Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.
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.
Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model
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
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. Copyright © 2013 Elsevier Inc. All rights reserved.
Chapman, Michael S.; Trzynka, Andrew; Chapman, Brynmor K.
2013-01-01
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. PMID:23376441
HYDROGEN ATOM THERMAL PARAMETERS.
JENSEN, L H; SUNDARALINGAM, M
1964-09-11
Isotropic hydrogen atom thermal parameters for N,N'- hexamethylenebispropionamide have been determined. They show a definite trend and vary from approximately the same as the mean thermal parameters for atoms other than hydrogen near the center of the molecule to appreciably greater for atoms near the end. The indicated trend for this compound, along with other results, provides the basis for a possible explanation of the anomolous values that have been obtained for hydrogen atom thermal parameters.
Nuclear magnetic resonance parameters of atomic xenon dissolved in Gay-Berne model liquid crystal.
Lintuvuori, Juho; Straka, Michal; Vaara, Juha
2007-03-01
We present constant-pressure Monte Carlo simulations of nuclear magnetic resonance (NMR) spectral parameters, nuclear magnetic shielding relative to the free atom as well as nuclear quadrupole coupling, for atomic xenon dissolved in a model thermotropic liquid crystal. The solvent is described by Gay-Berne (GB) molecules with parametrization kappa=4.4, kappa{'}=20.0 , and mu=nu=1 . The reduced pressure of P{*}=2.0 is used. Previous simulations of a pure GB system with this parametrization have shown that upon lowering the temperature, the model exhibits isotropic, nematic, smectic- A , and smectic- B /molecular crystal phases. We introduce spherical xenon solutes and adjust the energy and length scales of the GB-Xe interaction to those of the GB-GB interaction. This is done through first principles quantum chemical calculations carried out for a dimer of model mesogens as well as the mesogen-xenon complex. We preparametrize quantum chemically the Xe nuclear shielding and quadrupole coupling tensors when interacting with the model mesogen, and use the parametrization in a pairwise additive fashion in the analysis of the simulation. We present the temperature evolution of {129/131}Xe shielding and 131Xe quadrupole coupling in the different phases of the GB model. From the simulations, separate isotropic and anisotropic contributions to the experimentally available total shielding can be obtained. At the experimentally relevant concentration, the presence of the xenon atoms does not significantly affect the phase behavior as compared to the pure GB model. The simulations reproduce many of the characteristic experimental features of Xe NMR in real thermotropic LCs: Discontinuity in the value or trends of the shielding and quadrupole coupling at the nematic-isotropic and smectic-A-nematic phase transitions, nonlinear shift evolution in the nematic phase reflecting the behavior of the orientational order parameter, and decreasing shift in the smectic-A phase. The last
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.
Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water.
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.
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…
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…
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.
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.
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.
Stationary Electron Atomic Model
NASA Astrophysics Data System (ADS)
Pressler, David E.
1998-04-01
I will present a novel theory concerning the position and nature of the electron inside the atom. This new concept is consistant with present experimental evidence and adheres strictly to the valence-shell electron-pair repulsion (VSEPR) model presently used in chemistry for predicting the shapes of molecules and ions. In addition, I will discuss the atomic model concept as being a true harmonic oscillator, periodic motion at resonant frequency which produces radiation at discrete frequencies or line spectra is possible because the electron is under the action of two restoring forces, electrostatic attraction and superconducting respulsion of the electron's magnetic field by the nucleus.
A model for airblast atomization
Rizk, N.K.; Mongia, H.C.
1989-01-01
The objective of fuel injection modeling activities is generally to give support to the atomizer design effort to achieve improved spray quality. in gas turbine combustors, enhanced atomization is essential for satisfactory performance, since droplet sizes can have direct impact on almost all key aspects of combustion. A model that includes the integration of the submodels of air flow, fuel injection and atomization, and droplets turbulent dispersion has been formulated. The model was applied to an airblast atomizer that incorporated a short prefilming device. The predictions were validated against two-component phase Doppler interferometry data of that atomizer. The results of the present investigation demonstrate the capability of the developed model to predict satisfactorily the air flow field and spray characteristics. They indicate the need for detailed measurements in the near field of atomizer in order to quantitatively verify the modeling of the initial atomization processes in this region. 15 refs.
Atom Interferometer Modeling Tool
2011-08-08
definition is to import conductor geometry from an outside CAD tool such as AutoCAD . This allows users to specify the more complex layouts using a...fully-featured tool of their choice, while significantly reducing the complexity of LiveAtom. Furthermore, most groups have already been using a 2D ...specifying conductor geometry LiveAtom offers the user a 3D visualization of their experiment. Once the experiment is fully specified, computing the
NASA Technical Reports Server (NTRS)
Landman, D. A.
1986-01-01
The effects on calculated lower-level population densities of the truncation of Na and Sr(+) model atoms are determined in the context of the present spectral diagnostic scheme for solar prominences and spicules. It is shown that neglect of the upper atomic levels in Na, in particular, leads to overestimates in electron density and gas pressure by factors of about 2 and about 4, respectively, and to underestimates in the degree of hydrogen ionization and in the line-of-sight thickness of emitting material again by factors of about 2 and about 4, respectively. The implications of the revised emitting region extents, in particular, on the validity of the diagnostic method for these features are discussed.
Quantitative surface parameter maps using Intermodulation Atomic Force Microscopy
NASA Astrophysics Data System (ADS)
Forchheimer, Daniel; Platz, Daniel; Tholén, Erik; Hutter, Carsten; Haviland, David
2011-03-01
It is well known that the phase image in amplitude modulation atomic force microscopy (AM-AFM) is sensitive to material properties of the surface. However that information is not enough to fully quantify the tip-surface interaction. We have developed Intermodulation AFM, based on a spectral analysis of the cantilever's nonlinear dynamics, which increases the amount of information obtained without increasing scan time. We show how it is possible to extract quantitative material properties of the surface from this additional information. The method works under the assumption of a tip-surface force model, such as the DMT model, fitting the model parameters to the measured spectral data. The parameters are obtained at each pixel of the AFM image and form surface property maps which can be displayed together with topography. We demonstrate this on different surfaces such as polymer blends, extracting stiffness and adhesive properties. D. Platz, E. A. Tholen, D. Pesen, and D. B. Haviland, Appl. Phys. Lett., 92, 153106 (2008)
Recent advances in atomic modeling
Goldstein, W.H.
1988-10-12
Precision spectroscopy of solar plasmas has historically been the goad for advances in calculating the atomic physics and dynamics of highly ionized atoms. Recent efforts to understand the laboratory plasmas associated with magnetic and inertial confinement fusion, and with X-ray laser research, have played a similar role. Developments spurred by laboratory plasma research are applicable to the modeling of high-resolution spectra from both solar and cosmic X-ray sources, such as the photoionized plasmas associated with accretion disks. Three of these developments in large scale atomic modeling are reviewed: a new method for calculating large arrays of collisional excitation rates, a sum rule based method for extending collisional-radiative models and modeling the effects of autoionizing resonances, and a detailed level accounting calculation of resonant excitation rates in FeXVII. 21 refs., 5 figs., 2 tabs.
Four-Parameter Scheme for Ground Level of Helium Atom
NASA Astrophysics Data System (ADS)
Hu, Xian-Quan; Xu, Jie; Ma, Yong; Zheng, Rui-Lun
2006-05-01
In this paper, the ground state wave function of four parameters is developed and the expression of the ground state level is derived for the helium atom when the radial Schrödinger equation of the helium atom is solved. The ground energy is respectively computed by the optimized algorithms of Matlab 7.0 and the Monte Carlo methods. Furthermore, the ground state wave function is obtained. Compared with the experiment value and the value with the variation calculus in reference, the results of this paper show that in the four-parameter scheme, not only the calculations become more simplified and precise, but also the radial wave function of the helium atom meets the space symmetry automatically in ground state.
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)
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)
"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)
"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)
Semi-empirical determination of radiative parameters for atomic nickel
NASA Astrophysics Data System (ADS)
Ruczkowski, J.; Elantkowska, M.; Dembczyński, J.
2017-01-01
The aim of this article is to determine the values of the radiative parameters for atomic nickel by means of a semi-empirical method. The calculated values of oscillator strengths and lifetimes are, in the majority of cases, in good agreement with experimental data. Our calculation procedures allowed us to obtain the values of transition integrals and predict the values of oscillator strengths for transitions over a wide spectral range and radiative lifetimes for excited levels. Furthermore, the predicted values will be useful when the experimental values are not known.
Can atom-surface potential measurements test atomic structure models?
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.
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.
Parameter extraction and transistor models
NASA Technical Reports Server (NTRS)
Rykken, Charles; Meiser, Verena; Turner, Greg; Wang, QI
1985-01-01
Using specified mathematical models of the MOSFET device, the optimal values of the model-dependent parameters were extracted from data provided by the Jet Propulsion Laboratory (JPL). Three MOSFET models, all one-dimensional were used. One of the models took into account diffusion (as well as convection) currents. The sensitivity of the models was assessed for variations of the parameters from their optimal values. Lines of future inquiry are suggested on the basis of the behavior of the devices, of the limitations of the proposed models, and of the complexity of the required numerical investigations.
Photovoltaic module parameters acquisition model
NASA Astrophysics Data System (ADS)
Cibira, Gabriel; Koščová, Marcela
2014-09-01
This paper presents basic procedures for photovoltaic (PV) module parameters acquisition using MATLAB and Simulink modelling. In first step, MATLAB and Simulink theoretical model are set to calculate I-V and P-V characteristics for PV module based on equivalent electrical circuit. Then, limited I-V data string is obtained from examined PV module using standard measurement equipment at standard irradiation and temperature conditions and stated into MATLAB data matrix as a reference model. Next, the theoretical model is optimized to keep-up with the reference model and to learn its basic parameters relations, over sparse data matrix. Finally, PV module parameters are deliverable for acquisition at different realistic irradiation, temperature conditions as well as series resistance. Besides of output power characteristics and efficiency calculation for PV module or system, proposed model validates computing statistical deviation compared to reference model.
Ranjan, Alok Wang, Mingmei; Sherpa, Sonam D.; Rastogi, Vinayak; Koshiishi, Akira; Ventzek, Peter L. G.
2016-05-15
Atomic or layer by layer etching of silicon exploits temporally segregated self-limiting adsorption and material removal steps to mitigate the problems associated with continuous or quasicontinuous (pulsed) plasma processes: selectivity loss, damage, and profile control. Successful implementation of atomic layer etching requires careful choice of the plasma parameters for adsorption and desorption steps. This paper illustrates how process parameters can be arrived at through basic scaling exercises, modeling and simulation, and fundamental experimental tests of their predictions. Using chlorine and argon plasma in a radial line slot antenna plasma source as a platform, the authors illustrate how cycle time, ion energy, and radical to ion ratio can be manipulated to manage the deviation from ideality when cycle times are shortened or purges are incomplete. Cell based Monte Carlo feature scale modeling is used to illustrate profile outcomes. Experimental results of atomic layer etching processes are illustrated on silicon line and space structures such that iso-dense bias and aspect ratio dependent free profiles are produced. Experimental results also illustrate the profile control margin as processes move from atomic layer to multilayer by layer etching. The consequence of not controlling contamination (e.g., oxygen) is shown to result in deposition and roughness generation.
Algebraic direct methods for few-atoms structure models.
Hauptman, Herbert A; Guo, D Y; Xu, Hongliang; Blessing, Robert H
2002-07-01
As a basis for direct-methods phasing at very low resolution for macromolecular crystal structures, normalized structure-factor algebra is presented for few-atoms structure models with N = 1, 2, 3, em leader equal atoms or polyatomic globs per unit cell. Main results include: [see text]. Triplet discriminant Delta(hk) and triplet weight W(hk) parameters, a approximately 4.0 and b approximately 3.0, respectively, were determined empirically in numerical error analyses. Tests with phases calculated for few-atoms 'super-glob' models of the protein apo-D-glyceraldehyde-3-phosphate dehydrogenase (approximately 10000 non-H atoms) showed that low-resolution phases from the new few-atoms tangent formula were much better than conventional tangent formula phases for N = 2 and 3; phases from the two formulae were essentially the same for N > or = 4.
Nagaoka's atomic model and hyperfine interactions.
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.
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.
Atomic scale modeling of boron transient diffusion in silicon
Caturla, M. J.; Diaz de la Rubia, T.; Foad, M.; Giles, M.; Johnson, M. D.; Law, M.; Lilak, A.
1998-06-17
We presents results from a predictive atomic level simulation of Boron diffusion in Silicon under a wide variety of implant and annealing conditions. The parameters for this simulation have been extracted from first principle approximation models and molecular dynamics simulations. The results are compared with experiments showing good agreement in all cases. The parameters and reactions used have been implemented into a continuum-level model simulator.
Calibrating binary lumped parameter models
NASA Astrophysics Data System (ADS)
Morgenstern, Uwe; Stewart, Mike
2017-04-01
Groundwater at its discharge point is a mixture of water from short and long flowlines, and therefore has a distribution of ages rather than a single age. Various transfer functions describe the distribution of ages within the water sample. Lumped parameter models (LPMs), which are mathematical models of water transport based on simplified aquifer geometry and flow configuration can account for such mixing of groundwater of different age, usually representing the age distribution with two parameters, the mean residence time, and the mixing parameter. Simple lumped parameter models can often match well the measured time varying age tracer concentrations, and therefore are a good representation of the groundwater mixing at these sites. Usually a few tracer data (time series and/or multi-tracer) can constrain both parameters. With the building of larger data sets of age tracer data throughout New Zealand, including tritium, SF6, CFCs, and recently Halon-1301, and time series of these tracers, we realised that for a number of wells the groundwater ages using a simple lumped parameter model were inconsistent between the different tracer methods. Contamination or degradation of individual tracers is unlikely because the different tracers show consistent trends over years and decades. This points toward a more complex mixing of groundwaters with different ages for such wells than represented by the simple lumped parameter models. Binary (or compound) mixing models are able to represent a more complex mixing, with mixing of water of two different age distributions. The problem related to these models is that they usually have 5 parameters which makes them data-hungry and therefore difficult to constrain all parameters. Two or more age tracers with different input functions, with multiple measurements over time, can provide the required information to constrain the parameters of the binary mixing model. We obtained excellent results using tritium time series encompassing
Using symbolic computing in building probabilistic models for atoms
NASA Astrophysics Data System (ADS)
Guiasu, Silviu
This article shows how symbolic computing and the mathematical formalism induced by maximizing entropy and minimizing the mean deviation from statistical equilibrium may be effectively applied to obtaining probabilistic models for the structure of atoms, using trial wave functions compatible with an average shell picture of the atom. The objective is not only to recover the experimental value of the ground state mean energy of the atom, but rather to better approximate the unknown parameters of these trial functions and to calculate both correlations between electrons and the amount of interdependence among different subsets of electrons of the atoms. The examples and numerical results refer to the hydrogen, helium, lithium, and beryllium atoms. The main computer programs, using the symbolic computing software MATHEMATICA, are also given.
Simulation-based Extraction of Key Material Parameters from Atomic Force Microscopy
NASA Astrophysics Data System (ADS)
Alsafi, Huseen; Peninngton, Gray
Models for the atomic force microscopy (AFM) tip and sample interaction contain numerous material parameters that are often poorly known. This is especially true when dealing with novel material systems or when imaging samples that are exposed to complicated interactions with the local environment. In this work we use Monte Carlo methods to extract sample material parameters from the experimental AFM analysis of a test sample. The parameterized theoretical model that we use is based on the Virtual Environment for Dynamic AFM (VEDA) [1]. The extracted material parameters are then compared with the accepted values for our test sample. Using this procedure, we suggest a method that can be used to successfully determine unknown material properties in novel and complicated material systems. We acknowledge Fisher Endowment Grant support from the Jess and Mildred Fisher College of Science and Mathematics,Towson University.
Atempts to link Quanta & Atoms before the Bohr Atom model
NASA Astrophysics Data System (ADS)
Venkatesan, A.; Lieber, M.
2005-03-01
Attempts to quantize atomic phenomena before Bohr are hardly ever mentioned in elementary textbooks.This presentation will elucidate the contributions of A.Haas around 1910. Haas tried to quantize the Thomson atom model as an optical resonator made of positive and negative charges. The inherent ambiguity of charge distribution in the model made him choose a positive spherical distribution around which the electrons were distributed.He obtained expressions for the Rydberg constant and what is known today as the Bohr radius by balancing centrifugal energy with Coulomb energy and quantizing it with Planck's relation E=hν. We point out that Haas would have arrived at better estimates of these constants had he used the virial theorem apart from the fact that the fundamental constants were not well known. The crux of Haas's physical picture was to derive Planck's constant h from charge quantum e , mass of electron m and atomic radius. Haas faced severe criticism for applying thermodynamic concepts like Planck distribution to microscopic phenomena. We will try to give a flavor for how quantum phenomena were viewed at that time. It is of interest to note that the driving force behind Haas's work was to present a paper that would secure him a position as a Privatdozent in History of Physics. We end with comments by Bohr and Sommerfeld on Haas's work and with some brief biographical remarks.
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.
Identification of driver model parameters.
Reński, A
2001-01-01
The paper presents a driver model, which can be used in a computer simulation of a curved ride of a car. The identification of the driver parameters consisted in a comparison of the results of computer calculations obtained for the driver-vehicle-environment model with different driver data sets with test results of the double lane-change manoeuvre (Standard No. ISO/TR 3888:1975, International Organization for Standardization [ISO], 1975) and the wind gust manoeuvre. The optimisation method allows to choose for each real driver a set of driver model parameters for which the differences between test and calculation results are smallest. The presented driver model can be used in investigating the driver-vehicle control system, which allows to adapt the car construction to the psychophysical characteristics of a driver.
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
Modeling of atomic systems for atomic clocks and quantum information
NASA Astrophysics Data System (ADS)
Arora, Bindiya
This dissertation reports the modeling of atomic systems for atomic clocks and quantum information. This work is motivated by the prospects of optical frequency standards with trapped ions and the quantum computation proposals with neutral atoms in optical lattices. Extensive calculations of the electric-dipole matrix elements in monovalent atoms are conducted using the relativistic all-order method. This approach is a linearized version of the coupled-cluster method, which sums infinite sets of many-body perturbation theory terms. All allowed transitions between the lowest ns, np1/2, np 3/2 states and a large number of excited states of alkali-metal atoms are evaluated using the all-order method. For Ca+ ion, additional allowed transitions between nd5/2, np 3/2, nf5/2, nf 7/2 states and a large number of excited states are evaluated. We combine D1 lines measurements by Miller et al. [18] with our all-order calculations to determine the values of the electric-dipole matrix elements for the 4pj - 3d j' transitions in K and for the 5pj - 4dj' transitions in Rb to high precision. The resulting electric-dipole matrix elements are used for the high-precision calculation of frequency-dependent polarizabilities of ground state of alkali atoms. Our values of static polarizabilities are found to be in excellent agreement with available experiments. Calculations were done for the wavelength in the range 300--1600 nm, with particular attention to wavelengths of common infrared lasers. We parameterize our results so that they can be extended accurately to arbitrary wavelengths above 800 nm. Our data can be used to predict the oscillation frequencies of optically-trapped atoms, and particularly the ratios of frequencies of different species held in the same trap. We identify wavelengths at which two different alkali atoms have the same oscillation frequency. We present results of all-order calculations of static and frequency-dependent polarizabilities of excited np1/2 and np3
Detecting Clusters in Atom Probe Data with Gaussian Mixture Models.
Zelenty, Jennifer; Dahl, Andrew; Hyde, Jonathan; Smith, George D W; Moody, Michael P
2017-04-01
Accurately identifying and extracting clusters from atom probe tomography (APT) reconstructions is extremely challenging, yet critical to many applications. Currently, the most prevalent approach to detect clusters is the maximum separation method, a heuristic that relies heavily upon parameters manually chosen by the user. In this work, a new clustering algorithm, Gaussian mixture model Expectation Maximization Algorithm (GEMA), was developed. GEMA utilizes a Gaussian mixture model to probabilistically distinguish clusters from random fluctuations in the matrix. This machine learning approach maximizes the data likelihood via expectation maximization: given atomic positions, the algorithm learns the position, size, and width of each cluster. A key advantage of GEMA is that atoms are probabilistically assigned to clusters, thus reflecting scientifically meaningful uncertainty regarding atoms located near precipitate/matrix interfaces. GEMA outperforms the maximum separation method in cluster detection accuracy when applied to several realistically simulated data sets. Lastly, GEMA was successfully applied to real APT data.
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.
Quantum entanglement in two-electron atomic models
NASA Astrophysics Data System (ADS)
Manzano, D.; Plastino, A. R.; Dehesa, J. S.; Koga, T.
2010-07-01
We explore the main entanglement properties exhibited by the eigenfunctions of two exactly soluble two-electron models, the Crandall atom and the Hooke atom, and compare them with the entanglement features of helium-like systems. We compute the amount of entanglement associated with the wavefunctions corresponding to the fundamental and first few excited states of these models. We investigate the dependence of the entanglement on the parameters of the models and on the quantum numbers of the eigenstates. It is found that the amount of entanglement of the system tends to increase with energy in both models. In addition, we study the entanglement of a few states of helium-like systems, which we compute using high-quality Kinoshita-like eigenfunctions. The dependence of the entanglement of helium-like atoms on the nuclear charge and on energy is found to be consistent with the trends observed in the previous two model systems.
Modeling Atom Probe Tomography: A review.
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.
Simple empirical order parameter for a first-order quantum phase transition in atomic nuclei.
Bonatsos, Dennis; McCutchan, E A; Casten, R F; Casperson, R J
2008-04-11
A simple, empirical, easy-to-measure effective order parameter of a first-order phase transition in atomic nuclei is presented, namely, the ratio of the energies of the first excited 6+ and 0+ states, distinguishing between first- and second-order transitions, and taking on a special value in the critical region, as data in Nd-Dy show. In the large NB limit of the interacting boson approximation model, a repeating degeneracy between alternate yrast and successive 0+ states is found in the critical region around the line of a first-order phase transition, pointing to a possible underlying symmetry.
Atomization data for spray combustion modeling
NASA Technical Reports Server (NTRS)
Ferrenberg, A. J.; Varma, M. S.
1985-01-01
Computer models that simulate the energy release processes in spray combustion are highly dependent upon the quality of atomization data utilized. This paper presents results of analyses performed with a state-of-the-art rocket combustion code, demonstrating the important effects of initial droplet sizes and size distributions on combustion losses. Also, the questionable aspects and inapplicability of the generally available atomization data are discussed. One important and misunderstood aspect of the atomization process is the difference between spatial (concentration) and flux (temporal) droplet size distributions. These are addressed, and a computer model developed to assess this difference is described and results presented. Finally, experimental results are shown that demonstrate the often neglected effects of the local gas velocity field on the atomization process.
Atomization data for spray combustion modeling
NASA Technical Reports Server (NTRS)
Ferrenberg, A. J.; Varma, M. S.
1985-01-01
Computer models that simulate the energy release processes in spray combustion are highly dependent upon the quality of atomization data utilized. This paper presents results of analyses performed with a state-of-the-art rocket combustion code, demonstrating the important effects of initial droplet sizes and size distributions on combustion losses. Also, the questionable aspects and inapplicability of the generally available atomization data are discussed. One important and misunderstood aspect of the atomization process is the difference between spatial (concentration) and flux (temporal) droplet size distributions. These are addressed, and a computer model developed to assess this difference is described and results presented. Finally, experimental results are shown that demonstrate the often neglected effects of the local gas velocity field on the atomization process.
Monte Carlo Computational Modeling of Atomic Oxygen Interactions
NASA Technical Reports Server (NTRS)
Banks, Bruce A.; Stueber, Thomas J.; Miller, Sharon K.; De Groh, Kim K.
2017-01-01
which has the capability to tune the interactions of how the atomic oxygen reacts, scatters, or recombines on polymer or nonreactive surfaces. In addition to the specification of atomic oxygen arrival details, a total of 15 atomic oxygen interaction parameters have been identified as necessary to properly simulate observed interactions and resulting polymer erosion that have been observed in LEO. The tuning of the Monte Carlo model has been accomplished by adjusting interaction parameters so the erosion patterns produced by the model match those from several actual LEO space experiments. Surface texturing in LEO can also be predicted by the model. Such comparison of space tests with ground laboratory experiments have enabled confidence in ground laboratory lifetime prediction of protected polymers. Results of Monte Carlo tuning, examples of surface texturing and undercutting erosion prediction, and several examples of how the model can be used to predict other LEO and Mars orbital space results are presented.
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.
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.
Hirshfeld atom refinement for modelling strong hydrogen bonds.
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.
Atomization data requirements for rocket combustor modeling
NASA Technical Reports Server (NTRS)
Ferrenberg, A. J.; Varma, M. S.
1984-01-01
The complex computer codes, which model liquid rocket combustors, require information about the distribution and atomization of these liquid reactants. The available information is, in general, of questionable validity and applicability. Authors and users of combustion codes are often unaware of, or underestimate the importance of, these deficiencies in atomization data. These deficiencies and their importance are examined. Results of analyses performed with a state-of-the-art rocket combustion code are presented which demonstrate the important effects of such atomization information as initial droplet sizes and size distribution on vaporization rate and losses. Also, the questionable aspects and inapplicability of the available atomization data are discussed. One important and often neglected or misunderstood aspect of atomization data is the differences between spatial (concentration) and flux (often called temporal) droplet size distributions. These are described, and a computer model constructed to assess the difference between concentration and flux droplet size distributions is described and results presented. Experimental data are also given to demonstrate this difference. Finally, experimental results are presented that demonstrate the very great, and often neglected effect, of the local gas velocity field on atomization.
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…
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…
Balloon Thermal Model Design Parameters and Sensitivities
NASA Technical Reports Server (NTRS)
Ferguson, Douglas
2017-01-01
This presentation describes the thought process for determining balloon thermal model design parameters, including environmental parameters taken form NASA's top-of-atmosphere (TOA) database, and shows the sensitivity of an example model's key temperature results to those input parameters.
Jakobsen, Sofie; Jensen, Frank
2014-12-09
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.
Phenomenological model of spin crossover in molecular crystals as derived from atom-atom potentials.
Sinitskiy, Anton V; Tchougréeff, Andrei L; Dronskowski, Richard
2011-08-07
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.
Murzyn, Krzysztof; Bratek, Maciej; Pasenkiewicz-Gierula, Marta
2013-12-27
OPLS All-Atom (OPLS/AA) is a generic all-atom force field which was fine-tuned to accurately reproduce condensed phase properties of organic liquids. Its application in modeling of lipid membranes is, however, limited mainly due to the inability to correctly describe phase behavior and organization of the hydrophobic core of the model lipid bilayers. Here we report new OPLS/AA parameters for n-pentadecane, methyl acetate, and dimethyl phosphate anion. For the new force field parameters, we show very good agreement between calculated and numerous reference data, including liquid density, enthalpy of vaporization, free energy of hydration, and selected transport properties. The new OPLS/AA parameters have been used in successful submicrosecond MD simulations of bilayers made of bacterial glycolipids whose results will be published elsewhere shortly.
Application of the model of delocalized atoms to metallic glasses
NASA Astrophysics Data System (ADS)
Sanditov, D. S.; Darmaev, M. V.; Sanditov, B. D.
2017-01-01
The parameters of the model of delocalized atoms applied to metallic glasses have been calculated using the data on empirical constants of the Vogel-Fulcher-Tammann equation (for the temperature dependence of viscosity). It has been shown that these materials obey the same glass-formation criterion as amorphous organic polymers and inorganic glasses. This fact qualitatively confirms the universality of the main regularities of the liquid-glass transition process for all amorphous materials regardless of their origin. The energy of the delocalization of an atom in metallic glasses, Δɛ e ≈ 20-25 kJ/mol, coincides with the results obtained for oxide inorganic glasses. It is substantially lower than the activation energies for a viscous flow and for ion diffusion. The delocalization of an atom (its displacement from the equilibrium position) for amorphous metallic alloys is a low-energy small-scale process similar to that for other glass-like systems.
