WorldWideScience

Sample records for bundles atomistic simulations

  1. 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.

  2. 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...

  3. 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. (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  4. 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

  5. Atomistic Monte Carlo simulation of lipid membranes

    DEFF Research Database (Denmark)

    Wüstner, Daniel; Sklenar, Heinz

    2014-01-01

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

  6. Atomistic simulations of dislocation processes in copper

    DEFF Research Database (Denmark)

    Vegge, T.; Jacobsen, K.W.

    2002-01-01

    We discuss atomistic simulations of dislocation processes in copper based on effective medium theory interatomic potentials. Results on screw dislocation structures and processes are reviewed with particular focus on point defect mobilities and processes involving cross slip. For example, the sta...... of vacancy controlled climb show the jogs to climb easily in their extended form. The stability of small vacancy dipoles is discussed and it is seen that the introduction of jogs may lead to the formation of Z-type faulted vacancy dipoles....

  7. 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.

  8. 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.

  9. 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.

  10. 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,

  11. 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...

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

    DEFF Research Database (Denmark)

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

    2004-01-01

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

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

    Science.gov (United States)

    Rapaport, D C

    2009-04-01

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

  14. 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.

  15. 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.

  16. Atomistic Molecular Dynamic Simulations of Multiferroics

    Science.gov (United States)

    Wang, Dawei; Weerasinghe, Jeevaka; Bellaiche, L.

    2012-08-01

    A first-principles-based approach is developed to simulate dynamical properties, including complex permittivity and permeability in the GHz-THz range, of multiferroics at finite temperatures. It includes both structural degrees of freedom and magnetic moments as dynamic variables in Newtonian and Landau-Lifshitz-Gilbert (LLG) equations within molecular dynamics, respectively, with the couplings between these variables being incorporated. The use of a damping coefficient and of the fluctuation field in the LLG equations is required to obtain equilibrated magnetic properties at any temperature. No electromagnon is found in the spin-canted structure of BiFeO3. On the other hand, two magnons with very different frequencies are predicted via the use of this method. The smallest-in-frequency magnon corresponds to oscillations of the weak ferromagnetic vector in the basal plane being perpendicular to the polarization while the second magnon corresponds to magnetic dipoles going in and out of this basal plane. The large value of the frequency of this second magnon is caused by static couplings between magnetic dipoles with electric dipoles and oxygen octahedra tiltings.

  17. 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.

  18. 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.

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

    DEFF Research Database (Denmark)

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

    2007-01-01

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

  20. Atomistic Simulations of Dislocations in a Model BCC Multicomponent Concentrated Solid Solution Alloy (Postprint)

    Science.gov (United States)

    2016-12-19

    Dislocations ; Atomistic simulations; Concentrated multicomponent solid solution alloy; BCC crystal 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF...This has implications for higher-scale modeling ( dislocation dynamics or crystal plasticity) of HEA alloys, relative to elemental BCC metals, which...AFRL-RX-WP-JA-2017-0302 ATOMISTIC SIMULATIONS OF DISLOCATIONS IN A MODEL BCC MULTICOMPONENT CONCENTRATED SOLID SOLUTION ALLOY

  1. Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ

    DEFF Research Database (Denmark)

    Euro, Liliya; Haapanen, Outi; Róg, Tomasz

    2017-01-01

    of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable......DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform...

  2. Atomistic Simulation of Polymer Crystallization at Realistic Length Scales

    Energy Technology Data Exchange (ETDEWEB)

    Gee, R H; Fried, L E

    2005-01-28

    Understanding the dynamics of polymer crystallization during the induction period prior to crystal growth is a key goal in polymer physics. Here we present the first study of primary crystallization of polymer melts via molecular dynamics simulations at physically realistic (about 46 nm) length scales. Our results show that the crystallization mechanism involves a spinodal decomposition microphase separation caused by an increase in the average length of rigid trans segments along the polymer backbone during the induction period. Further, the characteristic length of the growing dense domains during the induction period is longer than predicted by classical nucleation theory. These results indicate a new 'coexistence period' in the crystallization, where nucleation and growth mechanisms coexist with a phase separation mechanism. Our results provide an atomistic verification of the fringed micelle model.

  3. Atomistic simulation of graphene-based polymer nanocomposites

    Energy Technology Data Exchange (ETDEWEB)

    Rissanou, Anastassia N.; Bačová, Petra; Harmandaris, Vagelis [Crete Center for Quantum Complexity and Nanotechnology (CQCN), Department of Physics, University of Crete, Heraklion, Crete (Greece)

    2016-05-18

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

  4. 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...

  5. Simulation of finite size effects of the fiber bundle model

    Science.gov (United States)

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

    2018-01-01

    In theory, the macroscopic fracture of materials should correspond with the thermodynamic limit of the fiber bundle model. However, the simulation of a fiber bundle model with an infinite size is unrealistic. To study the finite size effects of the fiber bundle model, fiber bundle models of various size are simulated in detail. The effects of system size on the constitutive behavior, critical stress, maximum avalanche size, avalanche size distribution, and increased step number of external load are explored. The simulation results imply that there is no feature size or cut size for macroscopic mechanical and statistical properties of the model. The constitutive curves near the macroscopic failure for various system size can collapse well with a simple scaling relationship. Simultaneously, the introduction of a simple extrapolation method facilitates the acquisition of more accurate simulation results in a large-limit system, which is better for comparison with theoretical results.

  6. 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

  7. 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.

  8. Atomistic simulation studies of iron sulphide, platinum antimonide and platinum arsenide

    CSIR Research Space (South Africa)

    Ngoepe, PE

    2005-09-01

    Full Text Available The authors present the results of atomistic simulations using derived interatomic potentials for the pyrite-structured metal chalcogenides FeS2, PtSb2 and PtAs2. Structural and elastic constants were calculated and compared with experimental...

  9. Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary.

    Science.gov (United States)

    Yang, Shengfeng; Chen, Youping

    2015-03-08

    In this paper, we present the development of a concurrent atomistic-continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic-continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] tilt GBs in bi-crystal strontium titanate obtained by CAC compare well with those obtained by existing experiments and density function theory calculations. Although 98.4% of the degrees of freedom of the simulated atomistic system have been eliminated in a coarsely meshed finite-element region, the CAC results, including the stress-strain responses, the GB-crack interaction mechanisms and the effect of the interaction on the fracture strength, are comparable with that of all-atom molecular dynamics simulation results. In addition, CAC simulation results show that the GB-crack interaction has a significant effect on the fracture behaviour of bi-crystal strontium titanate; not only the misorientation angle but also the atomic-level details of the GB structure influence the effect of the GB on impeding crack propagation.

  10. Atomistic simulations on intergranular fracture toughness of copper bicrystals with symmetric tilt grain boundaries

    Science.gov (United States)

    Cui, Cheng Bin; Beom, Hyeon Gyu

    2018-01-01

    The intergranular fracture toughness of Cu bicrystals with symmetric tilt grain boundaries was investigated using atomistic simulations. Mode I fracture of Cu bicrystals with an intergranular crack was considered. The boundary conditions were specified by the near-tip displacement fields obtained based on linear elastic fracture mechanics (LEFM). Based on the energy interpretation of the energy release rate, a two-specimen method was adopted to determine the fracture toughness. The simulation results of the fracture toughness matched well with those determined using LEFM. In contrast to the toughness obtained using the Griffith energy criterion, the atomistic simulation results for the same bicrystal were not constants, but dependent on the crack-tip circumstances. This behavior was mainly associated with the different local stress conditions and fracture patterns observed for the different models.

  11. Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations

    Science.gov (United States)

    2016-01-01

    Gangliosides are glycolipids in which an oligosaccharide headgroup containing one or more sialic acids is connected to a ceramide. Gangliosides reside in the outer leaflet of the plasma membrane and play a crucial role in various physiological processes such as cell signal transduction and neuronal differentiation by modulating structures and functions of membrane proteins. Because the detailed behavior of gangliosides and protein-ganglioside interactions are poorly known, we investigated the interactions between the gangliosides GM1 and GM3 and the proteins aquaporin (AQP1) and WALP23 using equilibrium molecular dynamics simulations and potential of mean force calculations at both coarse-grained (CG) and atomistic levels. In atomistic simulations, on the basis of the GROMOS force field, ganglioside aggregation appears to be a result of the balance between hydrogen bond interactions and steric hindrance of the headgroups. GM3 clusters are slightly larger and more ordered than GM1 clusters due to the smaller headgroup of GM3. The different structures of GM1 and GM3 clusters from atomistic simulations are not observed at the CG level based on the Martini model, implying a difference in driving forces for ganglioside interactions in atomistic and CG simulations. For protein-ganglioside interactions, in the atomistic simulations, GM1 lipids bind to specific sites on the AQP1 surface, whereas they are depleted from WALP23. In the CG simulations, the ganglioside binding sites on the AQP1 surface are similar, but ganglioside aggregation and protein-ganglioside interactions are more prevalent than in the atomistic simulations. Using the polarizable Martini water model, results were closer to the atomistic simulations. Although experimental data for validation is lacking, we proposed modified Martini parameters for gangliosides to more closely mimic the sizes and structures of ganglioside clusters observed at the atomistic level. PMID:27610460

  12. 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.

  13. 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.

  14. Molecular cooperativity and compatibility via full atomistic simulation

    Science.gov (United States)

    Kwan Yang, Kenny

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

  15. 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

  16. Vibrational Behavior of Single-Walled Carbon Nanotubes: Atomistic Simulations

    Science.gov (United States)

    Chang, I.-Ling; Huang, Chang-Ming

    2013-10-01

    This study examines the vibrational behaviors of both armchair and zigzag carbon nanotubes (CNTs). The natural longitudinal/flexural/torsional/radial frequencies of CNTs were extracted and analyzed simultaneously from an equilibrium molecular dynamics (MD) simulation without imposing any initial modal displacement or force. Initial random atomic velocities, which were assigned to fit the simulated temperature, could be considered as an excitation on CNTs composing of wide range of spatial frequencies. The position and velocity of each atom at every time step was calculated using finite difference algorithm, and fast Fourier transform (FFT) was used to perform time-to-frequency domain transform. The effects of CNT length, radius, chirality, and boundary condition on the vibrational behaviors of CNTs were systematically examined. Moreover, the simulated natural frequencies and mode shapes were compared with the predictions based on continuum theories, i.e., rod, Euler-Bernoulli beam and nonlocal Timoshenko beam, to examine their applicability in nanostructures.

  17. Atomistic simulation of the structural and elastic properties of ...

    Indian Academy of Sciences (India)

    Isshiki et al [3] found that magnesite transforms to an unknown form at pressures above 115 GPa. Skorodumova et al [9] used ab initio calculations to determine that mag- nesite can transform into a pyroxene structure at 113 GPa. Oganov et al [10] performed simulations using the universal structure prediction programme ...

  18. Atomistic Simulation of Frictional Sliding Between Cellulose Iß Nanocrystals

    Science.gov (United States)

    Xiawa Wu; Robert J. Moon; Ashlie Martini

    2013-01-01

    Sliding friction between cellulose Iß nanocrystals is studied using molecular dynamics simulation. The effects of sliding velocity, normal load, and relative angle between sliding surface are predicted, and the results analyzed in terms of the number of hydrogen bonds within and between the cellulose chains. We find that although the observed friction trends can be...

  19. Coding considerations for standalone molecular dynamics simulations of atomistic structures

    Science.gov (United States)

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

    2017-10-01

    The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

  20. A fast mollified impulse method for biomolecular atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Fath, L., E-mail: lukas.fath@kit.edu [Institute for App. and Num. Mathematics, Karlsruhe Institute of Technology (Germany); Hochbruck, M., E-mail: marlis.hochbruck@kit.edu [Institute for App. and Num. Mathematics, Karlsruhe Institute of Technology (Germany); Singh, C.V., E-mail: chandraveer.singh@utoronto.ca [Department of Materials Science & Engineering, University of Toronto (Canada)

    2017-03-15

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

  1. Thermochemistry of strontium incorporation in aragonite from atomistic simulations

    OpenAIRE

    Grau-Crespo, R.; Ruiz-Hernández, S. E.; Ruiz-Salvador, A. R.; De Leeuw, N. H.

    2010-01-01

    We have investigated the thermodynamics of mixing between aragonite (orthorhombic CaCO3) and strontianite (SrCO3). In agreement with experiment, our simulations predict that there is a miscibility gap between the two solids at ambient conditions. All SrxCa1 xCO3 solids with compositions 0.12 < x < 0.87 are metastable with respect to separation into a Ca-rich and a Sr-rich phase. The concentration of Sr in coral aragonites (x 0.01) lies in the miscibility region of the phase diagram...

  2. Voronoi Based Nanocrystalline Generation Algorithm for Atomistic Simulations

    Science.gov (United States)

    2016-12-22

    Modernization Program DOD Next Generation Workforce Development, HIP-15- 020 and HIP-16-005. This research was supported in part by an appointment to the...code)   Standard Form 298 (Rev. 8/98)    Prescribed by ANSI Std. Z39.18 December 2016 Technical Note Voronoi-Based Nanocrystalline Generation Algorithm...The objective herein is to discuss an algorithm for generating nanocrystalline structures for use in molecular dynamics simulations. This algorithm

  3. Atomistic simulations of focused ion beam machining of strained silicon

    Science.gov (United States)

    Guénolé, J.; Prakash, A.; Bitzek, E.

    2017-09-01

    The focused ion beam (FIB) technique has established itself as an indispensable tool in the material science community, both to analyze samples and to prepare specimens by FIB milling. In combination with digital image correlation (DIC), FIB milling can, furthermore, be used to evaluate intrinsic stresses by monitoring the strain release during milling. The irradiation damage introduced by such milling, however, results in a change in the stress/strain state and elastic properties of the material; changes in the strain state in turn affect the bonding strength, and are hence expected to implicitly influence irradiation damage formation and sputtering. To elucidate this complex interplay between strain, irradiation damage and sputtering, we perform TRIM calculations and molecular dynamics simulations on silicon irradiated by Ga+ ions, with slab and trench-like geometries, whilst simultaneously applying uniaxial tensile and compressive strains up to 4%. In addition we calculate the threshold displacement energy (TDE) and the surface binding energy (SBE) for various strain states. The sputter rate and amount of damage produced in the MD simulations show a clear influence of the strain state. The SBE shows no significant dependence on strain, but is strongly affected by surface reconstructions. The TDE shows a clear strain-dependence, which, however, cannot explain the influence of strain on the extent of the induced irradiation damage or the sputter rate.

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

    Science.gov (United States)

    Kim, Han Seul; Kim, Yong-Hoon

    2015-07-15

    We review recent advances in the DNA sequencing method based on measurements of transverse electrical currents. Device configurations proposed in the literature are classified according to whether the molecular fingerprints appear as the major (Mode I) or perturbing (Mode II) current signals. Scanning tunneling microscope and tunneling electrode gap configurations belong to the former category, while the nanochannels with or without an embedded nanopore belong to the latter. The molecular sensing mechanisms of Modes I and II roughly correspond to the electron tunneling and electrochemical gating, respectively. Special emphasis will be given on the computer simulation studies, which have been playing a critical role in the initiation and development of the field. We also highlight low-dimensional nanomaterials such as carbon nanotubes, graphene, and graphene nanoribbons that allow the novel Mode II approach. Finally, several issues in previous computational studies are discussed, which points to future research directions toward more reliable simulation of electrical current DNA sequencing devices. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Review of Nanoindentation Size Effect: Experiments and Atomistic Simulation

    Directory of Open Access Journals (Sweden)

    George Z. Voyiadjis

    2017-10-01

    Full Text Available Nanoindentation is a well-stablished experiment to study the mechanical properties of materials at the small length scales of micro and nano. Unlike the conventional indentation experiments, the nanoindentation response of the material depends on the corresponding length scales, such as indentation depth, which is commonly termed the size effect. In the current work, first, the conventional experimental observations and theoretical models of the size effect during nanoindentation are reviewed in the case of crystalline metals, which are the focus of the current work. Next, the recent advancements in the visualization of the dislocation structure during the nanoindentation experiment is discussed, and the observed underlying mechanisms of the size effect are addressed. Finally, the recent computer simulations using molecular dynamics are reviewed as a powerful tool to investigate the nanoindentation experiment and its governing mechanisms of the size effect.

  6. Surface effects in atomistic mechanical simulations of Al nanocrystals

    Science.gov (United States)

    Munilla, Javier; Castro, Mario; Carnicero, Alberto

    2009-07-01

    Detailed knowledge of the mechanical properties of nanocrystals is crucial for understanding the behavior of micromachining devices. Determining experimentally the elastic and plastic properties of nanocrystals can be very challenging. In this work, we present molecular-dynamics simulations of mechanical properties of Al nanocrystals, both using Lennard-Jones and embedded-atom method potentials. We show that this kind of tests borrowed from mechanical engineering provide helpful insight on the mechanical behavior of nanocrystals. We also provide evidence suggesting that the small scale effects, mainly due to the small surface-to-volume ratio of nanocrystals, are crucial. The main results of our work are the failure of the thermodynamical relations connecting the applied stress and the material strain (additionally, we introduce a simple mathematical framework to account for this effect), the nonequilibrium behavior at the onset of the plastic deformation related to the appearance of long tails (power law) in the distribution of dissipated heat and, finally, the existence of conditions under which the system can experience reversible load-unload cycles in the plastic state.

  7. 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.

  8. Thermal transport in phase-change materials from atomistic simulations

    Science.gov (United States)

    Sosso, Gabriele C.; Donadio, Davide; Caravati, Sebastiano; Behler, Jörg; Bernasconi, Marco

    2012-09-01

    We computed the thermal conductivity (κ) of amorphous GeTe by means of classical molecular dynamics and lattice dynamics simulations. GeTe is a phase change material of interest for applications in nonvolatile memories. An interatomic potential with close-to-ab initio accuracy was used as generated by fitting a huge ab initio database with a neural network method. It turns out that the majority of heat carriers are nonpropagating vibrations (diffusons), the small percentage of propagating modes giving a negligible contribution to the total value of κ. This result is in contrast with the properties of other amorphous semiconductors such as Si for which nonpropagating and propagating vibrations account for about one half of the value of κ each. This outcome suggests that the value of κ measured for the bulk amorphous phase can be used to model the thermal transport of GeTe and possibly of other materials in the same class also in nanoscaled memory devices. Actually, the contribution from propagating modes, which may endure ballistic transport at the scale of 10-20 nm, is negligible.

  9. 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.

  10. 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.

  11. Scaling of slip avalanches in sheared amorphous materials based on large-scale atomistic simulations

    Science.gov (United States)

    Zhang, Dansong; Dahmen, Karin A.; Ostoja-Starzewski, Martin

    2017-03-01

    Atomistic simulations of binary amorphous systems with over 4 million atoms are performed. Systems of two interatomic potentials of the Lennard-Jones type, LJ12-6 and LJ9-6, are simulated. The athermal quasistatic shearing protocol is adopted, where the shear strain is applied in a stepwise fashion with each step followed by energy minimization. For each avalanche event, the shear stress drop (Δ σ ), the hydrostatic pressure drop (Δ σh ), and the potential energy drop (Δ E ) are computed. It is found that, with the avalanche size increasing, the three become proportional to each other asymptotically. The probability distributions of avalanche sizes are obtained and values of scaling exponents fitted. In particular, the distributions follow a power law, P (Δ U )˜Δ U-τ , where Δ U is a measure of avalanche sizes defined based on shear stress drops. The exponent τ is 1.25 ±0.1 for the LJ12-6 systems, and 1.15 ±0.1 for the LJ9-6 systems. The value of τ for the LJ12-6 systems is consistent with that from an earlier atomistic simulation study by Robbins et al. [Phys. Rev. Lett. 109, 105703 (2012)], 10.1103/PhysRevLett.109.105703, but the fitted values of other scaling exponents differ, which may be because the shearing protocol used here differs from that in their study.

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

    Science.gov (United States)

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

    2017-10-01

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

  13. 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.

  14. 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

  15. Rate dependence of grain boundary sliding via time-scaling atomistic simulations

    Science.gov (United States)

    Hammami, Farah; Kulkarni, Yashashree

    2017-02-01

    Approaching experimentally relevant strain rates has been a long-standing challenge for molecular dynamics method which captures phenomena typically on the scale of nanoseconds or at strain rates of 107 s-1 and higher. Here, we use grain boundary sliding in nanostructures as a paradigmatic problem to investigate rate dependence using atomistic simulations. We employ a combination of time-scaling computational approaches, including the autonomous basin climbing method, the nudged elastic band method, and kinetic Monte Carlo, to access strain rates ranging from 0.5 s-1 to 107 s-1. Combined with a standard linear solid model for viscoelastic behavior, our simulations reveal that grain boundary sliding exhibits noticeable rate dependence only below strain rates on the order of 10 s-1 but is rate independent and consistent with molecular dynamics at higher strain rates.

  16. 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.

  17. Proton transport in functionalised additives for PEM fuel cells: contributions from atomistic simulations.

    Science.gov (United States)

    Tölle, Pia; Köhler, Christof; Marschall, Roland; Sharifi, Monir; Wark, Michael; Frauenheim, Thomas

    2012-08-07

    The conventional polymer electrolyte membrane (PEM) materials for fuel cell applications strongly rely on temperature and pressure conditions for optimal performance. In order to expand the range of operating conditions of these conventional PEM materials, mesoporous functionalised SiO(2) additives are developed. It has been demonstrated that these additives themselves achieve proton conductivities approaching those of conventional materials. However, the proton conduction mechanisms and especially factors influencing charge carrier mobility under different hydration conditions are not well known and difficult to separate from concentration effects in experiments. This tutorial review highlights contributions of atomistic computer simulations to the basic understanding and eventual design of these materials. Some basic introduction to the theoretical and computational framework is provided to introduce the reader to the field, the techniques are in principle applicable to a wide range of other situations as well. Simulation results are directly compared to experimental data as far as possible.

  18. 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.)

  19. Simulations of micron-scale fracture using atomistic-based boundary element method

    Science.gov (United States)

    Wu, Xiaojie; Li, Xiantao

    2017-12-01

    A new formulation of a boundary element method (BEM) is proposed in this paper to simulate cracks at the micron scale. The main departure from the traditional BEMs is that the current model is derived from the underlying atomistic model, which involves the interactions of atoms at the scale of Angstroms. By using the lattice Green’s function, the new BEM formulation eliminates the excessive atomic degrees of freedom away from crack tips, and directly couples the process zones with the physical boundary conditions. We show that with such a drastic reduction, one can simulate brittle fracture process on the scale of microns, for which the entire system consists of a few billion atoms. We discuss several numerical issues to make the implementation more efficient. Examples will be presented for cracks in the bcc iron system.

  20. Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations

    Science.gov (United States)

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

    2009-01-01

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

  1. 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

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

    Science.gov (United States)

    Pavlov, Alexander S; Khalatur, Pavel G

    2016-06-28

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

  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

    We used atomistic simulations to study the membrane-bound form of catechol-O-methyltransferase (MB-COMT). In particular we investigated the 26-residue transmembrane a-helical segment of MB-COMT together with the 24-residue fragment that links the transmembrane component to the main protein unit...

  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. Study of Structure and Deformation Pathways in Ti-7Al Using Atomistic Simulations, Experiments, and Characterization

    Science.gov (United States)

    Venkataraman, Ajey; Shade, Paul A.; Adebisi, R.; Sathish, S.; Pilchak, Adam L.; Viswanathan, G. Babu; Brandes, Matt C.; Mills, Michael J.; Sangid, Michael D.

    2017-05-01

    Ti-7Al is a good model material for mimicking the α phase response of near- α and α+ β phases of many widely used titanium-based engineering alloys, including Ti-6Al-4V. In this study, three model structures of Ti-7Al are investigated using atomistic simulations by varying the Ti and Al atom positions within the crystalline lattice. These atomic arrangements are based on transmission electron microscopy observations of short-range order. The elastic constants of the three model structures considered are calculated using molecular dynamics simulations. Resonant ultrasound spectroscopy experiments are conducted to obtain the elastic constants at room temperature and a good agreement is found between the simulation and experimental results, providing confidence that the model structures are reasonable. Additionally, energy barriers for crystalline slip are established for these structures by means of calculating the γ-surfaces for different slip systems. Finally, the positions of Al atoms in regards to solid solution strengthening are studied using density functional theory simulations, which demonstrate a higher energy barrier for slip when the Al solute atom is closer to (or at) the fault plane. These results provide quantitative insights into the deformation mechanisms of this alloy.

  6. 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.

  7. 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.

  8. Atomistic- and Meso-Scale Computational Simulations for Developing Multi-Timescale Theory for Radiation Degradation in Electronic and Optoelectronic Devices

    Science.gov (United States)

    2017-02-13

    AFRL-RV-PS- AFRL-RV-PS- TR-2016-0161 TR-2016-0161 ATOMISTIC- AND MESO-SCALE COMPUTATIONAL SIMULATIONS FOR DEVELOPING MULTI-TIMESCALE THEORY FOR...From - To) 18 Aug 2015 – 7 Dec 2016 4. TITLE AND SUBTITLE Atomistic- and Meso-Scale Computational Simulations for Developing Multi-Timescale Theory ...and knowledge gained from atomic- and meso-scale simulations will be input into rate-diffusion theory as initial conditions to calculate the steady

  9. 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.

  10. Effect of conjugation on phase transitions in thermoresponsive polymers: an atomistic and coarse-grained simulation study.

    Science.gov (United States)

    Condon, Joshua E; Martin, Tyler B; Jayaraman, Arthi

    2017-04-19

    Using atomistic and coarse-grained molecular dynamics (MD) simulations, we explain the shifts in lower critical solution temperature (LCST)-like phase transitions exhibited by elastin-like peptides (ELPs) upon conjugation to other macromolecules (e.g. collagen-like peptides or CLPs). First, using atomistic simulations, we study ELP oligomers with the sequence (VPGFG)6 in explicit water, and characterize the LCST-like transition temperature as one at which the ELP oligomers undergo a change in "hydration state". In agreement with past experimental observations of Luo and Kiick, upon anchoring ELP oligomers to a point to mimic ELP oligomers conjugated to another macromolecule, there is an apparent slight shift in the transition temperature to lower values compared to free (unconjugated) ELP oligomers. However, these atomistic simulations are limited to small systems of short ELPs, and as such do not capture the multiple chain aggregation/phase separation observed in experiments of ELPs. Therefore, we utilize phenomenological coarse-grained (CG) MD simulations to probe how conjugating a block of generic-LCST polymer to another rigid unresponsive macromolecular block impacts the transition temperatures at concentrations and length scales larger than atomistic simulations. We find that when multiple LCST polymer chains are conjugated to a rigid unresponsive polymer block, the increased local crowding of the LCST polymers shifts the transition marked by onset of chain aggregation to smaller effective polymer-polymer attraction energies compared to the free LCST polymer chains. The driving force needed for aggregation is reduced in the conjugates compared to free LCST polymer due to reduction in the loss of polymer configurational entropy upon aggregation.

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

    Science.gov (United States)

    Sen, Fatih Gurcag

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

  12. 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.

  13. 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.

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

    Science.gov (United States)

    Pan, Xiaoliang; Schwartz, Steven

    2015-03-01

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

  15. 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.

  16. 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.

  17. Controlling simulations of human-artifact interaction with scenario bundles

    NARCIS (Netherlands)

    Van der Vegte, W.F.; Rusák, Z.

    2008-01-01

    We introduce a methodology for modeling and simulating fully virtual human-artifact systems, aiming to resolve two issues in virtual prototyping: (i) integration of distinct modeling and simulation approaches, and (ii) extending the deployability of simulations towards conceptual design. We are

  18. Modeling root-reinforcement with a Fiber-Bundle Model and Monte Carlo simulation

    Science.gov (United States)

    This paper uses sensitivity analysis and a Fiber-Bundle Model (FBM) to examine assumptions underpinning root-reinforcement models. First, different methods for apportioning load between intact roots were investigated. Second, a Monte Carlo approach was used to simulate plants with heartroot, platero...

  19. Understanding the physical metallurgy of the CoCrFeMnNi high-entropy alloy: an atomistic simulation study

    Science.gov (United States)

    Choi, Won-Mi; Jo, Yong Hee; Sohn, Seok Su; Lee, Sunghak; Lee, Byeong-Joo

    2018-01-01

    Although high-entropy alloys (HEAs) are attracting interest, the physical metallurgical mechanisms related to their properties have mostly not been clarified, and this limits wider industrial applications, in addition to the high alloy costs. We clarify the physical metallurgical reasons for the materials phenomena (sluggish diffusion and micro-twining at cryogenic temperatures) and investigate the effect of individual elements on solid solution hardening for the equiatomic CoCrFeMnNi HEA based on atomistic simulations (Monte Carlo, molecular dynamics and molecular statics). A significant number of stable vacant lattice sites with high migration energy barriers exists and is thought to cause the sluggish diffusion. We predict that the hexagonal close-packed (hcp) structure is more stable than the face-centered cubic (fcc) structure at 0 K, which we propose as the fundamental reason for the micro-twinning at cryogenic temperatures. The alloying effect on the critical resolved shear stress (CRSS) is well predicted by the atomistic simulation, used for a design of non-equiatomic fcc HEAs with improved strength, and is experimentally verified. This study demonstrates the applicability of the proposed atomistic approach combined with a thermodynamic calculation technique to a computational design of advanced HEAs.

  20. 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

  1. Atomistic Molecular Dynamics Simulations of the Initial Crystallization Stage in an SWCNT-Polyetherimide Nanocomposite

    Directory of Open Access Journals (Sweden)

    Victor M. Nazarychev

    2017-10-01

    Full Text Available Crystallization of all-aromatic heterocyclic polymers typically results in an improvement of their thermo-mechanical properties. Nucleation agents may be used to promote crystallization, and it is well known that the incorporation of nanoparticles, and in particular carbon-based nanofillers, may induce or accelerate crystallization through nucleation. The present study addresses the structural properties of polyetherimide-based nanocomposites and the initial stages of polyetherimide crystallization as a result of single-walled carbon nanotube (SWCNT incorporation. We selected two amorphous thermoplastic polyetherimides ODPA-P3 and aBPDA-P3 based on 3,3′,4,4′-oxydiphthalic dianhydride (ODPA, 2,3′,3,4′-biphenyltetracarboxylic dianhydride (aBPDA and diamine 1,4-bis[4-(4-aminophenoxyphenoxy]benzene (P3 and simulated the onset of crystallization in the presence of SWCNTs using atomistic molecular dynamics. For ODPA-P3, we found that the planar phthalimide and phenylene moieties show pronounced ordering near the CNT (carbon nanotube surface, which can be regarded as the initial stage of crystallization. We will discuss two possible mechanisms for ODPA-P3 crystallization in the presence of SWCNTs: the spatial confinement caused by the CNTs and π–π interactions at the CNT-polymer matrix interface. Based on our simulation results, we propose that ODPA-P3 crystallization is most likely initiated by favorable π–π interactions between the carbon nanofiller surface and the planar ODPA-P3 phthalimide and phenylene moieties.

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

    Science.gov (United States)

    Durand, O.; Jaouen, S.; Soulard, L.; Heuzé, O.; Colombet, L.

    2017-10-01

    We compare, at similar scales, the processes of microjetting and ejecta production from shocked roughened metal surfaces by using atomistic and continuous approaches. The atomistic approach is based on very large scale molecular dynamics (MD) simulations with systems containing up to 700 × 106 atoms. The continuous approach is based on Eulerian hydrodynamics simulations with adaptive mesh refinement; the simulations take into account the effects of viscosity and surface tension, and the equation of state is calculated from the MD simulations. The microjetting is generated by shock-loading above its fusion point a three-dimensional tin crystal with an initial sinusoidal free surface perturbation, the crystal being set in contact with a vacuum. Several samples with homothetic wavelengths and amplitudes of defect are simulated in order to investigate the influence of viscosity and surface tension of the metal. The simulations show that the hydrodynamic code reproduces with very good agreement the profiles, calculated from the MD simulations, of the ejected mass and velocity along the jet. Both codes also exhibit a similar fragmentation phenomenology of the metallic liquid sheets ejected, although the fragmentation seed is different. We show in particular, that it depends on the mesh size in the continuous approach.

  3. Characterization of Plastic Deformation Evolution in Single Crystal and Nanocrystalline Cu During Shock by Atomistic Simulations

    Science.gov (United States)

    Mirzaei Sichani, Mehrdad

    The objective of this dissertation is to characterize the evolution of plastic deformation mechanisms in single crystal and nanocrystalline Cu models during shock by atomistic simulations. Molecular dynamics (MD) simulations are performed for a range of particle velocities from 0.5 to 1.7 km/s and initial temperatures of 5, 300 and 600 K for single crystal models as well as particle velocities from 1.5 to 3.4 km/s for nanocrystalline models with grain diameters of 6, 11, 16 and 26 nm. For single crystal models, four different shock directions are selected, , , and , and dislocation density behind the shock wave front generally increases with increasing particle velocity for all shock orientations. Plastic relaxation for shock in the , and directions is primarily due to a reduction in the Shockley partial dislocation density. In contrast, plastic relaxation is limited for shock in the orientation. This is partially due to the emergence of sessile stair-rod dislocations with Burgers vectors of 1/3 and 1/6 due to the reaction of Shockley partial dislocations with twin boundaries and stacking fault intersections. For shock, FCC Cu is uniaxially compressed towards the BCC structure behind the shock wave front; this process is more favorable at higher shock pressures and temperatures. For particle velocities above 0.9 km/s, regions of HCP crystal structure nucleate from uniaxially compressed Cu. Free energy calculations proves that the nucleation and growth of these HCP clusters are an artifact of the embedded-atom interatomic potential. In addition, simulated x-ray diffraction line profiles are created for shock models of single crystal Cu at the Hugoniot state. Generally, peak broadening in the x-ray diffraction line profiles increases with increasing particle velocity. For nanocrystalline models, the compression of the FCC lattice towards the BCC structure is more apparent at particle velocity of 2.4 km/s, and at this particle velocity, the atomic percentage of BCC

  4. 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.

  5. Atomistic Simulation of Dislocation Core Structures in b2 Nickel-Aluminum

    Science.gov (United States)

    Xie, Zhao-Yang

    A systematic study of the core structures of , , and dislocations in B2 NiAl has been conducted using atomistic simulations with an embedded atom method (EAM) potential. New flexible boundary conditions and a new method of graphic representation of dislocation core structure have been employed. The main findings are the following: Core structures. There are no planar core structures of the dislocations found in B2 NiAl. The core spreading of dislocations in NiAl can occur along a variety of planes depending on dislocation slip plane and line orientation. Discrete lattice effects reduced the high strain levels from anisotropic elasticity solution at the dislocation core considerably and resulted in asymmetrical core structures. The core structure of the dislocations is mutilayered with spreading on the plane. The extent of the same strain level comparing with and dislocations is much larger. The complete dislocations in NiAl are also highly non-planar and are stable with respect to splitting into exact 1/2 partials as well as to alternative splittings that correspond to the stable fault in the vicinity of the antiphase boundary (APB), in both and planes. Peierls stresses. Peierls stresses of the dislocations have been calculated and have been compared for their relative ease of motion. Local disordering effects. The local disordering effects on the core structure are found to be significant only in the immediate vicinity of the point defect. Compositional deviation from stoichiometry. The simulation results of , , and dislocations in off stoichiometric NiAl show that the core structures became more extended than the ones in the stoichiometric NiAl. The core structures are not only dependent on the overall composition but also on their local atomic arrangement near the core region. When compositional deviation from stoichiometry is introduced, the response to the applied stress is different for the various slip systems. The Peierls stresses for the usually easiest

  6. 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

  7. Atomistic simulations of cation hydration in sodium and calcium montmorillonite nanopores

    Science.gov (United States)

    Yang, Guomin; Neretnieks, Ivars; Holmboe, Michael

    2017-08-01

    During the last four decades, numerous studies have been directed to the swelling smectite-rich clays in the context of high-level radioactive waste applications and waste-liners for contaminated sites. The swelling properties of clay mineral particles arise due to hydration of the interlayer cations and the diffuse double layers formed near the negatively charged montmorillonite (MMT) surfaces. To accurately study the cation hydration in the interlayer nanopores of MMT, solvent-solute and solvent-clay surface interactions (i.e., the solvation effects and the shape effects) on the atomic level should be taken into account, in contrast to many recent electric double layer based methodologies using continuum models. Therefore, in this research we employed fully atomistic simulations using classical molecular dynamics (MD) simulations, the software package GROMACS along with the CLAYFF forcefield and the SPC/E water model. We present the ion distributions and the deformation of the hydrated coordination structures, i.e., the hydration shells of Na+ and Ca2+ in the interlayer, respectively, for MMT in the first-layer, the second-layer, the third-layer, the fourth-layer, and the fifth-layer (1W, 2W, 3W, 4W, and 5W) hydrate states. Our MD simulations show that Na+ in Na-MMT nanopores have an affinity to the ditrigonal cavities of the clay layers and form transient inner-sphere complexes at about 3.8 Å from clay midplane at water contents less than the 5W hydration state. However, these phenomena are not observed in Ca-MMT regardless of swelling states. For Na-MMT, each Na+ is coordinated to four water molecules and one oxygen atom of the clay basal-plane in the first hydration shell at the 1W hydration state, and with five to six water molecules in the first hydration shell within a radius of 3.1 Å at all higher water contents. In Ca-MMT, however each Ca2+ is coordinated to approximately seven water molecules in the first hydration shell at the 1W hydration state and

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

    Science.gov (United States)

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

    2012-06-07

    There is significant interest in the restoration of the double-bundle anatomy of the native ACL when performing ACL reconstruction. Possible techniques include those utilizing two separate grafts with independent tunnels and those that attempt to mimic this anatomy with a single graft and fewer tunnels. Many of the latter techniques require specific instrumentation and are technically challenging. We demonstrate that the double-bundle anatomy of the native ACL can theoretically be mimicked by a single-bundle reconstruction. We performed single bundle ACL reconstruction with a bone-patellar tendon-bone (BTB) graft in two cadaveric knees. Both grafts were placed to mimic the native ACL footprints - one reconstruction was performed with rectangular bone blocks and oval tunnels and one was performed utilizing a standard BTB graft and round tunnels. Qualitative assessment of graft behavior was made as the knees were taken through a range of motion. The ACL graft was able to qualitatively mimic the behavior of the native ACL in both knees provided the bone blocks were correctly orientated. ACL reconstruction with a single BTB graft can qualitatively mimic the behavior of the two bundles of the native ACL. The key to ensuring this behavior was noted to be appropriate orientation of the graft in the tunnels. Quantitative biomechanical investigations are necessary to evaluate the impact of graft orientation on function.

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

    Directory of Open Access Journals (Sweden)

    Jacobi Matthias

    2012-06-01

    Full Text Available Abstract Background There is significant interest in the restoration of the double-bundle anatomy of the native ACL when performing ACL reconstruction. Possible techniques include those utilizing two separate grafts with independent tunnels and those that attempt to mimic this anatomy with a single graft and fewer tunnels. Many of the latter techniques require specific instrumentation and are technically challenging. We demonstrate that the double-bundle anatomy of the native ACL can theoretically be mimicked by a single-bundle reconstruction. Methods We performed single bundle ACL reconstruction with a bone-patellar tendon-bone (BTB graft in two cadaveric knees. Both grafts were placed to mimic the native ACL footprints – one reconstruction was performed with rectangular bone blocks and oval tunnels and one was performed utilizing a standard BTB graft and round tunnels. Qualitative assessment of graft behavior was made as the knees were taken through a range of motion. Results The ACL graft was able to qualitatively mimic the behavior of the native ACL in both knees provided the bone blocks were correctly orientated. Conclusions ACL reconstruction with a single BTB graft can qualitatively mimic the behavior of the two bundles of the native ACL. The key to ensuring this behavior was noted to be appropriate orientation of the graft in the tunnels. Quantitative biomechanical investigations are necessary to evaluate the impact of graft orientation on function.

  10. Atomistic simulations of deformation mechanisms in ultralight weight Mg-Li alloys

    Science.gov (United States)

    Karewar, Shivraj

    Mg alloys have spurred a renewed academic and industrial interest because of their ultra-light-weight and high specific strength properties. Hexagonal close packed Mg has low deformability and a high plastic anisotropy between basal and non-basal slip systems at room temperature. Alloying with Li and other elements is believed to counter this deficiency by activating non-basal slip by reducing their nucleation stress. In this work I study how Li addition affects deformation mechanisms in Mg using atomistic simulations. In the first part, I create a reliable and transferable concentration dependent embedded atom method (CD-EAM) potential for my molecular dynamics study of deformation. This potential describes the Mg-Li phase diagram, which accurately describes the phase stability as a function of Li concentration and temperature. Also, it reproduces the heat of mixing, lattice parameters, and bulk moduli of the alloy as a function of Li concentration. Most importantly, our CD-EAM potential reproduces the variation of stacking fault energy for basal, prismatic, and pyramidal slip systems that in uences the deformation mechanisms as a function of Li concentration. This success of CD-EAM Mg-Li potential in reproducing different properties, as compared to literature data, shows its reliability and transferability. Next, I use this newly created potential to study the effect of Li addition on deformation mechanisms in Mg-Li nanocrystalline (NC) alloys. Mg-Li NC alloys show basal slip, pyramidal type-I slip, tension twinning, and two-compression twinning deformation modes. Li addition reduces the plastic anisotropy between basal and non-basal slip systems by modifying the energetics of Mg-Li alloys. This causes the solid solution softening. The inverse relationship between strength and ductility therefore suggests a concomitant increase in alloy ductility. A comparison of the NC results with single crystal deformation results helps to understand the qualitative and

  11. Quantifying chain reptation in entangled polymer melts: topological and dynamical mapping of atomistic simulation results onto the tube model.

