WorldWideScience

Sample records for model united atom

  1. 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...

  2. 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.

  3. 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.

  4. 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 ...

  5. 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.

  6. 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.

  7. 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.

  8. "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…

  9. 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.

  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. 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.

  12. 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

  13. Hard sphere model of atom

    CERN Document Server

    Tsekov, R

    2014-01-01

    The finite size effect of electron and nucleus is accounted for in the model of atom. Due to their hard sphere repulsion the energy of the 1s orbital decreases and the corrections amount up to 8 % in Uranium. Several models for boundary conditions on the atomic nucleus surface are discussed as well.

  14. Stochastic models for atomic clocks

    Science.gov (United States)

    Barnes, J. A.; Jones, R. H.; Tryon, P. V.; Allan, D. W.

    1983-01-01

    For the atomic clocks used in the National Bureau of Standards Time Scales, an adequate model is the superposition of white FM, random walk FM, and linear frequency drift for times longer than about one minute. The model was tested on several clocks using maximum likelihood techniques for parameter estimation and the residuals were acceptably random. Conventional diagnostics indicate that additional model elements contribute no significant improvement to the model even at the expense of the added model complexity.

  15. The Quantum Atomic Model "Electronium": A Successful Teaching Tool.

    Science.gov (United States)

    Budde, Marion; Niedderer, Hans; Scott, Philip; Leach, John

    2002-01-01

    Focuses on the quantum atomic model Electronium. Outlines the Bremen teaching approach in which this model is used, and analyzes the learning of two students as they progress through the teaching unit. (Author/MM)

  16. A Quantum Model of Atoms (the Energy Levels of Atoms).

    Science.gov (United States)

    Rafie, Francois

    2001-01-01

    Discusses the model for all atoms which was developed on the same basis as Bohr's model for the hydrogen atom. Calculates the radii and the energies of the orbits. Demonstrates how the model obeys the de Broglie's hypothesis that the moving electron exhibits both wave and particle properties. (Author/ASK)

  17. "Electronium": A Quantum Atomic Teaching Model.

    Science.gov (United States)

    Budde, Marion; Niedderer, Hans; Scott, Philip; Leach, John

    2002-01-01

    Outlines an alternative atomic model to the probability model, the descriptive quantum atomic model Electronium. Discusses the way in which it is intended to support students in learning quantum-mechanical concepts. (Author/MM)

  18. Project Physics Tests 5, Models of the Atom.

    Science.gov (United States)

    Harvard Univ., Cambridge, MA. Harvard Project Physics.

    Test items relating to Project Physics Unit 5 are presented in this booklet. Included are 70 multiple-choice and 23 problem-and-essay questions. Concepts of atomic model are examined on aspects of relativistic corrections, electron emission, photoelectric effects, Compton effect, quantum theories, electrolysis experiments, atomic number and mass,…

  19. Can atom-surface potential measurements test atomic structure models?

    Science.gov (United States)

    Lonij, Vincent P A; Klauss, Catherine E; Holmgren, William F; Cronin, Alexander D

    2011-06-30

    van der Waals (vdW) atom-surface potentials can be excellent benchmarks for atomic structure calculations. This is especially true if measurements are made with two different types of atoms interacting with the same surface sample. Here we show theoretically how ratios of vdW potential strengths (e.g., C₃(K)/C₃(Na)) depend sensitively on the properties of each atom, yet these ratios are relatively insensitive to properties of the surface. We discuss how C₃ ratios depend on atomic core electrons by using a two-oscillator model to represent the contribution from atomic valence electrons and core electrons separately. We explain why certain pairs of atoms are preferable to study for future experimental tests of atomic structure calculations. A well chosen pair of atoms (e.g., K and Na) will have a C₃ ratio that is insensitive to the permittivity of the surface, whereas a poorly chosen pair (e.g., K and He) will have a ratio of C₃ values that depends more strongly on the permittivity of the surface.

  20. 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...

  1. 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.

  2. Nagaoka's atomic model and hyperfine interactions.

    Science.gov (United States)

    Inamura, Takashi T

    2016-01-01

    The prevailing view of Nagaoka's "Saturnian" atom is so misleading that today many people have an erroneous picture of Nagaoka's vision. They believe it to be a system involving a 'giant core' with electrons circulating just outside. Actually, though, in view of the Coulomb potential related to the atomic nucleus, Nagaoka's model is exactly the same as Rutherford's. This is true of the Bohr atom, too. To give proper credit, Nagaoka should be remembered together with Rutherford and Bohr in the history of the atomic model. It is also pointed out that Nagaoka was a pioneer of understanding hyperfine interactions in order to study nuclear structure.

  3. Modeling Atom Probe Tomography: A review

    Energy Technology Data Exchange (ETDEWEB)

    Vurpillot, F., E-mail: francois.vurpillot@univ-rouen.fr [Groupe de Physique des Matériaux, UMR CNRS 6634, Université de Rouen, Saint Etienne du Rouvray 76801 (France); Oberdorfer, C. [Institut für Materialwissenschaft, Lehrstuhl für Materialphysik, Universität Stuttgart, Heisenbergstr. 3, 70569 Stuttgart (Germany)

    2015-12-15

    Improving both the precision and the accuracy of Atom Probe Tomography reconstruction requires a correct understanding of the imaging process. In this aim, numerical modeling approaches have been developed for 15 years. The injected ingredients of these modeling tools are related to the basic physic of the field evaporation mechanism. The interplay between the sample nature and structure of the analyzed sample and the reconstructed image artefacts have pushed to gradually improve and make the model more and more sophisticated. This paper reviews the evolution of the modeling approach in Atom Probe Tomography and presents some future potential directions in order to improve the method. - Highlights: • The basics of field evaporation. • The main aspects of Atom Probe Tomography modeling. • The intrinsic limitations of the current method and future potential directions to improve the understanding of tip to image ion projection.

  4. Students' Mental Models of Atomic Spectra

    Science.gov (United States)

    Körhasan, Nilüfer Didis; Wang, Lu

    2016-01-01

    Mental modeling, which is a theory about knowledge organization, has been recently studied by science educators to examine students' understanding of scientific concepts. This qualitative study investigates undergraduate students' mental models of atomic spectra. Nine second-year physics students, who have already taken the basic chemistry and…

  5. Atomic model of liquid pure Fe

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Using a θ-θX-ray diffractometer, the liquid structure of pure Fewas investigated and the diffraction intensity, structure factor, pair distribution function as well as the coordination number and atomic distance were obtained. The experimental results showed that there was also a pre-peak on the curve of the structure factor of liquid pure Fe. The pre-peak is a mark of medium-range order in melts. According to the characteristics of pre-peak, an atomic model of liquid pure Fe is constructed, namely, the structure of liquid pure Fe is a combination of clusters consisting of bcc cells with shared vertexes and other atoms with random dense atom distribution.

  6. Contemporary models of the atomic nucleus

    CERN Document Server

    Nemirovskii, P E

    2013-01-01

    Contemporary Models of the Atomic Nucleus discusses nuclear structure and properties, expounding contemporary theoretical concepts of the low-energy nuclear processes underlying in nuclear models. This book focuses on subjects such as the optical nuclear model, unified or collective model, and deuteron stripping reaction. Other topics discussed include the basic nuclear properties; shell model; theoretical analysis of the shell model; and radiative transitions and alpha-decay. The deuteron theory and the liquid drop nuclear model with its application to fission theory are also mentioned, but o

  7. Jaynes-Cummings model with a collective atomic mode

    OpenAIRE

    Zheng, Shi-Biao

    2012-01-01

    We study the dynamics of a single control atom and an atomic sample interacting with a nonresonant cavity mode. The control atom is driven by an auxiliary classical field. Under certain conditions, the coherent energy exchange between the control atom and the atomic sample induced by the cavity mode is described by the Jaynes-Cummings model. The idea provides a possibility for quantum-state engineering and reconstruction for collective atomic modes.

  8. Weber's planetary model of the atom

    Energy Technology Data Exchange (ETDEWEB)

    Koch Torres Assis, Andre; Wiederkehr, Karl Heinrich; Wolfschmidt, Gudrun

    2011-07-01

    Known is Wilhelm Weber together with Gaussfor the creation of the absolute measurement systems, foundation for the contemporary Si units. Here Weber's atomic model, originated around 1860, is presented.With the triumph of the field physics and the short-range interaction theory (Faraday, Maxwell, Heinrich Hertz) all to fastly the older electrodynamics was put as superseeded long-range interaction theory ad acta. Just at the end of the 19th century the idea of a substantial, atomistic structure of electricity (H. A. Lorentz, J. J. Thomson) had is way. On the base of Ampere's hypothesis of the molecular currents in Weber's atomic model electrical particles with electric charge and very small mass circulate around a ponderable atom or molecule, which carries also electrical charge. These circulating particles excite according to Weber in the ether light waves of constant frequency. The similarity with Bohr's atomic model - apart from the quantum conditions and quantum jumps - is amazing. Energetic consideration in the emission of the light waves Weber indeed not yet made. In the foundation of metal electronics Weber also started from Ampere's molecular currents. If voltage is put on the conductor ballistic motions of electrical particles result, which arrive so from the effective sphere of a ponderable atom in the effective sphere of a neighbouring atom. Based on these ideas then Riecke, Drude, and H. A. Lorentz created then the classical electron theory of the metals. Sommerfeld took up again the idea under usage of the quantum theory come into use, and solid-state physics began.

  9. Cumulative atomic multipole moments complement any atomic charge model to obtain more accurate electrostatic properties

    Science.gov (United States)

    Sokalski, W. A.; Shibata, M.; Ornstein, R. L.; Rein, R.

    1992-01-01

    The quality of several atomic charge models based on different definitions has been analyzed using cumulative atomic multipole moments (CAMM). This formalism can generate higher atomic moments starting from any atomic charges, while preserving the corresponding molecular moments. The atomic charge contribution to the higher molecular moments, as well as to the electrostatic potentials, has been examined for CO and HCN molecules at several different levels of theory. The results clearly show that the electrostatic potential obtained from CAMM expansion is convergent up to R-5 term for all atomic charge models used. This illustrates that higher atomic moments can be used to supplement any atomic charge model to obtain more accurate description of electrostatic properties.

  10. 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…

  11. Atom-Role-Based Access Control Model

    Science.gov (United States)

    Cai, Weihong; Huang, Richeng; Hou, Xiaoli; Wei, Gang; Xiao, Shui; Chen, Yindong

    Role-based access control (RBAC) model has been widely recognized as an efficient access control model and becomes a hot research topic of information security at present. However, in the large-scale enterprise application environments, the traditional RBAC model based on the role hierarchy has the following deficiencies: Firstly, it is unable to reflect the role relationships in complicated cases effectively, which does not accord with practical applications. Secondly, the senior role unconditionally inherits all permissions of the junior role, thus if a user is under the supervisor role, he may accumulate all permissions, and this easily causes the abuse of permission and violates the least privilege principle, which is one of the main security principles. To deal with these problems, we, after analyzing permission types and role relationships, proposed the concept of atom role and built an atom-role-based access control model, called ATRBAC, by dividing the permission set of each regular role based on inheritance path relationships. Through the application-specific analysis, this model can well meet the access control requirements.

  12. Big Atoms for Small Children: Building Atomic Models from Common Materials to Better Visualize and Conceptualize Atomic Structure

    Science.gov (United States)

    Cipolla, Laura; Ferrari, Lia A.

    2016-01-01

    A hands-on approach to introduce the chemical elements and the atomic structure to elementary/middle school students is described. The proposed classroom activity presents Bohr models of atoms using common and inexpensive materials, such as nested plastic balls, colored modeling clay, and small-sized pasta (or small plastic beads).

  13. Big Atoms for Small Children: Building Atomic Models from Common Materials to Better Visualize and Conceptualize Atomic Structure

    Science.gov (United States)

    Cipolla, Laura; Ferrari, Lia A.

    2016-01-01

    A hands-on approach to introduce the chemical elements and the atomic structure to elementary/middle school students is described. The proposed classroom activity presents Bohr models of atoms using common and inexpensive materials, such as nested plastic balls, colored modeling clay, and small-sized pasta (or small plastic beads).

  14. Making It Visual: Creating a Model of the Atom

    Science.gov (United States)

    Pringle, Rose M.

    2004-01-01

    This article describes a lesson in which students construct Bohr's planetary model of the atom. Niels Bohr's atomic model provides a framework for discussing with middle and high school students the historical development of our understanding of the structure of the atom. The model constructed in this activity will enable students to visualize the…

  15. Computer Model Of Fragmentation Of Atomic Nuclei

    Science.gov (United States)

    Wilson, John W.; Townsend, Lawrence W.; Tripathi, Ram K.; Norbury, John W.; KHAN FERDOUS; Badavi, Francis F.

    1995-01-01

    High Charge and Energy Semiempirical Nuclear Fragmentation Model (HZEFRG1) computer program developed to be computationally efficient, user-friendly, physics-based program for generating data bases on fragmentation of atomic nuclei. Data bases generated used in calculations pertaining to such radiation-transport applications as shielding against radiation in outer space, radiation dosimetry in outer space, cancer therapy in laboratories with beams of heavy ions, and simulation studies for designing detectors for experiments in nuclear physics. Provides cross sections for production of individual elements and isotopes in breakups of high-energy heavy ions by combined nuclear and Coulomb fields of interacting nuclei. Written in ANSI FORTRAN 77.

  16. Calculation of Al-Zn diagram from central atoms model

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    A slightly modified central atoms model was proposed. The probabilities of various clusters with the central atoms and their nearest neighboring shells can be calculated neglecting the assumption of the param eter of energy in the central atoms model in proportion to the number of other atoms i (referred with the central atom). A parameter Pα is proposed in this model, which equals to reciprocal of activity coefficient of a component, therefore, the new model can be understood easily. By this model, the Al-Zn phase diagram and its thermodynamic properties were calculated, the results coincide with the experimental data.

  17. The two-atom Jaynes-Cummings model's dynamic properties

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The model of two two-level atoms interact with a single-mode cavity was investigated. The formulation of the time evolution operator for the two-atom Jaynes-Cummings model is pressented by the bare-states approach. Besides, the time evolution of the two-atom common population probabilities is studied, and some novel features are obtained.

  18. 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)

  19. Harmonic oscillator model for the helium atom

    CERN Document Server

    Carlsen, Martin

    2015-01-01

    A harmonic oscillator model in four dimensions is presented for the helium atom to estimate the distance to the inner and outer electron from the nucleus, the angle between electrons and the energy levels. The method is algebraic and is not based on the choice of correct trial wave function. Three harmonic oscillators and thus three quantum numbers are sufficient to describe the two-electron system. We derive a simple formula for the energy in the general case and in the special case of the Wannier Ridge. For a set of quantum numbers the distance to the electrons and the angle between the electrons are uniquely determined as the intersection between three surfaces. We show that the excited states converge either towards ionization thresholds or towards extreme parallel or antiparallel states and provide an estimate of the ground state energy.

  20. Atomic force microscopy of model lipid membranes.

    Science.gov (United States)

    Morandat, Sandrine; Azouzi, Slim; Beauvais, Estelle; Mastouri, Amira; El Kirat, Karim

    2013-02-01

    Supported lipid bilayers (SLBs) are biomimetic model systems that are now widely used to address the biophysical and biochemical properties of biological membranes. Two main methods are usually employed to form SLBs: the transfer of two successive monolayers by Langmuir-Blodgett or Langmuir-Schaefer techniques, and the fusion of preformed lipid vesicles. The transfer of lipid films on flat solid substrates offers the possibility to apply a wide range of surface analytical techniques that are very sensitive. Among them, atomic force microscopy (AFM) has opened new opportunities for determining the nanoscale organization of SLBs under physiological conditions. In this review, we first focus on the different protocols generally employed to prepare SLBs. Then, we describe AFM studies on the nanoscale lateral organization and mechanical properties of SLBs. Lastly, we survey recent developments in the AFM monitoring of bilayer alteration, remodeling, or digestion, by incubation with exogenous agents such as drugs, proteins, peptides, and nanoparticles.

  1. Operation of the computer model for microenvironment atomic oxygen exposure

    Science.gov (United States)

    Bourassa, R. J.; Gillis, J. R.; Gruenbaum, P. E.

    1995-01-01

    A computer model for microenvironment atomic oxygen exposure has been developed to extend atomic oxygen modeling capability to include shadowing and reflections. The model uses average exposure conditions established by the direct exposure model and extends the application of these conditions to treat surfaces of arbitrary shape and orientation.

  2. Early Atomic Models - From Mechanical to Quantum (1904-1913)

    CERN Document Server

    Baily, Charles

    2012-01-01

    A complete history of early atomic models would fill volumes, but a reasonably coherent tale of the path from mechanical atoms to the quantum can be told by focusing on the relevant work of three great contributors to atomic physics, in the critically important years between 1904 and 1913: J. J. Thomson, Ernest Rutherford and Niels Bohr. We first examine the origins of Thomson's mechanical atomic models, from his ethereal vortex atoms in the early 1880's, to the myriad "corpuscular" atoms he proposed following the discovery of the electron in 1897. Beyond predictions for the periodicity of the elements, the application of Thomson's atoms to problems in scattering and absorption led to quantitative predictions that were confirmed by experiments with high-velocity electrons traversing thin sheets of metal. Still, the much more massive and energetic {\\alpha}-particles being studied by Rutherford were better suited for exploring the interior of the atom, and careful measurements on the angular dependence of their...

  3. An atomic model for neutral and singly ionized uranium

    Science.gov (United States)

    Maceda, E. L.; Miley, G. H.

    1979-01-01

    A model for the atomic levels above ground state in neutral, U(0), and singly ionized, U(+), uranium is described based on identified atomic transitions. Some 168 states in U(0) and 95 in U(+) are found. A total of 1581 atomic transitions are used to complete this process. Also discussed are the atomic inverse lifetimes and line widths for the radiative transitions as well as the electron collisional cross sections.

  4. Effect of energetic oxygen atoms on neutral density models.

    Science.gov (United States)

    Rohrbaugh, R. P.; Nisbet, J. S.

    1973-01-01

    The dissociative recombination of O2(+) and NO(+) in the F region results in the production of atomic oxygen and atomic nitrogen with substantially greater kinetic energy than the ambient atoms. In the exosphere these energetic atoms have long free paths. They can ascend to altitudes of several thousand kilometers and can travel horizontally to distances of the order of the earth's radius. The distribution of energetic oxygen atoms is derived by means of models of the ion and neutral densities for quiet and disturbed solar conditions. A distribution technique is used to study the motion of the atoms in the collision-dominated region. Ballistic trajectories are calculated in the spherical gravitational field of the earth. The present calculations show that the number densities of energetic oxygen atoms predominate over the ambient atomic oxygen densities above 1000 km under quiet solar conditions and above 1600 km under disturbed solar conditions.

  5. 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.

  6. 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

  7. INFERNO - A better model of atoms in dense plasmas

    Science.gov (United States)

    Liberman, D. A.

    1982-03-01

    A self-consistent field model of atoms in dense plasmas has been devised and incorporated in a computer program. In the model there is a uniform positive charge distribution with a hole in it and at the center of the hole an atomic nucleus. There are electrons, in both bound and continuum states, in sufficient number to form an electrically neutral system. The Dirac equation is used so that high Z atoms can be dealt with. A finite temperature is assumed, and a mean field (average atom) approximation is used in statistical averages. Applications have been made to equations of states and to photoabsorption.

  8. 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

  9. 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....

  10. 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…

  11. 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…

  12. Ab initio calculations and modelling of atomic cluster structure

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Lyalin, Andrey G.; Greiner, Walter

    2004-01-01

    framework for modelling the fusion process of noble gas clusters is presented. We report the striking correspondence of the peaks in the experimentally measured abundance mass spectra with the peaks in the size-dependence of the second derivative of the binding energy per atom calculated for the chain...... of the noble gas clusters up to 150 atoms....

  13. 100th anniversary of Bohr's model of the atom.

    Science.gov (United States)

    Schwarz, W H Eugen

    2013-11-18

    In the fall of 1913 Niels Bohr formulated his atomic models at the age of 27. This Essay traces Bohr's fundamental reasoning regarding atomic structure and spectra, the periodic table of the elements, and chemical bonding. His enduring insights and superseded suppositions are also discussed.

  14. Analytic Solutions of Three-Level Dressed-Atom Model

    Institute of Scientific and Technical Information of China (English)

    WANG Zheng-Ling; YIN Jian-Ping

    2004-01-01

    On the basis of the dressed-atom model, the general analytic expressions for the eigenenergies, eigenstates and their optical potentials of the A-configuration three-level atom system are derived and analysed. From the calculation of dipole matrix element of different dressed states, we obtain the spontaneous-emission rates in the dressed-atom picture. We find that our general expressions of optical potentials for the three-level dressed atom can be reduced to the same as ones in previous references under the approximation of a small saturation parameter. We also analyse the dependences of the optical potentials of a three-level 85Rb atom on the laser detuning and the dependences of spontaneous-emission rates on the radial position in the dark hollow beam, and discuss the probability (population) evolutions of dressed-atomic eigenstates in three levels in the hollow beam.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. Molecule-specific determination of atomic polarizabilities with the polarizable atomic multipole model.

    Science.gov (United States)

    Woo Kim, Hyun; Rhee, Young Min

    2012-07-30

    Recently, many polarizable force fields have been devised to describe induction effects between molecules. In popular polarizable models based on induced dipole moments, atomic polarizabilities are the essential parameters and should be derived carefully. Here, we present a parameterization scheme for atomic polarizabilities using a minimization target function containing both molecular and atomic information. The main idea is to adopt reference data only from quantum chemical calculations, to perform atomic polarizability parameterizations even when relevant experimental data are scarce as in the case of electronically excited molecules. Specifically, our scheme assigns the atomic polarizabilities of any given molecule in such a way that its molecular polarizability tensor is well reproduced. We show that our scheme successfully works for various molecules in mimicking dipole responses not only in ground states but also in valence excited states. The electrostatic potential around a molecule with an externally perturbing nearby charge also exhibits a near-quantitative agreement with the reference data from quantum chemical calculations. The limitation of the model with isotropic atoms is also discussed to examine the scope of its applicability.

  20. Atomic structure of graphene supported heterogeneous model catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Franz, Dirk

    2017-04-15

    Graphene on Ir(111) forms a moire structure with well defined nucleation centres. Therefore it can be utilized to create hexagonal metal cluster lattices with outstanding structural quality. At diffraction experiments these 2D surface lattices cause a coherent superposition of the moire cell structure factor, so that the measured signal intensity scales with the square of coherently scattering unit cells. This artificial signal enhancement enables the opportunity for X-ray diffraction to determine the atomic structure of small nano-objects, which are hardly accessible with any experimental technique. The uniform environment of every metal cluster makes the described metal cluster lattices on graphene/Ir(111) an attractive model system for the investigation of catalytic, magnetic and quantum size properties of ultra-small nano-objects. In this context the use of x-rays provides a maximum of flexibility concerning the possible sample environments (vacuum, selected gases, liquids, sample temperature) and allows in-situ/operando measurements. In the framework of the present thesis the structure of different metal clusters grown by physical vapor deposition in an UHV environment and after gas exposure have been investigated. On the one hand the obtained results will explore many aspects of the atomic structure of these small metal clusters and on the other hand the presented results will proof the capabilities of the described technique (SXRD on cluster lattices). For iridium, platinum, iridium/palladium and platinum/rhodium the growth on graphene/Ir(111) of epitaxial, crystalline clusters with an ordered hexagonal lattice arrangement has been confirmed using SXRD. The clusters nucleate at the hcp sites of the moire cell and bind via rehybridization of the carbon atoms (sp{sup 2} → sp{sup 3}) to the Ir(111) substrate. This causes small displacements of the substrate atoms, which is revealed by the diffraction experiments. All metal clusters exhibit a fcc structure

  1. A liquid drop model for embedded atom method cluster energies

    Science.gov (United States)

    Finley, C. W.; Abel, P. B.; Ferrante, J.

    1996-01-01

    Minimum energy configurations for homonuclear clusters containing from two to twenty-two atoms of six metals, Ag, Au, Cu, Ni, Pd, and Pt have been calculated using the Embedded Atom Method (EAM). The average energy per atom as a function of cluster size has been fit to a liquid drop model, giving estimates of the surface and curvature energies. The liquid drop model gives a good representation of the relationship between average energy and cluster size. As a test the resulting surface energies are compared to EAM surface energy calculations for various low-index crystal faces with reasonable agreement.

  2. Models for identification of erroneous atom-to-atom mapping of reactions performed by automated algorithms.

    Science.gov (United States)

    Muller, Christophe; Marcou, Gilles; Horvath, Dragos; Aires-de-Sousa, João; Varnek, Alexandre

    2012-12-21

    Machine learning (SVM and JRip rule learner) methods have been used in conjunction with the Condensed Graph of Reaction (CGR) approach to identify errors in the atom-to-atom mapping of chemical reactions produced by an automated mapping tool by ChemAxon. The modeling has been performed on the three first enzymatic classes of metabolic reactions from the KEGG database. Each reaction has been converted into a CGR representing a pseudomolecule with conventional (single, double, aromatic, etc.) bonds and dynamic bonds characterizing chemical transformations. The ChemAxon tool was used to automatically detect the matching atom pairs in reagents and products. These automated mappings were analyzed by the human expert and classified as "correct" or "wrong". ISIDA fragment descriptors generated for CGRs for both correct and wrong mappings were used as attributes in machine learning. The learned models have been validated in n-fold cross-validation on the training set followed by a challenge to detect correct and wrong mappings within an external test set of reactions, never used for learning. Results show that both SVM and JRip models detect most of the wrongly mapped reactions. We believe that this approach could be used to identify erroneous atom-to-atom mapping performed by any automated algorithm.

  3. Toward an anisotropic atom-atom model for the crystalline phases of the molecular S8 compound

    OpenAIRE

    Pastorino, C.; Gamba, Z.

    2000-01-01

    We analize two anisotropic atom-atom models used to describe the crystalline alpha,beta and gamma phases of S8 crystals, the most stable compound of elemental sulfur in solid phases, at ambient pressure and T

  4. Alpha-cluster model of atomic nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Sosin, Zbigniew; Kallunkathariyil, Jinesh [Jagiellonian University, M. Smoluchowski Institute of Physics, Krakow (Poland); Blocki, Jan [NCBJ, Theoretical Physics Division (BP2), Swierk (Poland); Lukasik, Jerzy; Pawlowski, Piotr [IFJ PAN, Krakow (Poland)

    2016-05-15

    The description of a nuclear system in its ground state and at low excitations based on the equation of state (EoS) around normal density is presented. In the expansion of the EoS around the saturation point, additional spin polarization terms are taken into account. These terms, together with the standard symmetry term, are responsible for the appearance of the α-like clusters in the ground-state configurations of the N=Z even-even nuclei. At the nuclear surface these clusters can be identified as alpha particles. A correction for the surface effects is introduced for atomic nuclei. Taking into account an additional interaction between clusters the binding energies and sizes of the considered nuclei are very accurately described. The limits of the EoS parameters are established from the properties of the α, {sup 3}He and t particles. (orig.)

  5. 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.

  6. Nagaoka’s atomic model and hyperfine interactions

    Science.gov (United States)

    INAMURA, Takashi T.

    2016-01-01

    The prevailing view of Nagaoka’s “Saturnian” atom is so misleading that today many people have an erroneous picture of Nagaoka’s vision. They believe it to be a system involving a ‘giant core’ with electrons circulating just outside. Actually, though, in view of the Coulomb potential related to the atomic nucleus, Nagaoka’s model is exactly the same as Rutherford’s. This is true of the Bohr atom, too. To give proper credit, Nagaoka should be remembered together with Rutherford and Bohr in the history of the atomic model. It is also pointed out that Nagaoka was a pioneer of understanding hyperfine interactions in order to study nuclear structure. PMID:27063182

  7. Detecting Clusters in Atom Probe Data with Gaussian Mixture Models.

    Science.gov (United States)

    Zelenty, Jennifer; Dahl, Andrew; Hyde, Jonathan; Smith, George D W; Moody, Michael P

    2017-04-01

    Accurately identifying and extracting clusters from atom probe tomography (APT) reconstructions is extremely challenging, yet critical to many applications. Currently, the most prevalent approach to detect clusters is the maximum separation method, a heuristic that relies heavily upon parameters manually chosen by the user. In this work, a new clustering algorithm, Gaussian mixture model Expectation Maximization Algorithm (GEMA), was developed. GEMA utilizes a Gaussian mixture model to probabilistically distinguish clusters from random fluctuations in the matrix. This machine learning approach maximizes the data likelihood via expectation maximization: given atomic positions, the algorithm learns the position, size, and width of each cluster. A key advantage of GEMA is that atoms are probabilistically assigned to clusters, thus reflecting scientifically meaningful uncertainty regarding atoms located near precipitate/matrix interfaces. GEMA outperforms the maximum separation method in cluster detection accuracy when applied to several realistically simulated data sets. Lastly, GEMA was successfully applied to real APT data.

  8. An extension of dynamic droplet deformation models to secondary atomization

    NARCIS (Netherlands)

    Bartz, F.O.; Schmehl, R.; Koch, R.; Bauer, H.J.

    2010-01-01

    A detailed model for secondary atomization of liquid droplets by aerodynamic forces is presented. As an empirical extension of dynamic droplet deformation models, it accounts for temporal variations of the relative velocity between droplet and gas phase during the deformation and breakup process and

  9. Hirshfeld atom refinement for modelling strong hydrogen bonds.

    Science.gov (United States)

    Woińska, Magdalena; Jayatilaka, Dylan; Spackman, Mark A; Edwards, Alison J; Dominiak, Paulina M; Woźniak, Krzysztof; Nishibori, Eiji; Sugimoto, Kunihisa; Grabowsky, Simon

    2014-09-01

    High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples of Z' > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O-H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (SHADE) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment, e.g. the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.

  10. Physically representative atomistic modeling of atomic-scale friction

    Science.gov (United States)

    Dong, Yalin

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

  11. Modeling noncontact atomic force microscopy resolution on corrugated surfaces

    Directory of Open Access Journals (Sweden)

    Kristen M. Burson

    2012-03-01

    Full Text Available Key developments in NC-AFM have generally involved atomically flat crystalline surfaces. However, many surfaces of technological interest are not atomically flat. We discuss the experimental difficulties in obtaining high-resolution images of rough surfaces, with amorphous SiO2 as a specific case. We develop a quasi-1-D minimal model for noncontact atomic force microscopy, based on van der Waals interactions between a spherical tip and the surface, explicitly accounting for the corrugated substrate (modeled as a sinusoid. The model results show an attenuation of the topographic contours by ~30% for tip distances within 5 Å of the surface. Results also indicate a deviation from the Hamaker force law for a sphere interacting with a flat surface.

  12. Gas Atomization of Aluminium Melts: Comparison of Analytical Models

    Directory of Open Access Journals (Sweden)

    Georgios Antipas

    2012-06-01

    Full Text Available A number of analytical models predicting the size distribution of particles during atomization of Al-based alloys by N2, He and Ar gases were compared. Simulations of liquid break up in a close coupled atomizer revealed that the finer particles are located near the center of the spray cone. Increasing gas injection pressures led to an overall reduction of particle diameters and caused a migration of the larger powder particles towards the outer boundary of the flow. At sufficiently high gas pressures the spray became monodisperse. The models also indicated that there is a minimum achievable mean diameter for any melt/gas system.

  13. Modeling sympathetic cooling of molecules by ultracold atoms

    CERN Document Server

    Lim, Jongseok; Hutson, Jeremy M; Tarbutt, M R

    2015-01-01

    We model sympathetic cooling of ground-state CaF molecules by ultracold Li and Rb atoms. The molecules are moving in a microwave trap, while the atoms are trapped magnetically. We calculate the differential elastic cross sections for CaF-Li and CaF-Rb collisions, using model Lennard-Jones potentials adjusted to give typical values for the s-wave scattering length. Together with trajectory calculations, these differential cross sections are used to simulate the cooling of the molecules, the heating of the atoms, and the loss of atoms from the trap. We show that a hard-sphere collision model based on an energy-dependent momentum transport cross section accurately predicts the molecule cooling rate but underestimates the rates of atom heating and loss. Our simulations suggest that Rb is a more effective coolant than Li for ground-state molecules, and that the cooling dynamics are less sensitive to the exact value of the s-wave scattering length when Rb is used. Using realistic experimental parameters, we find th...

  14. Explicit all-atom modeling of realistically sized ligand-capped nanocrystals.

    Science.gov (United States)

    Kaushik, Ananth P; Clancy, Paulette

    2012-03-21

    We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), "capped" with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes.

  15. Explicit all-atom modeling of realistically sized ligand-capped nanocrystals

    KAUST Repository

    Kaushik, Ananth P.

    2012-01-01

    We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), capped with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes. © 2012 American Institute of Physics.

  16. Atomic-scale modeling of cellulose nanocrystals

    Science.gov (United States)

    Wu, Xiawa

    Cellulose nanocrystals (CNCs), the most abundant nanomaterials in nature, are recognized as one of the most promising candidates to meet the growing demand of green, bio-degradable and sustainable nanomaterials for future applications. CNCs draw significant interest due to their high axial elasticity and low density-elasticity ratio, both of which are extensively researched over the years. In spite of the great potential of CNCs as functional nanoparticles for nanocomposite materials, a fundamental understanding of CNC properties and their role in composite property enhancement is not available. In this work, CNCs are studied using molecular dynamics simulation method to predict their material' behaviors in the nanoscale. (a) Mechanical properties include tensile deformation in the elastic and plastic regions using molecular mechanics, molecular dynamics and nanoindentation methods. This allows comparisons between the methods and closer connectivity to experimental measurement techniques. The elastic moduli in the axial and transverse directions are obtained and the results are found to be in good agreement with previous research. The ultimate properties in plastic deformation are reported for the first time and failure mechanism are analyzed in details. (b) The thermal expansion of CNC crystals and films are studied. It is proposed that CNC film thermal expansion is due primarily to single crystal expansion and CNC-CNC interfacial motion. The relative contributions of inter- and intra-crystal responses to heating are explored. (c) Friction at cellulose-CNCs and diamond-CNCs interfaces is studied. The effects of sliding velocity, normal load, and relative angle between sliding surfaces are predicted. The Cellulose-CNC model is analyzed in terms of hydrogen bonding effect, and the diamond-CNC model compliments some of the discussion of the previous model. In summary, CNC's material properties and molecular models are both studied in this research, contributing to

  17. Model based control of dynamic atomic force microscope

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Chibum [Department of Mechanical System Design Engineering, Seoul National University of Science and Technology, Seoul 139-743 (Korea, Republic of); Salapaka, Srinivasa M., E-mail: salapaka@illinois.edu [Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States)

    2015-04-15

    A model-based robust control approach is proposed that significantly improves imaging bandwidth for the dynamic mode atomic force microscopy. A model for cantilever oscillation amplitude and phase dynamics is derived and used for the control design. In particular, the control design is based on a linearized model and robust H{sub ∞} control theory. This design yields a significant improvement when compared to the conventional proportional-integral designs and verified by experiments.

  18. Model based control of dynamic atomic force microscope.

    Science.gov (United States)

    Lee, Chibum; Salapaka, Srinivasa M

    2015-04-01

    A model-based robust control approach is proposed that significantly improves imaging bandwidth for the dynamic mode atomic force microscopy. A model for cantilever oscillation amplitude and phase dynamics is derived and used for the control design. In particular, the control design is based on a linearized model and robust H(∞) control theory. This design yields a significant improvement when compared to the conventional proportional-integral designs and verified by experiments.

  19. 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...

  20. 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.

  1. Modeling and optimizing of the random atomic spin gyroscope drift based on the atomic spin gyroscope

    Science.gov (United States)

    Quan, Wei; Lv, Lin; Liu, Baiqi

    2014-11-01

    In order to improve the atom spin gyroscope's operational accuracy and compensate the random error caused by the nonlinear and weak-stability characteristic of the random atomic spin gyroscope (ASG) drift, the hybrid random drift error model based on autoregressive (AR) and genetic programming (GP) + genetic algorithm (GA) technique is established. The time series of random ASG drift is taken as the study object. The time series of random ASG drift is acquired by analyzing and preprocessing the measured data of ASG. The linear section model is established based on AR technique. After that, the nonlinear section model is built based on GP technique and GA is used to optimize the coefficients of the mathematic expression acquired by GP in order to obtain a more accurate model. The simulation result indicates that this hybrid model can effectively reflect the characteristics of the ASG's random drift. The square error of the ASG's random drift is reduced by 92.40%. Comparing with the AR technique and the GP + GA technique, the random drift is reduced by 9.34% and 5.06%, respectively. The hybrid modeling method can effectively compensate the ASG's random drift and improve the stability of the system.

  2. Modeling and optimizing of the random atomic spin gyroscope drift based on the atomic spin gyroscope

    Energy Technology Data Exchange (ETDEWEB)

    Quan, Wei; Lv, Lin, E-mail: lvlinlch1990@163.com; Liu, Baiqi [School of Instrument Science and Opto-Electronics Engineering, Beihang University, Beijing 100191 (China)

    2014-11-15

    In order to improve the atom spin gyroscope's operational accuracy and compensate the random error caused by the nonlinear and weak-stability characteristic of the random atomic spin gyroscope (ASG) drift, the hybrid random drift error model based on autoregressive (AR) and genetic programming (GP) + genetic algorithm (GA) technique is established. The time series of random ASG drift is taken as the study object. The time series of random ASG drift is acquired by analyzing and preprocessing the measured data of ASG. The linear section model is established based on AR technique. After that, the nonlinear section model is built based on GP technique and GA is used to optimize the coefficients of the mathematic expression acquired by GP in order to obtain a more accurate model. The simulation result indicates that this hybrid model can effectively reflect the characteristics of the ASG's random drift. The square error of the ASG's random drift is reduced by 92.40%. Comparing with the AR technique and the GP + GA technique, the random drift is reduced by 9.34% and 5.06%, respectively. The hybrid modeling method can effectively compensate the ASG's random drift and improve the stability of the system.

  3. Modeling and optimizing of the random atomic spin gyroscope drift based on the atomic spin gyroscope.

    Science.gov (United States)

    Quan, Wei; Lv, Lin; Liu, Baiqi

    2014-11-01

    In order to improve the atom spin gyroscope's operational accuracy and compensate the random error caused by the nonlinear and weak-stability characteristic of the random atomic spin gyroscope (ASG) drift, the hybrid random drift error model based on autoregressive (AR) and genetic programming (GP) + genetic algorithm (GA) technique is established. The time series of random ASG drift is taken as the study object. The time series of random ASG drift is acquired by analyzing and preprocessing the measured data of ASG. The linear section model is established based on AR technique. After that, the nonlinear section model is built based on GP technique and GA is used to optimize the coefficients of the mathematic expression acquired by GP in order to obtain a more accurate model. The simulation result indicates that this hybrid model can effectively reflect the characteristics of the ASG's random drift. The square error of the ASG's random drift is reduced by 92.40%. Comparing with the AR technique and the GP + GA technique, the random drift is reduced by 9.34% and 5.06%, respectively. The hybrid modeling method can effectively compensate the ASG's random drift and improve the stability of the system.

  4. 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.

  5. Model United Nations at CERN

    CERN Document Server

    2012-01-01

    From 20 to 22 January, 300 young people from international secondary schools in Switzerland, France and Turkey will meet at CERN to debate scientific topics at a Model UN Conference.   Representing some 50 countries, they will form committees and a model General Assembly to discuss the meeting’s chosen topic: “UN – World Science Pole for Progress”.

  6. 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.

  7. Application of the model of delocalized atoms to metallic glasses

    Science.gov (United States)

    Sanditov, D. S.; Darmaev, M. V.; Sanditov, B. D.

    2017-01-01

    The parameters of the model of delocalized atoms applied to metallic glasses have been calculated using the data on empirical constants of the Vogel-Fulcher-Tammann equation (for the temperature dependence of viscosity). It has been shown that these materials obey the same glass-formation criterion as amorphous organic polymers and inorganic glasses. This fact qualitatively confirms the universality of the main regularities of the liquid-glass transition process for all amorphous materials regardless of their origin. The energy of the delocalization of an atom in metallic glasses, Δɛ e ≈ 20-25 kJ/mol, coincides with the results obtained for oxide inorganic glasses. It is substantially lower than the activation energies for a viscous flow and for ion diffusion. The delocalization of an atom (its displacement from the equilibrium position) for amorphous metallic alloys is a low-energy small-scale process similar to that for other glass-like systems.

  8. Modeling molecular crystals formed by spin-active metal complexes by atom-atom potentials

    CERN Document Server

    Sinitskiy, Anton V; Tokmachev, Andrei M; Dronskowski, Richard

    2009-01-01

    We apply the atom-atom potentials to molecular crystals of iron (II) complexes with bulky organic ligands. The crystals under study are formed by low-spin or high-spin molecules of Fe(phen)$_{2}$(NCS)$_{2}$ (phen = 1,10-phenanthroline), Fe(btz)$_{2}$(NCS)$_{2}$ (btz = 5,5$^{\\prime }$,6,6$^{\\prime}$-tetrahydro-4\\textit{H},4$^{\\prime}$\\textit{H}-2,2$^{\\prime }$-bi-1,3-thiazine), and Fe(bpz)$_{2}$(bipy) (bpz = dihydrobis(1-pyrazolil)borate, and bipy = 2,2$^{\\prime}$-bipyridine). All molecular geometries are taken from the X-ray experimental data and assumed to be frozen. The unit cell dimensions and angles, positions of the centers of masses of molecules, and the orientations of molecules corresponding to the minimum energy at 1 atm and 1 GPa are calculated. The optimized crystal structures are in a good agreement with the experimental data. Sources of the residual discrepancies between the calculated and experimental structures are discussed. The intermolecular contributions to the enthalpy of the spin transiti...

  9. Theory and modelling of diamond fracture from an atomic perspective.

    Science.gov (United States)

    Brenner, Donald W; Shenderova, Olga A

    2015-03-28

    Discussed in this paper are several theoretical and computational approaches that have been used to better understand the fracture of both single-crystal and polycrystalline diamond at the atomic level. The studies, which include first principles calculations, analytic models and molecular simulations, have been chosen to illustrate the different ways in which this problem has been approached, the conclusions and their reliability that have been reached by these methods, and how these theory and modelling methods can be effectively used together.

  10. Non-linear Loudspeaker Unit Modelling

    DEFF Research Database (Denmark)

    Pedersen, Bo Rohde; Agerkvist, Finn T.

    2008-01-01

    Simulations of a 6½-inch loudspeaker unit are performed and compared with a displacement measurement. The non-linear loudspeaker model is based on the major nonlinear functions and expanded with time-varying suspension behaviour and flux modulation. The results are presented with FFT plots of three...... frequencies and different displacement levels. The model errors are discussed and analysed including a test with loudspeaker unit where the diaphragm is removed....

  11. Modeling of active beam units with Modelica

    DEFF Research Database (Denmark)

    Maccarini, Alessandro; Hultmark, Göran; Vorre, Anders

    2015-01-01

    This paper proposes an active beam model suitable for building energy simulations with the programming language Modelica. The model encapsulates empirical equations derived by a novel active beam terminal unit that operates with low-temperature heating and high-temperature cooling systems....... Measurements from a full-scale experiment are used to compare the thermal behavior of the active beam with the one predicted by simulations. The simulation results show that the model corresponds closely with the actual operation. The model predicts the outlet water temperature of the active beam...... with a maximum mean absolute error of 0.18 °C. In term of maximum mean absolute percentage error, simulation results differ by 0.9%. The methodology presented is general enough to be applied for modeling other active beam units. Modeling of active beam units with Modelica. Available from: https...

  12. A constructive model potential method for atomic interactions

    Science.gov (United States)

    Bottcher, C.; Dalgarno, A.

    1974-01-01

    A model potential method is presented that can be applied to many electron single centre and two centre systems. The development leads to a Hamiltonian with terms arising from core polarization that depend parametrically upon the positions of the valence electrons. Some of the terms have been introduced empirically in previous studies. Their significance is clarified by an analysis of a similar model in classical electrostatics. The explicit forms of the expectation values of operators at large separations of two atoms given by the model potential method are shown to be equivalent to the exact forms when the assumption is made that the energy level differences of one atom are negligible compared to those of the other.

  13. AtomDB and PyAtomDB: Atomic Data and Modelling Tools for High Energy and Non-Maxwellian Plasmas

    Science.gov (United States)

    Foster, Adam; Smith, Randall K.; Brickhouse, Nancy S.; Cui, Xiaohong

    2016-04-01

    The release of AtomDB 3 included a large wealth of inner shell ionization and excitation data allowing accurate modeling of non-equilibrium plasmas. We describe the newly calculated data and compare it to published literature data. We apply the new models to existing supernova remnant data such as W49B and N132D. We further outline progress towards AtomDB 3.1, including a new energy-dependent charge exchange cross sections.We present newly developed models for the spectra of electron-electron bremsstrahlung and those due to non-Maxwellian electron distributions.Finally, we present our new atomic database access tools, released as PyAtomDB, allowing powerful use of the underlying fundamental atomic data as well as the spectral emissivities.

  14. 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.

  15. Empirical model of atomic nitrogen in the upper thermosphere

    Science.gov (United States)

    Engebretson, M. J.; Mauersberger, K.; Kayser, D. C.; Potter, W. E.; Nier, A. O.

    1977-01-01

    Atomic nitrogen number densities in the upper thermosphere measured by the open source neutral mass spectrometer (OSS) on Atmosphere Explorer-C during 1974 and part of 1975 have been used to construct a global empirical model at an altitude of 375 km based on a spherical harmonic expansion. The most evident features of the model are large diurnal and seasonal variations of atomic nitrogen and only a moderate and latitude-dependent density increase during periods of geomagnetic activity. Maximum and minimum N number densities at 375 km for periods of low solar activity are 3.6 x 10 to the 6th/cu cm at 1500 LST (local solar time) and low latitude in the summer hemisphere and 1.5 x 10 to the 5th/cu cm at 0200 LST at mid-latitudes in the winter hemisphere.

  16. The Chocolate Shop and Atomic Orbitals: A New Atomic Model Created by High School Students to Teach Elementary Students

    Science.gov (United States)

    Liguori, Lucia

    2014-01-01

    Atomic orbital theory is a difficult subject for many high school and beginning undergraduate students, as it includes mathematical concepts not yet covered in the school curriculum. Moreover, it requires certain ability for abstraction and imagination. A new atomic orbital model "the chocolate shop" created "by" students…

  17. The Chocolate Shop and Atomic Orbitals: A New Atomic Model Created by High School Students to Teach Elementary Students

    Science.gov (United States)

    Liguori, Lucia

    2014-01-01

    Atomic orbital theory is a difficult subject for many high school and beginning undergraduate students, as it includes mathematical concepts not yet covered in the school curriculum. Moreover, it requires certain ability for abstraction and imagination. A new atomic orbital model "the chocolate shop" created "by" students…

  18. An interface capturing scheme for modeling atomization in compressible flows

    Science.gov (United States)

    Garrick, Daniel P.; Hagen, Wyatt A.; Regele, Jonathan D.

