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Sample records for atomic parameter model

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

    PubMed Central

    Pande, Vijay S.; Head-Gordon, Teresa; Ponder, Jay W.

    2016-01-01

    A set of improved parameters for the AMOEBA polarizable atomic multipole water model is developed. The protocol uses an automated procedure, ForceBalance, to adjust model parameters to enforce agreement with ab initio-derived results for water clusters and experimentally obtained 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 new AMOEBA14 water model accurately predicts the temperature of maximum density and qualitatively matches the experimental density curve across temperatures ranging from 249 K to 373 K. Excellent agreement is observed for the AMOEBA14 model in comparison to a variety of experimental properties as a function of temperature, including the 2nd 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 to 20 water molecules, the AMOEBA14 model yields results similar to the 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. PMID:25683601

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

    PubMed

    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.

  3. ATOMIC AND MOLECULAR PHYSICS: Four-parameter analytical local model potential for atoms

    NASA Astrophysics Data System (ADS)

    Yu, Fei; Sun, Jiu-Xun; Tian, Rong-Gang; Yang, Wei

    2009-10-01

    Analytical local model potential for modeling the interaction in an atom reduces the computational effort in electronic structure calculations significantly. A new four-parameter analytical local model potential is proposed for atoms Li through Lr, and the values of four parameters are shell-independent and obtained by fitting the results of Xa method. At the same time, the energy eigenvalues, the radial wave functions and the total energies of electrons are obtained by solving the radial Schrödinger equation with a new form of potential function by Numerov's numerical method. The results show that our new form of potential function is suitable for high, medium and low Z atoms. A comparison among the new potential function and other analytical potential functions shows the greater flexibility and greater accuracy of the present new potential function.

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

    PubMed

    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.

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

    PubMed

    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.

  6. Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water.

    PubMed

    Reinhardt, Aleks; Doye, Jonathan P K; Noya, Eva G; Vega, Carlos

    2012-11-21

    We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging.

  7. Hydration free energies using semiempirical quantum mechanical Hamiltonians and a continuum solvent model with multiple atomic-type parameters.

    PubMed

    Anisimov, Victor M; Cavasotto, Claudio N

    2011-06-23

    To build the foundation for accurate quantum mechanical (QM) simulation of biomacromolecules in an aqueous environment, we undertook the optimization of the COnductor-like Screening MOdel (COSMO) atomic radii and atomic surface tension coefficients for different semiempirical Hamiltonians adhering to the same computational conditions recently followed in the simulation of biomolecular systems. This optimization was achieved by reproducing experimental hydration free energies of a set consisting of 507 neutral and 99 ionic molecules. The calculated hydration free energies were significantly improved by introducing a multiple atomic-type scheme that reflects different chemical environments. The nonpolar contribution was treated according to the scaled particle Claverie-Pierotti formalism. Separate radii and surface tension coefficient sets have been developed for AM1, PM3, PM5, and RM1 semiempirical Hamiltonians, with an average unsigned error for neutral molecules of 0.64, 0.66, 0.73, and 0.71 kcal/mol, respectively. Free energy calculation of each molecule took on average 0.5 s on a single processor. The new sets of parameters will enhance the quality of semiempirical QM calculations using COSMO in biomolecular systems. Overall, these results further extend the utility of QM methods to chemical and biological systems in the condensed phase.

  8. "Bohr's Atomic Model."

    ERIC Educational Resources Information Center

    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. Stochastic models for atomic clocks

    NASA Technical Reports Server (NTRS)

    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.

  10. Computer Modeling Of Atomization

    NASA Technical Reports Server (NTRS)

    Giridharan, M.; Ibrahim, E.; Przekwas, A.; Cheuch, S.; Krishnan, A.; Yang, H.; Lee, J.

    1994-01-01

    Improved mathematical models based on fundamental principles of conservation of mass, energy, and momentum developed for use in computer simulation of atomization of jets of liquid fuel in rocket engines. Models also used to study atomization in terrestrial applications; prove especially useful in designing improved industrial sprays - humidifier water sprays, chemical process sprays, and sprays of molten metal. Because present improved mathematical models based on first principles, they are minimally dependent on empirical correlations and better able to represent hot-flow conditions that prevail in rocket engines and are too severe to be accessible for detailed experimentation.

  11. Semiclassical model for atoms

    PubMed Central

    Pearson, Ralph G.

    1981-01-01

    The energies of several two- and three-electron atoms, in both ground states and excited states, are calculated by a very simple semiclassical model. The only change from Bohr's original method is to replace definite orbits by probability distribution functions based on classical dynamics. The energies are better than Hartree-Fock values. There is still a need for an exchange-energy correction. Images PMID:16593047

  12. Origin of the Universal Three-body Parameter in Atomic Efimov Physic

    NASA Astrophysics Data System (ADS)

    Naidon, Pascal; Endo, Shimpei; Ueda, Masahito

    2013-05-01

    Several experiments with different kinds of ultra-cold atoms have revealed that the three-body parameter that fixes the Efimov spectrum of few-atom systems near broad Feshbach resonances is universally determined by the atoms' van der Waals length. Using model potential calculations we find that the three-body parameter originates from a deformation of the three-atom system due to universal two-body correlations at separations on the order of the van der Waals length scale. This simple physical picture is consistent with the universality of the three-body parameter observed in the experiments, as well as previous numerical calculations. It explains why the low-energy physics of three bosonic atoms near a broad resonance is solely determined by their two-body parameters.

  13. Finding New Thermoelectric Compounds Using Crystallographic Data: Atomic Displacement Parameters

    SciTech Connect

    Chakoumakos, B.C.; Mandrus, D.G.; Sales, B.C.; Sharp, J.W.

    1999-08-29

    A new structure-property relationship is discussed which links atomic displacement parameters (ADPs) and the lattice thermal conductivity of clathrate-like compounds. For many clathrate-like compounds, in which one of the atom types is weakly bound and ''rattles'' within its atomic cage, room temperature ADP information can be used to estimate the room temperature lattice thermal conductivity, the vibration frequency of the ''rattler'', and the temperature dependence of the heat capacity. Neutron data and X-ray crystallography data, reported in the literature, are used to apply this analysis to several promising classes of thermoelectric materials.

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

    ERIC Educational Resources Information Center

    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)

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

    ERIC Educational Resources Information Center

    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)

  16. Ultrahigh-resolution study of protein atomic displacement parameters at cryotemperatures obtained with a helium cryostat.

    SciTech Connect

    Petrova, T.; Ginell, S.; Mitschler, A.; Hazemann, I.; Schneider, T.; Cousido, A.; Lunin, V.; Joachimiak, A.; Podjarny, A,; Biosciences Division; Russian Academy of Sciences; IGBMC; Inst. of Molecular Oncology

    2006-01-01

    Two X-ray data sets for a complex of human aldose reductase (h-AR) with the inhibitor IDD 594 and the cofactor NADP(+) were collected from two different parts of the same crystal to a resolution of 0.81 A at 15 and 60 K using cold helium gas as cryogen. The contribution of temperature to the atomic B values was estimated by comparison of the independently refined models. It was found that although being slightly different for different kinds of atoms, the differences (deltaB) in the isotropic equivalents B of atomic displacement parameters (ADPs) were approximately constant (about 1.7 A(2)) for well ordered atoms as the temperature was increased from 15 to 60 K. The mean value of this difference varied according to the number of non-H atoms covalently bound to the parent atom. Atoms having a B value of higher than 8 A(2) at 15 K showed much larger deviations of deltaB from the average value, which might reflect partial occupancy of atomic sites. An analysis of the anisotropy of ADPs for individual atoms revealed an increase in the isotropy of ADPs with the increase of the temperature from 15 to 60 K. In a separate experiment, a 0.93 A resolution data set was collected from a different crystal of the same complex at 100 K using cold nitrogen as a cryogen. The effects of various errors on the atomic B values were estimated by comparison of the refined models and the temperature-dependent component was inferred. It was found that both decreasing the data redundancy and increasing the resolution cutoff led to an approximately constant increase in atomic B values for well ordered atoms.

  17. Parameter uncertainty for ASP models

    SciTech Connect

    Knudsen, J.K.; Smith, C.L.

    1995-10-01

    The steps involved to incorporate parameter uncertainty into the Nuclear Regulatory Commission (NRC) accident sequence precursor (ASP) models is covered in this paper. Three different uncertainty distributions (i.e., lognormal, beta, gamma) were evaluated to Determine the most appropriate distribution. From the evaluation, it was Determined that the lognormal distribution will be used for the ASP models uncertainty parameters. Selection of the uncertainty parameters for the basic events is also discussed. This paper covers the process of determining uncertainty parameters for the supercomponent basic events (i.e., basic events that are comprised of more than one component which can have more than one failure mode) that are utilized in the ASP models. Once this is completed, the ASP model is ready to be utilized to propagate parameter uncertainty for event assessments.

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

    PubMed

    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.

  19. False asymmetry, pseudosymmetry, disorder, polymorphism and atomic displacement parameters

    NASA Astrophysics Data System (ADS)

    Lombardo, Giuseppe M.; Punzo, Francesco

    2014-12-01

    Two similar sugars, with chemical formulas differing only by the presence of a methyl group connected to the molecule backbones in different positions, crystallize in the monoclinic P21 space group giving rise to Z‧ = 2 structures. They both bear an azide side chain which is the principal responsible for the lack of a higher symmetry for one compound only. We analyzed their most relevant features by means of X-ray single crystal diffraction coupled with a quantitative estimation of their potential tendency to crystallize in a different space group with higher symmetry. The latter tendency of the most promising of the two compounds is commented in the light of the anisotropic behaviour of the atomic displacement parameters.

  20. Parameter identification in continuum models

    NASA Technical Reports Server (NTRS)

    Banks, H. T.; Crowley, J. M.

    1983-01-01

    Approximation techniques for use in numerical schemes for estimating spatially varying coefficients in continuum models such as those for Euler-Bernoulli beams are discussed. The techniques are based on quintic spline state approximations and cubic spline parameter approximations. Both theoretical and numerical results are presented. Previously announced in STAR as N83-28934

  1. Parameter identification in continuum models

    NASA Technical Reports Server (NTRS)

    Banks, H. T.; Crowley, J. M.

    1983-01-01

    Approximation techniques for use in numerical schemes for estimating spatially varying coefficients in continuum models such as those for Euler-Bernoulli beams are discussed. The techniques are based on quintic spline state approximations and cubic spline parameter approximations. Both theoretical and numerical results are presented.

  2. Parameter estimation for transformer modeling

    NASA Astrophysics Data System (ADS)

    Cho, Sung Don

    Large Power transformers, an aging and vulnerable part of our energy infrastructure, are at choke points in the grid and are key to reliability and security. Damage or destruction due to vandalism, misoperation, or other unexpected events is of great concern, given replacement costs upward of $2M and lead time of 12 months. Transient overvoltages can cause great damage and there is much interest in improving computer simulation models to correctly predict and avoid the consequences. EMTP (the Electromagnetic Transients Program) has been developed for computer simulation of power system transients. Component models for most equipment have been developed and benchmarked. Power transformers would appear to be simple. However, due to their nonlinear and frequency-dependent behaviors, they can be one of the most complex system components to model. It is imperative that the applied models be appropriate for the range of frequencies and excitation levels that the system experiences. Thus, transformer modeling is not a mature field and newer improved models must be made available. In this work, improved topologically-correct duality-based models are developed for three-phase autotransformers having five-legged, three-legged, and shell-form cores. The main problem in the implementation of detailed models is the lack of complete and reliable data, as no international standard suggests how to measure and calculate parameters. Therefore, parameter estimation methods are developed here to determine the parameters of a given model in cases where available information is incomplete. The transformer nameplate data is required and relative physical dimensions of the core are estimated. The models include a separate representation of each segment of the core, including hysteresis of the core, lambda-i saturation characteristic, capacitive effects, and frequency dependency of winding resistance and core loss. Steady-state excitation, and de-energization and re-energization transients

  3. Nagaoka's atomic model and hyperfine interactions.

    PubMed

    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.

  4. The Hydrogen Atom: The Rutherford Model

    NASA Astrophysics Data System (ADS)

    Tilton, Homer Benjamin

    1996-06-01

    Early this century Ernest Rutherford established the nuclear model of the hydrogen atom, presently taught as representing the best visual model after modification by Niels Bohr and Arnold Sommerfeld. It replaced the so-called "plum pudding" model of J. J. Thomson which held sway previously. While the Rutherford model represented a large step forward in our understanding of the hydrogen atom, questions remained, and still do.

  5. Optimization of electrothermal atomization parameters for simultaneous multielement atomic absorption spectrometry

    USGS Publications Warehouse

    Harnly, J.M.; Kane, J.S.

    1984-01-01

    The effect of the acid matrix, the measurement mode (height or area), the atomizer surface (unpyrolyzed and pyrolyzed graphite), the atomization mode (from the wall or from a platform), and the atomization temperature on the simultaneous electrothermal atomization of Co, Cr, Cu, Fe, Mn, Mo, Ni, V, and Zn was examined. The 5% HNO3 matrix gave rise to severe irreproducibility using a pyrolyzed tube unless the tube was properly "prepared". The 5% HCl matrix did not exhibit this problem, and no problems were observed with either matrix using an unpyrolized tube or a pyrolyzed platform. The 5% HCl matrix gave better sensitivities with a pyrolyzed tube but the two matrices were comparable for atomization from a platform. If Mo and V are to be analyzed with the other seven elements, a high atomization temperature (2700??C or greater) is necessary regardless of the matrix, the measurement mode, the atomization mode, or the atomizer surface. Simultaneous detection limits (peak height with pyrolyzed tube atomization) were comparable to those of conventional atomic absorption spectrometry using electrothermal atomization above 280 nm. Accuracies and precisions of ??10-15% were found in the 10 to 120 ng mL-1 range for the analysis of NBS acidified water standards.

  6. Parameter estimation, model reduction and quantum filtering

    NASA Astrophysics Data System (ADS)

    Chase, Bradley A.

    This thesis explores the topics of parameter estimation and model reduction in the context of quantum filtering. The last is a mathematically rigorous formulation of continuous quantum measurement, in which a stream of auxiliary quantum systems is used to infer the state of a target quantum system. Fundamental quantum uncertainties appear as noise which corrupts the probe observations and therefore must be filtered in order to extract information about the target system. This is analogous to the classical filtering problem in which techniques of inference are used to process noisy observations of a system in order to estimate its state. Given the clear similarities between the two filtering problems, I devote the beginning of this thesis to a review of classical and quantum probability theory, stochastic calculus and filtering. This allows for a mathematically rigorous and technically adroit presentation of the quantum filtering problem and solution. Given this foundation, I next consider the related problem of quantum parameter estimation, in which one seeks to infer the strength of a parameter that drives the evolution of a probe quantum system. By embedding this problem in the state estimation problem solved by the quantum filter, I present the optimal Bayesian estimator for a parameter when given continuous measurements of the probe system to which it couples. For cases when the probe takes on a finite number of values, I review a set of sufficient conditions for asymptotic convergence of the estimator. For a continuous-valued parameter, I present a computational method called quantum particle filtering for practical estimation of the parameter. Using these methods, I then study the particular problem of atomic magnetometry and review an experimental method for potentially reducing the uncertainty in the estimate of the magnetic field beyond the standard quantum limit. The technique involves double-passing a probe laser field through the atomic system, giving

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

    PubMed

    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.

  8. Modeling Atom Probe Tomography: A review.

    PubMed

    Vurpillot, F; Oberdorfer, C

    2015-12-01

    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.

  9. A Nonlinear Model for Fuel Atomization in Spray Combustion

    NASA Technical Reports Server (NTRS)

    Liu, Nan-Suey (Technical Monitor); Ibrahim, Essam A.; Sree, Dave

    2003-01-01

    Most gas turbine combustion codes rely on ad-hoc statistical assumptions regarding the outcome of fuel atomization processes. The modeling effort proposed in this project is aimed at developing a realistic model to produce accurate predictions of fuel atomization parameters. The model involves application of the nonlinear stability theory to analyze the instability and subsequent disintegration of the liquid fuel sheet that is produced by fuel injection nozzles in gas turbine combustors. The fuel sheet is atomized into a multiplicity of small drops of large surface area to volume ratio to enhance the evaporation rate and combustion performance. The proposed model will effect predictions of fuel sheet atomization parameters such as drop size, velocity, and orientation as well as sheet penetration depth, breakup time and thickness. These parameters are essential for combustion simulation codes to perform a controlled and optimized design of gas turbine fuel injectors. Optimizing fuel injection processes is crucial to improving combustion efficiency and hence reducing fuel consumption and pollutants emissions.

  10. Atomic Calculations with a One-Parameter, Single Integral Method.

    ERIC Educational Resources Information Center

    Baretty, Reinaldo; Garcia, Carmelo

    1989-01-01

    Presents an energy function E(p) containing a single integral and one variational parameter, alpha. Represents all two-electron integrals within the local density approximation as a single integral. Identifies this as a simple treatment for use in an introductory quantum mechanics course. (MVL)

  11. Hirshfeld atom refinement for modelling strong hydrogen bonds.

    PubMed

    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.

  12. Biological parameters for lung cancer in mathematical models of carcinogenesis.

    PubMed

    Jacob, P; Jacob, V

    2003-01-01

    Applications of the two-step model of carcinogenesis with clonal expansion (TSCE) to lung cancer data are reviewed, including those on atomic bomb survivors from Hiroshima and Nagasaki. British doctors, Colorado Plateau miners and Chinese tin miners. Different sets of identifiable model parameters are used in the literature. The parameter set which could be determined with the lowest uncertainty consists of the net proliferation rate gamma of intermediate cells, the hazard h55 at an intermediate age and the hazard h(infinity) at an asymptotically large age. Also, the values of these three parameters obtained in the various studies are more consistent than other identifiable combinations of the biological parameters. Based on representative results for these three parameters, implications for the biological parameters in the TSCE model are derived. PMID:14579892

  13. Students' Mental Models of Atomic Spectra

    ERIC Educational Resources Information Center

    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…

  14. Effective microscopic models for sympathetic cooling of atomic gases

    NASA Astrophysics Data System (ADS)

    Onofrio, Roberto; Sundaram, Bala

    2015-09-01

    Thermalization of a system in the presence of a heat bath has been the subject of many theoretical investigations especially in the framework of solid-state physics. In this setting, the presence of a large bandwidth for the frequency distribution of the harmonic oscillators schematizing the heat bath is crucial, as emphasized in the Caldeira-Leggett model. By contrast, ultracold gases in atomic traps oscillate at well-defined frequencies and therefore seem to lie outside the Caldeira-Leggett paradigm. We introduce interaction Hamiltonians which allow us to adapt the model to an atomic physics framework. The intrinsic nonlinearity of these models differentiates them from the original Caldeira-Leggett model and calls for a nontrivial stability analysis to determine effective ranges for the model parameters. These models allow for molecular-dynamics simulations of mixtures of ultracold gases, which is of current relevance for optimizing sympathetic cooling in degenerate Bose-Fermi mixtures.

  15. Systematic Improvement of Potential-Derived Atomic Multipoles and Redundancy of the Electrostatic Parameter Space.

    PubMed

    Jakobsen, Sofie; Jensen, Frank

    2014-12-01

    We assess the accuracy of force field (FF) electrostatics at several levels of approximation from the standard model using fixed partial charges to conformational specific multipole fits including up to quadrupole moments. Potential-derived point charges and multipoles are calculated using least-squares methods for a total of ∼1000 different conformations of the 20 natural amino acids. Opposed to standard charge fitting schemes the procedure presented in the current work employs fitting points placed on a single isodensity surface, since the electrostatic potential (ESP) on such a surface determines the ESP at all points outside this surface. We find that the effect of multipoles beyond partial atomic charges is of the same magnitude as the effect due to neglecting conformational dependency (i.e., polarizability), suggesting that the two effects should be included at the same level in FF development. The redundancy at both the partial charge and multipole levels of approximation is quantified. We present an algorithm which stepwise reduces or increases the dimensionality of the charge or multipole parameter space and provides an upper limit of the ESP error that can be obtained at a given truncation level. Thereby, we can identify a reduced set of multipole moments corresponding to ∼40% of the total number of multipoles. This subset of parameters provides a significant improvement in the representation of the ESP compared to the simple point charge model and close to the accuracy obtained using the complete multipole parameter space. The selection of the ∼40% most important multipole sites is highly transferable among different conformations, and we find that quadrupoles are of high importance for atoms involved in π-bonding, since the anisotropic electric field generated in such regions requires a large degree of flexibility.

  16. Parameter Estimation of Partial Differential Equation Models.

    PubMed

    Xun, Xiaolei; Cao, Jiguo; Mallick, Bani; Carroll, Raymond J; Maity, Arnab

    2013-01-01

    Partial differential equation (PDE) models are commonly used to model complex dynamic systems in applied sciences such as biology and finance. The forms of these PDE models are usually proposed by experts based on their prior knowledge and understanding of the dynamic system. Parameters in PDE models often have interesting scientific interpretations, but their values are often unknown, and need to be estimated from the measurements of the dynamic system in the present of measurement errors. Most PDEs used in practice have no analytic solutions, and can only be solved with numerical methods. Currently, methods for estimating PDE parameters require repeatedly solving PDEs numerically under thousands of candidate parameter values, and thus the computational load is high. In this article, we propose two methods to estimate parameters in PDE models: a parameter cascading method and a Bayesian approach. In both methods, the underlying dynamic process modeled with the PDE model is represented via basis function expansion. For the parameter cascading method, we develop two nested levels of optimization to estimate the PDE parameters. For the Bayesian method, we develop a joint model for data and the PDE, and develop a novel hierarchical model allowing us to employ Markov chain Monte Carlo (MCMC) techniques to make posterior inference. Simulation studies show that the Bayesian method and parameter cascading method are comparable, and both outperform other available methods in terms of estimation accuracy. The two methods are demonstrated by estimating parameters in a PDE model from LIDAR data. PMID:24363476

  17. Phenomenological model of spin crossover in molecular crystals as derived from atom-atom potentials.

    PubMed

    Sinitskiy, Anton V; Tchougréeff, Andrei L; Dronskowski, Richard

    2011-08-01

    The method of atom-atom potentials, previously applied to the analysis of pure molecular crystals formed by either low-spin (LS) or high-spin (HS) forms (spin isomers) of Fe(II) coordination compounds (Sinitskiy et al., Phys. Chem. Chem. Phys., 2009, 11, 10983), is used to estimate the lattice enthalpies of mixed crystals containing different fractions of the spin isomers. The crystals under study were formed by LS and HS isomers of Fe(phen)(2)(NCS)(2) (phen = 1,10-phenanthroline), Fe(btz)(2)(NCS)(2) (btz = 5,5',6,6'-tetrahydro-4H,4'H-2,2'-bi-1,3-thiazine), and Fe(bpz)(2)(bipy) (bpz = dihydrobis(1-pyrazolil)borate, and bipy = 2,2'-bipyridine). For the first time the phenomenological parameters Γ pertinent to the Slichter-Drickamer model (SDM) of several materials were independently derived from the microscopic model of the crystals with use of atom-atom potentials of intermolecular interaction. The accuracy of the SDM was checked against the numerical data on the enthalpies of mixed crystals. Fair semiquantitative agreement with the experimental dependence of the HS fraction on temperature was achieved with use of these values. Prediction of trends in Γ values as a function of chemical composition and geometry of the crystals is possible with the proposed approach, which opens a way to rational design of spin crossover materials with desired properties.

  18. Automation of the CHARMM General Force Field (CGenFF) II: Assignment of bonded parameters and partial atomic charges

    PubMed Central

    Vanommeslaeghe, K.; Raman, E. Prabhu; MacKerell, A. D.

    2012-01-01

    Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug candidates interacting with biological systems. In these simulations, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters and partial atomic charges is required. In the present article, algorithms for the assignment of parameters and charges for the CHARMM General Force Field (CGenFF) are presented. These algorithms rely on the existing parameters and charges that were determined as part of the parametrization of the force field. Bonded parameters are assigned based on the similarity between the atom types that define said parameters, while charges are determined using an extended bond-charge increment scheme. Charge increments were optimized to reproduce the charges on model compounds that were part of the parametrization of the force field. A “penalty score” is returned for every bonded parameter and charge, allowing the user to quickly and conveniently assess the quality of the force field representation of different parts of the compound of interest. Case studies are presented to clarify the functioning of the algorithms and the significance of their output data. PMID:23145473

  19. Atomic Data Applications for Supernova Modeling

    NASA Astrophysics Data System (ADS)

    Fontes, Christopher J.

    2013-06-01

    The modeling of supernovae (SNe) incorporates a variety of disciplines, including hydrodynamics, radiation transport, nuclear physics and atomic physics. These efforts require numerical simulation of the final stages of a star's life, the supernova explosion phase, and the radiation that is subsequently emitted by the supernova remnant, which can occur over a time span of tens of thousands of years. While there are several different types of SNe, they all emit radiation in some form. The measurement and interpretation of these spectra provide important information about the structure of the exploding star and the supernova engine. In this talk, the role of atomic data is highlighted as iit pertains to the modeling of supernova spectra. Recent applications [1,2] involve the Los Alamos OPLIB opacity database, which has been used to provide atomic opacities for modeling supernova plasmas under local thermodynamic equilibrium (LTE) conditions. Ongoing work includes the application of atomic data generated by the Los Alamos suite of atomic physics codes under more complicated, non-LTE conditions [3]. As a specific, recent example, a portion of the x-ray spectrum produced by Tycho's supernova remnant (SN 1572) will be discussed [4]. [1] C.L. Fryer et al, Astrophys. J. 707, 193 (2009). [2] C.L. Fryer et al, Astrophys. J. 725, 296 (2009). [3] C.J. Fontes et al, Conference Proceedings for ICPEAC XXVII, J. of Phys: Conf. Series 388, 012022 (2012). [4] K.A. Eriksen et al, Presentation at the 2012 AAS Meeting (Austin, TX). (This work was performed under the auspices of the U.S. Department of Energy by Los Alamos National Laboratory under Contract No. DE-AC52-06NA25396.)

  20. Understanding Parameter Invariance in Unidimensional IRT Models

    ERIC Educational Resources Information Center

    Rupp, Andre A.; Zumbo, Bruno D.

    2006-01-01

    One theoretical feature that makes item response theory (IRT) models those of choice for many psychometric data analysts is parameter invariance, the equality of item and examinee parameters from different examinee populations or measurement conditions. In this article, using the well-known fact that item and examinee parameters are identical only…

  1. Model parameter updating using Bayesian networks

    SciTech Connect

    Treml, C. A.; Ross, Timothy J.

    2004-01-01

    This paper outlines a model parameter updating technique for a new method of model validation using a modified model reference adaptive control (MRAC) framework with Bayesian Networks (BNs). The model parameter updating within this method is generic in the sense that the model/simulation to be validated is treated as a black box. It must have updateable parameters to which its outputs are sensitive, and those outputs must have metrics that can be compared to that of the model reference, i.e., experimental data. Furthermore, no assumptions are made about the statistics of the model parameter uncertainty, only upper and lower bounds need to be specified. This method is designed for situations where a model is not intended to predict a complete point-by-point time domain description of the item/system behavior; rather, there are specific points, features, or events of interest that need to be predicted. These specific points are compared to the model reference derived from actual experimental data. The logic for updating the model parameters to match the model reference is formed via a BN. The nodes of this BN consist of updateable model input parameters and the specific output values or features of interest. Each time the model is executed, the input/output pairs are used to adapt the conditional probabilities of the BN. Each iteration further refines the inferred model parameters to produce the desired model output. After parameter updating is complete and model inputs are inferred, reliabilities for the model output are supplied. Finally, this method is applied to a simulation of a resonance control cooling system for a prototype coupled cavity linac. The results are compared to experimental data.

  2. Global Model Analysis by Parameter Space Partitioning

    ERIC Educational Resources Information Center

    Pitt, Mark A.; Kim, Woojae; Navarro, Daniel J.; Myung, Jay I.

    2006-01-01

    To model behavior, scientists need to know how models behave. This means learning what other behaviors a model can produce besides the one generated by participants in an experiment. This is a difficult problem because of the complexity of psychological models (e.g., their many parameters) and because the behavioral precision of models (e.g.,…

  3. Atomic model of supersymmetric Hubbard operators

    NASA Astrophysics Data System (ADS)

    Hopkinson, J.; Coleman, P.

    2003-02-01

    We apply the recently proposed supersymmetric Hubbard operators [P. Coleman, C. Pépin, and J. Hopkinson, Phys. Rev. B 63, 140411(R) (2001)] to an atomic model. In the limiting case of free spins, we derive exact results for the entropy which are compared with a mean-field + Gaussian corrections description. We show how these results can be extended to the case of charge fluctuations and calculate exact results for the partition function, free energy, and heat capacity of an atomic model for some simple examples. Wave-functions of possible states are listed. We compare the accuracy of large N expansions of the susy spin operators [P. Coleman, C. Pépin, and A. M. Tsvelik, Phys. Rev. B 62, 3852 (2000); Nucl. Phys. B 586, 641 (2000)] with those obtained using “Schwinger bosons” and “Abrikosov pseudofermions.” For the atomic model, we compare results of slave boson, slave fermion, and susy Hubbard operator approximations in the physically interesting but uncontrolled limiting case of N→2. For a mixed representation of spins, we estimate the accuracy of large N expansions of the atomic model. In the single box limit, we find that the lowest-energy susy saddle point reduces to simply either slave bosons or slave fermions, while for higher boxes this is not the case. The highest energy saddle point solution has the interesting feature that it admits a small region of a mixed representation, which bears a superficial resemblance to that observed experimentally close to an antiferromagnetic quantum critical point.

  4. Atomic Data For Core And Edge Modeling

    SciTech Connect

    O'Mullane, M. G.; Foster, A. R.; Whiteford, A. D.; Summers, H. P.; Loch, S. D.; Lauro-Taroni, L.

    2009-09-10

    Future magnetic fusion energy devices, will have both very high Z (tungsten) and low Z (beryllium) plasma facing components, are setting the agenda for current atomic data needs. Data for the light species are in good shape but the heavy species present some challenges. We outline an approach for systematic heavy element data production for fusion applications in addition to techniques for handling the large amount of data in modeling codes efficiently.

  5. On Interpreting the Model Parameters for the Three Parameter Logistic Model

    ERIC Educational Resources Information Center

    Maris, Gunter; Bechger, Timo

    2009-01-01

    This paper addresses two problems relating to the interpretability of the model parameters in the three parameter logistic model. First, it is shown that if the values of the discrimination parameters are all the same, the remaining parameters are nonidentifiable in a nontrivial way that involves not only ability and item difficulty, but also the…

  6. A Green's function quantum average atom model

    SciTech Connect

    Starrett, Charles Edward

    2015-05-21

    A quantum average atom model is reformulated using Green's functions. This allows integrals along the real energy axis to be deformed into the complex plane. The advantage being that sharp features such as resonances and bound states are broadened by a Lorentzian with a half-width chosen for numerical convenience. An implementation of this method therefore avoids numerically challenging resonance tracking and the search for weakly bound states, without changing the physical content or results of the model. A straightforward implementation results in up to a factor of 5 speed-up relative to an optimized orbital based code.

  7. Atomic Layer Deposition - Process Models and Metrologies

    SciTech Connect

    Burgess, D.R. Jr.; Maslar, J.E.; Hurst, W.S.; Moore, E.F.; Kimes, W.A.; Fink, R.R.; Nguyen, N.V.

    2005-09-09

    We report on the status of a combined experimental and modeling study for atomic layer deposition (ALD) of HfO2 and Al2O3. Hafnium oxide films were deposited from tetrakis(dimethylamino)hafnium and water. Aluminum oxide films from trimethyl aluminum and water are being studied through simulations. In this work, both in situ metrologies and process models are being developed. Optically-accessible ALD reactors have been constructed for in situ, high-sensitivity Raman and infrared absorption spectroscopic measurements to monitor gas phase and surface species. A numerical model using computational fluid dynamics codes has been developed to simulate the gas flow and temperature profiles in the experimental reactor. Detailed chemical kinetic models are being developed with assistance from quantum chemical calculations to explore reaction pathways and energetics. This chemistry is then incorporated into the overall reactor models.

  8. Atom-Role-Based Access Control Model

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Technical Reports Server (NTRS)

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

    NASA Technical Reports Server (NTRS)

    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. Making It Visual: Creating a Model of the Atom

    ERIC Educational Resources Information Center

    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…

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

    ERIC Educational Resources Information Center

    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. Computer Model Of Fragmentation Of Atomic Nuclei

    NASA Technical Reports Server (NTRS)

    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.

  14. Parameters and error of a theoretical model

    SciTech Connect

    Moeller, P.; Nix, J.R.; Swiatecki, W.

    1986-09-01

    We propose a definition for the error of a theoretical model of the type whose parameters are determined from adjustment to experimental data. By applying a standard statistical method, the maximum-likelihoodlmethod, we derive expressions for both the parameters of the theoretical model and its error. We investigate the derived equations by solving them for simulated experimental and theoretical quantities generated by use of random number generators. 2 refs., 4 tabs.

  15. Expanding the model: anisotropic displacement parameters in protein structure refinement.

    PubMed

    Merritt, E A

    1999-06-01

    Recent technological improvements in crystallographic data collection have led to a surge in the number of protein structures being determined at atomic or near-atomic resolution. At this resolution, structural models can be expanded to include anisotropic displacement parameters (ADPs) for individual atoms. New protocols and new tools are needed to refine, analyze and validate such models optimally. One such tool, PARVATI, has been used to examine all protein structures (peptide chains >50 residues) for which expanded models including ADPs are available from the Protein Data Bank. The distribution of anisotropy within each of these refined models is broadly similar across the entire set of structures, with a mean anisotropy A in the range 0.4-0.5. This is a significant departure from a purely isotropic model and explains why the inclusion of ADPs yields a substantial improvement in the crystallographic residuals R and Rfree. The observed distribution of anisotropy may prove useful in the validation of very high resolution structures. A more complete understanding of this distribution may also allow the development of improved protein structural models, even at lower resolution.

  16. Effects of detuning and atomic motion parameter on the dynamical behavior of the entanglement between two-level atom and SU(1,1) quantum system

    NASA Astrophysics Data System (ADS)

    Abdel-Khalek, S.; Quthami, M.; Ahmed, M. M. A.

    2015-02-01

    In this paper, we study the dynamics of the atomic inversion and von Neumann entropy for a moving and non-moving two-level atom interacting with multi SU(1,1) quantum system. The wave function and system density matrix using specific initial conditions are obtained. The effects of initial atomic state position and detuning parameters are examined in the absence and presence of the atomic motion effect. Important phenomena such as entanglement sudden death, sudden birth and long-living entanglement are explored during time evolution. The results show that the detuning parameter and excitation number is very useful in generating a high amount of entanglement.

  17. Entanglement swapping to a qutrit-qutrit atomic system in the presence of Kerr medium and detuning parameter

    NASA Astrophysics Data System (ADS)

    Ghasemi, M.; Tavassoly, M. K.

    2016-09-01

    In this paper we consider two independent systems, each consisting of a V-type three-level atom as a qutrit which interacts with a single-mode quantized field in the presence of a Kerr medium. The dynamics of atom-field interaction in each cavity is governed by the Jaynes-Cummings model. The analytical solution associated with each cavity is derived, showing that the atom and field in each cavity are clearly entangled. However, the two (identical) atoms have never interacted and so no entanglement between them exists. The aim of the present paper is to investigate about the possibility of entanglement swapping to a qutrit-qutrit system. We achieve the purpose with the help of the Bell state measurement (BSM) method on the field photons. In the continuation, we discuss on the influences of "Kerr medium" and "off-resonance condition" on success probability, the degree of entanglement and atomic inversion in detail and show that one can appropriately adjust these quantities by tuning the evolved parameters. The success probability of the order of 0.50 for the created qutrit-qutrit entangled state may be accessible.

  18. Models and parameters for environmental radiological assessments

    SciTech Connect

    Miller, C W

    1984-01-01

    This book presents a unified compilation of models and parameters appropriate for assessing the impact of radioactive discharges to the environment. Models examined include those developed for the prediction of atmospheric and hydrologic transport and deposition, for terrestrial and aquatic food-chain bioaccumulation, and for internal and external dosimetry. Chapters have been entered separately into the data base. (ACR)

  19. Bounds on collapse models from cold-atom experiments

    NASA Astrophysics Data System (ADS)

    Bilardello, Marco; Donadi, Sandro; Vinante, Andrea; Bassi, Angelo

    2016-11-01

    The spontaneous localization mechanism of collapse models induces a Brownian motion in all physical systems. This effect is very weak, but experimental progress in creating ultracold atomic systems can be used to detect it. In this paper, we considered a recent experiment (Kovachy et al., 2015), where an atomic ensemble was cooled down to picokelvins. Any Brownian motion induces an extra increase of the position variance of the gas. We study this effect by solving the dynamical equations for the Continuous Spontaneous Localizations (CSL) model, as well as for its non-Markovian and dissipative extensions. The resulting bounds, with a 95 % of confidence level, are beaten only by measurements of spontaneous X-ray emission and by experiments with cantilever (in the latter case, only for rC ≥ 10-7 m, where rC is one of the two collapse parameters of the CSL model). We show that, contrary to the bounds given by X-ray measurements, non-Markovian effects do not change the bounds, for any reasonable choice of a frequency cutoff in the spectrum of the collapse noise. Therefore the bounds here considered are more robust. We also show that dissipative effects are unimportant for a large spectrum of temperatures of the noise, while for low temperatures the excluded region in the parameter space is the more reduced, the lower the temperature.

  20. Atomic Models for Motional Stark Effects Diagnostics

    SciTech Connect

    Gu, M F; Holcomb, C; Jayakuma, J; Allen, S; Pablant, N A; Burrell, K

    2007-07-26

    We present detailed atomic physics models for motional Stark effects (MSE) diagnostic on magnetic fusion devices. Excitation and ionization cross sections of the hydrogen or deuterium beam traveling in a magnetic field in collisions with electrons, ions, and neutral gas are calculated in the first Born approximation. The density matrices and polarization states of individual Stark-Zeeman components of the Balmer {alpha} line are obtained for both beam into plasma and beam into gas models. A detailed comparison of the model calculations and the MSE polarimetry and spectral intensity measurements obtained at the DIII-D tokamak is carried out. Although our beam into gas models provide a qualitative explanation for the larger {pi}/{sigma} intensity ratios and represent significant improvements over the statistical population models, empirical adjustment factors ranging from 1.0-2.0 must still be applied to individual line intensities to bring the calculations into full agreement with the observations. Nevertheless, we demonstrate that beam into gas measurements can be used successfully as calibration procedures for measuring the magnetic pitch angle through {pi}/{sigma} intensity ratios. The analyses of the filter-scan polarization spectra from the DIII-D MSE polarimetry system indicate unknown channel and time dependent light contaminations in the beam into gas measurements. Such contaminations may be the main reason for the failure of beam into gas calibration on MSE polarimetry systems.

  1. Acoustic omni meta-atom for decoupled access to all octants of a wave parameter space

    NASA Astrophysics Data System (ADS)

    Koo, Sukmo; Cho, Choonlae; Jeong, Jun-Ho; Park, Namkyoo

    2016-09-01

    The common behaviour of a wave is determined by wave parameters of its medium, which are generally associated with the characteristic oscillations of its corresponding elementary particles. In the context of metamaterials, the decoupled excitation of these fundamental oscillations would provide an ideal platform for top-down and reconfigurable access to the entire constitutive parameter space; however, this has remained as a conceivable problem that must be accomplished, after being pointed out by Pendry. Here by focusing on acoustic metamaterials, we achieve the decoupling of density ρ, modulus B-1 and bianisotropy ξ, by separating the paths of particle momentum to conform to the characteristic oscillations of each macroscopic wave parameter. Independent access to all octants of wave parameter space (ρ, B-1, ξ)=(+/-,+/-,+/-) is thus realized using a single platform that we call an omni meta-atom; as a building block that achieves top-down access to the target properties of metamaterials.

  2. Acoustic omni meta-atom for decoupled access to all octants of a wave parameter space

    PubMed Central

    Koo, Sukmo; Cho, Choonlae; Jeong, Jun-ho; Park, Namkyoo

    2016-01-01

    The common behaviour of a wave is determined by wave parameters of its medium, which are generally associated with the characteristic oscillations of its corresponding elementary particles. In the context of metamaterials, the decoupled excitation of these fundamental oscillations would provide an ideal platform for top–down and reconfigurable access to the entire constitutive parameter space; however, this has remained as a conceivable problem that must be accomplished, after being pointed out by Pendry. Here by focusing on acoustic metamaterials, we achieve the decoupling of density ρ, modulus B−1 and bianisotropy ξ, by separating the paths of particle momentum to conform to the characteristic oscillations of each macroscopic wave parameter. Independent access to all octants of wave parameter space (ρ, B−1, ξ)=(+/−,+/−,+/−) is thus realized using a single platform that we call an omni meta-atom; as a building block that achieves top–down access to the target properties of metamaterials. PMID:27687689

  3. Calibration of reconstruction parameters in atom probe tomography using a single crystallographic orientation.

    PubMed

    Suram, Santosh K; Rajan, Krishna

    2013-09-01

    The purpose of this work is to develop a methodology to estimate the APT reconstruction parameters when limited crystallographic information is available. Reliable spatial scaling of APT data currently requires identification of multiple crystallographic poles from the field desorption image for estimating the reconstruction parameters. This requirement limits the capacity of accurately reconstructing APT data for certain complex systems, such as highly alloyed systems and nanostructured materials wherein more than one pole is usually not observed within one grain. To overcome this limitation, we develop a quantitative methodology for calibrating the reconstruction parameters in an APT dataset by ensuring accurate inter-planar spacing and optimizing the curvature correction for the atomic planes corresponding to a single crystallographic orientation. We validate our approach on an aluminum dataset and further illustrate its capabilities by computing geometric reconstruction parameters for W and Al-Mg-Sc datasets.

  4. Stability scale and atomic solvation parameters extracted from 1023 mutation experiments.

    PubMed

    Zhou, Hongyi; Zhou, Yaoqi

    2002-12-01

    The stability scale of 20 amino acid residues is derived from a database of 1023 mutation experiments on 35 proteins. The resulting scale of hydrophobic residues has an excellent correlation with the octanol-to-water transfer free energy corrected with an additional Flory-Huggins molar-volume term (correlation coefficient r = 0.95, slope = 1.05, and a near zero intercept). Thus, hydrophobic contribution to folding stability is characterized remarkably well by transfer experiments. However, no corresponding correlation is found for hydrophilic residues. Both the hydrophilic portion and the entire scale, however, correlate strongly with average burial accessible surface (r = 0.76 and 0.97, respectively). Such a strong correlation leads to a near uniform value of the atomic solvation parameters for atoms C, S, O/N, O(-0.5), and N(+0.5,1). All are in the range of 12-28 cal x mol(-1) A(-2), close to the original estimate of hydrophobic contribution of 25-30 cal x mol(-1) A(-2) to folding stability. Without any adjustable parameters, the new stability scale and new atomic solvation parameters yielded an accurate prediction of protein-protein binding free energy for a separate database of 21 protein-protein complexes (r = 0.80 and slope = 1.06, and r = 0.83 and slope = 0.93, respectively).

  5. Atomic force microscopy of model lipid membranes.

    PubMed

    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.

  6. Analysis of Modeling Parameters on Threaded Screws.

    SciTech Connect

    Vigil, Miquela S.; Brake, Matthew Robert; Vangoethem, Douglas

    2015-06-01

    Assembled mechanical systems often contain a large number of bolted connections. These bolted connections (joints) are integral aspects of the load path for structural dynamics, and, consequently, are paramount for calculating a structure's stiffness and energy dissipation prop- erties. However, analysts have not found the optimal method to model appropriately these bolted joints. The complexity of the screw geometry cause issues when generating a mesh of the model. This paper will explore different approaches to model a screw-substrate connec- tion. Model parameters such as mesh continuity, node alignment, wedge angles, and thread to body element size ratios are examined. The results of this study will give analysts a better understanding of the influences of these parameters and will aide in finding the optimal method to model bolted connections.

  7. Force Field Independent Metal Parameters Using a Nonbonded Dummy Model

    PubMed Central

    2014-01-01

    The cationic dummy atom approach provides a powerful nonbonded description for a range of alkaline-earth and transition-metal centers, capturing both structural and electrostatic effects. In this work we refine existing literature parameters for octahedrally coordinated Mn2+, Zn2+, Mg2+, and Ca2+, as well as providing new parameters for Ni2+, Co2+, and Fe2+. In all the cases, we are able to reproduce both M2+–O distances and experimental solvation free energies, which has not been achieved to date for transition metals using any other model. The parameters have also been tested using two different water models and show consistent performance. Therefore, our parameters are easily transferable to any force field that describes nonbonded interactions using Coulomb and Lennard-Jones potentials. Finally, we demonstrate the stability of our parameters in both the human and Escherichia coli variants of the enzyme glyoxalase I as showcase systems, as both enzymes are active with a range of transition metals. The parameters presented in this work provide a valuable resource for the molecular simulation community, as they extend the range of metal ions that can be studied using classical approaches, while also providing a starting point for subsequent parametrization of new metal centers. PMID:24670003

  8. Valence state parameters of all transition metal atoms in metalloproteins--development of ABEEMσπ fluctuating charge force field.

    PubMed

    Yang, Zhong-Zhi; Wang, Jian-Jiang; Zhao, Dong-Xia

    2014-09-01

    To promote accuracy of the atom-bond electronegativity equalization method (ABEEMσπ) fluctuating charge polarizable force fields, and extend it to include all transition metal atoms, a new parameter, the reference charge is set up in the expression of the total energy potential function. We select over 700 model molecules most of which model metalloprotein molecules that come from Protein Data Bank. We set reference charges for different apparent valence states of transition metals and calibrate the parameters of reference charges, valence state electronegativities, and valence state hardnesses for ABEEMσπ through linear regression and least square method. These parameters can be used to calculate charge distributions of metalloproteins containing transition metal atoms (Sc-Zn, Y-Cd, and Lu-Hg). Compared the results of ABEEMσπ charge distributions with those obtained by ab initio method, the quite good linear correlations of the two kinds of charge distributions are shown. The reason why the STO-3G basis set in Mulliken population analysis for the parameter calibration is specially explained in detail. Furthermore, ABEEMσπ method can also quickly and quite accurately calculate dipole moments of molecules. Molecular dynamics optimizations of five metalloproteins as the examples show that their structures obtained by ABEEMσπ fluctuating charge polarizable force field are very close to the structures optimized by the ab initio MP2/6–311G method. This means that the ABEEMσπ/MM can now be applied to molecular dynamics simulations of systems that contain metalloproteins with good accuracy.

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

    NASA Technical Reports Server (NTRS)

    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.

  10. Project Physics Text 5, Models of the Atom.

    ERIC Educational Resources Information Center

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

    Basic atomic theories are presented in this fifth unit of the Project Physics text for use by senior high students. Chemical basis of atomic models in the early years of the 18th Century is discussed n connection with Dalton's theory, atomic properties, and periodic tables. The discovery of electrons is described by using cathode rays, Millikan's…

  11. Atomic Oscillator Strengths for Stellar Atmosphere Modeling

    NASA Astrophysics Data System (ADS)

    Ruffoni, Matthew; Pickering, Juliet C.

    2015-08-01

    In order to correctly model stellar atmospheres, fundamental atomic data must be available to describe atomic lines observed in their spectra. Accurate, laboratory-measured oscillator strengths (f-values) for Fe peak elements in neutral or low-ionisation states are particularly important for determining chemical abundances.However, advances in astronomical spectroscopy in recent decades have outpaced those in laboratory astrophysics, with the latter frequently being overlooked at the planning stages of new projects. As a result, numerous big-budget astronomy projects have been, and continue to be hindered by a lack of suitable, accurately-measured reference data to permit the analysis of expensive astronomical spectra; a problem only likely to worsen in the coming decades as spectrographs at new facilities increasingly move to infrared wavelengths.At Imperial College London - and in collaboration with NIST, Wisconsin University and Lund University - we have been working with the astronomy community in an effort to provide new accurately-measured f-values for a range of projects. In particular, we have been working closely with the Gaia-ESO (GES) and SDSS-III/APOGEE surveys, both of which have discovered that many lines that would make ideal candidates for inclusion in their analyses have poorly defined f-values, or are simply absent from the database. Using high-resolution Fourier transform spectroscopy (R ~ 2,000,000) to provide atomic branching fractions, and combining these with level lifetimes measured with laser induced fluorescence, we have provided new laboratory-measured f-values for a range of Fe-peak elements, most recently including Fe I, Fe II, and V I. For strong, unblended lines, uncertainties are as low as ±0.02 dex.In this presentation, I will describe how experimental f-values are obtained in the laboratory and present our recent work for GES and APOGEE. In particular, I will also discuss the strengths and limitations of current laboratory

  12. An atomic model for neutral and singly ionized uranium

    NASA Technical Reports Server (NTRS)

    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.

  13. Bioelectrical impedance modelling of gentamicin pharmacokinetic parameters.

    PubMed

    Zarowitz, B J; Pilla, A M; Peterson, E L

    1989-10-01

    1. Bioelectrical impedance analysis was used to develop descriptive models of gentamicin pharmacokinetic parameters in 30 adult in-patients receiving therapy with gentamicin. 2. Serial blood samples obtained from each subject at steady state were analyzed and used to derive gentamicin pharmacokinetic parameters. 3. Multiple regression equations were developed for clearance, elimination rate constant and volume of distribution at steady state and were all statistically significant at P less than 0.05. 4. Clinical validation of this innovative technique is warranted before clinical use is recommended.

  14. Force-field parameters of the Psi and Phi around glycosidic bonds to oxygen and sulfur atoms.

    PubMed

    Saito, Minoru; Okazaki, Isao

    2009-12-01

    The Psi and Phi torsion angles around glycosidic bonds in a glycoside chain are the most important determinants of the conformation of a glycoside chain. We determined force-field parameters for Psi and Phi torsion angles around a glycosidic bond bridged by a sulfur atom, as well as a bond bridged by an oxygen atom as a preparation for the next study, i.e., molecular dynamics free energy calculations for protein-sugar and protein-inhibitor complexes. First, we extracted the Psi or Phi torsion energy component from a quantum mechanics (QM) total energy by subtracting all the molecular mechanics (MM) force-field components except for the Psi or Phi torsion angle. The Psi and Phi energy components extracted (hereafter called "the remaining energy components") were calculated for simple sugar models and plotted as functions of the Psi and Phi angles. The remaining energy component curves of Psi and Phi were well represented by the torsion force-field functions consisting of four and three cosine functions, respectively. To confirm the reliability of the force-field parameters and to confirm its compatibility with other force-fields, we calculated adiabatic potential curves as functions of Psi and Phi for the model glycosides by adopting the Psi and Phi force-field parameters obtained and by energetically optimizing other degrees of freedom. The MM potential energy curves obtained for Psi and Phi well represented the QM adiabatic curves and also these curves' differences with regard to the glycosidic oxygen and sulfur atoms. Our Psi and Phi force-fields of glycosidic oxygen gave MM potential energy curves that more closely represented the respective QM curves than did those of the recently developed GLYCAM force-field.

  15. Testing Linear Models for Ability Parameters in Item Response Models

    ERIC Educational Resources Information Center

    Glas, Cees A. W.; Hendrawan, Irene

    2005-01-01

    Methods for testing hypotheses concerning the regression parameters in linear models for the latent person parameters in item response models are presented. Three tests are outlined: A likelihood ratio test, a Lagrange multiplier test and a Wald test. The tests are derived in a marginal maximum likelihood framework. They are explicitly formulated…

  16. Computer simulation of liquid cesium using embedded atom model

    NASA Astrophysics Data System (ADS)

    Belashchenko, D. K.; Nikitin, N. Yu

    2008-02-01

    The new method is presented for the inventing an embedded atom potential (EAM potential) for liquid metals. This method uses directly the pair correlation function (PCF) of the liquid metal near the melting temperature. Because of the specific analytic form of this EAM potential, the pair term of potential can be calculated using the pair correlation function and, for example, Schommers algorithm. Other parameters of EAM potential may be found using the potential energy, module of compression and pressure at some conditions, mainly near the melting temperature, at very high temperature or in strongly compressed state. We used the simple exponential formula for effective EAM electronic density and a polynomial series for embedding energy. Molecular dynamics method was applied with L. Verlet algorithm. A series of models with 1968 atoms in the basic cube was constructed in temperature interval 323-1923 K. The thermodynamic properties of liquid cesium, structure data and self-diffusion coefficients are calculated. In general, agreement between the model data and known experimental ones is reasonable. The evaluation is given for the critical temperature of cesium models with EAM potential.

  17. Modelling affect in terms of speech parameters.

    PubMed

    Stassen, H H

    1988-01-01

    It is well known that the human voice contains important information about the affective state of a speaker at a nonverbal level. Accordingly, we started an extensive investigation which aims at modelling intraindividual changes of the global affective state over time, as this state is reflected by the human voice, and can be inferred from measurable speech parameters. For the purpose of this investigation, a speech-recording procedure was designed which is especially suited to reveal intraindividual changes of voice patterns over time since each person serves as his or her own reference. On the other hand, the chosen experimental setup is less suited to classify patients in the sense of a traditional diagnostic scheme. In order to find an appropriate mathematical model on the basis of speech parameters, a calibration study with 190 healthy subjects was carried out which enabled us to investigate each parameter for its reproducibility, sensitivity and specificity. In particular, this calibration study yielded the information of how to draw the line between 'normal' fluctuations and 'significant' intraindividual changes over time. All speech parameters under discussion turned out to be sufficiently stable over time, whereas, in regard to their sensitivity to form and content of text, significant differences showed up. In a second step, a pilot study with 6 depressive patients was carried out in order to investigate the specificity of voice parameters with regard to psychopathology. It turned out that the registration procedure is realizable even if patients are considerably handicapped by their illness. However, no consistent correlations could be revealed between single speech parameters and psychopathological rating scales.(ABSTRACT TRUNCATED AT 250 WORDS)

  18. Modelling spin Hamiltonian parameters of molecular nanomagnets.

    PubMed

    Gupta, Tulika; Rajaraman, Gopalan

    2016-07-12

    Molecular nanomagnets encompass a wide range of coordination complexes possessing several potential applications. A formidable challenge in realizing these potential applications lies in controlling the magnetic properties of these clusters. Microscopic spin Hamiltonian (SH) parameters describe the magnetic properties of these clusters, and viable ways to control these SH parameters are highly desirable. Computational tools play a proactive role in this area, where SH parameters such as isotropic exchange interaction (J), anisotropic exchange interaction (Jx, Jy, Jz), double exchange interaction (B), zero-field splitting parameters (D, E) and g-tensors can be computed reliably using X-ray structures. In this feature article, we have attempted to provide a holistic view of the modelling of these SH parameters of molecular magnets. The determination of J includes various class of molecules, from di- and polynuclear Mn complexes to the {3d-Gd}, {Gd-Gd} and {Gd-2p} class of complexes. The estimation of anisotropic exchange coupling includes the exchange between an isotropic metal ion and an orbitally degenerate 3d/4d/5d metal ion. The double-exchange section contains some illustrative examples of mixed valance systems, and the section on the estimation of zfs parameters covers some mononuclear transition metal complexes possessing very large axial zfs parameters. The section on the computation of g-anisotropy exclusively covers studies on mononuclear Dy(III) and Er(III) single-ion magnets. The examples depicted in this article clearly illustrate that computational tools not only aid in interpreting and rationalizing the observed magnetic properties but possess the potential to predict new generation MNMs. PMID:27366794

  19. Constant-parameter capture-recapture models

    USGS Publications Warehouse

    Brownie, C.; Hines, J.E.; Nichols, J.D.

