WorldWideScience

Sample records for united atom simulations

  1. Balancing simulation accuracy and efficiency with the Amber united atom force field.

    Science.gov (United States)

    Hsieh, Meng-Juei; Luo, Ray

    2010-03-04

    We have analyzed the quality of a recently proposed Amber united-atom model and its overall efficiency in ab initio folding and thermodynamic sampling of two stable beta-hairpins. It is found that the mean backbone structures are quite consistent between the simulations in the united-atom and its corresponding all-atom models in Amber. More importantly, the simulated beta turns are also consistent between the two models. Finally, the chemical shifts on H alpha are highly consistent between simulations in the two models, although the simulated chemical shifts are lower than experiment, indicating less structured peptides, probably due to the omission of the hydrophobic term in the simulations. More interestingly, the stabilities of both beta-hairpins at room temperature are similar to those derived from the NMR measurement, whether the united-atom or the all-atom model is used. Detailed analysis shows high percentages of backbone torsion angles within the beta region and high percentages of native contacts. Given the reasonable quality of the united-atom model with respect to experimental data, we have further studied the simulation efficiency of the united-atom model over the all-atom model. Our data shows that the united-atom model is a factor of 6-8 faster than the all-atom model as measured with the ab initio first pass folding time for the two tested beta-hairpins. Detailed structural analysis shows that all ab initio folded trajectories enter the native basin, whether the united-atom model or the all-atom model is used. Finally, we have also studied the simulation efficiency of the united-atom model as measured in terms of how fast thermodynamic convergence can be achieved. It is apparent that the united-atom simulations reach convergence faster than the all-atom simulations with respect to both mean potential energies and mean native contacts. These findings show that the efficiency of the united-atom model is clearly beyond the per-step dynamics simulation

  2. A comparison of united atom, explicit atom, and coarse-grained simulation models for poly(ethylene oxide).

    Science.gov (United States)

    Chen, Chunxia; Depa, Praveen; Sakai, Victoria García; Maranas, Janna K; Lynn, Jeffrey W; Peral, Inmaculada; Copley, John R D

    2006-06-21

    We compare static and dynamic properties obtained from three levels of modeling for molecular dynamics simulation of poly(ethylene oxide) (PEO). Neutron scattering data are used as a test of each model's accuracy. The three simulation models are an explicit atom (EA) model (all the hydrogens are taken into account explicitly), a united atom (UA) model (CH(2) and CH(3) groups are considered as a single unit), and a coarse-grained (CG) model (six united atoms are taken as one bead). All three models accurately describe the PEO static structure factor as measured by neutron diffraction. Dynamics are assessed by comparison to neutron time of flight data, which follow self-motion of protons. Hydrogen atom motion from the EA model and carbon/oxygen atom motion from the UA model closely follow the experimental hydrogen motion, while hydrogen atoms reinserted in the UA model are too fast. The EA and UA models provide a good description of the orientation properties of C-H vectors measured by nuclear magnetic resonance experiments. Although dynamic observables in the CG model are in excellent agreement with their united atom counterparts, they cannot be compared to neutron data because the time after which the CG model is valid is greater than the neutron decay times.

  3. Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins.

    Science.gov (United States)

    Kukol, Andreas

    2009-03-10

    United-atom force fields for molecular dynamics (MD) simulations provide a higher computational efficiency, especially in lipid membrane simulations, with little sacrifice in accuracy, when compared to all-atom force fields. Excellent united-atom lipid models are available, but in combination with depreciated protein force fields. In this work, a united-atom model of the lipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine has been built with standard parameters of the force field GROMOS96 53a6 that reproduces the experimental area per lipid of a lipid bilayer within 3% accuracy to a value of 0.623 ± 0.011 nm(2) without the assumption of a constant surface area or the inclusion of surface pressure. In addition, the lateral self-diffusion constant and deuterium order parameters of the acyl chains are in agreement with experimental data. Furthermore, models for 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) result in areas per lipid of 0.625 nm(2) (DMPC), 0.693 nm(2) (POPC), and 0.700 nm(2) (POPG) from 40 ns MD simulations. Experimental lateral self-diffusion coefficients are reproduced satisfactorily by the simulation. The lipid models can form the basis for molecular dynamics simulations of membrane proteins with current and future versions of united-atom protein force fields.

  4. Chemical Potential of Benzene Fluid from Monte Carlo Simulation with Anisotropic United Atom Model

    Directory of Open Access Journals (Sweden)

    Mahfuzh Huda

    2013-07-01

    Full Text Available The profile of chemical potential of benzene fluid has been investigated using Anisotropic United Atom (AUA model. A Monte Carlo simulation in canonical ensemble was done to obtain the isotherm of benzene fluid, from which the excess part of chemical potential was calculated. A surge of potential energy is observed during the simulation at high temperature which is related to the gas-liquid phase transition. The isotherm profile indicates the tendency of benzene to condensate due to the strong attractive interaction. The results show that the chemical potential of benzene rapidly deviates from its ideal gas counterpart even at low density.

  5. Predicting hydrophobic solvation by molecular simulation: 1. Testing united-atom alkane models.

    Science.gov (United States)

    Jorge, Miguel; Garrido, Nuno M; Simões, Carlos J V; Silva, Cândida G; Brito, Rui M M

    2017-03-05

    We present a systematic test of the performance of three popular united-atom force fields-OPLS-UA, GROMOS and TraPPE-at predicting hydrophobic solvation, more precisely at describing the solvation of alkanes in alkanes. Gibbs free energies of solvation were calculated for 52 solute/solvent pairs from Molecular Dynamics simulations and thermodynamic integration making use of the IBERCIVIS volunteer computing platform. Our results show that all force fields yield good predictions when both solute and solvent are small linear or branched alkanes (up to pentane). However, as the size of the alkanes increases, all models tend to increasingly deviate from experimental data in a systematic fashion. Furthermore, our results confirm that specific interaction parameters for cyclic alkanes in the united-atom representation are required to account for the additional excluded volume within the ring. Overall, the TraPPE model performs best for all alkanes, but systematically underpredicts the magnitude of solvation free energies by about 6% (RMSD of 1.2 kJ/mol). Conversely, both GROMOS and OPLS-UA systematically overpredict solvation free energies (by ∼13% and 15%, respectively). The systematic trends suggest that all models can be improved by a slight adjustment of their Lennard-Jones parameters. © 2016 Wiley Periodicals, Inc.

  6. Predicting hydrophobic solvation by molecular simulation: 2. New united-atom model for alkanes, alkenes, and alkynes.

    Science.gov (United States)

    Jorge, Miguel

    2017-03-05

    Existing united-atom models for non-polar hydrocarbons lead to systematic deviations in predicted solvation free energies in hydrophobic solvents. In this article, an improved set of parameters is proposed for alkane molecules that corrects this systematic deviation and accurately predicts solvation free energies in hydrophobic media, while simultaneously providing a very good description of pure liquid densities. The model is then extended to alkenes and alkynes, again yielding very accurate predictions of solvation free energies and densities for these classes of compounds. For alkynes in particular, this work represents the first attempt at a systematic parameterization using the united-atom approach. Averaging over all 95 solute/solvent pairs tested, the mean signed deviation from experimental data is very close to zero, indicating no systematic error in the predictions. The fact that predictions are robust even for relatively large molecules suggests that the new model may be applicable to solvation of non-polar macromolecules without accumulation of errors. The root mean squared deviation of the simulations is only 0.6 kJ/mol, which is lower than the estimated uncertainty in the experimental measurements. This excellent performance constitutes a solid basis on which a more general model can be parameterized to describe solvation in both polar and non-polar environments. © 2016 Wiley Periodicals, Inc.

  7. United States History Simulations, 1925-1964: The Scopes Trial, Dropping the Atomic Bomb on Japan, United States versus Alger Hiss, Mississippi--Summer 1964. ETC Simulations Number Three.

    Science.gov (United States)

    Hostrop, Richard W.

    This booklet provides instructions for simulation and role play of historical events in U.S. history from 1925-1964. Included for student research and participation are: the Scopes trial in Tennessee involving supporters of the teaching of evolution in the schools and of creationism; the decision to drop the atomic bomb on Japan ending World War…

  8. Atomic Force Microscopy and Real Atomic Resolution. Simple Computer Simulations

    NARCIS (Netherlands)

    Koutsos, V.; Manias, E.; Brinke, G. ten; Hadziioannou, G.

    1994-01-01

    Using a simple computer simulation for AFM imaging in the contact mode, pictures with true and false atomic resolution are demonstrated. The surface probed consists of two f.c.c. (111) planes and an atomic vacancy is introduced in the upper layer. Changing the size of the effective tip and its

  9. Simulations of atomic-scale sliding friction

    DEFF Research Database (Denmark)

    Sørensen, Mads Reinholdt; Jacobsen, Karsten Wedel; Stoltze, Per

    1996-01-01

    Simulation studies of atomic-scale sliding friction have been performed for a number of tip-surface and surface-surface contacts consisting of copper atoms. Both geometrically very simple tip-surface structures and more realistic interface necks formed by simulated annealing have been studied. Ki...

  10. NIC atomic operation unit with caching and bandwidth mitigation

    Science.gov (United States)

    Hemmert, Karl Scott; Underwood, Keith D.; Levenhagen, Michael J.

    2016-03-01

    A network interface controller atomic operation unit and a network interface control method comprising, in an atomic operation unit of a network interface controller, using a write-through cache and employing a rate-limiting functional unit.

  11. CHARMM36 united atom chain model for lipids and surfactants.

    Science.gov (United States)

    Lee, Sarah; Tran, Alan; Allsopp, Matthew; Lim, Joseph B; Hénin, Jérôme; Klauda, Jeffery B

    2014-01-16

    Molecular simulations of lipids and surfactants require accurate parameters to reproduce and predict experimental properties. Previously, a united atom (UA) chain model was developed for the CHARMM27/27r lipids (Hénin, J., et al. J. Phys. Chem. B. 2008, 112, 7008-7015) but suffers from the flaw that bilayer simulations using the model require an imposed surface area ensemble, which limits its use to pure bilayer systems. A UA-chain model has been developed based on the CHARMM36 (C36) all-atom lipid parameters, termed C36-UA, and agreed well with bulk, lipid membrane, and micelle formation of a surfactant. Molecular dynamics (MD) simulations of alkanes (heptane and pentadecane) were used to test the validity of C36-UA on density, heat of vaporization, and liquid self-diffusion constants. Then, simulations using C36-UA resulted in accurate properties (surface area per lipid, X-ray and neutron form factors, and chain order parameters) of various saturated- and unsaturated-chain bilayers. When mixed with the all-atom cholesterol model and tested with a series of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)/cholesterol mixtures, the C36-UA model performed well. Simulations of self-assembly of a surfactant (dodecylphosphocholine, DPC) using C36-UA suggest an aggregation number of 53 ± 11 DPC molecules at 0.45 M of DPC, which agrees well with experimental estimates. Therefore, the C36-UA force field offers a useful alternative to the all-atom C36 lipid force field by requiring less computational cost while still maintaining the same level of accuracy, which may prove useful for large systems with proteins.

  12. Four-component united-atom model of bitumen

    DEFF Research Database (Denmark)

    Hansen, Jesper Schmidt; Lemarchand, Claire; Nielsen, Erik

    2013-01-01

    We propose a four-component united-atom molecular model of bitumen. The model includes realistic chemical constituents and introduces a coarse graining level that suppresses the highest frequency modes. Molecular dynamics simulations of the model are carried out using graphic-processor-units based...... software in time spans in order of microseconds, which enables the study of slow relaxation processes characterizing bitumen. This paper also presents results of the model dynamics as expressed through the mean-square displacement, the stress autocorrelation function, and rotational relaxation...... the stress autocorrelation function, the shear viscosity and shear modulus are evaluated, showing a viscous response at frequencies below 100 MHz. The model predictions of viscosity and diffusivities are compared to experimental data, giving reasonable agreement. The model shows that the asphaltene, resin...

  13. The First Drinking Simulator Unit

    Directory of Open Access Journals (Sweden)

    Saied Mostafa Moazzami

    2014-03-01

    Full Text Available Introduction: Current Thermal cycling units fail to simulate the drinking behaviors, and oral balancing temperature. They cannot also simulate other oral conditions such as drink coloring, and chemicals like tea, coffee, carbonated and noncarbonated, citrus juices as well as alcoholic and nonalcoholic drinks and also saliva and milk itself. The main objective of this study is to introduce the designing and manufacturing the first Drinking Simulator Unit (DSU that reproduces the thermal, color and chemicalcycling as well as the drinking behavior and oral temperature in lab conditions uniquely. Methods: The invented system generally has two parts: the hardware and the software parts. The hardware consists of the mechanical and electronic parts. The software part is responsible for controlling the heating and cooling systems, electric valves, the pumps, and automatic filling systems of tanks as well as the sensors of the machine. Results: DSU is the first unit can reproduce the thermal, color and chemical cycling as well as the drinking behavior and oral temperature in lab conditions. Different kinds of colored and acidic drinks and also other chemical materials such as bleaching substances as well as detergents and antiseptics used for dentistry, industrial and medical purposes can be tested by DSU. DSU has also to be considered as an appliance performing in-vitro researches on dental structures. Conclusion: The invented system can greatly improve and validate the results of such researches.  

  14. Atomic simulations for surface-initiated melting of Nb(111)

    Institute of Scientific and Technical Information of China (English)

    YANG Xi-yuan; WU Dan

    2009-01-01

    A modified analytic embedded-atom model(MAEAM) was applied to investigate surface premelting and melting behaviors of Nb(111) plane by molecular dynamics(MD) simulations. First the relaxation of surface interface space at 300 K was studied. Then a number N of the disordered atoms per unit area was determined at the given temperatures to investigate the surface premelting and melting evolution. The obtained results indicated that the premelting phenomena occurred at about 1 100 K and a liquid-like layer emerged on (111) plane simultaneously. As temperature increased up to 2 200 K, the number N grew logarithmically for short-range metallic interactions. Upon 2 350 K surface melting generated originally and the number N increased exponentially with the incremental temperature.

  15. Stochastic electrodynamics simulations for collective atom response in optical cavities

    Science.gov (United States)

    Lee, Mark D.; Jenkins, Stewart D.; Bronstein, Yael; Ruostekoski, Janne

    2017-08-01

    We study the collective optical response of an atomic ensemble confined within a single-mode optical cavity by stochastic electrodynamics simulations that include the effects of atomic position correlations, internal level structure, and spatial variations in cavity coupling strength and atom density. In the limit of low light intensity, the simulations exactly reproduce the full quantum field-theoretical description for cold stationary atoms and at higher light intensities we introduce semiclassical approximations to atomic saturation that we compare with the exact solution in the case of two atoms. We find that collective subradiant modes of the atoms, with very narrow linewidths, can be coupled to the cavity field by spatial variation of the atomic transition frequency and resolved at low intensities, and show that they can be specifically driven by tailored transverse pumping beams. We show that the cavity optical response, in particular both the subradiant mode profile and the resonance shift of the cavity mode, can be used as a diagnostic tool for the position correlations of the atoms and hence the atomic quantum many-body phase. The quantum effects are found to be most prominent close to the narrow subradiant mode resonances at high light intensities. Although an optical cavity can generally strongly enhance quantum fluctuations via light confinement, we show that the semiclassical approximation to the stochastic electrodynamics model provides at least a qualitative agreement with the exact optical response outside the subradiant mode resonances even in the presence of significant saturation of the atoms.

  16. A heated vapor cell unit for DAVLL in atomic rubidium

    OpenAIRE

    McCarron, Daniel J.; Hughes, Ifan G.; Tierney, Patrick; Cornish, Simon L

    2007-01-01

    The design and performance of a compact heated vapor cell unit for realizing a dichroic atomic vapor laser lock (DAVLL) for the D2 transitions in atomic rubidium is described. A 5 cm-long vapor cell is placed in a double-solenoid arrangement to produce the required magnetic field; the heat from the solenoid is used to increase the vapor pressure and correspondingly the DAVLL signal. We have characterized experimentally the dependence of important features of the DAVLL signal on magnetic field...

  17. Spreadsheet-Based Program for Simulating Atomic Emission Spectra

    Science.gov (United States)

    Flannigan, David J.

    2014-01-01

    A simple Excel spreadsheet-based program for simulating atomic emission spectra from the properties of neutral atoms (e.g., energies and statistical weights of the electronic states, electronic partition functions, transition probabilities, etc.) is described. The contents of the spreadsheet (i.e., input parameters, formulas for calculating…

  18. ATOMIC-FORCE MICROSCOPY AND REAL ATOMIC-RESOLUTION - SIMPLE COMPUTER-SIMULATIONS

    NARCIS (Netherlands)

    KOUTSOS, [No Value; MANIAS, E; TENBRINKE, G; HADZIIOANNOU, G

    1994-01-01

    Using a simple computer simulation for AFM imaging in the contact mode, pictures with true and false atomic resolution are demonstrated. The surface probed consists of two f.c.c. (111) planes and an atomic vacancy is introduced in the upper layer. Changing the size of the effective tip and its regis

  19. Nanoscale magnetic atom chips for quantum simulation

    NARCIS (Netherlands)

    La Rooij, A.L.

    2017-01-01

    This thesis consists of five chapters that describe the different things that I have done in the past few years which all concern my effort to create lattices of ultracold gaseous atoms at length-scales of approximately 100 nano-meters (a millionth of a decimeter, or 200 times smaller than the diame

  20. A heated vapor cell unit for dichroic atomic vapor laser lock in atomic rubidium.

    Science.gov (United States)

    McCarron, Daniel J; Hughes, Ifan G; Tierney, Patrick; Cornish, Simon L

    2007-09-01

    The design and performance of a compact heated vapor cell unit for realizing a dichroic atomic vapor laser lock (DAVLL) for the D(2) transitions in atomic rubidium is described. A 5 cm long vapor cell is placed in a double-solenoid arrangement to produce the required magnetic field; the heat from the solenoid is used to increase the vapor pressure and correspondingly the DAVLL signal. We have characterized experimentally the dependence of important features of the DAVLL signal on magnetic field and cell temperature. For the weaker transitions both the amplitude and gradient of the signal are increased by an order of magnitude.

  1. Ultracold atoms for simulation of many body quantum systems

    Science.gov (United States)

    Hutchinson, David A. W.

    2017-01-01

    Feynman famously proposed simulating quantum physics using other, better controlled, quantum systems. This vision is now a reality within the realm of ultracold atomic physics. We discuss how these systems can be used to simulate many body physics, concentrating the Berezinskii-Kosterlitz-Thouless transition in 2D physics and the role of disorder.

  2. Simulation of Rutherford backscattering spectrometry from arbitrary atom structures

    Science.gov (United States)

    Zhang, S.; Nordlund, K.; Djurabekova, F.; Zhang, Y.; Velisa, G.; Wang, T. S.

    2016-10-01

    Rutherford backscattering spectrometry in a channeling direction (RBS/C) is a powerful tool for analysis of the fraction of atoms displaced from their lattice positions. However, it is in many cases not straightforward to analyze what is the actual defect structure underlying the RBS/C signal. To reveal insights of RBS/C signals from arbitrarily complex defective atomic structures, we develop here a method for simulating the RBS/C spectrum from a set of arbitrary read-in atom coordinates (obtained, e.g., from molecular dynamics simulations). We apply the developed method to simulate the RBS/C signals from Ni crystal structures containing randomly displaced atoms, Frenkel point defects, and extended defects, respectively. The RBS/C simulations show that, even for the same number of atoms in defects, the RBS/C signal is much stronger for the extended defects. Comparison with experimental results shows that the disorder profile obtained from RBS/C signals in ion-irradiated Ni is due to a small fraction of extended defects rather than a large number of individual random atoms.

  3. Classical simulation of atomic beam focusing and deposition for atom lithography

    Institute of Scientific and Technical Information of China (English)

    Xianzhong Chen(陈献忠); Hanmin Yao(姚汉民); Xunan Chen(陈旭南)

    2004-01-01

    We start from the intensity distribution of a standing wave (SW) laser field and deduce the classical equation of atomic motion. The image distortion is analyzed using transfer function approach. Atomic flux density distribution as a function of propagation distance is calculated based on Monte-Carlo scheme and trajectory tracing method. Simulation results have shown that source imperfection, especially beam spread, plays an important role in broadening the feature width, and the focus depth of atom lens for real atomic source is longer than that for perfect source. The ideal focal plane can be easily determined by the variation of atomic density at the minimal potential of the laser field as a function of traveling distance.

  4. Quantum Simulation of a 2D Quasicrystal with Cold Atoms

    Directory of Open Access Journals (Sweden)

    Nicolas Macé

    2016-09-01

    Full Text Available We describe a way to obtain a two-dimensional quasiperiodic tiling with eight-fold symmetry using cold atoms. One can obtain a series of such optical tilings, related by scale transformations, for a series of specific values of the chemical potential of the atoms. A theoretical model for the optical system is described and compared with that of the well-known cut-and-project method for the Ammann–Beenker tiling. The relation between the two tilings is discussed. This type of cold atom structure should allow the simulation of several important lattice models for interacting quantum particles and spins in quasicrystals.

  5. Atomic scale simulation of carbon nanotube nucleation from hydrocarbon precursors.

    Science.gov (United States)

    Khalilov, Umedjon; Bogaerts, Annemie; Neyts, Erik C

    2015-12-22

    Atomic scale simulations of the nucleation and growth of carbon nanotubes is essential for understanding their growth mechanism. In spite of over twenty years of simulation efforts in this area, limited progress has so far been made on addressing the role of the hydrocarbon growth precursor. Here we report on atomic scale simulations of cap nucleation of single-walled carbon nanotubes from hydrocarbon precursors. The presented mechanism emphasizes the important role of hydrogen in the nucleation process, and is discussed in relation to previously presented mechanisms. In particular, the role of hydrogen in the appearance of unstable carbon structures during in situ experimental observations as well as the initial stage of multi-walled carbon nanotube growth is discussed. The results are in good agreement with available experimental and quantum-mechanical results, and provide a basic understanding of the incubation and nucleation stages of hydrocarbon-based CNT growth at the atomic level.

  6. Quantum simulations with ultracold atoms in optical lattices.

    Science.gov (United States)

    Gross, Christian; Bloch, Immanuel

    2017-09-08

    Quantum simulation, a subdiscipline of quantum computation, can provide valuable insight into difficult quantum problems in physics or chemistry. Ultracold atoms in optical lattices represent an ideal platform for simulations of quantum many-body problems. Within this setting, quantum gas microscopes enable single atom observation and manipulation in large samples. Ultracold atom-based quantum simulators have already been used to probe quantum magnetism, to realize and detect topological quantum matter, and to study quantum systems with controlled long-range interactions. Experiments on many-body systems out of equilibrium have also provided results in regimes unavailable to the most advanced supercomputers. We review recent experimental progress in this field and comment on future directions. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  7. Molecular dynamics simulation of amplitude modulation atomic force microscopy.

    Science.gov (United States)

    Hu, Xiaoli; Egberts, Philip; Dong, Yalin; Martini, Ashlie

    2015-06-12

    Molecular dynamics (MD) simulations were used to model amplitude modulation atomic force microscopy (AM-AFM). In this novel simulation, the model AFM tip responds to both tip-substrate interactions and to a sinusoidal excitation signal. The amplitude and phase shift of the tip oscillation observed in the simulation and their variation with tip-sample distance were found to be consistent with previously reported trends from experiments and theory. These simulation results were also fit to an expression enabling estimation of the energy dissipation, which was found to be smaller than that in a corresponding experiment. The difference was analyzed in terms of the effects of tip size and substrate thickness. Development of this model is the first step toward using MD to gain insight into the atomic-scale phenomena that occur during an AM-AFM measurement.

  8. NQR detection of explosive simulants using RF atomic magnetometers

    Science.gov (United States)

    Monti, Mark C.; Alexson, Dimitri A.; Okamitsu, Jeffrey K.

    2016-05-01

    Nuclear Quadrupole Resonance (NQR) is a highly selective spectroscopic method that can be used to detect and identify a number of chemicals of interest to the defense, national security, and law enforcement community. In the past, there have been several documented attempts to utilize NQR to detect nitrogen bearing explosives using induction sensors to detect the NQR RF signatures. We present here our work on the NQR detection of explosive simulants using optically pumped RF atomic magnetometers. RF atomic magnetometers can provide an order of magnitude (or more) improvement in sensitivity versus induction sensors and can enable mitigation of RF interference, which has classically has been a problem for conventional NQR using induction sensors. We present the theory of operation of optically pumped RF atomic magnetometers along with the result of laboratory work on the detection of explosive simulant material. An outline of ongoing work will also be presented along with a path for a fieldable detection system.

  9. Estimation of atomic hydrophobicities using molecular dynamics simulation of peptides

    Science.gov (United States)

    Held, Marie; Nicolau, Dan V.

    2007-12-01

    The hydrophobic force is one of the main driving forces in protein folding and binding. However, its nature is not yet well understood and consequently there are more than 80 different scales published trying to quantify it. Most of the hydrophobicity scales are amino acid-based, but the interaction between the molecular surface of the proteins (and DNA) and surfaces they are immobilized on, e.g., on biomedical micro/nanodevices, occurs on fractions of, rather than whole amino acids. This fragmented structure of the biomolecular surface requires the derivation of atom-level hydrophobicity. Most attempts for the evaluation of atomic hydrophobicities are derived from amino acid-based values, which ignore dynamic and steric factors. This contribution reports on the Molecular Dynamics simulations that aim to overcome this simplification. The calculations examine various tripeptides in an aqueous solution and the analysis focuses on the distance of the nearest water molecules to the individual atoms in the peptides. Different environments result in a variation of average distances for similar atoms in different tripeptides. Comparison with the atomic hydrophobicities derived from the amino acid-based hydrophobicity obtained from peptide partition in water-octanol (Dgoct) and transport through the membrane interface (Dgwif) shows a similar trend to the calculated distances. The variations are likely due to the steric differences of similar types of atoms in different geometric contexts. Therefore, Molecular Dynamics simulations proved convenient for the evaluation of atomic hydrophobicities and open new research avenues. The atomic hydrophobicities can be used to design surfaces that mimic the biomolecular surfaces and therefore elicit an expected biomolecular activity from the immobilized biomolecules.

  10. High Fidelity Simulation of Primary Atomization in Diesel Engine Sprays

    Science.gov (United States)

    Ivey, Christopher; Bravo, Luis; Kim, Dokyun

    2014-11-01

    A high-fidelity numerical simulation of jet breakup and spray formation from a complex diesel fuel injector at ambient conditions has been performed. A full understanding of the primary atomization process in fuel injection of diesel has not been achieved for several reasons including the difficulties accessing the optically dense region. Due to the recent advances in numerical methods and computing resources, high fidelity simulations of atomizing flows are becoming available to provide new insights of the process. In the present study, an unstructured un-split Volume-of-Fluid (VoF) method coupled to a stochastic Lagrangian spray model is employed to simulate the atomization process. A common rail fuel injector is simulated by using a nozzle geometry available through the Engine Combustion Network. The working conditions correspond to a single orifice (90 μm) JP-8 fueled injector operating at an injection pressure of 90 bar, ambient condition at 29 bar, 300 K filled with 100% nitrogen with Rel = 16,071, Wel = 75,334 setting the spray in the full atomization mode. The experimental dataset from Army Research Lab is used for validation in terms of spray global parameters and local droplet distributions. The quantitative comparison will be presented and discussed. Supported by Oak Ridge Associated Universities and the Army Research Laboratory.

  11. The Atomic Simulation Environment - A Python library for working with atoms

    DEFF Research Database (Denmark)

    Larsen, Ask Hjorth; Mortensen, Jens Jørgen; Blomqvist, Jakob

    2017-01-01

    The Atomic Simulation Environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simula- tions. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library mak...

  12. The EAGLE simulations: atomic hydrogen associated with galaxies

    CERN Document Server

    Crain, Robert A; Lagos, Claudia del P; Rahmati, Alireza; Schaye, Joop; McCarthy, Ian G; Marasco, Antonino; Bower, Richard G; Schaller, Matthieu; Theuns, Tom; van der Hulst, Thijs

    2016-01-01

    We examine the properties of atomic hydrogen (HI) associated with galaxies in the EAGLE simulations of galaxy formation. EAGLE's feedback parameters were calibrated to reproduce the stellar mass function and galaxy sizes at $z=0.1$, and we assess whether this calibration also yields realistic HI properties. We estimate the self-shielding density with a fitting function calibrated using radiation transport simulations, and correct for molecular hydrogen with empirical or theoretical relations. The `standard-resolution' simulations systematically underestimate HI column densities, leading to an HI deficiency in low-mass ($M_\\star < 10^{10}M_\\odot$) galaxies and poor reproduction of the observed HI mass function. These shortcomings are largely absent from EAGLE simulations featuring a factor of 8 (2) better mass (spatial) resolution, within which the HI mass of galaxies evolves more mildly from $z=1$ to $0$ than in the standard-resolution simulations. The largest-volume simulation reproduces the observed clus...

  13. Simulation training for hyperacute stroke unit nurses.

    Science.gov (United States)

    Roots, Angela; Thomas, Libby; Jaye, Peter; Birns, Jonathan

    National clinical guidelines have emphasized the need to identify acute stroke as a clinical priority for early assessment and treatment of patients on hyperacute stroke units. Nurses working on hyperacute stroke units require stroke specialist training and development of competencies in dealing with neurological emergencies and working in multidisciplinary teams. Educational theory suggests that experiential learning with colleagues in real-life settings may provide transferable results to the workplace with improved performance. Simulation training has been shown to deliver situational training without compromising patient safety and has been shown to improve both technical and non-technical skills (McGaghie et al, 2010). This article describes the role that simulation training may play for nurses working on hyperacute stroke units explaining the modalities available and the educational potential. The article also outlines the development of a pilot course involving directly relevant clinical scenarios for hyperacute stroke unit patient care and assesses the benefits of simulation training for hyperacute stroke unit nurses, in terms of clinical performance and non-clinical abilities including leadership and communication.

  14. Nonlinear simulation of free surfaces and atomization in pressure swirl atomizers

    Science.gov (United States)

    Park, Hongbok; Heister, Stephen D.

    2006-05-01

    A fully nonlinear boundary element method (BEM) model has been developed to simulate the pressure swirl or simplex atomizer. The free surface inside the vortex chamber and within the hollow-cone/primary atomization zone is simulated with a fourth order scheme thereby permitting investigation of highly distorted surfaces up to the point where atomization occurs. For the axisymmetric calculations, annular rings of fluid are pinched from the main liquid domain. Swirling flow is simulated via a superposition of a potential vortex with the base axial flow emanating from the nozzle in a BEM formulation. Results show good comparison to film thicknesses from test data as well as from linear one-dimensional theory. Parametric studies are conducted to assess the influence of injector geometry and flow characteristics on film thickness and spray angle produced by the atomizer. Limited results are also provided to compare droplet sizes with experimental data. In this regard, the linear stability analysis of Ponstein is used to predict the number of droplets created from each ring of fluid shed by the axisymmetric calculation.

  15. Simulated mixed absorbers and effective atomic numbers for attenuation

    Indian Academy of Sciences (India)

    K Karunakaran Nair; N Ramachandran; K K Abdullah; K M Varier

    2006-09-01

    The total -ray interaction crosss-sections on mixed absorbers were determined at 662 keV with a view to study the effective atomic numbers for -ray absorption under narrow beam good geometry set-up. The measurements were taken for the combination of metallic absorbers like aluminium, copper, lead and mercury and also for the simulated absorbers by rotating the targets. ORTEC HPGe and NaI(Tl) detectors were used for detection of -rays.The experimental results compare favourably with theoretical values derived from XCOM package and suggest the usefulness of the concept of effective atomic numbers and the utility of the rotating absorbers technique.

  16. pH in atomic scale simulations of electrochemical interfaces

    DEFF Research Database (Denmark)

    Rossmeisl, Jan; Chan, Karen; Ahmed, Rizwan

    2013-01-01

    Electrochemical reaction rates can strongly depend on pH, and there is increasing interest in electrocatalysis in alkaline solution. To date, no method has been devised to address pH in atomic scale simulations. We present a simple method to determine the atomic structure of the metal......|solution interface at a given pH and electrode potential. Using Pt(111)|water as an example, we show the effect of pH on the interfacial structure, and discuss its impact on reaction energies and barriers. This method paves the way for ab initio studies of pH effects on the structure and electrocatalytic activity...

  17. High Fidelity Simulation of Atomization in Diesel Engine Sprays

    Science.gov (United States)

    2015-09-01

    sprays, volume of fluids, CFD, diesel 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT UU 18. NUMBER OF PAGES 16 19a. NAME OF...Reynolds number, Re = 3000. In a related study, Desjardins con- ducted detailed numerical simulations ( DNS ) of primary atomization for several values...model development. Note that, as with most other DNS studies, no quantitative comparison to experimental data is typically provided. The need to

  18. The atomic simulation environment—a Python library for working with atoms

    Science.gov (United States)

    Hjorth Larsen, Ask; Jørgen Mortensen, Jens; Blomqvist, Jakob; Castelli, Ivano E.; Christensen, Rune; Dułak, Marcin; Friis, Jesper; Groves, Michael N.; Hammer, Bjørk; Hargus, Cory; Hermes, Eric D.; Jennings, Paul C.; Bjerre Jensen, Peter; Kermode, James; Kitchin, John R.; Leonhard Kolsbjerg, Esben; Kubal, Joseph; Kaasbjerg, Kristen; Lysgaard, Steen; Bergmann Maronsson, Jón; Maxson, Tristan; Olsen, Thomas; Pastewka, Lars; Peterson, Andrew; Rostgaard, Carsten; Schiøtz, Jakob; Schütt, Ole; Strange, Mikkel; Thygesen, Kristian S.; Vegge, Tejs; Vilhelmsen, Lasse; Walter, Michael; Zeng, Zhenhua; Jacobsen, Karsten W.

    2017-07-01

    The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple ‘for-loop’ construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

  19. Magnetohydrodynamics simulations on graphics processing units

    CERN Document Server

    Wong, Hon-Cheng; Feng, Xueshang; Tang, Zesheng

    2009-01-01

    Magnetohydrodynamics (MHD) simulations based on the ideal MHD equations have become a powerful tool for modeling phenomena in a wide range of applications including laboratory, astrophysical, and space plasmas. In general, high-resolution methods for solving the ideal MHD equations are computationally expensive and Beowulf clusters or even supercomputers are often used to run the codes that implemented these methods. With the advent of the Compute Unified Device Architecture (CUDA), modern graphics processing units (GPUs) provide an alternative approach to parallel computing for scientific simulations. In this paper we present, to the authors' knowledge, the first implementation to accelerate computation of MHD simulations on GPUs. Numerical tests have been performed to validate the correctness of our GPU MHD code. Performance measurements show that our GPU-based implementation achieves speedups of 2 (1D problem with 2048 grids), 106 (2D problem with 1024^2 grids), and 43 (3D problem with 128^3 grids), respec...

  20. Kinetic Simulation and Energetic Neutral Atom Imaging of the Magnetosphere

    Science.gov (United States)

    Fok, Mei-Ching H.

    2011-01-01

    Advanced simulation tools and measurement techniques have been developed to study the dynamic magnetosphere and its response to drivers in the solar wind. The Comprehensive Ring Current Model (CRCM) is a kinetic code that solves the 3D distribution in space, energy and pitch-angle information of energetic ions and electrons. Energetic Neutral Atom (ENA) imagers have been carried in past and current satellite missions. Global morphology of energetic ions were revealed by the observed ENA images. We have combined simulation and ENA analysis techniques to study the development of ring current ions during magnetic storms and substorms. We identify the timing and location of particle injection and loss. We examine the evolution of ion energy and pitch-angle distribution during different phases of a storm. In this talk we will discuss the findings from our ring current studies and how our simulation and ENA analysis tools can be applied to the upcoming TRIO-CINAMA mission.

  1. Four-component united-atom model of bitumen

    CERN Document Server

    Hansen, Jesper S; Nielsen, Erik; Dyre, Jeppe C; Schrøder, Thomas B

    2013-01-01

    We propose a four-component molecular model of bitumen. The model includes realistic chemical constituents and introduces a coarse-graining level that suppresses the highest frequency modes. Molecular dynamics simulations of the model are being carried out using Graphic-Processor-Units based software in time spans in order of microseconds, and this enables the study of slow relaxation processes characterizing bitumen. This paper focuses on the high-temperature dynamics as expressed through the mean-square displacement, the stress autocorrelation function, and rotational relaxation. The diffusivity of the individual molecules changes little as a function of temperature and reveals distinct dynamical time scales as a result of the different constituents in the system. Different time scales are also observed for the rotational relaxation. The stress autocorrelation function features a slow non-exponential decay for all temperatures studied. From the stress autocorrelation function, the shear viscosity and shear ...

  2. Comparative simulations of Fresnel holography methods for atomic waveguides

    CERN Document Server

    Henderson, Victoria A; Riis, Erling; Arnold, Aidan S

    2016-01-01

    We have simulated the optical properties of micro-fabricated Fresnel zone plates (FZPs) as an alternative to spatial light modulators (SLMs) for producing non-trivial light potentials to trap atoms within a lensless Fresnel arrangement. We show that binary (1-bit) FZPs with wavelength (1 \\mu m) spatial resolution consistently outperform kinoforms of spatial and phase resolution comparable to commercial SLMs in root mean square error comparisons, with FZP kinoforms demonstrating increasing improvement for complex target intensity distributions. Moreover, as sub-wavelength resolution microfabrication is possible, FZPs provide an exciting possibility for the creation of static cold-atom trapping potentials useful to atomtronics, interferometry, and the study of fundamental physics.

  3. Learning scheme to predict atomic forces and accelerate materials simulations

    Science.gov (United States)

    Botu, V.; Ramprasad, R.

    2015-09-01

    The behavior of an atom in a molecule, liquid, or solid is governed by the force it experiences. If the dependence of this vectorial force on the atomic chemical environment can be learned efficiently with high fidelity from benchmark reference results—using "big-data" techniques, i.e., without resorting to actual functional forms—then this capability can be harnessed to enormously speed up in silico materials simulations. The present contribution provides several examples of how such a force field for Al can be used to go far beyond the length-scale and time-scale regimes presently accessible using quantum-mechanical methods. It is argued that pathways are available to systematically and continuously improve the predictive capability of such a learned force field in an adaptive manner, and that this concept can be generalized to include multiple elements.

  4. EON: software for long time simulations of atomic scale systems

    Science.gov (United States)

    Chill, Samuel T.; Welborn, Matthew; Terrell, Rye; Zhang, Liang; Berthet, Jean-Claude; Pedersen, Andreas; Jónsson, Hannes; Henkelman, Graeme

    2014-07-01

    The EON software is designed for simulations of the state-to-state evolution of atomic scale systems over timescales greatly exceeding that of direct classical dynamics. States are defined as collections of atomic configurations from which a minimization of the potential energy gives the same inherent structure. The time evolution is assumed to be governed by rare events, where transitions between states are uncorrelated and infrequent compared with the timescale of atomic vibrations. Several methods for calculating the state-to-state evolution have been implemented in EON, including parallel replica dynamics, hyperdynamics and adaptive kinetic Monte Carlo. Global optimization methods, including simulated annealing, basin hopping and minima hopping are also implemented. The software has a client/server architecture where the computationally intensive evaluations of the interatomic interactions are calculated on the client-side and the state-to-state evolution is managed by the server. The client supports optimization for different computer architectures to maximize computational efficiency. The server is written in Python so that developers have access to the high-level functionality without delving into the computationally intensive components. Communication between the server and clients is abstracted so that calculations can be deployed on a single machine, clusters using a queuing system, large parallel computers using a message passing interface, or within a distributed computing environment. A generic interface to the evaluation of the interatomic interactions is defined so that empirical potentials, such as in LAMMPS, and density functional theory as implemented in VASP and GPAW can be used interchangeably. Examples are given to demonstrate the range of systems that can be modeled, including surface diffusion and island ripening of adsorbed atoms on metal surfaces, molecular diffusion on the surface of ice and global structural optimization of nanoparticles.

  5. Computer simulation of electronic excitation in atomic collision cascades

    Energy Technology Data Exchange (ETDEWEB)

    Duvenbeck, A.

    2007-04-05

    The impact of an keV atomic particle onto a solid surface initiates a complex sequence of collisions among target atoms in a near-surface region. The temporal and spatial evolution of this atomic collision cascade leads to the emission of particles from the surface - a process usually called sputtering. In modern surface analysis the so called SIMS technology uses the flux of sputtered particles as a source of information on the microscopical stoichiometric structure in the proximity of the bombarded surface spots. By laterally varying the bombarding spot on the surface, the entire target can be scanned and chemically analyzed. However, the particle detection, which bases upon deflection in electric fields, is limited to those species that leave the surface in an ionized state. Due to the fact that the ionized fraction of the total flux of sputtered atoms often only amounts to a few percent or even less, the detection is often hampered by rather low signals. Moreover, it is well known, that the ionization probability of emitted particles does not only depend on the elementary species, but also on the local environment from which a particle leaves the surface. Therefore, the measured signals for different sputtered species do not necessarily represent the stoichiometric composition of the sample. In the literature, this phenomenon is known as the Matrix Effect in SIMS. In order to circumvent this principal shortcoming of SIMS, the present thesis develops an alternative computer simulation concept, which treats the electronic energy losses of all moving atoms as excitation sources feeding energy into the electronic sub-system of the solid. The particle kinetics determining the excitation sources are delivered by classical molecular dynamics. The excitation energy calculations are combined with a diffusive transport model to describe the spread of excitation energy from the initial point of generation. Calculation results yield a space- and time-resolved excitation

  6. Multimillion to billion atom simulations of nanosystems under extreme conditions

    Science.gov (United States)

    Vashishta, P.

    2008-12-01

    Advanced materials and devices with nanometer grain/feature sizes are being developed to achieve higher strength and toughness in ceramic materials and greater speeds in electronic devices. Below 100 nm, however, continuum description of materials and devices must be supplemented by atomistic descriptions. Current state of the art atomistic simulations involve 10 million - 1 billion atoms. We investigate initiation, growth and healing of wing cracks in confined silica glass by multimillion atom molecular dynamics (MD) simulations. Under dynamic compression, frictional sliding of pre-crack surfaces nucleates nanovoids, which evolve into nanocrack columns at the pre-crack tip. Nanocrack columns merge to form a wing crack, which grows via coalescence with nanovoids in the direction of maximum compression. Lateral confinement arrests the growth and partially heals the wing crack. Growth and arrest of the wing crack occur repeatedly, as observed in dynamic compression experiments on brittle solids under lateral confinement. MD simulation of hypervelocity projectile impact in aluminum nitride and alumina has also been studied. The simulations reveal strong interplay between shock- induced structural phase transformation, plastic deformation and brittle cracks. The shock wave splits into an elastic precursor and a wurtzite-to-rocksalt structural transformation wave. When the elastic wave reflected from the boundary of the sample interacts with the transformation wave front, nanocavities are generated along the penetration path of the projectile and dislocations in adjacent regions. The nanocavities coalesce to form mode I brittle cracks while dislocations generate kink bands that give rise to mode II cracks. These simulations provide a microscopic view of defects associated with simultaneous tensile and shear cracking at the structural phase transformation boundary due to shock impact in high-strength ceramics. Initiation of chemical reactions at shock fronts prior to

  7. Quantum simulation of disordered systems with cold atoms

    Science.gov (United States)

    Garreau, Jean-Claude

    2017-01-01

    This paper reviews the physics of quantum disorder in relation with a series of experiments using laser-cooled atoms exposed to "kicks" of a standing wave, realizing a paradigmatic model of quantum chaos, the kicked rotor. This dynamical system can be mapped onto a tight-binding Hamiltonian with pseudo-disorder, formally equivalent to the Anderson model of quantum disorder, with quantum chaos playing the role of disorder. This provides a very good quantum simulator for the Anderson physics. xml:lang="fr"

  8. The EAGLE simulations: atomic hydrogen associated with galaxies

    Science.gov (United States)

    Crain, Robert A.; Bahé, Yannick M.; Lagos, Claudia del P.; Rahmati, Alireza; Schaye, Joop; McCarthy, Ian G.; Marasco, Antonino; Bower, Richard G.; Schaller, Matthieu; Theuns, Tom; van der Hulst, Thijs

    2017-02-01

    We examine the properties of atomic hydrogen (H I) associated with galaxies in the Evolution and Assembly of GaLaxies and their Environments (EAGLE) simulations of galaxy formation. EAGLE's feedback parameters were calibrated to reproduce the stellar mass function and galaxy sizes at z = 0.1, and we assess whether this calibration also yields realistic H I properties. We estimate the self-shielding density with a fitting function calibrated using radiation transport simulations, and correct for molecular hydrogen with empirical or theoretical relations. The `standard-resolution' simulations systematically underestimate H I column densities, leading to an H I deficiency in low-mass (M⋆ standard-resolution simulations. The largest volume simulation reproduces the observed clustering of H I systems, and its dependence on H I richness. At fixed M⋆, galaxies acquire more H I in simulations with stronger feedback, as they become associated with more massive haloes and higher infall rates. They acquire less H I in simulations with a greater star formation efficiency, since the star formation and feedback necessary to balance the infall rate is produced by smaller gas reservoirs. The simulations indicate that the H I of present-day galaxies was acquired primarily by the smooth accretion of ionized, intergalactic gas at z ≃ 1, which later self-shields, and that only a small fraction is contributed by the reincorporation of gas previously heated strongly by feedback. H I reservoirs are highly dynamic: over 40 per cent of H I associated with z = 0.1 galaxies is converted to stars or ejected by z = 0.

  9. Derivation of Distributed Models of Atomic Polarizability for Molecular Simulations.

    Science.gov (United States)

    Soteras, Ignacio; Curutchet, Carles; Bidon-Chanal, Axel; Dehez, François; Ángyán, János G; Orozco, Modesto; Chipot, Christophe; Luque, F Javier

    2007-11-01

    The main thrust of this investigation is the development of models of distributed atomic polarizabilities for the treatment of induction effects in molecular mechanics simulations. The models are obtained within the framework of the induced dipole theory by fitting the induction energies computed via a fast but accurate MP2/Sadlej-adjusted perturbational approach in a grid of points surrounding the molecule. Particular care is paid in the examination of the atomic quantities obtained from models of implicitly and explicitly interacting polarizabilities. Appropriateness and accuracy of the distributed models are assessed by comparing the molecular polarizabilities recovered from the models and those obtained experimentally and from MP2/Sadlej calculations. The behavior of the models is further explored by computing the polarization energy for aromatic compounds in the context of cation-π interactions and for selected neutral compounds in a TIP3P aqueous environment. The present results suggest that the computational strategy described here constitutes a very effective tool for the development of distributed models of atomic polarizabilities and can be used in the generation of new polarizable force fields.

  10. Hybrid-structure atomic models for HED laboratory plasma diagnostics and simulations

    Science.gov (United States)

    Hansen, Stephanie

    2010-03-01

    While theoretical atomic physics calculations are well developed for isolated atoms and have been thoroughly benchmarked against low-density laboratory sources such as electron beam ion traps and tokamak plasmas, the high energy density (HED) regime offers significant challenges for atomic physics and spectroscopic modeling. High plasma densities lead to collective effects such as continuum lowering, line broadening, and significant populations in multiply excited atomic states. These effects change the plasma equation of state and the character of emission and absorption spectra and must be accounted for in order to accurately simulate radiative transfer in and apply spectroscopic diagnostics to HED plasmas. Modeling complex mid- and high-Z ions in the HED regime is a particular challenge because exponential growth in accessible configuration space overwhelms the reduction of the Rydberg levels through continuum lowering. This talk will discuss one approach to generating a tractable spectroscopic-quality atomic kinetics model and describe its application to HED laboratory plasmas produced on Sandia's Z facility. [4pt] Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  11. Simulation studies of atomic resolution X-ray holography

    Indian Academy of Sciences (India)

    Yogesh Kashyap; P S Sarkar; Amar Sinha; B K Godwal

    2004-02-01

    X-ray holography is a new method of structure determination based on measurement of interference of a known reference wave with an unknown object wave (containing information on atomic sites scattering the reference wave) so that phase information is preserved. Unlike X-ray diffraction, it does not demand for translational periodicity in the material. It is based on the idea similar to that of optical holography and has been tested on crystals, quasicrystals, thin films and doped semiconductors for their structure determination. In order to analyse potentials and limitations of this technique, we have carried out theoretical simulation studies on simple structures. In this paper we describe the basic algorithm of hologram generation and reconstruction of atomic positions from generated data. We illustrate this technique using Fe (bcc) single crystal as sample case to demonstrate its capabilities and limitations. Simulations were carried out on the Cu (fcc) structure and on complex structure such as the Al–Pd–Mn quasicrystal. Technical issues such as low signal to noise ratio, twin image problem etc have been discussed briefly to emphasize the need for high intensity X-ray source such as synchrotron for experiments and proper reconstruction algorithm. Finally the scope and potential of this technique have been discussed.

  12. A compressible multiphase framework for simulating supersonic atomization

    Science.gov (United States)

    Regele, Jonathan D.; Garrick, Daniel P.; Hosseinzadeh-Nik, Zahra; Aslani, Mohamad; Owkes, Mark

    2016-11-01

    The study of atomization in supersonic combustors is critical in designing efficient and high performance scramjets. Numerical methods incorporating surface tension effects have largely focused on the incompressible regime as most atomization applications occur at low Mach numbers. Simulating surface tension effects in high speed compressible flow requires robust numerical methods that can handle discontinuities caused by both material interfaces and shocks. A shock capturing/diffused interface method is developed to simulate high-speed compressible gas-liquid flows with surface tension effects using the five-equation model. This includes developments that account for the interfacial pressure jump that occurs in the presence of surface tension. A simple and efficient method for computing local interface curvature is developed and an acoustic non-dimensional scaling for the surface tension force is proposed. The method successfully captures a variety of droplet breakup modes over a range of Weber numbers and demonstrates the impact of surface tension in countering droplet deformation in both subsonic and supersonic cross flows.

  13. The Scales of Time, Length, Mass, Energy, and Other Fundamental Physical Quantities in the Atomic World and the Use of Atomic Units in Quantum Mechanical Calculations

    Science.gov (United States)

    Teo, Boon K.; Li, Wai-Kee

    2011-01-01

    This article is divided into two parts. In the first part, the atomic unit (au) system is introduced and the scales of time, space (length), and speed, as well as those of mass and energy, in the atomic world are discussed. In the second part, the utility of atomic units in quantum mechanical and spectroscopic calculations is illustrated with…

  14. Atomic Scale Computer Simulation for Early Precipitation Process of Ni75Al6Vi9 Alloy

    Institute of Scientific and Technical Information of China (English)

    Yuhong ZHAO; Hua HOU; Hong XU; Yongxin WANG; Zheng CHEN; Xiaodong SUN

    2003-01-01

    The atomic scale computer simulation for initial precipitation mechanism of Ni75Al6V19 alloy was carried out for the first time by employing the microscopic diffusion equation. The initial precipitation process was invest igated throughsimulating the atom

  15. Simulation and understanding of atomic and molecular quantum crystals

    Science.gov (United States)

    Cazorla, Claudio; Boronat, Jordi

    2017-07-01

    Quantum crystals abound in the whole range of solid-state species. Below a certain threshold temperature the physical behavior of rare gases (He 4 and Ne), molecular solids (H2 and CH4 ), and some ionic (LiH), covalent (graphite), and metallic (Li) crystals can be explained only in terms of quantum nuclear effects (QNE). A detailed comprehension of the nature of quantum solids is critical for achieving progress in a number of fundamental and applied scientific fields such as planetary sciences, hydrogen storage, nuclear energy, quantum computing, and nanoelectronics. This review describes the current physical understanding of quantum crystals formed by atoms and small molecules, as well as the wide palette of simulation techniques that are used to investigate them. Relevant aspects in these materials such as phase transformations, structural properties, elasticity, crystalline defects, and the effects of reduced dimensionality are discussed thoroughly. An introduction to quantum Monte Carlo techniques, which in the present context are the simulation methods of choice, and other quantum simulation approaches (e.g., path-integral molecular dynamics and quantum thermal baths) is provided. The overarching objective of this article is twofold: first, to clarify in which crystals and physical situations the disregard of QNE may incur in important bias and erroneous interpretations. And second, to promote the study and appreciation of QNE, a topic that traditionally has been treated in the context of condensed matter physics, within the broad and interdisciplinary areas of materials science.

  16. Characterization of fan spray atomizers through numerical simulation

    Energy Technology Data Exchange (ETDEWEB)

    Altimira, Mireia [Thermal and Fluids Engineering Division, Mechanical Engineering Department, Tecnun (University of Navarra), Manuel de Lardizabal 13, 20018 San Sebastian (Spain)], E-mail: maltimira@tecnun.es; Rivas, Alejandro; Larraona, Gorka S.; Anton, Raul; Ramos, Juan Carlos [Thermal and Fluids Engineering Division, Mechanical Engineering Department, Tecnun (University of Navarra), Manuel de Lardizabal 13, 20018 San Sebastian (Spain)

    2009-04-15

    The present paper focuses on the mathematical modeling of industrial fan spray atomizers. The two-phase flow taking place inside the nozzle's tip and the exterior region near the outlet of three different industrial nozzle designs has been modeled and simulated. As a result, valuable information has been obtained regarding the influence of the inner geometry on the flow and also the formation and development of the liquid sheet. Characteristic magnitudes such as the discharge coefficient and the liquid sheet thickness factor have been obtained and validated through experimental measurements. The accumulation of liquid at the border of fan-shaped liquid sheets, also known as rim, has been studied in the analyzed designs, revealing the presence of a tangential velocity component in the liquid sheet and a relationship between the incoming flow rate of the rim and the angle of the liquid sheet. The dependence of the results on turbulence modeling has also been analyzed, drawing interesting conclusions regarding their influence on the liquid sheet mean flow characteristics and on the surrounding gas. Thus, the mathematical model developed has been proved to be a useful tool for nozzle manufacturers; it provides the most important characteristic parameters of the liquid sheet formed given certain nozzle geometry and, additionally, those data necessary to carry out studies of instability, breakup and atomization of the liquid sheet.

  17. Simulation of primary fuel atomization processes at subcritical pressures.

    Energy Technology Data Exchange (ETDEWEB)

    Arienti, Marco

    2013-06-01

    This report documents results from an LDRD project for the first-principles simulation of the early stages of spray formation (primary atomization). The first part describes a Cartesian embedded-wall method for the calculation of flow internal to a real injector in a fully coupled primary calculation. The second part describes the extension to an all-velocity formulation by introducing a momentum-conservative semi-Lagrangian advection and by adding a compressible term in the Poissons equation. Accompanying the description of the new algorithms are verification tests for simple two-phase problems in the presence of a solid interface; a validation study for a scaled-up multi-hole Diesel injector; and demonstration calculations for the closing and opening transients of a single-hole injector and for the high-pressure injection of liquid fuel at supersonic velocity.

  18. Atomic dynamics of alumina melt: A molecular dynamics simulation study

    Directory of Open Access Journals (Sweden)

    S.Jahn

    2008-03-01

    Full Text Available The atomic dynamics of Al2O3 melt are studied by molecular dynamics simulation. The particle interactions are described by an advanced ionic interaction model that includes polarization effects and ionic shape deformations. The model has been shown to reproduce accurately the static structure factors S(Q from neutron and x-ray diffraction and the dynamic structure factor S(Q,ω from inelastic x-ray scattering. Analysis of the partial dynamic structure factors shows inelastic features in the spectra up to momentum transfers, Q, close to the principal peaks of partial static structure factors. The broadening of the Brillouin line widths is discussed in terms of a frequency dependent viscosity η(ω.

  19. Simulations of atomic deuterium exposure in self-damaged tungsten

    Science.gov (United States)

    Hodille, E. A.; Založnik, A.; Markelj, S.; Schwarz-Selinger, T.; Becquart, C. S.; Bisson, R.; Grisolia, C.

    2017-05-01

    Simulations of deuterium (D) atom exposure in self-damaged polycrystalline tungsten at 500 K and 600 K are performed using an evolution of the MHIMS (migration of hydrogen isotopes in materials) code in which a model to describe the interaction of D with the surface is implemented. The surface-energy barriers for both temperatures are determined analytically with a steady-state analysis. The desorption energy per D atom from the surface is 0.69  ±  0.02 eV at 500 K and 0.87  ±  0.03 eV at 600 K. These values are in good agreement with ab initio calculations as well as experimental determination of desorption energies. The absorption energy (from the surface to the bulk) is 1.33  ±  0.04 eV at 500 K, 1.55  ±  0.02 eV at 600 K when assuming that the resurfacing energy (from the bulk to the surface) is 0.2 eV. Thermal-desorption spectrometry data after D atom exposure at 500 K and isothermal desorption at 600 K after D atom exposure at 600 K can be reproduced quantitatively with three bulk-detrapping energies, namely 1.65  ±  0.01 eV, 1.85  ±  0.03 eV and 2.06  ±  0.04 eV, in addition to the intrinsic detrapping energies known for undamaged tungsten (0.85 eV and 1.00 eV). Thanks to analyses of the amount of traps during annealing at different temperatures and ab initio calculations, the 1.65 eV detrapping energy is attributed to jogged dislocations and the 1.85 eV detrapping energy is attributed to dislocation loops. Finally, the 2.06 eV detrapping energy is attributed to D trapping in cavities based on literature reporting observations on the growth of cavities, even though this could also be understood as D desorbing from the C-D bond in the case of hydrocarbon contamination in the experimental sample.

  20. United polarizable multipole water model for molecular mechanics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Rui; Wang, Qiantao; Ren, Pengyu, E-mail: pren@mail.utexas.edu [Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712 (United States); Wang, Lee-Ping; Pande, Vijay S. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)

    2015-07-07

    We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3–5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interaction site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water.

  1. From Atom to Eve: An Interdisciplinary Unit on Origins.

    Science.gov (United States)

    Dietrich, Karen C.; Letts, Kathleen P.

    1986-01-01

    Describes a Catholic high school science unit on the origins of energy, matter, stars, planets, and life. Explains how the three- to four-week unit seeks to promote a unifying vision of science and religion, physics and biology, art and chemistry, education and living. (DMM)

  2. Cascade Annealing of Tungsten Implanted with 5 keV Noble Gas Atoms : A Computer Simulation

    NARCIS (Netherlands)

    Kolk, G.J. van der; Veen, A. van; Caspers, L.M.; Hosson, J.Th.M. De

    1984-01-01

    The trapping of vacancies by implanted atoms is calculated. After low energy implantation (5 keV) of tungsten with heavy noble gas atoms most of the implanted atoms are in substitutional position with one or two vacancies closer than two lattice units. Under the influence of the lattice distortion a

  3. Multimillion Atom Simulations of Nanostructured Materials on Parallel Computers ---Sintering and Consolidation, Fracture, and Oxidation---

    Science.gov (United States)

    Vashishta, P.; Bachlechner, M. E.; Campbell, T.; Kalia, R. K.; Kikuchi, H.; Kodiyalam, S.; Nakano, A.; Ogata, S.; Shimojo, F.; Walsh, P.

    Multiresolution molecular-dynamics approach for multimillion atom simulations has been used to investigate structural properties, mechanical failure in ceramic materials, and atomic-level stresses in nanoscale semiconductor/ceramic mesas (Si/Si3N4). Crack propagation and fracture in silicon nitride, silicon carbide, gallium arsenide, and nanophase ceramics are investigated. We observe a crossover from slow to rapid fracture and a correlation between the speed of crack propagation and morphology of fracture surface. A 100 million atom simulation is carried out to study crack propagation in GaAs. Mechanical failure in the Si/Si3N4 interface is studied by applying tensile strain parallel to the interface. Ten million atom molecular dynamics simulations are performed to determine atomic-level stress distributions in a 54 nm nanopixel on a 0.1 μm silicon substrate. Multimillion atom simulations of oxidation of aluminum nanoclusters and nanoindentation in silicon nitride are also discussed.

  4. Molecular Dynamics Simulations of Atomic H Etching SiC Surface

    NARCIS (Netherlands)

    Sun, W.; Liu, H.; Lin, L.; Zhao, C. L.; Lu, X. D.; He, P. N.; Gou, F.

    2012-01-01

    In this paper, molecular dynamics simulations were performed to study interactions between atomic H and SiC, silicon carbon surfaces were continuously bombarded by atomic H with different energies. The Tersoff-Brenner potentials were implemented. The simulation results show that with increasing

  5. Atomically resolved tomography to directly inform simulations for structure-property relationships

    Science.gov (United States)

    Moody, Michael P.; Ceguerra, Anna V.; Breen, Andrew J.; Cui, Xiang Yuan; Gault, Baptiste; Stephenson, Leigh T.; Marceau, Ross K. W.; Powles, Rebecca C.; Ringer, Simon P.

    2014-11-01

    Microscopy encompasses a wide variety of forms and scales. So too does the array of simulation techniques developed that correlate to and build upon microstructural information. Nevertheless, a true nexus between microscopy and atomistic simulations is lacking. Atom probe has emerged as a potential means of achieving this goal. Atom probe generates three-dimensional atomistic images in a format almost identical to many atomistic simulations. However, this data is imperfect, preventing input into computational algorithms to predict material properties. Here we describe a methodology to overcome these limitations, based on a hybrid data format, blending atom probe and predictive Monte Carlo simulations. We create atomically complete and lattice-bound models of material specimens. This hybrid data can then be used as direct input into density functional theory simulations to calculate local energetics and elastic properties. This research demonstrates the role that atom probe combined with theoretical approaches can play in modern materials engineering.

  6. Torque and atomic forces for Cartesian tensor atomic multipoles with an application to crystal unit cell optimization.

    Science.gov (United States)

    Elking, Dennis M

    2016-08-15

    New equations for torque and atomic force are derived for use in flexible molecule force fields with atomic multipoles. The expressions are based on Cartesian tensors with arbitrary multipole rank. The standard method for rotating Cartesian tensor multipoles and calculating torque is to first represent the tensor with n indexes and 3(n) redundant components. In this work, new expressions for directly rotating the unique (n + 1)(n + 2)/2 Cartesian tensor multipole components Θpqr are given by introducing Cartesian tensor rotation matrix elements X(R). A polynomial expression and a recursion relation for X(R) are derived. For comparison, the analogous rotation matrix for spherical tensor multipoles are the Wigner functions D(R). The expressions for X(R) are used to derive simple equations for torque and atomic force. The torque and atomic force equations are applied to the geometry optimization of small molecule crystal unit cells. In addition, a discussion of computational efficiency as a function of increasing multipole rank is given for Cartesian tensors. © 2016 Wiley Periodicals, Inc.

  7. High-throughput all-atom molecular dynamics simulations using distributed computing.

    Science.gov (United States)

    Buch, I; Harvey, M J; Giorgino, T; Anderson, D P; De Fabritiis, G

    2010-03-22

    Although molecular dynamics simulation methods are useful in the modeling of macromolecular systems, they remain computationally expensive, with production work requiring costly high-performance computing (HPC) resources. We review recent innovations in accelerating molecular dynamics on graphics processing units (GPUs), and we describe GPUGRID, a volunteer computing project that uses the GPU resources of nondedicated desktop and workstation computers. In particular, we demonstrate the capability of simulating thousands of all-atom molecular trajectories generated at an average of 20 ns/day each (for systems of approximately 30 000-80 000 atoms). In conjunction with a potential of mean force (PMF) protocol for computing binding free energies, we demonstrate the use of GPUGRID in the computation of accurate binding affinities of the Src SH2 domain/pYEEI ligand complex by reconstructing the PMF over 373 umbrella sampling windows of 55 ns each (20.5 mus of total data). We obtain a standard free energy of binding of -8.7 +/- 0.4 kcal/mol within 0.7 kcal/mol from experimental results. This infrastructure will provide the basis for a robust system for high-throughput accurate binding affinity prediction.