    2017-09-01

    The study of atomization in supersonic flow is critical to ensuring reliable ignition of scramjet combustors under startup conditions. 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 compressible flow requires robust numerical methods that can handle discontinuities caused by both shocks and material interfaces with high density ratios. In this work, a shock and interface capturing scheme is developed that uses the Harten-Lax-van Leer-Contact (HLLC) Riemann solver while a Tangent of Hyperbola for INterface Capturing (THINC) interface reconstruction scheme retains the fluid immiscibility condition in the volume fraction and phasic densities in the context of the five equation model. The approach includes the effects of compressibility, surface tension, and molecular viscosity. One and two-dimensional benchmark problems demonstrate the desirable interface sharpening and conservation properties of the approach. Simulations of secondary atomization of a cylindrical water column after its interaction with a shockwave show good qualitative agreement with experimentally observed behavior. Three-dimensional examples of primary atomization of a liquid jet in a Mach 2 crossflow demonstrate the robustness of the method.

  19. Extended Hubbard models for ultracold atoms in optical lattices

    Energy Technology Data Exchange (ETDEWEB)

    Juergensen, Ole

    2015-06-05

    In this thesis, the phase diagrams and dynamics of various extended Hubbard models for ultracold atoms in optical lattices are studied. Hubbard models are the primary description for many interacting particles in periodic potentials with the paramount example of the electrons in solids. The very same models describe the behavior of ultracold quantum gases trapped in the periodic potentials generated by interfering beams of laser light. These optical lattices provide an unprecedented access to the fundamentals of the many-particle physics that govern the properties of solid-state materials. They can be used to simulate solid-state systems and validate the approximations and simplifications made in theoretical models. This thesis revisits the numerous approximations underlying the standard Hubbard models with special regard to optical lattice experiments. The incorporation of the interaction between particles on adjacent lattice sites leads to extended Hubbard models. Offsite interactions have a strong influence on the phase boundaries and can give rise to novel correlated quantum phases. The extended models are studied with the numerical methods of exact diagonalization and time evolution, a cluster Gutzwiller approximation, as well as with the strong-coupling expansion approach. In total, this thesis demonstrates the high relevance of beyond-Hubbard processes for ultracold atoms in optical lattices. Extended Hubbard models can be employed to tackle unexplained problems of solid-state physics as well as enter previously inaccessible regimes.

  20. 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).

  1. A Comprehensive X-Ray Absorption Model for Atomic Oxygen

    Science.gov (United States)

    Gorczyca, T. W.; Bautista, M. A.; Hasoglu, M. F.; Garcia, J.; Gatuzz, E.; Kaastra, J. S.; Kallman, T. R.; Manson, S. T.; Mendoza, C.; Raassen, A. J. J.; de Vries, C. P.; Zatsarinny, O.

    2013-01-01

    An analytical formula is developed to accurately represent the photoabsorption cross section of atomic Oxygen for all energies of interest in X-ray spectral modeling. In the vicinity of the K edge, a Rydberg series expression is used to fit R-matrix results, including important orbital relaxation effects, that accurately predict the absorption oscillator strengths below threshold and merge consistently and continuously to the above-threshold cross section. Further, minor adjustments are made to the threshold energies in order to reliably align the atomic Rydberg resonances after consideration of both experimental and observed line positions. At energies far below or above the K-edge region, the formulation is based on both outer- and inner-shell direct photoionization, including significant shake-up and shake-off processes that result in photoionization-excitation and double-photoionization contributions to the total cross section. The ultimate purpose for developing a definitive model for oxygen absorption is to resolve standing discrepancies between the astronomically observed and laboratory-measured line positions, and between the inferred atomic and molecular oxygen abundances in the interstellar medium from XSTAR and SPEX spectral models.

  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. Chemical domain of QSAR models from atom-centered fragments.

    Science.gov (United States)

    Kühne, Ralph; Ebert, Ralf-Uwe; Schüürmann, Gerrit

    2009-12-01

    A methodology to characterize the chemical domain of qualitative and quantitative structure-activity relationship (QSAR) models based on the atom-centered fragment (ACF) approach is introduced. ACFs decompose the molecule into structural pieces, with each non-hydrogen atom of the molecule acting as an ACF center. ACFs vary with respect to their size in terms of the path length covered in each bonding direction starting from a given central atom and how comprehensively the neighbor atoms (including hydrogen) are described in terms of element type and bonding environment. In addition to these different levels of ACF definitions, the ACF match mode as degree of strictness of the ACF comparison between a test compound and a given ACF pool (such as from a training set) has to be specified. Analyses of the prediction statistics of three QSAR models with their training sets as well as with external test sets and associated subsets demonstrate a clear relationship between the prediction performance and the levels of ACF definition and match mode. The findings suggest that second-order ACFs combined with a borderline match mode may serve as a generic and at the same time a mechanistically sound tool to define and evaluate the chemical domain of QSAR models. Moreover, four standard categories of the ACF-based membership to a given chemical domain (outside, borderline outside, borderline inside, inside) are introduced that provide more specific information about the expected QSAR prediction performance. As such, the ACF-based characterization of the chemical domain appears to be particularly useful for QSAR applications in the context of REACH and other regulatory schemes addressing the safety evaluation of chemical compounds.

  4. Atomic collision processes for modelling cool star spectra

    Science.gov (United States)

    Barklem, Paul

    2015-05-01

    The abundances of chemical elements in cool stars are very important in many problems in modern astrophysics. They provide unique insight into the chemical and dynamical evolution of the Galaxy, stellar processes such as mixing and gravitational settling, the Sun and its place in the Galaxy, and planet formation, to name a just few examples. Modern telescopes and spectrographs measure stellar spectral lines with precision of order 1 per cent, and planned surveys will provide such spectra for millions of stars. However, systematic errors in the interpretation of observed spectral lines leads to abundances with uncertainties greater than 20 per cent. Greater precision in the interpreted abundances should reasonably be expected to lead to significant discoveries, and improvements in atomic data used in stellar atmosphere models play a key role in achieving such advances in precision. In particular, departures from the classical assumption of local thermodynamic equilibrium (LTE) represent a significant uncertainty in the modelling of stellar spectra and thus derived chemical abundances. Non-LTE modelling requires large amounts of radiative and collisional data for the atomic species of interest. I will focus on inelastic collision processes due to electron and hydrogen atom impacts, the important perturbers in cool stars, and the progress that has been made. I will discuss the impact on non-LTE modelling, and what the modelling tells us about the types of collision processes that are important and the accuracy required. More specifically, processes of fundamentally quantum mechanical nature such as spin-changing collisions and charge transfer have been found to be very important in the non-LTE modelling of spectral lines of lithium, oxygen, sodium and magnesium.

  5. 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.

  6. Sudden birth of entanglement between two atoms in a double JC model

    Institute of Scientific and Technical Information of China (English)

    Mingdi Du; Maofa Fang; Xiang Liu

    2009-01-01

    Sudden birth of entanglement between two initially separate atoms interacting with two entangled photons in a double JC model is investigated,arid the influences of different atomic initial states on entanglement among atoms are discussed.The results show that sudden birth of entanglement can occur when the two atoms are initially in excited states.

  7. Model study in chemisorption: atomic hydrogen on beryllium clusters

    Energy Technology Data Exchange (ETDEWEB)

    Bauschlicher, C.W. Jr.

    1976-08-01

    The interaction between atomic hydrogen and the (0001) surface of Be metal has been studied by ab initio electronic structure theory. Self-consistent-field (SCF) calculations have been performed using minimum, optimized minimum, double zeta and mixed basis sets for clusters as large as 22 Be atoms. The binding energy and equilibrium geometry (the distance to the surface) were determined for 4 sites. Both spatially restricted (the wavefunction was constrained to transform as one of the irreducible representations of the molecular point group) and unrestricted SCF calculations were performed. Using only the optimized minimum basis set, clusters containing as many as 22 beryllium atoms have been investigated. From a variety of considerations, this cluster is seen to be nearly converged within the model used, providing the most reliable results for chemisorption. The site dependence of the frequency is shown to be a geometrical effect depending on the number and angle of the bonds. The diffusion of atomic hydrogen through a perfect beryllium crystal is predicted to be energetically unfavorable. The cohesive energy, the ionization energy and the singlet-triplet separation were computed for the clusters without hydrogen. These quantities can be seen as a measure of the total amount of edge effects. The chemisorptive properties are not related to the total amount of edge effects, but rather the edge effects felt by the adsorbate bonding berylliums. This lack of correlation with the total edge effects illustrates the local nature of the bonding, further strengthening the cluster model for chemisorption. A detailed discussion of the bonding and electronic structure is included. The remaining edge effects for the Be/sub 22/ cluster are discussed.

  8. Atom-field entanglement in two-atom Jaynes-Cummings model with intensity-dependent coupling

    OpenAIRE

    Bashkirov, E. K.

    2014-01-01

    An exact solution of the problem of two-atom one- and two-mode Jaynes-Cummings model with intensity-dependent coupling is presented. Asymptotic solutions for system state vectors are obtained in the approximation of large initial coherent fields. The atom-field entanglement is investigated on the basis of the reduced atomic entropy dynamics. The possibility of the system being initially in a pure disentangled state to revive into this state during the evolution process for both models is show...

  9. Lattice location of dopant atoms: An -body model calculation

    Indian Academy of Sciences (India)

    N K Deepak

    2010-03-01

    The channelling and scattering yields of 1 MeV -particles in the $\\langle 1 0 0 \\rangle$, $\\langle 1 1 0 \\rangle and $\\langle 1 1 1 \\rangle$ directions of silicon implanted with bismuth and ytterbium have been simulated using -body model. The close encounter yield from dopant atoms in silicon is determined from the flux density, using the Bontemps and Fontenille method. All previous works reported in literature so far have been done with computer programmes using a statistical analytical expression or by a binary collision model or a continuum model. These results at the best gave only the transverse displacement of the lattice site from the concerned channelling direction. Here we applied the superior -body model to study the yield from bismuth in silicon. The finding that bismuth atom occupies a position close to the silicon substitutional site is new. The transverse displacement of the suggested lattice site from the channelling direction is consistent with the experimental results. The above model is also applied to determine the location of ytterbium in silicon. The present values show good agreement with the experimental results.

  10. Atomic-level structural and functional model of a bacterial photosynthetic membrane vesicle.

    Science.gov (United States)

    Sener, Melih K; Olsen, John D; Hunter, C Neil; Schulten, Klaus

    2007-10-02

    The photosynthetic unit (PSU) of purple photosynthetic bacteria consists of a network of bacteriochlorophyll-protein complexes that absorb solar energy for eventual conversion to ATP. Because of its remarkable simplicity, the PSU can serve as a prototype for studies of cellular organelles. In the purple bacterium Rhodobacter sphaeroides the PSU forms spherical invaginations of the inner membrane, approximately 70 nm in diameter, composed mostly of light-harvesting complexes, LH1 and LH2, and reaction centers (RCs). Atomic force microscopy studies of the intracytoplasmic membrane have revealed the overall spatial organization of the PSU. In the present study these atomic force microscopy data were used to construct three-dimensional models of an entire membrane vesicle at the atomic level by using the known structure of the LH2 complex and a structural model of the dimeric RC-LH1 complex. Two models depict vesicles consisting of 9 or 18 dimeric RC-LH1 complexes and 144 or 101 LH2 complexes, representing a total of 3,879 or 4,464 bacteriochlorophylls, respectively. The in silico reconstructions permit a detailed description of light absorption and electronic excitation migration, including computation of a 50-ps excitation lifetime and a 95% quantum efficiency for one of the model membranes, and demonstration of excitation sharing within the closely packed RC-LH1 dimer arrays.

  11. Modeling Emission of Heavy Energetic Neutral Atoms from the Heliosphere

    Science.gov (United States)

    Swaczyna, Paweł; Bzowski, Maciej

    2017-09-01

    Observations of energetic neutral atoms (ENAs) are a fruitful tool for remote diagnosis of the plasma in the heliosphere and its vicinity. So far, instruments detecting ENAs from the heliosphere were configured for observations of hydrogen atoms. Here, we estimate emissions of ENAs of the heavy chemical elements helium, oxygen, nitrogen, and neon. A large portion of the heliospheric ENAs is created in the inner heliosheath from neutralized interstellar pick-up ions (PUIs). We modeled this process and calculated full-sky intensities of ENAs for energies 0.2–130 keV/nuc. We found that the largest fluxes among considered species are expected for helium, smaller for oxygen and nitrogen, and smallest for neon. The obtained intensities are 50–106 times smaller than the hydrogen ENA intensities observed by IBEX. The detection of heavy ENAs will be possible if a future ENA detector is equipped with the capability to measure the masses of observed atoms. Because of different reaction cross-sections among the different species, observations of heavy ENAs can allow for a better understanding of global structure of the heliosphere as well as the transport and energization of PUIs in the heliosphere.

  12. Quantum Rabi model in the Brillouin zone with ultracold atoms

    Science.gov (United States)

    Felicetti, Simone; Rico, Enrique; Sabin, Carlos; Ockenfels, Till; Koch, Johannes; Leder, Martin; Grossert, Christopher; Weitz, Martin; Solano, Enrique

    2017-01-01

    The quantum Rabi model describes the interaction between a two-level quantum system and a single bosonic mode. We propose a method to perform a quantum simulation of the quantum Rabi model, introducing an implementation of the two-level system provided by the occupation of Bloch bands in the first Brillouin zone by ultracold atoms in tailored optical lattices. The effective qubit interacts with a quantum harmonic oscillator implemented in an optical dipole trap. Our realistic proposal allows one to experimentally investigate the quantum Rabi model for extreme parameter regimes, which are not achievable with natural light-matter interactions. When the simulated wave function exceeds the validity region of the simulation, we identify a generalized version of the quantum Rabi model in a periodic phase space.

  13. An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

    Science.gov (United States)

    Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

    2009-05-01

    Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.

  14. Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.

    Science.gov (United States)

    Laury, Marie L; Wang, Lee-Ping; Pande, Vijay S; Head-Gordon, Teresa; Ponder, Jay W

    2015-07-23

    A set of improved parameters for the AMOEBA polarizable atomic multipole water model is developed. An automated procedure, ForceBalance, is used to adjust model parameters to enforce agreement with ab initio-derived results for water clusters and experimental data for a variety of liquid phase properties across a broad temperature range. The values reported here for the new AMOEBA14 water model represent a substantial improvement over the previous AMOEBA03 model. The AMOEBA14 model accurately predicts the temperature of maximum density and qualitatively matches the experimental density curve across temperatures from 249 to 373 K. Excellent agreement is observed for the AMOEBA14 model in comparison to experimental properties as a function of temperature, including the second virial coefficient, enthalpy of vaporization, isothermal compressibility, thermal expansion coefficient, and dielectric constant. The viscosity, self-diffusion constant, and surface tension are also well reproduced. In comparison to high-level ab initio results for clusters of 2-20 water molecules, the AMOEBA14 model yields results similar to AMOEBA03 and the direct polarization iAMOEBA models. With advances in computing power, calibration data, and optimization techniques, we recommend the use of the AMOEBA14 water model for future studies employing a polarizable water model.

  15. 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...

  16. Fully variational average atom model with ion-ion correlations.

    Science.gov (United States)

    Starrett, C E; Saumon, D

    2012-02-01

    An average atom model for dense ionized fluids that includes ion correlations is presented. The model assumes spherical symmetry and is based on density functional theory, the integral equations for uniform fluids, and a variational principle applied to the grand potential. Starting from density functional theory for a mixture of classical ions and quantum mechanical electrons, an approximate grand potential is developed, with an external field being created by a central nucleus fixed at the origin. Minimization of this grand potential with respect to electron and ion densities is carried out, resulting in equations for effective interaction potentials. A third condition resulting from minimizing the grand potential with respect to the average ion charge determines the noninteracting electron chemical potential. This system is coupled to a system of point ions and electrons with an ion fixed at the origin, and a closed set of equations is obtained. Solution of these equations results in a self-consistent electronic and ionic structure for the plasma as well as the average ionization, which is continuous as a function of temperature and density. Other average atom models are recovered by application of simplifying assumptions.

  17. Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters.

    Science.gov (United States)

    Chapman, Michael S; Trzynka, Andrew; Chapman, Brynmor K

    2013-04-01

    When refining the fit of component atomic structures into electron microscopic reconstructions, use of a resolution-dependent atomic density function makes it possible to jointly optimize the atomic model and imaging parameters of the microscope. Atomic density is calculated by one-dimensional Fourier transform of atomic form factors convoluted with a microscope envelope correction and a low-pass filter, allowing refinement of imaging parameters such as resolution, by optimizing the agreement of calculated and experimental maps. A similar approach allows refinement of atomic displacement parameters, providing indications of molecular flexibility even at low resolution. A modest improvement in atomic coordinates is possible following optimization of these additional parameters. Methods have been implemented in a Python program that can be used in stand-alone mode for rigid-group refinement, or embedded in other optimizers for flexible refinement with stereochemical restraints. The approach is demonstrated with refinements of virus and chaperonin structures at resolutions of 9 through 4.5 Å, representing regimes where rigid-group and fully flexible parameterizations are appropriate. Through comparisons to known crystal structures, flexible fitting by RSRef is shown to be an improvement relative to other methods and to generate models with all-atom rms accuracies of 1.5-2.5 Å at resolutions of 4.5-6 Å.

  18. Analysis and application of the scale effect of flood discharge atomization model

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    The phenomenon of discharge atomization occurs as hydraulic structures discharging,which influences the safety of power station,electrical equipment and produces environmental pollution.A series of physical model tests and feedback analysis are adapted to preliminarily study the scale effect of discharge atomization model by use of the field observation data of discharge atomization.The effect of Re and We numbers of flow on the atomization intensity is analyzed.A conversion relationship of atomization intensity between prototype and model results and the similarity criteria of the atomization range are developed. The conclusion is that the surface tension of discharge atomization model could be ignored when the Weber number is larger than 500.Some case studies are given by use of the similitude criteria of the atomization model.

  19. 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.

  20. Development of a Kohn-Sham like potential in the Self-Consistent Atomic Deformation Model

    CERN Document Server

    Mehl, M J; Stokes, H T

    1996-01-01

    This is a brief description of how to derive the local ``atomic'' potentials from the Self-Consistent Atomic Deformation (SCAD) model density function. Particular attention is paid to the spherically averaged case.

  1. Development of a Kohn-Sham like potential in the Self-Consistent Atomic Deformation Model

    OpenAIRE

    Mehl, M. J.; Boyer, L. L.; Stokes, H. T.

    1996-01-01

    This is a brief description of how to derive the local ``atomic'' potentials from the Self-Consistent Atomic Deformation (SCAD) model density function. Particular attention is paid to the spherically averaged case.

  2. Monte Carlo modeling of atomic oxygen attack of polymers with protective coatings on LDEF

    Science.gov (United States)

    Banks, Bruce A.; Degroh, Kim K.; Auer, Bruce M.; Gebauer, Linda; Edwards, Jonathan L.

    1993-01-01

    Characterization of the behavior of atomic oxygen interaction with materials on the Long Duration Exposure Facility (LDEF) assists in understanding of the mechanisms involved. Thus the reliability of predicting in-space durability of materials based on ground laboratory testing should be improved. A computational model which simulates atomic oxygen interaction with protected polymers was developed using Monte Carlo techniques. Through the use of an assumed mechanistic behavior of atomic oxygen interaction based on in-space atomic oxygen erosion of unprotected polymers and ground laboratory atomic oxygen interaction with protected polymers, prediction of atomic oxygen interaction with protected polymers on LDEF was accomplished. However, the results of these predictions are not consistent with the observed LDEF results at defect sites in protected polymers. Improved agreement between observed LDEF results and predicted Monte Carlo modeling can be achieved by modifying of the atomic oxygen interactive assumptions used in the model. LDEF atomic oxygen undercutting results, modeling assumptions, and implications are presented.

  3. Hidden Markov Model of atomic quantum jump dynamics in an optically probed cavity

    DEFF Research Database (Denmark)

    Gammelmark, S.; Molmer, K.; Alt, W.

    2014-01-01

    We analyze the quantum jumps of an atom interacting with a cavity field. The strong atom- field interaction makes the cavity transmission depend on the time dependent atomic state, and we present a Hidden Markov Model description of the atomic state dynamics which is conditioned in a Bayesian......, the atomic state is determined in a Bayesian manner from the measurement data, and we present an iterative protocol, which determines both the atomic state and the model parameters. As a new element in the treatment of observed quantum systems, we employ a Bayesian approach that conditions the atomic state...... manner on the detected signal. We suggest that small variations in the observed signal may be due to spatial motion of the atom within the cavity, and we represent the atomic system by a number of hidden states to account for both the small variations and the internal state jump dynamics. In our theory...

  4. Hidden Markov Model of atomic quantum jump dynamics in an optically probed cavity

    DEFF Research Database (Denmark)

    Gammelmark, S.; Molmer, K.; Alt, W.

    2014-01-01

    manner on the detected signal. We suggest that small variations in the observed signal may be due to spatial motion of the atom within the cavity, and we represent the atomic system by a number of hidden states to account for both the small variations and the internal state jump dynamics. In our theory......We analyze the quantum jumps of an atom interacting with a cavity field. The strong atom- field interaction makes the cavity transmission depend on the time dependent atomic state, and we present a Hidden Markov Model description of the atomic state dynamics which is conditioned in a Bayesian......, the atomic state is determined in a Bayesian manner from the measurement data, and we present an iterative protocol, which determines both the atomic state and the model parameters. As a new element in the treatment of observed quantum systems, we employ a Bayesian approach that conditions the atomic state...

  5. Ab initio determination of kinetics for atomic layer deposition modeling

    Science.gov (United States)

    Remmers, Elizabeth M.

    A first principles model is developed to describe the kinetics of atomic layer deposition (ALD) systems. This model requires no fitting parameters, as it is based on the reaction pathways, structures, and energetics obtained from quantum-chemical studies. Using transition state theory and partition functions from statistical mechanics, equilibrium constants and reaction rates can be calculated. Several tools were created in Python to aid in the calculation of these quantities, and this procedure was applied to two systems- zinc oxide deposition from diethyl zinc (DEZ) and water, and alumina deposition from trimethyl aluminum (TMA) and water. A Gauss-Jordan factorization is used to decompose the system dynamics, and the resulting systems of equations are solved numerically to obtain the temporal concentration profiles of these two deposition systems.

  6. Model of spacecraft atomic oxygen and solar exposure microenvironments

    Science.gov (United States)

    Bourassa, R. J.; Pippin, H. G.

    1993-01-01

    Computer models of environmental conditions in Earth orbit are needed for the following reasons: (1) derivation of material performance parameters from orbital test data, (2) evaluation of spacecraft hardware designs, (3) prediction of material service life, and (4) scheduling spacecraft maintenance. To meet these needs, Boeing has developed programs for modeling atomic oxygen (AO) and solar radiation exposures. The model allows determination of AO and solar ultraviolet (UV) radiation exposures for spacecraft surfaces (1) in arbitrary orientations with respect to the direction of spacecraft motion, (2) overall ranges of solar conditions, and (3) for any mission duration. The models have been successfully applied to prediction of experiment environments on the Long Duration Exposure Facility (LDEF) and for analysis of selected hardware designs for deployment on other spacecraft. The work on these models has been reported at previous LDEF conferences. Since publication of these reports, a revision has been made to the AO calculation for LDEF, and further work has been done on the microenvironments model for solar exposure.

  7. 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.

  8. Atomic scale modelling of hexagonal structured metallic fission product alloys.

    Science.gov (United States)

    Middleburgh, S C; King, D M; Lumpkin, G R

    2015-04-01

    Noble metal particles in the Mo-Pd-Rh-Ru-Tc system have been simulated on the atomic scale using density functional theory techniques for the first time. The composition and behaviour of the epsilon phases are consistent with high-entropy alloys (or multi-principal component alloys)-making the epsilon phase the only hexagonally close packed high-entropy alloy currently described. Configurational entropy effects were considered to predict the stability of the alloys with increasing temperatures. The variation of Mo content was modelled to understand the change in alloy structure and behaviour with fuel burnup (Mo molar content decreases in these alloys as burnup increases). The predicted structures compare extremely well with experimentally ascertained values. Vacancy formation energies and the behaviour of extrinsic defects (including iodine and xenon) in the epsilon phase were also investigated to further understand the impact that the metallic precipitates have on fuel performance.

  9. Penetration of alkali atoms throughout a graphene membrane: theoretical modeling.

    Science.gov (United States)

    Boukhvalov, D W; Virojanadara, C

    2012-03-07

    Theoretical studies of penetration of various alkali atoms (Li, Na, Rb, Cs) throughout a graphene membrane grown on a silicon carbide substrate are reported and compared with recent experimental results. Results of first principles modeling demonstrate a rather low (about 0.8 eV) energy barrier for the formation of temporary defects in the carbon layer required for the penetration of Li at a high concentration of adatoms, a higher (about 2 eV) barrier for Na, and barriers above 4 eV for Rb and Cs. Experiments prove migration of lithium adatoms from the graphene surface to the buffer layer and SiC substrate at room temperature, sodium at 100 °C and impenetrability of the graphene membrane for Rb and Cs. Differences between epitaxial and free-standing graphene for the penetration of alkali ions are also discussed.

  10. Independent-particle models for light negative atomic ions

    Science.gov (United States)

    Ganas, P. S.; Talman, J. D.; Green, A. E. S.

    1980-01-01

    For the purposes of astrophysical, aeronomical, and laboratory application, a precise independent-particle model for electrons in negative atomic ions of the second and third period is discussed. The optimum-potential model (OPM) of Talman et al. (1979) is first used to generate numerical potentials for eight of these ions. Results for total energies and electron affinities are found to be very close to Hartree-Fock solutions. However, the OPM and HF electron affinities both depart significantly from experimental affinities. For this reason, two analytic potentials are developed whose inner energy levels are very close to the OPM and HF levels but whose last electron eigenvalues are adjusted precisely with the magnitudes of experimental affinities. These models are: (1) a four-parameter analytic characterization of the OPM potential and (2) a two-parameter potential model of the Green, Sellin, Zachor type. The system O(-) or e-O, which is important in upper atmospheric physics is examined in some detail.

  11. Modelling laser-atom interactions in the strong field regime

    CERN Document Server

    Galstyan, A; Mota-Furtado, F; O'Mahony, P F; Janssens, N; Jenkins, S D; Chuluunbaatar, O; Piraux, B

    2016-01-01

    We consider the ionisation of atomic hydrogen by a strong infrared field. We extend and study in more depth an existing semi-analytical model. Starting from the time-dependent Schroedinger equation in momentum space and in the velocity gauge we substitute the kernel of the non-local Coulomb potential by a sum of N separable potentials, each of them supporting one hydrogen bound state. This leads to a set of N coupled one-dimensional linear Volterra integral equations to solve. We analyze the gauge problem for the model, the different ways of generating the separable potentials and establish a clear link with the strong field approximation which turns out to be a limiting case of the present model. We calculate electron energy spectra as well as the time evolution of electron wave packets in momentum space. We compare and discuss the results obtained with the model and with the strong field approximation and examine in this context, the role of excited states.

  12. Entanglement in Three-Atom Tavis-Cummings Model Induced by a Thermal Field

    Institute of Scientific and Technical Information of China (English)

    CAI Jin-Fang; LIU Hui-Ping

    2005-01-01

    The explicit form of the evolution operator for the three-atom Tavis-Cummings model is given. The atoms can be entangled through their interaction with a thermal field. The degree of entanglement depends on the mean photon number of the thermal field and the initial state of the atoms.

  13. Parallelizing the Cellular Potts Model on graphics processing units

    Science.gov (United States)

    Tapia, José Juan; D'Souza, Roshan M.

    2011-04-01

    The Cellular Potts Model (CPM) is a lattice based modeling technique used for simulating cellular structures in computational biology. The computational complexity of the model means that current serial implementations restrict the size of simulation to a level well below biological relevance. Parallelization on computing clusters enables scaling the size of the simulation but marginally addresses computational speed due to the limited memory bandwidth between nodes. In this paper we present new data-parallel algorithms and data structures for simulating the Cellular Potts Model on graphics processing units. Our implementations handle most terms in the Hamiltonian, including cell-cell adhesion constraint, cell volume constraint, cell surface area constraint, and cell haptotaxis. We use fine level checkerboards with lock mechanisms using atomic operations to enable consistent updates while maintaining a high level of parallelism. A new data-parallel memory allocation algorithm has been developed to handle cell division. Tests show that our implementation enables simulations of >10 cells with lattice sizes of up to 256 3 on a single graphics card. Benchmarks show that our implementation runs ˜80× faster than serial implementations, and ˜5× faster than previous parallel implementations on computing clusters consisting of 25 nodes. The wide availability and economy of graphics cards mean that our techniques will enable simulation of realistically sized models at a fraction of the time and cost of previous implementations and are expected to greatly broaden the scope of CPM applications.

  14. The Tübingen Model-Atom Database: A Revised Aluminum Model Atom and its Application for the Spectral Analysis of White Dwarfs

    Science.gov (United States)

    Löbling, L.

    2017-03-01

    Aluminum (Al) nucleosynthesis takes place during the asymptotic-giant-branch (AGB) phase of stellar evolution. Al abundance determinations in hot white dwarf stars provide constraints to understand this process. Precise abundance measurements require advanced non-local thermodynamic stellar-atmosphere models and reliable atomic data. In the framework of the German Astrophysical Virtual Observatory (GAVO), the Tübingen Model-Atom Database (TMAD) contains ready-to- use model atoms for elements from hydrogen to barium. A revised, elaborated Al model atom has recently been added. We present preliminary stellar-atmosphere models and emergent Al line spectra for the hot white dwarfs G191–B2B and RE 0503–289.

  15. 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

  16. 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.

  17. Global atmospheric model for mercury including oxidation by bromine atoms

    Directory of Open Access Journals (Sweden)

    C. D. Holmes

    2010-12-01

    Full Text Available Global models of atmospheric mercury generally assume that gas-phase OH and ozone are the main oxidants converting Hg0 to HgII and thus driving mercury deposition to ecosystems. However, thermodynamic considerations argue against the importance of these reactions. We demonstrate here the viability of atomic bromine (Br as an alternative Hg0 oxidant. We conduct a global 3-D simulation with the GEOS-Chem model assuming gas-phase Br to be the sole Hg0 oxidant (Hg + Br model and compare to the previous version of the model with OH and ozone as the sole oxidants (Hg + OH/O3 model. We specify global 3-D Br concentration fields based on our best understanding of tropospheric and stratospheric Br chemistry. In both the Hg + Br and Hg + OH/O3 models, we add an aqueous photochemical reduction of HgII in cloud to impose a tropospheric lifetime for mercury of 6.5 months against deposition, as needed to reconcile observed total gaseous mercury (TGM concentrations with current estimates of anthropogenic emissions. This added reduction would not be necessary in the Hg + Br model if we adjusted the Br oxidation kinetics downward within their range of uncertainty. We find that the Hg + Br and Hg + OH/O3 models are equally capable of reproducing the spatial distribution of TGM and its seasonal cycle at northern mid-latitudes. The Hg + Br model shows a steeper decline of TGM concentrations from the tropics to southern mid-latitudes. Only the Hg + Br model can reproduce the springtime depletion and summer rebound of TGM observed at polar sites; the snowpack component of GEOS-Chem suggests that 40% of HgII deposited to snow in the Arctic is transferred to the ocean and land reservoirs, amounting to a net deposition flux to the Arctic of 60 Mg a−1. Summertime events of depleted Hg0 at Antarctic sites due to subsidence are much better simulated by

  18. Global atmospheric model for mercury including oxidation by bromine atoms

    Directory of Open Access Journals (Sweden)

    C. D. Holmes

    2010-08-01

    Full Text Available Global models of atmospheric mercury generally assume that OH and ozone are the main oxidants converting Hg0 to HgII and thus driving mercury deposition to ecosystems. However, thermodynamic considerations argue against the importance of these reactions. We demonstrate here the viability of atomic bromine (Br as an alternative Hg0 oxidant. We conduct a global 3-D simulation with the GEOS-Chem model assuming Br to be the sole Hg0 oxidant (Hg + Br model and compare to the previous version of the model with OH and ozone as the sole oxidants (Hg + OH/O3 model. We specify global 3-D Br concentration fields based on our best understanding of tropospheric and stratospheric Br chemistry. In both the Hg + Br and Hg + OH/O3 models, we add an aqueous photochemical reduction of HgII in cloud to impose a tropospheric lifetime for mercury of 6.5 months against deposition, as needed to reconcile observed total gaseous mercury (TGM concentrations with current estimates of anthropogenic emissions. This added reduction would not be necessary in the Hg + Br model if we adjusted the Br oxidation kinetics downward within their range of uncertainty. We find that the Hg + Br and Hg + OH/O3 models are equally capable of reproducing the spatial distribution of TGM and its seasonal cycle at northern mid-latitudes. The Hg + Br model shows a steeper decline of TGM concentrations from the tropics to southern mid-latitudes. Only the Hg + Br model can reproduce the springtime depletion and summer rebound of TGM observed at polar sites; the snowpack component of GEOS-Chem suggests that 40% of HgII deposited to snow in the Arctic is transferred to the ocean and land reservoirs, amounting to a net deposition flux of 60 Mg a−1. Summertime events of depleted Hg0 at Antarctic sites due to subsidence are much better simulated by the Hg + Br model. Model

  19. Secondary Students' Mental Models of Atoms and Molecules: Implications for Teaching Chemistry.

    Science.gov (United States)

    Harrison, Allan G.; Treagust, David F.

    1996-01-01

    Examines the reasoning behind views of atoms and molecules held by students (n=48) and investigates how mental models may assist or hamper further instruction in chemistry. Reports that students prefer models of atoms and molecules that depict them as discrete, concrete structures. Recommends that teachers develop student modeling skills and…

  20. Development of a phenomenological model for coal slurry atomization

    Energy Technology Data Exchange (ETDEWEB)

    Dooher, J.P. [Adelphi Univ., Garden City, NY (United States)

    1995-11-01

    Highly concentrated suspensions of coal particles in water or alternate fluids appear to have a wide range of applications for energy production. For enhanced implementation of coal slurry fuel technology, an understanding of coal slurry atomization as a function coal and slurry properties for specific mechanical configurations of nozzle atomizers should be developed.

  1. General model of depolarization and transfer of polarization of singly ionized atoms by collisions with hydrogen atoms

    Science.gov (United States)

    Derouich, M.

    2017-02-01

    Simulations of the generation of the atomic polarization is necessary for interpreting the second solar spectrum. For this purpose, it is important to rigorously determine the effects of the isotropic collisions with neutral hydrogen on the atomic polarization of the neutral atoms, ionized atoms and molecules. Our aim is to treat in generality the problem of depolarizing isotropic collisions between singly ionized atoms and neutral hydrogen in its ground state. Using our numerical code, we computed the collisional depolarization rates of the p-levels of ions for large number of values of the effective principal quantum number n* and the Unsöld energy Ep. Then, genetic programming has been utilized to fit the available depolarization rates. As a result, strongly non-linear relationships between the collisional depolarization rates, n* and Ep are obtained, and are shown to reproduce the original data with accuracy clearly better than 10%. These relationships allow quick calculations of the depolarizing collisional rates of any simple ion which is very useful for the solar physics community. In addition, the depolarization rates associated to the complex ions and to the hyperfine levels can be easily derived from our results. In this work we have shown that by using powerful numerical approach and our collisional method, general model giving the depolarization of the ions can be obtained to be exploited for solar applications.

  2. Operation of the computer model for direct atomic oxygen exposure of Earth satellites

    Science.gov (United States)

    Bourassa, R. J.; Gruenbaum, P. E.; Gillis, J. R.; Hargraves, C. R.

    1995-01-01

    One of the primary causes of material degradation in low Earth orbit (LEO) is exposure to atomic oxygen. When atomic oxygen molecules collide with an orbiting spacecraft, the relative velocity is 7 to 8 km/sec and the collision energy is 4 to 5 eV per atom. Under these conditions, atomic oxygen may initiate a number of chemical and physical reactions with exposed materials. These reactions contribute to material degradation, surface erosion, and contamination. Interpretation of these effects on materials and the design of space hardware to withstand on-orbit conditions requires quantitative knowledge of the atomic oxygen exposure environment. Atomic oxygen flux is a function of orbit altitude, the orientation of the orbit plan to the Sun, solar and geomagnetic activity, and the angle between exposed surfaces and the spacecraft heading. We have developed a computer model to predict the atomic oxygen exposure of spacecraft in low Earth orbit. The application of this computer model is discussed.

  3. 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

  4. Multipole correction of atomic monopole models of molecular charge distribution. I. Peptides

    Science.gov (United States)

    Sokalski, W. A.; Keller, D. A.; Ornstein, R. L.; Rein, R.

    1993-01-01

    The defects in atomic monopole models of molecular charge distribution have been analyzed for several model-blocked peptides and compared with accurate quantum chemical values. The results indicate that the angular characteristics of the molecular electrostatic potential around functional groups capable of forming hydrogen bonds can be considerably distorted within various models relying upon isotropic atomic charges only. It is shown that these defects can be corrected by augmenting the atomic point charge models by cumulative atomic multipole moments (CAMMs). Alternatively, sets of off-center atomic point charges could be automatically derived from respective multipoles, providing approximately equivalent corrections. For the first time, correlated atomic multipoles have been calculated for N-acetyl, N'-methylamide-blocked derivatives of glycine, alanine, cysteine, threonine, leucine, lysine, and serine using the MP2 method. The role of the correlation effects in the peptide molecular charge distribution are discussed.

  5. Kinetic model of the bichromatic dark trap for atoms

    Science.gov (United States)

    Krasnov, I. V.

    2017-08-01

    A kinetic model of atom confinement in a bichromatic dark trap (BDT) is developed with the goal of describing its dissipative properties. The operating principle of the deep BDT is based on using the combination of multiple bichromatic cosine-Gaussian optical beams (CGBs) for creating high-potential barriers, which is described in our previous work (Krasnov 2016 Laser Phys. 26 105501). In the indicated work, particle motion in the BDT is described in terms of classical trajectories. In the present study, particle motion is analyzed by means of the Wigner function (phase-space distribution function (DF)), which allows one to properly take into account the quantum fluctuations of optical forces. Besides, we consider an improved scheme of the BDT, where CGBs create, apart from plane potential barriers, a narrow cooling layer. We find an asymptotic solution of the Fokker-Planck equation for the DF and show that the DF of particles deeply trapped in a BDT with a cooling layer is the Tsallis distribution with the effective temperature, which can be considerably lower than in a BDT without a cooling layer. Moreover, it can be adjusted by slightly changing the CGBs’ radii. We also study the effect of particle escape from the trap due to the scattering of resonant photons and show that the particle lifetime in a BDT can exceed several tens of hours when it is limited by photon scattering.

  6. MELCOR modeling of Fukushima unit 2 accident

    Energy Technology Data Exchange (ETDEWEB)

    Sevon, Tuomo [VTT Technical Research Centre of Finland, Espoo (Finland)

    2014-12-15

    A MELCOR model of the Fukushima Daiichi unit 2 accident was created in order to get a better understanding of the event and to improve severe accident modeling methods. The measured pressure and water level could be reproduced relatively well with the calculation. This required adjusting the RCIC system flow rates and containment leak area so that a good match to the measurements is achieved. Modeling of gradual flooding of the torus room with water that originated from the tsunami was necessary for a satisfactory reproduction of the measured containment pressure. The reactor lower head did not fail in this calculation, and all the fuel remained in the RPV. 13 % of the fuel was relocated from the core area, and all the fuel rods lost their integrity, releasing at least some volatile radionuclides. According to the calculation, about 90 % of noble gas inventory and about 0.08 % of cesium inventory was released to the environment. The release started 78 h after the earthquake, and a second release peak came at 90 h. Uncertainties in the calculation are very large because there is scarce public data available about the Fukushima power plant and because it is not yet possible to inspect the status of the reactor and the containment. Uncertainty in the calculated cesium release is larger than factor of ten.

  7. Effect of an external radiation field on the properties of the atoms and cavity field in the two-atom Tavis-Cummings model

    Institute of Scientific and Technical Information of China (English)

    王忠纯; 王琪; 张永生; 郭光灿

    2005-01-01

    We study the properties of atoms and cavity field in the two-atom Tavis-Cummings model where the two atoms interact with each other and are also driven by an external classical field. We consider the special case that the cavity is initially in a coherent state. The atomic inversion, the average photons number and the Mandel parameter in the driven Tavis-Cummings model are given and analysed numerically. We pay special attention to the dynamical behaviour of the atoms and the cavity field modified by the external field.

  8. APPROXIMATE MODEL OF INTENSE FIELD STABILIZATION FOR.HYDlROGEN ATOM

    Institute of Scientific and Technical Information of China (English)

    XIE BAI-SONG

    2000-01-01

    An approximate model is proposed to study the stabilization problem of hydrogen atoms under monochromatic intense laser field.The stabilization regime for system parameters such as laser field strength,laser field frequency and atomic magnetic quantum number are obtained by stability analysis of fixed points of the model.The results are consistent with those obtained by other methods.

  9. Squeezing effect of the cavity field in the two-atom Jay nes-Cummings model

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Authors investigate the model that two two-level atoms in terac t with a single-mode cavity. The formulation of the time evolution operator for the two-atom Jaynes-Cummings model is presented by the bare-states approach. Besides, squeezing effect of the cavity field is studied and some novel feature s are obtained.

  10. Photon statistical properties of the cavity field in the two-atom Jaynes-Cummings model

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The model that two two-level atoms interact with a singel-mode cavity is studied. The exact solution of the time evolution operator for the two-atom Jaynes-Cummings model is presented by the bare-states approach. Furthermore, we investigate the dynamical properties of the photon statistics of the cavity field, and obtain a number of novel features.

  11. Improving the Ni I atomic model for solar and stellar atmospheric models

    CERN Document Server

    Vieytes, Mariela C

    2013-01-01

    Neutral nickel (Ni I) is abundant in the solar atmosphere and is one of the important elements that contribute to the emission and absorption of radiation in the spectral range between 1900 and 3900 A. Previously, the Solar Radiation Physical Modeling (SRPM) models of the solar atmosphere considered only few levels of this species. Here we improve the Ni I atomic model by taking into account 61 levels and 490 spectral lines. We compute the populations of these levels in full NLTE using the SRPM code and compare the resulting emerging spectrum with observations. The present atomic model improves significantly the calculation of the solar spectral irradiance at near-UV wavelengths that are important for Earth atmo spheric studies, and particularly for ozone chemistry.

  12. Modeling Strongly Correlated Fermi Systems Using Ultra-Cold Atoms

    Science.gov (United States)

    2008-06-28

    exceeds the optical scattering rate Γsc). For the lattice described above, the Lamb Dicke parameter ER/hν = 0.12 and the festina lente criterion Γsc...zero entropy ). Initialization of the quantum register for quantum computations requires a gas of neutral atoms in a near-zero- entropy state...zero- entropy state is prepared by selectively removing atoms in the second band from the lattice potential. optical lattice experiments have

  13. Classical-field model of the hydrogen atom

    Science.gov (United States)

    Rashkovskiy, Sergey A.

    2017-02-01

    It is shown that all of the basic properties of the hydrogen atom can be consistently described in terms of classical electrodynamics if instead of considering the electron to be a particle, we consider an electrically charged classical wave field—an "electron wave"—which is held by the electrostatic field of the proton. It is shown that quantum mechanics must be considered not as a theory of particles but as a classical field theory in the spirit of classical electrodynamics. In this case, we are not faced with difficulties in interpreting the results of the theory. In the framework of classical electrodynamics, all of the well-known regularities of the spontaneous emission of the hydrogen atom are obtained, which is usually derived in the framework of quantum electrodynamics. It is shown that there are no discrete states and discrete energy levels of the atom: the energy of the atom and its states change continuously. An explanation of the conventional corpuscular-statistical interpretation of atomic phenomena is given. It is shown that this explanation is only a misinterpretation of continuous deterministic processes. In the framework of classical electrodynamics, the nonlinear Schrödinger equation is obtained, which accounts for the inverse action of self-electromagnetic radiation of the electron wave and completely describes the spontaneous emissions of an atom.

  14. 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...

  15. Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning

    CERN Document Server

    Rupp, Matthias; Müller, Klaus-Robert; von Lilienfeld, O Anatole

    2011-01-01

    We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schr\\"odinger equation is mapped onto a non-linear statistical regression problem of reduced complexity. Regression models are trained on and compared to atomization energies computed with hybrid density-functional theory. Cross-validation over more than seven thousand small organic molecules yields a mean absolute error of ~10 kcal/mol. Applicability is demonstrated for the prediction of molecular atomization potential energy curves.

  16. Modeling and understanding of effects of randomness in arrays of resonant meta-atoms

    DEFF Research Database (Denmark)

    Tretyakov, Sergei A.; Albooyeh, Mohammad; Alitalo, Pekka;

    2013-01-01

    In this review presentation we will discuss approaches to modeling and understanding electromagnetic properties of 2D and 3D lattices of small resonant particles (meta-atoms) in transition from regular (periodic) to random (amorphous) states. Nanostructured metasurfaces (2D) and metamaterials (3D......) are arrangements of optically small but resonant particles (meta-atoms). We will present our results on analytical modeling of metasurfaces with periodical and random arrangements of electrically and magnetically resonant meta-atoms with identical or random sizes, both for the normal and oblique-angle excitations......) of the arrangements of meta-atoms....

  17. Mapping trapped atomic gas with spin-orbit coupling to quantum Rabi-like model

    OpenAIRE

    Hu, Haiping; Chen, Shu

    2013-01-01

    We construct a connection of the ultracold atomic system in a harmonic trap with Raman-induced spin-orbit coupling to the quantum Rabi-like model. By mapping the trapped atomic system to a Rabi-like model, we can get the exact solution of the Rabi-like model following the methods to solve the quantum Rabi model. The existence of such a mapping implies that we can study the basic model in quantum optics by using trapped atomic gases with spin-orbit coupling.

  18. 'Bubble chamber model' of fast atom bombardment induced processes.