    1986-01-01

    Jolly (1982, Biometrics 38, 301-321) presented modifications of the Jolly-Seber model for capture-recapture data, which assume constant survival and/or capture rates. Where appropriate, because of the reduced number of parameters, these models lead to more efficient estimators than the Jolly-Seber model. The tests to compare models given by Jolly do not make complete use of the data, and we present here the appropriate modifications, and also indicate how to carry out goodness-of-fit tests which utilize individual capture history information. We also describe analogous models for the case where young and adult animals are tagged. The availability of computer programs to perform the analysis is noted, and examples are given using output from these programs.

  20. Independent-particle models for light negative atomic ions

    NASA Technical Reports Server (NTRS)

    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.

  1. Kane model parameters and stochastic spin current

    NASA Astrophysics Data System (ADS)

    Chowdhury, Debashree

    2015-11-01

    The spin current and spin conductivity is computed through thermally driven stochastic process. By evaluating the Kramers equation and with the help of k → . p → method we have studied the spin Hall scenario. Due to the thermal assistance, the Kane model parameters get modified, which consequently modulate the spin orbit coupling (SOC). This modified SOC causes the spin current to change in a finite amount.

  2. Perturbed atoms in molecules and solids: The PATMOS model.

    PubMed

    Røeggen, Inge; Gao, Bin

    2013-09-01

    A new computational method for electronic-structure studies of molecules and solids is presented. The key element in the new model - denoted the perturbed atoms in molecules and solids model - is the concept of a perturbed atom in a complex. The basic approximation of the new model is unrestricted Hartree Fock (UHF). The UHF orbitals are localized by the Edmiston-Ruedenberg procedure. The perturbed atoms are defined by distributing the orbitals among the nuclei in such a way that the sum of the intra-atomic UHF energies has a minimum. Energy corrections with respect to the UHF energy, are calculated within the energy incremental scheme. The most important three- and four-electron corrections are selected by introducing a modified geminal approach. Test calculations are performed on N2, Li2, and parallel arrays of hydrogen atoms. The character of the perturbed atoms is illustrated by calculations on H2, CH4, and C6H6.

  3. Atomic level modeling of the HIV capsid

    PubMed Central

    Pornillos, Owen; Ganser-Pornillos, Barbie K.; Yeager, Mark

    2010-01-01

    The mature capsids of human immunodeficiency virus type 1 (HIV-1) and other retroviruses are fullerene shells, composed of the viral CA protein, that enclose the viral genome and facilitate its delivery into new host cells1. Retroviral CA proteins contain independently-folded N-terminal and C-terminal domains (NTD and CTD) that are connected by a flexible linker2–4. The NTD forms either hexameric or pentameric rings, whereas the CTD forms symmetric homodimers that connect the rings into a hexagonal lattice3,5–13. We previously used a disulfide crosslinking strategy to enable isolation and crystallization of soluble HIV-1 CA hexamers11,14. By the same approach, we have now determined the X-ray structure of the HIV-1 CA pentamer at 2.5 Å resolution. Two mutant CA proteins with engineered disulfides at different positions (P17C/T19C and N21C/A22C) converged onto the same quaternary structure, indicating that the disulfide-crosslinked proteins recapitulate the structure of the native pentamer. Assembly of the quasi-equivalent hexamers and pentamers requires remarkably subtle rearrangements in subunit interactions, and appears to be controlled by an electrostatic switch that favors hexamers over pentamers. This study completes the gallery of sub-structures describing the components of the HIV-1 capsid and enables atomic level modeling of the complete capsid. Rigid-body rotations around two assembly interfaces appear sufficient to generate the full range of continuously varying lattice curvature in the fullerene cone. PMID:21248851

  4. Monte Carlo Computational Modeling of the Energy Dependence of Atomic Oxygen Undercutting of Protected Polymers

    NASA Technical Reports Server (NTRS)

    Banks, Bruce A.; Stueber, Thomas J.; Norris, Mary Jo

    1998-01-01

    A Monte Carlo computational model has been developed which simulates atomic oxygen attack of protected polymers at defect sites in the protective coatings. The parameters defining how atomic oxygen interacts with polymers and protective coatings as well as the scattering processes which occur have been optimized to replicate experimental results observed from protected polyimide Kapton on the Long Duration Exposure Facility (LDEF) mission. Computational prediction of atomic oxygen undercutting at defect sites in protective coatings for various arrival energies was investigated. The atomic oxygen undercutting energy dependence predictions enable one to predict mass loss that would occur in low Earth orbit, based on lower energy ground laboratory atomic oxygen beam systems. Results of computational model prediction of undercut cavity size as a function of energy and defect size will be presented to provide insight into expected in-space mass loss of protected polymers with protective coating defects based on lower energy ground laboratory testing.

  5. "Piekara's Chair": Mechanical Model for Atomic Energy Levels.

    ERIC Educational Resources Information Center

    Golab-Meyer, Zofia

    1991-01-01

    Uses the teaching method of models or analogies, specifically the model called "Piekara's chair," to show how teaching classical mechanics can familiarize students with the notion of energy levels in atomic physics. (MDH)

  6. Proposed reference models for atomic oxygen in the terrestrial atmosphere

    NASA Technical Reports Server (NTRS)

    Llewellyn, E. J.; Mcdade, I. C.; Lockerbie, M. D.

    1989-01-01

    A provisional Atomic Oxygen Reference model was derived from average monthly ozone profiles and the MSIS-86 reference model atmosphere. The concentrations are presented in tabular form for the altitude range 40 to 130 km.

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

    ERIC Educational Resources Information Center

    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)

  8. Model of spacecraft atomic oxygen and solar exposure microenvironments

    NASA Technical Reports Server (NTRS)

    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.

  9. Developing Models: What is the Atom Really Like?

    ERIC Educational Resources Information Center

    Records, Roger M.

    1982-01-01

    Five atomic theory activities feasible for high school students to perform are described based on the following models: (1) Dalton's Uniform Sphere Model; (2) Thomson's Raisin Pudding Model; (3) Rutherford's Nuclear Model; (4) Bohr's Energy Level Model, and (5) Orbital Model from quantum mechanics. (SK)

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

    PubMed

    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. PMID:27420398

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

    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.

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

    SciTech Connect

    Hamad, Said 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.

  14. Early atomic models - from mechanical to quantum (1904-1913)

    NASA Astrophysics Data System (ADS)

    Baily, C.

    2013-01-01

    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 qualitative 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 α-particles being studied by Rutherford were better suited for exploring the interior of the atom, and careful measurements on the angular dependence of their scattering eventually allowed him to infer the existence of an atomic nucleus. Niels Bohr was particularly troubled by the radiative instability inherent to any mechanical atom, and succeeded in 1913 where others had failed in the prediction of emission spectra, by making two bold hypotheses that were in contradiction to the laws of classical physics, but necessary in order to account for experimental facts.

  15. Parameter optimization in S-system models

    PubMed Central

    Vilela, Marco; Chou, I-Chun; Vinga, Susana; Vasconcelos, Ana Tereza R; Voit, Eberhard O; Almeida, Jonas S

    2008-01-01

    Background The inverse problem of identifying the topology of biological networks from their time series responses is a cornerstone challenge in systems biology. We tackle this challenge here through the parameterization of S-system models. It was previously shown that parameter identification can be performed as an optimization based on the decoupling of the differential S-system equations, which results in a set of algebraic equations. Results A novel parameterization solution is proposed for the identification of S-system models from time series when no information about the network topology is known. The method is based on eigenvector optimization of a matrix formed from multiple regression equations of the linearized decoupled S-system. Furthermore, the algorithm is extended to the optimization of network topologies with constraints on metabolites and fluxes. These constraints rejoin the system in cases where it had been fragmented by decoupling. We demonstrate with synthetic time series why the algorithm can be expected to converge in most cases. Conclusion A procedure was developed that facilitates automated reverse engineering tasks for biological networks using S-systems. The proposed method of eigenvector optimization constitutes an advancement over S-system parameter identification from time series using a recent method called Alternating Regression. The proposed method overcomes convergence issues encountered in alternate regression by identifying nonlinear constraints that restrict the search space to computationally feasible solutions. Because the parameter identification is still performed for each metabolite separately, the modularity and linear time characteristics of the alternating regression method are preserved. Simulation studies illustrate how the proposed algorithm identifies the correct network topology out of a collection of models which all fit the dynamical time series essentially equally well. PMID:18416837

  16. Using a scalar parameter to trace dislocation evolution in atomistic modeling

    SciTech Connect

    Yang, Jinbo; Zhang, Z F; Osetskiy, Yury N; Stoller, Roger E

    2015-01-01

    A scalar gamma-parameter is proposed from the Nye tensor. Its maximum value occurs along a dislocation line, either straight or curved, when the coordinate system is purposely chosen. This parameter can be easily obtained from the Nye tensor calculated at each atom in atomistic modeling. Using the gamma-parameter, a fully automated approach is developed to determine core atoms and the Burgers vectors of dislocations simultaneously. The approach is validated by revealing the smallest dislocation loop and by tracing the whole formation process of complicated dislocation networks on the fly.

  17. Optimized modulation parameters for a two-dimensional magneto-optical trap for cold fermionic potassium atoms

    NASA Astrophysics Data System (ADS)

    Lee, Jae Hoon; Mun, Jongchul

    2016-05-01

    We study optimized parameters for a high flux atomic beam source for 40 K fermionic atoms from a frequency modulated two-dimensional magneto-optical trap (2D MOT). The laser cooling beam frequencies of the 2D MOT were effectively broadened via elecro-optical modulators at 10MHz with modulation depths β ranging up to 7, depending on the laser intensity. A two-color pushing laser beam was also implemented for an asymmetrically directed atomic beam source. All laser parameters of the 2D MOT beams along with the magnetic field gradient were scanned for optimal atomic flux. With the added modulation, we were able to obtain 4 times enhancement of the atomic flux which was limited by the applied laser power. This work is supported by KRISS Creative Research Initiative.

  18. Moose models with vanishing S parameter

    SciTech Connect

    Casalbuoni, R.; De Curtis, S.; Dominici, D.

    2004-09-01

    In the linear moose framework, which naturally emerges in deconstruction models, we show that there is a unique solution for the vanishing of the S parameter at the lowest order in the weak interactions. We consider an effective gauge theory based on K SU(2) gauge groups, K+1 chiral fields, and electroweak groups SU(2){sub L} and U(1){sub Y} at the ends of the chain of the moose. S vanishes when a link in the moose chain is cut. As a consequence one has to introduce a dynamical nonlocal field connecting the two ends of the moose. Then the model acquires an additional custodial symmetry which protects this result. We examine also the possibility of a strong suppression of S through an exponential behavior of the link couplings as suggested by the Randall Sundrum metric.

  19. Model parameters for simulation of physiological lipids

    PubMed Central

    McGlinchey, Nicholas

    2016-01-01

    Coarse grain simulation of proteins in their physiological membrane environment can offer insight across timescales, but requires a comprehensive force field. Parameters are explored for multicomponent bilayers composed of unsaturated lipids DOPC and DOPE, mixed‐chain saturation POPC and POPE, and anionic lipids found in bacteria: POPG and cardiolipin. A nonbond representation obtained from multiscale force matching is adapted for these lipids and combined with an improved bonding description of cholesterol. Equilibrating the area per lipid yields robust bilayer simulations and properties for common lipid mixtures with the exception of pure DOPE, which has a known tendency to form nonlamellar phase. The models maintain consistency with an existing lipid–protein interaction model, making the force field of general utility for studying membrane proteins in physiologically representative bilayers. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26864972

  20. 100th anniversary of Bohr's model of the atom.

    PubMed

    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.

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

    ERIC Educational Resources Information Center

    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,…

  2. 100th anniversary of Bohr's model of the atom.

    PubMed

    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. PMID:24123759

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

    PubMed

    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.

  4. Modeling of atom-diatom scattering. Technical report

    SciTech Connect

    Sindoni, J.M.

    1992-05-30

    This report entails the work performed on modeling atom-diatom scattering processes utilizing the Impulse Approach (IA). Results of the model, obtained with a computer code, have proven to be in remarkable agreement with laboratory measurements for several atom-diatom scattering systems. Two scattering systems, in particular, that were successfully modeled and compared to measurements were Ar-KBr and Ar-CsF. The IA model provided an explanation for the rapid deactivation evident in the Ar-KBr system. Experimental results in the Ar-CsF experiment that could not be explained by conventional models were also successfully modeled using the IA. Results fit the experimental observations.

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

    NASA Technical Reports Server (NTRS)

    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.

  6. Multiscale modeling of failure in composites under model parameter uncertainty

    NASA Astrophysics Data System (ADS)

    Bogdanor, Michael J.; Oskay, Caglar; Clay, Stephen B.

    2015-09-01

    This manuscript presents a multiscale stochastic failure modeling approach for fiber reinforced composites. A homogenization based reduced-order multiscale computational model is employed to predict the progressive damage accumulation and failure in the composite. Uncertainty in the composite response is modeled at the scale of the microstructure by considering the constituent material (i.e., matrix and fiber) parameters governing the evolution of damage as random variables. Through the use of the multiscale model, randomness at the constituent scale is propagated to the scale of the composite laminate. The probability distributions of the underlying material parameters are calibrated from unidirectional composite experiments using a Bayesian statistical approach. The calibrated multiscale model is exercised to predict the ultimate tensile strength of quasi-isotropic open-hole composite specimens at various loading rates. The effect of random spatial distribution of constituent material properties on the composite response is investigated.

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

    PubMed

    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.

  8. Silicone hydrogel contact lens surface analysis by atomic force microscopy: shape parameters

    NASA Astrophysics Data System (ADS)

    Giraldez, M. J.; Garcia-Resua, C.; Lira, M.; Sánchez-Sellero, C.; Yebra-Pimentel, E.

    2011-05-01

    Purpose: Average roughness (Ra) is generally used to quantify roughness; however it makes no distinction between spikes and troughs. Shape parameters as kurtosis (Rku) and skewness (Rsk) serve to distinguish between two profiles with the same Ra. They have been reported in many biomedical fields, but they were no applied to contact lenses before. The aim of this study is to analyze surface properties of four silicone hydrogel contact lenses (CL) by Atomic Force Microscopy (AFM) evaluating Ra, Rku and Rsk. Methods: CL used in this study were disposable silicone hydrogel senofilcon A, comfilcon A, balafilcon A and lotrafilcon B. Unworn CL surfaces roughness and topography were measured by AFM (Veeco, multimode-nanoscope V) in tapping modeTM. Ra, Rku and Rsk for 25 and 196 μm2 areas were determined. Results: Surface topography and parameters showed different characteristics depending on the own nature of the contact lens (Ra/Rku/Rsk for 25 and 196 μm2 areas were: senofilcon A 3,33/3,74/0,74 and 3,76/18,16/1,75; comfilcon A: 1,56/31,09/2,93 and 2,76/45,82/3,60; balafilcon A: 2,01/33,62/-2,14 and 2,54/23,36/-1,96; lotrafilcon B: 26,97/4,11/-0,34 and 29,25/2,82/-0,23). In lotrafilcon B, with the highest Ra, Rku showed a lower degree of peakedness of its distribution. Negative Rsk value obtained for balafilcon A showed a clear predominance of valleys in this lens. Conclusions: Kku and Rsk are two statistical parameters useful to analyse CL surfaces, which complete information from Ra. Differences in values distribution and symmetry were observed between CL.

  9. Fixing the c Parameter in the Three-Parameter Logistic Model

    ERIC Educational Resources Information Center

    Han, Kyung T.

    2012-01-01

    For several decades, the "three-parameter logistic model" (3PLM) has been the dominant choice for practitioners in the field of educational measurement for modeling examinees' response data from multiple-choice (MC) items. Past studies, however, have pointed out that the c-parameter of 3PLM should not be interpreted as a guessing parameter. This…

  10. Problems associated with the measurement of coherence parameters - Superelastic electron scattering by laser-excited Ba-138(...6s6p1P1) atoms

    NASA Technical Reports Server (NTRS)

    Zetner, P. W.; Trajmar, S.; Csanak, G.; Clark, R. E. H.

    1989-01-01

    Measurements of superelastic scattering of electrons by laser-excited Ba-138(...6s6p1P1) atoms were carried out. An asymmetry observed has been explained using a model of scattering from a target with finite dimensions. This model employed coherence parameters which were calculated in the distorted-wave approximation. The results indicated that the interpretation of coherence experiments in terms of scattering from a pointlike target can lead to serious errors in the deduction of coherence parameters at low scattering angles.

  11. Tokamak plasma modelling and atomic processes

    NASA Astrophysics Data System (ADS)

    Kawamura, T.

    1986-06-01

    Topics addressed include: particle control in a tokomak device; ionizing and recombining plasmas; effects of data accuracy on tokamak impurity transport modeling; plasma modeling of tokamaks; and ultraviolet and X-ray spectroscopy of tokamak plasmas.

  12. Transferable Atomic Multipole Machine Learning Models for Small Organic Molecules.

    PubMed

    Bereau, Tristan; Andrienko, Denis; von Lilienfeld, O Anatole

    2015-07-14

    Accurate representation of the molecular electrostatic potential, which is often expanded in distributed multipole moments, is crucial for an efficient evaluation of intermolecular interactions. Here we introduce a machine learning model for multipole coefficients of atom types H, C, O, N, S, F, and Cl in any molecular conformation. The model is trained on quantum-chemical results for atoms in varying chemical environments drawn from thousands of organic molecules. Multipoles in systems with neutral, cationic, and anionic molecular charge states are treated with individual models. The models' predictive accuracy and applicability are illustrated by evaluating intermolecular interaction energies of nearly 1,000 dimers and the cohesive energy of the benzene crystal.

  13. Atomic Models of Strong Solids Interfaces Viewed as Composite Structures

    NASA Astrophysics Data System (ADS)

    Staffell, I.; Shang, J. L.; Kendall, K.

    2014-02-01

    This paper looks back through the 1960s to the invention of carbon fibres and the theories of Strong Solids. In particular it focuses on the fracture mechanics paradox of strong composites containing weak interfaces. From Griffith theory, it is clear that three parameters must be considered in producing a high strength composite:- minimising defects; maximising the elastic modulus; and raising the fracture energy along the crack path. The interface then introduces two further factors:- elastic modulus mismatch causing crack stopping; and debonding along a brittle interface due to low interface fracture energy. Consequently, an understanding of the fracture energy of a composite interface is needed. Using an interface model based on atomic interaction forces, it is shown that a single layer of contaminant atoms between the matrix and the reinforcement can reduce the interface fracture energy by an order of magnitude, giving a large delamination effect. The paper also looks to a future in which cars will be made largely from composite materials. Radical improvements in automobile design are necessary because the number of cars worldwide is predicted to double. This paper predicts gains in fuel economy by suggesting a new theory of automobile fuel consumption using an adaptation of Coulomb's friction law. It is demonstrated both by experiment and by theoretical argument that the energy dissipated in standard vehicle tests depends only on weight. Consequently, moving from metal to fibre construction can give a factor 2 improved fuel economy performance, roughly the same as moving from a petrol combustion drive to hydrogen fuel cell propulsion. Using both options together can give a factor 4 improvement, as demonstrated by testing a composite car using the ECE15 protocol.

  14. Atomic hydrogen distribution. [in Titan atmospheric model

    NASA Technical Reports Server (NTRS)

    Tabarie, N.

    1974-01-01

    Several possible H2 vertical distributions in Titan's atmosphere are considered with the constraint of 5 km-A a total quantity. Approximative calculations show that hydrogen distribution is quite sensitive to two other parameters of Titan's atmosphere: the temperature and the presence of other constituents. The escape fluxes of H and H2 are also estimated as well as the consequent distributions trapped in the Saturnian system.

  15. Nagaoka’s atomic model and hyperfine interactions

    PubMed Central

    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

  16. Transfer function modeling of damping mechanisms in distributed parameter models

    NASA Technical Reports Server (NTRS)

    Slater, J. C.; Inman, D. J.

    1994-01-01

    This work formulates a method for the modeling of material damping characteristics in distributed parameter models which may be easily applied to models such as rod, plate, and beam equations. The general linear boundary value vibration equation is modified to incorporate hysteresis effects represented by complex stiffness using the transfer function approach proposed by Golla and Hughes. The governing characteristic equations are decoupled through separation of variables yielding solutions similar to those of undamped classical theory, allowing solution of the steady state as well as transient response. Example problems and solutions are provided demonstrating the similarity of the solutions to those of the classical theories and transient responses of nonviscous systems.

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

    PubMed

    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.

  18. Parameter sensitivity analysis of nonlinear piezoelectric probe in tapping mode atomic force microscopy for measurement improvement

    SciTech Connect

    McCarty, Rachael; Nima Mahmoodi, S.

    2014-02-21

    The equations of motion for a piezoelectric microcantilever are derived for a nonlinear contact force. The analytical expressions for natural frequencies and mode shapes are obtained. Then, the method of multiple scales is used to analyze the analytical frequency response of the piezoelectric probe. The effects of nonlinear excitation force on the microcantilever beam's frequency and amplitude are analytically studied. The results show a frequency shift in the response resulting from the force nonlinearities. This frequency shift during contact mode is an important consideration in the modeling of AFM mechanics for generation of more accurate imaging. Also, a sensitivity analysis of the system parameters on the nonlinearity effect is performed. The results of a sensitivity analysis show that it is possible to choose parameters such that the frequency shift minimizes. Certain parameters such as tip radius, microcantilever beam dimensions, and modulus of elasticity have more influence on the nonlinearity of the system than other parameters. By changing only three parameters—tip radius, thickness, and modulus of elasticity of the microbeam—a more than 70% reduction in nonlinearity effect was achieved.

  19. Surface Adsorption in Nonpolarizable Atomic Models.

    PubMed

    Whitmer, Jonathan K; Joshi, Abhijeet A; Carlton, Rebecca J; Abbott, Nicholas L; de Pablo, Juan J

    2014-12-01

    Many ionic solutions exhibit species-dependent properties, including surface tension and the salting-out of proteins. These effects may be loosely quantified in terms of the Hofmeister series, first identified in the context of protein solubility. Here, our interest is to develop atomistic models capable of capturing Hofmeister effects rigorously. Importantly, we aim to capture this dependence in computationally cheap "hard" ionic models, which do not exhibit dynamic polarization. To do this, we have performed an investigation detailing the effects of the water model on these properties. Though incredibly important, the role of water models in simulation of ionic solutions and biological systems is essentially unexplored. We quantify this via the ion-dependent surface attraction of the halide series (Cl, Br, I) and, in so doing, determine the relative importance of various hypothesized contributions to ionic surface free energies. Importantly, we demonstrate surface adsorption can result in hard ionic models combined with a thermodynamically accurate representation of the water molecule (TIP4Q). The effect observed in simulations of iodide is commensurate with previous calculations of the surface potential of mean force in rigid molecular dynamics and polarizable density-functional models. Our calculations are direct simulation evidence of the subtle but sensitive role of water thermodynamics in atomistic simulations.

  20. Fast Three-Dimensional Method of Modeling Atomic Oxygen Undercutting of Protected Polymers

    NASA Technical Reports Server (NTRS)

    Snyder, Aaron; Banks, Bruce A.

    2002-01-01

    A method is presented to model atomic oxygen erosion of protected polymers in low Earth orbit (LEO). Undercutting of protected polymers by atomic oxygen occurs in LEO due to the presence of scratch, crack or pin-window defects in the protective coatings. As a means of providing a better understanding of undercutting processes, a fast method of modeling atomic-oxygen undercutting of protected polymers has been developed. Current simulation methods often rely on computationally expensive ray-tracing procedures to track the surface-to-surface movement of individual "atoms." The method introduced in this paper replaces slow individual particle approaches by substituting a model that utilizes both a geometric configuration-factor technique, which governs the diffuse transport of atoms between surfaces, and an efficient telescoping series algorithm, which rapidly integrates the cumulative effects stemming from the numerous atomic oxygen events occurring at the surfaces of an undercut cavity. This new method facilitates the systematic study of three-dimensional undercutting by allowing rapid simulations to be made over a wide range of erosion parameters.

  1. Optimization of a hydride generation metallic furnace atomic absorption spectrometry (HG-MF-AAS) method for tin determination: analytical and morphological parameters of a metallic atomizer.

    PubMed

    Moretto Galazzi, Rodrigo; Arruda, Marco Aurélio Zezzi

    2013-12-15

    The present work describes a metallic tube as hydride atomizer for atomic absorption spectrometry. Its performance is evaluated through tin determination, and the accuracy of the method assessed through the analysis of sediment and water samples. Some chemical parameters (referring to the generation of the hydride) such as acid, NaOH and THB concentrations, as well as physical parameters (referring to the transport of the hydride) such as carrier, acetylene, air flow-rates, flame composition, coil length, tube hole area, among others, are evaluated for optimization of the method. Scanning electron microscopy is used for evaluating morphological parameters in both new and used (after 150 h) tube atomizers. The method presents linear Sn concentration from 50 to 1000 µg L(-1) (r>0.9995; n=3) and the analytical frequency of ca. 40 h(-1). The limit of detection (LOD) is 7.1 µg L(-1) and the precision, expressed as RSD is less than 4% (200 µg L(-1); n=10). The accuracy is evaluated through reference materials, and the results are similar at 95% confidence level according to the t-test.

  2. Determination of the width of the absorption line of atomic iodine in optimization of the parameters of an iodine switch

    SciTech Connect

    Eroshenko, V.A.; Kirillov, G.A.; Mochalov, M.R.; Shemyakin, V.I.; Shurygin, V.K.

    1981-09-01

    A theoretical basis is given for the optimization of the parameters of an iodine switch. The results are reported of an experimental study of the pressure dependence of the width of the absorption line of atomic iodine. The broadening coefficient of molecular iodine is 3.2 MHz/Torr in the temperature range 800--1000 /sup 0/C.

  3. Physically representative atomistic modeling of atomic-scale friction

    NASA Astrophysics Data System (ADS)

    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

  4. Modeling of Turbulence Effects on Liquid Jet Atomization and Breakup

    NASA Technical Reports Server (NTRS)

    Trinh, Huu; Chen, C. P.

    2004-01-01

    Recent experimental investigations and physical modeling studies have indicated that turbulence behaviors within a liquid jet have considerable effects on the atomization process. For certain flow regimes, it has been observed that the liquid jet surface is highly turbulent. This turbulence characteristic plays a key role on the breakup of the liquid jet near to the injector exit. Other experiments also showed that the breakup length of the liquid core is sharply shortened as the liquid jet is changed from the laminar to the turbulent flow conditions. In the numerical and physical modeling arena, most of commonly used atomization models do not include the turbulence effect. Limited attempts have been made in modeling the turbulence phenomena on the liquid jet disintegration. The subject correlation and models treat the turbulence either as an only source or a primary driver in the breakup process. This study aims to model the turbulence effect in the atomization process of a cylindrical liquid jet. In the course of this study, two widely used models, Reitz's primary atomization (blob) and Taylor-Analogy-Break (TAB) secondary droplet breakup by O Rourke et al. are examined. Additional terms are derived and implemented appropriately into these two models to account for the turbulence effect on the atomization process. Since this enhancement effort is based on a framework of the two existing atomization models, it is appropriate to denote the two present models as T-blob and T-TAB for the primary and secondary atomization predictions, respectively. In the primary breakup model, the level of the turbulence effect on the liquid breakup depends on the characteristic time scales and the initial flow conditions. This treatment offers a balance of contributions of individual physical phenomena on the liquid breakup process. For the secondary breakup, an addition turbulence force acted on parent drops is modeled and integrated into the TAB governing equation. The drop size

  5. Atomic-scale modeling of cellulose nanocrystals

    NASA Astrophysics Data System (ADS)

    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

  6. Comparisons of selected methods for the determination of kinetic parameters from electrothermal atomic absorption data

    NASA Astrophysics Data System (ADS)

    Fonseca, Rodney W.; Pfefferkorn, Lisa L.; Holcombe, James A.

    1994-12-01

    Three of the methods available for the determination of kinetic parameters for atom formation in ETAAS were compared. In the approach of mcnally and holcombe [ Anal. Chem. 59, 1015 (1987)], Arrhenius-type plots are used to extract activation energy values while an approximation of the order of release is obtained by studying the alignment of the absorption maxima at increasing analyte concentrations. In the method of rojas and olivares [ Spectrochim. Acta47B, 387 (1992)], plots are prepared for different orders of release, with the correct order yielding a longer linear region from whose slope the activation energy is calculated. The method of yan et al. [ Spectrochim. Acta48B, 605 (1993)] uses a single absorption profile for the calculations. Activation energy and the order of release are obtained from the slope and intercept, respectively, on their graph. All three methods assume linear heating rate, constant activation energies, and furnace isothermality. The methods were tested with the same experimental data sets for Cu, Au and Ni using a spatially isothermal cuvette. Since intensive mathematical treatments commonly have deleterious effects on the uncertainty of the final result, the methods were compared using both the original data and a smoothed version of it. In general, the three methods yielded comparable results for the metals studied. However, choosing the most linear plot to determine the correct order of release when using Rojas and Olivares' method was sometimes subjective, and McNally and Holcombe's method provided only estimates for the orders of release that were neither zero nor unity.

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

    NASA Technical Reports Server (NTRS)

    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.

  8. Parameter Estimates in Differential Equation Models for Chemical Kinetics

    ERIC Educational Resources Information Center

    Winkel, Brian

    2011-01-01

    We discuss the need for devoting time in differential equations courses to modelling and the completion of the modelling process with efforts to estimate the parameters in the models using data. We estimate the parameters present in several differential equation models of chemical reactions of order n, where n = 0, 1, 2, and apply more general…

  9. A model to predict image formation in Atom probe Tomography.

    PubMed

    Vurpillot, F; Gaillard, A; Da Costa, G; Deconihout, B

    2013-09-01

    A model devoted to the modelling of the field evaporation of a tip is presented in this paper. The influence of length scales from the atomic scale to the macroscopic scale is taken into account in this approach. The evolution of the tip shape is modelled at the atomic scale in a three dimensional geometry with cylindrical symmetry. The projection law of ions is determined using a realistic representation of the tip geometry including the presence of electrodes in the surrounding area of the specimen. This realistic modelling gives a direct access to the voltage required to field evaporate, to the evolving magnification in the microscope and to the understanding of reconstruction artefacts when the presence of phases with different evaporation fields and/or different dielectric permittivity constants are modelled. This model has been applied to understand the field evaporation behaviour in bulk dielectric materials. In particular the role of the residual conductivity of dielectric materials is addressed.

  10. Model based control of dynamic atomic force microscope

    SciTech Connect

    Lee, Chibum; Salapaka, Srinivasa M.

    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.

  11. Model based control of dynamic atomic force microscope.

    PubMed

    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.

  12. Stokes parameters of resonance lines scattered by a moving, magnetic medium. Theory of the two-level atom

    NASA Astrophysics Data System (ADS)

    Raouafi, N.-E.

    2002-05-01

    The aim of the present work is to present theoretical results on the Stokes parameters of a resonance spectral line, scattered by moving atoms (or ions) in the presence of a local magnetic field. We assume that the scattered line is sensitive to the Hanle effect due to the magnetic field and also to Doppler redistribution due to the atomic motions. The present theory is developed for a two-level atom, in the framework of the density matrix formalism Blum (1981). Analogous results given in Sahal-Bréchot et al. (1986) for the magnetic-field effect alone, and in Sahal-Bréchot et al. (\\cite{Sahal98}) for the velocity-field effect alone, can be obtained from our theory by cancelling in the equations, respectively, the velocity field or the magnetic field. The results of our theory are general and can be used for astrophysical studies concerning the Hanle effect and the Doppler redistribution effect on the linear polarization parameters of the scattered radiation. They can be used particularly to interpret linear polarization of coronal spectral lines to get a complete determination of vectorial quantities such as the coronal magnetic field and the solar wind velocity field vectors. As an application, the atomic velocity field distribution is supposed to be Maxwellian with a drift velocity field vector. This latter describes the macroscopic motion of the scattering atoms. In the solar corona, it can be assimilated into the solar wind velocity field vector.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  14. Learning atomic human actions using variable-length Markov models.

    PubMed

    Liang, Yu-Ming; Shih, Sheng-Wen; Shih, Arthur Chun-Chieh; Liao, Hong-Yuan Mark; Lin, Cheng-Chung

    2009-02-01

    Visual analysis of human behavior has generated considerable interest in the field of computer vision because of its wide spectrum of potential applications. Human behavior can be segmented into atomic actions, each of which indicates a basic and complete movement. Learning and recognizing atomic human actions are essential to human behavior analysis. In this paper, we propose a framework for handling this task using variable-length Markov models (VLMMs). The framework is comprised of the following two modules: a posture labeling module and a VLMM atomic action learning and recognition module. First, a posture template selection algorithm, based on a modified shape context matching technique, is developed. The selected posture templates form a codebook that is used to convert input posture sequences into discrete symbol sequences for subsequent processing. Then, the VLMM technique is applied to learn the training symbol sequences of atomic actions. Finally, the constructed VLMMs are transformed into hidden Markov models (HMMs) for recognizing input atomic actions. This approach combines the advantages of the excellent learning function of a VLMM and the fault-tolerant recognition ability of an HMM. Experiments on realistic data demonstrate the efficacy of the proposed system.

  15. Atmospheric turbulence optical model (ATOM) based on fractal theory

    NASA Astrophysics Data System (ADS)

    Jaenisch, Holger M.; Handley, James W.; Scoggins, Jim; Carroll, Marvin P.

    1994-06-01

    An Atmospheric Turbulence Optical Model (ATOM) is presented that used cellular automata (CA) rules as the basis for modeling synthetic phase sheets. This method allows image fracture, scintillation and blur to be correctly models using the principle of convolution with a complex kernel derived from CA rules interaction. The model takes into account the changing distribution of turbules from micro-turbule domination at low altitudes to macro-domination at high altitudes. The wavelength of propagating images (such as a coherent laser beam) and the range are taken into account. The ATOM model is written in standard FORTRAN 77 and enables high-speed in-line calculation of atmospheric effects to be performed without resorting to computationally intensive solutions of Navier Stokes equations or Cn2 profiles.

  16. Measurement of atomic Stark parameters of many Mn I and Fe I spectral lines using GMAW process

    NASA Astrophysics Data System (ADS)

    Zielinska, S.; Pellerin, S.; Dzierzega, K.; Valensi, F.; Musiol, K.; Briand, F.

    2010-11-01

    The particular character of the welding arc working in pure argon, whose emission spectrum consists of many spectral lines strongly broadened by the Stark effect, has allowed measurement, sometimes for the first time, of the Stark parameters of 15 Mn I and 10 Fe I atomic spectral lines, and determination of the dependence on temperature of normalized Stark broadening in Ne = 1023 m-3 of the 542.4 nm atomic iron line. These results show that special properties of the MIG plasma may be useful in this domain because composition of the wire-electrode may be easily adapted to the needs of an experiment.

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

    PubMed

    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.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    SciTech Connect

    Quan, Wei; Lv, Lin Liu, Baiqi

    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.

  1. ATOMIC DATA AND SPECTRAL MODEL FOR Fe III

    SciTech Connect

    Bautista, Manuel A.; Ballance, Connor P.; Quinet, Pascal

    2010-08-01

    We present new atomic data (radiative transitions rates and collision strengths) from large-scale calculations and a non-LTE spectral model for Fe III. This model is in very good agreement with observed astronomical emission spectra, in contrast with previous models that yield large discrepancies in observations. The present atomic computations employ a combination of atomic physics methods, e.g., relativistic Hartree-Fock, the Thomas-Fermi-Dirac potential, and Dirac-Fock computation of A-values and the R-matrix with intermediate coupling frame transformation and the Dirac R-matrix. We study advantages and shortcomings of each method. It is found that the Dirac R-matrix collision strengths yield excellent agreement with observations, much improved over previously available models. By contrast, the transformation of the LS-coupling R-matrix fails to yield accurate effective collision strengths at around 10{sup 4} K, despite using very large configuration expansions, due to the limited treatment of spin-orbit effects in the near-threshold resonances of the collision strengths. The present work demonstrates that accurate atomic data for low-ionization iron-peak species are now within reach.

  2. Parameter redundancy in discrete state‐space and integrated models

    PubMed Central

    McCrea, Rachel S.

    2016-01-01

    Discrete state‐space models are used in ecology to describe the dynamics of wild animal populations, with parameters, such as the probability of survival, being of ecological interest. For a particular parametrization of a model it is not always clear which parameters can be estimated. This inability to estimate all parameters is known as parameter redundancy or a model is described as nonidentifiable. In this paper we develop methods that can be used to detect parameter redundancy in discrete state‐space models. An exhaustive summary is a combination of parameters that fully specify a model. To use general methods for detecting parameter redundancy a suitable exhaustive summary is required. This paper proposes two methods for the derivation of an exhaustive summary for discrete state‐space models using discrete analogues of methods for continuous state‐space models. We also demonstrate that combining multiple data sets, through the use of an integrated population model, may result in a model in which all parameters are estimable, even though models fitted to the separate data sets may be parameter redundant. PMID:27362826

  3. Parameter redundancy in discrete state-space and integrated models.

    PubMed

    Cole, Diana J; McCrea, Rachel S

    2016-09-01

    Discrete state-space models are used in ecology to describe the dynamics of wild animal populations, with parameters, such as the probability of survival, being of ecological interest. For a particular parametrization of a model it is not always clear which parameters can be estimated. This inability to estimate all parameters is known as parameter redundancy or a model is described as nonidentifiable. In this paper we develop methods that can be used to detect parameter redundancy in discrete state-space models. An exhaustive summary is a combination of parameters that fully specify a model. To use general methods for detecting parameter redundancy a suitable exhaustive summary is required. This paper proposes two methods for the derivation of an exhaustive summary for discrete state-space models using discrete analogues of methods for continuous state-space models. We also demonstrate that combining multiple data sets, through the use of an integrated population model, may result in a model in which all parameters are estimable, even though models fitted to the separate data sets may be parameter redundant.

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

    PubMed

    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.

  5. Estimation Methods for One-Parameter Testlet Models

    ERIC Educational Resources Information Center

    Jiao, Hong; Wang, Shudong; He, Wei

    2013-01-01

    This study demonstrated the equivalence between the Rasch testlet model and the three-level one-parameter testlet model and explored the Markov Chain Monte Carlo (MCMC) method for model parameter estimation in WINBUGS. The estimation accuracy from the MCMC method was compared with those from the marginalized maximum likelihood estimation (MMLE)…

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

    SciTech Connect

    Santos, G.; Tonel, A.; Foerster, A.; Links, J.

    2006-02-15

    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.

  7. Seamless continental-domain hydrologic model parameter estimations with Multi-Scale Parameter Regionalization

    NASA Astrophysics Data System (ADS)

    Mizukami, Naoki; Clark, Martyn; Newman, Andrew; Wood, Andy

    2016-04-01

    Estimation of spatially distributed parameters is one of the biggest challenges in hydrologic modeling over a large spatial domain. This problem arises from methodological challenges such as the transfer of calibrated parameters to ungauged locations. Consequently, many current large scale hydrologic assessments rely on spatially inconsistent parameter fields showing patchwork patterns resulting from individual basin calibration or spatially constant parameters resulting from the adoption of default or a-priori estimates. In this study we apply the Multi-scale Parameter Regionalization (MPR) framework (Samaniego et al., 2010) to generate spatially continuous and optimized parameter fields for the Variable Infiltration Capacity (VIC) model over the contiguous United States(CONUS). The MPR method uses transfer functions that relate geophysical attributes (e.g., soil) to model parameters (e.g., parameters that describe the storage and transmission of water) at the native resolution of the geophysical attribute data and then scale to the model spatial resolution with several scaling functions, e.g., arithmetic mean, harmonic mean, and geometric mean. Model parameter adjustments are made by calibrating the parameters of the transfer function rather than the model parameters themselves. In this presentation, we first discuss conceptual challenges in a "model agnostic" continental-domain application of the MPR approach. We describe development of transfer functions for the soil parameters, and discuss challenges associated with extending MPR for VIC to multiple models. Next, we discuss the "computational shortcut" of headwater basin calibration where we estimate the parameters for only 500 headwater basins rather than conducting simulations for every grid box across the entire domain. We first performed individual basin calibration to obtain a benchmark of the maximum achievable performance in each basin, and examined their transferability to the other basins. We then

  8. Adjoint method for estimating Jiles-Atherton hysteresis model parameters

    NASA Astrophysics Data System (ADS)

    Zaman, Mohammad Asif; Hansen, Paul C.; Neustock, Lars T.; Padhy, Punnag; Hesselink, Lambertus

    2016-09-01

    A computationally efficient method for identifying the parameters of the Jiles-Atherton hysteresis model is presented. Adjoint analysis is used in conjecture with an accelerated gradient descent optimization algorithm. The proposed method is used to estimate the Jiles-Atherton model parameters of two different materials. The obtained results are found to be in good agreement with the reported values. By comparing with existing methods of model parameter estimation, the proposed method is found to be computationally efficient and fast converging.

  9. Exactly solvable models for atom-molecule Hamiltonians.

    PubMed

    Dukelsky, J; Dussel, G G; Esebbag, C; Pittel, S

    2004-07-30

    We present a family of exactly solvable generalizations of the Jaynes-Cummings model involving the interaction of an ensemble of SU(2) or SU(1,1) quasispins with a single boson field. They are obtained from the trigonometric Richardson-Gaudin models by replacing one of the SU(2) or SU(1,1) degrees of freedom by an ideal boson. The application to a system of bosonic atoms and molecules is reported.

  10. Atomic Data and Modelling for Fusion: the ADAS Project

    NASA Astrophysics Data System (ADS)

    Summers, H. P.; O'Mullane, M. G.

    2011-05-01

    The paper is an update on the Atomic Data and Analysis Structure, ADAS, since ICAM-DATA06 and a forward look to its evolution in the next five years. ADAS is an international project supporting principally magnetic confinement fusion research. It has participant laboratories throughout the world, including ITER and all its partner countries. In parallel with ADAS, the ADAS-EU Project provides enhanced support for fusion research at Associated Laboratories and Universities in Europe and ITER. OPEN-ADAS, sponsored jointly by the ADAS Project and IAEA, is the mechanism for open access to principal ADAS atomic data classes and facilitating software for their use. EXTENDED-ADAS comprises a variety of special, integrated application software, beyond the purely atomic bounds of ADAS, tuned closely to specific diagnostic analyses and plasma models. The current scientific content and scope of these various ADAS and ADAS related activities are briefly reviewed. These span a number of themes including heavy element spectroscopy and models, charge exchange spectroscopy, beam emission spectroscopy and special features which provide a broad baseline of atomic modelling and support. Emphasis will be placed on `lifting the fundamental data baseline'—a principal ADAS task for the next few years. This will include discussion of ADAS and ADAS-EU coordinated and shared activities and some of the methods being exploited.

  11. Model-Based MR Parameter Mapping with Sparsity Constraints: Parameter Estimation and Performance Bounds

    PubMed Central

    Zhao, Bo; Lam, Fan; Liang, Zhi-Pei

    2014-01-01

    MR parameter mapping (e.g., T1 mapping, T2 mapping, T2∗ mapping) is a valuable tool for tissue characterization. However, its practical utility has been limited due to long data acquisition times. This paper addresses this problem with a new model-based parameter mapping method. The proposed method utilizes a formulation that integrates the explicit signal model with sparsity constraints on the model parameters, enabling direct estimation of the parameters of interest from highly undersampled, noisy k-space data. An efficient greedy-pursuit algorithm is described to solve the resulting constrained parameter estimation problem. Estimation-theoretic bounds are also derived to analyze the benefits of incorporating sparsity constraints and benchmark the performance of the proposed method. The theoretical properties and empirical performance of the proposed method are illustrated in a T2 mapping application example using computer simulations. PMID:24833520

  12. Ion-reversibility studies in amorphous solids using the two-atom scattering model. [Rutherford backscattering from disordered solids

    SciTech Connect

    Oen, O.S.

    1981-06-01

    An analytical two-atom scattering model has been developed to treat the recent discovery of the enhancement near 180/sup 0/ of Rutherford backscattering yields from disordered solids. In contrast to conventional calculations of Rutherford backscattering that treat scattering from a single atom only (the backscattering atom), the present model includes the interaction of a second atom lying between the target surface and the backscattering plane. The projectile ion makes a glancing collision with this second atom both before and after it is backscattered. The model predicts an enhancement effect whose physical origin arises from the tolerance of path for those ions whose inward and outward trajectories lie in the vicinity of the critical impact parameter. Results using Moliere scattering show how the yield enhancement depends on ion energy, backscattering depth, exit angle, scattering potential, atomic numbers of the projectile and target, and target density. In the model the critical impact parameter and critical angle play important roles. It is shown that these quantities depend on a single dimensionless parameter and analytical expressions for them are given which are accurate to better than 1%.

  13. Summary of the DREAM8 Parameter Estimation Challenge: Toward Parameter Identification for Whole-Cell Models

    PubMed Central

    Karr, Jonathan R.; Williams, Alex H.; Zucker, Jeremy D.; Raue, Andreas; Steiert, Bernhard; Timmer, Jens; Kreutz, Clemens; Wilkinson, Simon; Allgood, Brandon A.; Bot, Brian M.; Hoff, Bruce R.; Kellen, Michael R.; Covert, Markus W.; Stolovitzky, Gustavo A.; Meyer, Pablo

    2015-01-01

    Whole-cell models that explicitly represent all cellular components at the molecular level have the potential to predict phenotype from genotype. However, even for simple bacteria, whole-cell models will contain thousands of parameters, many of which are poorly characterized or unknown. New algorithms are needed to estimate these parameters and enable researchers to build increasingly comprehensive models. We organized the Dialogue for Reverse Engineering Assessments and Methods (DREAM) 8 Whole-Cell Parameter Estimation Challenge to develop new parameter estimation algorithms for whole-cell models. We asked participants to identify a subset of parameters of a whole-cell model given the model’s structure and in silico “experimental” data. Here we describe the challenge, the best performing methods, and new insights into the identifiability of whole-cell models. We also describe several valuable lessons we learned toward improving future challenges. Going forward, we believe that collaborative efforts supported by inexpensive cloud computing have the potential to solve whole-cell model parameter estimation. PMID:26020786

  14. A constructive model potential method for atomic interactions

    NASA Technical Reports Server (NTRS)

    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.

  15. Modeling of Turbulence Effect on Liquid Jet Atomization

    NASA Technical Reports Server (NTRS)

    Trinh, H. P.

    2007-01-01

    Recent studies indicate that turbulence behaviors within a liquid jet have considerable effect on the atomization process. Such turbulent flow phenomena are encountered in most practical applications of common liquid spray devices. This research aims to model the effects of turbulence occurring inside a cylindrical liquid jet to its atomization process. The two widely used atomization models Kelvin-Helmholtz (KH) instability of Reitz and the Taylor analogy breakup (TAB) of O'Rourke and Amsden portraying primary liquid jet disintegration and secondary droplet breakup, respectively, are examined. Additional terms are formulated and appropriately implemented into these two models to account for the turbulence effect. Results for the flow conditions examined in this study indicate that the turbulence terms are significant in comparison with other terms in the models. In the primary breakup regime, the turbulent liquid jet tends to break up into large drops while its intact core is slightly shorter than those without turbulence. In contrast, the secondary droplet breakup with the inside liquid turbulence consideration produces smaller drops. Computational results indicate that the proposed models provide predictions that agree reasonably well with available measured data.

  16. Extended Bose Hubbard model of interacting bosonic atoms in optical lattices: From superfluidity to density waves

    SciTech Connect

    Mazzarella, G.; Giampaolo, S. M.; Illuminati, F.

    2006-01-15

    For systems of interacting, ultracold spin-zero neutral bosonic atoms, harmonically trapped and subject to an optical lattice potential, we derive an Extended Bose Hubbard (EBH) model by developing a systematic expansion for the Hamiltonian of the system in powers of the lattice parameters and of a scale parameter, the lattice attenuation factor. We identify the dominant terms that need to be retained in realistic experimental conditions, up to nearest-neighbor interactions and nearest-neighbor hoppings conditioned by the on-site occupation numbers. In the mean field approximation, we determine the free energy of the system and study the phase diagram both at zero and at finite temperature. At variance with the standard on site Bose Hubbard model, the zero-temperature phase diagram of the EBH model possesses a dual structure in the Mott insulating regime. Namely, for specific ranges of the lattice parameters, a density wave phase characterizes the system at integer fillings, with domains of alternating mean occupation numbers that are the atomic counterparts of the domains of staggered magnetizations in an antiferromagnetic phase. We show as well that in the EBH model, a zero-temperature quantum phase transition to pair superfluidity is, in principle, possible, but completely suppressed at the lowest order in the lattice attenuation factor. Finally, we determine the possible occurrence of the different phases as a function of the experimentally controllable lattice parameters.

  17. Atomic Data and the Modeling of Supernova Spectra

    NASA Astrophysics Data System (ADS)

    Fontes, Christopher

    2012-06-01

    The modeling of supernovae (SNe) incorporates a variety of disciplines, including hydrodynamics, radiation transport, nuclear physics and atomic physics. These efforts require numerical simulation of the final stages of a star's life, the supernova explosion phase, and the radiation that is subsequently emitted by the supernova remnant, which can occur over a time span of tens of thousands of years. While there are several different types of SNe, they all emit radiation in some form. The measurement and interpretation of these spectra provide important information about the structure of the exploding star and the supernova engine. In this talk, the role of atomic data is highlighted as it pertains to the modeling of supernova spectra. Recent applications [1,2] involve the Los Alamos OPLIB opacity database, which has been used to provide atomic opacities for modeling supernova plasmas under local thermodynamic equilibrium (LTE) conditions. Ongoing work includes the application of atomic data generated by the Los Alamos suite of atomic physics codes under more complicated, non-LTE conditions [3]. As a specific, recent example, a portion of the x-ray spectrum produced by Tycho's supernova remnant (SN 1572) will be discussed [4].[4pt] [1] C.L. Fryer et al., Astrophys. J. 707, 193 (2009).[0pt] [2] C.L. Fryer et al., Astrophys. J. 725, 296 (2009).[0pt] [3] C.J. Fontes et al., Conference Proceedings for ICPEAC XXVII (Belfast, Northern Ireland), in press, (2011).[0pt] [4] K.A. Eriksen et al., Presentation at the 2012 AAS Meeting (Austin, TX).

  18. Parameter estimation in deformable models using Markov chain Monte Carlo

    NASA Astrophysics Data System (ADS)

    Chalana, Vikram; Haynor, David R.; Sampson, Paul D.; Kim, Yongmin

    1997-04-01

    Deformable models have gained much popularity recently for many applications in medical imaging, such as image segmentation, image reconstruction, and image registration. Such models are very powerful because various kinds of information can be integrated together in an elegant statistical framework. Each such piece of information is typically associated with a user-defined parameter. The values of these parameters can have a significant effect on the results generated using these models. Despite the popularity of deformable models for various applications, not much attention has been paid to the estimation of these parameters. In this paper we describe systematic methods for the automatic estimation of these deformable model parameters. These methods are derived by posing the deformable models as a Bayesian inference problem. Our parameter estimation methods use Markov chain Monte Carlo methods for generating samples from highly complex probability distributions.

  19. Agricultural and Environmental Input Parameters for the Biosphere Model

    SciTech Connect

    Kaylie Rasmuson; Kurt Rautenstrauch

    2003-06-20

    This analysis is one of nine technical reports that support the Environmental Radiation Model for Yucca Mountain Nevada (ERMYN) biosphere model. It documents input parameters for the biosphere model, and supports the use of the model to develop Biosphere Dose Conversion Factors (BDCF). The biosphere model is one of a series of process models supporting the Total System Performance Assessment (TSPA) for the repository at Yucca Mountain. The ERMYN provides the TSPA with the capability to perform dose assessments. A graphical representation of the documentation hierarchy for the ERMYN is presented in Figure 1-1. This figure shows the interrelationships between the major activities and their products (the analysis and model reports) that were planned in the biosphere Technical Work Plan (TWP, BSC 2003a). It should be noted that some documents identified in Figure 1-1 may be under development and therefore not available at the time this document is issued. The ''Biosphere Model Report'' (BSC 2003b) describes the ERMYN and its input parameters. This analysis report, ANL-MGR-MD-000006, ''Agricultural and Environmental Input Parameters for the Biosphere Model'', is one of the five reports that develop input parameters for the biosphere model. This report defines and justifies values for twelve parameters required in the biosphere model. These parameters are related to use of contaminated groundwater to grow crops. The parameter values recommended in this report are used in the soil, plant, and carbon-14 submodels of the ERMYN.

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

    NASA Technical Reports Server (NTRS)

    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

  1. On retrial queueing model with fuzzy parameters

    NASA Astrophysics Data System (ADS)

    Ke, Jau-Chuan; Huang, Hsin-I.; Lin, Chuen-Horng

    2007-01-01

    This work constructs the membership functions of the system characteristics of a retrial queueing model with fuzzy customer arrival, retrial and service rates. The α-cut approach is used to transform a fuzzy retrial-queue into a family of conventional crisp retrial queues in this context. By means of the membership functions of the system characteristics, a set of parametric non-linear programs is developed to describe the family of crisp retrial queues. A numerical example is solved successfully to illustrate the validity of the proposed approach. Because the system characteristics are expressed and governed by the membership functions, more information is provided for use by management. By extending this model to the fuzzy environment, fuzzy retrial-queue is represented more accurately and analytic results are more useful for system designers and practitioners.

  2. A simulation of water pollution model parameter estimation

    NASA Technical Reports Server (NTRS)

    Kibler, J. F.

    1976-01-01

    A parameter estimation procedure for a water pollution transport model is elaborated. A two-dimensional instantaneous-release shear-diffusion model serves as representative of a simple transport process. Pollution concentration levels are arrived at via modeling of a remote-sensing system. The remote-sensed data are simulated by adding Gaussian noise to the concentration level values generated via the transport model. Model parameters are estimated from the simulated data using a least-squares batch processor. Resolution, sensor array size, and number and location of sensor readings can be found from the accuracies of the parameter estimates.