  8. Homogeneous nucleation and microstructure evolution in million-atom molecular dynamics simulation.

    Science.gov (United States)

    Shibuta, Yasushi; Oguchi, Kanae; Takaki, Tomohiro; Ohno, Munekazu

    2015-08-27

    Homogeneous nucleation from an undercooled iron melt is investigated by the statistical sampling of million-atom molecular dynamics (MD) simulations performed on a graphics processing unit (GPU). Fifty independent instances of isothermal MD calculations with one million atoms in a quasi-two-dimensional cell over a nanosecond reveal that the nucleation rate and the incubation time of nucleation as functions of temperature have characteristic shapes with a nose at the critical temperature. This indicates that thermally activated homogeneous nucleation occurs spontaneously in MD simulations without any inducing factor, whereas most previous studies have employed factors such as pressure, surface effect, and continuous cooling to induce nucleation. Moreover, further calculations over ten nanoseconds capture the microstructure evolution on the order of tens of nanometers from the atomistic viewpoint and the grain growth exponent is directly estimated. Our novel approach based on the concept of "melting pots in a supercomputer" is opening a new phase in computational metallurgy with the aid of rapid advances in computational environments.

  9. Atoms

    Institute of Scientific and Technical Information of China (English)

    刘洪毓

    2007-01-01

    Atoms(原子)are all around us.They are something like the bricks (砖块)of which everything is made. The size of an atom is very,very small.In just one grain of salt are held millions of atoms. Atoms are very important.The way one object acts depends on what

  10. Materials simulations at the atom-continuum interface: Dislocation mobility and notched fracture initiation

    Science.gov (United States)

    Bailey, Nicholas Patrick

    We have solved three problems with a common theme of interfacing atomistic models with continuum models. The first is measuring the Peierls barrier for dislocation glide in a two dimensional material. The key features of this work are (1) efficient extrapolation of the infinite system limit from small simulations, through the use of multipole relaxation at the atom-continuum interface, and (2) the representation of the dependence on external parameters (in this case applied stress) in a compact way using a physically motivated functional form. The second problem is the initiation of fracture at sharp notches in single crystal silicon, a problem of current experimental interest in microfabrication. It is found that when expressed in atomic-scale units the critical stress intensity factor is almost independent of notch opening angle, as long as the interatomic potential does, in fact, produce brittle fracture. The third problem is the challenge of incorporating atomistic simulations in an adaptive manner in large scale continuum (finite element) simulations. Our method involves embedding such simulations within elements in an overlapping sense, and avoids some of the complexity associated with alternative methods. We solve these three problems through the development of a flexible, modern, powerful molecular dynamics package, known as DigitalMaterial. We describe the design of the software, which is fully object-oriented. What makes this package different from others is the use of a component-based approach based on software engineering methods known as Design Patterns. The interfaces for these components are very clearly defined, allowing components to be interoperable and to be easily driven from a high level scripting environment.

  11. Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

    Science.gov (United States)

    Shen, Lin; Hu, Hao

    2014-06-10

    We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

  12. Computer Simulation of Ordering and Atom Clustering in Aging Binary Al-Li Alloy

    Institute of Scientific and Technical Information of China (English)

    LI Xiao-ling; CHEN Zheng; WANG Yong-xin; HU Ming-juan

    2004-01-01

    Ordering and atom clustering in aging binary Al-Li alloy has been investigated by computer simulation through calculating the long range order (lro.) parameter and composition deviation order parameter from single-site occupation probabilities of Li atom. The results show that when the alloy lies in metastable region in the phase diagram ordering and atom clustering occur simultaneously. As the composition of the alloy increases ordering occurs earlier than atom clustering gradually. When the alloy lies in instable region atom clustering takes place after the congruent ordering completes. It has also been found that the incubation period of the phase transformation is shortened as the composition increases.

  13. Computer Simulation of Ordering and Atom Clustering in Aging Binary AI-Li Alloy

    Institute of Scientific and Technical Information of China (English)

    LIXiao-ling; CHENZheng; WANGYong-xin; HUMing-juan

    2004-01-01

    Ordering and atom clustering in aging binary Al-Li alloy has been investigated by computer simulation through calculating the long range order (lro.) parameter and composition deviation order parameter from single-site occupation probabilities of Li atom. The results show that when the alloy lies in metastable region in the phase diagram ordering and atom clustering occur simultaneously. As the composition of the alloy increases ordering occurs earlier than atom clustering gradually. When the alloy lies in instable region atom clustering takes place after the congruent ordering completes. It has also been found that the incubation period of the phase transformation is shortened as the composition increases.

  14. Hybrid statistics-simulations based method for atom-counting from ADF STEM images.

    Science.gov (United States)

    De Wael, Annelies; De Backer, Annick; Jones, Lewys; Nellist, Peter D; Van Aert, Sandra

    2017-01-25

    A hybrid statistics-simulations based method for atom-counting from annular dark field scanning transmission electron microscopy (ADF STEM) images of monotype crystalline nanostructures is presented. Different atom-counting methods already exist for model-like systems. However, the increasing relevance of radiation damage in the study of nanostructures demands a method that allows atom-counting from low dose images with a low signal-to-noise ratio. Therefore, the hybrid method directly includes prior knowledge from image simulations into the existing statistics-based method for atom-counting, and accounts in this manner for possible discrepancies between actual and simulated experimental conditions. It is shown by means of simulations and experiments that this hybrid method outperforms the statistics-based method, especially for low electron doses and small nanoparticles. The analysis of a simulated low dose image of a small nanoparticle suggests that this method allows for far more reliable quantitative analysis of beam-sensitive materials.

  15. Molecular dynamics simulations of the atom packing characteristics of three deformed silver nanoparticles at room temperature.

    Science.gov (United States)

    Zhang, Lin

    2016-03-14

    Deformation is of significance in controlling the shape of materials, but the key structural information of metal nanoparticles is still limited. Molecular dynamics simulations are performed to explore the microscopic details of atom packing differences in three deformed silver nanoparticles with one atom difference. Analytical tools are used to demonstrate the effects of external load and surface atoms of particles on the packing patterns in these deformed nanoparticles including internal energy per atom, pair numbers, and pair distribution functions as well as cross-sectional images. The simulation results show that under small compression, the particles present elastic behaviors. The increasing compression results in the sliding of the atoms in different parts of these particles, and some interfaces are formed between these parts. As the external load becomes large, these deformed particles are compressed into the thickness of several atomic layers. The unloaded particles present different behaviors.

  16. Automated military unit identification in battlefield simulation

    Energy Technology Data Exchange (ETDEWEB)

    Stroud, P.; Gordon, R.

    1997-05-01

    It is the nature of complex systems, composed of many interacting elements, that unanticipated phenomena develop. Computer simulation, in which the elements of a complex system are implemented as interacting software objects (actors), is an effective tool to study collective and emergent phenomena in complex systems. A new cognitive architecture is described for constructing simulation actors that can, like the intelligent elements they represent adapt to unanticipated conditions. This cognitive architecture generates trial behaviors, estimates their fitness using an internal representation of the system, and has an internal apparatus for evolving a population of trial behaviors to changing environmental conditions. A specific simulation actor is developed to evaluate surveillance radar images of moving vehicles on battlefields. The vehicle cluster location, characterization and discrimination processes currently performed by intelligent human operators were implemented into a parameterized formation recognition process by using a newly developed family of 2D cluster filters. The mechanics of these cluster filters are described. Preliminary results are presented in which this GSM actor demonstrates the ability not only to recognize military formations under prescribed conditions, but to adapt its behavior to unanticipated conditions that develop in the complex simulated battlefield system.

  17. Multimillion-atom molecular dynamics simulation of atomic level stresses in Si(111)/Si3N4(0001) nanopixels

    Science.gov (United States)

    Bachlechner, Martina E.; Omeltchenko, Andrey; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjö, Ingvar; Madhukar, Anupam; Messina, Paul

    1998-04-01

    Ten million atom multiresolution molecular-dynamics simulations are performed on parallel computers to determine atomic-level stress distributions in a 54 nm nanopixel on a 0.1 μm silicon substrate. Effects of surfaces, edges, and lattice mismatch at the Si(111)/Si3N4(0001) interface on the stress distributions are investigated. Stresses are found to be highly inhomogeneous in the nanopixel. The top surface of silicon nitride has a compressive stress of +3 GPa and the stress is tensile, -1 GPa, in silicon below the interface.

  18. A Simulator for Producing of High Flux Atomic Oxygen Beam by Using ECR Plasma Source

    Institute of Scientific and Technical Information of China (English)

    Shuwang DUO; Meishuan LI; Yaming ZHANG

    2004-01-01

    In order to study the atomic oxygen corrosion of spacecraft materials in low earth orbit environment, an atomic oxygen simulator was established. In the simulator, a 2.45 GHz microwave source with maximum power of 600 W was launched into the circular cavity to generate ECR (electron cyclotron resonance) plasma. The oxygen ion beam moved onto a negatively biased Mo plate under the condition of symmetry magnetic mirror field confine, then was neutralized and reflected to form oxygen atom beam. The properties of plasma density, electron temperature, plasma space potential and ion incident energy were characterized. The atomic oxygen beam flux was calibrated by measuring the mass loss rate of Kapton during the atomic 5~30 eV and a cross section of φ80 mm could be obtained under the operating pressure of 10-1~10-3 Pa. Such a high flux source can provide accelerated simulation tests of materials and coatings for space applications.

  19. SIMULATION OF THE ATOMIZED FLOW BY SLIT TYPE BUCKET ENERGY DISSIPATOR

    Institute of Scientific and Technical Information of China (English)

    LIU Shi-he; DUAN Hong-dong

    2005-01-01

    Slit type bucket is one kind of flip bucket for energy dissipation generally used in the hydraulic project.In this paper the atomized flow produced behind this energy dissipator is analyzed, a numerical model for the aerated jet considering air entrainment and air resistance force is suggested, and simulation of the rain resulted by the atomized flow is also discussed.Furthermore, the prototype observation data for the atomized flow of Dongjiang Hydropower Station is used to verify the model suggested.

  20. A new united atom force field for adsorption of alkenes in zeolites

    NARCIS (Netherlands)

    Liu, B.; Smit, B.; Rey, F.; Valencia, S.; Calero, S.

    2008-01-01

    A new united atom force field was developed that accurately describes the adsorption properties of linear alkenes in zeolites. The force field was specifically designed for use in the inhomogeneous system and therefore a truncated and shifted potential was used. With the determined force field, we p

  1. Polymer coating comprising 2-methoxyethyl acrylate units synthesized by surface-initiated atom transfer radical polymerization

    DEFF Research Database (Denmark)

    2011-01-01

    Source: US2012184029A The present invention relates to preparation of a polymer coating comprising or consisting of polymer chains comprising or consisting of units of 2-methoxyethyl acrylate synthesized by Surface-Initiated Atom Transfer Radical Polymerization (SI ATRP) such as ARGET SI ATRP...... or AGET SI ATRP and uses of said polymer coating....

  2. Energy from the Atom. A Basic Teaching Unit on Energy. Revised.

    Science.gov (United States)

    McDermott, Hugh, Ed.; Scharmann, Larry, Ed.

    Recommended for grades 9-12 social studies and/or physical science classes, this 4-8 day unit focuses on four topics: (1) the background and history of atomic development; (2) two common types of nuclear reactors (boiling water and pressurized water reactors); (3) disposal of radioactive waste; and (4) the future of nuclear energy. Each topic…

  3. The Atomic Mass Unit, the Avogadro Constant, and the Mole: A Way to Understanding

    Science.gov (United States)

    Baranski, Andrzej

    2012-01-01

    Numerous articles have been published that address problems encountered in teaching basic concepts of chemistry such as the atomic mass unit, Avogadro's number, and the mole. The origin of these problems is found in the concept definitions. If these definitions are adjusted for teaching purposes, understanding could be improved. In the present…

  4. Accelerating all-atom MD simulations of lipids using a modified virtual-sites technique

    DEFF Research Database (Denmark)

    Loubet, Bastien; Kopec, Wojciech; Khandelia, Himanshu

    2014-01-01

    We present two new implementations of the virtual sites technique which completely suppresses the degrees of freedom of the hydrogen atoms in a lipid bilayer allowing for an increased time step of 5 fs in all-atom simulations of the CHARMM36 force field. One of our approaches uses the derivation ...

  5. Index to the United States Atomic Energy Commission's Annual Report to Congress for 1961. Major activities in the atomic energy programs, January 1961 - December 1961

    Energy Technology Data Exchange (ETDEWEB)

    Seaborg, Glenn T.

    1962-01-31

    This volume contains a name and subject index for the 1961 report of the United States Atomic Energy Commission to Congress. The full semiannual report covers the major unclassified activities of the Commission from January through December 1961.

  6. Index to the United States Atomic Energy Commission's Annual Report to Congress for 1962. Major activities in the atomic energy programs, January 1962 - December 1962

    Energy Technology Data Exchange (ETDEWEB)

    Seaborg, Glenn T.

    1963-01-31

    This volume contains a name and subject index for the 1962 report of the United States Atomic Energy Commission to Congress. The full semiannual report covers the major unclassified activities of the Commission from January through December 1962.

  7. Index to the United States Atomic Energy Commission's Annual Report to Congress for 1960. Major activities in the atomic energy programs, January 1960 - December 1960

    Energy Technology Data Exchange (ETDEWEB)

    McCone, John A.

    1961-01-31

    This volume contains a name and subject index for the 1960 report of the United States Atomic Energy Commission to Congress. The full semiannual report covers the major unclassified activities of the Commission from January through December 1960.

  8. Index to the United States Atomic Energy Commission's Annual Report to Congress for 1959. Major activities in the atomic energy programs, January 1959 - December 1959

    Energy Technology Data Exchange (ETDEWEB)

    McCone, John A.

    1960-01-31

    This volume contains a name and subject index for the 1959 report of the United States Atomic Energy Commission to Congress. The full semiannual report covers the major unclassified activities of the Commission from January through December 1959.

  9. Thermodynamics of small clusters of atoms: A molecular dynamics simulation

    DEFF Research Database (Denmark)

    Damgaard Kristensen, W.; Jensen, E. J.; Cotterill, Rodney M J

    1974-01-01

    The thermodynamic properties of clusters containing 55, 135, and 429 atoms have been calculated using the molecular dynamics method. Structural and vibrational properties of the clusters were examined at different temperatures in both the solid and the liquid phase. The nature of the melting...

  10. Simulation and optimization of an industrial PSA unit

    Directory of Open Access Journals (Sweden)

    Barg C.

    2000-01-01

    Full Text Available The Pressure Swing Adsorption (PSA units have been used as a low cost alternative to the usual gas separation processes. Its largest commercial application is for hydrogen purification systems. Several studies have been made about the simulation of pressure swing adsorption units, but there are only few reports on the optimization of such processes. The objective of this study is to simulate and optimize an industrial PSA unit for hydrogen purification. This unit consists of six beds, each of them have three layers of different kinds of adsorbents. The main impurities are methane, carbon monoxide and sulfidric gas. The product stream has 99.99% purity in hydrogen, and the recovery is around 90%. A mathematical model for a commercial PSA unit is developed. The cycle time and the pressure swing steps are optimized. All the features concerning with complex commercial processes are considered.

  11. A dynamical atomic simulation for the Ni-Al Wulff nanoparticle

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Jianfeng [Department of Applied Physics, Hunan Agricultural University, Changsha 410128 (China); Yang, Jianyu, E-mail: wuliyangjianyu@yahoo.com.cn [Hunan Institute of Engineering, Xiangtan 411104 (China)

    2013-06-01

    Ni-Al bimetallic nanoparticle structures are studied from a kinetic point of view. The diffusion and growth of Ni (or Al) atoms on Al (or Ni) cores with the Wulff structure are simulated by molecular dynamics and nudged elastic band methods. An analytic embedded atom model is applied to the two metals. The energy barriers of several typical diffusion processes of the adatoms on the nanoparticle surface are calculated. Results show that the incorporation of the Ni atoms into the Al core easily occurs, and the reverse process does not readily proceed. The growth simulations reveal that a better core-shell nanoparticle is obtained when the Al atoms are deposited on the Ni core at lower temperatures, and the deposition of the Ni atoms on the Al core leads to an amorphous surface. - Highlights: • The diffusion barrier of Ni (or Al) on Al (or Ni) Wulff nanoparticle is studied. • Ni atom can diffuse easily into Al core, and Al atom generally segregate on surface. • A core-shell nanoparticle is obtained for the deposition of Al atoms on Ni core. • Amorphous nanoparticle surface is obtained by depositing Ni atoms on Al core.

  12. Unit testing, model validation, and biological simulation

    Science.gov (United States)

    Watts, Mark D.; Ghayoomie, S. Vahid; Larson, Stephen D.; Gerkin, Richard C.

    2016-01-01

    The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the biological sciences, it is important to examine how these practices can accelerate biological software development and improve research quality. In this article, we give a focused case study of our experience with the practices of unit testing and test-driven development in OpenWorm, an open-science project aimed at modeling Caenorhabditis elegans. We identify and discuss the challenges of incorporating test-driven development into a heterogeneous, data-driven project, as well as the role of model validation tests, a category of tests unique to software which expresses scientific models. PMID:27635225

  13. Quantum Computation and Simulation Using Neutral Fermionic Atoms

    Science.gov (United States)

    2014-06-06

    State Laser Source for Laser Cooling of Lithium , 39th Annual Meeting of the APS Division of Atomic, Molecular, and Optical Physics. 27-MAY-08...Prof. Lincoln Carr and Laith Haddad from the Colorado School of Mines , we have proposed a method to excite relativistic vortices in a Bose-Einstein...Savard, S. Bali, C. Freed, and J. Thomas, “Ultrastable CO2 laser trapping of lithium fermions,” Phys. Rev. Lett. 82, 4204–4207 (1999). [5] L. Carr

  14. Simulating atomic-scale phenomena on surfaces of unconventional superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Kreisel, Andreas; Andersen, Brian [Niels Bohr Institute (Denmark); Choubey, Peayush; Hirschfeld, Peter [Univ. of Florida (United States); Berlijn, Tom [CNMS and CSMD, Oak Ridge National Laboratory (United States)

    2016-07-01

    Interest in atomic scale effects in superconductors has increased because of two general developments: First, the discovery of new materials as the cuprate superconductors, heavy fermion and Fe-based superconductors where the coherence length of the cooper pairs is as small to be comparable to the lattice constant, rendering small scale effects important. Second, the experimental ability to image sub-atomic features using scanning-tunneling microscopy which allows to unravel numerous physical properties of the homogeneous system such as the quasi particle excitation spectra or various types of competing order as well as properties of local disorder. On the theoretical side, the available methods are based on lattice models restricting the spatial resolution of such calculations. In the present project we combine lattice calculations using the Bogoliubov-de Gennes equations describing the superconductor with wave function information containing sub-atomic resolution obtained from ab initio approaches. This allows us to calculate phenomena on surfaces of superconductors as directly measured in scanning tunneling experiments and therefore opens the possibility to identify underlying properties of these materials and explain observed features of disorder. It will be shown how this method applies to the cuprate material Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8} and a Fe based superconductor.

  15. Atom probe tomography simulations and density functional theory calculations of bonding energies in Cu3Au

    KAUST Repository

    Boll, Torben

    2012-10-01

    In this article the Cu-Au binding energy in Cu3Au is determined by comparing experimental atom probe tomography (APT) results to simulations. The resulting bonding energy is supported by density functional theory calculations. The APT simulations are based on the Müller-Schottky equation, which is modified to include different atomic neighborhoods and their characteristic bonds. The local environment is considered up to the fifth next nearest neighbors. To compare the experimental with simulated APT data, the AtomVicinity algorithm, which provides statistical information about the positions of the neighboring atoms, is applied. The quality of this information is influenced by the field evaporation behavior of the different species, which is connected to the bonding energies. © Microscopy Society of America 2012.

  16. Atomic oxygen distributions in the Venus thermosphere: Comparisons between Venus Express observations and global model simulations

    Science.gov (United States)

    Brecht, A. S.; Bougher, S. W.; Gérard, J.-C.; Soret, L.

    2012-02-01

    Nightglow emissions provide insight into the global thermospheric circulation, specifically in the transition region (˜70-120 km). The O 2 IR nightglow statistical map created from Venus Express (VEx) Visible and InfraRed Thermal Imaging Spectrometer (VIRTIS) observations has been used to deduce a three-dimensional atomic oxygen density map. In this study, the National Center of Atmospheric Research (NCAR) Venus Thermospheric General Circulation Model (VTGCM) is utilized to provide a self-consistent global view of the atomic oxygen density distribution. More specifically, the VTGCM reproduces a 2D nightside atomic oxygen density map and vertical profiles across the nightside, which are compared to the VEx atomic oxygen density map. Both the simulated map and vertical profiles are in close agreement with VEx observations within a ˜30° contour of the anti-solar point. The quality of agreement decreases past ˜30°. This discrepancy implies the employment of Rayleigh friction within the VTGCM may be an over-simplification for representing wave drag effects on the local time variation of global winds. Nevertheless, the simulated atomic oxygen vertical profiles are comparable with the VEx profiles above 90 km, which is consistent with similar O 2 ( 1Δ) IR nightglow intensities. The VTGCM simulations demonstrate the importance of low altitude trace species as a loss for atomic oxygen below 95 km. The agreement between simulations and observations provides confidence in the validity of the simulated mean global thermospheric circulation pattern in the lower thermosphere.

  17. Computer Simulations: A Tool to Predict Experimental Parameters with Cold Atoms

    Science.gov (United States)

    2013-04-01

    allowing us to look at the trap frequency, depth, and axes. It can also simulate the atom behavior using Monte Carlo simulations. Since the...ARL-TR-5787; U.S. Army Research Laboratory: Adelphi, MD, 2011. 21 1 DEFENSE TECHNICAL (PDF) INFORMATION CTR DTIC OCA 1 DIRECTOR

  18. Multimillion atom simulation of materials on parallel computers — nanopixel, interfacial fracture, nanoindentation, and oxidation

    Science.gov (United States)

    Vashishta, Priya; Bachlechner, Martina; Nakano, Aiichiro; Campbell, Timothy J.; Kalia, Rajiv K.; Kodiyalam, Sanjay; Ogata, Shuji; Shimojo, Fuyuki; Walsh, Phillip

    2001-10-01

    We have developed scalable space-time multiresolution algorithms to enable molecular dynamics simulations involving up to a billion atoms on massively parallel computers. Large-scale molecular dynamics simulations have been used to study stress domains and interfacial fracture in semiconductor/dielectric nanopixels, nanoindentation, and oxidation of metallic nanoparticles.

  19. Implementation of Shifted Periodic Boundary Conditions in the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Software

    Science.gov (United States)

    2015-08-01

    Atomic /Molecular Massively Parallel Simulator (LAMMPS) Software by N Scott Weingarten and James P Larentzos Approved for...0687 ● AUG 2015 US Army Research Laboratory Implementation of Shifted Periodic Boundary Conditions in the Large-Scale Atomic /Molecular...Shifted Periodic Boundary Conditions in the Large-Scale Atomic /Molecular Massively Parallel Simulator (LAMMPS) Software 5a. CONTRACT NUMBER 5b

  20. Process of Energetic Carbon Atom Deposition on Si (001) Substrate by Molecular Dynamics Simulation

    Institute of Scientific and Technical Information of China (English)

    于威; 滕晓云; 李晓苇; 傅广生

    2002-01-01

    The process of energetic C atom deposition on Si (001)-(2×1) is studied by the molecular dynamics method using the semi-empirical many-bond Tersoff potential. It is found that the incident energy of the carbon atom has an important effect on the collision process and its diffusion process on the substrate. Most of the incident energy of the carbon atom is transferred to the substrate atoms within the initial two vibration periods of substrate atoms and its value increases with the incident energy. The spreading distance and penetration depth of the incident atom increasing with the incident energy are also identified. The simulated results imply that an important effect of energy of incident carbon on the film growth at Iow substrate temperature provides activation energy for silicon carbide formation through the vibration enhancement of local substrate atoms. In addition, suppressing carbon atom inhomogeneous collection and dispensing with the silicon diffusion process may be effectively promoted by the spreading and penetration of the energetic carbon atom in the silicon substrate.

  1. Parallel algorithm of solidification process simulation for large-sized system of liquid metal atoms

    Institute of Scientific and Technical Information of China (English)

    董科军; 刘让苏; 郑采星; 刘海蓉; 彭平; 卢小勇; 胡庆丰; 何新芳

    2003-01-01

    A parallel arithmetic program for the molecular dynamics (MD) simulation study of a large-sized system consisting of 50 000-100 000 atoms of liquid metals is reformed, based on the cascade arithmetic program used for the molecular dynamics simulation study of a small-sized system consisting of 500-1 000 atoms. The program is used to simulate the rapid solidification processes of liquid metal Al system. Some new results, such as larger clusters composed of more than 3-6 smaller clusters (icosahedra or defect icosahedra) obtained in the system of 50 000 atoms, however, the larger clusters can not be seen in the small-sized system of 500-1 000 atoms. On the other hand, the results from this simulation study would be more closed to the real situation of the system under consideration because the influence of boundary conditions is decreased remarkably. It can be expected that from the parallel algorithm combined with the higher performance super-computer, the total number of atoms in simulation system can be enlarged again up to tens, even hundreds times in the near future.

  2. Atomic scale simulations for improved CRUD and fuel performance modeling

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, Anders David Ragnar [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Cooper, Michael William Donald [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-01-06

    A more mechanistic description of fuel performance codes can be achieved by deriving models and parameters from atomistic scale simulations rather than fitting models empirically to experimental data. The same argument applies to modeling deposition of corrosion products on fuel rods (CRUD). Here are some results from publications in 2016 carried out using the CASL allocation at LANL.

  3. Molecular dynamics simulations of lipid vesicle fusion in atomic detail

    NARCIS (Netherlands)

    Knecht, Volker; Marrink, Siewert-Jan

    The fusion of a membrane-bounded vesicle with a target membrane is a key step in intracellular trafficking, exocytosis, and drug delivery. Molecular dynamics simulations have been used to study the fusion of small unilamellar vesicles composed of a dipalmitoyl-phosphatidylcholine (DPPC)/palmitic

  4. Simulating quantum-optical phenomena with cold atoms in optical lattices

    Energy Technology Data Exchange (ETDEWEB)

    Navarrete-Benlloch, Carlos [Departament d' Optica, Universitat de Valencia, Dr Moliner 50, 46100 Burjassot (Spain); Vega, Ines de [Institut fuer Theoretische Physik, Albert-Einstein-Allee 11, Universitaet Ulm, D-89069 Ulm (Germany); Porras, Diego [Departamento de Fisica Teorica I, Universidad Complutense, 28040 Madrid (Spain); Ignacio Cirac, J, E-mail: carlos.navarrete@uv.es, E-mail: ines.devega@uni-ulm.de, E-mail: diego.porras@fis.ucm.es, E-mail: ignacio.cirac@mpq.mpg.de [Max-Planck-Institut fuer Quantenoptik, Hans-Kopfermann-Strasse 1, 85748 Garching (Germany)

    2011-02-15

    We propose a scheme involving cold atoms trapped in optical lattices to observe different phenomena traditionally linked to quantum-optical systems. The basic idea consists of connecting the trapped atomic state to a non-trapped state through a Raman scheme. The coupling between these two types of atoms (trapped and free) turns out to be similar to that describing light-matter interaction within the rotating-wave approximation, the role of matter and photons being played by the trapped and free atoms, respectively. We explain in particular how to observe phenomena arising from the collective spontaneous emission of atomic and harmonic oscillator samples, such as superradiance and directional emission. We also show how the same setup can simulate Bose-Hubbard Hamiltonians with extended hopping as well as Ising models with long-range interactions. We believe that this system can be realized with state of the art technology.

  5. Adsorption kinetics of surfactants at liquid-solid and liquid-vapor interfaces from atomic-scale simulations

    Science.gov (United States)

    Iskrenova, Eugeniya K.; Patnaik, Soumya S.

    2012-02-01

    Nucleate pool boiling of pure liquid is a complex process involving different size- and time-scale phenomena. The appearance of the first nanobubble in the liquid at the bottom of a hot pan, the detachment of the bubble from the solid surface, its subsequent coalescence with other bubbles, all represent complex multiscale phenomena. Surfactants added to water increase the complexity of the process by contributing to the dynamic surface tension at the liquid-vapor and liquid-solid interfaces and thus affecting the heat and mass transfer at those interfaces. We apply molecular dynamics simulations to study the adsorption kinetics of anionic, cationic, and non-ionic surfactants at liquid/solid and liquid/vapor interfaces. The all-atom vs. united-atom approaches for the solid and surfactants are surveyed in view of their applicability at near boiling temperatures and a range of model water potentials is assessed for reproducing the thermal properties of water at boiling conditions.

  6. Computer Simulation of Atoms Nuclei Structure Using Information Coefficients of Proportionality

    OpenAIRE

    Labushev, Mikhail M.

    2012-01-01

    The latest research of the proportionality of atomic weights of chemical elements made it possible to obtain 3 x 3 matrices for the calculation of information coefficients of proportionality Ip that can be used for 3D modeling of the structure of atom nucleus. The results of computer simulation show high potential of nucleus structure research for the characterization of their chemical and physical properties.

  7. Computer Simulation of Atoms Nuclei Structure Using Information Coefficients of Proportionality

    CERN Document Server

    Labushev, Mikhail M

    2012-01-01

    The latest research of the proportionality of atomic weights of chemical elements made it possible to obtain 3 x 3 matrices for the calculation of information coefficients of proportionality Ip that can be used for 3D modeling of the structure of atom nucleus. The results of computer simulation show high potential of nucleus structure research for the characterization of their chemical and physical properties.

  8. Accelerated discovery of OLED materials through atomic-scale simulation

    Science.gov (United States)

    Halls, Mathew D.; Giesen, David J.; Hughes, Thomas F.; Goldberg, Alexander; Cao, Yixiang; Kwak, H. Shaun; Mustard, Thomas J.; Gavartin, Jacob

    2016-09-01

    Organic light-emitting diode (OLED) devices are under widespread investigation to displace or complement inorganic optoelectronic devices for solid-state lighting and active displays. The materials in these devices are selected or designed according to their intrinsic and extrinsic electronic properties with concern for efficient charge injection and transport, and desired stability and light emission characteristics. The chemical design space for OLED materials is enormous and there is need for the development of computational approaches to help identify the most promising solutions for experimental development. In this work we will present examples of simulation approaches available to efficiently screen libraries of potential OLED materials; including first-principles prediction of key intrinsic properties, and classical simulation of amorphous morphology and stability. Also, an alternative to exhaustive computational screening is introduced based on a biomimetic evolutionary framework; evolving the molecular structure in the calculated OLED property design space.

  9. Molecular Dynamics Simulation of Macromolecules Using Graphics Processing Unit

    CERN Document Server

    Xu, Ji; Ge, Wei; Yu, Xiang; Yang, Xiaozhen; Li, Jinghai

    2010-01-01

    Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In recent years, graphics processing unit (GPU) provides unprecedented computational power for scientific applications. Many MD algorithms suit with the multithread nature of GPU. In this paper, MD algorithms for macromolecular systems that run entirely on GPU are presented. Compared to the MD simulation with free software GROMACS on a single CPU core, our codes achieve about 10 times speed-up on a single GPU. For validation, we have performed MD simulations of polymer crystallization on GPU, and the results observed perfectly agree with computations on CPU. Therefore, our single GPU codes have already provided an inexpensive alternative for macromolecular simulations on traditional CPU clusters and they can also be used as a basis to develop parallel GPU programs to further spee...

  10. Reparameterization of all-atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension

    DEFF Research Database (Denmark)

    Sonne, Jacob; Jensen, M.Ø.; Hansen, Flemming Yssing;

    2007-01-01

    represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting...... method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per...... fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field....

  11. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    CERN Document Server

    Erban, Radek

    2015-01-01

    Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parameterized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

  12. NUMERICAL SIMULATION OF ATOMIZATION RAINFALL AND THE GENERATED FLOW ON A SLOPE

    Institute of Scientific and Technical Information of China (English)

    LIU Shi-he; TAI Wei; FAN Min; LUO Qiu-shi

    2012-01-01

    This article studies the atomization rainfall and the generated flow on a slope by numerical simulations.The atomization rainfall is simulated by a unified model for splash droplets and a suspended mist,and the distribution of the diameter of splash rain drops is analyzed.The slope runoff generated by the atomization rainfall is simulated by a depth-averaged 2-D model,and the localization of the rainfall intensity in space is specially considered.The simulation results show that:(1) the median rain size of the atomization rainfall increases in the longitudinal direction at first,then monotonously decreases,and the maximum value is taken at the longitudinal position not in consistent with the position where the maximum rain intensity is taken.In the lateral direction the median rain size monotonously decreases,(2) since the atomization rainfall is distributed in a strongly localized area,it takes a longer time for its runoff yield to reach a steady state than that in the natural rainfall,the variation ranges of the water depth and the velocity in the longitudinal and lateral directions are larger than those in the natural rainfall.

  13. Cold-atom quantum simulation of U(1) lattice gauge-Higgs model

    Science.gov (United States)

    Kasamatsu, Kenichi; Kuno, Yoshihito; Takahashi, Yoshiro; Ichinose, Ikuo; Matsui, Tetsuo

    2015-03-01

    We discuss the possible methods to construct a quantum simulator of the U(1) lattice gauge-Higgs model using cold atoms in an optical lattice. These methods require no severe fine tunings of parameters of atomic-interactions in contrast with the other previous literature. We propose some realistic experimental setups to realize the atomic quantum simulator of the U(1) lattice gauge-Higgs model in a two-dimensional optical lattice. Our target gauge-Higgs model has a nontrivial phase structure, i.e., existence of the phase boundary between confinement and Higgs phases, and this phase boundary is to be observed by cold-atom experiments. As a reference to such experiments, we make numerical simulations of the time-dependent Gross-Pitaevskii equation and observe the real-time dynamics of the atomic simulators. Clarification of the dynamics of this gauge-Higgs model sheds some lights upon various unsolved problems including the inflation process of the early universe.

  14. Ultracold atoms in optical lattices simulating quantum many-body systems

    CERN Document Server

    Lewenstein, Maciej; Ahufinger, Verònica

    2012-01-01

    Quantum computers, though not yet available on the market, will revolutionize the future of information processing. Quantum computers for special purposes like quantum simulators are already within reach. The physics of ultracold atoms, ions and molecules offer unprecedented possibilities of control of quantum many body systems and novel possibilities of applications to quantum information processing and quantum metrology. Particularly fascinating is the possibility of usingultracold atoms in lattices to simulate condensed matter or even high energy physics.This book provides a complete and co

  15. Beyond Modeling: All-Atom Olfactory Receptor Model Simulations

    Directory of Open Access Journals (Sweden)

    Peter C Lai

    2012-05-01

    Full Text Available Olfactory receptors (ORs are a type of GTP-binding protein-coupled receptor (GPCR. These receptors are responsible for mediating the sense of smell through their interaction with odor ligands. OR-odorant interactions marks the first step in the process that leads to olfaction. Computational studies on model OR structures can validate experimental functional studies as well as generate focused and novel hypotheses for further bench investigation by providing a view of these interactions at the molecular level. Here we have shown the specific advantages of simulating the dynamic environment that is associated with OR-odorant interactions. We present a rigorous methodology that ranges from the creation of a computationally-derived model of an olfactory receptor to simulating the interactions between an OR and an odorant molecule. Given the ubiquitous occurrence of GPCRs in the membranes of cells, we anticipate that our OR-developed methodology will serve as a model for the computational structural biology of all GPCRs.

  16. Simulating Quantum Spin Models using Rydberg-Excited Atomic Ensembles in Magnetic Microtrap Arrays

    CERN Document Server

    Whitlock, Shannon; Hannaford, Peter

    2016-01-01

    We propose a scheme to simulate lattice spin models based on strong and long-range interacting Rydberg atoms stored in a large-spacing array of magnetic microtraps. Each spin is encoded in a collective spin state involving a single $nP$ Rydberg atom excited from an ensemble of ground-state alkali atoms prepared via Rydberg blockade. After the excitation laser is switched off the Rydberg spin states on neighbouring lattice sites interact via general isotropic or anisotropic spin-spin interactions. To read out the collective spin states we propose a single Rydberg atom triggered avalanche scheme in which the presence of a single Rydberg atom conditionally transfers a large number of ground-state atoms in the trap to an untrapped state which can be readily detected by site-resolved absorption imaging. Such a quantum simulator should allow the study of quantum spin systems in almost arbitrary two-dimensional configurations. This paves the way towards engineering exotic spin models, such as spin models based on tr...

  17. Acoustic Characterization of Compact Jet Engine Simulator Units

    Science.gov (United States)

    Doty, Michael J.; Haskin, Henry H.

    2013-01-01

    Two dual-stream, heated jet, Compact Jet Engine Simulator (CJES) units are designed for wind tunnel acoustic experiments involving a Hybrid Wing Body (HWB) vehicle. The newly fabricated CJES units are characterized with a series of acoustic and flowfield investigations to ensure successful operation with minimal rig noise. To limit simulator size, consistent with a 5.8% HWB model, the CJES units adapt Ultra Compact Combustor (UCC) technology developed at the Air Force Research Laboratory. Stable and controllable operation of the combustor is demonstrated using passive swirl air injection and backpressuring of the combustion chamber. Combustion instability tones are eliminated using nonuniform flow conditioners in conjunction with upstream screens. Through proper flow conditioning, rig noise is reduced by more than 20 dB over a broad spectral range, but it is not completely eliminated at high frequencies. The low-noise chevron nozzle concept designed for the HWB test shows expected acoustic benefits when installed on the CJES unit, and consistency between CJES units is shown to be within 0.5 dB OASPL.

  18. Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure.

    Science.gov (United States)

    van der Linden, Marx Gomes; Ferreira, Diogo César; de Oliveira, Leandro Cristante; Onuchic, José N; de Araújo, Antônio F Pereira

    2014-07-01

    The three-dimensional structure of proteins is determined by their linear amino acid sequences but decipherment of the underlying protein folding code has remained elusive. Recent studies have suggested that burials, as expressed by atomic distances to the molecular center, are sufficiently informative for structural determination while potentially obtainable from sequences. Here we provide direct evidence for this distinctive role of burials in the folding code, demonstrating that burial propensities estimated from local sequence can indeed be used to fold globular proteins in ab initio simulations. We have used a statistical scheme based on a Hidden Markov Model (HMM) to classify all heavy atoms of a protein into a small number of burial atomic types depending on sequence context. Molecular dynamics simulations were then performed with a potential that forces all atoms of each type towards their predicted burial level, while simple geometric constraints were imposed on covalent structure and hydrogen bond formation. The correct folded conformation was obtained and distinguished in simulations that started from extended chains for a selection of structures comprising all three folding classes and high burial prediction quality. These results demonstrate that atomic burials can act as informational intermediates between sequence and structure, providing a new conceptual framework for improving structural prediction and understanding the fundamentals of protein folding.

  19. Efficient molecular dynamics simulations with many-body potentials on graphics processing units

    Science.gov (United States)

    Fan, Zheyong; Chen, Wei; Vierimaa, Ville; Harju, Ari

    2017-09-01

    Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. In the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within different loops, which could result in write conflict between different threads in a CUDA kernel. In this work, we provide a new force evaluation algorithm, which is based on an explicit pairwise force expression for many-body potentials derived recently (Fan et al., 2015). In our algorithm, the force, virial stress, and heat current for a given atom can be accumulated within a single thread and is free of write conflicts. We discuss the formulations and algorithms and evaluate their performance. A new open-source code, GPUMD, is developed based on the proposed formulations. For the Tersoff many-body potential, the double precision performance of GPUMD using a Tesla K40 card is equivalent to that of the LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) molecular dynamics code running with about 100 CPU cores (Intel Xeon CPU X5670 @ 2.93 GHz).

  20. SPH Simulation of Liquid Scattering from the Edge of a Rotary Atomizer

    Science.gov (United States)

    Izawa, Seiichiro; Ito, Takuya; Shigeta, Masaya; Fukunishi, Yu

    2013-11-01

    Three-dimensional incompressible SPH method is used to simulate the behavior of liquid scattering from the edge of a rotary atomizer. Rotary atomizers have been widely used for spraying, painting and coating, for instance, in the automobile industry. However, how the spray droplets are formed after leaving the edge of the rotary atomizer is not well understood, because the scale of the phenomenon is very small and the speed of rotation is very fast. The present computational result shows that while the liquid forms a film on the surface of the rotating disk of the atomizer, it quickly deforms into many thin columns after leaving the disk edge, and these columns soon break up into fine droplets which spread out in the radial direction. The size of droplets tends to become smaller with the increase in the disk rotating speed. The results show good agreement with the experimental observations.

  1. Simulation of the transport of sputtered atoms and effects of processing conditions

    Energy Technology Data Exchange (ETDEWEB)

    Settaouti, A. [Electrotechnic Department, University of Sciences and Technology, P.O. Box 1505, EL-M' naouar, Oran (Algeria)], E-mail: settaouti@yahoo.fr; Settaouti, L. [Electrotechnic Department, University of Sciences and Technology, P.O. Box 1505, EL-M' naouar, Oran (Algeria)

    2008-07-15

    Sputter deposition is a complex process; it is obvious that the energy and direction of the particles arriving at the substrate is in close relation with the transport process from the target to the substrate, it is desirable to model this transport of atoms through the background gas. The transport of sputtered Ag atoms during sputter deposition through the gas phase in the facing targets sputtering system studied by Monte Carlo simulation is presented. The model calculates the flux of the atoms arriving at the substrate, their energy, direction and number of collisions they underwent. The dependence of the deposition rates of Ag atoms on the gas pressure and the distance between the targets and substrate were investigated.

  2. On new definitions of SI base units. Why is the "atomic" kilogram preferable

    CERN Document Server

    Bronnikov, K A; Kalinin, M I; Khruschov, V V; Kononogov, S A; Melnikov, V N

    2014-01-01

    We discuss the role of fundamental constants and measurement data for the Planck, Avogadro and Boltzmann constants and the elementary electric charge in connection with the planned transition to new definitions of four base SI units (the kilogram, mole, ampere and kelvin) in terms of fixed values of these constants. It is proposed to choose a new definition of any base SI unit in terms of a particular fundamental physical constant using a number of criteria, or principles, such as succession relative to the current SI, a sufficient stability of the new unit standards, and concordance between physical dimensions of the unit and the corresponding fundamental constant. It is argued that a redefinition of the kilogram and mole by fixing the values of the atomic mass unit and the Avogadro constant satisfies all these criteria and bears some more advantages against the version with fixed Planck constant: a well founded approach to definition of the ampere and the opportunity to preserve the current relationship bet...

  3. Molecular dynamics simulations investigating consecutive nucleation, solidification and grain growth in a twelve-million-atom Fe-system

    Science.gov (United States)

    Okita, Shin; Verestek, Wolfgang; Sakane, Shinji; Takaki, Tomohiro; Ohno, Munekazu; Shibuta, Yasushi

    2017-09-01

    Continuous processes of homogeneous nucleation, solidification and grain growth are spontaneously achieved from an undercooled iron melt without any phenomenological parameter in the molecular dynamics (MD) simulation with 12 million atoms. The nucleation rate at the critical temperature is directly estimated from the atomistic configuration by cluster analysis to be of the order of 1034 m-3 s-1. Moreover, time evolution of grain size distribution during grain growth is obtained by the combination of Voronoi and cluster analyses. The grain growth exponent is estimated to be around 0.3 from the geometric average of the grain size distribution. Comprehensive understanding of kinetic properties during continuous processes is achieved in the large-scale MD simulation by utilizing the high parallel efficiency of a graphics processing unit (GPU), which is shedding light on the fundamental aspects of production processes of materials from the atomistic viewpoint.

  4. Quantum simulation of the Hubbard model with dopant atoms in silicon.

    Science.gov (United States)

    Salfi, J; Mol, J A; Rahman, R; Klimeck, G; Simmons, M Y; Hollenberg, L C L; Rogge, S

    2016-04-20

    In quantum simulation, many-body phenomena are probed in controllable quantum systems. Recently, simulation of Bose-Hubbard Hamiltonians using cold atoms revealed previously hidden local correlations. However, fermionic many-body Hubbard phenomena such as unconventional superconductivity and spin liquids are more difficult to simulate using cold atoms. To date the required single-site measurements and cooling remain problematic, while only ensemble measurements have been achieved. Here we simulate a two-site Hubbard Hamiltonian at low effective temperatures with single-site resolution using subsurface dopants in silicon. We measure quasi-particle tunnelling maps of spin-resolved states with atomic resolution, finding interference processes from which the entanglement entropy and Hubbard interactions are quantified. Entanglement, determined by spin and orbital degrees of freedom, increases with increasing valence bond length. We find separation-tunable Hubbard interaction strengths that are suitable for simulating strongly correlated phenomena in larger arrays of dopants, establishing dopants as a platform for quantum simulation of the Hubbard model.

  5. Relaxation of a simulated lipid bilayer vesicle compressed by an atomic force microscope

    Science.gov (United States)

    Barlow, Ben M.; Bertrand, Martine; Joós, Béla

    2016-11-01

    Using coarse-grained molecular dynamics simulations, we study the relaxation of bilayer vesicles, uniaxially compressed by an atomic force microscope cantilever. The relaxation time exhibits a strong force dependence. Force-compression curves are very similar to recent experiments wherein giant unilamellar vesicles were compressed in a nearly identical manner.

  6. Disposal of radioactive wastes arising in the United Kingdom from the peaceful uses of atomic energy

    CERN Document Server

    Bryant, P M

    1971-01-01

    This paper describes United Kingdom policy in relation to radioactive waste and summarises the relevant legislation ad methods of control. Data are given on the amounts of radioactivity discharged as waste from establishments of the United Kingdom Atomic Energy Authority, the nuclear power stations operated by the Electricity Generating Boards and other users of radioactive materials. Studies of the behaviour of radioactivity in the environment are reported with particular reference to food chains and other potential sources of irradiation of the public. The results of environmental monitoring are presented and estimates are made of radiation doses received by individual members of the public and larger population groups as a result of waste disposal. It is concluded that the doses received are all within the appropriate limits recommended by the International Commission on Radiological Protection, and in most cases are trivial.

  7. An explicit algorithm for fully flexible unit cell simulation with recursive thermostat chains.

    Science.gov (United States)

    Jung, Kwangsub; Cho, Maenghyo

    2008-10-28

    Through the combination of the recursive multiple thermostat (RMT) Nose-Poincare and Parrinello-Rahman methods, the recursive multiple thermostat chained fully flexible unit cell (RMT-NsigmaT) molecular dynamics method is proposed for isothermal-isobaric simulation. The RMT method is known to have the advantage of achieving the ergodicity that is required for canonical sampling of the harmonic oscillator. Thus, an explicit time integration algorithm is developed for RMT-NsigmaT. We examine the ergodicity for various parameters of RMT-NsigmaT using bulk and thin film structures with different numbers of copper atoms and thicknesses in various environments. Through the numerical simulations, we conclude that the RMT-NsigmaT method is advantageous in the cases of lower temperatures.

  8. Efficient magnetohydrodynamic simulations on graphics processing units with CUDA

    Science.gov (United States)

    Wong, Hon-Cheng; Wong, Un-Hong; Feng, Xueshang; Tang, Zesheng

    2011-10-01

    Magnetohydrodynamic (MHD) simulations based on the ideal MHD equations have become a powerful tool for modeling phenomena in a wide range of applications including laboratory, astrophysical, and space plasmas. In general, high-resolution methods for solving the ideal MHD equations are computationally expensive and Beowulf clusters or even supercomputers are often used to run the codes that implemented these methods. With the advent of the Compute Unified Device Architecture (CUDA), modern graphics processing units (GPUs) provide an alternative approach to parallel computing for scientific simulations. In this paper we present, to the best of the author's knowledge, the first implementation of MHD simulations entirely on GPUs with CUDA, named GPU-MHD, to accelerate the simulation process. GPU-MHD supports both single and double precision computations. A series of numerical tests have been performed to validate the correctness of our code. Accuracy evaluation by comparing single and double precision computation results is also given. Performance measurements of both single and double precision are conducted on both the NVIDIA GeForce GTX 295 (GT200 architecture) and GTX 480 (Fermi architecture) graphics cards. These measurements show that our GPU-based implementation achieves between one and two orders of magnitude of improvement depending on the graphics card used, the problem size, and the precision when comparing to the original serial CPU MHD implementation. In addition, we extend GPU-MHD to support the visualization of the simulation results and thus the whole MHD simulation and visualization process can be performed entirely on GPUs.

  9. SIMULATION IN THERMAL DESIGN FOR ELECTRONIC CONTROL UNIT OF ELECTRONIC UNIT PUMP

    Institute of Scientific and Technical Information of China (English)

    XU Quankui; ZHU Keqing; ZHUO Bin; MAO Xiaojian; WANG Junxi

    2008-01-01

    The high working junction temperature of power component is the most common reason of its failure. So the thermal design is of vital importance in electronic control unit (ECU) design. By means of circuit simulation, the thermal design of ECU for electronic unit pump (EUP) fuel system is applied. The power dissipation model of each power component in the ECU is created and simulated. According to the analyses of simulation results, the factors which affect the power dissipation of components are analyzed. Then the ways for reducing the power dissipation of power components are carried out. The power dissipation of power components at different engine state is calculated and analyzed. The maximal power dissipation of each power component in all possible engine state is also carried out based on these simulations. A cooling system is designed based on these studies. The tests show that the maximum total power dissipation of ECU drops from 43.2 W to 33.84 W after these simulations and optimizations. These applications of simulations in thermal design of ECU can greatly increase the quality of the design, save the design cost and shorten design time

  10. Atomic Quantum Simulations of Abelian and non-Abelian Gauge Theories

    CERN Document Server

    CERN. Geneva

    2014-01-01

    Using a Fermi-Bose mixture of ultra-cold atoms in an optical lattice, in a collaboration of atomic and particle physicists, we have constructed a quantum simulator for a U(1) gauge theory coupled to fermionic matter. The construction is based on quantum link models which realize continuous gauge symmetry with discrete quantum variables. At low energies, quantum link models with staggered fermions emerge from a Hubbard-type model which can be quantum simulated. This allows investigations of string breaking as well as the real-time evolution after a quench in gauge theories, which are inaccessible to classical simulation methods. Similarly, using ultracold alkaline-earth atoms in optical lattices, we have constructed a quantum simulator for U(N) and SU(N) lattice gauge theories with fermionic matter based on quantum link models. These systems share qualitative features with QCD, including chiral symmetry breaking and restoration at non-zero temperature or baryon density. Unlike classical simulations, a quantum ...

  11. High-Fidelity Simulations of Electrically-Charged Atomizing Diesel-Type Jets

    Science.gov (United States)

    Gaillard, Benoit; Owkes, Mark; van Poppel, Bret

    2015-11-01

    Combustion of liquid fuels accounts for over a third of the energy usage today. Improving efficiency of combustion systems is critical to meet the energy needs while limiting environmental impacts. Additionally, a shift away from traditional fossil fuels to bio-derived alternatives requires fuel injection systems that can atomize fuels with a wide range of properties. In this work, the potential benefits of electrically-charged atomization is investigated using numerical simulations. Particularly, the electrostatic forces on the hydrodynamic jet are quantified and the impact of the forces is analyzed by comparing simulations of Diesel-type jets at realistic flow conditions. The simulations are performed using a state-of-the-art numerical framework that globally conserves mass, momentum, and the electric charge density even at the gas-liquid interface where discontinuities exist.

  12. Atom dynamics in optical lattices: Time-dependent simulation and decoherence suppression

    Science.gov (United States)

    de Rinaldis, Sergio; Lidar, Daniel A.

    2004-03-01

    We develop a model to simulate the dynamics of atoms trapped in an optical lattice with gravity in the presence of natural decoherence. The latter, measured by quantum process tomography, is dominated by pure dephasing. The wavefunction is represented on a grid and the time dependent evolution operator is expanded in Chebychev polynomials according to the (t,t') method (*), while a fictitious environment is introduced that simulates the observed dephasing. The control field consists in raising or lowering the potential wells of the atoms and modifying the phase of the laser fields (that results in a translation of the lattice). As an example relevant for quantum information processing, we simulate the effect of bang-bang pulses designed to suppress decoherence. (*) Ref. U.Peskin, R. Kosloff, N. Moiseyev, J. Chem. Phys. 8849 (1994)

  13. Atomic simulation of amorphization and crystallization of Ag50 Au50 alloy during rapid solidification

    Institute of Scientific and Technical Information of China (English)

    王丽; 杨华; 张均艳; 边秀房; 衣粟

    2002-01-01

    By means of constant temperature and constant pressure molecular dynamic simulation technique, a series of simulations of the glass transition and crystallization processes of Ag50Au50 were performed. The atoms interact via EAM potential function. Pair correlation functions of liquid Ag50Au50 during different cooling rates and temperatures were simulated to reveal the structural features of liquid, super-cooled liquid, glass state and crystal. The thermodynamics and kinetics of structure transition of Ag50Au50 during cooling processes were performed.

  14. Line-by-line spectroscopic simulations on graphics processing units

    Science.gov (United States)

    Collange, Sylvain; Daumas, Marc; Defour, David

    2008-01-01

    We report here on software that performs line-by-line spectroscopic simulations on gases. Elaborate models (such as narrow band and correlated-K) are accurate and efficient for bands where various components are not simultaneously and significantly active. Line-by-line is probably the most accurate model in the infrared for blends of gases that contain high proportions of H 2O and CO 2 as this was the case for our prototype simulation. Our implementation on graphics processing units sustains a speedup close to 330 on computation-intensive tasks and 12 on memory intensive tasks compared to implementations on one core of high-end processors. This speedup is due to data parallelism, efficient memory access for specific patterns and some dedicated hardware operators only available in graphics processing units. It is obtained leaving most of processor resources available and it would scale linearly with the number of graphics processing units in parallel machines. Line-by-line simulation coupled with simulation of fluid dynamics was long believed to be economically intractable but our work shows that it could be done with some affordable additional resources compared to what is necessary to perform simulations on fluid dynamics alone. Program summaryProgram title: GPU4RE Catalogue identifier: ADZY_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZY_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.: 62 776 No. of bytes in distributed program, including test data, etc.: 1 513 247 Distribution format: tar.gz Programming language: C++ Computer: x86 PC Operating system: Linux, Microsoft Windows. Compilation requires either gcc/g++ under Linux or Visual C++ 2003/2005 and Cygwin under Windows. It has been tested using gcc 4.1.2 under Ubuntu Linux 7.04 and using Visual C

  15. Modified morphology of graphene sheets by Argon-atom bombardment: molecular dynamics simulations.

    Science.gov (United States)

    Wei, Xiao-Lin; Zhang, Kai-Wang; Wang, Ru-Zhi; Liu, Wen-Liang; Zhong, Jian-Xin

    2011-12-01

    By a molecular dynamics method, we simulated the process of Argon-atom bombardment on a graphene sheet with 2720 carbon atoms. The results show that, the damage of the bombardment on the graphene sheet depends not only on the incident energy but also on the particle flux density of Argon atoms. To compare and analyze the effect of the incident energy and the particle flux density in the Argon-atom bombardment, we defined the impact factor on graphene sheet by calculating the broken-hole area. The results indicate that, there is an exponential accumulated-damage for the impact of both the incident energy and the particle flux density and there is a critical incident energy ranging from 20-30 eV/atom in Argon-atom bombardment. Different configurations, such as sieve-like and circle-like graphene can be formed by controlling of different particle flux density as the incident energy is more than the critical value. Our results supply a feasible method on fabrication of porous graphene-based materials for gas-storages and molecular sieves, and it also helps to understand the damage mechanism of graphene-based electronic devices under high particle radiation.

  16. Intermolecular orientations in liquid acetonitrile: new insights based on diffraction measurements and all-atom simulations

    CERN Document Server

    Pothoczki, Szilvia

    2016-01-01

    Intermolecular correlations in liquid acetonitrile (CH3CN) have been revisited by calculating orientational correlation functions. In the present approach, hydrogen atoms are included, so that a concept applicable for molecules of (nearly) tetrahedral shape can be exploited. In this way molecular arrangements are elucidated not only for closest neighbours but also extending well beyond the first coordination sphere. Thus a complementary viewpoint is provided to the more popular dipole-dipole correlations. Our calculations are based on large structural models that were obtained by applying diffraction data and partial radial distribution functions from potential-based (all-atom) molecular dynamics simulation simultaneously, within the framework of the Reverse Monte Carlo method.

  17. A Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision

    CERN Document Server

    Mansour, Andrew Abi

    2013-01-01

    Mesoscopic N-atom systems derive their structural and dynamical properties from processes coupled across multiple scales in space and time. An efficient method for understanding and simulating such systems from the underlying N-atom formulation is presented. The method integrates notions of multiscale analysis, Trotter factorization, and a hypothesis that the momenta conjugate to coarse-grained variables can be treated as a stationary random process. The method is demonstrated for Lactoferrin protein, Nudaurelia Capensis Omega Virus, and Cowpea Chlorotic Mottle Virus to assess its accuracy and scaling with system size.

  18. Monte Carlo simulations of phase transitions and lattice dynamics in an atom-phonon model for spin transition compounds

    Energy Technology Data Exchange (ETDEWEB)

    Apetrei, Alin Marian, E-mail: alin.apetrei@uaic.r [Department of Physics, Alexandru Ioan Cuza University of Iasi, 11 Blvd. Carol I, Iasi 700506 (Romania); Enachescu, Cristian; Tanasa, Radu; Stoleriu, Laurentiu; Stancu, Alexandru [Department of Physics, Alexandru Ioan Cuza University of Iasi, 11 Blvd. Carol I, Iasi 700506 (Romania)

    2010-09-01

    We apply here the Monte Carlo Metropolis method to a known atom-phonon coupling model for 1D spin transition compounds (STC). These inorganic molecular systems can switch under thermal or optical excitation, between two states in thermodynamical competition, i.e. high spin (HS) and low spin (LS). In the model, the ST units (molecules) are linked by springs, whose elastic constants depend on the spin states of the neighboring atoms, and can only have three possible values. Several previous analytical papers considered a unique average value for the elastic constants (mean-field approximation) and obtained phase diagrams and thermal hysteresis loops. Recently, Monte Carlo simulation papers, taking into account all three values of the elastic constants, obtained thermal hysteresis loops, but no phase diagrams. Employing Monte Carlo simulation, in this work we obtain the phase diagram at T=0 K, which is fully consistent with earlier analytical work; however it is more complex. The main difference is the existence of two supplementary critical curves that mark a hysteresis zone in the phase diagram. This explains the pressure hysteresis curves at low temperature observed experimentally and predicts a 'chemical' hysteresis in STC at very low temperatures. The formation and the dynamics of the domains are also discussed.

  19. Discrete Event Simulation of Patient Admissions to a Neurovascular Unit

    Directory of Open Access Journals (Sweden)

    S. Hahn-Goldberg

    2014-01-01

    Full Text Available Evidence exists that clinical outcomes improve for stroke patients admitted to specialized Stroke Units. The Toronto Western Hospital created a Neurovascular Unit (NVU using beds from general internal medicine, Neurology and Neurosurgery to care for patients with stroke and acute neurovascular conditions. Using patient-level data for NVU-eligible patients, a discrete event simulation was created to study changes in patient flow and length of stay pre- and post-NVU implementation. Varying patient volumes and resources were tested to determine the ideal number of beds under various conditions. In the first year of operation, the NVU admitted 507 patients, over 66% of NVU-eligible patient volumes. With the introduction of the NVU, length of stay decreased by around 8%. Scenario testing showed that the current level of 20 beds is sufficient for accommodating the current demand and would continue to be sufficient with an increase in demand of up to 20%.

  20. Diffusion simulation of Cr-Fe bcc systems at atomic level using a random walk algorithm

    Energy Technology Data Exchange (ETDEWEB)

    San Sebastian, I.; Aldazabal, J. [CEIT and Tecnun (University of Navarra), San Sebastian (Spain); Capdevila, C.; Garcia-Mateo, C. [MATERALIA Research Group, Department of Physical Metallurgy, Centro Nacional de Investigaciones Metalurgicas (CENIM-CSIC), Avda. Gregorio del Amo 8, 28040 Madrid (Spain)

    2008-06-15

    This paper proposes a model to simulate the diffusion of impurities in bcc atomic lattices. It works with three-dimensional volume, divided in small cubic elements (voxels), containing more than one atomic cell each. Once the domain is discretized, impurities jump from one voxel to another according to certain probability that takes into account the composition and geometry of the target voxel. In the present work, a model was applied to a prismatic volume and in order to deduce the relationship between the atomic jumping frequency and the temperature two different cases were studied. One consists of a Fe matrix with Cr impurities, and the other is based on a Cr matrix with Fe impurities. Results obtained from these simulations were compared with profiles obtained by Dictra software. Results for the atomic jumping frequencies were fitted to an Arrhenius type equation, as shown in following expressions: From these equations it is possible to obtain an activation energy for the atomic jumping phenomenon of {proportional_to}306 kJ/mol and {proportional_to}411 kJ/mol for the Fe-matrix and Cr-matrix systems, respectively. These energies match the empirical measured values for the diffusion of Cr and Fe impurities, 250 kJ/mol and 407 kJ/mol, respectively. Results obtained in this work assure that the proposed model is suitable for simulating the three-dimensional diffusion of substitutional impurities in Cr and Fe bcc systems. It could be easily expanded to other bcc matrix systems. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  1. PORFLOW Simulations Supporting Saltstone Disposal Unit Design Optimization

    Energy Technology Data Exchange (ETDEWEB)

    Flach, G. P. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Hang, T. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Taylor, G. A. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-12-10

    SRNL was requested by SRR to perform PORFLOW simulations to support potential cost-saving design modifications to future Saltstone Disposal Units in Z-Area (SRR-CWDA-2015-00120). The design sensitivity cases are defined in a modeling input specification document SRR-CWDA-2015-00133 Rev. 1. A high-level description of PORFLOW modeling and interpretation of results are provided in SRR-CWDA-2015-00169. The present report focuses on underlying technical issues and details of PORFLOW modeling not addressed by the input specification and results interpretation documents. Design checking of PORFLOW modeling is documented in SRNL-L3200-2015-00146.

  2. Simulating Lattice Spin Models on Graphics Processing Units

    CERN Document Server

    Levy, Tal; Rabani, Eran; 10.1021/ct100385b

    2012-01-01

    Lattice spin models are useful for studying critical phenomena and allow the extraction of equilibrium and dynamical properties. Simulations of such systems are usually based on Monte Carlo (MC) techniques, and the main difficulty is often the large computational effort needed when approaching critical points. In this work, it is shown how such simulations can be accelerated with the use of NVIDIA graphics processing units (GPUs) using the CUDA programming architecture. We have developed two different algorithms for lattice spin models, the first useful for equilibrium properties near a second-order phase transition point and the second for dynamical slowing down near a glass transition. The algorithms are based on parallel MC techniques, and speedups from 70- to 150-fold over conventional single-threaded computer codes are obtained using consumer-grade hardware.