    Science.gov (United States)

    Stephanou, Pavlos S; Baig, Chunggi; Tsolou, Georgia; Mavrantzas, Vlasis G; Kröger, Martin

    2010-03-28

    The topological state of entangled polymers has been analyzed recently in terms of primitive paths which allowed obtaining reliable predictions of the static (statistical) properties of the underlying entanglement network for a number of polymer melts. Through a systematic methodology that first maps atomistic molecular dynamics (MD) trajectories onto time trajectories of primitive chains and then documents primitive chain motion in terms of a curvilinear diffusion in a tubelike region around the coarse-grained chain contour, we are extending these static approaches here even further by computing the most fundamental function of the reptation theory, namely, the probability psi(s,t) that a segment s of the primitive chain remains inside the initial tube after time t, accounting directly for contour length fluctuations and constraint release. The effective diameter of the tube is independently evaluated by observing tube constraints either on atomistic displacements or on the displacement of primitive chain segments orthogonal to the initial primitive path. Having computed the tube diameter, the tube itself around each primitive path is constructed by visiting each entanglement strand along the primitive path one after the other and approximating it by the space of a small cylinder having the same axis as the entanglement strand itself and a diameter equal to the estimated effective tube diameter. Reptation of the primitive chain longitudinally inside the effective constraining tube as well as local transverse fluctuations of the chain driven mainly from constraint release and regeneration mechanisms are evident in the simulation results; the latter causes parts of the chains to venture outside their average tube surface for certain periods of time. The computed psi(s,t) curves account directly for both of these phenomena, as well as for contour length fluctuations, since all of them are automatically captured in the atomistic simulations. Linear viscoelastic

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2017-02-15

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

  13. Adhesion of single- and multi-walled carbon nanotubes to silicon substrate: atomistic simulations and continuum analysis

    Science.gov (United States)

    Yuan, Xuebo; Wang, Youshan

    2017-10-01

    The radial deformation of carbon nanotubes (CNTs) adhering to a substrate may prominently affect their mechanical and physical properties. In this study, both classical atomistic simulations and continuum analysis are carried out, to investigate the lateral adhesion of single-walled CNTs (SWCNTs) and multi-walled CNTs (MWCNTs) to a silicon substrate. A linear elastic model for analyzing the adhesion of 2D shells to a rigid semi-infinite substrate is constructed in the framework of continuum mechanics. Good agreement is achieved between the cross-section profiles of adhesive CNTs obtained by the continuum model and by the atomistic simulation approach. It is found that the adhesion of a CNT to the silicon substrate is significantly influenced by its initial diameter and the number of walls. CNTs with radius larger than a certain critical radius are deformed radially on the silicon substrate with flat contact regions. With increasing number of walls, the extent of radial deformation of a MWCNT on the substrate decreases dramatically, and the flat contact area reduces—and eventually vanishes—due to increasing equivalent bending stiffness. It is analytically predicted that large-diameter MWCNTs with a large number of walls are likely to ‘stand’ on the silicon substrate. The present work can be useful for understanding the radial deformation of CNTs adhering to a solid planar substrate.

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

    Science.gov (United States)

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

    2013-12-01

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

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

    DEFF Research Database (Denmark)

    Henneberg, Kaj-åge; F.A., Roberge

    1997-01-01

    Computer simulations are used to study passive fiber modulation of propagation in a tightly packed bundle of frog skeletal muscle fibers (uniform fiber radius of 50 mu m). With T = 20 degrees C and a uniform nominal interstitial cleft width (d) over bar = 0.35 mu m, about 92% of the active fiber...... source current (I-ma) enters the passive tissue as a radial load current (I-ep) while the rest flows longitudinally in the cleft between the active and adjacent passive fibers. The conduction velocity of 1.32 m/s was about 30% lower than on an isolated fiber in a Ringer bath, in close agreement...

  16. Coupled binding-bending-folding: The complex conformational dynamics of protein-DNA binding studied by atomistic molecular dynamics simulations.

    Science.gov (United States)

    van der Vaart, Arjan

    2015-05-01

    Protein-DNA binding often involves dramatic conformational changes such as protein folding and DNA bending. While thermodynamic aspects of this behavior are understood, and its biological function is often known, the mechanism by which the conformational changes occur is generally unclear. By providing detailed structural and energetic data, molecular dynamics simulations have been helpful in elucidating and rationalizing protein-DNA binding. This review will summarize recent atomistic molecular dynamics simulations of the conformational dynamics of DNA and protein-DNA binding. A brief overview of recent developments in DNA force fields is given as well. Simulations have been crucial in rationalizing the intrinsic flexibility of DNA, and have been instrumental in identifying the sequence of binding events, the triggers for the conformational motion, and the mechanism of binding for a number of important DNA-binding proteins. Molecular dynamics simulations are an important tool for understanding the complex binding behavior of DNA-binding proteins. With recent advances in force fields and rapid increases in simulation time scales, simulations will become even more important for future studies. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

  17. 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.

  18. 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 reaction mechanism of the cytochrome (cyt) bc(1) complex relies on proton and electron transfer to/from the substrate quinone/quinol, which in turn generate a proton gradient across the mitochondrial membrane. Cardiolipin (CL) have been suggested to play an important role in cyt bc(1) function...... by both ensuring the structural integrity of the protein complex and also by taking part in the proton uptake. Yet, the atom-scale understanding of these highly charged four-tail lipids in the cyt bc(1) function has remained quite unclear. We consider this issue through atomistic molecular dynamics...... the description of the role of the surrounding lipid environment: in addition to the specific CL-protein interactions, we observe the protein domains on the positive side of the membrane to settle against the lipids. Altogether, the simulations discussed in this article provide novel views into the dynamics...

  19. Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes.

    Science.gov (United States)

    Stadlbauer, Petr; Mazzanti, Liuba; Cragnolini, Tristan; Wales, David J; Derreumaux, Philippe; Pasquali, Samuela; Šponer, Jiří

    2016-12-13

    G-quadruplexes are the most important noncanonical DNA architectures. Many quadruplex-forming sequences, including the human telomeric sequence d(GGGTTA)n, have been investigated due to their implications in cancer and other diseases, and because of their potential in DNA-based nanotechnology. Despite the availability of atomistic structural studies of folded G-quadruplexes, their folding pathways remain mysterious, and mutually contradictory models of folding coexist in the literature. Recent experiments convincingly demonstrated that G-quadruplex folding often takes days to reach thermodynamic equilibrium. Based on atomistic simulations of diverse classes of intermediates in G-quadruplex folding, we have suggested that the folding is an extremely multipathway process combining a kinetic partitioning mechanism with conformational diffusion. However, complete G-quadruplex folding is far beyond the time scale of atomistic simulations. Here we use high-resolution coarse-grained simulations to investigate potential unfolding intermediates, whose structural dynamics are then further explored with all-atom simulations. This multiscale approach indicates how various pathways are interconnected in a complex network. Spontaneous conversions between different folds are observed. We demonstrate the inability of simple order parameters, such as radius of gyration or the number of native H-bonds, to describe the folding landscape of the G-quadruplexes. Our study also provides information relevant to further development of the coarse-grained force field.

  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. © The Authors Journal of Computational Chemistry

  1. Simulation of spatial and temporal properties of aftershocks by means of the fiber bundle model

    Science.gov (United States)

    Monterrubio-Velasco, Marisol; Zúñiga, F. R.; Márquez-Ramírez, Victor Hugo; Figueroa-Soto, Angel

    2017-09-01

    The rupture processes of any heterogeneous material constitute a complex physical problem. Earthquake aftershocks show temporal and spatial behaviors which are consequence of the heterogeneous stress distribution and multiple rupturing following the main shock. This process is difficult to model deterministically due to the number of parameters and physical conditions, which are largely unknown. In order to shed light on the minimum requirements for the generation of aftershock clusters, in this study, we perform a simulation of the main features of such a complex process by means of a fiber bundle (FB) type model. The FB model has been widely used to analyze the fracture process in heterogeneous materials. It is a simple but powerful tool that allows modeling the main characteristics of a medium such as the brittle shallow crust of the earth. In this work, we incorporate spatial properties, such as the Coulomb stress change pattern, which help simulate observed characteristics of aftershock sequences. In particular, we introduce a parameter (P) that controls the probability of spatial distribution of initial loads. Also, we use a "conservation" parameter (π), which accounts for the load dissipation of the system, and demonstrate its influence on the simulated spatio-temporal patterns. Based on numerical results, we find that P has to be in the range 0.06 system requires a small difference in the spatial distribution of initial stress, and a very particular fraction of load transfer in order to generate realistic aftershocks.

  2. Molecular simulation of bundle-like crystal nucleation from n-eicosane melts

    Science.gov (United States)

    Yi, Peng; Rutledge, Gregory C.

    2011-07-01

    Homogeneous nucleation of n-eicosane crystals from the supercooled melt was studied by molecular simulation using a realistic, united-atom model for n-alkanes. Using molecular dynamics simulation, we observed nucleation events directly at constant pressure and temperature, corresponding to about 19% supercooling. Under these conditions, the induction time is found to be 80.6 ± 8.8 ns for a system of volume (1.882 ± 0.006) × 10-19 cm3, corresponding to a nucleation rate of (6.59 ± 0.72) × 1025 cm-3 s-1. The nucleation free energy was calculated separately for three temperatures, ranging from 10% to 19% supercooling, by a Monte Carlo method with umbrella sampling. Values for the nucleation free energy range from 7.3 to 13.2 (in units of kBT). Detailed examination of the simulations reveals the critical nucleus to be a bundle of stretched segments about eight methylene groups long, organized into a cylindrical shape. The remaining methylene groups of the chains that participate in the nucleus form a disordered interfacial layer. By fitting the free energy curve to the cylindrical nucleus model, the solid-liquid interfacial free energies are calculated to be about 10 mJ/m2 for the side surface and 4 mJ/m2 for the end surface, both of which are relatively insensitive to temperature.

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

    Science.gov (United States)

    Hoang Viet, Man; Derreumaux, Philippe; Nguyen, Phuong H.

    2015-07-01

    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.

  4. Concurrent atomistic and continuum simulation of bi-crystal strontium titanate with tilt grain boundary

    OpenAIRE

    Yang, Shengfeng; Chen, Youping

    2015-01-01

    In this paper, we present the development of a concurrent atomistic–continuum (CAC) methodology for simulation of the grain boundary (GB) structures and their interaction with other defects in ionic materials. Simulation results show that the CAC simulation allows a smooth passage of cracks through the atomistic–continuum interface without the need for additional constitutive rules or special numerical treatment; both the atomic-scale structures and the energies of the four different [001] ti...

  5. 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.

  6. 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.

  7. 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

  8. The design of self-collapsed super-strong nanotube bundles

    Science.gov (United States)

    Pugno, Nicola Maria

    2010-09-01

    The study reported in this paper suggests that the influence of the surrounding nanotubes in a bundle is nearly identical to that of a liquid having surface tension equal to the surface energy of the nanotubes. This surprising behaviour is supported by the calculation of the polygonization and especially of the self-collapse diameters, and related dog-bone configurations, of nanotubes in a bundle, in agreement with atomistic simulations and nanoscale experiments. Accordingly, we have evaluated the strength of the nanotube bundle, with or without collapsed nanotubes, assuming a sliding failure: the self-collapse can increase the strength up to a value of about ˜30%, suggesting the design of self-collapsed super-strong nanotube bundles. Other systems, such as peapods and fullerites, can be similarly treated, including the effect of the presence of a liquid, as reported in the appendices.

  9. 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.

  10. Large eddy simulation of flow across in-line tube bundles

    Energy Technology Data Exchange (ETDEWEB)

    Sofiane Benhamadouche [Electricite de France R et D, MFTT, 6 quai Watier, 78400 Chatou (France); Dominique Laurence; Nicolas Jarrin [UMIST, MAME Dept, G. Begg Bldg, Sackville St. PO box 88, Manchester M601QD (United Kingdom); Electricite de France R et D, MFTT, 6 quai Watier, 78400 Chatou (France)

    2005-07-01

    Previously, Benhamadouche and Laurence (2003) produced very good results for the flow in a staggered tube bundle, using Large Eddy Simulation with EDF in-house finite volume code code-Saturne (Archambeau et al. (2004)). The discretization is based on a collocated arrangement for unstructured grids. A second order scheme in space and time is used with a standard Smagorinsky model. All the wall boundary cells are in the viscous layer, thus, no wall function is applied. The same numerical scheme is tested on a square in-line tube bundle with P/D = 1,44 and Re = 70000 (P is the vertical and horizontal tube spacing, D is the diameter of a tube and the Reynolds number is based on the gap velocity). The tube bundle is assumed infinite; periodic conditions are used in the three directions with an imposed flow rate. The dimensions of the computational domain have to be chosen (the computational cell, see figure 1 and the 3D elevation L{sub z}). Three computations are carried out (see table 1). Case 1 (1200000 cells) gives a non-symmetrical mean solution that impacts the tubes alternatively on the top and the bottom depending on the considered column (see figure 2). Case 2 gives the same behavior with fewer tubes. Case 3 gives a different solution in which the flow impacts the tubes on the same way whatever the column of the tubes (see figure 3). Note that the solution in also non-symmetrical in this case. A comparison of the total mean drag and lift coefficients and their rms values is given in table 2. The qualitative behavior is good for both cases; the rms value of the drag is between 30% to 50% lower than the rms value of the lift. However, Case 3 results are more realistic as the mean of the lift is almost zero and the other values are of the order of magnitude of the ones obtained for other tube bundles (P/D = 1,75 in Chen (1987)). One can conclude that the elevation in the third direction has a more important effect then the domain size and can impact seriously the

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

    DEFF Research Database (Denmark)

    Papaleo, Elena

    2015-01-01

    that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome...... 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....

  12. Atomistic-scale simulations of the initial chemical events in triacetonetriperoxide (TATP) detonation

    Science.gov (United States)

    van Duin, Adri; Zeiri, Yehuda; Goddard, William

    2005-03-01

    To study the initial chemical events related to the detonation of triacetonetriperoxide (TATP) we have performed a series of molecular dynamics (MD) simulations using the ReaxFF reactive force field [1,2], extended to reproduce the quantumchemical (QM)-derived relative energies of the reactants, products, intermediates and transition states related to the TATP unimolecular decomposition. We find excellent agreement between the reaction products predicted from QM and those observed from ReaxFF unimolecular cookoff simulations. Furthermore, the primary reaction products observed in the unimolecular cookoff simulations match closely with those observed from a TATP-condensed phase cookoff simulation, indicating that unimolecular decomposition dominates TATP-condensed phase initiation. [1] A.C.T. van Duin, S. Dasgupta, F. Lorant and W.A. Goddard (2001), J. Phys. Chem. A 105, 9396-9409.. [2] A. Strachan, A.C.T. van Duin, D. Chakraborty, S. Dasgupta and W.A. Goddard III (2003) Phys. Rev. Letters 91, 09301.

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

    NARCIS (Netherlands)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2017-12-01

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

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

    DEFF Research Database (Denmark)

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

    2001-01-01

    We have performed atomic-scare simulations of cross-slip processes of screw dislocations in copper, simulating jog-free dislocations as well as different types of jogged screw dislocations. Minimum-energy paths and corresponding transition state energies are obtained using the nudged......-elastic-band path technique. We find low barriers and effective masses for the conservative motion along the dislocations of elementary jogs on both ordinary {111}[110] and non-octahedral {110}[110] slip systems. The jogs are found to be constricted and therefore effectively act as pre-existing constrictions...

  16. An Overview of the State of the Art in Atomistic and Multiscale Simulation of Fracture

    Science.gov (United States)

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

    2009-01-01

    The emerging field of nanomechanics is providing a new focus in the study of the mechanics of materials, particularly in simulating fundamental atomic mechanisms involved in the initiation and evolution of damage. Simulating fundamental material processes using first principles in physics strongly motivates the formulation of computational multiscale methods to link macroscopic failure to the underlying atomic processes from which all material behavior originates. This report gives an overview of the state of the art in applying concurrent and sequential multiscale methods to analyze damage and failure mechanisms across length scales.

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

    Science.gov (United States)

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

    2015-12-01

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

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

    Indian Academy of Sciences (India)

    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 ...

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

    NARCIS (Netherlands)

    Klaver, T.P.C.

    2004-01-01

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

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

    NARCIS (Netherlands)

    Fan, Z.; Lin, L.; Buijs, W.; Vlugt, T.J.H.; van Huis, MA

    2016-01-01

    Cation exchange is a powerful tool for the synthesis of nanostructures such as core–shell nanocrystals, however, the underlying mechanism is poorly understood. Interactions of cations with ligands and solvent molecules are systematically ignored in simulations. Here, we introduce the concept of

  1. 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

  2. Simulation of spatial and temporal properties of aftershocks by means of the fiber bundle model

    Science.gov (United States)

    Monterrubio-Velasco, Marisol; Zúñiga, F. R.; Márquez-Ramírez, Victor Hugo; Figueroa-Soto, Angel

    2017-11-01

    The rupture processes of any heterogeneous material constitute a complex physical problem. Earthquake aftershocks show temporal and spatial behaviors which are consequence of the heterogeneous stress distribution and multiple rupturing following the main shock. This process is difficult to model deterministically due to the number of parameters and physical conditions, which are largely unknown. In order to shed light on the minimum requirements for the generation of aftershock clusters, in this study, we perform a simulation of the main features of such a complex process by means of a fiber bundle (FB) type model. The FB model has been widely used to analyze the fracture process in heterogeneous materials. It is a simple but powerful tool that allows modeling the main characteristics of a medium such as the brittle shallow crust of the earth. In this work, we incorporate spatial properties, such as the Coulomb stress change pattern, which help simulate observed characteristics of aftershock sequences. In particular, we introduce a parameter ( P) that controls the probability of spatial distribution of initial loads. Also, we use a "conservation" parameter ( π), which accounts for the load dissipation of the system, and demonstrate its influence on the simulated spatio-temporal patterns. Based on numerical results, we find that P has to be in the range 0.06 order to reproduce aftershocks pattern characteristics which resemble those of observed sequences. This means that the system requires a small difference in the spatial distribution of initial stress, and a very particular fraction of load transfer in order to generate realistic aftershocks.

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

    DEFF Research Database (Denmark)

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

    2013-01-01

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

  4. 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

    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......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...

  5. 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...

  6. Atomistic simulations of wetting properties and water films on hydrophilic surfaces

    Science.gov (United States)

    Kanduč, Matej; Netz, Roland R.

    2017-04-01

    We use molecular simulations to investigate the wetting behavior of water at flat polar surfaces. Introducing a computational procedure based on thermodynamic integration methods, we determine the equilibrium water film thickness on the surface at given vapor density as well as the corresponding change of the surface free energy. The wetting film is relevant on polar surfaces near the wetting transition and significantly alters the surface contact angle. For thin films, the surface free energy change increases linearly with the thickness, as predicted by simple thermodynamic arguments. For thick films we observe deviations from linearity, which we rationalize by the formation of hydrogen bonds between water molecules in the film. Our approach provides an efficient and accurate technique to calculate the wetting properties of surface layers, which we verify by simulating water droplets on the surfaces.

  7. A search for the dominant heat conducting phonon modes in graphene: An atomistic simulation study

    Science.gov (United States)

    Zhang, Hengji; Cho, Kyeongjae

    2011-03-01

    We have performed an equilibrium molecular dynamic (MD) simulation study to investigate phonon thermal transport in graphene at 300K with Green-Kubo method. Using a newly optimized reactive empirical bond order carbon potential (Lindsay, et al. Physical Review B 81, 205441, 2010), our calculated thermal conductivity (TC) of defect free graphene is about 3000 W/mK in good agreement with experiments(~ 3000-5000 W/mK). A maximum of ~ 1000 fold reduction in TC is possible to achieve for graphene with defects and surrounding viscous medium. As we decompose the in-plane and out-plane phonon vibration modes of graphene in MD simulations, the out of plane vibration modes (ZA phonon) contribute to about 50% of the overall TC. This large contribution from ZA modes is explained with density of states analysis. We have clarified a recent controversy on which polarization mode in graphene is the main heat carrier.

  8. Atomistic Simulations of Hyperthermal Collisions Between Closed-Shell Species and Organic and Inorganic Surfaces

    Science.gov (United States)

    2009-02-01

    perfluorinated organics, and 3) Investigation of energy exchange in collisions of closed- shell gases with alkanethiolate self-assembled monolayers. The...principal outcome of this project was the advancement of computational-chemistry techniques that can be used to simulate chemical reactions occurring on...8-98) Prescribed by ANSI Std. 239.18 20090410041 Final Performance Report Accurate characterization of the chemical reactions occurring on an

  9. Atomistic simulations of nanoindentation on the basal plane of crystalline molybdenum disulfide (MoS2)

    Science.gov (United States)

    Stewart, J. A.; Spearot, D. E.

    2013-06-01

    In the present work, nanoindentation on the basal surface of a crystalline molybdenum disulfide (MoS2) thin film is investigated by molecular statics (MS) calculations. A previously parameterized interatomic potential combining the reactive empirical bond-order and Lennard-Jones potentials is implemented into the LAMMPS molecular simulation package and refined for improved prediction of the mechanical properties of MoS2 at athermal conditions. Nanoindentation simulations are performed using three indenter sizes with specific focus on the incipient plastic deformation event within the MoS2single crystal. MS calculations show that a local phase transformation occurs beneath the indenter at plastic yield without the presence of broken Mo-S bonds. The structural characteristics of the phase transformation are captured using a slip vector analysis. The nanoindentation simulations provide insight into the mechanical response of MoS2 during contact deformation characteristic of both synthesis and application for better design of MoS2 nanoparticle lubricants.

  10. On interfacial properties of tetrahydrofuran: Atomistic and coarse-grained models from molecular dynamics simulation

    Science.gov (United States)

    Garrido, J. M.; Algaba, J.; Míguez, J. M.; Mendiboure, B.; Moreno-Ventas Bravo, A. I.; Piñeiro, M. M.; Blas, F. J.

    2016-04-01

    We have determined the interfacial properties of tetrahydrofuran (THF) from direct simulation of the vapor-liquid interface. The molecules are modeled using six different molecular models, three of them based on the united-atom approach and the other three based on a coarse-grained (CG) approach. In the first case, THF is modeled using the transferable parameters potential functions approach proposed by Chandrasekhar and Jorgensen [J. Chem. Phys. 77, 5073 (1982)] and a new parametrization of the TraPPE force fields for cyclic alkanes and ethers [S. J. Keasler et al., J. Phys. Chem. B 115, 11234 (2012)]. In both cases, dispersive and coulombic intermolecular interactions are explicitly taken into account. In the second case, THF is modeled as a single sphere, a diatomic molecule, and a ring formed from three Mie monomers according to the SAFT-γ Mie top-down approach [V. Papaioannou et al., J. Chem. Phys. 140, 054107 (2014)]. Simulations were performed in the molecular dynamics canonical ensemble and the vapor-liquid surface tension is evaluated from the normal and tangential components of the pressure tensor along the simulation box. In addition to the surface tension, we have also obtained density profiles, coexistence densities, critical temperature, density, and pressure, and interfacial thickness as functions of temperature, paying special attention to the comparison between the estimations obtained from different models and literature experimental data. The simulation results obtained from the three CG models as described by the SAFT-γ Mie approach are able to predict accurately the vapor-liquid phase envelope of THF, in excellent agreement with estimations obtained from TraPPE model and experimental data in the whole range of coexistence. However, Chandrasekhar and Jorgensen model presents significant deviations from experimental results. We also compare the predictions for surface tension as obtained from simulation results for all the models with

  11. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Sepehrinia, Kazem; Mohammadi, Aliasghar, E-mail: amohammadi@sharif.edu

    2016-05-15

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

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

    Science.gov (United States)

    Jin, Yu

    2016-01-01

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

  14. Construction of a kinetics model for liquid-solid transitions built from atomistic simulations

    Science.gov (United States)

    Benedict, Lorin; Zepeda-Ruiz, Luis; Haxhimali, Tomorr; Hamel, Sebastien; Sadigh, Babak; Chernov, Alexander; Belof, Jonathan

    We discuss work in progress towards a kinetics model for dynamically-driven liquid-solid transitions built from MD simulations. The growth of solid particles within a liquid is studied for a range of conditions, and careful attention is paid to the construction of an accurate multi-phase (equilibrium) equation of state for the system under consideration, in order to provide a framework upon which the non-equilibrium physics is based. His work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. Lawrence Livermore National Security, LLC.

  15. Effect of Interface on the Deformation of Aluminium Bicrystal: Atomistic Simulation Study

    Directory of Open Access Journals (Sweden)

    Yan Shaohua

    2016-01-01

    Full Text Available Molecular dynamic (MD simulation has been conducted to study the effect of interface structure on the mechanical response of eight symmetric tilt grain boundaries in high stacking-fault Al. It is found that the grain boundaries with E structure unit (SU have higher energy, but the grain boundary energy alone cannot be used as a parameter to determine the mechanical properties of grain boundary. The SUs, especially E units, do have an influence on the mechanical response of grain boundaries. Our results show that the dislocation imitates from E units preferably, but this depends on the dissociation at grain boundary.

  16. Mechanical Deformation Mechanisms and Properties of Prion Fibrils Probed by Atomistic Simulations

    Science.gov (United States)

    Choi, Bumjoon; Kim, Taehee; Ahn, Eue Soo; Lee, Sang Woo; Eom, Kilho

    2017-03-01

    Prion fibrils, which are a hallmark for neurodegenerative diseases, have recently been found to exhibit the structural diversity that governs disease pathology. Despite our recent finding concerning the role of the disease-specific structure of prion fibrils in determining their elastic properties, the mechanical deformation mechanisms and fracture properties of prion fibrils depending on their structures have not been fully characterized. In this work, we have studied the tensile deformation mechanisms of prion and non-prion amyloid fibrils by using steered molecular dynamics simulations. Our simulation results show that the elastic modulus of prion fibril, which is formed based on left-handed β-helical structure, is larger than that of non-prion fibril constructed based on right-handed β-helix. However, the mechanical toughness of prion fibril is found to be less than that of non-prion fibril, which indicates that infectious prion fibril is more fragile than non-infectious (non-prion) fibril. Our study sheds light on the role of the helical structure of amyloid fibrils, which is related to prion infectivity, in determining their mechanical deformation mechanisms and properties.

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

    Science.gov (United States)

    Sepehrinia, Kazem; Mohammadi, Aliasghar

    2016-05-01

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

  18. 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.

  19. Capillary fluctuations of surface steps: An atomistic simulation study for the model Cu(111) system

    Science.gov (United States)

    Freitas, Rodrigo; Frolov, Timofey; Asta, Mark

    2017-10-01

    Molecular dynamics (MD) simulations are employed to investigate the capillary fluctuations of steps on the surface of a model metal system. The fluctuation spectrum, characterized by the wave number (k ) dependence of the mean squared capillary-wave amplitudes and associated relaxation times, is calculated for 〈110 〉 and 〈112 〉 steps on the {111 } surface of elemental copper near the melting temperature of the classical potential model considered. Step stiffnesses are derived from the MD results, yielding values from the largest system sizes of (37 ±1 ) meV/A ˚ for the different line orientations, implying that the stiffness is isotropic within the statistical precision of the calculations. The fluctuation lifetimes are found to vary by approximately four orders of magnitude over the range of wave numbers investigated, displaying a k dependence consistent with kinetics governed by step-edge mediated diffusion. The values for step stiffness derived from these simulations are compared to step free energies for the same system and temperature obtained in a recent MD-based thermodynamic-integration (TI) study [Freitas, Frolov, and Asta, Phys. Rev. B 95, 155444 (2017), 10.1103/PhysRevB.95.155444]. Results from the capillary-fluctuation analysis and TI calculations yield statistically significant differences that are discussed within the framework of statistical-mechanical theories for configurational contributions to step free energies.

  20. 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.

  1. 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

    started, more or less independent of strain rate. The shear bands can also be characterized using a correlation function defined in terms of D-min(2), which, moreover, can detect incipient shear bands in cases where they do not fully form. By averaging the kinetic energy over small regions, the local...... 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.......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...

  2. Collapsed adhesion of carbon nanotubes on silicon substrates: continuum mechanics and atomistic simulations

    Science.gov (United States)

    Yuan, Xuebo; Wang, Youshan

    2018-02-01

    Carbon nanotubes (CNTs) can undergo collapse from the ordinary cylindrical configurations to bilayer ribbons when adhered on substrates. In this study, the collapsed adhesion of CNTs on the silicon substrates is investigated using both classical molecular dynamics (MD) simulations and continuum analysis. The governing equations and transversality conditions are derived based on the minimum potential energy principle and the energy-variational method, considering both the van der Waals interactions between CNTs and substrates and those inside CNTs. Closed-form solutions for the collapsed configuration are obtained which show good agreement with the results of MD simulations. The stability of adhesive configurations is investigated by analyzing the energy states. It is found that the adhesive states of single-walled CNTs (SWCNTs) (n, n) on the silicon substrates can be categorized by two critical radii, 0.716 and 0.892 nm. For SWCNTs with radius larger than 0.892 nm, they would fully collapse on the silicon substrates. For SWCNTs with radius less than 0.716 nm, the initial cylindrical configuration is energetically favorable. For SWCNTs with radius between two critical radii, the radially deformed state is metastable. The non-contact ends of all collapsed SWCNTs are identical with the same arc length of 2.38 nm. Finally, the role of number of walls on the adhesive configuration is investigated quantitatively. For multi-walled CNTs with the number of walls exceeding a certain value, the cylindrical configuration is stable due to the increasing bending stiffness. The present study can be useful for the design of CNT-based nanodevices.

  3. Atomistic Simulations of Defect Nucleation and Intralayer Fracture in Molybdenum Disulphide During Nanoindentation

    Science.gov (United States)

    Stewart, James A., Jr.

    Molybdenum disulphide (MoS2) is a layered, hexagonal crystal that has a very low coefficient of friction. Due to this low coefficient of friction, MoS2 has become a well-known solid lubricant and liquid lubricant additive. As such, nanoparticles of MoS2 have been proposed as an additive to traditional liquid lubricants to provide frictional properties that are sensitive to different temperature and pressure regimes. However, to properly design these MoS2 nanoparticles to be sensitive to different temperature and pressure regimes, it is necessary to understand the mechanical response of crystalline MoS2 under mechanical loading. Specifically, the fundamental mechanism associated with the nucleation and interaction of defects as well as intralayer fracture. This thesis addressed the mechanical response of crystalline MoS2 via contact deformation (nanoindentation) simulations, which is representative of the loading conditions experienced by these nanoparticles during synthesis and application. There are two main tasks to this thesis. First, a Mo-S interatomic potential (a combination of the reactive empirical bond-order (REBO) interatomic potential and the Lennard-Jones 12-6 interatomic potential) that has been parameterized specifically to investigate the tribological properties of MoS2 was implemented into the classical molecular simulation package, LAMMPS, and refined to provide improved predictions for the mechanical properties of MoS 2 via molecular statics calculations. Second, using this newly implemented interatomic potential, molecular statics calculations were performed to investigate the mechanical response of MoS2 via nanoindentation with specific focus on the nucleation of defects. Nanoindentation force - displacement curves were compared to the Hertzian contact theory prediction. It was shown that MoS2 does not follow the Hertzian prediction due it anisotropic nature. In addition, it was shown that the initial sudden force drop event in the force

  4. Atomistic simulations of thermodynamic properties of Xe gas bubbles in U10Mo fuels

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Shenyang; Setyawan, Wahyu; Joshi, Vineet V.; Lavender, Curt A.

    2017-04-15

    Xe gas bubble superlattice formation is observed in irradiated uranium–10 wt% molybdenum (U10Mo) fuels. However, the thermodynamic properties of the bubbles (the relationship among bubble size, equilibrium Xe concentration, and bubble pressure) and the mechanisms of bubble growth and superlattice formation are not well known. In this work, molecular dynamics is used to study these properties and mechanisms. The results provide important inputs for quantitative mesoscale models of gas bubble evolution and fuel performance. In the molecular dynamics simulations, the embedded-atom method (EAM) potential of U10Mo-Xe (Smirnova et al. 2013) is employed. Initial gas bubbles with low Xe concentration are generated in a U10Mo single crystal. Then Xe atom atoms are continuously added into the bubbles, and the evolution of pressure and dislocation emission around the bubbles is analyzed. The relationship between pressure, equilibrium Xe concentration, and radius of the bubbles is established. It was found that the gas bubble growth is accompanied by partial dislocation emission, which results in a star-shaped dislocation structure and an anisotropic stress field. The emitted partial dislocations have a Burgers vector along the <111> direction and a slip plane of (11-2). Dislocation loop punch-out was not observed. A tensile stress was found along <110> directions around the bubble, favoring the nucleation and formation of a face-centered cubic bubble superlattice in body-centered cubic U10Mo fuels.

  5. Atomistic simulation of water percolation and proton hopping in Nafion fuel cell membrane.

    Science.gov (United States)

    Devanathan, Ram; Venkatnathan, Arun; Rousseau, Roger; Dupuis, Michel; Frigato, Tomaso; Gu, Wei; Helms, Volkhard

    2010-11-04

    We have performed a detailed analysis of water clustering and percolation in hydrated Nafion configurations generated by classical molecular dynamics simulations. Our results show that at low hydration levels H(2)O molecules are isolated and a continuous hydrogen-bonded network forms as the hydration level is increased. Our quantitative analysis has established a hydration level (λ) between 5 and 6 H(2)O/SO(3)(-) as the percolation threshold of Nafion. We have also examined the effect of such a network on proton transport by studying the structural diffusion of protons using the quantum hopping molecular dynamics method. The mean residence time of the proton on a water molecule decreases by 2 orders of magnitude when the λ value is increased from 5 to 15. The proton diffusion coefficient in Nafion at a λ value of 15 is about 1.1 × 10(-5) cm(2)/s in agreement with experiment. The results provide quantitative atomic-level evidence of water network percolation in Nafion and its effect on proton conductivity.

  6. Atomistic simulations of deuterium irradiation on iron-based alloys in future fusion reactors

    Directory of Open Access Journals (Sweden)

    E. Safi

    2016-12-01

    Full Text Available Iron-based alloys are now being considered as plasma-facing materials for the first wall of future fusion reactors. Therefore, the iron (Fe and carbon (C erosion will play a key role in predicting the life-time and viability of reactors with steel walls. In this work, the surface erosion and morphology changes due to deuterium (D irradiation in pure Fe, Fe with 1% C impurity and the cementite, are studied using molecular dynamics (MD simulations, varying surface temperature and impact energy. The sputtering yields for both Fe and C were found to increase with incoming energy. In iron carbide, C sputtering was preferential to Fe and the deuterium was mainly trapped as D2 in bubbles, while mostly atomic D was present in Fe and Fe–1%C. The sputtering yields obtained from MD were compared to SDTrimSP yields. At lower impact energies, the sputtering mechanism was of both physical and chemical origin, while at higher energies (>100eV the physical sputtering dominated.

  7. 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.

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

    Science.gov (United States)

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

    2015-11-19

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

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

    Science.gov (United States)

    Berdiyorov, G.; Harrabi, K.; Mehmood, U.; Peeters, F. M.; Tabet, N.; Zhang, J.; Hussein, I. A.; McLachlan, M. A.

    2015-07-01

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

  10. Atomistic simulations of thermodynamic properties of Xe gas bubbles in U10Mo fuels

    Science.gov (United States)

    Hu, Shenyang; Setyawan, Wahyu; Joshi, Vineet V.; Lavender, Curt A.

    2017-07-01

    Xe gas bubble superlattice formation is observed in irradiated uranium-10 wt% molybdenum (U10Mo) fuels. However, the thermodynamic properties of the bubbles (the relationship among bubble size, equilibrium Xe concentration, and bubble pressure) and the mechanisms of bubble superlattice formation are not well known. In this work, the molecular dynamics (MD) method is used to study these properties and mechanisms. The results provide important inputs for quantitative mesoscale models of gas bubble evolution and fuel performance. In the MD simulations, the embedded-atom method (EAM) potential of U10Mo-Xe [1] is employed. Initial gas bubbles with a low Xe concentration (underpressured) are generated in a body-centered cubic (bcc) U10Mo single crystal. Then Xe atoms are sequentially added into the bubbles one by one, and the evolution of pressure and dislocation emission around the bubbles is analyzed. The relationship between pressure, equilibrium Xe concentration, and radius of the bubbles is established. It was found that an overpressured gas bubble emits partial dislocations with a Burgers vector along the direction and a slip plane of (11-2). Meanwhile, dislocation loop punch out was not observed. The overpressured bubble also induces an anisotropic stress field. A tensile stress was found along directions around the bubble, favoring the nucleation and formation of a face-centered cubic bubble superlattice in bcc U10Mo fuels.

  11. Transferability of Polymer Chain Properties between Coarse-Grained and Atomistic Models of Natural Rubber Molecule Validated by Molecular Dynamics Simulations

    Science.gov (United States)

    Kitjanon, Jiramate; Khuntawee, Wasinee; Sutthibutpong, Thana; Boonnoy, Phansiri; Phongphanphanee, Saree; Wong-ekkabut, Jirasak

    2017-09-01

    In this study, we have successfully parameterized the coarse-grained (CG) model of cis-1,4-polyisoprene (main component of natural rubber) based on the MARTINI force field. An isoprene monomer is mapped into one bead of CG model. The structure, bulk and thermodynamics properties of cis-1,4-polyisoprene with new CG model are well comparable to the atomistic simulation model and experiment. Our CG model of cis-1,4-polyisoprene will be helpful to study in the advanced rubber nanocomposite materials.

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

    Science.gov (United States)

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

    2015-06-01

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

  13. Improved atomistic Monte Carlo simulations demonstrate that poly-L-proline adopts heterogeneous ensembles of conformations of semi-rigid segments interrupted by kinks.

    Science.gov (United States)

    Radhakrishnan, Aditya; Vitalis, Andreas; Mao, Albert H; Steffen, Adam T; Pappu, Rohit V

    2012-06-14

    Poly-L-proline (PLP) polymers are useful mimics of biologically relevant proline-rich sequences. Biophysical and computational studies of PLP polymers in aqueous solutions are challenging because of the diversity of length scales and the slow time scales for conformational conversions. We describe an atomistic simulation approach that combines an improved ABSINTH implicit solvation model, with conformational sampling based on standard and novel Metropolis Monte Carlo moves. Refinements to forcefield parameters were guided by published experimental data for proline-rich systems. We assessed the validity of our simulation results through quantitative comparisons to experimental data that were not used in refining the forcefield parameters. Our analysis shows that PLP polymers form heterogeneous ensembles of conformations characterized by semirigid, rod-like segments interrupted by kinks, which result from a combination of internal cis peptide bonds, flexible backbone ψ angles, and the coupling between ring puckering and backbone degrees of freedom.

  14. Numerical Simulations on the Laser Spot Welding of Zirconium Alloy Endplate for Nuclear Fuel Bundle Assembly

    Science.gov (United States)

    Satyanarayana, G.; Narayana, K. L.; Boggarapu, Nageswara Rao

    2018-01-01

    In the nuclear industry, a critical welding process is joining of an end plate to a fuel rod to form a fuel bundle. Literature on zirconium welding in such a critical operation is limited. A CFD model is developed and performed for the three-dimensional non-linear thermo-fluid analysis incorporating buoyancy and Marnangoni stress and specifying temperature dependent properties to predict weld geometry and temperature field in and around the melt pool of laser spot during welding of a zirconium alloy E110 endplate with a fuel rod. Using this method, it is possible to estimate the weld pool dimensions for the specified laser power and laser-on-time. The temperature profiles will estimate the HAZ and microstructure. The adequacy of generic nature of the model is validated with existing experimental data.

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

    Science.gov (United States)

    Nie, Yifan; Liang, Chaoping; Cha, Pil-Ryung; Colombo, Luigi; Wallace, Robert M; Cho, Kyeongjae

    2017-06-07

    Controlled growth of crystalline solids is critical for device applications, and atomistic modeling methods have been developed for bulk crystalline solids. Kinetic Monte Carlo (KMC) simulation method provides detailed atomic scale processes during a solid growth over realistic time scales, but its application to the growth modeling of van der Waals (vdW) heterostructures has not yet been developed. Specifically, the growth of single-layered transition metal dichalcogenides (TMDs) is currently facing tremendous challenges, and a detailed understanding based on KMC simulations would provide critical guidance to enable controlled growth of vdW heterostructures. In this work, a KMC simulation method is developed for the growth modeling on the vdW epitaxy of TMDs. The KMC method has introduced full material parameters for TMDs in bottom-up synthesis: metal and chalcogen adsorption/desorption/diffusion on substrate and grown TMD surface, TMD stacking sequence, chalcogen/metal ratio, flake edge diffusion and vacancy diffusion. The KMC processes result in multiple kinetic behaviors associated with various growth behaviors observed in experiments. Different phenomena observed during vdW epitaxy process are analysed in terms of complex competitions among multiple kinetic processes. The KMC method is used in the investigation and prediction of growth mechanisms, which provide qualitative suggestions to guide experimental study.

  16. Voltage clamp simulations for multifiber bundles in a double sucrose gap: cable complications.

    Science.gov (United States)

    Solchenbach, K; Haas, H G; Brommundt, G

    1986-10-01

    A theoretical model is presented for voltage clamp of a bundle of cylindrical excitable cells in a double sucrose gap. The preparation in the test node is represented by a single one-dimensional cable (length/diameter ratio approximately) with standard Hodgkin-Huxley kinetics for transmembrane Na current. Imperfections of voltage control due to internal (longitudinal) resistivity and external (radial) resistance in series to the membrane are analysed. The electrical behavior of a fiber is described by the cable equation with appropriate boundary conditions and subsidiary equations reflecting the membrane characteristics. Membrane voltage and current distribution in response to a step command was obtained by numerical integration. The results are described in two papers. The present paper deals with the effect of internal resistivity with the external resistance being neglected. The closed loop response of a fiber displays a strong tendency to oscillate. To stabilize the system a phase lead was inserted and the gain of the control amplifier was reduced. Conditions for stability were examined by Nyquist analysis. When the Na system was activated by a command pulse below ENa, a voltage gradient developed between a depolarization (relative to the command signal) at the end where voltage was monitored and a hyperpolarization at the site of current injection. In spite of a poor voltage control the total measured current appeared to have a smooth transient. With large voltage gradients a small, second inward current was seen. At a low (high) Na conductance maximum peak inward current was larger (smaller) that the current expected from ideal space clamping.