    Science.gov (United States)

    Kosevich, Marina V; Shelkovsky, Vadim S; Boryak, Oleg A; Orlov, Vadim V

    2003-01-01

    A hypothesis concerning FAB mechanisms, referred to as a 'bubble chamber FAB model', is proposed. This model can provide an answer to the long-standing question as to how fragile biomolecules and weakly bound clusters can survive under high-energy particle impact on liquids. The basis of this model is a simple estimation of saturated vapour pressure over the surface of liquids, which shows that all liquids ever tested by fast atom bombardment (FAB) and liquid secondary ion mass spectrometry (SIMS) were in the superheated state under the experimental conditions applied. The result of the interaction of the energetic particles with superheated liquids is known to be qualitatively different from that with equilibrium liquids. It consists of initiation of local boiling, i.e., in formation of vapour bubbles along the track of the energetic particle. This phenomenon has been extensively studied in the framework of nuclear physics and provides the basis for construction of the well-known bubble chamber detectors. The possibility of occurrence of similar processes under FAB of superheated liquids substantiates a conceptual model of emission of secondary ions suggested by Vestal in 1983, which assumes formation of bubbles beneath the liquid surface, followed by their bursting accompanied by release of microdroplets and clusters as a necessary intermediate step for the creation of molecular ions. The main distinctive feature of the bubble chamber FAB model, proposed here, is that the bubbles are formed not in the space and time-restricted impact-excited zone, but in the nearby liquid as a 'normal' boiling event, which implies that the temperature both within the bubble and in the droplets emerging on its burst is practically the same as that of the bulk liquid sample. This concept can resolve the paradox of survival of intact biomolecules under FAB, since the part of the sample participating in the liquid-gas transition via the bubble mechanism has an ambient temperature

  19. Uncertainties in Atomic Data and Their Propagation Through Spectral Models. I.

    Science.gov (United States)

    Bautista, M. A.; Fivet, V.; Quinet, P.; Dunn, J.; Gull, T. R.; Kallman, T. R.; Mendoza, C.

    2013-01-01

    We present a method for computing uncertainties in spectral models, i.e., level populations, line emissivities, and emission line ratios, based upon the propagation of uncertainties originating from atomic data.We provide analytic expressions, in the form of linear sets of algebraic equations, for the coupled uncertainties among all levels. These equations can be solved efficiently for any set of physical conditions and uncertainties in the atomic data. We illustrate our method applied to spectral models of Oiii and Fe ii and discuss the impact of the uncertainties on atomic systems under different physical conditions. As to intrinsic uncertainties in theoretical atomic data, we propose that these uncertainties can be estimated from the dispersion in the results from various independent calculations. This technique provides excellent results for the uncertainties in A-values of forbidden transitions in [Fe ii]. Key words: atomic data - atomic processes - line: formation - methods: data analysis - molecular data - molecular processes - techniques: spectroscopic

  20. Model United Nations comes to CERN

    CERN Document Server

    Anaïs Schaeffer

    2012-01-01

    From 20 to 22 January pupils from international schools in Switzerland, France and Turkey came to CERN for three days of "UN-type" conferences.   The MUN organisers, who are all pupils at the Lycée international in Ferney-Voltaire, worked tirelessly for weeks to make the event a real success. The members of the MUN/MFNU association at the Lycée international in Ferney-Voltaire spent several months preparing for their first "Model United Nations" (MUN),  a simulation of a UN session at which young "diplomats" take on the role of delegates representing different nations to discuss a given topic. And as their chosen topic was science, it was only natural that they should hold the event at CERN. For three days, from 20 to 22 January, no fewer than 340 pupils from 12 international schools* in Switzerland, France and Turkey came together to deliberate, consult and debate on the importance of scientific progress fo...

  1. Modeling three-dimensional network formation with an atomic lattice model: application to silicic acid polymerization.

    Science.gov (United States)

    Jin, Lin; Auerbach, Scott M; Monson, Peter A

    2011-04-07

    We present an atomic lattice model for studying the polymerization of silicic acid in sol-gel and related processes for synthesizing silica materials. Our model is based on Si and O atoms occupying the sites of a body-centered-cubic lattice, with all atoms arranged in SiO(4) tetrahedra. This is the simplest model that allows for variation in the Si-O-Si angle, which is largely responsible for the versatility in silica polymorphs. The model describes the assembly of polymerized silica structures starting from a solution of silicic acid in water at a given concentration and pH. This model can simulate related materials-chalcogenides and clays-by assigning energy penalties to particular ring geometries in the polymerized structures. The simplicity of this approach makes it possible to study the polymerization process to higher degrees of polymerization and larger system sizes than has been possible with previous atomistic models. We have performed Monte Carlo simulations of the model at two concentrations: a low density state similar to that used in the clear solution synthesis of silicalite-1, and a high density state relevant to experiments on silica gel synthesis. For the high concentration system where there are NMR data on the temporal evolution of the Q(n) distribution, we find that the model gives good agreement with the experimental data. The model captures the basic mechanism of silica polymerization and provides quantitative structural predictions on ring-size distributions in good agreement with x-ray and neutron diffraction data.

  2. 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.

  3. Atomic charges for modeling metal–organic frameworks: Why and how

    Energy Technology Data Exchange (ETDEWEB)

    Hamad, Said, E-mail: said@upo.es; Balestra, Salvador R.G.; Bueno-Perez, Rocio; Calero, Sofia; Ruiz-Salvador, A. Rabdel

    2015-03-15

    Atomic partial charges are parameters of key importance in the simulation of Metal–Organic Frameworks (MOFs), since Coulombic interactions decrease with the distance more slowly than van der Waals interactions. But despite its relevance, there is no method to unambiguously assign charges to each atom, since atomic charges are not quantum observables. There are several methods that allow the calculation of atomic charges, most of them starting from the electronic wavefunction or the electronic density or the system, as obtained with quantum mechanics calculations. In this work, we describe the most common methods employed to calculate atomic charges in MOFs. In order to show the influence that even small variations of structure have on atomic charges, we present the results that we obtained for DMOF-1. We also discuss the effect that small variations of atomic charges have on the predicted structural properties of IRMOF-1. - Graphical abstract: We review the different method with which to calculate atomic partial charges that can be used in force field-based calculations. We also present two examples that illustrate the influence of the geometry on the calculated charges and the influence of the charges on structural properties. - Highlights: • The choice of atomic charges is crucial in modeling adsorption and diffusion in MOFs. • Methods for calculating atomic charges in MOFs are reviewed. • We discuss the influence of the framework geometry on the calculated charges. • We discuss the influence of the framework charges on structural the properties.

  4. Flame-in-gas-shield and miniature diffusion flame hydride atomizers for atomic fluorescence spectrometry: optimization and comparison

    OpenAIRE

    Marschner, K; Musil, S. (Stanislav); Dědina, J. (Jiří)

    2015-01-01

    A detailed optimization of relevant experimental parameters of two hydride atomizers for atomic fluorescence spectrometry: flame-in-gas-shield atomizer with a two-channel shielding unit and a standard atomizer for atomic fluorescence spectrometry, miniature diffusion flame, was performed. Arsine, generated by the reaction with NaBH4 in a flow injection arrangement, was chosen as the model hydride. Analytical characteristics of both the atomizers (sensitivity, noise, limits of detection) were ...

  5. Analytical model for relativistic corrections to the nuclear magnetic shielding constant in atoms

    Energy Technology Data Exchange (ETDEWEB)

    Romero, Rodolfo H. [Facultad de Ciencias Exactas, Universidad Nacional del Nordeste, Avenida Libertad 5500 (3400), Corrientes (Argentina)]. E-mail: rhromero@exa.unne.edu.ar; Gomez, Sergio S. [Facultad de Ciencias Exactas, Universidad Nacional del Nordeste, Avenida Libertad 5500 (3400), Corrientes (Argentina)

    2006-04-24

    We present a simple analytical model for calculating and rationalizing the main relativistic corrections to the nuclear magnetic shielding constant in atoms. It provides good estimates for those corrections and their trends, in reasonable agreement with accurate four-component calculations and perturbation methods. The origin of the effects in deep core atomic orbitals is manifestly shown.

  6. A calculation of internal kinetic energy and polarizability of compressed argon from the statistical atom model

    NARCIS (Netherlands)

    Seldam, C.A. ten; Groot, S.R. de

    From Jensen's and Gombás' modification of the statistical Thomas-Fermi atom model, a theory for compressed atoms is developed by changing the boundary conditions. Internal kinetic energy and polarizability of argon are calculated as functions of pressure. At 1000 atm. an internal kinetic energy of

  7. Nonclassical Effects of a Four-Level Excited-Doublet Atom Model

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jian-Song; XU Jing-Bo

    2006-01-01

    We adopt a dynamical algebraic method to study a four-level excited-doublet atom model and obtain the explicit expressions of the time-evolution operator and the density operator for the system. The nonclassical effects of the system, such as collapses and revivals of the atomic inversion and squeezing of the radiation field, are also discussed.

  8. Identifying Atomic Structure as a Threshold Concept: Student Mental Models and Troublesomeness

    Science.gov (United States)

    Park, Eun Jung; Light, Gregory

    2009-01-01

    Atomic theory or the nature of matter is a principal concept in science and science education. This has, however, been complicated by the difficulty students have in learning the concept and the subsequent construction of many alternative models. To understand better the conceptual barriers to learning atomic structure, this study explores the…

  9. Engineering the Dynamics of Effective Spin-Chain Models for Strongly Interacting Atomic Gases

    DEFF Research Database (Denmark)

    Volosniev, A. G.; Petrosyan, D.; Valiente, M.

    2015-01-01

    We consider a one-dimensional gas of cold atoms with strong contact interactions and construct an effective spin-chain Hamiltonian for a two-component system. The resulting Heisenberg spin model can be engineered by manipulating the shape of the external confining potential of the atomic gas. We...

  10. Mg I as a probe of the solar chromosphere - The atomic model

    Science.gov (United States)

    Mauas, Pablo J.; Avrett, Eugene H.; Loeser, Rudolf

    1988-01-01

    This paper presents a complete atomic model for Mg I line synthesis, where all the atomic parameters are based on recent experimental and theoretical data. It is shown how the computed profiles at 4571 A and 5173 A are influenced by the choice of these parameters and the number of levels included in the model atom. In addition, observed profiles of the 5173 A b2 line and theoretical profiles for comparison (based on a recent atmospheric model for the average quiet sun) are presented.

  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. Modelization of nanospace interaction involving a ferromagnetic atom: a spin polarization effect study by thermogravimetric analysis.

    Science.gov (United States)

    Santhanam, K S V; Chen, Xu; Gupta, S

    2014-04-01

    Ab initio studies of ferromagnetic atom interacting with carbon nanotubes have been reported in the literature that predict when the interaction is strong, a higher hybridization with confinement effect will result in spin polarization in the ferromagnetic atom. The spin polarization effect on the thermal oxidation to form its oxide is modeled here for the ferromagnetic atom and its alloy, as the above studies predict the 4s electrons are polarized in the atom. The four models developed here provide a pathway for distinguishing the type of interaction that exists in the real system. The extent of spin polarization in the ferromagnetic atom has been examined by varying the amount of carbon nanotubes in the composites in the thermogravimetric experiments. In this study we report the experimental results on the CoNi alloy which appears to show selective spin polarization. The products of the thermal oxidation has been analyzed by Fourier Transform Infrared Spectroscopy.

  13. UNIFIED MODEL FOR SPLASH DROPLETS AND SUSPENDED MIST OF ATOMIZED FLOW

    Institute of Scientific and Technical Information of China (English)

    LIU Shi-he; SUN Xiao-fei; LUO Jing

    2008-01-01

    In this article, the unified mathematical model for splash droplets and suspended mist of atomized flow was established, which classifies the atomized sources into the splash source and the suspended source. For the splash source, the Lagrangian method was used to simulate the random motion of splash water droplets, and for the suspended source the theory of air-water two-phase flow was used to simulate the mist flow moving in particle clouds. The rainfall intensity of the atomized flow was obtained by summarizing the rainfall intensities relative to the above two types of atomized sources. Both experimental data and prototype observation data were used for the verification of the mathematical model. For both the distribution of rainfall intensity, and the outer edge of the atomized flow, the simulation results are in agreement with the experimental data or prototype observation data.

  14. An Analytical Model for Adsorption and Diffusion of Atoms/Ions on Graphene Surface

    Directory of Open Access Journals (Sweden)

    Yan-Zi Yu

    2015-01-01

    Full Text Available Theoretical investigations are made on adsorption and diffusion of atoms/ions on graphene surface based on an analytical continuous model. An atom/ion interacts with every carbon atom of graphene through a pairwise potential which can be approximated by the Lennard-Jones (L-J potential. Using the Fourier expansion of the interaction potential, the total interaction energy between the adsorption atom/ion and a monolayer graphene is derived. The energy-distance relationships in the normal and lateral directions for varied atoms/ions, including gold atom (Au, platinum atom (Pt, manganese ion (Mn2+, sodium ion (Na1+, and lithium-ion (Li1+, on monolayer graphene surface are analyzed. The equilibrium position and binding energy of the atoms/ions at three particular adsorption sites (hollow, bridge, and top are calculated, and the adsorption stability is discussed. The results show that H-site is the most stable adsorption site, which is in agreement with the results of other literatures. What is more, the periodic interaction energy and interaction forces of lithium-ion diffusing along specific paths on graphene surface are also obtained and analyzed. The minimum energy barrier for diffusion is calculated. The possible applications of present study include drug delivery system (DDS, atomic scale friction, rechargeable lithium-ion graphene battery, and energy storage in carbon materials.

  15. QSTR with extended topochemical atom indices. 10. Modeling of toxicity of organic chemicals to humans using different chemometric tools.

    Science.gov (United States)

    Roy, Kunal; Ghosh, Gopinath

    2008-11-01

    In this communication, we have developed quantitative predictive models using human lethal concentration values of 26 organic compounds including some pharmaceuticals with extended topochemical atom (ETA) indices applying different chemometric tools and compared the extended topochemical atom models with the models developed from non-extended topochemical atom ones. Extended topochemical atom descriptors were also tried in combination with non-extended topochemical atom descriptors to develop better predictive models. The use of extended topochemical atom descriptors along with non-extended topochemical atom ones improved equation statistics and cross-validation quality. The best model with sound statistical quality was developed from partial least squares regression using extended topochemical atom descriptors in combination non-extended topochemical atom ones. Finally, to check true predictability of the ETA parameters, the data set was divided into training (n = 19) and test (n = 7) sets. Partial least squares and genetic partial least squares models were developed from the training set using extended topochemical atom indices and the models were validated using the test set. The extended topochemical atom models developed from different statistical tools suggest that the toxicity increases with bulk, chloro functionality, presence of electronegative atoms within a chain or ring and unsaturation, and decreases with hydroxy functionality and branching. The results suggest that the extended topochemical atom descriptors are sufficiently rich in chemical information to encode the structural features for QSAR/QSPR/QSTR modeling.

  16. Present status on atomic and molecular data relevant to fusion plasma diagnostics and modeling

    Energy Technology Data Exchange (ETDEWEB)

    Tawara, H. [ed.

    1997-01-01

    This issue is the collection of the paper presented status on atomic and molecular data relevant to fusion plasma diagnostics and modeling. The 10 of the presented papers are indexed individually. (J.P.N.)

  17. Modeling hydrogen storage in boron-substituted graphene decorated with potassium metal atoms

    CSIR Research Space (South Africa)

    Tokarev, A

    2015-03-01

    Full Text Available Boron-substituted graphene decorated with potassium metal atoms was considered as a novel material for hydrogen storage. Density functional theory calculations were used to model key properties of the material, such as geometry, hydrogen packing...

  18. Computational model for noncontact atomic force microscopy: energy dissipation of cantilever.

    Science.gov (United States)

    Senda, Yasuhiro; Blomqvist, Janne; Nieminen, Risto M

    2016-09-21

    We propose a computational model for noncontact atomic force microscopy (AFM) in which the atomic force between the cantilever tip and the surface is calculated using a molecular dynamics method, and the macroscopic motion of the cantilever is modeled by an oscillating spring. The movement of atoms in the tip and surface is connected with the oscillating spring using a recently developed coupling method. In this computational model, the oscillation energy is dissipated, as observed in AFM experiments. We attribute this dissipation to the hysteresis and nonconservative properties of the interatomic force that acts between the atoms in the tip and sample surface. The dissipation rate strongly depends on the parameters used in the computational model.

  19. Anisotropy modeling of terahertz metamaterials: polarization dependent resonance manipulation by meta-atom cluster.

    Science.gov (United States)

    Jung, Hyunseung; In, Chihun; Choi, Hyunyong; Lee, Hojin

    2014-06-09

    Recently metamaterials have inspired worldwide researches due to their exotic properties in transmitting, reflecting, absorbing or refracting specific electromagnetic waves. Most metamaterials are known to have anisotropic properties, but existing anisotropy models are applicable only to a single meta-atom and its properties. Here we propose an anisotropy model for asymmetrical meta-atom clusters and their polarization dependency. The proposed anisotropic meta-atom clusters show a unique resonance property in which their frequencies can be altered for parallel polarization, but fixed to a single resonance frequency for perpendicular polarization. The proposed anisotropic metamaterials are expected to pave the way for novel optical systems.

  20. QSPR modeling mineral crystal lattice energy by optimal descriptors of the graph of atomic orbitals

    Science.gov (United States)

    Toropova, A. P.; Toropov, A. A.; Maksudov, S. Kh.

    2006-09-01

    Models of the crystal lattice of minerals of general formula of A mC n: m, n = 1,2: A = Li, K, Na, Mg, Ca, Mn, Cu, Zn, Sr, Cd, Ba, Hg, Pb, Cs, and Rb ; C = Be, O, F, S, Cl, Br, and I; as a mathematical function of their structure have been constructed. Two elucidations of molecular structure have been used: molecular graph (vertexes are atoms, i.e., Li, Na, K, etc.) and graph of atomic orbitals, GAO (vertexes are atomic orbitals, i.e., 1s 2, 2p 5, 3d 10, etc). Statistical characteristics of the GAO-based models are better.

  1. Conceptual Model of Quantities, Units, Dimensions, and Values

    Science.gov (United States)

    Rouquette, Nicolas F.; DeKoenig, Hans-Peter; Burkhart, Roger; Espinoza, Huascar

    2011-01-01

    JPL collaborated with experts from industry and other organizations to develop a conceptual model of quantities, units, dimensions, and values based on the current work of the ISO 80000 committee revising the International System of Units & Quantities based on the International Vocabulary of Metrology (VIM). By providing support for ISO 80000 in SysML via the International Vocabulary of Metrology (VIM), this conceptual model provides, for the first time, a standard-based approach for addressing issues of unit coherence and dimensional analysis into the practice of systems engineering with SysML-based tools. This conceptual model provides support for two kinds of analyses specified in the International Vocabulary of Metrology (VIM): coherence of units as well as of systems of units, and dimension analysis of systems of quantities. To provide a solid and stable foundation, the model for defining quantities, units, dimensions, and values in SysML is explicitly based on the concepts defined in VIM. At the same time, the model library is designed in such a way that extensions to the ISQ (International System of Quantities) and SI Units (Systeme International d Unites) can be represented, as well as any alternative systems of quantities and units. The model library can be used to support SysML user models in various ways. A simple approach is to define and document libraries of reusable systems of units and quantities for reuse across multiple projects, and to link units and quantity kinds from these libraries to Unit and QuantityKind stereotypes defined in SysML user models.

  2. From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum.

    Science.gov (United States)

    Urzhumtsev, Alexandre; Afonine, Pavel V; Van Benschoten, Andrew H; Fraser, James S; Adams, Paul D

    2016-09-01

    Researcher feedback has indicated that in Urzhumtsev et al. [(2015) Acta Cryst. D71, 1668-1683] clarification of key parts of the algorithm for interpretation of TLS matrices in terms of elemental atomic motions and corresponding ensembles of atomic models is required. Also, it has been brought to the attention of the authors that the incorrect PDB code was reported for one of test models. These issues are addressed in this article.

  3. An atomic model of brome mosaic virus using direct electron detection and real-space optimization

    OpenAIRE

    Wang, Zhao; Hryc, Corey F.; Bammes, Benjamin; Afonine, Pavel V.; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L.; Kao, Cheng; Ludtke, Steven J; Schmid, Michael F.; Adams, Paul D.; Chiu, Wah

    2014-01-01

    Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiat...

  4. Logistic Regression Model on Antenna Control Unit Autotracking Mode

    Science.gov (United States)

    2015-10-20

    412TW-PA-15240 Logistic Regression Model on Antenna Control Unit Autotracking Mode DANIEL T. LAIRD AIR FORCE TEST CENTER EDWARDS AFB, CA...OCT 15 4. TITLE AND SUBTITLE Logistic Regression Model on Antenna Control Unit Autotracking Mode 5a. CONTRACT NUMBER 5b. GRANT...alternative-hypothesis. This paper will present an Antenna Auto- tracking model using Logistic Regression modeling. This paper presents an example of

  5. 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.)

  6. Kinetic modeling of primary and secondary oxygen atom fluxes at 1 AU

    Science.gov (United States)

    Balyukin, Igor; Katushkina, Olga; Alexashov, Dmitry; Izmodenov, Vladislav

    2016-07-01

    The first quantitative measurements of the interstellar heavy (oxygen and neon) neutral atoms obtained on the IBEX spacecraft were presented in Park et al. (ApJS, 2015). Qualitative analysis of these data shows that the secondary component of the interstellar oxygen atoms was also measured along with the primary interstellar atoms. This component is formed near the heliopause due to process of charge exchange of interstellar oxygen ions with hydrogen atoms and its existence in the heliosphere was previously predicted theoretically (Izmodenov et al, 1997, 1999, 2001). Quantitative analysis of fluxes of interstellar heavy neutral atoms is only possible with the help of a model which takes into account both filtration of the primary and origin of the secondary interstellar oxygen in the region of interaction of the solar wind with the local interstellar medium as well as a detailed simulation of the motion of interstellar atoms inside the heliosphere. This simulation must take into account the temporal and heliolatitudinal dependences of ionization, the process of charge exchange with the protons of the solar wind and the effect of the solar gravitational attraction. This paper presents the results of modeling interstellar oxygen and neon atoms in the heliospheric shock layer and inside the heliosphere based on a new three-dimensional kinetic-MHD model of the solar wind interaction with the local interstellar medium (Izmodenov and Alexashov, ApJS, 2015) and the comparison of this results with the data obtained on the IBEX spacecraft.

  7. Does God Play Dice with Universe The Hydrogen Atomic Model of Bohr and de Broglie

    CERN Document Server

    Kamenov, P S

    1999-01-01

    In this paper it is shown that if one accept assumption of de Broglie that "unitary wave-particle" exists simultaneously and this coexistence is real, then one can find the mean life time of the hydrogen atom of Bohr (intensities). Something more, the acceptance of de Broglie's ideas show that a single excited hydrogen atom decays at exactly predictable moment (after excitation). The natural width of excited hydrogen atoms are found using the Bohr's model of this atom and de Broglie's ideas. The mean life time of the excited states is a characteristic only of a statistical ensemble of many atoms and coincide exactly with experimental data and can be used for analytical applications. It is shown also that resonant Mossbauer absorption in time domain provides a qualitative evidence of the existence of "own lifetime" for first excited states of the nuclei.

  8. Classical trajectory perspective of atomic ionization in strong laser fields semiclassical modeling

    CERN Document Server

    Liu, Jie

    2014-01-01

    The ionization of atoms and molecules in strong laser fields is an active field in modern physics and has versatile applications in such as attosecond physics, X-ray generation, inertial confined fusion (ICF), medical science and so on. Classical Trajectory Perspective of Atomic Ionization in Strong Laser Fields covers the basic concepts in this field and discusses many interesting topics using the semiclassical model of classical trajectory ensemble simulation, which is one of the most successful ionization models and has the advantages of a clear picture, feasible computing and accounting for many exquisite experiments quantitatively. The book also presents many applications of the model in such topics as the single ionization, double ionization, neutral atom acceleration and other timely issues in strong field physics, and delivers useful messages to readers with presenting the classical trajectory perspective on the strong field atomic ionization. The book is intended for graduate students and researchers...

  9. Sound speed and oscillation frequencies for solar models evolved with Los Alamos ATOMIC opacities

    CERN Document Server

    Guzik, Joyce A; Walczak, P; Wood, S R; Mussack, K; Farag, E

    2016-01-01

    Los Alamos National Laboratory has calculated a new generation of radiative opacities (OPLIB data using the ATOMIC code) for elements with atomic number Z=1-30 with improved physics input, updated atomic data, and finer temperature grid to replace the Los Alamos LEDCOP opacities released in the year 2000. We calculate the evolution of standard solar models including these new opacities, and compare with models evolved using the Lawrence Livermore National Laboratory OPAL (Iglesias and Rogers 1996) opacities. We use the solar abundance mixture of Asplund et al. (2009). The new Los Alamos ATOMIC opacities have steeper opacity derivatives than those of OPAL for temperatures and densities of the solar interior radiative zone. We compare the calculated nonadiabatic solar oscillation frequencies and solar interior sound speed to observed frequencies and helioseismic inferences. The calculated sound-speed profiles are similar for models evolved using either the updated Iben evolution code (see \\cite{Guzik2010}), or ...

  10. Models of atoms in plasmas based on common formalism for bound and free electrons

    Science.gov (United States)

    Blenski, T.; Piron, R.; Caizergues, C.; Cichocki, B.

    2013-12-01

    Atom-in-plasma models: Thomas-Fermi (TF) and INFERNO, AJCI and VAAQP, that use the same formalism for all electrons are briefly described and analyzed from the point of view of their thermodynamic consistence. While the TF and VAAQP models may be derived from variational principle and respect the virial theorem, it appears that two earlier quantum extensions of the quasi-classical TF model, INFERNO and AJCI, are not fully variational. The problems of the two latter approaches are analyzed from the point of view of the VAAQP model. However all quantum models seem to give unrealistic description of atoms in plasma at low temperature and high plasma densities. These difficulties are connected with the Wigner-Seitz cavity approach to non-central ions that is present in all considered models. Comparison of some equation-of-state data from TF, INFERNO and VAAQP models are shown on a chosen example. We report also on the status of our research on the frequency-dependent linear-response theory of atoms in plasma. A new Ehrenfest-type sum rule, originally proposed in the quantum VAAQP model, was proven in the case of the response of the TF atom with the Bloch hydrodynamics (TFB) and checked by numerical example. The TFB case allows one to have a direct insight into the rather involved mathematics of the self-consistent linear response calculations in situations when both the central atom and its plasma vicinity are perturbed by an electric field.

  11. Modelling fluidized catalytic cracking unit stripper efficiency

    Directory of Open Access Journals (Sweden)

    García-Dopico M.

    2015-01-01

    Full Text Available This paper presents our modelling of a FCCU stripper, following our earlier research. This model can measure stripper efficiency against the most important variables: pressure, temperature, residence time and steam flow. Few models in the literature model the stripper and usually they do against only one variable. Nevertheless, there is general agreement on the importance of the stripper in the overall process, and the fact that there are few models maybe it is due to the difficulty to obtain a comprehensive model. On the other hand, the proposed model does use all the variables of the stripper, calculating efficiency on the basis of steam flow, pressure, residence time and temperature. The correctness of the model is then analysed, and we examine several possible scenarios, like decreasing the steam flow, which is achieved by increasing the temperature in the stripper.

  12. Some reflections on the role of semi-classical atomic models in the teaching and learning of introductory quantum mechanics

    Science.gov (United States)

    O'Sullivan, Colm

    2016-03-01

    The role of "semi-classical" (Bohr-Sommerfeld) and "semi-quantum-mechanical" (atomic orbital) models in the context of the teaching of atomic theory is considered. It is suggested that an appropriate treatment of such models can serve as a useful adjunct to quantum mechanical study of atomic systems.

  13. Continuous vs. discrete models for the quantum harmonic oscillator and the hydrogen atom

    CERN Document Server

    Lorente, M

    2001-01-01

    The Kravchuk and Meixner polynomials of discrete variable are introduced for the discrete models of the harmonic oscillator and hydrogen atom. Starting from Rodrigues formula we construct raising and lowering operators, commutation and anticommutation relations. The physical properties of discrete models are figured out through the equivalence with the continuous models obtained by limit process.

  14. Continuous vs. discrete models for the quantum harmonic oscillator and the hydrogen atom

    Science.gov (United States)

    Lorente, Miguel

    2001-07-01

    The Kravchuk and Meixner polynomials of discrete variable are introduced for the discrete models of the harmonic oscillator and hydrogen atom. Starting from Rodrigues formula we construct raising and lowering operators, commutation and anticommutation relations. The physical properties of discrete models are figured out through the equivalence with the continuous models obtained by limit process.

  15. Continuous vs. discrete models for the quantum harmonic oscillator and the hydrogen atom

    OpenAIRE

    Lorente, M.

    2004-01-01

    The Kravchuk and Meixner polynomials of discrete variable are introduced for the discrete models of the harmonic oscillator and hydrogen atom. Starting from Rodrigues formula we construct raising and lowering operators, commutation and anticommutation relations. The physical properties of discrete models are figured out through the equivalence with the continuous models obtained by limit process.

  16. Hydrogen ADPs with Cu Kα data? Invariom and Hirshfeld atom modelling of fluconazole.

    Science.gov (United States)

    Orben, Claudia M; Dittrich, Birger

    2014-06-01

    For the structure of fluconazole [systematic name: 2-(2,4-difluorophenyl)-1,3-bis(1H-1,2,4-triazol-1-yl)propan-2-ol] monohydrate, C13H12F2N6O·H2O, a case study on different model refinements is reported, based on single-crystal X-ray diffraction data measured at 100 K with Cu Kα radiation to a resolution of sin θ/λ of 0.6 Å(-1). The structure, anisotropic displacement parameters (ADPs) and figures of merit from the independent atom model are compared to `invariom' and `Hirshfeld atom' refinements. Changing from a spherical to an aspherical atom model lowers the figures of merit and improves both the accuracy and the precision of the geometrical parameters. Differences between results from the two aspherical-atom refinements are small. However, a refinement of ADPs for H atoms is only possible with the Hirshfeld atom density model. It gives meaningful results even at a resolution of 0.6 Å(-1), but requires good low-order data.

  17. Parity violation in atomic cesium and alternatives to the standard model of electroweak interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bouchiat, C.; Piketty, C.A. (Ecole Normale Superieure, 75 - Paris (France). Lab. de Physique Theorique)

    1983-08-18

    We study the implications of the recent observation of a parity violation in atomic cesium. After a discussion of the uncertainties associated with the atomic physics calculations we derive conservative bounds for the weak charge Qsub(W). These bounds are used to put constraints on alternatives to the standard electroweak model, involving an 'extra U(1)' gauge group. We analyze the possibility that the extra gauge boson might be very light and give, as a by-product, the typical range of momentum transfer explored in atomic parity violation experiments.

  18. Engineering the Dynamics of Effective Spin-Chain Models for Strongly Interacting Atomic Gases

    DEFF Research Database (Denmark)

    Volosniev, A. G.; Petrosyan, D.; Valiente, M.

    2015-01-01

    We consider a one-dimensional gas of cold atoms with strong contact interactions and construct an effective spin-chain Hamiltonian for a two-component system. The resulting Heisenberg spin model can be engineered by manipulating the shape of the external confining potential of the atomic gas. We...... find that bosonic atoms offer more flexibility for tuning independently the parameters of the spin Hamiltonian through interatomic (intra-species) interaction which is absent for fermions due to the Pauli exclusion principle. Our formalism can have important implications for control and manipulation...

  19. Generalized Kolbenstvedt model for electron impact ionization of K-, L- and M-shell atoms

    Energy Technology Data Exchange (ETDEWEB)

    Haque, A.K.F.; Uddin, M.A.; Patoary, M.A.R.; Basak, A.K. [Rajshahi Univ., Dept. of Physics (Bangladesh); Talukder, M.R. [Rajshahi Univ., Dept. of Applied Physics and Electronic Engineering (Bangladesh); Saha, B.C. [Florida A and M Univ., Dept. of Physics (United States); Karim, K.R. [Illinois State Univ., Dept. of Physics, IL (United States); Malik, F.B. [Southern Illinois Univ., Dept. of Physics, IL (United States); Washington Univ., St. Louis, Dept. of Physics, MO (United States)

    2007-05-15

    The recently modified Kolbenstvedt (MKLV) model, developed for electron impact ionization of the K-shell atomic targets, has been extended to generalize its two parameters in terms of the electronic orbitals nl. The generalized MKLV (GKLV) with two sets of the species independent parameters for the same nl, one set for the ionization of inner orbits and another for the outermost orbit, is found profoundly successful in accounting for the electron impact ionization cross section data of the K, L and M-shell neutral atoms with atomic numbers Z = 1-92 for the incident energies up to 1000 MeV in a consistent manner. (authors)

  20. Uncertainties in Atomic Data and Their Propagation Through Spectral Models. I

    CERN Document Server

    Bautista, Manuel A; Quinet, Pascal; Dunn, Jay; Kallman, Theodore R Gull Timothy R; Mendoza, Claudio

    2013-01-01

    We present a method for computing uncertainties in spectral models, i.e. level populations, line emissivities, and emission line ratios, based upon the propagation of uncertainties originating from atomic data. We provide analytic expressions, in the form of linear sets of algebraic equations, for the coupled uncertainties among all levels. These equations can be solved efficiently for any set of physical conditions and uncertainties in the atomic data. We illustrate our method applied to spectral models of O III and Fe II and discuss the impact of the uncertainties on atomic systems under different physical conditions. As to intrinsic uncertainties in theoretical atomic data, we propose that these uncertainties can be estimated from the dispersion in the results from various independent calculations. This technique provides excellent results for the uncertainties in A-values of forbidden transitions in [Fe II].

  1. 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.

  2. Size distribution of islands according to 2D growth model with 2 kinds of diffusion atoms

    CERN Document Server

    Yamauchi, R; Koyama, M; Sasakura, H; Nakata, Y; Muto, S

    2015-01-01

    We simulated the growth of 2D islands with 2 kinds of diffusion atoms using the kinetic Monte- Carlo (kMC) method. As a result, we found that the slow atoms tend to create nuclei and determine the island volume distribution, along with additional properties such as island density. We also conducted a theoretical analysis using the rate equation of the point-island model to confirm these results.

  3. Atomic and field dynamics in the time-dependent Jaynes-Cummings model with arbitrary detuning

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    We propose a general numerical method for solving the time -dependent Jaynes-Cummings model with arbitrary detuning by integrating relate d groups of coupled equations using Runge-Kutta numerical technique. The atomic and field dynamics such as evolution of atomic population inversion and second -order correlation function of photons are studied in case of different detunin g. The results show that the field tends to exhibit bunching effect due to the I ncreasing of detuning.

  4. Neural and Cognitive Modeling with Networks of Leaky Integrator Units

    Science.gov (United States)

    Graben, Peter beim; Liebscher, Thomas; Kurths, Jürgen

    After reviewing several physiological findings on oscillations in the electroencephalogram (EEG) and their possible explanations by dynamical modeling, we present neural networks consisting of leaky integrator units as a universal paradigm for neural and cognitive modeling. In contrast to standard recurrent neural networks, leaky integrator units are described by ordinary differential equations living in continuous time. We present an algorithm to train the temporal behavior of leaky integrator networks by generalized back-propagation and discuss their physiological relevance. Eventually, we show how leaky integrator units can be used to build oscillators that may serve as models of brain oscillations and cognitive processes.

  5. 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...

  6. The pediatric intensive care unit business model.

    Science.gov (United States)

    Schleien, Charles L

    2013-06-01

    All pediatric intensivists need a primer on ICU finance. The author describes potential alternate revenue sources for the division. Differentiating units by size or academic affiliation, the author describes drivers of expense. Strategies to manage the bottom line including negotiations for hospital services are covered. Some of the current trends in physician productivity and its described metrics, with particular focus on clinical FTE management is detailed. Methods of using this data to enhance revenue are discussed. Some of the other current trends in the ICU business related to changes at the federal and state level as well as in the insurance sector, moving away from fee-for-service are covered. Copyright © 2013 Elsevier Inc. All rights reserved.

  7. Mapping the Two-Component Atomic Fermi Gas to the Nuclear Shell-Model

    DEFF Research Database (Denmark)

    Özen, C.; Zinner, Nikolaj Thomas

    2014-01-01

    of the external potential becomes important. A system of two-species fermionic cold atoms with an attractive zero-range interaction is analogous to a simple model of nucleus in which neutrons and protons interact only through a residual pairing interaction. In this article, we discuss how the problem of a two......-component atomic fermi gas in a tight external trap can be mapped to the nuclear shell model so that readily available many-body techniques in nuclear physics, such as the Shell Model Monte Carlo (SMMC) method, can be directly applied to the study of these systems. We demonstrate an application of the SMMC method...

  8. Empirical model for electron impact ionization cross sections of neutral atoms

    Energy Technology Data Exchange (ETDEWEB)

    Talukder, M.R.; Bose, S. [Rajshahi Univ., Dept. of Applied Physics and Electronic Engineering (Bangladesh); Patoary, M.A.R.; Haque, A.K.F.; Uddin, M.A.; Basak, A.K. [Rajshahi Univ., Dept. of Physics (Bangladesh); Kando, M. [Shizuoka Univ., Graduate School of Electronic Science and Technology (Japan)

    2008-02-15

    A simple empirical formula is proposed for the rapid calculation of electron impact total ionization cross sections both for the open- and closed-shell neutral atoms considered in the range 1 {<=} Z {<=} 92 and the incident electron energies from threshold to about 10{sup 4} eV. The results of the present analysis are compared with the available experimental and theoretical data. The proposed model provides a fast method for calculating fairly accurate electron impact total ionization cross sections of atoms. This model may be a prudent choice, for the practitioners in the field of applied sciences e.g. in plasma modeling, due to its simple inherent structure. (authors)

  9. Low-resolution density maps from atomic models: how stepping "back" can be a step "forward".

    Science.gov (United States)

    Belnap, D M; Kumar, A; Folk, J T; Smith, T J; Baker, T S

    1999-01-01

    Atomic-resolution structures have had a tremendous impact on modern biological science. Much useful information also has been gleaned by merging and correlating atomic-resolution structural details with lower-resolution (15-40 A), three-dimensional (3D) reconstructions computed from images recorded with cryo-transmission electron microscopy (cryoTEM) procedures. One way to merge these structures involves reducing the resolution of an atomic model to a level comparable to a cryoTEM reconstruction. A low-resolution density map can be derived from an atomic-resolution structure by retrieving a set of atomic coordinates editing the coordinate file, computing structure factors from the model coordinates, and computing the inverse Fourier transform of the structure factors. This method is a useful tool for structural studies primarily in combination with 3D cryoTEM reconstructions. It has been used to assess the quality of 3D reconstructions, to determine corrections for the phase-contrast transfer function of the transmission electron microscope, to calibrate the dimensions and handedness of 3D reconstructions, to produce difference maps, to model features in macromolecules or macromolecular complexes, and to generate models to initiate model-based determination of particle orientation and origin parameters for 3D reconstruction.

  10. A theoretical-electron-density databank using a model of real and virtual spherical atoms.

    Science.gov (United States)

    Nassour, Ayoub; Domagala, Slawomir; Guillot, Benoit; Leduc, Theo; Lecomte, Claude; Jelsch, Christian

    2017-08-01

    A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

  11. Reasoning with Atomic-Scale Molecular Dynamic Models

    Science.gov (United States)

    Pallant, Amy; Tinker, Robert F.

    2004-01-01

    The studies reported in this paper are an initial effort to explore the applicability of computational models in introductory science learning. Two instructional interventions are described that use a molecular dynamics model embedded in a set of online learning activities with middle and high school students in 10 classrooms. The studies indicate…

  12. Modeled Thickness of the Overburden Geomodel Unit (obthk_f)

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The obthk_f grid represents the modeled thickness of the Overburden geomodel unit at a 500 foot resolution. It is one grid of a geomodel that consists of eleven...

  13. Quantum chemical modelling of Si sub-surface amorphisation due to incorporation of H atoms and its stabilisation by O atoms

    Energy Technology Data Exchange (ETDEWEB)

    Pushkarchuk, Alexander [Institute of Physical-Organic Chemistry NASB, Minsk (Belarus); Saad, Anis [Al-Balqa Applied University, Salt (Jordan); Pushkarchuk, Vadim [Belarusian State University of Informatics and Radioelectronics, Minsk (Belarus); Fedotov, Alexander; Mazanik, Alexander; Zinchuk, Olga [Belarusian State University, Minsk (Belarus); Turishchev, Sergey [Voronezh State University, Voronezh (Russian Federation)

    2010-04-15

    Here we present the results of systematic simulating studies of atomic configurations in silicon ''surface clusters'' with different numbers (per cluster) of interstitial H and O atoms as impurities, obtained by semi-empirical (PM3) and DFT quantum-chemical methods. The aim of modeling was to study the near-surface region Si amorphization caused by H-incorporation (from H-plasma, for example) and changes in the atomic structure of this amorphized sub-surface region by additionally incorporated O-atoms. A set of Si{sub x}H{sub y}[H{sub L}O{sub M}] clusters was used in order to reproduce a local atomic structure of H- or H-O-containing complexes with different numbers of impurity atoms per cluster for the corresponding Si(111) and Si(100) near-surface regions. Here x-number of Si atoms, y-number of H atoms which saturate dangling bonds at the cluster surface, L-number of incorporated H atoms which create hydrogen-containing defect complexes, M-number of O atoms incorporated in hydrogen-containing complexes. The optimization procedure, using the PM3 and DFT levels quantum chemical theory geometry optimisation of all Si clusters, allowed comparison of changes in the atomic structures of Si surface and sub-surface regions with different configurations of Si-H and Si-H-O impurity complexes (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  14. The effect of degenerate atomic levels on the field state dissipation in two-photon Jaynes-Cummings model

    Institute of Scientific and Technical Information of China (English)

    周玲; 宋鹤山; 李崇; 郭彦青

    2003-01-01

    The dissipation of the field in the two-photon Jaynes-Cummings model (JCM) with degenerate atomic levels was studied. The initial degenerate atomic state affects the field coherence loss. When the degenerate atom is initially in an equal probability superposition state, the field coherence loss is smallest. It is found that the degeneracy of the atomic level increases the period of entanglement between the atom and the field. When the degeneracy was considered, the coherence properties of the field could be affected by the reservoir qualitatively, if a nonlinear two-photon process is involved. This is different from the dissipation of one-photon JCM with degenerate atomic levels.

  15. Monte Carlo Technique Used to Model the Degradation of Internal Spacecraft Surfaces by Atomic Oxygen

    Science.gov (United States)

    Banks, Bruce A.; Miller, Sharon K.

    2004-01-01

    Atomic oxygen is one of the predominant constituents of Earth's upper atmosphere. It is created by the photodissociation of molecular oxygen (O2) into single O atoms by ultraviolet radiation. It is chemically very reactive because a single O atom readily combines with another O atom or with other atoms or molecules that can form a stable oxide. The effects of atomic oxygen on the external surfaces of spacecraft in low Earth orbit can have dire consequences for spacecraft life, and this is a well-known and much studied problem. Much less information is known about the effects of atomic oxygen on the internal surfaces of spacecraft. This degradation can occur when openings in components of the spacecraft exterior exist that allow the entry of atomic oxygen into regions that may not have direct atomic oxygen attack but rather scattered attack. Openings can exist because of spacecraft venting, microwave cavities, and apertures for Earth viewing, Sun sensors, or star trackers. The effects of atomic oxygen erosion of polymers interior to an aperture on a spacecraft were simulated at the NASA Glenn Research Center by using Monte Carlo computational techniques. A two-dimensional model was used to provide quantitative indications of the attenuation of atomic oxygen flux as a function of the distance into a parallel-walled cavity. The model allows the atomic oxygen arrival direction, the Maxwell Boltzman temperature, and the ram energy to be varied along with the interaction parameters of the degree of recombination upon impact with polymer or nonreactive surfaces, the initial reaction probability, the reaction probability dependence upon energy and angle of attack, degree of specularity of scattering of reactive and nonreactive surfaces, and the degree of thermal accommodation upon impact with reactive and non-reactive surfaces to be varied to allow the model to produce atomic oxygen erosion geometries that replicate actual experimental results from space. The degree of

  16. Nano Goes to School: A Teaching Model of the Atomic Force Microscope

    Science.gov (United States)

    Planinsic, Gorazd; Kovac, Janez

    2008-01-01

    The paper describes a teaching model of the atomic force microscope (AFM), which proved to be successful in the role of an introduction to nanoscience in high school. The model can demonstrate the two modes of operation of the AFM (contact mode and oscillating mode) as well as some basic principles that limit the resolution of the method. It can…

  17. Comparison of kinetic models for atom recombination on high-temperature reusable surface insulation

    Science.gov (United States)

    Willey, Ronald J.

    1993-01-01

    Five kinetic models are compared for their ability to predict recombination coefficients for oxygen and nitrogen atoms over high-temperature reusable surface insulation (HRSI). Four of the models are derived using Rideal-Eley or Langmuir-Hinshelwood catalytic mechanisms to describe the reaction sequence. The fifth model is an empirical expression that offers certain features unattainable through mechanistic description. The results showed that a four-parameter model, with temperature as the only variable, works best with data currently available. The model describes recombination coefficients for oxygen and nitrogen atoms for temperatures from 300 to 1800 K. Kinetic models, with atom concentrations, demonstrate the influence of atom concentration on recombination coefficients. These models can be used for the prediction of heating rates due to catalytic recombination during re-entry or aerobraking maneuvers. The work further demonstrates a requirement for more recombination experiments in the temperature ranges of 300-1000 K, and 1500-1850 K, with deliberate concentration variation to verify model requirements.

  18. A comparison of two atomic models for the radiative properties of dense hot low Z plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Minguez, E. E-mail: minguez@denim.upm.es; Sauvan, P.; Gil, J.M.; Rodriguez, R.; Rubiano, J.G.; Florido, R.; Martel, P.; Angelo, P.; Schott, R.; Philippe, F.; Leboucher-Dalimier, E.; Mancini, R

    2003-11-01

    In this work, two different atomic models (ANALOP based on parametric potentials and IDEFIX based on the dicenter model) are used to calculate the opacities for bound-bound transitions in hot dense, low Z plasmas, and the results are compared to each other. In addition, the ANALOP code has been used to compute free-bound cross sections for hydrogen-like ions.

  19. Nano Goes to School: A Teaching Model of the Atomic Force Microscope

    Science.gov (United States)

    Planinsic, Gorazd; Kovac, Janez

    2008-01-01

    The paper describes a teaching model of the atomic force microscope (AFM), which proved to be successful in the role of an introduction to nanoscience in high school. The model can demonstrate the two modes of operation of the AFM (contact mode and oscillating mode) as well as some basic principles that limit the resolution of the method. It can…

  20. Everyone Wants to Be a Model Teacher: Part III: Extensions to Atomic Structures and Bonding.

    Science.gov (United States)

    Schrader, C. L.

    1985-01-01

    Describes activities in which students: (1) propose creative atomic models that account for observed properties and predict additional experimental data; (2) calculate empirical formulas for 27 binary compounds; (3) propose a model to explain why certain elements have certain valences; and (4) arrange hypothetical elements into a periodic chart.…

  1. Supporting Students in Learning with Multiple Representation to Improve Student Mental Models on Atomic Structure Concepts

    Science.gov (United States)

    Sunyono; Yuanita, L.; Ibrahim, M.