  3. Polymer Field-Theory Simulations on Graphics Processing Units

    CERN Document Server

    Delaney, Kris T

    2012-01-01

    We report the first CUDA graphics-processing-unit (GPU) implementation of the polymer field-theoretic simulation framework for determining fully fluctuating expectation values of equilibrium properties for periodic and select aperiodic polymer systems. Our implementation is suitable both for self-consistent field theory (mean-field) solutions of the field equations, and for fully fluctuating simulations using the complex Langevin approach. Running on NVIDIA Tesla T20 series GPUs, we find double-precision speedups of up to 30x compared to single-core serial calculations on a recent reference CPU, while single-precision calculations proceed up to 60x faster than those on the single CPU core. Due to intensive communications overhead, an MPI implementation running on 64 CPU cores remains two times slower than a single GPU.

  4. A molecular dynamics simulation of hydrogen atoms collisions on an H-preadsorbed silica surface

    Science.gov (United States)

    Rutigliano, M.; Gamallo, P.; Sayós, R.; Orlandini, S.; Cacciatore, M.

    2014-08-01

    The interaction of hydrogen atoms and molecules with a silica surface is relevant for many research and technological areas. Here, the dynamics of hydrogen atoms colliding with an H-preadsorbed β-cristobalite (0 0 1) surface has been studied using a semiclassical collisional method in conjunction with a recently developed analytical potential energy surface based on density functional theory (DFT) calculations. The atomic recombination probability via an Eley-Rideal (E-R) mechanism, as well as the probabilities for other competitive surface processes, have been determined in a broad range of collision energies (0.04-3.0 eV) for off-normal (θv = 45°) and normal (θv = 0°) incidence and for two different surface temperatures (TS = 300 and 1000 K). H2,gas molecules form in roto-vibrational excited levels while the energy transferred to the solid surface is below 10% for all simulated conditions. Finally, the global atomic recombination coefficient (γE-R) and vibrational state resolved recombination coefficients (γ(v)) were calculated and compared with the available experimental values. The calculated collisional data are of interest in chemical kinetics studies and fluid dynamics simulations of silica surface processes in H-based low-temperature, low-pressure plasmas.

  5. Route to One Atomic Unit of Time: Development of a Broadband Attosecond Streak Camera

    Science.gov (United States)

    Zhao, Kun; Zhang, Qi; Chini, Michael; Chang, Zenghu

    A new attosecond streak camera based on a three-meter-long magnetic-bottle time-of-flight electron spectrometer (MBES) is developed. The temporal resolution of the photoelectron detection system is measured to be better than 250 ps, which is sufficient to achieve an energy resolution of 0.5 eV at 150 eV photoelectron energy. In preliminary experiments, a 94-as isolated XUV pulse was generated and characterized. With a new algorithm to retrieve the amplitude and phase of XUV pulses (PROOF—phase retrieval by omega oscillation filtering), the attosecond streak camera will be able to characterize isolated attosecond pulses as short as one atomic unit of time (25 as).

  6. Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations

    Science.gov (United States)

    Perilla, Juan R.; Schulten, Klaus

    2017-07-01

    Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of ~1,300 proteins with altogether 4 million atoms. Although the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical-physical properties of an empty HIV-1 capsid, including its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. The simulations reveal critical details about the capsid with implications to biological function.

  7. High Resolution Numerical Simulations of Primary Atomization in Diesel Sprays with Single Component Reference Fuels

    Science.gov (United States)

    2015-09-01

    NC. 14. ABSTRACT A high-resolution numerical simulation of jet breakup and spray formation from a complex diesel fuel injector at diesel engine ... diesel fuel injector at diesel engine type conditions has been performed. A full understanding of the primary atomization process in diesel fuel...the capability of a recently adopted high fidelity two phase flow solver in the context of diesel engine sprays. Previous works relating to this

  8. Synthesis, Characterization, and Multimillion-Atom Simulation of Halogen-Based Energetic Materials for Agent Defeat

    Science.gov (United States)

    2013-04-01

    Kolesnikov NIST: Liu New Discoveries, Inventions, or Patent Disclosures K. O. Christe and G. Drake, “Energetic Ionic Liquids ,” US Patent 7,771,549, Aug...DTRA-TR-13-23 Synthesis, Characterization, and Multimillion-Atom Simulation of Halogen -Based Energetic Materials for Agent Defeat Approved for...second foot foot-pound-force gallon (U.S. liquid ) inch jerk joule/kilogram (J/kg) radiation dose absorbed kilotons kip (1000 lbf) kip/inch 2

  9. MONTE-CARLO SIMULATION FOR ATOMIC DEPOSITION OF AMORPHOUS ELECTROLESS Ni80P20 COATING

    Institute of Scientific and Technical Information of China (English)

    K.S. Guan; H.R. Bai; Z.W. Wang; Y.S. Yin

    2002-01-01

    Atomic growth process and structure of Amorphous Electroless Coating have beenstudied, using Monte-Carlo simulation method. The simulation results of amorphousNi80P20 coating show that PDFs are in accordance with practical values. The mi-grations of adatoms in coating's growth are different from that of solidification ofamorphous materials. In some cases, the migrated adatoms in the process of growthof amorphous coating are not enough to occupy all vacancies and traps, so the amor-phous coating is micro-porous. The immovable probability k and the largest migrationdistance of adatoms, which lie on the electroless bath components, affect the PDF,volume density and microporosity remarkably.

  10. Fine-tuning of atomic point charges: Classical simulations of pyridine in different environments

    Science.gov (United States)

    Macchiagodena, Marina; Mancini, Giordano; Pagliai, Marco; Del Frate, Gianluca; Barone, Vincenzo

    2017-06-01

    A correct description of electrostatic contributions in force fields for classical simulations is mandatory for an accurate modeling of molecular interactions in pure liquids or solutions. Here, we propose a new protocol for point charge fitting, aimed to take into the proper account different polarization effects due to the environment employing virtual sites and tuning the point charge within the polarizable continuum model framework. The protocol has been validated by means of molecular dynamics simulations on pure pyridine liquid and on pyridine aqueous solution, reproducing a series of experimental observables and providing the information for their correct interpretation at atomic level.

  11. Atomic-scale simulations of the mechanical deformation of nanocrystalline metals

    DEFF Research Database (Denmark)

    Schiøtz, Jakob; Vegge, Tejs; Di Tolla, Francesco

    1999-01-01

    Nanocrystalline metals, i.e., metals in which the grain size is in the nanometer range, have a range of technologically interesting properties including increased hardness and yield strength. We present atomic-scale simulations of the plastic behavior of nanocrystalline copper. The simulations show...... leads to a hardening as the grain size is increased (reverse Hall-Fetch effect), implying a maximum in hardness for a grain size above the ones studied here. We investigate the effects of varying temperature, strain rate, and porosity, and discuss the relation to recent experiments. At increasing...

  12. Microstructure simulation of rapidly solidified ASP30 high-speed steel particles by gas atomization

    Science.gov (United States)

    Ma, Jie; Wang, Bo; Yang, Zhi-liang; Wu, Guang-xin; Zhang, Jie-yu; Zhao, Shun-li

    2016-03-01

    In this study, the microstructure evolution of rapidly solidified ASP30 high-speed steel particles was predicted using a simulation method based on the cellular automaton-finite element (CAFE) model. The dendritic growth kinetics, in view of the characteristics of ASP30 steel, were calculated and combined with macro heat transfer calculations by user-defined functions (UDFs) to simulate the microstructure of gas-atomized particles. The relationship among particle diameter, undercooling, and the convection heat transfer coefficient was also investigated to provide cooling conditions for simulations. The simulated results indicated that a columnar grain microstructure was observed in small particles, whereas an equiaxed microstructure was observed in large particles. In addition, the morphologies and microstructures of gas-atomized ASP30 steel particles were also investigated experimentally using scanning electron microscopy (SEM). The experimental results showed that four major types of microstructures were formed: dendritic, equiaxed, mixed, and multi-droplet microstructures. The simulated results and the available experimental data are in good agreement.

  13. Atomic and dislocation dynamics simulations of plastic deformation in reactor pressure vessel steel

    Science.gov (United States)

    Monnet, Ghiath; Domain, Christophe; Queyreau, Sylvain; Naamane, Sanae; Devincre, Benoit

    2009-11-01

    The collective behavior of dislocations in reactor pressure vessel (RPV) steel involves dislocation properties on different phenomenological scales. In the multiscale approach, adopted in this work, we use atomic simulations to provide input data for larger scale simulations. We show in this paper how first-principles calculations can be used to describe the Peierls potential of screw dislocations, allowing for the validation of the empirical interatomic potential used in molecular dynamics simulations. The latter are used to compute the velocity of dislocations as a function of the applied stress and the temperature. The mobility laws obtained in this way are employed in dislocation dynamics simulations in order to predict properties of plastic flow, namely dislocation-dislocation interactions and dislocation interactions with carbides at low and high temperature.

  14. First-Principles Atomic Force Microscopy Image Simulations with Density Embedding Theory.

    Science.gov (United States)

    Sakai, Yuki; Lee, Alex J; Chelikowsky, James R

    2016-05-11

    We present an efficient first-principles method for simulating noncontact atomic force microscopy (nc-AFM) images using a "frozen density" embedding theory. Frozen density embedding theory enables one to efficiently compute the tip-sample interaction by considering a sample as a frozen external field. This method reduces the extensive computational load of first-principles AFM simulations by avoiding consideration of the entire tip-sample system and focusing on the tip alone. We demonstrate that our simulation with frozen density embedding theory accurately reproduces full density functional theory simulations of freestanding hydrocarbon molecules while the computational time is significantly reduced. Our method also captures the electronic effect of a Cu(111) substrate on the AFM image of pentacene and reproduces the experimental AFM image of Cu2N on a Cu(100) surface. This approach is applicable for theoretical imaging applications on large molecules, two-dimensional materials, and materials surfaces.

  15. Simulating compact quantum electrodynamics with ultracold atoms: probing confinement and nonperturbative effects.

    Science.gov (United States)

    Zohar, Erez; Cirac, J Ignacio; Reznik, Benni

    2012-09-21

    Recently, there has been much interest in simulating quantum field theory effects of matter and gauge fields. In a recent work, a method for simulating compact quantum electrodynamics (CQED) using Bose-Einstein condensates has been suggested. We suggest an alternative approach, which relies on single atoms in an optical lattice, carrying 2l + 1 internal levels, which converges rapidly to CQED as l increases. That enables the simulation of CQED in 2 + 1 dimensions in both the weak and the strong coupling regimes, hence, allowing us to probe confinement as well as other nonperturbative effects of the theory. We provide an explicit construction for the case l = 1 which is sufficient for simulating the effect of confinement between two external static charges.

  16. Atomic and dislocation dynamics simulations of plastic deformation in reactor pressure vessel steel

    Energy Technology Data Exchange (ETDEWEB)

    Monnet, Ghiath, E-mail: ghiathmonnet@yahoo.f [EDF-R and D, MMC, Avenue des Renardieres, 77818 Moret sur Loing (France); Domain, Christophe; Queyreau, Sylvain; Naamane, Sanae [EDF-R and D, MMC, Avenue des Renardieres, 77818 Moret sur Loing (France); Devincre, Benoit [LEM, CNRS-ONERA, 29 av. de la division Leclerc, 92130 Chatillon (France)

    2009-11-15

    The collective behavior of dislocations in reactor pressure vessel (RPV) steel involves dislocation properties on different phenomenological scales. In the multiscale approach, adopted in this work, we use atomic simulations to provide input data for larger scale simulations. We show in this paper how first-principles calculations can be used to describe the Peierls potential of screw dislocations, allowing for the validation of the empirical interatomic potential used in molecular dynamics simulations. The latter are used to compute the velocity of dislocations as a function of the applied stress and the temperature. The mobility laws obtained in this way are employed in dislocation dynamics simulations in order to predict properties of plastic flow, namely dislocation-dislocation interactions and dislocation interactions with carbides at low and high temperature.

  17. Simulating Potential Switchgrass Production in the United States

    Energy Technology Data Exchange (ETDEWEB)

    Thomson, Allison M.; Izaurralde, Roberto C.; West, T. O.; Parrish, David J.; Tyler, Donald D.; Williams, Jimmy R.

    2009-12-31

    Using results from field trials of switchgrass (Panicum virgatum L.) in the United States, the EPIC (Environmental Policy Integrated Climate) process-level agroecosystem model was calibrated, validated, and applied to simulate potential productivity of switchgrass for use as a biofuel feedstock. The model was calibrated with a regional study of 10-yr switchgrass field trials and subsequently tested against a separate compiled dataset of field trials from across the eastern half of the country. An application of the model in a national database using 8-digit watersheds as the primary modeling unit produces 30-yr average switchgrass yield estimates that can be aggregated to 18 major watersheds. The model projects average annual switchgrass productivity of greater than 7 Mg ha-1 in the Upper Mississippi, Lower Mississippi, and Ohio watersheds. The major factors limiting simulated production vary by region; low precipitation is the primary limiting factor across the western half of the country, while moderately acidic soils limit yields on lands east of the Mississippi River. Average projected switchgrass production on all crop land in the continental US is 5.6 Mg ha-1. At this level of productivity, 28.6 million hectares of crop land would be required to produce the 16 billion gallons of cellulosic ethanol called for by 2022 in the 2007 Energy Independence and Security Act. The model described here can be applied as a tool to inform the land-use and environmental consequences of switchgrass production.

  18. All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer.

    Science.gov (United States)

    Perlmutter, Jason D; Drasler, William J; Xie, Wangshen; Gao, Jiali; Popot, Jean-Luc; Sachs, Jonathan N

    2011-09-06

    Amphipathic polymers called amphipols (APols) have been developed as an alternative to detergents for stabilizing membrane proteins (MPs) in aqueous solutions. APols provide MPs with a particularly mild environment and, as a rule, keep them in a native functional state for longer periods than do detergents. Amphipol A8-35, a derivative of polyacrylate, is widely used and has been particularly well studied experimentally. In aqueous solutions, A8-35 molecules self-assemble into well-defined globular particles with a mass of ∼40 kDa and a R(g) of ∼2.4 nm. As a first step towards describing MP/A8-35 complexes by molecular dynamics (MD), we present three sets of simulations of the pure APol particle. First, we performed a series of all-atom MD (AAMD) simulations of the particle in solution, starting from an arbitrary initial configuration. Although AAMD simulations result in stable cohesive particles over a 45 ns simulation, the equilibration of the particle organization is limited. This motivated the use of coarse-grained MD (CGMD), allowing us to investigate processes on the microsecond time scale, including de novo particle assembly. We present a detailed description of the parametrization of the CGMD model from the AAMD simulations and a characterization of the resulting CGMD particles. Our third set of simulations utilizes reverse coarse-graining (rCG), through which we obtain all-atom coordinates from a CGMD simulation. This allows a higher-resolution characterization of a configuration determined by a long-timescale simulation. Excellent agreement is observed between MD models and experimental, small-angle neutron scattering data. The MD data provides new insight into the structure and dynamics of A8-35 particles, which is possibly relevant to the stabilizing effects of APols on MPs, as well as a starting point for modeling MP/A8-35 complexes.

  19. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.

    Science.gov (United States)

    Raval, Alpan; Piana, Stefano; Eastwood, Michael P; Dror, Ron O; Shaw, David E

    2012-08-01

    Accurate computational prediction of protein structure represents a longstanding challenge in molecular biology and structure-based drug design. Although homology modeling techniques are widely used to produce low-resolution models, refining these models to high resolution has proven difficult. With long enough simulations and sufficiently accurate force fields, molecular dynamics (MD) simulations should in principle allow such refinement, but efforts to refine homology models using MD have for the most part yielded disappointing results. It has thus far been unclear whether MD-based refinement is limited primarily by accessible simulation timescales, force field accuracy, or both. Here, we examine MD as a technique for homology model refinement using all-atom simulations, each at least 100 μs long-more than 100 times longer than previous refinement simulations-and a physics-based force field that was recently shown to successfully fold a structurally diverse set of fast-folding proteins. In MD simulations of 24 proteins chosen from the refinement category of recent Critical Assessment of Structure Prediction (CASP) experiments, we find that in most cases, simulations initiated from homology models drift away from the native structure. Comparison with simulations initiated from the native structure suggests that force field accuracy is the primary factor limiting MD-based refinement. This problem can be mitigated to some extent by restricting sampling to the neighborhood of the initial model, leading to structural improvement that, while limited, is roughly comparable to the leading alternative methods.

  20. Microscopic phase-field simulation of atomic site occupation in ordering process of NiAl9Fe6 alloy

    Institute of Scientific and Technical Information of China (English)

    LIANG Min-jie; CHEN Zheng; ZHANG Ji-xiang; WANG Yong-xin

    2008-01-01

    The process of γ(fcc)→γ(fcc)+γ'(L12) phase transformation was simulated by using microscopic phase-field method for the low supersaturation NiAl9Fe6 alloy. It is found that in the γ' phase, the ordering degree of Al atoms is obviously higher than that of Fe atoms, and the ordering of Al atoms precedes their clustering, while the case of Fe atoms is opposite. The α site is mainly occupied by Ni atoms, while the β site is occupied in common by Al, Fe and Ni atoms. At order-disorder interphase boundary, the ordering degree of Al atoms is higher than that of Fe atoms, and at the β site, the Fe atomic site occupation probabilities vary from high to low during ordering; the Al atomic site occupation probabilities are similar to those of Fe atoms, but their values are much higher than those of Fe atoms; Ni atoms are opposite to both of them. Meanwhile, during the ordering transformation, γ' phase is always a complex Ni3(AlFeNi) single-phase, and it is precipitated by the non-classical nucleation and growth style. Finally, in the alloy system, the volume of γ' ordered phase is less than that of γ phase, and the volume ratio of order to disorder is about 77%.

  1. Fuzzy unit commitment solution - A novel twofold simulated annealing approach

    Energy Technology Data Exchange (ETDEWEB)

    Saber, Ahmed Yousuf; Senjyu, Tomonobu; Yona, Atsushi; Urasaki, Naomitsu [Faculty of Engineering, University of the Ryukyus, 1 Senbaru, Nishihara-cho Nakagami, Okinawa 903-0213 (Japan); Funabashi, Toshihisa [Meidensha Corporation, Riverside Building 36-2, Tokyo 103-8515 (Japan)

    2007-10-15

    The authors propose a twofold simulated annealing (twofold-SA) method for the optimization of fuzzy unit commitment formulation in this paper. In the proposed method, simulated annealing (SA) and fuzzy logic are combined to obtain SA acceptance probabilities from fuzzy membership degrees. Fuzzy load is calculated from error statistics and an initial solution is generated by a priority list method. The initial solution is decomposed into hourly-schedules and each hourly-schedule is modified by decomposed-SA using a bit flipping operator. Fuzzy membership degrees are the selection attributes of the decomposed-SA. A new solution consists of these hourly-schedules of entire scheduling period after repair, as unit-wise constraints may not be fulfilled at the time of an individual hourly-schedule modification. This helps to detect and modify promising schedules of appropriate hours. In coupling-SA, this new solution is accepted for the next iteration if its cost is less than that of current solution. However, a higher cost new solution is accepted with the temperature dependent total cost membership function. Computation time of the proposed method is also improved by the imprecise tolerance of the fuzzy model. Besides, excess units with the system dependent probability distribution help to handle constraints efficiently and imprecise economic load dispatch (ELD) calculations are modified to save the execution time. The proposed method is tested using standard reported data sets. Numerical results show an improvement in solution cost and time compared to the results obtained from other existing methods. (author)

  2. The application of quasi-steady approximation in atomic kinetics in simulation of hohlraum radiation drive

    Science.gov (United States)

    Ren, Guoli; Pei, Wenbing; Lan, Ke; Li, Xin; Hohlraum Physics Team

    2014-10-01

    In current routine 2D simulation of hohlraum physics, we adopt the principal-quantum-number (n-level) average atom model (AAM) in NLTE plasma description. The more sophisticated atomic kinetics description is better choice, but the in-line calculation consumes much more resource. By distinguishing the much more fast bound-bound atomic processes from the relative slow bound-free atomic processes, we found a method to built up a bound electron distribution (n-level or nl-level) using in-line n-level calculated plasma condition (such as temperature, density, average ionization degree). We name this method ``quasi-steady approximation.'' Using this method and the plasma condition calculated under n-level, we re-build the nl-level bound electron distribution (Pnl), and acquire a new hohlraum radiative drive by post-processing. Comparison with the n-level post-processed hohlraum drive shows that we get an almost identical radiation flux but with more-detailed frequency-dependant structures. Also we use this method in the benchmark gold sphere experiment, the constructed nl-level radiation drive resembles the experimental results and DCA results, while the n-level raditation does not.

  3. A comparative study of interatomic potentials for copper and aluminum gas phase sputter atom transport simulations

    CERN Document Server

    Kuwata, K T; Doyle, J R

    2003-01-01

    A comparative study of interatomic potential models for use in gas phase sputter atom transport simulations is presented. Quantum chemical interatomic potentials for argon-copper and argon-aluminum are calculated using Kohn-Sham density functional theory utilizing the PW91 functional. These potentials (PW91) are compared to the commonly used Born-Mayer potentials calculated by Abrahamson [Phys. Rev. 178 (1969) 76] using the Thomas-Fermi-Dirac model (TFD) and the screened Coulomb potentials derived from the 'universal' form calculated by Ziegler, Biersack and Littmark (ZBL). Monte Carlo simulations of gas phase sputter atom transport were performed to determine the average energy of atoms arriving at the substrate versus pressure for the three potential models. Overall, the ZBL potential gave results in much better agreement with the PW91 potential than the TFD potential. A characteristic thermalization pressure-distance product of approx 0.11 mTorr cm was found for both copper and aluminum using the PW91 pote...

  4. An atomic and molecular fluid model for efficient edge-plasma transport simulations at high densities

    Science.gov (United States)

    Rognlien, Thomas; Rensink, Marvin

    2016-10-01

    Transport simulations for the edge plasma of tokamaks and other magnetic fusion devices requires the coupling of plasma and recycling or injected neutral gas. There are various neutral models used for this purpose, e.g., atomic fluid model, a Monte Carlo particle models, transition/escape probability methods, and semi-analytic models. While the Monte Carlo method is generally viewed as the most accurate, it is time consuming, which becomes even more demanding for device simulations of high densities and size typical of fusion power plants because the neutral collisional mean-free path becomes very small. Here we examine the behavior of an extended fluid neutral model for hydrogen that includes both atoms and molecules, which easily includes nonlinear neutral-neutral collision effects. In addition to the strong charge-exchange between hydrogen atoms and ions, elastic scattering is included among all species. Comparisons are made with the DEGAS 2 Monte Carlo code. Work performed for U.S. DoE by LLNL under Contract DE-AC52-07NA27344.

  5. Analysis of Adhesive Characteristics of Asphalt Based on Atomic Force Microscopy and Molecular Dynamics Simulation.

    Science.gov (United States)

    Xu, Meng; Yi, Junyan; Feng, Decheng; Huang, Yudong; Wang, Dongsheng

    2016-05-18

    Asphalt binder is a very important building material in infrastructure construction; it is commonly mixed with mineral aggregate and used to produce asphalt concrete. Owing to the large differences in physical and chemical properties between asphalt and aggregate, adhesive bonds play an important role in determining the performance of asphalt concrete. Although many types of adhesive bonding mechanisms have been proposed to explain the interaction forces between asphalt binder and mineral aggregate, few have been confirmed and characterized. In comparison with chemical interactions, physical adsorption has been considered to play a more important role in adhesive bonding between asphalt and mineral aggregate. In this study, the silicon tip of an atomic force microscope was used to represent silicate minerals in aggregate, and a nanoscale analysis of the characteristics of adhesive bonding between asphalt binder and the silicon tip was conducted via an atomic force microscopy (AFM) test and molecular dynamics (MD) simulations. The results of the measurements and simulations could help in better understanding of the bonding and debonding procedures in asphalt-aggregate mixtures during hot mixing and under traffic loading. MD simulations on a single molecule of a component of asphalt and monocrystalline silicon demonstrate that molecules with a higher atomic density and planar structure, such as three types of asphaltene molecules, can provide greater adhesive strength. However, regarding the real components of asphalt binder, both the MD simulations and AFM test indicate that the colloidal structural behavior of asphalt also has a large influence on the adhesion behavior between asphalt and silicon. A schematic model of the interaction between asphalt and silicon is presented, which can explain the effect of aging on the adhesion behavior of asphalt.

  6. A Simple AIMD Approach to Derive Atomic Charges for Condensed Phase Simulation of Ionic Liquids

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Y; Maginn, EJ

    2012-08-23

    The atomic charges for two ionic liquids (ILs), 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM] [PF6]) and 1-ethyl-3-methylimidazolium hexafluorophosphate ([EMIM][PF6]), were derived from periodic crystal phase calculations with density functional theory (DFT) and plane wave basis sets (denoted as "AIMD-c charge"). For both ILs, the total charge was found to be +/- 0.8 e for the cation and anion, respectively, due to the charge transfer between ions and polarization caused by the environment. These atomic charges were used in a force field developed within the general Amber force field framework. Using this force field, static, dynamic, and thermodynamic properties were computed for the two ILs using molecular dynamics simulation. The results were compared against results obtained using the same Amber force field but four different sets of partial charges, denoted as full charge, scaled charge, AIMD-1 charge, and AIMD-b charge, respectively. The full charge was derived from quantum chemistry calculation of isolated ions in a vacuum and resulted in a total charge of unity on each ion. The scaled charge was obtained by uniformly scaling the full charge by 0.8. AIMD-1 and AIMD-b charges were derived from liquid phase ab initio molecular dynamics simulations. The scaled charges have the same total charge on the ions as the AIMD-c charge but different distributions. It was found that simulation results not only depend on the total charge of each ion, but they are also sensitive to the charge distribution within an ion, especially for dynamic and thermodynamic properties. Overall, for the two ILs under study, the AIMD-c charge was found to predict experimental results better than the other four sets of charges, indicating that fitting charges from crystal phase DFT calculations, instead of extensive sampling of the liquid phase configurations, is a simple and reliable way to derive atomic charges for condensed phase ionic liquid simulations.

  7. Mechanical Properties of Boehmite Evaluated by Atomic Force Microscopy Experiments and Molecular Dynamic Finite Element Simulations

    Directory of Open Access Journals (Sweden)

    J. Fankhänel

    2016-01-01

    Full Text Available Boehmite nanoparticles show great potential in improving mechanical properties of fiber reinforced polymers. In order to predict the properties of nanocomposites, knowledge about the material parameters of the constituent phases, including the boehmite particles, is crucial. In this study, the mechanical behavior of boehmite is investigated using Atomic Force Microscopy (AFM experiments and Molecular Dynamic Finite Element Method (MDFEM simulations. Young’s modulus of the perfect crystalline boehmite nanoparticles is derived from numerical AFM simulations. Results of AFM experiments on boehmite nanoparticles deviate significantly. Possible causes are identified by experiments on complementary types of boehmite, that is, geological and hydrothermally synthesized samples, and further simulations of imperfect crystals and combined boehmite/epoxy models. Under certain circumstances, the mechanical behavior of boehmite was found to be dominated by inelastic effects that are discussed in detail in the present work. The studies are substantiated with accompanying X-ray diffraction and Raman experiments.

  8. Design and Simulation of an Absorption Diffusion Solar Refrigeration Unit

    Directory of Open Access Journals (Sweden)

    B. Chaouachi

    2007-01-01

    Full Text Available The purpose of this study was the design and the simulation of an absorption diffusion refrigerator using solar as source of energy, for domestic use. The design holds account about the climatic conditions and the unit cost due to technical constraints imposed by the technology of the various components of the installation such as the solar generator, the condenser, the absorber and the evaporator. Mass and energy conservation equations were developed for each component of the cycle and solved numerically. The obtained results showed, that the new designed mono pressure absorption cycle of ammonia was suitable well for the cold production by means of the solar energy and that with a simple plate collector we can reach a power, of the order of 900 watts sufficient for domestic use.

  9. Atomic quantum simulation of the lattice gauge-Higgs model: Higgs couplings and emergence of exact local gauge symmetry.

    Science.gov (United States)

    Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo

    2013-09-13

    Recently, the possibility of quantum simulation of dynamical gauge fields was pointed out by using a system of cold atoms trapped on each link in an optical lattice. However, to implement exact local gauge invariance, fine-tuning the interaction parameters among atoms is necessary. In the present Letter, we study the effect of violation of the U(1) local gauge invariance by relaxing the fine-tuning of the parameters and showing that a wide variety of cold atoms is still a faithful quantum simulator for a U(1) gauge-Higgs model containing a Higgs field sitting on sites. The clarification of the dynamics of this gauge-Higgs model sheds some light upon various unsolved problems, including the inflation process of the early Universe. We study the phase structure of this model by Monte Carlo simulation and also discuss the atomic characteristics of the Higgs phase in each simulator.

  10. Effect of irradiation on mechanical properties of symmetrical grain boundaries investigated by atomic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, X. Y.; Gao, N.; Setyawan, W.; Xu, B.; Liu, W.; Wang, Z. G.

    2017-08-01

    Tensile response of irradiated symmetric grain boundaries to externally applied strain has been studied using atomic simulation methods. The absorption of irradiation induced defects by grain boundaries has been confirmed to degrade the mechanical properties of grain boundaries through the change of its under- taken deformation mechanism. Atomic rearrangement, the formations of a stress accumulation region and vacancy-rich zone and the nucleation and movement of dislocations under stress effect have been observed after the displacement cascades in grain boundaries, which are considered as main reasons to induce above degradation. These results suggest the necessity of considering both trap- ping efficiency to defects and the mechanical property change of irradiated grain boundaries for further development of radiation resistant materials.

  11. Simulation of Chromium Atom Deposition Pattern in a Gaussain Laser Standing Wave with Different Laser Power

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wen-Tao; ZHU Bao-Hua

    2009-01-01

    One-dimensional deposition of a neutral chromium atomic beam focused by a near-resonant Gaussian standing-laser field is discussed by using a fourth-order Runge-Kutta type algorithm. The deposition pattern of neutral chromium atoms in a laser standing wave with different laser power is discussed and the simulation result shows that the full width at half maximum (FWHM) of a nanometer stripe is 115nm and the contrast is 2.5:1 with laser power 3.93mW; the FWHM is 0.Snm and the contrast is 27:1 with laser power 16mW, the optimal laser power; but with laser power increasing to 50mW, the nanometer structure forms multi-crests and the quality worsens quickly with increasing laser power.

  12. Effect of irradiation on mechanical properties of symmetrical grain boundaries investigated by atomic simulations

    Science.gov (United States)

    Wang, X. Y.; Gao, N.; Setyawan, W.; Xu, B.; Liu, W.; Wang, Z. G.

    2017-08-01

    Tensile response of irradiated symmetric grain boundaries to the externally applied strain has been studied using atomic simulation methods. The absorption of irradiation induced defects by grain boundaries has been confirmed to degrade the mechanical properties of grain boundaries through the change of its undertaken deformation mechanism. Atomic rearrangement, the formations of a stress accumulation region and vacancy-rich zone and the nucleation and movement of dislocations under stress effect have been observed after the displacement cascades in grain boundaries, which are considered as main reasons to induce above degradation. These results suggest the necessity of considering both trapping efficiency to defects and the mechanical property change of irradiated grain boundaries for further development of radiation resistant materials.

  13. 75 FR 24755 - DTE ENERGY; Enrico Fermi Atomic Power Plant Unit 1; Exemption From Certain Low-Level Waste...

    Science.gov (United States)

    2010-05-05

    ... COMMISSION DTE ENERGY; Enrico Fermi Atomic Power Plant Unit 1; Exemption From Certain Low-Level Waste Shipment Tracking Requirements In 10 CFR Part 20 Appendix G 1.0 Background DTE Energy (DTE) is the licensee.... DTE is in the process of decommissioning Fermi-1 and radioactive waste shipments from the site are...

  14. Atomic-level simulations of nanoindentation-induced phase transformation in mono-crystalline silicon

    Science.gov (United States)

    Lin, Yen-Hung; Chen, Tei-Chen; Yang, Ping-Feng; Jian, Sheng-Rui; Lai, Yi-Shao

    2007-12-01

    Molecular dynamics (MD) simulations of nanoindentation are carried out to investigate the phase transformations in Si with a spherical indenter. Since the phase transformation induced by deformation in micro-scale is closely related to the carrier mobility of the material, it has become a key issue to be investigated for the chips especially with smaller feature size. Up to now, however, it is not possible to carry out the nanoindentation experimentally in such a small feature. Consequently, molecular dynamic simulation on nanoindentation is resorted to and becomes a powerful tool to understand the detailed mechanisms of stress-induced phase transformation in nano-scale. In this study, the inter-atomic interaction of Si atoms is modeled by Tersoff's potential, while the interaction between Si atoms and diamond indenter atoms is modeled by Morse potential. It is found that the diamond cubic structure of Si in the indentation zone transforms into a phase with body-centred tetragonal structure (β-Si) just underneath the indenter during loading stage and then changes to amorphous after unloading. By using the technique of coordinate number the results reveal that indentation on the (0 0 1) surface exhibits significant phase transformation along the direction. In addition, indentation on the (1 1 0) surface shows more significant internal slipping and spreading of phase transformation than on the (0 0 1) surface. Furthermore, during the indentation process phase transformations of Si are somewhat reversible. Parts of transformed phases that are distributed over the region of elastic deformation can be gradually recovered to original mono-crystal structure after unloading.

  15. Monte Carlo simulation of photon migration in 3D turbid media accelerated by graphics processing units.

    Science.gov (United States)

    Fang, Qianqian; Boas, David A

    2009-10-26

    We report a parallel Monte Carlo algorithm accelerated by graphics processing units (GPU) for modeling time-resolved photon migration in arbitrary 3D turbid media. By taking advantage of the massively parallel threads and low-memory latency, this algorithm allows many photons to be simulated simultaneously in a GPU. To further improve the computational efficiency, we explored two parallel random number generators (RNG), including a floating-point-only RNG based on a chaotic lattice. An efficient scheme for boundary reflection was implemented, along with the functions for time-resolved imaging. For a homogeneous semi-infinite medium, good agreement was observed between the simulation output and the analytical solution from the diffusion theory. The code was implemented with CUDA programming language, and benchmarked under various parameters, such as thread number, selection of RNG and memory access pattern. With a low-cost graphics card, this algorithm has demonstrated an acceleration ratio above 300 when using 1792 parallel threads over conventional CPU computation. The acceleration ratio drops to 75 when using atomic operations. These results render the GPU-based Monte Carlo simulation a practical solution for data analysis in a wide range of diffuse optical imaging applications, such as human brain or small-animal imaging.

  16. Simulation of the Cosmic Evolution of Atomic and Molecular Hydrogen in Galaxies

    CERN Document Server

    Obreschkow, D; De Lucia, G; Khochfar, S; Rawlings, S

    2009-01-01

    We present a simulation of the cosmic evolution of the atomic and molecular phases of the cold hydrogen gas in about 3e7 galaxies, obtained by post-processing the virtual galaxy catalog produced by (De Lucia et al. 2007) on the Millennium Simulation of cosmic structure (Springel et al. 2005). Our method uses a set of physical prescriptions to assign neutral atomic hydrogen (HI) and molecular hydrogen (H2) to galaxies, based on their total cold gas masses and a few additional galaxy properties. These prescriptions are specially designed for large cosmological simulations, where, given current computational limitations, individual galaxies can only be represented by simplistic model-objects with a few global properties. Our recipes allow us to (i) split total cold gas masses between HI, H2, and Helium, (ii) assign realistic sizes to both the HI- and H2-disks, and (iii) evaluate the corresponding velocity profiles and shapes of the characteristic radio emission lines. The results presented in this paper include ...

  17. Attosecond dissociation of the HT molecule from the He united-atom limit

    Science.gov (United States)

    Clark, Charles W.; Thompson, Alan K.; Coplan, Michael A.; Cooper, John W.; Hughes, Patrick; Vest, Robert E.

    2008-05-01

    From an AMO perspective, the n + ^3He ->t + p + 764 keV nuclear reaction can be viewed as unimolecular dissociation of the HT molecule proceeding from the ^4He united-atom limit. The speeds of the electrons in the ground state of He are comparable to those of the triton and proton fragments, thus fulfilling the Massey criterion which is conducive to subsequent charge-transfer and excitation collisions between the heavy fragments and ambient ^3He. We have measured Lyman α radiation produced in a ^3He gas cell irradiated by a cold neutron beam at the NIST Center for Neutron Research. For atmospheric pressure and room temperature in the cell, we find yields of tens of Lyman α photons for every neutron reaction [arXiv:0801.2614]. These results suggest a method of cold neutron detection by optical means that is complementary to existing proportional counter technologies, and offers greater sensitivity, wider dynamic range, suppression of background, and simpler manufacturability.

  18. Atomic quantum simulation of a three-dimensional U(1) gauge-Higgs model

    Science.gov (United States)

    Kuno, Yoshihito; Sakane, Shinya; Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo

    2016-12-01

    In this paper, we study theoretically atomic quantum simulations of a U(1) gauge-Higgs model on a three-dimensional (3D) spatial lattice by using an extended Bose-Hubbard model with intersite repulsions on a 3D optical lattice. Here, the phase and density fluctuations of the boson variable on each site of the optical lattice describe the vector potential and the electric field on each link of the gauge-model lattice, respectively. The target gauge model is different from the standard Wilson-type U(1) gauge-Higgs model because it has plaquette and Higgs interactions with asymmetric couplings in the space-time directions. Nevertheless, the corresponding quantum simulation is still important as it provides us with a platform to study unexplored time-dependent phenomena characteristic of each phase in the general gauge-Higgs models. To determine the phase diagram of the gauge-Higgs model at zero temperature, we perform Monte Carlo simulations of the corresponding 3+1-dimensional U(1) gauge-Higgs model, and obtain the confinement and Higgs phases. To investigate the dynamical properties of the gauge-Higgs model, we apply the Gross-Pitaevskii equations to the extended Bose-Hubbard model. We simulate the time evolution of an electric flux that initially is put on a straight line connecting two external point charges. We also calculate the potential energy between this pair of charges and obtain the string tension in the confinement phase. Finally, we propose a feasible experimental setup for the atomic simulations of this quantum gauge-Higgs model on the 3D optical lattice. These results may serve as theoretical guides for future experiments.

  19. Efficient molecular dynamics simulations with many-body potentials on graphics processing units

    CERN Document Server

    Fan, Zheyong; Vierimaa, Ville; Harju, Ari

    2016-01-01

    Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones. In the conventional force evaluation algorithm for many-body potentials, the force, virial stress, and heat current for a given atom are accumulated within different loops, which could result in write conflict between different threads in a CUDA kernel. In this work, we provide a new force evaluation algorithm, which is based on an explicit pairwise force expression for many-body potentials derived recently [Phys. Rev. B 92 (2015) 094301]. In our algorithm, the force, virial stress, and heat current for a given atom can be accumulated within a single thread and is free of write conflicts. We discuss the formulations and algorithms and evaluate their performance. A new open-source code, GPUMD, is developed based on the proposed formulations. For the Tersoff many-body potentia...

  20. An all-atom simulation study of the ordering of liquid squalane near a solid surface

    Science.gov (United States)

    Tsige, Mesfin; Patnaik, Soumya S.

    2008-05-01

    An all-atom molecular dynamics study using the OPLS force field has been carried out to obtain new insights in to the orientation and ordering of liquid squalane near a solid surface. As observed in previous experiments, the squalane molecules closest to a SiO 2 substrate are found to be tightly bound with their molecular axis preferentially parallel to the interface. Unlike linear alkanes, the squalane molecules are also found to lie preferentially parallel to the liquid/vapor interface. The simulation results predict that the molecular plane orientation of the squalane molecules changes from mainly parallel to perpendicular to the substrate in going further away from the substrate.

  1. GPGPU Approach: Simulation of the Interaction of Heavy Interstellar Atoms with the Heliosphere

    Science.gov (United States)

    DeStefano, A.

    2014-12-01

    Running simulations is an involved process taking many hours of computational time to complete. With the advent of cluster computing and parallel processing, problems may be solved in much less time compared to those run in serial. Specifically, NVIDIA released the parallel computing platform CUDA in 2007 giving researchers and programmers access to the GPU to solve generalized problems, and not those of just images.In current research, code has previously been developed to study the interaction of the heliosphere and heavy atoms from the local interstellar medium.Ionized species of hydrogen, helium and other heavy atoms are deflected by the heliosphere where as the neutral species are relatively unimpeded. Charge exchange of these neutral particles may occur between ionized species originating from the solar wind or other populations of pickup ions (PUI) modifying the shape and properties of the heliosphere, compared to one without neutrals. The details of the charge exchange interaction are element dependent and need to be investigated one by one. Current research has studied the interaction of local interstellar hydrogen with the heliosphere quite extensively with theory, simulations and modeling.Since hydrogen is the most abundant element care must be taken when coupling MHD equations with the charge exchange interactions. Simulation code has been developed to account for this dynamic problem and they have shown that the shape of the heliosphere is affected by this. Interstellar atoms heavier than hydrogen interacting with the heliosphere has been looked at as well, but not nearly with as much detail or sophisticated models as hydrogen. The heavy atom data collected by IBEX has in this sense been under-utilized by models.Previously, the simulation was computed with the use of MPI (Message Passing Interface) for parallelization. This approach provided a decrease in computational time. However, CUDA enables the programmer to take advantage of the computer

  2. Energy corrugation in atomic-scale friction on graphite revisited by molecular dynamics simulations

    Institute of Scientific and Technical Information of China (English)

    Xiao-Yu Sun; Yi-Zhou Qi; Wengen Ouyang; Xi-Qiao Feng; Qunyang Li

    2016-01-01

    Although atomic stick–slip friction has been extensively studied since its first demonstration on graphite, the physical understanding of this dissipation-dominated phenomenon is still very limited. In this work, we perform molecular dynamics (MD) simulations to study the frictional behavior of a diamond tip sliding over a graphite surface. In contrast to the common wisdom, our MD results suggest that the energy barrier associated lateral sliding (known as energy corrugation) comes not only from interaction between the tip and the top layer of graphite but also from interactions among the deformed atomic layers of graphite. Due to the competi-tion of these two subentries, friction on graphite can be tuned by controlling the relative adhesion of different interfaces. For relatively low tip-graphite adhesion, friction behaves nor-mally and increases with increasing normal load. However, for relatively high tip-graphite adhesion, friction increases unusually with decreasing normal load leading to an effec-tively negative coefficient of friction, which is consistent with the recent experimental observations on chemically modified graphite. Our results provide a new insight into the physical origins of energy corrugation in atomic scale friction.

  3. Simulation of dislocations in ordered Ni{sub 3}Al by atomic stiffness matrix method

    Energy Technology Data Exchange (ETDEWEB)

    Hsu, Y.E.; Chaki, T.K. [State Univ. of New York, Buffalo, NY (United States). Dept. of Mechanical and Aerospace Engineering

    1996-12-31

    A simulation of structure and motion of edge dislocations in ordered Ni{sub 3}Al was performed by atomic stiffness matrix method. In this method the equilibrium positions of the atoms were obtained by solving a set of linear equations formed by a stiffness matrix, whose terms consisted of derivatives of the interaction potential of EAM (embedded atom method) type. The superpartial dislocations, separated by an antiphase boundary (APB) on (111), dissociated into Shockley partials with complex stacking faults (CSF) on (111) plane. The core structure, represented by the Burgers vector density distribution and iso-strain contours, changed under applied stresses as well as upon addition of boron. The separation between the superpartials changed with the addition of B and antisite Ni. As one Shockley partial moved out to the surface, a Shockley partial in the interior moved a large distance to join the lone one near the surface, leaving behind a long CSF strip. The decrease in the width of the APB upon addition of B and antisite Ni has been explained by a reduction of the strength of directional bonding between Ni and Al as well as by the dragging of B atmosphere by the superpartials.

  4. Simulation of dislocations in ordered Ni{sub 3}Al by atomic stiffness matrix method

    Energy Technology Data Exchange (ETDEWEB)

    Hsu, Y.E.; Chaki, T.K. [State Univ. of New York, Buffalo, NY (United States). Dept. of Mechanical and Aerospace Engineering

    1996-12-01

    A simulation of structure and motion of edge dislocations in ordered Ni{sub 3}Al was performed by atomic stiffness matrix method. In this method the equilibrium positions of the atoms were obtained by solving a set of linear equations formed by a stiffness matrix, whose terms consisted of derivatives of the interaction potential of EAM (embedded atom method) type. The superpartial dislocations, separated by an antiphase boundary (APB) on (111), dissociated into Shockley partials with complex stacking faults (CSF) on (111) plane. The core structure, represented by the Burgers vector density distribution and iso-strain contours, changed under applied stresses as well as upon addition of boron. The separation between the superpartials changed with the addition of B and antisite Ni. As one Shockley partial moved out to the surface, a Shockley partial in the interior moved a large distance to join the lone one near the surface, leaving behind a long CSF strip. The decrease in the width of the APB upon addition of B and antisite Ni has been explained by a reduction of the strength of direction bonding between Ni and Al as well as by the dragging of B atmosphere by the superpartials.

  5. Molecular jamming—The cystine slipknot mechanical clamp in all-atom simulations

    Science.gov (United States)

    Pepłowski, Łukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek

    2011-02-01

    A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids.

  6. Energy corrugation in atomic-scale friction on graphite revisited by molecular dynamics simulations

    Science.gov (United States)

    Sun, Xiao-Yu; Qi, Yi-Zhou; Ouyang, Wengen; Feng, Xi-Qiao; Li, Qunyang

    2016-08-01

    Although atomic stick-slip friction has been extensively studied since its first demonstration on graphite, the physical understanding of this dissipation-dominated phenomenon is still very limited. In this work, we perform molecular dynamics (MD) simulations to study the frictional behavior of a diamond tip sliding over a graphite surface. In contrast to the common wisdom, our MD results suggest that the energy barrier associated lateral sliding (known as energy corrugation) comes not only from interaction between the tip and the top layer of graphite but also from interactions among the deformed atomic layers of graphite. Due to the competition of these two subentries, friction on graphite can be tuned by controlling the relative adhesion of different interfaces. For relatively low tip-graphite adhesion, friction behaves normally and increases with increasing normal load. However, for relatively high tip-graphite adhesion, friction increases unusually with decreasing normal load leading to an effectively negative coefficient of friction, which is consistent with the recent experimental observations on chemically modified graphite. Our results provide a new insight into the physical origins of energy corrugation in atomic scale friction.

  7. Interpretation of atom probe tomography data for the intermetallic TiAl+Nb by means of field evaporation simulation

    KAUST Repository

    Boll, Torben

    2013-01-01

    In this paper simulations of the field evaporation process during field ion microscopy (FIM) and atom probe tomography (APT) are presented and compared with experimental data. The Müller-Schottky-model [1] was extended to include the local atomic arrangement on the evaporation process of atoms. This arrangement was described by the sum of the next-neighbor-binding-energies, which differ for an atom of type A, depending on how many A-A, B-B or A-B bonds are present. Thus simulations of APT-data of intermetallic phases become feasible. In this study simulations of L10-TiAl with additions of Nb are compared with experimental data. Certain artifacts, which appear for experimental data are treated as well. © 2012 Elsevier B.V.

  8. Computing 1-D atomic densities in macromolecular simulations: the Density Profile Tool for VMD

    CERN Document Server

    Giorgino, Toni

    2013-01-01

    Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to analyze simulated trajectories, either interactively or via scripts, to derive quantities of interest and provide insight for further experiments. This paper presents the Density Profile Tool, a package that enhances the Visual Molecular Dynamics environment with the ability to interactively compute and visualize 1-D projections of various density functions of molecular models. We describe how the plugin is used to perform computations both via a graphical interface and programmatically. Results are presented for realistic examples, all-atom bilayer models, showing how mass and electron densities readily provide measurements such as membrane thickness, location of structural elements, and how they compare to X-ray diffraction experiments.

  9. MD simulation of atomic displacement cascades near chromium-rich clusters in FeCr alloy

    Energy Technology Data Exchange (ETDEWEB)

    Tikhonchev, M., E-mail: tikhonchev@sv.ulsu.ru [Ulyanovsk State University, Research Institute of Technology, 42 Leo Tolstoy St., 432970 Ulyanovsk (Russian Federation); Svetukhin, V. [Ulyanovsk State University, Research Institute of Technology, 42 Leo Tolstoy St., 432970 Ulyanovsk (Russian Federation); Gaganidze, E. [Karlsruhe Institute of Technology, Institute for Applied Materials, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Karlsruhe (Germany)

    2013-11-15

    The paper reports simulation of cascades in Fe–9 at.%Cr binary alloy containing chromium-rich clusters. The simulation is performed by the molecular dynamics method at the initial temperature of 300 K and primary knock-on atom energy of 15 and 20 keV. Spherical clusters containing 95 at.% of Cr with diameter of 1–5 nm have been considered. The properties of cascade evolution in the presence of chromium-rich cluster are studied. It is shown that these clusters tend to dissolve in collision cascades. However, clusters with diameter of ⩾3 nm exhibit only slight modifications and can be considered stable. Parameters of small (1–2 nm) clusters can change significantly and, in some cases, a 1 nm cluster can be totally dissolved.

  10. Reduced atomic pair-interaction design (RAPID) model for simulations of proteins.

    Science.gov (United States)

    Ni, Boris; Baumketner, Andrij

    2013-02-14

    Increasingly, theoretical studies of proteins focus on large systems. This trend demands the development of computational models that are fast, to overcome the growing complexity, and accurate, to capture the physically relevant features. To address this demand, we introduce a protein model that uses all-atom architecture to ensure the highest level of chemical detail while employing effective pair potentials to represent the effect of solvent to achieve the maximum speed. The effective potentials are derived for amino acid residues based on the condition that the solvent-free model matches the relevant pair-distribution functions observed in explicit solvent simulations. As a test, the model is applied to alanine polypeptides. For the chain with 10 amino acid residues, the model is found to reproduce properly the native state and its population. Small discrepancies are observed for other folding properties and can be attributed to the approximations inherent in the model. The transferability of the generated effective potentials is investigated in simulations of a longer peptide with 25 residues. A minimal set of potentials is identified that leads to qualitatively correct results in comparison with the explicit solvent simulations. Further tests, conducted for multiple peptide chains, show that the transferable model correctly reproduces the experimentally observed tendency of polyalanines to aggregate into β-sheets more strongly with the growing length of the peptide chain. Taken together, the reported results suggest that the proposed model could be used to succesfully simulate folding and aggregation of small peptides in atomic detail. Further tests are needed to assess the strengths and limitations of the model more thoroughly.

  11. Multimillion-atom molecular dynamics simulation of atomic level stresses in Si(111)/Si{sub 3}N{sub 4}(0001) nanopixels

    Energy Technology Data Exchange (ETDEWEB)

    Bachlechner, M.E.; Omeltchenko, A.; Nakano, A.; Kalia, R.K.; Vashishta, P. [Concurrent Computing Laboratory for Materials Simulations, Department of Physics Astronomy and Department of Computer Science, Louisiana State University, Baton Rouge, Louisiana70803-4001 (United States); Ebbsjoe, I. [Studsvik Neutron Research Laboratory, University of Uppsala, S-611 82Nykoeping (Sweden); Madhukar, A. [Department of Materials Science and Engineering, University of Southern California, Los Angeles, California90089-0241 (United States); Messina, P. [Center for Advanced Computing Research, California Institute of Technology, Pasadena, California91125 (United States)

    1998-04-01

    Ten million atom multiresolution molecular-dynamics simulations are performed on parallel computers to determine atomic-level stress distributions in a 54 nm nanopixel on a 0.1 {mu}m silicon substrate. Effects of surfaces, edges, and lattice mismatch at the Si(111)/Si{sub 3}N{sub 4}(0001) interface on the stress distributions are investigated. Stresses are found to be highly inhomogeneous in the nanopixel. The top surface of silicon nitride has a compressive stress of +3GPa and the stress is tensile, {minus}1GPa, in silicon below the interface. {copyright} {ital 1998 American Institute of Physics.}

  12. Numerical Integration with Graphical Processing Unit for QKD Simulation

    Science.gov (United States)

    2014-03-27

    existing and proposed Quantum Key Distribution (QKD) systems. This research investigates using graphical processing unit ( GPU ) technology to more...Time Pad GPU graphical processing unit API application programming interface CUDA Compute Unified Device Architecture SIMD single-instruction-stream...and can be passed by value or reference [2]. 2.3 Graphical Processing Units Programming with graphical processing unit ( GPU ) requires a different

  13. Theoretical simulations of atomic and polyatomic bombardment of an organic overlayer on a metallic substrate

    CERN Document Server

    Krantzman, K D; Delcorte, A; Garrison, B J

    2003-01-01

    Our previous molecular dynamics simulations on initial test systems have laid the foundation for understanding some of the effects of polyatomic bombardment. In this paper, we describe simulations of the bombardment of a more realistic model system, an overlayer of sec-butyl-terminated polystyrene tetramers on a Ag left brace 1 1 1 right brace substrate. We have used this model system to study the bombardment with Xe and SF sub 5 projectiles at kinetic energies ranging from 0.50 to 5.0 keV. SF sub 5 sputters more molecules than Xe, but a higher percentage of these are damaged rather than ejected intact when the bombarding energy is greater than 0.50 keV. Therefore, at energies comparable to experimental values, the efficiency, measured as the yield-to-damage ratio, is greater with Xe than SF sub 5. Stable and intact molecules are generally produced by upward moving substrate atoms, while fragments are produced by the upward and lateral motion of reflected projectile atoms and fragments from the target molecul...

  14. Learning about the Unit Cell and Crystal Lattice with Computerized Simulations and Games: A Pilot Study

    Science.gov (United States)

    Luealamai, Sutha; Panijpan, Bhinyo

    2012-01-01

    The authors have developed a computer-based learning module on the unit cell of various types of crystal. The module has two components: the virtual unit cell (VUC) part and the subsequent unit cell hunter part. The VUC is a virtual reality simulation for students to actively arrive at the unit cell from exploring, from a broad view, the crystal…

  15. Learning about the Unit Cell and Crystal Lattice with Computerized Simulations and Games: A Pilot Study

    Science.gov (United States)

    Luealamai, Sutha; Panijpan, Bhinyo

    2012-01-01

    The authors have developed a computer-based learning module on the unit cell of various types of crystal. The module has two components: the virtual unit cell (VUC) part and the subsequent unit cell hunter part. The VUC is a virtual reality simulation for students to actively arrive at the unit cell from exploring, from a broad view, the crystal…

  16. Specsim: A Software Simulator for Integral Field Unit Spectrometers

    Science.gov (United States)

    Lorente, N. P. F.; Glasse, A. C. H.; Wright, G. S.; Ramsay, S. K.; Evans, C. J.

    As the scale and complexity of each generation of telescopes and their instruments increases, the requirement for a means of furthering our understanding of their properties and limitations, from the initial design to the point of commissioning also grows. An effective way of learning about the behaviour of a new system is to employ a software simulator to generate synthetic astronomical data, based on a given set of telescope and instrument characteristics. The Specsim tool has been developed to model, in software, the operation of Integral Field Unit (IFU) spectrometers, so as to give the science, engineering and operations teams responsible for designing, building and running such instruments a preview of the data products before the system is operational. Specsim generates synthetic data frames approximating those which will be taken by the instrument. The program models astronomical sources and generates detector frames using the predicted and measured properties of the telescope and instrument. These frames can then be used to illustrate and inform a range of activities, including refining the design, developing calibration strategies and the development and testing of data reduction pipelines. Specsim is currently used to model the Medium Resolution Spectrograph on JWST-MIRI, and KMOS on the ESO VLT. The software has been designed in a modular fashion, thus allowing the tool to expand easily to model future instruments, by incorporating new models into the existing infrastructure.

  17. Atomic quantum simulation of a three-dimensional U(1) gauge-Higgs model

    CERN Document Server

    Kuno, Yoshihito; Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo

    2016-01-01

    In this paper, we study atomic quantum simulations of a U(1) gauge-Higgs model on a three-dimensional (3D) spatial lattice. We start from an extended 3D Bose-Hubbard model with nearest-neighbor repulsions and show that it can simulate a U(1) gauge-Higgs model with next nearest-neighbor Higgs couplings. Here the phase of the boson variable on each site of the optical lattice describes the vector potential on each link of the gauge-model lattice. To determine the phase diagram of the gauge-Higgs model at a zero temperature, we perform Monte-Carlo simulations of the corresponding 3+1-dimensional U(1) gauge-Higgs model, and obtain the three phases, i.e., the confinement, Coulomb and Higgs phases. To investigate the dynamical properties of the gauge-Higgs model, we apply the Gross-Pitaevskii equations to the extended Bose-Hubbard model. We simulate the time-evolution of an electric flux initially put on a straight line connecting two external point charges. We also calculate the potential energy between this pair ...

  18. Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.

    Directory of Open Access Journals (Sweden)

    Samuel Hertig

    2016-06-01

    Full Text Available Molecular dynamics (MD simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery-the fact that the two sites involved influence one another in a symmetrical manner-can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.

  19. Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations.

    Science.gov (United States)

    Hertig, Samuel; Latorraca, Naomi R; Dror, Ron O

    2016-06-01

    Molecular dynamics (MD) simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications including rational drug design and protein engineering. Here, we provide an introduction to the investigation of protein allostery using molecular dynamics simulation. We emphasize the importance of designing simulations that include appropriate perturbations to the molecular system, such as the addition or removal of ligands or the application of mechanical force. We also demonstrate how the bidirectional nature of allostery-the fact that the two sites involved influence one another in a symmetrical manner-can facilitate such investigations. Through a series of case studies, we illustrate how these concepts have been used to reveal the structural basis for allostery in several proteins and protein complexes of biological and pharmaceutical interest.

  20. Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses.

    Science.gov (United States)

    Hoang Man, Viet; Van-Oanh, Nguyen-Thi; Derreumaux, Philippe; Li, Mai Suan; Roland, Christopher; Sagui, Celeste; Nguyen, Phuong H

    2016-04-28

    Since the discovery of the plant pathogen tobacco mosaic virus as the first viral entity in the late 1800s, viruses traditionally have been mainly thought of as pathogens for disease-resistances. However, viruses have recently been exploited as nanoplatforms with applications in biomedicine and materials science. To this aim, a large majority of current methods and tools have been developed to improve the physical stability of viral particles, which may be critical to the extreme physical or chemical conditions that viruses may encounter during purification, fabrication processes, storage and use. However, considerably fewer studies are devoted to developing efficient methods to degrade or recycle such enhanced stability biomaterials. With this in mind, we carry out all-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, to dissociate viruses. Adopting the poliovirus as a representative example, we find that the primary step in the dissociation process is due to the strong resonance between the amide I vibrational modes of the virus and the tuned laser frequencies. This process is determined by a balance between the formation and dissociation of the protein shell, reflecting the highly plasticity of the virus. Furthermore, our method should provide a feasible approach to simulate viruses, which is otherwise too expensive for conventional equilibrium all-atom simulations of such very large systems. Our work shows a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials, provide an extremely valuable tool for elucidating mechanical aspects of viruses, and may well play an important role in future fighting against virus-related diseases.

  1. Structure and dynamics of interfaces in organic and inorganic materials using atomic level simulation

    Science.gov (United States)

    Lee, Donghwa

    Interfaces in materials play a key role for industrial applications. The structures and dynamics at various interfaces including ferroelectric domain walls, gas-organic interface, organic-semiconductor interface and metal-gas interface are investigated with different atomic levels of simulation approaches. Ferroelectricity: Due to their unique ferroelectric and nonlinear optical properties, trigonal ferroelectrics such as LiNbO3 and LiTaO 3, are of wide interest for their potential applications in optoelectronics and nonlinear optics. The properties of these materials are heavily influenced by the shape of ferroelectric domains and domain walls. Therefore, investigation of the local structure and energetics of the ferroelectric domain walls and their interaction with defects on atomic scales, which is not clearly understood, is extremely important. The structure and energetics of ferroelectric domain walls in LiNbO 3 are examined using density functional theory (DFT) and molecular dynamics (MD) methods. The energetically favorable structures of 180° domain walls and the activation energy for domain wall motion are determined by atomic level simulations. The variation of polarization due to the presence of domain walls is also discussed. Defects can be pinned by domain walls. Various defects-domain walls interactions and the effects on domain wall motion are described using atomic level simulation methods. Although the structure of LiTaO3 is very similar with LiNbO3, it has been said experimentally that the shapes of domain walls are different with the presence of particular defects. Using both DFT and a newly developed interatomic potential for LiTaO 3, the differences in domain wall structure are understood in terms of the difference in energetics of domain walls between two materials. Polymerization: Surface polymerization by ion-assisted deposition (SPIAD) enables the control of thin film chemistry and morphology on the nanoscale during growth of conductive

  2. Classroom Simulation of United Nations Conference on Climate Change

    Science.gov (United States)

    Hastings, D. W.

    2009-12-01

    Global climate change is widely recognized as the most important environmental problem today that requires complex, global solutions with international cooperation. Teaching the science of climate change is relatively simple compared to the challenges of determining solutions to this problem. It is important for students to learn that solutions do exist and that international negotiations are underway to achieve reductions. What are the (policy) solutions to this vexing problem, which countries should take responsibility, and specifically how can this be done? In the final week of an advanced undergraduate environmental science class: Global Environmental Change, students engage in a week-long classroom simulation of the annual United Nations Framework Convention on Climate Change Conference of the Parties (UNFCCC/COP). Small groups of students represent one nation that has a particular, and important, interest in the negotiations. Each group researches the positions their country has with respect to the negotiations, determines their possible allies, and who might have interests that are in conflict with their country. While NGOs such as environmental organizations and industry groups are not formally represented, I include some of these groups since they are influential and provide interesting insight into different interests. For simplicity, about 8-10 nations and NGOs are included. In preparation for the conference, students produce a background paper and draft resolution. At the end of the conference, they refine these documents to produce an updated position paper and resolution on how to mitigate global warming. Students are asked to focus on: 1. How much to change global greenhouse gas emissions over the next decade and over the next century; 2. How much of these emission reductions their country should be responsible for; 3. How will their country meet these goals? They must focus on whether and how to implement two mechanisms: a) Clean Development

  3. A ground-based radio frequency inductively coupled plasma apparatus for atomic oxygen simulation in low Earth orbit.

    Science.gov (United States)

    Huang, Yongxian; Tian, Xiubo; Yang, Shiqin; Chu, Paul K

    2007-10-01

    A radio frequency (rf) inductively coupled plasma apparatus has been developed to simulate the atomic oxygen environment encountered in low Earth orbit (LEO). Basing on the novel design, the apparatus can achieve stable, long lasting operation, pure and high density oxygen plasma beam. Furthermore, the effective atomic oxygen flux can be regulated. The equivalent effective atomic oxygen flux may reach (2.289-2.984) x 10(16) at.cm(2) s at an oxygen pressure of 1.5 Pa and rf power of 400 W. The equivalent atomic oxygen flux is about 100 times than that in the LEO environment. The mass loss measured from the polyimide sample changes linearly with the exposure time, while the density of the eroded holes becomes smaller. The erosion mechanism of the polymeric materials by atomic oxygen is complex and involves initial reactions at the gas-surface interface as well as steady-state material removal.