  17. 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.

  18. Free volume theory applied to lateral diffusion in Langmuir monolayers: atomistic simulations for a protein-free model of lung surfactant.

    Science.gov (United States)

    Javanainen, Matti; Monticelli, Luca; Bernardino de la Serna, Jorge; Vattulainen, Ilpo

    2010-10-05

    We hereby present a study on lateral diffusion of lipids in Langmuir monolayers. We apply atomistic molecular dynamics simulations to a model system whose composition is consistent with protein-free lung surfactant. Our main focus is on the assessment of the validity of the free volume theory for lateral diffusion and on the interpretation of the cross-sectional area and activation energy parameters appearing in the theory. We find that the diffusion results can be fitted to the description given by the free volume theory, but the interpretation of its parameters is not straightforward. While the cross-sectional area appears to be related to the hard-core cross-sectional area of a lipid, its role in the lateral diffusion process is unclear. Also, the activation energy derived using the free volume theory is different from the activation energy found through Arrhenius analysis, and its physical interpretation remains elusive. Finally, we find that lipid diffusion does not occur via rapid single-particle "jumps". Instead, lipids move in a concerted manner as loosely defined transient clusters, as observed earlier for lipid bilayers.

  19. Atomistic Molecular Dynamics Simulations of Carbon Dioxide Diffusivity in n-Hexane, n-Decane, n-Hexadecane, Cyclohexane, and Squalane.

    Science.gov (United States)

    Moultos, Othonas A; Tsimpanogiannis, Ioannis N; Panagiotopoulos, Athanassios Z; Trusler, J P Martin; Economou, Ioannis G

    2016-12-22

    Atomistic molecular dynamics simulations were carried out to obtain the diffusion coefficients of CO2 in n-hexane, n-decane, n-hexadecane, cyclohexane, and squalane at temperatures up to 423.15 K and pressures up to 65 MPa. Three popular models were used for the representation of hydrocarbons: the united atom TraPPE (TraPPE-UA), the all-atom OPLS, and an optimized version of OPLS, namely, L-OPLS. All models qualitatively reproduce the pressure dependence of the diffusion coefficient of CO2 in hydrocarbons measured recently, and L-OPLS was found to be the most accurate. Specifically for n-alkanes, L-OPLS also reproduced the measured viscosities and densities much more accurately than the original OPLS and TraPPE-UA models, indicating that the optimization of the torsional potential is crucial for the accurate description of transport properties of long chain molecules. The three force fields predict different microscopic properties such as the mean square radius of gyration for the n-alkane molecules and pair correlation functions for the CO2-n-alkane interactions. CO2 diffusion coefficients in all hydrocarbons studied are shown to deviate significantly from the Stokes-Einstein behavior.

  20. Effect of bundle size on cladding deformation in LOCA simulation tests. [PWR; BWR

    Energy Technology Data Exchange (ETDEWEB)

    Chapman, R.H.; Crowley, J.L.; Longest, A.W.

    1982-01-01

    Two LOCA simulation tests were conducted to investigate the effects of temperature uniformity and radial restraint boundary conditions on Zircaloy cladding deformation. In one of the tests (B-5), boundary conditions typical of a large array were imposed on an inner 4 x 4 square array by two concentric rings of interacting guard fuel pin simulators. In the other test (B-3), the boundary conditions were imposed on a 4 x 4 square array by a non-interacting heated shroud. Test parameters conducive to large deformation were selected in order to favor rod-to-rod interactions. The tests showed that rod-to-rod interactions play an important role in the deformation process.

  1. 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

  2. Super-micron-scale atomistic simulation for electronic transport with atomic vibration: Unified approach from quantum to classical transport

    Science.gov (United States)

    Ishizeki, Keisuke; Sasaoka, Kenji; Konabe, Satoru; Souma, Satofumi; Yamamoto, Takahiro

    2017-07-01

    We develop a powerful simulation method that can treat electronic transport in a super-micron-scale open system with atomic vibration at finite temperature. As an application of the developed method to realistic materials, we simulate electronic transport in metallic single-walled carbon nanotubes from nanometer scale to micrometer scale at room temperature. Based on the simulation results, we successfully identify two different crossovers, namely, ballistic to diffusive crossover and coherent to incoherent crossover, simultaneously and with equal footing, from which the mean free path and the phase coherence length can be extracted clearly. Moreover, we clarify the scaling behavior of the electrical resistance and the electronic current in the crossover regime.

  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...

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    be the method of choice to explore how carbohydrates function. However, the progress in the field is limited by the lack of appropriate tools for preparing carbohydrate structures and related topology files for the simulation models. Here we present tools that fill this gap. Applications where the tools...

  5. doGlycans-Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS

    Czech Academy of Sciences Publication Activity Database

    Danne, R.; Poojari, C.; Martinez-Seara, Hector; Rissanen, S.; Lolicato, F.; Róg, T.; Vattulainen, I.

    2017-01-01

    Roč. 57, č. 10 (2017), s. 2401-2406 ISSN 1549-9596 Institutional support: RVO:61388963 Keywords : molecular dynamics simulations * GROMOS force field * cellulose nanofibrils Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.760, year: 2016 http://pubs.acs.org/doi/full/10.1021/acs.jcim.7b00237

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

    Directory of Open Access Journals (Sweden)

    Pär Bjelkmar

    2009-02-01

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

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

    Science.gov (United States)

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

    2017-10-01

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

  8. 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

    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......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...... and significant thinning of the membrane also observed in experiments, this provides additional support for the predictive power of microsecond-scale membrane protein simulations....

  9. Atomistic simulations of nanocrystalline U0.5Th0.5O2 solid solution under uniaxial tension

    Directory of Open Access Journals (Sweden)

    Hongxing Xiao

    2017-12-01

    Full Text Available Molecular dynamics simulations were performed to investigate the uniaxial tensile properties of nanocrystalline U0.5Th0.5O2 solid solution with the Born–Mayer–Huggins potential. The results indicated that the elastic modulus increased linearly with the density relative to a single crystal, but decreased with increasing temperature. The simulated nanocrystalline U0.5Th0.5O2 exhibited a breakdown in the Hall–Petch relation with mean grain size varying from 3.0 nm to 18.0 nm. Moreover, the elastic modulus of U1-yThyO2 solid solutions with different content of thorium at 300 K was also studied and the results accorded well with the experimental data available in the literature. In addition, the fracture mode of nanocrystalline U0.5Th0.5O2 was inclined to be ductile because the fracture behavior was preceded by some moderate amount of plastic deformation, which is different from what has been seen earlier in simulations of pure UO2.

  10. Atomistic simulation studies of the α/β-glucoside and galactoside in anhydrous bilayers: effect of the anomeric and epimeric configurations.

    Science.gov (United States)

    Ahmadi, Sara; Manickam Achari, Vijayan; Nguan, Hockseng; Hashim, Rauzah

    2014-03-01

    Fully atomistic molecular dynamics simulation studies of thermotropic bilayers were performed using a set of glycosides namely n-octyl-β-D-glucopyranoside (β-C8Glc), n-octyl-α-D-glucopyranoside (α-C8Glc), n-octyl-β-D-galactopyranoside (β-C8Gal), and n-octyl-α-D-galactopyranoside (α-C8Gal) to investigate the stereochemical relationship of the epimeric/anomeric quartet liner glycolipids with the same octyl chain group. The results showed that, the anomeric stereochemistry or the axial/equatorial orientation of C1-O1 (α/β) is an important factor controlling the area and d-spacing of glycolipid bilayer systems in the thermotropic phase. The head group tilt angle and the chain ordering properties are affected by the anomeric effect. In addition, the L(C) phase of β-C8Gal, is tilting less compared to those in the fluid L(α). The stereochemistry of the C4-epimeric (axial/equatorial) and anomeric (α/β) centers simultaneously influence the inter-molecular hydrogen bond. Thus, the trend in the values of the hydrogen bond for these glycosides is β-C8Gal > α-C8Glc > β-C8Glc > α-C8Gal. The four bilayer systems showed anomalous diffusion behavior with an observed trend for the diffusion coefficients; and this trend is β-C8Gal > β-C8Glc > α-C8Gal > α-C8Glc. The "bent" configuration of the α-anomer results in an increase of the hydrophobic area, chain vibration and chain disorganization. Since thermal energy is dispensed more entropically for the chain region, the overall molecular diffusion decreases.

  11. Atomistic simulation of the trapping capability of He-vacancy defects at Ni {\\sum}^{}3\\left(1\\bar{1}2\\right)[110] grain boundary

    Science.gov (United States)

    Gong, Hengfeng; Wang, Chengbin; Zhang, Wei; Huai, Ping; Lu, Wei; Zhu, Zhiyuan

    2016-12-01

    He atoms tend to cluster and precipitate into bubbles that prefer to grow in the grain boundaries, resulting in high temperature He embrittlement with significantly degraded material properties. This is a major bottleneck in employing Ni-based alloys for applications such as molten salt reactors (MSRs). This paper focuses on understanding how the local grain boundary structure interacts with He atoms and how the local atomistic environment in the grain boundary influences the binding energy of He defects. Using molecular dynamics simulations, we have investigated the trapping capability of the Ni {\\sum}3≤ft(1 \\bar{1} 2\\right)≤ft[1 1 0\\right] grain boundary to He defects (He N ) and to He-vacancy defects (He N V M ). The two defects in the Ni grain boundary exhibit geometries with high symmetry. The binding energy of an interstitial He atom to He N V M defects is found to be generally larger in pure Ni than that in the grain boundary. We compared the binding energy of He N defects to the Ni vacancy and to the Ni grain boundary, finding that the Ni vacancy possesses a higher trapping strength to He N . We also found that the binding strength of He N to the grain boundary is stronger than that of He N V M to the grain boundary. The He-vacancy ratio in He N V M defects does not significantly affect the binding energy in the grain boundary plane. The current work will provide insight in understanding the experimentally observed He bubble formation in Ni-based alloys and bridge atomic scale events and damage with macroscopic failure.

  12. Phase Transformation in Monolayer Molybdenum Disulphide (MoS2) with and without Defects under Tension Predicted by Atomistic Simulations

    Science.gov (United States)

    Dillon, Keith

    In addition to its use as a solid lubricant, molybdenum disulphide (MoS 2) has gained recent attention as a possible substitute for silicon as it is increasingly difficult to keep shrinking down electronic devices made of silicon, the conventional electronic material. When thinned down to atomic thickness, monolayer MoS2 possesses very unique and promising electronic and electrical properties. Unlike electronic and electrical properties, knowledge of the mechanical properties and role of structural defects on these properties of monolayer MoS2 is unexplored. For this thesis, the two main objectives are (1) to gain insight about the failure mechanism of monolayer MoS2 by modeling nanoindentation performed on suspended free standing membrane with comparison to experiment and (2) to explore the influence of structural defects on the mechanical properties of monolayer MoS2 by modelling monolayer MoS2 membranes with defects and simulating the same nanoindentation process as in part (1). It is shown that the force required for fracture of the MoS2 monolayer increases with increasing indenter diameter. This relationship and the magnitudes of the breaking forces computed in this work are consistent with experiments presented in the literature. A phase transformation, caused by an abrupt drop in the S-S intralayer Z dimension, is observed prior to failure during both defect-free and defect-containing membrane simulations. This phase transformation is also observed in uniaxial tension simulations. Analysis suggests that structural defects alter the failure mechanisms of monolayer MoS2 and thus reduce its mechanical performance. For point defects, the phase transformation initiates from accumulated vacancies away from the center of the membrane and accelerates the new phase propagation process. For grain boundary structures, it was found that their fracture strength is independent of the grain boundary energy.

  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

    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-molecular......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...

  14. Primary radiation damage of Zr-0.5%Nb binary alloy: atomistic simulation by molecular dynamics method

    Science.gov (United States)

    Tikhonchev, M.; Svetukhin, V.; Kapustin, P.

    2017-09-01

    Ab initio calculations predict high positive binding energy (˜1 eV) between niobium atoms and self-interstitial configurations in hcp zirconium. It allows the expectation of increased niobium fraction in self-interstitials formed under neutron irradiation in atomic displacement cascades. In this paper, we report the results of molecular dynamics simulation of atomic displacement cascades in Zr-0.5%Nb binary alloy and pure Zr at the temperature of 300 K. Two sets of n-body interatomic potentials have been used for the Zr-Nb system. We consider a cascade energy range of 2-20 keV. Calculations show close estimations of the average number of produced Frenkel pairs in the alloy and pure Zr. A high fraction of Nb is observed in the self-interstitial configurations. Nb is mainly detected in single self-interstitial configurations, where its fraction reaches tens of percent, i.e. more than its tenfold concentration in the matrix. The basic mechanism of this phenomenon is the trapping of mobile self-interstitial configurations by niobium. The diffusion of pure zirconium and mixed zirconium-niobium self-interstitial configurations in the zirconium matrix at 300 K has been simulated. We observe a strong dependence of the estimated diffusion coefficients and fractions of Nb in self-interstitials produced in displacement cascades on the potential.

  15. Impact of hydration on the micromechanical properties of the polymer composite structure of wood investigated with atomistic simulations

    Science.gov (United States)

    Kulasinski, Karol; Derome, Dominique; Carmeliet, Jan

    2017-06-01

    A model of the secondary layer of wood cell wall consisting of crystalline cellulose, hemicellulose, and lignin is constructed and investigated with molecular dynamics simulations in the full range of hydration: from dry to saturated state. The model is considered a composite with the cellulose fibrils embedded in hemicellulose and lignin, forming a soft amorphous matrix. Its complex structure leads to nonlinear and anisotropic swelling and mechanical weakening. The water diffusivity through the pores is affected by an interplay between stiff cellulose fibers and weakening amorphous polymers. The formation and breaking of hydrogen bonds within the polymers and at the interfaces is found to be the underlying mechanism of adsorption-induced mechanical softening. The model is tested for adsorption isotherm, mechanical moduli, hydrogen bonds, and water diffusivity that all undergo a substantial change as the hydration increases. The determined physical and mechanical properties, changing with hydration, agree qualitatively with experimental measurements.

  16. Investigating interfacial contact configuration and behavior of single-walled carbon nanotube-based nanodevice with atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Cui, Jianlei, E-mail: cjlxjtu@mail.xjtu.edu.cn; Zhang, Jianwei [Xi’an Jiaotong University, State Key Laboratory for Manufacturing Systems Engineering (China); He, Xiaoqiao, E-mail: bcxqhe@cityu.edu.hk [City University of Hong Kong, Department of Architecture and Civil Engineering (Hong Kong); Mei, Xuesong; Wang, Wenjun [Xi’an Jiaotong University, State Key Laboratory for Manufacturing Systems Engineering (China); Yang, Xinju [Fudan University, State Key Laboratory of Surface Physics and Department of Physics (China); Xie, Hui; Yang, Lijun; Wang, Yang [Harbin Institute of Technology, State Key Laboratory of Robotics and Systems (China)

    2017-03-15

    Carbon nanotubes (CNTs), including single-walled carbon nanotubes (SWNTs) and multi-walled carbon nanotubes (MWNTs), are considered to be the promising candidates for next-generation interconnects with excellent physical and chemical properties ranging from ultrahigh mechanical strength, to electrical properties, to thermal conductivity, to optical properties, etc. To further study the interfacial contact configurations of SWNT-based nanodevice with a 13.56-Å diameter, the corresponding simulations are carried out with the molecular dynamic method. The nanotube collapses dramatically into the surface with the complete collapse on the Au/Ag/graphite electrode surface and slight distortion on the Si/SiO{sub 2} substrate surface, respectively. The related dominant mechanism is studied and explained. Meanwhile, the interfacial contact configuration and behavior, depended on other factors, are also analyzed in this article.

  17. 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.

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

    Science.gov (United States)

    Sun, Yunxiang; Qian, Zhenyu; Wei, Guanghong

    2016-05-14

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

  19. Atomistic simulations of the effects of polyglutamine chain length and solvent quality on conformational equilibria and spontaneous homodimerization.

    Science.gov (United States)

    Vitalis, Andreas; Wang, Xiaoling; Pappu, Rohit V

    2008-12-05

    Aggregation of expanded polyglutamine tracts is associated with nine different neurodegenerative diseases, including Huntington's disease. Experiments and computer simulations have demonstrated that monomeric forms of polyglutamine molecules sample heterogeneous sets of collapsed structures in water. The current work focuses on a mechanistic characterization of polyglutamine homodimerization as a function of chain length and temperature. These studies were carried out using molecular simulations based on a recently developed continuum solvation model that was designed for studying conformational and binding equilibria of intrinsically disordered molecules such as polyglutamine systems. The main results are as follows: Polyglutamine molecules form disordered, collapsed globules in aqueous solution. These molecules spontaneously associate at conditions approaching those of typical in vitro experiments for chains of length N>/=15. The spontaneity of these homotypic associations increases with increasing chain length and decreases with increasing temperature. Similar and generic driving forces govern both collapse and spontaneous homodimerization of polyglutamine in aqueous milieus. Collapse and dimerization maximize self-interactions and reduce the interface between polyglutamine molecules and the surrounding solvent. Other than these generic considerations, there do not appear to be any specific structural requirements for either chain collapse or chain dimerization; that is, both collapse and dimerization are nonspecific in that disordered globules form disordered dimers. In fact, it is shown that the driving force for intermolecular associations is governed by spontaneous conformational fluctuations within monomeric polyglutamine. These results suggest that polyglutamine aggregation is unlikely to follow a homogeneous nucleation mechanism with the monomer as the critical nucleus. Instead, the results support the formation of disordered, non-beta-sheet-like soluble

  20. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Cui, Jianlei, E-mail: cjlxjtu@mail.xjtu.edu.cn; Zhang, Jianwei [Xi’an Jiaotong University, State Key Laboratory for Manufacturing Systems Engineering (China); He, Xiaoqiao, E-mail: bcxqhe@cityu.edu.hk [City University of Hong Kong, Department of Architecture and Civil Engineering (Hong Kong); Yang, Xinjun [Fudan University, State Key Laboratory of Surface Physics and Department of Physics (China); Mei, Xuesong; Wang, Wenjun; Jiang, Gedong; Wang, Kedian [Xi’an Jiaotong University, State Key Laboratory for Manufacturing Systems Engineering (China); Yang, Lijun; Xie, Hui [Harbin Institute of Technology, State Key Laboratory of Robotics and Systems (China)

    2017-03-15

    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. 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.

  3. 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

    2017-02-13

    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.

  4. 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.

  5. 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

  6. Dynamics of flagellar bundling

    Science.gov (United States)

    Janssen, Pieter; Graham, Michael

    2010-11-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-08-21

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

  8. 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.

  9. 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...

  10. Atomistic spin dynamics and surface magnons

    Science.gov (United States)

    Etz, Corina; Bergqvist, Lars; Bergman, Anders; Taroni, Andrea; Eriksson, Olle

    2015-06-01

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

  11. Addressing uncertainty in atomistic machine learning

    DEFF Research Database (Denmark)

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

    2017-01-01

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

  12. 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.

  13. 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.

  14. Theoretical underpinning and prototype implementation of scenario bundle-based logical control for simulation of human–artifact interaction

    NARCIS (Netherlands)

    Van der Vegte, W.F.; Horváth, I.

    2012-01-01

    This article presents a new methodology that enables designers to include in simulations not only the physics aspects of artifact behavior, but also human actions. The motivation for this research came from the fact that none of the conventional approaches to engineering simulations includes

  15. Addressing uncertainty in atomistic machine learning.

    Science.gov (United States)

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

    2017-05-10

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

  16. Atomistic approach for modeling metal-semiconductor interfaces

    DEFF Research Database (Denmark)

    Stradi, Daniele; Martinez, Umberto; Blom, Anders

    2016-01-01

    We present a general framework for simulating interfaces using an atomistic approach based on density functional theory and non-equilibrium Green's functions. The method includes all the relevant ingredients, such as doping and an accurate value of the semiconductor band gap, required to model re...

  17. Concurrent multiscale modelling of atomistic and hydrodynamic processes in liquids

    Science.gov (United States)

    Markesteijn, Anton; Karabasov, Sergey; Scukins, Arturs; Nerukh, Dmitry; Glotov, Vyacheslav; Goloviznin, Vasily

    2014-01-01

    Fluctuations of liquids at the scales where the hydrodynamic and atomistic descriptions overlap are considered. The importance of these fluctuations for atomistic motions is discussed and examples of their accurate modelling with a multi-space–time-scale fluctuating hydrodynamics scheme are provided. To resolve microscopic details of liquid systems, including biomolecular solutions, together with macroscopic fluctuations in space–time, a novel hybrid atomistic–fluctuating hydrodynamics approach is introduced. For a smooth transition between the atomistic and continuum representations, an analogy with two-phase hydrodynamics is used that leads to a strict preservation of macroscopic mass and momentum conservation laws. Examples of numerical implementation of the new hybrid approach for the multiscale simulation of liquid argon in equilibrium conditions are provided. PMID:24982246

  18. Using molecular dynamics for the refinement of atomistic models of GPCRs by homology modeling.

    Science.gov (United States)

    Lupala, Cecylia S; Rasaeifar, Bahareh; Gomez-Gutierrez, Patricia; Perez, Juan J

    2017-08-14

    Despite GPCRs sharing a common seven helix bundle, analysis of the diverse crystallographic structures available reveal specific features that might be relevant for ligand design. Despite the number of crystallographic structures of GPCRs steadily increasing, there are still challenges that hamper the availability of new structures. In the absence of a crystallographic structure, homology modeling remains one of the important techniques for constructing 3D models of proteins. In the present study we investigated the use of molecular dynamics simulations for the refinement of GPCRs models constructed by homology modeling. Specifically, we investigated the relevance of template selection, ligand inclusion as well as the length of the simulation on the quality of the GPCRs models constructed. For this purpose we chose the crystallographic structure of the rat muscarinic M3 receptor as reference and constructed diverse atomistic models by homology modeling, using different templates. Specifically, templates used in the present work include the human muscarinic M2; the more distant human histamine H1 and the even more distant bovine rhodopsin as shown in the GPCRs phylogenetic tree. We also investigated the use or not of a ligand in the refinement process. Hence, we conducted the refinement process of the M3 model using the M2 muscarinic as template with tiotropium or NMS docked in the orthosteric site and compared with the results obtained with a model refined without any ligand bound.

  19. Atomistic Modeling of Corrosion Events at the Interface between a Metal and Its Environment

    Directory of Open Access Journals (Sweden)

    Christopher D. Taylor

    2012-01-01

    Full Text Available Atomistic simulation is a powerful tool for probing the structure and properties of materials and the nature of chemical reactions. Corrosion is a complex process that involves chemical reactions occurring at the interface between a material and its environment and is, therefore, highly suited to study by atomistic modeling techniques. In this paper, the complex nature of corrosion processes and mechanisms is briefly reviewed. Various atomistic methods for exploring corrosion mechanisms are then described, and recent applications in the literature surveyed. Several instances of the application of atomistic modeling to corrosion science are then reviewed in detail, including studies of the metal-water interface, the reaction of water on electrified metallic interfaces, the dissolution of metal atoms from metallic surfaces, and the role of competitive adsorption in controlling the chemical nature and structure of a metallic surface. Some perspectives are then given concerning the future of atomistic modeling in the field of corrosion science.

  20. Single Actin Bundle Rheology.

    Science.gov (United States)

    Strehle, Dan; Mollenkopf, Paul; Glaser, Martin; Golde, Tom; Schuldt, Carsten; Käs, Josef A; Schnauß, Jörg

    2017-10-24

    Bundled actin structures play an essential role in the mechanical response of the actin cytoskeleton in eukaryotic cells. Although responsible for crucial cellular processes, they are rarely investigated in comparison to single filaments and isotropic networks. Presenting a highly anisotropic structure, the determination of the mechanical properties of individual bundles was previously achieved through passive approaches observing bending deformations induced by thermal fluctuations. We present a new method to determine the bending stiffness of individual bundles, by measuring the decay of an actively induced oscillation. This approach allows us to systematically test anisotropic, bundled structures. Our experiments revealed that thin, depletion force-induced bundles behave as semiflexible polymers and obey the theoretical predictions determined by the wormlike chain model. Thickening an individual bundle by merging it with other bundles enabled us to study effects that are solely based on the number of involved filaments. These thicker bundles showed a frequency-dependent bending stiffness, a behavior that is inconsistent with the predictions of the wormlike chain model. We attribute this effect to internal processes and give a possible explanation with regard to the wormlike bundle theory.

  1. Single Actin Bundle Rheology

    Directory of Open Access Journals (Sweden)

    Dan Strehle

    2017-10-01

    Full Text Available Bundled actin structures play an essential role in the mechanical response of the actin cytoskeleton in eukaryotic cells. Although responsible for crucial cellular processes, they are rarely investigated in comparison to single filaments and isotropic networks. Presenting a highly anisotropic structure, the determination of the mechanical properties of individual bundles was previously achieved through passive approaches observing bending deformations induced by thermal fluctuations. We present a new method to determine the bending stiffness of individual bundles, by measuring the decay of an actively induced oscillation. This approach allows us to systematically test anisotropic, bundled structures. Our experiments revealed that thin, depletion force-induced bundles behave as semiflexible polymers and obey the theoretical predictions determined by the wormlike chain model. Thickening an individual bundle by merging it with other bundles enabled us to study effects that are solely based on the number of involved filaments. These thicker bundles showed a frequency-dependent bending stiffness, a behavior that is inconsistent with the predictions of the wormlike chain model. We attribute this effect to internal processes and give a possible explanation with regard to the wormlike bundle theory.

  2. Isothermal crystallization of short polymer chains induced by the oriented slab and the stretched bundle of polymer: a molecular dynamics simulation.

    Science.gov (United States)

    Yang, Jun-Sheng; Yang, Chuan-Lu; Wang, Mei-Shan; Chen, Bao-Dong; Ma, Xiao-Guang

    2012-02-23

    Information on the interfacial interaction is vital in understanding the crystallization of short polymer chains around oriented nuclei. However, this interaction is difficult to observe at the atomic level. Molecular dynamics simulations are performed to investigate the structural formation of polymer chains induced by the highly oriented slab or the stretched bundle of polymer chains. The results show that the surface-induced crystallization of polymer chains is greatly influenced by the foreign surface on the crystal structure and the morphology of the polymers, hence providing molecular-level support for previous experimental observations [Lotz et al. Macromolecules 1993, 26, 5915 and Yan et al. Macromolecules 2009, 42, 9321]. The order parameter S and the configurations show that the ability of the polypropylene (PP) slab to induce the polyethylene (PE) melt crystallization is weaker than that of the PE slab and that the short PE chains display multiple orientations on the PP slab. In addition, the crystallization rate was found to be dependent on the lattice matching between the free chains and the substrates on the contact lattice planes. © 2012 American Chemical Society

  3. Atomistic Modeling of Gas Adsorption in Nanocarbons

    Directory of Open Access Journals (Sweden)

    G. Zollo

    2012-01-01

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

  4. Cytoskeletal bundle mechanics

    NARCIS (Netherlands)

    Bathe, Mark; Heussinger, Claus; Claessens, Mireille Maria Anna Elisabeth; Bausch, Andreas R.; Frey, Erwin

    2008-01-01

    The mechanical properties of cytoskeletal actin bundles play an essential role in numerous physiological processes, including hearing, fertilization, cell migration, and growth. Cells employ a multitude of actin-binding proteins to actively regulate bundle dimensions and cross-linking properties to

  5. Baseline left bundle branch block with right bundle branch escape complexes in a patient with coronary artery disease, presents like an alternating bundle branch block: a case report

    Science.gov (United States)

    Bhimaraj, Arvind; Abusin, Salaheldin; Margeta, Bosko

    2008-01-01

    Alternating bundle branch block (ABBB) is a less commonly encountered phenomenon with the advent of re-perfusion therapy for acute myocardial infarction. ECGs simulating the appearance of an ABBB need to be carefully analysed. We present an ECG showing a baseline Left Bundle Branch Block(LBBB) progressing to a high grade AV block with escape complexes having a Right Bundle Branch Block (RBBB) morphology. Such an ECG can be mistaken for an ABBB if not analysed carefully. PMID:19116014

  6. Adaptive resolution simulations of biomolecular systems.

    Science.gov (United States)

    Zavadlav, Julija; Bevc, Staš; Praprotnik, Matej

    2017-12-01

    In this review article, we discuss and analyze some recently developed hybrid atomistic-mesoscopic solvent models for multiscale biomolecular simulations. We focus on the biomolecular applications of the adaptive resolution scheme (AdResS), which allows solvent molecules to change their resolution back and forth between atomistic and coarse-grained representations according to their positions in the system. First, we discuss coupling of atomistic and coarse-grained models of salt solution using a 1-to-1 molecular mapping-i.e., one coarse-grained bead represents one water molecule-for development of a multiscale salt solution model. In order to make use of coarse-grained molecular models that are compatible with the MARTINI force field, one has to resort to a supramolecular mapping, in particular to a 4-to-1 mapping, where four water molecules are represented with one coarse-grained bead. To this end, bundled atomistic water models are employed, i.e., the relative movement of water molecules that are mapped to the same coarse-grained bead is restricted by employing harmonic springs. Supramolecular coupling has recently also been extended to polarizable coarse-grained water models with explicit charges. Since these coarse-grained models consist of several interaction sites, orientational degrees of freedom of the atomistic and coarse-grained representations are coupled via a harmonic energy penalty term. The latter aligns the dipole moments of both representations. The reviewed multiscale solvent models are ready to be used in biomolecular simulations, as illustrated in a few examples.

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

    National Research Council Canada - National Science Library

    Yifan Nie; Chaoping Liang; Pil-Ryung Cha; Luigi Colombo; Robert M Wallace; Kyeongjae Cho

    2017-01-01

    .... Kinetic Monte Carlo (KMC) simulation method provides detailed atomic scale processes during a solid growth over realistic time scales, but its application to the growth modeling of van der Waals (vdW...

  8. 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.

    Science.gov (United States)

    Róg, Tomasz; Orłowski, Adam; Llorente, Alicia; Skotland, Tore; Sylvänne, Tuulia; Kauhanen, Dimple; Ekroos, Kim; Sandvig, Kirsten; Vattulainen, Ilpo

    2016-06-01

    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 in these models are: cholesterol (CHOL), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylethanolamine (POPE), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidyl-ethanolamine (SOPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (SOPS), N-palmitoyl-D-erythro-sphingosyl-phosphatidylcholine (SM16), and N-lignoceroyl-D-erythro-sphingosyl-phosphatidylcholine (SM24). The bilayers׳ compositions are based on lipidomic studies of PC-3 prostate cancer cells and exosomes discussed in Llorente et al. (2013) [1], showing an increase in the section of long-tail lipid species (SOPS, SOPE, and SM24) in the exosomes. Former knowledge about lipid asymmetry in cell membranes was accounted for in the models, meaning that the model of the inner leaflet is composed of a mixture of PC, PS, PE, and cholesterol, while the extracellular leaflet is composed of SM, PC and cholesterol discussed in Van Meer et al. (2008) [2]. The provided data include lipids׳ topologies, equilibrated structures of asymmetric bilayers, all force field parameters, and input files with parameters describing simulation conditions (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].

  9. The ABCDEF Implementation Bundle

    Directory of Open Access Journals (Sweden)

    Annachiara Marra

    2016-08-01

    Full Text Available Long-term morbidity, long-term cognitive impairment and hospitalization-associated disability are common occurrence in the survivors of critical illness, with significant consequences for patients and for the caregivers. The ABCDEF bundle represents an evidence-based guide for clinicians to approach the organizational changes needed for optimizing ICU patient recovery and outcomes. The ABCDEF bundle includes: Assess, Prevent, and Manage Pain, Both Spontaneous Awakening Trials (SAT and Spontaneous Breathing Trials (SBT, Choice of analgesia and sedation, Delirium: Assess, Prevent, and Manage, Early mobility and Exercise, and Family engagement. The purpose of this review is to describe the core features of the ABCDEF bundle.

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

    Energy Technology Data Exchange (ETDEWEB)

    Schwen, D. [Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Illinois 61801 (United States); Bringa, E. [CONICET and Instituto de Ciencias Basicas, Universidad Nacional de Cuyo, Mendoza 5500 (Argentina); Krauser, J. [Hochschule Harz, Friedrichstrasse 57-59, 38855 Werningerode (Germany); Weidinger, A. [Helmholtz-Zentrum Berlin fuer Materialien und Energie, 14109 Berlin (Germany); Trautmann, C. [GSI Helmholtzzentrum, Planckstr. 1, 64291, Darmstadt (Germany); Hofsaess, H. [II. Physikalisches Institut, Universitaet Goettingen, Friedrich-Hund-Platz 1, 37077 Goettingen (Germany)

    2012-09-10

    The formation of surface hillocks in diamond-like carbon is studied experimentally and by means of large-scale molecular dynamics simulations with 5 Multiplication-Sign 10{sup 6} atoms combined with a thermal spike model. The irradiation experiments with swift heavy ions cover a large electronic stopping range between {approx}12 and 72 keV/nm. Both experiments and simulations show that beyond a stopping power threshold, the hillock height increases linearly with the electronic stopping, and agree extremely well assuming an efficiency of approximately 20% in the transfer of electronic energy to the lattice. The simulations also show a transition of sp{sup 3} to sp{sup 2} bonding along the tracks with the hillocks containing almost no sp{sup 3} contribution.

  11. Bundle Branch Block

    Science.gov (United States)

    ... 2015. Bundle branch block Symptoms & causes Diagnosis & treatment Advertisement Mayo Clinic does not endorse companies or products. ... a Job Site Map About This Site Twitter Facebook Google YouTube Pinterest Mayo Clinic is a not- ...

  12. Thermodynamics of fiber bundles

    OpenAIRE

    Pride, Steven R.; Toussaint, Renaud

    2002-01-01

    A recent theory that determines the properties of disordered solids as the solid accumulates damage is applied to the special case of fiber bundles with global load sharing and is shown to be exact in this case. The theory postulates that the probability of observing a given emergent damage state is obtained by maximizing the emergent entropy as defined by Shannon subject to energetic constraints. This theory yields the known exact results for the fiber-bundle model with global load sharing a...

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    as ligand binding in this region can accelerate or decelerate the conformational inactivation. Plasticity in this region may thus be mechanistically linked to the conformational change, possibly through facilitation of further unfolding of the hydrophobic core, as previously reported. This study provides...... a promising example of how computer simulations can help tether out mechanisms of serpin function and dysfunction at a spatial and temporal resolution that is far beyond the reach of any experiment....

  14. Atomistic simulation of nanowires in the sp3d5s* tight-binding formalism: From boundary conditions to strain calculations

    Science.gov (United States)

    Luisier, Mathieu; Schenk, Andreas; Fichtner, Wolfgang; Klimeck, Gerhard

    2006-11-01

    As the active dimensions of metal-oxide field-effect transistors are approaching the atomic scale, the electronic properties of these “nanowire” devices must be treated on a quantum mechanical level. In this paper, the transmission coefficients and the density of states of biased and unbiased Si and GaAs nanowires are simulated using the sp3d5s* empirical tight-binding method. Each atom, as well as the connections to its nearest neighbors, is represented explicitly. The material parameters are optimized to reproduce bulk band-structure characteristics in various crystal directions and various strain conditions. A scattering boundary method to calculate the open boundary conditions in nanowire transistors is developed to reduce the computational burden. Existing methods such as iterative or generalized eigenvalue problem approaches are significantly more expensive than the transport simulation through the device. The algorithm can be coupled to nonequilibrium Green’s function and wave function transport calculations. The speed improvement is even larger if the wire transport direction is different from [100]. Finally, it is demonstrated that strain effects can be easily included in the present nanowire simulations.

  15. 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.

  16. Atomistic simulations of the equation of state and hybridization of liquid carbon at a temperature of 6000 K in the pressure range of 1-25 GPa

    Science.gov (United States)

    Dozhdikov, V. S.; Basharin, A. Yu.; Levashov, P. R.; Minakov, D. V.

    2017-12-01

    The equation of state and the structure of liquid carbon are studied by molecular simulation. Both classical and quantum molecular dynamics (QMD) are used to calculate the equation of state and the distribution of chemical bonds at 6000 K in the pressure range 1-25 GPa. Our calculations and results of other authors show that liquid carbon has a fairly low density on the order of 1.2-1.35 g/cm3 at pressures about 1 GPa. Owing to the coordination number analysis, this fact can be attributed to the high content of sp1-bonded atoms (more than 50% according to our ab initio computations). Six empirical potentials have been tested in order to describe the density dependence of pressure and structure at 6000 K. As a result, only one potential, ReaxFF/lg, was able to reproduce the QMD simulations for both the equation of state and the fraction of sp1, sp2, sp3-bonded atoms.

  17. Prediction of the concentration dependence of the surface tension and density of salt solutions: atomistic simulations using Drude oscillator polarizable and nonpolarizable models.

    Science.gov (United States)

    Neyt, Jean-Claude; Wender, Aurélie; Lachet, Véronique; Ghoufi, Aziz; Malfreyt, Patrice

    2013-07-28

    Molecular simulations using Drude oscillator polarizable and nonpolarizable models for water and ions are carried out to predict the dependence of the surface tension on salt concentration. The polarizable water and ion models are based only on the classical Drude oscillators. The temperature dependence of the surface tension of water is examined for different water models. The dependence of salt densities on salt concentration is investigated through the nonpolarizable and Drude oscillator polarizable models. Finally, the reproduction of the surface tension of salt solution over a large range of concentrations is analyzed through a number of combinations between ions and water force fields. The structure of the interface is then discussed as a function of polarization effects. We establish here the inability of the Drude oscillator polarizable force fields to reproduce the salt concentration dependence of surface tension of NaCl aqueous solutions.

  18. Atomistic Approach toward Selective Photocatalytic Oxidation of a Mustard-Gas Simulant: A Case Study with Heavy-Chalcogen-Containing PCN-57 Analogues.

    Science.gov (United States)

    Goswami, Subhadip; Miller, Claire E; Logsdon, Jenna L; Buru, Cassandra T; Wu, Yi-Lin; Bowman, David N; Islamoglu, Timur; Asiri, Abdullah M; Cramer, Christopher J; Wasielewski, Michael R; Hupp, Joseph T; Farha, Omar K

    2017-06-14

    Here we describe the synthesis of two Zr-based benzothiadiazole- and benzoselenadiazole-containing metal-organic frameworks (MOFs) for the selective photocatalytic oxidation of the mustard gas simulant, 2-chloroethyl ethyl sulfide (CEES). The photophysical properties of the linkers and MOFs are characterized by steady-state absorption and emission, time-resolved emission, and ultrafast transient absorption spectroscopy. The benzoselenadiazole-containing MOF shows superior catalytic activity compared to that containing benzothiadiazole with a half-life of 3.5 min for CEES oxidation to nontoxic 2-chloroethyl ethyl sulfoxide (CEESO). Transient absorption spectroscopy performed on the benzoselenadiazole linker reveals the presence of a triplet excited state, which decays with a lifetime of 9.4 μs, resulting in the generation of singlet oxygen for photocatalysis. This study demonstrates the effect of heavy chalcogen substitution within a porous framework for the modulation of photocatalytic activity.

  19. 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.

  20. Atomistic simulations and network-based modeling of the Hsp90-Cdc37 chaperone binding with Cdk4 client protein: A mechanism of chaperoning kinase clients by exploiting weak spots of intrinsically dynamic kinase domains.

    Directory of Open Access Journals (Sweden)

    Josh Czemeres

    Full Text Available A fundamental role of the Hsp90 and Cdc37 chaperones in mediating conformational development and activation of diverse protein kinase clients is essential in signal transduction. There has been increasing evidence that the Hsp90-Cdc37 system executes its chaperoning duties by recognizing conformational instability of kinase clients and modulating their folding landscapes. The recent cryo-electron microscopy structure of the Hsp90-Cdc37-Cdk4 kinase complex has provided a framework for dissecting regulatory principles underlying differentiation and recruitment of protein kinase clients to the chaperone machinery. In this work, we have combined atomistic simulations with protein stability and network-based rigidity decomposition analyses to characterize dynamic factors underlying allosteric mechanism of the chaperone-kinase cycle and identify regulatory hotspots that control client recognition. Through comprehensive characterization of conformational dynamics and systematic identification of stabilization centers in the unbound and client- bound Hsp90 forms, we have simulated key stages of the allosteric mechanism, in which Hsp90 binding can induce instability and partial unfolding of Cdk4 client. Conformational landscapes of the Hsp90 and Cdk4 structures suggested that client binding can trigger coordinated dynamic changes and induce global rigidification of the Hsp90 inter-domain regions that is coupled with a concomitant increase in conformational flexibility of the kinase client. This process is allosteric in nature and can involve reciprocal dynamic exchanges that exert global effect on stability of the Hsp90 dimer, while promoting client instability. The network-based rigidity analysis and emulation of thermal unfolding of the Cdk4-cyclin D complex and Hsp90-Cdc37-Cdk4 complex revealed weak spots of kinase instability that are present in the native Cdk4 structure and are targeted by the chaperone during client recruitment. Our findings

  1. Atomistic simulations and network-based modeling of the Hsp90-Cdc37 chaperone binding with Cdk4 client protein: A mechanism of chaperoning kinase clients by exploiting weak spots of intrinsically dynamic kinase domains.