Relativistic calculations of screening parameters and atomic radii of neutral atoms
NASA Astrophysics Data System (ADS)
Guerra, M.; Amaro, P.; Santos, J. P.; Indelicato, P.
2017-09-01
Calculations of the effective nuclear charge for elements with 1 ≤ Z ≤ 118 have been performed in a Dirac-Fock approach including all relativistic effects as well as contributions from quantum electrodynamics. Maximum charge density for every subshell of every element in the periodic table was also computed in the same framework as well as atomic radii based on the total charge density. Results were compared with the extensively cited works of Clementi et al., obtained in the 1960s with Roothan's self-consistent-field method.
CHARMM36 united atom chain model for lipids and surfactants.
Lee, Sarah; Tran, Alan; Allsopp, Matthew; Lim, Joseph B; Hénin, Jérôme; Klauda, Jeffery B
2014-01-16
Molecular simulations of lipids and surfactants require accurate parameters to reproduce and predict experimental properties. Previously, a united atom (UA) chain model was developed for the CHARMM27/27r lipids (Hénin, J., et al. J. Phys. Chem. B. 2008, 112, 7008-7015) but suffers from the flaw that bilayer simulations using the model require an imposed surface area ensemble, which limits its use to pure bilayer systems. A UA-chain model has been developed based on the CHARMM36 (C36) all-atom lipid parameters, termed C36-UA, and agreed well with bulk, lipid membrane, and micelle formation of a surfactant. Molecular dynamics (MD) simulations of alkanes (heptane and pentadecane) were used to test the validity of C36-UA on density, heat of vaporization, and liquid self-diffusion constants. Then, simulations using C36-UA resulted in accurate properties (surface area per lipid, X-ray and neutron form factors, and chain order parameters) of various saturated- and unsaturated-chain bilayers. When mixed with the all-atom cholesterol model and tested with a series of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC)/cholesterol mixtures, the C36-UA model performed well. Simulations of self-assembly of a surfactant (dodecylphosphocholine, DPC) using C36-UA suggest an aggregation number of 53 ± 11 DPC molecules at 0.45 M of DPC, which agrees well with experimental estimates. Therefore, the C36-UA force field offers a useful alternative to the all-atom C36 lipid force field by requiring less computational cost while still maintaining the same level of accuracy, which may prove useful for large systems with proteins.
A computer model for liquid jet atomization in rocket thrust chambers
NASA Astrophysics Data System (ADS)
Giridharan, M. G.; Lee, J. G.; Krishnan, A.; Yang, H. Q.; Ibrahim, E.; Chuech, S.; Przekwas, A. J.
1991-12-01
The process of atomization has been used as an efficient means of burning liquid fuels in rocket engines, gas turbine engines, internal combustion engines, and industrial furnaces. Despite its widespread application, this complex hydrodynamic phenomenon has not been well understood, and predictive models for this process are still in their infancy. The difficulty in simulating the atomization process arises from the relatively large number of parameters that influence it, including the details of the injector geometry, liquid and gas turbulence, and the operating conditions. In this study, numerical models are developed from first principles, to quantify factors influencing atomization. For example, the surface wave dynamics theory is used for modeling the primary atomization and the droplet energy conservation principle is applied for modeling the secondary atomization. The use of empirical correlations has been minimized by shifting the analyses to fundamental levels. During applications of these models, parametric studies are performed to understand and correlate the influence of relevant parameters on the atomization process. The predictions of these models are compared with existing experimental data. The main tasks of this study were the following: development of a primary atomization model; development of a secondary atomization model; development of a model for impinging jets; development of a model for swirling jets; and coupling of the primary atomization model with a CFD code.
NASA Astrophysics Data System (ADS)
Deal, M.; Escobar, M. E.; Vauclair, S.; Vauclair, G.; Hui-Bon-Hoa, A.; Richard, O.
2017-05-01
Context. A precision of the order of one percent is needed on the parameters of exoplanet-hosts stars to correctly characterise the planets themselves. This can be achieved by asteroseismology. It is important in this context to test the influence of introducing atomic diffusion with radiative accelerations in the models upon the derived parameters. In this paper, we begin this study with the case of the star 94 Ceti A. Aims: We aim to perform a complete asteroseismic analysis of the exoplanet-host F-type star 94 Ceti A, from the first radial-velocity observations with the High Accuracy Radial velocity Planet Searcher (HARPS) up to the final computed best models. We also aim to test the influence of atomic diffusion, including radiative accelerations, upon the computed frequencies and on the determined stellar parameters. 94 Ceti A is hot enough to suffer these effects. We also aim to test the effect of including a complete atmosphere in the stellar models. Methods: The radial velocity observations were performed with HARPS in 2007. The low degree modes were derived and identified using classical methods and compared with the results obtained from stellar models computed with the Toulouse Geneva Evolution Code (TGEC). Results: We obtained precise parameters for the star 94 Ceti A. We showed that including atomic diffusion with radiative accelerations can modify the age by a few percent, whereas adding a complete atmosphere does not change the results by more than one percent. Conclusions: Atomic diffusion including radiative accelerations should be taken into account in all the computations of stellar models with masses larger than 1.3 M⊙ in order to determine accurate parameters for observed stars.
Quantum model of the Thomson helium atom
NASA Astrophysics Data System (ADS)
Kazaryan, E. M.; Shakhnazaryan, V. A.; Sarkisyan, H. A.; Gusev, A. A.
2014-03-01
A quantum model of the Thomson helium atom is considered within the framework of stationary perturbation theory. It is shown that from a formal point of view this problem is similar to that of two-electron states in a parabolic quantum dot. The ground state energy of the quantum Thomson helium atom is estimated on the basis of Heisenberg's uncertainty principle. The ground state energies obtained in the first order of perturbation theory and qualitative estimate provide, respectively, upper and lower estimates of eigenvalues derived by numerically solving the problem for a quantum model. The conditions under which the Kohn theorem holds in this system, when the values of resonance absorption frequencies are independent of the Coulomb interaction between electrons, are discussed.
Vanommeslaeghe, K; Raman, E Prabhu; MacKerell, A D
2012-12-21
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.
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
Parameter estimation for distributed parameter models of complex, flexible structures
NASA Technical Reports Server (NTRS)
Taylor, Lawrence W., Jr.
1991-01-01
Distributed parameter modeling of structural dynamics has been limited to simple spacecraft configurations because of the difficulty of handling several distributed parameter systems linked at their boundaries. Although there is other computer software able to generate such models or complex, flexible spacecraft, unfortunately, neither is suitable for parameter estimation. Because of this limitation the computer software PDEMOD is being developed for the express purposes of modeling, control system analysis, parameter estimation and structure optimization. PDEMOD is capable of modeling complex, flexible spacecraft which consist of a three-dimensional network of flexible beams and rigid bodies. Each beam has bending (Bernoulli-Euler or Timoshenko) in two directions, torsion, and elongation degrees of freedom. The rigid bodies can be attached to the beam ends at any angle or body location. PDEMOD is also capable of performing parameter estimation based on matching experimental modal frequencies and static deflection test data. The underlying formulation and the results of using this approach for test data of the Mini-MAST truss will be discussed. The resulting accuracy of the parameter estimates when using such limited data can impact significantly the instrumentation requirements for on-orbit tests.
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.
A Green's function quantum average atom model
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.
Optimal Linking Design for Response Model Parameters
ERIC Educational Resources Information Center
Barrett, Michelle D.; van der Linden, Wim J.
2017-01-01
Linking functions adjust for differences between identifiability restrictions used in different instances of the estimation of item response model parameters. These adjustments are necessary when results from those instances are to be compared. As linking functions are derived from estimated item response model parameters, parameter estimation…
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).
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).
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…
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…
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.
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.
Low Resolution Refinement of Atomic Models Against Crystallographic Data.
Nicholls, Robert A; Kovalevskiy, Oleg; Murshudov, Garib N
2017-01-01
This review describes some of the problems encountered during low-resolution refinement and map calculation. Refinement is considered as an application of Bayes' theorem, allowing combination of information from various sources including crystallographic experimental data and prior chemical and structural knowledge. The sources of prior knowledge relevant to macromolecules include basic chemical information such as bonds and angles, structural information from reference models of known homologs, knowledge about secondary structures, hydrogen bonding patterns, and similarity of non-crystallographically related copies of a molecule. Additionally, prior information encapsulating local conformational conservation is exploited, keeping local interatomic distances similar to those in the starting atomic model. The importance of designing an accurate likelihood function-the only link between model parameters and observed data-is emphasized. The review also reemphasizes the importance of phases, and describes how the use of raw observed amplitudes could give a better correlation between the calculated and "true" maps. It is shown that very noisy or absent observations can be replaced by calculated structure factors, weighted according to the accuracy of the atomic model. This approach helps to smoothen the map. However, such replacement should be used sparingly, as the bias toward errors in the model could be too much to avoid. It is in general recommended that, whenever a new map is calculated, map quality should be judged by inspection of the parts of the map where there is no atomic model. It is also noted that it is advisable to work with multiple blurred and sharpened maps, as different parts of a crystal may exhibit different degrees of mobility. Doing so can allow accurate building of atomic models, accounting for overall shape as well as finer structural details. Some of the results described in this review have been implemented in the programs REFMAC5, Pro
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.
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.
Parameter Identifiability of Fundamental Pharmacodynamic Models
Janzén, David L. I.; Bergenholm, Linnéa; Jirstrand, Mats; Parkinson, Joanna; Yates, James; Evans, Neil D.; Chappell, Michael J.
2016-01-01
Issues of parameter identifiability of routinely used pharmacodynamics models are considered in this paper. The structural identifiability of 16 commonly applied pharmacodynamic model structures was analyzed analytically, using the input-output approach. Both fixed-effects versions (non-population, no between-subject variability) and mixed-effects versions (population, including between-subject variability) of each model structure were analyzed. All models were found to be structurally globally identifiable under conditions of fixing either one of two particular parameters. Furthermore, an example was constructed to illustrate the importance of sufficient data quality and show that structural identifiability is a prerequisite, but not a guarantee, for successful parameter estimation and practical parameter identifiability. This analysis was performed by generating artificial data of varying quality to a structurally identifiable model with known true parameter values, followed by re-estimation of the parameter values. In addition, to show the benefit of including structural identifiability as part of model development, a case study was performed applying an unidentifiable model to real experimental data. This case study shows how performing such an analysis prior to parameter estimation can improve the parameter estimation process and model performance. Finally, an unidentifiable model was fitted to simulated data using multiple initial parameter values, resulting in highly different estimated uncertainties. This example shows that although the standard errors of the parameter estimates often indicate a structural identifiability issue, reasonably “good” standard errors may sometimes mask unidentifiability issues. PMID:27994553
Parameter Estimation of Partial Differential Equation Models.
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.
Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N
2009-05-01
Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.
Whitford, Paul C.; Noel, Jeffrey K.; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y.; Onuchic, José N.
2012-01-01
Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Gō) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a Cα structure-based model and an all-atom empirical forcefield. Key findings include 1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature 2) folding mechanisms are robust to variations of the energetic parameters 3) protein folding free energy barriers can be manipulated through parametric modifications 4) the global folding mechanisms in a Cα model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model 5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Since this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035
Two-atom model in enhanced ion backscattering near 180/sup 0/ scattering angles
Oen, O.S.
1981-06-01
The recent discovery by Pronko, Appleton, Holland, and Wilson of an unusual enhancement of the yield of ions backscattered through angles close to 180/sup 0/ from the near surface regions of solids is investigated using a two-atom scattering model. The model predicts an enhancement effect in amorphous solids 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. Predictions are given of the dependence of the yield enhancement on the following parameters: ion energy, backscattering depth, exit angle, scattering potential, atomic numbers of projectile and target, and atomic density of target.
Quantum Rabi model for N-state atoms.
Albert, Victor V
2012-05-04
A tractable N-state Rabi Hamiltonian is introduced by extending the parity symmetry of the two-state model. The single-mode case provides a few-parameter description of a novel class of periodic systems, predicting that the ground state of certain four-state atom-cavity systems will undergo parity change at strong-coupling. A group-theoretical treatment provides physical insight into dynamics and a modified rotating wave approximation obtains accurate analytical energies. The dissipative case can be applied to study excitation energy transfer in molecular rings or chains.
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.
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…
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.
Screening parameters for the relativistic hydrogenic model
NASA Astrophysics Data System (ADS)
Lanzini, Fernando; Di Rocco, Héctor O.
2015-12-01
We present a Relativistic Screened Hydrogenic Model (RSHM) where the screening parameters depend on the variables (n , l , j) and the parameters (Z , N) . These screening parameters were derived theoretically in a neat form with no use of experimental values nor numerical values from self-consistent codes. The results of the model compare favorably with those obtained by using more sophisticated approaches. For the interested reader, a copy of our code can be requested from the corresponding author.
Atomic Models for Motional Stark Effects Diagnostics
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.
Quantum Rabi model in the Brillouin zone with ultracold atoms
NASA Astrophysics Data System (ADS)
Felicetti, Simone; Rico, Enrique; Sabin, Carlos; Ockenfels, Till; Koch, Johannes; Leder, Martin; Grossert, Christopher; Weitz, Martin; Solano, Enrique
2017-01-01
The quantum Rabi model describes the interaction between a two-level quantum system and a single bosonic mode. We propose a method to perform a quantum simulation of the quantum Rabi model, introducing an implementation of the two-level system provided by the occupation of Bloch bands in the first Brillouin zone by ultracold atoms in tailored optical lattices. The effective qubit interacts with a quantum harmonic oscillator implemented in an optical dipole trap. Our realistic proposal allows one to experimentally investigate the quantum Rabi model for extreme parameter regimes, which are not achievable with natural light-matter interactions. When the simulated wave function exceeds the validity region of the simulation, we identify a generalized version of the quantum Rabi model in a periodic phase space.
Atomic force microscopy of model lipid membranes.
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.
Parameter Space of Atomic Layer Deposition of Ultrathin Oxides on Graphene
2016-01-01
Atomic layer deposition (ALD) of ultrathin aluminum oxide (AlOx) films was systematically studied on supported chemical vapor deposition (CVD) graphene. We show that by extending the precursor residence time, using either a multiple-pulse sequence or a soaking period, ultrathin continuous AlOx films can be achieved directly on graphene using standard H2O and trimethylaluminum (TMA) precursors even at a high deposition temperature of 200 °C, without the use of surfactants or other additional graphene surface modifications. To obtain conformal nucleation, a precursor residence time of >2s is needed, which is not prohibitively long but sufficient to account for the slow adsorption kinetics of the graphene surface. In contrast, a shorter residence time results in heterogeneous nucleation that is preferential to defect/selective sites on the graphene. These findings demonstrate that careful control of the ALD parameter space is imperative in governing the nucleation behavior of AlOx on CVD graphene. We consider our results to have model system character for rational two-dimensional (2D)/non-2D material process integration, relevant also to the interfacing and device integration of the many other emerging 2D materials. PMID:27723305
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…
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.
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…
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…
Variable deceleration parameter and dark energy models
NASA Astrophysics Data System (ADS)
Bishi, Binaya K.
2016-03-01
This paper deals with the Bianchi type-III dark energy model and equation of state parameter in a first class of f(R,T) gravity. Here, R and T represents the Ricci scalar and trace of the energy momentum tensor, respectively. The exact solutions of the modified field equations are obtained by using (i) linear relation between expansion scalar and shear scalar, (ii) linear relation between state parameter and skewness parameter and (iii) variable deceleration parameter. To obtain the physically plausible cosmological models, the variable deceleration parameter with the suitable substitution leads to the scale factor of the form a(t) = [sinh(αt)] 1 n, where α and n > 0 are arbitrary constants. It is observed that our models are accelerating for 0 < n < 1 and for n > 1, transition phase from deceleration to acceleration. Further, we have discussed physical properties of the models.
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.
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.
Molecular-orbital model for slow hollow atoms colliding with atoms in a solid
Arnau, A.; Koehrbrueck, R.; Grether, M.; Spieler, A.; Stolterfoht, N.
1995-05-01
A model that has previously been used to calculate the molecular orbitals in atomic collisions between neutral atoms and ions is extended to describe hollow atoms colliding with a solid. The energy levels and screening functions are obtained from density-functional calculations. The results show that the inner-shell holes in the hollow projectile, as well as the screening cloud within the solid, create important effects that are essential for the description of the interaction of multicharged ions with solids.
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
Roy, Kunal; Ghosh, Gopinath
2008-11-01
In this communication, we have developed quantitative predictive models using human lethal concentration values of 26 organic compounds including some pharmaceuticals with extended topochemical atom (ETA) indices applying different chemometric tools and compared the extended topochemical atom models with the models developed from non-extended topochemical atom ones. Extended topochemical atom descriptors were also tried in combination with non-extended topochemical atom descriptors to develop better predictive models. The use of extended topochemical atom descriptors along with non-extended topochemical atom ones improved equation statistics and cross-validation quality. The best model with sound statistical quality was developed from partial least squares regression using extended topochemical atom descriptors in combination non-extended topochemical atom ones. Finally, to check true predictability of the ETA parameters, the data set was divided into training (n = 19) and test (n = 7) sets. Partial least squares and genetic partial least squares models were developed from the training set using extended topochemical atom indices and the models were validated using the test set. The extended topochemical atom models developed from different statistical tools suggest that the toxicity increases with bulk, chloro functionality, presence of electronegative atoms within a chain or ring and unsaturation, and decreases with hydroxy functionality and branching. The results suggest that the extended topochemical atom descriptors are sufficiently rich in chemical information to encode the structural features for QSAR/QSPR/QSTR modeling.
Acoustic omni meta-atom for decoupled access to all octants of a wave parameter space
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
Acoustic omni meta-atom for decoupled access to all octants of a wave parameter space.
Koo, Sukmo; Cho, Choonlae; Jeong, Jun-Ho; Park, Namkyoo
2016-09-30
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.
A Random Number Model for Beer's Law-Atom Shadowing
NASA Astrophysics Data System (ADS)
Daniels, R. Scott
1999-01-01
A random-number corpuscular-theory-of-light model for teaching Beer's law is presented. In this model, atoms are considered to have photon-capture cross-sectional areas and to exist in some finite volume. Where by chance one atom lies directly behind another, the first atom is said to cast a shadow on the second, thereby preventing the second atom from participating in the attenuation of radiation at that instant. This model not only produces the linear Beer's law relationship, but it also provides a simple and visual model from which the law can be demonstrated with the use of a computer-spreadsheet random number generator.
NASA Astrophysics Data System (ADS)
Lin, C. D.; Tunnell, L. N.
1980-07-01
Electron capture to the K shell of projectiles from the K and other subshells of multielectron target atoms is studied in the intermediate energy region using the single-active-electron approximation and the two-state, two-center atomic eigenfunction expansion method. It is concluded that the theoretical capture cross section is not sensitive to the atomic models used at high collision energies where the projectile velocity v is near or greater than the orbital velocity ve of the active electron. For v
Effect of energetic oxygen atoms on neutral density models.
NASA Technical Reports Server (NTRS)
Rohrbaugh, R. P.; Nisbet, J. S.
1973-01-01
The dissociative recombination of O2(+) and NO(+) in the F region results in the production of atomic oxygen and atomic nitrogen with substantially greater kinetic energy than the ambient atoms. In the exosphere these energetic atoms have long free paths. They can ascend to altitudes of several thousand kilometers and can travel horizontally to distances of the order of the earth's radius. The distribution of energetic oxygen atoms is derived by means of models of the ion and neutral densities for quiet and disturbed solar conditions. A distribution technique is used to study the motion of the atoms in the collision-dominated region. Ballistic trajectories are calculated in the spherical gravitational field of the earth. The present calculations show that the number densities of energetic oxygen atoms predominate over the ambient atomic oxygen densities above 1000 km under quiet solar conditions and above 1600 km under disturbed solar conditions.
On parameter estimation in population models.
Ross, J V; Taimre, T; Pollett, P K
2006-12-01
We describe methods for estimating the parameters of Markovian population processes in continuous time, thus increasing their utility in modelling real biological systems. A general approach, applicable to any finite-state continuous-time Markovian model, is presented, and this is specialised to a computationally more efficient method applicable to a class of models called density-dependent Markov population processes. We illustrate the versatility of both approaches by estimating the parameters of the stochastic SIS logistic model from simulated data. This model is also fitted to data from a population of Bay checkerspot butterfly (Euphydryas editha bayensis), allowing us to assess the viability of this population.
Exploiting intrinsic fluctuations to identify model parameters.
Zimmer, Christoph; Sahle, Sven; Pahle, Jürgen
2015-04-01
Parameterisation of kinetic models plays a central role in computational systems biology. Besides the lack of experimental data of high enough quality, some of the biggest challenges here are identification issues. Model parameters can be structurally non-identifiable because of functional relationships. Noise in measured data is usually considered to be a nuisance for parameter estimation. However, it turns out that intrinsic fluctuations in particle numbers can make parameters identifiable that were previously non-identifiable. The authors present a method to identify model parameters that are structurally non-identifiable in a deterministic framework. The method takes time course recordings of biochemical systems in steady state or transient state as input. Often a functional relationship between parameters presents itself by a one-dimensional manifold in parameter space containing parameter sets of optimal goodness. Although the system's behaviour cannot be distinguished on this manifold in a deterministic framework it might be distinguishable in a stochastic modelling framework. Their method exploits this by using an objective function that includes a measure for fluctuations in particle numbers. They show on three example models, immigration-death, gene expression and Epo-EpoReceptor interaction, that this resolves the non-identifiability even in the case of measurement noise with known amplitude. The method is applied to partially observed recordings of biochemical systems with measurement noise. It is simple to implement and it is usually very fast to compute. This optimisation can be realised in a classical or Bayesian fashion.
Ab initio determination of kinetics for atomic layer deposition modeling
NASA Astrophysics Data System (ADS)
Remmers, Elizabeth M.
A first principles model is developed to describe the kinetics of atomic layer deposition (ALD) systems. This model requires no fitting parameters, as it is based on the reaction pathways, structures, and energetics obtained from quantum-chemical studies. Using transition state theory and partition functions from statistical mechanics, equilibrium constants and reaction rates can be calculated. Several tools were created in Python to aid in the calculation of these quantities, and this procedure was applied to two systems- zinc oxide deposition from diethyl zinc (DEZ) and water, and alumina deposition from trimethyl aluminum (TMA) and water. A Gauss-Jordan factorization is used to decompose the system dynamics, and the resulting systems of equations are solved numerically to obtain the temporal concentration profiles of these two deposition systems.
NASA Astrophysics Data System (ADS)
Santos-Martins, Diogo; Fernandes, Pedro Alexandrino; Ramos, Maria João
2016-11-01
In the context of SAMPL5, we submitted blind predictions of the cyclohexane/water distribution coefficient (D) for a series of 53 drug-like molecules. Our method is purely empirical and based on the additive contribution of each solute atom to the free energy of solvation in water and in cyclohexane. The contribution of each atom depends on the atom type and on the exposed surface area. Comparatively to similar methods in the literature, we used a very small set of atomic parameters: only 10 for solvation in water and 1 for solvation in cyclohexane. As a result, the method is protected from overfitting and the error in the blind predictions could be reasonably estimated. Moreover, this approach is fast: it takes only 0.5 s to predict the distribution coefficient for all 53 SAMPL5 compounds, allowing its application in virtual screening campaigns. The performance of our approach (submission 49) is modest but satisfactory in view of its efficiency: the root mean square error (RMSE) was 3.3 log D units for the 53 compounds, while the RMSE of the best performing method (using COSMO-RS) was 2.1 (submission 16). Our method is implemented as a Python script available at https://github.com/diogomart/SAMPL5-DC-surface-empirical.
Modeling pattern in collections of parameters
Link, W.A.
1999-01-01
Wildlife management is increasingly guided by analyses of large and complex datasets. The description of such datasets often requires a large number of parameters, among which certain patterns might be discernible. For example, one may consider a long-term study producing estimates of annual survival rates; of interest is the question whether these rates have declined through time. Several statistical methods exist for examining pattern in collections of parameters. Here, I argue for the superiority of 'random effects models' in which parameters are regarded as random variables, with distributions governed by 'hyperparameters' describing the patterns of interest. Unfortunately, implementation of random effects models is sometimes difficult. Ultrastructural models, in which the postulated pattern is built into the parameter structure of the original data analysis, are approximations to random effects models. However, this approximation is not completely satisfactory: failure to account for natural variation among parameters can lead to overstatement of the evidence for pattern among parameters. I describe quasi-likelihood methods that can be used to improve the approximation of random effects models by ultrastructural models.
Recursive parameter estimation of hydrologic models
NASA Astrophysics Data System (ADS)
Rajaram, Harihar; Georgakakos, Konstantine P.
1989-02-01
Proposed is a nonlinear filtering approach to recursive parameter estimation of conceptual watershed response models in state-space form. The conceptual model state is augmented by the vector of free parameters which are to be estimated from input-output data, and the extended Kaiman filter is used to recursively estimate and predict the augmented state. The augmented model noise covariance is parameterized as the sum of two components: one due to errors in the augmented model input and another due to errors in the specification of augmented model constants that were estimated from other than input-output data (e.g., topographic and rating curve constants). These components depend on the sensitivity of the augmented model to input and uncertain constants. Such a novel parameterization allows for nonstationary model noise statistics that are consistent with the dynamics of watershed response as they are described by the conceptual watershed response model. Prior information regarding uncertainty in input and uncertain constants in the form of degree-of-belief estimates of hydrologists can be used directly within the proposed formulation. Even though model structure errors are not explicitly parameterized in the present formulation, such errors can be identified through the examination of the one-step ahead predicted normalized residuals and the parameter traces during convergence. The formulation is exemplified by the estimation of the parameters of a conceptual hydrologic model with data from the 2.1-km2 watershed of Woods Lake located in the Adirondack Mountains of New York.
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.
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.
Delineating parameter unidentifiabilities in complex models
NASA Astrophysics Data System (ADS)
Raman, Dhruva V.; Anderson, James; Papachristodoulou, Antonis
2017-03-01
Scientists use mathematical modeling as a tool for understanding and predicting the properties of complex physical systems. In highly parametrized models there often exist relationships between parameters over which model predictions are identical, or nearly identical. These are known as structural or practical unidentifiabilities, respectively. They are hard to diagnose and make reliable parameter estimation from data impossible. They furthermore imply the existence of an underlying model simplification. We describe a scalable method for detecting unidentifiabilities, as well as the functional relations defining them, for generic models. This allows for model simplification, and appreciation of which parameters (or functions thereof) cannot be estimated from data. Our algorithm can identify features such as redundant mechanisms and fast time-scale subsystems, as well as the regimes in parameter space over which such approximations are valid. We base our algorithm on a quantification of regional parametric sensitivity that we call `multiscale sloppiness'. Traditionally, the link between parametric sensitivity and the conditioning of the parameter estimation problem is made locally, through the Fisher information matrix. This is valid in the regime of infinitesimal measurement uncertainty. We demonstrate the duality between multiscale sloppiness and the geometry of confidence regions surrounding parameter estimates made where measurement uncertainty is non-negligible. Further theoretical relationships are provided linking multiscale sloppiness to the likelihood-ratio test. From this, we show that a local sensitivity analysis (as typically done) is insufficient for determining the reliability of parameter estimation, even with simple (non)linear systems. Our algorithm can provide a tractable alternative. We finally apply our methods to a large-scale, benchmark systems biology model of necrosis factor (NF)-κ B , uncovering unidentifiabilities.