  3. A Logical Difficulty of the Parameter Setting Model.

    ERIC Educational Resources Information Center

    Sasaki, Yoshinori

    1990-01-01

    Seeks to prove that the parameter setting model (PSM) of Chomsky's Universal Grammar theory contains an internal contradiction when it is seriously taken to model the internal state of language learners. (six references) (JL)

  4. Determining extreme parameter correlation in ground water models.

    USGS Publications Warehouse

    Hill, M.C.; Osterby, O.

    2003-01-01

    In ground water flow system models with hydraulic-head observations but without significant imposed or observed flows, extreme parameter correlation generally exists. As a result, hydraulic conductivity and recharge parameters cannot be uniquely estimated. In complicated problems, such correlation can go undetected even by experienced modelers. Extreme parameter correlation can be detected using parameter correlation coefficients, but their utility depends on the presence of sufficient, but not excessive, numerical imprecision of the sensitivities, such as round-off error. This work investigates the information that can be obtained from parameter correlation coefficients in the presence of different levels of numerical imprecision, and compares it to the information provided by an alternative method called the singular value decomposition (SVD). Results suggest that (1) calculated correlation coefficients with absolute values that round to 1.00 were good indicators of extreme parameter correlation, but smaller values were not necessarily good indicators of lack of correlation and resulting unique parameter estimates; (2) the SVD may be more difficult to interpret than parameter correlation coefficients, but it required sensitivities that were one to two significant digits less accurate than those that required using parameter correlation coefficients; and (3) both the SVD and parameter correlation coefficients identified extremely correlated parameters better when the parameters were more equally sensitive. When the statistical measures fail, parameter correlation can be identified only by the tedious process of executing regression using different sets of starting values, or, in some circumstances, through graphs of the objective function.

  5. Atomic coherence in the nonresonant Jaynes-Cummings model with thermocoherent field

    NASA Astrophysics Data System (ADS)

    Rastegar, N.; Baghshahi, H. R.; Mirafzali, S. Y.

    2016-11-01

    Using relative entropy of coherence, we study the atomic coherence (AC) in the nonresonant Jaynes-Cummings model, when the atom is initially prepared in an incoherent mixed state and the quantized field is in a thermocoherent (Glauber-Lachs) state. The influence of the increasing average number of thermal photons, average number of coherent photons and detuninig parameter on the AC are examined, separately in detail. We found that increasing the mean number of thermal (coherent) photons over a fixed mean number of the coherent (thermal) field has a destructive (constructive) effect on the AC. In addition, we see that the increment of detuning parameter leads to decrement of AC. Remarkably, we observe that in the particular case of thermal field, the AC cannot be created.

  6. On Interpreting the Parameters for Any Item Response Model

    ERIC Educational Resources Information Center

    Thissen, David

    2009-01-01

    Maris and Bechger's article is an exercise in technical virtuosity and provides much to be learned by students of psychometrics. In this commentary, the author begins with making two observations. The first is that the title, "On Interpreting the Model Parameters for the Three Parameter Logistic Model," belies the generality of parts of Maris and…

  7. Exploring the interdependencies between parameters in a material model.

    SciTech Connect

    Silling, Stewart Andrew; Fermen-Coker, Muge

    2014-01-01

    A method is investigated to reduce the number of numerical parameters in a material model for a solid. The basis of the method is to detect interdependencies between parameters within a class of materials of interest. The method is demonstrated for a set of material property data for iron and steel using the Johnson-Cook plasticity model.

  8. Influences of parameter uncertainties within the ICRP-66 respiratory tract model: a parameter sensitivity analysis.

    PubMed

    Huston, Thomas E; Farfán, Eduardo B; Bolch, W Emmett; Bolch, Wesley E

    2003-11-01

    An important aspect in model uncertainty analysis is the evaluation of input parameter sensitivities with respect to model outcomes. In previous publications, parameter uncertainties were examined for the ICRP-66 respiratory tract model. The studies were aided by the development and use of a computer code LUDUC (Lung Dose Uncertainty Code) which allows probabilities density functions to be specified for all ICRP-66 model input parameters. These density functions are sampled using Latin hypercube techniques with values subsequently propagated through the ICRP-66 model. In the present study, LUDUC has been used to perform a detailed parameter sensitivity analysis of the ICRP-66 model using input parameter density functions specified in previously published articles. The results suggest that most of the variability in the dose to a given target region is explained by only a few input parameters. For example, for particle diameters between 0.1 and 50 microm, about 50% of the variability in the total lung dose (weighted sum of target tissue doses) for 239PuO2 is due to variability in the dose to the alveolar-interstitial (AI) region. In turn, almost 90% of the variability in the dose to the AI region is attributable to uncertainties in only four parameters in the model: the ventilation rate, the AI deposition fraction, the clearance rate constant for slow-phase absorption of deposited material to the blood, and the clearance rate constant for particle transport from the AI2 to bb1 compartment. A general conclusion is that many input parameters do not significantly influence variability in final doses. As a result, future research can focus on improving density functions for those input variables that contribute the most to variability in final dose values. PMID:14571988

  9. NWP model forecast skill optimization via closure parameter variations

    NASA Astrophysics Data System (ADS)

    Järvinen, H.; Ollinaho, P.; Laine, M.; Solonen, A.; Haario, H.

    2012-04-01

    We present results of a novel approach to tune predictive skill of numerical weather prediction (NWP) models. These models contain tunable parameters which appear in parameterizations schemes of sub-grid scale physical processes. The current practice is to specify manually the numerical parameter values, based on expert knowledge. We developed recently a concept and method (QJRMS 2011) for on-line estimation of the NWP model parameters via closure parameter variations. The method called EPPES ("Ensemble prediction and parameter estimation system") utilizes ensemble prediction infra-structure for parameter estimation in a very cost-effective way: practically no new computations are introduced. The approach provides an algorithmic decision making tool for model parameter optimization in operational NWP. In EPPES, statistical inference about the NWP model tunable parameters is made by (i) generating an ensemble of predictions so that each member uses different model parameter values, drawn from a proposal distribution, and (ii) feeding-back the relative merits of the parameter values to the proposal distribution, based on evaluation of a suitable likelihood function against verifying observations. In this presentation, the method is first illustrated in low-order numerical tests using a stochastic version of the Lorenz-95 model which effectively emulates the principal features of ensemble prediction systems. The EPPES method correctly detects the unknown and wrongly specified parameters values, and leads to an improved forecast skill. Second, results with an ensemble prediction system emulator, based on the ECHAM5 atmospheric GCM show that the model tuning capability of EPPES scales up to realistic models and ensemble prediction systems. Finally, preliminary results of EPPES in the context of ECMWF forecasting system are presented.

  10. Semirelativistic model for ionization of atomic hydrogen by electron impact

    SciTech Connect

    Attaourti, Y.; Taj, S.; Manaut, B.

    2005-06-15

    We present a semirelativistic model for the description of the ionization process of atomic hydrogen by electron impact in the first Born approximation by using the Darwin wave function to describe the bound state of atomic hydrogen and the Sommerfeld-Maue wave function to describe the ejected electron. This model, accurate to first order in Z/c in the relativistic correction, shows that, even at low kinetic energies of the incident electron, spin effects are small but not negligible. These effects become noticeable with increasing incident electron energies. All analytical calculations are exact and our semirelativistic results are compared with the results obtained in the nonrelativistic Coulomb Born approximation both for the coplanar asymmetric and the binary coplanar geometries.

  11. Empirical model of atomic nitrogen in the upper thermosphere

    NASA Technical Reports Server (NTRS)

    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.

  12. Extended Bose-Hubbard models with ultracold magnetic atoms.

    PubMed

    Baier, S; Mark, M J; Petter, D; Aikawa, K; Chomaz, L; Cai, Z; Baranov, M; Zoller, P; Ferlaino, F

    2016-04-01

    The Hubbard model underlies our understanding of strongly correlated materials. Whereas its standard form only comprises interactions between particles at the same lattice site, extending it to encompass long-range interactions is predicted to profoundly alter the quantum behavior of the system. We realize the extended Bose-Hubbard model for an ultracold gas of strongly magnetic erbium atoms in a three-dimensional optical lattice. Controlling the orientation of the atomic dipoles, we reveal the anisotropic character of the onsite interaction and hopping dynamics and their influence on the superfluid-to-Mott insulator quantum phase transition. Moreover, we observe nearest-neighbor interactions, a genuine consequence of the long-range nature of dipolar interactions. Our results lay the groundwork for future studies of exotic many-body quantum phases. PMID:27124454

  13. Trends in Atomic Parameters for Crystals and Free Ions across the Lanthanide Series: The Case of LaCl3:Ln(3+).

    PubMed

    Yeung, Y Y; Tanner, P A

    2015-06-18

    Analyses of the crystal field energy levels of the series LaCl3:Ln(3+) using a semiempirical Hamiltonian shows that only five ions (Pr, Nd, Pm, Dy, Ho) meet the criteria to avoid overfitting of the atomic part. A new parameter (SNES) has been introduced to represent the strength of the normalized electrostatic repulsion for these ions. This parameter varies linearly (R(2)adj = 0.9994, N = 5) with the reciprocal of the radius of the tripositive lanthanide ion, as expected from the form of repulsive Coulomb interaction. The Slater parameters from the crystal field analyses, F(k)(corr) (i.e., corrected for the effects of the two-particle component of the three-body operator associated with the T(2) parameter), exhibit an exponential variation with the number of electrons, n, in 4f(n). This is explained by reference to the radial part of a hydrogen-like wave function. The ratio of F(k)(corr) with the ab initio free ion Slater parameter F(k)(ab initio) varies linearly with n. Fitted parameters F(k)(corr: free ion) from the free ion data for Pr(3+) and Nd(3+) show that the corresponding ab initio values are between 14 and 27% too high. The spin-orbit coupling constant from crystal field analyses (ζ4f) exhibits a quartic variation with atomic number, and the ratio ζ4f/ζ4f(ab initio) follows an exponential growth model with n. The results serve to confirm the hypothesis that smooth trends can be observed across the Ln(3+) series for the fitted parameters despite the fact that the majority of experimental data is lacking. PMID:25985076

  14. Trends in Atomic Parameters for Crystals and Free Ions across the Lanthanide Series: The Case of LaCl3:Ln(3+).

    PubMed

    Yeung, Y Y; Tanner, P A

    2015-06-18

    Analyses of the crystal field energy levels of the series LaCl3:Ln(3+) using a semiempirical Hamiltonian shows that only five ions (Pr, Nd, Pm, Dy, Ho) meet the criteria to avoid overfitting of the atomic part. A new parameter (SNES) has been introduced to represent the strength of the normalized electrostatic repulsion for these ions. This parameter varies linearly (R(2)adj = 0.9994, N = 5) with the reciprocal of the radius of the tripositive lanthanide ion, as expected from the form of repulsive Coulomb interaction. The Slater parameters from the crystal field analyses, F(k)(corr) (i.e., corrected for the effects of the two-particle component of the three-body operator associated with the T(2) parameter), exhibit an exponential variation with the number of electrons, n, in 4f(n). This is explained by reference to the radial part of a hydrogen-like wave function. The ratio of F(k)(corr) with the ab initio free ion Slater parameter F(k)(ab initio) varies linearly with n. Fitted parameters F(k)(corr: free ion) from the free ion data for Pr(3+) and Nd(3+) show that the corresponding ab initio values are between 14 and 27% too high. The spin-orbit coupling constant from crystal field analyses (ζ4f) exhibits a quartic variation with atomic number, and the ratio ζ4f/ζ4f(ab initio) follows an exponential growth model with n. The results serve to confirm the hypothesis that smooth trends can be observed across the Ln(3+) series for the fitted parameters despite the fact that the majority of experimental data is lacking.

  15. Charged Neutrinos and Atoms in the Standard Model

    NASA Astrophysics Data System (ADS)

    Takasugi, E.; Tanaka, M.

    1992-03-01

    The possibility of the charge quantization in the standard model is examined in the absence of the ``generation as copies'' rule. It is shown that neutrinos and atoms can have mini-charges, while neutron is neutral. If a triplet Higgs boson is introduced, neutrinos have masses. Two neutrinos form a Konopinski-Mahmoud Dirac particle and the other becomes a Majorana particle due to the hidden local anomaly free U(1) symmetry.

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

    NASA Technical Reports Server (NTRS)

    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.

  17. Atomic Data and Spectral Model for Fe II

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

    We present extensive calculations of radiative transition rates and electron impact collision strengths for Fe ii. The data sets involve 52 levels from the 3d7, 3d64s, and 3{d}54{s}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 ii absorption spectra. Finally, we provide diagnostic line ratios and line emissivities for emission spectroscopy as well as column densities for absorption spectroscopy. All atomic data and models are available online and through the AtomPy atomic data curation environment.

  18. Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models.

    PubMed

    Baker, Syed Murtuza; Poskar, C Hart; Junker, Björn H

    2011-01-01

    In systems biology, experimentally measured parameters are not always available, necessitating the use of computationally based parameter estimation. In order to rely on estimated parameters, it is critical to first determine which parameters can be estimated for a given model and measurement set. This is done with parameter identifiability analysis. A kinetic model of the sucrose accumulation in the sugar cane culm tissue developed by Rohwer et al. was taken as a test case model. What differentiates this approach is the integration of an orthogonal-based local identifiability method into the unscented Kalman filter (UKF), rather than using the more common observability-based method which has inherent limitations. It also introduces a variable step size based on the system uncertainty of the UKF during the sensitivity calculation. This method identified 10 out of 12 parameters as identifiable. These ten parameters were estimated using the UKF, which was run 97 times. Throughout the repetitions the UKF proved to be more consistent than the estimation algorithms used for comparison. PMID:21989173

  19. Modeling of Turbulence Effects on Liquid Jet Atomization and Breakup

    NASA Technical Reports Server (NTRS)

    Trinh, Huu P.; Chen, C. P.

    2005-01-01

    Recent experimental investigations and physical modeling studies have indicated that turbulence behaviors within a liquid jet have considerable effects on the atomization process. This study aims to model the turbulence effect in the atomization process of a cylindrical liquid jet. Two widely used models, the Kelvin-Helmholtz (KH) instability of Reitz (blob model) and the Taylor-Analogy-Breakup (TAB) secondary droplet breakup by O Rourke et al, are further extended to include turbulence effects. In the primary breakup model, the level of the turbulence effect on the liquid breakup depends on the characteristic scales and the initial flow conditions. For the secondary breakup, an additional turbulence force acted on parent drops is modeled and integrated into the TAB governing equation. The drop size formed from this breakup regime is estimated based on the energy balance before and after the breakup occurrence. This paper describes theoretical development of the current models, called "T-blob" and "T-TAB", for primary and secondary breakup respectivety. Several assessment studies are also presented in this paper.

  20. Relationship between Cole-Cole model parameters and spectral decomposition parameters derived from SIP data

    NASA Astrophysics Data System (ADS)

    Weigand, M.; Kemna, A.

    2016-06-01

    Spectral induced polarization (SIP) data are commonly analysed using phenomenological models. Among these models the Cole-Cole (CC) model is the most popular choice to describe the strength and frequency dependence of distinct polarization peaks in the data. More flexibility regarding the shape of the spectrum is provided by decomposition schemes. Here the spectral response is decomposed into individual responses of a chosen elementary relaxation model, mathematically acting as kernel in the involved integral, based on a broad range of relaxation times. A frequently used kernel function is the Debye model, but also the CC model with some other a priorly specified frequency dispersion (e.g. Warburg model) has been proposed as kernel in the decomposition. The different decomposition approaches in use, also including conductivity and resistivity formulations, pose the question to which degree the integral spectral parameters typically derived from the obtained relaxation time distribution are biased by the approach itself. Based on synthetic SIP data sampled from an ideal CC response, we here investigate how the two most important integral output parameters deviate from the corresponding CC input parameters. We find that the total chargeability may be underestimated by up to 80 per cent and the mean relaxation time may be off by up to three orders of magnitude relative to the original values, depending on the frequency dispersion of the analysed spectrum and the proximity of its peak to the frequency range limits considered in the decomposition. We conclude that a quantitative comparison of SIP parameters across different studies, or the adoption of parameter relationships from other studies, for example when transferring laboratory results to the field, is only possible on the basis of a consistent spectral analysis procedure. This is particularly important when comparing effective CC parameters with spectral parameters derived from decomposition results.

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

    ERIC Educational Resources Information Center

    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…

  2. Testing parameters in structural equation modeling: every "one" matters.

    PubMed

    Gonzalez, R; Griffin, D

    2001-09-01

    A problem with standard errors estimated by many structural equation modeling programs is described. In such programs, a parameter's standard error is sensitive to how the model is identified (i.e., how scale is set). Alternative but equivalent ways to identify a model may yield different standard errors, and hence different Z tests for a parameter, even though the identifications produce the same overall model fit. This lack of invariance due to model identification creates the possibility that different analysts may reach different conclusions about a parameter's significance level even though they test equivalent models on the same data. The authors suggest that parameters be tested for statistical significance through the likelihood ratio test, which is invariant to the identification choice. PMID:11570231

  3. Extraction of exposure modeling parameters of thick resist

    NASA Astrophysics Data System (ADS)

    Liu, Chi; Du, Jinglei; Liu, Shijie; Duan, Xi; Luo, Boliang; Zhu, Jianhua; Guo, Yongkang; Du, Chunlei

    2004-12-01

    Experimental and theoretical analysis indicates that many nonlinear factors existing in the exposure process of thick resist can remarkably affect the PAC concentration distribution in the resist. So the effects should be fully considered in the exposure model of thick resist, and exposure parameters should not be treated as constants because there exists certain relationship between the parameters and resist thickness. In this paper, an enhanced Dill model for the exposure process of thick resist is presented, and the experimental setup for measuring exposure parameters of thick resist is developed. We measure the intensity transmittance curve of thick resist AZ4562 under different processing conditions, and extract the corresponding exposure parameters based on the experiment results and the calculations from the beam propagation matrix of the resist films. With these modified modeling parameters and enhanced Dill model, simulation of thick-resist exposure process can be effectively developed in the future.

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

    PubMed

    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.

  5. Exchange energy gradients with respect to atomic positions and cell parameters within the Hartree-Fock Gamma-point approximation.

    PubMed

    Weber, Valéry; Daul, Claude; Challacombe, Matt

    2006-06-01

    Recently, linear scaling construction of the periodic exact Hartree-Fock exchange matrix within the Gamma-point approximation has been introduced [J. Chem. Phys. 122, 124105 (2005)]. In this article, a formalism for evaluation of analytical Hartree-Fock exchange energy gradients with respect to atomic positions and cell parameters at the Gamma-point approximation is presented. While the evaluation of exchange gradients with respect to atomic positions is similar to those in the gas phase limit, the gradients with respect to cell parameters involve the accumulation of atomic gradients multiplied by appropriate factors and a modified electron repulsion integral (ERI). This latter integral arises from use of the minimum image convention in the definition of the Gamma-point Hartree-Fock approximation. We demonstrate how this new ERI can be computed with the help of a modified vertical recurrence relation in the frame of the Obara-Saika and Head-Gordon-Pople algorithm. As an illustration, the analytical gradients have been used in conjunction with the QUICCA algorithm [K. Nemeth and M. Challacombe, J. Chem. Phys. 121, 2877 (2004)] to optimize periodic systems at the Hartree-Fock level of theory. PMID:16774396

  6. Exchange energy gradients with respect to atomic positions and cell parameters within the Hartree-Fock Γ-point approximation

    NASA Astrophysics Data System (ADS)

    Weber, Valéry; Daul, Claude; Challacombe, Matt

    2006-06-01

    Recently, linear scaling construction of the periodic exact Hartree-Fock exchange matrix within the Γ-point approximation has been introduced [J. Chem. Phys. 122, 124105 (2005)]. In this article, a formalism for evaluation of analytical Hartree-Fock exchange energy gradients with respect to atomic positions and cell parameters at the Γ-point approximation is presented. While the evaluation of exchange gradients with respect to atomic positions is similar to those in the gas phase limit, the gradients with respect to cell parameters involve the accumulation of atomic gradients multiplied by appropriate factors and a modified electron repulsion integral (ERI). This latter integral arises from use of the minimum image convention in the definition of the Γ-point Hartree-Fock approximation. We demonstrate how this new ERI can be computed with the help of a modified vertical recurrence relation in the frame of the Obara-Saika and Head-Gordon-Pople algorithm. As an illustration, the analytical gradients have been used in conjunction with the QUICCA algorithm [K. Németh and M. Challacombe, J. Chem. Phys. 121, 2877 (2004)] to optimize periodic systems at the Hartree-Fock level of theory.

  7. Identification of parameters of discrete-continuous models

    SciTech Connect

    Cekus, Dawid Warys, Pawel

    2015-03-10

    In the paper, the parameters of a discrete-continuous model have been identified on the basis of experimental investigations and formulation of optimization problem. The discrete-continuous model represents a cantilever stepped Timoshenko beam. The mathematical model has been formulated and solved according to the Lagrange multiplier formalism. Optimization has been based on the genetic algorithm. The presented proceeding’s stages make the identification of any parameters of discrete-continuous systems possible.

  8. Estimating parameters for generalized mass action models with connectivity information

    PubMed Central

    Ko, Chih-Lung; Voit, Eberhard O; Wang, Feng-Sheng

    2009-01-01

    Background Determining the parameters of a mathematical model from quantitative measurements is the main bottleneck of modelling biological systems. Parameter values can be estimated from steady-state data or from dynamic data. The nature of suitable data for these two types of estimation is rather different. For instance, estimations of parameter values in pathway models, such as kinetic orders, rate constants, flux control coefficients or elasticities, from steady-state data are generally based on experiments that measure how a biochemical system responds to small perturbations around the steady state. In contrast, parameter estimation from dynamic data requires time series measurements for all dependent variables. Almost no literature has so far discussed the combined use of both steady-state and transient data for estimating parameter values of biochemical systems. Results In this study we introduce a constrained optimization method for estimating parameter values of biochemical pathway models using steady-state information and transient measurements. The constraints are derived from the flux connectivity relationships of the system at the steady state. Two case studies demonstrate the estimation results with and without flux connectivity constraints. The unconstrained optimal estimates from dynamic data may fit the experiments well, but they do not necessarily maintain the connectivity relationships. As a consequence, individual fluxes may be misrepresented, which may cause problems in later extrapolations. By contrast, the constrained estimation accounting for flux connectivity information reduces this misrepresentation and thereby yields improved model parameters. Conclusion The method combines transient metabolic profiles and steady-state information and leads to the formulation of an inverse parameter estimation task as a constrained optimization problem. Parameter estimation and model selection are simultaneously carried out on the constrained

  9. Inverse estimation of parameters for an estuarine eutrophication model

    SciTech Connect

    Shen, J.; Kuo, A.Y.

    1996-11-01

    An inverse model of an estuarine eutrophication model with eight state variables is developed. It provides a framework to estimate parameter values of the eutrophication model by assimilation of concentration data of these state variables. The inverse model using the variational technique in conjunction with a vertical two-dimensional eutrophication model is general enough to be applicable to aid model calibration. The formulation is illustrated by conducting a series of numerical experiments for the tidal Rappahannock River, a western shore tributary of the Chesapeake Bay. The numerical experiments of short-period model simulations with different hypothetical data sets and long-period model simulations with limited hypothetical data sets demonstrated that the inverse model can be satisfactorily used to estimate parameter values of the eutrophication model. The experiments also showed that the inverse model is useful to address some important questions, such as uniqueness of the parameter estimation and data requirements for model calibration. Because of the complexity of the eutrophication system, degrading of speed of convergence may occur. Two major factors which cause degradation of speed of convergence are cross effects among parameters and the multiple scales involved in the parameter system.

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

    SciTech Connect

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

    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.

  11. Structural models and atomic distribution of bimetallic nanoparticles as investigated by X-ray absorption spectroscopy.

    PubMed

    Hwang, Bing-Joe; Sarma, Loka Subramanyam; Chen, Jiun-Ming; Chen, Ching-Hsiang; Shih, Shou-Chu; Wang, Guo-Rung; Liu, Din-Goa; Lee, Jyh-Fu; Tang, Mau-Tsu

    2005-08-10

    In this report, we describe a general methodology to determine the extent of alloying or atomic distribution quantitatively in bimetallic nanoparticles (NPs) by X-ray absorption spectroscopy (XAS). The structural parameters determined in these studies serve as a quantitative index and provide a general route to determine the structural aspects of the bimetallic NPs. We have derived various types of possible structural models based on the extent of alloying and coordination number parameters of bimetallic NPs. We also discussed the nature of homo- and heterometallic interactions in bimetallic NPs based on the extent of alloying. Herein, we use carbon-supported platinum-ruthenium bimetallic nanoparticles to demonstrate the proposed methodology, and this can be extended further to get more insights into the alloying extent or atomic distribution of other bimetallic systems. The results demonstrated in this paper open up methods to determine the atomic distribution of bimetallic NPs, which is an extremely important parameter that strongly influences the physicochemical properties of NPs and their applications.

  12. Optimization of FM spectroscopy parameters for a frequency locking loop in small scale CPT based atomic clocks.

    PubMed

    Ben-Aroya, I; Kahanov, M; Eisenstein, G

    2007-11-12

    We describe the optimization of a Frequency Locked Loop (FLL) in an atomic clock which is based on Coherent Population Trapping (CPT) in (87)Rb vapor using the D(2) transition. The FLL uses frequency modulation (FM) spectroscopy and we study the effect of FM parameters (modulation frequency and index) on the sensitivity and the signal to noise ratio of the feedback signal in the FLL. The clock which employs a small spherical glass cell containing (87)Rb atoms and a buffer gas, exhibits a short term stability of 3x10(-11)/ radicaltau. The long term relative frequency stability of the 10 MHz output is better than 10(-10) with a drift of 10(-11) per day.

  13. Collisional excitation of the highly excited hydrogen atoms in the dipole form of the semiclassical impact parameter and Born approximations

    NASA Technical Reports Server (NTRS)

    Omidvar, K.

    1971-01-01

    Expressions for the excitation cross section of the highly excited states of the hydrogenlike atoms by fast charged particles have been derived in the dipole approximation of the semiclassical impact parameter and the Born approximations, making use of a formula for the asymptotic expansion of the oscillator strength of the hydrogenlike atoms given by Menzel. When only the leading term in the asymptotic expansion is retained, the expression for the cross section becomes identical to the expression obtained by the method of the classical collision and correspondence principle given by Percival and Richards. Comparisons are made between the Bethe coefficients obtained here and the Bethe coefficients of the Born approximation for transitions where the Born calculation is available. Satisfactory agreement is obtained only for n yields n + 1 transitions, with n the principal quantum number of the excited state.

  14. Model and Parameter Discretization Impacts on Estimated ASR Recovery Efficiency

    NASA Astrophysics Data System (ADS)

    Forghani, A.; Peralta, R. C.

    2015-12-01

    We contrast computed recovery efficiency of one Aquifer Storage and Recovery (ASR) well using several modeling situations. Test situations differ in employed finite difference grid discretization, hydraulic conductivity, and storativity. We employ a 7-layer regional groundwater model calibrated for Salt Lake Valley. Since the regional model grid is too coarse for ASR analysis, we prepare two local models with significantly smaller discretization capable of analyzing ASR recovery efficiency. Some addressed situations employ parameters interpolated from the coarse valley model. Other situations employ parameters derived from nearby well logs or pumping tests. The intent of the evaluations and subsequent sensitivity analysis is to show how significantly the employed discretization and aquifer parameters affect estimated recovery efficiency. Most of previous studies to evaluate ASR recovery efficiency only consider hypothetical uniform specified boundary heads and gradient assuming homogeneous aquifer parameters. The well is part of the Jordan Valley Water Conservancy District (JVWCD) ASR system, that lies within Salt Lake Valley.

  15. Modeling exact exchange potential in spherically confined atoms.

    PubMed

    Vyboishchikov, Sergei F

    2015-10-15

    In this work, local exchange potentials corresponding to the Hartree-Fock (HF) electron density have been obtained using the Zhao-Morrison-Parr method for a number of closed-shell confined atoms and ions. The exchange potentials obtained and the resulting density were compared with those given by the Becke-Johnson (BJ) model potential. It is demonstrated that introducing a scaling factor to the BJ potential allows improving the quality of the resulting density. The optimum scaling factor increases with decreasing confinement radius. The performance of Karasiev and Ludeña's SCα-LDA method as well as of the Becke-88 exchange potential for reproducing the HF electron densities in confined atoms has been also examined.

  16. Neutral atomic absorption lines and far-UV extinction: Possible implications for depletions and grain parameters

    NASA Astrophysics Data System (ADS)

    Welty, Daniel E.

    1990-07-01

    Researchers examine nine lines of sight within the Galaxy and one in the Large Magellanic Cloud (LMC) for which data on both neutral atomic absorption lines (Snow 1984; White 1986; Welty, Hobbs, and York 1989) and far UV extinction (Bless and Savage 1972; Jenkins, Savage, and Spitzer 1986) are available, in order to test the assumption that variations in gamma/alpha will cancel in taking ratios of the ionization balance equation, and to try to determine to what extent that assumption has affected the aforementioned studies of depletions and grain properties.

  17. Neutral atomic absorption lines and far-UV extinction: Possible implications for depletions and grain parameters

    NASA Technical Reports Server (NTRS)

    Welty, Daniel E.

    1990-01-01

    Researchers examine nine lines of sight within the Galaxy and one in the Large Magellanic Cloud (LMC) for which data on both neutral atomic absorption lines (Snow 1984; White 1986; Welty, Hobbs, and York 1989) and far UV extinction (Bless and Savage 1972; Jenkins, Savage, and Spitzer 1986) are available, in order to test the assumption that variations in gamma/alpha will cancel in taking ratios of the ionization balance equation, and to try to determine to what extent that assumption has affected the aforementioned studies of depletions and grain properties.

  18. Parameter identifiability of power-law biochemical system models.

    PubMed

    Srinath, Sridharan; Gunawan, Rudiyanto

    2010-09-01

    Mathematical modeling has become an integral component in biotechnology, in which these models are frequently used to design and optimize bioprocesses. Canonical models, like power-laws within the Biochemical Systems Theory, offer numerous mathematical and numerical advantages, including built-in flexibility to simulate general nonlinear behavior. The construction of such models relies on the estimation of unknown case-specific model parameters by way of experimental data fitting, also known as inverse modeling. Despite the large number of publications on this topic, this task remains the bottleneck in canonical modeling of biochemical systems. The focus of this paper concerns with the question of identifiability of power-law models from dynamic data, that is, whether the parameter values can be uniquely and accurately identified from time-series data. Existing and newly developed parameter identifiability methods were applied to two power-law models of biochemical systems, and the results pointed to the lack of parametric identifiability as the root cause of the difficulty faced in the inverse modeling. Despite the focus on power-law models, the analyses and conclusions are extendable to other canonical models, and the issue of parameter identifiability is expected to be a common problem in biochemical system modeling. PMID:20197073

  19. Estimating winter wheat phenological parameters: Implications for crop modeling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Crop parameters, such as the timing of developmental events, are critical for accurate simulation results in crop simulation models, yet uncertainty often exists in determining the parameters. Factors contributing to the uncertainty include: a) sources of variation within a plant (i.e., within diffe...

  20. Partial Atomic Charges and Screened Charge Models of the Electrostatic Potential.

    PubMed

    Wang, Bo; Truhlar, Donald G

    2012-06-12

    We propose a new screened charge method for calculating partial atomic charges in molecules by electrostatic potential (ESP) fitting. The model, called full density screening (FDS), is used to approximate the screening effect of full charge densities of atoms in molecules. The results are compared to the conventional ESP fitting method based on point charges and to our previously proposed outer density screening (ODS) method, in which the parameters are reoptimized for the present purpose. In ODS, the charge density of an atom is represented by the sum of a point charge and a smeared negative charge distributed in a Slater-type orbital (STO). In FDS, the charge density of an atom is taken to be the sum of the charge density of the neutral atom and a partial atomic charge (of either sign) distributed in an STO. The ζ values of the STOs used in these two models are optimized in the present study to best reproduce the electrostatic potentials. The quality of the fit to the electrostatics is improved in the screened charge methods, especially for the regions that are within one van der Waals radius of the centers of atoms. It is also found that the charges derived by fitting electrostatic potentials with screened charges are less sensitive to the positions of the fitting points than are those derived with conventional electrostatic fitting. Moreover, we found that the electrostatic-potential-fitted (ESP) charges from the screened charge methods are similar to those from the point-charge method except for molecules containing the methyl group, where we have explored the use of restraints on nonpolar H atoms. We recommend the FDS model if the only goal is ESP fitting to obtain partial atomic charges or a fit to the ESP field. However, the ODS model is more accurate for electronic embedding in combined quantum mechanical and molecular mechanical (QM/MM) modeling and is more accurate than point-charge models for ESP fitting, and it is recommended for applications

  1. Bohr model and dimensional scaling analysis of atoms and molecules

    NASA Astrophysics Data System (ADS)

    Urtekin, Kerim

    It is generally believed that the old quantum theory, as presented by Niels Bohr in 1913, fails when applied to many-electron systems, such as molecules, and nonhydrogenic atoms. It is the central theme of this dissertation to display with examples and applications the implementation of a simple and successful extension of Bohr's planetary model of the hydrogenic atom, which has recently been developed by an atomic and molecular theory group from Texas A&M University. This "extended" Bohr model, which can be derived from quantum mechanics using the well-known dimentional scaling technique is used to yield potential energy curves of H2 and several more complicated molecules, such as LiH, Li2, BeH, He2 and H3, with accuracies strikingly comparable to those obtained from the more lengthy and rigorous "ab initio" computations, and the added advantage that it provides a rather insightful and pictorial description of how electrons behave to form chemical bonds, a theme not central to "ab initio" quantum chemistry. Further investigation directed to CH, and the four-atom system H4 (with both linear and square configurations), via the interpolated Bohr model, and the constrained Bohr model (with an effective potential), respectively, is reported. The extended model is also used to calculate correlation energies. The model is readily applicable to the study of molecular species in the presence of strong magnetic fields, as is the case in the vicinities of white dwarfs and neutron stars. We find that magnetic field increases the binding energy and decreases the bond length. Finally, an elaborative review of doubly coupled quantum dots for a derivation of the electron exchange energy, a straightforward application of Heitler-London method of quantum molecular chemistry, concludes the dissertation. The highlights of the research are (1) a bridging together of the pre- and post quantum mechanical descriptions of the chemical bond (Bohr-Sommerfeld vs. Heisenberg-Schrodinger), and

  2. Complexity, parameter sensitivity and parameter transferability in the modelling of floodplain inundation

    NASA Astrophysics Data System (ADS)

    Bates, P. D.; Neal, J. C.; Fewtrell, T. J.

    2012-12-01

    In this we paper we consider two related questions. First, we address the issue of how much physical complexity is necessary in a model in order to simulate floodplain inundation to within validation data error. This is achieved through development of a single code/multiple physics hydraulic model (LISFLOOD-FP) where different degrees of complexity can be switched on or off. Different configurations of this code are applied to four benchmark test cases, and compared to the results of a number of industry standard models. Second we address the issue of how parameter sensitivity and transferability change with increasing complexity using numerical experiments with models of different physical and geometric intricacy. Hydraulic models are a good example system with which to address such generic modelling questions as: (1) they have a strong physical basis; (2) there is only one set of equations to solve; (3) they require only topography and boundary conditions as input data; and (4) they typically require only a single free parameter, namely boundary friction. In terms of complexity required we show that for the problem of sub-critical floodplain inundation a number of codes of different dimensionality and resolution can be found to fit uncertain model validation data equally well, and that in this situation Occam's razor emerges as a useful logic to guide model selection. We find also find that model skill usually improves more rapidly with increases in model spatial resolution than increases in physical complexity, and that standard approaches to testing hydraulic models against laboratory data or analytical solutions may fail to identify this important fact. Lastly, we find that in benchmark testing studies significant differences can exist between codes with identical numerical solution techniques as a result of auxiliary choices regarding the specifics of model implementation that are frequently unreported by code developers. As a consequence, making sound

  3. Fundamentals, accuracy and input parameters of frost heave prediction models

    NASA Astrophysics Data System (ADS)

    Schellekens, Fons Jozef

    In this thesis, the frost heave knowledge of physical geographers and soil physicists, a detailed description of the frost heave process, methods to determine soil parameters, and analysis of the spatial variability of these soil parameters are connected to the expertise of civil engineers and mathematicians in the (computer) modelling of the process. A description is given of observations of frost heave in laboratory experiments and in the field. Frost heave modelling is made accessible by a detailed description of the main principles of frost heave modelling in a language which can be understood by persons who do not have a thorough mathematical background. Two examples of practical one-dimensional frost heave prediction models are described: a model developed by Wang (1994) and a model developed by Nixon (1991). Advantages, limitations and some improvements of these models are described. It is suggested that conventional frost heave prediction using estimated extreme input parameters may be improved by using locally measured input parameters. The importance of accurate input parameters in frost heave prediction models is demonstrated in a case study using the frost heave models developed by Wang and Nixon. Methods to determine the input parameters are discussed, concluding with a suite of methods, some of which are new, to determine the input parameters of frost heave prediction models from very basic grain size parameters. The spatial variability of the required input parameters is analysed using data obtained along the Norman Wells-Zama oil pipeline at Norman Wells, NWT, located in the transition between discontinuous and continuous permafrost regions at the northern end of Canada's northernmost oil pipeline. A method based on spatial variability analysis of the input parameters in frost heave models is suggested to optimize the improvement that arises from adequate sampling, while minimizing the costs of obtaining field data. A series of frost heave

  4. Magnetic and atomic structure parameters of Sc-doped barium hexagonal ferrites

    NASA Astrophysics Data System (ADS)

    Yang, Aria; Chen, Yajie; Chen, Zhaohui; Vittoria, Carmine; Harris, V. G.

    2008-04-01

    Scandium-doped M-type barium hexagonal ferrites of the composition BaFe12-xScxO19 are well suited for low frequency microwave device applications such as isolators and circulators. A series of Sc-doped M-type barium hexagonal ferrite powders (x =0-1.2) were prepared by conventional ceramic processing techniques. The resulting powders were verified to be pure phase and maintain the nominal chemical stoichiometry by x-ray diffraction and energy dispersive x-ray spectroscopy, respectively. Static magnetic measurements indicated that both saturation magnetization and uniaxial magnetocrystalline anisotropy field decreased with increasing concentration of scandium. Extended x-ray absorption fine structure measurements were carried out to clarify the correlation between the magnetic and atomic structure properties. It is found that the substituted Sc has a strong preference for the bipyramidal site. Nevertheless, the substitution did not introduce additional atomic structural disorder into the barium hexagonal structure. The structural study provided important evidence to quantitatively explain the change in dc and microwave magnetic properties due to Sc ion doping.

  5. Retrospective forecast of ETAS model with daily parameters estimate

    NASA Astrophysics Data System (ADS)

    Falcone, Giuseppe; Murru, Maura; Console, Rodolfo; Marzocchi, Warner; Zhuang, Jiancang

    2016-04-01

    We present a retrospective ETAS (Epidemic Type of Aftershock Sequence) model based on the daily updating of free parameters during the background, the learning and the test phase of a seismic sequence. The idea was born after the 2011 Tohoku-Oki earthquake. The CSEP (Collaboratory for the Study of Earthquake Predictability) Center in Japan provided an appropriate testing benchmark for the five 1-day submitted models. Of all the models, only one was able to successfully predict the number of events that really happened. This result was verified using both the real time and the revised catalogs. The main cause of the failure was in the underestimation of the forecasted events, due to model parameters maintained fixed during the test. Moreover, the absence in the learning catalog of an event similar to the magnitude of the mainshock (M9.0), which drastically changed the seismicity in the area, made the learning parameters not suitable to describe the real seismicity. As an example of this methodological development we show the evolution of the model parameters during the last two strong seismic sequences in Italy: the 2009 L'Aquila and the 2012 Reggio Emilia episodes. The achievement of the model with daily updated parameters is compared with that of same model where the parameters remain fixed during the test time.

  6. Parameter Estimates in Differential Equation Models for Population Growth

    ERIC Educational Resources Information Center

    Winkel, Brian J.

    2011-01-01

    We estimate the parameters present in several differential equation models of population growth, specifically logistic growth models and two-species competition models. We discuss student-evolved strategies and offer "Mathematica" code for a gradient search approach. We use historical (1930s) data from microbial studies of the Russian biologist,…

  7. NEFDS contamination model parameter estimation of powder contaminated surfaces

    NASA Astrophysics Data System (ADS)

    Gibbs, Timothy J.; Messinger, David W.

    2016-05-01

    Hyperspectral signatures of powdered contaminated surfaces are challenging to characterize due to intimate mixing between materials. Most radiometric models have difficulties in recreating these signatures due to non-linear interactions between particles with different physical properties. The Nonconventional Exploitation Factors Data System (NEFDS) Contamination Model is capable of recreating longwave hyperspectral signatures at any contamination mixture amount, but only for a limited selection of materials currently in the database. A method has been developed to invert the NEFDS model and perform parameter estimation on emissivity measurements from a variety of powdered materials on substrates. This model was chosen for its potential to accurately determine contamination coverage density as a parameter in the inverted model. Emissivity data were measured using a Designs and Prototypes fourier transform infrared spectrometer model 102 for different levels of contamination. Temperature emissivity separation was performed to convert data from measure radiance to estimated surface emissivity. Emissivity curves were then input into the inverted model and parameters were estimated for each spectral curve. A comparison of measured data with extrapolated model emissivity curves using estimated parameter values assessed performance of the inverted NEFDS contamination model. This paper will present the initial results of the experimental campaign and the estimated surface coverage parameters.

  8. Uncertainty in dual permeability model parameters for structured soils.

    PubMed

    Arora, B; Mohanty, B P; McGuire, J T

    2012-01-01

    Successful application of dual permeability models (DPM) to predict contaminant transport is contingent upon measured or inversely estimated soil hydraulic and solute transport parameters. The difficulty in unique identification of parameters for the additional macropore- and matrix-macropore interface regions, and knowledge about requisite experimental data for DPM has not been resolved to date. Therefore, this study quantifies uncertainty in dual permeability model parameters of experimental soil columns with different macropore distributions (single macropore, and low- and high-density multiple macropores). Uncertainty evaluation is conducted using adaptive Markov chain Monte Carlo (AMCMC) and conventional Metropolis-Hastings (MH) algorithms while assuming 10 out of 17 parameters to be uncertain or random. Results indicate that AMCMC resolves parameter correlations and exhibits fast convergence for all DPM parameters while MH displays large posterior correlations for various parameters. This study demonstrates that the choice of parameter sampling algorithms is paramount in obtaining unique DPM parameters when information on covariance structure is lacking, or else additional information on parameter correlations must be supplied to resolve the problem of equifinality of DPM parameters. This study also highlights the placement and significance of matrix-macropore interface in flow experiments of soil columns with different macropore densities. Histograms for certain soil hydraulic parameters display tri-modal characteristics implying that macropores are drained first followed by the interface region and then by pores of the matrix domain in drainage experiments. Results indicate that hydraulic properties and behavior of the matrix-macropore interface is not only a function of saturated hydraulic conductivity of the macroporematrix interface (Ksa ) and macropore tortuosity (lf ) but also of other parameters of the matrix and macropore domains.

  9. Assessment of Some Atomization Models Used in Spray Calculations

    NASA Technical Reports Server (NTRS)

    Raju, M. S.; Bulzin, Dan

    2011-01-01

    The paper presents the results from a validation study undertaken as a part of the NASA s fundamental aeronautics initiative on high altitude emissions in order to assess the accuracy of several atomization models used in both non-superheat and superheat spray calculations. As a part of this investigation we have undertaken the validation based on four different cases to investigate the spray characteristics of (1) a flashing jet generated by the sudden release of pressurized R134A from cylindrical nozzle, (2) a liquid jet atomizing in a subsonic cross flow, (3) a Parker-Hannifin pressure swirl atomizer, and (4) a single-element Lean Direct Injector (LDI) combustor experiment. These cases were chosen because of their importance in some aerospace applications. The validation is based on some 3D and axisymmetric calculations involving both reacting and non-reacting sprays. In general, the predicted results provide reasonable agreement for both mean droplet sizes (D32) and average droplet velocities but mostly underestimate the droplets sizes in the inner radial region of a cylindrical jet.

  10. Agricultural and Environmental Input Parameters for the Biosphere Model

    SciTech Connect

    K. Rasmuson; K. Rautenstrauch

    2004-09-14

    This analysis is one of 10 technical reports that support the Environmental Radiation Model for Yucca Mountain Nevada (ERMYN) (i.e., the biosphere model). It documents development of agricultural and environmental input parameters for the biosphere model, and supports the use of the model to develop biosphere dose conversion factors (BDCFs). The biosphere model is one of a series of process models supporting the total system performance assessment (TSPA) for the repository at Yucca Mountain. The ERMYN provides the TSPA with the capability to perform dose assessments. A graphical representation of the documentation hierarchy for the ERMYN is presented in Figure 1-1. This figure shows the interrelationships between the major activities and their products (the analysis and model reports) that were planned in ''Technical Work Plan for Biosphere Modeling and Expert Support'' (BSC 2004 [DIRS 169573]). The ''Biosphere Model Report'' (BSC 2004 [DIRS 169460]) describes the ERMYN and its input parameters.

  11. Combined Estimation of Hydrogeologic Conceptual Model and Parameter Uncertainty

    SciTech Connect

    Meyer, Philip D.; Ye, Ming; Neuman, Shlomo P.; Cantrell, Kirk J.

    2004-03-01

    The objective of the research described in this report is the development and application of a methodology for comprehensively assessing the hydrogeologic uncertainties involved in dose assessment, including uncertainties associated with conceptual models, parameters, and scenarios. This report describes and applies a statistical method to quantitatively estimate the combined uncertainty in model predictions arising from conceptual model and parameter uncertainties. The method relies on model averaging to combine the predictions of a set of alternative models. Implementation is driven by the available data. When there is minimal site-specific data the method can be carried out with prior parameter estimates based on generic data and subjective prior model probabilities. For sites with observations of system behavior (and optionally data characterizing model parameters), the method uses model calibration to update the prior parameter estimates and model probabilities based on the correspondence between model predictions and site observations. The set of model alternatives can contain both simplified and complex models, with the requirement that all models be based on the same set of data. The method was applied to the geostatistical modeling of air permeability at a fractured rock site. Seven alternative variogram models of log air permeability were considered to represent data from single-hole pneumatic injection tests in six boreholes at the site. Unbiased maximum likelihood estimates of variogram and drift parameters were obtained for each model. Standard information criteria provided an ambiguous ranking of the models, which would not justify selecting one of them and discarding all others as is commonly done in practice. Instead, some of the models were eliminated based on their negligibly small updated probabilities and the rest were used to project the measured log permeabilities by kriging onto a rock volume containing the six boreholes. These four

  12. Accuracy of Aerodynamic Model Parameters Estimated from Flight Test Data

    NASA Technical Reports Server (NTRS)

    Morelli, Eugene A.; Klein, Vladislav

    1997-01-01

    An important put of building mathematical models based on measured date is calculating the accuracy associated with statistical estimates of the model parameters. Indeed, without some idea of this accuracy, the parameter estimates themselves have limited value. An expression is developed for computing quantitatively correct parameter accuracy measures for maximum likelihood parameter estimates when the output residuals are colored. This result is important because experience in analyzing flight test data reveals that the output residuals from maximum likelihood estimation are almost always colored. The calculations involved can be appended to conventional maximum likelihood estimation algorithms. Monte Carlo simulation runs were used to show that parameter accuracy measures from the new technique accurately reflect the quality of the parameter estimates from maximum likelihood estimation without the need for correction factors or frequency domain analysis of the output residuals. The technique was applied to flight test data from repeated maneuvers flown on the F-18 High Alpha Research Vehicle. As in the simulated cases, parameter accuracy measures from the new technique were in agreement with the scatter in the parameter estimates from repeated maneuvers, whereas conventional parameter accuracy measures were optimistic.

  13. Development of a coincidence system for the measurement of X-ray emission atomic parameters

    NASA Astrophysics Data System (ADS)

    Martínez, Filiberto; Miranda, Javier

    2013-07-01

    Preliminary results obtained in experiments carried out with an x-ray spectrometer built at the Instituto de Física for Atomic Physics and environmental sciences studies are presented. The experiments are based on a coincidence method for signals produced by LEGe and Si(Li) detectors. The x-ray fluorescence yields (ωLi) and Coster-Kronig transition probabilities (fij) for elements with 55 ≤ Z ≤ 60 are among the quantities of interest. The method is based on the simultaneous detection of K x-rays with the LEGe detector and the L x-rays with the Si(Li) detector. The primary radiation source is an x-ray tube with Rh anode. The system was tested with the coincidence of the L x-rays from Ce with its K line, demonstrating the feasibility of the experiments.

  14. Development of a coincidence system for the measurement of X-ray emission atomic parameters

    SciTech Connect

    Martinez, Filiberto; Miranda, Javier

    2013-07-03

    Preliminary results obtained in experiments carried out with an x-ray spectrometer built at the Instituto de Fisica for Atomic Physics and environmental sciences studies are presented. The experiments are based on a coincidence method for signals produced by LEGe and Si(Li) detectors. The x-ray fluorescence yields ({omega}{sub Li}) and Coster-Kronig transition probabilities (f{sub ij}) for elements with 55 {<=} Z {<=} 60 are among the quantities of interest. The method is based on the simultaneous detection of K x-rays with the LEGe detector and the L x-rays with the Si(Li) detector. The primary radiation source is an x-ray tube with Rh anode. The system was tested with the coincidence of the L x-rays from Ce with its K line, demonstrating the feasibility of the experiments.

  15. Numerical modeling of piezoelectric transducers using physical parameters.

    PubMed

    Cappon, Hans; Keesman, Karel J

    2012-05-01

    Design of ultrasonic equipment is frequently facilitated with numerical models. These numerical models, however, need a calibration step, because usually not all characteristics of the materials used are known. Characterization of material properties combined with numerical simulations and experimental data can be used to acquire valid estimates of the material parameters. In our design application, a finite element (FE) model of an ultrasonic particle separator, driven by an ultrasonic transducer in thickness mode, is required. A limited set of material parameters for the piezoelectric transducer were obtained from the manufacturer, thus preserving prior physical knowledge to a large extent. The remaining unknown parameters were estimated from impedance analysis with a simple experimental setup combined with a numerical optimization routine using 2-D and 3-D FE models. Thus, a full set of physically interpretable material parameters was obtained for our specific purpose. The approach provides adequate accuracy of the estimates of the material parameters, near 1%. These parameter estimates will subsequently be applied in future design simulations, without the need to go through an entire series of characterization experiments. Finally, a sensitivity study showed that small variations of 1% in the main parameters caused changes near 1% in the eigenfrequency, but changes up to 7% in the admittance peak, thus influencing the efficiency of the system. Temperature will already cause these small variations in response; thus, a frequency control unit is required when actually manufacturing an efficient ultrasonic separation system.

  16. SPOTting Model Parameters Using a Ready-Made Python Package

    PubMed Central

    Houska, Tobias; Kraft, Philipp; Chamorro-Chavez, Alejandro; Breuer, Lutz

    2015-01-01

    The choice for specific parameter estimation methods is often more dependent on its availability than its performance. We developed SPOTPY (Statistical Parameter Optimization Tool), an open source python package containing a comprehensive set of methods typically used to calibrate, analyze and optimize parameters for a wide range of ecological models. SPOTPY currently contains eight widely used algorithms, 11 objective functions, and can sample from eight parameter distributions. SPOTPY has a model-independent structure and can be run in parallel from the workstation to large computation clusters using the Message Passing Interface (MPI). We tested SPOTPY in five different case studies to parameterize the Rosenbrock, Griewank and Ackley functions, a one-dimensional physically based soil moisture routine, where we searched for parameters of the van Genuchten-Mualem function and a calibration of a biogeochemistry model with different objective functions. The case studies reveal that the implemented SPOTPY methods can be used for any model with just a minimal amount of code for maximal power of parameter optimization. They further show the benefit of having one package at hand that includes number of well performing parameter search methods, since not every case study can be solved sufficiently with every algorithm or every objective function. PMID:26680783

  17. AUTOMATED FORCE FIELD PARAMETERIZATION FOR NON-POLARIZABLE AND POLARIZABLE ATOMIC MODELS BASED ON AB INITIO TARGET DATA.

    PubMed

    Huang, Lei; Roux, Benoît

    2013-08-13

    Classical molecular dynamics (MD) simulations based on atomistic models are increasingly used to study a wide range of biological systems. A prerequisite for meaningful results from such simulations is an accurate molecular mechanical force field. Most biomolecular simulations are currently based on the widely used AMBER and CHARMM force fields, which were parameterized and optimized to cover a small set of basic compounds corresponding to the natural amino acids and nucleic acid bases. Atomic models of additional compounds are commonly generated by analogy to the parameter set of a given force field. While this procedure yields models that are internally consistent, the accuracy of the resulting models can be limited. In this work, we propose a method, General Automated Atomic Model Parameterization (GAAMP), for generating automatically the parameters of atomic models of small molecules using the results from ab initio quantum mechanical (QM) calculations as target data. Force fields that were previously developed for a wide range of model compounds serve as initial guess, although any of the final parameter can be optimized. The electrostatic parameters (partial charges, polarizabilities and shielding) are optimized on the basis of QM electrostatic potential (ESP) and, if applicable, the interaction energies between the compound and water molecules. The soft dihedrals are automatically identified and parameterized by targeting QM dihedral scans as well as the energies of stable conformers. To validate the approach, the solvation free energy is calculated for more than 200 small molecules and MD simulations of 3 different proteins are carried out.

  18. An Effective Parameter Screening Strategy for High Dimensional Watershed Models

    NASA Astrophysics Data System (ADS)

    Khare, Y. P.; Martinez, C. J.; Munoz-Carpena, R.

    2014-12-01

    Watershed simulation models can assess the impacts of natural and anthropogenic disturbances on natural systems. These models have become important tools for tackling a range of water resources problems through their implementation in the formulation and evaluation of Best Management Practices, Total Maximum Daily Loads, and Basin Management Action Plans. For accurate applications of watershed models they need to be thoroughly evaluated through global uncertainty and sensitivity analyses (UA/SA). However, due to the high dimensionality of these models such evaluation becomes extremely time- and resource-consuming. Parameter screening, the qualitative separation of important parameters, has been suggested as an essential step before applying rigorous evaluation techniques such as the Sobol' and Fourier Amplitude Sensitivity Test (FAST) methods in the UA/SA framework. The method of elementary effects (EE) (Morris, 1991) is one of the most widely used screening methodologies. Some of the common parameter sampling strategies for EE, e.g. Optimized Trajectories [OT] (Campolongo et al., 2007) and Modified Optimized Trajectories [MOT] (Ruano et al., 2012), suffer from inconsistencies in the generated parameter distributions, infeasible sample generation time, etc. In this work, we have formulated a new parameter sampling strategy - Sampling for Uniformity (SU) - for parameter screening which is based on the principles of the uniformity of the generated parameter distributions and the spread of the parameter sample. A rigorous multi-criteria evaluation (time, distribution, spread and screening efficiency) of OT, MOT, and SU indicated that SU is superior to other sampling strategies. Comparison of the EE-based parameter importance rankings with those of Sobol' helped to quantify the qualitativeness of the EE parameter screening approach, reinforcing the fact that one should use EE only to reduce the resource burden required by FAST/Sobol' analyses but not to replace it.