    Science.gov (United States)

    Czemeres, Josh; Buse, Kurt; Verkhivker, Gennady M

    2017-01-01

    A fundamental role of the Hsp90 and Cdc37 chaperones in mediating conformational development and activation of diverse protein kinase clients is essential in signal transduction. There has been increasing evidence that the Hsp90-Cdc37 system executes its chaperoning duties by recognizing conformational instability of kinase clients and modulating their folding landscapes. The recent cryo-electron microscopy structure of the Hsp90-Cdc37-Cdk4 kinase complex has provided a framework for dissecting regulatory principles underlying differentiation and recruitment of protein kinase clients to the chaperone machinery. In this work, we have combined atomistic simulations with protein stability and network-based rigidity decomposition analyses to characterize dynamic factors underlying allosteric mechanism of the chaperone-kinase cycle and identify regulatory hotspots that control client recognition. Through comprehensive characterization of conformational dynamics and systematic identification of stabilization centers in the unbound and client- bound Hsp90 forms, we have simulated key stages of the allosteric mechanism, in which Hsp90 binding can induce instability and partial unfolding of Cdk4 client. Conformational landscapes of the Hsp90 and Cdk4 structures suggested that client binding can trigger coordinated dynamic changes and induce global rigidification of the Hsp90 inter-domain regions that is coupled with a concomitant increase in conformational flexibility of the kinase client. This process is allosteric in nature and can involve reciprocal dynamic exchanges that exert global effect on stability of the Hsp90 dimer, while promoting client instability. The network-based rigidity analysis and emulation of thermal unfolding of the Cdk4-cyclin D complex and Hsp90-Cdc37-Cdk4 complex revealed weak spots of kinase instability that are present in the native Cdk4 structure and are targeted by the chaperone during client recruitment. Our findings suggested that this

  2. Atomistic potential for graphene and other sp(2) carbon systems.

    Science.gov (United States)

    Fthenakis, Zacharias G; Kalosakas, George; Chatzidakis, Georgios D; Galiotis, Costas; Papagelis, Konstantinos; Lathiotakis, Nektarios N

    2017-11-14

    We introduce a torsional force field for sp(2) carbon to augment an in-plane atomistic potential of a previous work [G. Kalosakas et al., J. Appl. Phys., 2013, 113, 134307] so that it is applicable to out-of-plane deformations of graphene and related carbon materials. The introduced force field is fit to reproduce density-functional-theory calculation data of appropriately chosen structures. The aim is to create a force field that is as simple as possible so it can be efficient for large scale atomistic simulations of various sp(2) carbon structures without significant loss of accuracy. We show that the complete proposed potential reproduces characteristic properties of fullerenes and carbon nanotubes. In addition, it reproduces very accurately the out-of-plane acoustic and optical modes of graphene's phonon dispersion as well as all phonons with frequencies up to 1000 cm(-1).

  3. Right bundle branch block

    DEFF Research Database (Denmark)

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

    2013-01-01

    AimsTo determine the prevalence, predictors of newly acquired, and the prognostic value of right bundle branch block (RBBB) and incomplete RBBB (IRBBB) on a resting 12-lead electrocardiogram in men and women from the general population.Methods and resultsWe followed 18 441 participants included.......5%/2.3% in women, P Right bundle branch block was associated with significantly...... increased all-cause and cardiovascular mortality in both genders with age-adjusted hazard ratios (HR) of 1.31 [95% confidence interval (CI), 1.11-1.54] and 1.87 (95% CI, 1.48-2.36) in the gender pooled analysis with little attenuation after multiple adjustment. Right bundle branch block was associated...

  4. 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...

  5. 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.

  6. Monte Carlo simulation of the effect of shape and thickness on SEM-EDS microanalysis of asbestos fibres and bundles: the case of anthophyllite, tremolite and actinolite

    Science.gov (United States)

    Valdrè, G.; Moro, D.; Ulian, G.

    2018-01-01

    Asbestos is a generic term used for six types of silicate minerals that are found in fibres or bundles of fibres, which can be easily cleaved into thinner ones. Scanning electron microscopy energy-dispersive X-ray spectrometry (SEM-EDS) quantitative microanalysis of asbestos mineral fibres still represents a complex analytical issue because of the variable fibre shape and small thickness (asbestos. Realistic experimental conditions, such as sample geometry, SEM set-up and detector physics were taken into account. We report the results obtained on 100 μm long fibres and bundles of circular and square section and thicknesses from to 0.1 μm to 10 μm, for electron beam energies of 5, 15 and 25 keV. A strong influence of the asbestos mineral fibres and bundles shape and thickness on the detected EDS X-ray intensity was observed. In general, the X-ray intensities as a function of fibre thickness showed a considerable reduction below about 0.5 μm at 5 keV, 2 μm at 15 keV, and 5 μm at 25 keV for all the elements and minerals, with a non-linear dependence. Correction parameters, k-ratio, for the thickness effect were calculated and proposed.

  7. Buying bundles: the effects of bundle attributes on the value of bundling

    OpenAIRE

    Linthorst, M.M.; Telgen, Jan; Schotanus, Fredo

    2008-01-01

    We consider the situation in which a buyer has to find the optimal degree of bundling for buying goods and services. From a review of the literature we develop attributes associated with bundling. Each of these attributes has an effect on the value of a bundle. Combined, the attributes determine the value of a bundle. We describe how the various attributes of a bundle contribute to the value of a bundle given the context of the buying situation. Based on interviews, a further analysis of bund...

  8. Buying bundles: the effects of bundling attributes on the value of bundling

    OpenAIRE

    Linthorst, M.M.; Telgen, Jan; Schotanus, Fredo

    2008-01-01

    We consider the situation in which a buyer has to find the optimal degree of bundling for buying goods and services. From a review of the literature we develop attributes associated with bundling. Each of these attributes has an effect on the value of a bundle. Combined, the attributes determine the value of a bundle. We describe how the various attributes of a bundle contribute to the value of a bundle given the context of the buying situation. Based on interviews, a further analysis of bund...

  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. 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.

  11. Simulation-based Randomized Comparative Assessment of Out-of-Hospital Cardiac Arrest Resuscitation Bundle Completion by Emergency Medical Service Teams Using Standard Life Support or an Experimental Automation-assisted Approach.

    Science.gov (United States)

    Choi, Bryan; Asselin, Nicholas; Pettit, Catherine C; Dannecker, Max; Machan, Jason T; Merck, Derek L; Merck, Lisa H; Suner, Selim; Williams, Kenneth A; Jay, Gregory D; Kobayashi, Leo

    2016-12-01

    Effective resuscitation of out-of-hospital cardiac arrest (OHCA) patients is challenging. Alternative resuscitative approaches using electromechanical adjuncts may improve provider performance. Investigators applied simulation to study the effect of an experimental automation-assisted, goal-directed OHCA management protocol on EMS providers' resuscitation performance relative to standard protocols and equipment. Two-provider (emergency medical technicians (EMT)-B and EMT-I/C/P) teams were randomized to control or experimental group. Each team engaged in 3 simulations: baseline simulation (standard roles); repeat simulation (standard roles); and abbreviated repeat simulation (reversed roles, i.e., basic life support provider performing ALS tasks). Control teams used standard OHCA protocols and equipment (with high-performance cardiopulmonary resuscitation training intervention); for second and third simulations, experimental teams performed chest compression, defibrillation, airway, pulmonary ventilation, vascular access, medication, and transport tasks with goal-directed protocol and resuscitation-automating devices. Videorecorders and simulator logs collected resuscitation data. Ten control and 10 experimental teams comprised 20 EMT-B's; 1 EMT-I, 8 EMT-C's, and 11 EMT-P's; study groups were not fully matched. Both groups suboptimally performed chest compressions and ventilations at baseline. For their second simulations, control teams performed similarly except for reduced on-scene time, and experimental teams improved their chest compressions (P=0.03), pulmonary ventilations (Pautomation-assisted OHCA management augmented select resuscitation bundle element performance without comprehensive improvement.

  12. Bundle pricing with comparable items

    NARCIS (Netherlands)

    Grigoriev, Alexander; van Loon, Joyce; Sviridenko, Maxim; Uetz, Marc Jochen; Vredeveld, Tjark; Arge, L.; Hoffmann, M.; Welzl, E.

    2007-01-01

    We consider a revenue maximization problem where we are selling a set of items, each available in a certain quantity, to a set of bidders. Each bidder is interested in one or several bundles of items. We assume the bidders’ valuations for each of these bundles to be known. Whenever bundle prices are

  13. Bundling ecosystem services in Denmark

    DEFF Research Database (Denmark)

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

    2014-01-01

    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...

  14. Anisotropic solid-liquid interface kinetics in silicon: an atomistically informed phase-field model

    Science.gov (United States)

    Bergmann, S.; Albe, K.; Flegel, E.; Barragan-Yani, D. A.; Wagner, B.

    2017-09-01

    We present an atomistically informed parametrization of a phase-field model for describing the anisotropic mobility of liquid-solid interfaces in silicon. The model is derived from a consistent set of atomistic data and thus allows to directly link molecular dynamics and phase field simulations. Expressions for the free energy density, the interfacial energy and the temperature and orientation dependent interface mobility are systematically fitted to data from molecular dynamics simulations based on the Stillinger-Weber interatomic potential. The temperature-dependent interface velocity follows a Vogel-Fulcher type behavior and allows to properly account for the dynamics in the undercooled melt.

  15. Buying bundles: the effects of bundling attributes on the value of bundling

    NARCIS (Netherlands)

    Linthorst, M.M.; Telgen, Jan; Schotanus, Fredo

    2008-01-01

    We consider the situation in which a buyer has to find the optimal degree of bundling for buying goods and services. From a review of the literature we develop attributes associated with bundling. Each of these attributes has an effect on the value of a bundle. Combined, the attributes determine the

  16. Buying bundles: the effects of bundle attributes on the value of bundling

    NARCIS (Netherlands)

    Linthorst, M.M.; Telgen, Jan; Schotanus, Fredo

    2008-01-01

    We consider the situation in which a buyer has to find the optimal degree of bundling for buying goods and services. From a review of the literature we develop attributes associated with bundling. Each of these attributes has an effect on the value of a bundle. Combined, the attributes determine the

  17. 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).

  18. 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.

  19. 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

  20. 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.

  1. Bundled payments in orthopedic surgery.

    Science.gov (United States)

    Bushnell, Brandon D

    2015-02-01

    As a result of reading this article, physicians should be able to: 1. Describe the concept of bundled payments and the potential applications of bundled payments in orthopedic surgery. 2. For specific situations, outline a clinical episode of care, determine the participants in a bundling situation, and define care protocols and pathways. 3. Recognize the importance of resource utilization management, quality outcome measurement, and combined economic-clinical value in determining the value of bundled payment arrangements. 4. Identify the implications of bundled payments for practicing orthopedists, as well as the legal issues and potential future directions of this increasingly popular alternative payment method. Bundled payments, the idea of paying a single price for a bundle of goods and services, is a financial concept familiar to most American consumers because examples appear in many industries. The idea of bundled payments has recently gained significant momentum as a financial model with the potential to decrease the significant current costs of health care. Orthopedic surgery as a field of medicine is uniquely positioned for success in an environment of bundled payments. This article reviews the history, logistics, and implications of the bundled payment model relative to orthopedic surgery. Copyright 2015, SLACK Incorporated.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-04-15

    Highlights: • Investigate spacer grid with split-type mixing vanes. • Extent of predictability of experimental data by STAR-CCM+. • Reliability of two equation turbulence models. • Resistance to cross-flow through gaps. - Abstract: Mass transfer by diversion cross-flow through gaps is an important inter-subchannel interaction in fuel bundle of power reactors. It is normally due to the lateral pressure difference between adjacent sub-channels. This phenomenon is augmented in the presence of flow deflectors and is referred to as, directed cross-flow. Diversion cross-flow carries the momentum and energy of flow and hence affects the velocity and temperature profile in the rod bundle. The resistance to cross-flow in the transverse momentum equations is specified by the cross-flow resistant coefficient which is the subject of concern in the present study. In order to obtain data to correlate cross-flow resistance coefficient, computational fluid dynamic simulation using STAR-CCM+ was performed for flow of water at the bundle Reynolds number of Re1 = 3.4×10{sup 4} through a 5 × 5 rod bundle geometry supported by spacer grid with split mixing vanes for which the rod to rod pitch to diameter ratio was 1.33 and the rod to wall pitch to diameter ratio was 0.74. The two layer k-epsilon turbulence model with an all y+ automatic wall treatment function in STAR-CCM+ were adopted for an isothermal single phase (water) flow through the geometry. The objectives were to primarily investigate the extent of predictability of the experimental data by the computational fluid dynamic (CFD) simulation as a measure of reliability on the CFD code employed and also apply the simulation data to develop correlations for determining resistance coefficient to cross-flow. Validation of simulation results with experimental data showed good correlation of mean flow parameters with experimental data whiles turbulent fluctuations deviated largely from experimental trends. Generally, the

  3. 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.

  4. Muon bundles from the Universe

    Directory of Open Access Journals (Sweden)

    Kankiewicz P.

    2018-01-01

    Full Text Available Recently the CERN ALICE experiment, in its dedicated cosmic ray run, observed muon bundles of very high multiplicities, thereby confirming similar findings from the LEP era at CERN (in the CosmoLEP project. Significant evidence for anisotropy of arrival directions of the observed high multiplicity muonic bundles is found. Estimated directionality suggests their possible extragalactic provenance. We argue that muonic bundles of highest multiplicity are produced by strangelets, hypothetical stable lumps of strange quark matter infiltrating our Universe.

  5. 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.

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

    Science.gov (United States)

    Xiawa Wu; Robert J. Moon; Ashlie Martini

    2013-01-01

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

  7. 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

  8. 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.

  9. Literature review report on atomistic modeling tools for FeCrAl alloys

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yongfeng [Idaho National Lab. (INL), Idaho Falls, ID (United States); Schwen, Daniel [Idaho National Lab. (INL), Idaho Falls, ID (United States); Martinez, Enrique [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-12-01

    This reports summarizes the literature review results on atomistic tools, particularly interatomic potentials used in molecular dynamics simulations, for FeCrAl ternary alloys. FeCrAl has recently been identified as a possible cladding concept for accident tolerant fuels for its superior corrosion resistance. Along with several other concepts, an initial evaluation and recommendation are desired for FeCrAl before it’s used in realistic fuels. For this purpose, sufficient understanding on the in-reactor behavior of FeCrAl needs to be grained in a relatively short timeframe, and multiscale modeling and simulations have been selected as an efficient measure to supplement experiments and in-reactor testing for better understanding on FeCrAl. For the limited knowledge on FeCrAl alloys, the multiscale modeling approach relies on atomistic simulations to obtain the missing material parameters and properties. As a first step, atomistic tools have to be identified and this is the purpose of the present report. It was noticed during the literature survey that no interatomic potentials currently available for FeCrAl. Here, we summarize the interatomic potentials available for FeCr alloys for possible molecular dynamics studies using FeCr as surrogate materials. Other atomistic methods such as lattice kinetic Monte Carlo are also included in this report. A couple of research topics at the atomic scale are suggested based on the literature survey.

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

    Science.gov (United States)

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

    2018-01-01

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

  11. 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.

  12. Influence of knee flexion angle and transverse drill angle on creation of femoral tunnels in double-bundle anterior cruciate ligament reconstruction using the transportal technique: Three-dimensional computed tomography simulation analysis.

    Science.gov (United States)

    Choi, Chong Hyuk; Kim, Sung-Jae; Chun, Yong-Min; Kim, Sung-Hwan; Lee, Su-Keon; Eom, Nam-Kyu; Jung, Min

    2018-01-01

    The purpose of this study was to find appropriate flexion angle and transverse drill angle for optimal femoral tunnels of anteromedial (AM) bundle and posterolateral (PL) bundle in double-bundle ACL reconstruction using transportal technique. Thirty three-dimensional knee models were reconstructed. Knee flexion angles were altered from 100° to 130° at intervals of 10°. Maximum transverse drill angle (MTA), MTA minus 10° and 20° were set up. Twelve different tunnels were determined by four flexion angles and three transverse drill angles for each bundle. Tunnel length, wall breakage, inter-tunnel communication and graft-bending angle were assessed. Mean tunnel length of AM bundle was >30mm at 120° and 130° of flexion in all transverse drill angles. Mean tunnel length of PL bundle was >30mm during every condition. There were ≥1 cases of wall breakage except at 120° and 130° of flexion with MTA for AM bundle. There was no case of wall breakage for PL bundle. Considering inter-tunnel gap of >2mm without communication and obtuse graft-bending angle, 120° of flexion and MTA could be recommended as optimal condition for femoral tunnels of AM and PL bundles. Flexion angle and transverse drill angle had combined effect on femoral tunnel in double-bundle ACL reconstruction using transportal technique. Achieving flexion angle of 120° and transverse drill angle close to the medial femoral condyle could be recommended as optimal condition for femoral tunnels of AM and PL bundles to avoid insufficient tunnel length, wall breakage, inter-tunnel communication and acute graft-bending angle. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Atomistic Galois insertions for flow sensitive integrity

    DEFF Research Database (Denmark)

    Nielson, Flemming; Nielson, Hanne Riis

    2017-01-01

    and to obtain full automation we shall explore the over-approximating nature of static analysis. We demonstrate that the use of atomistic Galois insertions constitutes a stable framework in which to obtain sound and fully automatic enforcement of flow sensitive integrity. The framework is illustrated...

  14. 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.

  15. Biomechanical comparisons of knee stability after anterior cruciate ligament reconstruction between 2 clinically available transtibial procedures: anatomic double bundle versus single bundle.

    Science.gov (United States)

    Kondo, Eiji; Merican, Azhar M; Yasuda, Kazunori; Amis, Andrew A

    2010-07-01

    Several trials have compared the clinical results between anatomic double-bundle and single-bundle anterior cruciate ligament reconstruction procedures. However, it remains controversial whether the anatomic double-bundle procedure is superior to the single-bundle procedure. The anatomic double-bundle procedure will be better than the single-bundle procedure at resisting anterior laxity, internal rotation laxity, and pivot-shift instability. Controlled laboratory study. Eight cadaveric knees were tested in a 6 degrees of freedom rig using the following loading conditions: 90-N anterior tibialforce, 5-N.m internal and external tibial torques, and a simulated pivot-shift test. Tibiofemoral kinematics during the flexion-extension cycle were recorded with an optical tracking system for (1) intact, (2) anterior cruciate ligament-deficient knee, (3) anatomic double-bundle reconstruction, and (4) single-bundle reconstruction placed at 11 o'clock in the intercondylar notch. There were significant reductions of anterior laxity of 3.5 mm at 20 degrees of flexion, internal rotational laxity of 2.5 degrees at 20 degrees of flexion, and anterior translations (2 mm) and internal rotations (5 degrees ) in the simulated pivot-shift test in the double-bundle reconstruction com-pared with the single-bundle reconstruction. There were no significant differences between the 2 procedures for external rotation laxity. The postoperative anterior translation and internal rotation stability after anatomic double-bundle anterior cruciate ligament reconstruction were significantly better than after single-bundle reconstruction, in both static tests and the pivot shift. Unlike previous laboratory studies, this work used clinical arthroscopic methods for anterior cruciate ligament reconstruction, and found that the anatomic reconstruction was superior to a single graft placed at 11 o'clock.

  16. MAVEN EUV Modelled Data Bundle

    Data.gov (United States)

    National Aeronautics and Space Administration — This bundle contains solar irradiance spectra in 1-nm bins from 0-190 nm. The spectra are generated based upon the Flare Irradiance Spectra Model - Mars (FISM-M)...

  17. 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...

  18. MAVEN SWEA Calibrated Data Bundle

    Data.gov (United States)

    National Aeronautics and Space Administration — This bundle contains fully calibrated electron energy/angle (3D) distributions, pitch angle distributions, and omni-directional energy spectra. Tables of sensitivity...

  19. MAVEN LPW Derived Data Bundle

    Data.gov (United States)

    National Aeronautics and Space Administration — This bundle contains data which have been derived from other data products or determined by fits to other data. These are science quality data produced by the LPW...

  20. MAVEN LPW Calibrated Data Bundle

    Data.gov (United States)

    National Aeronautics and Space Administration — This bundle contains fully calibrated, science quality data produced by the LPW instrument. The data include spacecraft potential, electric field waveforms and wave...

  1. Modified NEGF method for atomistic modeling of field emission from carbon nanotube

    Science.gov (United States)

    Monshipouri, Mahta; Behrooz, Milad; Abdi, Yaser

    2017-09-01

    A model to simulate the atomistic properties of the field emission (FE) from a zigzag-single walled carbon nanotube (Z-SWCNT) is presented. By a modification of the self-energy in non-equilibrium Green's function (NEGF) method, we simulated the field emission current, considering the quantum transport of electrons within the CNT. The paper involves investigation on the effect of the n index of the (n , 0) Z-SWCNT and the number of carbon dimers in the length direction as well as the anode-cathode separation on the FE current. Effect of additional gate voltage and substitutional impurities on the FE current is also studied. A comparison between the experimental data and simulation results are also included in the paper. The model can be used to consider different quantum effects of the atomistic emitter structure on the FE current.

  2. A human ether-á-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug cardiotoxicity.

    Science.gov (United States)

    Anwar-Mohamed, Anwar; Barakat, Khaled H; Bhat, Rakesh; Noskov, Sergei Y; Tyrrell, D Lorne; Tuszynski, Jack A; Houghton, Michael

    2014-11-04

    Acquired cardiac long QT syndrome (LQTS) is a frequent drug-induced toxic event that is often caused through blocking of the human ether-á-go-go-related (hERG) K(+) ion channel. This has led to the removal of several major drugs post-approval and is a frequent cause of termination of clinical trials. We report here a computational atomistic model derived using long molecular dynamics that allows sensitive prediction of hERG blockage. It identified drug-mediated hERG blocking activity of a test panel of 18 compounds with high sensitivity and specificity and was experimentally validated using hERG binding assays and patch clamp electrophysiological assays. The model discriminates between potent, weak, and non-hERG blockers and is superior to previous computational methods. This computational model serves as a powerful new tool to predict hERG blocking thus rendering drug development safer and more efficient. As an example, we show that a drug that was halted recently in clinical development because of severe cardiotoxicity is a potent inhibitor of hERG in two different biological assays which could have been predicted using our new computational model. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  3. Atomistic design of semiconductor nanostructures with optimal thermoelectric properties

    Science.gov (United States)

    Galli, Giulia

    2008-03-01

    The search for novel materials with optimal thermoelectric properties (for either thermoelectric power generation or heat dissipation) is an active field of research. We present atomistic and ab-initio simulations of selected nanomaterials, aimed at predicting thermal conductivities and electronic transport properties, and ultimately at designing materials with optimal thermoelectric figure of merit. In particular we focus on carbon nanotubes [1], silicon wires [2] and nanoporous silicon [3] and we discuss both strategies and algorithms to optimize thermoelectric properties at the nanoscale. [1] D. Donadio and G.Galli, Phys. Rev. Lett. 2007 (in press). [2] T.Vo, A.Williamson, V.Lordi and G.Galli (submitted) and J.Reed, A.Williamson, E.Schwegler and G.Galli (submitted). [3] J.-H. Lee, J.C.Grossman, J.Reed and G.Galli, Appl. Phys. Lett. 2007 (in press).

  4. Atomistic modeling of ion implantation technologies in silicon

    Energy Technology Data Exchange (ETDEWEB)

    Marqués, Luis A., E-mail: lmarques@ele.uva.es; Santos, Iván; Pelaz, Lourdes; López, Pedro; Aboy, María

    2015-06-01

    Requirements for the manufacturing of electronic devices at the nanometric scale are becoming more and more demanding on each new technology node, driving the need for the fabrication of ultra-shallow junctions and finFET structures. Main implantation strategies, cluster and cold implants, are aimed to reduce the amount of end-of-range defects through substrate amorphization. During finFET doping the device body gets amorphized, and its regrowth is more problematic than in the case of conventional planar devices. Consequently, there is a renewed interest on the modeling of amorphization and recrystallization in the front-end processing of Si. We present multi-scale simulation schemes to model amorphization and recrystallization in Si from an atomistic perspective. Models are able to correctly predict damage formation, accumulation and regrowth, both in the ballistic and thermal-spike regimes, in very good agreement with conventional molecular dynamics techniques but at a much lower computational cost.

  5. Reaction pathways in atomistic models of thin film growth

    Science.gov (United States)

    Lloyd, Adam L.; Zhou, Ying; Yu, Miao; Scott, Chris; Smith, Roger; Kenny, Steven D.

    2017-10-01

    The atomistic processes that form the basis of thin film growth often involve complex multi-atom movements of atoms or groups of atoms on or close to the surface of a substrate. These transitions and their pathways are often difficult to predict in advance. By using an adaptive kinetic Monte Carlo (AKMC) approach, many complex mechanisms can be identified so that the growth processes can be understood and ultimately controlled. Here the AKMC technique is briefly described along with some special adaptions that can speed up the simulations when, for example, the transition barriers are small. Examples are given of such complex processes that occur in different material systems especially for the growth of metals and metallic oxides.

  6. Atomistic Determination of Cross-Slip Pathway and Energetics

    DEFF Research Database (Denmark)

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

    1997-01-01

    plane. The transition state and activation energy for cross slip as well as the energies of the involved dislocation constrictions are determined. One constriction has a negative energy compared to parallel partials. The energy vs splitting width for recombination of parallel partials into a perfect......The mechanism for cross slip of a screw dislocation in Cu is determined by atomistic simulations that only presume the initial and final states of the process. The dissociated dislocation constricts in the primary plane and redissociates into the cross-slip plane while still partly in the primary...... dislocation is determined. The breakdown of linear elasticity theory for small splitting widths is studied. [S0031-9007(97)04444-X]....

  7. Multiscale Simulations Using Particles

    DEFF Research Database (Denmark)

    Walther, Jens Honore

    We are developing particle methods as a general framework for large scale simulations of discrete and continuous systems in science and engineering. The specific application and research areas include: discrete element simulations of granular flow, smoothed particle hydrodynamics and particle...... vortex methods for problems in continuum fluid dynamics, dissipative particle dynamics for flow at the meso scale, and atomistic molecular dynamics simulations of nanofluidic systems. We employ multiscale techniques to breach the atomistic and continuum scales to study fundamental problems in fluid...

  8. GPU Parallel Bundle Block Adjustment

    Directory of Open Access Journals (Sweden)

    ZHENG Maoteng

    2017-09-01

    Full Text Available To deal with massive data in photogrammetry, we introduce the GPU parallel computing technology. The preconditioned conjugate gradient and inexact Newton method are also applied to decrease the iteration times while solving the normal equation. A brand new workflow of bundle adjustment is developed to utilize GPU parallel computing technology. Our method can avoid the storage and inversion of the big normal matrix, and compute the normal matrix in real time. The proposed method can not only largely decrease the memory requirement of normal matrix, but also largely improve the efficiency of bundle adjustment. It also achieves the same accuracy as the conventional method. Preliminary experiment results show that the bundle adjustment of a dataset with about 4500 images and 9 million image points can be done in only 1.5 minutes while achieving sub-pixel accuracy.

  9. Twist-off purification of hair bundles.

    Science.gov (United States)

    Shin, Jung-Bum; Pagana, James; Gillespie, Peter G

    2009-01-01

    Purification of hair bundles from inner-ear organs allows biochemical analysis of bundle constituents, including proteins and lipids. We describe here the "twist-off" method of bundle isolation, where dissected inner-ear organs are embedded in agarose, then subjected to a mechanical disruption that shears off bundles and leaves them in agarose blocks. With care in the dissection and in clean-up of the isolated bundles, contamination from cell bodies can be kept to a minimum. Isolated bundles can be analyzed by a variety of techniques, including immunocytochemistry, SDS-PAGE, immunoblotting, and mass spectrometry.

  10. 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.

  11. ADE bundles over surfaces with ADE singularities

    OpenAIRE

    Chen, Yunxia; Leung, Naichung Conan

    2012-01-01

    Given a complex projective surface with an ADE singularity and p_{g}=0, we construct ADE bundles over it and its minimal resolution. Furthermore, we descibe their minuscule representation bundles in terms of configurations of (reducible) (-1)-curves.

  12. PDS4 Bundle Creation Governance Using BPMN

    Science.gov (United States)

    Radulescu, C.; Levoe, S. R.; Algermissen, S. S.; Rye, E. D.; Hardman, S. H.

    2015-06-01

    The AMMOS-PDS Pipeline Service (APPS) provides a Bundle Builder tool, which governs the process of creating, and ultimately generates, PDS4 bundles incrementally, as science products are being generated.

  13. Developing the bundled glass column

    NARCIS (Netherlands)

    Oikonomopoulou, F.; Bristogianni, T; Veer, F.A.; Nijsse, R.; da Sousa Cruz, Paulo J.

    In this paper a bundled glass column is presented as a promising solution for a completely transparent, almost dematerialized structural compressive element. The aim is to ob-tain a glass column that can safely carry loads, achieve a high visual result and be relatively eas-ily manufactured.

  14. Line bundles and flat connections

    Indian Academy of Sciences (India)

    /fulltext/pmsc/127/03/0547-0549. Keywords. Calabi–Yau threefold; torsion; cocompact lattice; unitary representation. Abstract. We prove that there are cocompact lattices Γ in S L ( 2 , C ) with the property that there are holomorphic line bundles ...

  15. Line bundles and flat connections

    Indian Academy of Sciences (India)

    Calabi–Yau threefold; torsion; cocompact lattice; unitary representation. 2000 Mathematics Subject Classification. 81T30, 14D21, 53C07. 1. Stable bundles and unitary flat connections. 1.1 Admitting flat connections. Let X be a compact connected complex manifold of complex dimension δ. Let ω be the. (1, 1)-form on X ...

  16. Chemical vapor infiltration in single fiber bundles

    Energy Technology Data Exchange (ETDEWEB)

    Devlin, D.J.; Barbero, R.S.; Currier, R.P.

    1990-01-01

    Chemical vapor infiltration (CVI) in single fiber bundles is studied under isothermal conditions. Understanding infiltration dynamics in single bundles is essential to process design and modeling efforts. Deposition of pyrolytic carbon in carbon-fiber bundles is chosen as the experimental system, with densification data obtained from thermogravimetric analysis. Data are then compared to predictions from a recently proposed CVI model for fiber bundle densification. 10 refs., 5 figs., 1 tab.

  17. Principal G-bundles on nodal curves

    Indian Academy of Sciences (India)

    Springer Verlag Heidelberg #4 2048 1996 Dec 15 10:16:45

    If Y is reducible these notions depend on parameters a = (a1,...,aI ). The study of G-bundles on Y is done by extending the notion of (generalized) parabolic vector bundles [U1] to generalized parabolic principal G-bundles (called GPGs in short) on the curve C and using the correspondence between them and principal ...

  18. Strategic and welfare implications of bundling

    DEFF Research Database (Denmark)

    Martin, Stephen

    1999-01-01

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

  19. From atomistic interfaces to dendritic patterns

    Science.gov (United States)

    Galenko, P. K.; Alexandrov, D. V.

    2018-01-01

    Transport processes around phase interfaces, together with thermodynamic properties and kinetic phenomena, control the formation of dendritic patterns. Using the thermodynamic and kinetic data of phase interfaces obtained on the atomic scale, one can analyse the formation of a single dendrite and the growth of a dendritic ensemble. This is the result of recent progress in theoretical methods and computational algorithms calculated using powerful computer clusters. Great benefits can be attained from the development of micro-, meso- and macro-levels of analysis when investigating the dynamics of interfaces, interpreting experimental data and designing the macrostructure of samples. The review and research articles in this theme issue cover the spectrum of scales (from nano- to macro-length scales) in order to exhibit recently developing trends in the theoretical analysis and computational modelling of dendrite pattern formation. Atomistic modelling, the flow effect on interface dynamics, the transition from diffusion-limited to thermally controlled growth existing at a considerable driving force, two-phase (mushy) layer formation, the growth of eutectic dendrites, the formation of a secondary dendritic network due to coalescence, computational methods, including boundary integral and phase-field methods, and experimental tests for theoretical models-all these themes are highlighted in the present issue. This article is part of the theme issue `From atomistic interfaces to dendritic patterns'.

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

    Directory of Open Access Journals (Sweden)

    Qian Wang

    2017-01-01

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

  1. Thermal conductance of Teflon and Polyethylene: Insight from an atomistic, single-molecule level

    Science.gov (United States)

    Buerkle, Marius; Asai, Yoshihiro

    2017-02-01

    The thermal transport properties of teflon (polytetrafluoroethylene) and its polyethylene counterparts are, while highly desirable and widely used, only superficially understood. Here, we aim therefore to provide rigorous insight from an atomistic point of view in context of single-molecule devices. We show that for vinyl polymers adsorbed on metal-surfaces the thermal transport strongly depends on the properties of the metal-molecule interface and that the reduced thermal conductance observed for teflon derivatives originates in a reduced phonon injection life time. In asymmetric molecules phonon blocking on the intra molecular interface leads to a further reduction of thermal conductance. For hetrojunctions with different electrode materials we find that thermal conductance is suppressed due to a reduced overlap of the available phonon modes in the different electrodes. A detailed atomistic picture is thereby provided by studying the transport through perfluorooctane and octane on a single-molecule level using first principles transport calculations and nonequilibrium molecular dynamic simulations.

  2. 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.

  3. The Atiyah bundle and connections on a principal bundle

    Indian Academy of Sciences (India)

    INDRANIL BISWAS. School of Mathematics, Tata Institute of Fundamental Research, Homi Bhabha Road,. Mumbai 400 005 .... (U) on A(EG)(U) and (U, g ⊕ Rd) defined by multiplication. Therefore, the sheaf A(EG) is locally free over FC∞. (M) of rank dim(g ⊕ Rd). Hence. A(EG) defines a C. ∞ vector bundle over M of rank ...

  4. 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 $E$.

  5. 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...

  6. 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)

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

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Liangliang; Gubbins, Keith E., E-mail: keg@ncsu.edu [Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695 (United States); Seredych, Mykola; Bandosz, Teresa J. [Department of Chemistry, The City College of New York and the Graduate School of the City University of New York, New York 10031 (United States); Duin, Adri C. T. van [Department of Mechanical and Nuclear Engineering, Pennsylvania State University, University Park, Pennsylvania 16801 (United States); Lu, Xiaohua [State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing University of Technology, Nanjing 210009 (China)

    2013-11-21

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

  8. [Intermittent bundle branch block: a clinical model for the study of electrophysiological phenomena].

    Science.gov (United States)

    Costantini, Marcello

    2014-01-01

    uncommon to observe long periods of sinus rhythm with regular PP interval, conducted with alternating (2:1) bundle branch block. Intermittent left bundle branch block is a clinical model of cardiac memory: in these cases, negative T waves in the antero-septal leads during normal conduction are often evident. This negativity is an expression of cardiac memory, and not of ischemia as initially interpreted. Intermittent bundle branch block is an excellent model to study in vivo the effects of antiarrhythmic drugs on the pathological bundle branches. Narrowing of the QRS complex in the presence of bundle branch block is not always an expression of intermittent aberrancy: beware of late ectopic beats originating from the ipsilateral ventricle to the blocked branch, that merging with the antegrade beat conducted with bundle branch block, restrict the QRS, simulating intermittent aberrancy.

  9. Atomistic in situ investigation of the morphogenesis of grains during pressure-induced phase transitions: molecular dynamics simulations of the B1-B2 transformation of RbCl.

    Science.gov (United States)

    Zahn, Dirk; Tlatlik, Harald

    2010-12-03

    The mechanistic details of the pressure-induced B1-B2 phase transition of rubidium chloride are investigated in a series of transition path sampling molecular dynamics simulations. The B2→B1 transformation proceeds by nucleation and growth involving several, initially separated, nucleation centers. We show how independent and partially correlated nucleation events can function within a global mechanism and explore the evolution of phase domains during the transition. From this, the mechanisms of grain boundary formation are elaborated. The atomic structure of the domain-domain interfaces fully support the concept of Bernal polyhedra. Indeed, the manifold of different grain morphologies obtained from our simulations may be rationalized on the basis of essentially only two different kinds of Bernal polyhedra. The latter also play a crucial role for the B1→B2 transformation and specific grain boundary motifs are identified as preferred nucleation centers for this transition.

  10. Atomistic calculations of dislocation core energy in aluminium

    Science.gov (United States)

    Zhou, X. W.; Sills, R. B.; Ward, D. K.; Karnesky, R. A.

    2017-02-01

    A robust molecular-dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: It does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and the Burgers vector. These calculations show that, for the face-centered-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elastic energy: Ec=A sin2β +B cos2β , and this dependence is independent of temperature between 100 and 300 K. By further analyzing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and the core radius of a perfect versus an extended dislocation. With our methodology, the dislocation core energy can accurately be accounted for in models of dislocation-mediated plasticity.

  11. 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.

  12. An atomistic study of the deformation behavior of tungsten nanowires

    Science.gov (United States)

    Xu, Shuozhi; Su, Yanqing; Chen, Dengke; Li, Longlei

    2017-12-01

    Large-scale atomistic simulations are performed to study tensile and compressive loading of single-crystalline nanowires in body-centered cubic tungsten (W). Effects of loading mode, wire cross-sectional shape, wire size, strain rate, and crystallographic orientations of the lateral surfaces are explored. Uniaxial deformation of a W bulk single crystal is also investigated for reference. Our results reveal a strong tension-compression asymmetry in both the stress-strain response and the deformation behavior due to different yielding/failure modes: while the nanowires fail by brittle fracture under tensile loading, they yield by nucleation of dislocations from the wire surface under compressive loading. It is found that (1) nanowires have a higher strength than the bulk single crystal; (2) with a cross-sectional size larger than 10 nm, there exists a weak dependence of strength on wire size; (3) when the wire size is equal to or smaller than 10 nm, nanowires buckle under compressive loading; (4) the cross-sectional shape, strain rate, and crystallographic orientations of the lateral surfaces affect the strength and the site of defect initiation but not the overall deformation behavior.

  13. Compression deformation of WC: atomistic description of hard ceramic material

    Science.gov (United States)

    Feng, Qing; Song, Xiaoyan; Liu, Xuemei; Liang, Shuhua; Wang, Haibin; Nie, Zuoren

    2017-11-01

    The deformation characteristics of WC, as a typical hard ceramic material, were studied on the nanoscale using atomistic simulations for both the single-crystal and polycrystalline forms under uniaxial compression. In particular, the effects of crystallographic orientation, grain boundary coordination and grain size on the origin of deformation were investigated. The deformation behavior of the single-crystal and polycrystalline WC both depend strongly on the orientation towards the loading direction. The grain boundaries play a significant role in the deformation coordination and the potential high fracture toughness of the nanocrystalline WC. In contrast to conventional knowledge of ceramics, maximum strength was obtained at a critical grain size corresponding to the turning point from a Hall–Petch to an inverse Hall–Petch relationship. For this the mechanism of the combined effect of dislocation motion within grains and the coordination of stress concentration at the grain boundaries were proposed. The present work has moved forward our understanding of plastic deformability and the possibility of achieving a high strength of nanocrystalline ceramic materials.

  14. Static stress analysis of CANFLEX fuel bundles

    Energy Technology Data Exchange (ETDEWEB)

    Suk, Ho Chun; Kang, Hee Young; Sim, Ki Seop; Jeong, Jang Hwan; Jun, Gi Su; Park, Ju Hwan; Lee, Che Han; Kim, Tae Hyoung [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1996-02-01

    The static stress analysis of CANFLEX bundles is performed to evaluate the fuel structural integrity during the refuelling service. The structure analysis is carried out by predicting the drag force, stress and displacements of the fuel bundle. By the comparison of strength tests and analysis results, the displacement values are well agreed within 15%. The analysis shows that the CANFLEX fuel bundle keep its structural integrity. 24 figs., 6 tabs., 12 refs. (Author) .new.

  15. 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)

  16. Ulrich Schur bundles on flag varieties

    OpenAIRE

    Coskun, Izzet; Costa, Laura; Huizenga, Jack; Miró-Roig, Rosa Maria; Woolf, Matthew

    2015-01-01

    In this paper, we study equivariant vector bundles on partial flag varieties arising from Schur functors. We show that a partial flag variety with three or more steps does not admit an Ulrich bundle of this form with respect to the minimal ample class. We classify Ulrich bundles of this form on two-step flag varieties F(1,n-1;n), F(2,n-1;n), F(2,n-2;n), F(k,k+1;n) and F(k,k+2;n). We give a conjectural description of the two-step flag varieties which admit such Ulrich bundles.

  17. Equivariant Ulrich bundles on flag varieties

    OpenAIRE

    Coskun, Izzet; Huizenga, Jack; Woolf, Matthew

    2015-01-01

    In this paper, we study equivariant vector bundles on partial flag varieties arising from Schur functors. We show that a partial flag variety with three or more steps does not admit an Ulrich bundle of this form with respect to the minimal ample class. We classify Ulrich bundles of this form on two-step flag varieties F(2,n;n+1), F(2,n;n+2), F(k,k+1;n), and F(k,k+2;n). We give a conjectural description of the two-step flag varieties which admit such Ulrich bundles. Our results provide counter...

  18. Axis deviation without left bundle branch block.

    Science.gov (United States)

    Patanè, Salvatore; Marte, Filippo; Mancuso, Antonia

    2010-04-15

    It has been rarely reported changing axis deviation in the presence of left bundle branch block also during atrial fibrillation and with acute myocardial infarction too. It has also been rarely reported changing axis deviation with changing bundle branch block with onset of atrial fibrillation during acute myocardial infarction. We present a case of axis deviation without left bundle branch block and without atrial fibrillation and acute myocardial infarction in a 65-year-old Italian man. To our knowledge, this is the first report of axis deviation without left bundle branch block and without atrial fibrillation and acute myocardial infarction. Copyright 2008 Elsevier Ireland Ltd. All rights reserved.

  19. Atomistic simulations of radiation-induced defect formation in spinels: MgAl2O4 , MgGa2O4 , and MgIn2O4

    Science.gov (United States)

    Bacorisen, D.; Smith, Roger; Uberuaga, B. P.; Sickafus, K. E.; Ball, J. A.; Grimes, R. W.

    2006-12-01

    Molecular dynamics simulations of collision cascades were performed in three spinel oxides with varying inversion, namely normal magnesium aluminate, MgAl2O4 , half-inverse magnesium gallate, MgGa2O4 , and inverse magnesium indate, MgIn2O4 . The response of each of these oxides for energies of up to 10keV for the initial knock-on event was analyzed and compared. Defect production was characterized mainly by split interstitials/crowdions and cation antisite or disorder defects. The results show that cation interstitials preferentially occupy octahedral sites in all three materials. In the normal spinel, subcascade branching occurs and the defects at the end of the cascade are generally isolated, whereas in the half-inverse spinel, the higher energy cascades show a core damage region some of which consists of a partial rearrangement of atoms to the normal spinel structure and a partial transformation to a disordered rocksalt structure. In the fully inverse spinel a more connected region of the disordered rocksalt structure with the cascade core is evident.