Systematic parameter inference in stochastic mesoscopic modeling
NASA Astrophysics Data System (ADS)
Lei, Huan; Yang, Xiu; Li, Zhen; Karniadakis, George Em
2017-02-01
We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving dissipative particle dynamics (eDPD). The response surfaces of various target properties (viscosity, diffusivity, pressure, etc.) with respect to model parameters are constructed based on the generalized polynomial chaos (gPC) expansion using simulation results on sampling points (e.g., individual parameter sets). To alleviate the computational cost to evaluate the target properties, we employ the compressive sensing method to compute the coefficients of the dominant gPC terms given the prior knowledge that the coefficients are "sparse". The proposed method shows comparable accuracy with the standard probabilistic collocation method (PCM) while it imposes a much weaker restriction on the number of the simulation samples especially for systems with high dimensional parametric space. Fully access to the response surfaces within the confidence range enables us to infer the optimal force parameters given the desirable values of target properties at the macroscopic scale. Moreover, it enables us to investigate the intrinsic relationship between the model parameters, identify possible degeneracies in the parameter space, and optimize the model by eliminating model redundancies. The proposed method provides an efficient alternative approach for constructing mesoscopic models by inferring model parameters to recover target properties of the physics systems (e.g., from experimental measurements), where those force field parameters and formulation cannot be derived from the microscopic level in a straight forward way.
Relativistic Calculation of Scattering Parameters for Superelastic Electron-Atom Collisions
NASA Astrophysics Data System (ADS)
Zeman, V.; McEachran, R. P.; Stauffer, A. D.; Srivastava, R.
1996-05-01
Superelastic electron-atom scattering experiments are often more desirable to perform than inelastic experiments, in part due to the ability to excite specific fine-structure (and hyperfine-structure) states with relative ease. The superelastic scattering parameters measured, however, are often compared with inelastic parameters which have been measured or calculated by other groups, even though the two cases are not exactly the time-reverse of each other (inelastic experiments can't resolve hyperfine-structure states). To do this there must exist a theoretical framework by which the various parameters for the two cases can be compared. In the non-relativistic limit a general framework has been developed for n'p arrow ns transitions in quasi one-electron atoms(I.V. Hertel, M.H. Kelley and J.J. McClelland, Z. Phys. D, 6), 163 (1987). We extend these calculations to the relativistic case where jj-coupling, rather than LS-coupling, is employed. Examples of calculations using the relativistic distorted-wave approximation will be given.
Models and parameters for environmental radiological assessments
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)
Geometry-dependent atomic multipole models for the water molecule
NASA Astrophysics Data System (ADS)
Loboda, O.; Millot, C.
2017-10-01
Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.
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.
Atomic processes modeling of X-ray free electron laser produced plasmas using SCFLY code
NASA Astrophysics Data System (ADS)
Chung, H.-K.; Cho, B. I.; Ciricosta, O.; Vinko, S. M.; Wark, J. S.; Lee, R. W.
2017-03-01
With the development of X-ray free electron lasers (XFEL), a novel state of matter of highly transient and non-equilibrium plasma has been created in laboratories. As high intensity X-ray laser beams interact with a solid density target, electrons are ionized from inner-shell orbitals and these electrons and XFEL photons create dense and finite temperature plasmas. In order to study atomic processes in XFEL driven plasmas, the atomic kinetics model SCFLY containing an extensive set of configurations needed for solid density plasmas was applied to study atomic processes of XFEL driven systems. The code accepts the time-dependent conditions of the XFEL as input parameters, and computes time-dependent population distributions and ionization distributions self-consistently with electron temperatures and densities assuming an instantaneous equilibration of electron energies. The methods and assumptions in the atomic kinetics model and unique aspects of atomic processes in XFEL driven plasmas are described.
INFERNO - A better model of atoms in dense plasmas
NASA Astrophysics Data System (ADS)
Liberman, D. A.
1982-03-01
A self-consistent field model of atoms in dense plasmas has been devised and incorporated in a computer program. In the model there is a uniform positive charge distribution with a hole in it and at the center of the hole an atomic nucleus. There are electrons, in both bound and continuum states, in sufficient number to form an electrically neutral system. The Dirac equation is used so that high Z atoms can be dealt with. A finite temperature is assumed, and a mean field (average atom) approximation is used in statistical averages. Applications have been made to equations of states and to photoabsorption.
Inhibition of atomic dipole collapses by squeezed light: a Jaynes-Cummings model treatment
NASA Astrophysics Data System (ADS)
Ben-Aryeh, Y.; Miller, C. A.; Risken, H.; Schleich, W.
1992-06-01
We investigate the collapse of the atomic dipole caused by a squeezed vacuum in an ideal one-mode cavity. The difference between the collapse times of the two quadrature components of the dipole moments is increasing with increasing squeezing parameter. This phenomenon predicted by a hamiltonian Jaynes-Cummings model is similar to the inhibition and enhancement of atomic phase decay predicted by Gardiner for a markovian system.
Force Field Independent Metal Parameters Using a Nonbonded Dummy Model
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
Atomic charges for modeling metal–organic frameworks: Why and how
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.
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)
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.
"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)
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)
"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)
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.
Early Atomic Models - From Mechanical to Quantum (1904-1913)
NASA Astrophysics Data System (ADS)
Baily, Charles
2012-08-01
A complete history of early atomic models would fill volumes, but a reasonably coherent tale of the path from mechanical atoms to the quantum can be told by focusing on the relevant work of three great contributors to atomic physics, in the critically important years between 1904 and 1913: J. J. Thomson, Ernest Rutherford and Niels Bohr. We first examine the origins of Thomson's mechanical atomic models, from his ethereal vortex atoms in the early 1880's, to the myriad "corpuscular" atoms he proposed following the discovery of the electron in 1897. Beyond predictions for the periodicity of the elements, the application of Thomson's atoms to problems in scattering and absorption led to quantitative predictions that were confirmed by experiments with high-velocity electrons traversing thin sheets of metal. Still, the much more massive and energetic {\\alpha}-particles being studied by Rutherford were better suited for exploring the interior of the atom, and careful measurements on the angular dependence of their 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.
Analytical model of an isolated single-atom electron source.
Engelen, W J; Vredenbregt, E J D; Luiten, O J
2014-12-01
An analytical model of a single-atom electron source is presented, where electrons are created by near-threshold photoionization of an isolated atom. The model considers the classical dynamics of the electron just after the photon absorption, i.e. its motion in the potential of a singly charged ion and a uniform electric field used for acceleration. From closed expressions for the asymptotic transverse electron velocities and trajectories, the effective source temperature and the virtual source size can be calculated. The influence of the acceleration field strength and the ionization laser energy on these properties has been studied. With this model, a single-atom electron source with the optimum electron beam properties can be designed. Furthermore, we show that the model is also applicable to ionization of rubidium atoms, and thus also describes the ultracold electron source, which is based on photoionization of laser-cooled alkali atoms.
Computational model for noncontact atomic force microscopy: energy dissipation of cantilever.
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.
[Parameters adaptation in the populations models].
Il'ichev, V G
2005-01-01
Ecology-evolutionary models of low dimensions were developed on the basis of competitive selection criteria. Dynamics of variables (number of individuals) and the search of evolutionary-stable values of parameters (biological characterictics of populations) were monitored in the suggested models. If the environmental temperature is changing periodically, the average (a) and width (d) of temperature tolerance range appears to be the important parameters. By model experiments it was established that stable values of temperature (a), favorable for development of highly specialized algae (d is low) were close to minimum and maximum of temperature curve. And for the low specialized algae (d is high) this values were close to the average temperature of environment. In a similar manner, a set of evolutionally stable parameters (a, d) was established for either of the two interacted populations (competitors and "predator-prey"). The hypotheses concerning it's geometric structure and the process of coevolution is formulated.
Estimation of Model Parameters for Steerable Needles
Park, Wooram; Reed, Kyle B.; Okamura, Allison M.; Chirikjian, Gregory S.
2010-01-01
Flexible needles with bevel tips are being developed as useful tools for minimally invasive surgery and percutaneous therapy. When such a needle is inserted into soft tissue, it bends due to the asymmetric geometry of the bevel tip. This insertion with bending is not completely repeatable. We characterize the deviations in needle tip pose (position and orientation) by performing repeated needle insertions into artificial tissue. The base of the needle is pushed at a constant speed without rotating, and the covariance of the distribution of the needle tip pose is computed from experimental data. We develop the closed-form equations to describe how the covariance varies with different model parameters. We estimate the model parameters by matching the closed-form covariance and the experimentally obtained covariance. In this work, we use a needle model modified from a previously developed model with two noise parameters. The modified needle model uses three noise parameters to better capture the stochastic behavior of the needle insertion. The modified needle model provides an improvement of the covariance error from 26.1% to 6.55%. PMID:21643451
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.
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)
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)
Parameter identification and modeling of longitudinal aerodynamics
NASA Technical Reports Server (NTRS)
Aksteter, J. W.; Parks, E. K.; Bach, R. E., Jr.
1995-01-01
Using a comprehensive flight test database and a parameter identification software program produced at NASA Ames Research Center, a math model of the longitudinal aerodynamics of the Harrier aircraft was formulated. The identification program employed the equation error method using multiple linear regression to estimate the nonlinear parameters. The formulated math model structure adhered closely to aerodynamic and stability/control theory, particularly with regard to compressibility and dynamic manoeuvring. Validation was accomplished by using a three degree-of-freedom nonlinear flight simulator with pilot inputs from flight test data. The simulation models agreed quite well with the measured states. It is important to note that the flight test data used for the validation of the model was not used in the model identification.
Analysis of Modeling Parameters on Threaded Screws.
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.
Parameter Estimation of Spacecraft Fuel Slosh Model
NASA Technical Reports Server (NTRS)
Gangadharan, Sathya; Sudermann, James; Marlowe, Andrea; Njengam Charles
2004-01-01
Fuel slosh in the upper stages of a spinning spacecraft during launch has been a long standing concern for the success of a space mission. Energy loss through the movement of the liquid fuel in the fuel tank affects the gyroscopic stability of the spacecraft and leads to nutation (wobble) which can cause devastating control issues. The rate at which nutation develops (defined by Nutation Time Constant (NTC can be tedious to calculate and largely inaccurate if done during the early stages of spacecraft design. Pure analytical means of predicting the influence of onboard liquids have generally failed. A strong need exists to identify and model the conditions of resonance between nutation motion and liquid modes and to understand the general characteristics of the liquid motion that causes the problem in spinning spacecraft. A 3-D computerized model of the fuel slosh that accounts for any resonant modes found in the experimental testing will allow for increased accuracy in the overall modeling process. Development of a more accurate model of the fuel slosh currently lies in a more generalized 3-D computerized model incorporating masses, springs and dampers. Parameters describing the model include the inertia tensor of the fuel, spring constants, and damper coefficients. Refinement and understanding the effects of these parameters allow for a more accurate simulation of fuel slosh. The current research will focus on developing models of different complexity and estimating the model parameters that will ultimately provide a more realistic prediction of Nutation Time Constant obtained through simulation.
Churkin, Yu. V.; Fedortsov, A. B.; Klimchitskaya, G. L.; Yurova, V. A.
2010-10-15
The van der Waals and Casimir-Polder interaction of different atoms with graphene is investigated using the Dirac model which assumes that the energy of quasiparticles is linear with respect to the momentum. The obtained results for the van der Waals coefficients of hydrogen atoms and molecules and atoms of metastable He* and Na as a function of separation are compared with respective results found using the hydrodynamic model of graphene. It is shown that, regardless of the value of the gap parameter, the Dirac model leads to much smaller values of the van der Waals coefficients than the hydrodynamic model. The experiment on quantum reflection of metastable He* and Na atoms on graphene is proposed which is capable to discriminate between the two models of the electronic structure of graphene. In this respect, the parameters of the phenomenological potential for both these atoms interacting with graphene described by different models are determined.
A theoretical-electron-density databank using a model of real and virtual spherical atoms.
Nassour, Ayoub; Domagala, Slawomir; Guillot, Benoit; Leduc, Theo; Lecomte, Claude; Jelsch, Christian
2017-08-01
A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.
Combined atomic-scale modelling and experimental studies of nucleation in the solid state.
Cerezo, A; Hirosawa, S; Rozdilsky, I; Smith, G D W
2003-03-15
The process of solid-state nucleation in highly supersaturated solid solutions has been investigated on the atomic scale by a combination of three-dimensional atom probe analysis and atomistic modelling using dynamical Ising models. In binary Cu-Co alloys, a simple atom-exchange model with a single thermodynamic parameter derived from phase-diagram data was able to reproduce the atomic-scale microstructures observed in the atom probe, and also match the measured peak precipitate density. Modelling solute effects in complex copper-bearing steels required a more sophisticated model based on a vacancy-hopping mechanism and a larger number of thermodynamic and kinetic parameters derived from independent experimental data and theoretical calculations. The model gave an excellent match to the experimentally observed microstructures, and it reproduced features such as the clustering of Ni and Mn before the precipitation of Cu. The model also allowed time-dependent behaviour to be investigated, and it showed that solute clustering of Ni and Mn occurs during the cooling of the alloy. These clusters then act as heterogeneous nucleation sites for the formation of copper precipitates. Understanding such complex solute interaction effects through combined experiment and modelling is an essential step to controlling nucleation and hence the fine-scale microstructures in advanced engineering alloys.
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,…
100th anniversary of Bohr's model of the atom.
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. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Nonlinear, lumped parameter transformer model reduction technique
Degeneff, R.C.; Gutierrez, M.R.; Vakilian, M.
1995-04-01
Utility engineers often need nonlinear transformer models in order to investigate power system transient events. Methods exist to create accurate wideband reduced order linear transformer models, however, to date a method of creating a reduced order wideband nonlinear transformer model has not been presented. This paper describes a technique that starts with a detailed nonlinear transformer model used for insulation design studies and reduces its order so that it can be used conveniently in EMTP. The method is based on linearization of the core`s saturable characteristic during each solution time intervals. The technique uses Kron`s reduction approach in each solution time interval. It can be applied to any nonlinear lumped parameter network which uses electric parameter analogies (i.e., FEM networks). This paper outlines the nonlinear reduction technique. An illustrative example is given using the transient voltage response during saturation for a 785/345/34.5kV, YYD 500 MVA single phase auto transformer.
Hydrogen ADPs with Cu Kα data? Invariom and Hirshfeld atom modelling of fluconazole.
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.
A nonempirical anisotropic atom-atom model potential for chlorobenzene crystals.
Day, Graeme M; Price, Sarah L
2003-12-31
A nearly nonempirical, transferable model potential is developed for the chlorobenzene molecules (C6ClnH6-n, n = 1 to 6) with anisotropy in the atom-atom form of both electrostatic and repulsion interactions. The potential is largely derived from the charge densities of the molecules, using a distributed multipole electrostatic model and a transferable dispersion model derived from the molecular polarizabilities. A nonempirical transferable repulsion model is obtained by analyzing the overlap of the charge densities in dimers as a function of orientation and separation and then calibrating this anisotropic atom-atom model against a limited number of intermolecular perturbation theory calculations of the short-range energies. The resulting model potential is a significant improvement over empirical model potentials in reproducing the twelve chlorobenzene crystal structures. Further validation calculations of the lattice energies and rigid-body k = 0 phonon frequencies provide satisfactory agreement with experiment, with the discrepancies being primarily due to approximations in the theoretical methods rather than the model intermolecular potential. The potential is able to give a good account of the three polymorphs of p-dichlorobenzene in a detailed crystal structure prediction study. Thus, by introducing repulsion anisotropy into a transferable potential scheme, it is possible to produce a set of potentials for the chlorobenzenes that can account for their crystal properties in an unprecedentedly realistic fashion.
Parameter Estimation for Viscoplastic Material Modeling
NASA Technical Reports Server (NTRS)
Saleeb, Atef F.; Gendy, Atef S.; Wilt, Thomas E.
1997-01-01
A key ingredient in the design of engineering components and structures under general thermomechanical loading is the use of mathematical constitutive models (e.g. in finite element analysis) capable of accurate representation of short and long term stress/deformation responses. In addition to the ever-increasing complexity of recent viscoplastic models of this type, they often also require a large number of material constants to describe a host of (anticipated) physical phenomena and complicated deformation mechanisms. In turn, the experimental characterization of these material parameters constitutes the major factor in the successful and effective utilization of any given constitutive model; i.e., the problem of constitutive parameter estimation from experimental measurements.
Effects of model deficiencies on parameter estimation
NASA Technical Reports Server (NTRS)
Hasselman, T. K.
1988-01-01
Reliable structural dynamic models will be required as a basis for deriving the reduced-order plant models used in control systems for large space structures. Ground vibration testing and model verification will play an important role in the development of these models; however, fundamental differences between the space environment and earth environment, as well as variations in structural properties due to as-built conditions, will make on-orbit identification essential. The efficiency, and perhaps even the success, of on-orbit identification will depend on having a valid model of the structure. It is envisioned that the identification process will primarily involve parametric methods. Given a correct model, a variety of estimation algorithms may be used to estimate parameter values. This paper explores the effects of modeling errors and model deficiencies on parameter estimation by reviewing previous case histories. The effects depend at least to some extent on the estimation algorithm being used. Bayesian estimation was used in the case histories presented here. It is therefore conceivable that the behavior of an estimation algorithm might be useful in detecting and possibly even diagnosing deficiencies. In practice, the task is complicated by the presence of systematic errors in experimental procedures and data processing and in the use of the estimation procedures themselves.
YinYang atom: a simple combined ab initio quantum mechanical molecular mechanical model.
Shao, Yihan; Kong, Jing
2007-05-10
A simple interface is proposed for combined quantum mechanical (QM) molecular mechanical (MM) calculations for the systems where the QM and MM regions are connected through covalent bonds. Within this model, the atom that connects the two regions, called YinYang atom here, serves as an ordinary MM atom to other MM atoms and as a hydrogen-like atom to other QM atoms. Only one new empirical parameter is introduced to adjust the length of the connecting bond and is calibrated with the molecule propanol. This model is tested with the computation of equilibrium geometries and protonation energies for dozens of molecules. Special attention is paid on the influence of MM point charges on optimized geometry and protonation energy, and it is found that it is important to maintain local charge-neutrality in the MM region in order for the accurate calculation of the protonation and deprotonation energies. Overall the simple YinYang atom model yields comparable results to some other QM/MM models.
Hou, Tingjun; Zhang, Wei; Huang, Qin; Xu, Xiaojie
2005-02-01
than the other six solvation models. For proteins, the model classified the atoms into 20 basic types and the predicted aqueous free energies of solvation by PB/SA were used for fitting. The solvation model based on the new parameters was employed to predict the solvation free energies of 38 proteins. The predicted values from our model were in good agreement with those from the PB/SA model and were much better than those given by the other four models developed for proteins.
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.
Sonne, Jacob; Jensen, Morten Ø; Hansen, Flemming Y; Hemmingsen, Lars; Peters, Günther H
2007-06-15
Molecular dynamics simulations of dipalmitoylphosphatidylcholine (DPPC) lipid bilayers using the CHARMM27 force field in the tensionless isothermal-isobaric (NPT) ensemble give highly ordered, gel-like bilayers with an area per lipid of approximately 48 A(2). To obtain fluid (L(alpha)) phase properties of DPPC bilayers represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per lipid of 60.4 +/- 0.1 A(2). Compared to the 48 A(2), the new value of 60.4 A(2) is in fair agreement with the experimental value of 64 A(2). In addition, the simulated order parameter profile and electron density profile are in satisfactory agreement with experimental data. Thus, the biologically more interesting fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field.
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.
Dehzangi, Arash; Larki, Farhad; Hutagalung, Sabar D.; Goodarz Naseri, Mahmood; Majlis, Burhanuddin Y.; Navasery, Manizheh; Hamid, Norihan Abdul; Noor, Mimiwaty Mohd
2013-01-01
In this letter, we investigate the fabrication of Silicon nanostructure patterned on lightly doped (1015 cm−3) p-type silicon-on-insulator by atomic force microscope nanolithography technique. The local anodic oxidation followed by two wet etching steps, potassium hydroxide etching for silicon removal and hydrofluoric etching for oxide removal, are implemented to reach the structures. The impact of contributing parameters in oxidation such as tip materials, applying voltage on the tip, relative humidity and exposure time are studied. The effect of the etchant concentration (10% to 30% wt) of potassium hydroxide and its mixture with isopropyl alcohol (10%vol. IPA ) at different temperatures on silicon surface are expressed. For different KOH concentrations, the effect of etching with the IPA admixture and the effect of the immersing time in the etching process on the structure are investigated. The etching processes are accurately optimized by 30%wt. KOH +10%vol. IPA in appropriate time, temperature, and humidity. PMID:23776479
Reliability of parameter estimation in respirometric models.
Checchi, Nicola; Marsili-Libelli, Stefano
2005-09-01
When modelling a biochemical system, the fact that model parameters cannot be estimated exactly stimulates the definition of tests for checking unreliable estimates and design better experiments. The method applied in this paper is a further development from Marsili-Libelli et al. [2003. Confidence regions of estimated parameters for ecological systems. Ecol. Model. 165, 127-146.] and is based on the confidence regions computed with the Fisher or the Hessian matrix. It detects the influence of the curvature, representing the distortion of the model response due to its nonlinear structure. If the test is passed then the estimation can be considered reliable, in the sense that the optimisation search has reached a point on the error surface where the effect of nonlinearities is negligible. The test is used here for an assessment of respirometric model calibration, i.e. checking the experimental design and estimation reliability, with an application to real-life data in the ASM context. Only dissolved oxygen measurements have been considered, because this is a very popular experimental set-up in wastewater modelling. The estimation of a two-step nitrification model using batch respirometric data is considered, showing that the initial amount of ammonium-N and the number of data play a crucial role in obtaining reliable estimates. From this basic application other results are derived, such as the estimation of the combined yield factor and of the second step parameters, based on a modified kinetics and a specific nitrite experiment. Finally, guidelines for designing reliable experiments are provided.
Constant-parameter capture-recapture models
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.
NASA Astrophysics Data System (ADS)
Nakashima, Keiji; Ogawa, Teiichiro
1985-11-01
The angular dependence of Doppler profiles of atomic fluorescence produced in electron impact dissociation of molecules was simulated in consideration of the effect of the anisotropy of dissociation and the ``polarization'' in magnetic sublevel. The asymmetry parameter b and the polarization of the electric vector of emission Jp are key parameters of Doppler profiles for the excited atom of known translational energy distribution. The difference of two Doppler profiles taken at 90° and 45°, which is denoted as angular difference Doppler profile, is shown to be useful to estimate these two key parameters.
CHAMP: Changepoint Detection Using Approximate Model Parameters
2014-06-01
detecting changes in the parameters and mod- els that generate observed data. Commonly cited examples include detecting changes in stock market behavior [4...experimentally verified using artifi- cially generated data and are compared to those of Fearnhead and Liu [5]. 2 Related work Hidden Markov Models ( HMMs ) are...largely the de facto tool of choice when analyzing time series data, but the standard HMM formulation has several undesirable properties. The number of
Level set methods for modelling field evaporation in atom probe.
Haley, Daniel; Moody, Michael P; Smith, George D W
2013-12-01
Atom probe is a nanoscale technique for creating three-dimensional spatially and chemically resolved point datasets, primarily of metallic or semiconductor materials. While atom probe can achieve local high-level resolution, the spatial coherence of the technique is highly dependent upon the evaporative physics in the material and can often result in large geometric distortions in experimental results. The distortions originate from uncertainties in the projection function between the field evaporating specimen and the ion detector. Here we explore the possibility of continuum numerical approximations to the evaporative behavior during an atom probe experiment, and the subsequent propagation of ions to the detector, with particular emphasis placed on the solution of axisymmetric systems, such as isolated particles and multilayer systems. Ultimately, this method may prove critical in rapid modeling of tip shape evolution in atom probe tomography, which itself is a key factor in the rapid generation of spatially accurate reconstructions in atom probe datasets.
A 4096 atom model of amorphous silicon: Structure and dynamics
NASA Astrophysics Data System (ADS)
Feldman, Joseph L.; Bickham, Scott R.; Davidson, Brian N.; Wooten, Frederick
1997-03-01
We present structural and lattice dynamical information for a 4096 atom model of amorphous silicon. The structural model was obtained, similarly to previously published smaller models, using periodic boundary conditions, the Wooten-Winer-Weaire bond-switching algorithm, and the Broughton-Li relaxation with respect to the Stillinger-Weber potential. The structure is dynamically stable and there is no evidence in the radial distribution function of medium range order. For examining this large model, we use a 1000 processor Connection Machine to compute all the eigenvalues and eigenvectors exactly. The phonon density of states and inverse participation ratio are compared with results for related 216, 432 and 1000-atom models.
Solar Parameters for Modeling the Interplanetary Background
NASA Astrophysics Data System (ADS)
Bzowski, Maciej; Sokół, Justyna M.; Tokumaru, Munetoshi; Fujiki, Kenichi; Quémerais, Eric; Lallement, Rosine; Ferron, Stéphane; Bochsler, Peter; McComas, David J.
The goal of the working group on cross-calibration of past and present ultraviolet (UV) datasets of the International Space Science Institute (ISSI) in Bern, Switzerland was to establish a photometric cross-calibration of various UV and extreme ultraviolet (EUV) heliospheric observations. Realization of this goal required a credible and up-to-date model of the spatial distribution of neutral interstellar hydrogen in the heliosphere, and to that end, a credible model of the radiation pressure and ionization processes was needed. This chapter describes the latter part of the project: the solar factors responsible for shaping the distribution of neutral interstellar H in the heliosphere. In this paper we present the solar Lyman-α flux and the topics of solar Lyman-α resonant radiation pressure force acting on neutral H atoms in the heliosphere. We will also discuss solar EUV radiation and resulting photoionization of heliospheric hydrogen along with their evolution in time and the still hypothetical variation with heliolatitude. Furthermore, solar wind and its evolution with solar activity is presented, mostly in the context of charge exchange ionization of heliospheric neutral hydrogen, and dynamic pressure variations. Also electron-impact ionization of neutral heliospheric hydrogen and its variation with time, heliolatitude, and solar distance is discussed. After a review of the state of the art in all of those topics, we proceed to present an interim model of the solar wind and the other solar factors based on up-to-date in situ and remote sensing observations. This model was used by Izmodenov et al. (2013, this volume) to calculate the distribution of heliospheric hydrogen, which in turn was the basis for intercalibrating the heliospheric UV and EUV measurements discussed in Quémerais et al. (2013, this volume). Results of this joint effort will also be used to improve the model of the solar wind evolution, which will be an invaluable asset in interpretation of
Using a scalar parameter to trace dislocation evolution in atomistic modeling
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.
Modelling tourists arrival using time varying parameter
NASA Astrophysics Data System (ADS)
Suciptawati, P.; Sukarsa, K. G.; Kencana, Eka N.
2017-06-01
The importance of tourism and its related sectors to support economic development and poverty reduction in many countries increase researchers’ attentions to study and model tourists’ arrival. This work is aimed to demonstrate time varying parameter (TVP) technique to model the arrival of Korean’s tourists to Bali. The number of Korean tourists whom visiting Bali for period January 2010 to December 2015 were used to model the number of Korean’s tourists to Bali (KOR) as dependent variable. The predictors are the exchange rate of Won to IDR (WON), the inflation rate in Korea (INFKR), and the inflation rate in Indonesia (INFID). Observing tourists visit to Bali tend to fluctuate by their nationality, then the model was built by applying TVP and its parameters were approximated using Kalman Filter algorithm. The results showed all of predictor variables (WON, INFKR, INFID) significantly affect KOR. For in-sample and out-of-sample forecast with ARIMA’s forecasted values for the predictors, TVP model gave mean absolute percentage error (MAPE) as much as 11.24 percent and 12.86 percent, respectively.
Lipid Models for United-Atom Molecular Dynamics Simulations of Proteins.