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

    Science.gov (United States)

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

    2017-03-01

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

  5. Three-dimensional simulation on explosions of hydrogen atomic clusters irradiated by an intense femtosecond laser pulse

    Institute of Scientific and Technical Information of China (English)

    Xia Yong; Liu Jian-Sheng; Ni Guo-Quan; Xu Zhi-Zhan

    2004-01-01

    Using classic particle dynamics simulations, the interaction process between an intense femtosecond laser pulse and icosahedral hydrogen atomic clusters H13, H55 and H147 has been studied. It is revealed that with increasing number of atoms in the cluster, the kinetic energy of ions generated in the Coulomb explosion of the ionized hydrogen clusters increases. The expansion process of the clusters after laser irradiation has also been examined, showing that the expansion scale decreases with increasing cluster size.

  6. Accelerating development of metal organic framework membranes using atomically detailed simulations

    Science.gov (United States)

    Keskin, Seda

    A new group of nanoporous materials, metal organic frameworks (MOFs), have emerged as a fascinating alternative to more traditional nanoporous materials for membrane based gas separations. Although hundreds of different MOF structures have been synthesized in powder forms, very little is currently known about the potential performance of MOFs as membranes since fabrication and testing of membranes from new materials require a large amount of time and resources. The purpose of this thesis is to predict the macroscopic flux of multi-component gas mixtures through MOF-based membranes with information obtained from detailed atomistic simulations. First, atomically detailed simulations of gas adsorption and diffusion in MOFs combined with a continuum description of a membrane are introduced to predict the performance of MOF membranes. These results are compared with the only available experimental data for a MOF membrane. An efficient approximate method based on limited information from molecular simulations to accelerate the modeling of MOF membranes is then introduced. The accuracy and computational efficiency of different modeling approaches are discussed. A robust screening strategy is proposed to screen numerous MOF materials to identify the ones with the high membrane selectivity and to direct experimental efforts to the most promising of many possible MOF materials. This study provides the first predictions of any kind about the potential of MOFs as membranes and demonstrates that using molecular modeling for this purpose can be a useful means of identifying the phenomena that control the performance of MOFs as membranes.

  7. Multi-million Atom Electronic Structure Simulations using NEMO 3-D

    Science.gov (United States)

    Klimeck, Gerhard; Oyafuso, Fabiano; Boykin, Timothy B.; Bowen, R. Chris

    2002-03-01

    The detailed physical understanding of heterostructure interfaces enabled the creation of now well developed devices such as quantum well lasers, quantum well detectors, heterostructure field transistors and resonant tunneling diodes. The design and optimization of these devices and their implementation required the development and utilization of quantitative simulation tools. One such example is the nanoelectronic modeling tool (NEMO 1-D) originally developed by Texas Instruments. The need for such simulation tools is expected to only increase as device feature sizes and experimental characterization capabilities decrease and as manufacturing uncertainties increase. Quantum dot are a proptotypical 3-D nanoelectronic device and they have been studied experimentally and theoretically extensively in the past few years. The presentation will outline our recent developments to model such quantum dots on an atomistic level using the tight-binding method. The parallelization of the software on Intel-based Beowulfs and an SGI Origin, will be discussed. Simulation domains consisting of several million atoms will be analyzed for effects of random particle disorder, interfaces and confinement. More information about the work can be found at this website http://hpc.jpl.nasa.gov/PEP/ gekco.

  8. Beryllium Exposure Control Program at the Cardiff Atomic Weapons Establishment in the United Kingdom.

    Science.gov (United States)

    Johnson, J S; Foote, K; McClean, M; Cogbill, G

    2001-05-01

    The Cardiff Atomic Weapons Establishment (AWE) plant, located in Cardiff, Wales, United Kingdom, used metallic beryllium in their beryllium facility during the years of operation 1961-1997. The beryllium production processes included melting and casting, powder production, pressing, machining, and heat and surface treatments. As part of Cardiff's industrial hygiene program, extensive area measurements and personal lapel measurements of airborne beryllium concentrations were collected for Cardiff workers over the 36-year period of operation. In addition to extensive air monitoring, the beryllium control program also utilized surface contamination controls, building design, engineering controls, worker controls, material controls, and medical surveillance. The electronic database includes 367,757 area sampling records at 101 locations and 217,681 personal lapel sampling records collected from 194 employees over the period 1981-1997. Similar workplace samples were collected from 1961 to 1980, but they were not analyzed because they were not available electronically. Annual personal mean sampling concentrations for all workers ranged from 0.11 to 0.72 micrograms per cubic meter (microg/m3) with 95th percentiles ranging from 0.22 to 1.89 microg/m3; foundry workers worked in the highest concentration areas with a mean of 0.87 microg/m3 and a 95th percentile of 2.9 microg/m3. Area sampling concentrations, as expected, were lower than personal sampling concentrations. Mean annual area sample concentrations for all locations ranged from 0.02 to 0.32 microg/m3. The area sample 95th percentile concentrations for all years were below 0.5 microg/m3. For the overwhelming majority of samples, airborne beryllium concentrations were below the 2.0 microg/m3 standard. Although blood lymphocyte testing for beryllium sensitization has not been routinely conducted among these workers, this metal beryllium processing facility is the only large scale beryllium facility of its kind to have

  9. Molecular dynamics simulation of atomic-scale frictional behavior of corrugated nano-structured surfaces.

    Science.gov (United States)

    Kim, Hyun-Joon; Kim, Dae-Eun

    2012-07-01

    Surface morphology is one of the critical parameters that affect the frictional behavior of two contacting bodies in relative motion. It is important because the real contact area as well as the contact stiffness is dictated by the micro- and nano-scale geometry of the surface. In this regard, the frictional behavior may be controlled by varying the surface morphology through nano-structuring. In this study, molecular dynamics simulations were conducted to investigate the effects of contact area and structural stiffness of corrugated nano-structures on the fundamental frictional behavior at the atomic-scale. The nano-structured surface was modeled as an array of corrugated carbon atoms with a given periodicity. It was found that the friction coefficient of the nano-structured surface was lower than that of a smooth surface under specific contact conditions. The effect of applied load on the friction coefficient was dependent on the size of the corrugation. Furthermore, stiffness of the nano-structure was identified to be an important variable in dictating the frictional behavior.

  10. Simulation study for atomic size and alloying effects during forming processes of amorphous alloys

    Institute of Scientific and Technical Information of China (English)

    ZHENG Caixing; LIU Rangsu; PENG Ping; ZHOU Qunyi

    2004-01-01

    A molecular dynamics (MD) simulation study has been performed for the solidification processes of two binary liquid alloys Ag6Cu4 and CuNi by adopting the quantum Sutton-Chen many-body potentials. By analyzing bond-types, it is demonstrated that at the cooling rate of 2×1012K/s, the CuNi forms fcc crystal structures, while the Ag6Cu4 forms amorphous structures. The original reason is that the atomic radius ratio (1.13) of the CuAg is bigger than that (1.025) of the CuNi. This shows that the atomic size difference is indeed the main factor for forming amorphous alloys. Moreover, for Ag60Cu40,corresponding to the deep eutectic point in the phase diagram, it forms amorphous structure easily. This confirms that as to the forming tendency and stability of amorphous alloys, the alloying effect plays a key role. In addition, having analyzed the transformation of microstructures by using the bond-type index and cluster-type index methods, not only the key role of the icosahedral configuration to the formation and stability of amorphous alloys can be explained, but also the solidification processes of liquid metals and the characteristics of amorphous structures can be further understood.

  11. Simulations reveal the role of composition into the atomic-level flexibility of bioactive glass cements.

    Science.gov (United States)

    Tian, Kun Viviana; Chass, Gregory A; Di Tommaso, Devis

    2016-01-14

    Bioactive glass ionomer cements (GICs), the reaction product of a fluoro-alumino-silicate glass and polyacrylic acid, have been in effective use in dentistry for over 40 years and more recently in orthopaedics and medical implantation. Their desirable properties have affirmed GIC's place in the medical materials community, yet are limited to non-load bearing applications due to the brittle nature of the hardened composite cement, thought to arise from the glass component and the interfaces it forms. Towards helping resolve the fundamental bases of the mechanical shortcomings of GICs, we report the 1st ever computational models of a GIC-relevant component. Ab initio molecular dynamics simulations were employed to generate and characterise three fluoro-alumino-silicate glasses of differing compositions with focus on resolving the atomic scale structural and dynamic contributions of aluminium, phosphorous and fluorine. Analyses of the glasses revealed rising F-content leading to the expansion of the glass network, compression of Al-F bonding, angular constraint at Al-pivots, localisation of alumino-phosphates and increased fluorine diffusion. Together, these changes to the structure, speciation and dynamics with raised fluorine content impart an overall rigidifying effect on the glass network, and suggest a predisposition to atomic-level inflexibility, which could manifest in the ionomer cements they form.

  12. Fourth Semiannual Report to the Congress by the United States Atomic Energy Commission, July 1948

    Energy Technology Data Exchange (ETDEWEB)

    Lilienthal, David E.; Bacher, Robert F.; Pike, Sumner T.; Strauss, Lewis L.; Waymack, William W.

    1948-07-01

    The document includes the letter of submittal and the Fourth semiannual report. These reports are called for pursuant to Section 17 of the Atomic Energy Act of 1946. This fourth report incorporates some changes to the report. In order to make these reports of maximum value to Members of Congress, the Commission has prepared this mid-year report as a specialized document giving a comprehensive account of several major phases of the atomic energy program.

  13. Shifted Tietz-Wei oscillator for simulating the atomic interaction in diatomic molecules

    CERN Document Server

    Falaye, Babatunde J; Hamzavi, Majid

    2015-01-01

    The shifted Tietz-Wei (sTW) oscillator is as good as traditional Morse potential in simulating the atomic interaction in diatomic molecules. By using the Pekeris-type approximation to deal with the centrifugal term, we obtain the bound-state solutions of the radial Schr\\"odinger equation with this typical molecular model via the exact quantization rule (EQR). The energy spectrum for a set of diatomic molecules ($NO \\left(a^4\\Pi_i\\right)$, $NO \\left(B^2\\Pi_r\\right)$, $NO \\left(L'^2\\phi\\right)$, $NO \\left(b^4\\Sigma^{-}\\right)$, $ICl\\left(X^1\\Sigma_g^{+}\\right)$, $ICl\\left(A^3\\Pi_1\\right)$ and $ICl\\left(A'^3\\Pi_2\\right)$ for arbitrary values of $n$ and $\\ell$ quantum numbers are obtained. For the sake of completeness, we study the corresponding wavefunctions using the formula method.

  14. Representation of finite cracks by dislocation pileups: An application to atomic simulation of fracture

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-12-01

    The elastic displacement field solution of a semi-infinite crack in an anisotropic body, calculated using a complex variable approach due to Sih and Liebowitz, is usually used by atomistic simulations of fracture. The corresponding expression for the displacement field of a finite crack is numerically cumbersome since it involves multiple square roots of complex numbers. In this study, displacement field of the crack is calculated by superposing the displacements of dislocations in an equivalent double pileup, equilibrated under mode 1 conditions. An advantage of this method is its extensibility to atomistic studies of more complex systems containing multiple cracks or interfaces. The pileup representation of the finite crack is demonstrated as being equivalent to its corresponding continuum description using the example of a double ended crack in {alpha}-Fe, loaded in mode 1. In these examples, the interatomic interaction in {alpha}-Fe is described by an empirical embedded atom (EAM) potential.

  15. Representation of finite cracks by dislocation pileups: An application to atomic simulation of fracture

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-12-31

    The elastic displacement field solution of a semi-infinite crack in an anisotropic body, calculated using a complex variable approach due to Sih and Liebowitz, is usually used by atomistic simulations of fracture. The corresponding expression for the displacement field of a finite crack is numerically cumbersome since it involves multiple square roots of complex numbers. In this study, displacement field of the crack is calculated by superposing the displacements of dislocations in an equivalent double pileup, equilibrated under mode I conditions. An advantage of this method is its extensibility to atomistic studies of more complex systems containing multiple cracks or interfaces. The pileup representation of the finite crack is demonstrated as being equivalent to its corresponding continuum description using the example of a double ended crack in {alpha}-Fe, loaded in mode I. In these examples, the interatomic interaction in {alpha}-Fe is described by an empirical embedded atom (EAM) potential.

  16. Evolution of atomic structure in Al75Cu25 liquid from experimental and ab initio molecular dynamics simulation studies.

    Science.gov (United States)

    Xiong, L H; Yoo, H; Lou, H B; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z; Xie, H L; Xiao, T Q; Jeon, S; Lee, G W

    2015-01-28

    X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al(75)Cu(25) alloy have been performed from 800 to 1600 K. Experimental and ab initio molecular dynamics simulation results match well with each other. No abnormal changes were experimentally detected in the specific heat capacity over total hemispheric emissivity and density curves in the studied temperature range for a bulk liquid Al(75)Cu(25) alloy measured by the electrostatic levitation technique. The structure factors gained by the ab initio molecular dynamics simulation precisely coincide with the experimental data. The atomic structure analyzed by the Honeycutt-Andersen index and Voronoi tessellation methods shows that icosahedral-like atomic clusters prevail in the liquid Al(75)Cu(25) alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al(75)Cu(25) alloy in the studied temperature range.

  17. Excited-state intramolecular proton transfer to carbon atoms: nonadiabatic surface-hopping dynamics simulations.

    Science.gov (United States)

    Xia, Shu-Hua; Xie, Bin-Bin; Fang, Qiu; Cui, Ganglong; Thiel, Walter

    2015-04-21

    Excited-state intramolecular proton transfer (ESIPT) between two highly electronegative atoms, for example, oxygen and nitrogen, has been intensely studied experimentally and computationally, whereas there has been much less theoretical work on ESIPT to other atoms such as carbon. We have employed CASSCF, MS-CASPT2, RI-ADC(2), OM2/MRCI, DFT, and TDDFT methods to study the mechanistic photochemistry of 2-phenylphenol, for which such an ESIPT has been observed experimentally. According to static electronic structure calculations, irradiation of 2-phenylphenol populates the bright S1 state, which has a rather flat potential in the Franck-Condon region (with a shallow enol minimum at the CASSCF level) and may undergo an essentially barrierless ESIPT to the more stable S1 keto species. There are two S1/S0 conical intersections that mediate relaxation to the ground state, one in the enol region and one in the keto region, with the latter one substantially lower in energy. After S1 → S0 internal conversion, the transient keto species can return back to the S0 enol structure via reverse ground-state hydrogen transfer in a facile tautomerization. This mechanistic scenario is verified by OM2/MRCI-based fewest-switches surface-hopping simulations that provide detailed dynamic information. In these trajectories, ESIPT is complete within 118 fs; the corresponding S1 excited-state lifetime is computed to be 373 fs in vacuum. Most of the trajectories decay to the ground state via the S1/S0 conical intersection in the keto region (67%), and the remaining ones via the enol region (33%). The combination of static electronic structure computations and nonadiabatic dynamics simulations is expected to be generally useful for understanding the mechanistic photophysics and photochemistry of molecules with intramolecular hydrogen bonds.

  18. Modeling of adhesion in tablet compression - I. atomic force microscopy and molecular simulation.

    Energy Technology Data Exchange (ETDEWEB)

    Wang, J. J.; Li, T.; Bateman, S. D.; Erck, R.; Morris, K. R.; Energy Technology; Purdue Univ.; Novartis Pharmaceutical Corp.

    2003-04-01

    Adhesion problems during tablet manufacturing have been observed to be dependent on many formulation and process factors including the run time on the tablet press. Consequently, problems due to sticking may only become apparent towards the end of the development process when a prolonged run on the tablet press is attempted for the first time. It would be beneficial to predict in a relative sense if a formulation or new chemical entity has the potential for adhesion problems early in the development process. It was hypothesized that favorable intermolecular interaction between the drug molecules and the punch face is the first step or criterion in the adhesion process. Therefore, the rank order of adhesion during tablet compression should follow the rank order of these energies of interaction. The adhesion phenomenon was investigated using molecular simulations and contact mode atomic force microscopy (AFM). Three model compounds were chosen from a family of profen compounds. Silicon nitride AFM tips were modified by coating a 20-nm iron layer on the surfaces by sputter coating. Profen flat surfaces were made by melting and recrystallization. The modified AFM probe and each profen surface were immersed in the corresponding profen saturated water during force measurements using AFM. The work of adhesion between iron and ibuprofen, ketoprofen, and flurbiprofen in vacuum were determined to be -184.1, -2469.3, -17.3 mJ {center_dot} m-2, respectively. The rank order of the work of adhesion between iron and profen compounds decreased in the order: ketoprofen > ibuprofen > flurbiprofen. The rank order of interaction between the drug molecules and the iron superlattice as predicted by molecular simulation using Cerius2 is in agreement with the AFM measurements. It has been demonstrated that Atomic Force Microscopy is a powerful tool in studying the adhesion phenomena between organic drug compounds and metal surface. The study has provided insight into the adhesion problems

  19. Dynamic simulation model for ultra supercritical 1 000 MW unit boilers%Dynamic simulation model for ultra supercritical 1000 MW unit boilers

    Institute of Scientific and Technical Information of China (English)

    XU Hui; XU Ershu

    2013-01-01

    On the basis of heat transfer characteristics of working fluid at different pressures inside the water wall tube and structure of the ultra supercritical 1 000 MW unit once through boiler in Jianbi Power Plant,the varying phase transformation point method was adopted to establish the moving-boundary dynamic simulation model of water wall in ultra supercritical once through boilers,especially the length variation of hot water section,evaporation section and superheat section against the load changing.On this basis,the real-time dynamic simulation model for ultra-supercritical 1 000 MW unit boiler in Jianbi Power Plant was built on the STAR-90 simulation platform.The dynamic and static characteristics test showed that,this model can simulate the unit's startup/shutdown process and some typical fault conditions accurately,and had good dynamic and static performance.

  20. The Strength of Chaos: Accurate Simulation of Resonant Electron Scattering by Many-Electron Ions and Atoms in the Presence of Quantum Chaos

    Science.gov (United States)

    2017-01-20

    AFRL-AFOSR-JP-TR-2017-0012 The Strength of Chaos: accurate simulation of resonant electron scattering by many-electron ions and atoms in the presence...SUBTITLE The Strength of Chaos: accurate simulation of resonant electron scattering by many- electron ions and atoms in the presence of quantum chaos...Strength of Chaos: accurate simulation of resonant electron scattering by many-electron ions and atoms in the presence of quantum chaos” Date 13

  1. Simulating the rubble mound underlying armour units protecting a breakwater

    CSIR Research Space (South Africa)

    Cooper, Antony K

    2010-01-01

    Full Text Available mounds underlying the armour units. In its most primitive form, we model the rubble as a static structure with flat surfaces and then pack the selected armour units on top. This reduces the complexity, but the porosity of the packing close to the rubble...

  2. Finite element simulation for the mechanical characterization of soft biological materials by atomic force microscopy.

    Science.gov (United States)

    Valero, C; Navarro, B; Navajas, D; García-Aznar, J M

    2016-09-01

    The characterization of the mechanical properties of soft materials has been traditionally performed through uniaxial tensile tests. Nevertheless, this method cannot be applied to certain extremely soft materials, such as biological tissues or cells that cannot be properly subjected to these tests. Alternative non-destructive tests have been designed in recent years to determine the mechanical properties of soft biological tissues. One of these techniques is based on the use of atomic force microscopy (AFM) to perform nanoindentation tests. In this work, we investigated the mechanical response of soft biological materials to nanoindentation with spherical indenters using finite element simulations. We studied the responses of three different material constitutive laws (elastic, isotropic hyperelastic and anisotropic hyperelastic) under the same process and analyzed the differences thereof. Whereas linear elastic and isotropic hyperelastic materials can be studied using an axisymmetric simplification, anisotropic hyperelastic materials require three-dimensional analyses. Moreover, we established the limiting sample size required to determine the mechanical properties of soft materials while avoiding boundary effects. Finally, we compared the results obtained by simulation with an estimate obtained from Hertz theory. Hertz theory does not distinguish between the different material constitutive laws, and thus, we proposed corrections to improve the quantitative measurement of specific material properties by nanoindentation experiments.

  3. All-atom molecular dynamics simulation of a photosystem I/detergent complex

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Bradley J. [Univ. of Tennessee, Knoxville, TN (United States); Cheng, Xiaolin [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Frymier, Paul [Univ. of Tennessee, Knoxville, TN (United States)

    2014-09-18

    All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Moreover, we find that the docking of soluble electron mediators such as cytochrome c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.

  4. Grace: a Cross-platform Micromagnetic Simulator On Graphics Processing Units

    CERN Document Server

    Zhu, Ru

    2014-01-01

    A micromagnetic simulator running on graphics processing unit (GPU) is presented. It achieves significant performance boost as compared to previous central processing unit (CPU) simulators, up to two orders of magnitude for large input problems. Different from GPU implementations of other research groups, this simulator is developed with C++ Accelerated Massive Parallelism (C++ AMP) and is hardware platform compatible. It runs on GPU from venders include NVidia, AMD and Intel, which paved the way for fast micromagnetic simulation on both high-end workstations with dedicated graphics cards and low-end personal computers with integrated graphics card. A copy of the simulator software is publicly available.

  5. An Application of Simulated Annealing to Scheduling Army Unit Training

    Science.gov (United States)

    1986-10-01

    Simulated annealing operates by analogy to the metalurgy process which strengthens metals through successive heating and cooling. The method is highly...diminishing returns is observed. The simulated annealing heuristic operates by analogy to annealing in physical systems. Annealing in a physical

  6. MISCONCEPTION REMEDIATION OF ATOMIC ORBITAL, MOLECULAR ORBITAL, AND HIBRIDIZIATION CONCEPTS BY COMPUTER ASISSTED INSTRUCTION WITH ANIMATION AND SIMULATION MODEL

    Directory of Open Access Journals (Sweden)

    Sri Mursiti

    2010-06-01

    Full Text Available The research of Computer Asissted Instruction with animation and simulation was used to misconception remediation of atomic orbital, molecular orbital, and hibridiziation concepts. The applicated instruction model was focused on concept approach with macromedia flash player and power point programme. The subject of this research were the 2nd semestre students of Chemistry Department. The data were collected by using of true-false pre-test and post- test followed by the reason of its. The analysis reveals that the Computer Asissted Instruction with animation and simulation model increased the understanding of atomic orbital, molecular orbital, and hibridiziation concepts or remediation of concepts missconception, shown by the significant score gained between before and after the implementation of Computer Asissted Instruction with animation and simulation model. The instruction model developed the students's generic skills too.   Keywords: animation simulation,misconception remediation, orbital, hibridization

  7. Molecular dynamics simulation of protein adsorption at fluid interfaces: a comparison of all-atom and coarse-grained models.

    Science.gov (United States)

    Euston, Stephen R

    2010-10-11

    The adsorption of LTP at the decane-water interface was modeled using all-atom and coarse-grained (CG) molecular dynamics simulations. The CG model (300 ns simulation, 1200 ns scaled time) generates equilibrium adsorbed conformations in about 12 h, whereas the equivalent 1200 ns simulation would take about 300 days for the all-atom model. In both models the LTP molecule adsorbs with α-helical regions parallel to the interface with an average tilt angle normal to the interface of 73° for the all-atom model and 62° for the CG model. In the all-atom model, the secondary structure of the LTP is conserved upon adsorption. A considerable proportion of the N-terminal loop of LTP can be found in the decane phase for the all-atom model, whereas in the CG model the protein only penetrates as far as the mixed water-decane interfacial region. This difference may arise due to the different schemes used to parametrize force field parameters in the two models.

  8. Design and simulation of latent heat storage units. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Shamsundar, N.; Stein, E.; Rooz, E.; Bascaran, E.; Lee, T.C. [Houston Univ., TX (United States)

    1992-04-01

    This report presents the results of two years of research and development on passive latent heat storage systems. Analytical models have been developed and extended, and a computer code for simulating the performance of a latent heat storage has been developed. The code is intended to be merged into a larger solar energy system simulation code and used for making realistic system studies. Simulation studies using a code which has a flexible and accurate routine for handling the storage subsystem should lead to the development of better systems than those in which storage is added on after the rest of the system has already been selected and optimized.

  9. Design and simulation of latent heat storage units

    Energy Technology Data Exchange (ETDEWEB)

    Shamsundar, N.; Stein, E.; Rooz, E.; Bascaran, E.; Lee, T.C. (Houston Univ., TX (United States))

    1992-04-01

    This report presents the results of two years of research and development on passive latent heat storage systems. Analytical models have been developed and extended, and a computer code for simulating the performance of a latent heat storage has been developed. The code is intended to be merged into a larger solar energy system simulation code and used for making realistic system studies. Simulation studies using a code which has a flexible and accurate routine for handling the storage subsystem should lead to the development of better systems than those in which storage is added on after the rest of the system has already been selected and optimized.

  10. The data submitted by the United Kingdom to the United Nations Scientific Committee on the Effects of Atomic Radiation for the 1977 report to the General Assembly

    CERN Document Server

    Taylor, F E; Webb, G A M

    1976-01-01

    The United Nations Scientific Committee on the Effects of Atomic Radiation (UNSCEAR) was established by the General Assembly in 1955 to report on the exposure of man to ionising radiation. In the subsequent twenty years the Committee has covered most aspects of the subject with repeated reviews of the levels of exposure from fallout due to weapons testing. The Committee is currently preparing a further report on doses from all sources and an evaluation of their biological effects. This is expected to be published in 1977. To aid it in compiling this report the Committee requested Member States of the UN to submit national data on a wide range of sources of exposure. The Board was asked by the Foreign and Commonwealth Office to collate the information requested from the United Kingdom. Data were available in the scientific literature on some topics, such as medical irradiation and environmental radioactivity. On some other topics, particularly occupational exposure, data have been collected but seldom publishe...

  11. Use of a PhET Interactive Simulation in General Chemistry Laboratory: Models of the Hydrogen Atom

    Science.gov (United States)

    Clark, Ted M.; Chamberlain, Julia M.

    2014-01-01

    An activity supporting the PhET interactive simulation, Models of the Hydrogen Atom, has been designed and used in the laboratory portion of a general chemistry course. This article describes the framework used to successfully accomplish implementation on a large scale. The activity guides students through a comparison and analysis of the six…

  12. Interaction networks in protein folding via atomic-resolution experiments and long-time-scale molecular dynamics simulations

    DEFF Research Database (Denmark)

    Sborgi, Lorenzo; Verma, Abhinav; Piana, Stefano;

    2015-01-01

    The integration of atomic-resolution experimental and computational methods offers the potential for elucidating key aspects of protein folding that are not revealed by either approach alone. Here, we combine equilibrium NMR measurements of thermal unfolding and long molecular dynamics simulation...

  13. Atomic-scale wear of amorphous hydrogenated carbon during intermittent contact: a combined study using experiment, simulation, and theory.

    Science.gov (United States)

    Vahdat, Vahid; Ryan, Kathleen E; Keating, Pamela L; Jiang, Yijie; Adiga, Shashishekar P; Schall, J David; Turner, Kevin T; Harrison, Judith A; Carpick, Robert W

    2014-07-22

    In this study, we explore the wear behavior of amplitude modulation atomic force microscopy (AM-AFM, an intermittent-contact AFM mode) tips coated with a common type of diamond-like carbon, amorphous hydrogenated carbon (a-C:H), when scanned against an ultra-nanocrystalline diamond (UNCD) sample both experimentally and through molecular dynamics (MD) simulations. Finite element analysis is utilized in a unique way to create a representative geometry of the tip to be simulated in MD. To conduct consistent and quantitative experiments, we apply a protocol that involves determining the tip-sample interaction geometry, calculating the tip-sample force and normal contact stress over the course of the wear test, and precisely quantifying the wear volume using high-resolution transmission electron microscopy imaging. The results reveal gradual wear of a-C:H with no sign of fracture or plastic deformation. The wear rate of a-C:H is consistent with a reaction-rate-based wear theory, which predicts an exponential dependence of the rate of atom removal on the average normal contact stress. From this, kinetic parameters governing the wear process are estimated. MD simulations of an a-C:H tip, whose radius is comparable to the tip radii used in experiments, making contact with a UNCD sample multiple times exhibit an atomic-level removal process. The atomistic wear events observed in the simulations are correlated with under-coordinated atomic species at the contacting surfaces.

  14. Use of a PhET Interactive Simulation in General Chemistry Laboratory: Models of the Hydrogen Atom

    Science.gov (United States)

    Clark, Ted M.; Chamberlain, Julia M.

    2014-01-01

    An activity supporting the PhET interactive simulation, Models of the Hydrogen Atom, has been designed and used in the laboratory portion of a general chemistry course. This article describes the framework used to successfully accomplish implementation on a large scale. The activity guides students through a comparison and analysis of the six…

  15. Local elasticity of strained DNA studied by all-atom simulations

    Science.gov (United States)

    Mazur, Alexey K.

    2011-08-01

    Genomic DNA is constantly subjected to various mechanical stresses arising from its biological functions and cell packaging. If the local mechanical properties of DNA change under torsional and tensional stress, the activity of DNA-modifying proteins and transcription factors can be affected and regulated allosterically. To check this possibility, appropriate steady forces and torques were applied in the course of all-atom molecular dynamics simulations of DNA with AT- and GC-alternating sequences. It is found that the stretching rigidity grows with tension as well as twisting. The torsional rigidity is not affected by stretching, but it varies with twisting very strongly, and differently for the two sequences. Surprisingly, for AT-alternating DNA it passes through a minimum with the average twist close to the experimental value in solution. For this fragment, but not for the GC-alternating sequence, the bending rigidity noticeably changes with both twisting and stretching. The results have important biological implications and shed light on earlier experimental observations.

  16. Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods.

    Science.gov (United States)

    Kassem, Summer; Ahmed, Marawan; El-Sheikh, Salah; Barakat, Khaled H

    2015-11-01

    Entropy of binding constitutes a major, and in many cases a detrimental, component of the binding affinity in biomolecular interactions. While the enthalpic part of the binding free energy is easier to calculate, estimating the entropy of binding is further more complicated. A precise evaluation of entropy requires a comprehensive exploration of the complete phase space of the interacting entities. As this task is extremely hard to accomplish in the context of conventional molecular simulations, calculating entropy has involved many approximations. Most of these golden standard methods focused on developing a reliable estimation of the conformational part of the entropy. Here, we review these methods with a particular emphasis on the different techniques that extract entropy from atomic fluctuations. The theoretical formalisms behind each method is explained highlighting its strengths as well as its limitations, followed by a description of a number of case studies for each method. We hope that this brief, yet comprehensive, review provides a useful tool to understand these methods and realize the practical issues that may arise in such calculations.

  17. ALMOST: an all atom molecular simulation toolkit for protein structure determination.

    Science.gov (United States)

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea

    2014-05-30

    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost.

  18. Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.

    Science.gov (United States)

    Baron, Riccardo; Trzesniak, Daniel; de Vries, Alex H; Elsener, Andreas; Marrink, Siewert J; van Gunsteren, Wilfred F

    2007-02-19

    Thermodynamic data are often used to calibrate or test amomic-level (AL) force fields for molecular dynamics (MD) simulations. In contrast, the majority of coarse-grained (CG) force fields do not rely extensively on thermodynamic quantities. Recently, a CG force field for lipids, hydrocarbons, ions, and water, in which approximately four non-hydrogen atoms are mapped onto one interaction site, has been proposed and applied to study various aspects of lipid systems. To date, no extensive investigation of its capability to describe salvation thermodynamics has been undertaken. In the present study, a detailed picture of vaporization, solvation, and phase-partitioning thermodynamics for liquid hydrocarbons and water was obtained at CG and AL resolutions, in order to compare the two types or models and evaluate their ability to describe thermodynamic properties in the temperature range between 263 and 343 K. Both CG and AL models capture the experimental dependence of the thermodynamic properties on the temperature, albeit a systematically weaker dependence is found for the CG model. Moreover, deviations are found for solvation thermodynamics and for the corresponding enthalpy-entropy compensation for the CG model. Particularly water/oil repulsion seems to be overestimated. However, the results suggest that the thermodynamic properties considered should be reproducible by a CG model provided it is reparametrized on the basis of these liquid-phase properties.

  19. All-Atom Molecular Dynamics Simulation of Protein Translocation through an α-Hemolysin Nanopore

    KAUST Repository

    Di Marino, Daniele

    2015-08-06

    © 2015 American Chemical Society. Nanopore sensing is attracting the attention of a large and varied scientific community. One of the main issues in nanopore sensing is how to associate the measured current signals to specific features of the molecule under investigation. This is particularly relevant when the translocating molecule is a protein and the pore is sufficiently narrow to necessarily involve unfolding of the translocating protein. Recent experimental results characterized the cotranslocational unfolding of Thioredoxin (Trx) passing through an α-hemolisin pore, providing evidence for the existence of a multistep process. In this study we report the results of all-atom molecular dynamics simulations of the same system. Our data indicate that Trx translocation involves two main barriers. The first one is an unfolding barrier associated with a translocation intermediate where the N-terminal region of Trx is stuck at the pore entrance in a conformation that strongly resembles the native one. After the abrupt unfolding of the N-terminal region, the Trx enters the α-hemolisin vestibule. During this stage, the constriction is occupied not only by the translocating residue but also by a hairpin-like structure forming a tangle in the constriction. The second barrier is associated with the disentangling of this region.

  20. MD simulation of atomic displacement cascades in Fe-10 at.%Cr binary alloy

    Energy Technology Data Exchange (ETDEWEB)

    Tikhonchev, M., E-mail: tikhonchev@sv.ulsu.r [Ulyanovsk State University, Leo Tolstoy Str., 42, Ulyanovsk 432970 (Russian Federation); Joint Stock Company, ' State Scientific Center Research Institute of Atomic Reactors' , 433510 Dimitrovgrad-10 (Russian Federation); Svetukhin, V.; Kadochkin, A. [Ulyanovsk State University, Leo Tolstoy Str., 42, Ulyanovsk 432970 (Russian Federation); Gaganidze, E. [Forschungszentrum Karlsruhe, IMF II, 3640, D-76021 Karlsruhe (Germany)

    2009-12-15

    Molecular dynamics simulation of atomic displacement cascades up to 20 keV has been performed in Fe-10 at.%Cr binary alloy at a temperature of 600 K. The N-body interatomic potentials of Finnis-Sinclair type were used. According to the obtained results the dependence of 'surviving' defects amount is well approximated by power function that coincides with other researchers' results. Obtained cascade efficiency for damage energy in the range from 10 to 20 keV is approx0.2 NRT that is slightly higher than for pure alpha-Fe. In post-cascade area Cr fraction in interstitials is in range 2-5% that is essentially lower than Cr content in the base alloy. The results on size and amount of vacancy and interstitial clusters generated in displacement cascades are obtained. For energies of 2 keV and higher the defect cluster average size increases and it is well approximated by a linear dependence on cascade energy both for interstitials and vacancies.

  1. All-atom Molecular Dynamic Simulations and NMR Spectra Study on Intermolecular Interactions of N,N-dimethylacetamide-Water System

    Institute of Scientific and Technical Information of China (English)

    Rong Zhang; Zai-you Tan; San-lai Luo

    2008-01-01

    N,N-dimethylacetamide (DMA) has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA- water system. The radial distribution functions (RDFs) and the hydrogen-bonding network were used in MD simulations. There are strong hydrogen bonds and weak C-H…O contacts in the mixtures, as shown by the analysis of the RDFs. The insight structures in the DMA-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Chemical shifts of the hydrogen atom of water molecule with concentration and temperatures are adopted to study the interactions in the mixtures. The results of NMR spectra show good agreement with the statistical results of hydrogen bonds in MD simulations.

  2. Atomic quantum simulation of dynamical gauge fields coupled to fermionic matter: from string breaking to evolution after a quench.

    Science.gov (United States)

    Banerjee, D; Dalmonte, M; Müller, M; Rico, E; Stebler, P; Wiese, U-J; Zoller, P

    2012-10-26

    Using a Fermi-Bose mixture of ultracold atoms in an optical lattice, we construct a quantum simulator for a U(1) gauge theory coupled to fermionic matter. The construction is based on quantum links which realize continuous gauge symmetry with discrete quantum variables. At low energies, quantum link models with staggered fermions emerge from a Hubbard-type model which can be quantum simulated. This allows us to investigate string breaking as well as the real-time evolution after a quench in gauge theories, which are inaccessible to classical simulation methods.

  3. A three-axis flight simulator. [for testing and evaluating inertial measuring units, and flight platforms

    Science.gov (United States)

    Mason, M. G.

    1975-01-01

    A simulator is described, which was designed for testing and evaluating inertial measuring units, and flight platforms. Mechanical and electrical specifications for the outer, middle, and inner axis are presented. Test results are included.

  4. The UNITE-DSS Modelling System: Risk Simulation and Decision Conferencing

    DEFF Research Database (Denmark)

    Salling, Kim Bang; Barfod, Michael Bruhn

    This presentation introduces the brand new approach of integrating risk simulation and decision conferencing within transport project appraisal (UNITE-DSS model). The modelling approach is divided into various modules respectively as point estimates (cost-benefit analysis), stochastic interval...

  5. Spike library based simulator for extracellular single unit neuronal signals.

    Science.gov (United States)

    Thorbergsson, P T; Jorntell, H; Bengtsson, F; Garwicz, M; Schouenborg, J; Johansson, A

    2009-01-01

    A well defined set of design criteria is of great importance in the process of designing brain machine interfaces (BMI) based on extracellular recordings with chronically implanted micro-electrode arrays in the central nervous system (CNS). In order to compare algorithms and evaluate their performance under various circumstances, ground truth about their input needs to be present. Obtaining ground truth from real data would require optimal algorithms to be used, given that those exist. This is not possible since it relies on the very algorithms that are to be evaluated. Using realistic models of the recording situation facilitates the simulation of extracellular recordings. The simulation gives access to a priori known signal characteristics such as spike times and identities. In this paper, we describe a simulator based on a library of spikes obtained from recordings in the cat cerebellum and observed statistics of neuronal behavior during spontaneous activity. The simulator has proved to be useful in the task of generating extracellular recordings with realistic background noise and known ground truth to use in the evaluation of algorithms for spike detection and sorting.

  6. Investigation of the impact of high liquid viscosity on jet atomization in crossflow via high-fidelity simulations

    Science.gov (United States)

    Li, Xiaoyi; Gao, Hui; Soteriou, Marios C.

    2017-08-01

    Atomization of extremely high viscosity liquid can be of interest for many applications in aerospace, automotive, pharmaceutical, and food industries. While detailed atomization measurements usually face grand challenges, high-fidelity numerical simulations offer the advantage to comprehensively explore the atomization details. In this work, a previously validated high-fidelity first-principle simulation code HiMIST is utilized to simulate high-viscosity liquid jet atomization in crossflow. The code is used to perform a parametric study of the atomization process in a wide range of Ohnesorge numbers (Oh = 0.004-2) and Weber numbers (We = 10-160). Direct comparisons between the present study and previously published low-viscosity jet in crossflow results are performed. The effects of viscous damping and slowing on jet penetration, liquid surface instabilities, ligament formation/breakup, and subsequent droplet formation are investigated. Complex variations in near-field and far-field jet penetrations with increasing Oh at different We are observed and linked with the underlying jet deformation and breakup physics. Transition in breakup regimes and increase in droplet size with increasing Oh are observed, mostly consistent with the literature reports. The detailed simulations elucidate a distinctive edge-ligament-breakup dominated process with long surviving ligaments for the higher Oh cases, as opposed to a two-stage edge-stripping/column-fracture process for the lower Oh counterparts. The trend of decreasing column deflection with increasing We is reversed as Oh increases. A predominantly unimodal droplet size distribution is predicted at higher Oh, in contrast to the bimodal distribution at lower Oh. It has been found that both Rayleigh-Taylor and Kelvin-Helmholtz linear stability theories cannot be easily applied to interpret the distinct edge breakup process and further study of the underlying physics is needed.

  7. Molecular Dynamics Simulation Study of Atomic Segregation of (PdPt)147 during the Heating Process

    Science.gov (United States)

    Xiao, X. Y.; Cheng, Z. F.; Xia, J. H.

    Research on the influence of alloy concentration and distribution on bimetallic cluster plays a key role in exploring new structural material. This paper studies the melting process of icosahedral bimetallic cluster (PdPt)147 with different Pt concentrations and different atomic distributions by using molecular dynamics with an embedded atom method. The results indicate that the mixed Pd-Pt cluster shows an irregular phenomenon between 580 and 630 K, i.e. the atomic energy decreases with the increase of temperature. This is because the surface energy of Pd is lower than that of Pt; the decreased energy due to Pd atomic segregation is larger than the increased energy due to heating during the segregation process. In addition, the temperature of Pd atomic segregation is strongly related to Pt concentration. This leads to that Pd atoms prefer to remain on the surface even after the cluster melted.

  8. MEAM Simulation of Distribution of Nb Atoms in TiAl+Nb System

    Institute of Scientific and Technical Information of China (English)

    Xiaodong NI; Guoliang CHEN; Xitao WANG; Xudong HUI

    2001-01-01

    An accurate MEAM (modified embedded atom method) potential including angular dependence for TiAl compound has been developed. The properties of TiAl compound can be reproduced well. With this potential, the distribution of Nb atoms in L10 type TiAl compound with various composition are calculated by using an average-atom model similar to B-W (Bragg-Williams)method. The results of calculation showed that Nb atoms prefer to occupy the Ti sublattice of L10 structure, and with increasing atomic percent of Nb and Al, Nb atoms exhibited a trend of ordered distribution in Ti sublattice, and result in the formation of L10 derivative superlattice structure.

  9. Simulation-based patient flow analysis in an endoscopy unit

    DEFF Research Database (Denmark)

    Koo, Pyung-Hoi; Nielsen, Karl Brian; Jang, Jaejin

    2010-01-01

    One of the major elements in improving efficiency of healthcare services is patient flow. Patients require a variety of healthcare resources as they receive healthcare services. Poor management of patient flow results in long waiting time of patients, under/over utilization of medical resources......, low quality of care and high healthcare cost. This article addresses patient flow problems at a Gastrointestinal endoscopy unit. We attempt to analyze the main factors that contribute to the inefficient patient flow and process bottlenecks and to propose efficient patient scheduling and staff...

  10. Using the Large Fire Simulator System to map wildland fire potential for the conterminous United States

    Science.gov (United States)

    LaWen Hollingsworth; James Menakis

    2010-01-01

    This project mapped wildland fire potential (WFP) for the conterminous United States by using the large fire simulation system developed for Fire Program Analysis (FPA) System. The large fire simulation system, referred to here as LFSim, consists of modules for weather generation, fire occurrence, fire suppression, and fire growth modeling. Weather was generated with...

  11. 76 FR 48184 - Exelon Nuclear, Peach Bottom Atomic Power Station, Unit 1; Exemption From Certain Security...

    Science.gov (United States)

    2011-08-08

    ... a permanently shut down nuclear reactor facility. PBAPS Unit 1 was a high-temperature, gas-cooled... nuclear power reactors against radiological sabotage,'' paragraph (b)(1) states, ``The licensee shall... its objective to provide high assurance that activities involving special nuclear material are...

  12. Numerical simulation of the flow around a steerable propulsion unit

    Energy Technology Data Exchange (ETDEWEB)

    Pacuraru, F; Lungu, A; Ungureanu, C; Marcu, O, E-mail: florin.pacuraru@ugal.r [Department of Ship Hydrodynamics, ' Dunarea de Jos' University of Galati 47 Domneasca Street, Galati 800008 (Romania)

    2010-08-15

    Azimuth propulsion units have become during the last decade a more and more popular solution for all kinds of vessels. Azimuth thruster system, combining the propulsion and steering units of conventional ships replaces traditional propellers and lengthy drive shafts and rudders ensuring an excellent vessel steering. In many cases the interaction between the propeller and other components of the propulsion system strongly affects the inflow to the propeller and therefore its performance. The correct estimation of this influence is important for propulsion systems which consist of more than one element, such as pods (shaft, gondola and propeller), ducted propellers (duct, struts and propeller) or bow thrusters (ship form, tunnel, gondola and propeller). The paper proposes a numerical investigation based on RANS computation for solving the viscous flow around an azimuth thruster system to provide a detailed insight into the critical flow regions for determining the optimum inclination angle for struts, for studying the hydrodynamic interactions between various components of the system, for predicting the hydrodynamic performance of the propulsion system and to investigate regions with possible flow separations.

  13. Fat Tail Model for Simulating Test Systems in Multiperiod Unit Commitment

    Directory of Open Access Journals (Sweden)

    J. A. Marmolejo

    2015-01-01

    Full Text Available This paper describes the use of Chambers-Mallows-Stuck method for simulating stable random variables in the generation of test systems for economic analysis in power systems. A study that focused on generating test electrical systems through fat tail model for unit commitment problem in electrical power systems is presented. Usually, the instances of test systems in Unit Commitment are generated using normal distribution, but in this work, simulations data are based on a new method. For simulating, we used three original systems to obtain the demand behavior and thermal production costs. The estimation of stable parameters for the simulation of stable random variables was based on three generally accepted methods: (a regression, (b quantiles, and (c maximum likelihood, choosing one that has the best fit of the tails of the distribution. Numerical results illustrate the applicability of the proposed method by solving several unit commitment problems.

  14. Embedded atom approach for gold–silicon system from ab initio molecular dynamics simulations using the force matching method

    Indian Academy of Sciences (India)

    A NASSOUR

    2016-09-01

    In the present paper, an empirical embedded atom method (EAM) potential for gold–silicon (Au–Si) is developed by fitting to ab initio force (the ‘force matching’ method) and experimental data. The force database is generated within ab initio molecular dynamics (AIMD). The database includes liquid phase at various temperatures. Classical molecular dynamics simulations are performed to examine structural, coordination numbers, structure factors and dynamic properties of Au$_{81}$Si$_{19}$ alloy, with the interaction described via EAM model. The results are in good agreement with AIMD simulations and experimental data.

  15. Conformations of Carnosine in Aqueous Solutions by All-Atom Molecular Dynamics Simulations and 2D-NOSEY Spectrum

    Institute of Scientific and Technical Information of China (English)

    Rong Zhang; Dan Wang; Wen-juan Wu

    2013-01-01

    All-atom molecular simulations and two-dimensional nuclear overhauser effect spectrum have been used to study the conformations of carnosine in aqueous solution.Intramolecular distances,root-mean-square deviation,radius of gyration,and solvent-accessible surface are used to characterize the properties of the carnosine.Carnosine can shift between extended and folded states,but exists mostly in extended state in water.Its preference for extension in pure water has been proven by the 2D nuclear magnetic resonance (NMR) experiment.The NMR experimental results are consistent with the molecular dynamics simulations.

  16. Atomic Quantum Simulation of Dynamical Gauge Fields coupled to Fermionic Matter: From String Breaking to Evolution after a Quench

    OpenAIRE

    Banerjee D.; Dalmonte M.; Muller M; Rico E.; Stebler P.; Wiese U.-J.; Zoller P.

    2012-01-01

    Using a Fermi-Bose mixture of ultra-cold atoms in an optical lattice, we construct a quantum simulator for a U(1) gauge theory coupled to fermionic matter. The construction is based on quantum links which realize continuous gauge symmetry with discrete quantum variables. At low energies, quantum link models with staggered fermions emerge from a Hubbard-type model which can be quantum simulated. This allows us to investigate string breaking as well as the real-time evolution after a quench in ...

  17. Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails.

    Directory of Open Access Journals (Sweden)

    Peter M Kasson

    2010-06-01

    Full Text Available Membrane fusion is essential to both cellular vesicle trafficking and infection by enveloped viruses. While the fusion protein assemblies that catalyze fusion are readily identifiable, the specific activities of the proteins involved and nature of the membrane changes they induce remain unknown. Here, we use many atomic-resolution simulations of vesicle fusion to examine the molecular mechanisms for fusion in detail. We employ committor analysis for these million-atom vesicle fusion simulations to identify a transition state for fusion stalk formation. In our simulations, this transition state occurs when the bulk properties of each lipid bilayer remain in a lamellar state but a few hydrophobic tails bulge into the hydrophilic interface layer and make contact to nucleate a stalk. Additional simulations of influenza fusion peptides in lipid bilayers show that the peptides promote similar local protrusion of lipid tails. Comparing these two sets of simulations, we obtain a common set of structural changes between the transition state for stalk formation and the local environment of peptides known to catalyze fusion. Our results thus suggest that the specific molecular properties of individual lipids are highly important to vesicle fusion and yield an explicit structural model that could help explain the mechanism of catalysis by fusion proteins.

  18. Different Cooling Rate Dependences of Different Microstructure Units in Aluminium Glass by Molecular Dynamics Simulation

    Institute of Scientific and Technical Information of China (English)

    LIU Chang-Song; ZHU Zhen-Gang; XIA Jun-Chao; SUN De-Yan

    2000-01-01

    Constant-pressure molecular dynamics simulation and the pair analysis technique have been performed to study the microstructural evolution of aluminium during rapid solidification. The microstructure characteristics of icosahedral ordering increase with decrease of the cooling rate, whereas the microstructure unit characteristics of hcp crystalline structure decrease. There are two kinds of microstructure units which are similar to those in the fcc crystal containing interstitialcies. These two kinds of microscopic units are nearly independent of the cooling rate. The microscopic structural unit characteristics of fcc crystalline structure do not depend on the cooling rate either. These results may help us understand the microstructure of glass and its stability.

  19. Results and simulation of the prototype detection unit of KM3NeT-ARCA

    Directory of Open Access Journals (Sweden)

    Hugon C.M.F.

    2017-01-01

    Full Text Available KM3NeT-ARCA is a deep sea high energy neutrino detector. A detection unit prototype was deployed in the future KM3NeT-ARCA deep-sea site, off of the Sicilian coast. This detection unit is composed of a line of 3 digital optical modules with 31 photomultiplier tubes on each one. The prototype detection unit was operated since its deployment in May 2014 until its decommissioning in July 2015. The results of the calibration of this detection unit and its simulation are presented and discussed.

  20. United Nations scientific committee on the effects of atomic radiation 2000 report

    Energy Technology Data Exchange (ETDEWEB)

    Asano, Tomohiro [Japan Nuclear Cycle Development Inst., Tokai, Ibaraki (Japan); Sato, Koki; Onodera, Jun-ichi

    2001-06-01

    This article concerns the concept and discussion of the report in the title which was presented to General Assembly of UN in October, 2000. The report consists from the text and 10 subjects of Scientific Annex (Volume I: Sources and Volume II: Effects). The Annex involves A: Method to evaluate dose, B: Exposure from natural radiation, C: Public exposure due to artificial radiation sources, D: Exposure due to medical sources, E: Occupational dose, F: DNA repair and mutation, G: Biological effects due to low dose exposure, H: Complicated effects due to radiation and other factors, I: Epidemiological evaluation of radiation-carcinogenesis, and J: Exposure and effects in Chernobyl accident. Among these, described are followings: B; annual mean effective dose of 2.4 mSv, C; experiments and manufacturing of nuclear weapons, atomic power plant and others involving JCO criticality accident (September, 1999 in Japan), D; diagnostic and therapeutic exposures, E; population dose of 11,700 man-Sv, F: main concern on p53 gene, G; relation with cancer, H; relation with asbest, smoking, arsenic and others, I; concern on Hiroshima and Nagasaki survivors, Chernobyl accident, in-house Rn and in utero exposure, and J; release of radionuclides, exposure dose and health effects. In future, sources and effects will be examined dependently on each other. (K.H.)

  1. Medical exposure assessment: the global approach of the United Nations Scientific Committee on the Effects of Atomic Radiation.

    Science.gov (United States)

    Shannoun, F

    2015-07-01

    The United Nations Scientific Committee on the Effects of Atomic Radiation (UNSCEAR) was established in 1955 to systematically collect, evaluate, publish and share data on the global levels and effects of ionizing radiation from natural and artificial sources. Regular surveys have been conducted to determinate the frequencies of medical radiological procedure, the number of equipment and staffing and the level of global exposure using the health care level (HCL) extrapolation model. UNSCEAR surveys revealed a range of issues relating to participation, survey process, data quality and analysis. Thus, UNSCEAR developed an improvement strategy to address the existing deficiencies in data quality and collection. The major element of this strategy is the introduction of an on-line platform to facilitate the data collection and archiving process. It is anticipated that the number of countries participating in UNSCEAR's surveys will increase in the future, particularly from HCL II-IV countries.

  2. Transferable potentials for phase equilibria-united atom description of five- and six-membered cyclic alkanes and ethers.

    Science.gov (United States)

    Keasler, Samuel J; Charan, Sophia M; Wick, Collin D; Economou, Ioannis G; Siepmann, J Ilja

    2012-09-13

    While the transferable potentials for phase equilibria-united atom (TraPPE-UA) force field has generally been successful at providing parameters that are highly transferable between different molecules, the polarity and polarizability of a given functional group can be significantly perturbed in small cyclic structures, which limits the transferability of parameters obtained for linear molecules. This has motivated us to develop a version of the TraPPE-UA force field specifically for five- and six-membered cyclic alkanes and ethers. The Lennard-Jones parameters for the methylene group obtained from cyclic alkanes are transferred to the ethers for each ring size, and those for the oxygen atom are common to all compounds for a given ring size. However, the partial charges are molecule specific and parametrized using liquid-phase dielectric constants. This model yields accurate saturated liquid densities and vapor pressures, critical temperatures and densities, normal boiling points, heat capacities, and isothermal compressibilities for the following molecules: cyclopentane, tetrahydrofuran, 1,3-dioxolane, cyclohexane, oxane, 1,4-dioxane, 1,3-dioxane, and 1,3,5-trioxane. The azeotropic behavior and separation factor for the binary mixtures of 1,3-dioxolane/cyclohexane and ethanol/1,4-dioxane are qualitively reproduced.

  3. First-Principles United Atom Force Field for the Ionic Liquid BMIM(+)BF4(-): An Alternative to Charge Scaling.

    Science.gov (United States)

    Son, Chang Yun; McDaniel, Jesse G; Schmidt, J R; Cui, Qiang; Yethiraj, Arun

    2016-04-14

    Molecular dynamics study of ionic liquids (ILs) is a challenging task. While accurate fully polarizable atomistic models exist, they are computationally too demanding for routine use. Most nonpolarizable atomistic models predict diffusion constants that are much lower than experiment. Scaled charge atomistic models are cost-effective and give good results for single component ILs but are in qualitative error for the phase behavior of mixtures, due to inaccurate prediction of the IL cohesive energy. In this work, we present an alternative approach for developing computationally efficient models that importantly preserves both the correct dynamics and cohesive energy of the IL. Employing a "top-down" approach, a hierarchy of coarse-grained models for BMIM(+)BF4(-) are developed by systematically varying the polarization/atomic resolution of the distinct functional groups. Parametrization is based on symmetry-adapted perturbation theory (SAPT) calculations involving the homomolecular species; all cross interactions are obtained from mixing rules, and there are no adjustable parameters. We find that enhanced dynamics from a united-atom description counteracts the effect of reduced polarization, enabling computationally efficient models that exhibit quantitative agreement with experiment for both static and dynamic properties. We give explicit suggestions for reduced-description models that are computationally more efficient, more accurate, and more fundamentally sound than existing nonpolarizable atomistic models.

  4. Physics of non-steady state diffusion of lightweight atoms in a heavy atom matrix. Introducing an open-source tool for simulated-experiments in fluid mechanics

    CERN Document Server

    Serrano-López, Roberto; Tapia-Júdez, Oscar; Fradera, Jorge

    2013-01-01

    The practice-based learning methodologies offer to undergraduate professors different ways to illustrate certain general physic principles. Traditional experimental workbenches have been extensively used during decades for academic lessons in order to complete theoretical dissertations or lectures, aiming at assuring an adequate understanding. The high cost of materials and laboratory equipment, the excessive preparation time, and the difficulty for carrying out offsite-campus replications by students, are disadvantages that can discourage of trying new kinds of experimental tasks. This paper gives insight of simulated experiment possibilities through an open-source-based computational suite in teaching fluid mechanics. Physics underlying diffusion of a light specie in a heavier atom matrix, as function of time and position, were explained to students as an example to teach them the Fick's Second Law expression. We present a docent step-by-step programme, scheduled in three sessions. The expected solution is ...

  5. Temperature Dependence of the OH- + CH3I Reaction Kinetics. Experimental and Simulation Studies and Atomic-Level Dynamics (Postprint)

    Science.gov (United States)

    2013-11-25

    New Mexico 87117 5776, United States ABSTRACT: Direct dynamics simulations and selected ion flow tube {SIFT) experiments were performed to study...0.04 0.51 0.49 500 0.48 ± 0.06 0.05 ± O.ot 0.47 ± 0.05 0.46 0.54 aSee footnote a in Table 2 and IVA . I Simulation Results concerning the [CH3 I OHt

  6. Gaining insight into the physics of dynamic atomic force microscopy in complex environments using the VEDA simulator.

    Science.gov (United States)

    Kiracofe, Daniel; Melcher, John; Raman, Arvind

    2012-01-01

    Dynamic atomic force microscopy (dAFM) continues to grow in popularity among scientists in many different fields, and research on new methods and operating modes continues to expand the resolution, capabilities, and types of samples that can be studied. But many promising increases in capability are accompanied by increases in complexity. Indeed, interpreting modern dAFM data can be challenging, especially on complicated material systems, or in liquid environments where the behavior is often contrary to what is known in air or vacuum environments. Mathematical simulations have proven to be an effective tool in providing physical insight into these non-intuitive systems. In this article we describe recent developments in the VEDA (virtual environment for dynamic AFM) simulator, which is a suite of freely available, open-source simulation tools that are delivered through the cloud computing cyber-infrastructure of nanoHUB (www.nanohub.org). Here we describe three major developments. First, simulations in liquid environments are improved by enhancements in the modeling of cantilever dynamics, excitation methods, and solvation shell forces. Second, VEDA is now able to simulate many new advanced modes of operation (bimodal, phase-modulation, frequency-modulation, etc.). Finally, nineteen different tip-sample models are available to simulate the surface physics of a wide variety different material systems including capillary, specific adhesion, van der Waals, electrostatic, viscoelasticity, and hydration forces. These features are demonstrated through example simulations and validated against experimental data, in order to provide insight into practical problems in dynamic AFM.

  7. Atomic scale simulations of pyrochlore oxides with a tight-binding variable-charge model: implications for radiation tolerance.

    Science.gov (United States)

    Sattonnay, G; Tétot, R

    2014-02-05

    Atomistic simulations with new interatomic potentials derived from a tight-binding variable-charge model were performed in order to investigate the lattice properties and the defect formation energies in Gd2Ti2O7 and Gd2Zr2O7 pyrochlores. The main objective was to determine the role played by the defect stability on the radiation tolerance of these compounds. Calculations show that the titanate has a more covalent character than the zirconate. Moreover, the properties of oxygen Frenkel pairs, cation antisite defects and cation Frenkel pairs were studied. In Gd2Ti2O7 the cation antisite defect and the Ti-Frenkel pair are not stable: they evolve towards more stable defect configurations during the atomic relaxation process. This phenomenon is driven by a decrease of the Ti coordination number down to five which leads to a local atomic reorganization and strong structural distortions around the defects. These kinds of atomic rearrangements are not observed around defects in Gd2Zr2O7. Therefore, the defect stability in A2B2O7 depends on the ability of B atoms to accommodate high coordination number (higher than six seems impossible for Ti). The accumulation of structural distortions around Ti-defects due to this phenomenon could drive the Gd2Ti2O7 amorphization induced by irradiation.

  8. Descriptions and Implementations of DL_F Notation: A Natural Chemical Expression System of Atom Types for Molecular Simulations.

    Science.gov (United States)

    Yong, Chin W

    2016-08-22

    DL_F Notation is an easy-to-understand, standardized atom typesetting expression for molecular simulations for a range of organic force field (FF) schemes such as OPLSAA, PCFF, and CVFF. It is implemented within DL_FIELD, a software program that facilitates the setting up of molecular FF models for DL_POLY molecular dynamics simulation software. By making use of the Notation, a single core conversion module (the DL_F conversion Engine) implemented within DL_FIELD can be used to analyze a molecular structure and determine the types of atoms for a given FF scheme. Users only need to provide the molecular input structure in a simple xyz format and DL_FIELD can produce the necessary force field file for DL_POLY automatically. In commensurate with the development concept of DL_FIELD, which placed emphasis on robustness and user friendliness, the Engine provides a single-step solution to setup complex FF models. This allows users to switch from one of the above-mentioned FF seamlessly to another while at the same time provides a consistent atom typing that is expressed in a natural chemical sense.

  9. Real-time dynamics and proposal for feasible experiments of lattice gauge-Higgs model simulated by cold atoms

    Science.gov (United States)

    Kuno, Yoshihito; Kasamatsu, Kenichi; Takahashi, Yoshiro; Ichinose, Ikuo; Matsui, Tetsuo

    2015-06-01

    Lattice gauge theory has provided a crucial non-perturbative method in studying canonical models in high-energy physics such as quantum chromodynamics. Among other models of lattice gauge theory, the lattice gauge-Higgs model is a quite important one because it describes a wide variety of phenomena/models related to the Anderson-Higgs mechanism, such as superconductivity, the standard model of particle physics, and the inflation process of the early Universe. In this paper, we first show that atomic description of the lattice gauge model allows us to explore real-time dynamics of the gauge variables by using the Gross-Pitaevskii equations. Numerical simulations of the time development of an electric flux reveal some interesting characteristics of the dynamic aspect of the model and determine its phase diagram. Next, to realize a quantum simulator of the U(1) lattice gauge-Higgs model on an optical lattice filled by cold atoms, we propose two feasible methods: (i) Wannier states in the excited bands and (ii) dipolar atoms in a multilayer optical lattice. We pay attention to the constraint of Gauss's law and avoid nonlocal gauge interactions.

  10. High resolution transmission electron microscope Imaging and first-principles simulations of atomic-scale features in graphene membrane

    Science.gov (United States)

    Wang, Wei; Bhandari, Sagar; Yi, Wei; Bell, David; Westervelt, Robert; Kaxiras, Efthimios

    2012-02-01

    Ultra-thin membranes such as graphene[1] are of great importance for basic science and technology applications. Graphene sets the ultimate limit of thinness, demonstrating that a free-standing single atomic layer not only exists but can be extremely stable and strong [2--4]. However, both theory [5, 6] and experiments [3, 7] suggest that the existence of graphene relies on intrinsic ripples that suppress the long-wavelength thermal fluctuations which otherwise spontaneously destroy long range order in a two dimensional system. Here we show direct imaging of the atomic features in graphene including the ripples resolved using monochromatic aberration-corrected transmission electron microscopy (TEM). We compare the images observed in TEM with simulated images based on an accurate first-principles total potential. We show that these atomic scale features can be mapped through accurate first-principles simulations into high resolution TEM contrast. [1] Geim, A. K. & Novoselov, K. S. Nat. Mater. 6, 183-191, (2007). [2] Novoselov, K. S.et al. Science 306, 666-669, (2004). [3] Meyer, J. C. et al. Nature 446, 60-63, (2007). [4] Lee, C., Wei, X. D., Kysar, J. W. & Hone, J. Science 321, 385-388, (2008). [5] Nelson, D. R. & Peliti, L. J Phys-Paris 48, 1085-1092, (1987). [6] Fasolino, A., Los, J. H. & Katsnelson, M. I. Nat. Mater. 6, 858-861, (2007). [7] Meyer, J. C. et al. Solid State Commun. 143, 101-109, (2007).