  19. A comprehensive X-ray absorption model for atomic oxygen

    SciTech Connect

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

    2013-12-10

    An analytical formula is developed to accurately represent the photoabsorption cross section of O I 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.

  20. Application of physical parameter identification to finite element models

    NASA Technical Reports Server (NTRS)

    Bronowicki, Allen J.; Lukich, Michael S.; Kuritz, Steven P.

    1986-01-01

    A time domain technique for matching response predictions of a structural dynamic model to test measurements is developed. Significance is attached to prior estimates of physical model parameters and to experimental data. The Bayesian estimation procedure allows confidence levels in predicted physical and modal parameters to be obtained. Structural optimization procedures are employed to minimize an error functional with physical model parameters describing the finite element model as design variables. The number of complete FEM analyses are reduced using approximation concepts, including the recently developed convoluted Taylor series approach. The error function is represented in closed form by converting free decay test data to a time series model using Prony' method. The technique is demonstrated on simulated response of a simple truss structure.

  1. Parameter Identification in a Tuberculosis Model for Cameroon

    PubMed Central

    Moualeu-Ngangue, Dany Pascal; Röblitz, Susanna; Ehrig, Rainald; Deuflhard, Peter

    2015-01-01

    A deterministic model of tuberculosis in Cameroon is designed and analyzed with respect to its transmission dynamics. The model includes lack of access to treatment and weak diagnosis capacity as well as both frequency- and density-dependent transmissions. It is shown that the model is mathematically well-posed and epidemiologically reasonable. Solutions are non-negative and bounded whenever the initial values are non-negative. A sensitivity analysis of model parameters is performed and the most sensitive ones are identified by means of a state-of-the-art Gauss-Newton method. In particular, parameters representing the proportion of individuals having access to medical facilities are seen to have a large impact on the dynamics of the disease. The model predicts that a gradual increase of these parameters could significantly reduce the disease burden on the population within the next 15 years. PMID:25874885

  2. Regionalization parameters of conceptual rainfall-runoff model

    NASA Astrophysics Data System (ADS)

    Osuch, M.

    2003-04-01

    Main goal of this study was to develop techniques for the a priori estimation parameters of hydrological model. Conceptual hydrological model CLIRUN was applied to around 50 catchment in Poland. The size of catchments range from 1 000 to 100 000 km2. The model was calibrated for a number of gauged catchments with different catchment characteristics. The parameters of model were related to different climatic and physical catchment characteristics (topography, land use, vegetation and soil type). The relationships were tested by comparing observed and simulated runoff series from the gauged catchment that were not used in the calibration. The model performance using regional parameters was promising for most of the calibration and validation catchments.

  3. Parameter Sensitivity Evaluation of the CLM-Crop model

    NASA Astrophysics Data System (ADS)

    Drewniak, B. A.; Zeng, X.; Mametjanov, A.; Anitescu, M.; Norris, B.; Kotamarthi, V. R.

    2011-12-01

    In order to improve carbon cycling within Earth System Models, crop representation for corn, spring wheat, and soybean species has been incorporated into the latest version of the Community Land Model (CLM), the land surface model in the Community Earth System Model. As a means to evaluate and improve the CLM-Crop model, we will determine the sensitivity of various crop parameters on carbon fluxes (such as GPP and NEE), yields, and soil organic matter. The sensitivity analysis will perform small perturbations over a range of values for each parameter on individual grid sites, for comparison with AmeriFlux data, as well as globally so crop model parameters can be improved. Over 20 parameters have been identified for evaluation in this study including carbon-nitrogen ratios for leaves, stems, roots, and organs; fertilizer applications; growing degree days for each growth stage; and more. Results from this study will be presented to give a better understanding of the sensitivity of the various parameters used to represent crops, which will help improve the overall model performance and aid with determining future influences climate change will have on cropland ecosystems.

  4. Observation model and parameter partials for the JPL VLBI parameter estimation software MODEST, 19 94

    NASA Technical Reports Server (NTRS)

    Sovers, O. J.; Jacobs, C. S.

    1994-01-01

    This report is a revision of the document Observation Model and Parameter Partials for the JPL VLBI Parameter Estimation Software 'MODEST'---1991, dated August 1, 1991. It supersedes that document and its four previous versions (1983, 1985, 1986, and 1987). A number of aspects of the very long baseline interferometry (VLBI) model were improved from 1991 to 1994. Treatment of tidal effects is extended to model the effects of ocean tides on universal time and polar motion (UTPM), including a default model for nearly diurnal and semidiurnal ocean tidal UTPM variations, and partial derivatives for all (solid and ocean) tidal UTPM amplitudes. The time-honored 'K(sub 1) correction' for solid earth tides has been extended to include analogous frequency-dependent response of five tidal components. Partials of ocean loading amplitudes are now supplied. The Zhu-Mathews-Oceans-Anisotropy (ZMOA) 1990-2 and Kinoshita-Souchay models of nutation are now two of the modeling choices to replace the increasingly inadequate 1980 International Astronomical Union (IAU) nutation series. A rudimentary model of antenna thermal expansion is provided. Two more troposphere mapping functions have been added to the repertoire. Finally, corrections among VLBI observations via the model of Treuhaft and lanyi improve modeling of the dynamic troposphere. A number of minor misprints in Rev. 4 have been corrected.

  5. Absolute rate parameters for the reaction of ground state atomic oxygen with carbonyl sulfide

    NASA Technical Reports Server (NTRS)

    Klemm, R. B.; Stief, L. J.

    1974-01-01

    The rate parameters for the reaction of O(3P) with carbonyl sulfide, O(3P) + OCS yields CO + SO, have been determined directly by monitoring O(3P) using the flash photolysis-resonance fluorescence technique. The value for reaction rate was measured over a temperature range of 263-502 K and the data were fitted to an Arrhenius expression with good linearity. A comparison of the present results with those from previous studies of this reaction is also presented.

  6. Parameter Estimation for Groundwater Models under Uncertain Irrigation Data.

    PubMed

    Demissie, Yonas; Valocchi, Albert; Cai, Ximing; Brozovic, Nicholas; Senay, Gabriel; Gebremichael, Mekonnen

    2015-01-01

    The success of modeling groundwater is strongly influenced by the accuracy of the model parameters that are used to characterize the subsurface system. However, the presence of uncertainty and possibly bias in groundwater model source/sink terms may lead to biased estimates of model parameters and model predictions when the standard regression-based inverse modeling techniques are used. This study first quantifies the levels of bias in groundwater model parameters and predictions due to the presence of errors in irrigation data. Then, a new inverse modeling technique called input uncertainty weighted least-squares (IUWLS) is presented for unbiased estimation of the parameters when pumping and other source/sink data are uncertain. The approach uses the concept of generalized least-squares method with the weight of the objective function depending on the level of pumping uncertainty and iteratively adjusted during the parameter optimization process. We have conducted both analytical and numerical experiments, using irrigation pumping data from the Republican River Basin in Nebraska, to evaluate the performance of ordinary least-squares (OLS) and IUWLS calibration methods under different levels of uncertainty of irrigation data and calibration conditions. The result from the OLS method shows the presence of statistically significant (p < 0.05) bias in estimated parameters and model predictions that persist despite calibrating the models to different calibration data and sample sizes. However, by directly accounting for the irrigation pumping uncertainties during the calibration procedures, the proposed IUWLS is able to minimize the bias effectively without adding significant computational burden to the calibration processes.

  7. Parameter Estimation for Groundwater Models under Uncertain Irrigation Data.

    PubMed

    Demissie, Yonas; Valocchi, Albert; Cai, Ximing; Brozovic, Nicholas; Senay, Gabriel; Gebremichael, Mekonnen

    2015-01-01

    The success of modeling groundwater is strongly influenced by the accuracy of the model parameters that are used to characterize the subsurface system. However, the presence of uncertainty and possibly bias in groundwater model source/sink terms may lead to biased estimates of model parameters and model predictions when the standard regression-based inverse modeling techniques are used. This study first quantifies the levels of bias in groundwater model parameters and predictions due to the presence of errors in irrigation data. Then, a new inverse modeling technique called input uncertainty weighted least-squares (IUWLS) is presented for unbiased estimation of the parameters when pumping and other source/sink data are uncertain. The approach uses the concept of generalized least-squares method with the weight of the objective function depending on the level of pumping uncertainty and iteratively adjusted during the parameter optimization process. We have conducted both analytical and numerical experiments, using irrigation pumping data from the Republican River Basin in Nebraska, to evaluate the performance of ordinary least-squares (OLS) and IUWLS calibration methods under different levels of uncertainty of irrigation data and calibration conditions. The result from the OLS method shows the presence of statistically significant (p < 0.05) bias in estimated parameters and model predictions that persist despite calibrating the models to different calibration data and sample sizes. However, by directly accounting for the irrigation pumping uncertainties during the calibration procedures, the proposed IUWLS is able to minimize the bias effectively without adding significant computational burden to the calibration processes. PMID:25040235

  8. Ab initio calculation of Hubbard parameters for Rydberg-dressed atoms in a one-dimensional optical lattice

    NASA Astrophysics Data System (ADS)

    Chougale, Yashwant; Nath, Rejish

    2016-07-01

    We obtain ab initio the Hubbard parameters for Rydberg-dressed atoms in a one-dimensional (1D) sinusoidal optical lattice on the basis of maximally-localized Wannier states. Finite range, soft-core interatomic interactions become the trait of Rydberg admixed atoms, which can be extended over many neighboring lattice sites. In contrast to dipolar gases, where the interactions follow an inverse cubic law, the key feature of Rydberg-dressed interactions is the possibility of making neighboring couplings to the same magnitude as that of the onsite ones. The maximally-localized Wannier functions (MLWFs) are typically calculated via a spread-minimization procedure (Marzari N and Vanderbilt D 1997 Phys. Rev. B 56 12847) and are always found to be real functions apart from a trivial global phase when an isolated set of Bloch bands are considered. For an isolated single Bloch band, the above procedure reduces to a simple quasi-momentum-dependent unitary phase transformation. Here, instead of minimizing the spread, we employ a diagonal phase transformation which eliminates the imaginary part of the Wannier functions. The resulting Wannier states are found to be maximally localized and in exact agreement with those obtained via a spread-minimization procedure. Using these findings, we calculate the Hubbard couplings from the Rydberg admixed interactions, including dominant density-assisted tunneling (DAT) coefficients. Finally, we provide realistic lattice parameters for the state-of-the-art experimental Rydberg-dressed rubidium setup.

  9. Parameters of cosmological models and recent astronomical observations

    SciTech Connect

    Sharov, G.S.; Vorontsova, E.G. E-mail: elenavor@inbox.ru

    2014-10-01

    For different gravitational models we consider limitations on their parameters coming from recent observational data for type Ia supernovae, baryon acoustic oscillations, and from 34 data points for the Hubble parameter H(z) depending on redshift. We calculate parameters of 3 models describing accelerated expansion of the universe: the ΛCDM model, the model with generalized Chaplygin gas (GCG) and the multidimensional model of I. Pahwa, D. Choudhury and T.R. Seshadri. In particular, for the ΛCDM model 1σ estimates of parameters are: H{sub 0}=70.262±0.319 km {sup -1}Mp {sup -1}, Ω{sub m}=0.276{sub -0.008}{sup +0.009}, Ω{sub Λ}=0.769±0.029, Ω{sub k}=-0.045±0.032. The GCG model under restriction 0α≥ is reduced to the ΛCDM model. Predictions of the multidimensional model essentially depend on 3 data points for H(z) with z≥2.3.

  10. Material parameter computation for multi-layered vocal fold models.

    PubMed

    Schmidt, Bastian; Stingl, Michael; Leugering, Günter; Berry, David A; Döllinger, Michael

    2011-04-01

    Today, the prevention and treatment of voice disorders is an ever-increasing health concern. Since many occupations rely on verbal communication, vocal health is necessary just to maintain one's livelihood. Commonly applied models to study vocal fold vibrations and air flow distributions are self sustained physical models of the larynx composed of artificial silicone vocal folds. Choosing appropriate mechanical parameters for these vocal fold models while considering simplifications due to manufacturing restrictions is difficult but crucial for achieving realistic behavior. In the present work, a combination of experimental and numerical approaches to compute material parameters for synthetic vocal fold models is presented. The material parameters are derived from deformation behaviors of excised human larynges. The resulting deformations are used as reference displacements for a tracking functional to be optimized. Material optimization was applied to three-dimensional vocal fold models based on isotropic and transverse-isotropic material laws, considering both a layered model with homogeneous material properties on each layer and an inhomogeneous model. The best results exhibited a transversal-isotropic inhomogeneous (i.e., not producible) model. For the homogeneous model (three layers), the transversal-isotropic material parameters were also computed for each layer yielding deformations similar to the measured human vocal fold deformations.

  11. System for Predicting Pitzer Ion-Interaction Model Parameters

    NASA Astrophysics Data System (ADS)

    Schreiber, D. R.; Obias, T.

    2002-12-01

    Pitzer's Ion-Interaction Model has been widely utilized for the prediction of non-ideal solution behavior. The Pitzer model does an excellent job of predicting the solubility of minerals over a wide range of conditions for natural water systems. While Pitzer's equations have been successful in modeling systems when there are parameters available, there are still some systems that can't be modeled because parameters aren't available for all of the salts of interest. For example, there is little to no data for aluminum salts yet in acidified natural waters it may be present at significant concentrations. In addition, aluminum chemistry will also be important in the remediation of acidified High-level waste. Given the quantity of work involved in generating the needed parameters it would be advantageous to be able to predict Pitzer parameters for salt systems when there is no data available. Recently we began work on modeling High-level waste systems where Pitzer parameters are not available for some of the constituents of interest. We will discuss a set of relations we have developed for the prediction of Pitzer's binary ion-interaction parameters. In the binary parameter case, we reformulated the Pitzer's equations by replacing the parameters, β(0), β(1), β(2), and C, with expressions in ionic radii. Equations have been developed for salts of a particular anion with cations of similar charge. For example, there is a single equation for the 1:1 chloride salts. Relations for acids were developed separately. Also we have developed a separate set of equations for all salts of a particular charge type independent of the anion. While the latter set of equations are of lesser predictive value, they can be used in cases where we don't have a relation for a particular anion. Since any system used to predict parameters would result in a loss of accuracy, experimentally determined parameters should be used when available. The ability of parameters derived from our model

  12. Environmental Transport Input Parameters for the Biosphere Model

    SciTech Connect

    M. Wasiolek

    2004-09-10

    This analysis report is one of the technical reports documenting the Environmental Radiation Model for Yucca Mountain, Nevada (ERMYN), a biosphere model supporting the total system performance assessment for the license application (TSPA-LA) for the geologic repository at Yucca Mountain. A graphical representation of the documentation hierarchy for the ERMYN is presented in Figure 1-1. This figure shows relationships among the reports developed for biosphere modeling and biosphere abstraction products for the TSPA-LA, as identified in the ''Technical Work Plan for Biosphere Modeling and Expert Support'' (BSC 2004 [DIRS 169573]) (TWP). This figure provides an understanding of how this report contributes to biosphere modeling in support of the license application (LA). This report is one of the five reports that develop input parameter values for the biosphere model. The ''Biosphere Model Report'' (BSC 2004 [DIRS 169460]) describes the conceptual model and the mathematical model. The input parameter reports, shown to the right of the Biosphere Model Report in Figure 1-1, contain detailed description of the model input parameters. The output of this report is used as direct input in the ''Nominal Performance Biosphere Dose Conversion Factor Analysis'' and in the ''Disruptive Event Biosphere Dose Conversion Factor Analysis'' that calculate the values of biosphere dose conversion factors (BDCFs) for the groundwater and volcanic ash exposure scenarios, respectively. The purpose of this analysis was to develop biosphere model parameter values related to radionuclide transport and accumulation in the environment. These parameters support calculations of radionuclide concentrations in the environmental media (e.g., soil, crops, animal products, and air) resulting from a given radionuclide concentration at the source of contamination (i.e., either in groundwater or in volcanic ash). The analysis was performed in accordance with the TWP (BSC 2004 [DIRS 169573]).

  13. Spatial Variability and Interpolation of Stochastic Weather Simulation Model Parameters.

    NASA Astrophysics Data System (ADS)

    Johnson, Gregory L.; Daly, Christopher; Taylor, George H.; Hanson, Clayton L.

    2000-06-01

    The spatial variability of 58 precipitation and temperature parameters from the `generation of weather elements for multiple applications' (GEM) weather generator has been investigated over a region of significant complexity in topography and climate. GEM parameters were derived for 80 climate stations in southern Idaho and southeastern Oregon. A technique was developed and used to determine the GEM parameters from high-elevation snowpack telemetry stations that report precipitation in nonstandard 2.5-mm (versus 0.25 mm) increments. Important dependencies were noted between most of these parameters and elevation (both domainwide and local), location, and other factors. The `parameter-elevation regressions on independent slopes model' (PRISM) spatial modeling system was used to develop approximate 4-km gridded data fields of each of these parameters. A feature was developed in PRISM that models temperatures above and below mean inversions differently. Examples of the spatial fields derived from this study and a discussion of the applications of these spatial parameter fields are included.

  14. Inhalation Exposure Input Parameters for the Biosphere Model

    SciTech Connect

    K. Rautenstrauch

    2004-09-10

    This analysis is one of 10 reports that support the Environmental Radiation Model for Yucca Mountain, Nevada (ERMYN) biosphere model. The ''Biosphere Model Report'' (BSC 2004 [DIRS 169460]) describes in detail the conceptual model as well as the mathematical model and its input parameters. This report documents development of input parameters for the biosphere model that are related to atmospheric mass loading and supports the use of the model to develop biosphere dose conversion factors (BDCFs). The biosphere model is one of a series of process models supporting the total system performance assessment (TSPA) for a Yucca Mountain repository. Inhalation Exposure Input Parameters for the Biosphere Model is one of five reports that develop input parameters for the biosphere model. A graphical representation of the documentation hierarchy for the ERMYN is presented in Figure 1-1. This figure shows the interrelationships among the products (i.e., analysis and model reports) developed for biosphere modeling, and the plan for development of the biosphere abstraction products for TSPA, as identified in the Technical Work Plan for Biosphere Modeling and Expert Support (BSC 2004 [DIRS 169573]). This analysis report defines and justifies values of mass loading for the biosphere model. Mass loading is the total mass concentration of resuspended particles (e.g., dust, ash) in a volume of air. Mass loading values are used in the air submodel of ERMYN to calculate concentrations of radionuclides in air inhaled by a receptor and concentrations in air surrounding crops. Concentrations in air to which the receptor is exposed are then used in the inhalation submodel to calculate the dose contribution to the receptor from inhalation of contaminated airborne particles. Concentrations in air surrounding plants are used in the plant submodel to calculate the concentrations of radionuclides in foodstuffs contributed from uptake by foliar interception.

  15. Parameter uncertainty analysis of a biokinetic model of caesium.

    PubMed

    Li, W B; Klein, W; Blanchardon, E; Puncher, M; Leggett, R W; Oeh, U; Breustedt, B; Noßke, D; Lopez, M A

    2015-01-01

    Parameter uncertainties for the biokinetic model of caesium (Cs) developed by Leggett et al. were inventoried and evaluated. The methods of parameter uncertainty analysis were used to assess the uncertainties of model predictions with the assumptions of model parameter uncertainties and distributions. Furthermore, the importance of individual model parameters was assessed by means of sensitivity analysis. The calculated uncertainties of model predictions were compared with human data of Cs measured in blood and in the whole body. It was found that propagating the derived uncertainties in model parameter values reproduced the range of bioassay data observed in human subjects at different times after intake. The maximum ranges, expressed as uncertainty factors (UFs) (defined as a square root of ratio between 97.5th and 2.5th percentiles) of blood clearance, whole-body retention and urinary excretion of Cs predicted at earlier time after intake were, respectively: 1.5, 1.0 and 2.5 at the first day; 1.8, 1.1 and 2.4 at Day 10 and 1.8, 2.0 and 1.8 at Day 100; for the late times (1000 d) after intake, the UFs were increased to 43, 24 and 31, respectively. The model parameters of transfer rates between kidneys and blood, muscle and blood and the rate of transfer from kidneys to urinary bladder content are most influential to the blood clearance and to the whole-body retention of Cs. For the urinary excretion, the parameters of transfer rates from urinary bladder content to urine and from kidneys to urinary bladder content impact mostly. The implication and effect on the estimated equivalent and effective doses of the larger uncertainty of 43 in whole-body retention in the later time, say, after Day 500 will be explored in a successive work in the framework of EURADOS.

  16. Environmental Transport Input Parameters for the Biosphere Model

    SciTech Connect

    M. A. Wasiolek

    2003-06-27

    This analysis report is one of the technical reports documenting the Environmental Radiation Model for Yucca Mountain Nevada (ERMYN), a biosphere model supporting the total system performance assessment (TSPA) for the geologic repository at Yucca Mountain. A graphical representation of the documentation hierarchy for the ERMYN is presented in Figure 1-1. This figure shows relationships among the reports developed for biosphere modeling and biosphere abstraction products for the TSPA, as identified in the ''Technical Work Plan: for Biosphere Modeling and Expert Support'' (TWP) (BSC 2003 [163602]). Some documents in Figure 1-1 may be under development and not available when this report is issued. This figure provides an understanding of how this report contributes to biosphere modeling in support of the license application (LA), but access to the listed documents is not required to understand the contents of this report. This report is one of the reports that develops input parameter values for the biosphere model. The ''Biosphere Model Report'' (BSC 2003 [160699]) describes the conceptual model, the mathematical model, and the input parameters. The purpose of this analysis is to develop biosphere model parameter values related to radionuclide transport and accumulation in the environment. These parameters support calculations of radionuclide concentrations in the environmental media (e.g., soil, crops, animal products, and air) resulting from a given radionuclide concentration at the source of contamination (i.e., either in groundwater or volcanic ash). The analysis was performed in accordance with the TWP (BSC 2003 [163602]). This analysis develops values of parameters associated with many features, events, and processes (FEPs) applicable to the reference biosphere (DTN: M00303SEPFEPS2.000 [162452]), which are addressed in the biosphere model (BSC 2003 [160699]). The treatment of these FEPs is described in BSC (2003 [160699], Section 6.2). Parameter values

  17. Observation model and parameter partials for the JPL VLBI parameter estimation software MASTERFIT-1987

    NASA Technical Reports Server (NTRS)

    Sovers, O. J.; Fanselow, J. L.

    1987-01-01

    This report is a revision of the document of the same title (1986), dated August 1, which it supersedes. Model changes during 1986 and 1987 included corrections for antenna feed rotation, refraction in modelling antenna axis offsets, and an option to employ improved values of the semiannual and annual nutation amplitudes. Partial derivatives of the observables with respect to an additional parameter (surface temperature) are now available. New versions of two figures representing the geometric delay are incorporated. The expressions for the partial derivatives with respect to the nutation parameters have been corrected to include contributions from the dependence of UTI on nutation. The authors hope to publish revisions of this document in the future, as modeling improvements warrant.

  18. New modeling of scattering behaviors of argon atoms on tungsten substrate.

    PubMed

    Leu, Tzong-Shyng; Cheng, Chin-Hsiang; Ozhgibesov, Mikhail Sergeevich

    2011-11-01

    In this study argon beam-tungsten surface scattering processes were investigated numerically by applying molecular dynamics simulations. Energy transfer, momentum change and the scattering processes of argon gas atoms from the W(110) surface were discussed. The molecular dynamics results showed that Maxwell boundary conditions fail to describe the behaviors of a high mean kinetic energy argon beam impinging on a tungsten surface. A new three-dimensional model of argon-tungsten interaction was thus proposed, and its results proved to be in line with experimental and theoretical results that have been obtained previously by other researchers. Specifically, we developed a method for the normalization of the parameters of a gas beam scattered by a metal surface. We found that the ratio of the average velocity of the scattered beam to the appropriate root mean square deviation (RMSD) allowed us to determine whether the distribution of the scattered atoms was Maxwellian or not. We found that the shape of the functions representing the angular distributions of the scattered Ar atoms could be determined using the ratio of the RMSD of an angle (azimuthal or polar) of the scattered beam to the RMSD of a uniform distribution. The distribution of the azimuthal angle of the scattered atoms was found to be uniform regardless of the incident's kinetic energy, when the incident of the beam on the surface was normal.

  19. Application of Powder Diffraction Methods to the Analysis of the Atomic Structure of Nanocrystals: The Concept of the Apparent Lattice Parameter (ALP)

    NASA Technical Reports Server (NTRS)

    Palosz, B.; Grzanka, E.; Gierlotka, S.; Stelmakh, S.; Pielaszek, R.; Bismayer, U.; Weber, H.-P.; Palosz, W.; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    The applicability of standard methods of elaboration of powder diffraction data for determination of the structure of nano-size crystallites is analysed. Based on our theoretical calculations of powder diffraction data we show, that the assumption of the infinite crystal lattice for nanocrystals smaller than 20 nm in size is not justified. Application of conventional tools developed for elaboration of powder diffraction data, like the Rietveld method, may lead to erroneous interpretation of the experimental results. An alternate evaluation of diffraction data of nanoparticles, based on the so-called 'apparent lattice parameter' (alp) is introduced. We assume a model of nanocrystal having a grain core with well-defined crystal structure, surrounded by a surface shell with the atomic structure similar to that of the core but being under a strain (compressive or tensile). The two structural components, the core and the shell, form essentially a composite crystal with interfering, inseparable diffraction properties. Because the structure of such a nanocrystal is not uniform, it defies the basic definitions of an unambiguous crystallographic phase. Consequently, a set of lattice parameters used for characterization of simple crystal phases is insufficient for a proper description of the complex structure of nanocrystals. We developed a method of evaluation of powder diffraction data of nanocrystals, which refers to a core-shell model and is based on the 'apparent lattice parameter' methodology. For a given diffraction pattem, the alp values are calculated for every individual Bragg reflection. For nanocrystals the alp values depend on the diffraction vector Q. By modeling different a0tomic structures of nanocrystals and calculating theoretically corresponding diffraction patterns using the Debye functions we showed, that alp-Q plots show characteristic shapes which can be used for evaluation of the atomic structure of the core-shell system. We show, that using a simple

  20. Observation of antiferromagnetic correlations in the Hubbard model with ultracold atoms.

    PubMed

    Hart, Russell A; Duarte, Pedro M; Yang, Tsung-Lin; Liu, Xinxing; Paiva, Thereza; Khatami, Ehsan; Scalettar, Richard T; Trivedi, Nandini; Huse, David A; Hulet, Randall G

    2015-03-12

    Ultracold atoms in optical lattices have great potential to contribute to a better understanding of some of the most important issues in many-body physics, such as high-temperature superconductivity. The Hubbard model--a simplified representation of fermions moving on a periodic lattice--is thought to describe the essential details of copper oxide superconductivity. This model describes many of the features shared by the copper oxides, including an interaction-driven Mott insulating state and an antiferromagnetic (AFM) state. Optical lattices filled with a two-spin-component Fermi gas of ultracold atoms can faithfully realize the Hubbard model with readily tunable parameters, and thus provide a platform for the systematic exploration of its phase diagram. Realization of strongly correlated phases, however, has been hindered by the need to cool the atoms to temperatures as low as the magnetic exchange energy, and also by the lack of reliable thermometry. Here we demonstrate spin-sensitive Bragg scattering of light to measure AFM spin correlations in a realization of the three-dimensional Hubbard model at temperatures down to 1.4 times that of the AFM phase transition. This temperature regime is beyond the range of validity of a simple high-temperature series expansion, which brings our experiment close to the limit of the capabilities of current numerical techniques, particularly at metallic densities. We reach these low temperatures using a compensated optical lattice technique, in which the confinement of each lattice beam is compensated by a blue-detuned laser beam. The temperature of the atoms in the lattice is deduced by comparing the light scattering to determinant quantum Monte Carlo simulations and numerical linked-cluster expansion calculations. Further refinement of the compensated lattice may produce even lower temperatures which, along with light scattering thermometry, would open avenues for producing and characterizing other novel quantum states of

  1. Observation of antiferromagnetic correlations in the Hubbard model with ultracold atoms.

    PubMed

    Hart, Russell A; Duarte, Pedro M; Yang, Tsung-Lin; Liu, Xinxing; Paiva, Thereza; Khatami, Ehsan; Scalettar, Richard T; Trivedi, Nandini; Huse, David A; Hulet, Randall G

    2015-03-12

    Ultracold atoms in optical lattices have great potential to contribute to a better understanding of some of the most important issues in many-body physics, such as high-temperature superconductivity. The Hubbard model--a simplified representation of fermions moving on a periodic lattice--is thought to describe the essential details of copper oxide superconductivity. This model describes many of the features shared by the copper oxides, including an interaction-driven Mott insulating state and an antiferromagnetic (AFM) state. Optical lattices filled with a two-spin-component Fermi gas of ultracold atoms can faithfully realize the Hubbard model with readily tunable parameters, and thus provide a platform for the systematic exploration of its phase diagram. Realization of strongly correlated phases, however, has been hindered by the need to cool the atoms to temperatures as low as the magnetic exchange energy, and also by the lack of reliable thermometry. Here we demonstrate spin-sensitive Bragg scattering of light to measure AFM spin correlations in a realization of the three-dimensional Hubbard model at temperatures down to 1.4 times that of the AFM phase transition. This temperature regime is beyond the range of validity of a simple high-temperature series expansion, which brings our experiment close to the limit of the capabilities of current numerical techniques, particularly at metallic densities. We reach these low temperatures using a compensated optical lattice technique, in which the confinement of each lattice beam is compensated by a blue-detuned laser beam. The temperature of the atoms in the lattice is deduced by comparing the light scattering to determinant quantum Monte Carlo simulations and numerical linked-cluster expansion calculations. Further refinement of the compensated lattice may produce even lower temperatures which, along with light scattering thermometry, would open avenues for producing and characterizing other novel quantum states of

  2. Global-scale regionalization of hydrologic model parameters

    NASA Astrophysics Data System (ADS)

    Beck, Hylke E.; van Dijk, Albert I. J. M.; de Roo, Ad; Miralles, Diego G.; McVicar, Tim R.; Schellekens, Jaap; Bruijnzeel, L. Adrian

    2016-05-01

    Current state-of-the-art models typically applied at continental to global scales (hereafter called macroscale) tend to use a priori parameters, resulting in suboptimal streamflow (Q) simulation. For the first time, a scheme for regionalization of model parameters at the global scale was developed. We used data from a diverse set of 1787 small-to-medium sized catchments (10-10,000 km2) and the simple conceptual HBV model to set up and test the scheme. Each catchment was calibrated against observed daily Q, after which 674 catchments with high calibration and validation scores, and thus presumably good-quality observed Q and forcing data, were selected to serve as donor catchments. The calibrated parameter sets for the donors were subsequently transferred to 0.5° grid cells with similar climatic and physiographic characteristics, resulting in parameter maps for HBV with global coverage. For each grid cell, we used the 10 most similar donor catchments, rather than the single most similar donor, and averaged the resulting simulated Q, which enhanced model performance. The 1113 catchments not used as donors were used to independently evaluate the scheme. The regionalized parameters outperformed spatially uniform (i.e., averaged calibrated) parameters for 79% of the evaluation catchments. Substantial improvements were evident for all major Köppen-Geiger climate types and even for evaluation catchments > 5000 km distant from the donors. The median improvement was about half of the performance increase achieved through calibration. HBV with regionalized parameters outperformed nine state-of-the-art macroscale models, suggesting these might also benefit from the new regionalization scheme. The produced HBV parameter maps including ancillary data are available via www.gloh2o.org.

  3. Global-scale regionalization of hydrologic model parameters

    NASA Astrophysics Data System (ADS)

    Beck, Hylke; van Dijk, Albert; de Roo, Ad; Miralles, Diego; Schellekens, Jaap; McVicar, Tim; Bruijnzeel, Sampurno

    2016-04-01

    Current state-of-the-art models typically applied at continental to global scales (hereafter called macro-scale) tend to use a priori parameters, resulting in suboptimal streamflow (Q) simulation. For the first time, a scheme for regionalization of model parameters at the global scale was developed. We used data from a diverse set of 1787 small-to-medium sized catchments (10--10 000~km^2) and the simple conceptual HBV model to set up and test the scheme. Each catchment was calibrated against observed daily Q, after which 674 catchments with high calibration and validation scores, and thus presumably good-quality observed Q and forcing data, were selected to serve as donor catchments. The calibrated parameter sets for the donors were subsequently transferred to 0.5° grid cells with similar climatic and physiographic characteristics, resulting in parameter maps for HBV with global coverage. For each grid cell, we used the ten most similar donor catchments, rather than the single most similar donor, and averaged the resulting simulated Q, which enhanced model performance. The 1113 catchments not used as donors were used to independently evaluate the scheme. The regionalized parameters outperformed spatially-uniform (i.e., averaged calibrated) parameters for 79~% of the evaluation catchments. Substantial improvements were evident for all major Köppen-Geiger climate types and even for evaluation catchments >5000~km distance from the donors. The median improvement was about half of the performance increase achieved through calibration. HBV using regionalized parameters outperformed nine state-of-the-art macro-scale models, suggesting these might also benefit from the new regionalization scheme. The produced HBV parameter maps including ancillary data are available via http://water.jrc.ec.europa.eu/HBV/.

  4. Identification of Neurofuzzy models using GTLS parameter estimation.

    PubMed

    Jakubek, Stefan; Hametner, Christoph

    2009-10-01

    In this paper, nonlinear system identification utilizing generalized total least squares (GTLS) methodologies in neurofuzzy systems is addressed. The problem involved with the estimation of the local model parameters of neurofuzzy networks is the presence of noise in measured data. When some or all input channels are subject to noise, the GTLS algorithm yields consistent parameter estimates. In addition to the estimation of the parameters, the main challenge in the design of these local model networks is the determination of the region of validity for the local models. The method presented in this paper is based on an expectation-maximization algorithm that uses a residual from the GTLS parameter estimation for proper partitioning. The performance of the resulting nonlinear model with local parameters estimated by weighted GTLS is a product both of the parameter estimation itself and the associated residual used for the partitioning process. The applicability and benefits of the proposed algorithm are demonstrated by means of illustrative examples and an automotive application. PMID:19336320

  5. Dynamic Factor Analysis Models with Time-Varying Parameters

    ERIC Educational Resources Information Center

    Chow, Sy-Miin; Zu, Jiyun; Shifren, Kim; Zhang, Guangjian

    2011-01-01

    Dynamic factor analysis models with time-varying parameters offer a valuable tool for evaluating multivariate time series data with time-varying dynamics and/or measurement properties. We use the Dynamic Model of Activation proposed by Zautra and colleagues (Zautra, Potter, & Reich, 1997) as a motivating example to construct a dynamic factor model…

  6. Separability of Item and Person Parameters in Response Time Models.

    ERIC Educational Resources Information Center

    Van Breukelen, Gerard J. P.

    1997-01-01

    Discusses two forms of separability of item and person parameters in the context of response time models. The first is "separate sufficiency," and the second is "ranking independence." For each form a theorem stating sufficient conditions is proved. The two forms are shown to include several cases of models from psychometric and biometric…

  7. Atmospheric turbulence parameters for modeling wind turbine dynamics

    NASA Technical Reports Server (NTRS)

    Holley, W. E.; Thresher, R. W.

    1982-01-01

    A model which can be used to predict the response of wind turbines to atmospheric turbulence is given. The model was developed using linearized aerodynamics for a three-bladed rotor and accounts for three turbulent velocity components as well as velocity gradients across the rotor disk. Typical response power spectral densities are shown. The system response depends critically on three wind and turbulence parameters, and models are presented to predict desired response statistics. An equation error method, which can be used to estimate the required parameters from field data, is also presented.

  8. Uncertainty Analysis and Parameter Estimation For Nearshore Hydrodynamic Models

    NASA Astrophysics Data System (ADS)

    Ardani, S.; Kaihatu, J. M.

    2012-12-01

    Numerical models represent deterministic approaches used for the relevant physical processes in the nearshore. Complexity of the physics of the model and uncertainty involved in the model inputs compel us to apply a stochastic approach to analyze the robustness of the model. The Bayesian inverse problem is one powerful way to estimate the important input model parameters (determined by apriori sensitivity analysis) and can be used for uncertainty analysis of the outputs. Bayesian techniques can be used to find the range of most probable parameters based on the probability of the observed data and the residual errors. In this study, the effect of input data involving lateral (Neumann) boundary conditions, bathymetry and off-shore wave conditions on nearshore numerical models are considered. Monte Carlo simulation is applied to a deterministic numerical model (the Delft3D modeling suite for coupled waves and flow) for the resulting uncertainty analysis of the outputs (wave height, flow velocity, mean sea level and etc.). Uncertainty analysis of outputs is performed by random sampling from the input probability distribution functions and running the model as required until convergence to the consistent results is achieved. The case study used in this analysis is the Duck94 experiment, which was conducted at the U.S. Army Field Research Facility at Duck, North Carolina, USA in the fall of 1994. The joint probability of model parameters relevant for the Duck94 experiments will be found using the Bayesian approach. We will further show that, by using Bayesian techniques to estimate the optimized model parameters as inputs and applying them for uncertainty analysis, we can obtain more consistent results than using the prior information for input data which means that the variation of the uncertain parameter will be decreased and the probability of the observed data will improve as well. Keywords: Monte Carlo Simulation, Delft3D, uncertainty analysis, Bayesian techniques

  9. Quantitative composition determination at the atomic level using model-based high-angle annular dark field scanning transmission electron microscopy.

    PubMed

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

    2014-02-01

    High angle annular dark field scanning transmission electron microscopy (HAADF STEM) images provide sample information which is sensitive to the chemical composition. The image intensities indeed scale with the mean atomic number Z. To some extent, chemically different atomic column types can therefore be visually distinguished. However, in order to quantify the atomic column composition with high accuracy and precision, model-based methods are necessary. Therefore, an empirical incoherent parametric imaging model can be used of which the unknown parameters are determined using statistical parameter estimation theory (Van Aert et al., 2009, [1]). In this paper, it will be shown how this method can be combined with frozen lattice multislice simulations in order to evolve from a relative toward an absolute quantification of the composition of single atomic columns with mixed atom types. Furthermore, the validity of the model assumptions are explored and discussed.

  10. Masses of atomic nuclei in the infinite nuclear matter model

    SciTech Connect

    Satpathy, L.; Nayak, R.C.

    1988-07-01

    We present mass excesses of 3481 nuclei in the range 18less than or equal toAless than or equal to267 using the infinite nuclear matter model based on the Hugenholtz-Van Hove theorem. In this model the ground-state energy of a nucleus of asymmetry ..beta.. is considered equivalent to the energy of a perfect sphere made up of the infinite nuclear matter of the same asymmetry plus the residual energy due to shell effects, deformation, etc., called the local energy eta. In this model there are two kinds of parameters: global and local. The five global parameters characterizing the properties of the above sphere are determined by fitting the mass of all nuclei (756) in the recent mass table of Wapstra et al. having error bar less than 30 keV. The local parameters are determined for 25 regions each spanning 8 or 10 A values. The total number of parameters including the five global ones is 238. The root-mean-square deviation for the calculated masses from experiment is 397 keV for the 1572 nuclei used in the least-squares fit. copyright 1988 Academic Press, Inc.

  11. Sublattice model of atomic scale pairing inhomogeneity in a superconductor

    NASA Astrophysics Data System (ADS)

    Mishra, Vivek; Hirschfeld, P. J.; Barash, Yu. S.

    2008-10-01

    We study a toy model for a superconductor on a bipartite lattice where intrinsic pairing inhomogeneity is produced by two different coupling constants on the sublattices. The simplicity of the model allows for analytical solutions and tests of the consequences of atomic scale variations in pairing interactions, which have been considered recently in the cuprates. We present results for the transition temperature, density of states, and thermodynamics of the system over a phase diagram in the plane of two pairing coupling constants. For coupling constants of alternating sign, a gapless superconducting state is stable. Inhomogeneity is generally found to enhance the critical temperature, and at the same time the superfluid density is remarkably robust; at T=0 , it is suppressed only in the gapless phase.

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

    PubMed Central

    Lai, Peter C.; Crasto, Chiquito J.

    2012-01-01

    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 generate focused and novel hypotheses for further bench investigation by providing a view of these interactions at the molecular level beyond inferences that are drawn merely from static docking. Here we have shown the specific advantages of simulating the dynamic environment associated with OR-odorant interactions. We present a rigorous protocol which 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. PMID:22563330

  13. Bayesian methods for characterizing unknown parameters of material models

    DOE PAGES

    Emery, J. M.; Grigoriu, M. D.; Field Jr., R. V.

    2016-02-04

    A Bayesian framework is developed for characterizing the unknown parameters of probabilistic models for material properties. In this framework, the unknown parameters are viewed as random and described by their posterior distributions obtained from prior information and measurements of quantities of interest that are observable and depend on the unknown parameters. The proposed Bayesian method is applied to characterize an unknown spatial correlation of the conductivity field in the definition of a stochastic transport equation and to solve this equation by Monte Carlo simulation and stochastic reduced order models (SROMs). As a result, the Bayesian method is also employed tomore » characterize unknown parameters of material properties for laser welds from measurements of peak forces sustained by these welds.« less

  14. Soil-related Input Parameters for the Biosphere Model

    SciTech Connect

    A. J. Smith

    2003-07-02

    This analysis is one of the technical reports containing documentation of the Environmental Radiation Model for Yucca Mountain Nevada (ERMYN), a biosphere model supporting the Total System Performance Assessment (TSPA) for the geologic repository at Yucca Mountain. The biosphere model is one of a series of process models supporting the Total System Performance Assessment (TSPA) for the Yucca Mountain repository. A graphical representation of the documentation hierarchy for the ERMYN biosphere model is presented in Figure 1-1. This figure shows the interrelationships among the products (i.e., analysis and model reports) developed for biosphere modeling, and the plan for development of the biosphere abstraction products for TSPA, as identified in the ''Technical Work Plan: for Biosphere Modeling and Expert Support'' (BSC 2003 [163602]). It should be noted that some documents identified in Figure 1-1 may be under development at the time this report is issued and therefore not available. This figure is included to provide an understanding of how this analysis report contributes to biosphere modeling in support of the license application, and is not intended to imply that access to the listed documents is required to understand the contents of this report. This report, ''Soil Related Input Parameters for the Biosphere Model'', is one of the five analysis reports that develop input parameters for use in the ERMYN model. This report is the source documentation for the six biosphere parameters identified in Table 1-1. ''The Biosphere Model Report'' (BSC 2003 [160699]) describes in detail the conceptual model as well as the mathematical model and its input parameters. The purpose of this analysis was to develop the biosphere model parameters needed to evaluate doses from pathways associated with the accumulation and depletion of radionuclides in the soil. These parameters support the calculation of radionuclide concentrations in soil from on-going irrigation and ash

  15. Parameter Estimation for Single Diode Models of Photovoltaic Modules

    SciTech Connect

    Hansen, Clifford

    2015-03-01

    Many popular models for photovoltaic system performance employ a single diode model to compute the I - V curve for a module or string of modules at given irradiance and temperature conditions. A single diode model requires a number of parameters to be estimated from measured I - V curves. Many available parameter estimation methods use only short circuit, o pen circuit and maximum power points for a single I - V curve at standard test conditions together with temperature coefficients determined separately for individual cells. In contrast, module testing frequently records I - V curves over a wide range of irradi ance and temperature conditions which, when available , should also be used to parameterize the performance model. We present a parameter estimation method that makes use of a fu ll range of available I - V curves. We verify the accuracy of the method by recov ering known parameter values from simulated I - V curves . We validate the method by estimating model parameters for a module using outdoor test data and predicting the outdoor performance of the module.

  16. Atomic model of the type III secretion system needle.

    PubMed

    Loquet, Antoine; Sgourakis, Nikolaos G; Gupta, Rashmi; Giller, Karin; Riedel, Dietmar; Goosmann, Christian; Griesinger, Christian; Kolbe, Michael; Baker, David; Becker, Stefan; Lange, Adam

    2012-05-20

    Pathogenic bacteria using a type III secretion system (T3SS) to manipulate host cells cause many different infections including Shigella dysentery, typhoid fever, enterohaemorrhagic colitis and bubonic plague. An essential part of the T3SS is a hollow needle-like protein filament through which effector proteins are injected into eukaryotic host cells. Currently, the three-dimensional structure of the needle is unknown because it is not amenable to X-ray crystallography and solution NMR, as a result of its inherent non-crystallinity and insolubility. Cryo-electron microscopy combined with crystal or solution NMR subunit structures has recently provided a powerful hybrid approach for studying supramolecular assemblies, resulting in low-resolution and medium-resolution models. However, such approaches cannot deliver atomic details, especially of the crucial subunit-subunit interfaces, because of the limited cryo-electron microscopic resolution obtained in these studies. Here we report an alternative approach combining recombinant wild-type needle production, solid-state NMR, electron microscopy and Rosetta modelling to reveal the supramolecular interfaces and ultimately the complete atomic structure of the Salmonella typhimurium T3SS needle. We show that the 80-residue subunits form a right-handed helical assembly with roughly 11 subunits per two turns, similar to that of the flagellar filament of S. typhimurium. In contrast to established models of the needle in which the amino terminus of the protein subunit was assumed to be α-helical and positioned inside the needle, our model reveals an extended amino-terminal domain that is positioned on the surface of the needle, while the highly conserved carboxy terminus points towards the lumen.

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

    NASA Technical Reports Server (NTRS)

    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.

  18. Modeling smectic layers in confined geometries: order parameter and defects.

    PubMed

    Pevnyi, Mykhailo Y; Selinger, Jonathan V; Sluckin, Timothy J

    2014-09-01

    We identify problems with the standard complex order parameter formalism for smectic-A (SmA) liquid crystals and discuss possible alternative descriptions of smectic order. In particular, we suggest an approach based on the real smectic density variation rather than a complex order parameter. This approach gives reasonable numerical results for the smectic layer configuration and director field in sample geometries and can be used to model smectic liquid crystals under nanoscale confinement for technological applications.

  19. Parameter selection and testing the soil water model SOIL

    NASA Astrophysics Data System (ADS)

    McGechan, M. B.; Graham, R.; Vinten, A. J. A.; Douglas, J. T.; Hooda, P. S.

    1997-08-01

    The soil water and heat simulation model SOIL was tested for its suitability to study the processes of transport of water in soil. Required parameters, particularly soil hydraulic parameters, were determined by field and laboratory tests for some common soil types and for soils subjected to contrasting treatments of long-term grassland and tilled land under cereal crops. Outputs from simulations were shown to be in reasonable agreement with independently measured field drain outflows and soil water content histories.

  20. Simultaneous estimation of parameters in the bivariate Emax model.

    PubMed

    Magnusdottir, Bergrun T; Nyquist, Hans

    2015-12-10

    In this paper, we explore inference in multi-response, nonlinear models. By multi-response, we mean models with m > 1 response variables and accordingly m relations. Each parameter/explanatory variable may appear in one or more of the relations. We study a system estimation approach for simultaneous computation and inference of the model and (co)variance parameters. For illustration, we fit a bivariate Emax model to diabetes dose-response data. Further, the bivariate Emax model is used in a simulation study that compares the system estimation approach to equation-by-equation estimation. We conclude that overall, the system estimation approach performs better for the bivariate Emax model when there are dependencies among relations. The stronger the dependencies, the more we gain in precision by using system estimation rather than equation-by-equation estimation.

  1. Inelastic properties of magnetorheological composites: II. Model, identification of parameters

    NASA Astrophysics Data System (ADS)

    Kaleta, Jerzy; Lewandowski, Daniel; Zietek, Grazyna

    2007-10-01

    As a result of a two-part research project the inelastic properties of a selected group of magnetorheological composites in cyclic shear conditions have been identified. In the first part the fabrication of the composites, their structure, the control-measurement setup, the test methods and the experimental results were described. In the second part (presented here), the experimental data are used to construct a constitutive model and identify it. A four-parameter model of an elastic/viscoplastic body was adopted for description. The model coefficients were made dependent on magnetic field strength H. The model was analysed and procedures for its identification were designed. Two-phase identification of the model parameters was carried out. The model has been shown to be valid in a frequency range above 5 Hz.

  2. Application of physical parameter identification to finite-element models

    NASA Technical Reports Server (NTRS)

    Bronowicki, Allen J.; Lukich, Michael S.; Kuritz, Steven P.

    1987-01-01

    The time domain parameter identification method described previously is applied to TRW's Large Space Structure Truss Experiment. Only control sensors and actuators are employed in the test procedure. The fit of the linear structural model to the test data is improved by more than an order of magnitude using a physically reasonable parameter set. The electro-magnetic control actuators are found to contribute significant damping due to a combination of eddy current and back electro-motive force (EMF) effects. Uncertainties in both estimated physical parameters and modal behavior variables are given.

  3. Estimation of nonlinear pilot model parameters including time delay.

    NASA Technical Reports Server (NTRS)

    Schiess, J. R.; Roland, V. R.; Wells, W. R.

    1972-01-01

    Investigation of the feasibility of using a Kalman filter estimator for the identification of unknown parameters in nonlinear dynamic systems with a time delay. The problem considered is the application of estimation theory to determine the parameters of a family of pilot models containing delayed states. In particular, the pilot-plant dynamics are described by differential-difference equations of the retarded type. The pilot delay, included as one of the unknown parameters to be determined, is kept in pure form as opposed to the Pade approximations generally used for these systems. Problem areas associated with processing real pilot response data are included in the discussion.

  4. Improving ranking of models for protein complexes with side chain modeling and atomic potentials.

    PubMed

    Viswanath, Shruthi; Ravikant, D V S; Elber, Ron

    2013-04-01

    An atomically detailed potential for docking pairs of proteins is derived using mathematical programming. A refinement algorithm that builds atomically detailed models of the complex and combines coarse grained and atomic scoring is introduced. The refinement step consists of remodeling the interface side chains of the top scoring decoys from rigid docking followed by a short energy minimization. The refined models are then re-ranked using a combination of coarse grained and atomic potentials. The docking algorithm including the refinement and re-ranking, is compared favorably to other leading docking packages like ZDOCK, Cluspro, and PATCHDOCK, on the ZLAB 3.0 Benchmark and a test set of 30 novel complexes. A detailed analysis shows that coarse grained potentials perform better than atomic potentials for realistic unbound docking (where the exact structures of the individual bound proteins are unknown), probably because atomic potentials are more sensitive to local errors. Nevertheless, the atomic potential captures a different signal from the residue potential and as a result a combination of the two scores provides a significantly better prediction than each of the approaches alone.

  5. Parameter fitting for piano sound synthesis by physical modeling

    NASA Astrophysics Data System (ADS)

    Bensa, Julien; Gipouloux, Olivier; Kronland-Martinet, Richard

    2005-07-01

    A difficult issue in the synthesis of piano tones by physical models is to choose the values of the parameters governing the hammer-string model. In fact, these parameters are hard to estimate from static measurements, causing the synthesis sounds to be unrealistic. An original approach that estimates the parameters of a piano model, from the measurement of the string vibration, by minimizing a perceptual criterion is proposed. The minimization process that was used is a combination of a gradient method and a simulated annealing algorithm, in order to avoid convergence problems in case of multiple local minima. The criterion, based on the tristimulus concept, takes into account the spectral energy density in three bands, each allowing particular parameters to be estimated. The optimization process has been run on signals measured on an experimental setup. The parameters thus estimated provided a better sound quality than the one obtained using a global energetic criterion. Both the sound's attack and its brightness were better preserved. This quality gain was obtained for parameter values very close to the initial ones, showing that only slight deviations are necessary to make synthetic sounds closer to the real ones.

  6. Advanced parameter retrievals for metamaterial slabs using an inhomogeneous model

    NASA Astrophysics Data System (ADS)

    Li Hou, Ling; Chin, Jessie Yao; Yang, Xin Mi; Lin, Xian Qi; Liu, Ruopeng; Xu, Fu Yong; Cui, Tie Jun

    2008-03-01

    The S-parameter retrieval has proved to be an efficient approach to obtain electromagnetic parameters of metamaterials from reflection and transmission coefficients, where a slab of metamaterial with finite thickness is regarded as a homogeneous medium slab with the same thickness [D. R. Smith and S. Schultz, Phys. Rev. B 65, 195104 (2002)]. However, metamaterial structures composed of subwavelength unit cells are different from homogeneous materials, and the conventional retrieval method is, under certain circumstances, not accurate enough. In this paper, we propose an advanced parameter retrieval method for metamaterial slabs using an inhomogeneous model. Due to the coupling effects of unit cells in a metamaterial slab, the roles of edge and inner cells in the slab are different. Hence, the corresponding equivalent medium parameters are different, which results in the inhomogeneous property of the metamaterial slab. We propose the retrievals of medium parameters for edge and inner cells from S parameters by considering two- and three-cell metamaterial slabs, respectively. Then we set up an inhomogeneous three-layer model for arbitrary metamaterial slabs, which is much more accurate than the conventional homogeneous model. Numerical simulations verify the above conclusions.

  7. Control of the SCOLE configuration using distributed parameter models

    NASA Technical Reports Server (NTRS)

    Hsiao, Min-Hung; Huang, Jen-Kuang

    1994-01-01

    A continuum model for the SCOLE configuration has been derived using transfer matrices. Controller designs for distributed parameter systems have been analyzed. Pole-assignment controller design is considered easy to implement but stability is not guaranteed. An explicit transfer function of dynamic controllers has been obtained and no model reduction is required before the controller is realized. One specific LQG controller for continuum models had been derived, but other optimal controllers for more general performances need to be studied.