Kukol, Andreas
2009-03-10
United-atom force fields for molecular dynamics (MD) simulations provide a higher computational efficiency, especially in lipid membrane simulations, with little sacrifice in accuracy, when compared to all-atom force fields. Excellent united-atom lipid models are available, but in combination with depreciated protein force fields. In this work, a united-atom model of the lipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine has been built with standard parameters of the force field GROMOS96 53a6 that reproduces the experimental area per lipid of a lipid bilayer within 3% accuracy to a value of 0.623 ± 0.011 nm(2) without the assumption of a constant surface area or the inclusion of surface pressure. In addition, the lateral self-diffusion constant and deuterium order parameters of the acyl chains are in agreement with experimental data. Furthermore, models for 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) result in areas per lipid of 0.625 nm(2) (DMPC), 0.693 nm(2) (POPC), and 0.700 nm(2) (POPG) from 40 ns MD simulations. Experimental lateral self-diffusion coefficients are reproduced satisfactorily by the simulation. The lipid models can form the basis for molecular dynamics simulations of membrane proteins with current and future versions of united-atom protein force fields.
Transferable Atomic Multipole Machine Learning Models for Small Organic Molecules.
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.
Takechi-Haraya, Yuki; Sakai-Kato, Kumiko; Goda, Yukihiro
2017-07-01
We determined the permeability coefficient of a model hydrophilic drug, calcein, encapsulated within saturated lipid-based nano-sized liposomes of various lipid profiles. We demonstrated that the addition of cholesterol to liposomes containing saturated lipids increased the permeability of the liposomal membrane to calcein via a decrease in the membrane bending modulus, as determined by means of atomic force microscopy. We found an inverse correlation between the membrane bending modulus of saturated lipid-based nano-sized liposomes and the permeability coefficient of encapsulated calcein, demonstrating that bending modulus, as determined by means of atomic force microscopy, is a quantitative parameter describing the permeability of liposomal membranes to calcein.
NASA Astrophysics Data System (ADS)
Afrosimov, V. V.; Basalaev, A. A.; Panov, M. N.
2017-01-01
The absolute differential cross sections of scattering of fast particles formed in processes with capture of one or two electrons from Ar atoms have been measured for 6-keV He2+ ions in the interval of scattering angles within 0°-2.5°. The cross sections of electron capture and electron capture with ionization have been determined as functions of the impact parameter. The probabilities of these processes are compared to the distribution of electron density in various shells of target atoms. Applicability of the models of screened Coulomb interaction potentials to description of the scattering of recharged particles is assessed.
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.
Nagaoka’s atomic model and hyperfine interactions
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
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.
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.
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.
NASA Astrophysics Data System (ADS)
Topcu, Turker; Robicheaux, Francis
2012-06-01
It is common practice in strong-laser physics community that dynamical regime of atomic ionization is described by the Keldysh parameter, γ. Two distinct cases where γ1 and γ1 are associated with ionization mechanisms that are predominantly in tunneling and in multi-photon regimes, respectively. We report on our fully three-dimensional ab initio quantum simulations of ionization of hydrogen atoms in laser fields described in terms of the Keldysh parameter by solving the corresponding time-dependent Schr"odinger equation. We find that the Keldysh parameter is useful in inferring the dynamical ionization regime only when coupled with the scaled laser frequency, φ, when a large range of laser frequencies and peak intensities are considered. The additional parameter φ relates the laser frequency φ to the classical Kepler frequency φK of the electron, and together with the Keldysh parameter, they can be used to refer to an ionization regime.
Transferable Atomic Multipole Machine Learning Models for Small Organic Molecules
Bereau, Tristan; Andrienko, Denis; von Lilienfeld, O. Anatole
2015-07-01
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.
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.
Moose models with vanishing S parameter
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.
Model parameters for simulation of physiological lipids
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
Uncertainty quantification for optical model parameters
Lovell, A. E.; Nunes, F. M.; Sarich, J.; ...
2017-02-21
Although uncertainty quantification has been making its way into nuclear theory, these methods have yet to be explored in the context of reaction theory. For example, it is well known that different parameterizations of the optical potential can result in different cross sections, but these differences have not been systematically studied and quantified. The purpose of our work is to investigate the uncertainties in nuclear reactions that result from fitting a given model to elastic-scattering data, as well as to study how these uncertainties propagate to the inelastic and transfer channels. We use statistical methods to determine a best fitmore » and create corresponding 95% confidence bands. A simple model of the process is fit to elastic-scattering data and used to predict either inelastic or transfer cross sections. In this initial work, we assume that our model is correct, and the only uncertainties come from the variation of the fit parameters. Here, we study a number of reactions involving neutron and deuteron projectiles with energies in the range of 5–25 MeV/u, on targets with mass A=12–208. We investigate the correlations between the parameters in the fit. The case of deuterons on 12C is discussed in detail: the elastic-scattering fit and the prediction of 12C(d,p)13C transfer angular distributions, using both uncorrelated and correlated χ2 minimization functions. The general features for all cases are compiled in a systematic manner to identify trends. This work shows that, in many cases, the correlated χ2 functions (in comparison to the uncorrelated χ2 functions) provide a more natural parameterization of the process. These correlated functions do, however, produce broader confidence bands. Further optimization may require improvement in the models themselves and/or more information included in the fit.« less
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
Modeling noncontact atomic force microscopy resolution on corrugated surfaces.
Burson, Kristen M; Yamamoto, Mahito; Cullen, William G
2012-01-01
Key developments in NC-AFM have generally involved atomically flat crystalline surfaces. However, many surfaces of technological interest are not atomically flat. We discuss the experimental difficulties in obtaining high-resolution images of rough surfaces, with amorphous SiO(2) as a specific case. We develop a quasi-1-D minimal model for noncontact atomic force microscopy, based on van der Waals interactions between a spherical tip and the surface, explicitly accounting for the corrugated substrate (modeled as a sinusoid). The model results show an attenuation of the topographic contours by ~30% for tip distances within 5 Å of the surface. Results also indicate a deviation from the Hamaker force law for a sphere interacting with a flat surface.
Systemization and Use of Atomic Data for Astrophysical Modeling
NASA Astrophysics Data System (ADS)
Brickhouse, Nancy S.
The growth of supercomputing capabilities over the past decade has led to tremendous opportunities to produce theoretical atomic data for use in modeling astrophysical plasmas; however, not all data are created equally. Both accurate and complete atomic data are important to astrophysical modeling via plasma codes. Critical theoretical evaluations, experimental benchmarks, and even astrophysical observations themselves are all useful in assessing the temperatures, densities, opacities, abundances, and other physical quantities determined from spectroscopy. The database challenge for the future is to move toward increasing both flexibility and standardization of atomic data formats so that the quality of the data can be taken into account in modeling. Problems in X-ray spectroscopy will illustrate the importance of opening up what has often been a black box to many astronomers.
The atomic approach for the Coqblin-Schrieffer model
NASA Astrophysics Data System (ADS)
Figueira, M. S.; Saguia, A.; Foglio, M. E.; Silva-Valencia, J.; Franco, R.
2014-12-01
In this work we consider the Coqblin-Schrieffer model when the spin is S = 1 / 2. The atomic solution has eight states: four conduction and two localized states, and we can then calculate the eigenenergies and eigenstates analytically. From this solution, employing the cumulant Green's functions results of the Anderson model, we build a "seed", that works as the input of the atomic approach, developed earlier by some of us. We obtain the T-matrix as well as the conduction Green's function of the model, both for the impurity and the lattice cases. The generalization for other moments within N states follows the same steps. We present results both for the impurity as well as for the lattice case and we indicate possible applications of the method to study ultra cold atoms confined in optical superlattices and Kondo insulators. In this last case, our results support an insulator-metal transition as a function of the temperature.
NASA Astrophysics Data System (ADS)
Biondi, Filippo
2015-04-01
SAR Tomography is the extension of the conventional interferometric radar signal processing, where the radar image formation is extended in the height dimension. In order to improve the vertical resolution with respect to the classical Fourier methods, high resolution approaches, based on the Convex Optimization, has been implemented. This methods recast in the Compressed Sensing (CS) framework that optimizes tomographic smooth profiles via atomic decomposition, in order to retrieve the sparsity condition. The optimum solution has been estimated by Interior Point Methods. The problem for such kind of signal processing is the loss of the tomographic phase data, if optimizing by CS directly in the complex domain, so only the optimized energy information is available. In this paper a method to estimate an optimized spectra and phase information, is proposed by projecting both In phase and Quadrature (I-Q) vector components of each tomographic resolution cell spanned on the real and the imaginary components. The tomographic solutions has been estimated by processing sets of multi-baseline SAR data, in a full polarimetric configuration, acquired by the TropiSAR campaign in 2009 by ONERA. The performance enhancement of the principal decomposition parameters for the tomographic vertical planes analysis has been demonstrated.
Low-resolution density maps from atomic models: how stepping "back" can be a step "forward".
Belnap, D M; Kumar, A; Folk, J T; Smith, T J; Baker, T S
1999-01-01
Atomic-resolution structures have had a tremendous impact on modern biological science. Much useful information also has been gleaned by merging and correlating atomic-resolution structural details with lower-resolution (15-40 A), three-dimensional (3D) reconstructions computed from images recorded with cryo-transmission electron microscopy (cryoTEM) procedures. One way to merge these structures involves reducing the resolution of an atomic model to a level comparable to a cryoTEM reconstruction. A low-resolution density map can be derived from an atomic-resolution structure by retrieving a set of atomic coordinates editing the coordinate file, computing structure factors from the model coordinates, and computing the inverse Fourier transform of the structure factors. This method is a useful tool for structural studies primarily in combination with 3D cryoTEM reconstructions. It has been used to assess the quality of 3D reconstructions, to determine corrections for the phase-contrast transfer function of the transmission electron microscope, to calibrate the dimensions and handedness of 3D reconstructions, to produce difference maps, to model features in macromolecules or macromolecular complexes, and to generate models to initiate model-based determination of particle orientation and origin parameters for 3D reconstruction.
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.
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
Bayesian Inference of Initial Models in Cryo-Electron Microscopy Using Pseudo-atoms
Joubert, Paul; Habeck, Michael
2015-01-01
Single-particle cryo-electron microscopy is widely used to study the structure of macromolecular assemblies. Tens of thousands of noisy two-dimensional images of the macromolecular assembly viewed from different directions are used to infer its three-dimensional structure. The first step is to estimate a low-resolution initial model and initial image orientations. This is a challenging global optimization problem with many unknowns, including an unknown orientation for each two-dimensional image. Obtaining a good initial model is crucial for the success of the subsequent refinement step. We introduce a probabilistic algorithm for estimating an initial model. The algorithm is fast, has very few algorithmic parameters, and yields information about the precision of estimated model parameters in addition to the parameters themselves. Our algorithm uses a pseudo-atomic model to represent the low-resolution three-dimensional structure, with isotropic Gaussian components as moveable pseudo-atoms. This leads to a significant reduction in the number of parameters needed to represent the three-dimensional structure, and a simplified way of computing two-dimensional projections. It also contributes to the speed of the algorithm. We combine the estimation of the unknown three-dimensional structure and image orientations in a Bayesian framework. This ensures that there are very few parameters to set, and specifies how to combine different types of prior information about the structure with the given data in a systematic way. To estimate the model parameters we use Markov chain Monte Carlo sampling. The advantage is that instead of just obtaining point estimates of model parameters, we obtain an ensemble of models revealing the precision of the estimated parameters. We demonstrate the algorithm on both simulated and real data. PMID:25762328
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
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.
Richter, Wagner E; Silva, Arnaldo F; Bruns, Roy E
2017-04-07
The inclusion of atomic polarizations for describing molecular electronic structure changes on vibration is shown to be necessary for coherent infrared intensity modeling. Atomic charges from the ChelpG partition scheme and atomic charges and dipoles from Quantum Theory of Atoms in Molecules (QTAIM) were employed within two different models to describe the stretching and bending vibrational intensities of the C-H, C-F, and C=O groups. The model employing the QTAIM parameters was the Charge-Charge Transfer and Dipolar Polarization model (QTAIM/CCTDP), and the model employing the ChelpG charges was the Equilibrium Charge-Charge Flux (ChelpG/ECCF). The QTAIM/CCTDP models result in characteristic proportions of the charge-charge transfer-dipolar polarization contributions even though their sums giving the total intensities do not discriminate between these vibrations. According to the QTAIM/CCTDP model, the carbon monoxide intensity has electronic structure changes similar to those of the carbonyl stretches whereas they resemble those of the CH stretches for the ChelpG/ECCF model.
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.
Modelling of snow avalanche dynamics: influence of model parameters
NASA Astrophysics Data System (ADS)
Bozhinskiy, A. N.
The three-parameter hydraulic model of snow avalanche dynamics including the coefficients of dry and turbulent friction and the coefficient of new-snow-mass entrainment was investigated. The 'Domestic' avalanche site in Elbrus region, Caucasus, Russia, was chosen as the model avalanche range. According to the model, the fixed avalanche run-out can be achieved with various combinations of model parameters. At the fixed value of the coefficient of entrainment me, we have a curve on a plane of the coefficients of dry and turbulent friction. It was found that the family of curves (me is a parameter) are crossed at the single point. The value of the coefficient of turbulent friction at the cross-point remained practically constant for the maximum and average avalanche run-outs. The conclusions obtained are confirmed by the results of modelling for six arbitrarily chosen avalanche sites: three in the Khibiny mountains, Kola Peninsula, Russia, two in the Elbrus region and one idealized site with an exponential longitudinal profile. The dependences of run-out on the coefficient of dry friction are constructed for all the investigated avalanche sites. The results are important for the statistical simulation of avalanche dynamics since they suggest the possibility of using only one random model parameter, namely, the coefficient of dry friction, in the model. The histograms and distribution functions of the coefficient of dry friction are constructed and presented for avalanche sites Nos 22 and 43 (Khibiny mountains) and 'Domestic', with the available series of field data.
A model to predict image formation in Atom probe Tomography.
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.
Model based control of dynamic atomic force microscope
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.
Model based control of dynamic atomic force microscope
NASA Astrophysics Data System (ADS)
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.
Model based control of dynamic atomic force microscope.
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.
Estimation of Parameters in Latent Class Models with Constraints on the Parameters.
1986-06-01
parameter. This rules out models which characterize each Pkj in terms of conjoint effects of item and state parameters, as the Rasch model does, for... example . It also rules out models that impose ordering constraints on the Pkj’S. Thus, while many interesting models can be cast in terms of equality...ONR86-1 m 4 4. TITLE (mnd Subtitle) S. TYPE OF REPORT & PERIOD COVERED Estimation of Parameters in Latent Class Models with Constraints on the
Modeling and optimizing of the random atomic spin gyroscope drift based on the atomic spin gyroscope
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.
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.
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.
Chen, Chunxia; Depa, Praveen; Sakai, Victoria García; Maranas, Janna K; Lynn, Jeffrey W; Peral, Inmaculada; Copley, John R D
2006-06-21
We compare static and dynamic properties obtained from three levels of modeling for molecular dynamics simulation of poly(ethylene oxide) (PEO). Neutron scattering data are used as a test of each model's accuracy. The three simulation models are an explicit atom (EA) model (all the hydrogens are taken into account explicitly), a united atom (UA) model (CH(2) and CH(3) groups are considered as a single unit), and a coarse-grained (CG) model (six united atoms are taken as one bead). All three models accurately describe the PEO static structure factor as measured by neutron diffraction. Dynamics are assessed by comparison to neutron time of flight data, which follow self-motion of protons. Hydrogen atom motion from the EA model and carbon/oxygen atom motion from the UA model closely follow the experimental hydrogen motion, while hydrogen atoms reinserted in the UA model are too fast. The EA and UA models provide a good description of the orientation properties of C-H vectors measured by nuclear magnetic resonance experiments. Although dynamic observables in the CG model are in excellent agreement with their united atom counterparts, they cannot be compared to neutron data because the time after which the CG model is valid is greater than the neutron decay times.
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.
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…
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…
Local correlation energies of atoms, ions and model systems
NASA Astrophysics Data System (ADS)
Umrigar, Cyrus; Huang, Chien-Jung
1997-03-01
We present nearly local definitions of the correlation energy density, and its potential and kinetic components, and evaluate them for several atoms, ions and model systems. This information provides valuable guidance in constructing better correlation functionals than those in common use, such as the local density approximation (LDA) and the various generalized gradient approximations (GGAs). The true local correlation energy per electron has oscillations, reflecting the shell-structure, whereas the LDA approximation to it is monotonic. In addition we demonstrate that, for two-electron systems, the quantum chemistry and the density functional definitions of the correlation energy approach each other with increasing atomic number as 1/Z^3.
NASA Astrophysics Data System (ADS)
Smirnova, K. I.; Murga, M. S.; Wiebe, D. S.; Sobolev, A. M.
2017-08-01
The relationships between atomic and molecular hydrogen and dust of various sizes in extragalactic star-forming regions are considered, based on observational data from the Spitzer and Herschel infrared space telescopes, the Very Large Array (atomic hydrogen emission) and IRAM (CO emission). The source sample consists of approximately 300 star-forming regions in 11 nearby galaxies. Aperture photometry has been applied to measure the fluxes in eight infrared bands (3.6, 4.5, 5.8, 8, 24, 70, 100, and 160 μm), the atomic hydrogen 21 cm line, and CO (2-1) line. The parameters of the dust in the starforming regions were determined via synthetic-spectra fitting, such as the total dust mass, the fraction of polycyclic aromatic hydrocarbons (PAHs), etc. Comparison of the observed fluxes with the measured parameters shows that the relationships between atomic hydrogen, molecular hydrogen, and dust are different in low- and high-metallicity regions. Low-metallicity regions contain more atomic gas, but less molecular gas and dust, including PAHs. The mass of dust constitutes about 1% of the mass of molecular gas in all regions considered. Fluxes produced by atomic and molecular gas do not correlate with the parameters of the stellar radiation, whereas the dust fluxes grow with increasing mean intensity of stellar radiation and the fraction of enhanced stellar radiation. The ratio of the fluxes at 8 and 24 μm, which characterizes the PAH content, decreases with increasing intensity of the stellar radiation, possibly indicating evolutionary variations of the PAH content. The results confirm that the contribution of the 24 μm emission to the total IR luminosity of extragalactic star-forming regions does not depend on the metallicity.
Modeling Protein Structure at Near Atomic Resolutions With Gorgon
Baker, Matthew L.; Abeysinghe, Sasakthi S.; Schuh, Stephen; Coleman, Ross A.; Abrams, Austin; Marsh, Michael P.; Hryc, Corey F.; Ruths, Troy; Chiu, Wah; Ju, Tao
2011-01-01
Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure. PMID:21296162
Derivation of Distributed Models of Atomic Polarizability for Molecular Simulations.
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.
Atomic detection in microwave cavity experiments: A dynamical model
Rossi, R. Jr.; Nemes, M. C.; Peixoto de Faria, J. G.
2007-06-15
We construct a model for the atomic detection in the context of cavity quantum electrodynamics (QED) used to study coherence properties of superpositions of states of an electromagnetic mode. Analytic expressions for the atomic ionization are obtained, considering the imperfections of the measurement process due to the probabilistic nature of the interactions between the ionization field and the atoms. We provide for a dynamical content for the available expressions for the counting rates considering limited efficiency of detectors. Moreover, we include false countings. The influence of these imperfections on the information about the state of the cavity mode is obtained. In order to test the adequacy of our approach, we investigate a recent experiment reported by Maitre [X. Maitre et al., Phys. Rev. Lett. 79, 769 (1997)] and we obtain excellent agreement with the experimental results.
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.
Atomic Data and Modelling for Fusion: the ADAS Project
Summers, H. P.; O'Mullane, M. G.
2011-05-11
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.
Quantum-mechanical estimation of rectangular waveguide parameters with atomic entropy computation
NASA Astrophysics Data System (ADS)
Kumar, L.; Shankar Pandey, V.; Parthasarathy, H.; Shrimali, V.; Varshney, G.
2017-06-01
The field within a rectangular waveguide is associated with an electromagnetic four-potential which is used to excite a 3-dimensional (3D) quantum harmonic oscillator/atom within the guide and from the transition probabilities of the oscillators/atoms within the guide, we estimate the mode that has been excited as well as dimension of the guide. Finally, we make a small computation regarding the quantum information transmitted by the waveguide field (both classical and quantum e-m fields) having random phases and amplitudes to the atomic oscillator.
Theory and modelling of diamond fracture from an atomic perspective.
Brenner, Donald W; Shenderova, Olga A
2015-03-28
Discussed in this paper are several theoretical and computational approaches that have been used to better understand the fracture of both single-crystal and polycrystalline diamond at the atomic level. The studies, which include first principles calculations, analytic models and molecular simulations, have been chosen to illustrate the different ways in which this problem has been approached, the conclusions and their reliability that have been reached by these methods, and how these theory and modelling methods can be effectively used together.
[Calculation of parameters in forest evapotranspiration model].
Wang, Anzhi; Pei, Tiefan
2003-12-01
Forest evapotranspiration is an important component not only in water balance, but also in energy balance. It is a great demand for the development of forest hydrology and forest meteorology to simulate the forest evapotranspiration accurately, which is also a theoretical basis for the management and utilization of water resources and forest ecosystem. Taking the broadleaved Korean pine forest on Changbai Mountain as an example, this paper constructed a mechanism model for estimating forest evapotranspiration, based on the aerodynamic principle and energy balance equation. Using the data measured by the Routine Meteorological Measurement System and Open-Path Eddy Covariance Measurement System mounted on the tower in the broadleaved Korean pine forest, the parameters displacement height d, stability functions for momentum phi m, and stability functions for heat phi h were ascertained. The displacement height of the study site was equal to 17.8 m, near to the mean canopy height, and the functions of phi m and phi h changing with gradient Richarson number R i were constructed.
Elastic properties of compressed crystalline Ne in the model of deformable atoms
NASA Astrophysics Data System (ADS)
Troitskaya, E. P.; Chabanenko, V. V.; Zhikharev, I. V.; Gorbenko, Ie. Ie.; Pilipenko, E. A.
2013-02-01
An ab initio version of the model with deformable atoms has been constructed to investigate the elastic properties of compressed crystalline neon. Approximations for the calculating parameters of quadrupole deformation of atomic electron shells have been discussed. It has been shown that the pressure dependence of the deviation from the Cauchy relation δ is the result of two competitive interactions, namely, the many-body and electron-phonon interactions, which manifests itself in the deformation of atomic electron shells during the shift of nuclei. In the case of Ne, contributions of these interactions are compensated to a large degree, which provides a weakly pressure-dependent positive value for δ. The agreement of calculated elastic moduli and deviations from the Cauchy relation for Ne with the experiment is good.
Anisotropic character of atoms in a two-dimensional Frenkel—Kontorova model
NASA Astrophysics Data System (ADS)
Wang, Cang-Long; Duan, Wen-Shan; Chen, Jian-Min; Shi, Yu-Ren
2011-01-01
The dynamics of a certain density of interacting atoms arranged on a two-dimensional square lattice, which is made to slide over a two-dimensional periodic substrate potential with also the quare lattice symmetry, in the presence of dissipation, by an externally applied driving force, is studied. By rotating the misfit angle θ, the dynamical behaviour displays two different tribological regimes: one is smooth, the other becomes intermittent. We comment both on the nature of the atomic dynamics in the locked-to-sliding transition, and on the dynamical states displayed during the atom motion at different values of the driving force. In tribological applications, we also investigate how the main model parameters such as the stiffness strength and the magnitude of the adhesive force affect the static friction of the system. In particular, our simulation indicates that the superlubricity will appear.
Extracting Structure Parameters of Dimers for Molecular Tunneling Ionization Model
NASA Astrophysics Data System (ADS)
Song-Feng, Zhao; Fang, Huang; Guo-Li, Wang; Xiao-Xin, Zhou
2016-03-01
We determine structure parameters of the highest occupied molecular orbital (HOMO) of 27 dimers for the molecular tunneling ionization (so called MO-ADK) model of Tong et al. [Phys. Rev. A 66 (2002) 033402]. The molecular wave functions with correct asymptotic behavior are obtained by solving the time-independent Schrödinger equation with B-spline functions and molecular potentials which are numerically created using the density functional theory. We examine the alignment-dependent tunneling ionization probabilities from MO-ADK model for several molecules by comparing with the molecular strong-field approximation (MO-SFA) calculations. We show the molecular Perelomov-Popov-Terent'ev (MO-PPT) can successfully give the laser wavelength dependence of ionization rates (or probabilities). Based on the MO-PPT model, two diatomic molecules having valence orbital with antibonding systems (i.e., Cl2, Ne2) show strong ionization suppression when compared with their corresponding closest companion atoms. Supported by National Natural Science Foundation of China under Grant Nos. 11164025, 11264036, 11465016, 11364038, the Specialized Research Fund for the Doctoral Program of Higher Education of China under Grant No. 20116203120001, and the Basic Scientific Research Foundation for Institution of Higher Learning of Gansu Province
Photon Atomic Parameters of Nonessential Amino Acids for Radiotherapy and Diagnostics
Bursalıoğlu, Ertuğrul O.; İçelli, Orhan; Balkan, Begüm; Kavanoz, H. Birtan; Okutan, Mustafa
2014-01-01
The total mass attenuation coefficients (μt) (cm2/g) and atomic, molecular, and electronic effective cross sections have been calculated for nonessential amino acids that contain H, C, N, and O such as tyrosine, aspartate, glutamine, alanine, asparagine, aspartic acid, cysteine, and glycine in the wide energy region 0.015–15 MeV. The variations with energy of total mass attenuation coefficients and atomic, molecular, and electronic cross sections are shown for all photon interactions. PMID:25548658
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.
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.
GISAXS studies of model nanocatalysts synthesized by atomic cluster deposition.
Vajda, S.; Winans, R. E.; Ballentine, G. E.; Elam, J. W.; Lee, B.; Pellin, M. J.; Seifert, S.; Tikhonov, G. Y.; Tomczyk, N. A.
2006-01-01
Small nanoparticles possess unique, strongly size-dependent chemical and physical properties that make these particles ideal candidates for a number of applications, including catalysts or sensors due to their significantly higher activity and selectivity than their more bulk-like analogs. In the smallest size regime, nanocluster catalytic activity changes by orders of magnitude with the addition or removal of a single atom, thus allowing a tuning of the properties of these particles atom by atom. Equally effective tuning knobs for these model catalysts are the composition and morphology of the support, which can dramatically change the electronic structure of these particles, leading to drastic changes in both activity and specificity. However, the Achilles heal of these particles remains their sintering at elevated temperatures or when exposed to mixtures of reactive gases. In the presented paper, the issues of thermal stability, isomerization and growth of models of catalytic active sites - atomic gold and platinum clusters and nanoparticles produced by cluster deposition on technologically relevan oxide surfaces - is addressed by employing synchrotron X-ray radiation techniques.
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.
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
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.
AtomDB and PyAtomDB: Atomic Data and Modelling Tools for High Energy and Non-Maxwellian Plasmas
NASA Astrophysics Data System (ADS)
Foster, Adam; Smith, Randall K.; Brickhouse, Nancy S.; Cui, Xiaohong
2016-04-01
The release of AtomDB 3 included a large wealth of inner shell ionization and excitation data allowing accurate modeling of non-equilibrium plasmas. We describe the newly calculated data and compare it to published literature data. We apply the new models to existing supernova remnant data such as W49B and N132D. We further outline progress towards AtomDB 3.1, including a new energy-dependent charge exchange cross sections.We present newly developed models for the spectra of electron-electron bremsstrahlung and those due to non-Maxwellian electron distributions.Finally, we present our new atomic database access tools, released as PyAtomDB, allowing powerful use of the underlying fundamental atomic data as well as the spectral emissivities.
NASA Astrophysics Data System (ADS)
Miki, K.; Panesi, M.; Prudencio, E. E.; Prudhomme, S.