  11. Atomic-scale computer simulation for early precipitation process of Ni75Al10V15 alloy

    Institute of Scientific and Technical Information of China (English)

    ZHAO Yuhong; CHEN Zheng; WANG Yongxin; LU Yanli

    2004-01-01

    The kinetic model for a ternary system is introduced based on the microscopic diffusion form of the phase-field equations for a binary alloy. The equation is solved in the reciprocal space. This model is used to investigate the early precipitation process of Ni75-Al10V15 by simulating the atomic pictures of the two ordered phases and calculating the order parameters of γ′(Ni3Al) phase. Simulation results show that the γ′ ordered phases precipitate from the disordered matrix by a non-classical nucleation mechanism, and the nonstoichiometric γ′ ordered phase appears first and then transforms into the stoichiometric one. Clusters of V atoms appear at the γ′ phase boundaries followed by the formation of the nonstoichiometric θ ordered phase. The farther the location from γ′ phase boundary is, the lower the order degree of θ phase is. There exist two kinds of DO22 ordered domains: a horizontal one and a vertical one, related to their adjacent γ′ phase boundaries. The model could describe the atomic ordering and composition clustering simultaneously, and any a priori assumption about the new phase structure and precipitation mechanism etc. is unnecessary.

  12. Computer-delivered patient simulations in the United States Medical Licensing Examination (USMLE).

    Science.gov (United States)

    Dillon, Gerard F; Clauser, Brian E

    2009-01-01

    To obtain a full and unrestricted license to practice medicine in the United States, students and graduates of the MD-granting US medical schools and of medical schools located outside of the United States must take and pass the United States Medical Licensing Examination. United States Medical Licensing Examination began as a series of paper-and-pencil examinations in the early 1990s and converted to computer-delivery in 1999. With this change to the computerized format came the opportunity to introduce computer-simulated patients, which had been under development at the National Board of Medical Examiners for a number of years. This testing format, called a computer-based case simulation, requires the examinee to manage a simulated patient in simulated time. The examinee can select options for history-taking and physical examination. Diagnostic studies and treatment are ordered via free-text entry, and the examinee controls the advance of simulated time and the location of the patient in the health care setting. Although the inclusion of this format has brought a number of practical, psychometric, and security challenges, its addition has allowed a significant expansion in ways to assess examinees on their diagnostic decision making and therapeutic intervention skills and on developing and implementing a reasonable patient management plan.

  13. Simulations of quantum transport in nanoscale systems: application to atomic gold and silver wires

    DEFF Research Database (Denmark)

    Mozos, J.L.; Ordejon, P.; Brandbyge, Mads

    2002-01-01

    . The potential drop profile and induced electronic current (and therefore the conductance) are obtained from first principles. The method takes into account the atomic structure of both the nanoscale structure and the semi-infinite electrodes through which the potential is applied. Non-equilibrium Green......'s function techniques are used to calculate the quantum conductance. Here we apply the method to the study of the electronic transport in wires of gold and silver with atomic thickness. We show the results of our calculations, and compare with some of the abundant experimental data on these systems....

  14. Simulations of Edge Effect in 1D Spin Crossover Compounds by Atom-Phonon Coupling Model

    Science.gov (United States)

    Linares, J.; Chiruta, D.; Jureschi, C. M.; Alayli, Y.; Turcu, C. O.; Dahoo, P. R.

    2016-08-01

    We used the atom-phonon coupling model to explain and illustrate the behaviour of a linear nano-chain of molecules. The analysis of the system's behaviour was performed using Free Energy method, and by applying Monte Carlo Metropolis (MCM) method which take into account the phonon contribution. In particular we tested both the MCM algorithm and the dynamic-matrix method and we expose how the thermal behaviour of a 1D spin crossover system varies as a function of different factors. Furthermore we blocked the edge atoms of the chain in its high spin state to study the effect on the system's behaviour.

  15. Simulations of quantum transport in nanoscale systems: application to atomic gold and silver wires

    DEFF Research Database (Denmark)

    Mozos, J.L.; Ordejon, P.; Brandbyge, Mads

    2002-01-01

    's function techniques are used to calculate the quantum conductance. Here we apply the method to the study of the electronic transport in wires of gold and silver with atomic thickness. We show the results of our calculations, and compare with some of the abundant experimental data on these systems....

  16. ADATOM, VACANCY AND SPUTTERING YIELDS OF ENERGETIC Pt ATOMS IMPACTING ON Pt(100) BY MOLECULAR DYNAMICS SIMULATION

    Institute of Scientific and Technical Information of China (English)

    YE ZI-YAN; ZHANG QING-YU

    2001-01-01

    We have studied the influence of incident atoms with low energy on the Pt(100) surface by molecular dynamics simulation. The interaction potential obtained by the embedded atom method (EAM) was used in the simulation. The incident energy changes from 0.leV to 200eV, and the target temperature ranges from 100 to 500 K. The target scales are 6×6×4 and 8×8×4 fcc cells for lower and higher incident energies, respectively. The adatom, sputtering, vacancy and backscattering yields are calculated. It was found that there is a sputtering threshold for the incident energy. When the incident energy is higher than the sputtering threshold, the sputtering yield increases with the increase of incident energy, and the sputtering shows a symmetrical pattern. We found that the adatom and vacancy yields increase as the incident energy increases. The vacancy yields are much higher than those obtained by Monte Carlo simulation. The dependence of the adatom and sputtering yields on the incident energy and the relative atomistic mechanisms are discussed.

  17. Extended Bose-Hubbard model and atomic quantum simulation of U(1) gauge-Higgs model in (1 + 1) dimensions

    CERN Document Server

    Kuno, Yoshihito; Sakane, Shinya; Kasamatsu, Kenichi; Ichinose, Ikuo; Matsui, Tetsuo

    2016-01-01

    In this paper, we study atomic quantum simulations of $(1+1)$-dimensional($(1+1)$D) U(1) gauge-Higgs models (GHMs) defined on a lattice. We explain how U(1) lattice GHMs appear from an extended Bose-Hubbard model (EBHM) describing ultra-cold atoms with a nearest neighbor repulsion in a 1D optical lattice. We first study a phase diagram of the 1D EBHM at low fillings by means of a quantum Monte-Carlo(MC) simulation. Next, we study the EBHM at large fillings and also GHMs by the MC simulations in the path-integral formalism and show that there are four phases, i.e., the Higgs phase(superfluid), the confinement phase (Mott insulator), and phases corresponding to the density wave and the supersolid. With the obtained phase diagrams, we investigate the relationship between the two models. Finally, we study real-time dynamic of an electric flux in the GHMs by the Gross-Pitaevskii equations and the truncated Wigner approximation.

  18. Simulation of nucleation and growth of atomic layer deposition phosphorus for doping of advanced FinFETs

    Energy Technology Data Exchange (ETDEWEB)

    Seidel, Thomas E., E-mail: zoomtotom@gmail.com [Seitek50, Palm Coast, Florida 32135 (United States); Goldberg, Alexander; Halls, Mat D. [Schrödinger, Inc., San Diego, California 92122 (United States); Current, Michael I. [Current Scientific, San Jose, California 95124 (United States)

    2016-01-15

    Simulations for the nucleation and growth of phosphorus films were carried out using density functional theory. The surface was represented by a Si{sub 9}H{sub 12} truncated cluster surface model with 2 × 1-reconstructured (100) Si-OH terminations for the initial reaction sites. Chemistries included phosphorous halides (PF{sub 3}, PCl{sub 3}, and PBr{sub 3}) and disilane (Si{sub 2}H{sub 6}). Atomic layer deposition (ALD) reaction sequences were illustrated with three-dimensional molecular models using sequential PF{sub 3} and Si{sub 2}H{sub 6} reactions and featuring SiFH{sub 3} as a byproduct. Exothermic reaction pathways were developed for both nucleation and growth for a Si-OH surface. Energetically favorable reactions for the deposition of four phosphorus atoms including lateral P–P bonding were simulated. This paper suggests energetically favorable thermodynamic reactions for the growth of elemental phosphorus on (100) silicon. Phosphorus layers made by ALD are an option for doping advanced fin field-effect transistors (FinFETs). Phosphorus may be thermally diffused into the silicon or recoil knocked in; simulations of the recoil profile of phosphorus into a FinFET surface are illustrated.

  19. Monte Carlo Simulations of Random Frustrated Systems on Graphics Processing Units

    Science.gov (United States)

    Feng, Sheng; Fang, Ye; Hall, Sean; Papke, Ariane; Thomasson, Cade; Tam, Ka-Ming; Moreno, Juana; Jarrell, Mark

    2012-02-01

    We study the implementation of the classical Monte Carlo simulation for random frustrated models using the multithreaded computing environment provided by the the Compute Unified Device Architecture (CUDA) on modern Graphics Processing Units (GPU) with hundreds of cores and high memory bandwidth. The key for optimizing the performance of the GPU computing is in the proper handling of the data structure. Utilizing the multi-spin coding, we obtain an efficient GPU implementation of the parallel tempering Monte Carlo simulation for the Edwards-Anderson spin glass model. In the typical simulations, we find over two thousand times of speed-up over the single threaded CPU implementation.

  20. Development of a full-scale training simulator for an 800-MW power unit

    Science.gov (United States)

    Zhuravlev, S. K.; Andreev, A. M.

    2013-07-01

    Stages of work involving preparation of requirements specification, development, and subsequent implementation of a project for constructing a full-scale training simulator of an 800-MW power unit are considered. The training simulator is constructed using the Kosmotronika-Venets computerized automation system developed by PIK Progress (Moscow). The entire personnel training system, the arrangement of drills, and the concept of structuring the entire personnel education system at the Surgut GRES-2 district power station, a branch of E.ON Rossiya, had to be touched in drawing up the requirements specification for elaborating the training simulator. The article describes how these problems were solved.

  1. "Bohr's Atomic Model."

    Science.gov (United States)

    Willden, Jeff

    2001-01-01

    "Bohr's Atomic Model" is a small interactive multimedia program that introduces the viewer to a simplified model of the atom. This interactive simulation lets students build an atom using an atomic construction set. The underlying design methodology for "Bohr's Atomic Model" is model-centered instruction, which means the central model of the…

  2. Simulations and Modelling of Absorption Cooling Unit by Means of Peltier Module

    Directory of Open Access Journals (Sweden)

    Vladimír KOCÚR

    2011-07-01

    Full Text Available Article refers to function of absorption cooling unit simulated by means of Peltier module. Although, this system works on entirely different physical principle, it is necessary to use it as equivalent of absorption cooling what is proved in more detail in article.

  3. Simulations and Modelling of Absorption Cooling Unit by Means of Peltier Module

    OpenAIRE

    Vladimír KOCÚR; Jozef ŠURIANSKY

    2011-01-01

    Article refers to function of absorption cooling unit simulated by means of Peltier module. Although, this system works on entirely different physical principle, it is necessary to use it as equivalent of absorption cooling what is proved in more detail in article.

  4. Graphics Processing Unit-Based Bioheat Simulation to Facilitate Rapid Decision Making Associated with Cryosurgery Training.

    Science.gov (United States)

    Keelan, Robert; Zhang, Hong; Shimada, Kenji; Rabin, Yoed

    2016-04-01

    This study focuses on the implementation of an efficient numerical technique for cryosurgery simulations on a graphics processing unit as an alternative means to accelerate runtime. This study is part of an ongoing effort to develop computerized training tools for cryosurgery, with prostate cryosurgery as a developmental model. The ability to perform rapid simulations of various test cases is critical to facilitate sound decision making associated with medical training. Consistent with clinical practice, the training tool aims at correlating the frozen region contour and the corresponding temperature field with the target region shape. The current study focuses on the feasibility of graphics processing unit-based computation using C++ accelerated massive parallelism, as one possible implementation. Benchmark results on a variety of computation platforms display between 3-fold acceleration (laptop) and 13-fold acceleration (gaming computer) of cryosurgery simulation, in comparison with the more common implementation on a multicore central processing unit. While the general concept of graphics processing unit-based simulations is not new, its application to phase-change problems, combined with the unique requirements for cryosurgery optimization, represents the core contribution of the current study.

  5. Dislocation Emission at the Silicon/Silicon Nitride Interface: A Million Atom Molecular Dynamics Simulation on Parallel Computers

    Science.gov (United States)

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

    2000-01-01

    Mechanical behavior of the Si\\(111\\)/Si3N4\\(0001\\) interface is studied using million atom molecular dynamics simulations. At a critical value of applied strain parallel to the interface, a crack forms on the silicon nitride surface and moves toward the interface. The crack does not propagate into the silicon substrate; instead, dislocations are emitted when the crack reaches the interface. The dislocation loop propagates in the \\(1¯ 1¯1\\) plane of the silicon substrate with a speed of 500 \\(+/-100\\) m/s. Time evolution of the dislocation emission and nature of defects is studied.

  6. Dislocation Emission at the Silicon/Silicon Nitride Interface: A Million Atom Molecular Dynamics Simulation on Parallel Computers

    Energy Technology Data Exchange (ETDEWEB)

    Bachlechner, Martina E.; Omeltchenko, Andrey; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjoe, Ingvar; Madhukar, Anupam

    2000-01-10

    Mechanical behavior of the Si(111)/Si{sub 3}N{sub 4} (0001) interface is studied using million atom molecular dynamics simulations. At a critical value of applied strain parallel to the interface, a crack forms on the silicon nitride surface and moves toward the interface. The crack does not propagate into the silicon substrate; instead, dislocations are emitted when the crack reaches the interface. The dislocation loop propagates in the (1 11) plane of the silicon substrate with a speed of 500 ({+-}100) m/s . Time evolution of the dislocation emission and nature of defects is studied. (c) 2000 The American Physical Society.

  7. Simulation of Evaporator for Two-phase Flow in the New Plate-fin Desalination Unit

    Directory of Open Access Journals (Sweden)

    Shu Xu

    2013-04-01

    Full Text Available In this study a new desalination unit is established. It has four cells such as cooling cell, heating cell, evaporation cell and condensation cell. Seawater is pumped into cooling cell to be preheated and then goes to evaporation cell. In the new desalination unit the evaporation and condensation cell is heated and cooled by the heating and cooling cells respectively. The heating of the evaporation cell is ensured by hot water flowing upward along heating cells. The cooling of the condensation cell is ensured by seawater in cooling cell. Fluent 6.3 is used to simulate gas-liquid two-phase flow of boiling evaporation numerically. A simulation calculation to get fluid in a new desalination unit under the influence of the flow, pressure distribution and heat transfer performance of the evaporator.

  8. Study of Simulation Method of Time Evolution of Atomic and Molecular Systems by Quantum Electrodynamics

    CERN Document Server

    Ichikawa, Kazuhide; Tachibana, Akitomo

    2014-01-01

    We discuss a method to follow step-by-step time evolution of atomic and molecular systems based on QED (Quantum Electrodynamics). Our strategy includes expanding the electron field operator by localized wavepackets to define creation and annihilation operators and following the time evolution using the equations of motion of the field operator in the Heisenberg picture. We first derive a time evolution equation for the excitation operator, the product of two creation or annihilation operators, which is necessary for constructing operators of physical quantities such as the electronic charge density operator. We then describe our approximation methods to obtain time differential equations of the electronic density matrix, which is defined as the expectation value of the excitation operator. By solving the equations numerically, we show "electron-positron oscillations", the fluctuations originated from virtual electron-positron pair creations and annihilations, appear in the charge density of a hydrogen atom an...

  9. X-ray emission simulation from hollow atoms produced by high intensity laser irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Moribayashi, Kengo; Sasaki, Akira; Zhidkov, A. [Japan Atomic Energy Research Inst., Kansai Research Establishment, Neyagawa, Osaka (Japan); Suto, Keiko [Nara Women' s Univ., Graduate School of Human Culture, Nara (Japan); Kagawa, Takashi [Nara Women' s Univ., Department of Physics, Nara (Japan)

    2001-10-01

    We theoretically study the x-ray emission from hollow atoms produced by collisions of multiply charged ions accelerated by a short pulse laser with a solid or foil. By using the multistep-capture-and-loss (MSCL) model a high conversion efficiency to x-rays in an ultrafast atomic process is obtained. It is also proposed to apply this x-ray emission process to the x-ray source. For a few keV x-rays this x-ray source has a clear advantage. The number of x-ray photons increases as the laser energy becomes larger. For a laser energy of 10 J, the number of x-ray photons of 3x10{sup 11} is estimated. (author)

  10. Quantum Simulation of the Hubbard Model Using Ultra-Cold Atoms

    Science.gov (United States)

    2008-11-01

    gas of atoms. We also report on our observation of resonances in the three-body recombination rate in this gas which indicate the formation of Efimov ...recombination can also be used to test universal predictions for the quantum three-body problem such as the Efimov effect. We have already observed...two resonant features which indicate the formation of Efimov trimer states and are currently testing predictions of Efimov ¿s theory when the scattering

  11. United States of America activities relative to the International Atomic Energy Agency (IAEA) initiative: Records management for deep geologic repositories

    Energy Technology Data Exchange (ETDEWEB)

    Warner, P.J.

    1997-03-01

    The International Atomic Energy Agency (IAEA) has conducted consultant and advisory meetings to prepare a Technical Document which is intended to provide guidance to all IAEA Member States (otherwise known as countries) that are currently planning, designing, constructing or operating a deep or near surface geological repository for the storage and protection of vitrified high-level radioactive waste, spent fuel waste and TRU-waste (transuranic). Eleven countries of the international community are presently in various stages of siting, designing, or constructing deep geologic repositories. Member States of the IAEA have determined that the principle safety of such completed and operation sites must not rely solely on long term institutional arrangements for the retention of information. It is believed that repository siting, design, operation and postoperation information should be gathered, managed and retained in a manner that will provide information to future societies over a very long period of time. The radionuclide life is 10,000 years thus the retention of information must outlive current societies, languages, and be continually migrated to new technology to assure retrieval. This presentation will provide an overview of the status of consideration and implementation of these issues within the United States efforts relative to deep geologic repository projects.

  12. All-atom simulation study of protein PTH(1-34) by using the Wang-Landau sampling method

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seung-Yeon [Korea National University of Transportation, Chungju (Korea, Republic of); Kwak, Woo-Seop [Chosun University, Gwangju (Korea, Republic of)

    2014-12-15

    We perform simulations of the N-terminal 34-residue protein fragment PTH(1-34), consisting of 581 atoms, of the 84-residue human parathyroid hormone by using the all-atom ECEPP/3 force field and the Wang-Landau sampling method. Through a massive high-performance computation, the density of states and the partition function Z(T), as a continuous function of T, are obtained for PTH(1-34). From the continuous partition function Z(T), the partition function zeros of PTH(1-34) are evaluated for the first time. From both the specific heat and the partition function zeros, two characteristic transition temperatures are obtained for the all-atom protein PTH(1-34). The higher transition temperature T{sub 1} and the lower transition temperature T{sub 2} of PTH(1-34) can be interpreted as the collapse temperature T{sub θ} and the folding temperature T{sub f} , respectively.

  13. Simulation of the Ising model, memory for Bell states and generation of four-atom entangled states in cavity QED

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    A scheme is proposed to simulate the Ising model and preserve the maximum entangled states (Bell states) in cavity quantum electrodynamics (QED) driven by a classical field with large detuning. In the strong driving and large-detuning regime, the effective Hamiltonian of the system is the same as the standard Ising model, and the scheme can also make the initial four Bell states of two atoms at the maximum entanglement all the time. So it is a simple memory for the maximal entangled states. The system is insensitive to the cavity decay and the thermal field and more immune to decoherence. These advantages can warrant the experimental feasibility of the current scheme. Furthermore, the genuine four-atom entanglement may be acquired via two Bell states through one-step implementation on four two-level atoms in the strong-driven model, and when two Greenberger-Horne-Zeilinger (GHZ) states are prepared in our scheme, the entangled cluster state may be acquired easily. The success probability for the scheme is 1.

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

    Science.gov (United States)

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

    2000-02-01

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

  15. Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations.

    Science.gov (United States)

    Roberts, Christopher C; Chang, Chia-En A

    2016-08-25

    We present the second-generation GeomBD Brownian dynamics software for determining interenzyme intermediate transfer rates and substrate association rates in biomolecular complexes. Substrate and intermediate association rates for a series of enzymes or biomolecules can be compared between the freely diffusing disorganized configuration and various colocalized or complexed arrangements for kinetic investigation of enhanced intermediate transfer. In addition, enzyme engineering techniques, such as synthetic protein conjugation, can be computationally modeled and analyzed to better understand changes in substrate association relative to native enzymes. Tools are provided to determine nonspecific ligand-receptor association residence times, and to visualize common sites of nonspecific association of substrates on receptor surfaces. To demonstrate features of the software, interenzyme intermediate substrate transfer rate constants are calculated and compared for all-atom models of DNA origami scaffold-bound bienzyme systems of glucose oxidase and horseradish peroxidase. Also, a DNA conjugated horseradish peroxidase enzyme was analyzed for its propensity to increase substrate association rates and substrate local residence times relative to the unmodified enzyme. We also demonstrate the rapid determination and visualization of common sites of nonspecific ligand-receptor association by using HIV-1 protease and an inhibitor, XK263. GeomBD2 accelerates simulations by precomputing van der Waals potential energy grids and electrostatic potential grid maps, and has a flexible and extensible support for all-atom and coarse-grained force fields. Simulation software is written in C++ and utilizes modern parallelization techniques for potential grid preparation and Brownian dynamics simulation processes. Analysis scripts, written in the Python scripting language, are provided for quantitative simulation analysis. GeomBD2 is applicable to the fields of biophysics, bioengineering

  16. Wide-range length metrology by dual-imaging-unit atomic force microscope based on porous alumina.

    Science.gov (United States)

    Zhang, Dongxian; Zhang, Haijun; Lin, Xiaofeng

    2004-06-15

    A new dual-imaging-unit atomic force microscope (DIU-AFM) was developed for wide-range length metrology. In the DIU-AFM, two AFM units were combined, one as a reference unit, and the other a test one. Their probes with Z piezo elements and tips were horizontally set in parallel at the same height to reduce errors due to geometric asymmetry. An XY scanner was attached to an XY block that was able to move in the X direction with a step of about 500 nm. A standard porous alumina film was employed as the reference sample. Both reference sample and test sample were installed at the center of the XY scanner on the same surface and were simultaneously imaged. The two images had the same lateral size, and thus the length of the test sample image could be accurately measured by counting the number of periodic features of the reference one. The XY block together with the XY scanner were next moved in the X direction for about 1.5 microm and a second pair of reference and test images were obtained by activating the scanner. In this way, a series of pairs of images were acquired and could be spliced into two wide-range reference and test images, respectively. Again, the two spliced images were of the same size and the length of test image was measured based on the reference one. This article presents a discussion about the structure and control of the DIU-AFM system. Some experiments were carried out on the system to demonstrate the method of length calculation and measurement. Experiments show a satisfactory result of wide-range length metrology based on the hexagonal features of the porous alumina with a periodic length of several tens of nanometers. Using this method the DIU-AFM is capable of realizing nanometer-order accuracy length metrology when covering a wide range from micron to several hundreds of microns, or even up to millimeter order.

  17. Orbital origin of the electrical conduction in ferromagnetic atomic-size contacts: Insights from shot noise measurements and theoretical simulations

    Science.gov (United States)

    Vardimon, R.; Matt, M.; Nielaba, P.; Cuevas, J. C.; Tal, O.

    2016-02-01

    With the goal of elucidating the nature of spin-dependent electronic transport in ferromagnetic atomic contacts, we present here a combined experimental and theoretical study of the conductance and shot noise of metallic atomic contacts made of the 3 d ferromagnetic materials Fe, Co, and Ni. For comparison, we also present the corresponding results for the noble metal Cu. Conductance and shot noise measurements, performed using a low-temperature break-junction setup, show that in these ferromagnetic nanowires, (i) there is no conductance quantization of any kind, (ii) transport is dominated by several partially open conduction channels, even in the case of single-atom contacts, and (iii) the Fano factor of large contacts saturates to values that clearly differ from those of monovalent (nonmagnetic) metals. We rationalize these observations with the help of a theoretical approach that combines molecular dynamics simulations to describe the junction formation with nonequilibrium Green's function techniques to compute the transport properties within the Landauer-Büttiker framework. Our theoretical approach successfully reproduces all the basic experimental results and it shows that all the observations can be traced back to the fact that the d bands of the minority-spin electrons play a fundamental role in the transport through ferromagnetic atomic-size contacts. These d bands give rise to partially open conduction channels for any contact size, which in turn lead naturally to the different observations described above. Thus, the transport picture for these nanoscale ferromagnetic wires that emerges from the ensemble of our results is clearly at variance with the well established conduction mechanism that governs the transport in macroscopic ferromagnetic wires, where the d bands are responsible for the magnetism but do not take part in the charge flow. These insights provide a fundamental framework for ferromagnetic-based spintronics at the nanoscale.

  18. Molecular Dynamics Simulation of Atomic Force Microscopy at the Water-Muscovite Interface: Hydration Layer Structure and Force Analysis.

    Science.gov (United States)

    Kobayashi, Kazuya; Liang, Yunfeng; Amano, Ken-ichi; Murata, Sumihiko; Matsuoka, Toshifumi; Takahashi, Satoru; Nishi, Naoya; Sakka, Tetsuo

    2016-04-19

    With the development of atomic force microscopy (AFM), it is now possible to detect the buried liquid-solid interfacial structure in three dimensions at the atomic scale. One of the model surfaces used for AFM is the muscovite surface because it is atomically flat after cleavage along the basal plane. Although it is considered that force profiles obtained by AFM reflect the interfacial structures (e.g., muscovite surface and water structure), the force profiles are not straightforward because of the lack of a quantitative relationship between the force and the interfacial structure. In the present study, molecular dynamics simulations were performed to investigate the relationship between the muscovite-water interfacial structure and the measured AFM force using a capped carbon nanotube (CNT) AFM tip. We provide divided force profiles, where the force contributions from each water layer at the interface are shown. They reveal that the first hydration layer is dominant in the total force from water even after destruction of the layer. Moreover, the lateral structure of the first hydration layer transcribes the muscovite surface structure. It resembles the experimentally resolved surface structure of muscovite in previous AFM studies. The local density profile of water between the tip and the surface provides further insight into the relationship between the water structure and the detected force structure. The detected force structure reflects the basic features of the atomic structure for the local hydration layers. However, details including the peak-peak distance in the force profile (force-distance curve) differ from those in the density profile (density-distance curve) because of disturbance by the tip.

  19. Dynamic performance of duolayers at the air/water interface. 2. Mechanistic insights from all-atom simulations.

    Science.gov (United States)

    Christofferson, Andrew J; Yiapanis, George; Leung, Andy H M; Prime, Emma L; Tran, Diana N H; Qiao, Greg G; Solomon, David H; Yarovsky, Irene

    2014-09-18

    The novel duolayer system, comprising a monolayer of ethylene glycol monooctadecyl ether (C18E1) and the water-soluble polymer poly(vinylpyrrolidone) (PVP), has been shown to resist forces such as wind stress to a greater degree than the C18E1 monolayer alone. This paper reports all-atom molecular dynamics simulations comparing the monolayer (C18E1 alone) and duolayer systems under an applied force parallel to the air/water interface. The simulations show that, due to the presence of PVP at the interface, the duolayer film exhibits an increase in chain tilt, ordering, and density, as well as a lower lateral velocity compared to the monolayer. These results provide a molecular rationale for the improved performance of the duolayer system under wind conditions, as well as an atomic-level explanation for the observed efficacy of the duolayer system as an evaporation suppressant, which may serve as a useful guide for future development for thin films where resistance to external perturbation is desirable.

  20. A software architecture for multi-cellular system simulations on graphics processing units.

    Science.gov (United States)

    Jeannin-Girardon, Anne; Ballet, Pascal; Rodin, Vincent

    2013-09-01

    The first aim of simulation in virtual environment is to help biologists to have a better understanding of the simulated system. The cost of such simulation is significantly reduced compared to that of in vivo simulation. However, the inherent complexity of biological system makes it hard to simulate these systems on non-parallel architectures: models might be made of sub-models and take several scales into account; the number of simulated entities may be quite large. Today, graphics cards are used for general purpose computing which has been made easier thanks to frameworks like CUDA or OpenCL. Parallelization of models may however not be easy: parallel computer programing skills are often required; several hardware architectures may be used to execute models. In this paper, we present the software architecture we built in order to implement various models able to simulate multi-cellular system. This architecture is modular and it implements data structures adapted for graphics processing units architectures. It allows efficient simulation of biological mechanisms.

  1. Development of the NSSS thermal-hydraulic program for YGN unit 1 simulator

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kyung Doo; Jeong, Jae Jun; Lee, Won Jae; Chung, Bub Dong; Ha, Kwi Seok; Kang, Kyung Ho

    2000-09-01

    The NSSS thermal-hydraulic programs installed in the domestic full-scope power plant simulators were provided in early 1980s by foreign vendors. Because of limited computational capability at that time, they usually adopt very simplified physical models for a real-time simulation of NSSS thermal-hydraulic phenomena, which entails inaccurate results and the possibility of so-called 'negative training', especially for complicated two-phase flows in the reactor coolant system. To resolve the problem, we developed a realistic NSSS T/H program (named 'ARTS' code) for use in YongGwang Nuclear Unit 1 full-scope simulator. The best-estimate code RETRAN03, developed by EPRI and approved by USNRC, was selected as a reference code of ARTS. For the development of ARTS, the followings have been performed: -Improvement of the robustness of RETRAN - Improvement of the real-time simulation capability of RETRAN - Optimum input data generation for the NSSS simulation - New model development that cannot be efficiently modeled by RETRAN - Assessment of the ARTS code. The systematic assessment of ARTS has been conducted in both personal computers (Windows 98, Visual fortran) and the simulator development environment (Windows NT, GSE simulator development tool). The results were resonable in terms of accuracy, real-time simulation and robustness.

  2. Influence of atomic kinetics in the simulation of plasma microscopic properties and thermal instabilities for radiative bow shock experiments

    Science.gov (United States)

    Espinosa, G.; Rodríguez, R.; Gil, J. M.; Suzuki-Vidal, F.; Lebedev, S. V.; Ciardi, A.; Rubiano, J. G.; Martel, P.

    2017-03-01

    Numerical simulations of laboratory astrophysics experiments on plasma flows require plasma microscopic properties that are obtained by means of an atomic kinetic model. This fact implies a careful choice of the most suitable model for the experiment under analysis. Otherwise, the calculations could lead to inaccurate results and inappropriate conclusions. First, a study of the validity of the local thermodynamic equilibrium in the calculation of the average ionization, mean radiative properties, and cooling times of argon plasmas in a range of plasma conditions of interest in laboratory astrophysics experiments on radiative shocks is performed in this work. In the second part, we have made an analysis of the influence of the atomic kinetic model used to calculate plasma microscopic properties of experiments carried out on magpie on radiative bow shocks propagating in argon. The models considered were developed assuming both local and nonlocal thermodynamic equilibrium and, for the latter situation, we have considered in the kinetic model different effects such as external radiation field and plasma mixture. The microscopic properties studied were the average ionization, the charge state distributions, the monochromatic opacities and emissivities, the Planck mean opacity, and the radiative power loss. The microscopic study was made as a postprocess of a radiative-hydrodynamic simulation of the experiment. We have also performed a theoretical analysis of the influence of these atomic kinetic models in the criteria for the onset possibility of thermal instabilities due to radiative cooling in those experiments in which small structures were experimentally observed in the bow shock that could be due to this kind of instability.

  3. Point defects and irradiation in oxides: simulations at the atomic scale; Defauts ponctuels et irradiation dans les oxydes: simulation a l'echelle atomique

    Energy Technology Data Exchange (ETDEWEB)

    Crocombette, J.P

    2005-12-15

    The studies done by Jean-Paul Crocombette between 1996 and 2005 in the Service de Recherches de Metallurgie Physique of the Direction de l'Energie Nucleaire in Saclay are presented in this Habilitation thesis. These works were part of the material science researches on the ageing, especially under irradiation, of oxides of interest for the nuclear industry. In this context simulation studies at the atomic scale were performed on two elementary components of ageing under irradiation : point defects and displacement cascades ; using two complementary simulation techniques : ab initio electronic structure calculations and empirical potential molecular dynamics. The first part deals with point defects : self defects (vacancies or interstitials) or hetero-atomic dopants. One first recalls the energetics of such defects in oxides, the specific features of defects calculations and the expected accuracy of these calculations. Then one presents the results obtained on uranium dioxide, oxygen in silver and amorphous silica. The second part tackles the modelling of disintegration recoil nuclei in various?displacement cascades created by crystalline matrices for actinide waste disposal. Cascade calculations give access to the amorphization mechanisms under irradiation of these materials. One thus predicts that the amorphization in zircon takes place directly in the tracks whereas in lanthanum zirconate, the amorphization proceeds through the accumulation of point defects. Finally the prospects of these studies are discussed. (author)

  4. Computing 1-D atomic densities in macromolecular simulations: the Density Profile Tool for VMD

    OpenAIRE

    Giorgino, Toni

    2013-01-01

    Molecular dynamics simulations have a prominent role in biophysics and drug discovery due to the atomistic information they provide on the structure, energetics and dynamics of biomolecules. Specialized software packages are required to analyze simulated trajectories, either interactively or via scripts, to derive quantities of interest and provide insight for further experiments. This paper presents the Density Profile Tool, a package that enhances the Visual Molecular Dynamics environment w...

  5. Loss tangent imaging: Theory and simulations of repulsive-mode tapping atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Proksch, Roger [Asylum Research, Santa Barbara, California 93117 (United States); Yablon, Dalia G. [ExxonMobil Research and Engineering, Annandale, New Jersey (United States)

    2012-02-13

    An expression for loss tangent measurement of a surface in amplitude modulation atomic force microscopy is derived using only the cantilever phase and the normalized cantilever amplitude. This provides a direct measurement of substrate compositional information that only requires tuning of the cantilever resonance to provide quantitative information. Furthermore, the loss tangent expression incorporates both the lost and stored energy into one term that represents a fundamental interpretation of the phase signal in amplitude modulation imaging. Numerical solutions of a cantilever tip interacting with a simple Voigt modeled surface agree with the derived loss tangent to within a few percent.

  6. SciDAC - Center for Simulation of Wave Interactions with MHD -- General Atomics Support of ORNL Collaboration

    Energy Technology Data Exchange (ETDEWEB)

    Abla, G

    2012-11-09

    The Center for Simulation of Wave Interactions with Magnetohydrodynamics (SWIM) project is dedicated to conduct research on integrated multi-physics simulations. The Integrated Plasma Simulator (IPS) is a framework that was created by the SWIM team. It provides an integration infrastructure for loosely coupled component-based simulations by facilitating services for code execution coordination, computational resource management, data management, and inter-component communication. The IPS framework features improving resource utilization, implementing application-level fault tolerance, and support of the concurrent multi-tasking execution model. The General Atomics (GA) team worked closely with other team members on this contract, and conducted research in the areas of computational code monitoring, meta-data management, interactive visualization, and user interfaces. The original website to monitor SWIM activity was developed in the beginning of the project. Due to the amended requirements, the software was redesigned and a revision of the website was deployed into production in April of 2010. Throughout the duration of this project, the SWIM Monitoring Portal (http://swim.gat.com:8080/) has been a critical production tool for supporting the project's physics goals.

  7. Embedded atom computer simulation of lattice distortion and dislocation core structure and mobility in Fe-Cr alloys

    Energy Technology Data Exchange (ETDEWEB)

    Farkas, D.; Schon, C.G.; Lima, M.S.F. de [Virginia Polytechnic Inst., Blacksburg, VA (United States). Dept. of Materials Science and Engineering; Goldenstein, H. [Escola Politecnica USP, Sao Paulo (Brazil). Dept. de Metalurgia

    1996-01-01

    The atomistic structure of dislocation cores of <111> screw dislocations in disordered Fe-Cr b.c.c. alloys was simulated using embedded atom method potentials and molecular statics computer simulation. The mixed Fe-Cr interatomic potentials used were derived by fitting to the thermodynamic data of the disordered system and the measured lattice parameter changes of Fe upon Cr additions. The potentials predict phase separation as the most stable configuration for the central region of the phase diagram. The next most stable situation is the disordered b.c.c. phase. The structure of the screw 1/2 <111> dislocation core was studied using atomistic computer simulation and an improved visualization method for the representation of the resulting structures. The structure of the dislocation core is different from that typical of 1/2 <111> dislocations in pure b.c.c. materials. The core structure in the alloy tends to lose the threefold symmetry seen in pure b.c.c. materials and the stress necessary to initiate dislocation motion increases with Cr content. The mobility of kinks in these screw dislocations was also simulated and it was found that while the critical stress for kink motion in pure Fe is extremely low, it increases significantly with the addition of Cr. The implications of these differences for mechanical behavior are discussed.

  8. Simulation of UV atomic radiation for application in exhaust plume spectrometry

    Science.gov (United States)

    Wallace, T. L.; Powers, W. T.; Cooper, A. E.

    1993-06-01

    Quantitative analysis of exhaust plume spectral data has long been a goal of developers of advanced engine health monitoring systems which incorporate optical measurements of rocket exhaust constituents. Discussed herein is the status of present efforts to model and predict atomic radiation spectra and infer free-atom densities from emission/absorption measurements as part of the Optical Plume Anomaly Detection (OPAD) program at Marshall Space Flight Center (MSFC). A brief examination of the mathematical formalism is provided in the context of predicting radiation from the Mach disk region of the SSME exhaust flow at nominal conditions during ground level testing at MSFC. Computational results are provided for Chromium and Copper at selected transitions which indicate a strong dependence upon broadening parameter values determining the absorption-emission line shape. Representative plots of recent spectral data from the Stennis Space Center (SSC) Diagnostic Test Facility (DTF) rocket engine are presented and compared to numerical results from the present self-absorbing model; a comprehensive quantitative analysis will be reported at a later date.

  9. Simulation of operational processes in hospital emergency units as lean healthcare tool

    Directory of Open Access Journals (Sweden)

    Andreia Macedo Gomes

    2017-07-01

    Full Text Available Recently, the Lean philosophy is gaining importance due to a competitive environment, which increases the need to reduce costs. Lean practices and tools have been applied to manufacturing, services, supply chain, startups and, the next frontier is healthcare. Most lean techniques can be easily adapted to health organizations. Therefore, this paper intends to summarize Lean practices and tools that are already being applied in health organizations. Among the numerous techniques and lean tools used, this research highlights the Simulation. Therefore, in order to understand the use of Simulation as a Lean Healthcare tool, this research aims to analyze, through the simulation technique, the operational dynamics of the service process of a fictitious hospital emergency unit. Initially a systematic review of the literature on the practices and tools of Lean Healthcare was carried out, in order to identify the main techniques practiced. The research highlighted Simulation as the sixth most cited tool in the literature. Subsequently, a simulation of a service model of an emergency unit was performed through the Arena software. As a main result, it can be highlighted that the attendants of the built model presented a degree of idleness, thus, they are able to atend a greater demand. As a last conclusion, it was verified that the emergency room is the process with longer service time and greater overload.

  10. Density Functional Simulation of a Breaking Nanowire

    DEFF Research Database (Denmark)

    Nakamura, A.; Brandbyge, Mads; Hansen, Lars Bruno

    1999-01-01

    We study the deformation and breaking of an atomic-sized sodium wire using density functional simulations. The wire deforms through sudden atomic rearrangements and smoother atomic displacements. The conductance of the wire exhibits plateaus at integer values in units of 2e(2)/h corresponding...

  11. Nano-scale simulative measuring model for tapping mode atomic force microscopy and analysis for measuring a nano-scale ladder-shape standard sample.

    Science.gov (United States)

    Lin, Zone-Ching; Chou, Ming-Ho

    2010-07-01

    This study proposes to construct a nano-scale simulative measuring model of Tapping Mode Atomic Force Microscopy (TM-AFM), compare with the edge effect of simulative and measurement results. It combines with the Morse potential and vibration theory to calculate the tip-sample atomic interaction force between probe and sample. Used Silicon atoms (Si) arrange the shape of the rectangular cantilever probe and the nano-scale ladder-shape standard sample atomic model. The simulative measurements are compared with the results for the simulative measurements and experimental measurement. It is found that the scan rate and the probe tip's bevel angle are the two reasons to cause the surface error and edge effect of measuring the nano-scale ladder-shape standard sample by TM-AFM. And the bevel angle is about equal to the probe tip's bevel angle from the results of simulated and experimented on the vertical section of the sample edge. To compare with the edge effect between the simulation and experimental measurement, its error is small. It could be verified that the constructed simulative measuring model for TM-AFM in this article is reasonable.

  12. Quantum simulation of exotic PT -invariant topological nodal loop bands with ultracold atoms in an optical lattice

    Science.gov (United States)

    Zhang, Dan-Wei; Zhao, Y. X.; Liu, Rui-Bin; Xue, Zheng-Yuan; Zhu, Shi-Liang; Wang, Z. D.

    2016-04-01

    Since the well-known PT symmetry has its fundamental significance and implication in physics, where PT denotes a joint operation of space inversion P and time reversal T , it is important and intriguing to explore exotic PT -invariant topological metals and to physically realize them. Here we develop a theory for a different type of topological metals that are described by a two-band model of PT -invariant topological nodal loop states in a three-dimensional Brillouin zone, with the topological stability being revealed through the PT -symmetry-protected nontrivial Z2 topological charge even in the absence of both P and T symmetries. Moreover, the gapless boundary modes are demonstrated to originate from the nontrivial topological charge of the bulk nodal loop. Based on these exact results, we propose an experimental scheme to realize and to detect tunable PT -invariant topological nodal loop states with ultracold atoms in an optical lattice, in which atoms with two hyperfine spin states are loaded in a spin-dependent three-dimensional optical lattice and two pairs of Raman lasers are used to create out-of-plane spin-flip hopping with site-dependent phase. It is shown that such a realistic cold-atom setup can yield topological nodal loop states, having a tunable band-touching ring with the twofold degeneracy in the bulk spectrum and nontrivial surface states. The nodal loop states are actually protected by the combined PT symmetry and are characterized by a Z2-type invariant (or topological charge), i.e., a quantized Berry phase. Remarkably, we demonstrate with numerical simulations that (i) the characteristic nodal ring can be detected by measuring the atomic transfer fractions in a Bloch-Zener oscillation; (ii) the topological invariant may be measured based on the time-of-flight imaging; and (iii) the surface states may be probed through Bragg spectroscopy. The present proposal for realizing topological nodal loop states in cold-atom systems may provide a unique

  13. Coordinate space translation technique for simulation of electronic process in the ion-atom collision.

    Science.gov (United States)

    Wang, Feng; Hong, Xuhai; Wang, Jian; Kim, Kwang S

    2011-04-21

    Recently we developed a theoretical model of ion-atom collisions, which was made on the basis of a time-dependent density functional theory description of the electron dynamics and a classical treatment of the heavy particle motion. Taking advantage of the real-space grid method, we introduce a "coordinate space translation" technique to allow one to focus on a certain space of interest such as the region around the projectile or the target. Benchmark calculations are given for collisions between proton and oxygen over a wide range of impact energy. To extract the probability of charge transfer, the formulation of Lüdde and Dreizler [J. Phys. B 16, 3973 (1983)] has been generalized to ensemble-averaging application in the particular case of O((3)P). Charge transfer total cross sections are calculated, showing fairly good agreements between experimental data and present theoretical results.

  14. Atomic Force Microscopy Based Nanorobotics Modelling, Simulation, Setup Building and Experiments

    CERN Document Server

    Xie, Hui; Régnier, Stéphane; Sitti, Metin

    2012-01-01

    The atomic force microscope (AFM) has been successfully used to perform nanorobotic manipulation operations on nanoscale entities such as particles, nanotubes, nanowires, nanocrystals, and DNA since 1990s. There have been many progress on modeling, imaging, teleoperated or automated control, human-machine interfacing, instrumentation, and applications of AFM based nanorobotic manipulation systems in literature. This book aims to include all of such state-of-the-art progress in an organized, structured, and detailed manner as a reference book and also potentially a textbook in nanorobotics and any other nanoscale dynamics, systems and controls related research and education. Clearly written and well-organized, this text introduces designs and prototypes of the nanorobotic systems in detail with innovative principles of three-dimensional manipulation force microscopy and parallel imaging/manipulation force microscopy.

  15. Pairing preferences of the model mono-valence mono-atomic ions investigated by molecular simulation.

    Science.gov (United States)

    Zhang, Qiang; Zhang, Ruiting; Zhao, Ying; Li, HuanHuan; Gao, Yi Qin; Zhuang, Wei

    2014-05-14

    We carried out a series of potential of mean force calculations to study the pairing preferences of a series of model mono-atomic 1:1 ions with evenly varied sizes. The probabilities of forming the contact ion pair (CIP) and the single water separate ion pair (SIP) were presented in the two-dimensional plots with respect to the ion sizes. The pairing preferences reflected in these plots largely agree with the empirical rule of matching ion sizes in the small and big size regions. In the region that the ion sizes are close to the size of the water molecule; however, a significant deviation from this conventional rule is observed. Our further analysis indicated that this deviation originates from the competition between CIP and the water bridging SIP state. The competition is mainly an enthalpy modulated phenomenon in which the existing of the water bridging plays a significant role.

  16. Numerical simulation of flow in Hartmann resonance tube and flow in ultrasonic gas atomizer

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The gas flow in the Hartmann resonance tube is numerically investigated by the finite volume method based on the Roe solver. The oscillation of the flow is studied with the presence of a needle actuator set along the nozzle axis. Numerical results agree well with the theoretical and experimental results available. Numerical results indicate that the resonance mode of the resonance tube will switch by means of removing or adding the actuator. The gas flow in the ultrasonic gas atomization (USGA) nozzle is also studied by the same numerical methods. Oscillation caused by the Hartmann resonance tube structure, coupled with a secondary resonator, in the USGA nozzle isinvestigated. Effects of the variation of parameters on the iscillation are studied. The mechanism of the transition of subsonic flow to supersonic flow in the USGA nozzle is also discussed based on numerical results.

  17. High fidelity simulation and analysis of liquid jet atomization in a gaseous crossflow at intermediate Weber numbers

    Science.gov (United States)

    Li, Xiaoyi; Soteriou, Marios C.

    2016-08-01

    Recent advances in numerical methods coupled with the substantial enhancements in computing power and the advent of high performance computing have presented first principle, high fidelity simulation as a viable tool in the prediction and analysis of spray atomization processes. The credibility and potential impact of such simulations, however, has been hampered by the relative absence of detailed validation against experimental evidence. The numerical stability and accuracy challenges arising from the need to simulate the high liquid-gas density ratio across the sharp interfaces encountered in these flows are key reasons for this. In this work we challenge this status quo by presenting a numerical model able to deal with these challenges, employing it in simulations of liquid jet in crossflow atomization and performing extensive validation of its results against a carefully executed experiment with detailed measurements in the atomization region. We then proceed to the detailed analysis of the flow physics. The computational model employs the coupled level set and volume of fluid approach to directly capture the spatiotemporal evolution of the liquid-gas interface and the sharp-interface ghost fluid method to stably handle high liquid-air density ratio. Adaptive mesh refinement and Lagrangian droplet models are shown to be viable options for computational cost reduction. Moreover, high performance computing is leveraged to manage the computational cost. The experiment selected for validation eliminates the impact of inlet liquid and gas turbulence and focuses on the impact of the crossflow aerodynamic forces on the atomization physics. Validation is demonstrated by comparing column surface wavelengths, deformation, breakup locations, column trajectories and droplet sizes, velocities, and mass rates for a range of intermediate Weber numbers. Analysis of the physics is performed in terms of the instability and breakup characteristics and the features of downstream

  18. The Development of Models to Optimize Selection of Nuclear Fuels through Atomic-Level Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Prof. Simon Phillpot; Prof. Susan B. Sinnott; Prof. Hans Seifert; Prog. James Tulenko

    2009-01-26

    Demonstrated that FRAPCON can be modified to accept data generated from first principles studies, and that the result obtained from the modified FRAPCON make sense in terms of the inputs. Determined the temperature dependence of the thermal conductivity of single crystal UO2 from atomistic simulation.

  19. Simulations of the atomic structure, energetics, and cross slip of screw dislocations in copper

    DEFF Research Database (Denmark)

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

    1997-01-01

    Using nanoscale atomistic simulations it has been possible to address the problem of cross slip of a dissociated screw dislocation in an fee metal (Cu) by a method not suffering from the limitations imposed by elasticity theory. The focus has been on different dislocation configurations relevant...... to monitor the annihilation process, thereby determining the detailed dislocation reactions during annihilation....

  20. Reparameterization of all-atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension

    DEFF Research Database (Denmark)

    Sonne, Jacob; Jensen, M.Ø.; Hansen, Flemming Yssing

    2007-01-01

    lipid of 60.4 ± 0.1 Å2. Compared to the 48 Å2, the new value of 60.4 Å2 is in fair agreement with the experimental value of 64 Å2. In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting...

  1. Improved simulation design factors for unconventional crude vacuum units : cracked gas make and stripping section performance

    Energy Technology Data Exchange (ETDEWEB)

    Remesat, D. [Koch-Glitsch Canada LP, Calgary, AB (Canada)

    2008-10-15

    Operating data for unconventional heavy oil vacuum crude units were reviewed in order to optimize the design of vacuum columns. Operational data from heavy crude vacuum units operating with stripping and velocity were used to investigate the application of a proven vacuum distillation tower simulation topology designed for use with heavy oil and bitumen upgrader feeds. Design factors included a characterization of the crude oils or bitumens processed in the facility; the selection of thermodynamic models; and the non-equilibrium simulation topology. Amounts of generated cracked gas were calculated, and entrainment and stripping section performance was evaluated. Heater designs for ensuring the even distribution of heat flux were discussed. Data sets from vacuum units processing crude oils demonstrated that the amount of offgas flow increased as the transfer line temperature increased. The resulting instability caused increased coke generation and light hydrocarbon formation. Results also indicated that overhead vacuum ejector design and size as well as heat transfer capabilities of quench and pumparound zones must be considered when designing vacuum column units. Steam stripping lowered hydrocarbon partial pressure to allow materials to boil at lower temperatures. It was concluded that setting appropriate entrainment values will ensure the accuracy of sensitivity analyses for transfer line designs, inlet feed devices, and wash bed configurations. 9 refs., figs.

  2. Nonequilibrium all-atom molecular dynamics simulation of the bubble cavitation and application to dissociate amyloid fibrils.

    Science.gov (United States)

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

    2016-11-07

    The cavitation of gas bubbles in liquids has been applied to different disciplines in life and natural sciences, and in technologies. To obtain an appropriate theoretical description of effects induced by the bubble cavitation, we develop an all-atom nonequilibrium molecular-dynamics simulation method to simulate bubbles undergoing harmonic oscillation in size. This allows us to understand the mechanism of the bubble cavitation-induced liquid shear stress on surrounding objects. The method is then employed to simulate an Aβ fibril model in the presence of bubbles, and the results show that the bubble expansion and contraction exert water pressure on the fibril. This yields to the deceleration and acceleration of the fibril kinetic energy, facilitating the conformational transition between local free energy minima, and leading to the dissociation of the fibril. Our work, which is a proof-of-concept, may open a new, efficient way to dissociate amyloid fibrils using the bubble cavitation technique, and new venues to investigate the complex phenomena associated with amyloidogenesis.

  3. Calibration of quartz tuning fork spring constants for non-contact atomic force microscopy: direct mechanical measurements and simulations

    Directory of Open Access Journals (Sweden)

    Jens Falter

    2014-04-01

    Full Text Available Quartz tuning forks are being increasingly employed as sensors in non-contact atomic force microscopy especially in the “qPlus” design. In this study a new and easily applicable setup has been used to determine the static spring constant at several positions along the prong of the tuning fork. The results show a significant deviation from values calculated with the beam formula. In order to understand this discrepancy the complete sensor set-up has been digitally rebuilt and analyzed by using finite element method simulations. These simulations provide a detailed view of the strain/stress distribution inside the tuning fork. The simulations show quantitative agreement with the beam formula if the beam origin is shifted to the position of zero stress onset inside the tuning fork base and torsional effects are also included. We further found significant discrepancies between experimental calibration values and predictions from the shifted beam formula, which are related to a large variance in tip misalignment during the tuning fork assembling process.

  4. A simple and efficient quasi 3-dimensional viscoelastic model and software for simulation of tapping-mode atomic force microscopy.

    Science.gov (United States)

    Solares, Santiago D

    2015-01-01

    This paper introduces a quasi-3-dimensional (Q3D) viscoelastic model and software tool for use in atomic force microscopy (AFM) simulations. The model is based on a 2-dimensional array of standard linear solid (SLS) model elements. The well-known 1-dimensional SLS model is a textbook example in viscoelastic theory but is relatively new in AFM simulation. It is the simplest model that offers a qualitatively correct description of the most fundamental viscoelastic behaviors, namely stress relaxation and creep. However, this simple model does not reflect the correct curvature in the repulsive portion of the force curve, so its application in the quantitative interpretation of AFM experiments is relatively limited. In the proposed Q3D model the use of an array of SLS elements leads to force curves that have the typical upward curvature in the repulsive region, while still offering a very low computational cost. Furthermore, the use of a multidimensional model allows for the study of AFM tips having non-ideal geometries, which can be extremely useful in practice. Examples of typical force curves are provided for single- and multifrequency tapping-mode imaging, for both of which the force curves exhibit the expected features. Finally, a software tool to simulate amplitude and phase spectroscopy curves is provided, which can be easily modified to implement other controls schemes in order to aid in the interpretation of AFM experiments.

  5. Adsorption, X-ray Diffraction, Photoelectron, and Atomic Emission Spectroscopy Benchmark Studies for the Eighth Industrial Fluid Properties Simulation Challenge*+

    Science.gov (United States)

    Ross, Richard B.; Aeschliman, David B.; Ahmad, Riaz; Brennan, John K.; Brostrom, Myles L.; Frankel, Kevin A.; Moore, Jonathan D.; Moore, Joshua D.; Mountain, Raymond D.; Poirier, Derrick M.; Thommes, Matthias; Shen, Vincent K.; Schultz, Nathan E.; Siderius, Daniel W.; Smith, Kenneth D.

    2016-01-01

    The primary goal of the eighth industrial fluid properties simulation challenge was to test the ability of molecular simulation methods to predict the adsorption of organic adsorbates in activated carbon materials. The challenge focused on the adsorption of perfluorohexane in the activated carbon standard BAM-P109 (Panne and Thünemann 2010). Entrants were challenged to predict the adsorption of perfluorohexane in the activated carbon at a temperature of 273 K and at relative pressures of 0.1, 0.3, and 0.6. The relative pressure (P/Po) is defined as that relative to the bulk saturation pressure predicted by the fluid model at a given temperature (273 K in this case). The predictions were judged by comparison to a set of experimentally determined values, which are published here for the first time and were not disclosed to the entrants prior to the challenge. Benchmark experimental studies, described herein, were also carried out and provided to entrants in order to aid in the development of new force fields and simulation methods to be employed in the challenge. These studies included argon, carbon dioxide, and water adsorption in the BAM-P109 activated carbon as well as X-ray diffraction, X-ray microtomography, photoelectron spectroscopy, and atomic emission spectroscopy studies of BAM-P109. Several concurrent studies were carried out for the BAM-P108 activated carbon (Panne and Thünemann 2010). These are included in the current manuscript for comparison. PMID:27840543

  6. Investigation into nanoscratching mechanical response of AlCrCuFeNi high-entropy alloys using atomic simulations

    Science.gov (United States)

    Wang, Zining; Li, Jia; Fang, QiHong; Liu, Bin; Zhang, Liangchi

    2017-09-01

    The mechanical behaviors and deformation mechanisms of scratched AlCrCuFeNi high entropy alloys (HEAs) have been studied by molecular dynamics (MD) simulations, in terms of the scratching forces, atomic strain, atomic displacement, microstructural evolution and dislocation density. The results show that the larger tangential and normal forces and higher friction coefficient take place in AlCrCuFeNi HEA due to its outstanding strength and hardness, and high adhesion and fracture toughness over the pure metal materials. Moreover, the stacking fault energy (SFE) in HEA increases the probability to initiate dislocation and twinning, which is conducive to the formation of complex deformation modes. Compared to the single element metal workpieces, the segregation potency of solutes into twinning boundary (TB) is raised due to the decreasing segregation energy of TB, resulting in the stronger solute effects on improving twinning properties for HEA workpiece. The higher dislocation density and the more activated slipping planes lead to the outstanding plasticity of AlCrCuFeNi HEA. The solute atoms as barriers to hinder the motion of dislocation and the severe lattice distortion to suppress the free slipping of dislocation are significantly stronger obstacles to strengthen HEA. The excellent comprehensive scratching properties of the bulk AlCrCuFeNi HEAs are associated with the combined effects of multiple strengthening mechanisms, such as dislocation strengthening, deformation twinning strengthening as well as solute strengthening. This work provides a basis for further understanding and tailoring SFE in mechanical properties and deformation mechanism of HEAs, which maybe facilitate the design and preparation of new HEAs with high performance.

  7. Optimal Lead-lag Controller for Distributed Generation Unit in Island Mode Using Simulated Annealing

    Directory of Open Access Journals (Sweden)

    A. Akbarimajd

    2014-07-01

    Full Text Available Active and reactive power components of a Distributed Generation (DG is normally controlled by a conventional dq-current control strategy however, after islanding the dq-current which is not able to successfully complete the control task is disabled and a lead-lag control strategy based optimized by simulated annealing is proposed for control of DG unit in islanding mode. Integral of Time multiply by Absolute Error (ITEA criterion is used as cost function of simulated annealing in order to achieve smooth response and robust behavior. The proposed controller improved robust stability margins of the system. Simulations with different load and input operating conditions verify advantages of the proposed controller in comparison with a previously developed classic controller in terms of robustness and response time.

  8. Integrating the Electronic Health Record into high-fidelity interprofessional intensive care unit simulations.

    Science.gov (United States)

    Gold, Jeffrey A; Tutsch, Alycia S R; Gorsuch, Adriel; Mohan, Vishnu

    2015-01-01

    With the rapid adoption of electronic health records (EHR), there is a growing appreciation for the central role they play in clinical decision making and team communication, with many studies documenting new safety issues with integration of the EHR into the clinical enterprise. To study these issues, we created a high-fidelity simulation instance of our clinical EHR. In this paper, we describe the impact of integrating the EHR into high-fidelity, interprofessional intensive care unit (ICU) simulations, and the errors induced. We found a number of safety issues directly related to the EHR including alert fatigue, negative impacts on interprofessional communication, and problems with selective data gathering, and these issues were present for all members of the interprofessional team. Through successful integration of the EHR into high-fidelity team-based simulations, we now have an infrastructure to focus educational initiative and deploy informatics solutions to mitigate these safety issues.

  9. Atomic structure and thermal stability of interfaces between metallic glass and embedding nano-crystallites revealed by molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Gao, X.Z.; Yang, G.Q.; Xu, B.; Qi, C.; Kong, L.T., E-mail: konglt@sjtu.edu.cn; Li, J.F.

    2015-10-25

    Molecular dynamics simulations were performed to investigate the atomic structure and thermal stability of interfaces formed between amorphous Cu{sub 50}Zr{sub 50} matrix and embedding B2 CuZr nano-crystallites. The interfaces are found to be rather abrupt, and their widths show negligible dependence on the nano-crystallite size. Local atomic configuration in the interfacial region is dominated by geometry characterized by Voronoi polyhedra <0,5,2,6> and <0,4,4,6>, and the contents of these polyhedra also exhibit apparent size dependence, which in turn results in an increasing trend in the interfacial energy against the nano-crystallite size. Annealing of the interface models at elevated temperatures will also enrich these characterizing polyhedra. While when the temperature is as high as the glass transition temperature of the matrix, growth of the nano-crystallites will be appreciable. The growth activation energy also shows size dependence, which is lower for larger nano-crystallites, suggesting that large nano-crystallites are prone to grow upon thermal disturbance. - Highlights: • Special clusters characterizing the local geometry are abundant in the interfaces. • Their content varies with the size of the embedding nano-crystallite. • In turn, size dependences in interfacial thermodynamics and kinetics are observed.

  10. A New Determination of the Binding Energy of Atomic Oxygen on Dust Grain Surfaces: Experimental Results and Simulations

    CERN Document Server

    He, Jiao; Hopkins, Tyler; Vidali, Gianfranco; Kaufman, Michael J

    2015-01-01

    The energy to desorb atomic oxygen from an interstellar dust grain surface, $E_{\\rm des}$, is an important controlling parameter in gas-grain models; its value impacts the temperature range over which oxygen resides on a dust grain. However, no prior measurement has been done of the desorption energy. We report the first direct measurement of $E_{\\rm des}$ for atomic oxygen from dust grain analogs. The values of $E_{\\rm des}$ are $1660\\pm 60$~K and $1850\\pm 90$~K for porous amorphous water ice and for a bare amorphous silicate film, respectively, or about twice the value previously adopted in simulations of the chemical evolution of a cloud. We use the new values to study oxygen chemistry as a function of depth in a molecular cloud. For $n=10^4$ cm$^{-3}$ and $G_0$=10$^2$ ($G_0$=1 is the average local interstellar radiation field), the main result of the adoption of the higher oxygen binding energy is that H$_2$O can form on grains at lower visual extinction $A_{\\rm V}$, closer to the cloud surface. A higher ...

  11. A solar furnace coupled to a microwave induced plasma for the simulation of the space vehicles entry (atomic recombination)

    Energy Technology Data Exchange (ETDEWEB)

    Balat, M.; Badie, J.M.; Duqueroie, F.; Sauvage, S. [Institut de Science et de Genie des Materiaux et Procedes, IMP CNRS, UPR8521, 66 - Font Romeu (France)

    1999-03-01

    During the atmospheric entry phase, the surface temperature of the protective heat shield of hypersonic vehicles increases with the atom recombination from the dissociated gas plasma. The excess of heating coming from the oxygen and/or nitrogen recombinations (Earth entry) or carbon monoxide and/or oxygen (Mars entry) on the surface of the material depends on the entry environment (pressure, temperature, gas flow velocity) and on the protective coating material catalycity. A ground simulation has been realized to evaluate the catalycity of such materials using direct atom loss (chemical approach) and heat transfer (thermal approach) measurements. The set-up associates a solar radiation concentrator (for high temperature) and a microwave generator (for gas dissociation) to partially reproduce the atmospheric entry conditions. The catalytic activity of several ceramic materials (carbides, nitrides, oxides) under different pressure and temperature conditions is measured, using the two previous approaches. Finally, the experimental results obtained with both the approaches lead to the determination of a catalycity scale and the evaluation of the physico-chemical behaviour of ceramics under atmospheric entry conditions. (authors)

  12. Pore-Width-Dependent Preferential Interaction of sp2 Carbon Atoms in Cyclohexene with Graphitic Slit Pores by GCMC Simulation

    Directory of Open Access Journals (Sweden)

    Natsuko Kojima

    2011-01-01

    Full Text Available The adsorption of cyclohexene with two sp2 and four sp3 carbon atoms in graphitic slit pores was studied by performing grand canonical Monte Carlo simulation. The molecular arrangement of the cyclohexene on the graphitic carbon wall depends on the pore width. The distribution peak of the sp2 carbon is closer to the pore wall than that of the sp3 carbon except for the pore width of 0.7 nm, even though the Lennard-Jones size of the sp2 carbon is larger than that of the sp3 carbon. Thus, the difference in the interactions of the sp2 and sp3 carbon atoms of cyclohexene with the carbon pore walls is clearly observed in this study. The preferential interaction of sp2 carbon gives rise to a slight tilting of the cyclohexene molecule against the graphitic wall. This is suggestive of a π-π interaction between the sp2 carbon in the cyclohexene molecule and graphitic carbon.