    2015-01-01

    The aim of this research is identify the effectiveness of a multiple representation-based learning model, which builds a mental model within the concept of atomic structure. The research sample of 108 students in 3 classes is obtained randomly from among students of Mathematics and Science Education Studies using a stratified random sampling…

  2. Giant Atomic and Molecular Models and Other Lecture Demonstration Devices Designed for Concrete Operational Students.

    Science.gov (United States)

    Battino, Rubin

    1983-01-01

    Describes the design, construction, and use of oversize lecture-demonstration atomic/molecular models. These models appeal to both concrete and formal operational students. Also describes construction and use of an "spdf" sandwich board and an experiment using attribute blocks. (JN)

  3. Many-Body Quantum Optics with Decaying Atomic Spin States: ($\\gamma$, $\\kappa$) Dicke model

    CERN Document Server

    Gelhausen, Jan; Strack, Philipp

    2016-01-01

    We provide a theory for quantum-optical realizations of the open Dicke model with internal, atomic spin states subject to uncorrelated, single-site spontaneous emission with rate $\\gamma$. This introduces a second decay channel for excitations to irreversibly dissipate into the environment, in addition to the photon loss with rate $\\kappa$. We compute the mean-field non-equilibrium steady states for spin and photon observables in the long-time limit, $t\\rightarrow \\infty$. Although $\\gamma$ does not conserve the total angular momentum of the spin array, we argue that our solution is exact in the thermodynamic limit, for the number of atoms $N\\rightarrow \\infty$. In light of recent and upcoming experiments realizing superradiant phase transitions using internal atomic states with pinned atoms in optical lattices, our work lays the foundation for the pursuit of a new class of open quantum magnets coupled to quantum light.

  4. Personalised modelling of facial action unit intensity

    NARCIS (Netherlands)

    Yang, Shuang; Rudovic, Ognjen; Pavlovic, Vladimir; Pantic, Maja

    2014-01-01

    Facial expressions depend greatly on facial morphology and expressiveness of the observed person. Recent studies have shown great improvement of the personalized over non-personalized models in variety of facial expression related tasks, such as face and emotion recognition. However, in the context

  5. Relativistic Corrections to the Bohr Model of the Atom

    Science.gov (United States)

    Kraft, David W.

    1974-01-01

    Presents a simple means for extending the Bohr model to include relativistic corrections using a derivation similar to that for the non-relativistic case, except that the relativistic expressions for mass and kinetic energy are employed. (Author/GS)

  6. 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.

  7. Unit root modeling for trending stock market series

    Directory of Open Access Journals (Sweden)

    Afees A. Salisu

    2016-06-01

    Full Text Available In this paper, we examine how the unit root for stock market series should be modeled. We employ the Narayan and Liu (2015 trend GARCH-based unit root and its variants in order to more carefully capture the inherent statistical behavior of the series. We utilize daily, weekly and monthly data covering nineteen countries across the regions of America, Asia and Europe. We find that the nature of data frequency matters for unit root testing when dealing with stock market data. Our evidence also suggests that stock market data is better modeled in the presence of structural breaks, conditional heteroscedasticity and time trend.

  8. 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.

  9. Theory of quantum and classical connections in modeling atomic, molecular and electrodynamical systems

    CERN Document Server

    Popa, Alexandru

    2013-01-01

    Quantum and Classical Connections in Modeling Atomic, Molecular and Electrodynamic Systems is intended for scientists and graduate students interested in the foundations of quantum mechanics and applied scientists interested in accurate atomic and molecular models. This is a reference to those working in the new field of relativistic optics, in topics related to relativistic interactions between very intense laser beams and particles, and is based on 30 years of research. The novelty of this work consists of accurate connections between the properties of quantum equations and correspon

  10. The contribution of atom accessibility to site of metabolism models for cytochromes P450.

    Science.gov (United States)

    Rydberg, Patrik; Rostkowski, Michal; Gloriam, David E; Olsen, Lars

    2013-04-01

    Three different types of atom accessibility descriptors are investigated in relation to site of metabolism predictions. To enable the integration of local accessibility we have constructed 2DSASA, a method for the calculation of the atomic solvent accessible surface area that is independent of 3D coordinates. The method was implemented in the SMARTCyp site of metabolism prediction models and improved the results by up to 4 percentage points for nine cytochrome P450 isoforms. The final models are made available at http://www.farma.ku.dk/smartcyp.

  11. An atomic model of brome mosaic virus using direct electron detection and real-space optimization.

    Science.gov (United States)

    Wang, Zhao; Hryc, Corey F; Bammes, Benjamin; Afonine, Pavel V; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L; Kao, Cheng; Ludtke, Steven J; Schmid, Michael F; Adams, Paul D; Chiu, Wah

    2014-09-04

    Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure.

  12. 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.

  13. Galilean invariance in the exponential model of atomic collisions

    Energy Technology Data Exchange (ETDEWEB)

    del Pozo, A.; Riera, A.; Yaez, M.

    1986-11-01

    Using the X/sup n//sup +/(1s/sup 2/)+He/sup 2+/ colliding systems as specific examples, we study the origin dependence of results in the application of the two-state exponential model, and we show the relevance of polarization effects in that study. Our analysis shows that polarization effects of the He/sup +/(1s) orbital due to interaction with X/sup (//sup n//sup +1)+/ ion in the exit channel yield a very small contribution to the energy difference and render the dynamical coupling so strongly origin dependent that it invalidates the basic premises of the model. Further study, incorporating translation factors in the formalism, is needed.

  14. 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.

  15. General model of depolarization and transfer of polarization of singly ionized atoms by collisions with hydrogen atoms

    CERN Document Server

    Derouich, Moncef

    2016-01-01

    Simulations of the generation of the atomic polarization is necessary for interpreting the second solar spectrum. For this purpose, it is important to rigorously determine the effects of the isotropic collisions with neutral hydrogen on the atomic polarization of the neutral atoms, ionized atoms and molecules. Our aim is to treat in generality the problem of depolarizing isotropic collisions between singly ionized atoms and neutral hydrogen in its ground state. Using our numerical code, we computed the collisional depolarization rates of the $p$-levels of ions for large number of values of the effective principal quantum number $n^{*}$ and the Uns\\"old energy $E_p$. Then, genetic programming has been utilized to fit the available depolarization rates. As a result, strongly non-linear relationships between the collisional depolarization rates, $n^{*}$ and $E_p$ are obtained, and are shown to reproduce the original data with accuracy clearly better than 10\\%. These relationships allow quick calculations of the ...

  16. Modeling and understanding of effects of randomness in arrays of resonant meta-atoms

    DEFF Research Database (Denmark)

    Tretyakov, Sergei A.; Albooyeh, Mohammad; Alitalo, Pekka

    2013-01-01

    In this review presentation we will discuss approaches to modeling and understanding electromagnetic properties of 2D and 3D lattices of small resonant particles (meta-atoms) in transition from regular (periodic) to random (amorphous) states. Nanostructured metasurfaces (2D) and metamaterials (3D......) are arrangements of optically small but resonant particles (meta-atoms). We will present our results on analytical modeling of metasurfaces with periodical and random arrangements of electrically and magnetically resonant meta-atoms with identical or random sizes, both for the normal and oblique-angle excitations....... We show how the electromagnetic response of metasurfaces is related to the statistical parameters of the structure. Furthermore, we will discuss the phenomenon of anti-resonance in extracted effective parameters of metamaterials and clarify its relation to the periodicity (or amorphous nature...

  17. Spin-splitting calculation for zincblende semiconductors using an atomic bond-orbital model.

    Science.gov (United States)

    Kao, Hsiu-Fen; Lo, Ikai; Chiang, Jih-Chen; Chen, Chun-Nan; Wang, Wan-Tsang; Hsu, Yu-Chi; Ren, Chung-Yuan; Lee, Meng-En; Wu, Chieh-Lung; Gau, Ming-Hong

    2012-10-17

    We develop a 16-band atomic bond-orbital model (16ABOM) to compute the spin splitting induced by bulk inversion asymmetry in zincblende materials. This model is derived from the linear combination of atomic-orbital (LCAO) scheme such that the characteristics of the real atomic orbitals can be preserved to calculate the spin splitting. The Hamiltonian of 16ABOM is based on a similarity transformation performed on the nearest-neighbor LCAO Hamiltonian with a second-order Taylor expansion k at the Γ point. The spin-splitting energies in bulk zincblende semiconductors, GaAs and InSb, are calculated, and the results agree with the LCAO and first-principles calculations. However, we find that the spin-orbit coupling between bonding and antibonding p-like states, evaluated by the 16ABOM, dominates the spin splitting of the lowest conduction bands in the zincblende materials.

  18. Al13H-: Hydrogen atom site selectivity and the shell model

    Science.gov (United States)

    Grubisic, A.; Li, X.; Stokes, S. T.; Vetter, K.; Ganteför, G. F.; Bowen, K. H.; Jena, P.; Kiran, B.; Burgert, R.; Schnöckel, H.

    2009-09-01

    Using a combination of anion photoelectron spectroscopy and density functional theory calculations, we explored the influence of the shell model on H atom site selectivity in Al13H-. Photoelectron spectra revealed that Al13H- has two anionic isomers and for both of them provided vertical detachment energies (VDEs). Theoretical calculations found that the structures of these anionic isomers differ by the position of the hydrogen atom. In one, the hydrogen atom is radially bonded, while in the other, hydrogen caps a triangular face. VDEs for both anionic isomers as well as other energetic relationships were also calculated. Comparison of the measured versus calculated VDE values permitted the structure of each isomer to be confirmed and correlated with its observed photoelectron spectrum. Shell model, electron-counting considerations correctly predicted the relative stabilities of the anionic isomers and identified the stable structure of neutral Al13H.

  19. Atomic Data and Spectral Models for FeII

    CERN Document Server

    Bautista, Manuel A; Ballance, Connor; Quinet, Pascal; Ferland, Gary; Mendoza, Claudio; Kallman, Timothy R

    2015-01-01

    We present extensive calculations of radiative transition rates and electron impact collision strengths for Fe II. The data sets involve 52 levels from the $3d\\,^7$, $3d\\,^64s$, and $3d\\,^54s^2$ configurations. Computations of $A$-values are carried out with a combination of state-of-the-art multiconfiguration approaches, namely the relativistic Hartree--Fock, Thomas--Fermi--Dirac potential, and Dirac--Fock methods; while the $R$-matrix plus intermediate coupling frame transformation, Breit--Pauli $R$-matrix and Dirac $R$-matrix packages are used to obtain collision strengths. We examine the advantages and shortcomings of each of these methods, and estimate rate uncertainties from the resulting data dispersion. We proceed to construct excitation balance spectral models, and compare the predictions from each data set with observed spectra from various astronomical objects. We are thus able to establish benchmarks in the spectral modeling of [Fe II] emission in the IR and optical regions as well as in the UV Fe...

  20. Building a pseudo-atomic model of the anaphase-promoting complex

    Energy Technology Data Exchange (ETDEWEB)

    Kulkarni, Kiran; Zhang, Ziguo; Chang, Leifu; Yang, Jing; Fonseca, Paula C. A. da; Barford, David, E-mail: david.barford@icr.ac.uk [Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB (United Kingdom)

    2013-11-01

    This article describes an example of molecular replacement in which atomic models are used to interpret electron-density maps determined using single-particle electron-microscopy data. The anaphase-promoting complex (APC/C) is a large E3 ubiquitin ligase that regulates progression through specific stages of the cell cycle by coordinating the ubiquitin-dependent degradation of cell-cycle regulatory proteins. Depending on the species, the active form of the APC/C consists of 14–15 different proteins that assemble into a 20-subunit complex with a mass of approximately 1.3 MDa. A hybrid approach of single-particle electron microscopy and protein crystallography of individual APC/C subunits has been applied to generate pseudo-atomic models of various functional states of the complex. Three approaches for assigning regions of the EM-derived APC/C density map to specific APC/C subunits are described. This information was used to dock atomic models of APC/C subunits, determined either by protein crystallography or homology modelling, to specific regions of the APC/C EM map, allowing the generation of a pseudo-atomic model corresponding to 80% of the entire complex.

  1. Unified Model of Purification Units in Hydrogen Networks

    Institute of Scientific and Technical Information of China (English)

    吴思东; 王彧斐; 冯霄

    2014-01-01

    Purification processes are widely used in hydrogen networks of refineries to increase hydrogen reuse. In refineries, hydrogen purification techniques include hydrocarbon, hydrogen sulfide and CO removal units. In addi-tion, light hydrocarbon recovery from the hydrogen source streams can also result in hydrogen purification. In order to simplify the superstructure and mathematical model of hydrogen network integration, the models of different pu-rification processes are unified in this paper, including mass balance and the expressions for hydrogen recovery and impurity removal ratios, which are given for all the purification units in refineries. Based on the proposed unified model, a superstructure of hydrogen networks with purification processes is constructed.

  2. Dynamic decoupling and local atomic order of a model multicomponent metallic glass-former

    Science.gov (United States)

    Kim, Jeongmin; Sung, Bong June

    2015-06-01

    The dynamics of multicomponent metallic alloys is spatially heterogeneous near glass transition. The diffusion coefficient of one component of the metallic alloys may also decouple from those of other components, i.e., the diffusion coefficient of each component depends differently on the viscosity of metallic alloys. In this work we investigate the dynamic heterogeneity and decoupling of a model system for multicomponent Pd43Cu27Ni10P20 melts by using a hard sphere model that considers the size disparity of alloys but does not take chemical effects into account. We also study how such dynamic behaviors would relate to the local atomic structure of metallic alloys. We find, from molecular dynamics simulations, that the smallest component P of multicomponent Pd43Cu27Ni10P20 melts becomes dynamically heterogeneous at a translational relaxation time scale and that the largest major component Pd forms a slow subsystem, which has been considered mainly responsible for the stabilization of amorphous state of alloys. The heterogeneous dynamics of P atoms accounts for the breakdown of Stokes-Einstein relation and also leads to the dynamic decoupling of P and Pd atoms. The dynamically heterogeneous P atoms decrease the lifetime of the local short-range atomic orders of both icosahedral and close-packed structures by orders of magnitude.

  3. Dynamic decoupling and local atomic order of a model multicomponent metallic glass-former.

    Science.gov (United States)

    Kim, Jeongmin; Sung, Bong June

    2015-06-17

    The dynamics of multicomponent metallic alloys is spatially heterogeneous near glass transition. The diffusion coefficient of one component of the metallic alloys may also decouple from those of other components, i.e., the diffusion coefficient of each component depends differently on the viscosity of metallic alloys. In this work we investigate the dynamic heterogeneity and decoupling of a model system for multicomponent Pd43Cu27Ni10P20 melts by using a hard sphere model that considers the size disparity of alloys but does not take chemical effects into account. We also study how such dynamic behaviors would relate to the local atomic structure of metallic alloys. We find, from molecular dynamics simulations, that the smallest component P of multicomponent Pd43Cu27Ni10P20 melts becomes dynamically heterogeneous at a translational relaxation time scale and that the largest major component Pd forms a slow subsystem, which has been considered mainly responsible for the stabilization of amorphous state of alloys. The heterogeneous dynamics of P atoms accounts for the breakdown of Stokes-Einstein relation and also leads to the dynamic decoupling of P and Pd atoms. The dynamically heterogeneous P atoms decrease the lifetime of the local short-range atomic orders of both icosahedral and close-packed structures by orders of magnitude.

  4. Atom counting in HAADF STEM using a statistical model-based approach: methodology, possibilities, and inherent limitations.

    Science.gov (United States)

    De Backer, A; Martinez, G T; Rosenauer, A; Van Aert, S

    2013-11-01

    In the present paper, a statistical model-based method to count the number of atoms of monotype crystalline nanostructures from high resolution high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) images is discussed in detail together with a thorough study on the possibilities and inherent limitations. In order to count the number of atoms, it is assumed that the total scattered intensity scales with the number of atoms per atom column. These intensities are quantitatively determined using model-based statistical parameter estimation theory. The distribution describing the probability that intensity values are generated by atomic columns containing a specific number of atoms is inferred on the basis of the experimental scattered intensities. Finally, the number of atoms per atom column is quantified using this estimated probability distribution. The number of atom columns available in the observed STEM image, the number of components in the estimated probability distribution, the width of the components of the probability distribution, and the typical shape of a criterion to assess the number of components in the probability distribution directly affect the accuracy and precision with which the number of atoms in a particular atom column can be estimated. It is shown that single atom sensitivity is feasible taking the latter aspects into consideration.

  5. COUPLED ATOMIZATION AND SPRAY MODELLING IN THE SPRAY FORMING PROCESS USING OPENFOAM

    DEFF Research Database (Denmark)

    Gjesing, Rasmus; Hattel, Jesper Henri; Fritsching, Udo

    2009-01-01

    The paper presents a numerical model capable of simulating the atomization, break-up and in-flight spray phenomena in the spray forming process. The model is developed and implemented in the freeware code openFOAM. The focus is on studying the coupling effect of the melt break-up phenomena...... model for droplet cooling and solidification. The model is tested and validated against results from literature and experiments. Subsequently, the model is used to simulate the complex flow fields in the spray forming process and the results are discussed. The presented model of the spray forming...

  6. Modelling of liquid flow after a hydraulic jump on a rotating disk prior to centrifugal atomization

    Science.gov (United States)

    Zhao, Y. Y.; Dowson, A. L.; Jacobs, M. H.

    2000-01-01

    This paper describes a simplified numerical model which is used to calculate the height distribution, and the radial and tangential velocities of a liquid on a rotating disk after a hydraulic jump and prior to centrifugal atomization. The results obtained from this numerical model are compared with predictions made using previously derived `hydraulic jump' and `analytical' models. Calculations, in conjunction with experimental measurements relating to the trajectory of liquid flow on the atomizing disk, have shown that the numerical model can not only give a reasonable prediction of the hydraulic jump location, but also yields more accurate information regarding the variations in liquid height, and radial and tangential velocities. The model is ideally suited for engineering applications.

  7. Atomicrex—a general purpose tool for the construction of atomic interaction models

    Science.gov (United States)

    Stukowski, Alexander; Fransson, Erik; Mock, Markus; Erhart, Paul

    2017-07-01

    We introduce atomicrex, an open-source code for constructing interatomic potentials as well as more general types of atomic-scale models. Such effective models are required to simulate extended materials structures comprising many thousands of atoms or more, because electronic structure methods become computationally too expensive at this scale. atomicrex covers a wide range of interatomic potential types and fulfills many needs in atomistic model development. As inputs, it supports experimental property values as well as ab initio energies and forces, to which models can be fitted using various optimization algorithms. The open architecture of atomicrex allows it to be used in custom model development scenarios beyond classical interatomic potentials while thanks to its Python interface it can be readily integrated e.g., with electronic structure calculations or machine learning algorithms.

  8. Atomic Model and Micelle Dynamics of QS-21 Saponin

    Directory of Open Access Journals (Sweden)

    Conrado Pedebos

    2014-03-01

    Full Text Available QS-21 is a saponin extracted from Quillaja saponaria, widely investigated as a vaccine immunoadjuvant. However, QS-21 use is mainly limited by its chemical instability, significant variety in molecular composition and low tolerance dose in mammals. Also, this compound tends to form micelles in a concentration-dependent manner. Here, we aimed to characterize its conformation and the process of micelle formation, both experimentally and computationally. Therefore, molecular dynamics (MD simulations were performed in systems containing different numbers of QS-21 molecules in aqueous solution, in order to evaluate the spontaneous micelle formation. The applied methodology allowed the generation of micelles whose sizes were shown to be in high agreement with small-angle X-ray scattering (SAXS. Furthermore, the ester linkage between fucose and acyl chain was less solvated in the micellar form, suggesting a reduction in hydrolysis. This is the first atomistic interpretation of previous experimental data, the first micellar characterization of saponin micelles by SAXS and first tridimensional model of a micelle constituted of saponins, contributing to the understanding of the molecular basis of these compounds.

  9. Plasma-statistical models of the atom in the theory of some collisional and radiative processes

    NARCIS (Netherlands)

    Astapenko, VA

    2002-01-01

    A plasma-statistical model was used to describe collisional and radiative processes involving target ionization, namely, collisional ionization of atoms and incoherent polarization bremsstrahlung. The cross sections of these processes were expressed through the Compton profile of X-ray scattering, f

  10. Construction of an E. Coli genome-scale atom mapping model for MFA calculations.

    Science.gov (United States)

    Ravikirthi, Prabhasa; Suthers, Patrick F; Maranas, Costas D

    2011-06-01

    Metabolic flux analysis (MFA) has so far been restricted to lumped networks lacking many important pathways, partly due to the difficulty in automatically generating isotope mapping matrices for genome-scale metabolic networks. Here we introduce a procedure that uses a compound matching algorithm based on the graph theoretical concept of pattern recognition along with relevant reaction information to automatically generate genome-scale atom mappings which trace the path of atoms from reactants to products for every reaction. The procedure is applied to the iAF1260 metabolic reconstruction of Escherichia coli yielding the genome-scale isotope mapping model imPR90068. This model maps 90,068 non-hydrogen atoms that span all 2,077 reactions present in iAF1260 (previous largest mapping model included 238 reactions). The expanded scope of the isotope mapping model allows the complete tracking of labeled atoms through pathways such as cofactor and prosthetic group biosynthesis and histidine metabolism. An EMU representation of imPR90068 is also constructed and made available.

  11. New phases in an extended Hubbard model explicitly including atomic polarizabilities

    NARCIS (Netherlands)

    Brink, van de J.; Meinders, M.B.J.; Lorenzana, J.; Eder, R.; Sawatzky, G.A.

    1996-01-01

    We consider the influence of a nearest-neighbor Coulomb interaction in an extended Hubbard model and introduce a new interaction term which simulates atomic polarizabilities. This has the effect of screening the on-site Coulomb interaction for charged excitations, unlike a neighbor Coulomb interacti

  12. A simple model for atomic layer doped field-effect transistor (ALD-FET) electronic states

    Energy Technology Data Exchange (ETDEWEB)

    Mora R, M.E. [Centro de Investigaciones en Optica, Unidad Aguascalientes. Juan de Montoro 207, Zona Centro, 20000 Aguascalientes (Mexico); Gaggero S, L.M. [Escuela de Fisica, Universidad Autonoma de Zacatecas, Av. Preparatoria 301, 98060 Zacatecas (Mexico)

    1998-12-31

    We propose a simple potential model based on the Thomas-Fermi approximation to reproduce the main properties of the electronic structure of an atomic layer doped field effect transistor. Preliminary numerical results for a Si-based ALD-FET justify why bound electronic states are not observed in the experiment. (Author)

  13. Atomic Dipole Squeezing in the Correlated Two-Mode Two-Photon Jaynes-Cummings Model

    Science.gov (United States)

    Dong, Zhengchao; Zhao, Yonglin

    1996-01-01

    In this paper, we study the atomic dipole squeezing in the correlated two-mode two-photon JC model with the field initially in the correlated two-mode SU(1,1) coherent state. The effects of detuning, field intensity and number difference between the two field modes are investigated through numerical calculation.

  14. Kinetic model of II-VI(001) semiconductor surfaces : Growth rates in atomic layer epitaxy

    NARCIS (Netherlands)

    Volkmann, T; Ahr, M; Biehl, M

    2004-01-01

    We present a zinc-blende lattice gas model of II-VI(001) surfaces, which is investigated by means of kinetic Monte Carlo simulations. Anisotropic effective interactions between surface metal atoms allow for the description of, e.g., the sublimation of CdTe(001), including the reconstruction of Cd-te

  15. Modeling Mechanism and Growth Reactions for New Nanofabrication Processes by Atomic Layer Deposition.

    Science.gov (United States)

    Elliott, Simon D; Dey, Gangotri; Maimaiti, Yasheng; Ablat, Hayrensa; Filatova, Ekaterina A; Fomengia, Glen N

    2016-07-01

    Recent progress in the simulation of the chemistry of atomic layer deposition (ALD) is presented for technologically important materials such as alumina, silica, and copper metal. Self-limiting chemisorption of precursors onto substrates is studied using density functional theory so as to determine reaction pathways and aid process development. The main challenges for the future of ALD modeling are outlined.

  16. Aspherical-atom modeling of coordination compounds by single-crystal X-ray diffraction allows the correct metal atom to be identified.

    Science.gov (United States)

    Dittrich, Birger; Wandtke, Claudia M; Meents, Alke; Pröpper, Kevin; Mondal, Kartik Chandra; Samuel, Prinson P; Amin Sk, Nurul; Singh, Amit Pratap; Roesky, Herbert W; Sidhu, Navdeep

    2015-02-02

    Single-crystal X-ray diffraction (XRD) is often considered the gold standard in analytical chemistry, as it allows element identification as well as determination of atom connectivity and the solid-state structure of completely unknown samples. Element assignment is based on the number of electrons of an atom, so that a distinction of neighboring heavier elements in the periodic table by XRD is often difficult. A computationally efficient procedure for aspherical-atom least-squares refinement of conventional diffraction data of organometallic compounds is proposed. The iterative procedure is conceptually similar to Hirshfeld-atom refinement (Acta Crystallogr. Sect. A- 2008, 64, 383-393; IUCrJ. 2014, 1,61-79), but it relies on tabulated invariom scattering factors (Acta Crystallogr. Sect. B- 2013, 69, 91-104) and the Hansen/Coppens multipole model; disordered structures can be handled as well. Five linear-coordinate 3d metal complexes, for which the wrong element is found if standard independent-atom model scattering factors are relied upon, are studied, and it is shown that only aspherical-atom scattering factors allow a reliable assignment. The influence of anomalous dispersion in identifying the correct element is investigated and discussed.

  17. Modeling inelastic phonon scattering in atomic- and molecular-wire junctions

    DEFF Research Database (Denmark)

    Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads

    2005-01-01

    Computationally inexpensive approximations describing electron-phonon scattering in molecular-scale conductors are derived from the nonequilibrium Green's function method. The accuracy is demonstrated with a first-principles calculation on an atomic gold wire. Quantitative agreement between...... the full nonequilibrium Green's function calculation and the newly derived expressions is obtained while simplifying the computational burden by several orders of magnitude. In addition, analytical models provide intuitive understanding of the conductance including nonequilibrium heating and provide...... a convenient way of parameterizing the physics. This is exemplified by fitting the expressions to the experimentally observed conductances through both an atomic gold wire and a hydrogen molecule....

  18. Dynamics for a two-atom two-mode intensity-dependent Raman coupled model

    Science.gov (United States)

    Singh, S.; Gilhare, K.

    2016-06-01

    We study the quantum dynamics of a two-atom Raman coupled model interacting with a quantized bimodal field with intensity-dependent coupling terms in a lossless cavity. The unitary transformation method used to solve the time-dependent problem also gives the eigensolutions of the interaction Hamiltonian. We study the atomic-population dynamics and dynamics of the photon statistics in the two cavity modes, and present evidence of cooperative effects in the production of antibunching and anticorrelations between the modes. We also investigate the effect of detuning on the evolution of second-order correlation functions and observe that the oscillations become more rapid for large detuning.

  19. 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.

  20. Dynamics for a two-atom two-mode intensity-dependent Raman coupled model

    Energy Technology Data Exchange (ETDEWEB)

    Singh, S., E-mail: vasudha-rnc1@rediffmail.com, E-mail: sudhhasingh@gmail.com; Gilhare, K. [Ranchi University, Department of Physics (India)

    2016-06-15

    We study the quantum dynamics of a two-atom Raman coupled model interacting with a quantized bimodal field with intensity-dependent coupling terms in a lossless cavity. The unitary transformation method used to solve the time-dependent problem also gives the eigensolutions of the interaction Hamiltonian. We study the atomic-population dynamics and dynamics of the photon statistics in the two cavity modes, and present evidence of cooperative effects in the production of antibunching and anticorrelations between the modes. We also investigate the effect of detuning on the evolution of second-order correlation functions and observe that the oscillations become more rapid for large detuning.

  1. Application of sampling theory in modeling of continuum processes: photoionization cross-sections of atoms

    CERN Document Server

    Kozlov, Alex; Quiney, Harry

    2016-01-01

    We describe a method for the calculation of photoionization cross-sections using square-integrable amplitudes obtained from the diagonalization of finite-basis set representations of the electronic Hamiltonian. Three examples are considered: a model example in which the final state is a free particle, the hydrogen atom and neutral atomic sodium. The method exploits the Whittaker-Shannon-Kotel'nikov sampling theorem, which is widely used in digital signal sampling and reconstruction. The approach reproduces known data with very good accuracy and converges to the exact solution with increase of the basis set size.

  2. Model for Interaction Between Photon and Cold Atom in QED Cavity

    Institute of Scientific and Technical Information of China (English)

    ZHANG Li; WANG Cheng; LI Yan-Min; RUAN Sheng-Ping; XUAN Li

    2004-01-01

    A model has been established for the interaction between a single-mode optical field and a 2-energy-level cold atom with exact analytic solutions given. The processes of momentum and energy exchanges between the optical field and the cold atom due to the interaction between them are discussed in detail, and a formula has been given for the variation of momentum and energy exchange volumes with time t in dress state while both the effects of photon recoil and Doppler effect are taken into consideration.

  3. Application of sampling theory in modelling of continuum processes: photoionization cross-sections of atoms

    Science.gov (United States)

    Kozlov, A.; Saha, S.; Quiney, H. M.

    2017-01-01

    We describe a method for the calculation of photoionization cross-sections using square-integrable amplitudes obtained from the diagonalization of finite-basis set representations of the electronic Hamiltonian. Three examples are considered: a model example in which the final state is a free particle, the hydrogen atom and neutral atomic sodium. The method exploits the Whittaker-Shannon-Kotel’nikov sampling theorem, which is widely used in digital signal sampling and reconstruction. The approach reproduces known data with very good accuracy and converges to the exact solution with increase of the basis set size.

  4. Applications of quantum and classical connections in modeling atomic, molecular and electrodynamic systems

    CERN Document Server

    Popa, Alexandru

    2013-01-01

    Applications of Quantum and Classical Connections in Modeling Atomic, Molecular and Electrodynamical Systems is a reference on the new field of relativistic optics, examining topics related to relativistic interactions between very intense laser beams and particles. Based on 30 years of research, this unique book connects the properties of quantum equations to corresponding classical equations used to calculate the energetic values and the symmetry properties of atomic, molecular and electrodynamical systems. In addition, it examines applications for these methods, and for the calculation of

  5. Parametric time delay modeling for floating point units

    Science.gov (United States)

    Fahmy, Hossam A. H.; Liddicoat, Albert A.; Flynn, Michael J.

    2002-12-01

    A parametric time delay model to compare floating point unit implementations is proposed. This model is used to compare a previously proposed floating point adder using a redundant number representation with other high-performance implementations. The operand width, the fan-in of the logic gates and the radix of the redundant format are used as parameters to the model. The comparison is done over a range of operand widths, fan-in and radices to show the merits of each implementation.

  6. Approximate Teleportation of an Unknown Atomic-Entangled State with Dissipative Atom-Cavity Resonant Jaynes-Cummings Model

    Institute of Scientific and Technical Information of China (English)

    LIU Zong-Liang; LI Shao-Hua; CHEN Chang-Yong

    2008-01-01

    We propose a scheme for approximately and conditionally teleporting an unknown atomic-entangled state in dissipative cavity QED.It is the further development of the scheme of [Phys.Rev.A 69 (2004) 064302],where the cavity mode decay has not been considered and the state teleportated is an unknown atomic state.In this paper,we investigate the influence of the decay on the approximate and conditional teleportation of the unknown atomic-entangled state,which is different from that teleportated in [Phys.Rev.A 69 (2004) 064302] and then give the fidelity of the teleportation,which depends on the cavity mode decay.The scheme may be generalized to not only the teleportation of the cavity-mode-entangled-state by means of a single atom but also the teleportation of the unknown trapped-ion-entangled-state in a linear ion trap.

  7. Parity violation in atomic cesium and alternatives to the standard model of electroweak interactions

    Science.gov (United States)

    Bouchiat, C.; Piketty, C. A.

    1983-08-01

    We study the implications of the recent observation of a parity violation in atomic cesium. After a discussion of the uncertainties associated with the atomic physics calculations we derive conservative bounds for the weak charge QW. These bounds are used to put constraints on alternatives to the standard electroweak model, involving an ``extra U(1)'' gauge group. We analyze the possibility that the extra gauge boson might be very and give, as a by-product, the typical range of momentum transfer explored in atomic parity violation experiments. Laboratoire Propre du Centre National de la Recherche Scientifique associée à l'Ecole Normale Supérieure et à l'Université de Paris Sud.

  8. Finite Bias Calculations to Model Interface Dipoles in Electrochemical Cells at the Atomic Scale

    DEFF Research Database (Denmark)

    Hansen, Martin Hangaard; Jin, Chengjun; Thygesen, Kristian Sommer

    2016-01-01

    The structure of an electrochemical interface is not determined by any external electrostatic field, but rather by external chemical potentials. This paper demonstrates that the electric double layer should be understood fundamentally as an internal electric field set up by the atomic structure t...... to satisfy the thermodynamic constraints imposed by the environment. This is captured by the generalized computational hydrogen electrode model, which enables us to make efficient first-principles calculations of atomic scale properties of the electrochemical interface.......The structure of an electrochemical interface is not determined by any external electrostatic field, but rather by external chemical potentials. This paper demonstrates that the electric double layer should be understood fundamentally as an internal electric field set up by the atomic structure...

  9. Approximate and Conditional Teleportation of an Unknown Atomic State with Dissipative Jaynes-Cummings Model

    Institute of Scientific and Technical Information of China (English)

    ZHOU Yu-Rong; CHEN Chang-Yong; PAN Hui-Mei; GUO Feng; PANG Xiao-Feng

    2008-01-01

    A scheme for approximately and conditionally teleporting an unknown atomic state in dissipative cavity QED is proposed. It is the extension of the scheme of [Phys. Rev. A 69 (2004) 064302], where the cavity mode decay has not been considered and only a time point of system evolution and the corresponding fidelity implementing the teleportation are given. In fact, the cavity mode decay exists really and must be delt with. In this paper, we investigate the influence from the cavity mode decay on the implementation of the approximate and conditional teleportation by means of the dissipative Jaynes Cummings model and then show the analytical expression of the fidelity of realization of the teleportation, Alternatively, our scheme does not involve an additional atom, only requiring two atoms and one single-mode cavity.

  10. Model operator approach to the Lamb shift calculations in relativistic many-electron atoms

    CERN Document Server

    Shabaev, V M; Yerokhin, V A

    2013-01-01

    A model operator approach to calculations of the QED corrections to energy levels in relativistic many-electron atomic systems is developed. The model Lamb shift operator is represented by a sum of local and nonlocal potentials which are defined using the results of ab initio calculations of the diagonal and nondiagonal matrix elements of the one-loop QED operator with H-like wave functions. The model operator can be easily included in any calculations based on the Dirac-Coulomb-Breit Hamiltonian. Efficiency of the method is demonstrated by comparison of the model QED operator results for the Lamb shifts in many-electron atoms and ions with exact QED calculations.

  11. Kinetic model of atomic and molecular emissions in laser-induced breakdown spectroscopy of organic compounds.

    Science.gov (United States)

    Ma, Qianli; Dagdigian, Paul J

    2011-07-01

    A kinetic model previously developed to predict the relative intensities of atomic emission lines in laser-induced breakdown spectroscopy has been extended to include processes related to CN and C(2) molecular emissions. Simulations with this model were performed to predict the relative excited-state populations. The results from the simulations are compared with experimentally determined excited-state populations from 1,064 nm laser irradiation of organic residues on aluminum foil. The model reasonably predicts the relative intensity of the molecular emissions. Significantly, the model reproduces the vastly different temporal profiles of the atomic and molecular emissions. The latter are found to extend to much longer times after the laser pulse, and this appears to be due to the increasing concentration of the molecules versus time. From the simulations, the important processes affecting the CN and C(2) concentrations are identified.

  12. Berry phase in a two-atom Jaynes-Cummings model with Kerr medium

    Science.gov (United States)

    Bu, Shen-Ping; Zhang, Guo-Feng; Liu, Jia; Chen, Zi-Yu

    2008-12-01

    The Jaynes-Cummings model (JCM) is an very important model for describing interaction between quantized electromagnetic fields and atoms in cavity quantum electrodynamics (QED). This model is generalized in many different directions since it predicts many novel quantum effects that can be verified by modern physics experimental technologies. In this paper, the Berry phase and entropy of the ground state for arbitrary photon number n of a two-atom Jaynes-Cummings model with Kerr-like medium are investigated. It is found that there is some correspondence between their images, especially the existence of a curve in the Δ-ɛ plane along which the energy, Berry phase and entropy all reach their special values. So it is available for detecting entanglement by applying Berry phase.

  13. Forecasting Models for Hydropower Unit Stability Using LS-SVM

    Directory of Open Access Journals (Sweden)

    Liangliang Qiao

    2015-01-01

    Full Text Available This paper discusses a least square support vector machine (LS-SVM approach for forecasting stability parameters of Francis turbine unit. To achieve training and testing data for the models, four field tests were presented, especially for the vibration in Y-direction of lower generator bearing (LGB and pressure in draft tube (DT. A heuristic method such as a neural network using Backpropagation (NNBP is introduced as a comparison model to examine the feasibility of forecasting performance. In the experimental results, LS-SVM showed superior forecasting accuracies and performances to the NNBP, which is of significant importance to better monitor the unit safety and potential faults diagnosis.

  14. A Stochastic Unit Commitment Model for a Local CHP Plant

    DEFF Research Database (Denmark)

    Ravn, Hans V.; Riisom, Jannik; Schaumburg-Müller, Camilla

    2005-01-01

    Local CHP development in Denmark has during the 90’s been characterised by large growth primarily due to government subsidies in the form of feed-in tariffs. In line with the liberalisation process in the EU, Danish local CHPs of a certain size must operate on market terms from 2005. This paper...... presents a stochastic unit commitment model for a single local CHP plant (consisting of CHP unit, boiler, and heat storage facility) which takes into account varying spot prices. Further, additional technology is implemented in the model in the form of an immersion heater. Simulations are conducted using...

  15. Point process models for household distributions within small areal units

    Directory of Open Access Journals (Sweden)

    Zack W. Almquist

    2012-06-01

    Full Text Available Spatio-demographic data sets are increasingly available worldwide, permitting ever more realistic modeling and analysis of social processes ranging from mobility to disease trans- mission. The information provided by these data sets is typically aggregated by areal unit, for reasons of both privacy and administrative cost. Unfortunately, such aggregation does not permit fine-grained assessment of geography at the level of individual households. In this paper, we propose to partially address this problem via the development of point pro- cess models that can be used to effectively simulate the location of individual households within small areal units.

  16. Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling

    Energy Technology Data Exchange (ETDEWEB)

    Bonfanti, Matteo, E-mail: matteo.bonfanti@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, v. Golgi 19, 20133 Milano (Italy); Jackson, Bret [Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003 (United States); Hughes, Keith H. [School of Chemistry, Bangor University, Bangor, Gwynedd LL57 2UW (United Kingdom); Burghardt, Irene [Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt/Main (Germany); Martinazzo, Rocco, E-mail: rocco.martinazzo@unimi.it [Dipartimento di Chimica, Università degli Studi di Milano, v. Golgi 19, 20133 Milano (Italy); Istituto di Scienze e Tecnologie Molecolari, Consiglio Nazionale delle Richerche, v. Golgi 19, 20133 Milano (Italy)

    2015-09-28

    An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theory for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.

  17. 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.

  18. Accurate model annotation of a near-atomic resolution cryo-EM map.

    Science.gov (United States)

    Hryc, Corey F; Chen, Dong-Hua; Afonine, Pavel V; Jakana, Joanita; Wang, Zhao; Haase-Pettingell, Cameron; Jiang, Wen; Adams, Paul D; King, Jonathan A; Schmid, Michael F; Chiu, Wah

    2017-03-21

    Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.

  19. An unit commitment model for hydrothermal systems; Um modelo de unit commitment para sistemas hidrotermicos

    Energy Technology Data Exchange (ETDEWEB)

    Franca, Thiago de Paula; Luciano, Edson Jose Rezende; Nepomuceno, Leonardo [Universidade Estadual Paulista (UNESP), Bauru, SP (Brazil). Dept. de Engenharia Eletrica], Emails: ra611191@feb.unesp.br, edson.joserl@uol.com.br, leo@feb.unesp.br

    2009-07-01

    A model of Unit Commitment to hydrothermal systems that includes the costs of start/stop of generators is proposed. These costs has been neglected in a good part of the programming models for operation of hydrothermal systems (pre-dispatch). The impact of the representation of costs in total production costs is evaluated. The proposed model is solved by a hybrid methodology, which involves the use of genetic algorithms (to solve the entire part of the problem) and sequential quadratic programming methods. This methodology is applied to the solution of an IEEE test system. The results emphasize the importance of representation of the start/stop in the generation schedule.

  20. A Comparison between Elementary School Students' Mental Models and Visualizations in Textbooks for the Concept of Atom

    Science.gov (United States)

    Polat-Yaseen, Zeynep

    2012-01-01

    This study was designed for two major goals, which are to describe students' mental models about atom concept from 6th to 8th grade and to compare students' mental models with visual representations of atom in textbooks. Qualitative and quantitative data were collected with 4 open-ended questions including drawings which were quantified using the…

  1. Modeling the heating and atomic kinetics of a photoionized neon plasma experiment

    Science.gov (United States)

    Lockard, Tom E.

    Motivated by gas cell photoionized plasma experiments performed by our group at the Z facility of Sandia National Laboratories, we discuss in this dissertation a modeling study of the heating and ionization of the plasma for conditions characteristic of these experiments. Photoionized plasmas are non-equilibrium systems driven by a broadband x-ray radiation flux. They are commonly found in astrophysics but rarely seen in the laboratory. Several modeling tools have been employed: (1) a view-factor computer code constrained with side x-ray power and gated monochromatic image measurements of the z-pinch radiation, to model the time-history of the photon-energy resolved x-ray flux driving the photoionized plasma, (2) a Boltzmann self-consistent electron and atomic kinetics model to simulate the electron distribution function and configuration-averaged atomic kinetics, (3) a radiation-hydrodynamics code with inline non-equilibrium atomic kinetics to perform a comprehensive numerical simulation of the experiment and plasma heating, and (4) steady-state and time-dependent collisional-radiative atomic kinetics calculations with fine-structure energy level description to assess transient effects in the ionization and charge state distribution of the plasma. The results indicate that the photon-energy resolved x-ray flux impinging on the front window of the gas cell is very well approximated by a linear combination of three geometrically-diluted Planckian distributions. Knowledge of the spectral details of the x-ray drive turned out to be important for the heating and ionization of the plasma. The free electrons in the plasma thermalize quickly relative to the timescales associated with the time-history of the x-ray drive and the plasma atomic kinetics. Hence, electrons are well described by a Maxwellian energy distribution of a single temperature. This finding is important to support the application of a radiation-hydrodynamic model to simulate the experiment. It is found

  2. Protein Nano-Object Integrator (ProNOI for generating atomic style objects for molecular modeling

    Directory of Open Access Journals (Sweden)

    Smith Nicholas

    2012-12-01

    Full Text Available Abstract Background With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system. Results Here we report the Protein Nano-Object Integrator (ProNOI which allows for generating atomic-style geometrical objects with user desired shape and dimensions. Unlimited number of objects can be created and combined with biological macromolecules in Protein Data Bank (PDB format file. Once the objects are generated, the users can use sliders to manipulate their shape, dimension and absolute position. In addition, the software offers the option to charge the objects with either specified surface or volumetric charge density and to model them with user-desired dielectric constants. According to the user preference, the biological macromolecule atoms can be assigned charges and radii according to four different force fields: Amber, Charmm, OPLS and PARSE. The biological macromolecules and the atomic-style objects are exported as a position, charge and radius (PQR file, or if a default dielectric constant distribution is not selected, it is exported as a position, charge, radius and epsilon (PQRE file. As illustration of the capabilities of the ProNOI, we created a composite object in a shape of a robot, aptly named the Clemson Robot, whose parts are charged with various volumetric charge densities and holds the barnase-barstar protein complex in its hand. Conclusions The Protein Nano-Object Integrator (ProNOI is a convenient tool for

  3. Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling.

    Science.gov (United States)

    Smith, Nicholas; Campbell, Brandon; Li, Lin; Li, Chuan; Alexov, Emil

    2012-12-05

    With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system. Here we report the Protein Nano-Object Integrator (ProNOI) which allows for generating atomic-style geometrical objects with user desired shape and dimensions. Unlimited number of objects can be created and combined with biological macromolecules in Protein Data Bank (PDB) format file. Once the objects are generated, the users can use sliders to manipulate their shape, dimension and absolute position. In addition, the software offers the option to charge the objects with either specified surface or volumetric charge density and to model them with user-desired dielectric constants. According to the user preference, the biological macromolecule atoms can be assigned charges and radii according to four different force fields: Amber, Charmm, OPLS and PARSE. The biological macromolecules and the atomic-style objects are exported as a position, charge and radius (PQR) file, or if a default dielectric constant distribution is not selected, it is exported as a position, charge, radius and epsilon (PQRE) file. As illustration of the capabilities of the ProNOI, we created a composite object in a shape of a robot, aptly named the Clemson Robot, whose parts are charged with various volumetric charge densities and holds the barnase-barstar protein complex in its hand. The Protein Nano-Object Integrator (ProNOI) is a convenient tool for generating atomic-style nano shapes in conjunction with

  4. 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...

  5. Atomically informed nonlocal semi-discrete variational Peierls-Nabarro model for planar core dislocations.

    Science.gov (United States)

    Liu, Guisen; Cheng, Xi; Wang, Jian; Chen, Kaiguo; Shen, Yao

    2017-03-02

    Prediction of Peierls stress associated with dislocation glide is of fundamental concern in understanding and designing the plasticity and mechanical properties of crystalline materials. Here, we develop a nonlocal semi-discrete variational Peierls-Nabarro (SVPN) model by incorporating the nonlocal atomic interactions into the semi-discrete variational Peierls framework. The nonlocal kernel is simplified by limiting the nonlocal atomic interaction in the nearest neighbor region, and the nonlocal coefficient is directly computed from the dislocation core structure. Our model is capable of accurately predicting the displacement profile, and the Peierls stress, of planar-extended core dislocations in face-centered cubic structures. Our model could be extended to study more complicated planar-extended core dislocations, such as {111} dislocations in Al-based and Ti-based intermetallic compounds.

  6. Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy.

    Science.gov (United States)

    Klocke, Michael; Wolf, Dietrich E

    2016-01-01

    A molecular dynamics model is presented, which adds harmonic potentials to the atomic interactions to mimic the elastic properties of an AFM cantilever. It gives new insight into the correlation between the experimentally monitored frequency shift and cantilever damping due to the interaction between tip atoms and scanned surface. Applying the model to ionic crystals with rock salt structure two damping mechanisms are investigated, which occur separately or simultaneously depending on the tip position. These mechanisms are adhesion hysteresis on the one hand and lateral excitations of the cantilever on the other. We find that the short range Lennard-Jones part of the atomic interaction alone is sufficient for changing the predominant mechanism. When the long range ionic interaction is switched off, the two damping mechanisms occur with a completely different pattern, which is explained by the energy landscape for the apex atom of the tip. In this case the adhesion hysteresis is always associated with a distinct lateral displacement of the tip. It is shown how this may lead to a systematic shift between the periodic patterns obtained from the frequency and from the damping signal, respectively.