  20. Structural elucidation of transmembrane domain zero (TMD0) of EcdL: A multidrug resistance-associated protein (MRP) family of ATP-binding cassette transporter protein revealed by atomistic simulation.

    Science.gov (United States)

    Bera, Krishnendu; Rani, Priyanka; Kishor, Gaurav; Agarwal, Shikha; Kumar, Antresh; Singh, Durg Vijay

    2017-09-20

    ATP-Binding cassette (ABC) transporters play an extensive role in the translocation of diverse sets of biologically important molecules across membrane. EchnocandinB (antifungal) and EcdL protein of Aspergillus rugulosus are encoded by the same cluster of genes. Co-expression of EcdL and echinocandinB reflects tightly linked biological functions. EcdL belongs to Multidrug Resistance associated Protein (MRP) subfamily of ABC transporters with an extra transmembrane domain zero (TMD0). Complete structure of MRP subfamily comprising of TMD0 domain, at atomic resolution is not known. We hypothesized that the transportation of echonocandinB is mediated via EcdL protein. Henceforth, it is pertinent to know the topological arrangement of TMD0, with other domains of protein and its possible role in transportation of echinocandinB. Absence of effective template for TMD0 domain lead us to model by I-TASSER, further structure has been refined by multiple template modelling using homologous templates of remaining domains (TMD1, NBD1, TMD2, NBD2). The modelled structure has been validated for packing, folding and stereochemical properties. MD simulation for 0.1 μs has been carried out in the biphasic environment for refinement of modelled protein. Non-redundant structures have been excavated by clustering of MD trajectory. The structural alignment of modelled structure has shown Z-score -37.9; 31.6, 31.5 with RMSD; 2.4, 4.2, 4.8 with ABC transporters; PDB ID 4F4C, 4M1 M, 4M2T, respectively, reflecting the correctness of structure. EchinocandinB has been docked to the modelled as well as to the clustered structures, which reveals interaction of echinocandinB with TMD0 and other TM helices in the translocation path build of TMDs.

  1. 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.

  2. 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.

  3. The Q-Cycle Mechanism of the bc1 Complex: A Biologist's Perspective on Atomistic Studies.

    Science.gov (United States)

    Crofts, Antony R; Rose, Stuart W; Burton, Rodney L; Desai, Amit V; Kenis, Paul J A; Dikanov, Sergei A

    2017-04-20

    The Q-cycle mechanism of the bc1 complex is now well enough understood to allow application of advanced computational approaches to the study of atomistic processes. In addition to the main features of the mechanism, these include control and gating of the bifurcated reaction at the Qo-site, through which generation of damaging reactive oxygen species is minimized. We report a new molecular dynamics model of the Rhodobacter sphaeroides bc1 complex implemented in a native membrane, and constructed so as to eliminate blemishes apparent in earlier Rhodobacter models. Unconstrained MD simulations after equilibration with ubiquinol and ubiquinone respectively at Qo- and Qi-sites show that substrate binding configurations at both sites are different in important details from earlier models. We also demonstrate a new Qo-site intermediate, formed in the sub-ms time range, in which semiquinone remains complexed with the reduced iron sulfur protein. We discuss this, and a spring-loaded mechanism for modulating interactions of the iron sulfur protein with occupants of the Qo-site, in the context of control and gating roles. Such atomistic features of the mechanism can usefully be explored through simulation, but we stress the importance of constraints from physical chemistry and biology, both in setting up a simulation and in interpreting results.

  4. 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.

  5. Catastrophic Failure and Critical Scaling Laws of Fiber Bundle Material

    Directory of Open Access Journals (Sweden)

    Shengwang Hao

    2017-05-01

    Full Text Available This paper presents a spring-fiber bundle model used to describe the failure process induced by energy release in heterogeneous materials. The conditions that induce catastrophic failure are determined by geometric conditions and energy equilibrium. It is revealed that the relative rates of deformation of, and damage to the fiber bundle with respect to the boundary controlling displacement ε0 exhibit universal power law behavior near the catastrophic point, with a critical exponent of −1/2. The proportion of the rate of response with respect to acceleration exhibits a linear relationship with increasing displacement in the vicinity of the catastrophic point. This allows for the prediction of catastrophic failure immediately prior to failure by extrapolating the trajectory of this relationship as it asymptotes to zero. Monte Carlo simulations are completed and these two critical scaling laws are confirmed.

  6. 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.

  7. Why (almost) all bundles are chiral

    Science.gov (United States)

    Kost-Smith, Zachary V.; Blackwell, Robert A.; Glaser, Matthew A.

    2014-03-01

    We examine the self assembly of bundles of achiral hard rods with distributed, short-range attractive interactions. We show that in the majority of cases the equilibrium state of the bundle is chiral, with a double twist structure. We use biased Monte Carlo techniques and cell theory to compute the free energy as a function of an appropriately defined twist order parameter, and show that the formation of spontaneously chiral bundles is driven by maximization of orientational entropy. The finite curvature of the bundle boundary permits orientational escape, in which the circumferential angular range of motion of the rods is maximized for some finite average tilt. We map out the phase diagram of bundles in terms of the density, the ratio of rod length to bundle radius, L / R , and rod aspect ratio, L / D , and find transitions between untwisted, weakly twisted, and strongly twisted states. This work helps explain the common observation of twisted macroscopic bundles, and may provide insight into observations of twist in self-assembled membranes of colloidal rods.[2] This work funded by NSF MRSEC Grant DMR-0820579.

  8. Atomistic simulation of dislocation emission in nanosized grain boundaries

    Science.gov (United States)

    Derlet, P. M.; van Swygenhoven, H.; Hasnaoui, A.

    2003-11-01

    The present work deals with the atomic mechanism responsible for the emission of partial dislocations from grain boundaries (GB) in nanocrystalline metals. It is shown that, in a 12 nm grain-size sample, GBs containing grain-boundary dislocations (GBDs) can emit a partial dislocation during deformation by local atomic shuffling and stress-assisted free-volume migration. As in previous work, the nucleation occurs at a GBD, which, upon nucleation and propagation, is removed. In the present case, free-volume migration occurs away from the nucleation region both before and after the nucleation event.

  9. Atomistic simulation studies of the cement paste components

    OpenAIRE

    Manzano Moro, Hegoi

    2014-01-01

    230 p. El cemento y sus derivados, como los morteros o el hormigón, son generalmente considerados materiales de bajo nivel tecnológico. A pesar de ser el material manufacturado más empleado en el mundo, otros como los plásticos, los metales, el algodón, la lana, la madera e incluso las piedras, se valoran más en el día a día. De hecho, el cemento es comúnmente considerado como una pasta gris, con la única característica de endurecerse cuando se seca, y que se empleada para construir edific...

  10. Atomistic simulation of the structural and elastic properties of ...

    Indian Academy of Sciences (India)

    ZI-JIANG LIU1 2 3 XIAO-WEI SUN2 TING SONG2 YUAN GUO1 CAI-RONG ZHANG4 ZHENG-RONG ZHANG1. Department of Physics, Lanzhou City University, Lanzhou 730070, PR China; School of Mathematics and Physics, Lanzhou Jiaotong University, Lanzhou 730070, PR China; Key Laboratory of Atomic and ...

  11. Magnetic atomistic modelling and simulation of nanocrystalline thin films

    Science.gov (United States)

    Agudelo-Giraldo, J. D.; Ortiz-Álvarez, H. H.; Restrepo, J.; Restrepo-Parra, E.

    2017-05-01

    In this study, a methodology, for polycrystalline magnetic thin films construction composed by nano-grains, was developed. The size and shape of grains and samples under scale considerations of magnetic materials were developed, taking into account periodic boundary conditions. A comparative analysis of results obtained with experimental grains' distribution is presented. Lognormal distribution was proposed as a function of number of atoms per grain that agrees with experimental reports. A test of the magnetization as a function of the temperature was obtained by the parallelized Monte Carlo method dividing the sample in cells. The Hamiltonian considered variations of the exchange constant with atomic distance from RKKY approximation and a cubic magneto-crystalline anisotropy as a function of the temperature also was implemented. Results showed changes over critical behavior and different values for magnetization of saturation at low temperatures. Critical temperature is affected by the increments of disorder into the sample when grain size is reduced. A reduction of magnetization is correlated with mono-domain regimen in the sample for most of grains. These states are favored during the cooling process by the disorder in grain boundaries.

  12. Atomistic Design and Simulations of Nanoscale Machines and Assembly

    Science.gov (United States)

    Goddard, William A., III; Cagin, Tahir; Walch, Stephen P.

    2000-01-01

    Over the three years of this project, we made significant progress on critical theoretical and computational issues in nanoscale science and technology, particularly in:(1) Fullerenes and nanotubes, (2) Characterization of surfaces of diamond and silicon for NEMS applications, (3) Nanoscale machine and assemblies, (4) Organic nanostructures and dendrimers, (5) Nanoscale confinement and nanotribology, (6) Dynamic response of nanoscale structures nanowires (metals, tubes, fullerenes), (7) Thermal transport in nanostructures.

  13. 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.

  14. 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.

  15. 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.

  16. Thermodynamics of atomistic and coarse-grained models of water on nonpolar surfaces.

    Science.gov (United States)

    Ardham, Vikram Reddy; Leroy, Frédéric

    2017-08-21

    In order to study the phenomena where interfaces play a dominant role through molecular simulations, the proper representation of the interfacial thermodynamic properties of a given model is of crucial importance. The use of coarse-grained rather than atomistic models makes it possible to simulate interfacial systems with larger time and length scales. In the present work, we compare the structure and thermodynamic behavior of one atomistic and two single-site coarse-grained models of water on nonpolar surfaces, namely, graphite and the basal plane of molybdenum disulfide. The three models interact with the surfaces through Lennard-Jones potentials parametrized to reproduce recent experimental contact angle measurements. The models form a layered structure close to the surface, which is usually observed on sufficiently attractive nonpolar substrates. However, differences in the structure and thermodynamic behavior are observed between the models. These differences are explained by certain features of the water models, such as short range tetrahedral order and liquid density fluctuations. Besides these results, the approach employed in the present study may be used to assess the ability of coarse-grained models for solid-liquid systems to represent consistent interfacial thermodynamics.

  17. An Atomistic Carbide-Derived Carbon Model Generated Using ReaxFF-Based Quenched Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Matthew W. Thompson

    2017-10-01

    Full Text Available We report a novel atomistic model of carbide-derived carbons (CDCs, which are nanoporous carbons with high specific surface areas, synthesis-dependent degrees of graphitization, and well-ordered, tunable porosities. These properties make CDCs viable substrates in several energy-relevant applications, such as gas storage media, electrochemical capacitors, and catalytic supports. These materials are heterogenous, non-ideal structures and include several important parameters that govern their performance. Therefore, a realistic model of the CDC structure is needed in order to study these systems and their nanoscale and macroscale properties with molecular simulation. We report the use of the ReaxFF reactive force field in a quenched molecular dynamics routine to generate atomistic CDC models. The pair distribution function, pore size distribution, and adsorptive properties of this model are reported and corroborated with experimental data. Simulations demonstrate that compressing the system after quenching changes the pore size distribution to better match the experimental target. Ring size distributions of this model demonstrate the prevalence of non-hexagonal carbon rings in CDCs. These effects may contrast the properties of CDCs against those of activated carbons with similar pore size distributions and explain higher energy densities of CDC-based supercapacitors.

  18. 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

  19. Einstein metrics on tangent bundles of spheres

    Energy Technology Data Exchange (ETDEWEB)

    Dancer, Andrew S [Jesus College, Oxford University, Oxford OX1 3DW (United Kingdom); Strachan, Ian A B [Department of Mathematics, University of Hull, Hull HU6 7RX (United Kingdom)

    2002-09-21

    We give an elementary treatment of the existence of complete Kaehler-Einstein metrics with nonpositive Einstein constant and underlying manifold diffeomorphic to the tangent bundle of the (n+1)-sphere.

  20. Dynamic bi-product bundle pricing problem

    Directory of Open Access Journals (Sweden)

    Rafiei Hamed

    2014-01-01

    Full Text Available This paper addresses bundle pricing problem of two products in a stochastic environment so as to maximize net profit of a retailer. In the considered problem, it is assumed that customers are received upon a Poisson distribution and their demands follow a bi-variant distribution function. Also, it is assumed that products are sold individually or in the form of a bundle, which are offered from an initial stock of the products. To tackle the problem, a stochastic dynamic program is developed in which optimum values of the initial stock and order quantities of every planning period are determined. Moreover, prices of the individual products and their bundle are optimized. Also, the proposed dynamic program tackles bundling/ unbundling decisions taken in every planning period. A numerical example of a two planning period horizon is considered to validate the proposed model.

  1. 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. © 2016 Wiley Periodicals, Inc.

  2. Physiological mechanisms of QRS narrowing in bundle branch block patients undergoing permanent His bundle pacing.

    Science.gov (United States)

    Teng, Alexandra E; Massoud, Louis; Ajijola, Olujimi A

    2016-01-01

    His bundle pacing is increasingly used to avoid chronic right ventricular pacing, and electrically resynchronize ventricular activation by narrowing or normalizing the QRS interval in left and right bundle branch block. The mechanisms by which this occurs remain poorly understood. In this review, the proposed mechanisms and evidence supporting them are discussed. Also discussed are aspects of mechanisms that are not completely supported by the evidence. We also review the differences and physiological bases for direct vs. indirect His bundle capture, and the physiological mechanisms for QRS narrowing vs. normalization following His bundle pacing. Copyright © 2016 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    Amani, Ehsan; Movahed, Saeid

    2016-06-07

    In this study, for the first time, a hybrid continuum-atomistic based model is proposed for electrokinetics, electroosmosis and electrophoresis, through nanochannels. Although continuum based methods are accurate enough to model fluid flow and electric potential in nanofluidics (in dimensions larger than 4 nm), ionic concentration is too low in nanochannels for the continuum assumption to be valid. On the other hand, the non-continuum based approaches are too time-consuming and therefore is limited to simple geometries, in practice. Here, to propose an efficient hybrid continuum-atomistic method of modelling the electrokinetics in nanochannels; the fluid flow and electric potential are computed based on continuum hypothesis coupled with an atomistic Lagrangian approach for the ionic transport. The results of the model are compared to and validated by the results of the molecular dynamics technique for a couple of case studies. Then, the influences of bulk ionic concentration, external electric field, size of nanochannel, and surface electric charge on the electrokinetic flow and ionic mass transfer are investigated, carefully. The hybrid continuum-atomistic method is a promising approach to model more complicated geometries and investigate more details of the electrokinetics in nanofluidics. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Force Generation by Molecular-Motor-Powered Microtubule Bundles; Implications for Neuronal Polarization and Growth.

    Science.gov (United States)

    Jakobs, Maximilian; Franze, Kristian; Zemel, Assaf

    2015-01-01

    The heavily cross-linked microtubule (MT) bundles found in neuronal processes play a central role in the initiation, growth and maturation of axons and dendrites; however, a quantitative understanding of their mechanical function is still lacking. We here developed computer simulations to investigate the dynamics of force generation in 1D bundles of MTs that are cross-linked and powered by molecular motors. The motion of filaments and the forces they exert are investigated as a function of the motor type (unipolar or bipolar), MT density and length, applied load, and motor connectivity. We demonstrate that only unipolar motors (e.g., kinesin-1) can provide the driving force for bundle expansion, while bipolar motors (e.g., kinesin-5) oppose it. The force generation capacity of the bundles is shown to depend sharply on the fraction of unipolar motors due to a percolation transition that must occur in the bundle. Scaling laws between bundle length, force, MT length and motor fraction are presented. In addition, we investigate the dynamics of growth in the presence of a constant influx of MTs. Beyond a short equilibration period, the bundles grow linearly in time. In this growth regime, the bundle extends as one mass forward with most filaments sliding with the growth velocity. The growth velocity is shown to be dictated by the inward flux of MTs, to inversely scale with the load and to be independent of the free velocity of the motors. These findings provide important molecular-level insights into the mechanical function of the MT cytoskeleton in normal axon growth and regeneration after injury.

  5. 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

  6. Atomistic Force Field for Pyridinium-Based Ionic Liquids: Reliable Transport Properties

    DEFF Research Database (Denmark)

    Voroshylova, I. V.; Chaban, V. V.

    2014-01-01

    Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis(trifluoromethanesulfonyl)......Reliable force field (FF) is a central issue in successful prediction of physical chemical properties via computer simulations. This work introduces refined FF parameters for six popular ionic liquids (ILs) of the pyridinium family (butylpyridinium tetrafluoroborate, bis...... and elevated temperature. The developed atomistic models provide a systematic refinement upon the well-known Canongia LopesPadua (CL&P) FF. Together with the original CL&P parameters the present models foster a computational investigation of ionic liquids....

  7. 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.

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

    NARCIS (Netherlands)

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

    2015-01-01

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

  9. Representational analysis of extended disorder in atomistic ensembles derived from total scattering data.

    Science.gov (United States)

    Neilson, James R; McQueen, Tyrel M

    2015-10-01

    With the increased availability of high-intensity time-of-flight neutron and synchrotron X-ray scattering sources that can access wide ranges of momentum transfer, the pair distribution function method has become a standard analysis technique for studying disorder of local coordination spheres and at intermediate atomic separations. In some cases, rational modeling of the total scattering data (Bragg and diffuse) becomes intractable with least-squares approaches, necessitating reverse Monte Carlo simulations using large atomistic ensembles. However, the extraction of meaningful information from the resulting atomistic ensembles is challenging, especially at intermediate length scales. Representational analysis is used here to describe the displacements of atoms in reverse Monte Carlo ensembles from an ideal crystallographic structure in an approach analogous to tight-binding methods. Rewriting the displacements in terms of a local basis that is descriptive of the ideal crystallographic symmetry provides a robust approach to characterizing medium-range order (and disorder) and symmetry breaking in complex and disordered crystalline materials. This method enables the extraction of statistically relevant displacement modes (orientation, amplitude and distribution) of the crystalline disorder and provides directly meaningful information in a locally symmetry-adapted basis set that is most descriptive of the crystal chemistry and physics.

  10. A universal strategy for the creation of machine learning-based atomistic force fields

    Science.gov (United States)

    Huan, Tran Doan; Batra, Rohit; Chapman, James; Krishnan, Sridevi; Chen, Lihua; Ramprasad, Rampi

    2017-09-01

    Emerging machine learning (ML)-based approaches provide powerful and novel tools to study a variety of physical and chemical problems. In this contribution, we outline a universal strategy to create ML-based atomistic force fields, which can be used to perform high-fidelity molecular dynamics simulations. This scheme involves (1) preparing a big reference dataset of atomic environments and forces with sufficiently low noise, e.g., using density functional theory or higher-level methods, (2) utilizing a generalizable class of structural fingerprints for representing atomic environments, (3) optimally selecting diverse and non-redundant training datasets from the reference data, and (4) proposing various learning approaches to predict atomic forces directly (and rapidly) from atomic configurations. From the atomistic forces, accurate potential energies can then be obtained by appropriate integration along a reaction coordinate or along a molecular dynamics trajectory. Based on this strategy, we have created model ML force fields for six elemental bulk solids, including Al, Cu, Ti, W, Si, and C, and show that all of them can reach chemical accuracy. The proposed procedure is general and universal, in that it can potentially be used to generate ML force fields for any material using the same unified workflow with little human intervention. Moreover, the force fields can be systematically improved by adding new training data progressively to represent atomic environments not encountered previously.

  11. Biomechanics of the porcine triple bundle anterior cruciate ligament.

    Science.gov (United States)

    Kato, Yuki; Ingham, Sheila J M; Linde-Rosen, Monica; Smolinski, Patrick; Horaguchi, Takashi; Fu, Freddie H

    2010-01-01

    Several species of animals are used as a model to study human anterior cruciate ligament (ACL) reconstruction. In many animals, three bundles were clearly discernible during dissection in the ACL. However, there are few reports about the biomechanical role of each bundle in the porcine knee. The purpose of this study is to investigate the role of each of the three bundles in the porcine knee, especially the intermediate bundle. Ten porcine knees were tested using a robotic/universal forcemoment sensor system. This system applied anterior loading of 89 N at 30 degrees, 60 degrees and 90 degrees of flexion, and a combined 7 Nm valgus and 4 Nm internal tibial torque at 30 degrees and 60 degrees of flexion before and after each bundle was selectively cut. The in situ force (N) for each bundle of the ACL was measured. Both intermediate (IM) bundle and postero-lateral (PL) bundle had significantly lower in situ force than the antero-medial (AM) bundle in anterior loading. The IM and PL bundles carried a larger proportion of the force under the torsional loads than the anterior loads. But IM bundle had a significant lower in situ force during the combined torque at 60 degrees of knee flexion, when compared intact ACL. In summary, IM bundle has a subordinate role to the AM and PL bundles. AM bundle is more dominant than IM and PL bundles. The porcine knee is a suitable model for ACL studies, especially for AP stability.

  12. Computational Method for Atomistic-Continuum Homogenization

    National Research Council Canada - National Science Library

    Chung, Peter

    2002-01-01

    ...." Physical Review Letters. vol. 61, no. 25, pp. 2879-2882, 19 December 1988; Brenner, D. W. "Empirical Potential for Hydrocarbons for Use in Simulating the Chemical Vapor Deposition of Diamond Films...

  13. Stability of Picard bundle over moduli space of stable vector bundles ...

    Indian Academy of Sciences (India)

    Springer Verlag Heidelberg #4 2048 1996 Dec 15 10:16:45

    Stability of Picard bundle over moduli space of stable vector bundles of rank two over a curve. INDRANIL BISWAS and TOM ´AS L G ´OMEZ. School of Mathematics, Tata Institute of Fundamental Research, Homi Bhabha Road,. Mumbai 400 005, India. E-mail: indranil@math.tifr.res.in; tomas@math.tifr.res.in. MS received 14 ...

  14. Stability of Picard bundle over moduli space of stable vector bundles ...

    Indian Academy of Sciences (India)

    Abstract. 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.

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

    NARCIS (Netherlands)

    S. Jain (Shashi); C.W. Oosterlee (Cornelis)

    2015-01-01

    htmlabstractThis 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

  16. 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

  17. Stress-dependence of kinetic transitions at atomistic defects

    Science.gov (United States)

    Ball, S. L.; Alexander, K. C.; Schuh, C. A.

    2018-01-01

    The full second-rank activation volume tensors associated with vacancy migration in FCC copper and HCP titanium as well as transition events in the Σ5 (2 1 0) grain boundary in copper are calculated and analyzed. The full tensorial results quantitatively illustrate how the conventional use of an activation volume scalar in atomistic studies of the kinetic processes of complex defects can miss important stress dependencies, in that neither hydrostatic pressure nor deviatoric stress dependencies can be considered alone as dominating the response. The results speak to the importance of anisotropies in the stress-dependence of atomistic kinetics, including crystal structure anisotropy, elastic anisotropy, and defect structure or migration-path anisotropies.

  18. Exploring the membrane fusion mechanism through force-induced disassembly of HIV-1 six-helix bundle

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Kai [Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Zhang, Yong [Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Lou, Jizhong, E-mail: jlou@ibp.ac.cn [Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China); Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 (China)

    2016-05-13

    Enveloped virus, such as HIV-1, employs membrane fusion mechanism to invade into host cell. HIV-1 gp41 ectodomain uses six-helix bundle configuration to accomplish this process. Using molecular dynamic simulations, we confirmed the stability of this six-helix bundle by showing high occupancy of hydrogen bonds and hydrophobic interactions. Key residues and interactions important for the bundle integration were characterized by force-induced unfolding simulations of six-helix bundle, exhibiting the collapse order of these groups of interactions. Moreover, our results in some way concerted with a previous theory that the formation of coiled-coil choose a route which involved cooperative interactions between the N-terminal and C-terminal helix. -- Highlights: •Unfolding of HIV-1 gp41 six-helix bundle is studied by molecular dynamics simulations. •Specific interactions responsible for the stability of HIV-1 envelope post-fusion conformation were identified. •The gp41 six-helix bundle transition inducing membrane fusion might be a cooperative process of the three subunits.

  19. The atomistic representation of first strain-gradient elastic tensors

    Science.gov (United States)

    Admal, Nikhil Chandra; Marian, Jaime; Po, Giacomo

    2017-02-01

    We derive the atomistic representations of the elastic tensors appearing in the linearized theory of first strain-gradient elasticity for an arbitrary multi-lattice. In addition to the classical second-Piola) stress and elastic moduli tensors, these include the rank-three double-stress tensor, the rank-five tensor of mixed elastic moduli, and the rank-six tensor of strain-gradient elastic moduli. The atomistic representations are closed-form analytical expressions in terms of the first and second derivatives of the interatomic potential with respect to interatomic distances, and dyadic products of relative atomic positions. Moreover, all expressions are local, in the sense that they depend only on the atomic neighborhood of a lattice site. Our results emanate from the condition of energetic equivalence between continuum and atomistic representations of a crystal, when the kinematics of the latter is governed by the Cauchy-Born rule. Using the derived expressions, we prove that the odd-order tensors vanish if the lattice basis admits central-symmetry. The analytical expressions are implemented as a KIM compliant algorithm to compute the strain gradient elastic tensors for various materials. Numerical results are presented to compare representative interatomic potentials used in the literature for cubic crystals, including simple lattices (fcc Al and Cu and bcc Fe and W) and multi-lattices (diamond-cubic Si). We observe that central potentials exhibit generalized Cauchy relations for the rank-six tensor of strain-gradient elastic moduli. In addition, this tensor is found to be indefinite for many potentials. We discuss the relationship between indefiniteness and material stability. Finally, the atomistic representations are specialized to central potentials in simple lattices. These expressions are used with analytical potentials to study the sensitivity of the elastic tensors to the choice of the cutoff radius.

  20. Balance Ability and Proprioception after Single-Bundle, Single-Bundle Augmentation, and Double-Bundle ACL Reconstruction

    Directory of Open Access Journals (Sweden)

    Yubao Ma

    2014-01-01

    Full Text Available Purpose. The present study sought to determine the influences of single-bundle (SB, single-bundle augmentation (SBA, and double-bundle (DB reconstructions on balance ability and proprioceptive function. Methods. 67 patients who underwent a single- or double-bundle ACL reconstruction or a SBA using multistranded autologous hamstring tendons were included in this study with a 1-year follow-up. Body sway and knee kinesthesia (using the threshold to detect passive motion test (TTDPM were measured to indicate balance ability and proprioceptive function, respectively. Additionally, within-subject differences in anterior-posterior stability of the tibia and lower extremity muscle strength were evaluated before and after surgery. Results. At 6 and 12 months after surgery, DB reconstruction resulted in better balance and proprioceptive function than SB reconstruction (P<0.05. Although no significant difference was observed in balance ability or proprioceptive function between the SBA and DB reconstructions, knee stability was significantly better with SBA and DB reconstructions than SB reconstruction (P<0.05. No significant differences were found in quadriceps and hamstrings strength among the three reconstruction techniques. Conclusions. Our findings consider that joint stability, proprioceptive function, and balance ability were superior with SBA and DB reconstructions compared to SB reconstruction at 6 and 12 months after surgery.

  1. Atomistic study of structures and elastic properties of single crystalline ZnO nanotubes.

    Science.gov (United States)

    Moon, Wonha; Hwang, Hojung

    2008-06-04

    The structural stability and Young's modulus of single crystalline ZnO nanotubes are investigated using atomistic simulations. Unlike the case for conventional layered nanotubes, the energetic stability of single crystalline ZnO nanotubes is related to the wall thickness. The potential energy of ZnO nanotubes with fixed outer and inner diameters decreases with increasing wall thickness, while the nanotubes with the same wall thickness are independent of the outer and inner diameters. The transformation of single crystalline ZnO nanotubes with a double layer from wurtzite phase to graphitic phase suggests the possibility of wall-typed ZnO nanotubes. The size-dependent Young's modulus of ZnO nanotubes is also investigated. The wall thickness plays a significant role in the Young's modulus of single crystalline ZnO nanotubes, whereas the variation of outer and inner diameters slightly affects the Young's modulus of nanotubes with same wall thickness.

  2. Displacement field of a screw dislocation in a Cu nanowire: An atomistic study

    Science.gov (United States)

    Gailhanou, Marc; Roussel, Jean-Marc

    2013-12-01

    By performing atomistic calculations with a tight-binding potential, we study the displacement field induced by a screw dislocation lying along a free Cu cylindrical nanowire. For this anisotropic orientation that is often encountered experimentally, we show that the displacement field uz along the nanowire can be seen as the superposition of three different fields: the screw dislocation field in an infinite medium, the warping displacement field caused by the so-called Eshelby twist, and an additional image field induced by the free surfaces. A Fourier series analysis of this latter image displacement and stress fields is given. For a circular cross section of the wire, this image field corresponds mainly to an additional warping displacement uz∝xy. The dissociation mechanism of the dislocation into partials and the surface stress effects being also captured in our simulations, the present study enables one to quantify the various contributions to the formation of the x-ray diffractograms.

  3. Atomistic model of metal nanocrystals with line defects: contribution to diffraction line profile

    Directory of Open Access Journals (Sweden)

    Alberto eLeonardi

    2015-02-01

    Full Text Available Molecular Dynamics (MD was used to simulate cylindrical Pd and Ir domains with ideal dislocations parallel to the axis. Results show significant discrepancies with respect to predictions of traditional continuum mechanics. When MD atomistic models are used to generate powder diffraction patterns, strong deviations are observed from the usual paradigm of a small crystal perturbed by the strain field of lattice defects. The Krivoglaz-Wilkens model for dislocation effects of diffraction line profiles seems correct for the screw dislocation case if most parameters are known or strongly constrained. Nevertheless the practical implementation of the model, i.e., a free refinement of all microstructural parameters, leads to instability. Possible effects of the experimental practice based on Line Profile Analysis are discussed.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-10-14

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

  5. 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.

  6. Size scaling of failure strength with fat-tailed disorder in a fiber bundle model

    Science.gov (United States)

    Kádár, Viktória; Danku, Zsuzsa; Kun, Ferenc

    2017-09-01

    We investigate the size scaling of the macroscopic fracture strength of heterogeneous materials when microscopic disorder is controlled by fat-tailed distributions. We consider a fiber bundle model where the strength of single fibers is described by a power law distribution over a finite range. Tuning the amount of disorder by varying the power law exponent and the upper cutoff of fibers' strength, in the limit of equal load sharing an astonishing size effect is revealed: For small system sizes the bundle strength increases with the number of fibers, and the usual decreasing size effect of heterogeneous materials is restored only beyond a characteristic size. We show analytically that the extreme order statistics of fibers' strength is responsible for this peculiar behavior. Analyzing the results of computer simulations we deduce a scaling form which describes the dependence of the macroscopic strength of fiber bundles on the parameters of microscopic disorder over the entire range of system sizes.

  7. Void growth in metals: Atomistic calculations

    Energy Technology Data Exchange (ETDEWEB)

    Traiviratana, Sirirat [Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093 (United States); Bringa, Eduardo M. [Materials Science Department, Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Benson, David J. [Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093 (United States); Meyers, Marc A. [Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA 92093 (United States); NanoEngineering, University of California, San Diego, La Jolla, CA 92093 (United States)], E-mail: mameyers@ucsd.edu

    2008-09-15

    Molecular dynamics simulations in monocrystalline and bicrystalline copper were carried out with LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) to reveal void growth mechanisms. The specimens were subjected to tensile uniaxial strains; the results confirm that the emission of (shear) loops is the primary mechanism of void growth. It is observed that many of these shear loops develop along two slip planes (and not one, as previously thought), in a heretofore unidentified mechanism of cooperative growth. The emission of dislocations from voids is the first stage, and their reaction and interaction is the second stage. These loops, forming initially on different {l_brace}1 1 1{r_brace} planes, join at the intersection, if the Burgers vector of the dislocations is parallel to the intersection of two {l_brace}1 1 1{r_brace} planes: a <1 1 0> direction. Thus, the two dislocations cancel at the intersection and a biplanar shear loop is formed. The expansion of the loops and their cross slip leads to the severely work-hardened region surrounding a growing void. Calculations were carried out on voids with different sizes, and a size dependence of the stress threshold to emit dislocations was obtained by MD, in disagreement with the Gurson model which is scale independent. This disagreement is most marked for the nanometer sized voids. The scale dependence of the stress required to grow voids is interpreted in terms of the decreasing availability of optimally oriented shear planes and increased stress required to nucleate shear loops as the void size is reduced. The growth of voids simulated by MD is compared with the Cocks-Ashby constitutive model and significant agreement is found. The density of geometrically necessary dislocations as a function of void size is calculated based on the emission of shear loops and their outward propagation. Calculations are also carried out for a void at the interface between two grains to simulate polycrystalline

  8. Graph Bundling by Kernel Density Estimation

    NARCIS (Netherlands)

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

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

  9. Permanent His-Bundle Pacing: Case Studies.

    Science.gov (United States)

    Vijayaraman, Pugazhendhi; Dandamudi, Gopi

    2016-12-01

    His bundle pacing (HBP) is a physiological alternative to right ventricular pacing. In addition to patients with normal His-Purkinje conduction, HBP can be valuable in patients with infranodal atrioventricular (AV) block and patients undergoing AV node ablation. The following case studies illustrate the challenges associated with HBP. © 2016 Wiley Periodicals, Inc.

  10. Fluxes, bundle gerbes and 2-Hilbert spaces

    Science.gov (United States)

    Bunk, Severin; Szabo, Richard J.

    2017-10-01

    We elaborate on the construction of a prequantum 2-Hilbert space from a bundle gerbe over a 2-plectic manifold, providing the first steps in a programme of higher geometric quantisation of closed strings in flux compactifications and of M5-branes in C-fields. We review in detail the construction of the 2-category of bundle gerbes and introduce the higher geometrical structures necessary to turn their categories of sections into 2-Hilbert spaces. We work out several explicit examples of 2-Hilbert spaces in the context of closed strings and M5-branes on flat space. We also work out the prequantum 2-Hilbert space associated with an M-theory lift of closed strings described by an asymmetric cyclic orbifold of the SU(2) WZW model, providing an example of sections of a torsion gerbe on a curved background. We describe the dimensional reduction of M-theory to string theory in these settings as a map from 2-isomorphism classes of sections of bundle gerbes to sections of corresponding line bundles, which is compatible with the respective monoidal structures and module actions.

  11. The unintended consequences of bundled payments.

    Science.gov (United States)

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

    2013-01-01

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

  12. Meromorphic connections on vector bundles over curves

    Indian Academy of Sciences (India)

    Descartes,. 67084 Strasbourg Cedex, France. *Correspond author. E-mail: indranil@math.tifr.res.in; heu@math.unistra.fr. MS received 17 July 2013; revised 20 October 2013. Abstract. We give a criterion for filtered vector bundles over curves to admit a ...

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

    Science.gov (United States)

    Cheng, Bingqing; Tribello, Gareth A; Ceriotti, Michele

    2017-09-14

    In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable.

  14. Anterior cruciate ligament reconstruction with double bundle versus single bundle: experimental study

    National Research Council Canada - National Science Library

    Roberto F. Mota e Albuquerque; Sandra Umeda Sasaki; Marco Martins Amatuzzi; Fabio Janson Angelini

    2007-01-01

    OBJECTIVE: To test an intra-articular reconstruction of the anterior cruciate ligament of the knee in 10 human cadavers by replacing 2 anterior cruciate ligament bundles, with the purpose of producing...

  15. Functional aspects of His bundle physiology and pathophysiology: Clinical implications.

    Science.gov (United States)

    Scherlag, Benjamin J; Lazzara, Ralph

    In this review we present evidence from many experimental studies which challenge the concept of predestination of His bundle fibers. Using both intra- and extracellular His bundle pacing in the context of atrio-ventricular block and the development of bundle branch blocks these experimental studies provide the underlying mechanisms for the recent clinical findings showing the benefits of permanent His bundle pacing. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. A case of 'Masquerading' bundle branch block: a forgotten concept.

    Science.gov (United States)

    Choudhary, Dinesh; Namboodiri, Narayanan; Tharakan, Jaganmohan A

    2014-01-01

    'Masquerading' bundle branch block (right bundle branch block in the precordial leads with left bundle branch block in frontal leads and left axis deviation) is seen most commonly with coronary artery disease and hypertension. No definite explanation is available so far for these changes. We are presenting a case of rare congenital intranuclear inclusion myopathy with congestive heart failure and 'Masquerading' bundle branch block in ECG. Copyright © 2013 Cardiological Society of India. Published by Elsevier B.V. All rights reserved.

  17. Bundling revisited: substitute products and inter-firm discounts

    OpenAIRE

    Armstrong, Mark

    2010-01-01

    This paper extends the standard model of bundling to allow products to be substitutes and for products to be supplied by separate sellers. Whether integrated or separate, firms have an incentive to introduce bundling discounts when demand for the bundle is elastic relative to demand for stand-alone products. When products are partial substitutes, this typically gives an integrated firm a greater incentive to offer a bundle discount (relative to the standard model with additive preferences), w...

  18. 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.

  19. Compactifications of reductive groups as moduli stacks of bundles

    DEFF Research Database (Denmark)

    Martens, Johan; Thaddeus, Michael

    Let G be a reductive group. We introduce the moduli problem of "bundle chains" parametrizing framed principal G-bundles on chains of lines. Any fan supported in a Weyl chamber determines a stability condition on bundle chains. Its moduli stack provides an equivariant toroidal compactification of ...... studied by Losev-Manin....

  20. Turkish and Native English Academic Writers' Use of Lexical Bundles

    Science.gov (United States)

    Öztürk, Yusuf; Köse, Gül Durmusoglu

    2016-01-01

    Lexical bundles such as "on the other hand" and "as a result of" are extremely common and important in academic discourse. The appropriate use of lexical bundles typical of a specific academic discipline is important for writers and the absence of such bundles may not sound fluent and native-like. Recent studies (e.g. Adel…

  1. Quillen bundle and geometric prequantization of non-abelian ...

    Indian Academy of Sciences (India)

    In this paper we prequantize the moduli space of non-abelian vortices. We explicitly calculate the symplectic form arising from 2 metric and we construct a prequantum line bundle whose curvature is proportional to this symplectic form. The prequantum line bundle turns out to be Quillen's determinant line bundle with a ...

  2. The Bundle of His in Prosthetic Heart Valve Replacement*

    African Journals Online (AJOL)

    1973-01-27

    Jan 27, 1973 ... ventricular seplUm which transected the bundle of His. Blocks were then fashioned backwards and forwards.. to include the whole of the bundle and the AV node. as well as the bifurcation of the bundle into its left and right branches. According to Davies: in order to study the whole conduction system in an ...

  3. Real parabolic vector bundles over a real curve

    Indian Academy of Sciences (India)

    weights are integral multiples of 1/N, and the category of real -equivariant vector bundles on (Y,σY ). ... The notion of parabolic vector bundles over a compact Riemann surface was introduced by Seshadri [4] and their .... stable. If F is a direct sum of stable vector bundles having the same slope, then F is called polystable.

  4. Geometry of torus bundles in integrable Hamiltonian systems

    NARCIS (Netherlands)

    Lukina, Olga

    2008-01-01

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

  5. Masquerading bundle branch block: a variety of right bundle branch block with left anterior fascicular block.

    Science.gov (United States)

    Elizari, Marcelo V; Baranchuk, Adrian; Chiale, Pablo A

    2013-01-01

    The so-called 'masquerading' type of right bundle branch block is caused by the simultaneous presence of a high-degree left anterior fascicular block often accompanied with severe left ventricular enlargement and/or fibrotic block in the anterolateral wall of the left ventricle. These conditions tend to reorient the terminal electrical forces of the QRS complex towards the left and upwards, in such a way that the characteristic slurred S wave in lead I becomes smaller or even disappears. In many cases of standard masquerading right bundle branch block, a small Q wave in lead I is present due to the initial forces of the left anterior fascicular block, which are oriented rightwards and inferiorly. However, in some cases, the Q wave in lead I also vanishes, and the mimicking of a left bundle branch block becomes perfect in standard leads. This is commonly associated with an inferior myocardial infarction or severe inferior fibrosis in cardiomyopathies. The typical QRS changes of right bundle branch block may eventually be concealed even in the right precordial leads; under such circumstances, the ECG diagnosis may be mistaken and the right bundle branch block totally missed. The masquerading right bundle branch block carries a poor prognosis, since it always implies the presence of a severe underlying heart disease.

  6. Alignment of Multiple Electrospun Piezoelectric Fiber Bundles Across Serrated Gaps at an Incline: A Method to Generate Textile Strain Sensors.

    Science.gov (United States)

    Hsu, Yu-Hsiang; Chan, Chen-Hao; Tang, William C

    2017-11-13

    In this paper, we report a new type of electrospinning collector that allows simultaneous collection and alignment of multiple poly(vinylidene fluoride-trifluoroethylene) piezoelectric fiber bundles with a controlled separation. The key enabling feature is the serrated teeth along the edges across an inclined gap as a part of the conductive collector. As a result, the electrical field across the gap is shaped to direct the electrospun fibers to merge into multiple bundles. The sharp points on the serrated teeth provide favorable charge dissipation points and thus fibers are preferentially formed bridging two closest sharp points across the gap. To investigate the effectiveness of serrated teeth on the formation of multiple fiber bundles, three-dimensional finite element simulations are conducted. The corresponding collectors are implemented to experimentally study the resulting electrospun fibers. Both simulation and experimental results suggest that multiple fiber bundles can be formed under the condition of a low teeth pitch to gap distance ratio. Furthermore, a sharper tooth angle results in a higher preferential formation of fiber bundles. Finally, the total electrospinning time should be less than 60 seconds to maintain favorable electric field profile. We also demonstrate that these piezoelectric fiber bundles can serve as ultra-flexible textile sensors.