  13. Atomic level simulations of interaction between edge dislocations and irradiation induced ellipsoidal voids in alpha-iron

    Science.gov (United States)

    Zhu, Bida; Huang, Minsheng; Li, Zhenhuan

    2017-04-01

    High concentrations of vacancies tend to be formed inside the metal materials under irradiation, and then accumulate and cluster together gradually to promote the formation of nanovoids. Generally, these voids act as obstacles for dislocation glide and thereby change/degrade the mechanical behavior of irradiated materials. In this work, the interaction between ellipsoidal nanovoids with edge dislocations in alpha-iron has been studied by atomic simulations. The results illuminate that the ellipsoidal void's semi-major axis on the slip plane and parallel to the dislocation line is the dominant factor controlling the obstacle strength of ellipsoidal nanovoids. Two other semi-major axes, which are perpendicular to the glide plane and parallel to the Burgers vector, respectively, can also influence the critical resolved shear stress (CRSS) for dislocation shearing the ellipsoidal void. The intrinsic atomic mechanisms controlling above phenomena, such as nanovoid-geometry spatial constraint and nanovoid-surface curvature on dislocation evolution, have been discussed carefully. The classical continuum model has been amended to describe the dislocation-ellipsoidal nanovoid interaction base on current results. In addition, the influence of temperature on the CRSS of ellipsoidal nanovoids has also been investigated.

  14. Extremely scalable algorithm for 10$^8$-atom quantum material simulation on the full system of the K computer

    CERN Document Server

    Hoshi, Takeo; Kumahata, Kiyoshi; Terai, Masaaki; Miyamoto, Kengo; Minami, Kazuo; Shoji, Fumiyoshi

    2016-01-01

    An extremely scalable linear-algebraic algorithm was developed for quantum material simulation (electronic state calculation) with 10$^8$ atoms or 100-nm-scale materials. The mathematical foundation is generalized shifted linear equations ((zB - A) x = b), instead of conventional generalized eigenvalue equations. The method has a highly parallelizable mathematical structure. The fundamental theory is mathematical and is applicable also to other scientific fields. The benchmark shows an extreme strong scaling and a qualified time-to-solution on the full system of the K computer. The method was demonstrated in a real material research for ultra-flexible (organic) devices, key devices of next-generation IoT products. The present paper shows that an innovative scalable algorithm for a real research can appear by the co-design among application, algorithm and architecture.

  15. Experimental and Simulation Analysis of Hot Isostatic Pressing of Gas Atomized Stainless Steel 316L Powder Compacts

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Dongguo; Park, Seong Jin [Pohang University of Science and Technology, Pohang (Korea, Republic of); Ha, Sangyul [Samsung Electro-Mechanics, Suwon (Korea, Republic of); Shin, Youngho [Doosan Heavy Industries and Construction Co., Ltd., Changwon (Korea, Republic of); Park, Dong Yong [Korea Institute of Energy Research, Daejeon (Korea, Republic of); Chung, Sung Taek [CetaTech Inc., Sacheon (Korea, Republic of); Bollina, Ravi [Bahadurpally Jeedimetla, Hyderabad (India); See, Seongkyu [POSCO, Pohang (Korea, Republic of)

    2016-10-15

    In this work, both experimental and numerical studies were conducted to investigate the densification behavior of stainless steel 316L (STS 316L) powders during hot isostatic pressing (HIP), and to characterize the mechanical properties of HIPed specimens. The HIP experiments were conducted with gas atomized STS 316L powders with spherical particle shapes under controlled pressure and temperature conditions. The mechanical properties of HIPed samples were determined based on a series of tensile tests, and the results were compared to a reference STS 316L sample prepared by the conventional process, i.e., extrusion and annealing process. Corresponding microstructures before and after tensile tests were observed using scanning electron microscopy and their relationships to the mechanical properties were addressed. Furthermore, a finite element simulation based on the power-law creep model was carried out to predict the density distribution and overall shape change of the STS316L powder compact during HIP process, which agreed well with the experimental results.

  16. Observation of electromagnetically induced transparency in six-level Rb atoms and theoretical simulation of the observed spectra

    Science.gov (United States)

    Bhattacharyya, Dipankar; Ghosh, Arindam; Bandyopadhyay, Amitava; Saha, Satyajit; De, Sankar

    2015-09-01

    We report the observation of electromagnetically induced transparency (EIT) in a six-level Λ-type system in atomic Rb vapor containing both 87Rb and 85Rb. The experimental observation includes five velocity selective optically pumped (VSOP) absorption dips for both 87Rb and 85Rb. The EIT signal appears on the background of one such VSOP absorption dips. The measured EIT linewidth ({Γ }t) shows sub-natural ({Γ }t \\lt Γ ) values for both lower and higher values of pump Rabi-frequencies. The density matrix based theoretical model for the six-level system is developed and solved numerically by taking into account the Doppler broadening. A complete analytical solution (non perturbative) for a three level Λ-type system has been obtained and compared with the experimentally observed sub-natural EIT linewidth. The simulated spectra are in good agreement with the experimental findings.

  17. A two-dimensional algebraic quantum liquid produced by an atomic simulator of the quantum Lifshitz model.

    Science.gov (United States)

    Po, Hoi Chun; Zhou, Qi

    2015-08-13

    Bosons have a natural instinct to condense at zero temperature. It is a long-standing challenge to create a high-dimensional quantum liquid that does not exhibit long-range order at the ground state, as either extreme experimental parameters or sophisticated designs of microscopic Hamiltonians are required for suppressing the condensation. Here we show that synthetic gauge fields for ultracold atoms, using either the Raman scheme or shaken lattices, provide physicists a simple and practical scheme to produce a two-dimensional algebraic quantum liquid at the ground state. This quantum liquid arises at a critical Lifshitz point, where a two-dimensional quartic dispersion emerges in the momentum space, and many fundamental properties of two-dimensional bosons are changed in its proximity. Such an ideal simulator of the quantum Lifshitz model allows experimentalists to directly visualize and explore the deconfinement transition of topological excitations, an intriguing phenomenon that is difficult to access in other systems.

  18. Accelerating Wright-Fisher Forward Simulations on the Graphics Processing Unit.

    Science.gov (United States)

    Lawrie, David S

    2017-09-07

    Forward Wright-Fisher simulations are powerful in their ability to model complex demography and selection scenarios, but suffer from slow execution on the Central Processor Unit (CPU), thus limiting their usefulness. However, the single-locus Wright-Fisher forward algorithm is exceedingly parallelizable, with many steps that are so-called "embarrassingly parallel," consisting of a vast number of individual computations that are all independent of each other and thus capable of being performed concurrently. The rise of modern Graphics Processing Units (GPUs) and programming languages designed to leverage the inherent parallel nature of these processors have allowed researchers to dramatically speed up many programs that have such high arithmetic intensity and intrinsic concurrency. The presented GPU Optimized Wright-Fisher simulation, or "GO Fish" for short, can be used to simulate arbitrary selection and demographic scenarios while running over 250-fold faster than its serial counterpart on the CPU. Even modest GPU hardware can achieve an impressive speedup of over two orders of magnitude. With simulations so accelerated, one can not only do quick parametric bootstrapping of previously estimated parameters, but also use simulated results to calculate the likelihoods and summary statistics of demographic and selection models against real polymorphism data, all without restricting the demographic and selection scenarios that can be modeled or requiring approximations to the single-locus forward algorithm for efficiency. Further, as many of the parallel programming techniques used in this simulation can be applied to other computationally intensive algorithms important in population genetics, GO Fish serves as an exciting template for future research into accelerating computation in evolution. GO Fish is part of the Parallel PopGen Package available at: http://dl42.github.io/ParallelPopGen/. Copyright © 2017 Lawrie.

  19. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    Energy Technology Data Exchange (ETDEWEB)

    Markutsya, Sergiy [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Lamm, Monica H., E-mail: mhlamm@iastate.edu [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011 (United States)

    2014-11-07

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  20. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    Science.gov (United States)

    Markutsya, Sergiy; Lamm, Monica H.

    2014-11-01

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  1. 75 FR 23563 - Delegation of Certain Functions Under Section 104(g) of the United States-India Peaceful Atomic...

    Science.gov (United States)

    2010-05-04

    ...;#0; ] Memorandum of April 27, 2010 Delegation of Certain Functions Under Section 104(g) of the United... of the United States, including section 301 of title 3, United States Code, I hereby delegate to you the functions and authority conferred upon the President by section 104(g) of the United...

  2. Simulation of one-sided heating of boiler unit membrane-type water walls

    Science.gov (United States)

    Kurepin, M. P.; Serbinovskiy, M. Yu.

    2017-03-01

    This study describes the results of simulation of the temperature field and the stress-strain state of membrane-type gastight water walls of boiler units using the finite element method. The methods of analytical and standard calculation of one-sided heating of fin-tube water walls by a radiative heat flux are analyzed. The methods and software for input data calculation in the finite-element simulation, including thermoelastic moments in welded panels that result from their one-sided heating, are proposed. The method and software modules are used for water wall simulation using ANSYS. The results of simulation of the temperature field, stress field, deformations and displacement of the membrane-type panel for the boiler furnace water wall using the finite-element method, as well as the results of calculation of the panel tube temperature, stresses and deformations using the known methods, are presented. The comparison of the known experimental results on heating and bending by given moments of membrane-type water walls and numerical simulations is performed. It is demonstrated that numerical results agree with high accuracy with the experimental data. The relative temperature difference does not exceed 1%. The relative difference of the experimental fin mutual turning angle caused by one-sided heating by radiative heat flux and the results obtained in the finite element simulation does not exceed 8.5% for nondisplaced fins and 7% for fins with displacement. The same difference for the theoretical results and the simulation using the finite-element method does not exceed 3% and 7.1%, respectively. The proposed method and software modules for simulation of the temperature field and stress-strain state of the water walls are verified and the feasibility of their application in practical design is proven.

  3. In-Situ Statistical Analysis of Autotune Simulation Data using Graphical Processing Units

    Energy Technology Data Exchange (ETDEWEB)

    Ranjan, Niloo [ORNL; Sanyal, Jibonananda [ORNL; New, Joshua Ryan [ORNL

    2013-08-01

    Developing accurate building energy simulation models to assist energy efficiency at speed and scale is one of the research goals of the Whole-Building and Community Integration group, which is a part of Building Technologies Research and Integration Center (BTRIC) at Oak Ridge National Laboratory (ORNL). The aim of the Autotune project is to speed up the automated calibration of building energy models to match measured utility or sensor data. The workflow of this project takes input parameters and runs EnergyPlus simulations on Oak Ridge Leadership Computing Facility s (OLCF) computing resources such as Titan, the world s second fastest supercomputer. Multiple simulations run in parallel on nodes having 16 processors each and a Graphics Processing Unit (GPU). Each node produces a 5.7 GB output file comprising 256 files from 64 simulations. Four types of output data covering monthly, daily, hourly, and 15-minute time steps for each annual simulation is produced. A total of 270TB+ of data has been produced. In this project, the simulation data is statistically analyzed in-situ using GPUs while annual simulations are being computed on the traditional processors. Titan, with its recent addition of 18,688 Compute Unified Device Architecture (CUDA) capable NVIDIA GPUs, has greatly extended its capability for massively parallel data processing. CUDA is used along with C/MPI to calculate statistical metrics such as sum, mean, variance, and standard deviation leveraging GPU acceleration. The workflow developed in this project produces statistical summaries of the data which reduces by multiple orders of magnitude the time and amount of data that needs to be stored. These statistical capabilities are anticipated to be useful for sensitivity analysis of EnergyPlus simulations.

  4. Inclusion of pH and potential in atomic-scale simulations of the electrochemical interface

    DEFF Research Database (Denmark)

    Björketun, Mårten; Rossmeisl, Jan; Chan, Karen

    2013-01-01

    Recent improvements in computational power and theory have allowed for density functional theory calculations on electrochemical systems. Currently, there are two main types of ab initio studies on electrochemical systems. Catalyst screening/optimization studies focus on adsorption free energies...... interest in the development of efficient electrocatalysts for alkaline environments [2]. Consideration of pH is thus a crucial challenge in ab initio simulations. Here we present a generalization of the computational hydrogen electrode to explicitly capture the respective pH and potential effects...

  5. Dislocations and elementary processes of plasticity in FCC metals: atomic scale simulations; Dislocations et processus elementaires de la plasticite dans les metaux CFC: apports des simulations a l'echelle atomique

    Energy Technology Data Exchange (ETDEWEB)

    Rodney, D

    2000-07-01

    We present atomic-scale simulations of two elementary processes of FCC crystal plasticity. The first study consists in the simulation by molecular dynamics, in a nickel crystal, of the interactions between an edge dislocation and glissile interstitial loops of the type that form under irradiation in displacement cascades. The simulations show various atomic-scale interaction processes leading to the absorption and drag of the loops by the dislocation. These reactions certainly contribute to the formation of the 'clear bands' observed in deformed irradiated materials. The simulations also allow to study quantitatively the role of the glissile loops in irradiation hardening. In particular, dislocation unpinning stresses for certain pinning mechanisms are evaluated from the simulations. The second study consists first in the generalization in three dimensions of the quasi-continuum method (QCM), a multi-scale simulation method which couples atomistic techniques and the finite element method. In the QCM, regions close to dislocation cores are simulated at the atomic-scale while the rest of the crystal is simulated with a lower resolution by means of a discretization of the displacement fields using the finite element method. The QCM is then tested on the simulation of the formation and breaking of dislocation junctions in an aluminum crystal. Comparison of the simulations with an elastic model of dislocation junctions shows that the structure and strength of the junctions are dominated by elastic line tension effects, as is assumed in classical theories. (author)

  6. Filamentous Biopolymers on Surfaces: Atomic Force Microscopy Images Compared with Brownian Dynamics Simulation of Filament Deposition

    Science.gov (United States)

    Mücke, Norbert; Klenin, Konstantin; Kirmse, Robert; Bussiek, Malte; Herrmann, Harald; Hafner, Mathias; Langowski, Jörg

    2009-01-01

    Nanomechanical properties of filamentous biopolymers, such as the persistence length, may be determined from two-dimensional images of molecules immobilized on surfaces. For a single filament in solution, two principal adsorption scenarios are possible. Both scenarios depend primarly on the interaction strength between the filament and the support: i) For interactions in the range of the thermal energy, the filament can freely equilibrate on the surface during adsorption; ii) For interactions much stronger than the thermal energy, the filament will be captured by the surface without having equilibrated. Such a ‘trapping’ mechanism leads to more condensed filament images and hence to a smaller value for the apparent persistence length. To understand the capture mechanism in more detail we have performed Brownian dynamics simulations of relatively short filaments by taking the two extreme scenarios into account. We then compared these ‘ideal’ adsorption scenarios with observed images of immobilized vimentin intermediate filaments on different surfaces. We found a good agreement between the contours of the deposited vimentin filaments on mica (‘ideal’ trapping) and on glass (‘ideal’ equilibrated) with our simulations. Based on these data, we have developed a strategy to reliably extract the persistence length of short worm-like chain fragments or network forming filaments with unknown polymer-surface interactions. PMID:19888472

  7. Filamentous biopolymers on surfaces: atomic force microscopy images compared with Brownian dynamics simulation of filament deposition.

    Directory of Open Access Journals (Sweden)

    Norbert Mücke

    Full Text Available Nanomechanical properties of filamentous biopolymers, such as the persistence length, may be determined from two-dimensional images of molecules immobilized on surfaces. For a single filament in solution, two principal adsorption scenarios are possible. Both scenarios depend primarily on the interaction strength between the filament and the support: i For interactions in the range of the thermal energy, the filament can freely equilibrate on the surface during adsorption; ii For interactions much stronger than the thermal energy, the filament will be captured by the surface without having equilibrated. Such a 'trapping' mechanism leads to more condensed filament images and hence to a smaller value for the apparent persistence length. To understand the capture mechanism in more detail we have performed Brownian dynamics simulations of relatively short filaments by taking the two extreme scenarios into account. We then compared these 'ideal' adsorption scenarios with observed images of immobilized vimentin intermediate filaments on different surfaces. We found a good agreement between the contours of the deposited vimentin filaments on mica ('ideal' trapping and on glass ('ideal' equilibrated with our simulations. Based on these data, we have developed a strategy to reliably extract the persistence length of short worm-like chain fragments or network forming filaments with unknown polymer-surface interactions.

  8. c(4 × 2) and related structural units on the SrTiO3(001) surface: scanning tunneling microscopy, density functional theory, and atomic structure.

    Science.gov (United States)

    Becerra-Toledo, A E; Marshall, M S J; Castell, M R; Marks, L D

    2012-06-07

    Density functional theory is used to simulate high-bias, constant-current scanning tunneling micrographs for direct comparison with experimental images. Coupled to previous spectroscopic data, these simulations are used to determine the atomic structure of Ti-rich nanostructures on strontium titanate (001) surfaces. These nanostructures have three consecutive TiO(x) surface layers and exploit the distinctive structural motif of the c(4 × 2) reconstruction as their main building block. A structural model of a characteristic triline defect is also proposed.

  9. CFD simulation and optimization of the capillary throttling of air-flotation unit

    Science.gov (United States)

    Bin, Huang; Yi, Jiajing; Tao, Jiayue; Lu, Rongsheng

    2016-01-01

    With respect to orifice throttling or compensating, capillary throttling has following advantages: smaller mass flow rate and stronger anti-interference ability. This paper firstly gives the required average pressure of air-film when shipping a piece of LCD glass. Then, dimensional flow model of the capillary throttling of air-flotation unit is established. Based on the model, we firstly analyze the flowing process of the lubricated air through the capillary. Secondly, the pressure distribution equation of air-film is derived from the Navier-Stokes Equation. Furthermore, the approximate functional relations between model parameters and static characteristics of the air-film, such as mass flow rate, static bearing capacity, are obtained and then influence of the former on the latter is analyzed . Finally, according to the continuity of air flow, the function relation between model parameters and pressure of core nodes in the air-film is also derived. On foundation of theoretical analysis, the impacts of each model parameter on static characteristics of the air-film flow field, are respectively simulated and analyzed by CFD software Fluent. Based on these simulations and analysis, radius and length of the capillary, density of the gas supply orifices and other model parameters are optimized. Finally, the best unit model is acquired, which greatly improves the static working performance of air-film in air-flotation unit. Research results of this paper can provide guidance and basis for the design and optimization of air-flotation transporting system.

  10. The Atmospheric piston simulator as an integral part of the calibration unit of LINC - NIRVANA

    Science.gov (United States)

    Follert, R.; Herbst, T. M.; Bizenberger, P.; DeBonis, F.

    2010-07-01

    The atmospheric piston simulator is an integral part of the calibration unit of LINC-NIRVANA, the Fizeau interferometric imager for the Large Binocular Telescope. The calibration unit will be necessary to align and set up the different opto - mechanical subsystems of the instrument. It will assist in (1) the alignment of the optics via reference fibers; (2) establishing zero optical path difference using a balanced fiber splitter; (3) flat fielding of the detectors with an integrating sphere; (4) correction of the non-common path aberrations using a fiber-based phase diversity source; and (5) calibration of the adaptive optics with a rotating reference fiber plate. Substantial testing and verification of the fringe tracker under as realistic as possible conditions in the lab is desirable, since the performance of the fringe tracker will ultimately determine the high angular resolution imaging capability of LINC-NIRVANA as a whole. We are therefore also constructing an atmospheric piston simulator working in the J and H photometric bands. As with many of the other calibration unit sub-systems, our design concept is mainly fiber based. Opto - electronic phase modulators will be used to introduce the piston sequences. The control system of the piston modulators will allow for easy implementation of different vibration power spectra. This will enable us to test and demonstrate the capabilities of the fringe tracker under realistic conditions.

  11. Enhanced teaching and student learning through a simulator-based course in chemical unit operations design

    Science.gov (United States)

    Ghasem, Nayef

    2016-07-01

    This paper illustrates a teaching technique used in computer applications in chemical engineering employed for designing various unit operation processes, where the students learn about unit operations by designing them. The aim of the course is not to teach design, but rather to teach the fundamentals and the function of unit operation processes through simulators. A case study presenting the teaching method was evaluated using student surveys and faculty assessments, which were designed to measure the quality and effectiveness of the teaching method. The results of the questionnaire conclusively demonstrate that this method is an extremely efficient way of teaching a simulator-based course. In addition to that, this teaching method can easily be generalised and used in other courses. A student's final mark is determined by a combination of in-class assessments conducted based on cooperative and peer learning, progress tests and a final exam. Results revealed that peer learning can improve the overall quality of student learning and enhance student understanding.

  12. Simulation of abrasive water jet cutting process: Part 1. Unit event approach

    Science.gov (United States)

    Lebar, Andrej; Junkar, Mihael

    2004-11-01

    Abrasive water jet (AWJ) machined surfaces exhibit the texture typical of machining with high energy density beam processing technologies. It has a superior surface quality in the upper region and rough surface in the lower zone with pronounced texture marks called striations. The nature of the mechanisms involved in the domain of AWJ machining is still not well understood but is essential for AWJ control improvement. In this paper, the development of an AWJ machining simulation is reported on. It is based on an AWJ process unit event, which in this case represents the impact of a particular abrasive grain. The geometrical characteristics of the unit event are measured on a physical model of the AWJ process. The measured dependences and the proposed model relations are then implemented in the AWJ machining process simulation. The obtained results are in good agreement in the engraving regime of AWJ machining. To expand the validity of the simulation further, a cellular automata approach is explored in the second part of the paper.

  13. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations.

    Science.gov (United States)

    Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang

    2016-07-01

    Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases.

  14. Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions.

    Energy Technology Data Exchange (ETDEWEB)

    Mereghetti, Paolo; Wade, Rebecca C.

    2012-07-26

    High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. In this paper, we describe the implementation of mean field models of translational and rotational hydrodynamic interactions into an atomically detailed many-protein brownian dynamics simulation method. Concentrated solutions (30-40% volume fraction) of myoglobin, hemoglobin A, and sickle cell hemoglobin S were simulated, and static structure factors, oligomer formation, and translational and rotational self-diffusion coefficients were computed. Good agreement of computed properties with available experimental data was obtained. The results show the importance of both solvent mediated interactions and weak protein-protein interactions for accurately describing the dynamics and the association properties of concentrated protein solutions. Specifically, they show a qualitative difference in the translational and rotational dynamics of the systems studied. Although the translational diffusion coefficient is controlled by macromolecular shape and hydrodynamic interactions, the rotational diffusion coefficient is affected by macromolecular shape, direct intermolecular interactions, and both translational and rotational hydrodynamic interactions.

  15. Atomic simulation on evolution of nano-crystallizaion in amorphous metals

    Institute of Scientific and Technical Information of China (English)

    WANG Yu; WANG Xiu-xi; WANG Hai-long

    2006-01-01

    The deformation-induced nano-crystallization behavior of amorphous pure Ni was investigated by using a molecular dynamics simulation. The microevolution mechanism of the nano-crystallization,the crystallization process in the multicomponent amorphous Ni-Pd alloys and the temperature effect on the nano-crystallization behavior in amorphous metals were studied. The results show that the small nano-crystalline grain will nucleate and grow during the compression deformation. The deformation induces the growth of the ordered clusters in the amorphous metals and the nano-crystalline grain grows under the shearing combination and shearing deposition. The nano-crystalline grain will nucleate in a lower strain under a higher temperature. The combining severe plastic deformation with thermal annealing treatments presents a new opportunity for developing bulk nano-crystalline materials with controlled microstructures.

  16. 78 FR 63506 - Exelon Generation Company, LLC; Peach Bottom Atomic Power Station, Units 2 and 3; Proposed...

    Science.gov (United States)

    2013-10-24

    .... Units 2 and 3 at PBAPS have a common once-through heat dissipation system that draws water from and..., and as a source of public water. Units 2 and 3 use six circulating water pumps (three per unit), each... canal. Three adjustable discharge gates at the end of the discharge canal control the flow to Conowingo...

  17. The effect of deposition energy of energetic atoms on the growth and structure of ultrathin amorphous carbon films studied by molecular dynamics simulations

    KAUST Repository

    Wang, N

    2014-05-16

    The growth and structure of ultrathin amorphous carbon films was investigated by molecular dynamics simulations. The second-generation reactive-empirical-bond-order potential was used to model atomic interactions. Films with different structures were simulated by varying the deposition energy of carbon atoms in the range of 1-120 eV. Intrinsic film characteristics (e.g. density and internal stress) were determined after the system reached equilibrium. Short- and intermediate-range carbon atom ordering is examined in the context of atomic hybridization and ring connectivity simulation results. It is shown that relatively high deposition energy (i.e., 80 eV) yields a multilayer film structure consisting of an intermixing layer, bulk film and surface layer, consistent with the classical subplantation model. The highest film density (3.3 g cm-3), sp3 fraction (∼43%), and intermediate-range carbon atom ordering correspond to a deposition energy of ∼80 eV, which is in good agreement with experimental findings. © 2014 IOP Publishing Ltd.

  18. Test Results From a Direct Drive Gas Reactor Simulator Coupled to a Brayton Power Conversion Unit

    Science.gov (United States)

    Hervol, David S.; Briggs, Maxwell H.; Owen, Albert K.; Bragg-Sitton, Shannon M.

    2009-01-01

    The Brayton Power Conversion Unit (BPCU) located at NASA Glenn Research Center (GRC) in Cleveland, OH is a closed cycle system incorporating a turboaltemator, recuperator, and gas cooler connected by gas ducts to an external gas heater. For this series of tests, the BPCU was modified by replacing the gas heater with the Direct Drive Gas heater or DOG. The DOG uses electric resistance heaters to simulate a fast spectrum nuclear reactor similar to those proposed for space power applications. The combined system thermal transient behavior was the focus of these tests. The BPCU was operated at various steady state points. At each point it was subjected to transient changes involving shaft rotational speed or DOG electrical input. This paper outlines the changes made to the test unit and describes the testing that took place along with the test results.

  19. Atomic level insights into realistic molecular models of dendrimer-drug complexes through MD simulations

    Science.gov (United States)

    Jain, Vaibhav; Maiti, Prabal K.; Bharatam, Prasad V.

    2016-09-01

    Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH2) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH2) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH2) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an

  20. Simplified protein models can rival all atom simulations in predicting folding pathways and structure

    Science.gov (United States)

    Adhikari, Aashish N.; Freed, Karl F.; Sosnick, Tobin R.

    2014-01-01

    We demonstrate the ability of simultaneously determining a protein’s folding pathway and structure using a properly formulated model without prior knowledge of the native structure. Our model employs a natural coordinate system for describing proteins and a search strategy inspired by the observation that real proteins fold in a sequential fashion by incrementally stabilizing native-like substructures or "foldons". Comparable folding pathways and structures are obtained for the twelve proteins recently studied using atomistic molecular dynamics simulations [K. Lindorff-Larsen, S. Piana, R.O. Dror, D. E. Shaw, Science 334, 517 (2011)], with our calculations running several orders of magnitude faster. We find that native-like propensities in the unfolded state do not necessarily determine the order of structure formation, a departure from a major conclusion of the MD study. Instead, our results support a more expansive view wherein intrinsic local structural propensities may be enhanced or overridden in the folding process by environmental context. The success of our search strategy validates it as an expedient mechanism for folding both in silico and in vivo. PMID:23889448

  1. Free and open source simulation tools for the design of power processing units for photovoltaic systems

    Directory of Open Access Journals (Sweden)

    Sergio Morales-Hernández

    2015-06-01

    Full Text Available Renewable energy sources, including solar photovoltaic, require electronic circuits that serve as interface between the transducer device and the device or system that uses energy. Moreover, the energy efficiency and the cost of the system can be compromised if such electronic circuit is not designed properly. Given that the electrical characteristics of the photovoltaic devices are nonlinear and that the most efficient electronic circuits for power processing are naturally discontinuous, a detailed dynamic analysis to optimize the design is required. This analysis should be supported by computer simulation tools. In this paper a comparison between two software tools for dynamic system simulation is performed to determinate its usefulness in the design process of photovoltaic systems, mainly in what corresponds to the power processing units. Using as a case of study a photovoltaic system for battery charging it was determined that Scicoslab tool was the most suitable.

  2. X-ray photoelectron spectroscopy study of pyrolytically coated graphite platforms submitted to simulated electrothermal atomic absorption spectrometry conditions

    Energy Technology Data Exchange (ETDEWEB)

    Ruiz, Frine [Laboratorio de Quimica Analitica, Centro de Quimica, Instituto Venezolano de Investigaciones Cientificas, IVIC, Apartado Postal 21827, Caracas 1020-A (Venezuela); Benzo, Zully [Laboratorio de Quimica Analitica, Centro de Quimica, Instituto Venezolano de Investigaciones Cientificas, IVIC, Apartado Postal 21827, Caracas 1020-A (Venezuela); Quintal, Manuelita [Laboratorio de Quimica Analitica, Centro de Quimica, Instituto Venezolano de Investigaciones Cientificas, IVIC, Apartado Postal 21827, Caracas 1020-A (Venezuela); Garaboto, Angel [Laboratorio de Quimica Analitica, Centro de Quimica, Instituto Venezolano de Investigaciones Cientificas, IVIC, Apartado Postal 21827, Caracas 1020-A (Venezuela); Albornoz, Alberto [Laboratorio de Fisicoquimica de Superficies, Centro de Quimica, Instituto Venezolano de Investigaciones Cientificas, IVIC, Apartado Postal 21827, Caracas 1020-A (Venezuela); Brito, Joaquin L. [Laboratorio de Fisicoquimica de Superficies, Centro de Quimica, Instituto Venezolano de Investigaciones Cientificas, IVIC, Apartado Postal 21827, Caracas 1020-A (Venezuela)]. E-mail: joabrito@ivic.ve

    2006-10-15

    The present work is part of an ongoing project aiming to a better understanding of the mechanisms of atomization on graphite furnace platforms used for electrothermal atomic absorption spectrometry (ETAAS). It reports the study of unused pyrolytic graphite coated platforms of commercial origin, as well as platforms thermally or thermo-chemically treated under simulated ETAAS analysis conditions. X-ray photoelectron spectroscopy (XPS) was employed to study the elements present at the surfaces of the platforms. New, unused platforms showed the presence of molybdenum, of unknown origin, in concentrations up to 1 at.%. Species in two different oxidations states (Mo{sup 6+} and Mo{sup 2+}) were detected by analyzing the Mo 3d spectral region with high resolution XPS. The analysis of the C 1s region demonstrated the presence of several signals, one of these at 283.3 eV related to the presence of Mo carbide. The O 1s region showed also various peaks, including a signal that can be attributed to the presence of MoO{sub 3}. Some carbon and oxygen signals were consistent with the presence of C=O and C-O- (probably C-OH) groups on the platforms surfaces. Upon thermal treatment up to 2900 deg. C, the intensity of the Mo signal decreased, but peaks due to Mo oxides (Mo{sup 6+} and Mo{sup 5+}) and carbide (Mo{sup 2+}) were still apparent. Thermo-chemical treatment with 3 vol.% HCl solutions and heating up to 2900 deg. C resulted in further diminution of the Mo signal, with complete disappearance of Mo carbide species. Depth profiling of unused platforms by Ar{sup +} ion etching at increasing time periods demonstrated that, upon removal of several layers of carbonaceous material, the Mo signal disappears suggesting that this contamination is present only at the surface of the pyrolytic graphite platform.

  3. Multidisciplinary Simulation Acceleration using Multiple Shared-Memory Graphical Processing Units

    Science.gov (United States)

    Kemal, Jonathan Yashar

    For purposes of optimizing and analyzing turbomachinery and other designs, the unsteady Favre-averaged flow-field differential equations for an ideal compressible gas can be solved in conjunction with the heat conduction equation. We solve all equations using the finite-volume multiple-grid numerical technique, with the dual time-step scheme used for unsteady simulations. Our numerical solver code targets CUDA-capable Graphical Processing Units (GPUs) produced by NVIDIA. Making use of MPI, our solver can run across networked compute notes, where each MPI process can use either a GPU or a Central Processing Unit (CPU) core for primary solver calculations. We use NVIDIA Tesla C2050/C2070 GPUs based on the Fermi architecture, and compare our resulting performance against Intel Zeon X5690 CPUs. Solver routines converted to CUDA typically run about 10 times faster on a GPU for sufficiently dense computational grids. We used a conjugate cylinder computational grid and ran a turbulent steady flow simulation using 4 increasingly dense computational grids. Our densest computational grid is divided into 13 blocks each containing 1033x1033 grid points, for a total of 13.87 million grid points or 1.07 million grid points per domain block. To obtain overall speedups, we compare the execution time of the solver's iteration loop, including all resource intensive GPU-related memory copies. Comparing the performance of 8 GPUs to that of 8 CPUs, we obtain an overall speedup of about 6.0 when using our densest computational grid. This amounts to an 8-GPU simulation running about 39.5 times faster than running than a single-CPU simulation.

  4. The organizational context of ethical dilemmas: a role-playing simulation for the intensive care unit.

    Science.gov (United States)

    Strosberg, M A

    2001-01-01

    The allocation of health care resources often requires decision makers to balance conflicting ethical principles. The resource-constrained intensive care unit (ICU) provides an ideal setting to study how decision makers go about their balancing act in a complex and dynamic environment. The author presents a role-playing simulation exercise which models ICU admission and discharge decision making. Designed for the class-room, the simulation engages a variety of ethical, managerial, and public policy issues including end-of-life decision making, triage, and rationing. The simulation is based on a sequence of scenarios or "decision rounds" delineating conditions in the ICU in terms of disposition of ICU patients, number of available ICU beds, prognoses of candidates for admission, and other physiological and organizational information. Students, playing the roles of attending physician, hospital administrator, nurse manager, triage officer, and ethics committee member, are challenged to reach consensus in the context of multiple power centers and conflicting goals. An organization theory perspective, incorporated into the simulation, provides insight on how decisions are actually made and stimulates discussion on how decision making might be improved.

  5. High-speed nonlinear finite element analysis for surgical simulation using graphics processing units.

    Science.gov (United States)

    Taylor, Z A; Cheng, M; Ourselin, S

    2008-05-01

    The use of biomechanical modelling, especially in conjunction with finite element analysis, has become common in many areas of medical image analysis and surgical simulation. Clinical employment of such techniques is hindered by conflicting requirements for high fidelity in the modelling approach, and fast solution speeds. We report the development of techniques for high-speed nonlinear finite element analysis for surgical simulation. We use a fully nonlinear total Lagrangian explicit finite element formulation which offers significant computational advantages for soft tissue simulation. However, the key contribution of the work is the presentation of a fast graphics processing unit (GPU) solution scheme for the finite element equations. To the best of our knowledge, this represents the first GPU implementation of a nonlinear finite element solver. We show that the present explicit finite element scheme is well suited to solution via highly parallel graphics hardware, and that even a midrange GPU allows significant solution speed gains (up to 16.8 x) compared with equivalent CPU implementations. For the models tested the scheme allows real-time solution of models with up to 16,000 tetrahedral elements. The use of GPUs for such purposes offers a cost-effective high-performance alternative to expensive multi-CPU machines, and may have important applications in medical image analysis and surgical simulation.

  6. A combination method for simulation of secondary knock-on atoms of boron carbide induced by neutron irradiation in SPRR-300

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Jian-Chun [Key Laboratory of Radiation Physics and Technology of Education Ministry of China, Institute of Nuclear Science and Technology, Sichuan University, Chengdu, Sichuan 610064 (China); Feng, Qi-Jie; Liu, Xian-Kun [Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang, Sichuan 621900 (China); Zhan, Chang-Yong [Key Laboratory of Radiation Physics and Technology of Education Ministry of China, Institute of Nuclear Science and Technology, Sichuan University, Chengdu, Sichuan 610064 (China); Zou, Yu, E-mail: zouyu@scu.edu.cn [Key Laboratory of Radiation Physics and Technology of Education Ministry of China, Institute of Nuclear Science and Technology, Sichuan University, Chengdu, Sichuan 610064 (China); Liu, Yao-Guang [Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang, Sichuan 621900 (China)

    2016-02-01

    A multiscale sequence of simulation should be used to predict properties of materials under irradiation. Binary collision theory and molecular dynamics (MDs) method are commonly used to characterize the displacement cascades induced by neutrons in a material. In order to reduce the clock time spent for the MD simulation of damages induced by high-energy primary knock-on atoms (PKAs), the damage zones were split into sub-cascade according to the sub-cascade formation criteria. Two well-known codes, Geant4 and TRIM, were used to simulate high-energy PKA-induced cascades in B{sub 4}C and then produce the secondary knock-on atom (SKA) energy spectrum. It has been found that both high-energy primary knock-on B and C atoms move a long range in the boron carbide. These atoms produce sub-cascades at the tip of trajectory. The energy received by most of the SKAs is <10 keV, which can be used as input to reduce the clock time spent for MD simulation.

  7. Analysis of an Air Conditioning Coolant Solution for Metal Contamination Using Atomic Absorption Spectroscopy: An Undergraduate Instrumental Analysis Exercise Simulating an Industrial Assignment

    Science.gov (United States)

    Baird, Michael J.

    2004-01-01

    A real-life analytical assignment is presented to students, who had to examine an air conditioning coolant solution for metal contamination using an atomic absorption spectroscopy (AAS). This hands-on access to a real problem exposed the undergraduate students to the mechanism of AAS, and promoted participation in a simulated industrial activity.

  8. A combination method for simulation of secondary knock-on atoms of boron carbide induced by neutron irradiation in SPRR-300

    Science.gov (United States)

    Wu, Jian-Chun; Feng, Qi-Jie; Liu, Xian-Kun; Zhan, Chang-Yong; Zou, Yu; Liu, Yao-Guang

    2016-02-01

    A multiscale sequence of simulation should be used to predict properties of materials under irradiation. Binary collision theory and molecular dynamics (MDs) method are commonly used to characterize the displacement cascades induced by neutrons in a material. In order to reduce the clock time spent for the MD simulation of damages induced by high-energy primary knock-on atoms (PKAs), the damage zones were split into sub-cascade according to the sub-cascade formation criteria. Two well-known codes, Geant4 and TRIM, were used to simulate high-energy PKA-induced cascades in B4C and then produce the secondary knock-on atom (SKA) energy spectrum. It has been found that both high-energy primary knock-on B and C atoms move a long range in the boron carbide. These atoms produce sub-cascades at the tip of trajectory. The energy received by most of the SKAs is <10 keV, which can be used as input to reduce the clock time spent for MD simulation.

  9. Analysis of an Air Conditioning Coolant Solution for Metal Contamination Using Atomic Absorption Spectroscopy: An Undergraduate Instrumental Analysis Exercise Simulating an Industrial Assignment

    Science.gov (United States)

    Baird, Michael J.

    2004-01-01

    A real-life analytical assignment is presented to students, who had to examine an air conditioning coolant solution for metal contamination using an atomic absorption spectroscopy (AAS). This hands-on access to a real problem exposed the undergraduate students to the mechanism of AAS, and promoted participation in a simulated industrial activity.

  10. Molecular-dynamics simulation of lateral friction in contact-mode atomic force microscopy of alkane films: The role of molecular flexibility

    DEFF Research Database (Denmark)

    Soza, P.; Hansen, Flemming Yssing; Taub, H.

    2011-01-01

    Molecular-dynamics simulations are used to investigate lateral friction in contact-mode atomic force microscopy of tetracosane (n-C24H50) films. We find larger friction coefficients on the surface of monolayer and bilayer films in which the long axis of the molecules is parallel to the interface ...

  11. Neutral atom traps.

    Energy Technology Data Exchange (ETDEWEB)

    Pack, Michael Vern

    2008-12-01

    This report describes progress in designing a neutral atom trap capable of trapping sub millikelvin atom in a magnetic trap and shuttling the atoms across the atom chip from a collection area to an optical cavity. The numerical simulation and atom chip design are discussed. Also, discussed are preliminary calculations of quantum noise sources in Kerr nonlinear optics measurements based on electromagnetically induced transparency. These types of measurements may be important for quantum nondemolition measurements at the few photon limit.

  12. CNT welding through Ar bombardment using AIREBO potential and optimization of an extensionded AIREO potential for F atom to simulate hydrofluorocarbons

    Science.gov (United States)

    Kucukkal, Mustafa Umut

    Molecular Dynamics (MD) is an effective method to study diverse systems to gain atomistic level details from the trajectories of particles in the system. MD require a potential which describes the interaction of the particles within the system, which is then used to solve Newton's equation of motion to obtain the trajectories of the particles. For an accurate simulation of a system, an appropriate potential should be used for the MD simulations. The Adaptive Interactive Reactive Empirical Bond Order (AIREBO) potential is a promising potential for MD simulations of systems involving bond breakage or formation [1, 2]. The AIREBO potential is a Tersoff-style bond order potential which adds LJ and torsional interactions to REBO potential developed by Brenner et al [3, 4]. Currently, the AIREBO potential is well parameterized to study carbonaceous and hydrocarbon systems. In the first part of this study, the AIREBO potential is used in MD simulations to study the welding of single wall carbon nanotubes (SWCNTs) through Ar bombardment. SWCNTs have unique electronic properties which make them an appropriate candidate to use in nanoscale transistor and nanocomputer studies. An optimum conductivity through SWCNTs is required for these applications in electronic devices and it is achieved by the bonding arrangements of the carbon atoms in the junction area. This spatial bonding between SWCNTs can be obtained by various experimental methods such as electron beam radiation, fast atom bombardment and chemical vapor deposition. This study focuses on simulating Ar bombardment over cross junction of two SWCNTs placed on an imaginary Lennard-Jones surface perpendicular to each other. The cross junction area of SWCNTs was bombarded with Ar atoms of various kinetic energies in microcanical ensemble which is followed by annealing at various temperatures. The main goal of this study is to find optimum conditions to obtain the highest number of connections between the SWCNTs and the

  13. Methods of the aerodynamical experiments with simulation of massflow-traction ratio of the power unit

    Science.gov (United States)

    Lokotko, A. V.

    2016-10-01

    Modeling massflow-traction characteristics of the power unit (PU) may be of interest in the study of aerodynamic characteristics (ADC) aircraft models with full dynamic likeness, and in the study of the effect of interference PU. These studies require the use of a number of processing methods. These include: 1) The method of delivery of the high-pressure body of jets model engines on the sensitive part of the aerodynamic balance. 2) The method of estimate accuracy and reliability of measurement thrust generated by the jet device. 3) The method of implementation of the simulator SU in modeling the external contours of the nacelle, and the conditions at the inlet and outlet. 4) The method of determining the traction simulator PU. 5) The method of determining the interference effect from the work of power unit on the ADC of model. 6) The method of producing hot jets of jet engines. The paper examines implemented in ITAM methodology applied to testing in a supersonic wind tunnel T-313.

  14. Simulating three dimensional wave run-up over breakwaters covered by antifer units

    Directory of Open Access Journals (Sweden)

    A. Najafi-Jilani

    2014-06-01

    Full Text Available The paper presents the numerical analysis of wave run-up over rubble-mound breakwaters covered by antifer units using a technique integrating Computer-Aided Design (CAD and Computational Fluid Dynamics (CFD software. Direct application of Navier-Stokes equations within armour blocks, is used to provide a more reliable approach to simulate wave run-up over breakwaters. A well-tested Reynolds-averaged Navier-Stokes (RANS Volume of Fluid (VOF code (Flow-3D was adopted for CFD computations. The computed results were compared with experimental data to check the validity of the model. Numerical results showed that the direct three dimensional (3D simulation method can deliver accurate results for wave run-up over rubble mound breakwaters. The results showed that the placement pattern of antifer units had a great impact on values of wave run-up so that by changing the placement pattern from regular to double pyramid can reduce the wave run-up by approximately 30%. Analysis was done to investigate the influences of surface roughness, energy dissipation in the pores of the armour layer and reduced wave run-up due to inflow into the armour and stone layer.

  15. Fast Monte Carlo simulations of ultrasound-modulated light using a graphics processing unit.

    Science.gov (United States)

    Leung, Terence S; Powell, Samuel

    2010-01-01

    Ultrasound-modulated optical tomography (UOT) is based on "tagging" light in turbid media with focused ultrasound. In comparison to diffuse optical imaging, UOT can potentially offer a better spatial resolution. The existing Monte Carlo (MC) model for simulating ultrasound-modulated light is central processing unit (CPU) based and has been employed in several UOT related studies. We reimplemented the MC model with a graphics processing unit [(GPU), Nvidia GeForce 9800] that can execute the algorithm up to 125 times faster than its CPU (Intel Core Quad) counterpart for a particular set of optical and acoustic parameters. We also show that the incorporation of ultrasound propagation in photon migration modeling increases the computational time considerably, by a factor of at least 6, in one case, even with a GPU. With slight adjustment to the code, MC simulations were also performed to demonstrate the effect of ultrasonic modulation on the speckle pattern generated by the light model (available as animation). This was computed in 4 s with our GPU implementation as compared to 290 s using the CPU.

  16. Design and simulation of an activated sludge unit associated to a continuous reactor to remove heavy metals

    Energy Technology Data Exchange (ETDEWEB)

    D`Avila, J.S.; Nascimento, R.R. [Ambientec Consultoria Ltda., Aracaju, SE (Brazil)

    1993-12-31

    A software was developed to design and simulate an activated sludge unit associated to a new technology to remove heavy metals from wastewater. In this process, a continuous high efficiency biphasic reactor operates by using particles of activated peat in conjugation with the sludge unit. The results obtained may be useful to increase the efficiency or to reduce the design and operational costs involved in a activated sludge unit. (author). 5 refs., 2 tabs.

  17. Ground motion-simulations of 1811-1812 New Madrid earthquakes, central United States

    Science.gov (United States)

    Ramirez-Guzman, L.; Graves, Robert; Olsen, Kim B.; Boyd, Oliver; Cramer, Chris H.; Hartzell, Stephen; Ni, Sidao; Somerville, Paul G.; Williams, Robert; Zhong, Jinquan

    2015-01-01

    We performed a suite of numerical simulations based on the 1811–1812 New Madrid seismic zone (NMSZ) earthquakes, which demonstrate the importance of 3D geologic structure and rupture directivity on the ground‐motion response throughout a broad region of the central United States (CUS) for these events. Our simulation set consists of 20 hypothetical earthquakes located along two faults associated with the current seismicity trends in the NMSZ. The hypothetical scenarios range in magnitude from M 7.0 to 7.7 and consider various epicenters, slip distributions, and rupture characterization approaches. The low‐frequency component of our simulations was computed deterministically up to a frequency of 1 Hz using a regional 3D seismic velocity model and was combined with higher‐frequency motions calculated for a 1D medium to generate broadband synthetics (0–40 Hz in some cases). For strike‐slip earthquakes located on the southwest–northeast‐striking NMSZ axial arm of seismicity, our simulations show 2–10 s period energy channeling along the trend of the Reelfoot rift and focusing strong shaking northeast toward Paducah, Kentucky, and Evansville, Indiana, and southwest toward Little Rock, Arkansas. These waveguide effects are further accentuated by rupture directivity such that an event with a western epicenter creates strong amplification toward the northeast, whereas an eastern epicenter creates strong amplification toward the southwest. These effects are not as prevalent for simulations on the reverse‐mechanism Reelfoot fault, and large peak ground velocities (>40  cm/s) are typically confined to the near‐source region along the up‐dip projection of the fault. Nonetheless, these basin response and rupture directivity effects have a significant impact on the pattern and level of the estimated intensities, which leads to additional uncertainty not previously considered in magnitude estimates of the 1811–1812 sequence based only on historical

  18. Simulation Analysis as a Way to Assess the Performance of Important Unit Root and Change in Persistence Tests

    DEFF Research Database (Denmark)

    Fernández, Raúl O.; Vera-Valdés, J. Eduardo

    2013-01-01

    This chapter shows a way to, using simulation analysis, assess the performance of some of the most popular unit root and change in persistence tests. The authors do this by means of Monte Carlo simulations. The findings suggest that these tests show a lower than expected performance when dealing ...

  19. Simulation Analysis as a Way to Assess the Performance of Important Unit Root and Change in Persistence Tests

    DEFF Research Database (Denmark)

    Fernández, Raúl O.; Vera-Valdés, J. Eduardo

    2013-01-01

    This chapter shows a way to, using simulation analysis, assess the performance of some of the most popular unit root and change in persistence tests. The authors do this by means of Monte Carlo simulations. The findings suggest that these tests show a lower than expected performance when dealing ...

  20. Design of optimal operating conditions of simulated moving bed adsorptive separation units

    Energy Technology Data Exchange (ETDEWEB)

    Storti, G. (Univ. degli Studi di Padova (Italy)); Baciocchi, R.; Mazzotti, M.; Morbidelli, M. (Politecnico di Milano (Italy). Dipt. di Chimica Fisica Applicata)

    1995-01-01

    The design of the optimal operating conditions for simulated moving bed (SMB) adsorptive separation units is considered. A procedure for the a priori selection of the operating conditions to achieve an assigned separation requirement is developed in the frame of equilibrium theory for the equivalent four section countercurrent unit, using a model where the adsorption equilibria are described through the constant selectivity stoichiometric model, while both mass transfer resistance and axial dispersion are neglected. The space of the operating parameters, i.e. the mass flow rate ratios m[sub j], is divided in regions with different separation regimes. Curves at constant outlets purity and recovery are drawn in the (m[sub 2],m[sub 3]) plane. The introduction of three performance parameters, desorbent requirement, adsorbent requirement, and productivity, allows the development of a procedure for the design of optimal operating conditions. This procedure is completed, accounting for the effect of the switching time on the separation performances, with a detailed model of the SMB unit, considering both axial dispersion and mass transfer resistance. This result constitutes a useful tool for determining the range of operating conditions to achieve an assigned separation requirement and then for selecting the optimal operating condition within this range.

  1. Solving Unit Commitment Problem Using Modified Subgradient Method Combined with Simulated Annealing Algorithm

    Directory of Open Access Journals (Sweden)

    Ümmühan Başaran Filik

    2010-01-01

    Full Text Available This paper presents the solving unit commitment (UC problem using Modified Subgradient Method (MSG method combined with Simulated Annealing (SA algorithm. UC problem is one of the important power system engineering hard-solving problems. The Lagrangian relaxation (LR based methods are commonly used to solve the UC problem. The main disadvantage of this group of methods is the difference between the dual and the primal solution which gives some significant problems on the quality of the feasible solution. In this paper, MSG method which does not require any convexity and differentiability assumptions is used for solving the UC problem. MSG method depending on the initial value reaches zero duality gap. SA algorithm is used in order to assign the appropriate initial value for MSG method. The major advantage of the proposed approach is that it guarantees the zero duality gap independently from the size of the problem. In order to show the advantages of this proposed approach, the four-unit Tuncbilek thermal plant and ten-unit thermal plant which is usually used in literature are chosen as test systems. Penalty function (PF method is also used to compare with our proposed method in terms of total cost and UC schedule.

  2. Efficiency of endoscopy units can be improved with use of discrete event simulation modeling.

    Science.gov (United States)

    Sauer, Bryan G; Singh, Kanwar P; Wagner, Barry L; Vanden Hoek, Matthew S; Twilley, Katherine; Cohn, Steven M; Shami, Vanessa M; Wang, Andrew Y

    2016-11-01

    Background and study aims: The projected increased demand for health services obligates healthcare organizations to operate efficiently. Discrete event simulation (DES) is a modeling method that allows for optimization of systems through virtual testing of different configurations before implementation. The objective of this study was to identify strategies to improve the daily efficiencies of an endoscopy center with the use of DES. Methods: We built a DES model of a five procedure room endoscopy unit at a tertiary-care university medical center. After validating the baseline model, we tested alternate configurations to run the endoscopy suite and evaluated outcomes associated with each change. The main outcome measures included adequate number of preparation and recovery rooms, blocked inflow, delay times, blocked outflows, and patient cycle time. Results: Based on a sensitivity analysis, the adequate number of preparation rooms is eight and recovery rooms is nine for a five procedure room unit (total 3.4 preparation and recovery rooms per procedure room). Simple changes to procedure scheduling and patient arrival times led to a modest improvement in efficiency. Increasing the preparation/recovery rooms based on the sensitivity analysis led to significant improvements in efficiency. Conclusions: By applying tools such as DES, we can model changes in an environment with complex interactions and find ways to improve the medical care we provide. DES is applicable to any endoscopy unit and would be particularly valuable to those who are trying to improve on the efficiency of care and patient experience.

  3. Simulating Land Surface Hydrology at a 30-meter Spatial Resolution over the Contiguous United States

    Science.gov (United States)

    Wood, E. F.; Pan, M.; Cai, X.; Chaney, N.

    2016-12-01

    Big data, high performance computing, and recent advances in hydrologic similarity present a unique opportunity for macroscale hydrology: the land surface hydrology can be modeled at field scales over continental extents while ensuring computational efficiency to enable robust ensemble frameworks. In this presentation we will illustrate this potential breakthrough in macroscale hydrology by discussing results from a 30-meter simulation over the contiguous United States using the HydroBlocks land surface model. HydroBlocks is a novel land surface model that represents field-scale spatial heterogeneity of land surface processes through interacting hydrologic response units (HRUs) [Chaney et al., 2016]. The model is a coupling between the Noah-MP land surface model and the Dynamic TOPMODEL hydrologic model. The HRUs are defined by clustering proxies of the drivers of spatial heterogeneity using hyperresolution land data. For the simulations over CONUS, HydroBlocks is run at every HUC10 catchment using 100 HRUs per catchment between 2004 and 2014. The simulations are forced with the 4 km Stage IV radar rainfall product and a spatially downscaled version of NLDAS-2. We will show how this approach to macroscale hydrology ensures computational efficiency while providing field-scale hydrologic information over continental extents. We will illustrate how this approach provides a novel approach in both the application and validation of macroscale land surface and hydrologic models. Finally, using these results, we will discuss the important role that big data and high performance computing can play in providing solutions to longstanding challenges to not only flood and drought monitoring systems but also to numerical weather prediction, seasonal forecasting, and climate prediction. References Chaney, N., P. Metcalfe, and E. F. Wood (2016), HydroBlocks: A Field-scale Resolving Land Surface Model for Application Over Continental Extents, Hydrological Processes, (in press.)

  4. Quantum simulation of spin models and the discrete Truncated Wigner Approximation: from Rydberg atoms to trapped ions

    Science.gov (United States)

    Pineiro Orioli, Asier; Berges, Juergen; Signoles, Adrien; Schempp, Hanna; Whitlock, Shannon; Weidemueller, Matthias; Safavi-Naini, Arghavan; Wall, Michael; Schachenmayer, Johannes; Rey, Ana Maria

    2016-05-01

    Accurate description of the dynamics of quantum spin models is a theoretically challenging problem with widespread applications ranging from condensed matter to high-energy physics. Furthermore recent experimental progress in AMO experiments allows for the physical realization of these models in a variety of setups, such as Rydberg systems and trapped ion experiments, with an unprecedented degree of control and flexibility. Therefore, it is vital to develop efficient theoretical methods capable of simulating the many-body dynamics of such systems. In this work, we employ and extend the recently developed discrete Truncated Wigner Approximation (dTWA), an approximation based on the phase space description of quantum mechanics, to compute the dynamics of two types of spin models: the long-range XY model, which can be realized with Rydberg atoms, and a coupled spin-boson model, which is relevant to trapped ion experiments. Comparisons to experimental results and to available exact solutions to benchmark the method show that the dTWA is capable of capturing important features of the spin evolution and can also help uncovering some underlying non-equilibrium processes.

  5. Simulated Regional Yields of Spring Barley in the United Kingdom under Projected Climate Change

    Directory of Open Access Journals (Sweden)

    David O. Yawson

    2016-10-01

    Full Text Available This paper assessed the effect of projected climate change on the grain yield of barley in fourteen administrative regions in the United Kingdom (UK. Climate data for the 2030s, 2040s and 2050s for the high emission scenario (HES, medium emissions scenario (MES and low emissions scenario (LES were obtained from the UK Climate Projections 2009 (UKCP09 using the Weather Generator. Simulations were performed using the AquaCrop model and statistics of simulated future yields and baseline yields were compared. The results show that climate change could be beneficial to UK barley production. For all emissions scenarios and regions, differences between the simulated average future yields (2030s–2050s and the observed yields in the baseline period (1961–1990 ranged from 1.4 to 4 tons·ha−1. The largest increase in yields and yield variability occurred under the HES in the 2050s. Absolute increases in yields over baseline yields were substantially greater in the western half of the UK than in the eastern regions but marginally from south to north. These increases notwithstanding, yield reductions were observed for some individual years due to saturated soil conditions (most common in Wales, Northern Ireland and South-West Scotland. These suggest risks of yield penalties in any growing season in the future, a situation that should be considered for planning adaptation and risk management.

  6. Numerical simulation of physicochemical interactions between oxygen atom and phosphatidylcholine due to direct irradiation of atmospheric pressure nonequilibrium plasma to biological membrane with quantum mechanical molecular dynamics

    Science.gov (United States)

    Uchida, Satoshi; Yoshida, Taketo; Tochikubo, Fumiyoshi

    2017-10-01

    Plasma medicine is one of the most attractive applications using atmospheric pressure nonequilibrium plasma. With respect to direct contact of the discharge plasma with a biological membrane, reactive oxygen species play an important role in induction of medical effects. However, complicated interactions between the plasma radicals and membrane have not been understood well. In the present work, we simulated elemental processes at the first stage of physicochemical interactions between oxygen atom and phosphatidylcholine using the quantum mechanical molecular dynamics code in a general software AMBER. The change in the above processes was classified according to the incident energy of oxygen atom. At an energy of 1 eV, the abstraction of a hydrogen atom and recombination to phosphatidylcholine were simultaneously occurred in chemical attachment of incident oxygen atom. The exothermal energy of the reaction was about 80% of estimated one based on the bond energies of ethane. An oxygen atom over 10 eV separated phosphatidylcholine partially. The behaviour became increasingly similar to physical sputtering. The reaction probability of oxygen atom was remarkably high in comparison with that of hydrogen peroxide. These results suggest that we can uniformly estimate various physicochemical dynamics of reactive oxygen species against membrane lipids.

  7. Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection

    Directory of Open Access Journals (Sweden)

    Toofanny Rudesh D

    2011-08-01

    Full Text Available Abstract Background Molecular dynamics (MD simulations offer the ability to observe the dynamics and interactions of both whole macromolecules and individual atoms as a function of time. Taken in context with experimental data, atomic interactions from simulation provide insight into the mechanics of protein folding, dynamics, and function. The calculation of atomic interactions or contacts from an MD trajectory is computationally demanding and the work required grows exponentially with the size of the simulation system. We describe the implementation of a spatial indexing algorithm in our multi-terabyte MD simulation database that significantly reduces the run-time required for discovery of contacts. The approach is applied to the Dynameomics project data. Spatial indexing, also known as spatial hashing, is a method that divides the simulation space into regular sized bins and attributes an index to each bin. Since, the calculation of contacts is widely employed in the simulation field, we also use this as the basis for testing compression of data tables. We investigate the effects of compression of the trajectory coordinate tables with different options of data and index compression within MS SQL SERVER 2008. Results Our implementation of spatial indexing speeds up the calculation of contacts over a 1 nanosecond (ns simulation window by between 14% and 90% (i.e., 1.2 and 10.3 times faster. For a 'full' simulation trajectory (51 ns spatial indexing reduces the calculation run-time between 31 and 81% (between 1.4 and 5.3 times faster. Compression resulted in reduced table sizes but resulted in no significant difference in the total execution time for neighbour discovery. The greatest compression (~36% was achieved using page level compression on both the data and indexes. Conclusions The spatial indexing scheme significantly decreases the time taken to calculate atomic contacts and could be applied to other multidimensional neighbor discovery

  8. Parametric Limits of Efficient Use of a Centrifugal Water Atomizer in Contact Waste-Gas Heat-Utilization Units

    Science.gov (United States)

    Bezrodnyi, M. K.; Rachinskii, A. Yu.; Barabash, P. A.; Goliyad, N. N.

    2016-07-01

    The relation for the limiting temperature of water heating in a contact gas-droplet-type apparatus with a centrifugal atomizer has been determined experimentally in relation to the conditions of utilization of heat of power plant waste-gases. Investigations were carried out in the range of excess water pressures in front of the atomizer 0.2-0.6 MPa and of the volume fraction of steam in the vapor-gas mixture at the inlet of the apparatus from 0.02 to 0.45. The possibility of using the obtained dependence for calculating the limiting values of the vapor-gas flow parameters that limit the range of efficient operation of the contact apparatus with steam condensation and in the absence of heated liquid droplet evaporation is shown.

  9. Temperature dependence of the OH(-) + CH3I reaction kinetics. experimental and simulation studies and atomic-level dynamics.

    Science.gov (United States)

    Xie, Jing; Kohale, Swapnil C; Hase, William L; Ard, Shaun G; Melko, Joshua J; Shuman, Nicholas S; Viggiano, Albert A

    2013-12-27

    Direct dynamics simulations and selected ion flow tube (SIFT) experiments were performed to study the kinetics and dynamics of the OH(-) + CH3I reaction versus temperature. This work complements previous direct dynamics simulation and molecular beam ion imaging experiments of this reaction versus reaction collision energy (Xie et al. J. Phys. Chem. A 2013, 117, 7162). The simulations and experiments are in quite good agreement. Both identify the SN2, OH(-) + CH3I → CH3OH + I(-), and proton transfer, OH(-) + CH3I → CH2I(-) + H2O, reactions as having nearly equal importance. In the experiments, the SN2 pathway constitutes 0.64 ± 0.05, 0.56 ± 0.05, 0.51 ± 0.05, and 0.46 ± 0.05 of the total reaction at 210, 300, 400, and 500 K, respectively. For the simulations this fraction is 0.56 ± 0.06, 0.55 ± 0.04, and 0.50 ± 0.05 at 300, 400, and 500 K, respectively. The experimental total reaction rate constant is (2.3 ± 0.6) × 10(-9), (1.7 ± 0.4) × 10(-9), (1.9 ± 0.5) × 10(-9), and (1.8 ± 0.5) × 10(-9) cm(3) s(-1) at 210, 300, 400, and 500 K, respectively, which is approximately 25% smaller than the collision capture value. The simulation values for this rate constant are (1.7 ± 0.2) × 10(-9), (1.8 ± 0.1) × 10(-9), and (1.6 ± 0.1) × 10(-9) cm(3)s(-1) at 300, 400, and 500 K. From the simulations, direct rebound and stripping mechanisms as well as multiple indirect mechanisms are identified as the atomic-level reaction mechanisms for both the SN2 and proton-transfer pathways. For the SN2 reaction the direct and indirect mechanisms have nearly equal probabilities; the direct mechanisms are slightly more probable, and direct rebound is more important than direct stripping. For the proton-transfer pathway the indirect mechanisms are more important than the direct mechanisms, and stripping is significantly more important than rebound for the latter. Calculations were performed with the OH(-) quantum number J equal to 0, 3, and 6 to investigate the effect of

  10. Pegram Nuclear Physics Laboratories Progress Report for January 1969 through December 1969 to the United States Atomic Energy Commission

    Science.gov (United States)

    1969-12-01

    4 m N4 P 0Ca 40 V’ - ) 0 ein M Y Cd 116 Sternheimer (I) corrections are an example, considerably decrease the confidence and precision with which...interaction with this distribution can be accurately calculated. This suggests that muonic atoms may provide a means of testing Sternheimer as well as...and the first excited states. A satisfactory fit to the experimental data has IR. M. Sternheimer , Phys. Rev. 105, 158 (1957 and earlier papers. 2H. L

  11. Toward the credibility of Northeast United States summer precipitation projections in CMIP5 and NARCCAP simulations

    Science.gov (United States)

    Thibeault, Jeanne M.; Seth, A.