  7. Coupled molecular and cantilever dynamics model for frequency-modulated atomic force microscopy

    Directory of Open Access Journals (Sweden)

    Michael Klocke

    2016-05-01

    Full Text Available A molecular dynamics model is presented, which adds harmonic potentials to the atomic interactions to mimic the elastic properties of an AFM cantilever. It gives new insight into the correlation between the experimentally monitored frequency shift and cantilever damping due to the interaction between tip atoms and scanned surface. Applying the model to ionic crystals with rock salt structure two damping mechanisms are investigated, which occur separately or simultaneously depending on the tip position. These mechanisms are adhesion hysteresis on the one hand and lateral excitations of the cantilever on the other. We find that the short range Lennard-Jones part of the atomic interaction alone is sufficient for changing the predominant mechanism. When the long range ionic interaction is switched off, the two damping mechanisms occur with a completely different pattern, which is explained by the energy landscape for the apex atom of the tip. In this case the adhesion hysteresis is always associated with a distinct lateral displacement of the tip. It is shown how this may lead to a systematic shift between the periodic patterns obtained from the frequency and from the damping signal, respectively.

  8. 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.

  9. Mathematical model of layered metallurgical furnaces and units

    Science.gov (United States)

    Shvydkiy, V. S.; Spirin, N. A.; Lavrov, V. V.

    2016-09-01

    The basic approaches to mathematical modeling of the layered steel furnaces and units are considered. It is noted that the particular importance have the knowledge about the mechanisms and physical nature of processes of the charge column movement and the gas flow in the moving layer, as well as regularities of development of heat- and mass-transfer in them. The statement and mathematical description of the problem solution targeting the potential gas flow in the layered unit of an arbitrary profile are presented. On the basis of the proposed mathematical model the software implementation of information-modeling system of BF gas dynamics is carried out. The results of the computer modeling of BF non-isothermal gas dynamics with regard to the cohesion zone, gas dynamics of the combustion zone and calculation of hot-blast stoves are provided

  10. New Data for Modeling Hypersonic Entry into Earth's Atmosphere: Electron-impact Ionization of Atomic Nitrogen

    Science.gov (United States)

    Savin, Daniel Wolf; Ciccarino, Christopher

    2017-06-01

    Meteors passing through Earth’s atmosphere and space vehicles returning to Earth from beyond orbit enter the atmosphere at hypersonic velocities (greater than Mach 5). The resulting shock front generates a high temperature reactive plasma around the meteor or vehicle (with temperatures greater than 10,000 K). This intense heat is transferred to the entering object by radiative and convective processes. Modeling the processes a meteor undergoes as it passes through the atmosphere and designing vehicles to withstand these conditions requires an accurate understanding of the underlying non-equilibrium high temperature chemistry. Nitrogen chemistry is particularly important given the abundance of nitrogen in Earth's atmosphere. Line emission by atomic nitrogen is a major source of radiative heating during atomspheric entry. Our ability to accurately calculate this heating is hindered by uncertainties in the electron-impact ionization (EII) rate coefficient for atomic nitrogen.Here we present new EII calculations for atomic nitrogen. The atom is treated as a 69 level system, incorporating Rydberg values up to n=20. Level-specific cross sections are from published B-Spline R-Matrix-with-Pseudostates results for the first three levels and binary-encounter Bethe (BEB) calculations that we have carried out for the remaining 59 levels. These cross section data have been convolved into level-specific rate coefficients and fit with the commonly-used Arrhenius-Kooij formula for ease of use in hypersonic chemical models. The rate coefficient data can be readily scaled by the relevant atomic nitrogen partition function which varies in time and space around the meteor or reentry vehicle. Providing data up to n=20 also enables modelers to account for the density-dependent lowering of the continuum.

  11. Tunable two-dimensional arrays of single Rydberg atoms for realizing quantum Ising models.

    Science.gov (United States)

    Labuhn, Henning; Barredo, Daniel; Ravets, Sylvain; de Léséleuc, Sylvain; Macrì, Tommaso; Lahaye, Thierry; Browaeys, Antoine

    2016-06-30

    Spin models are the prime example of simplified many-body Hamiltonians used to model complex, strongly correlated real-world materials. However, despite the simplified character of such models, their dynamics often cannot be simulated exactly on classical computers when the number of particles exceeds a few tens. For this reason, quantum simulation of spin Hamiltonians using the tools of atomic and molecular physics has become a very active field over the past years, using ultracold atoms or molecules in optical lattices, or trapped ions. All of these approaches have their own strengths and limitations. Here we report an alternative platform for the study of spin systems, using individual atoms trapped in tunable two-dimensional arrays of optical microtraps with arbitrary geometries, where filling fractions range from 60 to 100 per cent. When excited to high-energy Rydberg D states, the atoms undergo strong interactions whose anisotropic character opens the way to simulating exotic matter. We illustrate the versatility of our system by studying the dynamics of a quantum Ising-like spin-1/2 system in a transverse field with up to 30 spins, for a variety of geometries in one and two dimensions, and for a wide range of interaction strengths. For geometries where the anisotropy is expected to have small effects on the dynamics, we find excellent agreement with ab initio simulations of the spin-1/2 system, while for strongly anisotropic situations the multilevel structure of the D states has a measurable influence. Our findings establish arrays of single Rydberg atoms as a versatile platform for the study of quantum magnetism.

  12. COST ESTIMATION MODELS FOR DRINKING WATER TREATMENT UNIT PROCESSES

    Science.gov (United States)

    Cost models for unit processes typically utilized in a conventional water treatment plant and in package treatment plant technology are compiled in this paper. The cost curves are represented as a function of specified design parameters and are categorized into four major catego...

  13. Modeled Top of the Overburden Geomodel Unit (obtop_f)

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The obtop_f grid represents the modeled elevation of the top of the Overburden geomodel unit at a 500 foot resolution. It is one grid of a geomodel that consists of...

  14. Social Innovation using the Best Practice Unit model

    NARCIS (Netherlands)

    Wilken, Jean Pierre

    2013-01-01

    The model of the Best Practice Unit (BPU) is a specific form of practice based research. It is a variation of the Community of Practice (CoP) as developed by Wenger, McDermott and Snyder (2002) with the specific aim to innovate a professional practice by combining learning, development and research.

  15. Model United Nations and Deep Learning: Theoretical and Professional Learning

    Science.gov (United States)

    Engel, Susan; Pallas, Josh; Lambert, Sarah

    2017-01-01

    This article demonstrates that the purposeful subject design, incorporating a Model United Nations (MUN), facilitated deep learning and professional skills attainment in the field of International Relations. Deep learning was promoted in subject design by linking learning objectives to Anderson and Krathwohl's (2001) four levels of knowledge or…

  16. Modeling the effect of short stay units on patient admissions

    NARCIS (Netherlands)

    Zonderland, Maartje E.; Boucherie, Richard J.; Carter, Michael W.; Stanford, David A.

    2015-01-01

    Two purposes of Short Stay Units (SSU) are the reduction of Emergency Department crowding and increased urgent patient admissions. At an SSU urgent patients are temporarily held until they either can go home or transferred to an inpatient ward. In this paper we present an overflow model to evaluate

  17. Effect of External Radiation Filed on the Properties of the Atoms and Cavity Field in the Tavis-Cummings Model

    Institute of Scientific and Technical Information of China (English)

    王忠纯

    2004-01-01

    @@ We study the properties of the atoms and cavity field in the Tavis-Cummings Model where the two atoms interact each other and also are driven by an external classical field.We consider the special case that the cavity is initially in a coherent state.After work out the atomic inversion, the average photons number and the Mandel parameter in the driven Tavis-Cummings Model, we do numerical analysis of them, and pay special attention to the dynamical behavior of the atoms and the cavity field modified by the external field.

  18. Solvation free energies and partition coefficients with the coarse-grained and hybrid all-atom/coarse-grained MARTINI models

    Science.gov (United States)

    Genheden, Samuel

    2017-09-01

    We present the estimation of solvation free energies of small solutes in water, n-octanol and hexane using molecular dynamics simulations with two MARTINI models at different resolutions, viz. the coarse-grained (CG) and the hybrid all-atom/coarse-grained (AA/CG) models. From these estimates, we also calculate the water/hexane and water/octanol partition coefficients. More than 150 small, organic molecules were selected from the Minnesota solvation database and parameterized in a semi-automatic fashion. Using either the CG or hybrid AA/CG models, we find considerable deviations between the estimated and experimental solvation free energies in all solvents with mean absolute deviations larger than 10 kJ/mol, although the correlation coefficient is between 0.55 and 0.75 and significant. There is also no difference between the results when using the non-polarizable and polarizable water model, although we identify some improvements when using the polarizable model with the AA/CG solutes. In contrast to the estimated solvation energies, the estimated partition coefficients are generally excellent with both the CG and hybrid AA/CG models, giving mean absolute deviations between 0.67 and 0.90 log units and correlation coefficients larger than 0.85. We analyze the error distribution further and suggest avenues for improvements.

  19. Building a pseudo-atomic model of the anaphase-promoting complex.

    Science.gov (United States)

    Kulkarni, Kiran; Zhang, Ziguo; Chang, Leifu; Yang, Jing; da Fonseca, Paula C A; Barford, David

    2013-11-01

    The anaphase-promoting complex (APC/C) is a large E3 ubiquitin ligase that regulates progression through specific stages of the cell cycle by coordinating the ubiquitin-dependent degradation of cell-cycle regulatory proteins. Depending on the species, the active form of the APC/C consists of 14-15 different proteins that assemble into a 20-subunit complex with a mass of approximately 1.3 MDa. A hybrid approach of single-particle electron microscopy and protein crystallography of individual APC/C subunits has been applied to generate pseudo-atomic models of various functional states of the complex. Three approaches for assigning regions of the EM-derived APC/C density map to specific APC/C subunits are described. This information was used to dock atomic models of APC/C subunits, determined either by protein crystallography or homology modelling, to specific regions of the APC/C EM map, allowing the generation of a pseudo-atomic model corresponding to 80% of the entire complex.

  20. Atomic density functional and diagram of structures in the phase field crystal model

    Science.gov (United States)

    Ankudinov, V. E.; Galenko, P. K.; Kropotin, N. V.; Krivilyov, M. D.

    2016-02-01

    The phase field crystal model provides a continual description of the atomic density over the diffusion time of reactions. We consider a homogeneous structure (liquid) and a perfect periodic crystal, which are constructed from the one-mode approximation of the phase field crystal model. A diagram of 2D structures is constructed from the analytic solutions of the model using atomic density functionals. The diagram predicts equilibrium atomic configurations for transitions from the metastable state and includes the domains of existence of homogeneous, triangular, and striped structures corresponding to a liquid, a body-centered cubic crystal, and a longitudinal cross section of cylindrical tubes. The method developed here is employed for constructing the diagram for the homogeneous liquid phase and the body-centered iron lattice. The expression for the free energy is derived analytically from density functional theory. The specific features of approximating the phase field crystal model are compared with the approximations and conclusions of the weak crystallization and 2D melting theories.

  1. Why has the bohr-sommerfeld model of the atom been ignoredby general chemistry textbooks?

    Science.gov (United States)

    Niaz, Mansoor; Cardellini, Liberato

    2011-12-01

    Bohr's model of the atom is considered to be important by general chemistry textbooks. A major shortcoming of this model was that it could not explain the spectra of atoms containing more than one electron. In order to increase the explanatory power of the model, Sommerfeld hypothesized the existence of elliptical orbits. This study has the following objectives: 1) Formulation of criteria based on a history and philosophy of science framework; and 2) Evaluation of university-level general chemistry textbooks based on the criteria, published in Italy and U.S.A. Presentation of a textbook was considered to be "satisfactory" if it included a description of the Bohr-Sommerfeld model along with diagrams of the elliptical orbits. Of the 28 textbooks published in Italy that were analyzed, only five were classified as "satisfactory". Of the 46 textbooks published in U.S.A., only three were classified as "satisfactory". This study has the following educational implications: a) Sommerfeld's innovation (auxiliary hypothesis) by introducing elliptical orbits, helped to restore the viability of Bohr's model; b) Bohr-Sommerfeld's model went no further than the alkali metals, which led scientists to look for other models; c) This clearly shows that scientific models are tentative in nature; d) Textbook authors and chemistry teachers do not consider the tentative nature of scientific knowledge to be important; e) Inclusion of the Bohr-Sommerfeld model in textbooks can help our students to understand how science progresses.

  2. Atoms in optical networks. A simple tridimensional model; Atomos en redes opticas. Un modelo tridimensional sencillo

    Energy Technology Data Exchange (ETDEWEB)

    Balleza D, E

    2004-07-01

    In the first chapter of this work we will show a detailed analysis of the one cooling Doppler phenomenon that appears when a laser induces a dipolar moment to the atoms in such a way that these may interact with him to transfer moment to the field with the subsequent decrease of kinetic energy that macroscopically it is translated in cooling of the atomic cloud. When the experiments of atomic cooling were carried out it was observed that the temperature was smaller to the one than it predicted the cooling Doppler, this originates the creation of a theory but it dies in which the over simplification is eliminated that the alone atom consists of two energy levels and levels are introduced of it structures fine that are able to explain the extra cooling. To this phenomenon it is called Sisifo effect and it is studied detailedly in the chapter two. The first two chapters talk each other about the atomic cooling, but it stops that the atomic cloud can be manipulated, before being confined, problem that we will expose in the chapter three with experimental solutions that at the moment they are implemented in the laboratories around the world. In particular we will concentrate on the traps FORT (Far Off Resonance Trap, trap very outside of resonance) that confine to the atoms in optic nets. The lasers gaussianos originate a potential sinusoidal along the propagation address and gaussiano in the perpendicular plane to this. In the I surrender four he/she intends a three-dimensional model that substitutes To the variation sinusoidal for a function crenel and he/she makes an approach To first order in the radial dependence to obtain an oscillator potential Harmonic instead of the gaussiano that you taenia. The pattern is solved in a similar way To the pattern unidimensional of bands: they are the functions of wave solution For every period and they are coupled among if so that they satisfy conditions of rhythm, When making this you arrives to a womb that couples the

  3. A MELCOR model of Fukushima Daiichi Unit 3 accident

    Energy Technology Data Exchange (ETDEWEB)

    Sevón, Tuomo, E-mail: tuomo.sevon@vtt.fi

    2015-04-01

    Highlights: • A MELCOR model of the Fukushima Unit 3 accident was developed. • The MELCOR input file is published as electronic supplementary data with this paper. • Reactor pressure vessel lower head failed about 53 h after the earthquake. • 70% of fuel was discharged from reactor to containment. • 0.95% of cesium inventory was released to the environment. - Abstract: A MELCOR model of the Fukushima Daiichi Unit 3 accident was developed. The model is based on publicly available information, and the MELCOR input file is published as electronic supplementary data with this paper. According to the calculation, the reactor pressure vessel lower head failed about 53 h after the earthquake. At the end of the calculation, 30% of the fuel was still inside the reactor and 70% had been discharged to the containment. Almost all of the radioactive noble gases and 0.95% of the cesium inventory were released to the environment during the accident.

  4. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    CERN Document Server

    Wabik, Jacek; Gront, Dominik; Kouza, Maksim; Kolinski, Andrzej

    2013-01-01

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  5. Ion-biomolecule collisions studied within the independent atom model including geometric screening corrections

    Science.gov (United States)

    Lüdde, H. J.; Achenbach, A.; Kalkbrenner, T.; Jankowiak, H. C.; Kirchner, T.

    2016-05-01

    A recently introduced model to account for geometric screening corrections in an independent-atom-model description of ion-molecule collisions is applied to proton collisions from amino acids and DNA and RNA nucleobases. The correction coefficients are obtained from using a pixel counting method (PCM) for the exact calculation of the effective cross sectional area that emerges when the molecular cross section is pictured as a structure of (overlapping) atomic cross sections. This structure varies with the relative orientation of the molecule with respect to the projectile beam direction and, accordingly, orientation-independent total cross sections are obtained from averaging the pixel count over many orientations. We present net capture and net ionization cross sections over wide ranges of impact energy and analyze the strength of the screening effect by comparing the PCM results with Bragg additivity rule cross sections and with experimental data where available. Work supported by NSERC, Canada.

  6. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Andrzej Koliński

    2013-05-01

    Full Text Available We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  7. Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.

    Science.gov (United States)

    Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej

    2013-05-10

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  8. Modeling of inelastic transport in one-dimensional metallic atomic wires

    DEFF Research Database (Denmark)

    Frederiksen, Thomas; Brandbyge, Mads; Lorente, N

    2004-01-01

    devices. A full description of the transport properties of atomic-size conductors therefore requires a quantum mechanical treatment of both the electronic and mechanical degrees of freedom. In this paper, we study a one-dimensional tight-binding model of the conducting electrons combined with a balls......Atomic-size conductors represent the ultimate limit of miniaturization, and understanding their properties is an important problem in the fields of nanoelectronics and molecular electronics. Quantum effects become important which leads to a physical behavior fundamentally different from macroscopic......-and-springs model for the mechanical motion of the nuclei comprising the wire. We determine the vibrational modes and frequencies for the wires. The electronic Hamiltonian is expanded to lowest order in these normal modes....

  9. Structure and Thermodynamic Properties of Liquid Transition Metals with Different Embedded-Atom Method Models

    Institute of Scientific and Technical Information of China (English)

    王金照; 陈民; 过增元

    2002-01-01

    Pair distribution functions and constant-volume heat capacities of liquid copper, silver and nickel have been calculated by molecular dynamics simulations with four different versions of the embedded-atom method (EAM) model, namely, the versions of Johnson, Mei, Cai and Pohlong. The simulated structural properties with the four potential models show reasonable agreement with experiments and have little difference with each other, while the calculated heat capacities with the different EAM versions show remarkable discrepancies. Detailed analyses of the energy of the liquid metallic system show that, to predict successfully the heat capacity, an EAM model should match the state equation first proposed by Rose.

  10. Argon 4s and 4p Excited States Atomic Data Applied in ARC-JET Modeling

    Directory of Open Access Journals (Sweden)

    K. Katsonis

    2011-01-01

    Full Text Available Evaluated atomic data concerning the 4s and 4p configurations of Ar I are averaged in order to simplify their use in various cases of Ar plasma modeling and diagnostics. These data are used here to model a low-power arcjet, running with Argon at low pressure. In so doing, they are explicitly introduced in the chemical processes included in a fluid Navier-Stokes type code, allowing for evaluation of the spectroscopically measurable level populations and of the electronic temperatures. The characteristics of the model are described and the main processes are discussed in view of the results of the calculations.

  11. Atom-field entanglement in the Jaynes Cummings model without rotating wave approximation

    Institute of Scientific and Technical Information of China (English)

    M. Mirzaee; M. Batavani

    2015-01-01

    In this paper, we present a structure for obtaining the exact eigenfunctions and eigenvalues of the Jaynes–Cummings model (JCM) without the rotating wave approximation (RWA). We study the evolution of the system in the strong coupling region using the time evolution operator without RWA. The entanglement of the system without RWA is investigated using the Von Neumann entropy as an entanglement measure. It is interesting that in the weak coupling regime, the population of the atomic levels and Von Neumann entropy without RWA model shows a good agreement with the RWA whereas in strong coupling domain, the results of these two models are quite different.

  12. Modeling of Electric Disturbance Signals Using Damped Sinusoids via Atomic Decompositions and Its Applications

    Directory of Open Access Journals (Sweden)

    Tcheou Michel P

    2007-01-01

    Full Text Available The number of waveforms monitored in power systems is increasing rapidly. This creates a demand for computational tools that aid in the analysis of the phenomena and also that allow efficient transmission and storage of the information acquired. In this context, signal processing techniques play a fundamental role. This work is a tutorial reviewing the principles and applications of atomic signal modeling of electric disturbance signals. The disturbance signal is modeled using a linear combination of damped sinusoidal components which are closely related to the phenomena typically observed in power systems. The signal model obtained is then employed for disturbance signal denoising, filtering of "DC components," and compression.

  13. Development of Wolsong Unit 2 Containment Analysis Model

    Energy Technology Data Exchange (ETDEWEB)

    Hoon, Choi [Korea Hydro and Nuclear Power Co., Ltd., Daejeon (Korea, Republic of); Jin, Ko Bong; Chan, Park Young [Hanbat National Univ., Daejeon (Korea, Republic of)

    2014-05-15

    To be prepared for the full scope safety analysis of Wolsong unit 2 with modified fuel, input decks for the various objectives, which can be read by GOTHIC 7.2b(QA), are developed and tested for the steady state simulation. A detailed nodalization of 39 control volumes and 92 flow paths is constructed to determine the differential pressure across internal walls or hydrogen concentration and distribution inside containment. A lumped model with 15 control volumes and 74 flow paths has also been developed to reduce the computer run time for the assessments in which the analysis results are not sensitive to detailed thermal hydraulic distribution inside containment such as peak pressure, pressure dependent signal and radionuclide release. The input data files provide simplified representations of the geometric layout of the containment building (volumes, dimensions, flow paths, doors, panels, etc.) and the performance characteristics of the various containment subsystems. The parameter values are based on best estimate or design values for that parameter. The analysis values are determined by conservatism depending on the analysis objective and may be different for various analysis objectives. Basic input decks of Wolsong unit 2 were developed for the various analysis purposes with GOTHIC 7.2b(QA). Depend on the analysis objective, two types of models are prepared. Detailed model models each confined room in the containment as a separate node. All of the geometric data are based on the drawings of Wolsong unit 2. Developed containment models are simulating the steady state well to the designated initial condition. These base models will be used for Wolsong unit 2 in case of safety analysis of full scope is needed.

  14. On model materials designed by atomic layer deposition for catalysis purposes

    OpenAIRE

    Diskus, Madeleine

    2011-01-01

    The aim of this work was to investigate the potential of model materials designed by atomic layer deposition toward applications in catalysis research. Molybdenum based catalysts promoted with cobalt were selected as target materials, considering their important roles in various industrial processes. Particular attention was paid to understand the growth dynamics of the ALD processes involved and further to characterize the obtained materials carefully. It was of main concern to verify the fe...

  15. Self-Diffusion Coefficients in Liquid Ag Using the Embedded Atom Model Based Effective Pair Potentials

    OpenAIRE

    DALGIÇ, Seyfettin; ÇOLAKOĞULLARI, Mutlu

    2006-01-01

    We present the dynamical properties of liquid Ag at different temperatures, using the Mishin and Doyoma-Kagure version of the Embedded Atom Model (EAM) potentials. They have been evaluated within the framework of the mode-coupling theory, using a self-consistent scheme that uses as input data only the static structure functions and the interatomic pair potentials of the liquid Ag. We have computed single-particle and collective time dependent properties of liquid Ag, and thereby calc...

  16. Mechanics of the IL2RA Gene Activation Revealed by Modeling and Atomic Force Microscopy

    OpenAIRE

    Pascale Milani; Monique Marilley; Albert Sanchez-Sevilla; Jean Imbert; Cédric Vaillant; Françoise Argoul; Jean-Marc Egly; José Rocca-Serra; Alain Arneodo

    2011-01-01

    Transcription implies recruitment of RNA polymerase II and transcription factors (TFs) by DNA melting near transcription start site (TSS). Combining atomic force microscopy and computer modeling, we investigate the structural and dynamical properties of the IL2RA promoter and identify an intrinsically negative supercoil in the PRRII region (containing Elf-1 and HMGA1 binding sites), located upstream of a curved DNA region encompassing TSS. Conformational changes, evidenced by time-lapse studi...

  17. THE POTENTIAL MODEL INVESTIGATION OF STARK EFFECT IN CAESIUM RYDBERG STATE ATOMS AND COMPARISON WITH EXPERIMENT

    Institute of Scientific and Technical Information of China (English)

    HU ZHENG-FA; ZHOU SHI-KANG; GONG SHUN-SHENG; ZHAN MING-SHENG

    2000-01-01

    The potential model method for computation of Stark structure of Cs Rydberg states atoms and oscillator strength is described,for external electric fields varying from 0 to 600V/cm.Anticrossing,l-mixing and n-mixing phenomena are observed clearly from the map of Stark.Corresponding experiment is performed under the same condition,and the two results are in good agreement with each other within the experimental uncertainty.

  18. Note: curve fit models for atomic force microscopy cantilever calibration in water.

    Science.gov (United States)

    Kennedy, Scott J; Cole, Daniel G; Clark, Robert L

    2011-11-01

    Atomic force microscopy stiffness calibrations performed on commercial instruments using the thermal noise method on the same cantilever in both air and water can vary by as much as 20% when a simple harmonic oscillator model and white noise are used in curve fitting. In this note, several fitting strategies are described that reduce this difference to about 11%. © 2011 American Institute of Physics

  19. Error sources in atomic force microscopy for dimensional measurements: Taxonomy and modeling

    DEFF Research Database (Denmark)

    Marinello, F.; Voltan, A.; Savio, E.

    2010-01-01

    This paper aimed at identifying the error sources that occur in dimensional measurements performed using atomic force microscopy. In particular, a set of characterization techniques for errors quantification is presented. The discussion on error sources is organized in four main categories......: scanning system, tip-surface interaction, environment, and data processing. The discussed errors include scaling effects, squareness errors, hysteresis, creep, tip convolution, and thermal drift. A mathematical model of the measurement system is eventually described, as a reference basis for errors...

  20. Classical and quantum dynamics of a model for atomic-molecular Bose--Einstein condensates

    OpenAIRE

    Santos Filho, Gilberto Nascimento; Tonel, Arlei Prestes; Foerster, Angela; Links, Jon(Centre for Mathematical Physics, School of Mathematics and Physics, The University of Queensland, 4072, Australia)

    2005-01-01

    We study a model for a two-mode atomic-molecular Bose--Einstein condensate. Starting with a classical analysis we determine the phase space fixed points of the system. It is found that bifurcations of the fixed points naturally separate the coupling parameter space into four regions. The different regions give rise to qualitatively different dynamics. We then show that this classification holds true for the quantum dynamics.

  1. Model for Atomic Oxygen Visible Line Emissions in Comet C/1995 O1 Hale-Bopp

    CERN Document Server

    Raghuram, Susarla

    2012-01-01

    We have recently developed a coupled chemistry-emission model for the green and red-doublet emissions of atomic oxygen on comet Hyakutake. In the present work we applied our model to comet Hale-Bopp, which had an order of magnitude higher H2O production rate than comet Hyakutake, to evaluate the photochemistry associated with the production and loss of O(1S) and O(1D) atoms and emission processes of green and red-doublet lines. We present the wavelength-dependent photo-attenuation rates for different photodissociation processes forming O(1S) and O(1D). The calculated radiative efficiency profiles of O(1S) and O(1D) atoms show that in comet Hale-Bopp the green and red-doublet emissions are emitted mostly above radial distances of 10^3 and 10^4 km, respectively. The model calculated [OI] 6300 A emission surface brightness and average intensity over the Fabry-P{\\'e}rot spectrometer field of view are consistent with the observation of Morgenthaler et al. (2001), while the intensity ratio of green to red-doublet e...

  2. 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...

  3. Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach

    Energy Technology Data Exchange (ETDEWEB)

    He, Yi; Scheraga, Harold A., E-mail: has5@cornell.edu [Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853 (United States); Liwo, Adam [Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk (Poland)

    2015-12-28

    Coarse-grained models are useful tools to investigate the structural and thermodynamic properties of biomolecules. They are obtained by merging several atoms into one interaction site. Such simplified models try to capture as much as possible information of the original biomolecular system in all-atom representation but the resulting parameters of these coarse-grained force fields still need further optimization. In this paper, a force field optimization method, which is based on maximum-likelihood fitting of the simulated to the experimental conformational ensembles and least-squares fitting of the simulated to the experimental heat-capacity curves, is applied to optimize the Nucleic Acid united-RESidue 2-point (NARES-2P) model for coarse-grained simulations of nucleic acids recently developed in our laboratory. The optimized NARES-2P force field reproduces the structural and thermodynamic data of small DNA molecules much better than the original force field.

  4. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models.

    Directory of Open Access Journals (Sweden)

    Hyuntae Na

    2015-10-01

    Full Text Available Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations--how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models.

  5. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models.

    Science.gov (United States)

    Na, Hyuntae; Jernigan, Robert L; Song, Guang

    2015-10-01

    Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations--how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models.

  6. Entropy squeezing for a two—level atom in the Jaynes—Cummings model with an intensity—depend coupling

    Institute of Scientific and Technical Information of China (English)

    李春先; 方卯发; 等

    2003-01-01

    We study the squeezing for a two-level atom in the Jaynes-Cumings model with intensity-dependent coupling using quantum information entropy,and examine the influences of the initial state of the system on the squeezed component number and direction of the information entropy squeezing.Our results show that,the squeezed component number depends on the atomic initial distribution angle,while the squeezed direction is determined by both the phases of the atom and the field for the information entropy squeezing.Quantum information entropy is shown to be a remarkable precision measure for atomic squeezing.

  7. Entropy squeezing for a two-level atom in the Jaynes-Cummings model with an intensity-depend coupling

    Institute of Scientific and Technical Information of China (English)

    李春先; 方卯发

    2003-01-01

    We study the squeezing for a two-level atom in the Jaynes-Cummings model with intensity-dependent coupling using quantum information entropy, and examine the influences of the initial state of the system on the squeezed component number and direction of the information entropy squeezing. Our results show that, the squeezed component number depends on the atomic initial distribution angle, while the squeezed direction is determined by both the phases of the atom and the field for the information entropy squeezing. Quantum information entropy is shown to be a remarkable precision measure for atomic squeezing.

  8. Mathematical modeling of chemical composition modification and etching of polymers under the atomic oxygen influence

    Science.gov (United States)

    Chirskaia, Natalia; Novikov, Lev; Voronina, Ekaterina

    2016-07-01

    Atomic oxygen (AO) of the upper atmosphere is one of the most important space factors that can cause degradation of spacecraft surface. In our previous mathematical model the Monte Carlo method and the "large particles" approximation were used for simulating processes of polymer etching under the influence of AO [1]. The interaction of enlarged AO particles with the polymer was described in terms of probabilities of reactions such as etching of polymer and specular and diffuse scattering of the AO particles on polymer. The effects of atomic oxygen on protected polymers and microfiller containing composites were simulated. The simulation results were in quite good agreement with the results of laboratory experiments on magnetoplasmadynamic accelerator of the oxygen plasma of SINP MSU [2]. In this paper we present a new model that describes the reactions of AO interactions with polymeric materials in more detail. Reactions of formation and further emission of chemical compounds such as CO, CO _{2}, H _{2}O, etc. cause the modification of the chemical composition of the polymer and change the probabilities of its consequent interaction with the AO. The simulation results are compared with the results of previous simulation and with the results of laboratory experiments. The reasons for the differences between the results of natural experiments on spacecraft, laboratory experiments and simulations are discussed. N. Chirskaya, M. Samokhina, Computer modeling of polymer structures degradation under the atomic oxygen exposure, WDS'12 Proceedings of Contributed Papers: Part III - Physics, Matfyzpress Prague, 2012, pp. 30-35. E. Voronina, L. Novikov, V. Chernik, N. Chirskaya, K. Vernigorov, G. Bondarenko, and A. Gaidar, Mathematical and experimental simulation of impact of atomic oxygen of the earth's upper atmosphere on nanostructures and polymer composites, Inorganic Materials: Applied Research, 2012, vol. 3, no. 2, pp. 95-101.

  9. History and Philosophy of Science through Models: Some Challenges in the Case of "The Atom".

    Science.gov (United States)

    Justi, Rosaria; Gilbert, John

    2000-01-01

    Suggests that the contribution of history and philosophy of science (HPS) to science education can be enhanced through a consideration of scientific models. Analyzes the curriculum and textbooks for 14-16 year olds in Brazil and the United Kingdom and identifies the use of hybrid models. (Contains 35 references.) (Author/YDS)

  10. Analogies in the teaching of Thomson and Bohr’s atomic models: A critic analysis about students’ reasoning

    Directory of Open Access Journals (Sweden)

    Vinícius Catão de Assis Souza

    2006-03-01

    Full Text Available Assuming (i the importance of using analogies in science teaching, (ii the learning difficulties related to the atomic models both discussed in the literature and observed in our previous research, and (iii the gap found in the literature concerning studies that probe how students really understand analogies presented to them in science teaching, we investigate, in this study, how students from the Medium Level understand the atomic models from analogies used to present and explain them. In order to limit the study, we chose only the atomic models proposed by J.J.Thomson and Niels Bohr. This was because the analogies of “the plum pudding” and “the solar system” are very often used in their teaching. This study aims at discussing the contributions and limitations of using such analogies in the teaching of the correspondent atomic models. Data were gathered from a written questionnaire answered by 99 1st year students (from one public and one private school. Data analysis made it evident that most students do not understand the analogies, as well as the atomic models to which they are associated. Moreover, there is no meaning for them in using two different analogies for the atom. From data analysis we discuss some teaching implications. We also propose new research questions that may contribute to foster the discussion and the improvement in the teaching of the atomic models.

  11. Atomically thin spherical shell-shaped superscatterers based on a Bohr model.

    Science.gov (United States)

    Li, Rujiang; Lin, Xiao; Lin, Shisheng; Liu, Xu; Chen, Hongsheng

    2015-12-18

    Graphene monolayers can be used for atomically thin three-dimensional shell-shaped superscatterer designs. Due to the excitation of the first-order resonance of transverse magnetic (TM) graphene plasmons, the scattering cross section of the bare subwavelength dielectric particle is enhanced significantly by five orders of magnitude. The superscattering phenomenon can be intuitively understood and interpreted with a Bohr model. In addition, based on the analysis of the Bohr model, it is shown that contrary to the TM case, superscattering is hard to achieve by exciting the resonance of transverse electric (TE) graphene plasmons due to their poor field confinements.

  12. A quasi-stationary numerical model of atomized metal droplets, II: Prediction and assessment

    DEFF Research Database (Denmark)

    Pryds, Nini H.; Hattel, Jesper Henri; Thorborg, Jesper

    1999-01-01

    by comparing experimental and calculated results for the powder particles of 12Cr-Mo-V steel. The study is also focusing on some aspects of the process which are not available experimentally, e.g. the effect of undercooling and gas/metal ratio on the solidification. The important effect of these parameters has......A new model which extends previous studies and includes the interaction between enveloping gas and an array of droplets has been developed and presented in a previous paper. The model incorporates the probability density function of atomized metallic droplets into the heat transfer equations...

  13. Self-consistent tight-binding atomic-relaxation model of titanium dioxide

    Energy Technology Data Exchange (ETDEWEB)

    Schelling, P.K.; Yu, N.; Halley, J.W. [School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455 (United States)

    1998-07-01

    We report a self-consistent tight-binding atomic-relaxation model for titanium dioxide. We fit the parameters of the model to first-principles electronic structure calculations of the band structure and energy as a function of lattice parameters in bulk rutile. We report the method and results for the surface structures and energies of relaxed (110), (100), and (001) surfaces of rutile TiO{sub 2} as well as work functions for these surfaces. Good agreement with first-principles calculations and experiments, where available, is found for these surfaces. We find significant charge transfer (increased covalency) at the surfaces. {copyright} {ital 1998} {ital The American Physical Society}

  14. Error analysis for momentum conservation in Atomic-Continuum Coupled Model

    Science.gov (United States)

    Yang, Yantao; Cui, Junzhi; Han, Tiansi

    2016-08-01

    Atomic-Continuum Coupled Model (ACCM) is a multiscale computation model proposed by Xiang et al. (in IOP conference series materials science and engineering, 2010), which is used to study and simulate dynamics and thermal-mechanical coupling behavior of crystal materials, especially metallic crystals. In this paper, we construct a set of interpolation basis functions for the common BCC and FCC lattices, respectively, implementing the computation of ACCM. Based on this interpolation approximation, we give a rigorous mathematical analysis of the error of momentum conservation equation introduced by ACCM, and derive a sequence of inequalities that bound the error. Numerical experiment is carried out to verify our result.

  15. Nonlinear mathematical modeling and sensitivity analysis of hydraulic drive unit

    Science.gov (United States)

    Kong, Xiangdong; Yu, Bin; Quan, Lingxiao; Ba, Kaixian; Wu, Liujie

    2015-09-01

    The previous sensitivity analysis researches are not accurate enough and also have the limited reference value, because those mathematical models are relatively simple and the change of the load and the initial displacement changes of the piston are ignored, even experiment verification is not conducted. Therefore, in view of deficiencies above, a nonlinear mathematical model is established in this paper, including dynamic characteristics of servo valve, nonlinear characteristics of pressure-flow, initial displacement of servo cylinder piston and friction nonlinearity. The transfer function block diagram is built for the hydraulic drive unit closed loop position control, as well as the state equations. Through deriving the time-varying coefficient items matrix and time-varying free items matrix of sensitivity equations respectively, the expression of sensitivity equations based on the nonlinear mathematical model are obtained. According to structure parameters of hydraulic drive unit, working parameters, fluid transmission characteristics and measured friction-velocity curves, the simulation analysis of hydraulic drive unit is completed on the MATLAB/Simulink simulation platform with the displacement step 2 mm, 5 mm and 10 mm, respectively. The simulation results indicate that the developed nonlinear mathematical model is sufficient by comparing the characteristic curves of experimental step response and simulation step response under different constant load. Then, the sensitivity function time-history curves of seventeen parameters are obtained, basing on each state vector time-history curve of step response characteristic. The maximum value of displacement variation percentage and the sum of displacement variation absolute values in the sampling time are both taken as sensitivity indexes. The sensitivity indexes values above are calculated and shown visually in histograms under different working conditions, and change rules are analyzed. Then the sensitivity

  16. An atomic charge model for graphene oxide for exploring its bioadhesive properties in explicit water.

    Science.gov (United States)

    Stauffer, D; Dragneva, N; Floriano, W B; Mawhinney, R C; Fanchini, G; French, S; Rubel, O

    2014-07-28

    Graphene Oxide (GO) has been shown to exhibit properties that are useful in applications such as biomedical imaging, biological sensors, and drug delivery. The binding properties of biomolecules at the surface of GO can provide insight into the potential biocompatibility of GO. Here we assess the intrinsic affinity of amino acids to GO by simulating their adsorption onto a GO surface. The simulation is done using Amber03 force-field molecular dynamics in explicit water. The emphasis is placed on developing an atomic charge model for GO. The adsorption energies are computed using atomic charges obtained from an ab initio electrostatic potential based method. The charges reported here are suitable for simulating peptide adsorption to GO.

  17. 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.

  18. 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.

  19. Sound speed and oscillation frequencies for a solar model evolved with Los Alamos ATOMIC opacities

    Science.gov (United States)

    Guzik, Joyce Ann; Fontes, Christopher; Walczak, Przemyslaw; Wood, Suzannah R.; Mussack, Katie

    2015-08-01

    Los Alamos has calculated a new generation of radiative opacities for elements with atomic number Z=1-30 with improved physics input, updated atomic data, and finer temperature grid to replace the Los Alamos LEDCOP opacities released in the year 2000. We calculate the evolution of a standard solar model including these new opacities, and compare with a model evolved using the Lawrence Livermore National Laboratory OPAL opacities released about 1996. We use the solar abundance mixture of Asplund, Grevesse, Sauval, and Scott (2009), including 2015 updates. The Los Alamos ATOMIC opacities (Colgan et al. 2013a,b) are somewhat higher than those of OPAL for temperatures and densities near the base of the solar convection zone. We compare the calculated nonadiabatic solar oscillation frequencies and solar interior sound speed to observed frequencies and helioseismic inferences. We discuss the potential for increased opacities to partially mitigate the ‘solar abundance problem’.References:J. Colgan, D.P. Kilcrease, N.H. Magee, Jr., G.S.J. Armstrong, J. Abdallah, Jr., M.E. Sherrill, C.J. Fontes, H.L. Zhang and P. Hakel, Eighth International Conference on Atomic and Molecular Data and their Applications: ICAMDATA, Gaithersburg, MD 2012, AIP Conf. Proc. No. 1545, (AIP, New York, 2013a), pp. 17-26.J. Colgan, D.P. Kilcrease, N.H. Magee, Jr, G.S.J. Armstrong, J. Abdallah, Jr., M.E. Sherrill, C.J. Fontes, H.L. Zhang and P. Hakel, High Energy Density Physics 9, 369 (2013b).

  20. Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method

    DEFF Research Database (Denmark)

    Valentin, Jan B.; Andreetta, Christian; Boomsma, Wouter

    2014-01-01

    We propose a method to formulate probabilistic models of protein structure in atomic detail, for a given amino acid sequence, based on Bayesian principles, while retaining a close link to physics. We start from two previously developed probabilistic models of protein structure on a local length...... scale, which concern the dihedral angles in main chain and side chains, respectively. Conceptually, this constitutes a probabilistic and continuous alternative to the use of discrete fragment and rotamer libraries. The local model is combined with a nonlocal model that involves a small number of energy...... terms according to a physical force field, and some information on the overall secondary structure content. In this initial study we focus on the formulation of the joint model and the evaluation of the use of an energy vector as a descriptor of a protein's nonlocal structure; hence, we derive...

  1. Testing the validity of the International Atomic Energy Agency (IAEA) safety culture model.

    Science.gov (United States)

    López de Castro, Borja; Gracia, Francisco J; Peiró, José M; Pietrantoni, Luca; Hernández, Ana

    2013-11-01

    This paper takes the first steps to empirically validate the widely used model of safety culture of the International Atomic Energy Agency (IAEA), composed of five dimensions, further specified by 37 attributes. To do so, three independent and complementary studies are presented. First, 290 students serve to collect evidence about the face validity of the model. Second, 48 experts in organizational behavior judge its content validity. And third, 468 workers in a Spanish nuclear power plant help to reveal how closely the theoretical five-dimensional model can be replicated. Our findings suggest that several attributes of the model may not be related to their corresponding dimensions. According to our results, a one-dimensional structure fits the data better than the five dimensions proposed by the IAEA. Moreover, the IAEA model, as it stands, seems to have rather moderate content validity and low face validity. Practical implications for researchers and practitioners are included.

  2. Use of atom probe techniques to support thermodynamic and atomistic modelling of phase transformations

    Energy Technology Data Exchange (ETDEWEB)

    Andren, Hans-Olof

    2003-07-25

    Atom probe field ion microscopy (APFIM) gives accurate data on phase composition for all elements and has a good sensitivity and excellent spatial resolution. APFIM data have therefore been used as support for thermodynamic modelling of phase equilibria and phase transformations. This paper describes a number of cases where atom probe data from Chalmers University have been used to judge the accuracy of modelling: the solubility of W and C in Co, the equilibrium volume fraction of VN in a complex chromium steel, the content of B in M{sub 23}C{sub 6} precipitates, the growth of Laves phase during ageing of a chromium steel, and the growth of secondary NbC precipitates in a stabilised austenitic stainless steel. Atomistic modelling is now emerging as a tool for materials science, in particular for modelling of interfacial structure and energies. The status of the activities in this field at Chalmers University is described, and the role of APFIM in atomistic modelling is discussed.

  3. What is the "best" atomic charge model to describe through-space charge-transfer excitations?

    Science.gov (United States)

    Jacquemin, Denis; Le Bahers, Tangui; Adamo, Carlo; Ciofini, Ilaria

    2012-04-28

    We investigate the efficiency of several partial atomic charge models (Mulliken, Hirshfeld, Bader, Natural, Merz-Kollman and ChelpG) for investigating the through-space charge-transfer in push-pull organic compounds with Time-Dependent Density Functional Theory approaches. The results of these models are compared to benchmark values obtained by determining the difference of total densities between the ground and excited states. Both model push-pull oligomers and two classes of "real-life" organic dyes (indoline and diketopyrrolopyrrole) used as sensitisers in solar cell applications have been considered. Though the difference of dipole moments between the ground and excited states is reproduced by most approaches, no atomic charge model is fully satisfactory for reproducing the distance and amount of charge transferred that are provided by the density picture. Overall, the partitioning schemes fitting the electrostatic potential (e.g. Merz-Kollman) stand as the most consistent compromises in the framework of simulating through-space charge-transfer, whereas the other models tend to yield qualitatively inconsistent values.

  4. Atomic phase diagram

    Institute of Scientific and Technical Information of China (English)

    LI Shichun

    2004-01-01

    Based on the Thomas-Fermi-Dirac-Cheng model, atomic phase diagram or electron density versus atomic radius diagram describing the interaction properties of atoms of different kinds in equilibrium state is developed. Atomic phase diagram is established based on the two-atoms model. Besides atomic radius, electron density and continuity condition for electron density on interfaces between atoms, the lever law of atomic phase diagram involving other physical parameters is taken into account, such as the binding energy, for the sake of simplicity.

  5. 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.

  6. Coqblin-Schrieffer model for an ultracold gas of ytterbium atoms with metastable state

    Science.gov (United States)

    Kuzmenko, Igor; Kuzmenko, Tetyana; Avishai, Yshai; Jo, Gyu-Boong

    2016-03-01

    Motivated by the impressive recent advance in manipulating cold ytterbium atoms, we explore and substantiate the feasibility of realizing the Coqblin-Schrieffer model in a gas of cold fermionic 173Yb atoms. Making use of different AC polarizabillity of the electronic ground state (electronic configuration S10) and the long lived metastable state (electronic configuration P30), it is substantiated that the latter can be localized and serve as a magnetic impurity while the former remains itinerant. The exchange mechanism between the itinerant S10 and the localized P30 atoms is analyzed and shown to be antiferromagnetic. The ensuing SU(6) symmetric Coqblin-Schrieffer Hamiltonian is constructed, and, using the calculated exchange constant J , perturbative renormalization group (RG) analysis yields the Kondo temperature TK that is experimentally accessible. A number of thermodynamic measurable observables are calculated in the weak-coupling regime T >TK (using perturbative RG analysis) and in the strong-coupling regime T

  7. Atomic oxygen dynamics in an air dielectric barrier discharge: a combined diagnostic and modeling approach

    Science.gov (United States)

    Baldus, Sabrina; Schröder, Daniel; Bibinov, Nikita; Schulz-von der Gathen, Volker; Awakowicz, Peter

    2015-06-01

    Cold atmospheric pressure plasmas are a promising alternative therapy for treatment of chronic wounds, as they have already shown in clinical trials. In this study an air dielectric barrier discharge (DBD) developed for therapeutic use in dermatology is characterized with respect to the plasma produced reactive oxygen species, namely atomic oxygen and ozone, which are known to be of great importance to wound healing. To understand the plasma chemistry of the applied DBD, xenon-calibrated two-photon laser-induced fluorescence spectroscopy and optical absorption spectroscopy are applied. The measured spatial distributions are shown and compared to each other. A model of the afterglow chemistry based on optical emission spectroscopy is developed to cross-check the measurement results and obtain insight into the dynamics of the considered reactive oxygen species. The atomic oxygen density is found to be located mostly between the electrodes with a maximum density of {{n}\\text{O}}=6× {{10}16} cm-3 . Time resolved measurements reveal a constant atomic oxygen density between two high voltage pulses. The ozone is measured up to 3 mm outside the active plasma volume, reaching a maximum value of {{n}{{\\text{O}3}}}=3× {{10}16} cm-3 between the electrodes.