  8. Kinetic modeling of α-hydrogen abstractions from unsaturated and saturated oxygenate compounds by hydrogen atoms.

    PubMed

    Paraskevas, Paschalis D; Sabbe, Maarten K; Reyniers, Marie-Françoise; Papayannakos, Nikos G; Marin, Guy B

    2014-10-01

    Hydrogen-abstraction reactions play a significant role in thermal biomass conversion processes, as well as regular gasification, pyrolysis, or combustion. In this work, a group additivity model is constructed that allows prediction of reaction rates and Arrhenius parameters of hydrogen abstractions by hydrogen atoms from alcohols, ethers, esters, peroxides, ketones, aldehydes, acids, and diketones in a broad temperature range (300-2000 K). A training set of 60 reactions was developed with rate coefficients and Arrhenius parameters calculated by the CBS-QB3 method in the high-pressure limit with tunneling corrections using Eckart tunneling coefficients. From this set of reactions, 15 group additive values were derived for the forward and the reverse reaction, 4 referring to primary and 11 to secondary contributions. The accuracy of the model is validated upon an ab initio and an experimental validation set of 19 and 21 reaction rates, respectively, showing that reaction rates can be predicted with a mean factor of deviation of 2 for the ab initio and 3 for the experimental values. Hence, this work illustrates that the developed group additive model can be reliably applied for the accurate prediction of kinetics of α-hydrogen abstractions by hydrogen atoms from a broad range of oxygenates. PMID:25209711

  9. Quantifying the parameters of Prusiner's heterodimer model for prion replication

    NASA Astrophysics Data System (ADS)

    Li, Z. R.; Liu, G. R.; Mi, D.

    2005-02-01

    A novel approach for the determination of parameters in prion replication kinetics is developed based on Prusiner's heterodimer model. It is proposed to employ a simple 2D HP lattice model and a two-state transition theory to determine kinetic parameters that play the key role in the prion replication process. The simulation results reveal the most important facts observed in the prion diseases, including the long incubation time, rapid death following symptom manifestation, the effect of inoculation size, different mechanisms of the familial and infectious prion diseases, etc. Extensive simulation with various thermodynamic parameters shows that the Prusiner's heterodimer model is applicable, and the putative protein X plays a critical role in replication of the prion disease.

  10. Radar altimeter waveform modeled parameter recovery. [SEASAT-1 data

    NASA Technical Reports Server (NTRS)

    1981-01-01

    Satellite-borne radar altimeters include waveform sampling gates providing point samples of the transmitted radar pulse after its scattering from the ocean's surface. Averages of the waveform sampler data can be fitted by varying parameters in a model mean return waveform. The theoretical waveform model used is described as well as a general iterative nonlinear least squares procedures used to obtain estimates of parameters characterizing the modeled waveform for SEASAT-1 data. The six waveform parameters recovered by the fitting procedure are: (1) amplitude; (2) time origin, or track point; (3) ocean surface rms roughness; (4) noise baseline; (5) ocean surface skewness; and (6) altitude or off-nadir angle. Additional practical processing considerations are addressed and FORTRAN source listing for subroutines used in the waveform fitting are included. While the description is for the Seasat-1 altimeter waveform data analysis, the work can easily be generalized and extended to other radar altimeter systems.

  11. Utilizing Soize's Approach to Identify Parameter and Model Uncertainties

    SciTech Connect

    Bonney, Matthew S.; Brake, Matthew Robert

    2014-10-01

    Quantifying uncertainty in model parameters is a challenging task for analysts. Soize has derived a method that is able to characterize both model and parameter uncertainty independently. This method is explained with the assumption that some experimental data is available, and is divided into seven steps. Monte Carlo analyses are performed to select the optimal dispersion variable to match the experimental data. Along with the nominal approach, an alternative distribution can be used along with corrections that can be utilized to expand the scope of this method. This method is one of a very few methods that can quantify uncertainty in the model form independently of the input parameters. Two examples are provided to illustrate the methodology, and example code is provided in the Appendix.

  12. SPOTting model parameters using a ready-made Python package

    NASA Astrophysics Data System (ADS)

    Houska, Tobias; Kraft, Philipp; Breuer, Lutz

    2015-04-01

    The selection and parameterization of reliable process descriptions in ecological modelling is driven by several uncertainties. The procedure is highly dependent on various criteria, like the used algorithm, the likelihood function selected and the definition of the prior parameter distributions. A wide variety of tools have been developed in the past decades to optimize parameters. Some of the tools are closed source. Due to this, the choice for a specific parameter estimation method is sometimes more dependent on its availability than the performance. A toolbox with a large set of methods can support users in deciding about the most suitable method. Further, it enables to test and compare different methods. We developed the SPOT (Statistical Parameter Optimization Tool), an open source python package containing a comprehensive set of modules, to analyze and optimize parameters of (environmental) models. SPOT comes along with a selected set of algorithms for parameter optimization and uncertainty analyses (Monte Carlo, MC; Latin Hypercube Sampling, LHS; Maximum Likelihood, MLE; Markov Chain Monte Carlo, MCMC; Scuffled Complex Evolution, SCE-UA; Differential Evolution Markov Chain, DE-MCZ), together with several likelihood functions (Bias, (log-) Nash-Sutcliff model efficiency, Correlation Coefficient, Coefficient of Determination, Covariance, (Decomposed-, Relative-, Root-) Mean Squared Error, Mean Absolute Error, Agreement Index) and prior distributions (Binomial, Chi-Square, Dirichlet, Exponential, Laplace, (log-, multivariate-) Normal, Pareto, Poisson, Cauchy, Uniform, Weibull) to sample from. The model-independent structure makes it suitable to analyze a wide range of applications. We apply all algorithms of the SPOT package in three different case studies. Firstly, we investigate the response of the Rosenbrock function, where the MLE algorithm shows its strengths. Secondly, we study the Griewank function, which has a challenging response surface for

  13. Synchronous Generator Model Parameter Estimation Based on Noisy Dynamic Waveforms

    NASA Astrophysics Data System (ADS)

    Berhausen, Sebastian; Paszek, Stefan

    2016-01-01

    In recent years, there have occurred system failures in many power systems all over the world. They have resulted in a lack of power supply to a large number of recipients. To minimize the risk of occurrence of power failures, it is necessary to perform multivariate investigations, including simulations, of power system operating conditions. To conduct reliable simulations, the current base of parameters of the models of generating units, containing the models of synchronous generators, is necessary. In the paper, there is presented a method for parameter estimation of a synchronous generator nonlinear model based on the analysis of selected transient waveforms caused by introducing a disturbance (in the form of a pseudorandom signal) in the generator voltage regulation channel. The parameter estimation was performed by minimizing the objective function defined as a mean square error for deviations between the measurement waveforms and the waveforms calculated based on the generator mathematical model. A hybrid algorithm was used for the minimization of the objective function. In the paper, there is described a filter system used for filtering the noisy measurement waveforms. The calculation results of the model of a 44 kW synchronous generator installed on a laboratory stand of the Institute of Electrical Engineering and Computer Science of the Silesian University of Technology are also given. The presented estimation method can be successfully applied to parameter estimation of different models of high-power synchronous generators operating in a power system.

  14. [Parameter uncertainty analysis for urban rainfall runoff modelling].

    PubMed

    Huang, Jin-Liang; Lin, Jie; Du, Peng-Fei

    2012-07-01

    An urban watershed in Xiamen was selected to perform the parameter uncertainty analysis for urban stormwater runoff modeling in terms of identification and sensitivity analysis based on storm water management model (SWMM) using Monte-Carlo sampling and regionalized sensitivity analysis (RSA) algorithm. Results show that Dstore-Imperv, Dstore-Perv and Curve Number (CN) are the identifiable parameters with larger K-S values in hydrological and hydraulic module, and the rank of K-S values in hydrological and hydraulic module is Dstore-Imperv > CN > Dstore-Perv > N-Perv > conductivity > Con-Mann > N-Imperv. With regards to water quality module, the parameters in exponent washoff model including Coefficient and Exponent and the Max. Buildup parameter of saturation buildup model in three land cover types are the identifiable parameters with the larger K-S values. In comparison, the K-S value of rate constant in three landuse/cover types is smaller than that of Max. Buildup, Coefficient and Exponent.

  15. Optimizing Muscle Parameters in Musculoskeletal Modeling Using Monte Carlo Simulations

    NASA Technical Reports Server (NTRS)

    Hanson, Andrea; Reed, Erik; Cavanagh, Peter

    2011-01-01

    Astronauts assigned to long-duration missions experience bone and muscle atrophy in the lower limbs. The use of musculoskeletal simulation software has become a useful tool for modeling joint and muscle forces during human activity in reduced gravity as access to direct experimentation is limited. Knowledge of muscle and joint loads can better inform the design of exercise protocols and exercise countermeasure equipment. In this study, the LifeModeler(TM) (San Clemente, CA) biomechanics simulation software was used to model a squat exercise. The initial model using default parameters yielded physiologically reasonable hip-joint forces. However, no activation was predicted in some large muscles such as rectus femoris, which have been shown to be active in 1-g performance of the activity. Parametric testing was conducted using Monte Carlo methods and combinatorial reduction to find a muscle parameter set that more closely matched physiologically observed activation patterns during the squat exercise. Peak hip joint force using the default parameters was 2.96 times body weight (BW) and increased to 3.21 BW in an optimized, feature-selected test case. The rectus femoris was predicted to peak at 60.1% activation following muscle recruitment optimization, compared to 19.2% activation with default parameters. These results indicate the critical role that muscle parameters play in joint force estimation and the need for exploration of the solution space to achieve physiologically realistic muscle activation.

  16. Estimation of the parameters of ETAS models by Simulated Annealing.

    PubMed

    Lombardi, Anna Maria

    2015-02-12

    This paper proposes a new algorithm to estimate the maximum likelihood parameters of an Epidemic Type Aftershock Sequences (ETAS) model. It is based on Simulated Annealing, a versatile method that solves problems of global optimization and ensures convergence to a global optimum. The procedure is tested on both simulated and real catalogs. The main conclusion is that the method performs poorly as the size of the catalog decreases because the effect of the correlation of the ETAS parameters is more significant. These results give new insights into the ETAS model and the efficiency of the maximum-likelihood method within this context.

  17. Estimation of the parameters of ETAS models by Simulated Annealing

    PubMed Central

    Lombardi, Anna Maria

    2015-01-01

    This paper proposes a new algorithm to estimate the maximum likelihood parameters of an Epidemic Type Aftershock Sequences (ETAS) model. It is based on Simulated Annealing, a versatile method that solves problems of global optimization and ensures convergence to a global optimum. The procedure is tested on both simulated and real catalogs. The main conclusion is that the method performs poorly as the size of the catalog decreases because the effect of the correlation of the ETAS parameters is more significant. These results give new insights into the ETAS model and the efficiency of the maximum-likelihood method within this context. PMID:25673036

  18. Extrinsic parameter extraction and RF modelling of CMOS

    NASA Astrophysics Data System (ADS)

    Alam, M. S.; Armstrong, G. A.

    2004-05-01

    An analytical approach for CMOS parameter extraction which includes the effect of parasitic resistance is presented. The method is based on small-signal equivalent circuit valid in all region of operation to uniquely extract extrinsic resistances, which can be used to extend the industry standard BSIM3v3 MOSFET model for radio frequency applications. The verification of the model was carried out through frequency domain measurements of S-parameters and direct time domain measurement at 2.4 GHz in a large signal non-linear mode of operation.

  19. Optimization of Parameter Selection for Partial Least Squares Model Development

    NASA Astrophysics Data System (ADS)

    Zhao, Na; Wu, Zhi-Sheng; Zhang, Qiao; Shi, Xin-Yuan; Ma, Qun; Qiao, Yan-Jiang

    2015-07-01

    In multivariate calibration using a spectral dataset, it is difficult to optimize nonsystematic parameters in a quantitative model, i.e., spectral pretreatment, latent factors and variable selection. In this study, we describe a novel and systematic approach that uses a processing trajectory to select three parameters including different spectral pretreatments, variable importance in the projection (VIP) for variable selection and latent factors in the Partial Least-Square (PLS) model. The root mean square errors of calibration (RMSEC), the root mean square errors of prediction (RMSEP), the ratio of standard error of prediction to standard deviation (RPD), and the determination coefficient of calibration (Rcal2) and validation (Rpre2) were simultaneously assessed to optimize the best modeling path. We used three different near-infrared (NIR) datasets, which illustrated that there was more than one modeling path to ensure good modeling. The PLS model optimizes modeling parameters step-by-step, but the robust model described here demonstrates better efficiency than other published papers.

  20. Climate change decision-making: Model & parameter uncertainties explored

    SciTech Connect

    Dowlatabadi, H.; Kandlikar, M.; Linville, C.

    1995-12-31

    A critical aspect of climate change decision-making is uncertainties in current understanding of the socioeconomic, climatic and biogeochemical processes involved. Decision-making processes are much better informed if these uncertainties are characterized and their implications understood. Quantitative analysis of these uncertainties serve to inform decision makers about the likely outcome of policy initiatives, and help set priorities for research so that outcome ambiguities faced by the decision-makers are reduced. A family of integrated assessment models of climate change have been developed at Carnegie Mellon. These models are distinguished from other integrated assessment efforts in that they were designed from the outset to characterize and propagate parameter, model, value, and decision-rule uncertainties. The most recent of these models is ICAM 2.1. This model includes representation of the processes of demographics, economic activity, emissions, atmospheric chemistry, climate and sea level change and impacts from these changes and policies for emissions mitigation, and adaptation to change. The model has over 800 objects of which about one half are used to represent uncertainty. In this paper we show, that when considering parameter uncertainties, the relative contribution of climatic uncertainties are most important, followed by uncertainties in damage calculations, economic uncertainties and direct aerosol forcing uncertainties. When considering model structure uncertainties we find that the choice of policy is often dominated by model structure choice, rather than parameter uncertainties.

  1. Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties.

    PubMed

    Beerepoot, Maarten T P; Steindal, Arnfinn Hykkerud; List, Nanna Holmgaard; Kongsted, Jacob; Olsen, Jógvan Magnus Haugaard

    2016-04-12

    We derive and validate averaged solvent parameters for embedding potentials to be used in polarizable embedding quantum mechanics/molecular mechanics (QM/MM) molecular property calculations of solutes in organic solvents. The parameters are solvent-specific atom-centered partial charges and isotropic polarizabilities averaged over a large number of geometries of solvent molecules. The use of averaged parameters reduces the computational cost to obtain the embedding potential, which can otherwise be a rate-limiting step in calculations involving large environments. The parameters are evaluated by analyzing the quality of the resulting molecular electrostatic potentials with respect to full QM potentials. We show that a combination of geometry-specific parameters for solvent molecules close to the QM region and averaged parameters for solvent molecules further away allows for efficient polarizable embedding multiscale modeling without compromising the accuracy. The results are promising for the development of general embedding parameters for biomolecules, where the reduction in computational cost can be considerable. PMID:26938368

  2. Inhalation Exposure Input Parameters for the Biosphere Model

    SciTech Connect

    M. Wasiolek

    2006-06-05

    This analysis is one of the technical reports that support the Environmental Radiation Model for Yucca Mountain, Nevada (ERMYN), referred to in this report as the biosphere model. ''Biosphere Model Report'' (BSC 2004 [DIRS 169460]) describes in detail the conceptual model as well as the mathematical model and its input parameters. This report documents development of input parameters for the biosphere model that are related to atmospheric mass loading and supports the use of the model to develop biosphere dose conversion factors (BDCFs). The biosphere model is one of a series of process models supporting the total system performance assessment (TSPA) for a Yucca Mountain repository. ''Inhalation Exposure Input Parameters for the Biosphere Model'' is one of five reports that develop input parameters for the biosphere model. A graphical representation of the documentation hierarchy for the biosphere model is presented in Figure 1-1 (based on BSC 2006 [DIRS 176938]). This figure shows the interrelationships among the products (i.e., analysis and model reports) developed for biosphere modeling and how this analysis report contributes to biosphere modeling. This analysis report defines and justifies values of atmospheric mass loading for the biosphere model. Mass loading is the total mass concentration of resuspended particles (e.g., dust, ash) in a volume of air. Mass loading values are used in the air submodel of the biosphere model to calculate concentrations of radionuclides in air inhaled by a receptor and concentrations in air surrounding crops. Concentrations in air to which the receptor is exposed are then used in the inhalation submodel to calculate the dose contribution to the receptor from inhalation of contaminated airborne particles. Concentrations in air surrounding plants are used in the plant submodel to calculate the concentrations of radionuclides in foodstuffs contributed from uptake by foliar interception. This report is concerned primarily with the

  3. Considerations for parameter optimization and sensitivity in climate models.

    PubMed

    Neelin, J David; Bracco, Annalisa; Luo, Hao; McWilliams, James C; Meyerson, Joyce E

    2010-12-14

    Climate models exhibit high sensitivity in some respects, such as for differences in predicted precipitation changes under global warming. Despite successful large-scale simulations, regional climatology features prove difficult to constrain toward observations, with challenges including high-dimensionality, computationally expensive simulations, and ambiguity in the choice of objective function. In an atmospheric General Circulation Model forced by observed sea surface temperature or coupled to a mixed-layer ocean, many climatic variables yield rms-error objective functions that vary smoothly through the feasible parameter range. This smoothness occurs despite nonlinearity strong enough to reverse the curvature of the objective function in some parameters, and to imply limitations on multimodel ensemble means as an estimator of global warming precipitation changes. Low-order polynomial fits to the model output spatial fields as a function of parameter (quadratic in model field, fourth-order in objective function) yield surprisingly successful metamodels for many quantities and facilitate a multiobjective optimization approach. Tradeoffs arise as optima for different variables occur at different parameter values, but with agreement in certain directions. Optima often occur at the limit of the feasible parameter range, identifying key parameterization aspects warranting attention--here the interaction of convection with free tropospheric water vapor. Analytic results for spatial fields of leading contributions to the optimization help to visualize tradeoffs at a regional level, e.g., how mismatches between sensitivity and error spatial fields yield regional error under minimization of global objective functions. The approach is sufficiently simple to guide parameter choices and to aid intercomparison of sensitivity properties among climate models. PMID:21115841

  4. Considerations for parameter optimization and sensitivity in climate models

    PubMed Central

    Neelin, J. David; Bracco, Annalisa; Luo, Hao; McWilliams, James C.; Meyerson, Joyce E.

    2010-01-01

    Climate models exhibit high sensitivity in some respects, such as for differences in predicted precipitation changes under global warming. Despite successful large-scale simulations, regional climatology features prove difficult to constrain toward observations, with challenges including high-dimensionality, computationally expensive simulations, and ambiguity in the choice of objective function. In an atmospheric General Circulation Model forced by observed sea surface temperature or coupled to a mixed-layer ocean, many climatic variables yield rms-error objective functions that vary smoothly through the feasible parameter range. This smoothness occurs despite nonlinearity strong enough to reverse the curvature of the objective function in some parameters, and to imply limitations on multimodel ensemble means as an estimator of global warming precipitation changes. Low-order polynomial fits to the model output spatial fields as a function of parameter (quadratic in model field, fourth-order in objective function) yield surprisingly successful metamodels for many quantities and facilitate a multiobjective optimization approach. Tradeoffs arise as optima for different variables occur at different parameter values, but with agreement in certain directions. Optima often occur at the limit of the feasible parameter range, identifying key parameterization aspects warranting attention—here the interaction of convection with free tropospheric water vapor. Analytic results for spatial fields of leading contributions to the optimization help to visualize tradeoffs at a regional level, e.g., how mismatches between sensitivity and error spatial fields yield regional error under minimization of global objective functions. The approach is sufficiently simple to guide parameter choices and to aid intercomparison of sensitivity properties among climate models. PMID:21115841

  5. Comparison between power-law rheological parameters of living cells in frequency and time domains measured by atomic force microscopy

    NASA Astrophysics Data System (ADS)

    Takahashi, Ryosuke; Okajima, Takaharu

    2016-08-01

    We investigated how stress relaxation mapping is quantified compared with the force modulation mapping of confluent epithelial cells using atomic force microscopy (AFM). Using a multi-frequency AFM technique, we estimated the power-law rheological behaviors of cells simultaneously in time and frequency domains. When the power-law exponent α was low (<0.1), the α values were almost the same in time and frequency domains. On the other hand, we found that at the high values (α > 0.1), α in the time domain was underestimated relative to that in the frequency domain, and the difference increased with α, whereas the cell modulus was overestimated in the time domain. These results indicate that power-law rheological parameters estimated by stress relaxation are sensitive to lag time during initial indentation, which is inevitable in time-domain AFM experiments.

  6. Investigation of the analysis parameters and background subtraction for high-k materials with atom probe tomography.

    PubMed

    Mutas, S; Klein, C; Gerstl, S S A

    2011-05-01

    In this paper we present depth profiles of a high-k layer consisting of HfO(2) with an embedded sub-nm thick ZrO(2) layer obtained with atom probe tomography (APT). In order to determine suitable measurement parameters for reliable, reproducible, and quantitative analysis, we have investigated the influence of the laser energy and the specimen temperature on the resulting elemental composition. In addition we devise a procedure for local background subtraction both for the composition and the depth scale that is crucial for gaining reproducible results. We find that the composition of the high-k material remains unaffected even for extreme laser energies and base temperatures, while higher laser energies lead to an accumulation of silicon at the upper interface of the high-k layer. Furthermore we show that APT is capable of providing sub-nm depth resolution for high-k materials with high reproducibility, good compositional accuracy, and high measurement yield.

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

    PubMed

    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.

  8. Simulating and Modeling Transport Through Atomically Thin Membranes

    NASA Astrophysics Data System (ADS)

    Ostrowski, Joseph; Eaves, Joel

    2014-03-01

    The world is running out of clean portable water. The efficacy of water desalination technologies using porous materials is a balance between membrane selectivity and solute throughput. These properties are just starting to be understood on the nanoscale, but in the limit of atomically thin membranes it is unclear whether one can apply typical continuous time random walk models. Depending on the size of the pore and thickness of the membrane, mass transport can range from single stochastic passage events to continuous flow describable by the usual hydrodynamic equations. We present a study of mass transport through membranes of various pore geometries using reverse nonequilibrium simulations, and analyze transport rates using stochastic master equations.

  9. SLIMP: Strong laser interaction model package for atoms and molecules

    NASA Astrophysics Data System (ADS)

    Zhang, Bin; Zhao, Zengxiu

    2015-07-01

    We present the SLIMP package, which provides an efficient way for the calculation of strong-field ionization rate and high-order harmonic spectra based on the single active electron approximation. The initial states are taken as single-particle orbitals directly from output files of the general purpose quantum chemistry programs GAMESS, Firefly and Gaussian. For ionization, the molecular Ammosov-Delone-Krainov theory, and both the length gauge and velocity gauge Keldysh-Faisal-Reiss theories are implemented, while the Lewenstein model is used for harmonic spectra. Furthermore, it is also efficient for the evaluation of orbital coordinates wavefunction, momentum wavefunction, orbital dipole moment and calculation of orbital integrations. This package can be applied to quite large basis sets and complex molecules with many atoms, and is implemented to allow easy extensions for additional capabilities.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26064629

  11. Atomic-level models of the bacterial carboxysome shell

    SciTech Connect

    Tanaka, S.; Kerfeld, C.A.; Sawaya, M.R.; Cai, F.; Heinhorst, S.; Cannon, G.C.; Yeates, T.O.

    2008-06-03

    The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation. The carboxysome shell is roughly 800 to 1400 angstroms in diameter and is assembled from several thousand protein subunits. Previous studies have revealed the three-dimensional structures of hexameric carboxysome shell proteins, which self-assemble into molecular layers that most likely constitute the facets of the polyhedral shell. Here, we report the three-dimensional structures of two proteins of previously unknown function, CcmL and OrfA (or CsoS4A), from the two known classes of carboxysomes, at resolutions of 2.4 and 2.15 angstroms. Both proteins assemble to form pentameric structures whose size and shape are compatible with formation of vertices in an icosahedral shell. Combining these pentamers with the hexamers previously elucidated gives two plausible, preliminary atomic models for the carboxysome shell.

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

    PubMed

    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.

  13. Parameter space for a dissipative Fermi-Ulam model

    NASA Astrophysics Data System (ADS)

    Oliveira, Diego F. M.; Leonel, Edson D.

    2011-12-01

    The parameter space for a dissipative bouncing ball model under the effect of inelastic collisions is studied. The system is described using a two-dimensional nonlinear area-contracting map. The introduction of dissipation destroys the mixed structure of phase space of the non-dissipative case, leading to the existence of a chaotic attractor and attracting fixed points, which may coexist for certain ranges of control parameters. We have computed the average velocity for the parameter space and made a connection with the parameter space based on the maximum Lyapunov exponent. For both cases, we found an infinite family of self-similar structures of shrimp shape, which correspond to the periodic attractors embedded in a large region that corresponds to the chaotic motion.

  14. Important observations and parameters for a salt water intrusion model

    USGS Publications Warehouse

    Shoemaker, W.B.

    2004-01-01

    Sensitivity analysis with a density-dependent ground water flow simulator can provide insight and understanding of salt water intrusion calibration problems far beyond what is possible through intuitive analysis alone. Five simple experimental simulations presented here demonstrate this point. Results show that dispersivity is a very important parameter for reproducing a steady-state distribution of hydraulic head, salinity, and flow in the transition zone between fresh water and salt water in a coastal aquifer system. When estimating dispersivity, the following conclusions can be drawn about the data types and locations considered. (1) The "toe" of the transition zone is the most effective location for hydraulic head and salinity observations. (2) Areas near the coastline where submarine ground water discharge occurs are the most effective locations for flow observations. (3) Salinity observations are more effective than hydraulic head observations. (4) The importance of flow observations aligned perpendicular to the shoreline varies dramatically depending on distance seaward from the shoreline. Extreme parameter correlation can prohibit unique estimation of permeability parameters such as hydraulic conductivity and flow parameters such as recharge in a density-dependent ground water flow model when using hydraulic head and salinity observations. Adding flow observations perpendicular to the shoreline in areas where ground water is exchanged with the ocean body can reduce the correlation, potentially resulting in unique estimates of these parameter values. Results are expected to be directly applicable to many complex situations, and have implications for model development whether or not formal optimization methods are used in model calibration.

  15. Important observations and parameters for a salt water intrusion model.

    PubMed

    Shoemaker, W Barclay

    2004-01-01

    Sensitivity analysis with a density-dependent ground water flow simulator can provide insight and understanding of salt water intrusion calibration problems far beyond what is possible through intuitive analysis alone. Five simple experimental simulations presented here demonstrate this point. Results show that dispersivity is a very important parameter for reproducing a steady-state distribution of hydraulic head, salinity, and flow in the transition zone between fresh water and salt water in a coastal aquifer system. When estimating dispersivity, the following conclusions can be drawn about the data types and locations considered. (1) The "toe" of the transition zone is the most effective location for hydraulic head and salinity observations. (2) Areas near the coastline where submarine ground water discharge occurs are the most effective locations for flow observations. (3) Salinity observations are more effective than hydraulic head observations. (4) The importance of flow observations aligned perpendicular to the shoreline varies dramatically depending on distance seaward from the shoreline. Extreme parameter correlation can prohibit unique estimation of permeability parameters such as hydraulic conductivity and flow parameters such as recharge in a density-dependent ground water flow model when using hydraulic head and salinity observations. Adding flow observations perpendicular to the shoreline in areas where ground water is exchanged with the ocean body can reduce the correlation, potentially resulting in unique estimates of these parameter values. Results are expected to be directly applicable to many complex situations, and have implications for model development whether or not formal optimization methods are used in model calibration.

  16. Estimation of growth parameters using a nonlinear mixed Gompertz model.

    PubMed

    Wang, Z; Zuidhof, M J

    2004-06-01

    In order to maximize the utility of simulation models for decision making, accurate estimation of growth parameters and associated variances is crucial. A mixed Gompertz growth model was used to account for between-bird variation and heterogeneous variance. The mixed model had several advantages over the fixed effects model. The mixed model partitioned BW variation into between- and within-bird variation, and the covariance structure assumed with the random effect accounted for part of the BW correlation across ages in the same individual. The amount of residual variance decreased by over 55% with the mixed model. The mixed model reduced estimation biases that resulted from selective sampling. For analysis of longitudinal growth data, the mixed effects growth model is recommended.

  17. Modelling Biophysical Parameters of Maize Using Landsat 8 Time Series

    NASA Astrophysics Data System (ADS)

    Dahms, Thorsten; Seissiger, Sylvia; Conrad, Christopher; Borg, Erik

    2016-06-01

    Open and free access to multi-frequent high-resolution data (e.g. Sentinel - 2) will fortify agricultural applications based on satellite data. The temporal and spatial resolution of these remote sensing datasets directly affects the applicability of remote sensing methods, for instance a robust retrieving of biophysical parameters over the entire growing season with very high geometric resolution. In this study we use machine learning methods to predict biophysical parameters, namely the fraction of absorbed photosynthetic radiation (FPAR), the leaf area index (LAI) and the chlorophyll content, from high resolution remote sensing. 30 Landsat 8 OLI scenes were available in our study region in Mecklenburg-Western Pomerania, Germany. In-situ data were weekly to bi-weekly collected on 18 maize plots throughout the summer season 2015. The study aims at an optimized prediction of biophysical parameters and the identification of the best explaining spectral bands and vegetation indices. For this purpose, we used the entire in-situ dataset from 24.03.2015 to 15.10.2015. Random forest and conditional inference forests were used because of their explicit strong exploratory and predictive character. Variable importance measures allowed for analysing the relation between the biophysical parameters with respect to the spectral response, and the performance of the two approaches over the plant stock evolvement. Classical random forest regression outreached the performance of conditional inference forests, in particular when modelling the biophysical parameters over the entire growing period. For example, modelling biophysical parameters of maize for the entire vegetation period using random forests yielded: FPAR: R² = 0.85; RMSE = 0.11; LAI: R² = 0.64; RMSE = 0.9 and chlorophyll content (SPAD): R² = 0.80; RMSE=4.9. Our results demonstrate the great potential in using machine-learning methods for the interpretation of long-term multi-frequent remote sensing datasets to model

  18. Prediction of interest rate using CKLS model with stochastic parameters

    SciTech Connect

    Ying, Khor Chia; Hin, Pooi Ah

    2014-06-19

    The Chan, Karolyi, Longstaff and Sanders (CKLS) model is a popular one-factor model for describing the spot interest rates. In this paper, the four parameters in the CKLS model are regarded as stochastic. The parameter vector φ{sup (j)} of four parameters at the (J+n)-th time point is estimated by the j-th window which is defined as the set consisting of the observed interest rates at the j′-th time point where j≤j′≤j+n. To model the variation of φ{sup (j)}, we assume that φ{sup (j)} depends on φ{sup (j−m)}, φ{sup (j−m+1)},…, φ{sup (j−1)} and the interest rate r{sub j+n} at the (j+n)-th time point via a four-dimensional conditional distribution which is derived from a [4(m+1)+1]-dimensional power-normal distribution. Treating the (j+n)-th time point as the present time point, we find a prediction interval for the future value r{sub j+n+1} of the interest rate at the next time point when the value r{sub j+n} of the interest rate is given. From the above four-dimensional conditional distribution, we also find a prediction interval for the future interest rate r{sub j+n+d} at the next d-th (d≥2) time point. The prediction intervals based on the CKLS model with stochastic parameters are found to have better ability of covering the observed future interest rates when compared with those based on the model with fixed parameters.

  19. Nilsson parameters κ and μ in relativistic mean field models

    NASA Astrophysics Data System (ADS)

    Sulaksono, A.; Mart, T.; Bahri, C.

    2005-03-01

    Nilsson parameters κ and μ have been studied in the framework of relativistic mean field (RMF) models. They are used to investigate the reason why RMF models give a relatively good prediction of the spin-orbit splitting but fail to reproduce the placement of the states with different orbital angular momenta. Instead of the relatively small effective mass M*, the independence of M* from the angular momentum l is found to be the reason.

  20. Atmosphere models and the determination of stellar parameters

    NASA Astrophysics Data System (ADS)

    Martins, F.

    2014-11-01

    We present the basic concepts necessary to build atmosphere models for any type of star. We then illustrate how atmosphere models can be used to determine stellar parameters. We focus on the effects of line-blanketing for hot stars, and on non-LTE and three dimensional effects for cool stars. We illustrate the impact of these effects on the determination of the ages of stars from the HR diagram.

  1. Consistency of Rasch Model Parameter Estimation: A Simulation Study.

    ERIC Educational Resources Information Center

    van den Wollenberg, Arnold L.; And Others

    1988-01-01

    The unconditional--simultaneous--maximum likelihood (UML) estimation procedure for the one-parameter logistic model produces biased estimators. The UML method is inconsistent and is not a good alternative to conditional maximum likelihood method, at least with small numbers of items. The minimum Chi-square estimation procedure produces unbiased…

  2. Parabolic problems with parameters arising in evolution model for phytromediation

    NASA Astrophysics Data System (ADS)

    Sahmurova, Aida; Shakhmurov, Veli

    2012-12-01

    The past few decades, efforts have been made to clean sites polluted by heavy metals as chromium. One of the new innovative methods of eradicating metals from soil is phytoremediation. This uses plants to pull metals from the soil through the roots. This work develops a system of differential equations with parameters to model the plant metal interaction of phytoremediation (see [1]).

  3. Atomic-scale simulations of atomic and molecular mobility in models of interstellar ice

    NASA Astrophysics Data System (ADS)

    Andersson, Stefan

    The mobility of atoms and molecular radicals at ice-covered dust particles controls the surprisingly rich chemistry of circumstellar and interstellar environments, where a large number of different organic molecules have been observed. Both thermal and non-thermal processes, for instance caused by UV radiation, have been inferred to play important roles in this chemistry. A growing number of experimental studies support previously suggested mechanisms and add to the understanding of possible astrochemical processes. Simulations, of both experiments and astrophysical environments, aid in interpreting experiments and suggesting important mechanisms. Still, the exact mechanisms behind the mobility of species in interstellar ice are far from fully understood. We have performed calculations at the molecular level on the mobility of H atoms and OH radicals at water ice surfaces of varying morphology. Calculations of binding energies and diffusion barriers of H atoms at crystalline and amorphous ice surfaces show that the experimentally observed slower diffusion at amorphous ice is due to considerably stronger binding energies and higher diffusion barriers than at crystalline ice. These results are in excellent agreement with recent experiments. It was also found that quantum tunneling is important for H atom mobility below 10 K. The binding energies and diffusion barriers of OH radicals at crystalline ice have been studied using the ONIOM(QM:AMOEBA) approach. Results indicate that OH diffusion over crystalline ice, contrary to the case of H atoms, might be slower at crystalline ice than at amorphous ice, due to a higher surface density of stronger binding sites at crystalline ice. We have also performed molecular dynamics simulations of the photoexcitation of vapor-deposited water at a range of surface temperatures. These results support that the experimentally observed desorption of H atoms following UV excitation is best explained by release of H atoms from

  4. Integrating microbial diversity in soil carbon dynamic models parameters

    NASA Astrophysics Data System (ADS)

    Louis, Benjamin; Menasseri-Aubry, Safya; Leterme, Philippe; Maron, Pierre-Alain; Viaud, Valérie

    2015-04-01

    Faced with the numerous concerns about soil carbon dynamic, a large quantity of carbon dynamic models has been developed during the last century. These models are mainly in the form of deterministic compartment models with carbon fluxes between compartments represented by ordinary differential equations. Nowadays, lots of them consider the microbial biomass as a compartment of the soil organic matter (carbon quantity). But the amount of microbial carbon is rarely used in the differential equations of the models as a limiting factor. Additionally, microbial diversity and community composition are mostly missing, although last advances in soil microbial analytical methods during the two past decades have shown that these characteristics play also a significant role in soil carbon dynamic. As soil microorganisms are essential drivers of soil carbon dynamic, the question about explicitly integrating their role have become a key issue in soil carbon dynamic models development. Some interesting attempts can be found and are dominated by the incorporation of several compartments of different groups of microbial biomass in terms of functional traits and/or biogeochemical compositions to integrate microbial diversity. However, these models are basically heuristic models in the sense that they are used to test hypotheses through simulations. They have rarely been confronted to real data and thus cannot be used to predict realistic situations. The objective of this work was to empirically integrate microbial diversity in a simple model of carbon dynamic through statistical modelling of the model parameters. This work is based on available experimental results coming from a French National Research Agency program called DIMIMOS. Briefly, 13C-labelled wheat residue has been incorporated into soils with different pedological characteristics and land use history. Then, the soils have been incubated during 104 days and labelled and non-labelled CO2 fluxes have been measured at ten

  5. Inhalation Exposure Input Parameters for the Biosphere Model

    SciTech Connect

    M. A. Wasiolek

    2003-09-24

    This analysis is one of the nine reports that support the Environmental Radiation Model for Yucca Mountain Nevada (ERMYN) biosphere model. The ''Biosphere Model Report'' (BSC 2003a) describes in detail the conceptual model as well as the mathematical model and its input parameters. This report documents a set of input parameters for the biosphere model, and supports the use of the model to develop biosphere dose conversion factors (BDCFs). The biosphere model is one of a series of process models supporting the Total System Performance Assessment (TSPA) for a Yucca Mountain repository. This report, ''Inhalation Exposure Input Parameters for the Biosphere Model'', is one of the five reports that develop input parameters for the biosphere model. A graphical representation of the documentation hierarchy for the ERMYN is presented in Figure 1-1. This figure shows the interrelationships among the products (i.e., analysis and model reports) developed for biosphere modeling, and the plan for development of the biosphere abstraction products for TSPA, as identified in the ''Technical Work Plan: for Biosphere Modeling and Expert Support'' (BSC 2003b). It should be noted that some documents identified in Figure 1-1 may be under development at the time this report is issued and therefore not available at that time. This figure is included to provide an understanding of how this analysis report contributes to biosphere modeling in support of the license application, and is not intended to imply that access to the listed documents is required to understand the contents of this analysis report. This analysis report defines and justifies values of mass loading, which is the total mass concentration of resuspended particles (e.g., dust, ash) in a volume of air. Measurements of mass loading are used in the air submodel of ERMYN to calculate concentrations of radionuclides in air surrounding crops and concentrations in air inhaled by a receptor. Concentrations in air to which the

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

    PubMed

    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.

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

    PubMed

    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. PMID:27467814

  8. Improving a regional model using reduced complexity and parameter estimation

    USGS Publications Warehouse

    Kelson, Victor A.; Hunt, Randall J.; Haitjema, Henk M.

    2002-01-01

    The availability of powerful desktop computers and graphical user interfaces for ground water flow models makes possible the construction of ever more complex models. A proposed copper-zinc sulfide mine in northern Wisconsin offers a unique case in which the same hydrologic system has been modeled using a variety of techniques covering a wide range of sophistication and complexity. Early in the permitting process, simple numerical models were used to evaluate the necessary amount of water to be pumped from the mine, reductions in streamflow, and the drawdowns in the regional aquifer. More complex models have subsequently been used in an attempt to refine the predictions. Even after so much modeling effort, questions regarding the accuracy and reliability of the predictions remain. We have performed a new analysis of the proposed mine using the two-dimensional analytic element code GFLOW coupled with the nonlinear parameter estimation code UCODE. The new model is parsimonious, containing fewer than 10 parameters, and covers a region several times larger in areal extent than any of the previous models. The model demonstrates the suitability of analytic element codes for use with parameter estimation codes. The simplified model results are similar to the more complex models; predicted mine inflows and UCODE-derived 95% confidence intervals are consistent with the previous predictions. More important, the large areal extent of the model allowed us to examine hydrological features not included in the previous models, resulting in new insights about the effects that far-field boundary conditions can have on near-field model calibration and parameterization. In this case, the addition of surface water runoff into a lake in the headwaters of a stream while holding recharge constant moved a regional ground watershed divide and resulted in some of the added water being captured by the adjoining basin. Finally, a simple analytical solution was used to clarify the GFLOW model

  9. Parameter Calibration of Mini-LEO Hill Slope Model

    NASA Astrophysics Data System (ADS)

    Siegel, H.

    2015-12-01

    The mini-LEO hill slope, located at Biosphere 2, is a small-scale catchment model that is used to study the ways landscapes change in response to biological, chemical, and hydrological processes. Previous experiments have shown that soil heterogeneity can develop as a result of groundwater flow; changing the characteristics of the landscape. To determine whether or not flow has caused heterogeneity within the mini-LEO hill slope, numerical models were used to simulate the observed seepage flow, water table height, and storativity. To begin a numerical model of the hill slope was created using CATchment Hydrology (CATHY). The model was then brought to an initial steady state by applying a rainfall event of 5mm/day for 180 days. Then a specific rainfall experiment of alternating intensities was applied to the model. Next, a parameter calibration was conducted, to fit the model to the observed data, by changing soil parameters individually. The parameters of the best fitting calibration were taken to be the most representative of those present within the mini-LEO hill slope. Our model concluded that heterogeneities had indeed arisen as a result of the rainfall event, resulting in a lower hydraulic conductivity downslope. The lower hydraulic conductivity downslope in turn caused in an increased storage of water and a decrease in seepage flow compared to homogeneous models. This shows that the hydraulic processes acting within a landscape can change the very characteristics of the landscape itself, namely the permeability and conductivity of the soil. In the future results from the excavation of soil in mini-LEO can be compared to the models results to improve the model and validate its findings.

  10. Electro-optical parameters of bond polarizability model for aluminosilicates.

    PubMed

    Smirnov, Konstantin S; Bougeard, Daniel; Tandon, Poonam

    2006-04-01

    Electro-optical parameters (EOPs) of bond polarizability model (BPM) for aluminosilicate structures were derived from quantum-chemical DFT calculations of molecular models. The tensor of molecular polarizability and the derivatives of the tensor with respect to the bond length are well reproduced with the BPM, and the EOPs obtained are in a fair agreement with available experimental data. The parameters derived were found to be transferable to larger molecules. This finding suggests that the procedure used can be applied to systems with partially ionic chemical bonds. The transferability of the parameters to periodic systems was tested in molecular dynamics simulation of the polarized Raman spectra of alpha-quartz. It appeared that the molecular Si-O bond EOPs failed to reproduce the intensity of peaks in the spectra. This limitation is due to large values of the longitudinal components of the bond polarizability and its derivative found in the molecular calculations as compared to those obtained from periodic DFT calculations of crystalline silica polymorphs by Umari et al. (Phys. Rev. B 2001, 63, 094305). It is supposed that the electric field of the solid is responsible for the difference of the parameters. Nevertheless, the EOPs obtained can be used as an initial set of parameters for calculations of polarizability related characteristics of relevant systems in the framework of BPM.

  11. Soil-Related Input Parameters for the Biosphere Model

    SciTech Connect

    A. J. Smith

    2004-09-09

    This report presents one of the analyses that support the Environmental Radiation Model for Yucca Mountain Nevada (ERMYN). The ''Biosphere Model Report'' (BSC 2004 [DIRS 169460]) describes the details of the conceptual model as well as the mathematical model and the required input parameters. The biosphere model is one of a series of process models supporting the postclosure Total System Performance Assessment (TSPA) for the Yucca Mountain repository. A schematic representation of the documentation flow for the Biosphere input to TSPA is presented in Figure 1-1. This figure shows the evolutionary relationships among the products (i.e., analysis and model reports) developed for biosphere modeling, and the biosphere abstraction products for TSPA, as identified in the ''Technical Work Plan for Biosphere Modeling and Expert Support'' (TWP) (BSC 2004 [DIRS 169573]). This figure is included to provide an understanding of how this analysis report contributes to biosphere modeling in support of the license application, and is not intended to imply that access to the listed documents is required to understand the contents of this report. This report, ''Soil-Related Input Parameters for the Biosphere Model'', is one of the five analysis reports that develop input parameters for use in the ERMYN model. This report is the source documentation for the six biosphere parameters identified in Table 1-1. The purpose of this analysis was to develop the biosphere model parameters associated with the accumulation and depletion of radionuclides in the soil. These parameters support the calculation of radionuclide concentrations in soil from on-going irrigation or ash deposition and, as a direct consequence, radionuclide concentration in other environmental media that are affected by radionuclide concentrations in soil. The analysis was performed in accordance with the TWP (BSC 2004 [DIRS 169573]) where the governing procedure was defined as AP-SIII.9Q, ''Scientific Analyses''. This

  12. Telescoping strategies for improved parameter estimation of environmental simulation models

    NASA Astrophysics Data System (ADS)

    Matott, L. Shawn; Hymiak, Beth; Reslink, Camden; Baxter, Christine; Aziz, Shirmin

    2013-10-01

    The parameters of environmental simulation models are often inferred by minimizing differences between simulated output and observed data. Heuristic global search algorithms are a popular choice for performing minimization but many algorithms yield lackluster results when computational budgets are restricted, as is often required in practice. One way for improving performance is to limit the search domain by reducing upper and lower parameter bounds. While such range reduction is typically done prior to optimization, this study examined strategies for contracting parameter bounds during optimization. Numerical experiments evaluated a set of novel “telescoping” strategies that work in conjunction with a given optimizer to scale parameter bounds in accordance with the remaining computational budget. Various telescoping functions were considered, including a linear scaling of the bounds, and four nonlinear scaling functions that more aggressively reduce parameter bounds either early or late in the optimization. Several heuristic optimizers were integrated with the selected telescoping strategies and applied to numerous optimization test functions as well as calibration problems involving four environmental simulation models. The test suite ranged from simple 2-parameter surfaces to complex 100-parameter landscapes, facilitating robust comparisons of the selected optimizers across a variety of restrictive computational budgets. All telescoping strategies generally improved the performance of the selected optimizers, relative to baseline experiments that used no bounds reduction. Performance improvements varied but were as high as 38% for a real-coded genetic algorithm (RGA), 21% for shuffled complex evolution (SCE), 16% for simulated annealing (SA), 8% for particle swarm optimization (PSO), and 7% for dynamically dimensioned search (DDS). Inter-algorithm comparisons suggest that the SCE and DDS algorithms delivered the best overall performance. SCE appears well

  13. Realistic uncertainties on Hapke model parameters from photometric measurement

    NASA Astrophysics Data System (ADS)

    Schmidt, Frédéric; Fernando, Jennifer

    2015-11-01

    The single particle phase function describes the manner in which an average element of a granular material diffuses the light in the angular space usually with two parameters: the asymmetry parameter b describing the width of the scattering lobe and the backscattering fraction c describing the main direction of the scattering lobe. Hapke proposed a convenient and widely used analytical model to describe the spectro-photometry of granular materials. Using a compilation of the published data, Hapke (Hapke, B. [2012]. Icarus 221, 1079-1083) recently studied the relationship of b and c for natural examples and proposed the hockey stick relation (excluding b > 0.5 and c > 0.5). For the moment, there is no theoretical explanation for this relationship. One goal of this article is to study a possible bias due to the retrieval method. We expand here an innovative Bayesian inversion method in order to study into detail the uncertainties of retrieved parameters. On Emission Phase Function (EPF) data, we demonstrate that the uncertainties of the retrieved parameters follow the same hockey stick relation, suggesting that this relation is due to the fact that b and c are coupled parameters in the Hapke model instead of a natural phenomena. Nevertheless, the data used in the Hapke (Hapke, B. [2012]. Icarus 221, 1079-1083) compilation generally are full Bidirectional Reflectance Diffusion Function (BRDF) that are shown not to be subject to this artifact. Moreover, the Bayesian method is a good tool to test if the sampling geometry is sufficient to constrain the parameters (single scattering albedo, surface roughness, b, c , opposition effect). We performed sensitivity tests by mimicking various surface scattering properties and various single image-like/disk resolved image, EPF-like and BRDF-like geometric sampling conditions. The second goal of this article is to estimate the favorable geometric conditions for an accurate estimation of photometric parameters in order to provide

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

    PubMed Central

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

    2015-01-01

    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. PMID:26249348

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

    PubMed

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

    2015-08-01

    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.

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

    SciTech Connect

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

    2015-07-28

    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.

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

    DOE PAGES

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

    2015-07-28

    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 severalmore » 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.« less

  18. Effect of discharge parameters on emission yields in a radio-frequency glow-discharge atomic-emission source

    NASA Astrophysics Data System (ADS)

    Parker, Mark; Hartenstein, Matthew L.; Marcus, R. Kenneth

    1997-05-01

    A study is performed on a radio-frequency glow-discharge atomic-emission (rf-GD-AES) source to determine the factors effecting the emission yields for both metallic and nonconductive sample types. Specifically, these studies focus on determining how the operating parameters (power and pressure) influence emission yields. The results follow predicted patterns as determined by Langmuir probe diagnostic studies of a similar source. In particular, discharge gas pressure is the key operating parameter as slight changes in pressure may significantly affect the emission yield of the analyte species. RF power is less important and is shown to produce only relatively small changes in the emission yield over the ranges typically used in rf-GD analyses. These studies indicate that the quantitative analysis of layered materials, depth-profiling, may be adversely affected if the data collection scheme, i.e. the quantitative algorithm, requires changing the pressure during an analysis to keep the operating current and voltage constant. A direct relationship is shown to exist between the Ar (discharge gas) emission intensity and that of sputtered species for nonconductors. This observance is used to compensate for differences in emission intensities observed in the analysis of various thickness nonconductive samples. The sputtered element emission signals are corrected based on the emission intensity of an Ar (1) transition, implying that quantitative analysis of nonconductive samples is not severely limited by the availability of matrix matched standards.

  19. Mass balance model parameter transferability on a tropical glacier

    NASA Astrophysics Data System (ADS)

    Gurgiser, Wolfgang; Mölg, Thomas; Nicholson, Lindsey; Kaser, Georg

    2013-04-01

    The mass balance and melt water production of glaciers is of particular interest in the Peruvian Andes where glacier melt water has markedly increased water supply during the pronounced dry seasons in recent decades. However, the melt water contribution from glaciers is projected to decrease with appreciable negative impacts on the local society within the coming decades. Understanding mass balance processes on tropical glaciers is a prerequisite for modeling present and future glacier runoff. As a first step towards this aim we applied a process-based surface mass balance model in order to calculate observed ablation at two stakes in the ablation zone of Shallap Glacier (4800 m a.s.l., 9°S) in the Cordillera Blanca, Peru. Under the tropical climate, the snow line migrates very frequently across most of the ablation zone all year round causing large temporal and spatial variations of glacier surface conditions and related ablation. Consequently, pronounced differences between the two chosen stakes and the two years were observed. Hourly records of temperature, humidity, wind speed, short wave incoming radiation, and precipitation are available from an automatic weather station (AWS) on the moraine near the glacier for the hydrological years 2006/07 and 2007/08 while stake readings are available at intervals of between 14 to 64 days. To optimize model parameters, we used 1000 model simulations in which the most sensitive model parameters were varied randomly within their physically meaningful ranges. The modeled surface height change was evaluated against the two stake locations in the lower ablation zone (SH11, 4760m) and in the upper ablation zone (SH22, 4816m), respectively. The optimal parameter set for each point achieved good model skill but if we transfer the best parameter combination from one stake site to the other stake site model errors increases significantly. The same happens if we optimize the model parameters for each year individually and transfer

  20. Estimating demographic parameters using hidden process dynamic models.

    PubMed

    Gimenez, Olivier; Lebreton, Jean-Dominique; Gaillard, Jean-Michel; Choquet, Rémi; Pradel, Roger

    2012-12-01

    Structured population models are widely used in plant and animal demographic studies to assess population dynamics. In matrix population models, populations are described with discrete classes of individuals (age, life history stage or size). To calibrate these models, longitudinal data are collected at the individual level to estimate demographic parameters. However, several sources of uncertainty can complicate parameter estimation, such as imperfect detection of individuals inherent to monitoring in the wild and uncertainty in assigning a state to an individual. Here, we show how recent statistical models can help overcome these issues. We focus on hidden process models that run two time series in parallel, one capturing the dynamics of the true states and the other consisting of observations arising from these underlying possibly unknown states. In a first case study, we illustrate hidden Markov models with an example of how to accommodate state uncertainty using Frequentist theory and maximum likelihood estimation. In a second case study, we illustrate state-space models with an example of how to estimate lifetime reproductive success despite imperfect detection, using a Bayesian framework and Markov Chain Monte Carlo simulation. Hidden process models are a promising tool as they allow population biologists to cope with process variation while simultaneously accounting for observation error. PMID:22373775

  1. Multiple beam interference model for measuring parameters of a capillary.

    PubMed

    Xu, Qiwei; Tian, Wenjing; You, Zhihong; Xiao, Jinghua

    2015-08-01

    A multiple beam interference model based on the ray tracing method and interference theory is built to analyze the interference patterns of a capillary tube filled with a liquid. The relations between the angular widths of the interference fringes and the parameters of both the capillary and liquid are derived. Based on these relations, an approach is proposed to simultaneously determine four parameters of the capillary, i.e., the inner and outer radii of the capillary, the refractive indices of the liquid, and the wall material. PMID:26368114

  2. Inversion of canopy reflectance models for estimation of vegetation parameters

    NASA Technical Reports Server (NTRS)

    Goel, Narendra S.

    1987-01-01

    One of the keys to successful remote sensing of vegetation is to be able to estimate important agronomic parameters like leaf area index (LAI) and biomass (BM) from the bidirectional canopy reflectance (CR) data obtained by a space-shuttle or satellite borne sensor. One approach for such an estimation is through inversion of CR models which relate these parameters to CR. The feasibility of this approach was shown. The overall objective of the research carried out was to address heretofore uninvestigated but important fundamental issues, develop the inversion technique further, and delineate its strengths and limitations.

  3. Multiple beam interference model for measuring parameters of a capillary.

    PubMed

    Xu, Qiwei; Tian, Wenjing; You, Zhihong; Xiao, Jinghua

    2015-08-01

    A multiple beam interference model based on the ray tracing method and interference theory is built to analyze the interference patterns of a capillary tube filled with a liquid. The relations between the angular widths of the interference fringes and the parameters of both the capillary and liquid are derived. Based on these relations, an approach is proposed to simultaneously determine four parameters of the capillary, i.e., the inner and outer radii of the capillary, the refractive indices of the liquid, and the wall material.

  4. Comparison of Cone Model Parameters for Halo Coronal Mass Ejections

    NASA Astrophysics Data System (ADS)

    Na, Hyeonock; Moon, Y.-J.; Jang, Soojeong; Lee, Kyoung-Sun; Kim, Hae-Yeon

    2013-11-01

    Halo coronal mass ejections (HCMEs) are a major cause of geomagnetic storms, hence their three-dimensional structures are important for space weather. We compare three cone models: an elliptical-cone model, an ice-cream-cone model, and an asymmetric-cone model. These models allow us to determine three-dimensional parameters of HCMEs such as radial speed, angular width, and the angle [ γ] between sky plane and cone axis. We compare these parameters obtained from three models using 62 HCMEs observed by SOHO/LASCO from 2001 to 2002. Then we obtain the root-mean-square (RMS) error between the highest measured projection speeds and their calculated projection speeds from the cone models. As a result, we find that the radial speeds obtained from the models are well correlated with one another ( R > 0.8). The correlation coefficients between angular widths range from 0.1 to 0.48 and those between γ-values range from -0.08 to 0.47, which is much smaller than expected. The reason may be the different assumptions and methods. The RMS errors between the highest measured projection speeds and the highest estimated projection speeds of the elliptical-cone model, the ice-cream-cone model, and the asymmetric-cone model are 376 km s-1, 169 km s-1, and 152 km s-1. We obtain the correlation coefficients between the location from the models and the flare location ( R > 0.45). Finally, we discuss strengths and weaknesses of these models in terms of space-weather application.