    2015-10-01

    Precipitation projections for the northeast United States and nearby Canada (Northeast) are examined for 15 Fifth Phase of the Coupled Model Intercomparison Project (CMIP5) models. A process-based evaluation of atmospheric circulation features associated with wet Northeast summers is performed to examine whether credibility can be differentiated within the multimodel ensemble. Based on these evaluations, and an analysis of the interannual statistical properties of area-averaged precipitation, model subsets were formed. Multimodel precipitation projections from each subset were compared to the multimodel projection from all of the models. Higher-resolution North American Regional Climate Change Assessment Program (NARCCAP) regional climate models (RCMs) were subjected to a similar evaluation, grouping into subsets, and examination of future projections. CMIP5 models adequately simulate most large-scale circulation features associated with wet Northeast summers, though all have errors in simulating observed sea level pressure and moisture divergence anomalies in the western tropical Atlantic/Gulf of Mexico. Relevant large-scale processes simulated by the RCMs resemble those of their driving global climate models (GCMs), which are not always realistic. Future RCM studies could benefit from a process analysis of potential driving GCMs prior to dynamical downscaling. No CMIP5 or NARCCAP models were identified as clearly more credible, but six GCMs and four RCMs performed consistently better. Among the "Better" models, there is no consistency in the direction of future summer precipitation change. CMIP5 projections suggest that the Northeast precipitation response depends on the dynamics of the North Atlantic anticyclone and associated circulation and moisture convergence patterns, which vary among "Better" models. Even when model credibility cannot be clearly differentiated, examination of simulated processes provides important insights into their evolution under

  12. Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations.

    Science.gov (United States)

    Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

    2015-06-15

    In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and

  13. Evaluation of the Contamination Control Unit during simulated transuranic waste retrieval

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, D.N.; Freeman, A.L.; Wixom, V.E.

    1993-11-01

    This report presents the results of a field demonstration at the INEL of the Contamination Control Unit (CCU). The CCU is a field deployable self-contained trailer mounted system to control contamination spread at the site of transuranic (TRU) handling operations. This is accomplished primarily by controlling dust spread. This demonstration was sponsored by the US Department of Energy`s Office of Waste Technology Development Buried Waste Integrated Demonstration. The CCU, housed in a mobile trailer for easy transport, supports four different contamination control systems: water misting, dust suppression application, soil fixative application, and vacuuming operations. Assessment of the CCU involved laboratory operational performance testing, operational testing and contamination control at a decommissioned Idaho National Engineering Laboratory reactor, and field testing in conjunction with a simulated TRU buried waste retrieval effort at the Cold Test Pit.

  14. AN APPROACH TO EFFICIENT FEM SIMULATIONS ON GRAPHICS PROCESSING UNITS USING CUDA

    Directory of Open Access Journals (Sweden)

    Björn Nutti

    2014-04-01

    Full Text Available The paper presents a highly efficient way of simulating the dynamic behavior of deformable objects by means of the finite element method (FEM with computations performed on Graphics Processing Units (GPU. The presented implementation reduces bottlenecks related to memory accesses by grouping the necessary data per node pairs, in contrast to the classical way done per element. This strategy reduces the memory access patterns that are not suitable for the GPU memory architecture. Furthermore, the presented implementation takes advantage of the underlying sparse-block-matrix structure, and it has been demonstrated how to avoid potential bottlenecks in the algorithm. To achieve plausible deformational behavior for large local rotations, the objects are modeled by means of a simplified co-rotational FEM formulation.

  15. Failure analysis of corrosion cracking and simulated testing for a fluid catalytic cracking unit

    Institute of Scientific and Technical Information of China (English)

    Hua Chen; Xiaogang Li; Chaofang Dong; Ming Li; Jinwen Yang

    2005-01-01

    The failure of a fluid catalysis and cracking unit (FCCU) in a Chinese refinery was investigated by using nondestructive detection methods, fracture surface examination, hardness measurement, chemical composition and corrosion products analysis. The results showed that the failure was caused by the dew point nitrate stress corrosion cracking. For a long operation period, the wall temperature of the regenerator in the FCCU was below the fume dew point. As a result, an acid fume NOx-SOx-H2O medium presented on the surface, resulting in stress corrosion cracking of the component with high residual stress. In order to confirm the relative conclusion, simulated testing was conducted in laboratory, and the results showed similar cracking characteristics. Finally, some suggestions have been made to prevent the stress corrosion cracking of an FCCU from re-occurring in the future.

  16. Approval of multiple unit trains by means of the simulation of contact wire/pantograph; Triebfahrzeugzulassung mithilfe der Simulation Fahrdraht/Stromabnehmer

    Energy Technology Data Exchange (ETDEWEB)

    Reichmann, Thomas; Raubold, Johannes [Siemens AG, Erlangen (Germany). Industry Sector, Mobility Div.

    2011-04-15

    The simulation program employed at Siemens adopting the finite element method delivers reliable findings about the dynamic interaction between pantographs and overhead contact lines and was verified by a validation according to EN 50318. In particular, a considerable reduction of measurement expenses for approval procedures of multiple unit trains with a lot of combination options for pantograph arrangements can be achieved by means of these simulations. (orig.)

  17. Atomic-Scale Kinetic Monte Carlo Simulation of {100}-Oriented Diamond Film Growth in C-H and C-H-Cl Systems by Chemical Vapour Deposition

    Institute of Scientific and Technical Information of China (English)

    安希忠; 张禹; 刘国权; 秦湘阁; 王辅忠; 刘胜新

    2002-01-01

    We simulate the { 100}-oriented diamond film growth of chemical vapour deposition (CVD) under different modelsin C-H and C-H-CI systems in an atomic scale by using the revised kinetic Monte Carlo method. The sirnulationresults show that: (1) the CVD diamond flm growth in the C-H system is suitable for high substrate temperature,and the flm surface roughness is very coarse; (2) the CVD diamond film can grow in the C-H-C1 system eitherat high temperature or at low temperature, and the film quality is outstanding; (3) atomic CI takes ala activerole for the growth of diamond film, especially at low temperatures. The concentration of atomic C1 should becontrolled in a proper range.

  18. Unit-Cell by Unit-Cell Homoepitaxial Growth Using Atomically Flat SrTiO3(001) Substrates and Pulsed Laser Deposition

    Institute of Scientific and Technical Information of China (English)

    FEI Yi-Yan; WANG Xu; LU Hui-Bin; YANG Guo-Zhen; ZHU Xiang-Dong

    2005-01-01

    @@ Using a combination of chemical etching and thermal annealing methods, we have obtained atomically flat TiO2-terminated SrTiO3 (001) with large terraces.The average width of the terrace is only determined by miscut angles.When we continuously grow tens of SrTiO3 monolayers on such a surface under pulsed laser ablation deposition condition at 621℃, the growth proceeds in a layer-by-layer mode characterized by un-damped oscillations of the specular RHEED intensity.After the growth of 180 monolayers, the surface morphology is restored to the pre-growth condition with similarly large terraces after annealing in vacuum for only 30 min, indicating efficient mass transfer on TiO2-terminated terraces.

  19. Energy and density analysis of the H2 molecule from the united atom to dissociation: The 3Σg+ and 3Σu+ states

    Science.gov (United States)

    Corongiu, Giorgina; Clementi, Enrico

    2009-11-01

    The first 14 Σ3g+ and the first 15 Σ3u+ states of the H2 molecule are computed with full configuration interaction both from Hartree-Fock molecular orbitals and Heitler-London atomic orbitals within the Born-Oppenheimer approximation, following recent studies for the Σ1g+ and Σ1u+ manifolds [Corongiu and Clementi, J. Chem. Phys. 131, 034301 (2009) and J. Phys. Chem. (in press)]. The basis sets utilized are extended and optimized Slater-type functions and spherical Gaussian functions. The states considered correspond to the configurations (1s1nl1) with n from 1 to 5; the internuclear separations sample the distances from 0.01 to 10 000 bohrs. For the first three Σ3g+ and Σ3u+ states and for the fourth and fifth Σ3g+ states, our computed energies at the equilibrium internuclear separation, when compared to the accurate values by Staszewska and Wolniewicz and by Kołos and Rychlewski, show deviations of about 0.006 kcal/mol, a test on the quality of our computations. Motivation for this work comes not only from obtaining potential energy curves for the high excited states of H2 but also from characterizing the electronic density evolution from the united atom to dissociation to provide a detailed analysis of the energy contributions from selected basis subsets and to quantitatively decompose the state energies into covalent and ionic components. Furthermore, we discuss the origin of the seemingly irregular patterns in potential energy curves in the two manifolds, between 4 and 6-9 bohrs—there are two systems of states: the first, from the united atom to about 4 bohrs, is represented by functions with principal quantum number higher than the one needed at dissociation; this system interacts at around 4 bohrs with the second system, which is represented by functions with principal quantum number corresponding to one of the dissociation products.

  20. A Performance Comparison of Different Graphics Processing Units Running Direct N-Body Simulations

    CERN Document Server

    Capuzzo-Dolcetta, Roberto

    2013-01-01

    Hybrid computational architectures based on the joint power of Central Processing Units and Graphic Processing Units (GPUs) are becoming popular and powerful hardware tools for a wide range of simulations in biology, chemistry, engineering, physics, etc.. In this paper we present a comparison of performance of various GPUs available on market when applied to the numerical integration of the classic, gravitational, N-body problem. To do this, we developed an OpenCL version of the parallel code (HiGPUs) to use for these tests, because this version is the only apt to work on GPUs of different makes. The main general result is that we confirm the reliability, speed and cheapness of GPUs when applied to the examined kind of problems (i.e. when the forces to evaluate are dependent on the mutual distances, as it happens in gravitational physics and molecular dynamics). More specifically, we find that also the cheap GPUs built to be employed just for gaming applications are very performant in terms of computing speed...

  1. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations

    Indian Academy of Sciences (India)

    Surjit B Dixit; Mihaly Mezei; David L Beveridge

    2012-07-01

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute–solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interactmore strongly with watermolecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning’s counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 Å from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general

  2. Adsorption of Synthetic Cationic Polymers on Model Phospholipid Membranes: Insight from Atomic-Scale Molecular Dynamics Simulations.

    Science.gov (United States)

    Kostritskii, Andrei Yu; Kondinskaia, Diana A; Nesterenko, Alexey M; Gurtovenko, Andrey A

    2016-10-11

    Although synthetic cationic polymers represent a promising class of effective antibacterial agents, the molecular mechanisms behind their antimicrobial activity remain poorly understood. To this end, we employ atomic-scale molecular dynamics simulations to explore adsorption of several linear cationic polymers of different chemical structure and protonation (polyallylamine (PAA), polyethylenimine (PEI), polyvinylamine (PVA), and poly-l-lysine (PLL)) on model bacterial membranes (4:1 mixture of zwitterionic phosphatidylethanolamine (PE) and anionic phosphatidylglycerol (PG) lipids). Overall, our findings show that binding of polycations to the anionic membrane surface effectively neutralizes its charge, leading to the reorientation of water molecules close to the lipid/water interface and to the partial release of counterions to the water phase. In certain cases, one has even an overcharging of the membrane, which was shown to be a cooperative effect of polymer charges and lipid counterions. Protonated amine groups of polycations are found to interact preferably with head groups of anionic lipids, giving rise to formation of hydrogen bonds and to a noticeable lateral immobilization of the lipids. While all the above findings are mostly defined by the overall charge of a polymer, we found that the polymer architecture also matters. In particular, PVA and PEI are able to accumulate anionic PG lipids on the membrane surface, leading to lipid segregation. In turn, PLL whose charge twice exceeds charges of PVA/PEI does not induce such lipid segregation due to its considerably less compact architecture and relatively long side chains. We also show that partitioning of a polycation into the lipid/water interface is an interplay between its protonation level (the overall charge) and hydrophobicity of the backbone. Therefore, a possible strategy in creating highly efficient antimicrobial polymeric agents could be in tuning these polycation's properties through proper

  3. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units.

    Science.gov (United States)

    Lindert, Steffen; Bucher, Denis; Eastman, Peter; Pande, Vijay; McCammon, J Andrew

    2013-11-12

    The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD method is shown to work in combination with the AMOEBA polarizable force field (AMOEBA-aMD), allowing the simulation of long time-scale events with a polarizable force field. Benchmarks are provided to show that the AMOEBA-aMD method is efficiently implemented and produces accurate results in its standard parametrization. For the BPTI protein, we demonstrate that the protein structure described with AMOEBA remains stable even on the extended time scales accessed at high levels of accelerations. For the DNA repair metalloenzyme endonuclease IV, we show that the use of the AMOEBA force field is a significant improvement over fixed charged models for describing the enzyme active-site. The new AMOEBA-aMD method is publicly available (http://wiki.simtk.org/openmm/VirtualRepository) and promises to be interesting for studying complex systems that can benefit from both the use of a polarizable force field and enhanced sampling.

  4. Experiment and modeling for the separation of guaifenesin enantiomers using simulated moving bed and Varicol units.

    Science.gov (United States)

    Gong, Rujin; Lin, Xiaojian; Li, Ping; Yu, Jianguo; Rodrigues, Alirio E

    2014-10-10

    The separation of guaifenesin enantiomers by both simulated moving bed (SMB) process and Varicol process was investigated experimentally and theoretically, where the columns were packed with cellulose tris 3,5-dimethylphenylcarbamate (Chiralcel OD) stationary phase and a mixture of n-hexane and ethanol was used as mobile phase. The operation conditions were designed based on the separation region with the consideration of mass transfer resistance and axial dispersion, and the experiments to separate guaifenesin enantiomers were carried out on VARICOL-Micro unit using SMB process with the column configuration of 1/2/2/1 and Varicol process with the column configuration of 1/1.5/1.5/1, respectively. Single enantiomer with more than 99.0% purity was obtained in both processes with the productivity of 0.42 genantiomer/dcm(3) CSP for SMB process and 054 genantiomer/dcm(3) CSP for Varicol process. These experimental results obtained from SMB and Varicol processes were compared with those reported from literatures. In addition, according to the numerical simulation, the effects of solid-film mass transfer resistance and axial dispersion on the internal profiles were discussed, and the effect of column configuration on the separation performance of SMB and Varicol processes was analyzed for a few columns system. The feasibility and efficiency for the separation of guaifenesin enantiomers by SMB and Varicol processes were evaluated. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. NUMERICAL SIMULATION OF TWO-DIMENSIONAL OVERTOPPING AGAINST SEAWALLS ARMORED WITH ARTIFICIAL UNITS IN REGULAR WAVES

    Institute of Scientific and Technical Information of China (English)

    LU Yong-jin; LIU Hua; WU Wei; ZHANG Jiu-shan

    2007-01-01

    A new mathematical model for the overtopping against seawalls armored with artificial units in regular waves was established. The 2-D numerical wave flume, based on the Reynolds Averaged Navier-Stokes (RANS) equations and the standard k-ε turbulence model, was developed to simulate the turbulent flows with the free surface, in which the Volume Of Fluid (VOF) method was used to handle the large deformation of the free surface and the relaxation approach of combined wave generation and absorbing was implemented. In order to consider the effects of energy dissipation due to the armors on a slope seawall, a porous media model was proposed and implemented in the numerical wave flume. A series of physical model experiments were carried out in the same condition of the numerical simulation to determine the drag coefficient in the porous media model in terms of the overtopping discharge. Compared the computational value of overtopping over the seawall with the experimental data, the values of the effective drag coefficient was calibrated for the layers of blocks at different locations along the seawalls.

  6. Simulation of Watts Bar Unit 1 Initial Startup Tests with Continuous Energy Monte Carlo Methods

    Energy Technology Data Exchange (ETDEWEB)

    Godfrey, Andrew T [ORNL; Gehin, Jess C [ORNL; Bekar, Kursat B [ORNL; Celik, Cihangir [ORNL

    2014-01-01

    The Consortium for Advanced Simulation of Light Water Reactors* is developing a collection of methods and software products known as VERA, the Virtual Environment for Reactor Applications. One component of the testing and validation plan for VERA is comparison of neutronics results to a set of continuous energy Monte Carlo solutions for a range of pressurized water reactor geometries using the SCALE component KENO-VI developed by Oak Ridge National Laboratory. Recent improvements in data, methods, and parallelism have enabled KENO, previously utilized predominately as a criticality safety code, to demonstrate excellent capability and performance for reactor physics applications. The highly detailed and rigorous KENO solutions provide a reliable nu-meric reference for VERAneutronics and also demonstrate the most accurate predictions achievable by modeling and simulations tools for comparison to operating plant data. This paper demonstrates the performance of KENO-VI for the Watts Bar Unit 1 Cycle 1 zero power physics tests, including reactor criticality, control rod worths, and isothermal temperature coefficients.

  7. Accelerated rescaling of single Monte Carlo simulation runs with the Graphics Processing Unit (GPU).

    Science.gov (United States)

    Yang, Owen; Choi, Bernard

    2013-01-01

    To interpret fiber-based and camera-based measurements of remitted light from biological tissues, researchers typically use analytical models, such as the diffusion approximation to light transport theory, or stochastic models, such as Monte Carlo modeling. To achieve rapid (ideally real-time) measurement of tissue optical properties, especially in clinical situations, there is a critical need to accelerate Monte Carlo simulation runs. In this manuscript, we report on our approach using the Graphics Processing Unit (GPU) to accelerate rescaling of single Monte Carlo runs to calculate rapidly diffuse reflectance values for different sets of tissue optical properties. We selected MATLAB to enable non-specialists in C and CUDA-based programming to use the generated open-source code. We developed a software package with four abstraction layers. To calculate a set of diffuse reflectance values from a simulated tissue with homogeneous optical properties, our rescaling GPU-based approach achieves a reduction in computation time of several orders of magnitude as compared to other GPU-based approaches. Specifically, our GPU-based approach generated a diffuse reflectance value in 0.08ms. The transfer time from CPU to GPU memory currently is a limiting factor with GPU-based calculations. However, for calculation of multiple diffuse reflectance values, our GPU-based approach still can lead to processing that is ~3400 times faster than other GPU-based approaches.

  8. Convection-Permitting Regional Climate Simulations over the Contiguous United States Including Potential Climate Change Scenarios

    Science.gov (United States)

    Liu, Changhai; Rasmussen, Roy; Ikeda, Kyoko; Barlage, Michael; Chen, Fei; Clark, Martyn; Dai, Aiguo; Dudhia, Jimy; Gochis, David; Gutmann, Ethan; Li, Yanping; Newman, Andrew; Thompson, Gregory

    2016-04-01

    The WRF model with a domain size of 1360x1016x51 points, using a 4 km spacing to encompass most of North America, is employed to investigate the water cycle and climate change impacts over the Contiguous United States (CONUS). Four suites of numerical experiments are being conducted, consisting of a 13-year retrospective simulation forced with ERA-I reanalysis, a 13-year climate sensitivity or Pseudo-Global Warming (PGW) simulation, and two 10-year CMIP5-based historical/future period simulations based on a revised bias-correction method. The major objectives are: 1) to evaluate high-resolution WRF's capability to capture orographic precipitation and snow mass balance over the western CONUS and convective precipitation over the eastern CONUS; 2) to assess future changes of seasonal snowfall and snowpack and associated hydrological cycles along with their regional variability across the different mountain barriers and elevation dependency, in response to the CMIP5 projected 2071-2100 climate warming; 3) to examine the precipitation changes under the projected global warming, with an emphasis on precipitation extremes and the warm-season precipitation corridor in association with MCS tracks in the central US; and 4) to provide a valuable community dataset for regional climate change and impact studies. Preliminary analysis of the retrospective simulation shows both seasonal/sub-seasonal precipitation and temperature are well reproduced, with precipitation bias being within 10% of the observations and temperature bias being below 1 degree C in most seasons and locations. The observed annual cycle of snow water equivalent (SWE), such as peak time and disappearance time, is also realistically replicated, even though the peak value is somewhat underestimated. The PGW simulation shows a large cold-season warming in northeast US and eastern Canada, possibly associated with snow albedo feedback, and a strong summer warming in north central US in association with

  9. Dynamic evaluation of two decades of WRF-CMAQ ozone simulations over the contiguous United States

    Science.gov (United States)

    Astitha, Marina; Luo, Huiying; Rao, S. Trivikrama; Hogrefe, Christian; Mathur, Rohit; Kumar, Naresh

    2017-09-01

    Dynamic evaluation of the fully coupled Weather Research and Forecasting (WRF)- Community Multi-scale Air Quality (CMAQ) model ozone simulations over the contiguous United States (CONUS) using two decades of simulations covering the period from 1990 to 2010 is conducted to assess how well the changes in observed ozone air quality are simulated by the model. The changes induced by variations in meteorology and/or emissions are also evaluated during the same timeframe using spectral decomposition of observed and modeled ozone time series with the aim of identifying the underlying forcing mechanisms that control ozone exceedances and making informed recommendations for the optimal use of regional-scale air quality models. The evaluation is focused on the warm season's (i.e., May-September) daily maximum 8-hr (DM8HR) ozone concentrations, the 4th highest (4th) and average of top 10 DM8HR ozone values (top10), as well as the spectrally-decomposed components of the DM8HR ozone time series using the Kolmogorov-Zurbenko (KZ) filter. Results of the dynamic evaluation are presented for six regions in the U.S., consistent with the National Oceanic and Atmospheric Administration (NOAA) climatic regions. During the earlier 11-yr period (1990-2000), the simulated and observed regional average trends are not statistically significant. During the more recent 2000-2010 period, all observed trends are statistically significant and WRF-CMAQ captures the observed downward trend in the Southwest and Midwest but under-predicts the downward trends in observations for the other regions. Observational analysis reveals that it is the magnitude of the long-term forcing that dictates the maximum ozone exceedance potential; there is a strong linear relationship between the long-term forcing and the 4th highest or the average of the top10 ozone concentrations in both observations and model output. This finding indicates that improving the model's ability to reproduce the long-term component

  10. Evaluation of structural deformations of a mechanical connecting unit oxidizer supplies by thermo-mechanical simulation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Sang Woo [Dept. of Mechanical Engineering, Institute of Machine Convergence Technology, Hankyong National University, Anseong (Korea, Republic of)

    2016-10-15

    A Mechanical connecting unit (MCU) used in ground facilities for a Liquid propellant rocket (LPR) acts as a bridge between the onboard system and the ground oxidizer filling system. It should be resistant to structural deformations in order to guarantee successful supply of a cryogenic oxidizer and high pressure gases without reduction of sealing capability. The MCU consists of many components and linkages and operates under harsh conditions induced by a cryogenic oxidizer, high pressure gases and other mechanical forces. Thus, the evaluation of structural deformation of the MCU considering complex conditions is expensive and time consuming. The present study efficiently evaluates the structural deformations of the key components of the MCU by Thermo-mechanical simulation (TMS) based on the superposition principle. Deformations due to the mechanical loadings including weights, pressures, and spring forces are firstly evaluated by using a non-linear flexible body simulation module (FFlex) of Multi-body dynamics (MBD) software, RecurDyn. Then, thermal deformations for the deformed geometries obtained by RecurDyn were subsequently calculated. It was conducted by using a Finite element (FE) analysis software, ANSYS. The total deformations for the onboard plate and multi-channel plate in the connecting section due to the mechanical and thermal loadings were successfully evaluated. Moreover, the outer gaps at six points between two plates were calculated and verified by comparison to the measured data. Their values and tendencies showed a good agreement. The author concluded that the TMS using MBD software considering flexible bodies and an FE simulator can efficiently evaluate structural deformations of the MCU operating under the complex load and boundary conditions.

  11. Simulating the hydrodynamic conditions in the United States Pharmacopeia paddle dissolution apparatus.

    Science.gov (United States)

    McCarthy, Leonard G; Kosiol, Carolin; Healy, Anne Marie; Bradley, Geoff; Sexton, James C; Corrigan, Owen I

    2003-01-01

    The objective of this work was to examine the feasibility of developing a high-performance computing software system to simulate the United States Pharmacopeia (USP) dissolution apparatus 2 (paddle apparatus) and thus aid in characterizing the fluid hydrodynamics in the method. The USP apparatus was modeled using the hydrodynamic package Fluent. The Gambit program was used to create a "wireframe" of the apparatus and generate the 3-dimensional grids for the computational fluid dynamics solver. The Fluent solver was run on an IBM RS/6000 SP distributed memory parallel processor system, using 8 processors. Configurations with and without a tablet present were developed and examined. Simulations for a liquid-filled vessel at a paddle speed of 50 rpm were generated. Large variations in fluid velocity magnitudes with position in the vessel were evident. Fluid velocity predictions were in good agreement with those previously published, using laser Doppler velocity measurements. A low-velocity domain was evident directly below the center of the rotating paddle. The model was extended to simulate the impact of the presence of a cylindrical tablet in the base of the dissolution vessel. The presence of the tablet complicated the local fluid flow, and large fluid shear rates were evident at the base of the compact. Fluid shear rates varied depending on the tablet surface and the location on the surface and were consistent with the reported asymmetrical dissolution of model tablets. The approach has the potential to explain the variable dissolution results reported and to aid in the design/prediction of optimal dissolution conditions for in vitro--in vivo correlations.

  12. Large eddy simulations of turbulent flows on graphics processing units: Application to film-cooling flows

    Science.gov (United States)

    Shinn, Aaron F.

    Computational Fluid Dynamics (CFD) simulations can be very computationally expensive, especially for Large Eddy Simulations (LES) and Direct Numerical Simulations (DNS) of turbulent ows. In LES the large, energy containing eddies are resolved by the computational mesh, but the smaller (sub-grid) scales are modeled. In DNS, all scales of turbulence are resolved, including the smallest dissipative (Kolmogorov) scales. Clusters of CPUs have been the standard approach for such simulations, but an emerging approach is the use of Graphics Processing Units (GPUs), which deliver impressive computing performance compared to CPUs. Recently there has been great interest in the scientific computing community to use GPUs for general-purpose computation (such as the numerical solution of PDEs) rather than graphics rendering. To explore the use of GPUs for CFD simulations, an incompressible Navier-Stokes solver was developed for a GPU. This solver is capable of simulating unsteady laminar flows or performing a LES or DNS of turbulent ows. The Navier-Stokes equations are solved via a fractional-step method and are spatially discretized using the finite volume method on a Cartesian mesh. An immersed boundary method based on a ghost cell treatment was developed to handle flow past complex geometries. The implementation of these numerical methods had to suit the architecture of the GPU, which is designed for massive multithreading. The details of this implementation will be described, along with strategies for performance optimization. Validation of the GPU-based solver was performed for fundamental bench-mark problems, and a performance assessment indicated that the solver was over an order-of-magnitude faster compared to a CPU. The GPU-based Navier-Stokes solver was used to study film-cooling flows via Large Eddy Simulation. In modern gas turbine engines, the film-cooling method is used to protect turbine blades from hot combustion gases. Therefore, understanding the physics of

  13. Atomic motions in poly(vinyl methyl ether): A combined study by quasielastic neutron scattering and molecular dynamics simulations in the light of the mode coupling theory.

    Science.gov (United States)

    Capponi, S; Arbe, A; Alvarez, F; Colmenero, J; Frick, B; Embs, J P

    2009-11-28

    Quasielastic neutron scattering experiments (time-of-flight, neutron spin echo, and backscattering) on protonated poly(vinyl methyl ether) (PVME) have revealed the hydrogen dynamics above the glass-transition temperature. Fully atomistic molecular dynamics simulations properly validated with the neutron scattering results have allowed further characterization of the atomic motions accessing the correlation functions directly in real space. Deviations from Gaussian behavior are found in the high-momentum transfer range, which are compatible with the predictions of mode coupling theory (MCT). We have applied the MCT phenomenological version to the self-correlation functions of PVME atoms calculated from our simulation data, obtaining consistent results. The unusually large value found for the lambda-exponent parameter is close to that recently reported for polybutadiene and simple polymer models with intramolecular barriers.

  14. 76 FR 29277 - Exelon Generation Company, LLC; Peach Bottom Atomic Power Station Unit Nos. 2 and 3...

    Science.gov (United States)

    2011-05-20

    ... From the Federal Register Online via the Government Publishing Office NUCLEAR REGULATORY... Assessment and Finding of No Significant Impact The U.S. Nuclear Regulatory Commission (NRC) is considering... waste (LLRW), from Exelon's Limerick Generating Station, Units 1 and 2 (LGS). The LLRW will be stored in...

  15. All-atom Molecular-level Computational Simulations of Planar Longitudinal Shockwave Interactions with Polyurea, Soda-lime Glass and Polyurea/Glass Interfaces

    Science.gov (United States)

    2014-01-01

    All-atom molecular-level computational simulations of planar longitudinal shockwave interactions with polyurea, soda- lime glass and polyurea/glass...of this paper is to study the mechanical response of polyurea, soda- lime glass (glass, for short), polyurea/glass/polyurea and glass/polyurea/glass...methods, the interaction of shockwaves with material boundaries. Keywords Polyurea, Material interface, Shockwaves, Soda- lime glass Paper type Research

  16. Unraveling low-resolution structural data of large biomolecules by constructing atomic models with experiment-targeted parallel cascade selection simulations

    Science.gov (United States)

    Peng, Junhui; Zhang, Zhiyong

    2016-07-01

    Various low-resolution experimental techniques have gained more and more popularity in obtaining structural information of large biomolecules. In order to interpret the low-resolution structural data properly, one may need to construct an atomic model of the biomolecule by fitting the data using computer simulations. Here we develop, to our knowledge, a new computational tool for such integrative modeling by taking the advantage of an efficient sampling technique called parallel cascade selection (PaCS) simulation. For given low-resolution structural data, this PaCS-Fit method converts it into a scoring function. After an initial simulation starting from a known structure of the biomolecule, the scoring function is used to pick conformations for next cycle of multiple independent simulations. By this iterative screening-after-sampling strategy, the biomolecule may be driven towards a conformation that fits well with the low-resolution data. Our method has been validated using three proteins with small-angle X-ray scattering data and two proteins with electron microscopy data. In all benchmark tests, high-quality atomic models, with generally 1-3 Å from the target structures, are obtained. Since our tool does not need to add any biasing potential in the simulations to deform the structure, any type of low-resolution data can be implemented conveniently.

  17. All-atom Molecular Dynamic Simulations Combined with the Chemical Shifts Study on the Weak Interactions of Ethanol-water System

    Institute of Scientific and Technical Information of China (English)

    ZHANG Rong; LUO San-Lai; WU Wen-Juan

    2008-01-01

    All-atom molecular dynamics(MD)simulation combined with chemical shifts was performed to investigate the interactions over the entire concentration range of the ethanol(EtOH)-water system.The results of the simulation were adopted to explain the NMR experiments by hydrogen bonding analysis.The strong hydrogen bonds and weak C-H…O contacts coexist in the mixtures through the analysis of the radial distribution functions.And the liquid structures in the whole concentration of EtOH-water mixtures can be classified into three regions by the statistic analysis of the hydrogen-bonding network in the MD simulations.Moreover,the chemical shifts of the hydrogen atom are in agreement witb the statistical results of the average number hydrogen bonds in the MD simulations.Interestingly,the excess relative extent Eηrel calculated by the MD simulations and chemical shifts in the EtOH aqueous solutions shows the largest deviation at XEtOH≈0.18.The excess properties present good agreement with the excess enthalpy in the concentration dependence.

  18. Synthesis-atomic structure-properties relationships in metallic nanoparticles by total scattering experiments and 3D computer simulations: case of Pt-Ru nanoalloy catalysts.

    Science.gov (United States)

    Prasai, Binay; Ren, Yang; Shan, Shiyao; Zhao, Yinguang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian; Petkov, Valeri

    2015-05-07

    An approach to determining the 3D atomic structure of metallic nanoparticles (NPs) in fine detail and using the unique knowledge obtained for rationalizing their synthesis and properties targeted for optimization is described and exemplified on Pt-Ru alloy NPs of importance to the development of devices for clean energy conversion such as fuel cells. In particular, PtxRu100-x alloy NPs, where x = 31, 49 and 75, are synthesized by wet chemistry and activated catalytically by a post-synthesis treatment involving heating under controlled N2-H2 atmosphere. So-activated NPs are evaluated as catalysts for gas-phase CO oxidation and ethanol electro-oxidation reactions taking place in fuel cells. Both as-synthesized and activated NPs are characterized structurally by total scattering experiments involving high-energy synchrotron X-ray diffraction coupled to atomic pair distribution functions (PDFs) analysis. 3D structure models both for as-synthesized and activated NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modelling Sutton-Chen method. Models are refined against the experimental PDF data by reverse Monte Carlo simulations and analysed in terms of prime structural characteristics such as metal-to-metal bond lengths, bond angles and first coordination numbers for Pt and Ru atoms. Analysis indicates that, though of a similar type, the atomic structure of as-synthesized and respective activated NPs differ in several details of importance to NP catalytic properties. Structural characteristics of activated NPs and data for their catalytic activity are compared side by side and strong evidence found that electronic effects, indicated by significant changes in Pt-Pt and Ru-Ru metal bond lengths at NP surface, and practically unrecognized so far atomic ensemble effects, indicated by distinct stacking of atomic layers near NP surface and prevalence of particular configurations of Pt and Ru atoms in these layers, contribute to the

  19. The effect of a simulation-based training intervention on the performance of established critical care unit teams.

    Science.gov (United States)

    Frengley, Robert W; Weller, Jennifer M; Torrie, Jane; Dzendrowskyj, Peter; Yee, Bevan; Paul, Adam M; Shulruf, Boaz; Henderson, Kaylene M

    2011-12-01

    We evaluated the effectiveness of a simulation-based intervention on improving teamwork in multidisciplinary critical care teams managing airway and cardiac crises and compared simulation-based learning and case-based learning on scores for performance. Self-controlled randomized crossover study design with blinded assessors. A simulated critical care ward, using a high-fidelity patient simulator, in a university simulation center. Forty teams from critical care units within the region comprising one doctor and three nurses. At the beginning and end of the 10-hr study day, each team undertook two preintervention and two postintervention assessment simulations (one airway, one cardiac on both occasions). The study day included presentations and discussions on human factors and crisis management, and airway and cardiac skills stations. For the intervention, teams were randomized to case-based learning or simulation-based learning for cardiac or airway scenarios. Each simulation was recorded and independently rated by three blinded expert assessors using a structured rating tool with technical and behavioral components. Participants were surveyed 3 months later. We demonstrated significant improvements in scores for overall teamwork (p ≤ .002) and the two behavioral factors, "Leadership and Team Coordination" (p ≤ .002) and "Verbalizing Situational Information" (p ≤ .02). Scores for clinical management also improved significantly (p ≤ .003). We found no significant difference between simulation-based learning and case-based learning in the context of this study. Survey data supported the effectiveness of study day with responders reporting retention of learning and changes made to patient management. A simulation-based study day can improve teamwork in multidisciplinary critical care unit teams as measured in pre- and postcourse simulations with some evidence of subsequent changes to patient management. In the context of a full-day course, using a mix of

  20. Cold Matter Assembled Atom-by-Atom

    CERN Document Server

    Endres, Manuel; Keesling, Alexander; Levine, Harry; Anschuetz, Eric R; Krajenbrink, Alexandre; Senko, Crystal; Vuletic, Vladan; Greiner, Markus; Lukin, Mikhail D

    2016-01-01

    The realization of large-scale fully controllable quantum systems is an exciting frontier in modern physical science. We use atom-by-atom assembly to implement a novel platform for the deterministic preparation of regular arrays of individually controlled cold atoms. In our approach, a measurement and feedback procedure eliminates the entropy associated with probabilistic trap occupation and results in defect-free arrays of over 50 atoms in less than 400 ms. The technique is based on fast, real-time control of 100 optical tweezers, which we use to arrange atoms in desired geometric patterns and to maintain these configurations by replacing lost atoms with surplus atoms from a reservoir. This bottom-up approach enables controlled engineering of scalable many-body systems for quantum information processing, quantum simulations, and precision measurements.

  1. Simulation and Optimization of Vacuum Swing Adsorption Units for Spacesuit Carbon Dioxide and Humidity Control

    Science.gov (United States)

    Swickrath, Michael J.; Anderson, Molly; McMillin, Summer; Broerman, Craig

    2011-01-01

    Controlling carbon dioxide (CO2) and humidity levels in a spacesuit is critical to ensuring both the safety and comfort of an astronaut during extra-vehicular activity (EVA). Traditionally, this has been accomplished utilizing either non-regenerative lithium hydroxide (LiOH) or regenerative but heavy metal oxide (MetOx) canisters which pose a significant weight burden. Although such technology enables air revitalization, the volume requirements to store the waste canisters as well as the mass to transport multiple units become prohibitive as mission durations increase. Consequently, motivation exists toward developing a fully regenerative technology for spacesuit environmental control. The application of solid amine materials with vacuum swing adsorption technology has shown the capacity to control CO2 while concomitantly managing humidity levels through a fully regenerative cycle eliminating constraints imposed with the traditional technologies. Prototype air revitalization units employing this technology have been fabricated in both a rectangular and cylindrical geometry. Experimental results for these test articles have been collected and are described herein. In order to accelerate the developmental efforts, an axially-dispersed plug flow model with an accompanying energy balance has been established and correlated with the experimental data. The experimental and simulation results display good agreement for a variety of flow rates (110-170 ALM), replicated metabolic challenges (100-590 Watts), and atmosphere pressures under consideration for the spacesuit (248 and 760 mm Hg). The testing and model results lend insight into the operational capabilities of these devices as well as the influence the geometry of the device has on performance. In addition, variable metabolic profiles were imposed on the test articles in order to assess the ability of the technology to transition to new metabolic conditions. The advent of the model provides the capacity to apply

  2. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Wenjun, E-mail: wjzheng@buffalo.edu; Glenn, Paul [Department of Physics, University at Buffalo, Buffalo, New York 14260 (United States)

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  3. Understanding Atom Probe Tomography of Oxide-Supported Metal Nanoparticles by Correlation with Atomic-Resolution Electron Microscopy and Field Evaporation Simulation.

    Science.gov (United States)

    Devaraj, Arun; Colby, Robert; Vurpillot, François; Thevuthasan, Suntharampillai

    2014-04-17

    Oxide-supported metal nanoparticles are widely used in heterogeneous catalysis. The increasingly detailed design of such catalysts necessitates three-dimensional characterization with high spatial resolution and elemental selectivity. Laser-assisted atom probe tomography (APT) is uniquely suited to the task but faces challenges with the evaporation of metal/insulator systems. Correlation of APT with aberration-corrected scanning transmission electron microscopy (STEM), for Au nanoparticles embedded in MgO, reveals preferential evaporation of the MgO and an inaccurate assessment of nanoparticle composition. Finite element field evaporation modeling is used to illustrate the evolution of the evaporation front. Nanoparticle composition is most accurately predicted when the MgO is treated as having a locally variable evaporation field, indicating the importance of considering laser-oxide interactions and the evaporation of various molecular oxide ions. These results demonstrate the viability of APT for analysis of oxide-supported metal nanoparticles, highlighting the need for developing a theoretical framework for the evaporation of heterogeneous materials.

  4. New ways to boost molecular dynamics simulations

    NARCIS (Netherlands)

    Krieger, E.; Vriend, G.

    2015-01-01

    We describe a set of algorithms that allow to simulate dihydrofolate reductase (DHFR, a common benchmark) with the AMBER all-atom force field at 160 nanoseconds/day on a single Intel Core i7 5960X CPU (no graphics processing unit (GPU), 23,786 atoms, particle mesh Ewald (PME), 8.0 A cutoff, correct

  5. Simulation and comparison of forest carbon sequestration in the United States and China in recent decades

    Science.gov (United States)

    Liu, Jinxun; Sleeter, Benjamin; Zhu, Zhiliang; Hawbaker, Todd; Zhu, Qiuan; Ju, Weimin; Wilson, Tamara; Sherba, Jason; Xin, Xiaoping; Gong, Peng; Chen, Jing

    2016-04-01

    Terrestrial ecosystems sequester roughly 30% of anthropogenic carbon emissions globally. While climate change is believed to drive ecosystem carbon cycles, land use and land cover (LULC) changes are becoming increasingly recognized as dominant drivers as well. The United States and China are the top two CO2 emitting countries in the world. On the other hand, the two countries both have tremendous land extent and thus enormous potential to sequester carbon. In this study, we focused on quantifying and comparing the climate effect and the LULC change effect on forest carbon sequestration in the two countries. The process-based Integrated Biosphere Simulator (IBIS) was used to simulate the effects of atmospheric CO2 fertilization, nitrogen deposition, climate change, fire disturbance, logging, and deforestation/reforestation on ecosystem carbon changes. Output variables included carbon stocks, such as live and dead biomass, and carbon fluxes, such as fire carbon combustion, logging removal, net ecosystem productivity (NPP) and net biome productivity (NBP). A comprehensive environmental input spatial dataset (1-km to 10-km resolution) was developed and used in IBIS, which included land cover change information derived from the Landsat data archive (1973 -2010), wildland fire scar and burn severity information (1984-2010), forest canopy percentage and live biomass (~2000), spatially heterogeneous atmospheric CO2 concentration and nitrogen deposition (2003-2009), and newly available climate and soil variables. In addition, forest field inventory data were used to calibrate the IBIS model. Initial comparison of results indicate that although the two countries have significant differences in forest land area, forest age structure, biomass stock level, and disturbance type, the overall annual carbon sequestration rates are comparable.

  6. Development and Evaluation of High-Resolution Climate Simulations Over the Mountainous Northeastern United States

    Science.gov (United States)

    Winter, Jonathan M.; Beckage, Brian; Bucini, Gabriela; Horton, Radley M.; Clemins, Patrick J.

    2016-01-01

    The mountain regions of the northeastern United States are a critical socioeconomic resource for Vermont, New York State, New Hampshire, Maine, and southern Quebec. While global climate models (GCMs) are important tools for climate change risk assessment at regional scales, even the increased spatial resolution of statistically downscaled GCMs (commonly approximately 1/ 8 deg) is not sufficient for hydrologic, ecologic, and land-use modeling of small watersheds within the mountainous Northeast. To address this limitation, an ensemble of topographically downscaled, high-resolution (30"), daily 2-m maximum air temperature; 2-m minimum air temperature; and precipitation simulations are developed for the mountainous Northeast by applying an additional level of downscaling to intermediately downscaled (1/ 8 deg) data using high-resolution topography and station observations. First, observed relationships between 2-m air temperature and elevation and between precipitation and elevation are derived. Then, these relationships are combined with spatial interpolation to enhance the resolution of intermediately downscaled GCM simulations. The resulting topographically downscaled dataset is analyzed for its ability to reproduce station observations. Topographic downscaling adds value to intermediately downscaled maximum and minimum 2-m air temperature at high-elevation stations, as well as moderately improves domain-averaged maximum and minimum 2-m air temperature. Topographic downscaling also improves mean precipitation but not daily probability distributions of precipitation. Overall, the utility of topographic downscaling is dependent on the initial bias of the intermediately downscaled product and the magnitude of the elevation adjustment. As the initial bias or elevation adjustment increases, more value is added to the topographically downscaled product.

  7. A CALCULATION OF SEMI-EMPIRICAL ONE-ELECTRON WAVE FUNCTIONS FOR MULTI-ELECTRON ATOMS USED FOR ELEMENTARY PROCESS SIMULATION IN NONLOCAL PLASMA

    Directory of Open Access Journals (Sweden)

    M. V. Tchernycheva

    2017-01-01

    Full Text Available Subject of Research. The paper deals with development outcomes for creation method of one-electron wave functions of complex atoms, relatively simple, symmetrical for all atom electrons and free from hard computations. The accuracy and resource intensity of the approach are focused on systematic calculations of cross sections and rate constants of elementary processes of inelastic collisions of atoms or molecules with electrons (ionization, excitation, excitation transfer, and others. Method. The method is based on a set of two iterative processes. At the first iteration step the Schrödinger equation was solved numerically for the radial parts of the electron wave functions in the potential of the atomic core self-consistent field. At the second iteration step the new approximationfor the atomic core field is created that uses found solutions for all one-electron wave functions. The solution optimization for described multiparameter problem is achieved by the use of genetic algorithm. The suitability of the developed method was verified by comparing the calculation results with numerous data on the energies of atoms in the ground and excited states. Main Results. We have created the run-time version of the program for creation of sets of one-electron wave functions and calculation of the cross sections and constants of collisional transition rates in the first Born approximation. The priori available information about binding energies of the electrons for any many-particle system for creation of semi-empirical refined solutions for the one-electron wave functions can be considered at any step of this procedure. Practical Relevance. The proposed solution enables a simple and rapid preparation of input data for the numerical simulation of nonlocal gas discharge plasma. The approach is focused on the calculation of discharges in complex gas mixtures requiring inclusion in the model of a large number of elementary collisional and radiation

  8. Ge Implantation to Improve Crystallinity and Productivity for Solid Phase Epitaxy Prepared by Atomic Mass Unit Cross Contamination-Free Technique

    Science.gov (United States)

    Lee, Kong-Soo; Yoo, Dae-Han; Han, Jae-Jong; Son, Gil-Hwan; Lee, Chang-Hun; Noh, Ju-Hee; Kim, Seok-Jae; Kim, Yong-Kwon; You, Young-Sub; Hyung, Yong-Woo; Lee, Hyeon-Deok

    2006-11-01

    Germanium (Ge) ion implantation was investigated for crystallinity enhancement during solid phase epitaxial (SPE) regrowth. Electron back-scatter diffraction (EBSD) measurement showed numerical increase of 19% of (100) signal, which might be due to the effect of pre-amorphization implantation (PAI) on silicon layer. On the other hand, electrical property such as off-leakage current of n-channel metal oxide semiconductor (NMOS) transistor degraded in specific regions of wafers. It was confirmed that arsenic (As) atoms were incorporated into channel area during Ge ion implantation. Since the equipment for Ge PAI was using several source gases such as BF3 and AsH3, atomic mass unit (AMU) contamination during PAI of Ge with AMU 74 caused the incorporation of As with AMU 75 which resided in arc-chamber and other parts of the equipment. It was effective to use Ge isotope of AMU 72 to suppress AMU contamination. It was effective to use enriched Ge source gas with AMU 72 in order to improve productivity.

  9. Solid-fluid and solid-solid equilibrium in hard sphere united atom models of n-alkanes: rotator phase stability.

    Science.gov (United States)

    Cao, M; Monson, P A

    2009-10-22

    We present a study of the phase behavior for models of n-alkanes with chain lengths up to C(21) based on hard sphere united atom models of methyl and methylene groups, with fixed bond lengths and C-C-C bond angles. We extend earlier work on such models of shorter alkanes by allowing for gauche conformations in the chains. We focus particularly on the orientational order about the chain axes in the solid phase near the melting point, and our model shows how the loss of this orientational order leads to the formation of rotator phases. We have made extensive calculations of the thermodynamic properties of the models as well as order parameters for tracking the degree of orientational order around the chain axis. Depending on the chain length and whether the carbon number is even or odd, the model exhibits both a rotator phase and a more orientationally ordered solid phase in addition to the fluid phase. Our results indicate that the transition between the two solid phases is first-order with a small density change. The results are qualitatively similar to those seen experimentally and show that rotator phases can appear in models of alkanes without explicit treatment of attractive forces or explicit treatment of the hydrogen atoms in the chains.

  10. Energy and Density Analyses of the 1Σu+ States in the H2 Molecule from the United Atom to Dissociation

    Science.gov (United States)

    Corongiu, Giorgina; Clementi, Enrico

    2009-07-01

    The 1Σu+ excited states of the H2 molecule are computed following a recent study by Corongiu and Clementi (J. Chem. Phys. 2009, 131, 034301) on the 1Σg+ states. Full configuration interaction computations both from Hartree-Fock molecular orbitals and Heitler-London atomic orbitals are presented and correlated with a comprehensive analysis. The basis sets utilized are either extended and optimized Slater type functions, STO, or spherical Gaussian functions, GTO. Computations and analyses are presented for states 1 to 14, covering the internuclear distances from 0.01 to 10000 bohr. The accurate data by L. Wolniewicz and collaborators, available for the first six excited states, verify the good quality of our computations. We focus on the characterization of the orbitals in the excited state wave functions, on the electronic density evolution from the united atom to dissociation, on quantitative decomposition of the total energy into covalent and ionic components and on detailed analyses of energy contributions to the total state energy from selected STO subsets. Each manifold has one state, specifically the states 1, 3 and 6, where the second minimum has strong ionic character. State 10 dissociates into the ion pair H+H-.

  11. Energy and density analyses of the 1Sigma(u)+ states in the H2 molecule from the united atom to dissociation.

    Science.gov (United States)

    Corongiu, Giorgina; Clementi, Enrico

    2009-12-31

    The 1Sigma(u)+ excited states of the H2 molecule are computed following a recent study by Corongiu and Clementi (J. Chem. Phys. 2009, 131, 034301) on the 1Sigma(g)+ states. Full configuration interaction computations both from Hartree-Fock molecular orbitals and Heitler-London atomic orbitals are presented and correlated with a comprehensive analysis. The basis sets utilized are either extended and optimized Slater type functions, STO, or spherical Gaussian functions, GTO. Computations and analyses are presented for states 1 to 14, covering the internuclear distances from 0.01 to 10000 bohr. The accurate data by L. Wolniewicz and collaborators, available for the first six excited states, verify the good quality of our computations. We focus on the characterization of the orbitals in the excited state wave functions, on the electronic density evolution from the united atom to dissociation, on quantitative decomposition of the total energy into covalent and ionic components and on detailed analyses of energy contributions to the total state energy from selected STO subsets. Each manifold has one state, specifically the states 1, 3 and 6, where the second minimum has strong ionic character. State 10 dissociates into the ion pair H+H-.

  12. Computer-assisted learning and simulation lab with 40 DentSim units.

    Science.gov (United States)

    Welk, A; Maggio, M P; Simon, J F; Scarbecz, M; Harrison, J A; Wicks, R A; Gilpatrick, R O

    2008-01-01

    There are an increasing number of studies about the computer-assisted dental patient simulator DentSim (DenX, Israel), by which dental students can acquire cognitive motor skills in a multimedia environment. However, only a very few studies have been published dealing with efficient ways to use and to manage a computer-assisted dental simulation lab with 40 DentSim units. The current approach and optimization steps of the College of Dentistry at the University of Tennessee Health Science Center were evaluated based on theoretical and practical tests and by questionnaires (partial 5-point Likert scale). Half of the D1 (first-year) students (2004/05) already had experience with computer-assisted learning at their undergraduate college and most of the students even expected to be taught via computer-assisted learning systems (83.5%) at the dental school. 87.3% of the students working with DentSim found the experience to be very interesting or interesting. Before the students carried out the preparation exercises, they were trained in the skills they needed to work with the sophisticated technology, eg, system-specific operation skills (66.6% attained maximal reachable points) and information searching skills (79.5% attained maximal reachable points). The indirect knowledge retention rate / incidental learning rate of the preparation exercises in the sense of computer-assisted problem-oriented learning regarding anatomy, preparation procedures, and cavity design was promising. The wide- ranging number of prepared teeth needed to acquire the necessary skills shows the varied individual learning curves of the students. The acceptance of, and response to, additional elective training time in the computer-assisted simulation lab were very high. Integrating the DentSim technology into the existing curriculum is a way to improve dental education, but it is also a challenge for both teachers and the students. It requires a shift in both curriculum and instructional goals that

  13. Dynamic simulation of industrial Fluidized-bed Catalytic Cracking - FCC unit

    Energy Technology Data Exchange (ETDEWEB)

    Secchi, Argimiro R.; Neumann, Gustavo A.; Trierweiler, Jorge O. [Rio Grande do Sul Univ., Porto Alegre, RS (Brazil). Dept. de Engenharia Quimica]. E-mail: arge@enq.ufrgs.br; gneumann@enq.ufrgs.br; jorge@enq.ufrgs.br; Santos, Marlova G. [PETROBRAS S.A., Canoas, RS (Brazil). Refinaria Alberto Pasqualini]. E-mail: marlova@petrobras.com.br

    2000-07-01

    In this work a mathematical model for the dynamic simulation of the Fluidized-bed Catalytic Cracking (FCC) Reactor, to be used in the analysis, control, and optimization of this system is developed. Based on the full range of published data in FCC performance and kinetic rates, and adapted to the industrial unit of the PETROBRAS' Alberto Pasqualini Refinery (REFAP), an integrated dynamic model is build up. The model is sufficiently complex to capture the major dynamics effects that occur in this system. The regenerator is modeled as emulsion and bubble phases that exchange mass and heat. The riser is modeled as an adiabatic plug flow reactor. The fluid dynamic is taking into account for the catalyst circulation, and the dynamics of the gas phase and the riser are also considered into the model. The model, represented by a non-linear system of differential-algebraic equations, was written in language C and implemented in MATLAB/SIMULINK. The results are compared with the data obtained from the industrial plant of REFAP. (author)

  14. Improving streamflow simulations in the Western United States via ensemble snow data assimilation

    Science.gov (United States)

    Huang, C.; Newman, A. J.; Clark, M. P.; Wood, A. W.; Zheng, X.

    2015-12-01

    The seasonal snowpack is a critical source of water in the western US. Past studies of snow data assimilation (DA) show that the better estimates of snow have the potential to enhance the precision of runoff prediction. In this study we select nine basins across the western United States, with a clear snow cover period and supporting snow water equivalent (SWE) measuring gauges, to test the ability of DA of SWE to improve streamflow simulations made with the coupled Snow17 and Sacramento Soil Moisture Accounting (SAC) models. We find that the relatively drier basins with little snow or runoff and basins with relatively complex snow runoff dynamics have less potential for improvement using SWE DA. For the higher potential basins, sensitivity analysis of the Ensemble Kalman Filter (EnKF) DA behavior shows that the correct estimation of SWE mean value is more important than accurately estimating of observed and forecasted error variance, which nonetheless can strongly influence SWE DA performance. This presentation describes key findings from the study, and also comments on different strategies for representing observed SWE, which typically differs from modeled SWE, in performing SWE DA.

  15. Simulation team training for improved teamwork in an intensive care unit.

    Science.gov (United States)

    Sandahl, Christer; Gustafsson, Helena; Wallin, Carl-Johan; Meurling, Lisbet; Øvretveit, John; Brommels, Mats; Hansson, Johan

    2013-01-01

    This study aims to describe implementation of simulator-based medical team training and the effect of this programme on inter-professional working in an intensive care unit (ICU). Over a period of two years, 90 percent (n = 152) of the staff of the general ICU at Karolinska University Hospital, Huddinge, Sweden, received inter-professional team training in a fully equipped patient room in their own workplace. A case study method was used to describe and explain the planning, formation, and results of the training programme. In interviews, the participants reported that the training had increased their awareness of the importance of effective communication for patient safety. The intervention had even had an indirect impact by creating a need to talk, not only about how to communicate efficaciously, but also concerning difficult care situations in general. This, in turn, had led to regular reflection meetings for nurses held three times a week. Examples of better communication in acute situations were also reported. However, the findings indicate that the observed improvements will not last, unless organisational features such as staffing rotas and scheduling of rounds and meetings can be changed to enable use of the learned behaviours in everyday work. Other threats to sustainability include shortage of staff, overtime for staff, demands for hospital beds, budget cuts, and poor staff communication due to separate meetings for nurses and physicians. The present results broaden our understanding of how to create and sustain an organizational system that supports medical team training.

  16. Two-Dimensional Simulation of Mass Transfer in Unitized Regenerative Fuel Cells under Operation Mode Switching

    Directory of Open Access Journals (Sweden)

    Lulu Wang

    2016-01-01

    Full Text Available A two-dimensional, single-phase, isothermal, multicomponent, transient model is built to investigate the transport phenomena in unitized regenerative fuel cells (URFCs under the condition of switching from the fuel cell (FC mode to the water electrolysis (WE mode. The model is coupled with an electrochemical reaction. The proton exchange membrane (PEM is selected as the solid electrolyte of the URFC. The work is motivated by the need to elucidate the complex mass transfer and electrochemical process under operation mode switching in order to improve the performance of PEM URFC. A set of governing equations, including conservation of mass, momentum, species, and charge, are considered. These equations are solved by the finite element method. The simulation results indicate the distributions of hydrogen, oxygen, water mass fraction, and electrolyte potential response to the transient phenomena via saltation under operation mode switching. The hydrogen mass fraction gradients are smaller than the oxygen mass fraction gradients. The average mass fractions of the reactants (oxygen and hydrogen and product (water exhibit evident differences between each layer in the steady state of the FC mode. By contrast, the average mass fractions of the reactant (water and products (oxygen and hydrogen exhibit only slight differences between each layer in the steady state of the WE mode. Under either the FC mode or the WE mode, the duration of the transient state is only approximately 0.2 s.

  17. Cycle simulation of the low-temperature triple-effect absorption chiller with vapor compression unit

    Energy Technology Data Exchange (ETDEWEB)

    Kim, J.S.; Lee, H.

    1999-07-01

    The construction of a triple-effect absorption chiller machine using the lithium bromide-water solution as a working fluid is strongly limited by corrosion problems caused by the high generator temperature. In this work, three new cycles having the additional vapor compression units were suggested in order to lower the generator temperature of a triple-effect absorption chiller. Each new cycle has one compressor located at the different position which was used to elevate the pressure of the refrigerant vapor. Computer simulations were carried out in order to examine both the basic triple-effect cycle and three new cycles. All types of triple-effect absorption chiller cycles were found to be able to lower the temperature of high-temperature generator to the more favorable operation range. The COPs of three cycles calculated by considering the additional compressor works showed a small level of decrease or increase compared with that of the basic triple-effect cycle. Consequently, a low-temperature triple-effect absorption chiller can be possibly constructed by adapting one of three new cycles. A great advantage of these new cycles over the basic one is that the conventionally used lithium bromide-water solution can be successfully used as a working fluid without the danger of corrosion.

  18. Critical evaluation of the nonradiological environmental technical specifications. Volume 3. Peach Bottom Atomic Power Station Units 2 and 3

    Energy Technology Data Exchange (ETDEWEB)

    Adams, S.M.; Cunningham, P.A.; Gray, D.D.; Kumar, K.D.; Witten, A.J.

    1976-08-10

    A comprehensive study of the data collected as part of the environmental Technical Specifications program for Units 2 and 3 of the Peach Bottom Nuclear Power Plant was conducted for the Office of Regulatory Research of the U.S. Nuclear Regulatory Commission. The program included an analysis of both the hydrothermal and ecological monitoring data collected from 1967 through 1976. Specific recommendations are made for improving both the present hydrothermal and ecological monitoring programs. Hydrothermal monitoring would be improved by more complete reporting of in-plant operating parameters. In addition, the present boat surveys could be discontinued, and monitoring efforts could be directed toward expanding the present thermograph network. Ecological monitoring programs were judged to be of high quality because standardized collection techniques, consistent reporting formats, and statistical analyses were performed on all of the data and were presented in an annual report. Sampling for all trophic groups was adequate for the purposes of assessing power plant induced perturbations. Considering the extensive period of preoperational data (six years) and operational data (three years) available for analysis, consideration could be given to reducing monitoring effort after data have been collected for a period when both units are operating at full capacity. In this way, an assessment of the potential ecological impact of the Peach Bottom facility can be made under conditions of maximum plant induced perturbations.

  19. High performance direct gravitational N-body simulations on graphics processing units II: An implementation in CUDA

    NARCIS (Netherlands)

    Belleman, R.G.; Bédorf, J.; Portegies Zwart, S.F.

    2008-01-01

    We present the results of gravitational direct N-body simulations using the graphics processing unit (GPU) on a commercial NVIDIA GeForce 8800GTX designed for gaming computers. The force evaluation of the N-body problem is implemented in "Compute Unified Device Architecture" (CUDA) using the GPU to

  20. High performance direct gravitational N-body simulations on graphics processing units II: An implementation in CUDA

    NARCIS (Netherlands)

    Belleman, R.G.; Bédorf, J.; Portegies Zwart, S.F.

    2008-01-01

    We present the results of gravitational direct N-body simulations using the graphics processing unit (GPU) on a commercial NVIDIA GeForce 8800GTX designed for gaming computers. The force evaluation of the N-body problem is implemented in "Compute Unified Device Architecture" (CUDA) using the GPU to

  1. Synthesis-atomic structure-properties relationships in metallic nanoparticles by total scattering experiments and 3D computer simulations: case of Pt-Ru nanoalloy catalysts

    Science.gov (United States)

    Prasai, Binay; Ren, Yang; Shan, Shiyao; Zhao, Yinguang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian; Petkov, Valeri

    2015-04-01

    An approach to determining the 3D atomic structure of metallic nanoparticles (NPs) in fine detail and using the unique knowledge obtained for rationalizing their synthesis and properties targeted for optimization is described and exemplified on Pt-Ru alloy NPs of importance to the development of devices for clean energy conversion such as fuel cells. In particular, PtxRu100-x alloy NPs, where x = 31, 49 and 75, are synthesized by wet chemistry and activated catalytically by a post-synthesis treatment involving heating under controlled N2-H2 atmosphere. So-activated NPs are evaluated as catalysts for gas-phase CO oxidation and ethanol electro-oxidation reactions taking place in fuel cells. Both as-synthesized and activated NPs are characterized structurally by total scattering experiments involving high-energy synchrotron X-ray diffraction coupled to atomic pair distribution functions (PDFs) analysis. 3D structure models both for as-synthesized and activated NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modelling Sutton-Chen method. Models are refined against the experimental PDF data by reverse Monte Carlo simulations and analysed in terms of prime structural characteristics such as metal-to-metal bond lengths, bond angles and first coordination numbers for Pt and Ru atoms. Analysis indicates that, though of a similar type, the atomic structure of as-synthesized and respective activated NPs differ in several details of importance to NP catalytic properties. Structural characteristics of activated NPs and data for their catalytic activity are compared side by side and strong evidence found that electronic effects, indicated by significant changes in Pt-Pt and Ru-Ru metal bond lengths at NP surface, and practically unrecognized so far atomic ensemble effects, indicated by distinct stacking of atomic layers near NP surface and prevalence of particular configurations of Pt and Ru atoms in these layers, contribute to the

  2. Chemical Kinetics of Hydrogen Atom Abstraction from Allylic Sites by (3)O2; Implications for Combustion Modeling and Simulation.