  8. 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.

  9. Electron crystallography of ultrathin 3D protein crystals: atomic model with charges.

    Science.gov (United States)

    Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi

    2015-03-17

    Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase.

  10. Atomic spin-chain realization of a model for quantum criticality

    Science.gov (United States)

    Toskovic, R.; van den Berg, R.; Spinelli, A.; Eliens, I. S.; van den Toorn, B.; Bryant, B.; Caux, J.-S.; Otte, A. F.

    2016-07-01

    The ability to manipulate single atoms has opened up the door to constructing interesting and useful quantum structures from the ground up. On the one hand, nanoscale arrangements of magnetic atoms are at the heart of future quantum computing and spintronic devices; on the other hand, they can be used as fundamental building blocks for the realization of textbook many-body quantum models, illustrating key concepts such as quantum phase transitions, topological order or frustration as a function of system size. Here, we use low-temperature scanning tunnelling microscopy to construct arrays of magnetic atoms on a surface, designed to behave like spin-1/2 XXZ Heisenberg chains in a transverse field, for which a quantum phase transition from an antiferromagnetic to a paramagnetic phase is predicted in the thermodynamic limit. Site-resolved measurements on these finite-size realizations reveal a number of sudden ground state changes when the field approaches the critical value, each corresponding to a new domain wall entering the chains. We observe that these state crossings become closer for longer chains, suggesting the onset of critical behaviour. Our results present opportunities for further studies on quantum behaviour of many-body systems, as a function of their size and structural complexity.

  11. From deep TLS validation to ensembles of atomic models built from elemental motions

    Energy Technology Data Exchange (ETDEWEB)

    Urzhumtsev, Alexandre, E-mail: sacha@igbmc.fr [Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch (France); Université de Lorraine, BP 239, 54506 Vandoeuvre-les-Nancy (France); Afonine, Pavel V. [Lawrence Berkeley National Laboratory, Berkeley, California (United States); Van Benschoten, Andrew H.; Fraser, James S. [University of California, San Francisco, San Francisco, CA 94158 (United States); Adams, Paul D. [Lawrence Berkeley National Laboratory, Berkeley, California (United States); University of California Berkeley, Berkeley, CA 94720 (United States); Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch (France)

    2015-07-28

    Procedures are described for extracting the vibration and libration parameters corresponding to a given set of TLS matrices and their simultaneous validation. Knowledge of these parameters allows the generation of structural ensembles corresponding to these matrices. The translation–libration–screw model first introduced by Cruickshank, Schomaker and Trueblood describes the concerted motions of atomic groups. Using TLS models can improve the agreement between calculated and experimental diffraction data. Because the T, L and S matrices describe a combination of atomic vibrations and librations, TLS models can also potentially shed light on molecular mechanisms involving correlated motions. However, this use of TLS models in mechanistic studies is hampered by the difficulties in translating the results of refinement into molecular movement or a structural ensemble. To convert the matrices into a constituent molecular movement, the matrix elements must satisfy several conditions. Refining the T, L and S matrix elements as independent parameters without taking these conditions into account may result in matrices that do not represent concerted molecular movements. Here, a mathematical framework and the computational tools to analyze TLS matrices, resulting in either explicit decomposition into descriptions of the underlying motions or a report of broken conditions, are described. The description of valid underlying motions can then be output as a structural ensemble. All methods are implemented as part of the PHENIX project.

  12. Pairwise energies for polypeptide coarse-grained models derived from atomic force fields

    Science.gov (United States)

    Betancourt, Marcos R.; Omovie, Sheyore J.

    2009-05-01

    The energy parametrization of geometrically simplified versions of polypeptides, better known as polypeptide or protein coarse-grained models, is obtained from molecular dynamics and statistical methods. Residue pairwise interactions are derived by performing atomic-level simulations in explicit water for all 210 pairs of amino acids, where the amino acids are modified to closer match their structure and charges in polypeptides. Radial density functions are computed from equilibrium simulations for each pair of residues, from which statistical energies are extracted using the Boltzmann inversion method. The resulting models are compared to similar potentials obtained by knowledge based methods and to hydrophobic scales, resulting in significant similarities in spite of the model simplicity. However, it was found that glutamine, asparagine, lysine, and arginine are more attractive to other residues than anticipated, in part, due to their amphiphilic nature. In addition, equally charged residues appear more repulsive than expected. Difficulties in the calculation of knowledge based potentials and hydrophobicity scale for these cases, as well as sensitivity of the force field to polarization effects are suspected to cause this discrepancy. It is also shown that the coarse-grained model can identify native structures in decoy databases nearly as well as more elaborate knowledge based methods, in spite of its resolution limitations. In a test conducted with several proteins and corresponding decoys, the coarse-grained potential was able to identify the native state structure but not the original atomic force field.

  13. Partial ionization in dense plasmas: Comparisons among average-atom density functional models

    Science.gov (United States)

    Murillo, Michael S.; Weisheit, Jon; Hansen, Stephanie B.; Dharma-wardana, M. W. C.

    2013-06-01

    Nuclei interacting with electrons in dense plasmas acquire electronic bound states, modify continuum states, generate resonances and hopping electron states, and generate short-range ionic order. The mean ionization state (MIS), i.e, the mean charge Z of an average ion in such plasmas, is a valuable concept: Pseudopotentials, pair-distribution functions, equations of state, transport properties, energy-relaxation rates, opacity, radiative processes, etc., can all be formulated using the MIS of the plasma more concisely than with an all-electron description. However, the MIS does not have a unique definition and is used and defined differently in different statistical models of plasmas. Here, using the MIS formulations of several average-atom models based on density functional theory, we compare numerical results for Be, Al, and Cu plasmas for conditions inclusive of incomplete atomic ionization and partial electron degeneracy. By contrasting modern orbital-based models with orbital-free Thomas-Fermi models, we quantify the effects of shell structure, continuum resonances, the role of exchange and correlation, and the effects of different choices of the fundamental cell and boundary conditions. Finally, the role of the MIS in plasma applications is illustrated in the context of x-ray Thomson scattering in warm dense matter.

  14. Partial ionization in dense plasmas: comparisons among average-atom density functional models.

    Science.gov (United States)

    Murillo, Michael S; Weisheit, Jon; Hansen, Stephanie B; Dharma-wardana, M W C

    2013-06-01

    Nuclei interacting with electrons in dense plasmas acquire electronic bound states, modify continuum states, generate resonances and hopping electron states, and generate short-range ionic order. The mean ionization state (MIS), i.e, the mean charge Z of an average ion in such plasmas, is a valuable concept: Pseudopotentials, pair-distribution functions, equations of state, transport properties, energy-relaxation rates, opacity, radiative processes, etc., can all be formulated using the MIS of the plasma more concisely than with an all-electron description. However, the MIS does not have a unique definition and is used and defined differently in different statistical models of plasmas. Here, using the MIS formulations of several average-atom models based on density functional theory, we compare numerical results for Be, Al, and Cu plasmas for conditions inclusive of incomplete atomic ionization and partial electron degeneracy. By contrasting modern orbital-based models with orbital-free Thomas-Fermi models, we quantify the effects of shell structure, continuum resonances, the role of exchange and correlation, and the effects of different choices of the fundamental cell and boundary conditions. Finally, the role of the MIS in plasma applications is illustrated in the context of x-ray Thomson scattering in warm dense matter.

  15. Mechanistic modeling study on process optimization and precursor utilization with atmospheric spatial atomic layer deposition

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Zhang; He, Wenjie; Duan, Chenlong [State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Chen, Rong, E-mail: rongchen@mail.hust.edu.cn [State Key Laboratory of Digital Manufacturing Equipment and Technology, School of Mechanical Science and Engineering, School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China); Shan, Bin [State Key Laboratory of Material Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074 (China)

    2016-01-15

    Spatial atomic layer deposition (SALD) is a promising technology with the aim of combining the advantages of excellent uniformity and conformity of temporal atomic layer deposition (ALD), and an industrial scalable and continuous process. In this manuscript, an experimental and numerical combined model of atmospheric SALD system is presented. To establish the connection between the process parameters and the growth efficiency, a quantitative model on reactant isolation, throughput, and precursor utilization is performed based on the separation gas flow rate, carrier gas flow rate, and precursor mass fraction. The simulation results based on this model show an inverse relation between the precursor usage and the carrier gas flow rate. With the constant carrier gas flow, the relationship of precursor usage and precursor mass fraction follows monotonic function. The precursor concentration, regardless of gas velocity, is the determinant factor of the minimal residual time. The narrow gap between precursor injecting heads and the substrate surface in general SALD system leads to a low Péclet number. In this situation, the gas diffusion act as a leading role in the precursor transport in the small gap rather than the convection. Fluid kinetics from the numerical model is independent of the specific structure, which is instructive for the SALD geometry design as well as its process optimization.

  16. Mg line formation in late-type stellar atmospheres: I. The model atom

    CERN Document Server

    Osorio, Y; Lind, K; Belyaev, A K; Spielfiedel, A; Guitou, M; Feautrier, N

    2015-01-01

    Mg is often traced in late-type stars using lines of neutral magnesium, which is expected to be subject to departures from LTE. The astrophysical importance of Mg as well as its relative simplicity from an atomic physics point of view, makes it a prime target and test bed for detailed ab initio non-LTE modelling in stellar atmospheres. For the low-lying states of Mg i, electron collision data were calculated using the R-matrix method. Calculations for collisional broadening by neutral hydrogen were also performed where data were missing. These calculations, together with data from the literature, were used to build a model atom. First, the modelling was tested by comparisons with observed spectra of benchmark stars with well-known parameters. Second, the spectral line behaviour and uncertainties were explored by extensive experiments in which sets of collisional data were changed or removed. The modelled spectra agree well with observed spectra. The line-to-line scatter in the derived abundances shows improve...

  17. A computer code for calculations in the algebraic collective model of the atomic nucleus

    CERN Document Server

    Welsh, T A

    2016-01-01

    A Maple code is presented for algebraic collective model (ACM) calculations. The ACM is an algebraic version of the Bohr model of the atomic nucleus, in which all required matrix elements are derived by exploiting the model's SU(1,1) x SO(5) dynamical group. This, in particular, obviates the use of coefficients of fractional parentage. This paper reviews the mathematical formulation of the ACM, and serves as a manual for the code. The code makes use of expressions for matrix elements derived elsewhere and newly derived matrix elements of the operators [pi x q x pi]_0 and [pi x pi]_{LM}, where q_M are the model's quadrupole moments, and pi_N are corresponding conjugate momenta (-2>=M,N<=2). The code also provides ready access to SO(3)-reduced SO(5) Clebsch-Gordan coefficients through data files provided with the code.

  18. Charge-state-dependent energy loss of slow ions. II. Statistical atom model

    Science.gov (United States)

    Wilhelm, Richard A.; Möller, Wolfhard

    2016-05-01

    A model for charge-dependent energy loss of slow ions is developed based on the Thomas-Fermi statistical model of atoms. Using a modified electrostatic potential which takes the ionic charge into account, nuclear and electronic energy transfers are calculated, the latter by an extension of the Firsov model. To evaluate the importance of multiple collisions even in nanometer-thick target materials we use the charge-state-dependent potentials in a Monte Carlo simulation in the binary collision approximation and compare the results to experiment. The Monte Carlo results reproduce the incident charge-state dependence of measured data well [see R. A. Wilhelm et al., Phys. Rev. A 93, 052708 (2016), 10.1103/PhysRevA.93.052708], even though the experimentally observed charge exchange dependence is not included in the model.

  19. Why Do We Believe that an Atom Is Colourless? Reflections about the Teaching of the Particle Model.

    Science.gov (United States)

    Albanese, Alessandro; Vicentini, Matilde

    1997-01-01

    Highlights students' ideas about the particle model of matter and its use. Discusses the atomic model in teaching and the rules of the particle modeling game. Demonstrates how a complete understanding of the rules of the model construction yields guidelines for didactic practice. Focuses on problems connected with visual communication through…

  20. 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.

  1. Ab Initio Atom-Atom Potentials Using CamCASP: Theory and Application to Many-Body Models for the Pyridine Dimer.

    Science.gov (United States)

    Misquitta, Alston J; Stone, Anthony J

    2016-09-13

    Creating accurate, analytic atom-atom potentials for small organic molecules from first principles can be a time-consuming and computationally intensive task, particularly if we also require them to include explicit polarization terms, which are essential in many systems. We describe how the CamCASP suite of programs can be used to generate such potentials using some of the most accurate electronic structure methods currently applicable. We derive the long-range terms from monomer properties and determine the short-range anisotropy parameters by a novel and robust method based on the iterated stockholder atom approach. Using these techniques, we develop distributed multipole models for the electrostatic, polarization, and dispersion interactions in the pyridine dimer and develop a series of many-body potentials for the pyridine system. Even the simplest of these potentials exhibits root mean square errors of only about 0.6 kJ mol(-1) for the low-energy pyridine dimers, significantly surpassing the best empirical potentials. Our best model is shown to support eight stable minima, four of which have not been reported before in the literature. Further, the functional form can be made systematically more elaborate so as to improve the accuracy without a significant increase in the human-time spent in their generation. We investigate the effects of anisotropy, rank of multipoles, and choice of polarizability and dispersion models.

  2. 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

  3. 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.

  4. Mapping the Two-Component Atomic Fermi Gas to the Nuclear Shell-Model

    DEFF Research Database (Denmark)

    Özen, C.; Zinner, Nikolaj Thomas

    2014-01-01

    The physics of a two-component cold fermi gas is now frequently addressed in laboratories. Usually this is done for large samples of tens to hundreds of thousands of particles. However, it is now possible to produce few-body systems (1-100 particles) in very tight traps where the shell structure...... of the external potential becomes important. A system of two-species fermionic cold atoms with an attractive zero-range interaction is analogous to a simple model of nucleus in which neutrons and protons interact only through a residual pairing interaction. In this article, we discuss how the problem of a two...

  5. Excited Electronic States of Atoms described by the Model of Oscillations in a Chain System

    Directory of Open Access Journals (Sweden)

    Ries A.

    2011-10-01

    Full Text Available We analyzed the numerical values of half-lifes of excited electronic states of the H, He and Li atom, as well as the Li + ion. By means of a fractal scaling model originally published by Müller in this journal, we interprete these half-lifes as proton resonance periods. On the logarithmic scale, the half-lifes were expressed by short continued fractions, where all numerators are Euler’s number. From this representation it was concluded that the half-lifes are heavily located in nodes or sub-nodes of the spectrum of proton resonance periods.

  6. Effective Approximation of Molecular Volume Using Atom-Centered Dielectric Functions in Generalized Born Models.

    Science.gov (United States)

    Chen, Jianhan

    2010-09-14

    The generalized Born (GB) theory is a prime choice for implicit treatment of solvent that provides a favorable balance between efficiency and accuracy for reliable simulation of protein conformational equilibria. In GB, the dielectric boundary is a key physical property that needs to be properly described. While it is widely accepted that the molecular surface (MS) should provide the most physical description, most existing GB models are based on van der Waals (vdW)-like surfaces for computational simplicity and efficiency. A simple and effective approximation to molecular volume is explored here using atom-centered dielectric functions within the context of a generalized Born model with simple switching (GBSW). The new model, termed GBSW/MS2, is as efficient as the original vdW-like-surface-based GBSW model, but is able to reproduce the Born radii calculated from the "exact" Poisson-Boltzmann theory with a correlation of 0.95. More importantly, examination of the potentials of mean force of hydrogen-bonding and charge-charge interactions demonstrates that GBSW/MS2 correctly captures the first desolvation peaks, a key signature of true MS. Physical parameters including atomic input radii and peptide backbone torsion were subsequently optimized on the basis of solvation free energies of model compounds, potentials of mean force of their interactions, and conformational equilibria of a set of helical and β-hairpin model peptides. The resulting GBSW/MS2 protein force field reasonably recapitulates the structures and stabilities of these model peptides. Several remaining limitations and possible future developments are also discussed.

  7. Atomic charge transfer-counter polarization effects determine infrared CH intensities of hydrocarbons: a quantum theory of atoms in molecules model.

    Science.gov (United States)

    Silva, Arnaldo F; Richter, Wagner E; Meneses, Helen G C; Bruns, Roy E

    2014-11-14

    Atomic charge transfer-counter polarization effects determine most of the infrared fundamental CH intensities of simple hydrocarbons, methane, ethylene, ethane, propyne, cyclopropane and allene. The quantum theory of atoms in molecules/charge-charge flux-dipole flux model predicted the values of 30 CH intensities ranging from 0 to 123 km mol(-1) with a root mean square (rms) error of only 4.2 km mol(-1) without including a specific equilibrium atomic charge term. Sums of the contributions from terms involving charge flux and/or dipole flux averaged 20.3 km mol(-1), about ten times larger than the average charge contribution of 2.0 km mol(-1). The only notable exceptions are the CH stretching and bending intensities of acetylene and two of the propyne vibrations for hydrogens bound to sp hybridized carbon atoms. Calculations were carried out at four quantum levels, MP2/6-311++G(3d,3p), MP2/cc-pVTZ, QCISD/6-311++G(3d,3p) and QCISD/cc-pVTZ. The results calculated at the QCISD level are the most accurate among the four with root mean square errors of 4.7 and 5.0 km mol(-1) for the 6-311++G(3d,3p) and cc-pVTZ basis sets. These values are close to the estimated aggregate experimental error of the hydrocarbon intensities, 4.0 km mol(-1). The atomic charge transfer-counter polarization effect is much larger than the charge effect for the results of all four quantum levels. Charge transfer-counter polarization effects are expected to also be important in vibrations of more polar molecules for which equilibrium charge contributions can be large.

  8. Modeling Forest Succession among Ecological Land Units in Northern Minnesota

    Directory of Open Access Journals (Sweden)

    George Host

    1998-12-01

    Full Text Available Field and modeling studies were used to quantify potential successional pathways among fine-scale ecological classification units within two geomorphic regions of north-central Minnesota. Soil and overstory data were collected on plots stratified across low-relief ground moraines and undulating sand dunes. Each geomorphic feature was sampled across gradients of topography or soil texture. Overstory conditions were sampled using five variable-radius point samples per plot; soil samples were analyzed for carbon and nitrogen content. Climatic, forest composition, and soil data were used to parameterize the sample plots for use with LINKAGES, a forest growth model that simulates changes in composition and soil characteristics over time. Forest composition and soil properties varied within and among geomorphic features. LINKAGES simulations were using "bare ground" and the current overstory as starting conditions. Northern hardwoods or pines dominated the late-successional communities of morainal and dune landforms, respectively. The morainal landforms were dominated by yellow birch and sugar maple; yellow birch reached its maximum abundance in intermediate landscape positions. On the dune sites, pine was most abundant in drier landscape positions, with white spruce increasing in abundance with increasing soil moisture and N content. The differences in measured soil properties and predicted late-successional composition indicate that ecological land units incorporate some of the key variables that govern forest composition and structure. They further show the value of ecological classification and modeling for developing forest management strategies that incorporate the spatial and temporal dynamics of forest ecosystems.

  9. State-to-state modeling of non equilibrium low-temperature atomic plasmas

    Science.gov (United States)

    Bultel, Arnaud; Morel, Vincent; Annaloro, Julien; Druguet, Marie-Claude

    2017-03-01

    The most relevant approach leading to a thorough understanding of the behavior of non equilibrium atomic plasmas is to elaborate state-to-state models in which the mass conservation equation is applied directly to atoms or ions on their excited states. The present communication reports the elaboration of such models and the results obtained. Two situations close to each other are considered. First, the plasmas produced behind shock fronts obtained in ground test facilities (shock tubes) or during planetary atmospheric entries of spacecrafts are discussed. We focused our attention on the nitrogen case for which a complete implementation of the CoRaM-N2 collisional-radiative model has been performed in a steady one-dimensional computation code based on the Rankine-Hugoniot assumptions. Second, the plasmas produced by the interaction between an ultra short laser pulse and a tungsten sample are discussed in the framework of the elaboration of the Laser-Induced Breakdown Spectroscopy (LIBS) technique. In the present case, tungsten has been chosen in the purpose of validating an in situ experimental method able to provide the elemental composition of the divertor wall of a tokamak like WEST or ITER undergoing high energetic deuterium and tritium nuclei fluxes.

  10. Effect of elliptical deformation on molecular polarizabilities of model carbon nanotubes from atomic increments.

    Science.gov (United States)

    Torrens, Francisco

    2003-08-01

    The interacting induced dipole polarization model implemented in our program POLAR is used for the calculation of the dipole-dipole polarizability alpha. The method is tested with single-wall carbon nanotube models as a function of nanotube radius and elliptical deformation. The results for polarizability follow the same trend as reference calculations performed with our version of the program PAPID. For the zigzag tubes, the polarizability is found to follow a remarkably simple law, that is, it varies as the inverse of the radius. A dramatic effect is also found with elliptical deformation. It is found that the polarizability and related properties can be modified continuously and reversibly by the external radial deformation. These results suggest an interesting technology in which mechanical deformation can control chemical properties of the carbon nanotubes. POLAR calculations differentiate more effectively than PAPID computations among single-wall nanotube models with increasing radial deformation. Different effective polarizabilities are calculated for the atoms at the highest and lowest curvature sites. POLAR calculations discriminate more efficiently than PAPID computations between the effective polarizabilities of the highest and lowest curvature sites. This remarkable and significant tunable polarizability can have important implications for metal coverage of metals on nanotubes and selective adsorption and desorption of foreign atoms and molecules on nanotubes and can lead to a wide variety of technological applications, such as catalysts, hydrogen storage, magnetic tubes, etc.

  11. Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method.

    Science.gov (United States)

    Valentin, Jan B; Andreetta, Christian; Boomsma, Wouter; Bottaro, Sandro; Ferkinghoff-Borg, Jesper; Frellsen, Jes; Mardia, Kanti V; Tian, Pengfei; Hamelryck, Thomas

    2014-02-01

    We propose a method to formulate probabilistic models of protein structure in atomic detail, for a given amino acid sequence, based on Bayesian principles, while retaining a close link to physics. We start from two previously developed probabilistic models of protein structure on a local length scale, which concern the dihedral angles in main chain and side chains, respectively. Conceptually, this constitutes a probabilistic and continuous alternative to the use of discrete fragment and rotamer libraries. The local model is combined with a nonlocal model that involves a small number of energy terms according to a physical force field, and some information on the overall secondary structure content. In this initial study we focus on the formulation of the joint model and the evaluation of the use of an energy vector as a descriptor of a protein's nonlocal structure; hence, we derive the parameters of the nonlocal model from the native structure without loss of generality. The local and nonlocal models are combined using the reference ratio method, which is a well-justified probabilistic construction. For evaluation, we use the resulting joint models to predict the structure of four proteins. The results indicate that the proposed method and the probabilistic models show considerable promise for probabilistic protein structure prediction and related applications.

  12. Lumped Parameter Modeling for Rapid Vibration Response Prototyping and Test Correlation for Electronic Units

    Science.gov (United States)

    Van Dyke, Michael B.

    2013-01-01

    Present preliminary work using lumped parameter models to approximate dynamic response of electronic units to random vibration; Derive a general N-DOF model for application to electronic units; Illustrate parametric influence of model parameters; Implication of coupled dynamics for unit/board design; Demonstrate use of model to infer printed wiring board (PWB) dynamics from external chassis test measurement.

  13. Unit physics performance of a mix model in Eulerian fluid computations

    Energy Technology Data Exchange (ETDEWEB)

    Vold, Erik [Los Alamos National Laboratory; Douglass, Rod [Los Alamos National Laboratory

    2011-01-25

    In this report, we evaluate the performance of a K-L drag-buoyancy mix model, described in a reference study by Dimonte-Tipton [1] hereafter denoted as [D-T]. The model was implemented in an Eulerian multi-material AMR code, and the results are discussed here for a series of unit physics tests. The tests were chosen to calibrate the model coefficients against empirical data, principally from RT (Rayleigh-Taylor) and RM (Richtmyer-Meshkov) experiments, and the present results are compared to experiments and to results reported in [D-T]. Results show the Eulerian implementation of the mix model agrees well with expectations for test problems in which there is no convective flow of the mass averaged fluid, i.e., in RT mix or in the decay of homogeneous isotropic turbulence (HIT). In RM shock-driven mix, the mix layer moves through the Eulerian computational grid, and there are differences with the previous results computed in a Lagrange frame [D-T]. The differences are attributed to the mass averaged fluid motion and examined in detail. Shock and re-shock mix are not well matched simultaneously. Results are also presented and discussed regarding model sensitivity to coefficient values and to initial conditions (IC), grid convergence, and the generation of atomically mixed volume fractions.

  14. 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.

  15. Multiscale Modeling of Damage Processes in fcc Aluminum: From Atoms to Grains

    Science.gov (United States)

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

    2008-01-01

    Molecular dynamics (MD) methods are opening new opportunities for simulating the fundamental processes of material behavior at the atomistic level. However, current analysis is limited to small domains and increasing the size of the MD domain quickly presents intractable computational demands. A preferred approach to surmount this computational limitation has been to combine continuum mechanics-based modeling procedures, such as the finite element method (FEM), with MD analyses thereby reducing the region of atomic scale refinement. Such multiscale modeling strategies can be divided into two broad classifications: concurrent multiscale methods that directly incorporate an atomistic domain within a continuum domain and sequential multiscale methods that extract an averaged response from the atomistic simulation for later use as a constitutive model in a continuum analysis.

  16. Topological phases of the kicked Harper-Kitaev model with ultracold atoms

    Science.gov (United States)

    Chen, M. N.; Mei, Feng; Su, W.; Wang, Huai-Qiang; Zhu, Shi-Liang; Sheng, L.; Xing, D. Y.

    2017-01-01

    We propose using ultracold atoms trapped in a one-dimensional periodically driven optical lattice to realize the Harper-Kitaev model, where the on-site energies are periodically kicked. Such a system provides a natural platform to study both Chern insulators and Majorana fermions. Based on calculating the quasienergy spectra, we find that both Floquet Majorana modes and Hall chiral edge modes could appear at the sample boundary in the gaps between the quasienergy bands. We also study the competition of topological superconductor and Chern insulator states in the model. We calculate the {{{Z}}2}× {{{Z}}2} index and Floquet Chern number to characterize the above two different topological states, including the topological phase transitions in the kicked Harper-Kitaev model with the increase in the strength of the kick.

  17. Model for fast, nonadiabatic collisions between alkali atoms and diatomic molecules

    Science.gov (United States)

    Hickman, A. P.

    1980-11-01

    Equations for collisions involving two potential surfaces are presented in the impact parameter approximation. In this approximation, a rectilinear classical trajectory is assumed for the translational motion, leading to a time-dependent Schroedinger's equation for the remaining degrees of freedom. Model potentials are considered for collisions of alkali atoms with diatomic molecules that lead to a particularly simple form of the final equations. Using the Magnus approximation, these equations are solved for parameters chosen to model the process Cs+O2→Cs++O2-, and total cross sections for ion-pair formation are obtained as a function of energy. The results exhibit oscillations that correspond qualitatively to those seen in recent measurements. In addition, the model predicts that the oscillations will become less pronounced as the initial vibrational level of O2 is increased.

  18. Modeling of Electric Disturbance Signals Using Damped Sinusoids via Atomic Decompositions and Its Applications

    Directory of Open Access Journals (Sweden)

    Marco A. M. Rodrigues

    2007-01-01

    Full Text Available The number of waveforms monitored in power systems is increasing rapidly. This creates a demand for computational tools that aid in the analysis of the phenomena and also that allow efficient transmission and storage of the information acquired. In this context, signal processing techniques play a fundamental role. This work is a tutorial reviewing the principles and applications of atomic signal modeling of electric disturbance signals. The disturbance signal is modeled using a linear combination of damped sinusoidal components which are closely related to the phenomena typically observed in power systems. The signal model obtained is then employed for disturbance signal denoising, filtering of “DC components,” and compression.

  19. Application of atomic force microscopy to the study of natural and model soil particles.

    Science.gov (United States)

    Cheng, S; Bryant, R; Doerr, S H; Rhodri Williams, P; Wright, C J

    2008-09-01

    The structure and surface chemistry of soil particles has extensive impact on many bulk scale properties and processes of soil systems and consequently the environments that they support. There are a number of physiochemical mechanisms that operate at the nanoscale which affect the soil's capability to maintain native vegetation and crops; this includes soil hydrophobicity and the soil's capacity to hold water and nutrients. The present study used atomic force microscopy in a novel approach to provide unique insight into the nanoscale properties of natural soil particles that control the physiochemical interaction of material within the soil column. There have been few atomic force microscopy studies of soil, perhaps a reflection of the heterogeneous nature of the system. The present study adopted an imaging and force measurement research strategy that accounted for the heterogeneity and used model systems to aid interpretation. The surface roughness of natural soil particles increased with depth in the soil column a consequence of the attachment of organic material within the crevices of the soil particles. The roughness root mean square calculated from ten 25 microm(2) images for five different soil particles from a Netherlands soil was 53.0 nm, 68.0 nm, 92.2 nm and 106.4 nm for the respective soil depths of 0-10 cm, 10-20 cm, 20-30 cm and 30-40 cm. A novel analysis method of atomic force microscopy phase images based on phase angle distribution across a surface was used to interpret the nanoscale distribution of organic material attached to natural and model soil particles. Phase angle distributions obtained from phase images of model surfaces were found to be bimodal, indicating multiple layers of material, which changed with the concentration of adsorbed humic acid. Phase angle distributions obtained from phase images of natural soil particles indicated a trend of decreasing surface coverage with increasing depth in the soil column. This was consistent with

  20. Scrape-off layer modeling with kinetic or diffusion description of charge-exchange atoms

    Science.gov (United States)

    Tokar, M. Z.

    2016-12-01

    Hydrogen isotope atoms, generated by charge-exchange (c-x) of neutral particles recycling from the first wall of a fusion reactor, are described either kinetically or in a diffusion approximation. In a one-dimensional (1-D) geometry, kinetic calculations are accelerated enormously by applying an approximate pass method for the assessment of integrals in the velocity space. This permits to perform an exhaustive comparison of calculations done with both approaches. The diffusion approximation is deduced directly from the velocity distribution function of c-x atoms in the limit of charge-exchanges with ions occurring much more frequently than ionization by electrons. The profiles across the flux surfaces of the plasma parameters averaged along the main part of the scrape-off layer (SOL), beyond the X-point and divertor regions, are calculated from the one-dimensional equations where parallel flows of charged particles and energy towards the divertor are taken into account as additional loss terms. It is demonstrated that the heat losses can be firmly estimated from the SOL averaged parameters only; for the particle loss the conditions in the divertor are of importance and the sensitivity of the results to the so-called "divertor impact factor" is investigated. The coupled 1-D models for neutral and charged species, with c-x atoms described either kinetically or in the diffusion approximation, are applied to assess the SOL conditions in a fusion reactor, with the input parameters from the European DEMO project. It is shown that the diffusion approximation provides practically the same profiles across the flux surfaces for the plasma density, electron, and ion temperatures, as those obtained with the kinetic description for c-x atoms. The main difference between the two approaches is observed in the characteristics of these species themselves. In particular, their energy flux onto the wall is underestimated in calculations with the diffusion approximation by 20 %-30

  1. 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 ...

  2. 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.

  3. 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.

  4. A convolution model of rock bed thermal storage units

    Science.gov (United States)

    Sowell, E. F.; Curry, R. L.

    1980-01-01

    A method is presented whereby a packed-bed thermal storage unit is dynamically modeled for bi-directional flow and arbitrary input flow stream temperature variations. The method is based on the principle of calculating the output temperature as the sum of earlier input temperatures, each multiplied by a predetermined 'response factor', i.e., discrete convolution. A computer implementation of the scheme, in the form of a subroutine for a widely used solar simulation program (TRNSYS) is described and numerical results compared with other models. Also, a method for efficient computation of the required response factors is described; this solution is for a triangular input pulse, previously unreported, although the solution method is also applicable for other input functions. This solution requires a single integration of a known function which is easily carried out numerically to the required precision.

  5. 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.

  6. Non-equilibrium dynamical phases of the two-atom Dicke model

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacherjee, Aranya B.

    2014-09-12

    In this paper, we investigate the non-equilibrium dynamical phases of the two-atom Dicke model, which can be realized in a two species Bose–Einstein condensate interacting with a single light mode in an optical cavity. Apart from the usual non-equilibrium normal and inverted phases, a non-equilibrium mixed phase is possible which is a combination of normal and inverted phase. A new kind of dynamical phase transition is predicted from non-superradiant mixed phase to the superradiant phase which can be achieved by tuning the two different atom–photon couplings. We also show that a dynamical phase transition from the non-superradiant mixed phase to the superradiant phase is forbidden for certain values of the two atom–photon coupling strengths. - Highlights: • We investigate the non-equilibrium dynamical phases of the two-atom Dicke model. • The dynamical phase diagram reveals a new kind of non-equilibrium mixed phase. • A new kind of dynamical phase transition is predicted from mixed phase to the superradiant phase. • In the dynamical phase diagram of the mixed phase, there are regions where the superradiant phase cannot exist.

  7. Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights.

    Science.gov (United States)

    Shimizu, Masahiro; Noguchi, Yasunori; Sakiyama, Yukari; Kawakami, Hironori; Katayama, Tsutomu; Takada, Shoji

    2016-12-13

    Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes.

  8. Atomic model for the membrane-embedded VO motor of a eukaryotic V-ATPase.

    Science.gov (United States)

    Mazhab-Jafari, Mohammad T; Rohou, Alexis; Schmidt, Carla; Bueler, Stephanie A; Benlekbir, Samir; Robinson, Carol V; Rubinstein, John L

    2016-11-03

    Vacuolar-type ATPases (V-ATPases) are ATP-powered proton pumps involved in processes such as endocytosis, lysosomal degradation, secondary transport, TOR signalling, and osteoclast and kidney function. ATP hydrolysis in the soluble catalytic V1 region drives proton translocation through the membrane-embedded VO region via rotation of a rotor subcomplex. Variability in the structure of the intact enzyme has prevented construction of an atomic model for the membrane-embedded motor of any rotary ATPase. We induced dissociation and auto-inhibition of the V1 and VO regions of the V-ATPase by starving the yeast Saccharomyces cerevisiae, allowing us to obtain a ~3.9-Å resolution electron cryomicroscopy map of the VO complex and build atomic models for the majority of its subunits. The analysis reveals the structures of subunits ac8c'c″de and a protein that we identify and propose to be a new subunit (subunit f). A large cavity between subunit a and the c-ring creates a cytoplasmic half-channel for protons. The c-ring has an asymmetric distribution of proton-carrying Glu residues, with the Glu residue of subunit c″ interacting with Arg735 of subunit a. The structure suggests sequential protonation and deprotonation of the c-ring, with ATP-hydrolysis-driven rotation causing protonation of a Glu residue at the cytoplasmic half-channel and subsequent deprotonation of a Glu residue at a luminal half-channel.

  9. Electric dipole moments of nucleons, nuclei, and atoms: The Standard Model and beyond

    Science.gov (United States)

    Engel, Jonathan; Ramsey-Musolf, Michael J.; van Kolck, U.

    2013-07-01

    Searches for the permanent electric dipole moments (EDMs) of molecules, atoms, nucleons and nuclei provide powerful probes of CP violation both within the Standard Model and beyond the Standard Model (BSM). The interpretation of experimental EDM limits requires careful delineation of physics at a wide range of scales, from the long-range atomic and molecular scales to the short-distance dynamics of physics at or beyond the Fermi scale. In this review, we provide a framework for disentangling contributions from physics at these disparate scales, building out from the set of dimension four and six effective operators that embody CP violation at the Fermi scale. We survey computations of hadronic and nuclear matrix elements associated with Fermi-scale CP violation in systems of experimental interest and quantify the present level of theoretical uncertainty in these calculations. Using representative BSM scenarios of current interest, we discuss ways in which the interplay of physics at various scales can generate EDMs at a potentially observable level.

  10. Linking atomic and mesoscopic scales for the modelling of the transport properties of uranium dioxide under irradiation

    Science.gov (United States)

    Bertolus, Marjorie; Freyss, Michel; Dorado, Boris; Martin, Guillaume; Hoang, Kiet; Maillard, Serge; Skorek, Richard; Garcia, Philippe; Valot, Carole; Chartier, Alain; Van Brutzel, Laurent; Fossati, Paul; Grimes, Robin W.; Parfitt, David C.; Bishop, Clare L.; Murphy, Samuel T.; Rushton, Michael J. D.; Staicu, Dragos; Yakub, Eugen; Nichenko, Sergii; Krack, Matthias; Devynck, Fabien; Ngayam-Happy, Raoul; Govers, Kevin; Deo, Chaitanya S.; Behera, Rakesh K.

    2015-07-01

    This article presents a synthesis of the investigations at the atomic scale of the transport properties of defects and fission gases in uranium dioxide, as well as of the transfer of results from the atomic scale to models at the mesoscopic scale, performed during the F-BRIDGE European project (2008-2012). We first present the mesoscale models used to investigate uranium oxide fuel under irradiation, and in particular the cluster dynamics and kinetic Monte Carlo methods employed to model the behaviour of defects and fission gases in UO2, as well as the parameters of these models. Second, we describe briefly the atomic scale methods employed, i.e. electronic structure calculations and empirical potential methods. Then, we show the results of the calculation of the data necessary for the mesoscale models using these atomic scale methods. Finally, we summarise the links built between the atomic and mesoscopic scale by listing the data calculated at the atomic scale which are to be used as input in mesoscale modelling. Despite specific difficulties in the description of fuel materials, the results obtained in F-BRIDGE show that atomic scale modelling methods are now mature enough to obtain precise data to feed higher scale models and help interpret experiments on nuclear fuels. These methods bring valuable insight, in particular the formation, binding and migration energies of point and extended defects, fission product localization, incorporation energies and migration pathways, elementary mechanisms of irradiation induced processes. These studies open the way for the investigation of other significant phenomena involved in fuel behaviour, in particular the thermochemical and thermomechanical properties and their evolution in-pile, complex microstructures, as well as of more complex fuels.

  11. Linking atomic and mesoscopic scales for the modelling of the transport properties of uranium dioxide under irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Bertolus, Marjorie, E-mail: marjorie.bertolus@cea.fr [CEA, DEN, DEC/SESC, Centre de Cadarache, 13108 Saint-Paul-lez-Durance (France); Freyss, Michel; Dorado, Boris; Martin, Guillaume; Hoang, Kiet; Maillard, Serge; Skorek, Richard; Garcia, Philippe; Valot, Carole [CEA, DEN, DEC/SESC, Centre de Cadarache, 13108 Saint-Paul-lez-Durance (France); Chartier, Alain; Van Brutzel, Laurent; Fossati, Paul [CEA, DEN, DPC/SCCME, 91191 Gif-sur-Yvette (France); Grimes, Robin W.; Parfitt, David C.; Bishop, Clare L.; Murphy, Samuel T.; Rushton, Michael J.D. [Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom); Staicu, Dragos; Yakub, Eugen; Nichenko, Sergii [European Commission, Joint Research Centre, Institute for Transuranium Elements, 76125 Karlsruhe (Germany); and others

    2015-07-15

    This article presents a synthesis of the investigations at the atomic scale of the transport properties of defects and fission gases in uranium dioxide, as well as of the transfer of results from the atomic scale to models at the mesoscopic scale, performed during the F-BRIDGE European project (2008–2012). We first present the mesoscale models used to investigate uranium oxide fuel under irradiation, and in particular the cluster dynamics and kinetic Monte Carlo methods employed to model the behaviour of defects and fission gases in UO{sub 2}, as well as the parameters of these models. Second, we describe briefly the atomic scale methods employed, i.e. electronic structure calculations and empirical potential methods. Then, we show the results of the calculation of the data necessary for the mesoscale models using these atomic scale methods. Finally, we summarise the links built between the atomic and mesoscopic scale by listing the data calculated at the atomic scale which are to be used as input in mesoscale modelling. Despite specific difficulties in the description of fuel materials, the results obtained in F-BRIDGE show that atomic scale modelling methods are now mature enough to obtain precise data to feed higher scale models and help interpret experiments on nuclear fuels. These methods bring valuable insight, in particular the formation, binding and migration energies of point and extended defects, fission product localization, incorporation energies and migration pathways, elementary mechanisms of irradiation induced processes. These studies open the way for the investigation of other significant phenomena involved in fuel behaviour, in particular the thermochemical and thermomechanical properties and their evolution in-pile, complex microstructures, as well as of more complex fuels.

  12. Pair potential modeling of atomic rearrangement in GeTe-Sb2Te3 superlattice via first-principles calculations

    Science.gov (United States)

    Song, Young-Sun; Kim, Jeongwoo; Jhi, Seung-Hoon

    2017-03-01

    We study the nature of atomic rearrangement during the phase-change processes in the superlattice of GeTe and Sb2Te3 by developing a new approach combining the first-principles calculations and a pair-potential model. We investigate the phase-change process in terms of energy changes from individual pairs or atoms by applying the pair (atom)-projection analysis to the intermediate structures between the initial and final states obtained from the climbing-image nudged elastic band method. Among the prototypical steps that can lead to the atomic layer rearrangement, we find that the required energy for the phase change is dominated by specific atoms responsible for the intrinsic energy barrier and the response to external pressure. Our approach of combining the first-principles methods and pair potential model with the projecting analysis can be a very efficient method in revealing the detailed atomic motions and the mechanism of fast atomic transition of the phase-change materials.

  13. Kinematic modelling of disc galaxies using graphics processing units

    Science.gov (United States)

    Bekiaris, G.; Glazebrook, K.; Fluke, C. J.; Abraham, R.

    2016-01-01

    With large-scale integral field spectroscopy (IFS) surveys of thousands of galaxies currently under-way or planned, the astronomical community is in need of methods, techniques and tools that will allow the analysis of huge amounts of data. We focus on the kinematic modelling of disc galaxies and investigate the potential use of massively parallel architectures, such as the graphics processing unit (GPU), as an accelerator for the computationally expensive model-fitting procedure. We review the algorithms involved in model-fitting and evaluate their suitability for GPU implementation. We employ different optimization techniques, including the Levenberg-Marquardt and nested sampling algorithms, but also a naive brute-force approach based on nested grids. We find that the GPU can accelerate the model-fitting procedure up to a factor of ˜100 when compared to a single-threaded CPU, and up to a factor of ˜10 when compared to a multithreaded dual CPU configuration. Our method's accuracy, precision and robustness are assessed by successfully recovering the kinematic properties of simulated data, and also by verifying the kinematic modelling results of galaxies from the GHASP and DYNAMO surveys as found in the literature. The resulting GBKFIT code is available for download from: http://supercomputing.swin.edu.au/gbkfit.

  14. A cluster expansion model for predicting activation barrier of atomic processes

    Energy Technology Data Exchange (ETDEWEB)

    Rehman, Tafizur; Jaipal, M. [Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur 208 016 (India); Chatterjee, Abhijit, E-mail: achatter@iitk.ac.in [Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur 208 016 (India); Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400 076 (India)

    2013-06-15

    We introduce a procedure based on cluster expansion models for predicting the activation barrier of atomic processes encountered while studying the dynamics of a material system using the kinetic Monte Carlo (KMC) method. Starting with an interatomic potential description, a mathematical derivation is presented to show that the local environment dependence of the activation barrier can be captured using cluster interaction models. Next, we develop a systematic procedure for training the cluster interaction model on-the-fly, which involves: (i) obtaining activation barriers for handful local environments using nudged elastic band (NEB) calculations, (ii) identifying the local environment by analyzing the NEB results, and (iii) estimating the cluster interaction model parameters from the activation barrier data. Once a cluster expansion model has been trained, it is used to predict activation barriers without requiring any additional NEB calculations. Numerical studies are performed to validate the cluster expansion model by studying hop processes in Ag/Ag(100). We show that the use of cluster expansion model with KMC enables efficient generation of an accurate process rate catalog.

  15. 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.

  16. An analytic technique for statistically modeling random atomic clock errors in estimation

    Science.gov (United States)

    Fell, P. J.

    1981-01-01

    Minimum variance estimation requires that the statistics of random observation errors be modeled properly. If measurements are derived through the use of atomic frequency standards, then one source of error affecting the observable is random fluctuation in frequency. This is the case, for example, with range and integrated Doppler measurements from satellites of the Global Positioning and baseline determination for geodynamic applications. An analytic method is presented which approximates the statistics of this random process. The procedure starts with a model of the Allan variance for a particular oscillator and develops the statistics of range and integrated Doppler measurements. A series of five first order Markov processes is used to approximate the power spectral density obtained from the Allan variance.

  17. Atomic physics modeling of transmission spectra of Sc-doped aerogel foams to support OMEGA experiments

    Science.gov (United States)

    Johns, H. M.; Lanier, N. E.; Kline, J. L.; Fontes, C. J.; Perry, T. S.; Fryer, C. L.; Brown, C. R. D.; Morton, J. W.; Hager, J. D.; Sherrill, M. E.

    2016-11-01

    We present synthetic transmission spectra generated with PrismSPECT utilizing both the ATBASE model and the Los Alamos opacity library (OPLIB) to evaluate whether an alternative choice in atomic data will impact modeling of experimental data from radiation transport experiments using Sc-doped aerogel foams (ScSi6O12 at 75 mg/cm3 density). We have determined that in the 50-200 eV Te range there is a significant difference in the 1s-3p spectra, especially below 100 eV, and for Te = 200 eV above 5000 eV in photon energy. Examining synthetic spectra generated using OPLIB with 300 resolving power reveals spectral sensitivity to Te changes of ˜3 eV.

  18. Coverage effects under atomic chemisorption: Morse-potential modeling based on bond-order conservation

    Science.gov (United States)

    Shustorovich, Evgeny

    1985-11-01

    Our recent analytical Morse-potential model based on bond-order conservation has been extended to treat coverage (θ) effects on the heat of atomic chemisorption Q. For highly symmetric surfaces such as fcc(111), fcc(100), and bcc(100), explicit expressions for Q versus θ have been obtained projecting regularities of Q( θ) and of the overlayer structures, in encouraging agreement with experiment. In particular, the model predicts that Q should typically decrease with θ (though at very low θ, Q can sometimes increase) and that there may be some critical coverage θc<1 beyond which the second-order phase transition (hollow→bridge or on-top) will occur.

  19. Dynamic Modeling for the Design and Cyclic Operation of an Atomic Layer Deposition (ALD Reactor

    Directory of Open Access Journals (Sweden)

    Curtisha D. Travis

    2013-08-01

    Full Text Available A laboratory-scale atomic layer deposition (ALD reactor system model is derived for alumina deposition using trimethylaluminum and water as precursors. Model components describing the precursor thermophysical properties, reactor-scale gas-phase dynamics and surface reaction kinetics derived from absolute reaction rate theory are integrated to simulate the complete reactor system. Limit-cycle solutions defining continuous cyclic ALD reactor operation are computed with a fixed point algorithm based on collocation discretization in time, resulting in an unambiguous definition of film growth-per-cycle (gpc. A key finding of this study is that unintended chemical vapor deposition conditions can mask regions of operation that would otherwise correspond to ideal saturating ALD operation. The use of the simulator for assisting in process design decisions is presented.