  7. 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

  8. Non-abelian higher gauge theory and categorical bundle

    Science.gov (United States)

    Viennot, David

    2016-12-01

    A gauge theory is associated with a principal bundle endowed with a connection permitting to define horizontal lifts of paths. The horizontal lifts of surfaces cannot be defined into a principal bundle structure. An higher gauge theory is an attempt to generalize the bundle structure in order to describe horizontal lifts of surfaces. A such attempt is particularly difficult for the non-abelian case. Some structures have been proposed to realize this goal (twisted bundle, gerbes with connection, bundle gerbe, 2-bundle). Each of them uses a category in place of the total space manifold of the usual principal bundle structure. Some of them replace also the structure group by a category (more precisely a Lie crossed module viewed as a category). But the base space remains still a simple manifold (possibly viewed as a trivial category with only identity arrows). We propose a new principal categorical bundle structure, with a Lie crossed module as structure groupoid, but with a base space belonging to a bigger class of categories (which includes non-trivial categories), that we called affine 2-spaces. We study the geometric structure of the categorical bundles built on these categories (which are a more complicated structure than the 2-bundles) and the connective structures on these bundles. Finally we treat an example interesting for quantum dynamics which is associated with the Bloch wave operator theory.

  9. SIKAP KONSUMEN TERHADAP PRODUK BUNDLING AGRIBISNIS

    Directory of Open Access Journals (Sweden)

    Didi Junaedi

    2017-04-01

    implementation to Dekalb brand hybrid corn and Round-up brand herbicide. By analyzes how consumer attitudes toward buying intention in this regard farmers as buyer and retailers as products services. The data used is primary data. Primary data is obtained using 2 kind of respondents are retailers and farmers. The data obtained by distributed 30 questionnaires for retailers and 110 farmers in Grobogan. The descriptive statistic employed to analyzed data by using multiple linear regressions with t test, F test and coefficient of determination. The result showed that on retailers respondents attribute the product bundling has no significant influence to consumer buying intention but consumer attitudes significantly influence the buying intention. On the farmers respondents showed that attributes of the product bundling and consumer attitudes positive and significant influence to buying intention.

  10. Covariance and the hierarchy of frame bundles

    Science.gov (United States)

    Estabrook, Frank B.

    1987-01-01

    This is an essay on the general concept of covariance, and its connection with the structure of the nested set of higher frame bundles over a differentiable manifold. Examples of covariant geometric objects include not only linear tensor fields, densities and forms, but affinity fields, sectors and sector forms, higher order frame fields, etc., often having nonlinear transformation rules and Lie derivatives. The intrinsic, or invariant, sets of forms that arise on frame bundles satisfy the graded Cartan-Maurer structure equations of an infinite Lie algebra. Reduction of these gives invariant structure equations for Lie pseudogroups, and for G-structures of various orders. Some new results are introduced for prolongation of structure equations, and for treatment of Riemannian geometry with higher-order moving frames. The use of invariant form equations for nonlinear field physics is implicitly advocated.

  11. 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.

  12. Uncovering Ecosystem Service Bundles through Social Preferences

    Science.gov (United States)

    Martín-López, Berta; Iniesta-Arandia, Irene; García-Llorente, Marina; Palomo, Ignacio; Casado-Arzuaga, Izaskun; Amo, David García Del; Gómez-Baggethun, Erik; Oteros-Rozas, Elisa; Palacios-Agundez, Igone; Willaarts, Bárbara; González, José A.; Santos-Martín, Fernando; Onaindia, Miren; López-Santiago, Cesar; Montes, Carlos

    2012-01-01

    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. PMID:22720006

  13. Twisted vector bundles on pointed nodal curves

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    DEFINITION 2.5. Let C → S be an n-pointed nodal curve over a k-scheme S and let ξ be a principal G- bundle on Cgen. A chart (U, η, ) for ξ is called balanced, if for each ... branches is via multiplication with primitive roots of unity which are inverse to each other. ...... Condition (16) implies that A0 is a block matrix of the form.

  14. Principal bundles on the projective line

    Indian Academy of Sciences (India)

    M. Senthilkumar (Newgen Imaging) 1461 1996 Oct 15 13:05:22

    LetX be a complete nonsingular curve over the algebraic closurek ofk andGa reductive group over k. Let E → X be a principal G-bundle on X. E is said to be semistable if, for every reduction of structure group EP ⊂ E to a maximal parabolic subgroup P of G, we have degree EP (p) ≤ 0, where p is the Lie algebra of P and EP ...

  15. Abelian conformal field theory and determinant bundles

    DEFF Research Database (Denmark)

    Andersen, Jørgen Ellegaard; Ueno, K.

    2007-01-01

    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...... nodal curves. These results are used in [4] to construct modular functors form the conformal field theories given in [14, 16] by twisting with an appropriate factional power of this Abelian theory....

  16. 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.

  17. Uncovering ecosystem service bundles through social preferences.

    Science.gov (United States)

    Martín-López, Berta; Iniesta-Arandia, Irene; García-Llorente, Marina; Palomo, Ignacio; Casado-Arzuaga, Izaskun; Amo, David García Del; Gómez-Baggethun, Erik; Oteros-Rozas, Elisa; Palacios-Agundez, Igone; Willaarts, Bárbara; González, José A; Santos-Martín, Fernando; Onaindia, Miren; López-Santiago, Cesar; Montes, Carlos

    2012-01-01

    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.

  18. Bundling harvester; Harvennuspuun automaattisen nippukorjausharvesterin kehittaeminen

    Energy Technology Data Exchange (ETDEWEB)

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

    1997-12-01

    The starting 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, automating of the harvester, and automated 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 utilisation 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 utilised without loosing the profitability of transportation. The results have been promising, and will promote the profitable utilisation of wood-energy. (orig.)

  19. An analytical fiber bundle model for pullout mechanics of root bundles

    Science.gov (United States)

    Cohen, D.; Schwarz, M.; Or, D.

    2011-09-01

    Roots in soil contribute to the mechanical stability of slopes. Estimation of root reinforcement is challenging because roots form complex biological networks whose geometrical and mechanical characteristics are difficult to characterize. Here we describe an analytical model that builds on simple root descriptors to estimate root reinforcement. Root bundles are modeled as bundles of heterogeneous fibers pulled along their long axes neglecting root-soil friction. Analytical expressions for the pullout force as a function of displacement are derived. The maximum pullout force and corresponding critical displacement are either derived analytically or computed numerically. Key model inputs are a root diameter distribution (uniform, Weibull, or lognormal) and three empirical power law relations describing tensile strength, elastic modulus, and length of roots as functions of root diameter. When a root bundle with root tips anchored in the soil matrix is pulled by a rigid plate, a unique parameter, ?, that depends only on the exponents of the power law relations, dictates the order in which roots of different diameters break. If ? 1, large roots break first. When ? = 1, all fibers break simultaneously, and the maximum tensile force is simply the roots' mean force times the number of roots in the bundle. Based on measurements of root geometry and mechanical properties, the value of ? is less than 1, usually ranging between 0 and 0.7. Thus, small roots always fail first. The model shows how geometrical and mechanical characteristics of roots and root diameter distribution affect the pullout force, its maximum and corresponding displacement. Comparing bundles of roots that have similar mean diameters, a bundle with a narrow variance in root diameter will result in a larger maximum force and a smaller displacement at maximum force than a bundle with a wide diameter distribution. Increasing the mean root diameter of a bundle without changing the distribution's shape increases

  20. Ion-irradiation-induced defects in bundles of carbon nanotubes

    CERN Document Server

    Salonen, E; Nordlund, K

    2002-01-01

    We study the structure and formation yields of atomic-scale defects produced by low-dose Ar ion irradiation in bundles of single-wall carbon nanotubes. For this, we employ empirical potential molecular dynamics and simulate ion impact events over an energy range of 100-1000 eV. We show that the most common defects produced at all energies are vacancies on nanotube walls, which at low temperatures are metastable but long-lived defects. We further calculate the spatial distribution of the defects, which proved to be highly non-uniform. We also show that ion irradiation gives rise to the formations of inter-tube covalent bonds mediated by carbon recoils and nanotube lattice distortions due to dangling bond saturation. The number of inter-tube links, as well as the overall damage, linearly grows with the energy of incident ions.

  1. Atomistic methodologies for material properties of 2D materials at the nanoscale

    Science.gov (United States)

    Zhang, Zhen

    Research on two dimensional (2D) materials, such as graphene and MoS2, now involves thousands of researchers worldwide cutting across physics, chemistry, engineering and biology. Due to the extraordinary properties of 2D materials, research extends from fundamental science to novel applications of 2D materials. From an engineering point of view, understanding the material properties of 2D materials under various conditions is crucial for tailoring the electrical and mechanical properties of 2D-material-based devices at the nanoscale. Even at the nanoscale, molecular systems typically consist of a vast number of atoms. Molecular dynamics (MD) simulations enable us to understand the properties of assemblies of molecules in terms of their structure and the microscopic interactions between them. From a continuum approach, mechanical properties and thermal properties, such as strain, stress, and heat capacity, are well defined and experimentally measurable. In MD simulations, material systems are considered to be discrete, and only interatomic potential, interatomic forces, and atom positions are directly obtainable. Besides, most of the fracture mechanics concepts, such as stress intensity factors, are not applicable since there is no singularity in MD simulations. However, energy release rate still remains to be a feasible and crucial physical quantity to characterize the fracture mechanical property of materials at the nanoscale. Therefore, equivalent definition of a physical quantity both in atomic scale and macroscopic scale is necessary in order to understand molecular and continuum scale phenomena concurrently. This work introduces atomistic simulation methodologies, based on interatomic potential and interatomic forces, as a tool to unveil the mechanical properties, thermal properties and fracture mechanical properties of 2D materials at the nanoscale. Among many 2D materials, graphene and MoS2 have attracted intense interest. Therefore, we applied our

  2. Atomistic modeling of nanoparticle generation in short pulse laser ablation of thin metal films in water.

    Science.gov (United States)

    Shih, Cheng-Yu; Wu, Chengping; Shugaev, Maxim V; Zhigilei, Leonid V

    2017-03-01

    Laser ablation in liquids is actively used for generation of clean colloidal nanoparticles with unique shapes and functionalities. The fundamental mechanisms of the laser ablation in liquids and the key processes that control the nanoparticle structure, composition, and size distribution, however, are not yet fully understood. In this paper, we report the results of first atomistic simulations of laser ablation of metal targets in liquid environment. A model combining a coarse-grained representation of the liquid environment (parameterized for water), a fully atomistic description of laser interactions with metal targets, and acoustic impedance matching boundary conditions is developed and applied for simulation of laser ablation of a thin silver film deposited on a silica substrate. The simulations, performed at two laser fluences in the regime of phase explosion, predict a rapid deceleration of the ejected ablation plume and the formation of a dense superheated molten layer at the water-plume interface. The water in contact with the hot metal layer is brought to the supercritical state and transforms into an expanding low density metal-water mixing region that serves as a precursor for the formation of a cavitation bubble. Two distinct mechanisms of the nanoparticle formation are predicted in the simulations: (1) the nucleation and growth of small (mostly ⩽10nm) nanoparticles in the metal-water mixing region and (2) the formation of larger (tens of nm) nanoparticles through the breakup of the superheated molten metal layer triggered by the emergence of complex morphological features attributed to the Rayleigh-Taylor instability of the interface between at the superheated metal layer and the supercritical water. The first mechanism is facilitated by the rapid cooling of the growing nanoparticles in the supercritical water environment, resulting in solidification of the nanoparticles located in the upper part of the mixing region on the timescale of nanoseconds

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-10-01

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

  4. Deductive multiscale simulation using order parameters

    Science.gov (United States)

    Ortoleva, Peter J.

    2017-05-16

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

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

    Science.gov (United States)

    Gromalova, Natalia; Nikishaeva, Nadezhda; Eremin, Nikolay

    2017-04-01

    potential. The other sets of interatomic potentials («Zircon 2, Zircon 3») differed from the first in that parameters was found with the help of quantum-chemical calculations of the structure «ab initio».The surface energies for different faces of zircon were calculated using Metadise code (Watson et al., 1996) at P4-3000 personal computer with Windows XP operating system. The computation time for one simple form was from 30 minutes to 12 hours. Calculations have shown that depending on the chosen model the surface energy of zircons faces several changes. For example, Esurf of face (331) obtained using models of potentials «Zircon 2», «Zircon 3» sufficiently similar (2.82 and 3.01 J/mol2 respectively). Meaning of Esurf of this face, calculated on the basis of set «Zircon 1» significantly lower (1,54 J/mol2). With regard to the face (100), it has low surface energies when selecting all three models, with a minimum value (1,14 J/mol2) in the model «Zircon 1». References: Gromalova N.A., Eremin N.N., Urusov V.S. Atomistic computer modeling of the crystal-morpology of corundum group minerals // Zapiski RMO. V. 144. №4. 2015. p. 84-92. Watson G.W., Kelsey E.T., de Leeuw N.H., Harris D.J, Parker S.C. Atomistic simulation of dislocations, surfaces and interfaces in MgO. Journal of the Chemical Society Faraday Transactions. 1996. V.92 P. 433-438.

  6. Critical Power in 7-Rod Tight Lattice Bundle

    Science.gov (United States)

    Liu, Wei; Kureta, Masatoshi; Akimoto, Hajime

    The Reduced-Moderation Water Reactor (RMWR) has recently becomes of great concern. The RMWR is expected to promote the effective utilization of uranium recourse. The RMWR is based on water-cooled reactor technology, with achieved under lower core water volume and water flow rate. In comparison with the current light water reactors whose water-to-fuel volume ratio is about 2-3, in the RMWR, this value is reduced to less than 0.5. Thereby, there is a need to research its cooling characteristics. Experimental research on critical power in tight lattice bundle that simulates the RMWR has been carried out in Japan Atomic Energy Research Institute (JAERI). The bundle consists one center rod and six peripheral rods. The 7 rods are arranged on a 14.3mm equilateral triangular pitch. Each rod is 13mm in outside diameter. An axial 12-step power distribution is employed to simulate the complicate heating condition in RMWR. Experiments are carried out under G=100-1400kg/m2s, Pex=2-8.5MPa. Effects of mass velocity, inlet temperature, pressure, radial peaking factor and axial peaking factor on critical power and critical quality are discussed. Compared with axial uniform heating condition, the axial non-uniform heating condition causes an obvious decrease in critical quality. Arai correlation, which is the only correlation that has been optimized for tight lattice condition, is verified with the present experimental data. The correlation is found to be able to give reasonable prediction only around RMWR nominal operating condition.

  7. Atomistically derived cohesive zone model of intergranular fracture in polycrystalline graphene

    Energy Technology Data Exchange (ETDEWEB)

    Guin, Laurent [LMS, École Polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau (France); Department of Mechanical Engineering, Columbia University, New York, New York 10027 (United States); Raphanel, Jean L. [LMS, École Polytechnique, CNRS, Université Paris-Saclay, 91128 Palaiseau (France); Kysar, Jeffrey W. [Department of Mechanical Engineering, Columbia University, New York, New York 10027 (United States)

    2016-06-28

    Pristine single crystal graphene is the strongest known two-dimensional material, and its nonlinear anisotropic mechanical properties are well understood from the atomic length scale up to a continuum description. However, experiments indicate that grain boundaries in the polycrystalline form reduce the mechanical behavior of polycrystalline graphene. Herein, we perform atomistic-scale molecular dynamics simulations of the deformation and fracture of graphene grain boundaries and express the results as continuum cohesive zone models (CZMs) that embed notions of the grain boundary ultimate strength and fracture toughness. To facilitate energy balance, we employ a new methodology that simulates a quasi-static controlled crack propagation which renders the kinetic energy contribution to the total energy negligible. We verify good agreement between Griffith's critical energy release rate and the work of separation of the CZM, and we note that the energy of crack edges and fracture toughness differs by about 35%, which is attributed to the phenomenon of bond trapping. This justifies the implementation of the CZM within the context of the finite element method (FEM). To enhance computational efficiency in the FEM implementation, we discuss the use of scaled traction-separation laws (TSLs) for larger element sizes. As a final result, we have established that the failure characteristics of pristine graphene and high tilt angle bicrystals differ by less than 10%. This result suggests that one could use a unique or a few typical TSLs as a good approximation for the CZMs associated with the mechanical simulations of the polycrystalline graphene.

  8. Are current atomistic force fields accurate enough to study proteins in crowded environments?

    Directory of Open Access Journals (Sweden)

    Drazen Petrov

    2014-05-01

    Full Text Available The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins, including their structural stabilities, intermolecular binding affinities and enzymatic rates. Moreover, various structural biology methods, such as NMR or different spectroscopies, typically involve samples with relatively high protein concentration. Due to large sampling requirements, however, the accuracy of classical molecular dynamics (MD simulations in capturing protein behavior at high concentration still remains largely untested. Here, we use explicit-solvent MD simulations and a total of 6.4 µs of simulated time to study wild-type (folded and oxidatively damaged (unfolded forms of villin headpiece at 6 mM and 9.2 mM protein concentration. We first perform an exhaustive set of simulations with multiple protein molecules in the simulation box using GROMOS 45a3 and 54a7 force fields together with different types of electrostatics treatment and solution ionic strengths. Surprisingly, the two villin headpiece variants exhibit similar aggregation behavior, despite the fact that their estimated aggregation propensities markedly differ. Importantly, regardless of the simulation protocol applied, wild-type villin headpiece consistently aggregates even under conditions at which it is experimentally known to be soluble. We demonstrate that aggregation is accompanied by a large decrease in the total potential energy, with not only hydrophobic, but also polar residues and backbone contributing substantially. The same effect is directly observed for two other major atomistic force fields (AMBER99SB-ILDN and CHARMM22-CMAP as well as indirectly shown for additional two (AMBER94, OPLS-AAL, and is possibly due to a general overestimation of the potential energy of protein-protein interactions at the expense of water-water and water-protein interactions. Overall, our results suggest that current MD force fields

  9. Influence of Bundle Diameter and Attachment Point on Kinematic Behavior in Double Bundle Anterior Cruciate Ligament Reconstruction Using Computational Model

    Directory of Open Access Journals (Sweden)

    Oh Soo Kwon

    2014-01-01

    Full Text Available A protocol to choose the graft diameter attachment point of each bundle has not yet been determined since they are usually dependent on a surgeon’s preference. Therefore, the influence of bundle diameters and attachment points on the kinematics of the knee joint needs to be quantitatively analyzed. A three-dimensional knee model was reconstructed with computed tomography images of a 26-year-old man. Based on the model, models of double bundle anterior cruciate ligament (ACL reconstruction were developed. The anterior tibial translations for the anterior drawer test and the internal tibial rotation for the pivot shift test were investigated according to variation of bundle diameters and attachment points. For the model in this study, the knee kinematics after the double bundle ACL reconstruction were dependent on the attachment point and not much influenced by the bundle diameter although larger sized anterior-medial bundles provided increased stability in the knee joint. Therefore, in the clinical setting, the bundle attachment point needs to be considered prior to the bundle diameter, and the current selection method of graft diameters for both bundles appears justified.

  10. Monopoles and Modifications of Bundles over Elliptic Curves

    Directory of Open Access Journals (Sweden)

    Andrey M. Levin

    2009-06-01

    Full Text Available Modifications of bundles over complex curves is an operation that allows one to construct a new bundle from a given one. Modifications can change a topological type of bundle. We describe the topological type in terms of the characteristic classes of the bundle. Being applied to the Higgs bundles modifications establish an equivalence between different classical integrable systems. Following Kapustin and Witten we define the modifications in terms of monopole solutions of the Bogomolny equation. We find the Dirac monopole solution in the case R × (elliptic curve. This solution is a three-dimensional generalization of the Kronecker series. We give two representations for this solution and derive a functional equation for it generalizing the Kronecker results. We use it to define Abelian modifications for bundles of arbitrary rank. We also describe non-Abelian modifications in terms of theta-functions with characteristic.

  11. Trivalent Cation Induced Bundle Formation of Filamentous fd Phages.

    Science.gov (United States)

    Korkmaz Zirpel, Nuriye; Park, Eun Jin

    2015-09-01

    Bacteriophages are filamentous polyelectrolyte viral rods infecting only bacteria. In this study, we investigate the bundle formation of fd phages with trivalent cations having different ionic radii (Al(3+) , La(3+) and Y(3+) ) at various phage and counterion concentrations, and at varying bundling times. Aggregated phage bundles were detected at relatively low trivalent counterion concentrations (1 mM). Although 10 mM and 100 mM Y(3+) and La(3+) treatments formed larger and more intertwined phage bundles, Al(3+) and Fe(3+) treatments lead to the formation of networking filaments. Energy dispersive X-ray spectroscopy (EDX) analyses confirmed the presence of C, N and O peaks on densely packed phage bundles. Immunofluorescence labelling and ELISA analyses with anti-p8 antibodies showed the presence of phage filaments after bundling. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Control algorithm for multiscale flow simulations of water

    DEFF Research Database (Denmark)

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

    2009-01-01

    We present a multiscale algorithm to couple atomistic water models with continuum incompressible flow simulations via a Schwarz domain decomposition approach. The coupling introduces an inhomogeneity in the description of the atomistic domain and prevents the use of periodic boundary conditions....... The use of a mass conserving specular wall results in turn to spurious oscillations in the density profile of the atomistic description of water. These oscillations can be eliminated by using an external boundary force that effectively accounts for the virial component of the pressure. In this Rapid...

  13. Heat Transfer Analysis in Wire Bundles for Aerospace Vehicles

    Science.gov (United States)

    Rickman, S. L.; Iamello, C. J.

    2016-01-01

    Design of wiring for aerospace vehicles relies on an understanding of "ampacity" which refers to the current carrying capacity of wires, either, individually or in wire bundles. Designers rely on standards to derate allowable current flow to prevent exceedance of wire temperature limits due to resistive heat dissipation within the wires or wire bundles. These standards often add considerable margin and are based on empirical data. Commercial providers are taking an aggressive approach to wire sizing which challenges the conventional wisdom of the established standards. Thermal modelling of wire bundles may offer significant mass reduction in a system if the technique can be generalized to produce reliable temperature predictions for arbitrary bundle configurations. Thermal analysis has been applied to the problem of wire bundles wherein any or all of the wires within the bundle may carry current. Wire bundles present analytical challenges because the heat transfer path from conductors internal to the bundle is tortuous, relying on internal radiation and thermal interface conductance to move the heat from within the bundle to the external jacket where it can be carried away by convective and radiative heat transfer. The problem is further complicated by the dependence of wire electrical resistivity on temperature. Reduced heat transfer out of the bundle leads to higher conductor temperatures and, hence, increased resistive heat dissipation. Development of a generalized wire bundle thermal model is presented and compared with test data. The steady state heat balance for a single wire is derived and extended to the bundle configuration. The generalized model includes the effects of temperature varying resistance, internal radiation and thermal interface conductance, external radiation and temperature varying convective relief from the free surface. The sensitivity of the response to uncertainties in key model parameters is explored using Monte Carlo analysis.

  14. Isomonodromic Deformations and Very Stable Vector Bundles of Rank Two

    Science.gov (United States)

    Biswas, Indranil; Heu, Viktoria; Hurtubise, Jacques

    2017-12-01

    For the universal isomonodromic deformation of an irreducible logarithmic rank two connection over a smooth complex projective curve of genus at least two, consider the family of holomorphic vector bundles over curves underlying this universal deformation. In a previous work we proved that the vector bundle corresponding to a general parameter of this family is stable. Here we prove that the vector bundle corresponding to a general parameter is in fact very stable, meaning it does not admit any nonzero nilpotent Higgs field.

  15. Bundling Products and Services Through Modularization Strategies

    DEFF Research Database (Denmark)

    Bask, Anu; Hsuan, Juliana; Rajahonka, Mervi

    2012-01-01

    Modularity has been recognized as a powerful tool in improving the efficiency and management of product design and manufacturing. However, the integrated view on covering both, product and service modularity for product-service systems (PSS), is under researched. Therefore, in this paper our...... objective is to contribute to the PSS modularity. Thus, we describe configurations of PSSs and the bundling of products and services through modularization strategies. So far there have not been tools to analyze and determine the correct combinations of degrees of product and service modularities....

  16. Differential geometry bundles, connections, metrics and curvature

    CERN Document Server

    Taubes, Clifford Henry

    2011-01-01

    Bundles, connections, metrics and curvature are the 'lingua franca' of modern differential geometry and theoretical physics. This book will supply a graduate student in mathematics or theoretical physics with the fundamentals of these objects. Many of the tools used in differential topology are introduced and the basic results about differentiable manifolds, smooth maps, differential forms, vector fields, Lie groups, and Grassmanians are all presented here. Other material covered includes the basic theorems about geodesics and Jacobi fields, the classification theorem for flat connections, the

  17. Affine Flag Manifolds and Principal Bundles

    CERN Document Server

    Schmitt, Alexander HW

    2010-01-01

    Affine flag manifolds are infinite dimensional versions of familiar objects such as Gramann varieties. The book features lecture notes, survey articles, and research notes - based on workshops held in Berlin, Essen, and Madrid - explaining the significance of these and related objects (such as double affine Hecke algebras and affine Springer fibers) in representation theory (e.g., the theory of symmetric polynomials), arithmetic geometry (e.g., the fundamental lemma in the Langlands program), and algebraic geometry (e.g., affine flag manifolds as parameter spaces for principal bundles). Novel

  18. Vector bundles on complex projective spaces

    CERN Document Server

    Okonek, Christian; Spindler, Heinz

    1980-01-01

    This expository treatment is based on a survey given by one of the authors at the Séminaire Bourbaki in November 1978 and on a subsequent course held at the University of Göttingen. It is intended to serve as an introduction to the topical question of classification of holomorphic vector bundles on complex projective spaces, and can easily be read by students with a basic knowledge of analytic or algebraic geometry. Short supplementary sections describe more advanced topics, further results, and unsolved problems.

  19. Machine learning of correlated dihedral potentials for atomistic molecular force fields.

    Science.gov (United States)

    Friederich, Pascal; Konrad, Manuel; Strunk, Timo; Wenzel, Wolfgang

    2018-02-07

    Computer simulation increasingly complements experimental efforts to describe nanoscale structure formation. Molecular mechanics simulations and related computational methods fundamentally rely on the accuracy of classical atomistic force fields for the evaluation of inter- and intramolecular energies. One indispensable component of such force fields, in particular for large organic molecules, is the accuracy of molecule-specific dihedral potentials which are the key determinants of molecular flexibility. We show in this work that non-local correlations of dihedral potentials play a decisive role in the description of the total molecular energy-an effect which is neglected in most state-of-the-art dihedral force fields. We furthermore present an efficient machine learning approach to compute intramolecular conformational energies. We demonstrate with the example of α-NPD, a molecule frequently used in organic electronics, that this approach outperforms traditional force fields by decreasing the mean absolute deviations by one order of magnitude to values smaller than 0.37 kcal/mol (16.0 meV) per dihedral angle.

  20. Atomistic Modeling of Mechanical Loss in Pure and Doped Amorphous Oxides

    Science.gov (United States)

    Trinastic, Jonathan; Hamdan, Rashid; Cheng, Hai-Ping

    2014-03-01

    The mechanical dissipation in the oxide coatings of many precision measurement systems is a major source of thermal noise that limits the performance of such devices. A good candidate for a coating material to reduce the mechanical loss is tantala (Ta2O5) doped with titania (TiO2). Here, we numerically calculate the mechanical loss (internal friction) in these and other promising oxides based on the double well model. Using classical, atomistic molecular dynamics simulations, we estimate the density of double wells in the energy landscape of the amorphous oxides and the distribution of barrier heights, in addition to the deformation potentials, the elastic constants and vibrational frequencies at both the bottom of the potential wells and at the saddle points, all of which are relevant to the internal friction calculation. We use two versions of the bisection method to find the double well densities and distributions. All methods used in these calculations are implemented in DL-POLY molecular dynamics simulation software. These calculations will provide experimentalists with a better guide into which material combinations might be better choice for reducing the mechanical loss.

  1. Atomistic investigation on the detachment of oil molecules from defective alumina surface

    Science.gov (United States)

    Xie, W. K.; Sun, Y. Z.; Liu, H. T.

    2017-12-01

    The mechanism of oil detachment from defective alumina surface in aqueous solution was investigated via atomistic molecular dynamics (MD) simulations. Special attention was focused on the effect of surface defect on the oil detachment. Our simulation results suggest that compared with perfect Al2O3 surface, defective substrate surface provides much more sites for the adsorption of oil molecules, thus it has higher oil adsorption energy. However, higher oil-solid adsorption energy does not mean that oil contaminants are much more difficult to be detached. It is found that surface defect could induce the spontaneous imbibition of water molecules, effectively promoting the detachment of oil molecules. Thus, compared with perfect alumina surface, the detachment of oil molecules from defective alumina surface tends to be much easier. Moreover, surface defect could lead to the oil residues inside surface defect. In water solution, the entire detachment process of oil molecules on defective surface consists of following stages, including the early detachment of oil molecules inside surface defect induced by capillary-driven spontaneous imbibition of water molecules, the following conformational change of oil molecules on topmost surface and the final migration of detached oil molecules from solid surface. These findings may help to sufficiently enrich the removal mechanism of oil molecules adhered onto defective solid surface.

  2. Discontinuous conduction in mouse bundle branches is caused by bundle-branch architecture

    NARCIS (Netherlands)

    van Veen, Toon A. B.; van Rijen, Harold V. M.; van Kempen, Marjan J. A.; Miquerol, Lucile; Opthof, Tobias; Gros, Daniel; Vos, Marc A.; Jongsma, Habo J.; de Bakker, Jacques M. T.

    2005-01-01

    Background - Recordings of the electrical activity of mouse bundle branches ( BBs) suggest reduced conduction velocity ( CV) in the midseptal compared with the proximal part of the BB. The present study was performed to elucidate the mechanism responsible for this slowing of conduction. Methods and

  3. Enthalpy and void distributions in subchannels of PHWR fuel bundles

    Energy Technology Data Exchange (ETDEWEB)

    Park, J. W.; Choi, H.; Rhee, B. W. [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1998-12-31

    Two different types of the CANDU fuel bundles have been modeled for the ASSERT-IV code subchannel analysis. From calculated values of mixture enthalpy and void fraction distribution in the fuel bundles, it is found that net buoyancy effect is pronounced in the central region of the DUPIC fuel bundle when compared with the standard CANDU fuel bundle. It is also found that the central region of the DUPIC fuel bundle can be cooled more efficiently than that of the standard fuel bundle. From the calculated mixture enthalpy distribution at the exit of the fuel channel, it is found that the mixture enthalpy and void fraction can be highest in the peripheral region of the DUPIC fuel bundle. On the other hand, the enthalpy and the void fraction were found to be highest in the central region of the standard CANDU fuel bundle at the exit of the fuel channel. This study shows that the subchannel analysis is very useful in assessing thermal behavior of the fuel bundle that could be used in CANDU reactors. 10 refs., 4 figs., 2 tabs. (Author)

  4. Atomistic Conversion Reaction Mechanism of WO 3 in Secondary Ion Batteries of Li, Na, and Ca

    Energy Technology Data Exchange (ETDEWEB)

    He, Yang [Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh PA 15261 USA; Gu, Meng [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA 99352 USA; Xiao, Haiyan [School of Physical Electronics, University of Electronic Science and Technology of China, Chengdu 610054 China; Luo, Langli [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA 99352 USA; Shao, Yuyan [Energy and Environmental Directorate, Pacific Northwest National Laboratory, Richland WA 99352 USA; Gao, Fei [Department of Nuclear Engineering and Radiological Sciences, University of Michigan, Ann Arbor MI 48109 USA; Du, Yingge [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA 99352 USA; Mao, Scott X. [Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh PA 15261 USA; Wang, Chongmin [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland WA 99352 USA

    2016-04-13

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

  5. Assessing the fracture strength of geological and related materials via an atomistically based J-integral

    Science.gov (United States)

    Jones, R. E.; Criscenti, L. J.; Rimsza, J.

    2016-12-01

    Predicting fracture initiation and propagation in low-permeability geomaterials is a critical yet un- solved problem crucial to assessing shale caprocks at carbon dioxide sequestration sites, and controlling fracturing for gas and oil extraction. Experiments indicate that chemical reactions at fluid-geomaterial interfaces play a major role in subcritical crack growth by weakening the material and altering crack nu- cleation and growth rates. Engineering the subsurface fracture environment, however, has been hindered by a lack of understanding of the mechanisms relating chemical environment to mechanical outcome, and a lack of capability directly linking atomistic insight to macroscale observables. We have developed a fundamental atomic-level understanding of the chemical-mechanical mecha- nisms that control subcritical cracks through coarse-graining data from reactive molecular simulations. Previous studies of fracture at the atomic level have typically been limited to producing stress-strain curves, quantifying either the system-level stress or energy at which fracture propagation occurs. As such, these curves are neither characteristic of nor insightful regarding fracture features local to the crack tip. In contrast, configurational forces, such as the J-integral, are specific to the crack in that they measure the energy available to move the crack and truly quantify fracture resistance. By development and use of field estimators consistent with the continuum conservation properties we are able to connect the data produced by atomistic simulation to the continuum-level theory of fracture mechanics and thus inform engineering decisions. In order to trust this connection we have performed theoretical consistency tests and validation with experimental data. Although we have targeted geomaterials, this capability can have direct impact on other unsolved technological problems such as predicting the corrosion and embrittlement of metals and ceramics. Sandia National

  6. Calculation of Elastic Bond Constants in Atomistic Strain Analysis

    Science.gov (United States)

    Chen, Haiyuan; Wang, Juanjuan; Ashalley, Eric; Li, Handong; Niu, Xiaobin

    2015-10-01

    Strain analysis has significance both for tailoring material properties and designing nanoscale devices. In particular, strain plays a vital role in engineering the growth thermodynamics and kinetics and is applicable for designing optoelectronic devices. In this paper, we present a methodology for establishing the relationship between elastic bond constants and measurable parameters, i.e., Poisson's ratio ν and systematic elastic constant K. At the atomistic level, this approach is within the framework of linear elastic theory and encompasses the neighbor interactions when an atom is introduced to stress. Departing from the force equilibrium equations, the relationships between ν, K, and spring constants are successfully established. Both the two-dimensional (2D) square lattice and common three-dimensional (3D) structures are taken into account in the procedure for facilitating, bridging the gap between structural complexity and numerical experiments. A new direction for understanding the physical phenomena in strain engineering is established.

  7. Diffusion in energy materials: Governing dynamics from atomistic modelling

    Science.gov (United States)

    Parfitt, D.; Kordatos, A.; Filippatos, P. P.; Chroneos, A.

    2017-09-01

    Understanding diffusion in energy materials is critical to optimising the performance of solid oxide fuel cells (SOFCs) and batteries both of which are of great technological interest as they offer high efficiency for cleaner energy conversion and storage. In the present review, we highlight the insights offered by atomistic modelling of the ionic diffusion mechanisms in SOFCs and batteries and how the growing predictive capability of high-throughput modelling, together with our new ability to control compositions and microstructures, will produce advanced materials that are designed rather than chosen for a given application. The first part of the review focuses on the oxygen diffusion mechanisms in cathode and electrolyte materials for SOFCs and in particular, doped ceria and perovskite-related phases with anisotropic structures. The second part focuses on disordered oxides and two-dimensional materials as these are very promising systems for battery applications.

  8. Molybdenum-99-producing 37-element fuel bundle neutronically and thermal-hydraulically equivalent to a standard CANDU fuel bundle

    Energy Technology Data Exchange (ETDEWEB)

    Nichita, E., E-mail: Eleodor.Nichita@uoit.ca; Haroon, J., E-mail: Jawad.Haroon@uoit.ca

    2016-10-15

    Highlights: • A 37-element fuel bundle modified for {sup 99}Mo production in CANDU reactors is presented. • The modified bundle is neutronically and thermal-hydraulically equivalent to the standard bundle. • The modified bundle satisfies all safety criteria satisfied by the standard bundle. - Abstract: {sup 99m}Tc, the most commonly used radioisotope in diagnostic nuclear medicine, results from the radioactive decay of {sup 99}Mo which is currently being produced at various research reactors around the globe. In this study, the potential use of CANDU power reactors for the production of {sup 99}Mo is investigated. A modified 37-element fuel bundle, suitable for the production of {sup 99}Mo in existing CANDU-type reactors is proposed. The new bundle is specifically designed to be neutronically and thermal-hydraulically equivalent to the standard 37-element CANDU fuel bundle in normal, steady-state operation and, at the same time, be able to produce significant quantities of {sup 99}Mo when irradiated in a CANDU reactor. The proposed bundle design uses fuel pins consisting of a depleted-uranium centre surrounded by a thin layer of low-enriched uranium. The new molybdenum-producing bundle is analyzed using the lattice transport code DRAGON and the diffusion code DONJON. The proposed design is shown to produce 4081 six-day Curies of {sup 99}Mo activity per bundle when irradiated in the peak-power channel of a CANDU core, while maintaining the necessary reactivity and power rating limits. The calculated {sup 99}Mo yield corresponds to approximately one third of the world weekly demand. A production rate of ∼3 bundles per week can meet the global demand of {sup 99}Mo.

  9. Design and evaluate finned tube bundles

    Energy Technology Data Exchange (ETDEWEB)

    Ganapathy, V. [ABCO Industries, Abilene, TX (United States)

    1996-09-01

    Finned tube bundles are widely used in heat exchangers, air coolers, waste heat boilers and fired heaters where energy transfer occurs between clean flue gases and a fluid with a high heat-transfer coefficient. They have several advantages including compactness, low gas pressure drop and low weight for a given duty compared to bare tube bundles. Choosing a fin type, arrangement and fin configuration requires a thorough analysis and economic evaluation. The solution is not unique since it depends on material and labor costs. Surface areas vary widely in finned tube designs for the same duty and gas pressure drop. Therefore, decisions should not be based on surface area alone. Plant engineers and consultants should consider operating costs in their evaluation because they accrue year after year. Selecting a boiler based on initial costs alone is not prudent. The paper discusses heat transfer and gas pressure drop with finned tubes, determining fin efficiency and effectiveness,g as pressure drop, tube wall and fin top temperatures, an example calculation, the effect of fin configuration on design, the effect of inline versus staggered arrangements and solid versus serrated fins, and concerns with high fin-density designs.

  10. Development boiling to sprinkled tube bundle

    Directory of Open Access Journals (Sweden)

    Kracík Petr

    2016-01-01

    Full Text Available This paper presents results of a studied heat transfer coefficient at the surface of a sprinkled tube bundle where boiling occurs. Research in the area of sprinkled exchangers can be divided into two major parts. The first part is research on heat transfer and determination of the heat transfer coefficient at sprinkled tube bundles for various liquids, whether boiling or not. The second part is testing of sprinkle modes for various tube diameters, tube pitches and tube materials and determination of individual modes’ interface. All results published so far for water as the falling film liquid apply to one to three tubes for which the mentioned relations studied are determined in rigid laboratory conditions defined strictly in advance. The sprinkled tubes were not viewed from the operational perspective where there are more tubes and various modes may occur in different parts with various heat transfer values. The article focuses on these processes. The tube is located in a low-pressure chamber where vacuum is generated using an exhauster via ejector. The tube consists of smooth copper tubes of 12 mm diameter placed horizontally one above another.

  11. Evaluation of Single-Bundle versus Double-Bundle PCL Reconstructions with More Than 10-Year Follow-Up

    Directory of Open Access Journals (Sweden)

    Masataka Deie

    2015-01-01

    Full Text Available Background. Posterior cruciate ligament (PCL injuries are not rare in acute knee injuries, and several recent anatomical studies of the PCL and reconstructive surgical techniques have generated improved patient results. Now, we have evaluated PCL reconstructions performed by either the single-bundle or double-bundle technique in a patient group followed up retrospectively for more than 10 years. Methods. PCL reconstructions were conducted using the single-bundle (27 cases or double-bundle (13 cases method from 1999 to 2002. The mean age at surgery was 34 years in the single-bundle group and 32 years in the double-bundle group. The mean follow-up period was 12.5 years. Patients were evaluated by Lysholm scoring, the gravity sag view, and knee arthrometry. Results. The Lysholm score after surgery was 89.1±5.6 points for the single-bundle group and 91.9±4.5 points for the double-bundle group. There was no significant difference between the methods in the side-to-side differences by gravity sag view or knee arthrometer evaluation, although several cases in both groups showed a side-to-side difference exceeding 5 mm by the latter evaluation method. Conclusions. We found no significant difference between single- and double-bundle PCL reconstructions during more than 10 years of follow-up.

  12. Pierced Lasso Bundles are a new class of knot-like motifs.

    Directory of Open Access Journals (Sweden)

    Ellinor Haglund

    2014-06-01

    Full Text Available A four-helix bundle is a well-characterized motif often used as a target for designed pharmaceutical therapeutics and nutritional supplements. Recently, we discovered a new structural complexity within this motif created by a disulphide bridge in the long-chain helical bundle cytokine leptin. When oxidized, leptin contains a disulphide bridge creating a covalent-loop through which part of the polypeptide chain is threaded (as seen in knotted proteins. We explored whether other proteins contain a similar intriguing knot-like structure as in leptin and discovered 11 structurally homologous proteins in the PDB. We call this new helical family class the Pierced Lasso Bundle (PLB and the knot-like threaded structural motif a Pierced Lasso (PL. In the current study, we use structure-based simulation to investigate the threading/folding mechanisms for all the PLBs along with three unthreaded homologs as the covalent loop (or lasso in leptin is important in folding dynamics and activity. We find that the presence of a small covalent loop leads to a mechanism where structural elements slipknot to thread through the covalent loop. Larger loops use a piercing mechanism where the free terminal plugs through the covalent loop. Remarkably, the position of the loop as well as its size influences the native state dynamics, which can impact receptor binding and biological activity. This previously unrecognized complexity of knot-like proteins within the helical bundle family comprises a completely new class within the knot family, and the hidden complexity we unraveled in the PLBs is expected to be found in other protein structures outside the four-helix bundles. The insights gained here provide critical new elements for future investigation of this emerging class of proteins, where function and the energetic landscape can be controlled by hidden topology, and should be take into account in ab initio predictions of newly identified protein targets.