2012-05-01
The objective in this paper is to analyze some stochastic models for estimating the ionization reaction rate constant of atomic Nitrogen (N + e- → N+ + 2e-). Parameters of the models are identified by means of Bayesian inference using spatially resolved absolute radiance data obtained from the Electric Arc Shock Tube (EAST) wind-tunnel. The proposed methodology accounts for uncertainties in the model parameters as well as physical model inadequacies, providing estimates of the rate constant that reflect both types of uncertainties. We present four different probabilistic models by varying the error structure (either additive or multiplicative) and by choosing different descriptions of the statistical correlation among data points. In order to assess the validity of our methodology, we first present some calibration results obtained with manufactured data and then proceed by using experimental data collected at EAST experimental facility. In order to simulate the radiative signature emitted in the shock-heated air plasma, we use a one-dimensional flow solver with Park's two-temperature model that simulates non-equilibrium effects. We also discuss the implications of the choice of the stochastic model on the estimation of the reaction rate and its uncertainties. Our analysis shows that the stochastic models based on correlated multiplicative errors are the most plausible models among the four models proposed in this study. The rate of the atomic Nitrogen ionization is found to be (6.2 ± 3.3) × 1011 cm3 mol-1 s-1 at 10,000 K.
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.
Improvement of hydrological model calibration by selecting multiple parameter ranges
NASA Astrophysics Data System (ADS)
Wu, Qiaofeng; Liu, Shuguang; Cai, Yi; Li, Xinjian; Jiang, Yangming
2017-01-01
The parameters of hydrological models are usually calibrated to achieve good performance, owing to the highly non-linear problem of hydrology process modelling. However, parameter calibration efficiency has a direct relation with parameter range. Furthermore, parameter range selection is affected by probability distribution of parameter values, parameter sensitivity, and correlation. A newly proposed method is employed to determine the optimal combination of multi-parameter ranges for improving the calibration of hydrological models. At first, the probability distribution was specified for each parameter of the model based on genetic algorithm (GA) calibration. Then, several ranges were selected for each parameter according to the corresponding probability distribution, and subsequently the optimal range was determined by comparing the model results calibrated with the different selected ranges. Next, parameter correlation and sensibility were evaluated by quantifying two indexes, RC Y, X and SE, which can be used to coordinate with the negatively correlated parameters to specify the optimal combination of ranges of all parameters for calibrating models. It is shown from the investigation that the probability distribution of calibrated values of any particular parameter in a Xinanjiang model approaches a normal or exponential distribution. The multi-parameter optimal range selection method is superior to the single-parameter one for calibrating hydrological models with multiple parameters. The combination of optimal ranges of all parameters is not the optimum inasmuch as some parameters have negative effects on other parameters. The application of the proposed methodology gives rise to an increase of 0.01 in minimum Nash-Sutcliffe efficiency (ENS) compared with that of the pure GA method. The rising of minimum ENS with little change of the maximum may shrink the range of the possible solutions, which can effectively reduce uncertainty of the model performance.
Atomically precise gold nanoclusters as new model catalysts.
Li, Gao; Jin, Rongchao
2013-08-20
Many industrial catalysts involve nanoscale metal particles (typically 1-100 nm), and understanding their behavior at the molecular level is a major goal in heterogeneous catalyst research. However, conventional nanocatalysts have a nonuniform particle size distribution, while catalytic activity of nanoparticles is size dependent. This makes it difficult to relate the observed catalytic performance, which represents the average of all particle sizes, to the structure and intrinsic properties of individual catalyst particles. To overcome this obstacle, catalysts with well-defined particle size are highly desirable. In recent years, researchers have made remarkable advances in solution-phase synthesis of atomically precise nanoclusters, notably thiolate-protected gold nanoclusters. Such nanoclusters are composed of a precise number of metal atoms (n) and of ligands (m), denoted as Aun(SR)m, with n ranging up to a few hundred atoms (equivalent size up to 2-3 nm). These protected nanoclusters are well-defined to the atomic level (i.e., to the point of molecular purity), rather than defined based on size as in conventional nanoparticle synthesis. The Aun(SR)m nanoclusters are particularly robust under ambient or thermal conditions (<200 °C). In this Account, we introduce Aun(SR)m nanoclusters as a new, promising class of model catalyst. Research on the catalytic application of Aun(SR)m nanoclusters is still in its infancy, but we use Au₂₅(SR)₁₈ as an example to illustrate the promising catalytic properties of Aun(SR)m nanoclusters. Compared with conventional metallic nanoparticle catalysts, Aun(SR)m nanoclusters possess several distinct features. First of all, while gold nanoparticles typically adopt a face-centered cubic (fcc) structure, Aun(SR)m nanoclusters (<2 nm) tend to adopt different atom-packing structures; for example, Au₂₅(SR)₁₈ (1 nm metal core, Au atomic center to center distance) has an icosahedral structure. Secondly, their ultrasmall
Sample Size and Item Parameter Estimation Precision When Utilizing the One-Parameter "Rasch" Model
ERIC Educational Resources Information Center
Custer, Michael
2015-01-01
This study examines the relationship between sample size and item parameter estimation precision when utilizing the one-parameter model. Item parameter estimates are examined relative to "true" values by evaluating the decline in root mean squared deviation (RMSD) and the number of outliers as sample size increases. This occurs across…
Semirelativistic model for ionization of atomic hydrogen by electron impact
NASA Astrophysics Data System (ADS)
Attaourti, Y.; Taj, S.; Manaut, B.
2005-06-01
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.
Extended Bose-Hubbard models with ultracold magnetic atoms.
Baier, S; Mark, M J; Petter, D; Aikawa, K; Chomaz, L; Cai, Z; Baranov, M; Zoller, P; Ferlaino, F
2016-04-08
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.
Extended Bose-Hubbard models with ultracold magnetic atoms
NASA Astrophysics Data System (ADS)
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.
Semirelativistic model for ionization of atomic hydrogen by electron impact
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.
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.
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.
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…
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…
An interface capturing scheme for modeling atomization in compressible flows
NASA Astrophysics Data System (ADS)
Garrick, Daniel P.; Hagen, Wyatt A.; Regele, Jonathan D.
2017-09-01
The study of atomization in supersonic flow is critical to ensuring reliable ignition of scramjet combustors under startup conditions. Numerical methods incorporating surface tension effects have largely focused on the incompressible regime as most atomization applications occur at low Mach numbers. Simulating surface tension effects in compressible flow requires robust numerical methods that can handle discontinuities caused by both shocks and material interfaces with high density ratios. In this work, a shock and interface capturing scheme is developed that uses the Harten-Lax-van Leer-Contact (HLLC) Riemann solver while a Tangent of Hyperbola for INterface Capturing (THINC) interface reconstruction scheme retains the fluid immiscibility condition in the volume fraction and phasic densities in the context of the five equation model. The approach includes the effects of compressibility, surface tension, and molecular viscosity. One and two-dimensional benchmark problems demonstrate the desirable interface sharpening and conservation properties of the approach. Simulations of secondary atomization of a cylindrical water column after its interaction with a shockwave show good qualitative agreement with experimentally observed behavior. Three-dimensional examples of primary atomization of a liquid jet in a Mach 2 crossflow demonstrate the robustness of the method.
Mg line formation in late-type stellar atmospheres. I. The model atom
NASA Astrophysics Data System (ADS)
Osorio, Y.; Barklem, P. S.; Lind, K.; Belyaev, A. K.; Spielfiedel, A.; Guitou, M.; Feautrier, N.
2015-07-01
Context. Magnesium is an element of significant astrophysical importance, often traced in late-type stars using lines of neutral magnesium, which is expected to be subject to departures from local thermodynamic equilibrium (LTE). The importance of Mg , together with the unique range of spectral features in late-type stars probing different parts of the atom, as well as its relative simplicity from an atomic physics point of view, makes it a prime target and test bed for detailed ab initio non-LTE modelling in stellar atmospheres. Previous non-LTE modelling of spectral line formation has, however, been subject to uncertainties due to lack of accurate data for inelastic collisions with electrons and hydrogen atoms. Aims: In this paper we build and test a Mg model atom for spectral line formation in late-type stars with new or recent inelastic collision data and no associated free parameters. We aim to reduce these uncertainties and thereby improve the accuracy of Mg non-LTE modelling in late-type stars. Methods: For the low-lying states of Mg i, electron collision data were calculated using the R-matrix method. Hydrogen collision data, including charge transfer processes, were taken from recent calculations by some of us. Calculations for collisional broadening by neutral hydrogen were also performed where data were missing. These calculations, together with data from the literature, were used to build a model atom. This model was then employed in the context of standard non-LTE modelling in 1D (including average 3D) model atmospheres in a small set of stellar atmosphere models. First, the modelling was tested by comparisons with observed spectra of benchmark stars with well-known parameters. Second, the spectral line behaviour and uncertainties were explored by extensive experiments in which sets of collisional data were changed or removed. Results: The modelled spectra agree well with observed spectra from benchmark stars, showing much better agreement with line
Modeling of Atomic Processes for X-Ray Laser Plasmas
1988-07-01
temperatures where models such as Thomas-Fermi or Debye - Huckel are known to be inadequate. The calculations done here show that, with increasing plasma... theory . Comparison of experimental data with the IPA calculations shows that for some simple systems such as a neutral few-electron atom (Lithium, for...linear fashion - unlike Debye -screening, which is known to be inadequate for screening by bound electrons. The two-component DFM is applicable for
NASA Technical Reports Server (NTRS)
Lee, J. H.; Timmons, R. B.; Stief, L. J.
1976-01-01
It is pointed out that the investigated reaction of oxygen with dimethyl sulfide may play an important role in photochemical smog formation and in the chemical evolution of dense interstellar clouds. Kinetic data were obtained with the aid of the flash photolysis-resonance fluorescence method. The photodecomposition of molecular oxygen provided the oxygen atoms for the experiments. The decay of atomic oxygen was studied on the basis of resonance fluorescence observations. Both reactions investigated were found to be fast processes. A negative temperature dependence of the rate constants for reactions with dimethyl sulfide was observed.
Comparison of liposome entrapment parameters by optical and atomic absorption spectrophotometry.
Yoss, N L; Popescu, O; Pop, V I; Porutiu, D; Kummerow, F A; Benga, G
1985-01-01
Methods for the complete characterization of liposomes prepared by ether-injection are described in detail. The validity of atomic absorption spectrophotometry for measuring markers of trapped volume was checked by comparative determinations of markers with established optical spectrophotometrical methods. The favorable results using atomic absorption spectrophotometry to quantitate the marker Mn2+ are of particular relevance as manganese ion is also the paramagnetic probe in n.m.r. measurements of water permeability of liposomes; our results indicate that in such measurements no other marker need be incorporated.
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.
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.
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.
Chemical domain of QSAR models from atom-centered fragments.
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.
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…
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…
Bichara, C.; Bergman, C.; Mathieu, J.-C.
1985-01-01
Monte Carlo calculations are carried out to give exact values of some thermodynamic properties of alloys. The calculations are performed within the framework of the surrounded atom model the main assumptions of which are: quasilattice structure of the alloy, nearest neighbour interactions, description of the configuration in terms of ''surrounded atoms''. The results are then compared wit those obtained using current approximations: the Bragg-Williams treatment and the quasichemical treatment. This work enables the authors to generalize the previous conclusions drawn in the study of the regular solution model. In every case, whatever the sign of the interactions (ordering or clustering tendency) Monte Carlo calculations yield a local order that both approximations fail to reproduce. In order to compare the calculations with experimental data, Cowley's short range order parameter is calculated by Monte Carlo and by the approximate methods (the parameters of the surrounded atom model are derived from thermodynamic data). The Monte Carlo values compare better than the quasichemical ones with the data obtained by X-ray or neutron diffraction in three actual systems.
Atomic collision processes for modelling cool star spectra
NASA Astrophysics Data System (ADS)
Barklem, Paul
2015-05-01
The abundances of chemical elements in cool stars are very important in many problems in modern astrophysics. They provide unique insight into the chemical and dynamical evolution of the Galaxy, stellar processes such as mixing and gravitational settling, the Sun and its place in the Galaxy, and planet formation, to name a just few examples. Modern telescopes and spectrographs measure stellar spectral lines with precision of order 1 per cent, and planned surveys will provide such spectra for millions of stars. However, systematic errors in the interpretation of observed spectral lines leads to abundances with uncertainties greater than 20 per cent. Greater precision in the interpreted abundances should reasonably be expected to lead to significant discoveries, and improvements in atomic data used in stellar atmosphere models play a key role in achieving such advances in precision. In particular, departures from the classical assumption of local thermodynamic equilibrium (LTE) represent a significant uncertainty in the modelling of stellar spectra and thus derived chemical abundances. Non-LTE modelling requires large amounts of radiative and collisional data for the atomic species of interest. I will focus on inelastic collision processes due to electron and hydrogen atom impacts, the important perturbers in cool stars, and the progress that has been made. I will discuss the impact on non-LTE modelling, and what the modelling tells us about the types of collision processes that are important and the accuracy required. More specifically, processes of fundamentally quantum mechanical nature such as spin-changing collisions and charge transfer have been found to be very important in the non-LTE modelling of spectral lines of lithium, oxygen, sodium and magnesium.
Bayesian approach to decompression sickness model parameter estimation.
Howle, L E; Weber, P W; Nichols, J M
2017-03-01
We examine both maximum likelihood and Bayesian approaches for estimating probabilistic decompression sickness model parameters. Maximum likelihood estimation treats parameters as fixed values and determines the best estimate through repeated trials, whereas the Bayesian approach treats parameters as random variables and determines the parameter probability distributions. We would ultimately like to know the probability that a parameter lies in a certain range rather than simply make statements about the repeatability of our estimator. Although both represent powerful methods of inference, for models with complex or multi-peaked likelihoods, maximum likelihood parameter estimates can prove more difficult to interpret than the estimates of the parameter distributions provided by the Bayesian approach. For models of decompression sickness, we show that while these two estimation methods are complementary, the credible intervals generated by the Bayesian approach are more naturally suited to quantifying uncertainty in the model parameters. Copyright © 2017 Elsevier Ltd. All rights reserved.
Elastic properties of compressed cryocrystals in a deformed atom model
NASA Astrophysics Data System (ADS)
Gorbenko, Ie. Ie.; Zhikharev, I. V.; Troitskaya, E. P.; Chabanenko, Val. V.; Pilipenko, E. A.
2013-06-01
A model with deformed atom shells was built to investigate the elastic properties of rare-gas Ne and Kr crystals under high pressure. It is shown that the observed deviation from the Cauchy relation δ cannot be adequately reproduced when taking into account only the many-body interaction. The individual pressure dependence of δ is the result of competition of the many-body interaction and the quadrupole interaction associated with the quadrupole-type deformation of electron shells of the atoms during the displacement of the nuclei. Each kind of interaction makes a strongly pressure dependent contribution to δ. In the case of Ne and Kr, contributions of these interactions are compensated to a good precision, providing δ being almost constant against pressure.
From deep TLS validation to ensembles of atomic models built from elemental motions
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.
Theoretical model for electrophilic oxygen atom insertion into hydrocarbons
Bach, R.D.; Su, M.D. ); Andres, J.L. Wayne State Univ., Detroit, MI ); McDouall, J.J.W. )
1993-06-30
A theoretical model suggesting the mechanistic pathway for the oxidation of saturated-alkanes to their corresponding alcohols and ketones is described. Water oxide (H[sub 2]O-O) is employed as a model singlet oxygen atom donor. Molecular orbital calculations with the 6-31G basis set at the MP2, QCISD, QCISD(T), CASSCF, and MRCI levels of theory suggest that oxygen insertion by water oxide occurs by the interaction of an electrophilic oxygen atom with a doubly occupied hydrocarbon fragment orbital. The electrophilic oxygen approaches the hydrocarbon along the axis of the atomic carbon p orbital comprising a [pi]-[sub CH(2)] or [pi]-[sub CHCH(3)] fragment orbital to form a carbon-oxygen [sigma] bond. A concerted hydrogen migration to an adjacent oxygen lone pair of electrons affords the alcohol insertion product in a stereoselective fashion with predictable stereochemistry. Subsequent oxidation of the alcohol to a ketone (or aldehyde) occurs in a similar fashion and has a lower activation barrier. The calculated (MP4/6-31G*//MP2/6-31G*) activation barriers for oxygen atom insertion into the C-H bonds of methane, ethane, propane, butane, isobutane, and methanol are 10.7, 8.2, 3.9, 4.8, 4.5, and 3.3 kcal/mol, respectively. We use ab initio molecular orbital calculations in support of a frontier MO theory that provides a unique rationale for both the stereospecificity and the stereoselectivity of insertion of electrophilic oxygen and related electrophiles into the carbon-hydrogen bond. 13 refs., 7 figs., 2 tabs.
DINA Model and Parameter Estimation: A Didactic
ERIC Educational Resources Information Center
de la Torre, Jimmy
2009-01-01
Cognitive and skills diagnosis models are psychometric models that have immense potential to provide rich information relevant for instruction and learning. However, wider applications of these models have been hampered by their novelty and the lack of commercially available software that can be used to analyze data from this psychometric…
Building Relativistic Mean-Field Models for Atomic Nuclei and Neutron Stars
NASA Astrophysics Data System (ADS)
Chen, Wei-Chia; Piekarewicz, Jorge
2014-03-01
Nuclear energy density functional (EDF) theory has been quite successful in describing nuclear systems such as atomic nuclei and nuclear matter. However, when building new models, attention is usually paid to the best-fit parameters only. In recent years, focus has been shifted to the neighborhood around the minimum of the chi-square function as well. This powerful covariance analysis is able to provide important information bridging experiments, observations, and theories. In this work, we attempt to build a specific type of nuclear EDFs, the relativistic mean-field models, which treat atomic nuclei, nuclear matter, and neutron stars on the same footing. The application of covariance analysis can reveal correlations between observables of interest. The purpose is to elucidate the alleged relations between the neutron skin of heavy nuclei and the size of neutron stars, and to develop insight into future investigations.
Intrinsic chirp of attosecond pulses: Single-atom model versus experiment
Kazamias, S.; Balcou, Ph.
2004-06-01
We demonstrate and evaluate the importance of an intrinsic chirp inherent to attosecond pulse creation accompanying high-order harmonic generation in recently published experimental data by Dinu et al. [Phys. Rev. Lett. 91, 063901 (2003)]. We present an analytical model, from which the atomic origin of the harmonic chirp is clearly understood. Moreover, the behavior of the chirp as a function of experimental parameters such as laser intensity is inferred. The comparison between our model and the experimental data provides us with useful information about the conditions in which the high-order harmonics is generated.
Dependence of microwave-excitation signal parameters on frequency stability of caesium atomic clock
NASA Astrophysics Data System (ADS)
Petrov, A. A.; Davydov, V. V.; Vologdin, V. A.; Zalyotov, D. V.
2015-11-01
New scheme of the microwave - excitation signal for the caesium atomic clock is based on method of direct digital synthesis. The theoretical calculations and experimental research showed decrease step frequency tuning by several orders and improvement the spectral characteristics of the output signal of frequency synthesizer. A range of generated output frequencies is expanded, and the possibility of detuning the frequency of the neighboring resonance of spectral line that makes it possible to adjust the C-field in quantum frequency standard is implemented. Experimental research of the metrological characteristics of the quantum frequency standard on the atoms of caesium - 133 with new design scheme of the microwave - excitation signal showed improvement in daily frequency stability on 1.2*10-14.
Distributed parameter modeling of repeated truss structures
NASA Technical Reports Server (NTRS)
Wang, Han-Ching
1994-01-01
A new approach to find homogeneous models for beam-like repeated flexible structures is proposed which conceptually involves two steps. The first step involves the approximation of 3-D non-homogeneous model by a 1-D periodic beam model. The structure is modeled as a 3-D non-homogeneous continuum. The displacement field is approximated by Taylor series expansion. Then, the cross sectional mass and stiffness matrices are obtained by energy equivalence using their additive properties. Due to the repeated nature of the flexible bodies, the mass, and stiffness matrices are also periodic. This procedure is systematic and requires less dynamics detail. The first step involves the homogenization from a 1-D periodic beam model to a 1-D homogeneous beam model. The periodic beam model is homogenized into an equivalent homogeneous beam model using the additive property of compliance along the generic axis. The major departure from previous approaches in literature is using compliance instead of stiffness in homogenization. An obvious justification is that the stiffness is additive at each cross section but not along the generic axis. The homogenized model preserves many properties of the original periodic model.
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
Parameter redundancy in discrete state‐space and integrated models
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
Parameter redundancy in discrete state-space and integrated models.
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. © 2016 The Author. Biometrical Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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)…
Equating Parameter Estimates from the Generalized Graded Unfolding Model.
ERIC Educational Resources Information Center
Roberts, James S.
Three common methods for equating parameter estimates from binary item response theory models are extended to the generalized grading unfolding model (GGUM). The GGUM is an item response model in which single-peaked, nonmonotonic expected value functions are implemented for polytomous responses. GGUM parameter estimates are equated using extended…
Tweaking Model Parameters: Manual Adjustment and Self Calibration
NASA Astrophysics Data System (ADS)
Schulz, B.; Tuffs, R. J.; Laureijs, R. J.; Lu, N.; Peschke, S. B.; Gabriel, C.; Khan, I.
2002-12-01
The reduction of P32 data is not always straight forward and the application of the transient model needs tight control by the user. This paper describes how to access the model parameters within the P32Tools software and how to work with the "Inspect signals per pixel" panel, in order to explore the parameter space and improve the model fit.
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)…
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.
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.
First-Order Quantum Phase Transition for Dicke Model Induced by Atom-Atom Interaction
NASA Astrophysics Data System (ADS)
Zhao, Xiu-Qin; Liu, Ni; Liang, Jiu-Qing
2017-05-01
In this article, we use the spin coherent state transformation and the ground state variational method to theoretically calculate the ground function. In order to consider the influence of the atom-atom interaction on the extended Dicke model’s ground state properties, the mean photon number, the scaled atomic population and the average ground energy are displayed. Using the self-consistent field theory to solve the atom-atom interaction, we discover the system undergoes a first-order quantum phase transition from the normal phase to the superradiant phase, but a famous Dicke-type second-order quantum phase transition without the atom-atom interaction. Meanwhile, the atom-atom interaction makes the phase transition point shift to the lower atom-photon collective coupling strength. Supported by the National Natural Science Foundation of China under Grant Nos. 11275118, 11404198, 91430109, 61505100, 51502189, and the Scientific and Technological Innovation Programs of Higher Education Institutions in Shanxi Province (STIP) under Grant No. 2014102, and the Launch of the Scientific Research of Shanxi University under Grant No. 011151801004, and the National Fundamental Fund of Personnel Training under Grant No. J1103210. The Natural Science Foundation of Shanxi Province under Grant No. 2015011008
Modeling Emission of Heavy Energetic Neutral Atoms from the Heliosphere
NASA Astrophysics Data System (ADS)
Swaczyna, Paweł; Bzowski, Maciej
2017-09-01
Observations of energetic neutral atoms (ENAs) are a fruitful tool for remote diagnosis of the plasma in the heliosphere and its vicinity. So far, instruments detecting ENAs from the heliosphere were configured for observations of hydrogen atoms. Here, we estimate emissions of ENAs of the heavy chemical elements helium, oxygen, nitrogen, and neon. A large portion of the heliospheric ENAs is created in the inner heliosheath from neutralized interstellar pick-up ions (PUIs). We modeled this process and calculated full-sky intensities of ENAs for energies 0.2–130 keV/nuc. We found that the largest fluxes among considered species are expected for helium, smaller for oxygen and nitrogen, and smallest for neon. The obtained intensities are 50–106 times smaller than the hydrogen ENA intensities observed by IBEX. The detection of heavy ENAs will be possible if a future ENA detector is equipped with the capability to measure the masses of observed atoms. Because of different reaction cross-sections among the different species, observations of heavy ENAs can allow for a better understanding of global structure of the heliosphere as well as the transport and energization of PUIs in the heliosphere.
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.
Modelling laser-atom interactions in the strong field regime
NASA Astrophysics Data System (ADS)
Galstyan, Alexander; Popov, Yuri V.; Mota-Furtado, Francisca; O'Mahony, Patrick F.; Janssens, Noël; Jenkins, Samuel D.; Chuluunbaatar, Ochbadrakh; Piraux, Bernard
2017-04-01
We consider the ionisation of atomic hydrogen by a strong infrared field. We extend and study in more depth an existing semi-analytical model. Starting from the time-dependent Schrödinger equation in momentum space and in the velocity gauge we substitute the kernel of the non-local Coulomb potential by a sum of N separable potentials, each of them supporting one hydrogen bound state. This leads to a set of N coupled one-dimensional linear Volterra integral equations to solve. We analyze the gauge problem for the model, the different ways of generating the separable potentials and establish a clear link with the strong field approximation which turns out to be a limiting case of the present model. We calculate electron energy spectra as well as the time evolution of electron wave packets in momentum space. We compare and discuss the results obtained with the model and with the strong field approximation and examine in this context the role of excited states. Contribution to the Topical Issue "Many Particle Spectroscopy of Atoms, Molecules, Clusters and Surfaces", edited by A.N. Grum-Grzhimailo, E.V. Gryzlova, Yu V. Popov, and A.V. Solov'yov.
Euston, Stephen R
2010-10-11
The adsorption of LTP at the decane-water interface was modeled using all-atom and coarse-grained (CG) molecular dynamics simulations. The CG model (300 ns simulation, 1200 ns scaled time) generates equilibrium adsorbed conformations in about 12 h, whereas the equivalent 1200 ns simulation would take about 300 days for the all-atom model. In both models the LTP molecule adsorbs with α-helical regions parallel to the interface with an average tilt angle normal to the interface of 73° for the all-atom model and 62° for the CG model. In the all-atom model, the secondary structure of the LTP is conserved upon adsorption. A considerable proportion of the N-terminal loop of LTP can be found in the decane phase for the all-atom model, whereas in the CG model the protein only penetrates as far as the mixed water-decane interfacial region. This difference may arise due to the different schemes used to parametrize force field parameters in the two models.
Henry, Eric R; Best, Robert B; Eaton, William A
2013-10-29
Advances in computing have enabled microsecond all-atom molecular dynamics trajectories of protein folding that can be used to compare with and test critical assumptions of theoretical models. We show that recent simulations by the Shaw group (10, 11, 14, 15) are consistent with a key assumption of an Ising-like theoretical model that native structure grows in only a few regions of the amino acid sequence as folding progresses. The distribution of mechanisms predicted by simulating the master equation of this native-centric model for the benchmark villin subdomain, with only two adjustable thermodynamic parameters and one temperature-dependent kinetic parameter, is remarkably similar to the distribution in the molecular dynamics trajectories.
Model for fast, nonadiabatic collisions between alkali atoms and diatomic molecules
NASA Astrophysics Data System (ADS)
Hickman, A. P.
1980-11-01
Equations for collisions involving two potential surfaces are presented in the impact parameter approximation. In this approximation, a rectilinear classical trajectory is assumed for the translational motion, leading to a time-dependent Schroedinger's equation for the remaining degrees of freedom. Model potentials are considered for collisions of alkali atoms with diatomic molecules that lead to a particularly simple form of the final equations. Using the Magnus approximation, these equations are solved for parameters chosen to model the process Cs+O2→Cs++O2-, and total cross sections for ion-pair formation are obtained as a function of energy. The results exhibit oscillations that correspond qualitatively to those seen in recent measurements. In addition, the model predicts that the oscillations will become less pronounced as the initial vibrational level of O2 is increased.
Parameter estimation of hydrologic models using data assimilation
NASA Astrophysics Data System (ADS)
Kaheil, Y. H.
2005-12-01
The uncertainties associated with the modeling of hydrologic systems sometimes demand that data should be incorporated in an on-line fashion in order to understand the behavior of the system. This paper represents a Bayesian strategy to estimate parameters for hydrologic models in an iterative mode. The paper presents a modified technique called localized Bayesian recursive estimation (LoBaRE) that efficiently identifies the optimum parameter region, avoiding convergence to a single best parameter set. The LoBaRE methodology is tested for parameter estimation for two different types of models: a support vector machine (SVM) model for predicting soil moisture, and the Sacramento Soil Moisture Accounting (SAC-SMA) model for estimating streamflow. The SAC-SMA model has 13 parameters that must be determined. The SVM model has three parameters. Bayesian inference is used to estimate the best parameter set in an iterative fashion. This is done by narrowing the sampling space by imposing uncertainty bounds on the posterior best parameter set and/or updating the "parent" bounds based on their fitness. The new approach results in fast convergence towards the optimal parameter set using minimum training/calibration data and evaluation of fewer parameter sets. The efficacy of the localized methodology is also compared with the previously used Bayesian recursive estimation (BaRE) algorithm.