    Science.gov (United States)

    Zhou, Chong-Wen; Simmie, John M; Somers, Kieran P; Goldsmith, C Franklin; Curran, Henry J

    2017-03-09

    Hydrogen atom abstraction from allylic C-H bonds by molecular oxygen plays a very important role in determining the reactivity of fuel molecules having allylic hydrogen atoms. Rate constants for hydrogen atom abstraction by molecular oxygen from molecules with allylic sites have been calculated. A series of molecules with primary, secondary, tertiary, and super secondary allylic hydrogen atoms of alkene, furan, and alkylbenzene families are taken into consideration. Those molecules include propene, 2-butene, isobutene, 2-methylfuran, and toluene containing the primary allylic hydrogen atom; 1-butene, 1-pentene, 2-ethylfuran, ethylbenzene, and n-propylbenzene containing the secondary allylic hydrogen atom; 3-methyl-1-butene, 2-isopropylfuran, and isopropylbenzene containing tertiary allylic hydrogen atom; and 1-4-pentadiene containing super allylic secondary hydrogen atoms. The M06-2X/6-311++G(d,p) level of theory was used to optimize the geometries of all of the reactants, transition states, products and also the hinder rotation treatments for lower frequency modes. The G4 level of theory was used to calculate the electronic single point energies for those species to determine the 0 K barriers to reaction. Conventional transition state theory with Eckart tunnelling corrections was used to calculate the rate constants. The comparison between our calculated rate constants with the available experimental results from the literature shows good agreement for the reactions of propene and isobutene with molecular oxygen. The rate constant for toluene with O2 is about an order magnitude slower than that experimentally derived from a comprehensive model proposed by Oehlschlaeger and coauthors. The results clearly indicate the need for a more detailed investigation of the combustion kinetics of toluene oxidation and its key pyrolysis and oxidation intermediates. Despite this, our computed barriers and rate constants retain an important internal consistency. Rate constants

  3. Atomic-scale computer simulation for early precipitation process of Ni75AlxV25-x alloy with intermediate Al composition

    Institute of Scientific and Technical Information of China (English)

    ZHAO Yuhong; JU Dongying; CHEN Zheng; HOU Hua

    2005-01-01

    The microscopic phase-field approach is applied to model the early precipitation process of Ni75AlxV25-x alloy. Without any prior assumptions, this model can be used to simulate the temporal evolution of arbitrary morphologies and microstructures on atomic scale. By simulating the atomic pictures, and calculating the order parameters and volume fraction of the θ (Ni3V) and γ'(Ni3Al) ordered phases, we study Ni75AlxV25-x alloys with Al composition of 0.05, 0. 053 and 0. 055 (atom fraction). Our calculated results show that,for these alloys, θ and γ' phases precipitate at the same time; with the increase of Al content, the amount of γ' phase increases and that of θ phase decreases; the precipitation characteristic of γ' phase transforms from Non-Classical Nucleation and Growth (NCNG) to Congruent Ordering + Spinodal Decomposition (CO + SD) gradually; otherwise, the precipitation characteristic of θ phase transforms from Congruent Ordering + Spinodal Decomposition (CO+ SD) to Non-Classical Nucleation and Growth (NCNG) mechanism gradually. Both θ and γ' phases have undergone the transition process of mixture precipitation mechanism characterized by both NCNG and CO + SD mechanisms. No incontinuous transition of precipitation mechanism has been found.

  4. Atomic rivals

    Energy Technology Data Exchange (ETDEWEB)

    Goldschmidt, B.

    1990-01-01

    This book is a memoir of rivalries among the Allies over the bomb, by a participant and observer. Nuclear proliferation began in the uneasy wartime collaboration of the United States, England, Canada, and Free France to produce the atom bomb. Through the changes of history, a young French chemist had a role in almost every act of this international drama. This memoir is based on Goldschmidt's own recollections, interviews with other leading figures, and 3,000 pages of newly declassified documents in Allied archives. From his own start as Marie Curie's lab assistant, Goldschmidt's career was closely intertwined with Frances complicated rise to membership in the nuclear club. As a refugee from the Nazis, he became part of the wartime nuclear energy project in Canada and found himself the only French scientist to work (although briefly) on the American atom bomb project.

  5. Atomic scale KMC simulation of {100} oriented CVD diamond film growth under low substrate temperature—Part Ⅰ Simulation of CVD diamond film growth under Joe-Badgwell-Hauge model

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The growth of {100} oriented CVD (Chemical Vapor Deposition)diamond film under Joe-Badgwell-Hauge (J-B-H) model is simulated at atomic scale by using revised KMC (Kinetic Monte Carlo) method. The results show that: (1) under Joe's model, the growth mechanism from single carbon species is suitable for the growth of {100} oriented CVD diamond film in low temperature; (2) the deposition rate and surface roughness () under Joe's model are influenced intensively by temperature ()and not evident bymass fraction of atom chlorine; (3)the surface roughness increases with the deposition rate, i.e. the film quality becomes worse with elevated temperature, in agreement with Grujicic's prediction; (4) the simulation results cannot make sure the role of single carbon insertion.

  6. Atomic scale KMC simulation of {100} oriented CVD diamond film growth under low substrate temperature-Part II Simulation of CVD diamond film growth in C-H system and in Cl-containing systems

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The growth of {100}-oriented CVD diamond film under two modifications of J-B-H model at low substrate temperatures was simulated by using a revised KMC method at atomic scale. The results were compared both in Cl-containing systems and in C-H system as follows: (1) Substrate temperature can produce an important effect both on film deposition rate and on surface roughness; (2) Aomic Cl takes an active role for the growth of diamond film at low temperatures; (3) {100}-oriented diamond film cannot deposit under single carbon insertion mechanism, which disagrees with the predictions before; (4) The explanation of the exact role of atomic Cl is not provided in the simulation results.

  7. Atomic scale KMC simulation of {100} oriented CVD diamond film growth under low substrate temperature—Part I simulation of CVD diamond film growth under Joe—Badgwell—Hauge model

    Institute of Scientific and Technical Information of China (English)

    Xizhong; YuZhang; 等

    2002-01-01

    The growth of {100} oriented CVD( Chemical Vapor Deposition) diamond film under Joe-Badgwell-Hauge(J-B-H) model is simulated at atomic scale by using revised KMC(Kinetic Monte Carlo)method.The results show that:(1) under Joe's model,the growth mechanism from single carbon species is suitable for the growth of {100} oriented CVD diamond film in low temperature;(2) the deposition rate and surface roughness(Rq) under Joe's model are influenced intensively by temperature(Ts) and not evident bymass fraction Wc1 of atom chlorine;(3) the surface roughness increases with the deposition rate.i.e.the film quality becomes worse with elevated temperature,in agreement with Grujicic's prediction;(4) the simulation results cannot make sure the role of single carbon insertion.

  8. Modelling, experimentation and simulation of a reversible HP/ORC unit to get a Positive Energy Building

    DEFF Research Database (Denmark)

    Dumont, Olivier; Carmo, Carolina; Quoilin, Sylvain

    2015-01-01

    covering the building annual heating needs and, furthermore, electricity is produced thanks to the surplus of heat in a so-called HP/ORC reversible unit. This paper focus on these three main points: sizing, experimentation and simulation of the reversible unit. First, an optimal sizing of the components...... storage, the solar roof and the reversible HP/ORC unit is developed and allows to perform a sensivity analysis. Annual results show that this technology leads to a Positive Energy Building....... and fluid R134a shows promising performance with a net electrical energy produced over one year reaching 4030 kWh. Following that, a prototype has been built and has proven the feasibility of the technology. Finally, a simulation code including the building, the ground heat exchanger, the thermal energy...

  9. Energy and density analysis of the H2 molecule from the united atom to dissociation: the 3Sigma(g)+ and 3Sigma(u)+ states.

    Science.gov (United States)

    Corongiu, Giorgina; Clementi, Enrico

    2009-11-14

    The first 14 (3)Sigma(g)(+) and the first 15 (3)Sigma(u)(+) states of the H(2) molecule are computed with full configuration interaction both from Hartree-Fock molecular orbitals and Heitler-London atomic orbitals within the Born-Oppenheimer approximation, following recent studies for the (1)Sigma(g)(+) and (1)Sigma(u)(+) manifolds [Corongiu and Clementi, J. Chem. Phys. 131, 034301 (2009) and J. Phys. Chem. (in press)]. The basis sets utilized are extended and optimized Slater-type functions and spherical Gaussian functions. The states considered correspond to the configurations (1s(1)nl(1)) with n from 1 to 5; the internuclear separations sample the distances from 0.01 to 10,000 bohrs. For the first three (3)Sigma(g)(+) and (3)Sigma(u)(+) states and for the fourth and fifth (3)Sigma(g)(+) states, our computed energies at the equilibrium internuclear separation, when compared to the accurate values by Staszewska and Wolniewicz and by Kołos and Rychlewski, show deviations of about 0.006 kcal/mol, a test on the quality of our computations. Motivation for this work comes not only from obtaining potential energy curves for the high excited states of H(2) but also from characterizing the electronic density evolution from the united atom to dissociation to provide a detailed analysis of the energy contributions from selected basis subsets and to quantitatively decompose the state energies into covalent and ionic components. Furthermore, we discuss the origin of the seemingly irregular patterns in potential energy curves in the two manifolds, between 4 and 6-9 bohrs--there are two systems of states: the first, from the united atom to about 4 bohrs, is represented by functions with principal quantum number higher than the one needed at dissociation; this system interacts at around 4 bohrs with the second system, which is represented by functions with principal quantum number corresponding to one of the dissociation products.

  10. An Overview of the Cooperative Effort between the United States Department of Energy and the China Atomic Energy Authority to Enhance MPC&A Inspections for Civil Nuclear Facilities in China

    Energy Technology Data Exchange (ETDEWEB)

    Ahern, Keith [U.S. Enrichment Corporation Paducah Gaseous Diffusion Plant; Daming, Liu [China Institute of Atomic Energy (CIAE); Hanley, Tim [U.S. Department of Energy, NNSA; Livingston, Linwood [Pacific Northwest National Laboratory (PNNL); McAninch, Connie [U.S. Department of Energy, NNSA; McGinnis, Brent R [ORNL; Ning, Shen [China Institute of Atomic Energy (CIAE); Qun, Yang [China Institute of Atomic Energy (CIAE); Roback, Jason William [ORNL; Tuttle, Glenn [U.S. Nuclear Regulatory Commission; Xuemei, Gao [China Institute of Atomic Energy (CIAE); Galer, Regina [U.S. National Nuclear Security Administration; Peterson, Nancy [U.S. National Nuclear Security Administration; Jia, Jinlie [China Atomic Energy Authority (CAEA)

    2011-01-01

    The United States Department of Energy, National Nuclear Security Administration (DOE/NNSA) and the China Atomic Energy Authority (CAEA) are cooperating to enhance the domestic regulatory inspections capacity for special nuclear material protection, control and accounting (MPC&A) requirements for civil nuclear facilities in China. This cooperation is conducted under the auspices of the Agreement between the Department of Energy of the United States of America and the State Development and Planning Commission of the People s Republic of China on Cooperation Concerning Peaceful Uses of Nuclear Technology. This initial successful effort was conducted in three phases. Phase I focused on introducing CAEA personnel to DOE and U. S. Nuclear Regulatory Commission inspection methods for U. S. facilities. This phase was completed in January 2008 during meetings in Beijing. Phase II focused on developing physical protection and material control and accounting inspection exercises that enforced U. S. inspection methods identified during Phase 1. Hands on inspection activities were conducted in the United States over a two week period in July 2009. Simulated deficiencies were integrated into the inspection exercises. The U. S. and Chinese participants actively identified and discussed deficiencies noted during the two week training course. The material control and accounting inspection exercises were conducted at the Paducah Gaseous Diffusion Plant (PGDP) in Paducah, KY. The physical protection inspection exercises were conducted at the Oak Ridge National Laboratory (ORNL) in Oak Ridge, TN. Phase III leveraged information provided under Phase I and experience gained under Phase II to develop a formal inspection guide that incorporates a systematic approach to training for Chinese MPC&A field inspectors. Additional hands on exercises that are applicable to Chinese regulations were incorporated into the Phase III training material. Phase III was completed in May 2010 at the China

  11. Shock-tube studies of atomic silicon emission in the spectral range 180 to 300 nm. [environment simulation for Jupiter probes

    Science.gov (United States)

    Prakash, S. G.; Park, C.

    1978-01-01

    Emission spectroscopy of shock-heated atomic silicon was performed in the spectral range 180 to 300 nm, in an environment simulating the ablation layer expected around a Jovian entry probe with a silica heat shield. From the spectra obtained at temperatures from 6000 to 10,000 K and electron number densities from 1 quadrillion to 100 quadrillion per cu cm, the Lorentzian line-widths were determined. The results showed that silicon lines are broadened significantly by both electrons (Stark broadening) and hydrogen atoms (Van der Waals broadening), and the combined line-widths are much larger than previously assumed. From the data, the Stark and the Van der Waals line-widths were determined for 34 silicon lines. Radiative transport through a typical shock layer was computed using the new line-width data. The computations showed that silicon emission in the hot region is large, but it is mostly absorbed in the colder region adjacent to the wall.

  12. Numerical Study of Atomized Make-up Water in Exhaust Pipe for Direct Air-cooled Unit%直接空冷机组排汽管道内雾化补水的数值研究

    Institute of Scientific and Technical Information of China (English)

    李慧君; 焦英智

    2015-01-01

    In order to reduce the heat load of the condenser and the unit cold source loss and improve the unit vacuum and thermal economy ,changing make-up water method from entering hot well directly to entering hot well after it was atomized at the appropriate location within the exhaust pipe .Taking an example of exhaust pipe of NK 600-24.2/566/56,applying the heat and mass transfer theory for air-water two-phase flow ,establishing the model of atomized make-up water for direct air-cooled unit .performing a numerical simulation about atomizing effect of different nozzle arrangement ,nozzle position ,spray direction,spray pressure and nozzle diameter by using CFD software and analyzing the temperature fields of exhaust of the best spraying effect .The results showed that: the smaller the nozzle diameter is and the higher the spray pressure is ,the more help to improve the degree of atomization ,strengthen the effect of heat and mass transfer for air-water and increase the amount of condensed steam .When the nozzles diameter is 0.3mm,spray pressure is 0.35MPa,the nozzles are arranged in the pipe centerline of 0.5m,1.5m,2.5m in a symmetrical manner on the x=4m cross section,and the spray angle with the positive x-axis in yz plane is 120°,the amount of steam condensation reaches a maximum of 0.079kg/s.%为降低空冷凝汽器的热负荷和机组冷源损失,提高机组真空和热经济性,将补水方式由直接进入热井改为在排汽管道内适当位置雾化后再进入热井。以NK600-24.2/566/566机组排汽管道为例,应用汽水两相流的传热传质理论,建立了直接空冷机组雾化补水模型。利用CFD软件对不同喷嘴位置、喷嘴角度、喷雾压力及喷嘴孔径下的雾化效果进行了数值摸拟,得到了最佳的喷嘴布置方案,并分析了最佳喷雾效果时排汽的温度场。结果表明:喷嘴孔径越小、喷雾压力越高,越有利于提高雾化程度,加强汽、液的传热传质效

  13. 氢原子斯塔克效应的结构平衡模型仿真%Structural Equation Modeling Simulation of Hydrogen Atom Stark Effect

    Institute of Scientific and Technical Information of China (English)

    周志祥

    2015-01-01

    斯塔克效应常应用于原子分子结构的研究,对氢原子进行结构平衡模型数学建模和仿真,可以准确分析氢原子在外电场作用下能级和光谱特性.传统的氢原子斯塔克效应结构平衡采用双线间隔分离模型,对原始读数和测量值的等价分析具有随机性,不能有效实现结构平衡.提出一种基于固有电偶极矩外电场分析的氢原子斯塔克效应的结构平衡模型.首先分析氢原子的原子特性,进行斯塔克效应数学建模,分析氢原子的晶体反应谱线分裂特征模型,光谱的发射是由于价电子的跃迁形成,电场一定会改变原子内部电荷的分布,得出斯塔克效应下的结构平衡和模型的能级分裂,其裂距与电场强度成正比,采用固有电偶极矩外电场分析,实现数学模型构建,并通过Matlab进行仿真实现.实验结果表明,模型能有效反映氢原子斯塔库克效应下的光谱特征,基于固有电偶极矩外电场分析,外电场能耗降低,性能稳定.%The study of Stark effect applied to atomic and molecular structure, structural balance model for mathematical modeling and Simulation of the hydrogen atom, can accurate analysis of the hydrogen atom in the level in the external elec-tric field and spectral characteristics. The traditional hydrogen atomic Stark effect structure equilibrium separation model adopts double spaced, randomness is equivalent to the original reading and analysis of the measured value, can not effec-tively to achieve structural balance. Put forward a kind of intrinsic electric dipole moment equilibrium structure analysis of external electric field of the hydrogen atom Stark effect model based on. The first atomic properties analysis of atomic and hydrogen, Stark effect on mathematical modeling, analysis of crystal reaction of hydrogen atomic spectral line splitting fea-ture model, spectral emission is due to transition of the valence electron, electric field distribution will

  14. Simulation of nitrate, sulfate, and ammonium aerosols over the United States

    Directory of Open Access Journals (Sweden)

    J. M. Walker

    2012-11-01

    Full Text Available Atmospheric concentrations of inorganic gases and aerosols (nitrate, sulfate, and ammonium are simulated for 2009 over the United States using the chemical transport model GEOS-Chem. Predicted aerosol concentrations are compared with surface-level measurement data from the Interagency Monitoring of Protected Visual Environments (IMPROVE, the Clean Air Status and Trends Network (CASTNET, and the California Air Resources Board (CARB. Sulfate predictions nationwide are in reasonably good agreement with observations, while nitrate and ammonium are over-predicted in the East and Midwest, but under-predicted in California, where observed concentrations are the highest in the country. Over-prediction of nitrate in the East and Midwest is consistent with results of recent studies, which suggest that nighttime nitric acid formation by heterogeneous hydrolysis of N2O5 is over-predicted based on current values of the N2O5 uptake coefficient, γ, onto aerosols. After reducing the value of γ by a factor of 10, predicted nitrate levels in the US Midwest and East still remain higher than those measured, and over-prediction of nitrate in this region remains unexplained. Comparison of model predictions with satellite measurements of ammonia from the Tropospheric Emissions Spectrometer (TES indicates that ammonia emissions in GEOS-Chem are underestimated in California and that the nationwide seasonality applied to ammonia emissions in GEOS-Chem does not represent California very well, particularly underestimating winter emissions. An ammonia sensitivity study indicates that GEOS-Chem simulation of nitrate is ammonia-limited in southern California and much of the state, suggesting that an underestimate of ammonia emissions is likely the main cause for the under-prediction of nitrate aerosol in many areas of California. An approximate doubling of ammonia emissions is needed to reproduce observed nitrate concentrations in

  15. Simulation of 64-bit MAC Unit using Kogge Stone Adder and Ancient Indian Mathematics

    Directory of Open Access Journals (Sweden)

    Aapurva Kaul

    2016-05-01

    Full Text Available This paper describes that multiply and accumulate (MAC unit plays a very vital role in various Digital Signal Processing applications. Speed of these applications depends on the speed of these three sub units of MAC multiply unit, adder unit and accumulator unit. In this paper the delay of 64-bit MAC unit is decreased as compared to the previous MAC units. In this Kogge Stone Adder is used as adder in design Vedic Multiplier using Urdhva Tiryakbhyam sutra. The designing of MAC unit is done under VIRTEX-4 family, XC4VFX140 device, FF1517 package and -11 speed and comparison of proposed MAC unit design is done under SPARTAN- 3E family, XC3S500 device, FG320 package and -5 speed in Xilinx ISE 8.1i. The combinational path delay of the 64-bit MAC unit is 59.705ns in SPARTAN-3E family. Ancient Indian mathematics is being used for designing of multiplier unit to decrease the overall delay of the MAC unit.

  16. Predicting the stability of atom-like and molecule-like unit-charge Coulomb three-particle systems

    Energy Technology Data Exchange (ETDEWEB)

    King, Andrew W.; Herlihy, Patrick E.; Cox, Hazel, E-mail: h.cox@sussex.ac.uk [Department of Chemistry, University of Sussex, Falmer, Brighton BN1 9QJ (United Kingdom)

    2014-07-28

    Non-relativistic quantum chemical calculations of the particle mass, m{sub 2}{sup ±}, corresponding to the dissociation threshold in a range of Coulomb three-particle systems of the form (m{sub 1}{sup ±}m{sub 2}{sup ±}m{sub 3}{sup ∓}), are performed variationally using a series solution method with a Laguerre-based wavefunction. These masses are used to calculate an accurate stability boundary, i.e., the line that separates the stability domain from the instability domains, in a reciprocal mass fraction ternary diagram. This result is compared to a lower bound to the stability domain derived from symmetric systems and reveals the importance of the asymmetric (mass-symmetry breaking) terms in the Hamiltonian at dissociation. A functional fit to the stability boundary data provides a simple analytical expression for calculating the minimum mass of a third particle required for stable binding to a two-particle system, i.e., for predicting the bound state stability of any unit-charge three-particle system.

  17. The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

    Science.gov (United States)

    Cortini, Ruggero; Cheng, Xiaolin; Smith, Jeremy C.

    2017-03-01

    Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to  ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning’s theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order of 1{{k}\\text{B}}T . Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.

  18. Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.

    Science.gov (United States)

    Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

    2012-12-07

    We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

  19. Planning intensive care unit design using computer simulation modeling: optimizing integration of clinical, operational, and architectural requirements.

    Science.gov (United States)

    OʼHara, Susan

    2014-01-01

    Nurses have increasingly been regarded as critical members of the planning team as architects recognize their knowledge and value. But the nurses' role as knowledge experts can be expanded to leading efforts to integrate the clinical, operational, and architectural expertise through simulation modeling. Simulation modeling allows for the optimal merge of multifactorial data to understand the current state of the intensive care unit and predict future states. Nurses can champion the simulation modeling process and reap the benefits of a cost-effective way to test new designs, processes, staffing models, and future programming trends prior to implementation. Simulation modeling is an evidence-based planning approach, a standard, for integrating the sciences with real client data, to offer solutions for improving patient care.

  20. Stress Domains in Si\\(111\\)/a-Si3N4 Nanopixel: Ten-Million-Atom Molecular Dynamics Simulations on Parallel Computers

    Science.gov (United States)

    Omeltchenko, Andrey; Bachlechner, Martina E.; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya; Ebbsjö, Ingvar; Madhukar, Anupam; Messina, Paul

    2000-01-01

    Parallel molecular dynamics simulations are performed to determine atomic-level stresses in Si\\(111\\)/Si3N4\\(0001\\) and Si\\(111\\)/a-Si3N4 nanopixels. Compared to the crystalline case, the stresses in amorphous Si3N4 are highly inhomogeneous in the plane of the interface. In silicon below the interface, for a 25 nm square mesa stress domains with triangular symmetry are observed, whereas for a rectangular, 54 nm×33 nm, mesa tensile stress domains \\(~300 Å\\) are separated by Y-shaped compressive domain wall. Maximum stresses in the domains and domain walls are -2 GPa and +2 GPa, respectively.

  1. Stress domains in Si(111)/a-Si3N4 nanopixel: ten-million-atom molecular dynamics simulations on parallel computers

    Science.gov (United States)

    Omeltchenko; Bachlechner; Nakano; Kalia; Vashishta; Ebbsjo; Madhukar; Messina

    2000-01-10

    Parallel molecular dynamics simulations are performed to determine atomic-level stresses in Si(111)/Si(3)N4(0001) and Si(111)/a-Si3N4 nanopixels. Compared to the crystalline case, the stresses in amorphous Si3N4 are highly inhomogeneous in the plane of the interface. In silicon below the interface, for a 25 nm square mesa stress domains with triangular symmetry are observed, whereas for a rectangular, 54 nmx33 nm, mesa tensile stress domains ( approximately 300 A) are separated by Y-shaped compressive domain wall. Maximum stresses in the domains and domain walls are -2 GPa and +2 GPa, respectively.

  2. Experimental Study of the Atomic and Molecular Processes Related to Plasma Detachment in Steady-State Divertor Simulator MAP-II

    Institute of Scientific and Technical Information of China (English)

    S.Kado; S.Kajita; Y.Iida; B.Xiao; T.Shikama; D.Yamasaki; T.Oishi; S.Tanaka

    2004-01-01

    Atomic and molecular processes relevant to the volumetric recombination phenomena were investigated in a linear divertor plasma simulator MAP-II. Volumetric recombination is induced in He plasma by puffing of He or H2. In the He puffing case, the reduction of the ion flux is dominated by the electron-ion recombination. In the H2 puffing case, however, it is dominated by the molecule-assisted recombination (MAR), which is characterized by the disappearance of the Helium Rydberg spectra and by the existence of the hydrogen negative ions. Current achievement and the future prospect are described.

  3. A Survey of Simulation Utilization in Anesthesiology Residency Programs in the United States.

    Science.gov (United States)

    Rochlen, Lauryn R; Housey, Michelle; Gannon, Ian; Tait, Alan R; Naughton, Norah; Kheterpal, Sachin

    2016-06-01

    Given the evolution of competency-based education and evidence supporting the benefits of incorporating simulation into anesthesiology residency training, simulation will likely play an important role in the training and assessment of anesthesiology residents. Currently, there are little data available regarding the current status of simulation-based curricula across US residency programs. In this study, we assessed simulation-based training and assessment in US anesthesiology programs using a survey designed to elicit information regarding the type, frequency, and content of the simulation courses offered at the 132 Accreditation Council of Graduate Medical Education-certified anesthesiology training programs. The response rate for the survey was 66%. Although most of the responding programs offered simulation-based courses for interns and residents and during CA-1 orientation, the curriculum varied greatly among programs. Approximately 40% of responding programs use simulation for resident assessment and remediation. The majority of responding programs favored standard simulation-based training as part of residency training (89%), and the most common perceived obstacles to doing so were time, money, and human resources. The results from this survey highlight that there are currently large variations in simulation-based training and assessment among training programs. It also confirms that many program directors feel that standardizing some components of simulation-based education and assessment would be beneficial. Given the positive impact simulation has on skill retention and operating room preparedness, it may be worthwhile to consider developing a standard curriculum.

  4. 3D modeling of stratigraphic units and simulation of seismic facies in the Lion gulf margin; Modelisation 3D des unites stratigraphiques et simulation des facies sismiques dans la marge du golfe du Lion

    Energy Technology Data Exchange (ETDEWEB)

    Chihi, H.

    1997-05-12

    This work aims at providing a contribution to the studies carried out on reservoir characterization by use of seismic data. The study mainly consisted in the use of geostatistical methods in order to model the geometry of stratigraphic units of the Golfe du Lion margin and to simulate the seismic facies from high resolution seismic data. We propose, for the geometric modelling, a methodology based on the estimation of the surfaces and calculation afterwards of the thicknesses, if the modelling of the depth is possible. On the other hand the method consists in estimating the thickness variable directly and in deducing the boundary surfaces afterwards. In order to simulate the distribution of seismic facies within the units of the western domain, we used the truncated Gaussian method. The used approach gave a satisfactory results, when the seismic facies present slightly dipping reflectors with respect to the reference level. Otherwise the method reaches its limits because of the problems of definition of a reference level which allows to follow the clino-forms. In spite of these difficulties, this simulation allows us to estimate the distribution of seismic facies within the units and then to deduce their probable extension. (author) 150 refs.

  5. Atom Tunneling in the Hydroxylation Process of Taurine/α-Ketoglutarate Dioxygenase Identified by Quantum Mechanics/Molecular Mechanics Simulations.

    Science.gov (United States)

    Álvarez-Barcia, Sonia; Kästner, Johannes

    2017-06-01

    Taurine/α-ketoglutarate dioxygenase is one of the most studied α-ketoglutarate-dependent dioxygenases (αKGDs), involved in several biotechnological applications. We investigated the key step in the catalytic cycle of the αKGDs, the hydrogen transfer process, by a quantum mechanics/molecular mechanics approach (B3LYP/CHARMM22). Analysis of the charge and spin densities during the reaction demonstrates that a concerted mechanism takes place, where the H atom transfer happens simultaneously with the electron transfer from taurine to the Fe═O cofactor. We found the quantum tunneling of the hydrogen atom to increase the rate constant by a factor of 40 at 5 °C. As a consequence, a quite high kinetic isotope effect close to 60 is obtained, which is consistent with the experimental value.

  6. Modeling and Simulation of the Microstructure Evolution of the Gas-atomized Alloy Droplets during Spray Forming

    Institute of Scientific and Technical Information of China (English)

    Jiuzhou ZHAO; Dongming LIU; Hengqiang YE

    2003-01-01

    In order to understand the solidification process of an atomized droplet and predict the fraction solidification ofdroplets with flight distance during spray forming, a numerical model based on the population dynamics approach isdeveloped to describe the microstructure evolution under the common action of the nucleation and growth of grains.The model is coupled with droplets heat transfer controlling equations and solved for Al-4.5 wt pct Cu alloy. It isdemonstrated that the numerical results describe the solidification process well.

  7. Gaining insight into the physics of dynamic atomic force microscopy in complex environments using the VEDA simulator

    OpenAIRE

    Kiracofe, Daniel; Melcher, John; Raman, Arvind

    2012-01-01

    Dynamic atomic force microscopy (dAFM) continues to grow in popularity among scientists in many different fields, and research on new methods and operating modes continues to expand the resolution, capabilities, and types of samples that can be studied. But many promising increases in capability are accompanied by increases in complexity. Indeed, interpreting modern dAFM data can be challenging, especially on complicated material systems, or in liquid environments where the behavior is often ...

  8. Evaluation of Thermal Control Coatings and Polymeric Materials Exposed to Ground Simulated Atomic Oxygen and Vacuum Ultraviolet Radiation

    Science.gov (United States)

    Kamenetzky, R. R.; Vaughn, J. A.; Finckenor, M. M.; Linton, R. C.

    1995-01-01

    Numerous thermal control and polymeric samples with potential International Space Station applications were evaluated for atomic oxygen and vacuum ultraviolet radiation effects in the Princeton Plasma Physics Laboratory 5 eV Neutral Atomic Oxygen Facility and in the MSFC Atomic Oxygen Drift Tube System. Included in this study were samples of various anodized aluminum samples, ceramic paints, polymeric materials, and beta cloth, a Teflon-impregnated fiberglass cloth. Aluminum anodizations tested were black duranodic, chromic acid anodize, and sulfuric acid anodize. Paint samples consisted of an inorganic glassy black paint and Z-93 white paint made with the original PS7 binder and the new K2130 binder. Polymeric samples evaluated included bulk Halar, bulk PEEK, and silverized FEP Teflon. Aluminized and nonaluminized Chemfab 250 beta cloth were also exposed. Samples were evaluated for changes in mass, thickness, solar absorptance, and infrared emittance. In addition to material effects, an investigation was made comparing diffuse reflectance/solar absorptance measurements made using a Beckman DK2 spectroreflectometer and like measurements made using an AZ Technology-developed laboratory portable spectroreflectometer.

  9. Computer simulations on resonant fluorescence spectra in atomic gases in two monochromatic laser fields of arbitrary intensity and magnetic field

    Science.gov (United States)

    Karagodova, Tamara Y.

    1996-03-01

    In the intense radiation fields with power density from 104W/cm2 to 109W/cm2 the essential modification of electronic states of atoms occurs displaying, in particular, in modifications of resonant fluorescence (rf) spectra. We use 'Fermi golden rule' for calculations of relative intensities and frequencies for rf multiplet for real multilevel initially unexcited atoms in two monochromatic laser fields of arbitrary intensity resonant to adjacent transitions of (Xi) or (Lambda) types and magnetic field, giving the level splittings of different values from Zeeman to Paschen-Back effect. The dependence of quasienergies on parameters obtained with the help of a sorting program permits us to define the values of parameters for which the states of the system are mixed and so to receive the correct probability amplitudes for instantaneous or adiabatic regimes of switching the perturbation. The analysis of the quasienergies and form of rf spectra permits us to get relations between the form of the spectra and modifications of electronic structure of the atom due to radiation fields and external magnetic field.

  10. Investigation of the on-axis atom number density in the supersonic gas jet under high gas backing pressure by simulation

    Directory of Open Access Journals (Sweden)

    Guanglong Chen

    2015-10-01

    Full Text Available The supersonic gas jets from conical nozzles are simulated using 2D model. The on-axis atom number density in gas jet is investigated in detail by comparing the simulated densities with the idealized densities of straight streamline model in scaling laws. It is found that the density is generally lower than the idealized one and the deviation between them is mainly dependent on the opening angle of conical nozzle, the nozzle length and the gas backing pressure. The density deviation is then used to discuss the deviation of the equivalent diameter of a conical nozzle from the idealized deq in scaling laws. The investigation on the lateral expansion of gas jet indicates the lateral expansion could be responsible for the behavior of the density deviation. These results could be useful for the estimation of cluster size and the understanding of experimental results in laser-cluster interaction experiments.

  11. Density functional theory (DFT)-based modified embedded atom method potentials: Bridging the gap between nanoscale theoretical simulations and DFT calculations

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A density functional theory (DFT)-calculation scheme for constructing the modified embedded atom method (MEAM) potentials for face-centered cubic (fcc) metals is presented. The input quantities are carefully selected and a more reliable DFT approach for surface energy determination is introduced in the parameterization scheme, enabling MEAM to precisely predict the surface and nanoscale properties of metallic materials. Molecular dynamics simulations on Pt and Au crystals show that the parameterization employed leads to significantly improved accuracy of MEAM in calculating the surface and nanoscale properties, with the results agreeing well with both DFT calculations and experimental observations. The present study implies that rational DFT parameterization of MEAM may lead to a theoretical tool to bridge the gap between nanoscale theoretical simulations and DFT calculations.

  12. Evaluation of SPACE code for simulation of inadvertent opening of spray valve in Shin Kori unit 1

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seyun; Youn, Bumsoo [KHNP Central Research Institute, Daejeon (Korea, Republic of)

    2013-05-15

    SPACE code is expected to be applied to the safety analysis for LOCA (Loss of Coolant Accident) and Non-LOCA scenarios. SPACE code solves two-fluid, three-field governing equations and programmed with C++ computer language using object-oriented concepts. To evaluate the analysis capability for the transient phenomena in the actual nuclear power plant, an inadvertent opening of spray valve in startup test phase of Shin Kori unit 1 was simulated with SPACE code. To evaluate the analysis capability for the transient phenomena in the actual nuclear power plant, an inadvertent opening of spray valve in startup test phase of Shin Kori unit 1 was simulated with SPACE code.

  13. Assessment of power step performances of variable speed pump-turbine unit by means of hydro-electrical system simulation

    Science.gov (United States)

    Béguin, A.; Nicolet, C.; Hell, J.; Moreira, C.

    2017-04-01

    The paper explores the improvement in ancillary services that variable speed technologies can provide for the case of an existing pumped storage power plant of 2x210 MVA which conversion from fixed speed to variable speed is investigated with a focus on the power step performances of the units. First two motor-generator variable speed technologies are introduced, namely the Doubly Fed Induction Machine (DFIM) and the Full Scale Frequency Converter (FSFC). Then a detailed numerical simulation model of the investigated power plant used to simulate power steps response and comprising the waterways, the pump-turbine unit, the motor-generator, the grid connection and the control systems is presented. Hydroelectric system time domain simulations are performed in order to determine the shortest response time achievable, taking into account the constraints from the maximum penstock pressure and from the rotational speed limits. It is shown that the maximum instantaneous power step response up and down depends on the hydro-mechanical characteristics of the pump-turbine unit and of the motor-generator speed limits. As a results, for the investigated test case, the FSFC solution offer the best power step response performances.

  14. Evaluation of interatomic potentials for noble gas atoms from rainbow scattering under axial channeling at Ag(1 1 1) surface by computer simulations based on binary collision approximation

    Energy Technology Data Exchange (ETDEWEB)

    Takeuchi, Wataru, E-mail: take@sp.ous.ac.jp

    2016-01-01

    The rainbow angles corresponding to pronounced peaks in the angular distributions of scattered projectiles with small angle, attributed to rainbow scattering (RS), under axial surface channeling conditions are strongly dependent on the interatomic potentials between projectiles and target atoms. The dependence of rainbow angles on normal energy of projectile energy to the target surface that has been experimentally obtained by Schüller and Winter (SW) (2007) for RS of He, Ne and Ar atoms from a Ag(1 1 1) surface with projectile energies of 3–60 keV was evaluated by the three-dimensional computer simulations using the ACOCT code based on the binary collision approximation with interatomic pair potentials. Consequently, the ACOCT results employing the Moliere pair potential with screening length correction close to adjustable one of O’Connor and Biersack (OB) formula are almost in agreement with the experimental ones, being self-consistent with the SW’s ones analyzed by computer simulations of classical trajectory calculations as RS from corrugated equipotential planes based on continuum potentials including the Moliere pair potential with screening length correction of the OB formula.

  15. Contribution of the North Atlantic subtropical high to regional climate model (RCM) skill in simulating southeastern United States summer precipitation

    Science.gov (United States)

    Li, Laifang; Li, Wenhong; Jin, Jiming

    2015-07-01

    This study assesses the skill of advanced regional climate models (RCMs) in simulating southeastern United States (SE US) summer precipitation and explores the physical mechanisms responsible for the simulation skill at a process level. Analysis of the RCM output for the North American Regional Climate Change Assessment Program indicates that the RCM simulations of summer precipitation show the largest biases and a remarkable spread over the SE US compared to other regions in the contiguous US. The causes of such a spread are investigated by performing simulations using the Weather Research and Forecasting (WRF) model, a next-generation RCM developed by the US National Center for Atmospheric Research. The results show that the simulated biases in SE US summer precipitation are due mainly to the misrepresentation of the modeled North Atlantic subtropical high (NASH) western ridge. In the WRF simulations, the NASH western ridge shifts 7° northwestward when compared to that in the reanalysis ensemble, leading to a dry bias in the simulated summer precipitation according to the relationship between the NASH western ridge and summer precipitation over the southeast. Experiments utilizing the four dimensional data assimilation technique further suggest that the improved representation of the circulation patterns (i.e., wind fields) associated with the NASH western ridge substantially reduces the bias in the simulated SE US summer precipitation. Our analysis of circulation dynamics indicates that the NASH western ridge in the WRF simulations is significantly influenced by the simulated planetary boundary layer (PBL) processes over the Gulf of Mexico. Specifically, a decrease (increase) in the simulated PBL height tends to stabilize (destabilize) the lower troposphere over the Gulf of Mexico, and thus inhibits (favors) the onset and/or development of convection. Such changes in tropical convection induce a tropical-extratropical teleconnection pattern, which modulates the

  16. The Chocolate Milk Crisis: A Consumer Economics Simulation Unit for Grades 1-6.

    Science.gov (United States)

    Derrico, Patricia; Karsotis, A. Thomas

    1981-01-01

    Describes a simulation game developed to introduce elementary school students to basic economic concepts, including scarcity, availability, resource utilization, trade-offs, and demand and barter. The simulation, based on a shortage of chocolate milk in the elementary school lunch room, stressed problem solving skills. (DB)

  17. Intercultural Simulation Games: A Review (of the United States and beyond)

    Science.gov (United States)

    Fowler, Sandra M.; Pusch, Margaret D.

    2010-01-01

    Intercultural simulations are instructional activities that engage and challenge participants with experiences integral to encounters between people of more than one cultural group. Simulations designed specifically to support intercultural encounters have been in use since the 1970s. This article examines the conceptual bases for intercultural…

  18. Shock-induced poration, cholesterol flip-flop and small interfering RNA transfection in a phospholipid membrane: Multimillion atom, microsecond molecular dynamics simulations

    Science.gov (United States)

    Choubey, Amit

    Biological cell membranes provide mechanical stability to cells and understanding their structure, dynamics and mechanics are important biophysics problems. Experiments coupled with computational methods such as molecular dynamics (MD) have provided insight into the physics of membranes. We use long-time and large-scale MD simulations to study the structure, dynamics and mechanical behavior of membranes. We investigate shock-induced collapse of nanobubbles in water using MD simulations based on a reactive force field. We observe a focused jet at the onset of bubble shrinkage and a secondary shock wave upon bubble collapse. The jet length scales linearly with the nanobubble radius, as observed in experiments on micron-to-millimeter size bubbles. Shock induces dramatic structural changes, including an ice-VII-like structural motif at a particle velocity of 1 km/s. The incipient ice VII formation and the calculated Hugoniot curve are in good agreement with experimental results. We also investigate molecular mechanisms of poration in lipid bilayers due to shock-induced collapse of nanobubbles. Our multimillion-atom MD simulations reveal that the jet impact generates shear flow of water on bilayer leaflets and pressure gradients across them. This transiently enhances the bilayer permeability by creating nanopores through which water molecules translocate rapidly across the bilayer. Effects of nanobubble size and temperature on the porosity of lipid bilayers are examined. The second research project focuses on cholesterol (CHOL) dynamics in phospholipid bilayers. Several experimental and computational studies have been performed on lipid bilayers consisting of dipalmitoylphosphatidylcholine (DPPC) and CHOL molecules. CHOL interleaflet transport (flip-flop) plays an important role in interleaflet coupling and determining CHOL flip-flop rate has been elusive. Various studies report that the rate ranges between milliseconds to seconds. We calculate CHOL flip-flop rates by

  19. FASIMA II - modelling and simulation of any drive unit concepts; FASIMA II - Modellierung und Simulation beliebiger Antriebsstrangkonzepte

    Energy Technology Data Exchange (ETDEWEB)

    Spoerl, T.; Flaig, A.; Lechner, G.

    1995-12-31

    In FASIMA II, the Institute for Machine Elements at the University of Stuttgart has a tool available which makes possible the examination of complex drive unit configurations. The examination of a vehicle of the compact class is introduced as an example of an application. The mass-production variant of the vehicle with a 5 speed manual gearbox was compared with two hybrid variants and a variant with a continuous variable transmission instead of the standard gearbox. It was found that hybrid drives do not necessarily lead to fuel savings. (orig.) [Deutsch] Mit FASIMA II steht am Institut fuer Maschinenelemente der Universitaet Stuttgart ein Werkzeug zur Verfuegung, das die Untersuchung auch komplexer Antriebsstrahkonfigurationen ermoeglicht. Als Anwendungsbeispiel wird eine Untersuchung eines Fahrzeugs der Kompaktklasse vorgestellt. Die Serienvariante des Fahrzeugs mit 5-Gang-Handschaltgetriebe wurde mit zwei hybriden Varianten und einer Variante mit einem CVT anstelle des Seriengetriebes verglichen. Hierbei zeigte sich, dass Hybridantriebe nicht zwangslaeufig zu Kraftstoffeinsparungen fuehren. (orig.)

  20. Simulation of the atomic and ionic densities in the ionization layer of a plasma arc with a binary cathode

    Energy Technology Data Exchange (ETDEWEB)

    Ortega, D; Marin, J A Sillero; Munoz-Serrano, E; Casado, E, E-mail: f92orhed@uco.e [Departamento de Fisica, Universidad de Cordoba, 14071 Cordoba (Spain)

    2009-04-21

    A physical model was developed to study the behaviour of the cathode material evaporated from a thoriated tungsten cathode of an atmospheric-pressure argon plasma arc. The densities of tungsten and thorium atoms and ions in the ionization layer were obtained, and the influence of the different physical processes on the evaporated cathode material was established. It was found that almost all of the neutral atoms evaporated from the cathode are ionized near the beginning of the ionization layer, i.e. near the boundary between the sheath and the ionization layer. Thorium ions are concentrated in a 4 {mu}m region near the beginning of this layer, while tungsten ions are found in a region of 9 {mu}m. The contribution of the electric force to the velocity of ions is the dominant contribution only near the beginning of the ionization layer. At a distance from the interface between the sheath and the ionization layer greater than 3.8 {mu}m in the case of thorium ions, and greater than 5 {mu}m in the case of tungsten ions, the contributions of the density gradient forces and the frictional forces are more important than the electric force contribution.

  1. Software for simulation of utilization schemes of secondary energy from the exhaust gases of metallurgical units

    Science.gov (United States)

    Olennikov, A. A.; Tsymbal, V. P.

    2016-09-01

    The work is devoted to the program complex intended for designing schemes of secondary energy utilization from metallurgical units. The structure of the software system is based on three levels of complex systems assembled from subsystems. The mathematical models of a complex process of heat transfer and gas dynamics occurring in the energy utilization units and gas cleaning devices. We describe the user interaction with the software package, and show the calculation results in the form of plots.

  2. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Das, Anuradha; Das, Suman; Biswas, Ranjit, E-mail: ranjit@bose.res.in [Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, West Bengal 700098 (India)

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH{sub 3}CONH{sub 2}) and urea (NH{sub 2}CONH{sub 2}) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH{sub 3}CONH{sub 2} + (1 − f)NH{sub 2}CONH{sub 2}] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α{sub 2}) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  3. Motion Regular Analysis and Its Simulation of the Rodless Drilling Unit's Guiding & Positioning Board

    Institute of Scientific and Technical Information of China (English)

    HU Chang-sheng; ZHAO Wei-min; MA Qiang

    2009-01-01

    To analyze the stress of the guiding & positioning board and the effectiveness of the guiding & positioning device, aeenrding to guiding & positioning device's operational principle and structure, the guiding & positioning board's motion regular was analyzed bydiagrammatical method based on 2 postulated conditions. Considering about the working conditions' change, simulations in 5 different kinds of working conditions were done to cheek the correctness of the motion regulars obtained by diagrammatical method. Simulation results prove that the motion regulars are right, the postulated conditions have no effect on the obtained motion regulars. According to the simulation results, the motion processs's characters were drawn out at the same time.

  4. Simulation of picosecond pulse propagation in fibre-based radiation shaping units

    Science.gov (United States)

    Kuptsov, G. V.; Petrov, V. V.; Laptev, A. V.; Petrov, V. A.; Pestryakov, E. V.

    2016-09-01

    We have performed a numerical simulation of picosecond pulse propagation in a combined stretcher consisting of a segment of a telecommunication fibre and diffraction holographic gratings. The process of supercontinuum generation in a nonlinear photoniccrystal fibre pumped by picosecond pulses is simulated by solving numerically the generalised nonlinear Schrödinger equation; spectral and temporal pulse parameters are determined. Experimental data are in good agreement with simulation results. The obtained results are used to design a high-power femtosecond laser system with a pulse repetition rate of 1 kHz.

  5. Massive Parallelism of Monte-Carlo Simulation on Low-End Hardware using Graphic Processing Units

    Energy Technology Data Exchange (ETDEWEB)

    Mburu, Joe Mwangi; Hah, Chang Joo Hah [KEPCO International Nuclear Graduate School, Ulsan (Korea, Republic of)

    2014-05-15

    Within the past decade, research has been done on utilizing GPU massive parallelization in core simulation with impressive results but unfortunately, not much commercial application has been done in the nuclear field especially in reactor core simulation. The purpose of this paper is to give an introductory concept on the topic and illustrate the potential of exploiting the massive parallel nature of GPU computing on a simple monte-carlo simulation with very minimal hardware specifications. To do a comparative analysis, a simple two dimension monte-carlo simulation is implemented for both the CPU and GPU in order to evaluate performance gain based on the computing devices. The heterogeneous platform utilized in this analysis is done on a slow notebook with only 1GHz processor. The end results are quite surprising whereby high speedups obtained are almost a factor of 10. In this work, we have utilized heterogeneous computing in a GPU-based approach in applying potential high arithmetic intensive calculation. By applying a complex monte-carlo simulation on GPU platform, we have speed up the computational process by almost a factor of 10 based on one million neutrons. This shows how easy, cheap and efficient it is in using GPU in accelerating scientific computing and the results should encourage in exploring further this avenue especially in nuclear reactor physics simulation where deterministic and stochastic calculations are quite favourable in parallelization.

  6. FINAL–REPORT NO. 2: INDEPENDENT CONFIRMATORY SURVEY SUMMARY AND RESULTS FOR THE ENRICO FERMI ATOMIC POWER PLANT, UNIT 1, NEWPORT, MICHIGAN (DOCKET NO. 50 16; RFTA 10-004)

    Energy Technology Data Exchange (ETDEWEB)

    Erika Bailey

    2011-07-07

    The Enrico Fermi Atomic Power Plant, Unit 1 (Fermi 1) was a fast breeder reactor design that was cooled by sodium and operated at essentially atmospheric pressure. On May 10, 1963, the Atomic Energy Commission (AEC) granted an operating license, DPR-9, to the Power Reactor Development Company (PRDC), a consortium specifically formed to own and operate a nuclear reactor at the Fermi 1 site. The reactor was designed for a maximum capability of 430 megawatts (MW); however, the maximum reactor power with the first core loading (Core A) was 200 MW. The primary system was filled with sodium in December 1960 and criticality was achieved in August 1963.

  7. Chemical gradients across phase boundaries between martensite and austenite in steel studied by atom probe tomography and simulation

    Energy Technology Data Exchange (ETDEWEB)

    Dmitrieva, O.; Ponge, D.; Inden, G.; Millan, J.; Choi, P. [Max-Planck-Institut fuer Eisenforschung, Max-Planck-Str. 1, 40237 Duesseldorf (Germany); Sietsma, J. [Delft University of Technology, Faculty 3mE, Dept. MSE, 2628 CD Delft (Netherlands); Raabe, D., E-mail: d.raabe@mpie.de [Max-Planck-Institut fuer Eisenforschung, Max-Planck-Str. 1, 40237 Duesseldorf (Germany)

    2011-01-15

    Partitioning at phase boundaries of complex steels is important for their properties. We present atom probe tomography results across martensite/austenite interfaces in a precipitation-hardened maraging-TRIP steel (12.2 Mn, 1.9 Ni, 0.6 Mo, 1.2 Ti, 0.3 Al; at.%). The system reveals compositional changes at the phase boundaries: Mn and Ni are enriched while Ti, Al, Mo and Fe are depleted. More specific, we observe up to 27 at.% Mn in a 20 nm layer at the phase boundary. This is explained by the large difference in diffusivity between martensite and austenite. The high diffusivity in martensite leads to a Mn flux towards the retained austenite. The low diffusivity in the austenite does not allow accommodation of this flux. Consequently, the austenite grows with a Mn composition given by local equilibrium. The interpretation is based on DICTRA and mixed-mode diffusion calculations (using a finite interface mobility).

  8. Cholesterol Flip-Flop Dynamics in a Phospholipid Bilayer: A 10 Microsecond All-Atom Molecular Dynamics Simulation

    Science.gov (United States)

    Choubey, Amit; Nomura, Ken-Ichi; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya

    2012-02-01

    Cholesterol (CHOL) molecules play a key role in modulating the rigidity of cell membranes, and controlling intracellular transport and signal transduction. Using all-atom molecular dynamics and the parallel replica approach, we study the effect of CHOL molecules on mechanical stresses across a dipalmitoylphosphatidycholine (DPPC)-CHOL bilayer, and the mechanism by which CHOL molecules migrate from one bilayer leaflet to the other (flip-flop events). On average, we observe a CHOL flip-flop event in half-a-microsecond. Once a CHOL flip-flop event is triggered, the inter-leaflet migration occurs in about 62 nanoseconds. The energy barrier associated with flip-flop events is found to be 73 kJ/mol. Results for membrane rigidity as a function of CHOL concentration will also be presented.

  9. Genetic Algorithm Based Simulated Annealing Method for Solving Unit Commitment Problem in Utility System

    Science.gov (United States)

    Rajan, C. Christober Asir

    2010-10-01

    The objective of this paper is to find the generation scheduling such that the total operating cost can be minimized, when subjected to a variety of constraints. This also means that it is desirable to find the optimal generating unit commitment in the power system for the next H hours. Genetic Algorithms (GA's) are general-purpose optimization techniques based on principles inspired from the biological evolution using metaphors of mechanisms such as neural section, genetic recombination and survival of the fittest. In this, the unit commitment schedule is coded as a string of symbols. An initial population of parent solutions is generated at random. Here, each schedule is formed by committing all the units according to their initial status ("flat start"). Here the parents are obtained from a pre-defined set of solution's i.e. each and every solution is adjusted to meet the requirements. Then, a random recommitment is carried out with respect to the unit's minimum down times. And SA improves the status. A 66-bus utility power system with twelve generating units in India demonstrates the effectiveness of the proposed approach. Numerical results are shown comparing the cost solutions and computation time obtained by using the Genetic Algorithm method and other conventional methods.

  10. Modeling the Self-assembly and Stability of DHPC Micelles using Atomic Resolution and Coarse Grained MD Simulations

    DEFF Research Database (Denmark)

    Kraft, Johan Frederik; Vestergaard, Mikkel; Schiøtt, Birgit

    2012-01-01

    Membrane mimics such as micelles and bicelles are widely used in experiments involving membrane proteins. With the aim of being able to carry out molecular dynamics simulations in environments comparable to experimental conditions, we set out to test the ability of both coarse grained and atomist...

  11. Computer Simulations of Quantum Theory of Hydrogen Atom for Natural Science Education Students in a Virtual Lab

    Science.gov (United States)

    Singh, Gurmukh

    2012-01-01

    The present article is primarily targeted for the advanced college/university undergraduate students of chemistry/physics education, computational physics/chemistry, and computer science. The most recent software system such as MS Visual Studio .NET version 2010 is employed to perform computer simulations for modeling Bohr's quantum theory of…

  12. Computer Simulations of Quantum Theory of Hydrogen Atom for Natural Science Education Students in a Virtual Lab

    Science.gov (United States)

    Singh, Gurmukh

    2012-01-01

    The present article is primarily targeted for the advanced college/university undergraduate students of chemistry/physics education, computational physics/chemistry, and computer science. The most recent software system such as MS Visual Studio .NET version 2010 is employed to perform computer simulations for modeling Bohr's quantum theory of…

  13. Efficient particle-in-cell simulation of auroral plasma phenomena using a CUDA enabled graphics processing unit

    Science.gov (United States)

    Sewell, Stephen

    This thesis introduces a software framework that effectively utilizes low-cost commercially available Graphic Processing Units (GPUs) to simulate complex scientific plasma phenomena that are modeled using the Particle-In-Cell (PIC) paradigm. The software framework that was developed conforms to the Compute Unified Device Architecture (CUDA), a standard for general purpose graphic processing that was introduced by NVIDIA Corporation. This framework has been verified for correctness and applied to advance the state of understanding of the electromagnetic aspects of the development of the Aurora Borealis and Aurora Australis. For each phase of the PIC methodology, this research has identified one or more methods to exploit the problem's natural parallelism and effectively map it for execution on the graphic processing unit and its host processor. The sources of overhead that can reduce the effectiveness of parallelization for each of these methods have also been identified. One of the novel aspects of this research was the utilization of particle sorting during the grid interpolation phase. The final representation resulted in simulations that executed about 38 times faster than simulations that were run on a single-core general-purpose processing system. The scalability of this framework to larger problem sizes and future generation systems has also been investigated.

  14. Simulation analysis of Shadow Factor and unit cost in the booster mirror arrangement for a solar panel

    Directory of Open Access Journals (Sweden)

    Nivas.V

    2013-10-01

    Full Text Available A simulation and experimental study was attempted to increase the power output from a 75 W mono and multi crystalline solar panel using V Trough solar concentrators, thus estimating its ideal concentration ratio for domestic applications in the absence of automatic tracking. The net radiation falling on the panel due to reflection from concentrators and the shading caused by the reflectors was simulated using TRACE PRO and PV Syst Software, calculating the net power output, losses and output energy. Through the simulated values, the calculated unit cost of energy for the concentrator arrangement with 1 X, 2 X, 3 X and 4 X configurations are found to be 0.81, 0.70, 0.74 and 0.75 $/kWh respectively for the 1st year. It is estimated that 2 X configuration having a surface temperature of less than 70°C, CO2 savings of 28 % higher than the reference model and a unit cost of 0.7 $/kWh is the optimum concentration ratio for a solar V Trough concentrator.

  15. DAYCENT national-scale simulations of nitrous oxide emissions from cropped soils in the United States.

    Science.gov (United States)

    Del Grosso, S J; Parton, W J; Mosier, A R; Walsh, M K; Ojima, D S; Thornton, P E

    2006-01-01

    Until recently, Intergovernmental Panel on Climate Change (IPCC) emission factor methodology, based on simple empirical relationships, has been used to estimate carbon (C) and nitrogen (N) fluxes for regional and national inventories. However, the 2005 USEPA greenhouse gas inventory includes estimates of N2O emissions from cultivated soils derived from simulations using DAYCENT, a process-based biogeochemical model. DAYCENT simulated major U.S. crops at county-level resolution and IPCC emission factor methodology was used to estimate emissions for the approximately 14% of cropped land not simulated by DAYCENT. The methodology used to combine DAYCENT simulations and IPCC methodology to estimate direct and indirect N2O emissions is described in detail. Nitrous oxide emissions from simulations of presettlement native vegetation were subtracted from cropped soil N2O to isolate anthropogenic emissions. Meteorological data required to drive DAYCENT were acquired from DAYMET, an algorithm that uses weather station data and accounts for topography to predict daily temperature and precipitation at 1-km2 resolution. Soils data were acquired from the State Soil Geographic Database (STATSGO). Weather data and dominant soil texture class that lie closest to the geographical center of the largest cluster of cropped land in each county were used to drive DAYCENT. Land management information was implemented at the agricultural-economic region level, as defined by the Agricultural Sector Model. Maps of model-simulated county-level crop yields were compared with yields estimated by the USDA for quality control. Combining results from DAYCENT simulations of major crops and IPCC methodology for remaining cropland yielded estimates of approximately 109 and approximately 70 Tg CO2 equivalents for direct and indirect, respectively, mean annual anthropogenic N2O emissions for 1990-2003.

  16. A Geant4-based Simulation to Evaluate the Feasibility of Using Nuclear Resonance Fluorescence (NRF) in Determining Atomic Compositions of Body Tissue in Cancer Diagnostics and Irradiation

    Science.gov (United States)

    Gilbo, Yekaterina; Wijesooriya, Krishni; Liyanage, Nilanga

    2017-01-01

    Customarily applied in homeland security for identifying concealed explosives and chemical weapons, NRF (Nuclear Resonance Fluorescence) may have high potential in determining atomic compositions of body tissue. High energy photons incident on a target excite the target nuclei causing characteristic re-emission of resonance photons. As the nuclei of each isotope have well-defined excitation energies, NRF uniquely indicates the isotopic content of the target. NRF radiation corresponding to nuclear isotopes present in the human body is emitted during radiotherapy based on Bremsstrahlung photons generated in a linear electron accelerator. We have developed a Geant4 simulation in order to help assess NRF capabilities in detecting, mapping, and characterizing tumors. We have imported a digital phantom into the simulation using anatomical data linked to known chemical compositions of various tissues. Work is ongoing to implement the University of Virginia's cancer center treatment setup and patient geometry, and to collect and analyze the simulation's physics quantities to evaluate the potential of NRF for medical imaging applications. Preliminary results will be presented.

  17. Self-Consistent Determination of Atomic Charges of Ionic Liquid through a Combination of Molecular Dynamics Simulation and Density Functional Theory.

    Science.gov (United States)

    Ishizuka, Ryosuke; Matubayasi, Nobuyuki

    2016-02-09

    A self-consistent scheme is developed to determine the atomic partial charges of ionic liquid. Molecular dynamics (MD) simulation was conducted to sample a set of ion configurations, and these configurations were subject to density functional theory (DFT) calculations to determine the partial charges. The charges were then averaged and used as inputs for the subsequent MD simulation, and MD and DFT calculations were repeated until the MD results are not altered any more. We applied this scheme to 1,3-dimethylimidazolium bis(trifluoromethylsulfonyl) imide ([C1mim][NTf2]) and investigated its structure and dynamics as a function of temperature. At convergence, the average ionic charges were ±0.84 e at 350 K due to charge transfer among ions, where e is the elementary charge, while the reduced ionic charges do not affect strongly the density of [C1mim][NTf2] and radial distribution function. Instead, major effects are found on the energetics and dynamics, with improvements of the overestimated heat of vaporization and the too slow motions of ions observed in MD simulations using commonly used force fields.

  18. All-atom molecular dynamics simulations reveal significant differences in interaction between antimycin and conserved amino acid residues in bovine and bacterial bc1 complexes.

    Science.gov (United States)

    Kokhan, Oleksandr; Shinkarev, Vladimir P

    2011-02-02

    Antimycin A is the most frequently used specific and powerful inhibitor of the mitochondrial respiratory chain. We used all-atom molecular dynamics (MD) simulations to study the dynamic aspects of the interaction of antimycin A with the Q(i) site of the bacterial and bovine bc(1) complexes embedded in a membrane. The MD simulations revealed considerable conformational flexibility of antimycin and significant mobility of antimycin, as a whole, inside the Q(i) pocket. We conclude that many of the differences in antimycin binding observed in high-resolution x-ray structures may have a dynamic origin and result from fluctuations of protein and antimycin between multiple conformational states of similar energy separated by low activation barriers, as well as from the mobility of antimycin within the Q(i) pocket. The MD simulations also revealed a significant difference in interaction between antimycin and conserved amino acid residues in bovine and bacterial bc(1) complexes. The strong hydrogen bond between antimycin and conserved Asp-228 (bovine numeration) was observed to be frequently broken in the bacterial bc(1) complex and only rarely in the bovine bc(1) complex. In addition, the distances between antimycin and conserved His-201 and Lys-227 were consistently larger in the bacterial bc(1) complex. The observed differences could be responsible for a weaker interaction of antimycin with the bacterial bc(1) complex.

  19. Cation-modulated electron-transfer channel: H-atom transfer vs proton-coupled electron transfer with a variable electron-transfer channel in acylamide units.

    Science.gov (United States)

    Chen, Xiaohua; Bu, Yuxiang

    2007-08-08

    The mechanism of proton transfer (PT)/electron transfer (ET) in acylamide units was explored theoretically using density functional theory in a representative model (a cyclic coupling mode between formamide and the N-dehydrogenated formamidic radical, FF). In FF, PT/ET normally occurs via a seven-center cyclic proton-coupled electron transfer (PCET) mechanism with a N-->N PT and an O-->O ET. However, when different hydrated metal ions are bound to the two oxygen sites of FF, the PT/ET mechanism may significantly change. In addition to their inhibition of PT/ET rate, the hydrated metal ions can effectively regulate the FF PT/ET cooperative mechanism to produce a single pathway hydrogen atom transfer (HAT) or a flexible proton coupled electron transfer (PCET) mechanism by changing the ET channel. The regulation essentially originates from the change in the O...O bond strength in the transition state, subject to the binding ability of the hydrated metal ions. In general, the high valent metal ions and those with large binding energies can promote HAT, and the low valent metal ions and those with small binding energies favor PCET. Hydration may reduce the Lewis acidity of cations, and thus favor PCET. Good correlations among the binding energies, barrier heights, spin density distributions, O...O contacts, and hydrated metal ion properties have been found, which can be used to interpret the transition in the PT/ET mechanism. These findings regarding the modulation of the PT/ET pathway via hydrated metal ions may provide useful information for a greater understanding of PT/ET cooperative mechanisms, and a possible method for switching conductance in nanoelectronic devices.

  20. A comprehensive picture in the view of atomic scale on piezoelectricity of ZnO tunnel junctions: The first principles simulation

    Directory of Open Access Journals (Sweden)

    Genghong Zhang

    2016-06-01

    Full Text Available Piezoelectricity is closely related with the performance and application of piezoelectric devices. It is a crucial issue to understand its detailed fundamental for designing functional devices with more peculiar performances. Basing on the first principles simulations, the ZnO piezoelectric tunnel junction is taken as an example to systematically investigate its piezoelectricity (including the piezopotential energy, piezoelectric field, piezoelectric polarization and piezocharge and explore their correlation. The comprehensive picture of the piezoelectricity in the ZnO tunnel junction is revealed at atomic scale and it is verified to be the intrinsic characteristic of ZnO barrier, independent of its terminated surface but dependent on its c axis orientation and the applied strain. In the case of the ZnO c axis pointing from right to left, an in-plane compressive strain will induce piezocharges (and a piezopotential energy drop with positive and negative signs (negative and positive signs emerging respectively at the left and right terminated surfaces of the ZnO barrier. Meanwhile a piezoelectric polarization (and a piezoelectric field pointing from right to left (from left to right are also induced throughout the ZnO barrier. All these piezoelectric physical quantities would reverse when the applied strain switches from compressive to tensile. This study provides an atomic level insight into the fundamental behavior of the piezoelectricity of the piezoelectric tunnel junction and should have very useful information for future designs of piezoelectric devices.