  5. Revised digestive parameter estimates for the Molly cow model.

    PubMed

    Hanigan, M D; Appuhamy, J A D R N; Gregorini, P

    2013-06-01

    The Molly cow model represents nutrient digestion and metabolism based on a mechanistic representation of the key biological elements. Digestive parameters were derived ad hoc from literature observations or were assumed. Preliminary work determined that several of these parameters did not represent the true relationships. The current work was undertaken to derive ruminal and postruminal digestive parameters and to use a meta-approach to assess the effects of interactions among nutrients and identify areas of model weakness. Model predictions were compared with a database of literature observations containing 233 treatment means. Mean square prediction errors were assessed to characterize model performance. Ruminal pH prediction equations had substantial mean bias, which caused problems in fiber digestion and microbial growth predictions. The pH prediction equation was reparameterized simultaneously with the several ruminal and postruminal digestion parameters, resulting in more realistic parameter estimates for ruminal fiber digestion, and moderate reductions in prediction errors for pH, neutral detergent fiber, acid detergent fiber, and microbial N outflow from the rumen; and postruminal digestion of neutral detergent fiber, acid detergent fiber, and protein. Prediction errors are still large for ruminal ammonia and outflow of starch from the rumen. The gain in microbial efficiency associated with fat feeding was found to be more than twice the original estimate, but in contrast to prior assumptions, fat feeding did not exert negative effects on fiber and protein degradation in the rumen. Microbial responses to ruminal ammonia concentrations were half saturated at 0.2mM versus the original estimate of 1.2mM. Residuals analyses indicated that additional progress could be made in predicting microbial N outflow, volatile fatty acid production and concentrations, and cycling of N between blood and the rumen. These additional corrections should lead to an even more

  6. Test models for improving filtering with model errors through stochastic parameter estimation

    SciTech Connect

    Gershgorin, B.; Harlim, J. Majda, A.J.

    2010-01-01

    The filtering skill for turbulent signals from nature is often limited by model errors created by utilizing an imperfect model for filtering. Updating the parameters in the imperfect model through stochastic parameter estimation is one way to increase filtering skill and model performance. Here a suite of stringent test models for filtering with stochastic parameter estimation is developed based on the Stochastic Parameterization Extended Kalman Filter (SPEKF). These new SPEKF-algorithms systematically correct both multiplicative and additive biases and involve exact formulas for propagating the mean and covariance including the parameters in the test model. A comprehensive study is presented of robust parameter regimes for increasing filtering skill through stochastic parameter estimation for turbulent signals as the observation time and observation noise are varied and even when the forcing is incorrectly specified. The results here provide useful guidelines for filtering turbulent signals in more complex systems with significant model errors.

  7. Thermodynamics of various F420 coenzyme models as sources of electrons, hydride ions, hydrogen atoms and protons in acetonitrile.

    PubMed

    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.

  8. Thermodynamics of various F420 coenzyme models as sources of electrons, hydride ions, hydrogen atoms and protons in acetonitrile.

    PubMed

    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

  9. Unrealistic parameter estimates in inverse modelling: A problem or a benefit for model calibration?

    USGS Publications Warehouse

    Poeter, E.P.; Hill, M.C.

    1996-01-01

    Estimation of unrealistic parameter values by inverse modelling is useful for constructed model discrimination. This utility is demonstrated using the three-dimensional, groundwater flow inverse model MODFLOWP to estimate parameters in a simple synthetic model where the true conditions and character of the errors are completely known. When a poorly constructed model is used, unreasonable parameter values are obtained even when using error free observations and true initial parameter values. This apparent problem is actually a benefit because it differentiates accurately and inaccurately constructed models. The problems seem obvious for a synthetic problem in which the truth is known, but are obscure when working with field data. Situations in which unrealistic parameter estimates indicate constructed model problems are illustrated in applications of inverse modelling to three field sites and to complex synthetic test cases in which it is shown that prediction accuracy also suffers when constructed models are inaccurate.

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

    ERIC Educational Resources Information Center

    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…

  11. Dynamic imaging model and parameter optimization for a star tracker.

    PubMed

    Yan, Jinyun; Jiang, Jie; Zhang, Guangjun

    2016-03-21

    Under dynamic conditions, star spots move across the image plane of a star tracker and form a smeared star image. This smearing effect increases errors in star position estimation and degrades attitude accuracy. First, an analytical energy distribution model of a smeared star spot is established based on a line segment spread function because the dynamic imaging process of a star tracker is equivalent to the static imaging process of linear light sources. The proposed model, which has a clear physical meaning, explicitly reflects the key parameters of the imaging process, including incident flux, exposure time, velocity of a star spot in an image plane, and Gaussian radius. Furthermore, an analytical expression of the centroiding error of the smeared star spot is derived using the proposed model. An accurate and comprehensive evaluation of centroiding accuracy is obtained based on the expression. Moreover, analytical solutions of the optimal parameters are derived to achieve the best performance in centroid estimation. Finally, we perform numerical simulations and a night sky experiment to validate the correctness of the dynamic imaging model, the centroiding error expression, and the optimal parameters.

  12. Modeling crash spatial heterogeneity: random parameter versus geographically weighting.

    PubMed

    Xu, Pengpeng; Huang, Helai

    2015-02-01

    The widely adopted techniques for regional crash modeling include the negative binomial model (NB) and Bayesian negative binomial model with conditional autoregressive prior (CAR). The outputs from both models consist of a set of fixed global parameter estimates. However, the impacts of predicting variables on crash counts might not be stationary over space. This study intended to quantitatively investigate this spatial heterogeneity in regional safety modeling using two advanced approaches, i.e., random parameter negative binomial model (RPNB) and semi-parametric geographically weighted Poisson regression model (S-GWPR). Based on a 3-year data set from the county of Hillsborough, Florida, results revealed that (1) both RPNB and S-GWPR successfully capture the spatially varying relationship, but the two methods yield notably different sets of results; (2) the S-GWPR performs best with the highest value of Rd(2) as well as the lowest mean absolute deviance and Akaike information criterion measures. Whereas the RPNB is comparable to the CAR, in some cases, it provides less accurate predictions; (3) a moderately significant spatial correlation is found in the residuals of RPNB and NB, implying the inadequacy in accounting for the spatial correlation existed across adjacent zones. As crash data are typically collected with reference to location dimension, it is desirable to firstly make use of the geographical component to explore explicitly spatial aspects of the crash data (i.e., the spatial heterogeneity, or the spatially structured varying relationships), then is the unobserved heterogeneity by non-spatial or fuzzy techniques. The S-GWPR is proven to be more appropriate for regional crash modeling as the method outperforms the global models in capturing the spatial heterogeneity occurring in the relationship that is model, and compared with the non-spatial model, it is capable of accounting for the spatial correlation in crash data.

  13. Modeling crash spatial heterogeneity: random parameter versus geographically weighting.

    PubMed

    Xu, Pengpeng; Huang, Helai

    2015-02-01

    The widely adopted techniques for regional crash modeling include the negative binomial model (NB) and Bayesian negative binomial model with conditional autoregressive prior (CAR). The outputs from both models consist of a set of fixed global parameter estimates. However, the impacts of predicting variables on crash counts might not be stationary over space. This study intended to quantitatively investigate this spatial heterogeneity in regional safety modeling using two advanced approaches, i.e., random parameter negative binomial model (RPNB) and semi-parametric geographically weighted Poisson regression model (S-GWPR). Based on a 3-year data set from the county of Hillsborough, Florida, results revealed that (1) both RPNB and S-GWPR successfully capture the spatially varying relationship, but the two methods yield notably different sets of results; (2) the S-GWPR performs best with the highest value of Rd(2) as well as the lowest mean absolute deviance and Akaike information criterion measures. Whereas the RPNB is comparable to the CAR, in some cases, it provides less accurate predictions; (3) a moderately significant spatial correlation is found in the residuals of RPNB and NB, implying the inadequacy in accounting for the spatial correlation existed across adjacent zones. As crash data are typically collected with reference to location dimension, it is desirable to firstly make use of the geographical component to explore explicitly spatial aspects of the crash data (i.e., the spatial heterogeneity, or the spatially structured varying relationships), then is the unobserved heterogeneity by non-spatial or fuzzy techniques. The S-GWPR is proven to be more appropriate for regional crash modeling as the method outperforms the global models in capturing the spatial heterogeneity occurring in the relationship that is model, and compared with the non-spatial model, it is capable of accounting for the spatial correlation in crash data. PMID:25460087

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

    PubMed

    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.

  15. Development of a phenomenological model for coal slurry atomization

    SciTech Connect

    Dooher, J.P.

    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.

  16. Important observations and parameters for a salt water intrusion model.

    PubMed

    Shoemaker, W Barclay

    2004-01-01

    Sensitivity analysis with a density-dependent ground water flow simulator can provide insight and understanding of salt water intrusion calibration problems far beyond what is possible through intuitive analysis alone. Five simple experimental simulations presented here demonstrate this point. Results show that dispersivity is a very important parameter for reproducing a steady-state distribution of hydraulic head, salinity, and flow in the transition zone between fresh water and salt water in a coastal aquifer system. When estimating dispersivity, the following conclusions can be drawn about the data types and locations considered. (1) The "toe" of the transition zone is the most effective location for hydraulic head and salinity observations. (2) Areas near the coastline where submarine ground water discharge occurs are the most effective locations for flow observations. (3) Salinity observations are more effective than hydraulic head observations. (4) The importance of flow observations aligned perpendicular to the shoreline varies dramatically depending on distance seaward from the shoreline. Extreme parameter correlation can prohibit unique estimation of permeability parameters such as hydraulic conductivity and flow parameters such as recharge in a density-dependent ground water flow model when using hydraulic head and salinity observations. Adding flow observations perpendicular to the shoreline in areas where ground water is exchanged with the ocean body can reduce the correlation, potentially resulting in unique estimates of these parameter values. Results are expected to be directly applicable to many complex situations, and have implications for model development whether or not formal optimization methods are used in model calibration. PMID:15584297

  17. Estimation of Time-Varying Pilot Model Parameters

    NASA Technical Reports Server (NTRS)

    Zaal, Peter M. T.; Sweet, Barbara T.

    2011-01-01

    Human control behavior is rarely completely stationary over time due to fatigue or loss of attention. In addition, there are many control tasks for which human operators need to adapt their control strategy to vehicle dynamics that vary in time. In previous studies on the identification of time-varying pilot control behavior wavelets were used to estimate the time-varying frequency response functions. However, the estimation of time-varying pilot model parameters was not considered. Estimating these parameters can be a valuable tool for the quantification of different aspects of human time-varying manual control. This paper presents two methods for the estimation of time-varying pilot model parameters, a two-step method using wavelets and a windowed maximum likelihood estimation method. The methods are evaluated using simulations of a closed-loop control task with time-varying pilot equalization and vehicle dynamics. Simulations are performed with and without remnant. Both methods give accurate results when no pilot remnant is present. The wavelet transform is very sensitive to measurement noise, resulting in inaccurate parameter estimates when considerable pilot remnant is present. Maximum likelihood estimation is less sensitive to pilot remnant, but cannot detect fast changes in pilot control behavior.

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

    PubMed

    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.

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

    PubMed Central

    Yazdani, Nuri; Chawla, Vipin; Edwards, Eve; Wood, Vanessa

    2014-01-01

    Summary 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. PMID:24778944

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

    PubMed

    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. PMID:24778944

  1. Collision cross sections and diffusion parameters for H and D in atomic oxygen. [in upper earth and Venus atmospheres

    NASA Technical Reports Server (NTRS)

    Hodges, R. R., Jr.

    1993-01-01

    Modeling the behavior of H and D in planetary exospheres requires detailed knowledge of the differential scattering cross sections for all of the important neutral-neutral and ion-neutral collision processes affecting these species over their entire ranges of interaction energies. In the upper atmospheres of Earth, Venus, and other planets as well, the interactions of H and D with atomic oxygen determine the rates of diffusion of escaping hydrogen isotopes through the thermosphere, the velocity distributions of exospheric atoms that encounter the upper thermosphere, the lifetimes of exospheric orbiters with periapsides near the exobase, and the transfer of momentum in collisions with hot O. The nature of H-O and D-O collisions and the derivation of a data base consisting of phase shifts and the differential, total, and momentum transfer cross sections for these interactions in the energy range 0.001 - 10 eV are discussed. Coefficients of mutual diffusion and thermal diffusion factors are calculated for temperatures of planetary interest.

  2. Parameter discovery in stochastic biological models using simulated annealing and statistical model checking.

    PubMed

    Hussain, Faraz; Jha, Sumit K; Jha, Susmit; Langmead, Christopher J

    2014-01-01

    Stochastic models are increasingly used to study the behaviour of biochemical systems. While the structure of such models is often readily available from first principles, unknown quantitative features of the model are incorporated into the model as parameters. Algorithmic discovery of parameter values from experimentally observed facts remains a challenge for the computational systems biology community. We present a new parameter discovery algorithm that uses simulated annealing, sequential hypothesis testing, and statistical model checking to learn the parameters in a stochastic model. We apply our technique to a model of glucose and insulin metabolism used for in-silico validation of artificial pancreata and demonstrate its effectiveness by developing parallel CUDA-based implementation for parameter synthesis in this model. PMID:24989866

  3. Empirical flow parameters : a tool for hydraulic model validity

    USGS Publications Warehouse

    Asquith, William H.; Burley, Thomas E.; Cleveland, Theodore G.

    2013-01-01

    The objectives of this project were (1) To determine and present from existing data in Texas, relations between observed stream flow, topographic slope, mean section velocity, and other hydraulic factors, to produce charts such as Figure 1 and to produce empirical distributions of the various flow parameters to provide a methodology to "check if model results are way off!"; (2) To produce a statistical regional tool to estimate mean velocity or other selected parameters for storm flows or other conditional discharges at ungauged locations (most bridge crossings) in Texas to provide a secondary way to compare such values to a conventional hydraulic modeling approach. (3.) To present ancillary values such as Froude number, stream power, Rosgen channel classification, sinuosity, and other selected characteristics (readily determinable from existing data) to provide additional information to engineers concerned with the hydraulic-soil-foundation component of transportation infrastructure.

  4. ATOMIC AND MOLECULAR PHYSICS: Model Potential Calculations of Oscillator Strength Spectra of Rydberg Li Atoms in External Fields

    NASA Astrophysics Data System (ADS)

    Meng, Hui-Yan; Shi, Ting-Yun

    2009-08-01

    By combining the B-spline basis set with model potential (B-spline + MP), we present oscillator strength spectra of Rydberg Li atoms in external fields. The photoabsorption spectra are analyzed. Over the narrow energy ranges considered in this paper, the structure of the spectra can be independent of the initial state chosen for a given atom. Our results are in good agreement with previous high-precision experimental data and theoretical calculations, where the R-matrix approach together with multichannel quantum defect theory (R-matrix+MQDT) was used. It is suggested that the present methods can be applied to deal with the oscillator strength spectra of Rydberg atoms in crossed electric and magnetic fields.

  5. Atomic forces for geometry-dependent point multipole and gaussian multipole models.

    PubMed

    Elking, Dennis M; Perera, Lalith; Duke, Robert; Darden, Thomas; Pedersen, Lee G

    2010-11-30

    In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise because of (1) the transfer of torque between neighboring atoms and (2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In this study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives partial derivative D(m'm)(l)/partial derivative Omega. The force equations can be applied to electrostatic models based on atomic point multipoles or gaussian multipole charge density. Hydrogen-bonded dimers are used to test the intermolecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential. The electrostatic energies and forces are compared with their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, whereas geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models.

  6. Numerical model for thermal parameters in optical materials

    NASA Astrophysics Data System (ADS)

    Sato, Yoichi; Taira, Takunori

    2016-04-01

    Thermal parameters of optical materials, such as thermal conductivity, thermal expansion, temperature coefficient of refractive index play a decisive role for the thermal design inside laser cavities. Therefore, numerical value of them with temperature dependence is quite important in order to develop the high intense laser oscillator in which optical materials generate excessive heat across mode volumes both of lasing output and optical pumping. We already proposed a novel model of thermal conductivity in various optical materials. Thermal conductivity is a product of isovolumic specific heat and thermal diffusivity, and independent modeling of these two figures should be required from the viewpoint of a clarification of physical meaning. Our numerical model for thermal conductivity requires one material parameter for specific heat and two parameters for thermal diffusivity in the calculation of each optical material. In this work we report thermal conductivities of various optical materials as Y3Al5O12 (YAG), YVO4 (YVO), GdVO4 (GVO), stoichiometric and congruent LiTaO3, synthetic quartz, YAG ceramics and Y2O3 ceramics. The dependence on Nd3+-doping in laser gain media in YAG, YVO and GVO is also studied. This dependence can be described by only additional three parameters. Temperature dependence of thermal expansion and temperature coefficient of refractive index for YAG, YVO, and GVO: these are also included in this work for convenience. We think our numerical model is quite useful for not only thermal analysis in laser cavities or optical waveguides but also the evaluation of physical properties in various transparent materials.

  7. Automated parameter estimation for biological models using Bayesian statistical model checking

    PubMed Central

    2015-01-01

    Background Probabilistic models have gained widespread acceptance in the systems biology community as a useful way to represent complex biological systems. Such models are developed using existing knowledge of the structure and dynamics of the system, experimental observations, and inferences drawn from statistical analysis of empirical data. A key bottleneck in building such models is that some system variables cannot be measured experimentally. These variables are incorporated into the model as numerical parameters. Determining values of these parameters that justify existing experiments and provide reliable predictions when model simulations are performed is a key research problem. Domain experts usually estimate the values of these parameters by fitting the model to experimental data. Model fitting is usually expressed as an optimization problem that requires minimizing a cost-function which measures some notion of distance between the model and the data. This optimization problem is often solved by combining local and global search methods that tend to perform well for the specific application domain. When some prior information about parameters is available, methods such as Bayesian inference are commonly used for parameter learning. Choosing the appropriate parameter search technique requires detailed domain knowledge and insight into the underlying system. Results Using an agent-based model of the dynamics of acute inflammation, we demonstrate a novel parameter estimation algorithm by discovering the amount and schedule of doses of bacterial lipopolysaccharide that guarantee a set of observed clinical outcomes with high probability. We synthesized values of twenty-eight unknown parameters such that the parameterized model instantiated with these parameter values satisfies four specifications describing the dynamic behavior of the model. Conclusions We have developed a new algorithmic technique for discovering parameters in complex stochastic models of

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

    NASA Technical Reports Server (NTRS)

    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.

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

    NASA Astrophysics Data System (ADS)

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

    1995-08-01

    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.

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

    NASA Technical Reports Server (NTRS)

    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.

  11. Modelling spatial-temporal and coordinative parameters in swimming.

    PubMed

    Seifert, L; Chollet, D

    2009-07-01

    This study modelled the changes in spatial-temporal and coordinative parameters through race paces in the four swimming strokes. The arm and leg phases in simultaneous strokes (butterfly and breaststroke) and the inter-arm phases in alternating strokes (crawl and backstroke) were identified by video analysis to calculate the time gaps between propulsive phases. The relationships among velocity, stroke rate, stroke length and coordination were modelled by polynomial regression. Twelve elite male swimmers swam at four race paces. Quadratic regression modelled the changes in spatial-temporal and coordinative parameters with velocity increases for all four strokes. First, the quadratic regression between coordination and velocity showed changes common to all four strokes. Notably, the time gaps between the key points defining the beginning and end of the stroke phases decreased with increases in velocity, which led to decreases in glide times and increases in the continuity between propulsive phases. Conjointly, the quadratic regression among stroke rate, stroke length and velocity was similar to the changes in coordination, suggesting that these parameters may influence coordination. The main practical application for coaches and scientists is that ineffective time gaps can be distinguished from those that simply reflect an individual swimmer's profile by monitoring the glide times within a stroke cycle. In the case of ineffective time gaps, targeted training could improve the swimmer's management of glide time. PMID:18547862

  12. Modeling and Extraction of Parasitic Thermal Conductance and Intrinsic Model Parameters of Thermoelectric Modules

    NASA Astrophysics Data System (ADS)

    Sim, Minseob; Park, Hyunbin; Kim, Shiho

    2015-11-01

    We have presented both modeling and a method for extracting parasitic thermal conductance as well as intrinsic device parameters of a thermoelectric module based on information readily available in vendor datasheets. An equivalent circuit model that is compatible with circuit simulators is derived, followed by a methodology for extracting both intrinsic and parasitic model parameters. For the first time, the effective thermal resistance of the ceramic and copper interconnect layers of the thermoelectric module is extracted using only parameters listed in vendor datasheets. In the experimental condition, including under condition of varying electric current, the parameters extracted from the model accurately reproduce the performance of commercial thermoelectric modules.

  13. Nonlocal Order Parameters for the 1D Hubbard Model

    NASA Astrophysics Data System (ADS)

    Montorsi, Arianna; Roncaglia, Marco

    2012-12-01

    We characterize the Mott-insulator and Luther-Emery phases of the 1D Hubbard model through correlators that measure the parity of spin and charge strings along the chain. These nonlocal quantities order in the corresponding gapped phases and vanish at the critical point Uc=0, thus configuring as hidden order parameters. The Mott insulator consists of bound doublon-holon pairs, which in the Luther-Emery phase turn into electron pairs with opposite spins, both unbinding at Uc. The behavior of the parity correlators is captured by an effective free spinless fermion model.

  14. [Research on optimization of mathematical model of flow injection-hydride generation-atomic fluorescence spectrometry].

    PubMed

    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.

  15. Modeling precursor diffusion and reaction of atomic layer deposition in porous structures

    SciTech Connect

    Keuter, Thomas Menzler, Norbert Heribert; Mauer, Georg; Vondahlen, Frank; Vaßen, Robert; Buchkremer, Hans Peter

    2015-01-01

    Atomic layer deposition (ALD) is a technique for depositing thin films of materials with a precise thickness control and uniformity using the self-limitation of the underlying reactions. Usually, it is difficult to predict the result of the ALD process for given external parameters, e.g., the precursor exposure time or the size of the precursor molecules. Therefore, a deeper insight into ALD by modeling the process is needed to improve process control and to achieve more economical coatings. In this paper, a detailed, microscopic approach based on the model developed by Yanguas-Gil and Elam is presented and additionally compared with the experiment. Precursor diffusion and second-order reaction kinetics are combined to identify the influence of the porous substrate's microstructural parameters and the influence of precursor properties on the coating. The thickness of the deposited film is calculated for different depths inside the porous structure in relation to the precursor exposure time, the precursor vapor pressure, and other parameters. Good agreement with experimental results was obtained for ALD zirconiumdioxide (ZrO{sub 2}) films using the precursors tetrakis(ethylmethylamido)zirconium and O{sub 2}. The derivation can be adjusted to describe other features of ALD processes, e.g., precursor and reactive site losses, different growth modes, pore size reduction, and surface diffusion.

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

    SciTech Connect

    Vieytes, M. C.; Fontenla, J. M. E-mail: johnf@digidyna.com

    2013-06-01

    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 Å. Previously, the Solar Radiation Physical Modeling (SRPM) models of the solar atmosphere only considered a 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 significantly improves the calculation of the solar spectral irradiance at near-UV wavelengths, which is important for Earth atmospheric studies, and particularly for ozone chemistry.

  17. Parameter and uncertainty estimation for mechanistic, spatially explicit epidemiological models

    NASA Astrophysics Data System (ADS)

    Finger, Flavio; Schaefli, Bettina; Bertuzzo, Enrico; Mari, Lorenzo; Rinaldo, Andrea

    2014-05-01

    Epidemiological models can be a crucially important tool for decision-making during disease outbreaks. The range of possible applications spans from real-time forecasting and allocation of health-care resources to testing alternative intervention mechanisms such as vaccines, antibiotics or the improvement of sanitary conditions. Our spatially explicit, mechanistic models for cholera epidemics have been successfully applied to several epidemics including, the one that struck Haiti in late 2010 and is still ongoing. Calibration and parameter estimation of such models represents a major challenge because of properties unusual in traditional geoscientific domains such as hydrology. Firstly, the epidemiological data available might be subject to high uncertainties due to error-prone diagnosis as well as manual (and possibly incomplete) data collection. Secondly, long-term time-series of epidemiological data are often unavailable. Finally, the spatially explicit character of the models requires the comparison of several time-series of model outputs with their real-world counterparts, which calls for an appropriate weighting scheme. It follows that the usual assumption of a homoscedastic Gaussian error distribution, used in combination with classical calibration techniques based on Markov chain Monte Carlo algorithms, is likely to be violated, whereas the construction of an appropriate formal likelihood function seems close to impossible. Alternative calibration methods, which allow for accurate estimation of total model uncertainty, particularly regarding the envisaged use of the models for decision-making, are thus needed. Here we present the most recent developments regarding methods for parameter and uncertainty estimation to be used with our mechanistic, spatially explicit models for cholera epidemics, based on informal measures of goodness of fit.

  18. Coupling of an average-atom model with a collisional-radiative equilibrium model

    SciTech Connect

    Faussurier, G. Blancard, C.; Cossé, P.

    2014-11-15

    We present a method to combine a collisional-radiative equilibrium model and an average-atom model to calculate bound and free electron wavefunctions in hot dense plasmas by taking into account screening. This approach allows us to calculate electrical resistivity and thermal conductivity as well as pressure in non local thermodynamic equilibrium plasmas. Illustrations of the method are presented for dilute titanium plasma.

  19. Inter-atomic potential energy and Grüneisen parameter: A new method for equation of state of solids

    NASA Astrophysics Data System (ADS)

    Parish, Peter G.; Moore, John

    2015-05-01

    This paper presents a rational foundation for the computation of equation of state (EOS) data for solids at high pressure. We demonstrate a new method which makes use of an accurate relation expressing the Grüneisen parameter γ (as a function of the specific volume V of the material) in terms of the specific inter-atomic potential energy ϕ (V). Existing expressions for γ in the literature are usually approximations in terms of total pressure P. There is a variety of such " (γ, P)" formulas and one needs experience in deciding which to use in any particular application. The alternative " (γ, ϕ)" relationship presented here is both unique and exact within the Debye and harmonic approximations and allows the individual terms of the EOS to be determined separately. It is rigorously derived in this paper and solved numerically, using experimental input data for aluminium, copper, lead and gold, to predict ϕ, dϕ / dV, γ, dγ / dV and EOS data for the four metals. Comparison is made with existing computations in the literature showing good agreement. The method can be applied to any metal or non-metal using experimental input data from any suitable volume-dependent locus.

  20. Discussion of parameters associated with the determination of arsenic by electrothermal atomic absorption spectrometry in slurried environmental samples.

    PubMed

    Vassileva, E; Baeten, H; Hoenig, M

    2001-01-01

    A slurry sampling-fast program procedure has been developed for the determination of arsenic in plants, soils and sediments by electrothermal atomic absorption spectrometry. Efficiencies of various single and mixed modifiers for thermal stabilization of arsenic and for a better removal of the matrix during pyrolysis step were compared. The influence of the slurry concentration, amounts of modifier and parameters of the pyrolysis step on the As integrated absorbance signals have been studied and a comparison between fast and conventional furnace programs was also made. The ultrasonic agitation of the slurry followed by a fast electrothermal program using an Ir/Mg modifier provides the most consistent performance in terms of precision and accuracy. The reliability of the whole procedure has been compared with results obtained after application of a wet digestion method with an HF step and validated by analyzing eleven certified reference materials. Arsenic detection and quantitation limits expressed on dry sample matter were about 30 and 100 micrograms kg-1, respectively.

  1. Accelerated gravitational wave parameter estimation with reduced order modeling.

    PubMed

    Canizares, Priscilla; Field, Scott E; Gair, Jonathan; Raymond, Vivien; Smith, Rory; Tiglio, Manuel

    2015-02-20

    Inferring the astrophysical parameters of coalescing compact binaries is a key science goal of the upcoming advanced LIGO-Virgo gravitational-wave detector network and, more generally, gravitational-wave astronomy. However, current approaches to parameter estimation for these detectors require computationally expensive algorithms. Therefore, there is a pressing need for new, fast, and accurate Bayesian inference techniques. In this Letter, we demonstrate that a reduced order modeling approach enables rapid parameter estimation to be performed. By implementing a reduced order quadrature scheme within the LIGO Algorithm Library, we show that Bayesian inference on the 9-dimensional parameter space of nonspinning binary neutron star inspirals can be sped up by a factor of ∼30 for the early advanced detectors' configurations (with sensitivities down to around 40 Hz) and ∼70 for sensitivities down to around 20 Hz. This speedup will increase to about 150 as the detectors improve their low-frequency limit to 10 Hz, reducing to hours analyses which could otherwise take months to complete. Although these results focus on interferometric gravitational wave detectors, the techniques are broadly applicable to any experiment where fast Bayesian analysis is desirable. PMID:25763948

  2. Order-parameter model for unstable multilane traffic flow

    NASA Astrophysics Data System (ADS)

    Lubashevsky, Ihor A.; Mahnke, Reinhard

    2000-11-01

    We discuss a phenomenological approach to the description of unstable vehicle motion on multilane highways that explains in a simple way the observed sequence of the ``free flow <--> synchronized mode <--> jam'' phase transitions as well as the hysteresis in these transitions. We introduce a variable called an order parameter that accounts for possible correlations in the vehicle motion at different lanes. So, it is principally due to the ``many-body'' effects in the car interaction in contrast to such variables as the mean car density and velocity being actually the zeroth and first moments of the ``one-particle'' distribution function. Therefore, we regard the order parameter as an additional independent state variable of traffic flow. We assume that these correlations are due to a small group of ``fast'' drivers and by taking into account the general properties of the driver behavior we formulate a governing equation for the order parameter. In this context we analyze the instability of homogeneous traffic flow that manifested itself in the above-mentioned phase transitions and gave rise to the hysteresis in both of them. Besides, the jam is characterized by the vehicle flows at different lanes which are independent of one another. We specify a certain simplified model in order to study the general features of the car cluster self-formation under the ``free flow <--> synchronized motion'' phase transition. In particular, we show that the main local parameters of the developed cluster are determined by the state characteristics of vehicle motion only.

  3. Computational approaches to parameter estimation and model selection in immunology

    NASA Astrophysics Data System (ADS)

    Baker, C. T. H.; Bocharov, G. A.; Ford, J. M.; Lumb, P. M.; Norton, S. J.; Paul, C. A. H.; Junt, T.; Krebs, P.; Ludewig, B.

    2005-12-01

    One of the significant challenges in biomathematics (and other areas of science) is to formulate meaningful mathematical models. Our problem is to decide on a parametrized model which is, in some sense, most likely to represent the information in a set of observed data. In this paper, we illustrate the computational implementation of an information-theoretic approach (associated with a maximum likelihood treatment) to modelling in immunology.The approach is illustrated by modelling LCMV infection using a family of models based on systems of ordinary differential and delay differential equations. The models (which use parameters that have a scientific interpretation) are chosen to fit data arising from experimental studies of virus-cytotoxic T lymphocyte kinetics; the parametrized models that result are arranged in a hierarchy by the computation of Akaike indices. The practical illustration is used to convey more general insight. Because the mathematical equations that comprise the models are solved numerically, the accuracy in the computation has a bearing on the outcome, and we address this and other practical details in our discussion.

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

    SciTech Connect

    Rehman, Tafizur; Jaipal, M.; Chatterjee, Abhijit

    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.

  5. How many parameters does a quark mass matrix model need

    SciTech Connect

    Koide, Y. )

    1990-11-01

    An investigation independent of matrix form is made of how many parameters, which characterize the difference between up- and down-quark mass matrices, are, at least, required from the present data on quark masses and mixings. From a general study of the model with hierarchical three-step mass generations described by the three parameters {alpha}{sub {ital q}}, {beta}{sub {ital q}}, and {gamma}{sub {ital q}} ({vert bar}{alpha}{sub {ital q}}{vert bar}{much gt}{vert bar}{beta}{sub {ital q}}{vert bar}{much gt}{vert bar}{gamma}{sub {ital q}}{vert bar}; {ital q}={ital u},{ital d}), it is pointed out that the model with {beta}{sub {ital u}}/{beta}{sub {ital d}}={gamma}{sub {ital u}}/{gamma}{sub {ital d}} (i.e., with two independent parameters {alpha}{sub {ital q}} and {beta}{sub {ital q}}) is ruled out.

  6. [Temperature dependence of parameters of plant photosynthesis models: a review].

    PubMed

    Borjigidai, Almaz; Yu, Gui-Rui

    2013-12-01

    This paper reviewed the progress on the temperature response models of plant photosynthesis. Mechanisms involved in changes in the photosynthesis-temperature curve were discussed based on four parameters, intercellular CO2 concentration, activation energy of the maximum rate of RuBP (ribulose-1,5-bisphosphate) carboxylation (V (c max)), activation energy of the rate of RuBP regeneration (J(max)), and the ratio of J(max) to V(c max) All species increased the activation energy of V(c max) with increasing growth temperature, while other parameters changed but differed among species, suggesting the activation energy of V(c max) might be the most important parameter for the temperature response of plant photosynthesis. In addition, research problems and prospects were proposed. It's necessary to combine the photosynthesis models at foliage and community levels, and to investigate the mechanism of plants in response to global change from aspects of leaf area, solar radiation, canopy structure, canopy microclimate and photosynthetic capacity. It would benefit the understanding and quantitative assessment of plant growth, carbon balance of communities and primary productivity of ecosystems.

  7. Parameter and Process Significance in Mechanistic Modeling of Cellulose Hydrolysis

    NASA Astrophysics Data System (ADS)

    Rotter, B.; Barry, A.; Gerhard, J.; Small, J.; Tahar, B.

    2005-12-01

    The rate of cellulose hydrolysis, and of associated microbial processes, is important in determining the stability of landfills and their potential impact on the environment, as well as associated time scales. To permit further exploration in this field, a process-based model of cellulose hydrolysis was developed. The model, which is relevant to both landfill and anaerobic digesters, includes a novel approach to biomass transfer between a cellulose-bound biofilm and biomass in the surrounding liquid. Model results highlight the significance of the bacterial colonization of cellulose particles by attachment through contact in solution. Simulations revealed that enhanced colonization, and therefore cellulose degradation, was associated with reduced cellulose particle size, higher biomass populations in solution, and increased cellulose-binding ability of the biomass. A sensitivity analysis of the system parameters revealed different sensitivities to model parameters for a typical landfill scenario versus that for an anaerobic digester. The results indicate that relative surface area of cellulose and proximity of hydrolyzing bacteria are key factors determining the cellulose degradation rate.

  8. A method of estimating optimal catchment model parameters

    NASA Astrophysics Data System (ADS)

    Ibrahim, Yaacob; Liong, Shie-Yui

    1993-09-01

    A review of a calibration method developed earlier (Ibrahim and Liong, 1992) is presented. The method generates optimal values for single events. It entails randomizing the calibration parameters over bounds such that a system response under consideration is bounded. Within the bounds, which are narrow and generated automatically, explicit response surface representation of the response is obtained using experimental design techniques and regression analysis. The optimal values are obtained by searching on the response surface for a point at which the predicted response is equal to the measured response and the value of the joint probability density function at that point in a transformed space is the highest. The method is demonstrated on a catchment in Singapore. The issue of global optimal values is addressed by applying the method on wider bounds. The results indicate that the optimal values arising from the narrow set of bounds are, indeed, global. Improvements which are designed to achieve comparably accurate estimates but with less expense are introduced. A linear response surface model is used. Two approximations of the model are studied. The first is to fit the model using data points generated from simple Monte Carlo simulation; the second is to approximate the model by a Taylor series expansion. Very good results are obtained from both approximations. Two methods of obtaining a single estimate from the individual event's estimates of the parameters are presented. The simulated and measured hydrographs of four verification storms using these estimates compare quite well.

  9. Estimating recharge rates with analytic element models and parameter estimation

    USGS Publications Warehouse

    Dripps, W.R.; Hunt, R.J.; Anderson, M.P.

    2006-01-01

    Quantifying the spatial and temporal distribution of recharge is usually a prerequisite for effective ground water flow modeling. In this study, an analytic element (AE) code (GFLOW) was used with a nonlinear parameter estimation code (UCODE) to quantify the spatial and temporal distribution of recharge using measured base flows as calibration targets. The ease and flexibility of AE model construction and evaluation make this approach well suited for recharge estimation. An AE flow model of an undeveloped watershed in northern Wisconsin was optimized to match median annual base flows at four stream gages for 1996 to 2000 to demonstrate the approach. Initial optimizations that assumed a constant distributed recharge rate provided good matches (within 5%) to most of the annual base flow estimates, but discrepancies of >12% at certain gages suggested that a single value of recharge for the entire watershed is inappropriate. Subsequent optimizations that allowed for spatially distributed recharge zones based on the distribution of vegetation types improved the fit and confirmed that vegetation can influence spatial recharge variability in this watershed. Temporally, the annual recharge values varied >2.5-fold between 1996 and 2000 during which there was an observed 1.7-fold difference in annual precipitation, underscoring the influence of nonclimatic factors on interannual recharge variability for regional flow modeling. The final recharge values compared favorably with more labor-intensive field measurements of recharge and results from studies, supporting the utility of using linked AE-parameter estimation codes for recharge estimation. Copyright ?? 2005 The Author(s).

  10. Optimal vibration control of curved beams using distributed parameter models

    NASA Astrophysics Data System (ADS)

    Liu, Fushou; Jin, Dongping; Wen, Hao

    2016-12-01

    The design of linear quadratic optimal controller using spectral factorization method is studied for vibration suppression of curved beam structures modeled as distributed parameter models. The equations of motion for active control of the in-plane vibration of a curved beam are developed firstly considering its shear deformation and rotary inertia, and then the state space model of the curved beam is established directly using the partial differential equations of motion. The functional gains for the distributed parameter model of curved beam are calculated by extending the spectral factorization method. Moreover, the response of the closed-loop control system is derived explicitly in frequency domain. Finally, the suppression of the vibration at the free end of a cantilevered curved beam by point control moment is studied through numerical case studies, in which the benefit of the presented method is shown by comparison with a constant gain velocity feedback control law, and the performance of the presented method on avoidance of control spillover is demonstrated.

  11. Parameter estimation for models of ligninolytic and cellulolytic enzyme kinetics

    SciTech Connect

    Wang, Gangsheng; Post, Wilfred M; Mayes, Melanie; Frerichs, Joshua T; Jagadamma, Sindhu

    2012-01-01

    While soil enzymes have been explicitly included in the soil organic carbon (SOC) decomposition models, there is a serious lack of suitable data for model parameterization. This study provides well-documented enzymatic parameters for application in enzyme-driven SOC decomposition models from a compilation and analysis of published measurements. In particular, we developed appropriate kinetic parameters for five typical ligninolytic and cellulolytic enzymes ( -glucosidase, cellobiohydrolase, endo-glucanase, peroxidase, and phenol oxidase). The kinetic parameters included the maximum specific enzyme activity (Vmax) and half-saturation constant (Km) in the Michaelis-Menten equation. The activation energy (Ea) and the pH optimum and sensitivity (pHopt and pHsen) were also analyzed. pHsen was estimated by fitting an exponential-quadratic function. The Vmax values, often presented in different units under various measurement conditions, were converted into the same units at a reference temperature (20 C) and pHopt. Major conclusions are: (i) Both Vmax and Km were log-normal distributed, with no significant difference in Vmax exhibited between enzymes originating from bacteria or fungi. (ii) No significant difference in Vmax was found between cellulases and ligninases; however, there was significant difference in Km between them. (iii) Ligninases had higher Ea values and lower pHopt than cellulases; average ratio of pHsen to pHopt ranged 0.3 0.4 for the five enzymes, which means that an increase or decrease of 1.1 1.7 pH units from pHopt would reduce Vmax by 50%. (iv) Our analysis indicated that the Vmax values from lab measurements with purified enzymes were 1 2 orders of magnitude higher than those for use in SOC decomposition models under field conditions.

  12. Multi-criteria parameter estimation for the Unified Land Model

    NASA Astrophysics Data System (ADS)

    Livneh, B.; Lettenmaier, D. P.

    2012-08-01

    We describe a parameter estimation framework for the Unified Land Model (ULM) that utilizes multiple independent data sets over the continental United States. These include a satellite-based evapotranspiration (ET) product based on MODerate resolution Imaging Spectroradiometer (MODIS) and Geostationary Operational Environmental Satellites (GOES) imagery, an atmospheric-water balance based ET estimate that utilizes North American Regional Reanalysis (NARR) atmospheric fields, terrestrial water storage content (TWSC) data from the Gravity Recovery and Climate Experiment (GRACE), and streamflow (Q) primarily from the United States Geological Survey (USGS) stream gauges. The study domain includes 10 large-scale (≥105 km2) river basins and 250 smaller-scale (<104 km2) tributary basins. ULM, which is essentially a merger of the Noah Land Surface Model and Sacramento Soil Moisture Accounting Model, is the basis for these experiments. Calibrations were made using each of the data sets individually, in addition to combinations of multiple criteria, with multi-criteria skill scores computed for all cases. At large scales, calibration to Q resulted in the best overall performance, whereas certain combinations of ET and TWSC calibrations lead to large errors in other criteria. At small scales, about one-third of the basins had their highest Q performance from multi-criteria calibrations (to Q and ET) suggesting that traditional calibration to Q may benefit by supplementing observed Q with remote sensing estimates of ET. Model streamflow errors using optimized parameters were mostly due to over (under) estimation of low (high) flows. Overall, uncertainties in remote-sensing data proved to be a limiting factor in the utility of multi-criteria parameter estimation.

  13. Multi-criteria parameter estimation for the unified land model

    NASA Astrophysics Data System (ADS)

    Livneh, B.; Lettenmaier, D. P.

    2012-04-01

    We describe a parameter estimation framework for the Unified Land Model (ULM) that utilizes multiple independent data sets over the Continental United States. These include a satellite-based evapotranspiration (ET) product based on MODerate resolution Imaging Spectroradiometer (MODIS) and Geostationary Operation Environmental Satellites (GOES) imagery, an atmospheric-water balance based ET estimate that utilizes North American Regional Reanalysis (NARR) atmospheric fields, terrestrial water storage content (TWSC) data from the Gravity Recovery and Climate Experiment (GRACE), and streamflow (Q) primarily from the United States Geological Survey (USGS) stream gauges. The study domain includes 10 large-scale (≥105 km2) river basins and 250 smaller-scale (<104 km2) tributary basins. ULM, which is essentially a merger of the Noah Land Surface Model and Sacramento Soil Moisture Accounting model, is the basis for these experiments. Calibrations were made using each of the criteria individually, in addition to combinations of multiple criteria, with multi-criteria skill scores computed for all cases. At large-scales calibration to Q resulted in the best overall performance, whereas certain combinations of ET and TWSC calibrations lead to large errors in other criteria. At small scales, about one-third of the basins had their highest Q performance from multi-criteria calibrations (to Q and ET) suggesting that traditional calibration to Q may benefit by supplementing observed Q with remote sensing estimates of ET. Model streamflow errors using optimized parameters were mostly due to over (under) estimation of low (high) flows. Overall, uncertainties in remote-sensing data proved to be a limiting factor in the utility of multi-criteria parameter estimation.

  14. Sensitivity Analysis of Parameters in Linear-Quadratic Radiobiologic Modeling

    SciTech Connect

    Fowler, Jack F.

    2009-04-01

    Purpose: Radiobiologic modeling is increasingly used to estimate the effects of altered treatment plans, especially for dose escalation. The present article shows how much the linear-quadratic (LQ) (calculated biologically equivalent dose [BED] varies when individual parameters of the LQ formula are varied by {+-}20% and by 1%. Methods: Equivalent total doses (EQD2 = normalized total doses (NTD) in 2-Gy fractions for tumor control, acute mucosal reactions, and late complications were calculated using the linear- quadratic formula with overall time: BED = nd (1 + d/ [{alpha}/{beta}]) - log{sub e}2 (T - Tk) / {alpha}Tp, where BED is BED = total dose x relative effectiveness (RE = nd (1 + d/ [{alpha}/{beta}]). Each of the five biologic parameters in turn was altered by {+-}10%, and the altered EQD2s tabulated; the difference was finally divided by 20. EQD2 or NTD is obtained by dividing BED by the RE for 2-Gy fractions, using the appropriate {alpha}/{beta} ratio. Results: Variations in tumor and acute mucosal EQD ranged from 0.1% to 0.45% per 1% change in each parameter for conventional schedules, the largest variation being caused by overall time. Variations in 'late' EQD were 0.4% to 0.6% per 1% change in the only biologic parameter, the {alpha}/{beta} ratio. For stereotactic body radiotherapy schedules, variations were larger, up to 0.6 to 0.9 for tumor and 1.6% to 1.9% for late, per 1% change in parameter. Conclusions: Robustness occurs similar to that of equivalent uniform dose (EUD), for the same reasons. Total dose, dose per fraction, and dose-rate cause their major effects, as well known.

  15. Simulation-based parameter estimation for complex models: a breast cancer natural history modelling illustration.

    PubMed

    Chia, Yen Lin; Salzman, Peter; Plevritis, Sylvia K; Glynn, Peter W

    2004-12-01

    Simulation-based parameter estimation offers a powerful means of estimating parameters in complex stochastic models. We illustrate the application of these ideas in the setting of a natural history model for breast cancer. Our model assumes that the tumor growth process follows a geometric Brownian motion; parameters are estimated from the SEER registry. Our discussion focuses on the use of simulation for computing the maximum likelihood estimator for this class of models. The analysis shows that simulation provides a straightforward means of computing such estimators for models of substantial complexity.

  16. Parameter uncertainty in biochemical models described by ordinary differential equations.

    PubMed

    Vanlier, J; Tiemann, C A; Hilbers, P A J; van Riel, N A W

    2013-12-01

    Improved mechanistic understanding of biochemical networks is one of the driving ambitions of Systems Biology. Computational modeling allows the integration of various sources of experimental data in order to put this conceptual understanding to the test in a quantitative manner. The aim of computational modeling is to obtain both predictive as well as explanatory models for complex phenomena, hereby providing useful approximations of reality with varying levels of detail. As the complexity required to describe different system increases, so does the need for determining how well such predictions can be made. Despite efforts to make tools for uncertainty analysis available to the field, these methods have not yet found widespread use in the field of Systems Biology. Additionally, the suitability of the different methods strongly depends on the problem and system under investigation. This review provides an introduction to some of the techniques available as well as gives an overview of the state-of-the-art methods for parameter uncertainty analysis.

  17. Modelling of some parameters from thermoelectric power plants

    NASA Astrophysics Data System (ADS)

    Popa, G. N.; Diniş, C. M.; Deaconu, S. I.; Maksay, Şt; Popa, I.

    2016-02-01

    Paper proposing new mathematical models for the main electrical parameters (active power P, reactive power Q of power supplies) and technological (mass flow rate of steam M from boiler and dust emission E from the output of precipitator) from a thermoelectric power plants using industrial plate-type electrostatic precipitators with three sections used in electrical power plants. The mathematical models were used experimental results taken from industrial facility, from boiler and plate-type electrostatic precipitators with three sections, and has used the least squares method for their determination. The modelling has been used equations of degree 1, 2 and 3. The equations were determined between dust emission depending on active power of power supplies and mass flow rate of steam from boiler, and, also, depending on reactive power of power supplies and mass flow rate of steam from boiler. These equations can be used to control the process from electrostatic precipitators.

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

    PubMed

    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. Quantitative analysis of doped/undoped ZnO nanomaterials using laser assisted atom probe tomography: Influence of the analysis parameters

    SciTech Connect

    Amirifar, Nooshin; Lardé, Rodrigue Talbot, Etienne; Pareige, Philippe; Rigutti, Lorenzo; Mancini, Lorenzo; Houard, Jonathan; Castro, Celia; Sallet, Vincent; Zehani, Emir; Hassani, Said; Sartel, Corine; Ziani, Ahmed; Portier, Xavier

    2015-12-07

    In the last decade, atom probe tomography has become a powerful tool to investigate semiconductor and insulator nanomaterials in microelectronics, spintronics, and optoelectronics. In this paper, we report an investigation of zinc oxide nanostructures using atom probe tomography. We observed that the chemical composition of zinc oxide is strongly dependent on the analysis parameters used for atom probe experiments. It was observed that at high laser pulse energies, the electric field at the specimen surface is strongly dependent on the crystallographic directions. This dependence leads to an inhomogeneous field evaporation of the surface atoms, resulting in unreliable measurements. We show that the laser pulse energy has to be well tuned to obtain reliable quantitative chemical composition measurements of undoped and doped ZnO nanomaterials.

  20. Quantitative analysis of doped/undoped ZnO nanomaterials using laser assisted atom probe tomography: Influence of the analysis parameters

    NASA Astrophysics Data System (ADS)

    Amirifar, Nooshin; Lardé, Rodrigue; Talbot, Etienne; Pareige, Philippe; Rigutti, Lorenzo; Mancini, Lorenzo; Houard, Jonathan; Castro, Celia; Sallet, Vincent; Zehani, Emir; Hassani, Said; Sartel, Corine; Ziani, Ahmed; Portier, Xavier

    2015-12-01

    In the last decade, atom probe tomography has become a powerful tool to investigate semiconductor and insulator nanomaterials in microelectronics, spintronics, and optoelectronics. In this paper, we report an investigation of zinc oxide nanostructures using atom probe tomography. We observed that the chemical composition of zinc oxide is strongly dependent on the analysis parameters used for atom probe experiments. It was observed that at high laser pulse energies, the electric field at the specimen surface is strongly dependent on the crystallographic directions. This dependence leads to an inhomogeneous field evaporation of the surface atoms, resulting in unreliable measurements. We show that the laser pulse energy has to be well tuned to obtain reliable quantitative chemical composition measurements of undoped and doped ZnO nanomaterials.

  1. Anisotropic Effects on Constitutive Model Parameters of Aluminum Alloys

    NASA Astrophysics Data System (ADS)

    Brar, Nachhatter; Joshi, Vasant

    2011-06-01

    Simulation of low velocity impact on structures or high velocity penetration in armor materials heavily rely on constitutive material models. The model constants are required input to computer codes (LS-DYNA, DYNA3D or SPH) to accurately simulate fragment impact on structural components made of high strength 7075-T651 aluminum alloys. Johnson-Cook model constants determined for Al7075-T651 alloy bar material failed to simulate correctly the penetration into 1' thick Al-7075-T651plates. When simulations go well beyond minor parameter tweaking and experimental results are drastically different it is important to determine constitutive parameters from the actual material used in impact/penetration experiments. To investigate anisotropic effects on the yield/flow stress of this alloy we performed quasi-static and high strain rate tensile tests on specimens fabricated in the longitudinal, transverse, and thickness directions of 1' thick Al7075-T651 plate. Flow stresses at a strain rate of ~1100/s in the longitudinal and transverse direction are similar around 670MPa and decreases to 620 MPa in the thickness direction. These data are lower than the flow stress of 760 MPa measured in Al7075-T651 bar stock.

  2. The relative variational model - A topological view of matter and its properties: Space occupancy by the atoms

    SciTech Connect

    Dias, M. S.; De Vasconcelos, V.; Mattos, J. R. L.; Jordao, E.

    2012-07-01

    Formal definitions of convergence, connected-ness and continuity were established to characterize and describe the crystalline solid and its properties as a unified notion in the topological space. In this unified notion, physical and material properties are modeled by means of an intrinsic and invariable form function: the Relative Variational Model. The crystalline solid is assumed an empty space that has been filled with atoms and phonons, i.e., the crystal is built with packages of matter and energy in a regular and orderly repetitive pattern along three orthogonal dimensions of the space. The spatial occupation of the atom in the crystalline structure is determined by its mean vibrational volume, which also defines the lattice parameter or interatomic distance. However, as packages of vibrational energy, phonons can only exist as vibrations of atoms. Any variation of internal energy is in fact the discretized variations of phonon's population. These variations occur in the quantized modes of vibration, and therefore the balance between the frequency and amplitude of vibrations also is a dynamic variable. In this paper, the Relative Variational Model was applied to de-convolutions of frequency spectra of the inelastic neutron scatterings. Some dynamic aspects of atom vibration were presented and evaluated in support to the model's fundamentals. (authors)

  3. Microbial Communities Model Parameter Calculation for TSPA/SR

    SciTech Connect

    D. Jolley

    2001-07-16

    This calculation has several purposes. First the calculation reduces the information contained in ''Committed Materials in Repository Drifts'' (BSC 2001a) to useable parameters required as input to MING V1.O (CRWMS M&O 1998, CSCI 30018 V1.O) for calculation of the effects of potential in-drift microbial communities as part of the microbial communities model. The calculation is intended to replace the parameters found in Attachment II of the current In-Drift Microbial Communities Model revision (CRWMS M&O 2000c) with the exception of Section 11-5.3. Second, this calculation provides the information necessary to supercede the following DTN: M09909SPAMING1.003 and replace it with a new qualified dataset (see Table 6.2-1). The purpose of this calculation is to create the revised qualified parameter input for MING that will allow {Delta}G (Gibbs Free Energy) to be corrected for long-term changes to the temperature of the near-field environment. Calculated herein are the quadratic or second order regression relationships that are used in the energy limiting calculations to potential growth of microbial communities in the in-drift geochemical environment. Third, the calculation performs an impact review of a new DTN: M00012MAJIONIS.000 that is intended to replace the currently cited DTN: GS9809083 12322.008 for water chemistry data used in the current ''In-Drift Microbial Communities Model'' revision (CRWMS M&O 2000c). Finally, the calculation updates the material lifetimes reported on Table 32 in section 6.5.2.3 of the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000c) based on the inputs reported in BSC (2001a). Changes include adding new specified materials and updating old materials information that has changed.

  4. Parameter optimization in differential geometry based solvation models

    PubMed Central

    Wang, Bao; Wei, G. W.