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
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.
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.
NASA Astrophysics Data System (ADS)
Allain, P. E.; Damiron, D.; Miyazaki, Y.; Kaminishi, K.; Pop, F. V.; Kobayashi, D.; Sasaki, N.; Kawakatsu, H.
2017-09-01
Atomic force microscopy has enabled imaging at the sub-molecular level, and 3D mapping of the tip-surface potential field. However, fast identification of the surface still remains a challenging topic for the microscope to enjoy widespread use as a tool with chemical contrast. In this paper, as a step towards implementation of such function, we introduce a control scheme and mathematical treatment of the acquired data that enable retrieval of essential information characterizing this potential field, leading to fast acquisition of images with chemical contrast. The control scheme is based on the tip sample distance modulation at an angular frequency ω, and null-control of the ω component of the measured self-excitation frequency of the oscillator. It is demonstrated that this control is robust, and that effective Morse Parameters that give satisfactory curve fit to the measured frequency shift can be calculated at rates comparable to the scan. Atomic features with similar topography were distinguished by differences in these parameters. The decay length parameter was resolved with a resolution of 10 pm. The method was demonstrated on quenched silicon at a scan rate comparable to conventional imaging.
Distributed parameter modeling for the control of flexible spacecraft
NASA Technical Reports Server (NTRS)
Taylor, Lawrence W., Jr.
1990-01-01
The use of FEMs of spacecraft structural dynamics is a common practice, but it has a number of shortcomings. Distributed-parameter models offer an alternative, but present both advantages and difficulties. First, the model order does not have to be reduced prior to the inclusion of control system dynamics. This advantage eliminates the risk involved with model 'order reduction'. Second, distributed parameter models inherently involve fewer parameters, thereby enabling more accurate parameter estimation using experimental data. Third, it is possible to include the damping in the basic model, thereby increasing the accuracy of the structural damping. The difficulty in generating distributed parameter models of complex spacecraft configurations has been greatly alleviated by the use of PDEMOD, BUNVIS-RG, or DISTEL. PDEMOD is being developed for simultaneously modeling structural dynamics and control system dynamics.
Bayesian Estimation in the One-Parameter Latent Trait Model.
1980-03-01
parameter, difficulty, is commonly known as the Rasch model or the one-parameter logistic model . For a detailed description of this model and its prop...Journal of Mathematical and Statistical Psychology, 1973, 26, 31-44. (a) Andersen, E. B. A goodness of fit test for the Rasch model . Psychometrika, 1973, 28...Psychometrika, 1972, 37, 29-51. Bock, R. D., & Lieberman, M. Fitting a response model for n dichotomously scored items. Psychometrika, 1970, 35, 179-197
Isolating parameter sensitivity in reach scale transient storage modeling
NASA Astrophysics Data System (ADS)
Schmadel, Noah M.; Neilson, Bethany T.; Heavilin, Justin E.; Wörman, Anders
2016-03-01
Parameter sensitivity analyses, although necessary to assess identifiability, may not lead to an increased understanding or accurate representation of transient storage processes when associated parameter sensitivities are muted. Reducing the number of uncertain calibration parameters through field-based measurements may allow for more realistic representations and improved predictive capabilities of reach scale stream solute transport. Using a two-zone transient storage model, we examined the spatial detail necessary to set parameters describing hydraulic characteristics and isolate the sensitivity of the parameters associated with transient storage processes. We represented uncertain parameter distributions as triangular fuzzy numbers and used closed form statistical moment solutions to express parameter sensitivity thus avoiding copious model simulations. These solutions also allowed for the direct incorporation of different levels of spatial information regarding hydraulic characteristics. To establish a baseline for comparison, we performed a sensitivity analysis considering all model parameters as uncertain. Next, we set hydraulic parameters as the reach averages, leaving the transient storage parameters as uncertain, and repeated the analysis. Lastly, we incorporated high resolution hydraulic information assessed from aerial imagery to examine whether more spatial detail was necessary to isolate the sensitivity of transient storage parameters. We found that a reach-average hydraulic representation, as opposed to using detailed spatial information, was sufficient to highlight transient storage parameter sensitivity and provide more information regarding the potential identifiability of these parameters.
A comprehensive X-ray absorption model for atomic oxygen
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.
Fully variational average atom model with ion-ion correlations.
Starrett, C E; Saumon, D
2012-02-01
An average atom model for dense ionized fluids that includes ion correlations is presented. The model assumes spherical symmetry and is based on density functional theory, the integral equations for uniform fluids, and a variational principle applied to the grand potential. Starting from density functional theory for a mixture of classical ions and quantum mechanical electrons, an approximate grand potential is developed, with an external field being created by a central nucleus fixed at the origin. Minimization of this grand potential with respect to electron and ion densities is carried out, resulting in equations for effective interaction potentials. A third condition resulting from minimizing the grand potential with respect to the average ion charge determines the noninteracting electron chemical potential. This system is coupled to a system of point ions and electrons with an ion fixed at the origin, and a closed set of equations is obtained. Solution of these equations results in a self-consistent electronic and ionic structure for the plasma as well as the average ionization, which is continuous as a function of temperature and density. Other average atom models are recovered by application of simplifying assumptions.
Accuracy of Parameter Estimation in Gibbs Sampling under the Two-Parameter Logistic Model.
ERIC Educational Resources Information Center
Kim, Seock-Ho; Cohen, Allan S.
The accuracy of Gibbs sampling, a Markov chain Monte Carlo procedure, was considered for estimation of item and ability parameters under the two-parameter logistic model. Memory test data were analyzed to illustrate the Gibbs sampling procedure. Simulated data sets were analyzed using Gibbs sampling and the marginal Bayesian method. The marginal…
Reviews and syntheses: parameter identification in marine planktonic ecosystem modelling
NASA Astrophysics Data System (ADS)
Schartau, Markus; Wallhead, Philip; Hemmings, John; Löptien, Ulrike; Kriest, Iris; Krishna, Shubham; Ward, Ben A.; Slawig, Thomas; Oschlies, Andreas
2017-03-01
To describe the underlying processes involved in oceanic plankton dynamics is crucial for the determination of energy and mass flux through an ecosystem and for the estimation of biogeochemical element cycling. Many planktonic ecosystem models were developed to resolve major processes so that flux estimates can be derived from numerical simulations. These results depend on the type and number of parameterizations incorporated as model equations. Furthermore, the values assigned to respective parameters specify a model's solution. Representative model results are those that can explain data; therefore, data assimilation methods are utilized to yield optimal estimates of parameter values while fitting model results to match data. Central difficulties are (1) planktonic ecosystem models are imperfect and (2) data are often too sparse to constrain all model parameters. In this review we explore how problems in parameter identification are approached in marine planktonic ecosystem modelling. We provide background information about model uncertainties and estimation methods, and how these are considered for assessing misfits between observations and model results. We explain differences in evaluating uncertainties in parameter estimation, thereby also discussing issues of parameter identifiability. Aspects of model complexity are addressed and we describe how results from cross-validation studies provide much insight in this respect. Moreover, approaches are discussed that consider time- and space-dependent parameter values. We further discuss the use of dynamical/statistical emulator approaches, and we elucidate issues of parameter identification in global biogeochemical models. Our review discloses many facets of parameter identification, as we found many commonalities between the objectives of different approaches, but scientific insight differed between studies. To learn more from results of planktonic ecosystem models we recommend finding a good balance in the level
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.
Magnetic and Atomic Structure Parameters of Sc-doped Barium Hexagonal Ferrites
Yang,A.; Chen, Y.; Chen, Z.; Vittoria, C.; Harris, V.
2008-01-01
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.
Statistical mechanical approaches to models with many poorly known parameters
NASA Astrophysics Data System (ADS)
Brown, Kevin S.; Sethna, James P.
2003-08-01
Models of biochemical regulation in prokaryotes and eukaryotes, typically consisting of a set of first-order nonlinear ordinary differential equations, have become increasingly popular of late. These systems have large numbers of poorly known parameters, simplified dynamics, and uncertain connectivity: three key features of a class of problems we call sloppy models, which are shared by many other high-dimensional multiparameter nonlinear models. We use a statistical ensemble method to study the behavior of these models, in order to extract as much useful predictive information as possible from a sloppy model, given the available data used to constrain it. We discuss numerical challenges that emerge in using the ensemble method for a large system. We characterize features of sloppy model parameter fluctuations by various spectral decompositions and find indeed that five parameters can be used to fit an elephant. We also find that model entropy is as important to the problem of model choice as model energy is to parameter choice.
Dynamics in the Parameter Space of a Neuron Model
NASA Astrophysics Data System (ADS)
Paulo, C. Rech
2012-06-01
Some two-dimensional parameter-space diagrams are numerically obtained by considering the largest Lyapunov exponent for a four-dimensional thirteen-parameter Hindmarsh—Rose neuron model. Several different parameter planes are considered, and it is shown that depending on the combination of parameters, a typical scenario can be preserved: for some choice of two parameters, the parameter plane presents a comb-shaped chaotic region embedded in a large periodic region. It is also shown that there exist regions close to these comb-shaped chaotic regions, separated by the comb teeth, organizing themselves in period-adding bifurcation cascades.
Low energy neutral atoms in the earth's magnetosphere: Modeling
Moore, K.R.; McComas, D.J.; Funsten, H.O.; Thomsen, M.F.
1992-01-01
Detection of low energy neutral atoms (LENAs) produced by the interaction of the Earth's geocorona with ambient space plasma has been proposed as a technique to obtain global information about the magnetosphere. Recent instrumentation advances reported previously and in these proceedings provide an opportunity for detecting LENAs in the energy range of <1 keV to {approximately}50 keV. In this paper, we present results from a numerical model which calculates line of sight LENA fluxes expected at a remote orbiting spacecraft for various magnetospheric plasma regimes. This model uses measured charge exchange cross sections, either of two neural hydrogen geocorona models, and various empirical modes of the ring current and plasma sheet to calculate the contribution to the integrated directional flux from each point along the line of sight of the instrument. We discuss implications for LENA imaging of the magnetosphere based on these simulations. 22 refs.
Numerical modeling for primary atomization of liquid jets
NASA Technical Reports Server (NTRS)
Przekwas, A. J.; Chuech, S. G.; Singhal, A. K.
1989-01-01
In the proposed numerical model for primary atomization, surface-wave dispersion equations are solved in conjunction with the jet-embedding technique of solving mean flow equations of a liquid jet. Linear and approximate nonlinear models have been considered. In each case, the dispersion equation is solved over the whole wavelength spectrum to predict drop sizes, frequency, and liquid-mass breakup rates without using any empirical constants. The present model has been applied to several low-speed and high-speed jets. For the high-speed case (the LOX/H2 coaxial injector of the Space Shuttle Main Engine Preburner), predicted drop sizes and liquid breakup rates are in good agreement with the results of the CICM code, which have been calibrated against measured data.
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
Statistical Parameters for Describing Model Accuracy
1989-03-20
mean and the standard deviation, approximately characterizes the accuracy of the model, since the width of the confidence interval whose center is at...Using a modified version of Chebyshev’s inequality, a similar result is obtained for the upper bound of the confidence interval width for any
NASA Astrophysics Data System (ADS)
Mai, Juliane; Cuntz, Matthias; Zink, Matthias; Thober, Stephan; Kumar, Rohini; Schäfer, David; Schrön, Martin; Craven, John; Rakovec, Oldrich; Spieler, Diana; Prykhodko, Vladyslav; Dalmasso, Giovanni; Musuuza, Jude; Langenberg, Ben; Attinger, Sabine; Samaniego, Luis
2016-04-01
Environmental models tend to require increasing computational time and resources as physical process descriptions are improved or new descriptions are incorporated. Many-query applications such as sensitivity analysis or model calibration usually require a large number of model evaluations leading to high computational demand. This often limits the feasibility of rigorous analyses. Here we present a fully automated sequential screening method that selects only informative parameters for a given model output. The method requires a number of model evaluations that is approximately 10 times the number of model parameters. It was tested using the mesoscale hydrologic model mHM in three hydrologically unique European river catchments. It identified around 20 informative parameters out of 52, with different informative parameters in each catchment. The screening method was evaluated with subsequent analyses using all 52 as well as only the informative parameters. Subsequent Sobol's global sensitivity analysis led to almost identical results yet required 40% fewer model evaluations after screening. mHM was calibrated with all and with only informative parameters in the three catchments. Model performances for daily discharge were equally high in both cases with Nash-Sutcliffe efficiencies above 0.82. Calibration using only the informative parameters needed just one third of the number of model evaluations. The universality of the sequential screening method was demonstrated using several general test functions from the literature. We therefore recommend the use of the computationally inexpensive sequential screening method prior to rigorous analyses on complex environmental models.
New modeling of scattering behaviors of argon atoms on tungsten substrate.
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. Crown Copyright © 2011. Published by Elsevier Inc. All rights reserved.
An approach to adjustment of relativistic mean field model parameters
NASA Astrophysics Data System (ADS)
Bayram, Tuncay; Akkoyun, Serkan
2017-09-01
The Relativistic Mean Field (RMF) model with a small number of adjusted parameters is powerful tool for correct predictions of various ground-state nuclear properties of nuclei. Its success for describing nuclear properties of nuclei is directly related with adjustment of its parameters by using experimental data. In the present study, the Artificial Neural Network (ANN) method which mimics brain functionality has been employed for improvement of the RMF model parameters. In particular, the understanding capability of the ANN method for relations between the RMF model parameters and their predictions for binding energies (BEs) of 58Ni and 208Pb have been found in agreement with the literature values.
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.
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)
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)
Determining extreme parameter correlation in ground water models.
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.
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.
A generalized model of atomic processes in dense plasmas
NASA Astrophysics Data System (ADS)
Chung, Hyun-Kyung; Chen, M.; Ciricosta, O.; Vinko, S.; Wark, J.; Lee, R. W.
2015-11-01
A generalized model of atomic processes in plasmas, FLYCHK, has been developed over a decade to provide experimentalists fast and simple but reasonable predictions of atomic properties of plasmas. For a given plasma condition, it provides charge state distributions and spectroscopic properties, which have been extensively used for experimental design and data analysis and currently available through NIST web site. In recent years, highly transient and non-equilibrium plasmas have been created with X-ray free electron lasers (XFEL). As high intensity x-rays interact with matter, the inner-shell electrons are ionized and Auger electrons and photo electrons are generated. With time, electrons participate in the ionization processes and collisional ionization by these electrons dominates photoionization as electron density increases. To study highly complex XFEL produced plasmas, SCFLY, an extended version of FLYCHK code has been used. The code accepts the time-dependent history of x-ray energy and intensity to compute population distribution and ionization distribution self-consistently with electron temperature and density assuming an instantaneous equilibration. The model and its applications to XFEL experiments will be presented as well as its limitations.
NASA Astrophysics Data System (ADS)
Daw, A.; Calamai, A.; Brewer, S.; Estes, C.; Kanoy, J.; Myer, B.; Stamilio, R.
2005-05-01
For the purpose of providing accurate atomic and molecular data for applications to the Earth's ionosphere and astrophysical plasmas, this project will provide measurements of: the radiative lifetime of the 5S metastable level of N+, the dissociation rate of doubly charged molecular nitrogen ions, electron capture rates from molecular nitrogen for both these ions, and the cross section for dissociative electron impact ionization of molecular nitrogen into metastable 5S N+, which is responsible for auroral 214 nm emission. Preliminary data and results are be presented. Ions are created in a radiofrequency ion trap by electron bombardment on nitrogen gas, and the UV radiation emitted by the stored ion population is then measured as a function of time. The primary source of radiation is the decaying metastable N+ ions, which emit photons at a wavelength of 214 nm. In addition to the atomic N+, doubly charged molecular ions (dications) are created and stored. Electron capture from neutral molecules into excited states of singly charged molecular nitrogen results in emission in bands that overlap with 214 nm. The decay rate of these two sources of radiation is measured as a function of nitrogen gas pressure to determine: the electron capture rates for both ions, the radiative decay rate of the metastable N+, and the dissociation rate of the dications. The photon observations are corrected for ion losses using the technique presented in Daw, Parkinson, Smith, & Calamai, ApJ 533, L179, 2000. Limits on the cross section for dissociative electron impact ionization of molecular nitrogen into metastable 5S N+ will be determined relative to the (well-known) cross section for dication production, by comparing the photon rate at 214 nm to the photon rate generated in different bandpasses as a result of dication electron capture.
Observation of antiferromagnetic correlations in the Hubbard model with ultracold atoms
NASA Astrophysics Data System (ADS)
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.
2015-03-01
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
WATGIS: A GIS-Based Lumped Parameter Water Quality Model
Glenn P. Fernandez; George M. Chescheir; R. Wayne Skaggs; Devendra M. Amatya
2002-01-01
A Geographic Information System (GIS)Âbased, lumped parameter water quality model was developed to estimate the spatial and temporal nitrogenÂloading patterns for lower coastal plain watersheds in eastern North Carolina. The model uses a spatially distributed delivery ratio (DR) parameter to account for nitrogen retention or loss along a drainage network. Delivery...
Exploring the interdependencies between parameters in a material model.
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.
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…
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…
Improving Model Performance by Dynamically Varying the Sensitive Parameters.
NASA Astrophysics Data System (ADS)
Girija, L.; Sudheer, K.
2016-12-01
Distributed hydrologic models are being extensively used for watershed modeling these days as they can account the heterogeneity of the catchment to a great extent. The large number of parameters that need to be calibrated, however, increases the complexity of the modelling. The various parameters may be representing a physical process that can have seasonal variability. However, most of the hydrologic models assume temporal invariability of the model parameters and their respective optimal values. This assumption, though, helps in reducing the computational burden, may compromise the ability of the model to extract information from the observed data having seasonal changes. In addition, the model may not simulate acceptable watershed responses during wet and dry seasons of the year if the same value for parameters is employed. Consequently, this study aims at considering varying values for parameters along the seasons in an year, and evaluate the performance. A demonstrative case study is conducted using SWAT model considering the data pertaining to Mississinewa watershed, Indiana, USA. The seasonally sensitive parameters of the model are identified, and are varied during the four different seasons of the year considering the antecedent moisture conditions. The model is expected to simulate the high and low flows more accurately compared to the conventional method of using a single set of parameter values for the entire simulation.
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.
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.
Sampling Kinetic Protein Folding Pathways using All-Atom Models
NASA Astrophysics Data System (ADS)
Bolhuis, P. G.
This chapter summarizes several computational strategies to study the kinetics of two-state protein folding using all atom models. After explaining the background of two state folding using energy landscapes I introduce common protein models and computational tools to study folding thermodynamics and kinetics. Free energy landscapes are able to capture the thermodynamics of two-state protein folding, and several methods for efficient sampling of these landscapes are presented. An accurate estimate of folding kinetics, the main topic of this chapter, is more difficult to achieve. I argue that path sampling methods are well suited to overcome the problems connected to the sampling of folding kinetics. Some of the major issues are illustrated in the case study on the folding of the GB1 hairpin.
Beyond modeling: all-atom olfactory receptor model simulations.
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.
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.
Four-component united-atom model of bitumen.
Hansen, J S; Lemarchand, Claire A; Nielsen, Erik; Dyre, Jeppe C; Schrøder, Thomas
2013-03-07
We propose a four-component united-atom molecular model of bitumen. The model includes realistic chemical constituents and introduces a coarse graining level that suppresses the highest frequency modes. Molecular dynamics simulations of the model are carried out using graphic-processor-units based software in time spans in order of microseconds, which enables the study of slow relaxation processes characterizing bitumen. This paper also presents results of the model dynamics as expressed through the mean-square displacement, the stress autocorrelation function, and rotational relaxation. The diffusivity of the individual molecules changes little as a function of temperature and reveals distinct dynamical time scales. Different time scales are also observed for the rotational relaxation. The stress autocorrelation function features a slow non-exponential decay for all temperatures studied. From the stress autocorrelation function, the shear viscosity and shear modulus are evaluated, showing a viscous response at frequencies below 100 MHz. The model predictions of viscosity and diffusivities are compared to experimental data, giving reasonable agreement. The model shows that the asphaltene, resin, and resinous oil tend to form nano-aggregates. The characteristic dynamical relaxation time of these aggregates is larger than that of the homogeneously distributed parts of the system, leading to strong dynamical heterogeneity.
Four-component united-atom model of bitumen
NASA Astrophysics Data System (ADS)
Hansen, J. S.; Lemarchand, Claire A.; Nielsen, Erik; Dyre, Jeppe C.; Schrøder, Thomas
2013-03-01
We propose a four-component united-atom molecular model of bitumen. The model includes realistic chemical constituents and introduces a coarse graining level that suppresses the highest frequency modes. Molecular dynamics simulations of the model are carried out using graphic-processor-units based software in time spans in order of microseconds, which enables the study of slow relaxation processes characterizing bitumen. This paper also presents results of the model dynamics as expressed through the mean-square displacement, the stress autocorrelation function, and rotational relaxation. The diffusivity of the individual molecules changes little as a function of temperature and reveals distinct dynamical time scales. Different time scales are also observed for the rotational relaxation. The stress autocorrelation function features a slow non-exponential decay for all temperatures studied. From the stress autocorrelation function, the shear viscosity and shear modulus are evaluated, showing a viscous response at frequencies below 100 MHz. The model predictions of viscosity and diffusivities are compared to experimental data, giving reasonable agreement. The model shows that the asphaltene, resin, and resinous oil tend to form nano-aggregates. The characteristic dynamical relaxation time of these aggregates is larger than that of the homogeneously distributed parts of the system, leading to strong dynamical heterogeneity.
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.
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.
Identification of hydrological model parameter variation using ensemble Kalman filter
NASA Astrophysics Data System (ADS)
Deng, Chao; Liu, Pan; Guo, Shenglian; Li, Zejun; Wang, Dingbao
2016-12-01
Hydrological model parameters play an important role in the ability of model prediction. In a stationary context, parameters of hydrological models are treated as constants; however, model parameters may vary with time under climate change and anthropogenic activities. The technique of ensemble Kalman filter (EnKF) is proposed to identify the temporal variation of parameters for a two-parameter monthly water balance model (TWBM) by assimilating the runoff observations. Through a synthetic experiment, the proposed method is evaluated with time-invariant (i.e., constant) parameters and different types of parameter variations, including trend, abrupt change and periodicity. Various levels of observation uncertainty are designed to examine the performance of the EnKF. The results show that the EnKF can successfully capture the temporal variations of the model parameters. The application to the Wudinghe basin shows that the water storage capacity (SC) of the TWBM model has an apparent increasing trend during the period from 1958 to 2000. The identified temporal variation of SC is explained by land use and land cover changes due to soil and water conservation measures. In contrast, the application to the Tongtianhe basin shows that the estimated SC has no significant variation during the simulation period of 1982-2013, corresponding to the relatively stationary catchment properties. The evapotranspiration parameter (C) has temporal variations while no obvious change patterns exist. The proposed method provides an effective tool for quantifying the temporal variations of the model parameters, thereby improving the accuracy and reliability of model simulations and forecasts.
Parameters Estimation of Geographically Weighted Ordinal Logistic Regression (GWOLR) Model
NASA Astrophysics Data System (ADS)
Zuhdi, Shaifudin; Retno Sari Saputro, Dewi; Widyaningsih, Purnami
2017-06-01
A regression model is the representation of relationship between independent variable and dependent variable. The dependent variable has categories used in the logistic regression model to calculate odds on. The logistic regression model for dependent variable has levels in the logistics regression model is ordinal. GWOLR model is an ordinal logistic regression model influenced the geographical location of the observation site. Parameters estimation in the model needed to determine the value of a population based on sample. The purpose of this research is to parameters estimation of GWOLR model using R software. Parameter estimation uses the data amount of dengue fever patients in Semarang City. Observation units used are 144 villages in Semarang City. The results of research get GWOLR model locally for each village and to know probability of number dengue fever patient categories.
Universally Sloppy Parameter Sensitivities in Systems Biology Models
Gutenkunst, Ryan N; Waterfall, Joshua J; Casey, Fergal P; Brown, Kevin S; Myers, Christopher R; Sethna, James P
2007-01-01
Quantitative computational models play an increasingly important role in modern biology. Such models typically involve many free parameters, and assigning their values is often a substantial obstacle to model development. Directly measuring in vivo biochemical parameters is difficult, and collectively fitting them to other experimental data often yields large parameter uncertainties. Nevertheless, in earlier work we showed in a growth-factor-signaling model that collective fitting could yield well-constrained predictions, even when it left individual parameters very poorly constrained. We also showed that the model had a “sloppy” spectrum of parameter sensitivities, with eigenvalues roughly evenly distributed over many decades. Here we use a collection of models from the literature to test whether such sloppy spectra are common in systems biology. Strikingly, we find that every model we examine has a sloppy spectrum of sensitivities. We also test several consequences of this sloppiness for building predictive models. In particular, sloppiness suggests that collective fits to even large amounts of ideal time-series data will often leave many parameters poorly constrained. Tests over our model collection are consistent with this suggestion. This difficulty with collective fits may seem to argue for direct parameter measurements, but sloppiness also implies that such measurements must be formidably precise and complete to usefully constrain many model predictions. We confirm this implication in our growth-factor-signaling model. Our results suggest that sloppy sensitivity spectra are universal in systems biology models. The prevalence of sloppiness highlights the power of collective fits and suggests that modelers should focus on predictions rather than on parameters. PMID:17922568
Universally sloppy parameter sensitivities in systems biology models.
Gutenkunst, Ryan N; Waterfall, Joshua J; Casey, Fergal P; Brown, Kevin S; Myers, Christopher R; Sethna, James P
2007-10-01
Quantitative computational models play an increasingly important role in modern biology. Such models typically involve many free parameters, and assigning their values is often a substantial obstacle to model development. Directly measuring in vivo biochemical parameters is difficult, and collectively fitting them to other experimental data often yields large parameter uncertainties. Nevertheless, in earlier work we showed in a growth-factor-signaling model that collective fitting could yield well-constrained predictions, even when it left individual parameters very poorly constrained. We also showed that the model had a "sloppy" spectrum of parameter sensitivities, with eigenvalues roughly evenly distributed over many decades. Here we use a collection of models from the literature to test whether such sloppy spectra are common in systems biology. Strikingly, we find that every model we examine has a sloppy spectrum of sensitivities. We also test several consequences of this sloppiness for building predictive models. In particular, sloppiness suggests that collective fits to even large amounts of ideal time-series data will often leave many parameters poorly constrained. Tests over our model collection are consistent with this suggestion. This difficulty with collective fits may seem to argue for direct parameter measurements, but sloppiness also implies that such measurements must be formidably precise and complete to usefully constrain many model predictions. We confirm this implication in our growth-factor-signaling model. Our results suggest that sloppy sensitivity spectra are universal in systems biology models. The prevalence of sloppiness highlights the power of collective fits and suggests that modelers should focus on predictions rather than on parameters.
Tube-Load Model Parameter Estimation for Monitoring Arterial Hemodynamics
Zhang, Guanqun; Hahn, Jin-Oh; Mukkamala, Ramakrishna
2011-01-01
A useful model of the arterial system is the uniform, lossless tube with parametric load. This tube-load model is able to account for wave propagation and reflection (unlike lumped-parameter models such as the Windkessel) while being defined by only a few parameters (unlike comprehensive distributed-parameter models). As a result, the parameters may be readily estimated by accurate fitting of the model to available arterial pressure and flow waveforms so as to permit improved monitoring of arterial hemodynamics. In this paper, we review tube-load model parameter estimation techniques that have appeared in the literature for monitoring wave reflection, large artery compliance, pulse transit time, and central aortic pressure. We begin by motivating the use of the tube-load model for parameter estimation. We then describe the tube-load model, its assumptions and validity, and approaches for estimating its parameters. We next summarize the various techniques and their experimental results while highlighting their advantages over conventional techniques. We conclude the review by suggesting future research directions and describing potential applications. PMID:22053157
Rate parameters for the reaction of atomic hydrogen with dimethyl ether and dimethyl sulfide
NASA Astrophysics Data System (ADS)
Lee, J. H.; Machen, R. C.; Nava, D. F.; Stief, L. J.