  13. Nudged Elastic Band Simulations of Kink Pairs in Tungsten

    Energy Technology Data Exchange (ETDEWEB)

    Cereceda, D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Marian, J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-01-16

    Atomistic techniques have been used to calculate energy barriers for dislocation motion that control the strength (yield stress and flow stress) of the material. In particular, the calculations focus on the change in enthalpy as a straight dislocation moves through the crystal lattice (the Peierls barrier) and kink pair formation enthalpy that controls the thermally activated double-kink mechanism important at low to moderate stresses. A novel means of assessing kink widths within atomistic simulations is introduced.

  14. Simulations

    CERN Document Server

    Ngada, Narcisse

    2015-06-15

    The complexity and cost of building and running high-power electrical systems make the use of simulations unavoidable. The simulations available today provide great understanding about how systems really operate. This paper helps the reader to gain an insight into simulation in the field of power converters for particle accelerators. Starting with the definition and basic principles of simulation, two simulation types, as well as their leading tools, are presented: analog and numerical simulations. Some practical applications of each simulation type are also considered. The final conclusion then summarizes the main important items to keep in mind before opting for a simulation tool or before performing a simulation.

  15. The Vibration Analysis of Tube Bundles Induced by Fluid Elastic Excitation in Shell Side of Heat Exchanger

    Science.gov (United States)

    Bao, Minle; Wang, Lu; Li, Wenyao; Gao, Tianze

    2017-09-01

    Fluid elastic excitation in shell side of heat exchanger was deduced theoretically in this paper. Model foundation was completed by using Pro / Engineer software. The finite element model was constructed and imported into the FLUENT module. The flow field simulation adopted the dynamic mesh model, RNG k-ε model and no-slip boundary conditions. Analysing different positions vibration of tube bundles by selecting three regions in shell side of heat exchanger. The results show that heat exchanger tube bundles at the inlet of the shell side are more likely to be failure due to fluid induced vibration.

  16. An integral Riemann-Roch theorem for surface bundles

    DEFF Research Database (Denmark)

    Madsen, Ib Henning

    2010-01-01

    This paper is a response to a conjecture by T. Akita about an integral Riemann–Roch theorem for surface bundles.......This paper is a response to a conjecture by T. Akita about an integral Riemann–Roch theorem for surface bundles....

  17. Restriction Theorem for Principal bundles in Arbitrary Characteristic

    DEFF Research Database (Denmark)

    Gurjar, Sudarshan

    2015-01-01

    The aim of this paper is to prove two basic restriction theorem for principal bundles on smooth projective varieties in arbitrary characteristic generalizing the analogues theorems of Mehta-Ramanathan for vector bundles. More precisely, let G be a reductive algebraic group over an algebraically c...

  18. Phase Space Reduction of Star Products on Cotangent Bundles.

    NARCIS (Netherlands)

    Kowalzig, N.; Neumaier, N.; Pflaum, M.

    2005-01-01

    In this paper we construct star products on Marsden-Weinstein reduced spaces in case both the original phase space and the reduced phase space are (symplectomorphic to) cotangent bundles. Under the assumption that the original cotangent bundle $T^*Q$ carries a symplectic structure of form

  19. Monoubiquitination Inhibits the Actin Bundling Activity of Fascin.

    Science.gov (United States)

    Lin, Shengchen; Lu, Shuang; Mulaj, Mentor; Fang, Bin; Keeley, Tyler; Wan, Lixin; Hao, Jihui; Muschol, Martin; Sun, Jianwei; Yang, Shengyu

    2016-12-30

    Fascin is an actin bundling protein that cross-links individual actin filaments into straight, compact, and stiff bundles, which are crucial for the formation of filopodia, stereocillia, and other finger-like membrane protrusions. The dysregulation of fascin has been implicated in cancer metastasis, hearing loss, and blindness. Here we identified monoubiquitination as a novel mechanism that regulates fascin bundling activity and dynamics. The monoubiquitination sites were identified to be Lys247 and Lys250, two residues located in a positive charge patch at the actin binding site 2 of fascin. Using a chemical ubiquitination method, we synthesized chemically monoubiquitinated fascin and determined the effects of monoubiquitination on fascin bundling activity and dynamics. Our data demonstrated that monoubiquitination decreased the fascin bundling EC50, delayed the initiation of bundle assembly, and accelerated the disassembly of existing bundles. By analyzing the electrostatic properties on the solvent-accessible surface of fascin, we proposed that monoubiquitination introduced steric hindrance to interfere with the interaction between actin filaments and the positively charged patch at actin binding site 2. We also identified Smurf1 as a E3 ligase regulating the monoubiquitination of fascin. Our findings revealed a previously unidentified regulatory mechanism for fascin, which will have important implications for the understanding of actin bundle regulation under physiological and pathological conditions. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. Lexical Bundles in L1 and L2 Academic Writing

    Science.gov (United States)

    Chen, Yu-Hua; Baker, Paul

    2010-01-01

    This paper adopts an automated frequency-driven approach to identify frequently-used word combinations (i.e., "lexical bundles") in academic writing. Lexical bundles retrieved from one corpus of published academic texts and two corpora of student academic writing (one L1, the other L2), were investigated both quantitatively and qualitatively.…

  1. Lexical Bundles: Facilitating University "Talk" in Group Discussions

    Science.gov (United States)

    Heng, Chan Swee; Kashiha, Hadi; Tan, Helen

    2014-01-01

    Group discussion forms an integral language experience for most language learners, providing them with an opportunity to express themselves in a naturalistic setting. Multi-word expressions are commonly used and one of them is lexical bundles. Lexical bundles are types of extended collocations that occur more commonly than we expect; they are…

  2. A novel microbond bundle pullout technique to evaluate the ...

    Indian Academy of Sciences (India)

    2017-07-26

    Jul 26, 2017 ... to be a need to develop a microbond bundle pullout test that is comparable in all aspects to the semi-empirical resin slab/fibre bundle pullout approach [9]. The improvement of the known draw backs of the single fibre microbond pullout method [7], such as the difficulty in formulation and testing (with lack.

  3. Hair bundles are specialized for ATP delivery via creatine kinase.

    NARCIS (Netherlands)

    Shin, J.B.; Streijger, F.; Beynon, A.J.; Peters, T.; Gadzala, L.; McMillen, D.; Bystrom, C.; Zee, C.E.E.M. van der; Wallimann, T.; Gillespie, P.G.

    2007-01-01

    When stimulated strongly, a hair cell's mechanically sensitive hair bundle may consume ATP too rapidly for replenishment by diffusion. To provide a broad view of the bundle's protein complement, including those proteins participating in energy metabolism, we used shotgun mass spectrometry methods to

  4. Smooth Bundling of Large Streaming and Sequence Graphs

    NARCIS (Netherlands)

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

    2013-01-01

    Dynamic graphs are increasingly pervasive in modern information systems. However, understanding how a graph changes in time is difficult. We present here two techniques for simplified visualization of dynamic graphs using edge bundles. The first technique uses a recent image-based graph bundling

  5. Computational imaging through a fiber-optic bundle

    Science.gov (United States)

    Lodhi, Muhammad A.; Dumas, John Paul; Pierce, Mark C.; Bajwa, Waheed U.

    2017-05-01

    Compressive sensing (CS) has proven to be a viable method for reconstructing high-resolution signals using low-resolution measurements. Integrating CS principles into an optical system allows for higher-resolution imaging using lower-resolution sensor arrays. In contrast to prior works on CS-based imaging, our focus in this paper is on imaging through fiber-optic bundles, in which manufacturing constraints limit individual fiber spacing to around 2 μm. This limitation essentially renders fiber-optic bundles as low-resolution sensors with relatively few resolvable points per unit area. These fiber bundles are often used in minimally invasive medical instruments for viewing tissue at macro and microscopic levels. While the compact nature and flexibility of fiber bundles allow for excellent tissue access in-vivo, imaging through fiber bundles does not provide the fine details of tissue features that is demanded in some medical situations. Our hypothesis is that adapting existing CS principles to fiber bundle-based optical systems will overcome the resolution limitation inherent in fiber-bundle imaging. In a previous paper we examined the practical challenges involved in implementing a highly parallel version of the single-pixel camera while focusing on synthetic objects. This paper extends the same architecture for fiber-bundle imaging under incoherent illumination and addresses some practical issues associated with imaging physical objects. Additionally, we model the optical non-idealities in the system to get lower modelling errors.

  6. Frobenius pull backs of vector bundles in higher dimensions

    Indian Academy of Sciences (India)

    Frobenius pull backs; instability degree, vector bundles. 1. Introduction. Let X be a nonsingular projective variety defined over an algebraically closed field k of an arbitrary characteristic, and let H be a very ample line bundle on X. Let E be a torsion free sheaf on X. Then the notion of E being stable (resp. semistable) is well- ...

  7. On Harder–Narasimhan reductions for Higgs principal bundles

    Indian Academy of Sciences (India)

    in Ramanathan's paper. The aim of this paper is to generalize the methods of Biswas and Holla to give a unified approach to the case of principal bundles with Higgs structure on smooth projective varieties as well as the case of ramified bundles on smooth curves [4] (see §2, §5 for definitions). Recall that for the case of ...

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

    Directory of Open Access Journals (Sweden)

    Yunqiang Bian

    2014-04-01

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

  9. Atomistic simulation and ab initio study of the defect structure of spinel-related Li{sub 0.5−0.5x}Mg{sub x}Fe{sub 2.5−0.5x}O{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Widatallah, H.M., E-mail: hishammw@squ.edu.om [Physics Department, College of Science, Sultan Qaboos University, PO Box 36, Al-Khoudh, 123 Muscat (Oman); Moore, E.A. [Department of Life, Health and Chemical Sciences, Faculty of Science, The Open University, Walton Hall, Milton Keynes MK7 6AA (United Kingdom); Babo, A.A. [Physics Department, Faculty of Science, University of Khartoum, PO Box 123, Khartoum 11115 (Sudan); Al-Barwani, M.S.; Elzain, M. [Physics Department, College of Science, Sultan Qaboos University, PO Box 36, Al-Khoudh, 123 Muscat (Oman)

    2012-12-15

    Graphical abstract: Unit cell of Li0{sub 5−0.5x}Mg{sub x}Fe{sub 2.5−0.5x}O{sub 4}, showing the lowest energy structure obtained using interatomic potential and DFT ab initio calculations. Large white spheres O{sup 2−}; small light grey spheres Mg{sup 2+} (evenly substituting of Li{sup +} and Fe{sup 3+} at octahedral sites); small dark grey spheres Fe{sup 3+}; small black spheres Li{sup +}. Display Omitted Highlights: ► Defect structure of Li{sub 0.5−0.5x}Mg{sub x}Fe{sub 2.5−x}O{sub 4} is studied with atomistic and DFT methods. ► 19 possible defect structure models with ∼60 defect configurations are investigated. ► The most favourable model found is when Mg{sup 2+} ions evenly replace Li{sup +} and octahedral Fe{sup 3+}. ► This defect structure decreases the magnetisation relative to that of Li{sub 0.5}Fe{sub 2.5}O{sub 4}. ► Experimentally-deduced models, at variance with the one obtained here, are discussed. -- Abstract: The position of magnesium ions in Mg{sup 2+}-doped lithium ferrite of the composition Li{sub 0.5−0.5x}Mg{sub x}Fe{sub 2.5−0.5x}O{sub 4}, which has been a matter of uncertainty among some experimentalists, is investigated using interatomic potential and ab initio DFT calculations. Among possible 19 defect structure models, some of which have been reported experimentally to be the most favorable, the lowest energy is found for Mg{sup 2+} ions evenly replacing Li{sup +} and Fe{sup 3+} ion on octahedral sites. This gives a decrease in magnetisation for the Mg{sup 2+}-doped ferrite relative to the un-doped lithium ferrite. The results suggest that some experimental observations of increased magnetisation of spinel lithium ferrite on Mg{sup 2+}-doping could be due to substitution of Mg{sup 2+} or Li{sup +} on tetrahedral sites at the high temperatures used in preparation of the solid and/or the presence of undetected defects in the initial precursors.

  10. [Bundle-branch block depending on the heart rate].

    Science.gov (United States)

    Apostolov, L

    1975-01-01

    Five patients are reported, admitted to the hospital, with diseases predominantly of the cardio-vascular system. During the electrocardiographic examinations bundle branch block was established, depending on heart rate. It fluctuated within the physiological limits from 50 to 90/min. In three of the patients, the bundle branch block appeared with the quickening of the heart rate (tachycardia-depending bundle branch block) and in two of the patients--the bundle branch block appeared during the slowing down of the heart action and disappeared with its quickening (bradicardia-depending bundle branch block). A brief literature review is presented and attention is paid to the possible diagnostic errors and the treatment mode of those patients with cardiac tonic and antiarrhythmic medicaments.

  11. Bundles over Quantum RealWeighted Projective Spaces

    Directory of Open Access Journals (Sweden)

    Tomasz Brzeziński

    2012-09-01

    Full Text Available The algebraic approach to bundles in non-commutative geometry and the definition of quantum real weighted projective spaces are reviewed. Principal U(1-bundles over quantum real weighted projective spaces are constructed. As the spaces in question fall into two separate classes, the negative or odd class that generalises quantum real projective planes and the positive or even class that generalises the quantum disc, so do the constructed principal bundles. In the negative case the principal bundle is proven to be non-trivial and associated projective modules are described. In the positive case the principal bundles turn out to be trivial, and so all the associated modules are free. It is also shown that the circle (coactions on the quantum Seifert manifold that define quantum real weighted projective spaces are almost free.

  12. Artificial ciliary bundles with nano fiber tip links

    CERN Document Server

    Asadnia, Mohsen; Miao, Jianmin; Triantafyllou, Michael

    2015-01-01

    Mechanosensory ciliary bundles in fishes are the inspiration for carefully engineered artificial flow sensors. We report the development of a new class of ultrasensitive MEMS flow sensors that mimic the intricate morphology of the ciliary bundles, including the stereocilia, tip links, and the cupula, and thereby achieve threshold detection limits that match the biological example. An artificial ciliary bundle is achieved by fabricating closely-spaced arrays of polymer micro-pillars with gradiating heights. Tip links that form the fundamental sensing elements are realized through electrospinning aligned PVDF piezoelectric nano-fibers that link the distal tips of the polymer cilia. An optimized synthesis of hyaluronic acid-methacrylic anhydride hydrogel that results in properties close to the biological cupula, together with drop-casting method are used to form the artificial cupula that encapsulates the ciliary bundle. In testing, fluid drag force causes the ciliary bundle to slide, stretching the flexible nan...

  13. Determination of the turbulence integral model parameters for a case of a coolant angular flow in regular rod-bundle

    Science.gov (United States)

    Bayaskhalanov, M. V.; Vlasov, M. N.; Korsun, A. S.; Merinov, I. G.; Philippov, M. Ph

    2017-11-01

    Research results of “k-ε” turbulence integral model (TIM) parameters dependence on the angle of a coolant flow in regular smooth cylindrical rod-bundle are presented. TIM is intended for the definition of efficient impulse and heat transport coefficients in the averaged equations of a heat and mass transfer in the regular rod structures in an anisotropic porous media approximation. The TIM equations are received by volume-averaging of the “k-ε” turbulence model equations on periodic cell of rod-bundle. The water flow across rod-bundle under angles from 15 to 75 degrees was simulated by means of an ANSYS CFX code. Dependence of the TIM parameters on flow angle was as a result received.

  14. A model for the anisotropic response of fibrous soft tissues using six discrete fibre bundles

    KAUST Repository

    Flynn, Cormac

    2011-06-30

    The development of constitutive models of fibrous soft-tissues is a challenging problem. Many consider the tissue to be a collection of fibres with a continuous distribution function representing their orientations. A discrete fibre model is presented consisting of six weighted fibre-bundles. Each bundle is oriented such that it passes through opposing vertices of a regular icosahedron. A novel aspect is the use of simple analytical distribution functions to simulate undulated collagen fibres. This approach yields closed-form analytical expressions for the strain energy of the collagen fibre-bundle that avoids the sometimes costly numerical integration of some statistical distribution functions. The elastin fibres are characterized by a modified neo-Hookean type strain energy function which does not allow for fibre compression. The model accurately simulates biaxial stretching of rabbit-skin (error-of-fit 8.7), uniaxial stretching of pig-skin (error-of-fit 7.6), equibiaxial loading of aortic valve cusp (error-of-fit 0.8), and simple shear of rat septal myocardium (error-of-fit 8.9). It compares favourably with previous soft-tissue models and alternative methods of representing undulated collagen fibres. Predicted collagen fibre stiffnesses range from 8.0thinspaceMPa to 930MPa. Elastin fibre stiffnesses range from 2.0 kPa to 154.4 kPa. © 2011 John Wiley & Sons, Ltd.

  15. Biomolecular interactions modulate macromolecular structure and dynamics in atomistic model of a bacterial cytoplasm

    Science.gov (United States)

    Yu, Isseki; Mori, Takaharu; Ando, Tadashi; Harada, Ryuhei; Jung, Jaewoon; Sugita, Yuji; Feig, Michael

    2016-01-01

    Biological macromolecules function in highly crowded cellular environments. The structure and dynamics of proteins and nucleic acids are well characterized in vitro, but in vivo crowding effects remain unclear. Using molecular dynamics simulations of a comprehensive atomistic model cytoplasm we found that protein-protein interactions may destabilize native protein structures, whereas metabolite interactions may induce more compact states due to electrostatic screening. Protein-protein interactions also resulted in significant variations in reduced macromolecular diffusion under crowded conditions, while metabolites exhibited significant two-dimensional surface diffusion and altered protein-ligand binding that may reduce the effective concentration of metabolites and ligands in vivo. Metabolic enzymes showed weak non-specific association in cellular environments attributed to solvation and entropic effects. These effects are expected to have broad implications for the in vivo functioning of biomolecules. This work is a first step towards physically realistic in silico whole-cell models that connect molecular with cellular biology. DOI: http://dx.doi.org/10.7554/eLife.19274.001 PMID:27801646

  16. Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

    Energy Technology Data Exchange (ETDEWEB)

    Vlasic, Thomas M.; Servio, Phillip; Rey, Alejandro D., E-mail: alejandro.rey@mcgill.ca [Department of Chemical Engineering, McGill University, Montreal H3A 0C5 (Canada)

    2016-08-15

    This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

  17. Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

    Directory of Open Access Journals (Sweden)

    Thomas M. Vlasic

    2016-08-01

    Full Text Available This work uses density functional theory (DFT to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane, at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

  18. Development and assessment of atomistic models for predicting static friction coefficients

    Science.gov (United States)

    Jahangiri, Soran; Heverly-Coulson, Gavin S.; Mosey, Nicholas J.

    2016-08-01

    The friction coefficient relates friction forces to normal loads and plays a key role in fundamental and applied areas of science and technology. Despite its importance, the relationship between the friction coefficient and the properties of the materials forming a sliding contact is poorly understood. We illustrate how simple relationships regarding the changes in energy that occur during slip can be used to develop a quantitative model relating the friction coefficient to atomic-level features of the contact. The slip event is considered as an activated process and the load dependence of the slip energy barrier is approximated with a Taylor series expansion of the corresponding energies with respect to load. The resulting expression for the load-dependent slip energy barrier is incorporated in the Prandtl-Tomlinson (PT) model and a shear-based model to obtain expressions for friction coefficient. The results indicate that the shear-based model reproduces the static friction coefficients μs obtained from first-principles molecular dynamics simulations more accurately than the PT model. The ability of the model to provide atomistic explanations for differences in μs amongst different contacts is also illustrated. As a whole, the model is able to account for fundamental atomic-level features of μs, explain the differences in μs for different materials based on their properties, and might be also used in guiding the development of contacts with desired values of μs.

  19. Atomistic study on dopant-distributions in realistically sized, highly P-doped Si nanowires.

    Science.gov (United States)

    Ryu, Hoon; Kim, Jongseob; Hong, Ki-Ha

    2015-01-14

    The dependency of dopant-distributions on channel diameters in realistically sized, highly phosphorus-doped silicon nanowires is investigated with an atomistic tight-binding approach coupled to self-consistent Schrödinger-Poisson simulations. By overcoming the limit in channel sizes and doping densities of previous studies, this work examines electronic structures and electrostatics of free-standing circular silicon nanowires that are phosphorus-doped with a high density of ∼ 2 × 10(19) cm(-3) and have 12 nm-28 nm cross-sections. Results of analysis on the channel energy indicate that the uniformly distributed dopant profile would be hardly obtained when the nanowire cross-section is smaller than 20 nm. Insufficient room to screen donor ions and shallower impurity bands are the primary reasons of the nonuniform dopant-distributions in smaller nanowires. Being firmly connected to the recent experimental study (Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 15254-15258), this work establishes the first theoretical framework for understanding dopant-distributions in over-10 nm highly doped silicon nanowires.

  20. Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics

    Science.gov (United States)

    Zhang, Wenjun; Wang, Ming L.; Cranford, Steven W.

    2016-01-01

    DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring.

  1. Framework for shape analysis of white matter fiber bundles.

    Science.gov (United States)

    Glozman, Tanya; Bruckert, Lisa; Pestilli, Franco; Yecies, Derek W; Guibas, Leonidas J; Yeom, Kristen W

    2017-12-02

    Diffusion imaging coupled with tractography algorithms allows researchers to image human white matter fiber bundles in-vivo. These bundles are three-dimensional structures with shapes that change over time during the course of development as well as in pathologic states. While most studies on white matter variability focus on analysis of tissue properties estimated from the diffusion data, e.g. fractional anisotropy, the shape variability of white matter fiber bundle is much less explored. In this paper, we present a set of tools for shape analysis of white matter fiber bundles, namely: (1) a concise geometric model of bundle shapes; (2) a method for bundle registration between subjects; (3) a method for deformation estimation. Our framework is useful for analysis of shape variability in white matter fiber bundles. We demonstrate our framework by applying our methods on two datasets: one consisting of data for 6 normal adults and another consisting of data for 38 normal children of age 11 days to 8.5 years. We suggest a robust and reproducible method to measure changes in the shape of white matter fiber bundles. We demonstrate how this method can be used to create a model to assess age-dependent changes in the shape of specific fiber bundles. We derive such models for an ensemble of white matter fiber bundles on our pediatric dataset and show that our results agree with normative human head and brain growth data. Creating these models for a large pediatric longitudinal dataset may improve understanding of both normal development and pathologic states and propose novel parameters for the examination of the pediatric brain. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Bundling of elastic filaments induced by hydrodynamic interactions

    Science.gov (United States)

    Man, Yi; Page, William; Poole, Robert J.; Lauga, Eric

    2017-12-01

    Peritrichous bacteria swim in viscous fluids by rotating multiple helical flagellar filaments. As the bacterium swims forward, all its flagella rotate in synchrony behind the cell in a tight helical bundle. When the bacterium changes its direction, the flagellar filaments unbundle and randomly reorient the cell for a short period of time before returning to their bundled state and resuming swimming. This rapid bundling and unbundling is, at its heart, a mechanical process whereby hydrodynamic interactions balance with elasticity to determine the time-varying deformation of the filaments. Inspired by this biophysical problem, we present in this paper what is perhaps the simplest model of bundling whereby two or more straight elastic filaments immersed in a viscous fluid rotate about their centerline, inducing rotational flows which tend to bend the filaments around each other. We derive an integrodifferential equation governing the shape of the filaments resulting from mechanical balance in a viscous fluid at low Reynolds number. We show that such equation may be evaluated asymptotically analytically in the long-wavelength limit, leading to a local partial differential equation governed by a single dimensionless bundling number. A numerical study of the dynamics predicted by the model reveals the presence of two configuration instabilities with increasing bundling numbers: first to a crossing state where filaments touch at one point and then to a bundled state where filaments wrap along each other in a helical fashion. We also consider the case of multiple filaments and the unbundling dynamics. We next provide an intuitive physical model for the crossing instability and show that it may be used to predict analytically its threshold and adapted to address the transition to a bundling state. We then use a macroscale experimental implementation of the two-filament configuration in order to validate our theoretical predictions and obtain excellent agreement. This long

  3. Restriction of Preferences to the Set of Consumption Bundles, In a Model with Production and Consumption Bundles

    NARCIS (Netherlands)

    Schalk, S.

    1999-01-01

    In contrast to the neo-classical theory of Arrow and Debreu, a model of a private ownership economy is presented, in which production and consumption bundles are treated separately. Each of the two types of bundles is assumed to establish a con- vex cone. Production technologies can convert

  4. Single-Bundle Versus Double-Bundle Reconstruction for Anterior Cruciate Ligament Rupture: A Meta-Analysis-Does Anatomy Matter?

    NARCIS (Netherlands)

    Eck, Carola F. Van; Kopf, Sebastian; Irrgang, James J.; Blankevoort, Leendert; Bhandari, Mohit; Fu, Freddie H.; Poolman, Rudolf W.

    2012-01-01

    Purpose: To determine whether double-bundle anterior cruciate ligament reconstruction leads to better restoration of anterior and rotational laxity and range of motion than single-bundle reconstruction. Methods: A search was performed in the Medline, Embase, CINAHL, and Cochrane databases. All

  5. The glass transition in cured epoxy thermosets: A comparative molecular dynamics study in coarse-grained and atomistic resolution

    Energy Technology Data Exchange (ETDEWEB)

    Langeloth, Michael; Böhm, Michael C.; Müller-Plathe, Florian [Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Center of Smart Interfaces, Technische Universität Darmstadt, Alarich Weiss Straße 4, D-64287 Darmstadt (Germany); Sugii, Taisuke, E-mail: taisuke.sugii.zs@hitachi.com [Center for Technology Innovation – Mechanical Engineering, Research & Development Group, Hitachi, Ltd., 832-2, Horiguchi, Hitachinaka, Ibaraki 312-0034 (Japan)

    2015-12-28

    We investigate the volumetric glass transition temperature T{sub g} in epoxy thermosets by means of molecular dynamics simulations. The epoxy thermosets consist of the resin bisphenol A diglycidyl ether and the hardener diethylenetriamine. A structure based coarse-grained (CG) force field has been derived using iterative Boltzmann inversion in order to facilitate simulations of larger length scales. We observe that T{sub g} increases clearly with the degree of cross-linking for all-atomistic (AA) and CG simulations. The transition T{sub g} in CG simulations of uncured mixtures is much lower than in AA-simulations due to the soft nature of the CG potentials, but increases all the more with the formation of rigid cross-links. Additional simulations of the CG mixtures in contact with a surface show the existence of an interphase region of about 3 nm thickness in which the network properties deviate significantly from the bulk. In accordance to experimental studies, we observe that T{sub g} is reduced in this interphase region and gradually increases to its bulk value with distance from the surface. The present study shows that the glass transition is a local phenomenon that depends on the network structure in the immediate environment.

  6. Study of hadron bundles observed in Chacaltaya two-story emulsion chamber

    Science.gov (United States)

    Aoki, H.

    1985-01-01

    The existence of hadron-rich families associated with few gamma-ray emission named Centauro and Mini-Centauro phemonena was reported. It was investigated whether these are produced by the special type of interaction different from the ordinary pion multiple production or not. The experimental results are compared with simulation calculation based on ordinary multiple pion production model. Both hadron multiplicity distribution, obtained from the present observation and the simulation calculation, show almost the same distribution which means that hadron bundles of such smaller multiplicities are considered to originate from successive interactions of surviving nucleon with the nature of multiple production during passage through the atmosphere.

  7. Cost-effectiveness of a central venous catheter care bundle.

    Directory of Open Access Journals (Sweden)

    Kate A Halton

    Full Text Available BACKGROUND: A bundled approach to central venous catheter care is currently being promoted as an effective way of preventing catheter-related bloodstream infection (CR-BSI. Consumables used in the bundled approach are relatively inexpensive which may lead to the conclusion that the bundle is cost-effective. However, this fails to consider the nontrivial costs of the monitoring and education activities required to implement the bundle, or that alternative strategies are available to prevent CR-BSI. We evaluated the cost-effectiveness of a bundle to prevent CR-BSI in Australian intensive care patients. METHODS AND FINDINGS: A Markov decision model was used to evaluate the cost-effectiveness of the bundle relative to remaining with current practice (a non-bundled approach to catheter care and uncoated catheters, or use of antimicrobial catheters. We assumed the bundle reduced relative risk of CR-BSI to 0.34. Given uncertainty about the cost of the bundle, threshold analyses were used to determine the maximum cost at which the bundle remained cost-effective relative to the other approaches to infection control. Sensitivity analyses explored how this threshold alters under different assumptions about the economic value placed on bed-days and health benefits gained by preventing infection. If clinicians are prepared to use antimicrobial catheters, the bundle is cost-effective if national 18-month implementation costs are below $1.1 million. If antimicrobial catheters are not an option the bundle must cost less than $4.3 million. If decision makers are only interested in obtaining cash-savings for the unit, and place no economic value on either the bed-days or the health benefits gained through preventing infection, these cost thresholds are reduced by two-thirds. CONCLUSIONS: A catheter care bundle has the potential to be cost-effective in the Australian intensive care setting. Rather than anticipating cash-savings from this intervention, decision

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

    CERN Document Server

    Djurabekova, Flyura; Pohjonen, Aarne; Nordlund, Kai

    2011-01-01

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

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

    DEFF Research Database (Denmark)

    Stradi, Daniele; Martinez, Umberto; Blom, Anders

    2016-01-01

    Metal-semiconductor contacts are a pillar of modern semiconductor technology. Historically, their microscopic understanding has been hampered by the inability of traditional analytical and numerical methods to fully capture the complex physics governing their operating principles. Here we introduce...... an atomistic approach based on density functional theory and nonequilibrium Green's function, which includes all the relevant ingredients required to model realistic metal-semiconductor interfaces and allows for a direct comparison between theory and experiments via I-Vbias curve simulations. We apply...... this method to characterize an Ag/Si interface relevant for photovoltaic applications and study the rectifying-to-Ohmic transition as a function of the semiconductor doping. We also demonstrate that the standard “activation energy” method for the analysis of I-Vbias data might be inaccurate for nonideal...

  10. TREAT Neutronics Analysis of Water-Loop Concept Accommodating LWR 9-rod Bundle

    Energy Technology Data Exchange (ETDEWEB)

    Hill, Connie M.; Woolstenhulme, Nicolas E.; Parry, James R.; Bess, John D.; Housley, Gregory K.

    2016-09-01

    Abstract. Simulation of a variety of transient conditions has been successfully achieved in the Transient Reactor Test (TREAT) facility during operation between 1959 and 1994 to support characterization and safety analysis of nuclear fuels and materials. A majority of previously conducted tests were focused on supporting sodium-cooled fast reactor (SFR) designs. Experiments evolved in complexity. Simulation of thermal-hydraulic conditions expected to be encountered by fuels and materials in a reactor environment was realized in the development of TREAT sodium loop experiment vehicles. These loops accommodated up to 7-pin fuel bundles and served to simulate more closely the reactor environment while safely delivering large quantities of energy into the test specimen. Some of the immediate TREAT restart operations will be focused on testing light water reactor (LWR) accident tolerant fuels (ATF). Similar to the sodium loop objectives, a water loop concept, developed and analyzed in the 1990’s, aimed at achieving thermal-hydraulic conditions encountered in commercial power reactors. The historic water loop concept has been analyzed in the context of a reactivity insertion accident (RIA) simulation for high burnup LWR 2-pin and 3-pin fuel bundles. Findings showed sufficient energy could be deposited into the specimens for evaluation. Similar results of experimental feasibility for the water loop concept (past and present) have recently been obtained using MCNP6.1 with ENDF/B-VII.1 nuclear data libraries. The old water loop concept required only two central TREAT core grid spaces. Preparation for future experiments has resulted in a modified water loop conceptual design designated the TREAT water environment recirculating loop (TWERL). The current TWERL design requires nine TREAT core grid spaces in order to place the water recirculating pump under the TREAT core. Due to the effectiveness of water moderation, neutronics analysis shows that removal of seven additional

  11. Continuum simulations of water flow past fullerene molecules

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  12. Bundling Actin Filaments From Membranes: Some Novel Players

    Directory of Open Access Journals (Sweden)

    Clément eThomas

    2012-08-01

    Full Text Available Progress in live-cell imaging of the cytoskeleton has significantly extended our knowledge about the organization and dynamics of actin filaments near the plasma membrane of plant cells. Noticeably, two populations of filamentous structures can be distinguished. On the one hand, fine actin filaments which exhibit an extremely dynamic behavior basically characterized by fast polymerization and prolific severing events, a process referred to as actin stochastic dynamics. On the other hand, thick actin bundles which are composed of several filaments and which are comparatively more stable although they constantly remodel as well. There is evidence that the actin cytoskeleton plays critical roles in trafficking and signaling at both the cell cortex and organelle periphery but the exact contribution of actin bundles remains unclear. A common view is that actin bundles provide the long-distance tracks used by myosin motors to deliver their cargo to growing regions and accordingly play a particularly important role in cell polarization. However, several studies support that actin bundles are more than simple passive highways and display multiple and dynamic roles in the regulation of many processes, such as cell elongation, polar auxin transport, stomatal and chloroplast movement, and defense against pathogens. The list of identified plant actin-bundling proteins is ever expanding, supporting that plant cells shape structurally and functionally different actin bundles. Here I review the most recently characterized actin-bundling proteins, with a particular focus on those potentially relevant to membrane trafficking and/or signaling.

  13. Aerosol retention in the flooded steam generator bundle during SGTR

    Energy Technology Data Exchange (ETDEWEB)

    Lind, Terttaliisa, E-mail: terttaliisa.lind@psi.c [Paul Scherrer Institut, Department of Nuclear Energy and Safety, 5232 Villigen (Switzerland); Dehbi, Abdel; Guentay, Salih [Paul Scherrer Institut, Department of Nuclear Energy and Safety, 5232 Villigen (Switzerland)

    2011-01-15

    Research highlights: High retention of aerosol particles in a steam generator bundle flooded with water. Increasing particle inertia, i.e., particle size and velocity, increases retention. Much higher retention of aerosol particles in the steam generator bundle flooded with water than in a dry bundle. Much higher retention of aerosol particles in the steam generator bundle than in a bare pool. Bare pool models have to be adapted to be applicable for flooded bundles. - Abstract: A steam generator tube rupture in a pressurized water reactor may cause accidental release of radioactive particles into the environment. Its specific significance is in its potential to bypass the containment thereby providing a direct pathway of the radioactivity from the primary circuit to the environment. Under certain severe accident scenarios, the steam generator bundle may be flooded with water. In addition, some severe accident management procedures are designed to minimize the release of radioactivity into the environment by flooding the defective steam generator secondary side with water when the steam generator has dried out. To extend our understanding of the particle retention phenomena in the flooded steam generator bundle, tests were conducted in the ARTIST and ARTIST II programs to determine the effect of different parameters on particle retention. The effects of particle type (spherical or agglomerate), particle size, gas mass flow rate, and the break submergence on particle retention were investigated. Results can be summarized as follows: increasing particle inertia was found to increase retention in the flooded bundle. Particle shape, i.e., agglomerate or spherical structure, did not affect retention significantly. Even with a very low submergence, 0.3 m above the tube break, significant aerosol retention took place underlining the importance of the jet-bundle interactions close to the tube break. Droplets were entrained from the water surface with high gas flow rates

  14. Matching conditions in the quasicontinuum method: Removal of the error introduced at the interface between the coarse-grained and fully atomistic region

    DEFF Research Database (Denmark)

    Shimokawa, T.; Mortensen, Jens Jørgen; Schiøtz, Jakob

    2004-01-01

    The quasicontinuum method is a way of reducing the number of degrees of freedom in an atomistic simulation by removing the majority of the atoms in regions of slowly varying strain fields. Due to the different ways the energy of the atoms is calculated in the coarse-grained regions and the regions...... the quasicontinuum method without these problems by introducing a buffer layer between the two regions of space. The method is applicable to short-ranged potentials in the face-centered cubic, body-centered cubic, and hexagonal close-packed crystal structures....

  15. Dark-field illuminated reflectance fiber bundle endoscopic microscope

    Science.gov (United States)

    Liu, Xuan; Huang, Yong; Kang, Jin U.

    2011-04-01

    We propose a reflectance fiber bundle microscope using a dark-field illumination configuration for applications in endoscopic medical imaging and diagnostics. Our experiment results show that dark-field illumination can effectively suppress strong specular reflection from the proximal end of the fiber bundle. We realized a lateral resolution of 4.4 μm using the dark-field illuminated fiber bundle configuration. To demonstrate the feasibility of using the system to study cell morphology, we obtained still and video images of two thyroid cancer cell lines. Our results clearly allow differentiation of different cancer cell types.

  16. Moduli of Parabolic Higgs Bundles and Atiyah Algebroids

    DEFF Research Database (Denmark)

    Logares, Marina; Martens, Johan

    2010-01-01

    In this paper we study the geometry of the moduli space of (non-strongly) parabolic Higgs bundles over a Riemann surface with marked points. We show that this space possesses a Poisson structure, extending the one on the dual of an Atiyah algebroid over the moduli space of parabolic vector bundles....... By considering the case of full flags, we get a Grothendieck–Springer resolution for all other flag types, in particular for the moduli spaces of twisted Higgs bundles, as studied by Markman and Bottacin and used in the recent work of Laumon–Ngô. We discuss the Hitchin system, and demonstrate that all...

  17. Application and Performance Analysis of a New Bundle Adjustment Model

    Science.gov (United States)

    Sun, Y.; Liu, X.; Chen, R.; Wan, J.; Wang, Q.; Wang, H.; Li, Y.; Yan, L.

    2017-09-01

    As the basis for photogrammetry, Bundle Adjustment (BA) can restore the pose of cameras accurately, reconstruct the 3D models of environment, and serve as the criterion of digital production. For the classical nonlinear optimization of BA model based on the Euclidean coordinate, it suffers the problem of being seriously dependent on the initial values, making it unable to converge fast or converge to a global minimum. This paper first introduces a new BA model based on parallax angle feature parametrization, and then analyses the applications and performance of the model used in photogrammetry field. To discuss the impact and the performance of the model (especially in aerial photogrammetry), experiments using two aerial datasets under different initial values were conducted. The experiment results are better than some well-known software packages of BA, and the simulation results illustrate the stability of the new model than the normal BA under the Euclidean coordinate. In all, the new BA model shows promising applications in faster and more efficient aerial photogrammetry with good convergence and fast convergence speed.

  18. Atomistic tensile deformation mechanisms of Fe with gradient nano-grained structure

    Directory of Open Access Journals (Sweden)

    Wenbin Li

    2015-08-01

    Full Text Available Large-scale molecular dynamics (MD simulations have been performed to investigate the tensile properties and the related atomistic deformation mechanisms of the gradient nano-grained (GNG structure of bcc Fe (gradient grains with d from 25 nm to 105 nm, and comparisons were made with the uniform nano-grained (NG structure of bcc Fe (grains with d = 25 nm. The grain size gradient in the nano-scale converts the applied uniaxial stress to multi-axial stresses and promotes the dislocation behaviors in the GNG structure, which results in extra hardening and flow strength. Thus, the GNG structure shows slightly higher flow stress at the early plastic deformation stage when compared to the uniform NG structure (even with smaller grain size. In the GNG structure, the dominant deformation mechanisms are closely related to the grain sizes. For grains with d = 25 nm, the deformation mechanisms are dominated by GB migration, grain rotation and grain coalescence although a few dislocations are observed. For grains with d = 54 nm, dislocation nucleation, propagation and formation of dislocation wall near GBs are observed. Moreover, formation of dislocation wall and dislocation pile-up near GBs are observed for grains with d = 105 nm, which is the first observation by MD simulations to our best knowledge. The strain compatibility among different layers with various grain sizes in the GNG structure should promote the dislocation behaviors and the flow stress of the whole structure, and the present results should provide insights to design the microstructures for developing strong-and-ductile metals.

  19. Effects of fuel relocation on reflood in a partially-blocked rod bundle

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Byoung Jae [School of Mechanical Engineering, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134 (Korea, Republic of); Kim, Jongrok; Kim, Kihwan; Bae, Sung Won [Thermal-Hydraulic Safety Research Division, Korea Atomic Energy Research Division, 111 Daedeok-daero, Yuseong-gu, Daejeon 34057 (Korea, Republic of); Moon, Sang-Ki, E-mail: skmoon@kaeri.re.kr [Thermal-Hydraulic Safety Research Division, Korea Atomic Energy Research Division, 111 Daedeok-daero, Yuseong-gu, Daejeon 34057 (Korea, Republic of)

    2017-02-15

    Ballooning of the fuel rods has been an important issue, since it can influence the coolability of the rod bundle in a large-break loss-of-coolant accident (LBLOCA). Numerous past studies have investigated the effect of blockage geometry on the heat transfer in a partially blocked rod bundle. However, they did not consider the occurrence of fuel relocation and the corresponding effect on two-phase heat transfer. Some fragmented fuel particles located above the ballooned region may drop into the enlarged volume of the balloon. Accordingly, the fuel relocation brings in a local power increase in the ballooned region. The present study’s objective is to investigate the effect of the fuel relocation on the reflood under a LBLOCA condition. Toward this end, experiments were performed in a 5 × 5 partially-blocked rod bundle. Two power profiles were tested: one is a typical cosine shape and the other is the modified shape considering the effect of the fuel relocation. For a typical power shape, the peak temperature in the ballooned rods was lower than that in the intact rods. On the other hand, for the modified power shape, the peak temperature in the ballooned rods was higher than that in the intact rods. Numerical simulations were also performed using the MARS code. The tendencies of the peak clad temperatures were well predicted.