    2015-01-01

    Differential geometry (DG) based solvation models are a new class of variational implicit solvent approaches that are able to avoid unphysical solvent-solute boundary definitions and associated geometric singularities, and dynamically couple polar and non-polar interactions in a self-consistent framework. Our earlier study indicates that DG based non-polar solvation model outperforms other methods in non-polar solvation energy predictions. However, the DG based full solvation model has not shown its superiority in solvation analysis, due to its difficulty in parametrization, which must ensure the stability of the solution of strongly coupled nonlinear Laplace-Beltrami and Poisson-Boltzmann equations. In this work, we introduce new parameter learning algorithms based on perturbation and convex optimization theories to stabilize the numerical solution and thus achieve an optimal parametrization of the DG based solvation models. An interesting feature of the present DG based solvation model is that it provides accurate solvation free energy predictions for both polar and non-polar molecules in a unified formulation. Extensive numerical experiment demonstrates that the present DG based solvation model delivers some of the most accurate predictions of the solvation free energies for a large number of molecules. PMID:26450304

  5. Parameter optimization in differential geometry based solvation models.

    PubMed

    Wang, Bao; Wei, G W

    2015-10-01

    Differential geometry (DG) based solvation models are a new class of variational implicit solvent approaches that are able to avoid unphysical solvent-solute boundary definitions and associated geometric singularities, and dynamically couple polar and non-polar interactions in a self-consistent framework. Our earlier study indicates that DG based non-polar solvation model outperforms other methods in non-polar solvation energy predictions. However, the DG based full solvation model has not shown its superiority in solvation analysis, due to its difficulty in parametrization, which must ensure the stability of the solution of strongly coupled nonlinear Laplace-Beltrami and Poisson-Boltzmann equations. In this work, we introduce new parameter learning algorithms based on perturbation and convex optimization theories to stabilize the numerical solution and thus achieve an optimal parametrization of the DG based solvation models. An interesting feature of the present DG based solvation model is that it provides accurate solvation free energy predictions for both polar and non-polar molecules in a unified formulation. Extensive numerical experiment demonstrates that the present DG based solvation model delivers some of the most accurate predictions of the solvation free energies for a large number of molecules.

  6. Bayesian analysis of inflation: Parameter estimation for single field models

    SciTech Connect

    Mortonson, Michael J.; Peiris, Hiranya V.; Easther, Richard

    2011-02-15

    Future astrophysical data sets promise to strengthen constraints on models of inflation, and extracting these constraints requires methods and tools commensurate with the quality of the data. In this paper we describe ModeCode, a new, publicly available code that computes the primordial scalar and tensor power spectra for single-field inflationary models. ModeCode solves the inflationary mode equations numerically, avoiding the slow roll approximation. It is interfaced with CAMB and CosmoMC to compute cosmic microwave background angular power spectra and perform likelihood analysis and parameter estimation. ModeCode is easily extendable to additional models of inflation, and future updates will include Bayesian model comparison. Errors from ModeCode contribute negligibly to the error budget for analyses of data from Planck or other next generation experiments. We constrain representative single-field models ({phi}{sup n} with n=2/3, 1, 2, and 4, natural inflation, and 'hilltop' inflation) using current data, and provide forecasts for Planck. From current data, we obtain weak but nontrivial limits on the post-inflationary physics, which is a significant source of uncertainty in the predictions of inflationary models, while we find that Planck will dramatically improve these constraints. In particular, Planck will link the inflationary dynamics with the post-inflationary growth of the horizon, and thus begin to probe the ''primordial dark ages'' between TeV and grand unified theory scale energies.

  7. Important Scaling Parameters for Testing Model-Scale Helicopter Rotors

    NASA Technical Reports Server (NTRS)

    Singleton, Jeffrey D.; Yeager, William T., Jr.

    1998-01-01

    An investigation into the effects of aerodynamic and aeroelastic scaling parameters on model scale helicopter rotors has been conducted in the NASA Langley Transonic Dynamics Tunnel. The effect of varying Reynolds number, blade Lock number, and structural elasticity on rotor performance has been studied and the performance results are discussed herein for two different rotor blade sets at two rotor advance ratios. One set of rotor blades were rigid and the other set of blades were dynamically scaled to be representative of a main rotor design for a utility class helicopter. The investigation was con-densities permits the acquisition of data for several Reynolds and Lock number combinations.

  8. Dielectric spectroscopy at the nanoscale by atomic force microscopy: A simple model linking materials properties and experimental response

    SciTech Connect

    Miccio, Luis A. Colmenero, Juan; Kummali, Mohammed M.; Alegría, Ángel; Schwartz, Gustavo A.

    2014-05-14

    The use of an atomic force microscope for studying molecular dynamics through dielectric spectroscopy with spatial resolution in the nanometer scale is a recently developed approach. However, difficulties in the quantitative connection of the obtained data and the material dielectric properties, namely, frequency dependent dielectric permittivity, have limited its application. In this work, we develop a simple electrical model based on physically meaningful parameters to connect the atomic force microscopy (AFM) based dielectric spectroscopy experimental results with the material dielectric properties. We have tested the accuracy of the model and analyzed the relevance of the forces arising from the electrical interaction with the AFM probe cantilever. In this way, by using this model, it is now possible to obtain quantitative information of the local dielectric material properties in a broad frequency range. Furthermore, it is also possible to determine the experimental setup providing the best sensitivity in the detected signal.

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

    NASA Technical Reports Server (NTRS)

    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

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

    PubMed

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

    2011-04-01

    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.

  11. Influence of the "surface effect" on the segregation parameters of S in Fe(100): A multi-scale modelling and Auger Electron Spectroscopy study

    NASA Astrophysics Data System (ADS)

    Barnard, P. E.; Terblans, J. J.; Swart, H. C.

    2015-12-01

    The article takes a new look at the process of atomic segregation by considering the influence of surface relaxation on the segregation parameters; the activation energy (Q), segregation energy (ΔG), interaction parameter (Ω) and the pre-exponential factor (D0). Computational modelling, namely Density Functional Theory (DFT) and the Modified Darken Model (MDM) in conjunction with Auger Electron Spectroscopy (AES) was utilized to study the variation of the segregation parameters for S in the surface region of Fe(100). Results indicate a variation in each of the segregation parameters as a function of the atomic layer under consideration. Values of the segregation parameters varied more dramatically as the surface layer is approached, with atomic layer 2 having the largest deviations in comparison to the bulk values. This atomic layer had the highest Q value and formed the rate limiting step for the segregation of S towards the Fe(100) surface. It was found that the segregation process is influenced by two sets of segregation parameters, those of the surface region formed by atomic layer 2, and those in the bulk material. This article is the first to conduct a full scale investigation on the influence of surface relaxation on segregation and labelled it the "surface effect".

  12. Identification of material parameters for continuum modeling of phase transformations in multicomponent systems

    NASA Astrophysics Data System (ADS)

    Umantsev, Alex

    2007-01-01

    The continuum (field theoretic) method has become the method of choice for multiscale structure-formation modeling of very different phase transformations in the past decade. One of the challenges in application of the method to transformations in real materials is to obtain the mesoscopic parameters, which characterize the thermodynamic system of interest. Significant progress has been made in the case of pure systems; however, one would like to know what changes need to be made in the case of binary or multicomponent systems. We consider an exactly solvable case of the linear multicomponent system undergoing a phase transformation and derive equations that relate parameters of the continuum method, like barrier height, gradient energy, and relaxation coefficients, to the measurable quantities, like interface energy, interfacial thickness, and kinetic coefficient. We find that the contribution of chemical interactions in the system can be expressed as the renormalization of the barrier-height parameter of the continuum method and replacement of the latent heat with the chemical modulus. Atomic-scale simulations data for a solid/liquid transition in a binary Cu-Ni system were chosen for comparison with the theory and the fitting yields the estimates for the continuum-method parameters. Analysis of the temperature dependence of the interfacial energy allowed us to shed light on the magnitudes of the internal energy and entropy contributions into the solid/liquid interface.

  13. Insight into model mechanisms through automatic parameter fitting: a new methodological framework for model development

    PubMed Central

    2014-01-01

    Background Striking a balance between the degree of model complexity and parameter identifiability, while still producing biologically feasible simulations using modelling is a major challenge in computational biology. While these two elements of model development are closely coupled, parameter fitting from measured data and analysis of model mechanisms have traditionally been performed separately and sequentially. This process produces potential mismatches between model and data complexities that can compromise the ability of computational frameworks to reveal mechanistic insights or predict new behaviour. In this study we address this issue by presenting a generic framework for combined model parameterisation, comparison of model alternatives and analysis of model mechanisms. Results The presented methodology is based on a combination of multivariate metamodelling (statistical approximation of the input–output relationships of deterministic models) and a systematic zooming into biologically feasible regions of the parameter space by iterative generation of new experimental designs and look-up of simulations in the proximity of the measured data. The parameter fitting pipeline includes an implicit sensitivity analysis and analysis of parameter identifiability, making it suitable for testing hypotheses for model reduction. Using this approach, under-constrained model parameters, as well as the coupling between parameters within the model are identified. The methodology is demonstrated by refitting the parameters of a published model of cardiac cellular mechanics using a combination of measured data and synthetic data from an alternative model of the same system. Using this approach, reduced models with simplified expressions for the tropomyosin/crossbridge kinetics were found by identification of model components that can be omitted without affecting the fit to the parameterising data. Our analysis revealed that model parameters could be constrained to a standard

  14. System parameters for erythropoiesis control model: Comparison of normal values in human and mouse model

    NASA Technical Reports Server (NTRS)

    1979-01-01

    The computer model for erythropoietic control was adapted to the mouse system by altering system parameters originally given for the human to those which more realistically represent the mouse. Parameter values were obtained from a variety of literature sources. Using the mouse model, the mouse was studied as a potential experimental model for spaceflight. Simulation studies of dehydration and hypoxia were performed. A comparison of system parameters for the mouse and human models is presented. Aside from the obvious differences expected in fluid volumes, blood flows and metabolic rates, larger differences were observed in the following: erythrocyte life span, erythropoietin half-life, and normal arterial pO2.

  15. Estimation of Enthalpy of Formation of Liquid Transition Metal Alloys: A Modified Prescription Based on Macroscopic Atom Model of Cohesion

    NASA Astrophysics Data System (ADS)

    Raju, Subramanian; Saibaba, Saroja

    2016-09-01

    The enthalpy of formation Δo H f is an important thermodynamic quantity, which sheds significant light on fundamental cohesive and structural characteristics of an alloy. However, being a difficult one to determine accurately through experiments, simple estimation procedures are often desirable. In the present study, a modified prescription for estimating Δo H f L of liquid transition metal alloys is outlined, based on the Macroscopic Atom Model of cohesion. This prescription relies on self-consistent estimation of liquid-specific model parameters, namely electronegativity ( ϕ L) and bonding electron density ( n b L ). Such unique identification is made through the use of well-established relationships connecting surface tension, compressibility, and molar volume of a metallic liquid with bonding charge density. The electronegativity is obtained through a consistent linear scaling procedure. The preliminary set of values for ϕ L and n b L , together with other auxiliary model parameters, is subsequently optimized to obtain a good numerical agreement between calculated and experimental values of Δo H f L for sixty liquid transition metal alloys. It is found that, with few exceptions, the use of liquid-specific model parameters in Macroscopic Atom Model yields a physically consistent methodology for reliable estimation of mixing enthalpies of liquid alloys.

  16. Application of Powder Diffraction Methods to the Analysis of Short- and Long-Range Atomic Order in Nanocrystalline Diamond and SiC: The Concept of the Apparent Lattice Parameter (alp)

    NASA Technical Reports Server (NTRS)

    Palosz, B.; Grzanka, E.; Gierlotka, S.; Stelmakh, S.; Pielaszek, R.; Bismayer, U.; Weber, H.-P.; Palosz, W.

    2003-01-01

    Two methods of the analysis of powder diffraction patterns of diamond and SiC nanocrystals are presented: (a) examination of changes of the lattice parameters with diffraction vector Q ('apparent lattice parameter', alp) which refers to Bragg scattering, and (b), examination of changes of inter-atomic distances based on the analysis of the atomic Pair Distribution Function, PDF. Application of these methods was studied based on the theoretical diffraction patterns computed for models of nanocrystals having (i) a perfect crystal lattice, and (ii), a core-shell structure, i.e. constituting a two-phase system. The models are defined by the lattice parameter of the grain core, thickness of the surface shell, and the magnitude and distribution of the strain field in the shell. X-ray and neutron experimental diffraction data of nanocrystalline SiC and diamond powders of the grain diameter from 4 nm up to micrometers were used. The effects of the internal pressure and strain at the grain surface on the structure are discussed based on the experimentally determined dependence of the alp values on the Q-vector, and changes of the interatomic distances with the grain size determined experimentally by the atomic Pair Distribution Function (PDF) analysis. The experimental results lend a strong support to the concept of a two-phase, core and the surface shell structure of nanocrystalline diamond and SiC.

  17. A Lumped Parameter Model for Feedback Studies in Tokamaks

    NASA Astrophysics Data System (ADS)

    Chance, M. S.; Chu, M. S.; Okabayashi, M.; Glasser, A. H.

    2004-11-01

    A lumped circuit model of the feedback stabilization studies in tokamaks is calculated. This work parallels the formulation by Boozer^a, is analogous to the studies done on axisymmetric modes^b, and generalizes the cylindrical model^c. The lumped circuit parameters are derived from the DCON derived eigenfunctions of the plasma, the resistive shell and the feedback coils. The inductances are calculated using the VACUUM code which is designed to calculate the responses between the various elements in the feedback system. The results are compared with the normal mode^d and the system identification^e approaches. ^aA.H. Boozer, Phys. Plasmas 5, 3350 (1998). ^b E.A. Lazarus et al., Nucl. Fusion 30, 111 (1990). ^c M. Okabayashi et al., Nucl. Fusion 38, 1607 (1998). ^dM.S. Chu et al., Nucl. Fusion 43, 441 (2003). ^eY.Q. Liu et al., Phys. Plasmas 7, 3681 (2000).

  18. PET-Specific Parameters and Radiotracers in Theoretical Tumour Modelling

    PubMed Central

    Marcu, Loredana G.; Bezak, Eva

    2015-01-01

    The innovation of computational techniques serves as an important step toward optimized, patient-specific management of cancer. In particular, in silico simulation of tumour growth and treatment response may eventually yield accurate information on disease progression, enhance the quality of cancer treatment, and explain why certain therapies are effective where others are not. In silico modelling is demonstrated to considerably benefit from information obtainable with PET and PET/CT. In particular, models have successfully integrated tumour glucose metabolism, cell proliferation, and cell oxygenation from multiple tracers in order to simulate tumour behaviour. With the development of novel radiotracers to image additional tumour phenomena, such as pH and gene expression, the value of PET and PET/CT data for use in tumour models will continue to grow. In this work, the use of PET and PET/CT information in in silico tumour models is reviewed. The various parameters that can be obtained using PET and PET/CT are detailed, as well as the radiotracers that may be used for this purpose, their utility, and limitations. The biophysical measures used to quantify PET and PET/CT data are also described. Finally, a list of in silico models that incorporate PET and/or PET/CT data is provided and reviewed. PMID:25788973

  19. Non-local correlation and quantum discord in two atoms in the non-degenerate model

    SciTech Connect

    Mohamed, A.-B.A.

    2012-12-15

    By using geometric quantum discord (GQD) and measurement-induced nonlocality (MIN), quantum correlation is investigated for two atoms in the non-degenerate two-photon Tavis-Cummings model. It is shown that there is no asymptotic decay for MIN while asymptotic decay exists for GQD. Quantum correlations can be strengthened by introducing the dipole-dipole interaction. The evolvement period of quantum correlation gets shorter with the increase in the dipole-dipole parameter. It is found that there exists not only quantum nonlocality without entanglement but also quantum nonlocality without quantum discord. Also, the MIN and GQD are raised rather than entanglement, and also with weak initial entanglement, there are MIN and entanglement in a interval of death quantum discord. - Highlights: Black-Right-Pointing-Pointer Geometric quantum discord (GQD) and measurement induced nonlocality (MIN) are used to investigate the correlations of two two-level atoms. Black-Right-Pointing-Pointer There is no asymptotic decay for MIN while asymptotic decay exists for GQD. Black-Right-Pointing-Pointer Quantum correlations can be strengthened by introducing the dipole-dipole interaction. Black-Right-Pointing-Pointer There exists not only quantum nonlocality without entanglement but also without discord. Black-Right-Pointing-Pointer Weak initial entanglement leads to MIN and entanglement in intervals of death discord.

  20. Project Physics Reader 5, Models of the Atom.

    ERIC Educational Resources Information Center

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

    As a supplement to Project Physics Unit 5, a collection of articles is presented in this reader for student browsing. Nine excerpts are given under the following headings: failure and success, Einstein, Mr. Tompkins and simultaneity, parable of the surveyors, outside and inside the elevator, the teacher and the Bohr theory of atom, Dirac and Born,…

  1. Variational methods to estimate terrestrial ecosystem model parameters

    NASA Astrophysics Data System (ADS)

    Delahaies, Sylvain; Roulstone, Ian

    2016-04-01

    Carbon is at the basis of the chemistry of life. Its ubiquity in the Earth system is the result of complex recycling processes. Present in the atmosphere in the form of carbon dioxide it is adsorbed by marine and terrestrial ecosystems and stored within living biomass and decaying organic matter. Then soil chemistry and a non negligible amount of time transform the dead matter into fossil fuels. Throughout this cycle, carbon dioxide is released in the atmosphere through respiration and combustion of fossils fuels. Model-data fusion techniques allow us to combine our understanding of these complex processes with an ever-growing amount of observational data to help improving models and predictions. The data assimilation linked ecosystem carbon (DALEC) model is a simple box model simulating the carbon budget allocation for terrestrial ecosystems. Over the last decade several studies have demonstrated the relative merit of various inverse modelling strategies (MCMC, ENKF, 4DVAR) to estimate model parameters and initial carbon stocks for DALEC and to quantify the uncertainty in the predictions. Despite its simplicity, DALEC represents the basic processes at the heart of more sophisticated models of the carbon cycle. Using adjoint based methods we study inverse problems for DALEC with various data streams (8 days MODIS LAI, monthly MODIS LAI, NEE). The framework of constraint optimization allows us to incorporate ecological common sense into the variational framework. We use resolution matrices to study the nature of the inverse problems and to obtain data importance and information content for the different type of data. We study how varying the time step affect the solutions, and we show how "spin up" naturally improves the conditioning of the inverse problems.

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

    PubMed

    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. Symmetric eikonal model for projectile-electron excitation and loss in relativistic ion-atom collisions

    SciTech Connect

    Voitkiv, A. B.; Najjari, B.; Shevelko, V. P.

    2010-08-15

    At impact energies > or approx. 1 GeV/u the projectile-electron excitation and loss occurring in collisions between highly charged ions and neutral atoms is already strongly influenced by the presence of atomic electrons. To treat these processes in collisions with heavy atoms we generalize the symmetric eikonal model, used earlier for considerations of electron transitions in ion-atom collisions within the scope of a three-body Coulomb problem. We show that at asymptotically high collision energies this model leads to an exact transition amplitude and is very well suited to describe the projectile-electron excitation and loss at energies above a few GeV/u. In particular, by considering a number of examples we demonstrate advantages of this model over the first Born approximation at impact energies of {approx}1-30 GeV/u, which are of special interest for atomic physics experiments at the future GSI facilities.

  4. Pressure pulsation in roller pumps: a validated lumped parameter model.

    PubMed

    Moscato, Francesco; Colacino, Francesco M; Arabia, Maurizio; Danieli, Guido A

    2008-11-01

    During open-heart surgery roller pumps are often used to keep the circulation of blood through the patient body. They present numerous key features, but they suffer from several limitations: (a) they normally deliver uncontrolled pulsatile inlet and outlet pressure; (b) blood damage appears to be more than that encountered with centrifugal pumps. A lumped parameter mathematical model of a roller pump (Sarns 7000, Terumo CVS, Ann Arbor, MI, USA) was developed to dynamically simulate pressures at the pump inlet and outlet in order to clarify the uncontrolled pulsation mechanism. Inlet and outlet pressures obtained by the mathematical model have been compared with those measured in various operating conditions: different rollers' rotating speed, different tube occlusion rates, and different clamping degree at the pump inlet and outlet. Model results agree with measured pressure waveforms, whose oscillations are generated by the tube compression/release mechanism during the rollers' engaging and disengaging phases. Average Euclidean Error (AEE) was 20mmHg and 33mmHg for inlet and outlet pressure estimates, respectively. The normalized AEE never exceeded 0.16. The developed model can be exploited for designing roller pumps with improved performances aimed at reducing the undesired pressure pulsation.

  5. Analysing DNA structural parameters using a mesoscopic model

    NASA Astrophysics Data System (ADS)

    Amarante, Tauanne D.; Weber, Gerald

    2014-03-01

    The Peyrard-Bishop model is a mesoscopic approximation to model DNA and RNA molecules. Several variants of this model exists, from 3D Hamiltonians, including torsional angles, to simpler 2D versions. Currently, we are able to parametrize the 2D variants of the model which allows us to extract important information about the molecule. For example, with this technique we were able recently to obtain the hydrogen bonds of RNA from melting temperatures, which previously were obtainable only from NMR measurements. Here, we take the 3D torsional Hamiltonian and set the angles to zero. Curiously, in doing this we do not recover the traditional 2D Hamiltonians. Instead, we obtain a different 2D Hamiltonian which now includes a base pair step distance, commonly known as rise. A detailed knowledge of the rise distance is important as it determines the overall length of the DNA molecule. This 2D Hamiltonian provides us with the exciting prospect of obtaining DNA structural parameters from melting temperatures. Our results of the rise distance at low salt concentration are in good qualitative agreement with those from several published x-ray measurements. We also found an important dependence of the rise distance with salt concentration. In contrast to our previous calculations, the elastic constants now show little dependence with salt concentrations which appears to be closer to what is seen experimentally in DNA flexibility experiments.

  6. Multi-objective parameter optimization of common land model using adaptive surrogate modeling

    NASA Astrophysics Data System (ADS)

    Gong, W.; Duan, Q.; Li, J.; Wang, C.; Di, Z.; Dai, Y.; Ye, A.; Miao, C.

    2015-05-01

    Parameter specification usually has significant influence on the performance of land surface models (LSMs). However, estimating the parameters properly is a challenging task due to the following reasons: (1) LSMs usually have too many adjustable parameters (20 to 100 or even more), leading to the curse of dimensionality in the parameter input space; (2) LSMs usually have many output variables involving water/energy/carbon cycles, so that calibrating LSMs is actually a multi-objective optimization problem; (3) Regional LSMs are expensive to run, while conventional multi-objective optimization methods need a large number of model runs (typically ~105-106). It makes parameter optimization computationally prohibitive. An uncertainty quantification framework was developed to meet the aforementioned challenges, which include the following steps: (1) using parameter screening to reduce the number of adjustable parameters, (2) using surrogate models to emulate the responses of dynamic models to the variation of adjustable parameters, (3) using an adaptive strategy to improve the efficiency of surrogate modeling-based optimization; (4) using a weighting function to transfer multi-objective optimization to single-objective optimization. In this study, we demonstrate the uncertainty quantification framework on a single column application of a LSM - the Common Land Model (CoLM), and evaluate the effectiveness and efficiency of the proposed framework. The result indicate that this framework can efficiently achieve optimal parameters in a more effective way. Moreover, this result implies the possibility of calibrating other large complex dynamic models, such as regional-scale LSMs, atmospheric models and climate models.

  7. Incorporation of shuttle CCT parameters in computer simulation models

    NASA Technical Reports Server (NTRS)

    Huntsberger, Terry

    1990-01-01

    Computer simulations of shuttle missions have become increasingly important during recent years. The complexity of mission planning for satellite launch and repair operations which usually involve EVA has led to the need for accurate visibility and access studies. The PLAID modeling package used in the Man-Systems Division at Johnson currently has the necessary capabilities for such studies. In addition, the modeling package is used for spatial location and orientation of shuttle components for film overlay studies such as the current investigation of the hydrogen leaks found in the shuttle flight. However, there are a number of differences between the simulation studies and actual mission viewing. These include image blur caused by the finite resolution of the CCT monitors in the shuttle and signal noise from the video tubes of the cameras. During the course of this investigation the shuttle CCT camera and monitor parameters are incorporated into the existing PLAID framework. These parameters are specific for certain camera/lens combinations and the SNR characteristics of these combinations are included in the noise models. The monitor resolution is incorporated using a Gaussian spread function such as that found in the screen phosphors in the shuttle monitors. Another difference between the traditional PLAID generated images and actual mission viewing lies in the lack of shadows and reflections of light from surfaces. Ray tracing of the scene explicitly includes the lighting and material characteristics of surfaces. The results of some preliminary studies using ray tracing techniques for the image generation process combined with the camera and monitor effects are also reported.

  8. Impact of parameter uncertainty on carbon sequestration modeling

    NASA Astrophysics Data System (ADS)

    Bandilla, K.; Celia, M. A.

    2013-12-01

    Geologic carbon sequestration through injection of supercritical carbon dioxide (CO2) into the subsurface is one option to reduce anthropogenic CO¬2 emissions. Widespread industrial-scale deployment, on the order of giga-tonnes of CO2 injected per year, will be necessary for carbon sequestration to make a significant contribution to solving the CO2 problem. Deep saline formations are suitable targets for CO2 sequestration due to their large storage capacity, high injectivity, and favorable pressure and temperature regimes. Due to the large areal extent of saline formations, and the need to inject very large amounts of CO2, multiple sequestration operations are likely to be developed in the same formation. The injection-induced migration of both CO2 and resident formation fluids (brine) needs to be predicted to determine the feasibility of industrial-scale deployment of carbon sequestration. Due to the larger spatial scale of the domain, many of the modeling parameters (e.g., permeability) will be highly uncertain. In this presentation we discuss a sensitivity analysis of both pressure response and CO2 plume migration to variations of model parameters such as permeability, compressibility and temperature. The impact of uncertainty in the stratigraphic succession is also explored. The sensitivity analysis is conducted using a numerical vertically-integrated modeling approach. The Illinois Basin, USA is selected as the test site for this study, due to its large storage capacity and large number of stationary CO2 sources. As there is currently only one active CO2 injection operation in the Illinois Basin, a hypothetical injection scenario is used, where CO2 is injected at the locations of large CO2 emitters related to electricity generation, ethanol production and hydrocarbon refinement. The Area of Review (AoR) is chosen as the comparison metric, as it includes both the CO2 plume size and pressure response.

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

    ERIC Educational Resources Information Center

    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…

  10. ORBSIM- ESTIMATING GEOPHYSICAL MODEL PARAMETERS FROM PLANETARY GRAVITY DATA

    NASA Technical Reports Server (NTRS)

    Sjogren, W. L.

    1994-01-01

    The ORBSIM program was developed for the accurate extraction of geophysical model parameters from Doppler radio tracking data acquired from orbiting planetary spacecraft. The model of the proposed planetary structure is used in a numerical integration of the spacecraft along simulated trajectories around the primary body. Using line of sight (LOS) Doppler residuals, ORBSIM applies fast and efficient modelling and optimization procedures which avoid the traditional complex dynamic reduction of data. ORBSIM produces quantitative geophysical results such as size, depth, and mass. ORBSIM has been used extensively to investigate topographic features on the Moon, Mars, and Venus. The program has proven particulary suitable for modelling gravitational anomalies and mascons. The basic observable for spacecraft-based gravity data is the Doppler frequency shift of a transponded radio signal. The time derivative of this signal carries information regarding the gravity field acting on the spacecraft in the LOS direction (the LOS direction being the path between the spacecraft and the receiving station, either Earth or another satellite). There are many dynamic factors taken into account: earth rotation, solar radiation, acceleration from planetary bodies, tracking station time and location adjustments, etc. The actual trajectories of the spacecraft are simulated using least squares fitted to conic motion. The theoretical Doppler readings from the simulated orbits are compared to actual Doppler observations and another least squares adjustment is made. ORBSIM has three modes of operation: trajectory simulation, optimization, and gravity modelling. In all cases, an initial gravity model of curved and/or flat disks, harmonics, and/or a force table are required input. ORBSIM is written in FORTRAN 77 for batch execution and has been implemented on a DEC VAX 11/780 computer operating under VMS. This program was released in 1985.

  11. Modeling the magnetic properties of lanthanide complexes: relationship of the REC parameters with Pauling electronegativity and coordination number.

    PubMed

    Baldoví, José J; Gaita-Ariño, Alejandro; Coronado, Eugenio

    2015-07-28

    In a previous study, we introduced the Radial Effective Charge (REC) model to study the magnetic properties of lanthanide single ion magnets. Now, we perform an empirical determination of the effective charges (Zi) and radial displacements (Dr) of this model using spectroscopic data. This systematic study allows us to relate Dr and Zi with chemical factors such as the coordination number and the electronegativities of the metal and the donor atoms. This strategy is being used to drastically reduce the number of free parameters in the modeling of the magnetic and spectroscopic properties of f-element complexes.

  12. Hubbard Model for Atomic Impurities Bound by the Vortex Lattice of a Rotating Bose-Einstein Condensate.

    PubMed

    Johnson, T H; Yuan, Y; Bao, W; Clark, S R; Foot, C; Jaksch, D

    2016-06-17

    We investigate cold bosonic impurity atoms trapped in a vortex lattice formed by condensed bosons of another species. We describe the dynamics of the impurities by a bosonic Hubbard model containing occupation-dependent parameters to capture the effects of strong impurity-impurity interactions. These include both a repulsive direct interaction and an attractive effective interaction mediated by the Bose-Einstein condensate. The occupation dependence of these two competing interactions drastically affects the Hubbard model phase diagram, including causing the disappearance of some Mott lobes. PMID:27367366

  13. Graphite furnace atomic absorption spectrophotometry--a novel method to quantify blood volume in experimental models of intracerebral hemorrhage.

    PubMed

    Kashefiolasl, Sepide; Foerch, Christian; Pfeilschifter, Waltraud

    2013-02-15

    Intracerebral hemorrhage (ICH) accounts for 10% of all strokes and has a significantly higher mortality than cerebral ischemia. For decades, ICH has been neglected by experimental stroke researchers. Recently, however, clinical trials on acute blood pressure lowering or hyperacute supplementation of coagulation factors in ICH have spurred an interest to also design and improve translational animal models of spontaneous and anticoagulant-associated ICH. Hematoma volume is a substantial outcome parameter of most experimental ICH studies. We present graphite furnace atomic absorption spectrophotometric analysis (AAS) as a suitable method to precisely quantify hematoma volumes in rodent models of ICH.

  14. Hubbard Model for Atomic Impurities Bound by the Vortex Lattice of a Rotating Bose-Einstein Condensate.

    PubMed

    Johnson, T H; Yuan, Y; Bao, W; Clark, S R; Foot, C; Jaksch, D

    2016-06-17

    We investigate cold bosonic impurity atoms trapped in a vortex lattice formed by condensed bosons of another species. We describe the dynamics of the impurities by a bosonic Hubbard model containing occupation-dependent parameters to capture the effects of strong impurity-impurity interactions. These include both a repulsive direct interaction and an attractive effective interaction mediated by the Bose-Einstein condensate. The occupation dependence of these two competing interactions drastically affects the Hubbard model phase diagram, including causing the disappearance of some Mott lobes.

  15. Modeling parameter extraction for DNQ-novolak thick film resists

    NASA Astrophysics Data System (ADS)

    Henderson, Clifford L.; Scheer, Steven A.; Tsiartas, Pavlos C.; Rathsack, Benjamen M.; Sagan, John P.; Dammel, Ralph R.; Erdmann, Andreas; Willson, C. Grant

    1998-06-01

    Optical lithography with special thick film DNQ-novolac photoresists have been practiced for many years to fabricate microstructures that require feature heights ranging from several to hundreds of microns such as thin film magnetic heads. It is common in these thick film photoresist systems to observe interesting non-uniform profiles with narrow regions near the top surface of the film that transition into broader and more concave shapes near the bottom of the resist profile. A number of explanations have been proposed for these various observations including the formation of `dry skins' at the resist surface and the presence of solvent gradients in the film which serve to modify the local development rate of the photoresist. There have been few detailed experimental studies of the development behavior of thick films resists. This has been due to part to the difficulty in studying these films with conventional dissolution rate monitors (DRMs). In general, this lack of experimental data along with other factors has made simulation and modeling of thick film resist performance difficult. As applications such as thin film head manufacturing drive to smaller features with higher aspect ratios, the need for accurate thick film simulation capability continues to grow. A new multi-wavelength DRM tool has been constructed and used in conjunction with a resist bleaching tool and rigorous parameter extraction techniques to establish exposure and development parameters for two thick film resists, AZTM 4330-RS and AZTM 9200. Simulations based on these parameters show good agreement to resist profiles for these two resists.

  16. Inverse modeling of hydrologic parameters using surface flux and runoff observations in the Community Land Model

    NASA Astrophysics Data System (ADS)

    Sun, Y.; Hou, Z.; Huang, M.; Tian, F.; Leung, L. R.

    2013-04-01

    This study demonstrates the possibility of inverting hydrologic parameters using surface flux and runoff observations in version 4 of the Community Land Model (CLM4). Previous studies showed that surface flux and runoff calculations are sensitive to major hydrologic parameters in CLM4 over different watersheds, and illustrated the necessity and possibility of parameter calibration. Two inversion strategies, the deterministic least-square fitting and stochastic Markov-Chain Monte-Carlo (MCMC) Bayesian inversion approaches, are evaluated by applying them to CLM4 at selected sites. The unknowns to be estimated include surface and subsurface runoff generation parameters and vadose zone soil water parameters. We find that using model parameters calibrated by the least-square fitting provides little improvements in the model simulations but the sampling-based stochastic inversion approaches are consistent - as more information comes in, the predictive intervals of the calibrated parameters become narrower and the misfits between the calculated and observed responses decrease. In general, parameters that are identified to be significant through sensitivity analyses and statistical tests are better calibrated than those with weak or nonlinear impacts on flux or runoff observations. Temporal resolution of observations has larger impacts on the results of inverse modeling using heat flux data than runoff data. Soil and vegetation cover have important impacts on parameter sensitivities, leading to different patterns of posterior distributions of parameters at different sites. Overall, the MCMC-Bayesian inversion approach effectively and reliably improves the simulation of CLM under different climates and environmental conditions. Bayesian model averaging of the posterior estimates with different reference acceptance probabilities can smooth the posterior distribution and provide more reliable parameter estimates, but at the expense of wider uncertainty bounds.

  17. A model for energy transfer in collisions of atoms with highly excited molecules.

    PubMed

    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. PMID:25907301

  18. Modeling soil detachment capacity by rill flow using hydraulic parameters

    NASA Astrophysics Data System (ADS)

    Wang, Dongdong; Wang, Zhanli; Shen, Nan; Chen, Hao

    2016-04-01

    The relationship between soil detachment capacity (Dc) by rill flow and hydraulic parameters (e.g., flow velocity, shear stress, unit stream power, stream power, and unit energy) at low flow rates is investigated to establish an accurate experimental model. Experiments are conducted using a 4 × 0.1 m rill hydraulic flume with a constant artificial roughness on the flume bed. The flow rates range from 0.22 × 10-3 m2 s-1 to 0.67 × 10-3 m2 s-1, and the slope gradients vary from 15.8% to 38.4%. Regression analysis indicates that the Dc by rill flow can be predicted using the linear equations of flow velocity, stream power, unit stream power, and unit energy. Dc by rill flow that is fitted to shear stress can be predicted with a power function equation. Predictions based on flow velocity, unit energy, and stream power are powerful, but those based on shear stress, especially on unit stream power, are relatively poor. The prediction based on flow velocity provides the best estimates of Dc by rill flow because of the simplicity and availability of its measurements. Owing to error in measuring flow velocity at low flow rates, the predictive abilities of Dc by rill flow using all hydraulic parameters are relatively lower in this study compared with the results of previous research. The measuring accuracy of experiments for flow velocity should be improved in future research.

  19. Atomic nitrogen: a parameter study of a micro-scale atmospheric pressure plasma jet by means of molecular beam mass spectrometry

    NASA Astrophysics Data System (ADS)

    Schneider, Simon; Dünnbier, Mario; Hübner, Simon; Reuter, Stephan; Benedikt, Jan

    2014-12-01

    Absolute atomic nitrogen densities (N) in the effluent of a micro-scale atmospheric pressure plasma jet (µ-APPJ) operated in He with small admixtures of molecular nitrogen (N2) are measured by means of molecular beam mass spectrometry. Focusing on changes of the external plasma parameters, the dependency of the atomic nitrogen density on the admixture of molecular nitrogen to the plasma, the variation of applied electrode voltage and the variation of distance between the jet nozzle and the sampling orifice of the mass spectrometer are analysed. When varying the N2 admixture, a maximum density of atomic nitrogen of approximately 1.5  ×  1014 cm-3 (~6 ppm) is reached at about 0.25% N2 admixture. Moreover, the N density increases approximately linearly with the applied voltage. Both results are comparable to atomic oxygen (O) behaviour of the µ-APPJ operated at equal plasma conditions except for admixing molecular O2 instead of nitrogen (Ellerweg et al 2010 New J. Phys. 12 013021). The N density decreases continuously with increasing distance, but the decrease is slower than in the case of O atoms in He/O2 plasma. N atoms with a density of 2.0  ×  1013 cm-3 (~0.8 ppm) are still detected at 40 mm distance from the jet nozzle in controlled He/N2 atmosphere. The simple fluid simulation of N diffusion does not reproduce the measured densities of N. Nevertheless, a simulation taking into account atomic nitrogen reactions with gas impurities are able to reproduce the measured data, indicating that these reactions are an important loss mechanism of N atoms. The presented results are relevant for the future investigation of interactions of reactive nitrogen species with biological substrates.

  20. Parameters-related uncertainty in modeling sugar cane yield with an agro-Land Surface Model

    NASA Astrophysics Data System (ADS)

    Valade, A.; Ciais, P.; Vuichard, N.; Viovy, N.; Ruget, F.; Gabrielle, B.

    2012-12-01

    Agro-Land Surface Models (agro-LSM) have been developed from the coupling of specific crop models and large-scale generic vegetation models. They aim at accounting for the spatial distribution and variability of energy, water and carbon fluxes within soil-vegetation-atmosphere continuum with a particular emphasis on how crop phenology and agricultural management practice influence the turbulent fluxes exchanged with the atmosphere, and the underlying water and carbon pools. A part of the uncertainty in these models is related to the many parameters included in the models' equations. In this study, we quantify the parameter-based uncertainty in the simulation of sugar cane biomass production with the agro-LSM ORCHIDEE-STICS on a multi-regional approach with data from sites in Australia, La Reunion and Brazil. First, the main source of uncertainty for the output variables NPP, GPP, and sensible heat flux (SH) is determined through a screening of the main parameters of the model on a multi-site basis leading to the selection of a subset of most sensitive parameters causing most of the uncertainty. In a second step, a sensitivity analysis is carried out on the parameters selected from the screening analysis at a regional scale. For this, a Monte-Carlo sampling method associated with the calculation of Partial Ranked Correlation Coefficients is used. First, we quantify the sensitivity of the output variables to individual input parameters on a regional scale for two regions of intensive sugar cane cultivation in Australia and Brazil. Then, we quantify the overall uncertainty in the simulation's outputs propagated from the uncertainty in the input parameters. Seven parameters are identified by the screening procedure as driving most of the uncertainty in the agro-LSM ORCHIDEE-STICS model output at all sites. These parameters control photosynthesis (optimal temperature of photosynthesis, optimal carboxylation rate), radiation interception (extinction coefficient), root

  1. CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling

    PubMed Central

    Guvench, Olgun; Mallajosyula, Sairam S.; Raman, E. Prabhu; Hatcher, Elizabeth; Vanommeslaeghe, Kenno; Foster, Theresa J.; Jamison, Francis W.; MacKerell, Alexander D.

    2011-01-01

    Monosaccharide derivatives such as xylose, fucose, N-acetylglucosamine (GlcNAc), N-acetylgalactosamine (GlaNAc), glucuronic acid, iduronic acid, and N-acetylneuraminic acid (Neu5Ac) are important components of eukaryotic glycans. The present work details development of force-field parameters for these monosaccharides and their covalent connections to proteins via O-linkages to serine or threonine sidechains and via N-linkages to asparagine sidechains. The force field development protocol was designed to explicitly yield parameters that are compatible with the existing CHARMM additive force field for proteins, nucleic acids, lipids, carbohydrates, and small molecules. Therefore, when combined with previously developed parameters for pyranose and furanose monosaccharides, for glycosidic linkages between monosaccharides, and for proteins, the present set of parameters enables the molecular simulation of a wide variety of biologically-important molecules such as complex carbohydrates and glycoproteins. Parametrization included fitting to quantum mechanical (QM) geometries and conformational energies of model compounds, as well as to QM pair interaction energies and distances of model compounds with water. Parameters were validated in the context of crystals of relevant monosaccharides, as well NMR and/or x-ray crystallographic data on larger systems including oligomeric hyaluronan, sialyl Lewis X, O- and N-linked glycopeptides, and a lectin:sucrose complex. As the validated parameters are an extension of the CHARMM all-atom additive biomolecular force field, they further broaden the types of heterogeneous systems accessible with a consistently-developed force-field model. PMID:22125473

  2. Maximum likelihood identification of aircraft parameters with unsteady aerodynamic modelling

    NASA Technical Reports Server (NTRS)

    Keskar, D. A.; Wells, W. R.

    1979-01-01

    A simplified aerodynamic force model based on the physical principle of Prandtl's lifting line theory and trailing vortex concept has been developed to account for unsteady aerodynamic effects in aircraft dynamics. Longitudinal equations of motion have been modified to include these effects. The presence of convolution integrals in the modified equations of motion led to a frequency domain analysis utilizing Fourier transforms. This reduces the integro-differential equations to relatively simple algebraic equations, thereby reducing computation time significantly. A parameter extraction program based on the maximum likelihood estimation technique is developed in the frequency domain. The extraction algorithm contains a new scheme for obtaining sensitivity functions by using numerical differentiation. The paper concludes with examples using computer generated and real flight data

  3. Sound propagation and absorption in foam - A distributed parameter model.

    NASA Technical Reports Server (NTRS)

    Manson, L.; Lieberman, S.

    1971-01-01

    Liquid-base foams are highly effective sound absorbers. A better understanding of the mechanisms of sound absorption in foams was sought by exploration of a mathematical model of bubble pulsation and coupling and the development of a distributed-parameter mechanical analog. A solution by electric-circuit analogy was thus obtained and transmission-line theory was used to relate the physical properties of the foams to the characteristic impedance and propagation constants of the analog transmission line. Comparison of measured physical properties of the foam with values obtained from measured acoustic impedance and propagation constants and the transmission-line theory showed good agreement. We may therefore conclude that the sound propagation and absorption mechanisms in foam are accurately described by the resonant response of individual bubbles coupled to neighboring bubbles.

  4. Atomic Forces for Geometry-Dependent Point Multipole and Gaussian Multipole Models

    PubMed Central

    Elking, Dennis M.; Perera, Lalith; Duke, Robert; Darden, Thomas; Pedersen, Lee G.

    2010-01-01

    In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise due to 1) the transfer of torque between neighboring atoms, and 2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In the current study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives ∂Dlm′m/∂Ω. The force equations can be applied to electrostatic models based on atomic point multipoles or Gaussian multipole charge density. Hydrogen bonded dimers are used to test the inter-molecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential (ESP). The electrostatic energies and forces are compared to their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, while geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models. PMID:20839297

  5. Verification Techniques for Parameter Selection and Bayesian Model Calibration Presented for an HIV Model

    NASA Astrophysics Data System (ADS)

    Wentworth, Mami Tonoe

    Uncertainty quantification plays an important role when making predictive estimates of model responses. In this context, uncertainty quantification is defined as quantifying and reducing uncertainties, and the objective is to quantify uncertainties in parameter, model and measurements, and propagate the uncertainties through the model, so that one can make a predictive estimate with quantified uncertainties. Two of the aspects of uncertainty quantification that must be performed prior to propagating uncertainties are model calibration and parameter selection. There are several efficient techniques for these processes; however, the accuracy of these methods are often not verified. This is the motivation for our work, and in this dissertation, we present and illustrate verification frameworks for model calibration and parameter selection in the context of biological and physical models. First, HIV models, developed and improved by [2, 3, 8], describe the viral infection dynamics of an HIV disease. These are also used to make predictive estimates of viral loads and T-cell counts and to construct an optimal control for drug therapy. Estimating input parameters is an essential step prior to uncertainty quantification. However, not all the parameters are identifiable, implying that they cannot be uniquely determined by the observations. These unidentifiable parameters can be partially removed by performing parameter selection, a process in which parameters that have minimal impacts on the model response are determined. We provide verification techniques for Bayesian model calibration and parameter selection for an HIV model. As an example of a physical model, we employ a heat model with experimental measurements presented in [10]. A steady-state heat model represents a prototypical behavior for heat conduction and diffusion process involved in a thermal-hydraulic model, which is a part of nuclear reactor models. We employ this simple heat model to illustrate verification

  6. A hierarchy of local electron correlation models based on atomic truncations

    NASA Astrophysics Data System (ADS)

    Head-Gordon, Martin; Lee, Michael S.; Maslen, Paul E.

    1999-11-01

    While wavefunction-based treatments of electron correlation have been very successful for the study of small molecules, they cannot be readily applied to large molecules because their computational cost rises too steeply with molecular size. For example, second order Møller-Plesset perturbation theory (MP2), the simplest such method, involves computational costs that asymptotically increase with the 5th power of molecular size. In this article we discuss the development of new local electron correlation models that ameliorate this problem, by truncating the number of substituted determinants that are included in the correlation treatment. Using atom-centered functions to span the occupied and virtual subspaces permits the truncations to be made by an atomic criterion, that satisfies all of the requirements of a well-defined theoretical model chemistry. The double substitutions that arise in MP2 theory generally involve promoting electrons from occupied orbitals on two atoms to unoccupied (virtual) orbitals on two other atoms, or tetra-atomics in molecules. The simplest restriction is to require one occupied and one virtual orbital to be on a common atom, leading to a triatomics in molecules (TRIM) model. A stronger approximation is to model double substitutions by the direct product of two such atomic excitations, which is a diatomics in molecules (DIM) model of electron correlation. The still more drastic approximation of forcing all double substitutions to be centered on single atoms, cannot describe dispersion interactions, and is not considered here. The theory of the DIM and TRIM models is outlined, and methods for obtaining the atom-centered functions spanning the occupied and virtual subspaces are discussed. Some numerical results are provided to compare the performance of the DIM and TRIM models against untruncated MP2 theory. Finally the outlook for the application of these methods to large molecules is discussed.

  7. Analysis of solvation structure and thermodynamics of ethane and propane in water by reference interaction site model theory using all-atom models

    NASA Astrophysics Data System (ADS)

    Cui, Qizhi; Smith, Vedene H.

    2001-08-01

    Following our previous paper on methane [Cui and Smith, J. Chem. Phys. 113, 10240 (2000)], we study the solvation structures and thermodynamics of ethane and propane in water at the infinite dilution limit by using the hypernetted chain closure reference interaction site model (HNC-RISM) theory with all-atom representations for solute molecules. At four thermodynamic states: temperature T=283.15, 298.15, 313.15, 328.15 K and the corresponding bulk water density ρ=0.9997, 0.9970, 0.9922, 0.9875 g cm-3, all the atomic solute-solvent radial distribution functions are obtained, and the corresponding running coordination numbers and the hydration free energies, energies, enthalpies, and entropies are calculated with the radial distribution functions as input. The hydration structures of ethane and propane are presented and analyzed at the atomic level in terms of the atomic solute-solvent radial distribution functions. With the optimized nonbonded potential parameters based on the CHARMM96 all-atom model for alkanes [Yin and Mackerell, J. Comput. Chem. 19, 334 (1998)], the ethane and propane hydration thermodynamic properties predicted by the HNC-RISM theory are improved in the specified temperature range (10-55 °C).

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

    PubMed

    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. PMID:24734699

  9. The atomic approach to the Anderson model for the finite U case: application to a quantum dot.

    PubMed

    Lobo, T; Figueira, M S; Foglio, M E

    2010-07-01

    In the present work we apply the atomic approach to the single-impurity Anderson model (SIAM). A general formulation of this approach, that can be applied both to the impurity and to the lattice Anderson Hamiltonian, was developed in a previous work (Foglio et al 2009 arxiv: 0903.0139v2 [cond-mat.str-el]). The method starts from the cumulant expansion of the periodic Anderson model, employing the hybridization as a perturbation. The atomic Anderson limit is analytically solved and its sixteen eigenenergies and eigenstates are obtained. This atomic Anderson solution, which we call the AAS, has all the fundamental excitations that generate the Kondo effect, and in the atomic approach is employed as a 'seed' to generate the approximate solutions for finite U. The width of the conduction band is reduced to zero in the AAS, and we choose its position such that the Friedel sum rule is satisfied, close to the chemical potential mu. We perform a complete study of the density of states of the SIAM over the whole relevant range of parameters: the empty dot, intermediate valence, Kondo and magnetic regimes. In the Kondo regime we obtain a density of states that characterizes well the structure of the Kondo peak. To show the usefulness of the method we have calculated the conductance of a quantum dot, side-coupled to a conduction band.

  10. Molecular Modeling of Triton X Micelles: Force Field Parameters, Self-Assembly, and Partition Equilibria.

    PubMed

    Yordanova, D; Smirnova, I; Jakobtorweihen, S

    2015-05-12

    Nonionic surfactants of the Triton X-series find various applications in extraction processes and as solubilizing agents for the purification of membrane proteins. However, so far no optimized parameters are available to perform molecular simulations with a biomolecular force field. Therefore, we have determined the first optimized set of CHARMM parameters for the Triton X-series, enabling all-atom molecular dynamics (MD) simulations. In order to validate the new parameters, micellar sizes (aggregation numbers) of Triton X-114 and Triton X-100 have been investigated as a function of temperature and surfactant concentration. These results are comparable with experimental results. Furthermore, we have introduced a new algorithm to obtain micelle structures from self-assembly MD simulations for the COSMOmic method. This model allows efficient partition behavior predictions once a representative micelle structure is available. The predicted partition coefficients for the systems Triton X-114/water and Triton X-100/water are in excellent agreement with experimental results. Therefore, this method can be applied as a screening tool to find optimal solute-surfactant combinations or suitable surfactant systems for a specific application.

  11. Numerical modeling of ozone production in a pulsed homogeneous discharge: A parameter study

    SciTech Connect

    Nilsson, J.O.; Eninger, J.E.

    1997-02-01

    The pulsed volume discharge is an alternative for the efficient generation of ozone in compact systems. This paper presents a parameter study of the reactions in this kind of homogeneous discharge by using a numerical model which solves plasma chemical kinetic rate and energy equations. Results are presented of ozone generation efficiency versus ozone concentration for different parameter combinations. Two parameter regimes are identified and analyzed. In the plasma phase ozone formation regime, where significant amounts of ozone are produced during the discharge pulse, it is found that higher ozone concentrations can be obtained than in the neutral phase ozone formation regime, where most of the ozone is formed after the discharge pulse. In the two-step ozone formation process, the rate of conversion of atomic oxygen plays a key role. In both regimes the ozone generation efficiency increases as n is increased or T{sub 0} decreased. The maximum concentration is 3% at 10 amagat and 100 K. The results on ozone accumulation in multiple pulse discharges are presented. In contrast to the single pulse case, higher efficiency is achieved at lower gas density. This scaling can be explained by losses due to ion currents. A tradeoff can be made between ozone generation efficiency and the number of pulses required to reach a certain concentration.

  12. Hydrological modeling in alpine catchments: sensing the critical parameters towards an efficient model calibration.

    PubMed

    Achleitner, S; Rinderer, M; Kirnbauer, R

    2009-01-01

    For the Tyrolean part of the river Inn, a hybrid model for flood forecast has been set up and is currently in its test phase. The system is a hybrid system which comprises of a hydraulic 1D model for the river Inn, and the hydrological models HQsim (Rainfall-runoff-discharge model) and the snow and ice melt model SES for modeling the rainfall runoff form non-glaciated and glaciated tributary catchment respectively. Within this paper the focus is put on the hydrological modeling of the totally 49 connected non-glaciated catchments realized with the software HQsim. In the course of model calibration, the identification of the most sensitive parameters is important aiming at an efficient calibration procedure. The indicators used for explaining the parameter sensitivities were chosen specifically for the purpose of flood forecasting. Finally five model parameters could be identified as being sensitive for model calibration when aiming for a well calibrated model for flood conditions. In addition two parameters were identified which are sensitive in situations where the snow line plays an important role.

  13. Hydrological modeling in alpine catchments: sensing the critical parameters towards an efficient model calibration.

    PubMed

    Achleitner, S; Rinderer, M; Kirnbauer, R

    2009-01-01

    For the Tyrolean part of the river Inn, a hybrid model for flood forecast has been set up and is currently in its test phase. The system is a hybrid system which comprises of a hydraulic 1D model for the river Inn, and the hydrological models HQsim (Rainfall-runoff-discharge model) and the snow and ice melt model SES for modeling the rainfall runoff form non-glaciated and glaciated tributary catchment respectively. Within this paper the focus is put on the hydrological modeling of the totally 49 connected non-glaciated catchments realized with the software HQsim. In the course of model calibration, the identification of the most sensitive parameters is important aiming at an efficient calibration procedure. The indicators used for explaining the parameter sensitivities were chosen specifically for the purpose of flood forecasting. Finally five model parameters could be identified as being sensitive for model calibration when aiming for a well calibrated model for flood conditions. In addition two parameters were identified which are sensitive in situations where the snow line plays an important role. PMID:19759453

  14. Inverse Modeling of Hydrologic Parameters Using Surface Flux and Streamflow Observations in the Community Land Model

    NASA Astrophysics Data System (ADS)

    Sun, Y.; Hou, Z.; Huang, M.; Tian, F.; Leung, L.

    2012-12-01

    This study aims at demonstrating the possibility of calibrating hydrologic parameters using surface flux and streamflow observations in version 4 of the Community Land Model (CLM4). Previously we showed that surface flux and streamflow calculations are sensitive to several key hydrologic parameters in CLM4, and discussed the necessity and possibility of parameter calibration. In this study, we evaluate performances of several different inversion strategies, including least-square fitting, quasi Monte-Carlo (QMC) sampling based Bayesian updating, and a Markov-Chain Monte-Carlo (MCMC) Bayesian inversion approach. The parameters to be calibrated include the surface and subsurface runoff generation parameters and vadose zone soil water parameters. We discuss the effects of surface flux and streamflow observations on the inversion results and compare their consistency and reliability using both monthly and daily observations at various flux tower and MOPEX sites. We find that the sampling-based stochastic inversion approaches behaved consistently - as more information comes in, the predictive intervals of the calibrated parameters as well as the misfits between the calculated and observed observations decrease. In general, the parameters that are identified to be significant through sensitivity analyses and statistical tests are better calibrated than those with weak or nonlinear impacts on flux or streamflow observations. We also evaluated the possibility of probabilistic model averaging for more consistent parameter estimation.

  15. Modeling Atoms and Molecules: A New Lesson for Upper Elementary and Middle School Students.

    ERIC Educational Resources Information Center

    Schwaner, Terry D.; And Others

    1994-01-01

    Describes a study involving 86 fifth-grade science students to enhance their understandings of basic biological chemistry. Contains a lesson that allows students to build models of atoms and molecules. (ZWH)

  16. Rovibrationally Inelastic Atom-Molecule Collision Cross Sections from a Hard Sphere Model

    NASA Astrophysics Data System (ADS)

    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.

  17. Physical property parameter set for modeling ICPP aqueous wastes with ASPEN electrolyte NRTL model

    SciTech Connect

    Schindler, R.E.