1981-03-01
Absolute rate constants for the reaction of atomic hydrogen with dimethyl ether (DME) and dimethyl sulfide (DMS) were obtained using the flash photolysis-resonance fluorescence technique. Under conditions where secondary reactions are avoided, rate constants for the H+DME reaction over the temperature range 273-426 K are well represented by the Arrhenius expression k1=(4.38±0.59)×10-12 exp(-1956±43/T) cm3 molecule-1 s-1. The corresponding Arrhenius expression for the H+DMS reaction over the temperature range 212-500 K is k2=(1.30±0.43)×10-11exp(-1118±81/T) cm3 molecule-1 s-1. The Arrhenius plot for k2 shows signs of curvature, however, and separate Arrhenius expressions are derived for the data above and below room temperature. These results are discussed and comparisons are made with previous determinations which employed flow discharge and product analysis techniques.
Predicting hydrophobic solvation by molecular simulation: 1. Testing united-atom alkane models.
Jorge, Miguel; Garrido, Nuno M; Simões, Carlos J V; Silva, Cândida G; Brito, Rui M M
2017-03-05
We present a systematic test of the performance of three popular united-atom force fields-OPLS-UA, GROMOS and TraPPE-at predicting hydrophobic solvation, more precisely at describing the solvation of alkanes in alkanes. Gibbs free energies of solvation were calculated for 52 solute/solvent pairs from Molecular Dynamics simulations and thermodynamic integration making use of the IBERCIVIS volunteer computing platform. Our results show that all force fields yield good predictions when both solute and solvent are small linear or branched alkanes (up to pentane). However, as the size of the alkanes increases, all models tend to increasingly deviate from experimental data in a systematic fashion. Furthermore, our results confirm that specific interaction parameters for cyclic alkanes in the united-atom representation are required to account for the additional excluded volume within the ring. Overall, the TraPPE model performs best for all alkanes, but systematically underpredicts the magnitude of solvation free energies by about 6% (RMSD of 1.2 kJ/mol). Conversely, both GROMOS and OPLS-UA systematically overpredict solvation free energies (by ∼13% and 15%, respectively). The systematic trends suggest that all models can be improved by a slight adjustment of their Lennard-Jones parameters. © 2016 Wiley Periodicals, Inc.
Paraskevas, Paschalis D; Sabbe, Maarten K; Reyniers, Marie-Françoise; Papayannakos, Nikos G; Marin, Guy B
2014-10-09
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.
Modeling a semiconductor laser with an intracavity atomic absorber
Masoller, C.; Vilaseca, R.; Oria, M.
2009-07-15
The dynamics of a semiconductor laser with an intracavity atomic absorber is studied numerically. The study is motivated by the experiments of Barbosa et al. [Opt. Lett. 32, 1869 (2007)], using a semiconductor junction as an active medium, with its output face being antireflection coated, and a cell containing cesium vapor placed in a cavity that was closed by a diffraction grating (DG). The DG allowed scanning the lasing frequency across the D{sub 2} line in the Cs spectrum, and different regimes such as frequency bistability or dynamic instability were observed depending on the operating conditions. Here we propose a rate-equation model that takes into account the dispersive losses and the dispersive refractive index change in the laser cavity caused by the presence of the Cs vapor cell. These effects are described through a modification of the complex susceptibility. The numerical results are found to be in qualitative good agreement with some of the observations; however, some discrepancies are also noticed, which can be attributed to multi-longitudinal-mode emission in the experiments. The simulations clearly show the relevant role of the Lamb dips and crossover resonances, which arise on top of the Doppler-broadened D{sub 2} line in the Cs spectrum, and are due to the forward and backward intracavity fields interacting resonantly with the Cs atoms. When the laser frequency is locked in a dip, a reduction in the frequency noise and of the intensity noise is demonstrated.
Beyond Modeling: All-Atom Olfactory Receptor Model Simulations
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
The definition of hydrologic model parameters using remote sensing techniques
NASA Technical Reports Server (NTRS)
Ragan, R. M.; Salomonson, V. V.
1978-01-01
The reported investigation is concerned with the use of Landsat remote sensing to define input parameters for an array of hydrologic models which are used to synthesize streamflow and water quality parameters in the planning or management process. The ground truth sampling and problems involved in translating the remotely sensed information into hydrologic model parameters are discussed. Questions related to the modification of existing models for compatibility with remote sensing capabilities are also examined. It is shown that the input parameters of many models are presently overdefined in terms of the sensitivity and accuracy of the model. When this overdefinition is recognized many of the models currently considered to be incompatible with remote sensing capabilities can be modified to make possible use with sensors having rather low resolutions.
State and parameter estimation for canonic models of neural oscillators.
Tyukin, Ivan; Steur, Erik; Nijmeijer, Henk; Fairhurst, David; Song, Inseon; Semyanov, Alexey; Van Leeuwen, Cees
2010-06-01
We consider the problem of how to recover the state and parameter values of typical model neurons, such as Hindmarsh-Rose, FitzHugh-Nagumo, Morris-Lecar, from in-vitro measurements of membrane potentials. In control theory, in terms of observer design, model neurons qualify as locally observable. However, unlike most models traditionally addressed in control theory, no parameter-independent diffeomorphism exists, such that the original model equations can be transformed into adaptive canonic observer form. For a large class of model neurons, however, state and parameter reconstruction is possible nevertheless. We propose a method which, subject to mild conditions on the richness of the measured signal, allows model parameters and state variables to be reconstructed up to an equivalence class.
Evaluation of the storage function model parameter characteristics
NASA Astrophysics Data System (ADS)
Sugiyama, Hironobu; Kadoya, Mutsumi; Nagai, Akihiro; Lansey, Kevin
1997-04-01
The storage function hydrograph model is one of the most commonly used models for flood runoff analysis in Japan. This paper studies the generality of the approach and its application to Japanese basins. Through a comparison of the basic equations for the models, the storage function model parameters, K, P, and T1, are shown to be related to the terms, k and p, in the kinematic wave model. This analysis showed that P and p are identical and K and T1 can be related to k, the basin area and its land use. To apply the storage function model throughout Japan, regional parameter relationships for K and T1 were developed for different land-use conditions using data from 22 watersheds and 91 flood events. These relationships combine the kinematic wave parameters with general topographic information using Hack's Law. The sensitivity of the parameters and their physical significance are also described.
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.
Modeling a short cold cathode DC discharge device with controllable plasma parameters
NASA Astrophysics Data System (ADS)
Kudryavtsev, Anatoly; Adams, Steven; Demidov, Vladimir; Bogdanov, Yevgeny
2009-11-01
A short (without positive column) DC gas-discharge device with a cold cathode has been modeled. The device consists of the plane disk-shaped cathode and anode while the inter-electrode gap is bounded by a cylindrical wall. The cathode and anode are each 2.5 cm in diameter, and the inter-electrode gap is 12 mm. The wall is made of conducting parts divided by an insulator. The modeling has been performed for argon plasma at 1 Torr pressure. It is demonstrated in the model that spatial distributions of electron density and temperature and argon metastable atom density depend on the DC voltage applied to different conducting parts of the wall. Applied voltage can trap within the device volume energetic electrons arising from atomic and molecular processes in the plasma. This leads to a modification in the heating of slow electrons by energetic electrons and as a result modifies the controlling plasma parameters.
A one parameter class of fractional Maxwell-like models
NASA Astrophysics Data System (ADS)
Colombaro, Ivano; Giusti, Andrea; Mainardi, Francesco
2017-06-01
In this paper we discuss a one parameter modification of the well known fractional Maxwell model of viscoelasticity. Such models appear to be particularly interesting because they describe the short time asymptotic limit of a more general class of viscoelastic models known in the literature as Bessel models.
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
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
NASA Astrophysics Data System (ADS)
Farchioni, Riccardo; Grosso, Giuseppe; Parravicini, Giuseppe Pastori
2012-04-01
By means of a tight-binding model we study the electronic and transport properties of a one-dimensional system with short-range spatially correlated disorder composed by a periodic chain functionalized by a random distribution of side-attached atoms with enegies EA or EB assigned in pairs as in the random dimer model. The attached atoms are spatially distributed so as to make the original periodic chain a random binary dimer model alloy with energy-dependent on-site parameters. We first consider the case of a single atom and of a couple of atoms, with the same site energy, side-attached to consecutive chain sites. In the case of a couple of attached atoms we evidence significative differences in the local density of states with respect to the case of a single side-attached atom; moreover we find the presence of two transmitting states instead of a single one as it happens in the case of a single substitutional dimer in the chain. We then address the case in which each chain site is decorated by an attached atom as specified above. After a decimation-renormalization procedure we are led to a random binary dimer system with energy-dependent site parameters. We study the localization properties of this system by evaluating the Lyapunov coefficient; we find for it the existence of four delocalized states in the spectrum instead of the two found for embedded random dimers. The Lyapunov coefficient as a function of the electron Fermi energy shows a quite complex behavior with zeros, relative minima, and maxima; their energy positions and heights depend on the site parameters and the coupling interaction of the attached atoms. The analysis of the average transmittivity of finite samples allows us also to show the effects of the competition between the strong localization induced by the presence of the attached atoms and the delocalization of the states due to the short-range order in the distribution of their energy. We show that it is possible to individuate specific
NASA Astrophysics Data System (ADS)
Bertolus, Marjorie; Freyss, Michel; Dorado, Boris; Martin, Guillaume; Hoang, Kiet; Maillard, Serge; Skorek, Richard; Garcia, Philippe; Valot, Carole; Chartier, Alain; Van Brutzel, Laurent; Fossati, Paul; Grimes, Robin W.; Parfitt, David C.; Bishop, Clare L.; Murphy, Samuel T.; Rushton, Michael J. D.; Staicu, Dragos; Yakub, Eugen; Nichenko, Sergii; Krack, Matthias; Devynck, Fabien; Ngayam-Happy, Raoul; Govers, Kevin; Deo, Chaitanya S.; Behera, Rakesh K.
2015-07-01
This article presents a synthesis of the investigations at the atomic scale of the transport properties of defects and fission gases in uranium dioxide, as well as of the transfer of results from the atomic scale to models at the mesoscopic scale, performed during the F-BRIDGE European project (2008-2012). We first present the mesoscale models used to investigate uranium oxide fuel under irradiation, and in particular the cluster dynamics and kinetic Monte Carlo methods employed to model the behaviour of defects and fission gases in UO2, as well as the parameters of these models. Second, we describe briefly the atomic scale methods employed, i.e. electronic structure calculations and empirical potential methods. Then, we show the results of the calculation of the data necessary for the mesoscale models using these atomic scale methods. Finally, we summarise the links built between the atomic and mesoscopic scale by listing the data calculated at the atomic scale which are to be used as input in mesoscale modelling. Despite specific difficulties in the description of fuel materials, the results obtained in F-BRIDGE show that atomic scale modelling methods are now mature enough to obtain precise data to feed higher scale models and help interpret experiments on nuclear fuels. These methods bring valuable insight, in particular the formation, binding and migration energies of point and extended defects, fission product localization, incorporation energies and migration pathways, elementary mechanisms of irradiation induced processes. These studies open the way for the investigation of other significant phenomena involved in fuel behaviour, in particular the thermochemical and thermomechanical properties and their evolution in-pile, complex microstructures, as well as of more complex fuels.
Identification of parameters of discrete-continuous models
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.
Inverse estimation of parameters for an estuarine eutrophication model
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.
CIMI simulations with recently developed multi-parameter chorus and plasmaspheric hiss models
NASA Astrophysics Data System (ADS)
Aryan, Homayon; Sibeck, David; Kang, Suk-bin; Balikhin, Michael; Fok, Mei-ching
2017-04-01
Simulation studies of the Earth's radiation belts are very useful in understanding the acceleration and loss of energetic particles. The Comprehensive Inner Magnetosphere-Ionosphere (CIMI) model considers the effects of the ring current and plasmasphere on the radiation belts. CIMI was formed by merging the Comprehensive Ring Current Model (CRCM) and the Radiation Belt Environment (RBE) model to solves for many essential quantities in the inner magnetosphere, including radiation belt enhancements and dropouts. It incorporates chorus and plasmaspheric hiss wave diffusion of energetic electrons in energy, pitch angle, and cross terms. Usually the chorus and plasmaspheric hiss models used in CIMI are based on single-parameter geomagnetic index (AE). Here we integrate recently developed multi-parameter chorus and plasmaspheric hiss wave models based on geomagnetic index and solar wind parameters. We then perform CIMI simulations for different storms and compare the results with data from the Van Allen Probes and the Two Wide-angle Imaging Neutral-atom Spectrometers and Akebono satellites. We find that the CIMI simulations with multi-parameter chorus and plasmaspheric hiss wave models are more comparable to data than the single-parameter wave models.
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.
Malinska, Maura; Dauter, Zbigniew
2016-01-01
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. PMID:27303797
The Role of Theoretical Atomic Physics in Astrophysical Plasma Modeling
NASA Astrophysics Data System (ADS)
Gorczyca, Tom
2008-05-01
The interpretation of cosmic spectra relies on a vast sea of atomic data which are not readily obtainable from analytic expressions or simple calculations. Since experimental determination of the multitude of atomic excitation, ionization, and recombination rates is clearly impossible, theoretical calculations are required for all transitions of all ionization stages of all elements through the iron peak elements, and to achieve the accuracy necessary for interpreting the most recently observed, high-resolution spectra, state-of-the-art atomic theoretical techniques need to be used. In this talk, I will give an overview of the latest status of the theoretical treatments of atomic processes in astrophysical plasmas, including a description of the available atomic databases. The successes of atomic theory, as assessed by benchmarking computational results with experimental measurements, where available, will be discussed as well as the present challenges facing the theoretical atomic laboratory astrophysics community.
Atomic scale modelling of hexagonal structured metallic fission product alloys
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
Atomic scale modelling of hexagonal structured metallic fission product alloys.
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.
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.
Experimental modelling of material interfaces with ultracold atoms
NASA Astrophysics Data System (ADS)
Corcovilos, Theodore A.; Brooke, Robert W. A.; Gillis, Julie; Ruggiero, Anthony C.; Tiber, Gage D.; Zaccagnini, Christopher A.
2014-05-01
We present a design for a new experimental apparatus for studying the physics of junctions using ultracold potassium atoms (K-39 and K-40). Junctions will be modeled using holographically projected 2D optical potentials. These potentials can be engineered to contain arbitrary features such as junctions between dissimilar lattices or the intentional insertion of defects. Long-term investigation goals include edge states, scattering at defects, and quantum depletion at junctions. In this poster we show our overall apparatus design and our progress in building experimental subsystems including the vacuum system, extended cavity diode lasers, digital temperature and current control circuits for the lasers, and the saturated absorption spectroscopy system. Funding provided by the Bayer School of Natural and Environmental.
Atomic-level models of the bacterial carboxysome shell
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.
Toward predictive food process models: A protocol for parameter estimation.
Vilas, Carlos; Arias-Méndez, Ana; García, Míriam R; Alonso, Antonio A; Balsa-Canto, E
2016-05-31
Mathematical models, in particular, physics-based models, are essential tools to food product and process design, optimization and control. The success of mathematical models relies on their predictive capabilities. However, describing physical, chemical and biological changes in food processing requires the values of some, typically unknown, parameters. Therefore, parameter estimation from experimental data is critical to achieving desired model predictive properties. This work takes a new look into the parameter estimation (or identification) problem in food process modeling. First, we examine common pitfalls such as lack of identifiability and multimodality. Second, we present the theoretical background of a parameter identification protocol intended to deal with those challenges. And, to finish, we illustrate the performance of the proposed protocol with an example related to the thermal processing of packaged foods.
Variability in sensitivity of catchment model parameters in Austria
NASA Astrophysics Data System (ADS)
Sleziak, Patrik; Parajka, Juraj; Hlavčová, Kamila; Szolgay, Ján
2017-04-01
The main objective of this study is to assess the spatial and temporal changes in sensitivity of model parameters in Austria. The sensitivity is assessed for a conceptual rainfall-runoff model (TUW model) by using Latin hypercube sampling method. The spatial variability in sensitivity of model parameters is evaluated over 213 Austrian basins. The temporal variability is compared for three 10-year periods from 1981-2010. The results show two distinct regions with different sensitivity of model parameters. In the alpine and flatlands regions, the most sensitive are parameters related to snow (degree-day melt factor) and soil (maximum soil field capacity) processes, respectively. The evaluation of temporal variability indicates that despite some changes in climate characteristics over the analyzed decades (i.e. a clear increase in air temperature and precipitation), the sensitivity changes are not large. Our contribution will discuss the factors that control the temporal stability of sensitivity changes in Austria.
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.
Algorithms and physical parameters involved in the calculation of model stellar atmospheres
NASA Astrophysics Data System (ADS)
Merlo, D. C.
This contribution summarizes the Doctoral Thesis presented at Facultad de Matemática, Astronomía y Física, Universidad Nacional de Córdoba for the degree of PhD in Astronomy. We analyze some algorithms and physical parameters involved in the calculation of model stellar atmospheres, such as atomic partition functions, functional relations connecting gaseous and electronic pressure, molecular formation, temperature distribution, chemical compositions, Gaunt factors, atomic cross-sections and scattering sources, as well as computational codes for calculating models. Special attention is paid to the integration of hydrostatic equation. We compare our results with those obtained by other authors, finding reasonable agreement. We make efforts on the implementation of methods that modify the originally adopted temperature distribution in the atmosphere, in order to obtain constant energy flux throughout. We find limitations and we correct numerical instabilities. We integrate the transfer equation solving directly the integral equation involving the source function. As a by-product, we calculate updated atomic partition functions of the light elements. Also, we discuss and enumerate carefully selected formulae for the monochromatic absorption and dispersion of some atomic and molecular species. Finally, we obtain a flexible code to calculate model stellar atmospheres.
A dimensionless parameter model for arc welding processes
Fuerschbach, P.W.
1994-12-31
A dimensionless parameter model previously developed for C0{sub 2} laser beam welding has been shown to be applicable to GTAW and PAW autogenous arc welding processes. The model facilitates estimates of weld size, power, and speed based on knowledge of the material`s thermal properties. The dimensionless parameters can also be used to estimate the melting efficiency, which eases development of weld schedules with lower heat input to the weldment. The mathematical relationship between the dimensionless parameters in the model has been shown to be dependent on the heat flow geometry in the weldment.
Estimation of the input parameters in the Feller neuronal model
NASA Astrophysics Data System (ADS)
Ditlevsen, Susanne; Lansky, Petr
2006-06-01
The stochastic Feller neuronal model is studied, and estimators of the model input parameters, depending on the firing regime of the process, are derived. Closed expressions for the first two moments of functionals of the first-passage time (FTP) through a constant boundary in the suprathreshold regime are derived, which are used to calculate moment estimators. In the subthreshold regime, the exponentiality of the FTP is utilized to characterize the input parameters. The methods are illustrated on simulated data. Finally, approximations of the first-passage-time moments are suggested, and biological interpretations and comparisons of the parameters in the Feller and the Ornstein-Uhlenbeck models are discussed.
Computationally Inexpensive Identification of Non-Informative Model Parameters
NASA Astrophysics Data System (ADS)
Mai, J.; Cuntz, M.; Kumar, R.; Zink, M.; Samaniego, L. E.; Schaefer, D.; Thober, S.; Rakovec, O.; Musuuza, J. L.; Craven, J. R.; Spieler, D.; Schrön, M.; Prykhodko, V.; Dalmasso, G.; Langenberg, B.; Attinger, S.
2014-12-01
Sensitivity analysis is used, for example, to identify parameters which induce the largest variability in model output and are thus informative during calibration. Variance-based techniques are employed for this purpose, which unfortunately require a large number of model evaluations and are thus ineligible for complex environmental models. We developed, therefore, a computational inexpensive screening method, which is based on Elementary Effects, that automatically separates informative and non-informative model parameters. The method was tested using the mesoscale hydrologic model (mHM) with 52 parameters. The model was applied in three European catchments with different hydrological characteristics, i.e. Neckar (Germany), Sava (Slovenia), and Guadalquivir (Spain). The method identified the same informative parameters as the standard Sobol method but with less than 1% of model runs. In Germany and Slovenia, 22 of 52 parameters were informative mostly in the formulations of evapotranspiration, interflow and percolation. In Spain 19 of 52 parameters were informative with an increased importance of soil parameters. We showed further that Sobol' indexes calculated for the subset of informative parameters are practically the same as Sobol' indexes before the screening but the number of model runs was reduced by more than 50%. The model mHM was then calibrated twice in the three test catchments. First all 52 parameters were taken into account and then only the informative parameters were calibrated while all others are kept fixed. The Nash-Sutcliffe efficiencies were 0.87 and 0.83 in Germany, 0.89 and 0.88 in Slovenia, and 0.86 and 0.85 in Spain, respectively. This minor loss of at most 4% in model performance comes along with a substantial decrease of at least 65% in model evaluations. In summary, we propose an efficient screening method to identify non-informative model parameters that can be discarded during further applications. We have shown that sensitivity
Field measurements and neural network modeling of water quality parameters
NASA Astrophysics Data System (ADS)
Qishlaqi, Afishin; Kordian, Sediqeh; Parsaie, Abbas
2017-01-01
Rivers are one of the main resources for water supplying the agricultural, industrial, and urban use; therefore, unremitting surveying the quality of them is necessary. Recently, artificial neural networks have been proposed as a powerful tool for modeling and predicting the water quality parameters in natural streams. In this paper, to predict water quality parameters of Tireh River located at South West of Iran, a multilayer neural network model (MLP) was developed. The T.D.S, Ec, pH, HCO3, Cl, Na, So4, Mg, and Ca as main parameters of water quality parameters were measured and predicted using the MLP model. The architecture of the proposed MLP model included two hidden layers that at the first and second hidden layers, eight and six neurons were considered. The tangent sigmoid and pure-line functions were selected as transfer function for the neurons in hidden and output layers, respectively. The results showed that the MLP model has suitable performance to predict water quality parameters of Tireh River. For assessing the performance of the MLP model in the water quality prediction along the studied area, in addition to existing sampling stations, another 14 stations along were considered by authors. Evaluating the performance of developed MLP model to map relation between the water quality parameters along the studied area showed that it has suitable accuracy and minimum correlation between the results of MLP model and measured data was 0.85.
NASA Astrophysics Data System (ADS)
Stener, M.; De Alti, G.; Fronzoni, G.; Decleva, P.
1997-10-01
Absolute photoionization cross-section and asymmetry parameter profiles of Be, Mg and Ca have been calculated at TDLDA and LDA level, employing a very accurate B-spline basis set and the modified Sternheimer approach. The van Leeuwen-Baerends (VLB) exchange correlation potential has been used, since its correct asymptotic behaviour is able to support virtual states and to describe core-excited resonances. The results have been compared with other calculations and experiment when available. The autoionization resonances have been successfully fitted with a suitable Fano profile. The Ca 3p → 3d 'giant-resonance' has been properly described, despite of the dramatic screening effects involved in the process. The success of the TDLDA method for describing the cross-section profiles in the present systems which display a wide range of many-body effects, seems to suggest that further efforts to apply the present method to molecules are justified.
Estimating winter wheat phenological parameters: Implications for crop modeling
USDA-ARS?s Scientific Manuscript database
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...
Crop parameters for modeling sugarcane under rainfed conditions in Mexico
USDA-ARS?s Scientific Manuscript database
Crop models with well-tested parameters can improve sugarcane productivity for food and biofuel generation. This study aimed to (i) calibrate the light extinction coefficient (k) and other crop parameters for the sugarcane cultivar CP 72-2086, an early-maturing cultivar grown in Mexico and many oth...
Atomic charges for modeling metal-organic frameworks: Why and how
NASA Astrophysics Data System (ADS)
Hamad, Said; Balestra, Salvador R. G.; Bueno-Perez, Rocio; Calero, Sofia; Ruiz-Salvador, A. Rabdel
2015-03-01
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.
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.
Analysis of the Second Model Parameter Estimation Experiment Workshop Results
NASA Astrophysics Data System (ADS)
Duan, Q.; Schaake, J.; Koren, V.; Mitchell, K.; Lohmann, D.
2002-05-01
The goal of Model Parameter Estimation Experiment (MOPEX) is to investigate techniques for the a priori parameter estimation for land surface parameterization schemes of atmospheric models and for hydrologic models. A comprehensive database has been developed which contains historical hydrometeorologic time series data and land surface characteristics data for 435 basins in the United States and many international basins. A number of international MOPEX workshops have been convened or planned for MOPEX participants to share their parameter estimation experience. The Second International MOPEX Workshop is held in Tucson, Arizona, April 8-10, 2002. This paper presents the MOPEX goal/objectives and science strategy. Results from our participation in developing and testing of the a priori parameter estimation procedures for the National Weather Service (NWS) Sacramento Soil Moisture Accounting (SAC-SMA) model, the Simple Water Balance (SWB) model, and the National Center for Environmental Prediction Center (NCEP) NOAH Land Surface Model (NOAH LSM) are highlighted. The test results will include model simulations using both a priori parameters and calibrated parameters for 12 basins selected for the Tucson MOPEX Workshop.
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.
Scrape-off layer modeling with kinetic or diffusion description of charge-exchange atoms
NASA Astrophysics Data System (ADS)
Tokar, M. Z.
2016-12-01
Hydrogen isotope atoms, generated by charge-exchange (c-x) of neutral particles recycling from the first wall of a fusion reactor, are described either kinetically or in a diffusion approximation. In a one-dimensional (1-D) geometry, kinetic calculations are accelerated enormously by applying an approximate pass method for the assessment of integrals in the velocity space. This permits to perform an exhaustive comparison of calculations done with both approaches. The diffusion approximation is deduced directly from the velocity distribution function of c-x atoms in the limit of charge-exchanges with ions occurring much more frequently than ionization by electrons. The profiles across the flux surfaces of the plasma parameters averaged along the main part of the scrape-off layer (SOL), beyond the X-point and divertor regions, are calculated from the one-dimensional equations where parallel flows of charged particles and energy towards the divertor are taken into account as additional loss terms. It is demonstrated that the heat losses can be firmly estimated from the SOL averaged parameters only; for the particle loss the conditions in the divertor are of importance and the sensitivity of the results to the so-called "divertor impact factor" is investigated. The coupled 1-D models for neutral and charged species, with c-x atoms described either kinetically or in the diffusion approximation, are applied to assess the SOL conditions in a fusion reactor, with the input parameters from the European DEMO project. It is shown that the diffusion approximation provides practically the same profiles across the flux surfaces for the plasma density, electron, and ion temperatures, as those obtained with the kinetic description for c-x atoms. The main difference between the two approaches is observed in the characteristics of these species themselves. In particular, their energy flux onto the wall is underestimated in calculations with the diffusion approximation by 20 % - 30
Effect of Noise in the Three-Parameter Logistic Model.
ERIC Educational Resources Information Center
Samejima, Fumiko
In a preceding research report, ONR/RR-82-1 (Information Loss Caused by Noise in Models for Dichotomous Items), observations were made on the effect of noise accommodated in different types of models on the dichotomous response level. In the present paper, focus is put upon the three-parameter logistic model, which is widely used among…
Effect of Noise in the Three-Parameter Logistic Model.