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

    Science.gov (United States)

    Suzuki, Yuichi; Nagaoka, Masataka

    2017-05-28

    Atomistic information of a whole chemical reaction system, e.g., instantaneous microscopic molecular structures and orientations, offers important and deeper insight into clearly understanding unknown chemical phenomena. In accordance with the progress of a number of simultaneous chemical reactions, the Red Moon method (a hybrid Monte Carlo/molecular dynamics reaction method) is capable of simulating atomistically the chemical reaction process from an initial state to the final one of complex chemical reaction systems. In the present study, we have proposed a transformation theory to interpret the chemical reaction process of the Red Moon methodology as the time evolution process in harmony with the chemical kinetics. For the demonstration of the theory, we have chosen the gas reaction system in which the reversible second-order reaction H2 + I2 ⇌ 2HI occurs. First, the chemical reaction process was simulated from the initial configurational arrangement containing a number of H2 and I2 molecules, each at 300 K, 500 K, and 700 K. To reproduce the chemical equilibrium for the system, the collision frequencies for the reactions were taken into consideration in the theoretical treatment. As a result, the calculated equilibrium concentrations [H2]eq and equilibrium constants Keq at all the temperatures were in good agreement with their corresponding experimental values. Further, we applied the theoretical treatment for the time transformation to the system and have shown that the calculated half-life τ's of [H2] reproduce very well the analytical ones at all the temperatures. It is, therefore, concluded that the application of the present theoretical treatment with the Red Moon method makes it possible to analyze reasonably the time evolution of complex chemical reaction systems to chemical equilibrium at the atomistic level.

  1. Improved Conjugate Gradient Bundle Adjustment of Dunhuang Wall Painting Images

    Science.gov (United States)

    Hu, K.; Huang, X.; You, H.

    2017-09-01

    Bundle adjustment with additional parameters is identified as a critical step for precise orthoimage generation and 3D reconstruction of Dunhuang wall paintings. Due to the introduction of self-calibration parameters and quasi-planar constraints, the structure of coefficient matrix of the reduced normal equation is banded-bordered, making the solving process of bundle adjustment complex. In this paper, Conjugate Gradient Bundle Adjustment (CGBA) method is deduced by calculus of variations. A preconditioning method based on improved incomplete Cholesky factorization is adopt to reduce the condition number of coefficient matrix, as well as to accelerate the iteration rate of CGBA. Both theoretical analysis and experimental results comparison with conventional method indicate that, the proposed method can effectively conquer the ill-conditioned problem of normal equation and improve the calculation efficiency of bundle adjustment with additional parameters considerably, while maintaining the actual accuracy.

  2. Bundles of Norms About Teen Sex and Pregnancy.

    Science.gov (United States)

    Mollborn, Stefanie; Sennott, Christie

    2015-09-01

    Teen pregnancy is a cultural battleground in struggles over morality, education, and family. At its heart are norms about teen sex, contraception, pregnancy, and abortion. Analyzing 57 interviews with college students, we found that "bundles" of related norms shaped the messages teens hear. Teens did not think their communities encouraged teen sex or pregnancy, but normative messages differed greatly, with either moral or practical rationalizations. Teens readily identified multiple norms intended to regulate teen sex, contraception, abortion, childbearing, and the sanctioning of teen parents. Beyond influencing teens' behavior, norms shaped teenagers' public portrayals and post hoc justifications of their behavior. Although norm bundles are complex to measure, participants could summarize them succinctly. These bundles and their conflicting behavioral prescriptions create space for human agency in negotiating normative pressures. The norm bundles concept has implications for teen pregnancy prevention policies and can help revitalize social norms for understanding health behaviors. © The Author(s) 2014.

  3. Some applications on tangent bundle with Kaluza-Klein metric

    Directory of Open Access Journals (Sweden)

    Murat Altunbaş

    2017-01-01

    Full Text Available In this paper, differential equations of geodesics; parallelism, incompressibility and closeness conditions of the horizontal and complete lift of the vector fields are investigated with respect to Kaluza-Klein metric on tangent bundle.

  4. Algebraic Frobenius splitting of cotangent bundles of flag varieties

    National Research Council Canada - National Science Library

    Hague, Chuck

    2013-01-01

    Following the program of algebraic Frobenius splitting begun by Kumar and Littelmann, we use representation-theoretic techniques to construct a Frobenius splitting of the cotangent bundle of the flag...

  5. Design and synthesis of DNA four-helix bundles.

    Science.gov (United States)

    Rangnekar, Abhijit; Gothelf, Kurt V; LaBean, Thomas H

    2011-06-10

    The field of DNA nanotechnology has evolved significantly in the past decade. Researchers have succeeded in synthesizing tile-based structures and using them to form periodic lattices in one, two and three dimensions. Origami-based structures have also been used to create nanoscale structures in two and three dimensions. Design and construction of DNA bundles with fixed circumference has added a new dimension to the field. Here we report the design and synthesis of a DNA four-helix bundle. It was found to be extremely rigid and stable. When several such bundles were assembled using appropriate sticky-ends, they formed micrometre-long filaments. However, when creation of two-dimensional sheet-like arrays of the four-helix bundles was attempted, nanoscale rings were observed instead. The exact reason behind the nanoring formation is yet to be ascertained, but it provides an exciting prospect for making programmable circular nanostructures using DNA.

  6. IMPROVED CONJUGATE GRADIENT BUNDLE ADJUSTMENT OF DUNHUANG WALL PAINTING IMAGES

    Directory of Open Access Journals (Sweden)

    K. Hu

    2017-09-01

    Full Text Available Bundle adjustment with additional parameters is identified as a critical step for precise orthoimage generation and 3D reconstruction of Dunhuang wall paintings. Due to the introduction of self-calibration parameters and quasi-planar constraints, the structure of coefficient matrix of the reduced normal equation is banded-bordered, making the solving process of bundle adjustment complex. In this paper, Conjugate Gradient Bundle Adjustment (CGBA method is deduced by calculus of variations. A preconditioning method based on improved incomplete Cholesky factorization is adopt to reduce the condition number of coefficient matrix, as well as to accelerate the iteration rate of CGBA. Both theoretical analysis and experimental results comparison with conventional method indicate that, the proposed method can effectively conquer the ill-conditioned problem of normal equation and improve the calculation efficiency of bundle adjustment with additional parameters considerably, while maintaining the actual accuracy.

  7. CANFLEX fuel bundle cross-flow endurance test (test report)

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Sung Deok; Chung, C. H.; Chang, S. K.; Kim, B. D.

    1997-04-01

    As part of the normal refuelling sequence of CANDU nuclear reactor, both new and irradiated bundles can be parked in the cross-flow region of the liner tubes. This situation occurs normally for a few minutes. The fuel bundle which is subjected to the cross-flow should be capable of withstanding the consequences of cross flow for normal periods, and maintain its mechanical integrity. The cross-flow endurance test was conducted for CANFLEX bundle, latest developed nuclear fuel, at CANDU-Hot Test Loop. The test was carried out during 4 hours at the inlet cross-flow region. After the test, the bundle successfully met all acceptance criteria after the 4 hours cross-flow test. (author). 2 refs., 3 tabs.

  8. Introductory lectures on fibre bundles and topology for physicists

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, G.H.

    1978-05-01

    These lectures may provide useful background material for understanding gauge theories, particularly the nonperturbative effects such as instantons and monopoles. The mathematical language of topology and fibre bundles is introduced.

  9. Bohr--Sommerfeld Lagrangians of moduli spaces of Higgs bundles

    DEFF Research Database (Denmark)

    Biswas, Indranil; Gammelgaard, Niels Leth; Logares, Marina

    Let $X$ be a compact connected Riemann surface of genus at least two. Let $M_H(r,d)$ denote the moduli space of semistable Higgs bundles on $X$ of rank $r$ and degree $d$. We prove that the compact complex Bohr-Sommerfeld Lagrangians of $M_H(r,d)$ are precisely the irreducible components of the n......Let $X$ be a compact connected Riemann surface of genus at least two. Let $M_H(r,d)$ denote the moduli space of semistable Higgs bundles on $X$ of rank $r$ and degree $d$. We prove that the compact complex Bohr-Sommerfeld Lagrangians of $M_H(r,d)$ are precisely the irreducible components...... of the nilpotent cone in $M_H(r,d)$. This generalizes to Higgs $G$-bundles and also to the parabolic Higgs bundles....

  10. Design and synthesis of DNA four-helix bundles

    Energy Technology Data Exchange (ETDEWEB)

    Rangnekar, Abhijit; Gothelf, Kurt V [Department of Chemistry, Centre for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C (Denmark); LaBean, Thomas H, E-mail: kvg@chem.au.dk, E-mail: thl@cs.duke.edu [Department of Chemistry, Duke University, Durham, NC 27708 (United States)

    2011-06-10

    The field of DNA nanotechnology has evolved significantly in the past decade. Researchers have succeeded in synthesizing tile-based structures and using them to form periodic lattices in one, two and three dimensions. Origami-based structures have also been used to create nanoscale structures in two and three dimensions. Design and construction of DNA bundles with fixed circumference has added a new dimension to the field. Here we report the design and synthesis of a DNA four-helix bundle. It was found to be extremely rigid and stable. When several such bundles were assembled using appropriate sticky-ends, they formed micrometre-long filaments. However, when creation of two-dimensional sheet-like arrays of the four-helix bundles was attempted, nanoscale rings were observed instead. The exact reason behind the nanoring formation is yet to be ascertained, but it provides an exciting prospect for making programmable circular nanostructures using DNA.

  11. A Discrete Theory of Connections on Principal Bundles

    OpenAIRE

    Leok, M; Marsden, JE; Weinstein, AD

    2017-01-01

    Connections on principal bundles play a fundamental role in expressing the equations of motion for mechanical systems with symmetry in an intrinsic fashion. A discrete theory of connections on principal bundles is constructed by introducing the discrete analogue of the Atiyah sequence, with a connection corresponding to the choice of a splitting of the short exact sequence. Equivalent representations of a discrete connection are considered, and an extension of the pair groupoid composition, t...

  12. On the Geometry of Cotangent Bundles of Lie Groups

    OpenAIRE

    Manga, Bakary

    2015-01-01

    Lie groups of automorphisms of cotangent bundles of Lie groups are completely characterized and interesting results are obtained. We give prominence to the fact that the Lie groups of automorphisms of cotangent bundles of Lie groups are super symmetric Lie groups. In the cases of orthogonal Lie lgebras, semi-simple Lie algebras and compact Lie algebras we recover by simple methods interesting co-homological known results. The Lie algebra of prederivations encompasses the one of derivations as...

  13. CHF prediction in rod bundles using round tube data

    Energy Technology Data Exchange (ETDEWEB)

    Souza, Wallen F.; Veloso, Maria A.F.; Pereira, Cláubia; Costa, Antonella L., E-mail: wallenfds@yahoo.com.br, E-mail: mdora@nuclear.ufmg.br [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Departamento de Engenharia Nuclear

    2017-07-01

    The present work concerns the use of 1995 CHF table for uniformly heated round tubes, developed jointly by Canadian and Russian researchers, for the prediction of critical heat fluxes in rod bundles geometries. Comparisons between measured and calculated critical heat fluxes indicate that this table could be applied to rod bundles provided that a suitable correction factor is employed. The tolerance limits associated with the departure from nucleate boiling ratio (DNBR) are evaluated by using statistical analysis. (author)

  14. Page 1 Moduli for bundles over curves - 325 through the ...

    Indian Academy of Sciences (India)

    (B End V, with the reduced structure. Note that C is an open subscheme in C and C is a multicone in G) End V. By the hypothesis of the lemma and assumption Mo = G, for te Twe have an isomorphism (p, Eo- ºr, We can interpret p, as a section of the fiber bundle (e. X ..) (G) with fiber G associated to the G × G. bundle Eo * Č, ...

  15. Mitotic spindle: kinetochore fibers hold on tight to interpolar bundles.

    Science.gov (United States)

    Tolić, Iva M

    2017-07-19

    When a cell starts to divide, it forms a spindle, a micro-machine made of microtubules, which separates the duplicated chromosomes. The attachment of microtubules to chromosomes is mediated by kinetochores, protein complexes on the chromosome. Spindle microtubules can be divided into three major classes: kinetochore microtubules, which form k-fibers ending at the kinetochore; interpolar microtubules, which extend from the opposite sides of the spindle and interact in the middle; and astral microtubules, which extend towards the cell cortex. Recent work in human cells has shown a close relationship between interpolar and kinetochore microtubules, where interpolar bundles are attached laterally to kinetochore fibers almost all along their length, acting as a bridge between sister k-fibers. Most of the interpolar bundles are attached to a pair of sister kinetochore fibers and vice versa. Thus, the spindle is made of modules consisting of a pair of sister kinetochore fibers and a bundle of interpolar microtubules that connects them. These interpolar bundles, termed bridging fibers, balance the forces acting at kinetochores and support the rounded shape of the spindle during metaphase. This review discusses the structure, function, and formation of kinetochore fibers and interpolar bundles, with an emphasis on how they interact. Their connections have an impact on the force balance in the spindle and on chromosome movement during mitosis because the forces in interpolar bundles are transmitted to kinetochore fibers and hence to kinetochores through these connections.

  16. 3D Quantum thermodynamic description of the non-equilibrium behavior of an unbounded system at an atomistic level

    Energy Technology Data Exchange (ETDEWEB)

    Smith, C E; Spakovsky, M R von [Center for Energy Systems Research, M.E. Department Virginia Polytechnic Institute and State University, Blacksburg, VA (United States); Sciacovelli, A; Verda, V, E-mail: vonspako@vt.ed [Department of Energy Engineering, Politecnico di Torino, c.so Duca degli Abruzzi 24, 10129 Torino (Italy)

    2010-06-01

    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 model the storage of hydrogen on and in a carbon nanotube. The tube is placed at the center of a tank with a volume of 250 nm{sup 3}. The thermodynamic system of interest is the hydrogen, which is assumed isolated and having boundaries that coincide with the walls of the tank and the carbon nanotube. The hydrogen is initially prepared in a state far from stable equilibrium (i.e., with the hydrogen molecules probabilistically near one of the outer tank walls) after which the system is allowed to relax (evolve) to a state of stable equilibrium. To predict this evolution in state, the so-called energy eigenvalue problem, which entails a many-body problem that for dilute and moderately dense gases can be modeled using virial expansion theory, is first solved for the geometry involved. The energy eigenvalues and eigenstates of the system found are then used by the nonlinear Beretta equation of motion of QT to determine the evolution of the thermodynamic state of the system as well as the 3D spatial distributions of the hydrogen molecules in time. The simulation results provide a quantification of the entropy generated due to irreversibilities at an atomistic level and show in detail the trajectory of the thermodynamic 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 probabilistically more concentrated near the carbon atoms, which make up the nanotube.

  17. A framework for solving atomistic phonon-structure scattering problems in the frequency domain using perfectly matched layer boundaries

    Energy Technology Data Exchange (ETDEWEB)

    Kakodkar, Rohit R.; Feser, Joseph P., E-mail: jpfeser@udel.edu [Department of Mechanical Engineering, University of Delaware, Newark, Delaware 19716 (United States)

    2015-09-07

    We present a numerical approach to the solution of elastic phonon-interface and phonon-nanostructure scattering problems based on a frequency-domain decomposition of the atomistic equations of motion and the use of perfectly matched layer (PML) boundaries. Unlike molecular dynamic wavepacket analysis, the current approach provides the ability to simulate scattering from individual phonon modes, including wavevectors in highly dispersive regimes. Like the atomistic Green's function method, the technique reduces scattering problems to a system of linear algebraic equations via a sparse, tightly banded matrix regardless of dimensionality. However, the use of PML boundaries enables rapid absorption of scattered wave energies at the boundaries and provides a simple and inexpensive interpretation of the scattered phonon energy flux calculated from the energy dissipation rate in the PML. The accuracy of the method is demonstrated on connected monoatomic chains, for which an analytic solution is known. The parameters defining the PML are found to affect the performance and guidelines for selecting optimal parameters are given. The method is used to study the energy transmission coefficient for connected diatomic chains over all available wavevectors for both optical and longitudinal phonons; it is found that when there is discontinuity between sublattices, even connected chains of equivalent acoustic impedance have near-zero transmission coefficient for short wavelengths. The phonon scattering cross section of an embedded nanocylinder is calculated in 2D for a wide range of frequencies to demonstrate the extension of the method to high dimensions. The calculations match continuum theory for long-wavelength phonons and large cylinder radii, but otherwise show complex physics associated with discreteness of the lattice. Examples include Mie oscillations which terminate when incident phonon frequencies exceed the maximum available frequency in the embedded nanocylinder

  18. Splitting 3-plane sub-bundles over the product of two real projective spaces

    Directory of Open Access Journals (Sweden)

    Maria Hermínia de Paula Leite Mello

    2003-11-01

    Full Text Available Let α be a real vector bundle of fiber dimension three over the product RP(m×RP(n which splits as a Whitney sum of line bundles. We show that the necessary and sufficient conditions for α to embed as a sub-bundle of a certain family of vector bundles β of fiber dimension m+n is the vanishing of the last three Stiefel-Whitney classes of the virtual bundle0 β−α. Among the target bundles β we consider the tangent bundle.

  19. ADAPTIVE QUASICONTINUUM SIMULATION OF ELASTIC-BRITTLE DISORDERED LATTICES

    Directory of Open Access Journals (Sweden)

    Karel Mikeš

    2017-11-01

    Full Text Available The quasicontinuum (QC method is a computational technique that can efficiently handle atomistic lattices by combining continuum and atomistic approaches. In this work, the QC method is combined with an adaptive algorithm, to obtain correct predictions of crack trajectories in failure simulations. Numerical simulations of crack propagation in elastic-brittle disordered lattices are performed for a two-dimensional example. The obtained results are compared with the fully resolved particle model. It is shown that the adaptive QC simulation provides a significant reduction of the computational demand. At the same time, the macroscopic crack trajectories and the shape of the force-displacement diagram are very well captured.

  20. Nonadiabatic Dynamics in Atomistic Environments: Harnessing Quantum-Classical Theory with Generalized Quantum Master Equations.

    Science.gov (United States)

    Pfalzgraff, William C; Kelly, Aaron; Markland, Thomas E

    2015-12-03

    The development of methods that can efficiently and accurately treat nonadiabatic dynamics in quantum systems coupled to arbitrary atomistic environments remains a significant challenge in problems ranging from exciton transport in photovoltaic materials to electron and proton transfer in catalysis. Here we show that our recently introduced MF-GQME approach, which combines Ehrenfest mean field theory with the generalized quantum master equation framework, is able to yield quantitative accuracy over a wide range of charge-transfer regimes in fully atomistic environments. This is accompanied by computational speed-ups of up to 3 orders of magnitude over a direct application of Ehrenfest theory. This development offers the opportunity to efficiently investigate the atomistic details of nonadiabatic quantum relaxation processes in regimes where obtaining accurate results has previously been elusive.

  1. A quantitative histopathological study of right bundle branch block complicating acute anteroseptal myocardial infarction.

    OpenAIRE

    Okabe, M; Fukuda, K; Nakashima, Y; Hiroki, T; Arakawa, K; Kikuchi, M

    1991-01-01

    The aim of the present study was to evaluate whether necrosis of the right bundle branch is responsible for development of right bundle branch block in acute myocardial infarction. Twenty patients with acute anteroseptal myocardial infarction were studied--10 with right bundle branch block (group A) and 10 without (group B)--to evaluate by serial sectioning the pathological extent of myocardial infarction surrounding the right bundle branch and also that of right bundle branch necrosis. Myoca...

  2. SCADOP: Phenomenological modeling of dryout in nuclear fuel rod bundles

    Energy Technology Data Exchange (ETDEWEB)

    Dasgupta, Arnab, E-mail: arnie@barc.gov.in; Chandraker, D.K., E-mail: dineshkc@barc.gov.in; Vijayan, P.K., E-mail: vijayanp@barc.gov.in

    2015-11-15

    Highlights: • Phenomenological model for annular flow dryout is presented. • The model evaluates initial entrained fraction using a new methodology. • The history effect in annular flow is predicted and validated. • Rod bundle dryout is predicted using subchannel methodology. • Model is validated against experimental dryout data in tubes and rod bundles. - Abstract: Analysis and prediction of dryout is of important consequence to safety of nuclear fuel clusters of boiling water type of reactors. Traditionally, experimental correlations are used for dryout predictions. Since these correlations are based on operating parameters and do not aim to model the underlying phenomena, there has been a proliferation of the correlations, each catering to some specific bundle geometry under a specific set of operating conditions. Moreover, such experiments are extremely costly. In general, changes in tested bundle geometry for improvement in thermal-hydraulic performance would require re-experimentation. Understanding and modeling the basic processes leading to dryout in flow boiling thus has great incentive. Such a model has the ability to predict dryout in any rod bundle geometry, unlike the operating parameter based correlation approach. Thus more informed experiments can be carried out. A good model can, reduce the number of experiments required during the iterations in bundle design. In this paper, a phenomenological model as indicated above is presented. The model incorporates a new methodology to estimate the Initial Entrained Fraction (IEF), i.e., entrained fraction at the onset of annular flow. The incorporation of this new methodology is important since IEF is often assumed ad-hoc and sometimes also used as a parameter to tune the model predictions to experimental data. It is highlighted that IEF may be low under certain conditions against the general perception of a high IEF due to influence of churn flow. It is shown that the same phenomenological model is

  3. Atomistic study of hydrogen embrittlement of grain boundaries in nickel: II. Decohesion

    Science.gov (United States)

    Tehranchi, A.; Curtin, W. A.

    2017-10-01

    Atomistic simulations of bicrystal samples containing a grain boundary are used to examine the effect of hydrogen atoms on the nucleation of intergranular cracks in Ni. Specifically, the theoretical strength is obtained by rigid separation of the two crystals above and below the GB and the yield strength (point of dislocation emission) is obtained by standard tension testing normal to the GB. These strengths are computed in pure Ni and Ni with H segregated to the grain boundaries under conditions typical of H embrittlement in Ni, and in artificially highly-H-saturated states. In all GBs studied here, the theoretical strength \\hat{σ } is not significantly reduced by the presence of the hydrogen atoms. Similarly, with the exception of the Ni {{Σ }}27(115) boundary, the yield strength {σ }{{y}} is not significantly altered by the presence of segregated H atoms. In all cases, the theoretical strengths are ˜25 GPa and the yield strengths are ˜10 GPa, so that (i) the theoretical strength is always well above the yield strength, with or without H, and (ii) both strengths are far above the bulk plastic flow stress, {σ }{{y}}{{B}} of Ni and Ni alloys. Significant reductions in fracture energy (25%-45%) are only achieved for some of the artificially high-H-segregation cases and then only when all the H around the GB is allow to diffuse locally to the fracture surface, which corresponds to unlikely out-of-equilibrium segregation plus local kinetics. Complementing recent work showing that H does not change the ability of GB cracks to emit dislocations and blunt, the present work indicates that equilibrium segregation of hydrogen atoms to GBs has little effect on lowering the GB strength and energy, and so does not significantly facilitate nucleation of intergranular cracks.

  4. Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex

    Science.gov (United States)

    Postila, Pekka A.; Kaszuba, Karol; Kuleta, Patryk; Vattulainen, Ilpo; Sarewicz, Marcin; Osyczka, Artur; Róg, Tomasz

    2016-09-01

    The cytochrome (cyt) bc1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme’s substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Qi-site of the cyt bc1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Qi-site to facilitate binding of half-protonated semiquinone - a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Qi-site.

  5. Single-tunnel double-bundle anterior cruciate ligament reconstruction with anatomical placement of hamstring tendon graft: can it restore normal knee joint kinematics?

    Science.gov (United States)

    Gadikota, Hemanth R; Wu, Jia-Lin; Seon, Jong Keun; Sutton, Karen; Gill, Thomas J; Li, Guoan

    2010-04-01

    Anatomical reconstruction techniques that can restore normal joint kinematics without increasing surgical complications could potentially improve clinical outcomes and help manage anterior cruciate ligament injuries more efficiently. Single-tunnel double-bundle anterior cruciate ligament reconstruction with anatomical placement of hamstring tendon graft can more closely restore normal knee anterior-posterior, medial-lateral, and internal-external kinematics than can conventional single-bundle anterior cruciate ligament reconstruction. Controlled laboratory study. Kinematic responses after single-bundle anterior cruciate ligament reconstruction and single-tunnel double-bundle anterior cruciate ligament reconstruction with anatomical placement of hamstring tendon graft were compared with the intact knee in 9 fresh-frozen human cadaveric knee specimens using a robotic testing system. Kinematics of each knee were determined under an anterior tibial load (134 N), a simulated quadriceps load (400 N), and combined torques (10 N.m valgus and 5 N.m internal tibial torques) at 0 degrees , 15 degrees , 30 degrees , 60 degrees , and 90 degrees of flexion. Anterior tibial translations were more closely restored to the intact knee level after single-tunnel double-bundle reconstruction with anatomical placement of hamstring tendon graft than with a single-bundle reconstruction under the 3 external loading conditions. Under simulated quadriceps load, the mean internal tibial rotations after both reconstructions were lower than that of the anterior cruciate ligament-intact knee with no significant differences between these 3 knee conditions at 0 degrees and 30 degrees of flexion (P > .05). The increased medial tibial shifts of the anterior cruciate ligament-deficient knees were restored to the intact level by both reconstruction techniques under the 3 external loading conditions. Single-tunnel double-bundle anterior cruciate ligament reconstruction with anatomical placement of

  6. Histones bundle F-actin filaments and affect actin structure.

    Science.gov (United States)

    Blotnick, Edna; Sol, Asaf; Muhlrad, Andras

    2017-01-01

    Histones are small polycationic proteins complexed with DNA located in the cell nucleus. Upon apoptosis they are secreted from the cells and react with extracellular polyanionic compounds. Actin which is a polyanionic protein, is also secreted from necrotic cells and interacts with histones. We showed that both histone mixture (histone type III) and the recombinant H2A histone bundles F-actin, increases the viscosity of the F-actin containing solution and polymerizes G-actin. The histone-actin bundles are relatively insensitive to increase of ionic strength, unlike other polycation, histatin, lysozyme, spermine and LL-37 induced F-actin bundles. The histone-actin bundles dissociate completely only in the presence of 300-400 mM NaCl. DNA, which competes with F-actin for histones, disassembles histone induced actin bundles. DNase1, which depolymerizes F- to G-actin, actively unbundles the H2A histone induced but slightly affects the histone mixture induced actin bundles. Cofilin decreases the amount of F-actin sedimented by low speed centrifugation, increases light scattering and viscosity of F-actin-histone mixture containing solutions and forms star like superstructures by copolymerizing G-actin with H2A histone. The results indicate that histones are tightly attached to F-actin by strong electrostatic and hydrophobic forces. Since both histones and F-actin are present in the sputum of patients with cystic fibrosis, therefore, the formation of the stable histone-actin bundles can contribute to the pathology of this disease by increasing the viscosity of the sputum. The actin-histone interaction in the nucleus might affect gene expression.

  7. Histones bundle F-actin filaments and affect actin structure.

    Directory of Open Access Journals (Sweden)

    Edna Blotnick

    Full Text Available Histones are small polycationic proteins complexed with DNA located in the cell nucleus. Upon apoptosis they are secreted from the cells and react with extracellular polyanionic compounds. Actin which is a polyanionic protein, is also secreted from necrotic cells and interacts with histones. We showed that both histone mixture (histone type III and the recombinant H2A histone bundles F-actin, increases the viscosity of the F-actin containing solution and polymerizes G-actin. The histone-actin bundles are relatively insensitive to increase of ionic strength, unlike other polycation, histatin, lysozyme, spermine and LL-37 induced F-actin bundles. The histone-actin bundles dissociate completely only in the presence of 300-400 mM NaCl. DNA, which competes with F-actin for histones, disassembles histone induced actin bundles. DNase1, which depolymerizes F- to G-actin, actively unbundles the H2A histone induced but slightly affects the histone mixture induced actin bundles. Cofilin decreases the amount of F-actin sedimented by low speed centrifugation, increases light scattering and viscosity of F-actin-histone mixture containing solutions and forms star like superstructures by copolymerizing G-actin with H2A histone. The results indicate that histones are tightly attached to F-actin by strong electrostatic and hydrophobic forces. Since both histones and F-actin are present in the sputum of patients with cystic fibrosis, therefore, the formation of the stable histone-actin bundles can contribute to the pathology of this disease by increasing the viscosity of the sputum. The actin-histone interaction in the nucleus might affect gene expression.

  8. Scalable and portable visualization of large atomistic datasets

    Science.gov (United States)

    Sharma, Ashish; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya

    2004-10-01

    A scalable and portable code named Atomsviewer has been developed to interactively visualize a large atomistic dataset consisting of up to a billion atoms. The code uses a hierarchical view frustum-culling algorithm based on the octree data structure to efficiently remove atoms outside of the user's field-of-view. Probabilistic and depth-based occlusion-culling algorithms then select atoms, which have a high probability of being visible. Finally a multiresolution algorithm is used to render the selected subset of visible atoms at varying levels of detail. Atomsviewer is written in C++ and OpenGL, and it has been tested on a number of architectures including Windows, Macintosh, and SGI. Atomsviewer has been used to visualize tens of millions of atoms on a standard desktop computer and, in its parallel version, up to a billion atoms. Program summaryTitle of program: Atomsviewer Catalogue identifier: ADUM Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUM Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested: 2.4 GHz Pentium 4/Xeon processor, professional graphics card; Apple G4 (867 MHz)/G5, professional graphics card Operating systems under which the program has been tested: Windows 2000/XP, Mac OS 10.2/10.3, SGI IRIX 6.5 Programming languages used: C++, C and OpenGL Memory required to execute with typical data: 1 gigabyte of RAM High speed storage required: 60 gigabytes No. of lines in the distributed program including test data, etc.: 550 241 No. of bytes in the distributed program including test data, etc.: 6 258 245 Number of bits in a word: Arbitrary Number of processors used: 1 Has the code been vectorized or parallelized: No Distribution format: tar gzip file Nature of physical problem: Scientific visualization of atomic systems Method of solution: Rendering of atoms using computer graphic techniques, culling algorithms for data

  9. Simulation

    DEFF Research Database (Denmark)

    Gould, Derek A; Chalmers, Nicholas; Johnson, Sheena J

    2012-01-01

    Recognition of the many limitations of traditional apprenticeship training is driving new approaches to learning medical procedural skills. Among simulation technologies and methods available today, computer-based systems are topical and bring the benefits of automated, repeatable, and reliable...... performance assessments. Human factors research is central to simulator model development that is relevant to real-world imaging-guided interventional tasks and to the credentialing programs in which it would be used....

  10. An in vitro biomechanical comparison of anterior cruciate ligament reconstruction: single bundle versus anatomical double bundle techniques

    Directory of Open Access Journals (Sweden)

    Sandra Umeda Sasaki

    2008-01-01

    Full Text Available INTRODUCTION: Anterior cruciate ligament ruptures are frequent, especially in sports. Surgical reconstruction with autologous grafts is widely employed in the international literature. Controversies remain with respect to technique variations as continuous research for improvement takes place. One of these variations is the anatomical double bundle technique, which is performed instead of the conventional single bundle technique. More recently, there has been a tendency towards positioning the two bundles through double bone tunnels in the femur and tibia (anatomical reconstruction. OBJECTIVES: To compare, through biomechanical tests, the practice of anatomical double bundle anterior cruciate ligament reconstruction with a patellar graft to conventional single bundle reconstruction with the same amount of patellar graft in a paired experimental cadaver study. METHODS: Nine pairs of male cadaver knees ranging in age from 44 to 63 years were randomized into two groups: group A (single bundle and group B (anatomical reconstruction. Each knee was biomechanically tested under three conditions: intact anterior cruciate ligament, reconstructed anterior cruciate ligament, and injured anterior cruciate ligament. Maximum anterior dislocation, rigidity, and passive internal tibia rotation were recorded with knees submitted to a 100 N horizontal anterior dislocation force applied to the tibia with the knees at 30, 60 and 90 degrees of flexion. RESULTS: There were no differences between the two techniques for any of the measurements by ANOVA tests. CONCLUSION: The technique of anatomical double bundle reconstruction of the anterior cruciate ligament with bone-patellar tendon-bone graft has a similar biomechanical behavior with regard to anterior tibial dislocation, rigidity, and passive internal tibial rotation.

  11. Effects of different initial bundle tensioning strategies on the outcome of double-bundle ACL reconstruction: a cohort study

    Directory of Open Access Journals (Sweden)

    Muneta Takeshi

    2011-07-01

    Full Text Available Abstract Background This study was performed to investigate the effects of different strategies and initial tension applied to each one of the bundles, antero-medial (AM and postero-lateral (PL, on clinical outcome in double bundle (DB ACL reconstruction. Methods One hundred fifty-one primary unilateral DB ACL reconstructions performed by a single surgeon from 1994 through 2002 were included in the study with a follow-up of at least 24 months. They were divided in the following 3 groups: Group I - Higher initial tension applied manually in the AM bundle compared to PL. II - Higher tension applied in the PL bundle compared to AM. III - The 2 bundles were attempted to be equally tensioned. All fixations were performed in 30 degrees of flexion. Group I = 59 patients, group II = 53 patients and group III = 39 patients. The groups had no statistical differences concerning demographic distribution. Clinical outcome was retrospectively evaluated by use of knee range of motion, manual knee laxity tests, KT-1000, Lysholm knee scale, subjective recovery scale and sports performance recovery scale. The differences of data were analyzed among the three groups. Results Group I showed a significant extension deficit compared with groups II and III. ANOVA revealed a significant difference of anterior laxity measured by the KT-1000 (average KT difference of 2.1, 2.1 and 1.2 mm in Group I, II and III, respectively. A statistical difference was found among the three groups regarding subjective and sports performance recovery scales with Group II showing higher scores in recovery than Group I. Conclusions The current clinical study does not recommend manual maximum of initial tension applied to the anteromedial or posterolateral bundles with graft tension imbalance at 30 degrees of flexion in double-bundle ACL reconstruction to achieve a better clinical outcome.

  12. The 2-Hilbert space of a prequantum bundle gerbe

    Science.gov (United States)

    Bunk, Severin; Sämann, Christian; Szabo, Richard J.

    We construct a prequantum 2-Hilbert space for any line bundle gerbe whose Dixmier-Douady class is torsion. Analogously to usual prequantization, this 2-Hilbert space has the category of sections of the line bundle gerbe as its underlying 2-vector space. These sections are obtained as certain morphism categories in Waldorf’s version of the 2-category of line bundle gerbes. We show that these morphism categories carry a monoidal structure under which they are semisimple and abelian. We introduce a dual functor on the sections, which yields a closed structure on the morphisms between bundle gerbes and turns the category of sections into a 2-Hilbert space. We discuss how these 2-Hilbert spaces fit various expectations from higher prequantization. We then extend the transgression functor to the full 2-category of bundle gerbes and demonstrate its compatibility with the additional structures introduced. We discuss various aspects of Kostant-Souriau prequantization in this setting, including its dimensional reduction to ordinary prequantization.

  13. Improvements to Wire Bundle Thermal Modeling for Ampacity Determination

    Science.gov (United States)

    Rickman, Steve L.; Iannello, Christopher J.; Shariff, Khadijah

    2017-01-01

    Determining current carrying capacity (ampacity) of wire bundles in aerospace vehicles is critical not only to safety but also to efficient design. Published standards provide guidance on determining wire bundle ampacity but offer little flexibility for configurations where wire bundles of mixed gauges and currents are employed with varying external insulation jacket surface properties. Thermal modeling has been employed in an attempt to develop techniques to assist in ampacity determination for these complex configurations. Previous developments allowed analysis of wire bundle configurations but was constrained to configurations comprised of less than 50 elements. Additionally, for vacuum analyses, configurations with very low emittance external jackets suffered from numerical instability in the solution. A new thermal modeler is presented allowing for larger configurations and is not constrained for low bundle infrared emissivity calculations. Formulation of key internal radiation and interface conductance parameters is discussed including the effects of temperature and air pressure on wire to wire thermal conductance. Test cases comparing model-predicted ampacity and that calculated from standards documents are presented.

  14. Anatomy of an Oligourea Six-Helix Bundle.

    Science.gov (United States)

    Lombardo, Caterina M; Collie, Gavin W; Pulka-Ziach, Karolina; Rosu, Frederic; Gabelica, Valerie; Mackereth, Cameron D; Guichard, Gilles

    2016-08-24

    Non-natural synthetic oligomers that adopt well-defined secondary structures (i.e., foldamers) represent appealing components for the fabrication of bioinspired self-assembled architectures at the nanometer scale. Recently, peptidomimetic N,N'-linked oligourea helices have been designed de novo with the ability to fold into discrete helix bundles in aqueous conditions. In order to gain better insight into the determinants of oligourea helix bundle formation, we have investigated the sequence-to-structure relationship of an 11-mer oligourea previously shown to assemble into a six-helix bundle. Using circular dichroism, NMR spectroscopy, native mass-spectrometry and X-ray crystallography, we studied how bundle formation was affected by systematic replacement of the hydrophobic surface of the oligourea helix with either polar or different hydrophobic side chains. The molecular information gathered here has revealed several key requirements for foldamer bundle formation in aqueous conditions, and provides valuable insight toward the development of foldamer quaternary assemblies with improved (bio)physical properties and divergent topologies.

  15. Ecosystem service bundles for analyzing tradeoffs in diverse landscapes

    Science.gov (United States)

    Raudsepp-Hearne, C.; Peterson, G. D.; Bennett, E. M.

    2010-01-01

    A key challenge of ecosystem management is determining how to manage multiple ecosystem services across landscapes. Enhancing important provisioning ecosystem services, such as food and timber, often leads to tradeoffs between regulating and cultural ecosystem services, such as nutrient cycling, flood protection, and tourism. We developed a framework for analyzing the provision of multiple ecosystem services across landscapes and present an empirical demonstration of ecosystem service bundles, sets of services that appear together repeatedly. Ecosystem service bundles were identified by analyzing the spatial patterns of 12 ecosystem services in a mixed-use landscape consisting of 137 municipalities in Quebec, Canada. We identified six types of ecosystem service bundles and were able to link these bundles to areas on the landscape characterized by distinct social–ecological dynamics. Our results show landscape-scale tradeoffs between provisioning and almost all regulating and cultural ecosystem services, and they show that a greater diversity of ecosystem services is positively correlated with the provision of regulating ecosystem services. Ecosystem service-bundle analysis can identify areas on a landscape where ecosystem management has produced exceptionally desirable or undesirable sets of ecosystem services. PMID:20194739

  16. Syntheses of Nanostructure Bundles Based on Semiconducting Metal Silicides

    Science.gov (United States)

    Li, Wen; Ishikawa, Daisuke; Tatsuoka, Hirokazu

    2013-08-01

    A variety of nanostructure bundles and arrays based on semiconducting metal silicides have been synthesized using abundant and non-toxic starting materials. Three types of fabrication techniques of the nanostructure bundles or arrays, including direct growth, template synthesis using natural nanostructured materials and template synthesis using artificially fabricated nanostructured materials are demonstrated. CrSi2 nanowire bundles were directly grown by the exposure of Si substrates to CrCl2 vapor at atmospheric pressure. A hexagonal MoSi2 nanosheet, Mg2Si/MgO composite nanowire and Mg2Si nanowire bundles and MnSi1.7 nanowire array were synthesized using a MoS2 layered material, a SiOx nanofiber bundle, a Si nanowire array, and a Si nanowire array as the templates, respectively. Additionally, the fabrication phenomenon and structural properties of the nanostructured semiconducting metal silicides were investigated. These reactions provided the low-cost and controllable synthetic techniques to synthesize large scale and one-dimensional semiconducting metal silicides for thermoelectric applications.

  17. A prospective comparative study of clinical and functional outcomes between anatomic double bundle and single bundle hamstring grafts for arthroscopic anterior cruciate ligament reconstruction.

    Science.gov (United States)

    Morey, Vivek M; Nag, Hira Lal; Chowdhury, Buddhadev; Sankineani, Sukesh Rao; Naranje, Sameer M

    2015-09-01

    Despite a number of studies comparing postoperative stability and function after anatomic single bundle and double bundle anterior cruciate ligament reconstruction, it remains unclear whether double bundle reconstruction has better functional outcome than single bundle anterior cruciate ligament reconstruction. To compare the subjective functional outcome as well as clinical stability in patients treated with either anatomic single bundle or anatomic double bundle anterior cruciate ligament (ACL) reconstruction. We hypothesized that there would be no difference in the postoperative functional outcome and clinical stability between anatomical double bundle anterior cruciate ligament reconstructions when compared to single bundle anterior cruciate ligament reconstructions. We prospectively followed 40 patients out of which, 20 patients were operated for anatomic single bundle ACL reconstruction and other 20 patients underwent anatomic double bundle ACL reconstruction. Patient evaluation using the laxity tests and outcome scales was done preoperatively and at 12, 24 and 48 months after the surgery. Clinical stability was assessed by Lachman test, Pivot shift test and Delhi active test. Functional outcome was assessed by International Knee Documentation Committee (IKDC), Lysholm and Modified Cincinnati scores. Patients in both groups were evaluated at regular intervals for a minimum period of 48 months (mean 51 months, range 48-56 months). For all subjective scores, double bundle group patients reported statistically significant higher scores compared to single bundle group patients. Graded stability results of the Lachman, and Pivot shift tests were significantly higher in the anatomically reconstructed double bundle patient group. We suggest that functional outcome and clinical stability may be better with anatomical double bundle anterior cruciate ligament reconstruction as compared to anatomical single bundle anterior cruciate ligament reconstruction. Copyright

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

    African Journals Online (AJOL)

    The "paradox of migration and the interests of the atomistic nation-states" interrogates the phenomenon of migration in general and in the Southern African Development Community in particular. The point of departure of the paper is the African Union and the Southern African Development Community's legal framework on ...

  19. A Mathematical Analysis of Atomistic-to-Continuum (AtC) Multiscale Coupling Methods

    Energy Technology Data Exchange (ETDEWEB)

    Gunzburger, Max

    2013-11-13

    We have worked on several projects aimed at improving the efficiency and understanding of multiscale methods, especially those applicable to problems involving atomistic-to-continuum coupling. Activities include blending methods for AtC coupling and efficient quasi-continuum methods for problems with long-range interactions.

  20. Electron and phonon transport in silicon nanowires: Atomistic approach to thermoelectric properties

    DEFF Research Database (Denmark)

    Markussen, Troels; Jauho, Antti-Pekka; Brandbyge, Mads

    2009-01-01

    We compute both electron and phonon transmissions in thin disordered silicon nanowires (SiNWs). Our atomistic approach is based on tight-binding and empirical potential descriptions of the electronic and phononic systems, respectively. Surface disorder is modeled by introducing surface silicon va...