  20. Modeling and optimization of atomic layer deposition processes on vertically aligned carbon nanotubes.

    Science.gov (United States)

    Yazdani, Nuri; Chawla, Vipin; Edwards, Eve; Wood, Vanessa; Park, Hyung Gyu; Utke, Ivo

    2014-01-01

    Many energy conversion and storage devices exploit structured ceramics with large interfacial surface areas. Vertically aligned carbon nanotube (VACNT) arrays have emerged as possible scaffolds to support large surface area ceramic layers. However, obtaining conformal and uniform coatings of ceramics on structures with high aspect ratio morphologies is non-trivial, even with atomic layer deposition (ALD). Here we implement a diffusion model to investigate the effect of the ALD parameters on coating kinetics and use it to develop a guideline for achieving conformal and uniform thickness coatings throughout the depth of ultra-high aspect ratio structures. We validate the model predictions with experimental data from ALD coatings of VACNT arrays. However, the approach can be applied to predict film conformality as a function of depth for any porous topology, including nanopores and nanowire arrays.

  1. Modeling and optimization of atomic layer deposition processes on vertically aligned carbon nanotubes

    Directory of Open Access Journals (Sweden)

    Nuri Yazdani

    2014-03-01

    Full Text Available Many energy conversion and storage devices exploit structured ceramics with large interfacial surface areas. Vertically aligned carbon nanotube (VACNT arrays have emerged as possible scaffolds to support large surface area ceramic layers. However, obtaining conformal and uniform coatings of ceramics on structures with high aspect ratio morphologies is non-trivial, even with atomic layer deposition (ALD. Here we implement a diffusion model to investigate the effect of the ALD parameters on coating kinetics and use it to develop a guideline for achieving conformal and uniform thickness coatings throughout the depth of ultra-high aspect ratio structures. We validate the model predictions with experimental data from ALD coatings of VACNT arrays. However, the approach can be applied to predict film conformality as a function of depth for any porous topology, including nanopores and nanowire arrays.

  2. Refined Dummy Atom Model of Mg(2+) by Simple Parameter Screening Strategy with Revised Experimental Solvation Free Energy.

    Science.gov (United States)

    Jiang, Yang; Zhang, Haiyang; Feng, Wei; Tan, Tianwei

    2015-12-28

    Metal ions play an important role in the catalysis of metalloenzymes. To investigate metalloenzymes via molecular modeling, a set of accurate force field parameters for metal ions is highly imperative. To extend its application range and improve the performance, the dummy atom model of metal ions was refined through a simple parameter screening strategy using the Mg(2+) ion as an example. Using the AMBER ff03 force field with the TIP3P model, the refined model accurately reproduced the experimental geometric and thermodynamic properties of Mg(2+). Compared with point charge models and previous dummy atom models, the refined dummy atom model yields an enhanced performance for producing reliable ATP/GTP-Mg(2+)-protein conformations in three metalloenzyme systems with single or double metal centers. Similar to other unbounded models, the refined model failed to reproduce the Mg-Mg distance and favored a monodentate binding of carboxylate groups, and these drawbacks needed to be considered with care. The outperformance of the refined model is mainly attributed to the use of a revised (more accurate) experimental solvation free energy and a suitable free energy correction protocol. This work provides a parameter screening strategy that can be readily applied to refine the dummy atom models for metal ions.

  3. 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...

  4. An atomic model of the tropomyosin cable on F-actin.

    Science.gov (United States)

    Orzechowski, Marek; Li, Xiaochuan Edward; Fischer, Stefan; Lehman, William

    2014-08-05

    Tropomyosin regulates a wide variety of actin filament functions and is best known for the role that it plays together with troponin in controlling muscle activity. For effective performance on actin filaments, adjacent 42-nm-long tropomyosin molecules are joined together by a 9- to 10-residue head-to-tail overlapping domain to form a continuous cable that wraps around the F-actin helix. Yet, despite the apparent simplicity of tropomyosin's coiled-coil structure and its well-known periodic association with successive actin subunits along F-actin, the structure of the tropomyosin cable on actin is uncertain. This is because the conformation of the overlap region that joins neighboring molecules is poorly understood, thus leaving a significant gap in our understanding of thin-filament structure and regulation. However, recent molecular-dynamics simulations of overlap segments defined their overall shape and provided unique and sufficient cues to model the whole actin-tropomyosin filament assembly in atomic detail. In this study, we show that these MD structures merge seamlessly onto the ends of tropomyosin coiled-coils. Adjacent tropomyosin molecules can then be joined together to provide a comprehensive model of the tropomyosin cable running continuously on F-actin. The resulting complete model presented here describes for the first time (to our knowledge) an atomic-level structure of αα-striated muscle tropomyosin bound to an actin filament that includes the critical overlap domain. Thus, the model provides a structural correlate to evaluate thin-filament mechanics, self-assembly mechanisms, and the effect of disease-causing mutations.

  5. Meta-model Based Model Organization and Transformation of Design Pattern Units in MDA

    Institute of Scientific and Technical Information of China (English)

    Chang-chun YANG; Zi-yi ZHAO; Jing Sun

    2010-01-01

    Tb achieve the purpose of applying design patterns which are various in kind and constant in changing in MDA from idea and application,one way is used to solve the problem of pattern disappearance which occurs at the process of pattern instantiation,to guarantee the independenceJpatterns,and at the same time,to apply this process to miltiple design patterns.Ib solve these two problems,the modeling method of design pattern units based on seta-models is adopted,I.e.,to divide the basic operations into atones in the metamodel tier and then combine the atones to complete design pattern units seta-models without business logic.After one process of conversion,the kxupose of making up various pattern units seta-model and dividing business logic and pattern logic is achieved.

  6. Transport of Pathogen Surrogates in Soil Treatment Units: Numerical Modeling

    Directory of Open Access Journals (Sweden)

    Ivan Morales

    2014-04-01

    Full Text Available Segmented mesocosms (n = 3 packed with sand, sandy loam or clay loam soil were used to determine the effect of soil texture and depth on transport of two septic tank effluent (STE-borne microbial pathogen surrogates—green fluorescent protein-labeled E. coli (GFPE and MS-2 coliphage—in soil treatment units. HYDRUS 2D/3D software was used to model the transport of these microbes from the infiltrative surface. Mesocosms were spiked with GFPE and MS-2 coliphage at 105 cfu/mL STE and 105–106 pfu/mL STE, respectively. In all soils, removal rates were >99.99% at 25 cm. The transport simulation compared (1 optimization; and (2 trial-and-error modeling approaches. Only slight differences between the transport parameters were observed between these approaches. Treating both the die-off rates and attachment/detachment rates as variables resulted in an overall better model fit, particularly for the tailing phase of the experiments. Independent of the fitting procedure, attachment rates computed by the model were higher in sandy and sandy loam soils than clay, which was attributed to unsaturated flow conditions at lower water content in the coarser-textured soils. Early breakthrough of the bacteria and virus indicated the presence of preferential flow in the system in the structured clay loam soil, resulting in faster movement of water and microbes through the soil relative to a conservative tracer (bromide.

  7. Kinematic Modelling of Disc Galaxies using Graphics Processing Units

    CERN Document Server

    Bekiaris, Georgios; Fluke, Christopher J; Abraham, Roberto

    2015-01-01

    With large-scale Integral Field Spectroscopy (IFS) surveys of thousands of galaxies currently under-way or planned, the astronomical community is in need of methods, techniques and tools that will allow the analysis of huge amounts of data. We focus on the kinematic modelling of disc galaxies and investigate the potential use of massively parallel architectures, such as the Graphics Processing Unit (GPU), as an accelerator for the computationally expensive model-fitting procedure. We review the algorithms involved in model-fitting and evaluate their suitability for GPU implementation. We employ different optimization techniques, including the Levenberg-Marquardt and Nested Sampling algorithms, but also a naive brute-force approach based on Nested Grids. We find that the GPU can accelerate the model-fitting procedure up to a factor of ~100 when compared to a single-threaded CPU, and up to a factor of ~10 when compared to a multi-threaded dual CPU configuration. Our method's accuracy, precision and robustness a...

  8. Thermodynamic Evaluation of Reaction Abilities of Structural Units in Fe-O Binary Melts Based on the Atom-Molecule Coexistence Theory

    Science.gov (United States)

    Yang, Xue-min; Li, Jin-yan; Wei, Meng-fang; Zhang, Jian

    2016-02-01

    A thermodynamic model for calculating the mass action concentrations Ni of structural units in Fe-O binary melts based on the atom-molecule coexistence theory, i.e., AMCT- Ni model, has been developed and verified to be valid through comparing with the calculated activities a_{R,i} of both O and Fe over a temperature range from 1833 K to 1973 K (1560 °C to 1700 °C). Moreover, activity coefficients γ_{O} or f_{{%,O} or f_{H,O} of O coupled with activity a_{R,O} or a_{%, O} or a_{H,O} of O and the corresponding first-order activity interaction coefficient \\varepsilon_{O}^{O} or e_{O}^{O} or h_{O}^{O} of O to O have also been determined by the developed AMCT- Ni model and verified to be credible. In addition, the molar mixing thermodynamic properties of Fe-O binary melts have been determined to be accurate. Values of the calculated mass action concentration N_{Fe} of free Fe are in good agreement with results of the calculated activity a_{R,Fe} of Fe relative to pure liquid Fe(l) as standard state in Fe-O binary melts. The calculated mass action concentration N_{O} of free O has a closely corresponding relationship with the calculated activity a_{R,O} of O relative to ideal O2 at 101,325 Pa as standard state in Fe-O binary melts. However, values of the calculated mass action concentration N_{O} of free O are much greater than results of the calculated activity a_{R,O} of O in Fe-O binary melts. The converted mass action concentration N_{O}^' of total O relative to ideal O2 at 101,325 Pa as standard state can be obtained through transferring standard state of the calculated mass action concentration N_{O} of free O. The converted mass action concentration N_{O}^' of total O or the converted activity a_{{R,O}^{AMCT} of O can well be matched with the calculated activity a_{R,O} of O in Fe-O binary melts. Although the obtained expression of first-order activity interaction coefficient \\varepsilon_{O}^{O} or e_{O}^{O} or h_{O}^{O} by the developed AMCT- Ni model for

  9. Transferable aspherical atom model refinement of protein and DNA structures against ultrahigh-resolution X-ray data.

    Science.gov (United States)

    Malinska, Maura; Dauter, Zbigniew

    2016-06-01

    In contrast to the independent-atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules, e.g. proteins and nucleic acids, against ultrahigh-resolution X-ray diffraction data. The University at Buffalo theoretical databank of aspherical pseudo-atoms has been used in the refinement of an oligopeptide, of Z-DNA hexamer and dodecamer duplexes, and of bovine trypsin. The application of the TAAM to these data improves the quality of the electron-density maps and the visibility of H atoms. It also lowers the conventional R factors and improves the atomic displacement parameters and the results of the Hirshfeld rigid-bond test. An additional advantage is that the transferred charge density allows the estimation of Coulombic interaction energy and electrostatic potential.

  10. 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.

  11. Modeling the human invader in the United States

    Science.gov (United States)

    Stohlgren, Thomas J.; Jarnevich, Catherine S.; Giri, Chandra P.

    2010-02-01

    Modern biogeographers recognize that humans are seen as constituents of ecosystems, drivers of significant change, and perhaps, the most invasive species on earth. We found it instructive to model humans as invasive organisms with the same environmental factors. We present a preliminary model of the spread of modern humans in the conterminous United States between 1992 and 2001 based on a subset of National Land Cover Data (NLCD), a time series LANDSAT product. We relied on the commonly used Maxent model, a species-environmental matching model, to map urbanization. Results: Urban areas represented 5.1% of the lower 48 states in 2001, an increase of 7.5% (18,112 km2) in the nine year period. At this rate, an area the size of Massachusetts is converted to urban land use every ten years. We used accepted models commonly used for mapping plant and animal distributions and found that climatic and environmental factors can strongly predict our spread (i.e., the conversion of forests, shrub/grass, and wetland areas into urban areas), with a 92.5% success rate (Area Under the Curve). Adding a roads layer in the model improved predictions to a 95.5% success rate. 8.8% of the 1-km2 cells in the conterminous U.S. now have a major road in them. In 2001, 0.8% of 1-km2 cells in the U.S. had an urbanness value of > 800, (>89% of a 1-km2 cell is urban), while we predict that 24.5% of 1-km2 cells in the conterminous U.S. will be > 800 eventually. Main conclusion: Humans have a highly predictable pattern of urbanization based on climatic and topographic variables. Conservation strategies may benefit from that predictability.

  12. Development of Spectral and Atomic Models for Diagnosing Energetic Particle Characteristics in Fast Ignition Experiments

    Energy Technology Data Exchange (ETDEWEB)

    MacFarlane, Joseph J [Prism Computational Sciences

    2009-08-07

    This Final Report summarizes work performed under DOE STTR Phase II Grant No. DE-FG02-05ER86258 during the project period from August 2006 to August 2009. The project, “Development of Spectral and Atomic Models for Diagnosing Energetic Particle Characteristics in Fast Ignition Experiments,” was led by Prism Computational Sciences (Madison, WI), and involved collaboration with subcontractors University of Nevada-Reno and Voss Scientific (Albuquerque, NM). In this project, we have: Developed and implemented a multi-dimensional, multi-frequency radiation transport model in the LSP hybrid fluid-PIC (particle-in-cell) code [1,2]. Updated the LSP code to support the use of accurate equation-of-state (EOS) tables generated by Prism’s PROPACEOS [3] code to compute more accurate temperatures in high energy density physics (HEDP) plasmas. Updated LSP to support the use of Prism’s multi-frequency opacity tables. Generated equation of state and opacity data for LSP simulations for several materials being used in plasma jet experimental studies. Developed and implemented parallel processing techniques for the radiation physics algorithms in LSP. Benchmarked the new radiation transport and radiation physics algorithms in LSP and compared simulation results with analytic solutions and results from numerical radiation-hydrodynamics calculations. Performed simulations using Prism radiation physics codes to address issues related to radiative cooling and ionization dynamics in plasma jet experiments. Performed simulations to study the effects of radiation transport and radiation losses due to electrode contaminants in plasma jet experiments. Updated the LSP code to generate output using NetCDF to provide a better, more flexible interface to SPECT3D [4] in order to post-process LSP output. Updated the SPECT3D code to better support the post-processing of large-scale 2-D and 3-D datasets generated by simulation codes such as LSP. Updated atomic physics modeling to provide for

  13. The Pre-Service Science Teachers' Mental Models for Concept of Atoms and Learning Difficulties

    Science.gov (United States)

    Kiray, Seyit Ahmet

    2016-01-01

    The purpose of this study is to reveal the pre-service science teachers' difficulties about the concept of atoms. The data was collected from two different sources: The Draw an Atom Test (DAAT) and face-to-face interviews. Draw an atom test (DAAT) were administered to the 142 science teacher candidates. To elaborate the results, the researcher…

  14. Modeling Small Scale Solar Powered ORC Unit for Standalone Application

    Directory of Open Access Journals (Sweden)

    Enrico Bocci

    2012-01-01

    Full Text Available When the electricity from the grid is not available, the generation of electricity in remote areas is an essential challenge to satisfy important needs. In many developing countries the power generation from Diesel engines is the applied technical solution. However the cost and supply of fuel make a strong dependency of the communities on the external support. Alternatives to fuel combustion can be found in photovoltaic generators, and, with suitable conditions, small wind turbines or microhydroplants. The aim of the paper is to simulate the power generation of a generating unit using the Rankine Cycle and using refrigerant R245fa as a working fluid. The generation unit has thermal solar panels as heat source and photovoltaic modules for the needs of the auxiliary items (pumps, electronics, etc.. The paper illustrates the modeling of the system using TRNSYS platform, highlighting standard and “ad hoc” developed components as well as the global system efficiency. In the future the results of the simulation will be compared with the data collected from the 3 kW prototype under construction in the Tuscia University in Italy.

  15. Cooperative Fish and Wildlife Research Units - A model partnership program

    Science.gov (United States)

    Dennerline, Donald E.; Childs, Dawn E.

    2017-04-20

    The U.S. Geological Survey (USGS) Cooperative Fish and Wildlife Research Units (CRU) program is a unique model of cooperative partnership among the USGS, other U.S. Department of the Interior and Federal agencies, universities, State fish and wildlife agencies, and the Wildlife Management Institute. These partnerships are maintained as one of the USGS’s strongest links to Federal and State land and natural resource management agencies.Established in 1935 to meet the need for trained professionals in the growing field of wildlife management, the program currently consists of 40 Cooperative Fish and Wildlife Research Units located on university campuses in 38 States and supports 119 research scientist positions when fully funded. The threefold mission of the CRU program is to (1) conduct scientific research for the management of fish, wildlife, and other natural resources; (2) provide technical assistance to natural resource managers in the application of scientific information to natural resource policy and management; and (3) train future natural resource professionals.

  16. How Sommerfeld extended Bohr's model of the atom (1913-1916)

    Science.gov (United States)

    Eckert, Michael

    2014-04-01

    Sommerfeld's extension of Bohr's atomic model was motivated by the quest for a theory of the Zeeman and Stark effects. The crucial idea was that a spectral line is made up of coinciding frequencies which are decomposed in an applied field. In October 1914 Johannes Stark had published the results of his experimental investigation on the splitting of spectral lines in hydrogen (Balmer lines) in electric fields, which showed that the frequency of each Balmer line becomes decomposed into a multiplet of frequencies. The number of lines in such a decomposition grows with the index of the line in the Balmer series. Sommerfeld concluded from this observation that the quantization in Bohr's model had to be altered in order to allow for such decompositions. He outlined this idea in a lecture in winter 1914/15, but did not publish it. The First World War further delayed its elaboration. When Bohr published new results in autumn 1915, Sommerfeld finally developed his theory in a provisional form in two memoirs which he presented in December 1915 and January 1916 to the Bavarian Academy of Science. In July 1916 he published the refined version in the Annalen der Physik. The focus here is on the preliminary Academy memoirs whose rudimentary form is better suited for a historical approach to Sommerfeld's atomic theory than the finished Annalen-paper. This introductory essay reconstructs the historical context (mainly based on Sommerfeld's correspondence). It will become clear that the extension of Bohr's model did not emerge in a singular stroke of genius but resulted from an evolving process.

  17. Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.

    Science.gov (United States)

    DiMaio, F; Chiu, W

    2016-01-01

    Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data.

  18. A computer code for calculations in the algebraic collective model of the atomic nucleus

    Science.gov (United States)

    Welsh, T. A.; Rowe, D. J.

    2016-03-01

    A Maple code is presented for algebraic collective model (ACM) calculations. The ACM is an algebraic version of the Bohr model of the atomic nucleus, in which all required matrix elements are derived by exploiting the model's SU(1 , 1) × SO(5) dynamical group. This paper reviews the mathematical formulation of the ACM, and serves as a manual for the code. The code enables a wide range of model Hamiltonians to be analysed. This range includes essentially all Hamiltonians that are rational functions of the model's quadrupole moments qˆM and are at most quadratic in the corresponding conjugate momenta πˆN (- 2 ≤ M , N ≤ 2). The code makes use of expressions for matrix elements derived elsewhere and newly derived matrix elements of the operators [ π ˆ ⊗ q ˆ ⊗ π ˆ ] 0 and [ π ˆ ⊗ π ˆ ] LM. The code is made efficient by use of an analytical expression for the needed SO(5)-reduced matrix elements, and use of SO(5) ⊃ SO(3) Clebsch-Gordan coefficients obtained from precomputed data files provided with the code.

  19. 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.

  20. Modeling of the CTEx subcritical unit using MCNPX code

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Avelino [Divisao de Defesa Quimica, Biologica e Nuclear. Centro Tecnologico do Exercito - CTEx, Guaratiba, Rio de Janeiro, RJ (Brazil); Silva, Ademir X. da, E-mail: ademir@con.ufrj.br [Programa de Engenharia Nuclear. Universidade Federal do Rio de Janeiro - UFRJ Centro de Tecnologia, Rio de Janeiro, RJ (Brazil); Rebello, Wilson F. [Secao de Engenharia Nuclear - SE/7 Instituto Militar de Engenharia - IME Rio de Janeiro, RJ (Brazil); Cunha, Victor L. Lassance [Instituto de Engenharia Nuclear (IEN/CNEN-RJ), Rio de Janeiro, RJ (Brazil)

    2011-07-01

    The present work aims at simulating the subcritical unit of Army Technology Center (CTEx) namely ARGUS pile (subcritical uranium-graphite arrangement) by using the computational code MCNPX. Once such modeling is finished, it could be used in k-effective calculations for systems using natural uranium as fuel, for instance. ARGUS is a subcritical assembly which uses reactor-grade graphite as moderator of fission neutrons and metallic uranium fuel rods with aluminum cladding. The pile is driven by an Am-Be spontaneous neutron source. In order to achieve a higher value for k{sub eff}, a higher concentration of U235 can be proposed, provided it safely remains below one. (author)

  1. Air pollution modelling using a graphics processing unit with CUDA

    CERN Document Server

    Molnar, Ferenc; Meszaros, Robert; Lagzi, Istvan; 10.1016/j.cpc.2009.09.008

    2010-01-01

    The Graphics Processing Unit (GPU) is a powerful tool for parallel computing. In the past years the performance and capabilities of GPUs have increased, and the Compute Unified Device Architecture (CUDA) - a parallel computing architecture - has been developed by NVIDIA to utilize this performance in general purpose computations. Here we show for the first time a possible application of GPU for environmental studies serving as a basement for decision making strategies. A stochastic Lagrangian particle model has been developed on CUDA to estimate the transport and the transformation of the radionuclides from a single point source during an accidental release. Our results show that parallel implementation achieves typical acceleration values in the order of 80-120 times compared to CPU using a single-threaded implementation on a 2.33 GHz desktop computer. Only very small differences have been found between the results obtained from GPU and CPU simulations, which are comparable with the effect of stochastic tran...

  2. Parameter estimation in a spatial unit root autoregressive model

    CERN Document Server

    Baran, Sándor

    2011-01-01

    Spatial autoregressive model $X_{k,\\ell}=\\alpha X_{k-1,\\ell}+\\beta X_{k,\\ell-1}+\\gamma X_{k-1,\\ell-1}+\\epsilon_{k,\\ell}$ is investigated in the unit root case, that is when the parameters are on the boundary of the domain of stability that forms a tetrahedron with vertices $(1,1,-1), \\ (1,-1,1),\\ (-1,1,1)$ and $(-1,-1,-1)$. It is shown that the limiting distribution of the least squares estimator of the parameters is normal and the rate of convergence is $n$ when the parameters are in the faces or on the edges of the tetrahedron, while on the vertices the rate is $n^{3/2}$.

  3. Modeling low impact development potential with hydrological response units.

    Science.gov (United States)

    Eric, Marija; Fan, Celia; Joksimovic, Darko; Li, James Y

    2013-01-01

    Evaluations of benefits of implementing low impact development (LID) stormwater management techniques can extend up to a watershed scale. This presents a challenge for representing them in watershed models, since they are typically orders of magnitude smaller in size. This paper presents an approach that is focused on trying to evaluate the benefits of implementing LIDs on a lot level. The methodology uses the concept of urban hydrological response Unit and results in developing and applying performance curves that are a function of lot properties to estimate the potential benefit of large-scale LID implementation. Lot properties are determined using a municipal geographic information system database and processed to determine groups of lots with similar properties. A representative lot from each group is modeled over a typical rainfall year using USEPA Stormwater Management Model to develop performance functions that relate the lot properties and the change in annual runoff volume and corresponding phosphorus loading with different LIDs implemented. The results of applying performance functions on all urban areas provide the potential locations, benefit and cost of implementation of all LID techniques, guiding future decisions for LID implementation by watershed area municipalities.

  4. Analysis of structural correlations in a model binary 3D liquid through the eigenvalues and eigenvectors of the atomic stress tensors

    CERN Document Server

    Levashov, Valentin A

    2015-01-01

    It is possible to associate with every atom or molecule in a liquid its own atomic stress tensor. These atomic stress tensors can be used to describe liquids' structures and to investigate the connection between structural and dynamic properties. In particular, atomic stresses allow to address atomic scale correlations relevant to the Green-Kubo expression for viscosity. Previously correlations between the atomic stresses of different atoms were studied using the Cartesian representation of the stress tensors or the representation based on spherical harmonics. In this paper we address structural correlations in a model 3D binary liquid using the eigenvalues and eigenvectors of the atomic stress tensors. Thus correlations relevant to the Green-Kubo expression for viscosity are interpreted in a simple geometric way. On decrease of temperature the changes in the relevant stress correlation function between different atoms are significantly more pronounced than the changes in the pair density function. We demonst...

  5. A fast empirical GAFF compatible partial atomic charge assignment scheme for modeling interactions of small molecules with biomolecular targets.

    Science.gov (United States)

    Mukherjee, Goutam; Patra, Niladri; Barua, Poranjyoti; Jayaram, B

    2011-04-15

    We report here a new and fast approach [Transferable Partial Atomic Charge Model (TPACM4)-upto four bonds] for deriving the partial atomic charges of small molecules for use in protein/DNA-ligand docking and scoring. We have created a look-up table of 5302 atom types to cover the chemical space of C, H, O, N, S, P, F, Cl, and Br atoms in small molecules together with their quantum mechanical RESP fit charges. The atom types defined span diverse plausible chemical environments of each atom in a molecule. The partial charge on any atom in a given molecule is then assigned by a reference to the look-up table. We tested the sensitivity of the TPACM4 partial charges in estimates of hydrogen bond dimers energies, solvation free energies and protein-ligand binding free energies. An average error ±1.11 kcal/mol and a correlation coefficient of 0.90 is obtained in the calculated protein-ligand binding free energies vis-à-vis an RMS error of ±1.02 kcal/mol and a correlation coefficient of 0.92 obtained with RESP fit charges in comparison to experiment. Similar accuracies are realized in predictions of hydrogen bond energies and solvation free energies of small molecules. For a molecule containing 50-55 atoms, the method takes on the order of milliseconds on a single processor machine to assign partial atomic charges. The TPACM4 programme has been web-enabled and made freely accessible at http://www.scfbio-iitd.res.in/software/drugdesign/charge.jsp.

  6. Is the Oxygen Atom Static or Dynamic? The Effect of Generating Animations on Students' Mental Models of Atomic Structure

    Science.gov (United States)

    Akaygun, Sevil

    2016-01-01

    Visualizing the chemical structure and dynamics of particles has been challenging for many students; therefore, various visualizations and tools have been used in chemistry education. For science educators, it has been important to understand how students visualize and represent particular phenomena--i.e., their mental models-- to design more…

  7. Mechanics of the IL2RA gene activation revealed by modeling and atomic force microscopy.

    Science.gov (United States)

    Milani, Pascale; Marilley, Monique; Sanchez-Sevilla, Albert; Imbert, Jean; Vaillant, Cédric; Argoul, Françoise; Egly, Jean-Marc; Rocca-Serra, José; Arneodo, Alain

    2011-04-13

    Transcription implies recruitment of RNA polymerase II and transcription factors (TFs) by DNA melting near transcription start site (TSS). Combining atomic force microscopy and computer modeling, we investigate the structural and dynamical properties of the IL2RA promoter and identify an intrinsically negative supercoil in the PRRII region (containing Elf-1 and HMGA1 binding sites), located upstream of a curved DNA region encompassing TSS. Conformational changes, evidenced by time-lapse studies, result in the progressive positioning of curvature apex towards the TSS, likely facilitating local DNA melting. In vitro assays confirm specific binding of the General Transcription Factors (GTFs) TBP and TFIIB over TATA-TSS position, where an inhibitory nucleosome prevented preinitiation complex (PIC) formation and uncontrolled DNA melting. These findings represent a substantial advance showing, first, that the structural properties of the IL2RA promoter are encoded in the DNA sequence and second, that during the initiation process DNA conformation is dynamic and not static.

  8. Extreme ultraviolet spectroscopy and atomic models of highly charged heavy ions in the Large Helical Device

    Science.gov (United States)

    Suzuki, C.; Murakami, I.; Koike, F.; Tamura, N.; Sakaue, H. A.; Morita, S.; Goto, M.; Kato, D.; Ohashi, H.; Higashiguchi, T.; Sudo, S.; O'Sullivan, G.

    2017-01-01

    We report recent results of extreme ultraviolet (EUV) spectroscopy of highly charged heavy ions in plasmas produced in the Large Helical Device (LHD). The LHD is an ideal source of experimental databases of EUV spectra because of high brightness and low opacity, combined with the availability of pellet injection systems and reliable diagnostic tools. The measured heavy elements include tungsten, tin, lanthanides and bismuth, which are motivated by ITER as well as a variety of plasma applications such as EUV lithography and biological microscopy. The observed spectral features drastically change between quasicontinuum and discrete depending on the plasma temperature, which leads to some new experimental identifications of spectral lines. We have developed collisional-radiative models for some of these ions based on the measurements. The atomic number dependence of the spectral feature is also discussed.

  9. 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.

  10. Fast low-rank approximations of multidimensional integrals in ion-atomic collisions modelling

    CERN Document Server

    Litsarev, M S

    2015-01-01

    An efficient technique based on low-rank separated approximations is proposed for computation of three-dimensional integrals arising in the energy deposition model that describes ion-atomic collisions. Direct tensor-product quadrature requires grids of size $4000^3$ which is unacceptable. Moreover, several of such integrals have to be computed simultaneously for different values of parameters. To reduce the complexity, we use the structure of the integrand and apply numerical linear algebra techniques for the construction of low-rank approximation. The resulting algorithm is $10^3$ faster than spectral quadratures in spherical coordinates used in the original DEPOSIT code. The approach can be generalized to other multidimensional problems in physics.

  11. The Challenge of Teaching Blind Students Atomic Models and the Process of Teacher Education

    Directory of Open Access Journals (Sweden)

    Renata Cardoso de Sá Ribeiro Razuck

    2014-04-01

    Full Text Available Based on the National Special Education in the Perspective of Inclusive Education (2008, students with special educational needs have to be included in the regular schools. Specifically blind students, because of their specific characteristics, they need necessary resources and suitable materials that can provide overcoming the lack of visualization. In this context, chemistry has a great visual appeal and provides a huge challenge for the acquisition of its concepts by the blinds. In order to try to fill some gaps in Chemistry contents with great visual appeal, this paper proposes a discussion on the importance of applying alternative pedagogical resources that enable visually impaired to understand and construct this imaginary science, working to this with prototypes of atomic models. This work is intended not only to contribute to the teaching-learning process, but also for the training of undergraduate courses to work towards inclusion.

  12. 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.

  13. Atomic Force Microscopy Study of the Interactions of Indolicidin with Model Membranes and DNA.

    Science.gov (United States)

    Fojan, Peter; Gurevich, Leonid

    2017-01-01

    The cell membrane is the first barrier and quite often the primary target that antimicrobial peptides (AMPs) have to destroy or penetrate to fulfill their mission. Upon penetrating through the membrane, the peptides can further attack intracellular targets, in particular DNA. Studying the interaction of an antimicrobial peptide with a cell membrane and DNA holds keys to understanding its killing mechanisms. Commonly, these interactions are studied by using optical or scanning electron microscopy and appropriately labeled peptides. However, labeling can significantly affect the hydrophobicity, conformation, and size of the peptide, hence altering the interaction significantly. Here, we describe the use of atomic force microscopy (AFM) for a label-free study of the interactions of peptides with model membranes under physiological conditions and DNA as a possible intracellular target.

  14. An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation.

    Science.gov (United States)

    Schur, Florian K M; Obr, Martin; Hagen, Wim J H; Wan, William; Jakobi, Arjen J; Kirkpatrick, Joanna M; Sachse, Carsten; Kräusslich, Hans-Georg; Briggs, John A G

    2016-07-29

    Immature HIV-1 assembles at and buds from the plasma membrane before proteolytic cleavage of the viral Gag polyprotein induces structural maturation. Maturation can be blocked by maturation inhibitors (MIs), thereby abolishing infectivity. The CA (capsid) and SP1 (spacer peptide 1) region of Gag is the key regulator of assembly and maturation and is the target of MIs. We applied optimized cryo-electron tomography and subtomogram averaging to resolve this region within assembled immature HIV-1 particles at 3.9 angstrom resolution and built an atomic model. The structure reveals a network of intra- and intermolecular interactions mediating immature HIV-1 assembly. The proteolytic cleavage site between CA and SP1 is inaccessible to protease. We suggest that MIs prevent CA-SP1 cleavage by stabilizing the structure, and MI resistance develops by destabilizing CA-SP1.

  15. Kubo-Greenwood approach to conductivity in dense plasmas with average atom models

    CERN Document Server

    Starrett, C E

    2016-01-01

    A new formulation of the Kubo-Greenwood conductivity for average atom models is given. The new formulation improves upon previous by explicitly including the ionic-structure factor. Calculations based on this new expression lead to much improved agreement with ab initio results for DC conductivity of warm dense hydrogen and beryllium, and for thermal conductivity of hydrogen. We also give and test a slightly modified Ziman-Evans formula for the resistivity that includes a non-free electron density of states, thus removing an ambiguity in the original Ziman-Evans formula. Again results based on this expression are in good agreement with ab initio simulations for warm dense beryllium and hydrogen. However, for both these expressions, calculations of the electrical conductivity of warm dense aluminum lead to poor agreement at low temperatures compared to ab initio simulations.

  16. A quasi-stationary numerical model of atomized metal droplets, I: Model formulation

    DEFF Research Database (Denmark)

    Hattel, Jesper Henri; Pryds, Nini H; Thorborg, Jesper

    1999-01-01

    A mathematical model for accelerating powder particles by a gas and for their thermal behavior during flight has been developed. Usually, dealing with the solidification of metal droplets, the interaction between an array of droplets and the surrounding gas is not integrated into the modeling...... temperature proposed in the literature has been discussed in relation to the present model. One of the major advantages of the present modeling is that it provides a tool to predict the thermal behavior of droplets during flight without the need of experimental parameters, i.e. gas temperature. Furthermore...

  17. Energetic Neutral Atom Imaging with the POLAR CEPPAD/ IPS Instrument : Initial Forward Modeling Results

    Science.gov (United States)

    Henderson, M. G.; Reeves, G. D.; Moore, K. R.; Spence, H. E.; Jorgensen, A. M.; Fennell, J. F.; Blake, J. B.; Roelof, E. C.

    1999-01-01

    Although the primary function of the CEPPAD/IPS instrument on Polar is the measurement of energetic ions in-situ, it has also proven to be a very capable Energetic Neutral Atom (ENA) imager. Raw ENA images are currently being constructed on a routine basis with a temporal resolution of minutes during both active and quiet times. However, while analyses of these images by themselves provide much information on the spatial distribution and dynamics of the energetic ion population in the ring current. detailed modeling is required to extract the actual ion distributions. In this paper. we present the initial results of forward modeling an IPS ENA image obtained during a small geo-magnetic storm on June 9, 1997. The equatorial ion distribution inferred with this technique reproduces the expected large noon/midnight and dawn/dusk asymmetries. The limitations of the model are discussed and a number of modifications to the basic forward modeling technique are proposed which should significantly improve its performance in future studies.

  18. Atomic resolution model of the antibody Fc interaction with the complement C1q component.

    Science.gov (United States)

    Schneider, Sebastian; Zacharias, Martin

    2012-05-01

    The globular C1q heterotrimer is a subunit of the C1 complement factor. Binding of the C1q subunit to the constant (Fc) part of antibody molecules is a first step and key event of complement activation. Although three-dimensional structures of C1q and antibody Fc subunits have been determined experimentally no atomic resolution structure of the C1q-Fc complex is known so far. Based on systematic protein-protein docking searches and Molecular Dynamics simulations a structural model of the C1q-IgG1-Fc-binding geometry has been obtained. The structural model is compatible with available experimental data on the interaction between the two partner proteins. It predicts a binding geometry that involves mainly the B-subunit of the C1q-trimer and both subunits of the IgG1-Fc-dimer with small conformational adjustments with respect to the unbound partners to achieve high surface complementarity. In addition to several charge-charge and polar contacts in the rim region of the interface it also involves nonpolar contacts between the two proteins and is compatible with the carbohydrate moiety of the Fc subunit. The model for the complex structure provides a working model for rationalizing available biochemical data on this important interaction and can form the basis for the design of Fc variants with a greater capacity to activate the complement system for example on binding to cancer cells or other target structures.

  19. A model for energy transfer in collisions of atoms with highly excited molecules.

    Science.gov (United States)

    Houston, Paul L; Conte, Riccardo; Bowman, Joel M

    2015-05-21

    A model for energy transfer in the collision between an atom and a highly excited target molecule has been developed on the basis of classical mechanics and turning point analysis. The predictions of the model have been tested against the results of trajectory calculations for collisions of five different target molecules with argon or helium under a variety of temperatures, collision energies, and initial rotational levels. The model predicts selected moments of the joint probability distribution, P(Jf,ΔE) with an R(2) ≈ 0.90. The calculation is efficient, in most cases taking less than one CPU-hour. The model provides several insights into the energy transfer process. The joint probability distribution is strongly dependent on rotational energy transfer and conservation laws and less dependent on vibrational energy transfer. There are two mechanisms for rotational excitation, one due to motion normal to the intermolecular potential and one due to motion tangential to it and perpendicular to the line of centers. Energy transfer is found to depend strongly on the intermolecular potential and only weakly on the intramolecular potential. Highly efficient collisions are a natural consequence of the energy transfer and arise due to collisions at "sweet spots" in the space of impact parameter and molecular orientation.

  20. Atomic model of rabbit hemorrhagic disease virus by cryo-electron microscopy and crystallography.

    Science.gov (United States)

    Wang, Xue; Xu, Fengting; Liu, Jiasen; Gao, Bingquan; Liu, Yanxin; Zhai, Yujia; Ma, Jun; Zhang, Kai; Baker, Timothy S; Schulten, Klaus; Zheng, Dong; Pang, Hai; Sun, Fei

    2013-01-01

    Rabbit hemorrhagic disease, first described in China in 1984, causes hemorrhagic necrosis of the liver. Its etiological agent, rabbit hemorrhagic disease virus (RHDV), belongs to the Lagovirus genus in the family Caliciviridae. The detailed molecular structure of any lagovirus capsid has yet to be determined. Here, we report a cryo-electron microscopic (cryoEM) reconstruction of wild-type RHDV at 6.5 Å resolution and the crystal structures of the shell (S) and protruding (P) domains of its major capsid protein, VP60, each at 2.0 Å resolution. From these data we built a complete atomic model of the RHDV capsid. VP60 has a conserved S domain and a specific P2 sub-domain that differs from those found in other caliciviruses. As seen in the shell portion of the RHDV cryoEM map, which was resolved to ~5.5 Å, the N-terminal arm domain of VP60 folds back onto its cognate S domain. Sequence alignments of VP60 from six groups of RHDV isolates revealed seven regions of high variation that could be mapped onto the surface of the P2 sub-domain and suggested three putative pockets might be responsible for binding to histo-blood group antigens. A flexible loop in one of these regions was shown to interact with rabbit tissue cells and contains an important epitope for anti-RHDV antibody production. Our study provides a reliable, pseudo-atomic model of a Lagovirus and suggests a new candidate for an efficient vaccine that can be used to protect rabbits from RHDV infection.

  1. 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.

  2. 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-.

  3. 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-.

  4. Object-Oriented Approach to Modeling Units of Pneumatic Systems

    Directory of Open Access Journals (Sweden)

    Yu. V. Kyurdzhiev

    2014-01-01

    Full Text Available The article shows the relevance of the approaches to the object-oriented programming when modeling the pneumatic units (PU.Based on the analysis of the calculation schemes of aggregates pneumatic systems two basic objects, namely a cavity flow and a material point were highlighted.Basic interactions of objects are defined. Cavity-cavity interaction: ex-change of matter and energy with the flows of mass. Cavity-point interaction: force interaction, exchange of energy in the form of operation. Point-point in-teraction: force interaction, elastic interaction, inelastic interaction, and inter-vals of displacement.The authors have developed mathematical models of basic objects and interactions. Models and interaction of elements are implemented in the object-oriented programming.Mathematical models of elements of PU design scheme are implemented in derived from the base class. These classes implement the models of flow cavity, piston, diaphragm, short channel, diaphragm to be open by a given law, spring, bellows, elastic collision, inelastic collision, friction, PU stages with a limited movement, etc.A numerical integration of differential equations for the mathematical models of PU design scheme elements is based on the Runge-Kutta method of the fourth order. On request each class performs a tact of integration i.e. calcu-lation of the coefficient method.The paper presents an integration algorithm of the system of differential equations. All objects of the PU design scheme are placed in a unidirectional class list. Iterator loop cycle initiates the integration tact of all the objects in the list. One in four iteration makes a transition to the next step of integration. Calculation process stops when any object shows a shutdowns flag.The proposed approach was tested in the calculation of a number of PU designs. With regard to traditional approaches to modeling, the authors-proposed method features in easy enhancement, code reuse, high reliability

  5. 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.

  6. Optimal oppor tunistic maintenance model of multi-unit systems

    Institute of Scientific and Technical Information of China (English)

    Zhijun Cheng; Zheng Yang; Bo Guo

    2013-01-01

    An opportunistic maintenance model is presented for a continuously deteriorating series system with economical de-pendence. The system consists of two kinds of units, which are respectively subjected to the deterioration failure described by Gamma process and the random failure described by Poisson process. A two-level opportunistic policy defined by three decision parameters is proposed to coordinate the different maintenance actions and minimize the long-run maintenance cost rate of the system. A computable expression of the average cost rate is es-tablished by using the renewal property of the stochastic process of the maintained system state. The optimal values of three deci-sion parameters are derived by an iteration approach based on the characteristic of Gamma process. The behavior of the proposed policy is il ustrated through a numerical experiment. Comparative study with the widely used corrective maintenance policy demon-strates the advantage of the proposed opportunistic maintenance method in significantly reducing the maintenance cost. Simultane-ously, the applicable area of this opportunistic model is discussed by the sensitivity analysis of the set-up cost and random failure rate.

  7. A ranking efficiency unit by restrictions using DEA models

    Science.gov (United States)

    Arsad, Roslah; Abdullah, Mohammad Nasir; Alias, Suriana

    2014-12-01

    In this paper, a comparison regarding the efficiency shares of listed companies in Bursa Malaysia was made, through the application of estimation method of Data Envelopment Analysis (DEA). In this study, DEA is used to measure efficiency shares of listed companies in Bursa Malaysia in terms of the financial performance. It is believed that only good financial performer will give a good return to the investors in the long run. The main objectives were to compute the relative efficiency scores of the shares in Bursa Malaysia and rank the shares based on Balance Index with regard to relative efficiency. The methods of analysis using Alirezaee and Afsharian's model were employed to this study; where the originality of Charnes, Cooper and Rhode model (CCR) with assumption of constant return to scale (CRS) still holds. This method of ranking relative efficiency of decision making units (DMUs) was value-added by using Balance Index. From the result, the companies that were recommended for investors based on ranking were NATWIDE, YTL and MUDA. These companies were the top three efficient companies with good performance in 2011 whereas in 2012 the top three companies were NATWIDE, MUDA and BERNAS.

  8. 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.

  9. Handling geophysical flows: Numerical modelling using Graphical Processing Units

    Science.gov (United States)

    Garcia-Navarro, Pilar; Lacasta, Asier; Juez, Carmelo; Morales-Hernandez, Mario

    2016-04-01

    Computational tools may help engineers in the assessment of sediment transport during the decision-making processes. The main requirements are that the numerical results have to be accurate and simulation models must be fast. The present work is based on the 2D shallow water equations in combination with the 2D Exner equation [1]. The resulting numerical model accuracy was already discussed in previous work. Regarding the speed of the computation, the Exner equation slows down the already costly 2D shallow water model as the number of variables to solve is increased and the numerical stability is more restrictive. On the other hand, the movement of poorly sorted material over steep areas constitutes a hazardous environmental problem. Computational tools help in the predictions of such landslides [2]. In order to overcome this problem, this work proposes the use of Graphical Processing Units (GPUs) for decreasing significantly the simulation time [3, 4]. The numerical scheme implemented in GPU is based on a finite volume scheme. The mathematical model and the numerical implementation are compared against experimental and field data. In addition, the computational times obtained with the Graphical Hardware technology are compared against Single-Core (sequential) and Multi-Core (parallel) CPU implementations. References [Juez et al.(2014)] Juez, C., Murillo, J., & Garca-Navarro, P. (2014) A 2D weakly-coupled and efficient numerical model for transient shallow flow and movable bed. Advances in Water Resources. 71 93-109. [Juez et al.(2013)] Juez, C., Murillo, J., & Garca-Navarro, P. (2013) . 2D simulation of granular flow over irregular steep slopes using global and local coordinates. Journal of Computational Physics. 225 166-204. [Lacasta et al.(2014)] Lacasta, A., Morales-Hernndez, M., Murillo, J., & Garca-Navarro, P. (2014) An optimized GPU implementation of a 2D free surface simulation model on unstructured meshes Advances in Engineering Software. 78 1-15. [Lacasta

  10. Characterization of atomic-level structure in Fe-based amorphous and nanocrystalline alloy by experimental and modeling methods

    Energy Technology Data Exchange (ETDEWEB)

    Babilas, Rafał, E-mail: rafal.babilas@polsl.pl

    2015-09-15

    The atomic structure of Fe{sub 70}Nb{sub 10}B{sub 20} alloy in “as-cast” state and after annealing was investigated using high-energy X-ray diffraction (XRD), Mössbauer spectroscopy (MS) and high resolution transmission electron microscopy (HRTEM). The HRTEM observations allowed to indicate some medium-range order (MRO) regions about 2 nm in size and formation of some kinds of short-range order (SRO) structures represented by atomic clusters with diameter ca. 0.5 nm. The Reverse Monte Carlo (RMC) method basing on the results of XRD measurements was used in modeling the atomic structure of Fe-based alloy. The structural model was described by peak values of partial pair correlation functions and coordination numbers determined by Mössbauer spectroscopy investigations. The three-dimensional configuration box of atoms was obtained from the RMC simulation and the representative Fe-centered clusters were taken from the calculated structure. According to the Gonser et al. approach, the measured spectra of alloy studied were decomposed into 5 subspectra representing average Fe–Fe coordination numbers. Basing on the results of disaccommodation of magnetic permeability, which is sensitive to the short order of the random packing of atoms, it was stated that an occurrence of free volume is not detected after nanocrystallization process. - Highlights: • Atomic cluster model of amorphous structure was proposed for studied glassy alloy. • Short range order (ca. 0.5 nm) regions interpreted as clusters were identified by HREM. • Clusters correspond to coordination numbers (N = 4,6,8,9) calculated by using Gonser approach. • Medium-range order (ca. 2 nm) could be referred to few atomic clusters. • SRO regions are able to grow up as nuclei of crystalline bcc Fe and iron borides. • Crystalline particles have spherical morphology with an average diameter of 20 nm.