    1996-09-01

    The aqueous waste evaporators at the Idaho Chemical Processing Plant (ICPP) are being modeled using ASPEN software. The ASPEN software calculates chemical and vapor-liquid equilibria with activity coefficients calculated using the electrolyte Non-Random Two Liquid (NRTL) model for local excess Gibbs free energies of interactions between ions and molecules in solution. The use of the electrolyte NRTL model requires the determination of empirical parameters for the excess Gibbs free energies of the interactions between species in solution. This report covers the development of a set parameters, from literature data, for the use of the electrolyte NRTL model with the major solutes in the ICPP aqueous wastes.

  18. Sensitivity of numerical dispersion modeling to explosive source parameters

    SciTech Connect

    Baskett, R.L. ); Cederwall, R.T. )

    1991-02-13

    The calculation of downwind concentrations from non-traditional sources, such as explosions, provides unique challenges to dispersion models. The US Department of Energy has assigned the Atmospheric Release Advisory Capability (ARAC) at the Lawrence Livermore National Laboratory (LLNL) the task of estimating the impact of accidental radiological releases to the atmosphere anywhere in the world. Our experience includes responses to over 25 incidents in the past 16 years, and about 150 exercises a year. Examples of responses to explosive accidents include the 1980 Titan 2 missile fuel explosion near Damascus, Arkansas and the hydrogen gas explosion in the 1986 Chernobyl nuclear power plant accident. Based on judgment and experience, we frequently estimate the source geometry and the amount of toxic material aerosolized as well as its particle size distribution. To expedite our real-time response, we developed some automated algorithms and default assumptions about several potential sources. It is useful to know how well these algorithms perform against real-world measurements and how sensitive our dispersion model is to the potential range of input values. In this paper we present the algorithms we use to simulate explosive events, compare these methods with limited field data measurements, and analyze their sensitivity to input parameters. 14 refs., 7 figs., 2 tabs.

  19. Parameter Estimation and Parameterization Uncertainty Using Bayesian Model Averaging

    NASA Astrophysics Data System (ADS)

    Tsai, F. T.; Li, X.

    2007-12-01

    This study proposes Bayesian model averaging (BMA) to address parameter estimation uncertainty arisen from non-uniqueness in parameterization methods. BMA provides a means of incorporating multiple parameterization methods for prediction through the law of total probability, with which an ensemble average of hydraulic conductivity distribution is obtained. Estimation uncertainty is described by the BMA variances, which contain variances within and between parameterization methods. BMA shows the facts that considering more parameterization methods tends to increase estimation uncertainty and estimation uncertainty is always underestimated using a single parameterization method. Two major problems in applying BMA to hydraulic conductivity estimation using a groundwater inverse method will be discussed in the study. The first problem is the use of posterior probabilities in BMA, which tends to single out one best method and discard other good methods. This problem arises from Occam's window that only accepts models in a very narrow range. We propose a variance window to replace Occam's window to cope with this problem. The second problem is the use of Kashyap information criterion (KIC), which makes BMA tend to prefer high uncertain parameterization methods due to considering the Fisher information matrix. We found that Bayesian information criterion (BIC) is a good approximation to KIC and is able to avoid controversial results. We applied BMA to hydraulic conductivity estimation in the 1,500-foot sand aquifer in East Baton Rouge Parish, Louisiana.

  20. Fundamental parameters of pulsating stars from atmospheric models

    NASA Astrophysics Data System (ADS)

    Barcza, S.

    2006-12-01

    A purely photometric method is reviewed to determine distance, mass, equilibrium temperature, and luminosity of pulsating stars by using model atmospheres and hydrodynamics. T Sex is given as an example: on the basis of Kurucz atmospheric models and UBVRI (in both Johnson and Kron-Cousins systems) data, variation of angular diameter, effective temperature, and surface gravity is derived as a function of phase, mass M=(0.76± 0.09) M⊙, distance d=530± 67 pc, Rmax=2.99R⊙, Rmin=2.87R⊙, magnitude averaged visual absolute brightness < MVmag>=1.17± 0.26 mag are found. During a pulsation cycle four standstills of the atmosphere are pointed out indicating the occurrence of two shocks in the atmosphere. The derived equilibrium temperature Teq=7781 K and luminosity (28.3± 8.8)L⊙ locate T Sex on the blue edge of the instability strip in a theoretical Hertzsprung-Russell diagram. The differences of the physical parameters from this study and Liu & Janes (1990) are discussed.

  1. Mechanical models for insect locomotion: stability and parameter studies

    NASA Astrophysics Data System (ADS)

    Schmitt, John; Holmes, Philip

    2001-08-01

    We extend the analysis of simple models for the dynamics of insect locomotion in the horizontal plane, developed in [Biol. Cybern. 83 (6) (2000) 501] and applied to cockroach running in [Biol. Cybern. 83 (6) (2000) 517]. The models consist of a rigid body with a pair of effective legs (each representing the insect’s support tripod) placed intermittently in ground contact. The forces generated may be prescribed as functions of time, or developed by compression of a passive leg spring. We find periodic gaits in both cases, and show that prescribed (sinusoidal) forces always produce unstable gaits, unless they are allowed to rotate with the body during stride, in which case a (small) range of physically unrealistic stable gaits does exist. Stability is much more robust in the passive spring case, in which angular momentum transfer at touchdown/liftoff can result in convergence to asymptotically straight motions with bounded yaw, fore-aft and lateral velocity oscillations. Using a non-dimensional formulation of the equations of motion, we also develop exact and approximate scaling relations that permit derivation of gait characteristics for a range of leg stiffnesses, lengths, touchdown angles, body masses and inertias, from a single gait family computed at ‘standard’ parameter values.

  2. Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator.

    PubMed

    Harder, Edward; Anisimov, Victor M; Vorobyov, Igor V; Lopes, Pedro E M; Noskov, Sergei Y; MacKerell, Alexander D; Roux, Benoît

    2006-11-01

    Electron pairs in the valence shell of an atom that do not participate in the bonding of a molecule ("lone pairs") give rise to a concentrated electron density away from the atom center. To account for the asymmetry in the electron charge density that arises from lone pairs, an electrostatic model is developed that is parametrically anisotropic at the atomic level. The model uses virtual interaction sites with partial charges that are associated but not coincident with the nuclei. In addition, the model incorporates anisotropic atomic polarizabilities. The protocol previously outlined in Anisimov et al. [J. Chem. Theory Comput. 2005, 1, 153] for parametrizing the electrostatic potential energy of a polarizable force field using classical Drude oscillators is extended to incorporate additional lone pair parameters. To probe the electrostatic environment around the lone pairs, the static (molecule alone) and perturbed (molecule in the presence of a test charge) electrostatic potential (ESP) are evaluated and compared to high level quantum mechanical (QM) electronic structure calculations. The parametrization of the virtual sites relies on data from the QM static ESP. The contribution to the perturbed ESP from the electronic polarization of the molecule is used to resolve the components of the atomic polarizability tensor. The model is tested in the case of four molecules:  methanol, acetone, methylamine, and pyridine. Interaction energies with water and sodium are used to assess the accuracy of the model. The results are compared with simpler models placing all the charge on the nuclei as well as using only isotropic atomic polarizabilities. Analysis shows that the addition of virtual sites reduces the average error relative to the QM calculations. In contrast to models with atom centered charges, the virtual site models correctly predict the minimum energy conformation for acetone and methanol, with water, to be closely coordinated with the lone pair direction

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

    PubMed

    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.

  4. Anisotropy Modeling of Terahertz Metamaterials: Polarization Dependent Resonance Manipulation by Meta-Atom Cluster

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    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.

  5. Invited Review Article: The statistical modeling of atomic clocks and the design of time scales

    SciTech Connect

    Levine, Judah

    2012-02-15

    I will show how the statistical models that are used to describe the performance of atomic clocks are derived from their internal design. These statistical models form the basis for time scales, which are used to define international time scales such as International Atomic Time and Coordinated Universal Time. These international time scales are realized by ensembles of clocks at national laboratories such as the National Institute of Standards and Technology, and I will describe how ensembles of atomic clocks are characterized and managed.

  6. Invited review article: The statistical modeling of atomic clocks and the design of time scales.

    PubMed

    Levine, Judah; Ibarra-Manzano, O

    2012-02-01

    I will show how the statistical models that are used to describe the performance of atomic clocks are derived from their internal design. These statistical models form the basis for time scales, which are used to define international time scales such as International Atomic Time and Coordinated Universal Time. These international time scales are realized by ensembles of clocks at national laboratories such as the National Institute of Standards and Technology, and I will describe how ensembles of atomic clocks are characterized and managed.

  7. Invited review article: The statistical modeling of atomic clocks and the design of time scales.

    PubMed

    Levine, Judah; Ibarra-Manzano, O

    2012-02-01

    I will show how the statistical models that are used to describe the performance of atomic clocks are derived from their internal design. These statistical models form the basis for time scales, which are used to define international time scales such as International Atomic Time and Coordinated Universal Time. These international time scales are realized by ensembles of clocks at national laboratories such as the National Institute of Standards and Technology, and I will describe how ensembles of atomic clocks are characterized and managed. PMID:22380071

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

    PubMed Central

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

    2016-01-01

    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. PMID:27599739

  9. Atomic bomb survivors and the sigmoidal response model

    SciTech Connect

    Kondo, S.

    1994-12-31

    Epidemiological data on health effects of low-level radiation based on 40-yr followup studies of 75000 atomic bomb survivors and 35000 control people show that there were no measurable risks from low-level radiation in regard to noncancer diseases, genetic, teratogenic, and carcinogenic effects. However, seemingly sigmoidal responses of bomb radiation-induced cancers, which must have been caused by tumorigenic mutations contradict experimental results that mutations linearly increase with increase in radiation dose. An explanation is proposed for this superficial contradiction.

  10. Parameters of an electric-discharge generator of iodine atoms for a chemical oxygen-iodine laser

    SciTech Connect

    Azyazov, V N; Vorob'ev, M V; Voronov, A I; Kupryaev, Nikolai V; Mikheev, P A; Ufimtsev, N I

    2009-01-31

    Laser-induced fluorescence is used for measuring the concentration of iodine molecules at the output of an electric-discharge generator of atomic iodine. Methyl iodide CH{sub 3}I is used as the donor of atomic iodine. The fraction of iodine extracted from CH{sub 3}I in the generator is {approx}50%. The optimal operation regimes are found in which 80%-90% of iodine contained in the output flow of the generator was in the atomic state. This fraction decreased during the iodine transport due to recombination and was 20%-30% at the place where iodine was injected into the oxygen flow. The fraction of the discharge power spent for dissociation was {approx}3%. (elements of laser setups)

  11. An Adaptive Sequential Design for Model Discrimination and Parameter Estimation in Non-Linear Nested Models

    SciTech Connect

    Tommasi, C.; May, C.

    2010-09-30

    The DKL-optimality criterion has been recently proposed for the dual problem of model discrimination and parameter estimation, for the case of two rival models. A sequential version of the DKL-optimality criterion is herein proposed in order to discriminate and efficiently estimate more than two nested non-linear models. Our sequential method is inspired by the procedure of Biswas and Chaudhuri (2002), which is however useful only in the set up of nested linear models.

  12. Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems

    PubMed Central

    2013-01-01

    Background Model development is a key task in systems biology, which typically starts from an initial model candidate and, involving an iterative cycle of hypotheses-driven model modifications, leads to new experimentation and subsequent model identification steps. The final product of this cycle is a satisfactory refined model of the biological phenomena under study. During such iterative model development, researchers frequently propose a set of model candidates from which the best alternative must be selected. Here we consider this problem of model selection and formulate it as a simultaneous model selection and parameter identification problem. More precisely, we consider a general mixed-integer nonlinear programming (MINLP) formulation for model selection and identification, with emphasis on dynamic models consisting of sets of either ODEs (ordinary differential equations) or DAEs (differential algebraic equations). Results We solved the MINLP formulation for model selection and identification using an algorithm based on Scatter Search (SS). We illustrate the capabilities and efficiency of the proposed strategy with a case study considering the KdpD/KdpE system regulating potassium homeostasis in Escherichia coli. The proposed approach resulted in a final model that presents a better fit to the in silico generated experimental data. Conclusions The presented MINLP-based optimization approach for nested-model selection and identification is a powerful methodology for model development in systems biology. This strategy can be used to perform model selection and parameter estimation in one single step, thus greatly reducing the number of experiments and computations of traditional modeling approaches. PMID:23938131

  13. Nonlinear Jaynes–Cummings model for two interacting two-level atoms

    NASA Astrophysics Data System (ADS)

    de los Santos-Sánchez, O.; González-Gutiérrez, C.; Récamier, J.

    2016-08-01

    In this work we examine a nonlinear version of the Jaynes–Cummings model for two identical two-level atoms allowing for Ising-like and dipole–dipole interplays between them. The model is said to be nonlinear in the sense that it can incorporate both a general intensity-dependent interaction between the atomic system and the cavity field and/or the presence of a nonlinear medium inside the cavity. As an example, we consider a particular type of atom-field coupling based upon the so-called Buck–Sukumar model and a lossless Kerr-like cavity. We describe the possible effects of such features on the evolution of some quantities of current interest, such as atomic excitation, purity, concurrence, the entropy of the field and the evolution of the latter in phase space.

  14. Three-dimensional time-dependent computer modeling of the electrothermal atomizers for analytical spectrometry

    NASA Astrophysics Data System (ADS)

    Tsivilskiy, I. V.; Nagulin, K. Yu.; Gilmutdinov, A. Kh.

    2016-02-01

    A full three-dimensional nonstationary numerical model of graphite electrothermal atomizers of various types is developed. The model is based on solution of a heat equation within solid walls of the atomizer with a radiative heat transfer and numerical solution of a full set of Navier-Stokes equations with an energy equation for a gas. Governing equations for the behavior of a discrete phase, i.e., atomic particles suspended in a gas (including gas-phase processes of evaporation and condensation), are derived from the formal equations molecular kinetics by numerical solution of the Hertz-Langmuir equation. The following atomizers test the model: a Varian standard heated electrothermal vaporizer (ETV), a Perkin Elmer standard THGA transversely heated graphite tube with integrated platform (THGA), and the original double-stage tube-helix atomizer (DSTHA). The experimental verification of computer calculations is carried out by a method of shadow spectral visualization of the spatial distributions of atomic and molecular vapors in an analytical space of an atomizer.

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

    NASA Astrophysics Data System (ADS)

    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.

  16. Recommended direct simulation Monte Carlo collision model parameters for modeling ionized air transport processes

    NASA Astrophysics Data System (ADS)

    Swaminathan-Gopalan, Krishnan; Stephani, Kelly A.

    2016-02-01

    A systematic approach for calibrating the direct simulation Monte Carlo (DSMC) collision model parameters to achieve consistency in the transport processes is presented. The DSMC collision cross section model parameters are calibrated for high temperature atmospheric conditions by matching the collision integrals from DSMC against ab initio based collision integrals that are currently employed in the Langley Aerothermodynamic Upwind Relaxation Algorithm (LAURA) and Data Parallel Line Relaxation (DPLR) high temperature computational fluid dynamics solvers. The DSMC parameter values are computed for the widely used Variable Hard Sphere (VHS) and the Variable Soft Sphere (VSS) models using the collision-specific pairing approach. The recommended best-fit VHS/VSS parameter values are provided over a temperature range of 1000-20 000 K for a thirteen-species ionized air mixture. Use of the VSS model is necessary to achieve consistency in transport processes of ionized gases. The agreement of the VSS model transport properties with the transport properties as determined by the ab initio collision integral fits was found to be within 6% in the entire temperature range, regardless of the composition of the mixture. The recommended model parameter values can be readily applied to any gas mixture involving binary collisional interactions between the chemical species presented for the specified temperature range.

  17. Observation model and parameter partials for the JPL geodetic GPS modeling software GPSOMC

    NASA Technical Reports Server (NTRS)

    Sovers, O. J.; Border, J. S.

    1988-01-01

    The physical models employed in GPSOMC and the modeling module of the GIPSY software system developed at JPL for analysis of geodetic Global Positioning Satellite (GPS) measurements are described. Details of the various contributions to range and phase observables are given, as well as the partial derivatives of the observed quantities with respect to model parameters. A glossary of parameters is provided to enable persons doing data analysis to identify quantities in the current report with their counterparts in the computer programs. There are no basic model revisions, with the exceptions of an improved ocean loading model and some new options for handling clock parametrization. Such misprints as were discovered were corrected. Further revisions include modeling improvements and assurances that the model description is in accord with the current software.

  18. YUP.SCX: coaxing atomic models into medium resolution electron density maps.

    PubMed

    Tan, Robert K-Z; Devkota, Batsal; Harvey, Stephen C

    2008-08-01

    The structures of large macromolecular complexes in different functional states can be determined by cryo-electron microscopy, which yields electron density maps of low to intermediate resolutions. The maps can be combined with high-resolution atomic structures of components of the complex, to produce a model for the complex that is more accurate than the formal resolution of the map. To this end, methods have been developed to dock atomic models into density maps rigidly or flexibly, and to refine a docked model so as to optimize the fit of the atomic model into the map. We have developed a new refinement method called YUP.SCX. The electron density map is converted into a component of the potential energy function to which terms for stereochemical restraints and volume exclusion are added. The potential energy function is then minimized (using simulated annealing) to yield a stereochemically-restrained atomic structure that fits into the electron density map optimally. We used this procedure to construct an atomic model of the 70S ribosome in the pre-accommodation state. Although some atoms are displaced by as much as 33A, they divide themselves into nearly rigid fragments along natural boundaries with smooth transitions between the fragments.

  19. Model inversion by parameter fit using NN emulating the forward model: evaluation of indirect measurements.

    PubMed

    Schiller, Helmut

    2007-05-01

    The usage of inverse models to derive parameters of interest from measurements is widespread in science and technology. The operational usage of many inverse models became feasible just by emulation of the inverse model via a neural net (NN). This paper shows how NNs can be used to improve inversion accuracy by minimizing the sum of error squares. The procedure is very fast as it takes advantage of the Jacobian which is a byproduct of the NN calculation. An example from remote sensing is shown. It is also possible to take into account a non-diagonal covariance matrix of the measurement to derive the covariance matrix of the retrieved parameters.

  20. Geomagnetically induced currents in Uruguay: Sensitivity to modelling parameters

    NASA Astrophysics Data System (ADS)

    Caraballo, R.

    2016-11-01

    According to the traditional wisdom, geomagnetically induced currents (GIC) should occur rarely at mid-to-low latitudes, but in the last decades a growing number of reports have addressed their effects on high-voltage (HV) power grids at mid-to-low latitudes. The growing trend to interconnect national power grids to meet regional integration objectives, may lead to an increase in the size of the present energy transmission networks to form a sort of super-grid at continental scale. Such a broad and heterogeneous super-grid can be exposed to the effects of large GIC if appropriate mitigation actions are not taken into consideration. In the present study, we present GIC estimates for the Uruguayan HV power grid during severe magnetic storm conditions. The GIC intensities are strongly dependent on the rate of variation of the geomagnetic field, conductivity of the ground, power grid resistances and configuration. Calculated GIC are analysed as functions of these parameters. The results show a reasonable agreement with measured data in Brazil and Argentina, thus confirming the reliability of the model. The expansion of the grid leads to a strong increase in GIC intensities in almost all substations. The power grid response to changes in ground conductivity and resistances shows similar results in a minor extent. This leads us to consider GIC as a non-negligible phenomenon in South America. Consequently, GIC must be taken into account in mid-to-low latitude power grids as well.

  1. Observation model and parameter partials for the JPL geodetic (GPS) modeling software 'GPSOMC'

    NASA Technical Reports Server (NTRS)

    Sovers, O. J.

    1990-01-01

    The physical models employed in GPSOMC, the modeling module of the GIPSY software system developed at JPL for analysis of geodetic Global Positioning Satellite (GPS) measurements are described. Details of the various contributions to range and phase observables are given, as well as the partial derivatives of the observed quantities with respect to model parameters. A glossary of parameters is provided to enable persons doing data analysis to identify quantities with their counterparts in the computer programs. The present version is the second revision of the original document which it supersedes. The modeling is expanded to provide the option of using Cartesian station coordinates; parameters for the time rates of change of universal time and polar motion are also introduced.

  2. Experiments and modeling of discharge characteristics in water-mist sprays generated by pressure-swirl atomizers

    NASA Astrophysics Data System (ADS)

    Santangelo, Paolo E.

    2012-12-01

    Pressure-swirl atomizers are often employed to generate a water-mist spray, typically employed in fire suppression. In the present study, an experimental characterization of dispersion (velocity and cone angle) and atomization (drop-size axial evolution) was carried out following a previously developed methodology, with specific reference to the initial region of the spray. Laser-based techniques were used to quantitatively evaluate the considered phenomena: velocity field was reconstructed through a Particle Image Velocimetry analysis; drop-size distribution was measured by a Malvern Spraytec device, highlighting secondary atomization and subsequent coalescence along the spray axis. Moreover, a comprehensive set of relations was validated as predictive of the involved parameters, following an inviscid-fluid approach. The proposed model pertains to early studies on pressure-swirl atomizers and primarily yields to determine both initial velocity and cone angle. The spray thickness is also predicted and a classic correlation for Sauter Mean Diameter is shown to provide good agreement with experimental results. The analysis was carried out at the operative pressure of 80 bar; two injectors were employed featuring different orifice diameters and flow numbers, as a sort of parametric approach to this spray typology.

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

    NASA Astrophysics Data System (ADS)

    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.

  4. Hydrodynamic, Atomic Kinetic, and Monte Carlo Radiation Transfer Models of the X-ray Spectra of Compact Binaries

    SciTech Connect

    Mauche, C W; Liedahl, D A; Akiyama, S; Plewa, T

    2008-02-08

    We describe the results of an effort, funded by the Lawrence Livermore National Laboratory Directed Research and Development Program, to model, using FLASH time-dependent adaptive-mesh hydrodynamic simulations, XSTAR photoionization calculations, HULLAC atomic data, and Monte Carlo radiation transport, the radiatively-driven photoionized wind and accretion flow of high-mass X-ray binaries (HMXBs). In this final report, we describe the purpose, approach, and technical accomplishments of this effort, including maps of the density, temperature, velocity, ionization parameter, and emissivity distributions of the X-ray emission lines of the well-studied HMXB Vela X-1.

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

    NASA Astrophysics Data System (ADS)

    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.

  6. Photoelectron angular distributions for states of any mixed character: an experiment-friendly model for atomic, molecular, and cluster anions.

    PubMed

    Khuseynov, Dmitry; Blackstone, Christopher C; Culberson, Lori M; Sanov, Andrei

    2014-09-28

    We present a model for laboratory-frame photoelectron angular distributions in direct photodetachment from (in principle) any molecular orbital using linearly polarized light. A transparent mathematical approach is used to generalize the Cooper-Zare central-potential model to anionic states of any mixed character. In the limit of atomic-anion photodetachment, the model reproduces the Cooper-Zare formula. In the case of an initial orbital described as a superposition of s and p-type functions, the model yields the previously obtained s-p mixing formula. The formalism is further advanced using the Hanstorp approximation, whereas the relative scaling of the partial-wave cross-sections is assumed to follow the Wigner threshold law. The resulting model describes the energy dependence of photoelectron anisotropy for any atomic, molecular, or cluster anions, usually without requiring a direct calculation of the transition dipole matrix elements. As a benchmark case, we apply the p-d variant of the model to the experimental results for NO(-) photodetachment and show that the observed anisotropy trend is described well using physically meaningful values of the model parameters. Overall, the presented formalism delivers insight into the photodetachment process and affords a new quantitative strategy for analyzing the photoelectron angular distributions and characterizing mixed-character molecular orbitals using photoelectron imaging spectroscopy of negative ions.

  7. Photoelectron angular distributions for states of any mixed character: An experiment-friendly model for atomic, molecular, and cluster anions

    SciTech Connect

    Khuseynov, Dmitry; Blackstone, Christopher C.; Culberson, Lori M.; Sanov, Andrei

    2014-09-28

    We present a model for laboratory-frame photoelectron angular distributions in direct photodetachment from (in principle) any molecular orbital using linearly polarized light. A transparent mathematical approach is used to generalize the Cooper-Zare central-potential model to anionic states of any mixed character. In the limit of atomic-anion photodetachment, the model reproduces the Cooper-Zare formula. In the case of an initial orbital described as a superposition of s and p-type functions, the model yields the previously obtained s-p mixing formula. The formalism is further advanced using the Hanstorp approximation, whereas the relative scaling of the partial-wave cross-sections is assumed to follow the Wigner threshold law. The resulting model describes the energy dependence of photoelectron anisotropy for any atomic, molecular, or cluster anions, usually without requiring a direct calculation of the transition dipole matrix elements. As a benchmark case, we apply the p-d variant of the model to the experimental results for NO{sup −} photodetachment and show that the observed anisotropy trend is described well using physically meaningful values of the model parameters. Overall, the presented formalism delivers insight into the photodetachment process and affords a new quantitative strategy for analyzing the photoelectron angular distributions and characterizing mixed-character molecular orbitals using photoelectron imaging spectroscopy of negative ions.

  8. Roughness parameter optimization using Land Parameter Retrieval Model and Soil Moisture Deficit: Implementation using SMOS brightness temperatures

    NASA Astrophysics Data System (ADS)

    Srivastava, Prashant K.; O'Neill, Peggy; Han, Dawei; Rico-Ramirez, Miguel A.; Petropoulos, George P.; Islam, Tanvir; Gupta, Manika

    2015-04-01

    Roughness parameterization is necessary for nearly all soil moisture retrieval algorithms such as single or dual channel algorithms, L-band Microwave Emission of Biosphere (LMEB), Land Parameter Retrieval Model (LPRM), etc. At present, roughness parameters can be obtained either by field experiments, although obtaining field measurements all over the globe is nearly impossible, or by using a land cover-based look up table, which is not always accurate everywhere for individual fields. From a catalogue of models available in the technical literature domain, the LPRM model was used here because of its robust nature and applicability to a wide range of frequencies. LPRM needs several parameters for soil moisture retrieval -- in particular, roughness parameters (h and Q) are important for calculating reflectivity. In this study, the h and Q parameters are optimized using the soil moisture deficit (SMD) estimated from the probability distributed model (PDM) and Soil Moisture and Ocean Salinity (SMOS) brightness temperatures following the Levenberg-Marquardt (LM) algorithm over the Brue catchment, Southwest of England, U.K.. The catchment is predominantly a pasture land with moderate topography. The PDM-based SMD is used as it is calibrated and validated using locally available ground-based information, suitable for large scale areas such as catchments. The optimal h and Q parameters are determined by maximizing the correlation between SMD and LPRM retrieved soil moisture. After optimization the values of h and Q have been found to be 0.32 and 0.15, respectively. For testing the usefulness of the estimated roughness parameters, a separate set of SMOS datasets are taken into account for soil moisture retrieval using the LPRM model and optimized roughness parameters. The overall analysis indicates a satisfactory result when compared against the SMD information. This work provides quantitative values of roughness parameters suitable for large scale applications. The

  9. Examining Pre-Service Teachers' Use of Atomic Models in Explaining Subsequent Ionisation Energy Values

    NASA Astrophysics Data System (ADS)

    Wheeldon, Ruth

    2012-06-01

    Chemistry students' explanations of ionisation energy phenomena often involve a number of non-scientific or inappropriate ideas being used to form causality arguments. Research has attributed this to many science teachers using these ideas themselves (Tan and Taber, in J Chem Educ 86(5):623-629, 2009). This research extends this work by considering which atomic models are used in pre-service teachers' explanations and how that relates to the causality ideas expressed. Thirty-one pre-service teachers were interviewed. Each was asked to describe and explain four different atomic representations (Rutherford, Electron cloud micrograph, Bohr and Schrödinger types) in as much detail as they could. They also provided an explanation for the subsequent ionisation energy values for an oxygen atom and identified which representations were helpful in explaining the values. Significantly, when pre-service teachers only used Bohr type representations, they did not use repelling electron ideas in their explanations. However, arguments that were based on electron-electron repulsion used features from Schrödinger type atoms. These findings suggest that many pre-service teachers need to develop their atomic modelling skills so that they select and use models more expertly and that subsequent ionisation explanations offer a context in which to explore different atomic models' limitations and their deployment as explanatory resources.

  10. Observation model and parameter partials for the JPL VLBI parameter estimation software MODEST/1991

    NASA Technical Reports Server (NTRS)

    Sovers, O. J.

    1991-01-01

    A revision is presented of MASTERFIT-1987, which it supersedes. Changes during 1988 to 1991 included introduction of the octupole component of solid Earth tides, the NUVEL tectonic motion model, partial derivatives for the precession constant and source position rates, the option to correct for source structure, a refined model for antenna offsets, modeling the unique antenna at Richmond, FL, improved nutation series due to Zhu, Groten, and Reigber, and reintroduction of the old (Woolard) nutation series for simulation purposes. Text describing the relativistic transformations and gravitational contributions to the delay model was also revised in order to reflect the computer code more faithfully.

  11. Efficient Nonlinear Atomization Model for Thin 3D Free Liquid Films

    NASA Astrophysics Data System (ADS)

    Mehring, Carsten

    2007-03-01

    Reviewed is a nonlinear reduced-dimension thin-film model developed by the author and aimed at the prediction of spray formation from thin films such as those found in gas-turbine engines (e.g., prefilming air-blast atomizers), heavy-fuel-oil burners (e.g., rotary-cup atomizers) and in the paint industry (e.g., flat-fan atomizers). Various implementations of the model focusing on different model-aspects, i.e., effect of film geometry, surface tension, liquid viscosity, coupling with surrounding gas-phase flow, influence of long-range intermolecular forces during film rupture are reviewed together with a validation of the nonlinear wave propagation characteristics predicted by the model for inviscid planar films using a two-dimensional vortex- method. An extension and generalization of the current nonlinear film model for implementation into a commercial flow- solver is outlined.

  12. Putting structure into context: fitting of atomic models into electron microscopic and electron tomographic reconstructions.

    PubMed

    Volkmann, Niels

    2012-02-01

    A complete understanding of complex dynamic cellular processes such as cell migration or cell adhesion requires the integration of atomic level structural information into the larger cellular context. While direct atomic-level information at the cellular level remains inaccessible, electron microscopy, electron tomography and their associated computational image processing approaches have now matured to a point where sub-cellular structures can be imaged in three dimensions at the nanometer scale. Atomic-resolution information obtained by other means can be combined with this data to obtain three-dimensional models of large macromolecular assemblies in their cellular context. This article summarizes some recent advances in this field.

  13. Multi-Variable Model-Based Parameter Estimation Model for Antenna Radiation Pattern Prediction

    NASA Technical Reports Server (NTRS)

    Deshpande, Manohar D.; Cravey, Robin L.

    2002-01-01

    A new procedure is presented to develop multi-variable model-based parameter estimation (MBPE) model to predict far field intensity of antenna. By performing MBPE model development procedure on a single variable at a time, the present method requires solution of smaller size matrices. The utility of the present method is demonstrated by determining far field intensity due to a dipole antenna over a frequency range of 100-1000 MHz and elevation angle range of 0-90 degrees.

  14. Influence of atomic modeling on integrated simulations of laser-produced Au plasmas.

    PubMed

    Frank, Yechiel; Raicher, Erez; Ehrlich, Yosi; Hurvitz, Gilad; Shpilman, Zeev; Fraenkel, Moshe; Zigler, Arie; Henis, Zohar

    2015-11-01

    Time-integrated x-ray emission spectra of laser-irradiated Au disks were recorded using transmission grating spectrometry, at laser intensities of 10(13) to 10(14) W/cm(2). Radiation-hydrodynamics and atomic physics calculations were used to simulate the emitted spectra. Three major plasma regions can be recognized: the heat wave, the corona, and an intermediate region connecting them. An analysis of the spectral contribution of these three plasma regions to the integrated recorded spectrum is presented. The importance of accurate atomic modeling of the intermediate plasma region, between the corona and the heat wave, is highlighted. The influence of several aspects of the atomic modeling is demonstrated, in particular multiply-excited atomic configurations and departure from local thermal equilibrium.

  15. UNCERTAINTIES IN ATOMIC DATA AND THEIR PROPAGATION THROUGH SPECTRAL MODELS. I

    SciTech Connect

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

    2013-06-10

    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].

  16. A Note on the Item Information Function of the Four-Parameter Logistic Model

    ERIC Educational Resources Information Center

    Magis, David

    2013-01-01

    This article focuses on four-parameter logistic (4PL) model as an extension of the usual three-parameter logistic (3PL) model with an upper asymptote possibly different from 1. For a given item with fixed item parameters, Lord derived the value of the latent ability level that maximizes the item information function under the 3PL model. The…

  17. Fundamental M-dwarf parameters from high-resolution spectra using PHOENIX ACES models. I. Parameter accuracy and benchmark stars

    NASA Astrophysics Data System (ADS)

    Passegger, V. M.; Wende-von Berg, S.; Reiners, A.

    2016-03-01

    M-dwarf stars are the most numerous stars in the Universe; they span a wide range in mass and are in the focus of ongoing and planned exoplanet surveys. To investigate and understand their physical nature, detailed spectral information and accurate stellar models are needed. We use a new synthetic atmosphere model generation and compare model spectra to observations. To test the model accuracy, we compared the models to four benchmark stars with atmospheric parameters for which independent information from interferometric radius measurements is available. We used χ2-based methods to determine parameters from high-resolution spectroscopic observations. Our synthetic spectra are based on the new PHOENIX grid that uses the ACES description for the equation of state. This is a model generation expected to be especially suitable for the low-temperature atmospheres. We identified suitable spectral tracers of atmospheric parameters and determined the uncertainties in Teff, log g, and [Fe/H] resulting from degeneracies between parameters and from shortcomings of the model atmospheres. The inherent uncertainties we find are σTeff = 35 K, σlog g = 0.14, and σ[Fe/H] = 0.11. The new model spectra achieve a reliable match to our observed data; our results for Teff and log g are consistent with literature values to within 1σ. However, metallicities reported from earlier photometric and spectroscopic calibrations in some cases disagree with our results by more than 3σ. A possible explanation are systematic errors in earlier metallicity determinations that were based on insufficient descriptions of the cool atmospheres. At this point, however, we cannot definitely identify the reason for this discrepancy, but our analysis indicates that there is a large uncertainty in the accuracy of M-dwarf parameter estimates. Based on observations carried out with UVES at ESO VLT.

  18. Physical parameters of galaxies with star formation through mid-infrared SED models

    NASA Astrophysics Data System (ADS)

    Ramos P., A. F.; Martínez-Galarza, J. R.; Higuera-G., M. A.; Quintero, S.

    2014-10-01

    We present a mid-infrared study of a sample of 19 Starburst galaxies in the local (z<0.2) universe. We derive physical parameters such as Metallicity, Interstellar Medium Pressure, Compactness Parameter C (related to the dust heating flux), PDR Fraction f_{PDR} and Extinction A_{V} by fitting the Spitzer-IRS spectra of these systems using state-of-the-art radiative transfer models and Bayesian techniques. Our results are fundamental in the understanding of massive star formation in the local counterparts of intermediate and high redshift Ultra Luminous Infrared Galaxies (ULIRGs). We reconstruct the star forming histories of these systems by obtaining posterior probability distribution functions (PDFs) for the star formation rates in different epochs an estimate the contribution to the bolometric luminosity from very recent (< 1 Myr) star formation events, and the contribution of Polycyclic Aromatic Hydrocarbons, which is significant in some cases. By comparing the derived PDFs with particular spectral signatures, such as the nebular emission of atomic species like [NeII] and [NeIII], and the H_{2} temperatures we also relate the global pattern of star formation in Starburst galaxies with the internal physics of the ISM.

  19. Modeling viscoelasticity through spring-dashpot models in intermittent-contact atomic force microscopy.

    PubMed

    López-Guerra, Enrique A; Solares, Santiago D

    2014-01-01

    We examine different approaches to model viscoelasticity within atomic force microscopy (AFM) simulation. Our study ranges from very simple linear spring-dashpot models to more sophisticated nonlinear systems that are able to reproduce fundamental properties of viscoelastic surfaces, including creep, stress relaxation and the presence of multiple relaxation times. Some of the models examined have been previously used in AFM simulation, but their applicability to different situations has not yet been examined in detail. The behavior of each model is analyzed here in terms of force-distance curves, dissipated energy and any inherent unphysical artifacts. We focus in this paper on single-eigenmode tip-sample impacts, but the models and results can also be useful in the context of multifrequency AFM, in which the tip trajectories are very complex and there is a wider range of sample deformation frequencies (descriptions of tip-sample model behaviors in the context of multifrequency AFM require detailed studies and are beyond the scope of this work).

  20. Optical Pattern Formation in Spatially Bunched Atoms: A Self-Consistent Model and Experiment

    NASA Astrophysics Data System (ADS)

    Schmittberger, Bonnie L.; Gauthier, Daniel J.

    2014-05-01

    The nonlinear optics and optomechanical physics communities use different theoretical models to describe how optical fields interact with a sample of atoms. There does not yet exist a model that is valid for finite atomic temperatures but that also produces the zero temperature results that are generally assumed in optomechanical systems. We present a self-consistent model that is valid for all atomic temperatures and accounts for the back-action of the atoms on the optical fields. Our model provides new insights into the competing effects of the bunching-induced nonlinearity and the saturable nonlinearity. We show that it is crucial to keep the fifth and seventh-order nonlinearities that arise when there exists atomic bunching, even at very low optical field intensities. We go on to apply this model to the results of our experimental system where we observe spontaneous, multimode, transverse optical pattern formation at ultra-low light levels. We show that our model accurately predicts our experimentally observed threshold for optical pattern formation, which is the lowest threshold ever reported for pattern formation. We gratefully acknowledge the financial support of the NSF through Grant #PHY-1206040.

  1. Interactions between C and Cu atoms in single-layer graphene: direct observation and modelling

    NASA Astrophysics Data System (ADS)

    Kano, Emi; Hashimoto, Ayako; Kaneko, Tomoaki; Tajima, Nobuo; Ohno, Takahisa; Takeguchi, Masaki

    2015-12-01

    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.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. Electronic supplementary information (ESI) available: Three TEM movies, additional TEM data corresponding to movies, calculated models, and lifetime results. See DOI: 10.1039/c5nr05913e

  2. [Application of model 4650 type I compressor atomizer in bronchial challenge test].

    PubMed

    Yuan, Y; Wang, Y; Zeng, J; He, T

    2000-06-01

    This study was directed to the feasibility of applying a simple atomizer-model 4650 type I (abbrev. M)-to bronchial challenge test. 92 cases of asthma were divided into 3 groups randomly. All of them were subjected to the bronchial challenge test by M atomizer, and by standard Dosimeter atomizer (abbrev. D) as a comparison. In the test by M atomizer, the times for inspiring challenging medicine were 1, 1.5 and 2 minutes for the 3 groups respectively, while the time for D atomizer was 1 minute for all. The results showed no significant differences (P > 0.2-0.5) between the two atomizers in the 3 groups, their values were linear correlated. When the inspiring time was 1 minute for both M and D, the test needed a higher concentration of challenging medicine for M than for D, their coefficient of correlation (r = 0.285) was relatively low. When inspiring time postponed to 1.5 minute for M, the difference in medicine concentration between M and D was smallest (-0.075 g/L), r = 0.665. However, a further postponed inspiring time to 2 minute for M reversely broadened their difference. These results indicated that the efficiency of M atomizer was a little lower than that of D, postponing the inspiring time for M could make up this weakness. A 1.5 minute inspiring time for M atomizer was the suggestion. Some modifications on M atomizer were done by us for a better efficiency, and the cheap and popular M atomizer could be a good replacement in bronchial challenge test.

  3. An atomic-scale model of fcc crystal-growth

    NASA Astrophysics Data System (ADS)

    van de Waal, B. W.

    1991-03-01

    Nearly perfect fcc growth may be simulated by the application of a simple growth-algorithm — only sites that are at least 4-coordinated are occupied — to a selected seed. The seed is a 22-atom cluster, being the smallest close-packed structure with two crossing stacking-faults. The stacking-faults produce active surface-sites, that can not be exhausted by occupation; they are arranged in non-vanishing steps, similar to those produced by screw-dislocations. The algorithm prevents further stacking-faults, and ensures ABC-stacking of close-packed (111)-layers, characteristic of the fcc structure. The same algorithm would not produce further growth of perfect fcc clusters or of Mackay icosahedra. It is proposed that the ability to grow fast under near-equilibrium conditions is a better criterion to select clusters as precursors of the bulk-structure than their cohesive energy. The crystal structure problem of the rare gases — why fcc, not hcp? — is discussed in connection with the apparent impossibility to simulate hcp growth by an analogous procedure.

  4. Student perception and conceptual development as represented by student mental models of atomic structure

    NASA Astrophysics Data System (ADS)

    Park, Eun Jung

    The nature of matter based upon atomic theory is a principal concept in science; hence, how to teach and how to learn about atoms is an important subject for science education. To this end, this study explored student perceptions of atomic structure and how students learn about this concept by analyzing student mental models of atomic structure. Changes in student mental models serve as a valuable resource for comprehending student conceptual development. Data was collected from students who were taking the introductory chemistry course. Responses to course examinations, pre- and post-questionnaires, and pre- and post-interviews were used to analyze student mental models of atomic structure. First, this study reveals that conceptual development can be achieved, either by elevating mental models toward higher levels of understanding or by developing a single mental model. This study reinforces the importance of higher-order thinking skills to enable students to relate concepts in order to construct a target model of atomic structure. Second, Bohr's orbital structure seems to have had a strong influence on student perceptions of atomic structure. With regard to this finding, this study suggests that it is instructionally important to teach the concept of "orbitals" related to "quantum theory." Third, there were relatively few students who had developed understanding at the level of the target model, which required student understanding of the basic ideas of quantum theory. This study suggests that the understanding of atomic structure based on the idea of quantum theory is both important and difficult. Fourth, this study included different student assessments comprised of course examinations, questionnaires, and interviews. Each assessment can be used to gather information to map out student mental models. Fifth, in the comparison of the pre- and post-interview responses, this study showed that high achieving students moved toward more improved models or to advanced

  5. Stochastic modelling of daily rainfall in Nigeria: intra-annual variation of model parameters

    NASA Astrophysics Data System (ADS)

    Jimoh, O. D.; Webster, P.

    1999-09-01

    A Markov model of order 1 may be used to describe the occurrence of wet and dry days in Nigeria. Such models feature two parameter sets; P01 to characterise the probability of a wet day following a dry day and P11 to characterise the probability of a wet day following a wet day. The model parameter sets, when estimated from historical records, are characterised by a distinctive seasonal behaviour. However, the comparison of this seasonal behaviour between rainfall stations is hampered by the noise reflecting the high variability of parameters on successive days. The first part of this article is concerned with methods for smoothing these inherently noisy parameter sets. Smoothing has been approached using Fourier series, averaging techniques, or a combination thereof. It has been found that different methods generally perform well with respect to estimation of the average number of wet events and the frequency duration curves of wet and dry events. Parameterisation of the P01 parameter set is more successful than the P11 in view of the relatively small number of wet events lasting two or more days. The second part of the article is concerned with describing the regional variation in smoothed parameter sets. There is a systematic variation in the P01 parameter set as one moves northwards. In contrast, there is limited regional variation in the P11 set. Although this regional variation in P01 appears to be related to the gradual movement of the Inter Tropical Convergence Zone, the contrasting behaviour of the two parameter sets is difficult to explain on physical grounds.

  6. Folding of proteins with an all-atom Go-model.

    PubMed

    Wu, L; Zhang, J; Qin, M; Liu, F; Wang, W

    2008-06-21

    The Go-like potential at a residual level has been successfully applied to the folding of proteins in many previous works. However, taking into consideration more detailed structural information in the atomic level, the definition of contacts used in these traditional Go-models may not be suitable for all-atom simulations. Here, in this work, we develop a rational definition of contacts considering the screening effect in the crowded intramolecular environment. In such a scheme, a large amount of screened atom pairs are excluded and the number of contacts is decreased compared to the case of the traditional definition. These contacts defined by such a new definition are compatible with the all-atom representation of protein structures. To verify the rationality of the new definition of contacts, the folding of proteins CI2 and SH3 is simulated by all-atom molecular dynamics simulations. A high folding cooperativity and good correlation of the simulated Phi-values with those obtained experimentally, especially for CI2, are found. This suggests that the all-atom Go-model is improved compared to the traditional Go-model. Based on the comparison of the Phi-values, the roles of side chains in the folding are discussed, and it is concluded that the side-chain structures are more important for local contacts in determining the transition state structures. Moreover, the relations between side chain and backbone orderings are also discussed.

  7. Dynamic hydrologic modeling using the zero-parameter Budyko model with instantaneous dryness index

    NASA Astrophysics Data System (ADS)

    Biswal, Basudev

    2016-09-01

    Long-term partitioning of hydrologic quantities is achieved by using the zero-parameter Budyko model which defines a dryness index. However, this approach is not suitable for dynamic partitioning particularly at diminishing timescales, and therefore, a universally applicable zero-parameter model remains elusive. Here an instantaneous dryness index is proposed which enables dynamic hydrologic modeling using the Budyko model. By introducing a "decay function" that characterizes the effects of antecedent rainfall and solar energy on the dryness state of a basin at a time, I propose the concept of instantaneous dryness index and use the Budyko function to perform continuous hydrologic partitioning. Using the same decay function, I then obtain discharge time series from the effective rainfall time series. The model is evaluated by considering data form 63 U.S. Geological Survey basins. Results indicate the possibility of using the proposed framework as an alternative platform for prediction in ungagued basins.

  8. Reasoning with Atomic-Scale Molecular Dynamic Models

    ERIC Educational Resources Information Center

    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…

  9. Modeling STM tips by single absorbed atoms on W(100) films: 3d and 4d transition-metal atoms

    NASA Astrophysics Data System (ADS)

    Hofer, W. A.; Redinger, J.; Podloucky, R.

    2001-09-01

    In order to provide comprehensive data on the electronic structure of realistic STM tips we have studied tungsten (100) films with adsorbed single 3d and 4d transition-metal atoms by ab initio molecular-dynamics and full potential methods. Molecular dynamics using ultrasoft pseudopotentials has been used to determine the relaxation of adsorbate and surface layers. Subsequently the electronic structure of the relaxed model tip has been calculated with an all-electron full potential method. The results suggest that the chemical nature of the tip apex to a high degree determines achievable corrugations and that results for current and corrugation values in a perturbation approach might be considerably improved by including the electronic structure of the tip.

  10. Ecosystem Modeling of College Drinking: Parameter Estimation and Comparing Models to Data*

    PubMed Central

    Ackleh, Azmy S.; Fitzpatrick, Ben G.; Scribner, Richard; Simonsen, Neal; Thibodeaux, Jeremy J.

    2009-01-01

    Recently we developed a model composed of five impulsive differential equations that describes the changes in drinking patterns (that persist at epidemic level) amongst college students. Many of the model parameters cannot be measured directly from data; thus, an inverse problem approach, which chooses the set of parameters that results in the “best” model to data fit, is crucial for using this model as a predictive tool. The purpose of this paper is to present the procedure and results of an unconventional approach to parameter estimation that we developed after more common approaches were unsuccessful for our specific problem. The results show that our model provides a good fit to survey data for 32 campuses. Using these parameter estimates, we examined the effect of two hypothetical intervention policies: 1) reducing environmental wetness, and 2) penalizing students who are caught drinking. The results suggest that reducing campus wetness may be a very effective way of reducing heavy episodic (binge) drinking on a college campus, while a policy that penalizes students who drink is not nearly as effective. PMID:20161275

  11. Relativistic Corrections to the Bohr Model of the Atom

    ERIC Educational Resources Information Center

    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)

  12. Structural modelling and control design under incomplete parameter information: The maximum-entropy approach

    NASA Technical Reports Server (NTRS)

    Hyland, D. C.

    1983-01-01

    A stochastic structural control model is described. In contrast to the customary deterministic model, the stochastic minimum data/maximum entropy model directly incorporates the least possible a priori parameter information. The approach is to adopt this model as the basic design model, thus incorporating the effects of parameter uncertainty at a fundamental level, and design mean-square optimal controls (that is, choose the control law to minimize the average of a quadratic performance index over the parameter ensemble).

  13. Long wave atmospheric noise model, phase 1. Volume 2: Mode parameters

    NASA Astrophysics Data System (ADS)

    Warber, Chris R.

    1989-04-01

    The full wave propagation code is used to calculate waveguide mode parameters in spread debris environments in order to develop a long wave atmospheric noise model. The parameters are stored for retrieval whenever the model is exercised. Because the noise-model data encompass parameters of all significant modes for a wide range of ground conductivities, frequencies, and nuclear environment intensities, graphs of those parameters are presented in this volume handbook format.

  14. A stochastic optimization model under modeling uncertainty and parameter certainty for groundwater remediation design--part I. Model development.

    PubMed

    He, L; Huang, G H; Lu, H W

    2010-04-15

    Solving groundwater remediation optimization problems based on proxy simulators can usually yield optimal solutions differing from the "true" ones of the problem. This study presents a new stochastic optimization model under modeling uncertainty and parameter certainty (SOMUM) and the associated solution method for simultaneously addressing modeling uncertainty associated with simulator residuals and optimizing groundwater remediation processes. This is a new attempt different from the previous modeling efforts. The previous ones focused on addressing uncertainty in physical parameters (i.e. soil porosity) while this one aims to deal with uncertainty in mathematical simulator (arising from model residuals). Compared to the existing modeling approaches (i.e. only parameter uncertainty is considered), the model has the advantages of providing mean-variance analysis for contaminant concentrations, mitigating the effects of modeling uncertainties on optimal remediation strategies, offering confidence level of optimal remediation strategies to system designers, and reducing computational cost in optimization processes.

  15. NMR provides checklist of generic properties for atomic-scale models of periodic mesoporous silicas.

    PubMed

    Shenderovich, Ilja G; Mauder, Daniel; Akcakayiran, Dilek; Buntkowsky, Gerd; Limbach, Hans-Heinrich; Findenegg, Gerhard H

    2007-10-25

    MCM-41 and SBA-15 silicas were studied by (29)Si solid-state NMR and (15)N NMR in the presence of (15)N-pyridine with the aim to formulate generic structural parameters that may be used as a checklist for atomic-scale structural models of this class of ordered mesoporous materials. High-quality MCM-41 silica constitutes quasi-ideal arrays of uniform-size pores with thin pore walls, while SBA-15 silica has thicker pore walls with framework and surface defects. The numbers of silanol (Q(3)) and silicate (Q(4)) groups were found to be in the ratio of about 1:3 for MCM-41 and about 1:4 for our SBA-15 materials. Combined with the earlier finding that the density of surface silanol groups is about three per nm(2) in MCM-41 (Shenderovich, et al. J. Phys. Chem. B 2003, 107, 11924) this allows us to discriminate between different atomic-scale models of these materials. Neither tridymite nor edingtonite meet both of these requirements. On the basis of the hexagonal pore shape model, the experimental Q(3):Q(4) ratio yields a wall thickness of about 0.95 nm for MCM-41 silica, corresponding to the width of ca. four silica tetrahedra. The arrangement of Q(3) groups at the silica surfaces was analyzed using postsynthesis surface functionalization. It was found that the number of covalent bonds to the surface formed by the functional reagents is affected by the surface morphology. It is concluded that for high-quality MCM-41 silicas the distance between neighboring surface silanol groups is greater than 0.5 nm. As a result, di- and tripodical reagents like (CH(3))(2)Si(OH)(2) and CH(3)Si(OH)(3) can form only one covalent bond to the surface. The residual hydroxyl groups of surface-bonded functional reagents either remain free or interact with other reagent molecules. Accordingly, the number of surface silanol groups at a given MCM-41 or SBA-15 silica may not decrease but increase after treatment with CH(3)Si(OH)(3) reagent. On the other hand, nearly all surface silanol groups

  16. Modeling of Transmittance Degradation Caused by Optical Surface Contamination by Atomic Oxygen Reaction with Adsorbed Silicones

    NASA Technical Reports Server (NTRS)

    Snyder, Aaron; Banks, Bruce; Miller, Sharon; Stueber, Thomas; Sechkar, Edward

    2001-01-01

    A numerical procedure is presented to calculate transmittance degradation caused by contaminant films on spacecraft surfaces produced through the interaction of orbital atomic oxygen (AO) with volatile silicones and hydrocarbons from spacecraft components. In the model, contaminant accretion is dependent on the adsorption of species, depletion reactions due to gas-surface collisions, desorption, and surface reactions between AO and silicone producing SiO(x), (where x is near 2). A detailed description of the procedure used to calculate the constituents of the contaminant layer is presented, including the equations that govern the evolution of fractional coverage by specie type. As an illustrative example of film growth, calculation results using a prototype code that calculates the evolution of surface coverage by specie type is presented and discussed. An example of the transmittance degradation caused by surface interaction of AO with deposited contaminant is presented for the case of exponentially decaying contaminant flux. These examples are performed using hypothetical values for the process parameters.

  17. Simultaneous estimation of plasma parameters from spectroscopic data of neutral helium using least square fitting of CR-model

    NASA Astrophysics Data System (ADS)

    Jain, Jalaj; Prakash, Ram; Vyas, Gheesa Lal; Pal, Udit Narayan; Chowdhuri, Malay Bikas; Manchanda, Ranjana; Halder, Nilanjan; Choyal, Yaduvendra

    2015-12-01

    In the present work an effort has been made to estimate the plasma parameters simultaneously like—electron density, electron temperature, ground state atom density, ground state ion density and metastable state density from the observed visible spectra of penning plasma discharge (PPD) source using least square fitting. The analysis is performed for the prominently observed neutral helium lines. The atomic data and analysis structure (ADAS) database is used to provide the required collisional-radiative (CR) photon emissivity coefficients (PECs) values under the optical thin plasma condition in the analysis. With this condition the estimated plasma temperature from the PPD is found rather high. It is seen that the inclusion of opacity in the observed spectral lines through PECs and addition of diffusion of neutrals and metastable state species in the CR-model code analysis improves the electron temperature estimation in the simultaneous measurement.

  18. Mathematical modelling of the liquid atomization process by cocurrent gas flow

    NASA Astrophysics Data System (ADS)

    Arkhipov, V. A.; Boiko, V. M.; Goldin, V. D.; Maslov, E. A.; Orlov, S. E.; Poplavskiy, S. V.; Usanina, A. S.; Zharova, I. K.

    2016-04-01

    This paper focuses on the physical-mathematical model of liquid atomization in the spray pattern of an ejection nozzle. A flow field of a gas phase behind the nozzle section is computed using the Ansys Fluent package. Dynamics of molten metal droplets in the gas phase within a trajectory approach is calculated. Using the presented model, numerical calculation results are given.

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

    ERIC Educational Resources Information Center

    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)

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

    ERIC Educational Resources Information Center

    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.…