  11. 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.

  12. Rovibrationally Inelastic Atom-Molecule Collision Cross Sections from a Hard Sphere Model

    Science.gov (United States)

    Lashner, Jacob; Stewart, Brian

    2016-05-01

    Hard-shell models have long been used to elucidate the principal features of molecular energy transfer and exchange reaction in the A + BC system. Nevertheless, no three-dimensional hard-shell calculation of inelastic collision cross sections has been reported. This work aims to fill that void. A particular motivation comes from our experimental results, which show the importance of equatorial impacts in the vibrational excitation process. Working with the simple hard-sphere model, we incorporated secondary impacts, defined as those in which A strikes C after striking B. Such collisions are important in systems such as Li2 - X, in which vibrational energy transfer occurs principally through side impacts. We discuss the complexity this adds to the model and present fully three-dimensional cross sections for rovibrational excitation of an initially stationary molecule in the homonuclear A + B2 system, examining the cross section as a function of the masses and radii of the atoms. We show how the features in the cross section evolve as these parameters are varied and calculate the contribution of secondary (near-equatorial) impacts to the dynamics. We compare with recent measurements in our laboratory and with the results of quasiclassical trajectories.

  13. An analytic model for accurate spring constant calibration of rectangular atomic force microscope cantilevers.

    Science.gov (United States)

    Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang

    2015-10-29

    Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson's ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers.

  14. The photospheric solar oxygen project: I. Abundance analysis of atomic lines and influence of atmospheric models

    CERN Document Server

    Caffau, Elisabetta; Steffen, Matthias; Ayres, Thomas R; Bonifacio, Piercarlo; Cayrel, Roger; Freytag, Bernd; Plez, Bertrand

    2008-01-01

    The solar oxygen abundance has undergone a major downward revision in the last decade, the most noticeable one being the update including 3D hydrodynamical simulations to model the solar photosphere. Up to now, such an analysis has been carried out only by one group using one radiation-hydrodynamics code. We investigate the photospheric oxygen abundance considering lines from atomic transitions. We also consider the relationship between the solar model used and the resulting solar oxygen abundance, to understand whether the downward abundance revision is specifically related to 3D hydrodynamical effects. We perform a new determination of the solar photospheric oxygen abundance by analysing different high-resolution high signal-to-noise ratio atlases of the solar flux and disc-centre intensity making use of the latest generation of CO5BOLD 3D solar model atmospheres. We find 8.73 < logNoxygen/Nhydrogen +12 < 8.79. The lower and upper value represent extreme assumptions on the role of collisional excitati...

  15. Van der Waals interactions and the limits of isolated atom models at interfaces.

    Science.gov (United States)

    Kawai, Shigeki; Foster, Adam S; Björkman, Torbjörn; Nowakowska, Sylwia; Björk, Jonas; Canova, Filippo Federici; Gade, Lutz H; Jung, Thomas A; Meyer, Ernst

    2016-05-13

    Van der Waals forces are among the weakest, yet most decisive interactions governing condensation and aggregation processes and the phase behaviour of atomic and molecular matter. Understanding the resulting structural motifs and patterns has become increasingly important in studies of the nanoscale regime. Here we measure the paradigmatic van der Waals interactions represented by the noble gas atom pairs Ar-Xe, Kr-Xe and Xe-Xe with a Xe-functionalized tip of an atomic force microscope at low temperature. Individual rare gas atoms were fixed at node sites of a surface-confined two-dimensional metal-organic framework. We found that the magnitude of the measured force increased with the atomic radius, yet detailed simulation by density functional theory revealed that the adsorption induced charge redistribution strengthened the van der Waals forces by a factor of up to two, thus demonstrating the limits of a purely atomic description of the interaction in these representative systems.

  16. Modeling non local thermodynamic equilibrium plasma using the Flexible Atomic Code data

    CERN Document Server

    Han, Bo; Salzmann, David; Zhao, Gang

    2015-01-01

    We present a new code, RCF("Radiative-Collisional code based on FAC"), which is used to simulate steady-state plasmas under non local thermodynamic equilibrium condition, especially photoinization dominated plasmas. RCF takes almost all of the radiative and collisional atomic processes into rate equation to interpret the plasmas systematically. The Flexible Atomic Code (FAC) supplies all the atomic data RCF needed, which insures calculating completeness and consistency of atomic data. With four input parameters relating to the radiation source and target plasma, RCF calculates the population of levels and charge states, as well as potentially emission spectrum. In preliminary application, RCF successfully reproduces the results of a photoionization experiment with reliable atomic data. The effects of the most important atomic processes on the charge state distribution are also discussed.

  17. Immobilization of single argon atoms in nano-cages of two-dimensional zeolite model systems

    Science.gov (United States)

    Zhong, Jian-Qiang; Wang, Mengen; Akter, Nusnin; Kestell, John D.; Boscoboinik, Alejandro M.; Kim, Taejin; Stacchiola, Dario J.; Lu, Deyu; Boscoboinik, J. Anibal

    2017-07-01

    The confinement of noble gases on nanostructured surfaces, in contrast to bulk materials, at non-cryogenic temperatures represents a formidable challenge. In this work, individual Ar atoms are trapped at 300 K in nano-cages consisting of (alumino)silicate hexagonal prisms forming a two-dimensional array on a planar surface. The trapping of Ar atoms is detected in situ using synchrotron-based ambient pressure X-ray photoelectron spectroscopy. The atoms remain in the cages upon heating to 400 K. The trapping and release of Ar is studied combining surface science methods and density functional theory calculations. While the frameworks stay intact with the inclusion of Ar atoms, the permeability of gasses (for example, CO) through them is significantly affected, making these structures also interesting candidates for tunable atomic and molecular sieves. These findings enable the study of individually confined noble gas atoms using surface science methods, opening up new opportunities for fundamental research.

  18. An atomic finite element model for biodegradable polymers. Part 1. Formulation of the finite elements.

    Science.gov (United States)

    Gleadall, Andrew; Pan, Jingzhe; Ding, Lifeng; Kruft, Marc-Anton; Curcó, David

    2015-11-01

    Molecular dynamics (MD) simulations are widely used to analyse materials at the atomic scale. However, MD has high computational demands, which may inhibit its use for simulations of structures involving large numbers of atoms such as amorphous polymer structures. An atomic-scale finite element method (AFEM) is presented in this study with significantly lower computational demands than MD. Due to the reduced computational demands, AFEM is suitable for the analysis of Young's modulus of amorphous polymer structures. This is of particular interest when studying the degradation of bioresorbable polymers, which is the topic of an accompanying paper. AFEM is derived from the inter-atomic potential energy functions of an MD force field. The nonlinear MD functions were adapted to enable static linear analysis. Finite element formulations were derived to represent interatomic potential energy functions between two, three and four atoms. Validation of the AFEM was conducted through its application to atomic structures for crystalline and amorphous poly(lactide).

  19. Immobilization of single argon atoms in nano-cages of two-dimensional zeolite model systems.

    Science.gov (United States)

    Zhong, Jian-Qiang; Wang, Mengen; Akter, Nusnin; Kestell, John D; Boscoboinik, Alejandro M; Kim, Taejin; Stacchiola, Dario J; Lu, Deyu; Boscoboinik, J Anibal

    2017-07-17

    The confinement of noble gases on nanostructured surfaces, in contrast to bulk materials, at non-cryogenic temperatures represents a formidable challenge. In this work, individual Ar atoms are trapped at 300 K in nano-cages consisting of (alumino)silicate hexagonal prisms forming a two-dimensional array on a planar surface. The trapping of Ar atoms is detected in situ using synchrotron-based ambient pressure X-ray photoelectron spectroscopy. The atoms remain in the cages upon heating to 400 K. The trapping and release of Ar is studied combining surface science methods and density functional theory calculations. While the frameworks stay intact with the inclusion of Ar atoms, the permeability of gasses (for example, CO) through them is significantly affected, making these structures also interesting candidates for tunable atomic and molecular sieves. These findings enable the study of individually confined noble gas atoms using surface science methods, opening up new opportunities for fundamental research.

  20. 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.

  1. 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

  2. Viscoelastic Finite Difference Modeling Using Graphics Processing Units

    Science.gov (United States)

    Fabien-Ouellet, G.; Gloaguen, E.; Giroux, B.

    2014-12-01

    Full waveform seismic modeling requires a huge amount of computing power that still challenges today's technology. This limits the applicability of powerful processing approaches in seismic exploration like full-waveform inversion. This paper explores the use of Graphics Processing Units (GPU) to compute a time based finite-difference solution to the viscoelastic wave equation. The aim is to investigate whether the adoption of the GPU technology is susceptible to reduce significantly the computing time of simulations. The code presented herein is based on the freely accessible software of Bohlen (2002) in 2D provided under a General Public License (GNU) licence. This implementation is based on a second order centred differences scheme to approximate time differences and staggered grid schemes with centred difference of order 2, 4, 6, 8, and 12 for spatial derivatives. The code is fully parallel and is written using the Message Passing Interface (MPI), and it thus supports simulations of vast seismic models on a cluster of CPUs. To port the code from Bohlen (2002) on GPUs, the OpenCl framework was chosen for its ability to work on both CPUs and GPUs and its adoption by most of GPU manufacturers. In our implementation, OpenCL works in conjunction with MPI, which allows computations on a cluster of GPU for large-scale model simulations. We tested our code for model sizes between 1002 and 60002 elements. Comparison shows a decrease in computation time of more than two orders of magnitude between the GPU implementation run on a AMD Radeon HD 7950 and the CPU implementation run on a 2.26 GHz Intel Xeon Quad-Core. The speed-up varies depending on the order of the finite difference approximation and generally increases for higher orders. Increasing speed-ups are also obtained for increasing model size, which can be explained by kernel overheads and delays introduced by memory transfers to and from the GPU through the PCI-E bus. Those tests indicate that the GPU memory size

  3. HYBRID ORBITALS OF CARBON ATOMS IN THE D6hC36 MOLECULE UNDER THE ROTATING ELLIPSOID MODEL

    Institute of Scientific and Technical Information of China (English)

    Tong Guo-ping

    2000-01-01

    The hybrid orbitals of carbon atoms in the D6h C36 molecule arestudied using two rotating ellipsoid models. The model 1 is 1.66R for theshort semi-axis and 2.34R for the long semi-axis, and the model 2 is 1.78R and 2.26R respectively, where R is the C-C bond length. By comparison,we think the model 2 to be more proper in revealing the electronic properties of the D6h C36 molecule. The component of s orbitals in the states hybridized for each of the atoms is much larger than C60, in which the sorbit component is 0.0380 and the porbit is 0.9620. The most component is 0.2098and the least is 0.0482 for model 1; the most is 0.1764 and the least is0.0656 for model 2.

  4. Aerosol cluster impact and break-up : II. Atomic and Cluster Scale Models.

    Energy Technology Data Exchange (ETDEWEB)

    Lechman, Jeremy B.; Takato, Yoichi (State University of New York at Buffalo, Buffalo, NY)

    2010-09-01

    Understanding the interaction of aerosol particle clusters/flocs with surfaces is an area of interest for a number of processes in chemical, pharmaceutical, and powder manufacturing as well as in steam-tube rupture in nuclear power plants. Developing predictive capabilities for these applications involves coupled phenomena on multiple length and timescales from the process macroscopic scale ({approx}1m) to the multi-cluster interaction scale (1mm-0.1m) to the single cluster scale ({approx}1000 - 10000 particles) to the particle scale (10nm-10{micro}m) interactions, and on down to the sub-particle, atomic scale interactions. The focus of this report is on the single cluster scale; although work directed toward developing better models of particle-particle interactions by considering sub-particle scale interactions and phenomena is also described. In particular, results of mesoscale (i.e., particle to single cluster scale) discrete element method (DEM) simulations for aerosol cluster impact with rigid walls are presented. The particle-particle interaction model is based on JKR adhesion theory and is implemented as an enhancement to the granular package in the LAMMPS code. The theory behind the model is outlined and preliminary results are shown. Additionally, as mentioned, results from atomistic classical molecular dynamics simulations are also described as a means of developing higher fidelity models of particle-particle interactions. Ultimately, the results from these and other studies at various scales must be collated to provide systems level models with accurate 'sub-grid' information for design, analysis and control of the underlying systems processes.

  5. Analytical Model of the Nonlinear Dynamics of Cantilever Tip-Sample Surface Interactions for Various Acoustic-Atomic Force Microscopies

    Science.gov (United States)

    Cantrell, John H., Jr.; Cantrell, Sean A.

    2008-01-01

    A comprehensive analytical model of the interaction of the cantilever tip of the atomic force microscope (AFM) with the sample surface is developed that accounts for the nonlinearity of the tip-surface interaction force. The interaction is modeled as a nonlinear spring coupled at opposite ends to linear springs representing cantilever and sample surface oscillators. The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a standard iteration procedure. Solutions are obtained for the phase and amplitude signals generated by various acoustic-atomic force microscope (A-AFM) techniques including force modulation microscopy, atomic force acoustic microscopy, ultrasonic force microscopy, heterodyne force microscopy, resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM), and the commonly used intermittent contact mode (TappingMode) generally available on AFMs. The solutions are used to obtain a quantitative measure of image contrast resulting from variations in the Young modulus of the sample for the amplitude and phase images generated by the A-AFM techniques. Application of the model to RDF-AFUM and intermittent soft contact phase images of LaRC-cp2 polyimide polymer is discussed. The model predicts variations in the Young modulus of the material of 24 percent from the RDF-AFUM image and 18 percent from the intermittent soft contact image. Both predictions are in good agreement with the literature value of 21 percent obtained from independent, macroscopic measurements of sheet polymer material.

  6. 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.

  7. Confining diffuse potential versus square-well-potential in modeling A@C60 atoms

    CERN Document Server

    Dolmatov, V K; Oglesby, J C

    2011-01-01

    It is shown that discontinuity, inherit to a square-well potential which is often used for mimicking the C60 cage potential, results neither in qualitative nor, what is even more important, quantitative artifacts in problems of endohedral A@C60 atoms, such as their photoionization. Moreover, it is demonstrated that, upon mimicking a square-well potential by a potential with diffuse boarders, calculated photoionization spectra are largely insensitive to the degree {\\eta} of diffuseness of the potential boarders, in a reasonably broad range of {\\eta}'s. The proof is based on results of comparison between calculated data for H@C60 and Xe@C60 photoionization cross sections and photoelectron angular asymmetries obtained by modeling the C$_{60}$ cage by confining square-well and diffuse potentials. Thus, it matters little which of these potentials to use in A@C60 problems. The diffuse potential is modeled by a combination of two Woods-Saxon potentials. Calculated data for the photoionization of Xe@C60 are separatel...

  8. [Research on optimization of mathematical model of flow injection-hydride generation-atomic fluorescence spectrometry].

    Science.gov (United States)

    Cui, Jian; Zhao, Xue-Hong; Wang, Yan; Xiao, Ya-Bing; Jiang, Xue-Hui; Dai, Li

    2014-01-01

    Flow injection-hydride generation-atomic fluorescence spectrometry was a widely used method in the industries of health, environmental, geological and metallurgical fields for the merit of high sensitivity, wide measurement range and fast analytical speed. However, optimization of this method was too difficult as there exist so many parameters affecting the sensitivity and broadening. Generally, the optimal conditions were sought through several experiments. The present paper proposed a mathematical model between the parameters and sensitivity/broadening coefficients using the law of conservation of mass according to the characteristics of hydride chemical reaction and the composition of the system, which was proved to be accurate as comparing the theoretical simulation and experimental results through the test of arsanilic acid standard solution. Finally, this paper has put a relation map between the parameters and sensitivity/broadening coefficients, and summarized that GLS volume, carrier solution flow rate and sample loop volume were the most factors affecting sensitivity and broadening coefficients. Optimizing these three factors with this relation map, the relative sensitivity was advanced by 2.9 times and relative broadening was reduced by 0.76 times. This model can provide a theoretical guidance for the optimization of the experimental conditions.

  9. Adsorption of metal atoms at a buckled graphene grain boundary using model potentials

    Energy Technology Data Exchange (ETDEWEB)

    Helgee, Edit E.; Isacsson, Andreas [Department of Applied Physics, Chalmers University of Technology, SE-412 96, Göteborg (Sweden)

    2016-01-15

    Two model potentials have been evaluated with regard to their ability to model adsorption of single metal atoms on a buckled graphene grain boundary. One of the potentials is a Lennard-Jones potential parametrized for gold and carbon, while the other is a bond-order potential parametrized for the interaction between carbon and platinum. Metals are expected to adsorb more strongly to grain boundaries than to pristine graphene due to their enhanced adsorption at point defects resembling those that constitute the grain boundary. Of the two potentials considered here, only the bond-order potential reproduces this behavior and predicts the energy of the adsorbate to be about 0.8 eV lower at the grain boundary than on pristine graphene. The Lennard-Jones potential predicts no significant difference in energy between adsorbates at the boundary and on pristine graphene. These results indicate that the Lennard-Jones potential is not suitable for studies of metal adsorption on defects in graphene, and that bond-order potentials are preferable.

  10. Thermodynamics of various F420 coenzyme models as sources of electrons, hydride ions, hydrogen atoms and protons in acetonitrile.

    Science.gov (United States)

    Xia, Ke; Shen, Guang-Bin; Zhu, Xiao-Qing

    2015-06-14

    32 F420 coenzyme models with alkylation of the three different N atoms (N1, N3 and N10) in the core structure (XFH(-)) were designed and synthesized and the thermodynamic driving forces (defined in terms of the molar enthalpy changes or the standard redox potentials in this work) of the 32 XFH(-) releasing hydride ions, hydrogen atoms and electrons, the thermodynamic driving forces of the 32 XFH˙ releasing protons and hydrogen atoms and the thermodynamic driving forces of XF(-)˙ releasing electrons in acetonitrile were determined using titration calorimetry and electrochemical methods. The effects of the methyl group at N1, N3 and N10 and a negative charge on N1 and N10 atoms on the six thermodynamic driving forces of the F420 coenzyme models and their related reaction intermediates were examined; the results show that seating arrangements of the methyl group and the negative charge have remarkably different effects on the thermodynamic properties of the F420 coenzyme models and their related reaction intermediates. The effects of the substituents at C7 and C8 on the six thermodynamic driving forces of the F420 coenzyme models and their related reaction intermediates were also examined; the results show that the substituents at C7 and C8 have good Hammett linear free energy relationships with the six thermodynamic parameters. Meanwhile, a reasonable determination of possible reactions between members of the F420 family and NADH family in vivo was given according to a thermodynamic analysis platform constructed using the elementary step thermodynamic parameter of F420 coenzyme model 2FH(-) and NADH model MNAH releasing hydride ions in acetonitrile. The information disclosed in this work can not only fill a gap in the chemical thermodynamics of F420 coenzyme models as a class of very important organic sources of electrons, hydride ions, hydrogen atoms and protons, but also strongly promote the fast development of the chemistry and applications of F420 coenzyme.

  11. The atom-surface interaction potential for He-NaCl: A model based on pairwise additivity

    Science.gov (United States)

    Hutson, Jeremy M.; Fowler, P. W.

    1986-08-01

    The recently developed semi-empirical model of Fowler and Hutson is applied to the He-NaCl atom-surface interaction potential. Ab initio self-consistent field calculations of the repulsive interactions between He atoms and in-crystal Cl - and Na + ions are performed. Dispersion coefficients involving in-crystal ions are also calculated. The atom-surface potential is constructed using a model based on pairwise additivity of atom-ion forces. With a small adjustment of the repulsive part, this potential gives good agreement with the experimental bound state energies obtained from selective adsorption resonances in low-energy atom scattering experiments. Close-coupling calculations of the resonant scattering are performed, and good agreement with the experimental peak positions and intensity patterns is obtained. It is concluded that there are no bound states deeper than those observed in the selective adsorption experiments, and that the well depth of the He-NaCl potential is 6.0 ± 0.2 meV.

  12. Capturing the multiscale dynamics of membrane protein complexes with all-atom, mixed-resolution, and coarse-grained models.

    Science.gov (United States)

    Liao, Chenyi; Zhao, Xiaochuan; Liu, Jiyuan; Schneebeli, Severin T; Shelley, John C; Li, Jianing

    2017-03-20

    The structures and dynamics of protein complexes are often challenging to model in heterogeneous environments such as biological membranes. Herein, we meet this fundamental challenge at attainable cost with all-atom, mixed-resolution, and coarse-grained models of vital membrane proteins. We systematically simulated five complex models formed by two distinct G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-μs timescales. These models, which suggest the swinging motion of an intracellular loop, for the first time, provide the molecular details for the regulatory role of such a loop. For the models at different resolutions, we observed consistent structural stability but various levels of speed-ups in protein dynamics. The mixed-resolution and coarse-grained models show two and four times faster protein diffusion than the all-atom models, in addition to a 4- and 400-fold speed-up in the simulation performance. Furthermore, by elucidating the strengths and challenges of combining all-atom models with reduced resolution models, this study can serve as a guide to simulating other complex systems in heterogeneous environments efficiently.

  13. The contribution of atom accessibility to site of metabolism models for cytochromes P450

    DEFF Research Database (Denmark)

    Rydberg, Patrik; Rostkowski, M.; Gloriam, D.E.

    2013-01-01

    Three different types of atom accessibility descriptors are investigated in relation to site of metabolism predictions. To enable the integration of local accessibility we have constructed 2DSASA, a method for the calculation of the atomic solvent accessible surface area that is independent of 3D...

  14. Identifying student and teacher difficulties in interpreting atomic spectra using a quantum model of emission and absorption of radiation

    Science.gov (United States)

    Savall-Alemany, Francisco; Domènech-Blanco, Josep Lluís; Guisasola, Jenaro; Martínez-Torregrosa, Joaquín

    2016-06-01

    Our study sets out to identify the difficulties that high school students, teachers, and university students encounter when trying to explain atomic spectra. To do so, we identify the key concepts that any quantum model for the emission and absorption of electromagnetic radiation must include to account for the gas spectra and we then design two questionnaires, one for teachers and the other for students. By analyzing the responses, we conclude that (i) teachers lack a quantum model for the emission and absorption of electromagnetic radiation capable of explaining the spectra, (ii) teachers and students share the same difficulties, and (iii) these difficulties concern the model of the atom, the model of radiation, and the model of the interaction between them.

  15. Interactions between C and Cu atoms in single-layer graphene: direct observation and modelling.

    Science.gov (United States)

    Kano, Emi; Hashimoto, Ayako; Kaneko, Tomoaki; Tajima, Nobuo; Ohno, Takahisa; Takeguchi, Masaki

    2016-01-07

    Metal doping into the graphene lattice has been studied recently to develop novel nanoelectronic devices and to gain an understanding of the catalytic activities of metals in nanocarbon structures. Here we report the direct observation of interactions between Cu atoms and single-layer graphene by transmission electron microscopy. We document stable configurations of Cu atoms in the graphene sheet and unique transformations of graphene promoted by Cu atoms. First-principles calculations based on density functional theory reveal a reduction of energy barrier that caused rotation of C-C bonds near Cu atoms. We discuss two driving forces, electron irradiation and in situ heating, and conclude that the observed transformations were mainly promoted by electron irradiation. Our results suggest that individual Cu atoms can promote reconstruction of single-layer graphene.

  16. A reaction-diffusion model for atomic oxygen interacting with spacecraft surface protective materials in low earth orbit environment

    Institute of Scientific and Technical Information of China (English)

    CHEN LaiWen; WANG JingHua; LEE Chun-Hian

    2009-01-01

    When hyperthermal atomic oxygen collides with a silicon surface, an ultrathin oxidation regime characterized by fractional atomic-oxygen anions having low diffusive and reactive barriers, along with their enhanced diffusion due to both the electric field and image potential, will form on the surface. In accordance with these properties, an attempt was made in the present study to modify the AlmeidaGoncalves-Baumvol (AGB) model by setting the diffusivity and reaction rate constant to be diffusion-length dependence. According to the modified model, numerical parametric studies for oxidation thin growth were performed. The dependencies of the diffusion coefficient, the reaction rate constant,the attenuation length, and the adjustable parameter upon the translational kinetic energy, flux, temperature, and tangential flux of atomic oxygen were analyzed briefly via the fitting of the experimental data given by Tagawa et al. The numerical results confirmed the rationality of the modified diffusion-reaction model. The model together with the computer code developed in this study would be a useful tool for thickness evaluation of the protective film against the oxidation of atomic oxygen toward spacecraft surface materials in LEO environment.

  17. A reaction-diffusion model for atomic oxygen interacting with spacecraft surface protective materials in low earth orbit environment

    Institute of Scientific and Technical Information of China (English)

    LEE; Chun-Hian

    2009-01-01

    When hyperthermal atomic oxygen collides with a silicon surface, an ultrathin oxidation regime characterized by fractional atomic-oxygen anions having low diffusive and reactive barriers, along with their enhanced diffusion due to both the electric field and image potential, will form on the surface. In ac- cordance with these properties, an attempt was made in the present study to modify the Almeida- Goncalves-Baumvol (AGB) model by setting the diffusivity and reaction rate constant to be diffu- sion-length dependence. According to the modified model, numerical parametric studies for oxidation thin growth were performed. The dependencies of the diffusion coefficient, the reaction rate constant, the attenuation length, and the adjustable parameter upon the translational kinetic energy, flux, tem- perature, and tangential flux of atomic oxygen were analyzed briefly via the fitting of the experimental data given by Tagawa et al. The numerical results confirmed the rationality of the modified diffu- sion-reaction model. The model together with the computer code developed in this study would be a useful tool for thickness evaluation of the protective film against the oxidation of atomic oxygen toward spacecraft surface materials in LEO environment.

  18. 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…

  19. Identifying Student and Teacher Difficulties in Interpreting Atomic Spectra Using a Quantum Model of Emission and Absorption of Radiation

    Science.gov (United States)

    Savall-Alemany, Francisco; Domènech-Blanco, Josep Lluís; Guisasola, Jenaro; Martínez-Torregrosa, Joaquín

    2016-01-01

    Our study sets out to identify the difficulties that high school students, teachers, and university students encounter when trying to explain atomic spectra. To do so, we identify the key concepts that any quantum model for the emission and absorption of electromagnetic radiation must include to account for the gas spectra and we then design two…

  20. Using Concept Maps as Instructional Materials to Foster the Understanding of the Atomic Model and Matter-Energy Interaction

    Science.gov (United States)

    Aguiar, Joana G.; Correia, Paulo R. M.

    2016-01-01

    In this paper, we explore the use of concept maps (Cmaps) as instructional materials prepared by teachers, to foster the understanding of chemistry. We choose fireworks as a macroscopic event to teach basic chemical principles related to the Bohr atomic model and matter-energy interaction. During teachers' Cmap navigation, students can experience…

  1. 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…

  2. Precast concrete unit assessment through GPR survey and FDTD modelling

    Science.gov (United States)

    Campo, Davide

    2017-04-01

    Precast concrete elements are widely used within United Kingdom house building offering ease in assembly and added values as structural integrity, sound and thermal insulation; most common concrete components include walls, beams, floors, panels, lintels, stairs, etc. The lack of respect of the manufacturer instruction during assembling, however, may induce cracking and short/long term loss of bearing capacity. GPR is a well-established not destructive technique employed in the assessment of structural elements because of real-time imaging, quickness of data collecting and ability to discriminate finest structural details. In this work, GPR has been used to investigate two different precast elements: precast reinforced concrete planks constituting the roof slab of a school and precast wood-cement blocks with insulation material pre-fitted used to build a perimeter wall of a private building. Visible cracks affected both constructions. For the assessment surveys, a GSSI 2.0 GHz GPR antenna has been used because of the high resolution required and the small size of the antenna case (155 by 90 by 105mm) enabling scanning up to 45mm from any obstruction. Finite Difference Time Domain (FDTD) numerical modelling was also performed to build a scenario of the expected GPR signal response for a preliminary real-time interpretation and to help solve uncertainties due to complex reflection patterns: simulated radargrams were built using Reflex Software v. 8.2, reproducing the same GPR pulse used for the surveys in terms of wavelet, nominal frequency, sample frequency and time window. Model geometries were derived from the design projects available both for the planks and the blocks; the electromagnetic properties of the materials (concrete, reinforcing bars, air-filled void, insulation and wooden concrete) were inferred from both values reported in literature and a preliminary interpretation of radargrams where internal layer interfaces were clearly recognizable and

  3. 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.

  4. Sputtering of copper atoms by keV atomic and molecular ions A comparison of experiment with analytical and computer based models

    CERN Document Server

    Gillen, D R; Goelich,

    2002-01-01

    Non-resonant multiphoton ionisation combined with quadrupole and time-of-flight analysis has been used to measure energy distributions of sputtered copper atoms. The sputtering of a polycrystalline copper target by 3.6 keV Ar sup + , N sup + and CF sub 2 sup + and 1.8 keV N sup + and CF sub 2 sup + ion bombardment at 45 deg. has been investigated. The linear collision model in the isotropic limit fails to describe the high energy tail of the energy distributions. However the TRIM.SP computer simulation has been shown to provide a good description. The results indicate that an accurate description of sputtering by low energy, molecular ions requires the use of computer simulation rather than analytical approaches. This is particularly important when considering plasma-surface interactions in plasma etching and deposition systems.

  5. ENHANCING THE ATOMIC-LEVEL UNDERSTANDING OF CO2 MINERAL SEQUESTRATION MECHANISMS VIA ADVANCED COMPUTATIONAL MODELING

    Energy Technology Data Exchange (ETDEWEB)

    A.V.G. Chizmeshya; M.J. McKelvy; G.H. Wolf; R.W. Carpenter; D.A. Gormley; J.R. Diefenbacher; R. Marzke

    2006-03-01

    have already significantly improved our understanding of mineral carbonation. Group members at the Albany Research Center have recently shown that carbonation of olivine and serpentine, which naturally occurs over geological time (i.e., 100,000s of years), can be accelerated to near completion in hours. Further process refinement will require a synergetic science/engineering approach that emphasizes simultaneous investigation of both thermodynamic processes and the detailed microscopic, atomic-level mechanisms that govern carbonation kinetics. Our previously funded Phase I Innovative Concepts project demonstrated the value of advanced quantum-mechanical modeling as a complementary tool in bridging important gaps in our understanding of the atomic/molecular structure and reaction mechanisms that govern CO2 mineral sequestration reaction processes for the model Mg-rich lamellar hydroxide feedstock material Mg(OH)2. In the present simulation project, improved techniques and more efficient computational schemes have allowed us to expand and augment these capabilities and explore more complex Mg-rich, lamellar hydroxide-based feedstock materials, including the serpentine-based minerals. These feedstock materials are being actively investigated due to their wide availability, and low-cost CO2 mineral sequestration potential. Cutting-edge first principles quantum chemical, computational solid-state and materials simulation methodology studies proposed herein, have been strategically integrated with our new DOE supported (ASU-Argonne National Laboratory) project to investigate the mechanisms that govern mineral feedstock heat-treatment and aqueous/fluid-phase serpentine mineral carbonation in situ. This unified, synergetic theoretical and experimental approach has provided a deeper understanding of the key reaction mechanisms than either individual approach can alone. We used ab initio techniques to significantly advance our understanding of atomic-level processes at the solid

  6. ENHANCING THE ATOMIC-LEVEL UNDERSTANDING OF CO2 MINERAL SEQUESTRATION MECHANISMS VIA ADVANCED COMPUTATIONAL MODELING

    Energy Technology Data Exchange (ETDEWEB)

    A.V.G. Chizmeshya

    2003-12-19

    DOE/NETL managed National Mineral Sequestration Working Group we have already significantly improved our understanding of mineral carbonation. Group members at the Albany Research Center have recently shown that carbonation of olivine and serpentine, which naturally occurs over geological time (i.e., 100,000s of years), can be accelerated to near completion in hours. Further process refinement will require a synergetic science/engineering approach that emphasizes simultaneous investigation of both thermodynamic processes and the detailed microscopic, atomic-level mechanisms that govern carbonation kinetics. Our previously funded Phase I Innovative Concepts project demonstrated the value of advanced quantum-mechanical modeling as a complementary tool in bridging important gaps in our understanding of the atomic/molecular structure and reaction mechanisms that govern CO{sub 2} mineral sequestration reaction processes for the model Mg-rich lamellar hydroxide feedstock material Mg(OH){sub 2}. In the present simulation project, improved techniques and more efficient computational schemes have allowed us to expand and augment these capabilities and explore more complex Mg-rich, lamellar hydroxide-based feedstock materials, including the serpentine-based minerals. These feedstock materials are being actively investigated due to their wide availability, and low-cost CO{sub 2} mineral sequestration potential. Cutting-edge first principles quantum chemical, computational solid-state and materials simulation methodology studies proposed herein, have been strategically integrated with our new DOE supported (ASU-Argonne National Laboratory) project to investigate the mechanisms that govern mineral feedstock heat-treatment and aqueous/fluid-phase serpentine mineral carbonation in situ. This unified, synergetic theoretical and experimental approach will provide a deeper understanding of the key reaction mechanisms than either individual approach can alone. Ab initio techniques will

  7. Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models.

    Science.gov (United States)

    Kouza, Maksim; Co, Nguyen Truong; Nguyen, Phuong H; Kolinski, Andrzej; Li, Mai Suan

    2015-04-14

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  8. Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models

    Energy Technology Data Exchange (ETDEWEB)

    Kouza, Maksim, E-mail: mkouza@chem.uw.edu.pl; Kolinski, Andrzej [Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warszaw (Poland); Co, Nguyen Truong [Department of Physics, Institute of Technology, National University of HCM City, 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City (Viet Nam); Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City (Viet Nam); Nguyen, Phuong H. [Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris (France); Li, Mai Suan, E-mail: masli@ifpan.edu.pl [Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw (Poland)

    2015-04-14

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  9. Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions.

    Science.gov (United States)

    Antoniewicz, Maciek R; Kelleher, Joanne K; Stephanopoulos, Gregory

    2007-01-01

    Metabolic flux analysis (MFA) has emerged as a tool of great significance for metabolic engineering and mammalian physiology. An important limitation of MFA, as carried out via stable isotope labeling and GC/MS and nuclear magnetic resonance (NMR) measurements, is the large number of isotopomer or cumomer equations that need to be solved, especially when multiple isotopic tracers are used for the labeling of the system. This restriction reduces the ability of MFA to fully utilize the power of multiple isotopic tracers in elucidating the physiology of realistic situations comprising complex bioreaction networks. Here, we present a novel framework for the modeling of isotopic labeling systems that significantly reduces the number of system variables without any loss of information. The elementary metabolite unit (EMU) framework is based on a highly efficient decomposition method that identifies the minimum amount of information needed to simulate isotopic labeling within a reaction network using the knowledge of atomic transitions occurring in the network reactions. The functional units generated by the decomposition algorithm, called EMUs, form the new basis for generating system equations that describe the relationship between fluxes and stable isotope measurements. Isotopomer abundances simulated using the EMU framework are identical to those obtained using the isotopomer and cumomer methods, however, require significantly less computation time. For a typical (13)C-labeling system the total number of equations that needs to be solved is reduced by one order-of-magnitude (100s EMUs vs. 1000s isotopomers). As such, the EMU framework is most efficient for the analysis of labeling by multiple isotopic tracers. For example, analysis of the gluconeogenesis pathway with (2)H, (13)C, and (18)O tracers requires only 354 EMUs, compared to more than two million isotopomers.

  10. Spatially-explicit model of mercury accumulation in the forest floor of the United States

    Science.gov (United States)

    Perry, C. H.; Zimmerman, P.

    2009-12-01

    Atmospherically-deposited Hg has a strong affinity for soil organic matter. The Forest Service, US Department of Agriculture, Forest Inventory and Analysis (FIA) program collects soil samples from forested areas across the United States as part of its sampling program, and annual soils inventories are underway or completed in 46 of the 50 states (Alaska, Hawaii, New Mexico, and Oklahoma have yet to be sampled). Our objective is to describe the spatial distribution of forest floor Hg for a transect running across the United States, from Arizona in the southwest to Maine in the northeast. The collection of forest floor samples was accomplished as part of the standard FIA Phase 3 Soil Quality Indicator program. Field protocols include the measurement of the thickness of the forest floor and the collection of the entire forest floor found within a 30-cm diameter sampling frame. We removed approximately 0.1 g of the sample for plots in our region of interest, and these were sent to two different laboratories for Hg analysis by cold-vapor atomic absorption. The two laboratories calibrated their instruments against common Hg standards. We found good agreement between samples analyzed at both laboratories. Observations of mercury concentrations were joined with the Forest Inventory and Analysis Database and other geospatial databases to assign basic location information and associated inventory data. Ecoprovince and forest-type group are significant predictors of Hg storage; conifer species tend to store more mercury than hardwood species. Additionally, models created using spatially-explicit techniques yield distinct patterns of Hg storage that vary across forest-type groups.

  11. Microfabricated Waveguide Atom Traps.

    Energy Technology Data Exchange (ETDEWEB)

    Jau, Yuan-Yu

    2017-09-01

    A nano - scale , microfabricated waveguide structure can in - principle be used to trap atoms in well - defined locations and enable strong photon - atom interactions . A neutral - atom platf orm based on this microfabrication technology will be pre - aligned , which is especially important for quantum - control applications. At present, there is still no reported demonstration of evanescent - field atom trapping using a microfabricated waveguide structure. We described the capabilities established by our team for future development of the waveguide atom - trapping technology at SNL and report our studies to overcome the technical challenges of loading cold atoms into the waveguide atom traps, efficient and broadband optical coupling to a waveguide, and the waveguide material for high - power optical transmission. From the atomic - physics and the waveguide modeling, w e have shown that a square nano - waveguide can be utilized t o achieve better atomic spin squeezing than using a nanofiber for first time.

  12. Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel.

    Science.gov (United States)

    Li, Xianfeng; Murthy, N Sanjeeva; Becker, Matthew L; Latour, Robert A

    2016-06-24

    A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications.

  13. Efimov studies of an ultracold cloud of 39 K atoms in microgravity: Numerical modelling and experimental design

    Science.gov (United States)

    Mossman, Maren; Engels, Peter; D'Incao, Jose; Jin, Deborah; Cornell, Eric

    2016-05-01

    Ultracold atomic gases at or near quantum degeneracy provide a powerful tool for the investigation of few-body physics. A particularly intriguing few-body phenomenon is the existence of Efimov trimer states at large interatomic scattering lengths. These trimers are predicted to exhibit universal geometric scaling relations, but in practice the situation is complicated e.g. by finite-range and finite-temperature effects. While some Efimov trimers have already been experimentally observed by several groups in ground-based experiments, NASA's Cold Atom Laboratory (CAL) onboard the ISS will greatly enhance the experimentally accessible regimes by providing ultracold clouds of 39 K atoms with temperatures at or below 1 nK, low densities, and long observation times. We present results of numerical modelling and simulations that lay out Efimov experiments capitalizing on the particular strengths of CAL.

  14. 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

  15. Modeling the Atomic-to-Molecular Transition and Chemical Distributions of Turbulent Star-Forming Clouds

    CERN Document Server

    Offner, Stella S R; Viti, Serena; Bell, Thomas A

    2013-01-01

    We use 3D-PDR, a three-dimensional astrochemistry code for modeling photodissociation regions (PDRs), to post-process hydrodynamic simulations of turbulent, star-forming clouds. We focus on the transition from atomic to molecular gas, with specific attention to the formation and distribution of H, C+, C, H2 and CO. First, we demonstrate that the details of the cloud chemistry and our conclusions are insensitive to the simulation spatial resolution, to the resolution at the cloud edge, and to the ray angular resolution. We then investigate the effect of geometry and simulation parameters on chemical abundances and find weak dependence on cloud morphology as dictated by gravity and turbulent Mach number. For a uniform external radiation field, we find similar distributions to those derived using a one-dimensional PDR code. However, we demonstrate that a three-dimensional treatment is necessary for a spatially varying external field, and we caution against using one-dimensional treatments for non-symmetric probl...

  16. MODELING THE ATOMIC-TO-MOLECULAR TRANSITION AND CHEMICAL DISTRIBUTIONS OF TURBULENT STAR-FORMING CLOUDS

    Energy Technology Data Exchange (ETDEWEB)

    Offner, Stella S. R. [Department of Astronomy, Yale University, New Haven, CT 06511 (United States); Bisbas, Thomas G.; Viti, Serena [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6B (United Kingdom); Bell, Tom A., E-mail: stella.offner@yale.edu [Centro de Astrobiologia (CSIC-INTA), Carretera de Ajalvir, km 4, E-28850 Madrid (Spain)

    2013-06-10

    We use 3D-PDR, a three-dimensional astrochemistry code for modeling photodissociation regions (PDRs), to post-process hydrodynamic simulations of turbulent, star-forming clouds. We focus on the transition from atomic to molecular gas, with specific attention to the formation and distribution of H, C{sup +}, C, H{sub 2}, and CO. First, we demonstrate that the details of the cloud chemistry and our conclusions are insensitive to the simulation spatial resolution, to the resolution at the cloud edge, and to the ray angular resolution. We then investigate the effect of geometry and simulation parameters on chemical abundances and find weak dependence on cloud morphology as dictated by gravity and turbulent Mach number. For a uniform external radiation field, we find similar distributions to those derived using a one-dimensional PDR code. However, we demonstrate that a three-dimensional treatment is necessary for a spatially varying external field, and we caution against using one-dimensional treatments for non-symmetric problems. We compare our results with the work of Glover et al., who self-consistently followed the time evolution of molecule formation in hydrodynamic simulations using a reduced chemical network. In general, we find good agreement with this in situ approach for C and CO abundances. However, the temperature and H{sub 2} abundances are discrepant in the boundary regions (A{sub v} {<=} 5), which is due to the different number of rays used by the two approaches.

  17. Near-atomic resolution structural model of the yeast 26S proteasome.

    Science.gov (United States)

    Beck, Florian; Unverdorben, Pia; Bohn, Stefan; Schweitzer, Andreas; Pfeifer, Günter; Sakata, Eri; Nickell, Stephan; Plitzko, Jürgen M; Villa, Elizabeth; Baumeister, Wolfgang; Förster, Friedrich

    2012-09-11

    The 26S proteasome operates at the executive end of the ubiquitin-proteasome pathway. Here, we present a cryo-EM structure of the Saccharomyces cerevisiae 26S proteasome at a resolution of 7.4 Å or 6.7 Å (Fourier-Shell Correlation of 0.5 or 0.3, respectively). We used this map in conjunction with molecular dynamics-based flexible fitting to build a near-atomic resolution model of the holocomplex. The quality of the map allowed us to assign α-helices, the predominant secondary structure element of the regulatory particle subunits, throughout the entire map. We were able to determine the architecture of the Rpn8/Rpn11 heterodimer, which had hitherto remained elusive. The MPN domain of Rpn11 is positioned directly above the AAA-ATPase N-ring suggesting that Rpn11 deubiquitylates substrates immediately following commitment and prior to their unfolding by the AAA-ATPase module. The MPN domain of Rpn11 dimerizes with that of Rpn8 and the C-termini of both subunits form long helices, which are integral parts of a coiled-coil module. Together with the C-terminal helices of the six PCI-domain subunits they form a very large coiled-coil bundle, which appears to serve as a flexible anchoring device for all the lid subunits.

  18. Mechanics of the IL2RA gene activation revealed by modeling and atomic force microscopy.

    Directory of Open Access Journals (Sweden)

    Pascale Milani

    Full Text Available Transcription implies recruitment of RNA polymerase II and transcription factors (TFs by DNA melting near transcription start site (TSS. Combining atomic force microscopy and computer modeling, we investigate the structural and dynamical properties of the IL2RA promoter and identify an intrinsically negative supercoil in the PRRII region (containing Elf-1 and HMGA1 binding sites, located upstream of a curved DNA region encompassing TSS. Conformational changes, evidenced by time-lapse studies, result in the progressive positioning of curvature apex towards the TSS, likely facilitating local DNA melting. In vitro assays confirm specific binding of the General Transcription Factors (GTFs TBP and TFIIB over TATA-TSS position, where an inhibitory nucleosome prevented preinitiation complex (PIC formation and uncontrolled DNA melting. These findings represent a substantial advance showing, first, that the structural properties of the IL2RA promoter are encoded in the DNA sequence and second, that during the initiation process DNA conformation is dynamic and not static.

  19. Modeling of an atomizer for two fluids; Modelacion de un atomizador de dos fluidos

    Energy Technology Data Exchange (ETDEWEB)

    Tapia Ramirez, Zoili [Instituto de Investigaciones Electricas, Cuernavaca (Mexico)

    1998-09-01

    The work reported in this article presents the results of the effort to improve the basic understanding of the flow structure that is formed in a two fluid sprayer before and after the interaction between the sprayed fluid and the spraying fluid. The images in the interior of the mixing chamber of the atomizer are shown, which were taken with a high velocity video camera. Also the results of the numerical simulation of the internal flow obtained by means of a package of commercial modeling are shown. [Espanol] El trabajo reportado en este articulo presenta los resultados del esfuerzo por mejorar el entendimiento basico de la estructura del flujo que se forma en un atomizador de dos fluidos antes y despues de la interaccion entre el fluido atomizado y el fluido atomizante. Se muestran imagenes del flujo en el interior de la camara de mezclado del atomizador, las cuales fueron tomadas con una camara de video de alta velocidad. Tambien se incluyen los resultados de la simulacion numerica del flujo interno obtenidas por medio de un paquete de modelacion comercial.

  20. Optimized Model Surfaces for Advanced Atomic Force Microscopy Studies of Surface Nanobubbles.

    Science.gov (United States)

    Song, Bo; Zhou, Yi; Schönherr, Holger

    2016-11-01

    The formation of self-assembled monolayers (SAMs) of binary mixtures of 16-mercaptohexadecanoic acid (MHDA) and 1-octadecanethiol (ODT) on ultraflat template-stripped gold (TSG) surfaces was systematically investigated to clarify the assembly behavior, composition, and degree of possible phase segregation in light of atomic force microscopy (AFM) studies of surface nanobubbles on these substrates. The data for SAMs on TSG were compared to those obtained by adsorption on rough evaporated gold, as reported in a previous study. Quartz crystal microbalance and surface plasmon resonance data acquired in situ on TSG indicate that similar to SAM formation on conventional evaporated gold substrates ODT and MHDA form monolayers and bilayers, respectively. The second layer on MHDA, whose formation is attributed to hydrogen bonding, can be easily removed by adequate rinsing with water. The favorable agreement of the grazing incidence reflection Fourier transform infrared (GIR FTIR) spectroscopy and contact angle data analyzed with the Israelachvili-Gee model suggests that the binary SAMs do not segregate laterally. This conclusion is fully validated by high-resolution friction force AFM observations down to a length scale of 8-10 nm, which is much smaller than the typical observed surface nanobubble radii. Finally, correspondingly functionalized TSG substrates are shown to be valuable supports for studying surface nanobubbles by AFM in water and for addressing the relation between surface functionality and nanobubble formation and properties.