ERIC Educational Resources Information Center
Samejima, Fumiko
In a preceding research report, ONR/RR-82-1 (Information Loss Caused by Noise in Models for Dichotomous Items), observations were made on the effect of noise accommodated in different types of models on the dichotomous response level. In the present paper, focus is put upon the three-parameter logistic model, which is widely used among…
REVIEW OF INDOOR EMISSION SOURCE MODELS: PART 2. PARAMETER ESTIMATION
This review consists of two sections. Part I provides an overview of 46 indoor emission source models. Part 2 (this paper) focuses on parameter estimation, a topic that is critical to modelers but has never been systematically discussed. A perfectly valid model may not be a usefu...
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,…
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,…
Lumped Parameter Model (LPM) for Light-Duty Vehicles
EPA’s Lumped Parameter Model (LPM) is a free, desktop computer application that estimates the effectiveness (CO2 Reduction) of various technology combinations or “packages,” in a manner that accounts for synergies between technologies.
Dynamic Load Model using PSO-Based Parameter Estimation
NASA Astrophysics Data System (ADS)
Taoka, Hisao; Matsuki, Junya; Tomoda, Michiya; Hayashi, Yasuhiro; Yamagishi, Yoshio; Kanao, Norikazu
This paper presents a new method for estimating unknown parameters of dynamic load model as a parallel composite of a constant impedance load and an induction motor behind a series constant reactance. An adequate dynamic load model is essential for evaluating power system stability, and this model can represent the behavior of actual load by using appropriate parameters. However, the problem of this model is that a lot of parameters are necessary and it is not easy to estimate a lot of unknown parameters. We propose an estimating method based on Particle Swarm Optimization (PSO) which is a non-linear optimization method by using the data of voltage, active power and reactive power measured at voltage sag.
Parameter Estimation for the Thurstone Case III Model.
ERIC Educational Resources Information Center
Mackay, David B.; Chaiy, Seoil
1982-01-01
The ability of three estimation criteria to recover parameters of the Thurstone Case V and Case III models from comparative judgment data was investigated via Monte Carlo techniques. Significant differences in recovery are shown to exist. (Author/JKS)
Online parameter estimation for surgical needle steering model.
Yan, Kai Guo; Podder, Tarun; Xiao, Di; Yu, Yan; Liu, Tien-I; Ling, Keck Voon; Ng, Wan Sing
2006-01-01
Estimation of the system parameters, given noisy input/output data, is a major field in control and signal processing. Many different estimation methods have been proposed in recent years. Among various methods, Extended Kalman Filtering (EKF) is very useful for estimating the parameters of a nonlinear and time-varying system. Moreover, it can remove the effects of noises to achieve significantly improved results. Our task here is to estimate the coefficients in a spring-beam-damper needle steering model. This kind of spring-damper model has been adopted by many researchers in studying the tissue deformation. One difficulty in using such model is to estimate the spring and damper coefficients. Here, we proposed an online parameter estimator using EKF to solve this problem. The detailed design is presented in this paper. Computer simulations and physical experiments have revealed that the simulator can estimate the parameters accurately with fast convergent speed and improve the model efficacy.
Uncertainty in dual permeability model parameters for structured soils
NASA Astrophysics Data System (ADS)
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.
NASA Astrophysics Data System (ADS)
Xia, Youlong; Yang, Zong-Liang; Stoffa, Paul L.; Sen, Mrinal K.
2005-01-01
Most previous land-surface model calibration studies have defined global ranges for their parameters to search for optimal parameter sets. Little work has been conducted to study the impacts of realistic versus global ranges as well as model complexities on the calibration and uncertainty estimates. The primary purpose of this paper is to investigate these impacts by employing Bayesian Stochastic Inversion (BSI) to the Chameleon Surface Model (CHASM). The CHASM was designed to explore the general aspects of land-surface energy balance representation within a common modeling framework that can be run from a simple energy balance formulation to a complex mosaic type structure. The BSI is an uncertainty estimation technique based on Bayes theorem, importance sampling, and very fast simulated annealing. The model forcing data and surface flux data were collected at seven sites representing a wide range of climate and vegetation conditions. For each site, four experiments were performed with simple and complex CHASM formulations as well as realistic and global parameter ranges. Twenty eight experiments were conducted and 50 000 parameter sets were used for each run. The results show that the use of global and realistic ranges gives similar simulations for both modes for most sites, but the global ranges tend to produce some unreasonable optimal parameter values. Comparison of simple and complex modes shows that the simple mode has more parameters with unreasonable optimal values. Use of parameter ranges and model complexities have significant impacts on frequency distribution of parameters, marginal posterior probability density functions, and estimates of uncertainty of simulated sensible and latent heat fluxes. Comparison between model complexity and parameter ranges shows that the former has more significant impacts on parameter and uncertainty estimations.
Oscillating Quintom Model with Time Periodic Varying Deceleration Parameter
NASA Astrophysics Data System (ADS)
Shen, Ming; Zhao, Liang
2014-01-01
We propose a new law for the deceleration parameter that varies periodically with time. According to the law, we give a model of the oscillating universe with quintom matter in the framework of a 4-dimensional Friedmann—Robertson—Walker background. We find that, in the model, the Hubble parameter oscillates and keeps positive. The universe undergoes decelerating expansion and accelerating expansion alternately without singularity
Agricultural and Environmental Input Parameters for the Biosphere Model
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.
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.
NASA Astrophysics Data System (ADS)
Löbling, L.
2017-03-01
Aluminum (Al) nucleosynthesis takes place during the asymptotic-giant-branch (AGB) phase of stellar evolution. Al abundance determinations in hot white dwarf stars provide constraints to understand this process. Precise abundance measurements require advanced non-local thermodynamic stellar-atmosphere models and reliable atomic data. In the framework of the German Astrophysical Virtual Observatory (GAVO), the Tübingen Model-Atom Database (TMAD) contains ready-to- use model atoms for elements from hydrogen to barium. A revised, elaborated Al model atom has recently been added. We present preliminary stellar-atmosphere models and emergent Al line spectra for the hot white dwarfs G191-B2B and RE 0503-289.
Combined Estimation of Hydrogeologic Conceptual Model and Parameter Uncertainty
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
From deep TLS validation to ensembles of atomic models built from elemental motions
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.
From deep TLS validation to ensembles of atomic models built from elemental motions
Urzhumtsev, Alexandre; Afonine, Pavel V.; Van Benschoten, Andrew H.; ...
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
Deng, Zhang; He, Wenjie; Duan, Chenlong; Chen, Rong; Shan, Bin
2016-01-15
Spatial atomic layer deposition (SALD) is a promising technology with the aim of combining the advantages of excellent uniformity and conformity of temporal atomic layer deposition (ALD), and an industrial scalable and continuous process. In this manuscript, an experimental and numerical combined model of atmospheric SALD system is presented. To establish the connection between the process parameters and the growth efficiency, a quantitative model on reactant isolation, throughput, and precursor utilization is performed based on the separation gas flow rate, carrier gas flow rate, and precursor mass fraction. The simulation results based on this model show an inverse relation between the precursor usage and the carrier gas flow rate. With the constant carrier gas flow, the relationship of precursor usage and precursor mass fraction follows monotonic function. The precursor concentration, regardless of gas velocity, is the determinant factor of the minimal residual time. The narrow gap between precursor injecting heads and the substrate surface in general SALD system leads to a low Péclet number. In this situation, the gas diffusion act as a leading role in the precursor transport in the small gap rather than the convection. Fluid kinetics from the numerical model is independent of the specific structure, which is instructive for the SALD geometry design as well as its process optimization.
From deep TLS validation to ensembles of atomic models built from elemental motions.
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.
From deep TLS validation to ensembles of atomic models built from elemental motions
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
Critical parameters of consistent relativistic mean-field models
NASA Astrophysics Data System (ADS)
Lourenço, O.; Dutra, M.; Menezes, D. P.
2017-06-01
In the present work, the critical temperature, critical pressure, and critical density, known as the critical parameters related to the liquid-gas phase transition are calculated for 34 relativistic mean-field models, which were shown to satisfy nuclear matter constraints in a comprehensive study involving 263 models. The compressibility factor was calculated and all 34 models present values lower than the one obtained with the van der Waals equation of state. The critical temperatures were compared with experimental data and just two classes of models can reach values close to them. A correlation between the critical parameters and the incompressibility was obtained.
SPOTting Model Parameters Using a Ready-Made Python Package
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
SPOTting Model Parameters Using a Ready-Made Python Package.
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.
Parameter Estimation and Model Selection in Computational Biology
Lillacci, Gabriele; Khammash, Mustafa
2010-01-01
A central challenge in computational modeling of biological systems is the determination of the model parameters. Typically, only a fraction of the parameters (such as kinetic rate constants) are experimentally measured, while the rest are often fitted. The fitting process is usually based on experimental time course measurements of observables, which are used to assign parameter values that minimize some measure of the error between these measurements and the corresponding model prediction. The measurements, which can come from immunoblotting assays, fluorescent markers, etc., tend to be very noisy and taken at a limited number of time points. In this work we present a new approach to the problem of parameter selection of biological models. We show how one can use a dynamic recursive estimator, known as extended Kalman filter, to arrive at estimates of the model parameters. The proposed method follows. First, we use a variation of the Kalman filter that is particularly well suited to biological applications to obtain a first guess for the unknown parameters. Secondly, we employ an a posteriori identifiability test to check the reliability of the estimates. Finally, we solve an optimization problem to refine the first guess in case it should not be accurate enough. The final estimates are guaranteed to be statistically consistent with the measurements. Furthermore, we show how the same tools can be used to discriminate among alternate models of the same biological process. We demonstrate these ideas by applying our methods to two examples, namely a model of the heat shock response in E. coli, and a model of a synthetic gene regulation system. The methods presented are quite general and may be applied to a wide class of biological systems where noisy measurements are used for parameter estimation or model selection. PMID:20221262
Parameter estimation and model selection in computational biology.
Lillacci, Gabriele; Khammash, Mustafa
2010-03-05
A central challenge in computational modeling of biological systems is the determination of the model parameters. Typically, only a fraction of the parameters (such as kinetic rate constants) are experimentally measured, while the rest are often fitted. The fitting process is usually based on experimental time course measurements of observables, which are used to assign parameter values that minimize some measure of the error between these measurements and the corresponding model prediction. The measurements, which can come from immunoblotting assays, fluorescent markers, etc., tend to be very noisy and taken at a limited number of time points. In this work we present a new approach to the problem of parameter selection of biological models. We show how one can use a dynamic recursive estimator, known as extended Kalman filter, to arrive at estimates of the model parameters. The proposed method follows. First, we use a variation of the Kalman filter that is particularly well suited to biological applications to obtain a first guess for the unknown parameters. Secondly, we employ an a posteriori identifiability test to check the reliability of the estimates. Finally, we solve an optimization problem to refine the first guess in case it should not be accurate enough. The final estimates are guaranteed to be statistically consistent with the measurements. Furthermore, we show how the same tools can be used to discriminate among alternate models of the same biological process. We demonstrate these ideas by applying our methods to two examples, namely a model of the heat shock response in E. coli, and a model of a synthetic gene regulation system. The methods presented are quite general and may be applied to a wide class of biological systems where noisy measurements are used for parameter estimation or model selection.
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.
Parameter Transferability Across Spatial and Temporal Resolutions in Hydrological Modelling
NASA Astrophysics Data System (ADS)
Melsen, L. A.; Teuling, R.; Torfs, P. J.; Zappa, M.; Mizukami, N.; Clark, M. P.; Uijlenhoet, R.
2015-12-01
Improvements in computational power and data availability provided new opportunities for hydrological modeling. The increased complexity of hydrological models, however, also leads to time consuming optimization procedures. Moreover, observations are still required to calibrate the model. Both to decrease calculation time of the optimization and to be able to apply the model in poorly gauged basins, many studies have focused on transferability of parameters. We adopted a probabilistic approach to systematically investigate parameter transferability across both temporal and spatial resolution. A Variable Infiltration Capacity model for the Thur basin (1703km2, Switzerland) was set-up and run at four different spatial resolutions (1x1, 5x5, 10x10km, lumped) and three different temporal resolutions (hourly, daily, monthly). Three objective functions were used to evaluate the model: Kling-Gupta Efficiency (KGE(Q)), Nash-Sutcliffe Efficiency (NSE(Q)) and NSE(logQ). We used a Hierarchical Latin Hypercube Sample (Vorechovsky, 2014) to efficiently sample the most sensitive parameters. The model was run 3150 times and the best 1% of the runs was selected as behavioral. The overlap in selected behavioral sets for different spatial and temporal resolutions was used as indicators for parameter transferability. There was a large overlap in selected sets for the different spatial resolutions, implying that parameters were to a large extent transferable across spatial resolutions. The temporal resolution, however, had a larger impact on the parameters; it significantly affected the parameter distributions for at least four out of seven parameters. The parameter values for the monthly time step were found to be substantially different from those for daily and hourly time steps. This suggests that the output from models which are calibrated on a monthly time step, cannot be interpreted or analysed on an hourly or daily time step. It was also shown that the selected objective
Crystal structures and atomic model of NADPH oxidase.
Magnani, Francesca; Nenci, Simone; Millana Fananas, Elisa; Ceccon, Marta; Romero, Elvira; Fraaije, Marco W; Mattevi, Andrea
2017-06-27
NADPH oxidases (NOXs) are the only enzymes exclusively dedicated to reactive oxygen species (ROS) generation. Dysregulation of these polytopic membrane proteins impacts the redox signaling cascades that control cell proliferation and death. We describe the atomic crystal structures of the catalytic flavin adenine dinucleotide (FAD)- and heme-binding domains of Cylindrospermum stagnale NOX5. The two domains form the core subunit that is common to all seven members of the NOX family. The domain structures were then docked in silico to provide a generic model for the NOX family. A linear arrangement of cofactors (NADPH, FAD, and two membrane-embedded heme moieties) injects electrons from the intracellular side across the membrane to a specific oxygen-binding cavity on the extracytoplasmic side. The overall spatial organization of critical interactions is revealed between the intracellular loops on the transmembrane domain and the NADPH-oxidizing dehydrogenase domain. In particular, the C terminus functions as a toggle switch, which affects access of the NADPH substrate to the enzyme. The essence of this mechanistic model is that the regulatory cues conformationally gate NADPH-binding, implicitly providing a handle for activating/deactivating the very first step in the redox chain. Such insight provides a framework to the discovery of much needed drugs that selectively target the distinct members of the NOX family and interfere with ROS signaling.
Behaviour of the cosmological model with variable deceleration parameter
NASA Astrophysics Data System (ADS)
Tiwari, R. K.; Beesham, A.; Shukla, B. K.
2016-12-01
We consider the Bianchi type-VI0 massive string universe with decaying cosmological constant Λ. To solve Einstein's field equations, we assume that the shear scalar is proportional to the expansion scalar and that the deceleration parameter q is a linear function of the Hubble parameter H, i.e., q=α +β H, which yields the scale factor a = e^{1/β√{2β t+k1}}. The model expands exponentially with cosmic time t. The value of the cosmological constant Λ is small and positive. Also, we discuss physical parameters as well as the jerk parameter j, which predict that the universe in this model originates as in the Λ CDM model.
Improved input parameters for diffusion models of skin absorption.
Hansen, Steffi; Lehr, Claus-Michael; Schaefer, Ulrich F
2013-02-01
To use a diffusion model for predicting skin absorption requires accurate estimates of input parameters on model geometry, affinity and transport characteristics. This review summarizes methods to obtain input parameters for diffusion models of skin absorption focusing on partition and diffusion coefficients. These include experimental methods, extrapolation approaches, and correlations that relate partition and diffusion coefficients to tabulated physico-chemical solute properties. Exhaustive databases on lipid-water and corneocyte protein-water partition coefficients are presented and analyzed to provide improved approximations to estimate lipid-water and corneocyte protein-water partition coefficients. The most commonly used estimates of lipid and corneocyte diffusion coefficients are also reviewed. In order to improve modeling of skin absorption in the future diffusion models should include the vertical stratum corneum heterogeneity, slow equilibration processes, the absorption from complex non-aqueous formulations, and an improved representation of dermal absorption processes. This will require input parameters for which no suitable estimates are yet available.
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.
A six-parameter Iwan model and its application
NASA Astrophysics Data System (ADS)
Li, Yikun; Hao, Zhiming
2016-02-01
Iwan model is a practical tool to describe the constitutive behaviors of joints. In this paper, a six-parameter Iwan model based on a truncated power-law distribution with two Dirac delta functions is proposed, which gives a more comprehensive description of joints than the previous Iwan models. Its analytical expressions including backbone curve, unloading curves and energy dissipation are deduced. Parameter identification procedures and the discretization method are also provided. A model application based on Segalman et al.'s experiment works with bolted joints is carried out. Simulation effects of different numbers of Jenkins elements are discussed. The results indicate that the six-parameter Iwan model can be used to accurately reproduce the experimental phenomena of joints.
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…
Piecewise parameter estimation for stochastic models in COPASI.
Bergmann, Frank T; Sahle, Sven; Zimmer, Christoph
2016-05-15
Computational modeling is widely used for deepening the understanding of biological processes. Parameterizing models to experimental data needs computationally efficient techniques for parameter estimation. Challenges for parameter estimation include in general the high dimensionality of the parameter space with local minima and in specific for stochastic modeling the intrinsic stochasticity. We implemented the recently suggested multiple shooting for stochastic systems (MSS) objective function for parameter estimation in stochastic models into COPASI. This MSS objective function can be used for parameter estimation in stochastic models but also shows beneficial properties when used for ordinary differential equation models. The method can be applied with all of COPASI's optimization algorithms, and can be used for SBML models as well. The methodology is available in COPASI as of version 4.15.95 and can be downloaded from http://www.copasi.org frank.bergmann@bioquant.uni-heidelberg.de or fbergman@caltech.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
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.
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.
Parameter estimation for groundwater models under uncertain irrigation data
Demissie, Yonas; Valocchi, Albert J.; 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.
Parameter Estimation for Groundwater Models under Uncertain Irrigation Data.
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.
Development of a phenomenological model for coal slurry atomization
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.
NASA Astrophysics Data System (ADS)
Derouich, M.
2017-02-01
Simulations of the generation of the atomic polarization is necessary for interpreting the second solar spectrum. For this purpose, it is important to rigorously determine the effects of the isotropic collisions with neutral hydrogen on the atomic polarization of the neutral atoms, ionized atoms and molecules. Our aim is to treat in generality the problem of depolarizing isotropic collisions between singly ionized atoms and neutral hydrogen in its ground state. Using our numerical code, we computed the collisional depolarization rates of the p-levels of ions for large number of values of the effective principal quantum number n* and the Unsöld energy Ep. Then, genetic programming has been utilized to fit the available depolarization rates. As a result, strongly non-linear relationships between the collisional depolarization rates, n* and Ep are obtained, and are shown to reproduce the original data with accuracy clearly better than 10%. These relationships allow quick calculations of the depolarizing collisional rates of any simple ion which is very useful for the solar physics community. In addition, the depolarization rates associated to the complex ions and to the hyperfine levels can be easily derived from our results. In this work we have shown that by using powerful numerical approach and our collisional method, general model giving the depolarization of the ions can be obtained to be exploited for solar applications.
Parameters of cosmological models and recent astronomical observations
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.
Parameters of cosmological models and recent astronomical observations
NASA Astrophysics Data System (ADS)
Sharov, G. S.; Vorontsova, E. G.
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: H0=70.262±0.319 km -1Mp -1, Ωm=0.276-0.008+0.009, ΩΛ=0.769±0.029, Ωk=-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.
On two-parameter models of photon cross sections: application to dual-energy CT imaging.
Williamson, Jeffrey F; Li, Sicong; Devic, Slobodan; Whiting, Bruce R; Lerma, Fritz A
2006-11-01
The goal of this study is to evaluate the theoretically achievable accuracy in estimating photon cross sections at low energies (20-1000 keV) from idealized dual-energy x-ray computed tomography (CT) images. Cross-section estimation from dual-energy measurements requires a model that can accurately represent photon cross sections of any biological material as a function of energy by specifying only two characteristic parameters of the underlying material, e.g., effective atomic number and density. This paper evaluates the accuracy of two commonly used two-parameter cross-section models for postprocessing idealized measurements derived from dual-energy CT images. The parametric fit model (PFM) accounts for electron-binding effects and photoelectric absorption by power functions in atomic number and energy and scattering by the Klein-Nishina cross section. The basis-vector model (BVM) assumes that attenuation coefficients of any biological substance can be approximated by a linear combination of mass attenuation coefficients of two dissimilar basis substances. Both PFM and BVM were fit to a modern cross-section library for a range of elements and mixtures representative of naturally occurring biological materials (Z = 2-20). The PFM model, in conjunction with the effective atomic number approximation, yields estimated the total linear cross-section estimates with mean absolute and maximum error ranges of 0.6%-2.2% and 1%-6%, respectively. The corresponding error ranges for BVM estimates were 0.02%-0.15% and 0.1%-0.5%. However, for photoelectric absorption frequency, the PFM absolute mean and maximum errors were 10.8%-22.4% and 29%-50%, compared with corresponding BVM errors of 0.4%-11.3% and 0.5%-17.0%, respectively. Both models were found to exhibit similar sensitivities to image-intensity measurement uncertainties. Of the two models, BVM is the most promising approach for realizing dual-energy CT cross-section measurement.
A Bayesian Approach for Parameter Estimation and Prediction using a Computationally Intensive Model
Higdon, Dave; McDonnell, Jordan D.; Schunck, Nicolas; Sarich, Jason; Wild, Stefan M.
2015-03-01
Bayesian methods have been successful in quantifying uncertainty in physics-based problems in parameter estimation and prediction. In these cases, physical measurements y are modeled as the best fit of a physics-based model eta(theta), where theta denotes the uncertain, best input setting. Hence the statistical model is of the form y = eta(theta) + c, where epsilon accounts for measurement, and possibly other, error sources. When nonlinearity is present in eta(center dot), the resulting posterior distribution for the unknown parameters in the Bayesian formulation is typically complex and nonstandard, requiring computationally demanding computational approaches such as Markov chain Monte Carlo (MCMC) to produce multivariate draws from the posterior. Although generally applicable, MCMC requires thousands (or even millions) of evaluations of the physics model eta(center dot). This requirement is problematic if the model takes hours or days to evaluate. To overcome this computational bottleneck, we present an approach adapted from Bayesian model calibration. This approach combines output from an ensemble of computational model runs with physical measurements, within a statistical formulation, to carry out inference. A key component of this approach is a statistical response surface, or emulator, estimated from the ensemble of model runs. We demonstrate this approach with a case study in estimating parameters for a density functional theory model, using experimental mass/binding energy measurements from a collection of atomic nuclei. We also demonstrate how this approach produces uncertainties in predictions for recent mass measurements obtained at Argonne National Laboratory.
A Bayesian approach for parameter estimation and prediction using a computationally intensive model
Higdon, Dave; McDonnell, Jordan D.; Schunck, Nicolas; Sarich, Jason; Wild, Stefan M.
2015-02-05
Bayesian methods have been successful in quantifying uncertainty in physics-based problems in parameter estimation and prediction. In these cases, physical measurements y are modeled as the best fit of a physics-based model $\\eta (\\theta )$, where θ denotes the uncertain, best input setting. Hence the statistical model is of the form $y=\\eta (\\theta )+\\epsilon ,$ where $\\epsilon $ accounts for measurement, and possibly other, error sources. When nonlinearity is present in $\\eta (\\cdot )$, the resulting posterior distribution for the unknown parameters in the Bayesian formulation is typically complex and nonstandard, requiring computationally demanding computational approaches such as Markov chain Monte Carlo (MCMC) to produce multivariate draws from the posterior. Although generally applicable, MCMC requires thousands (or even millions) of evaluations of the physics model $\\eta (\\cdot )$. This requirement is problematic if the model takes hours or days to evaluate. To overcome this computational bottleneck, we present an approach adapted from Bayesian model calibration. This approach combines output from an ensemble of computational model runs with physical measurements, within a statistical formulation, to carry out inference. A key component of this approach is a statistical response surface, or emulator, estimated from the ensemble of model runs. We demonstrate this approach with a case study in estimating parameters for a density functional theory model, using experimental mass/binding energy measurements from a collection of atomic nuclei. We also demonstrate how this approach produces uncertainties in predictions for recent mass measurements obtained at Argonne National Laboratory.
Modelling of Atomic Oxygen Visible emissions from Comets
NASA Astrophysics Data System (ADS)
Raghuram, Susarla; Bhardwaj, Anil
Green (5577 Å) and red-doublet (6300, 6364 Å) lines are prompt emissions of metastable oxygen atoms of O((1) S) and O((1) D) respectively, that have been observed in several comets. The observed red-doublet emission intensity is used to estimate the H_{2}O production rate, whereas the green to red-doublet intensity ratio (G/R ratio) has been used to confirm the parent molecule of oxygen lines as H_{2}O. The observed higher G/R ratio values are ascribed to higher CO_{2} and CO relative abundances. A coupled chemistry-emission model is developed to study the production and loss mechanisms of O((1) S) and O((1) D) atoms and the generation of red and green lines in comets. Our model calculations on different comets suggest that the G/R ratio depends not only on photochemistry, but also on the projected area observed for cometary coma, which is a function of the dimension of the slit used and the geocentric distance of the comet. Our calculated mean excess energy in various photodissociation processes show that the high energy photons dissociate CO_{2} and produce O((1) S) with large velocities than that in photodissociation of H_{2}O which is consistent with larger width of green line compared to that of the red-doublet lines observed in several comets The photodissociation of H_{2}O mainly governs the red-doublet emission, whereas CO_{2} plays an important role in controlling the green line emission. The collisional quenching of O((1) S) and O((1) D) can alter the G/R ratio more than that can be due to variation in the CO_{2} and CO relative abundances. The role of CO photodissociation is found to be insignificant in producing green and red-doublet emission lines and consequently in determining the G/R ratio. If a comet has equal composition of CO_{2} and H_{2}O, which happens when comet is at larger heliocentric distances, then ˜50% of red-doublet emission intensity is controlled by the photodissociation of CO_{2}. References: Festou, M.C., & Feldman, P.D., Astron
Environmental Transport Input Parameters for the Biosphere Model
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]).
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.
Inhalation Exposure Input Parameters for the Biosphere Model
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.
Parameter uncertainty analysis of a biokinetic model of caesium
Li, W. B.; Klein, W.; Blanchardon, Eric; ...
2014-04-17
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 atmore » 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.« less
Parameter uncertainty analysis of a biokinetic model of caesium
Li, W. B.; Klein, W.; Blanchardon, Eric; Puncher, M; Leggett, Richard Wayne; Oeh, U.; Breustedt, B.; Nosske, Dietmar; Lopez, M.
2014-04-17
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.
Parameter uncertainty analysis of a biokinetic model of caesium.
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.
Environmental Transport Input Parameters for the Biosphere Model
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
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.
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.
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.
Advances in Parameter Estimation and Data Assimilation for Hydrologic Modeling
NASA Astrophysics Data System (ADS)
Sorooshian, S.
2001-12-01
In the past two decades, the availability of new data sources (particularly remotely sensed information) and improved computational tools has resulted in significant developments in the field of hydrologic modeling, from simple flow models to complex numerical models which simulate the coupled behavior of multiple fluxes (hydrologic, chemical, energy, etc.). At the same time, significant improvements have taken place in the data assimilation and parameter estimation methods. Although the increasing complexity of models has outpaced the development of appropriate systems identification methodologies, there is a need to design models that are properly constrained by observational data. Independent and collaborative research efforts by various groups worldwide have led to improved modeling techniques, optimization methods for parameter estimation, methods for estimating predictive uncertainty, and methods for evaluating the relative merits of competing models. This talk will review some of the key developments during the past 20 years and speculate on future directions.
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.
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/.
Sensor placement for calibration of spatially varying model parameters
NASA Astrophysics Data System (ADS)
Nath, Paromita; Hu, Zhen; Mahadevan, Sankaran
2017-08-01
This paper presents a sensor placement optimization framework for the calibration of spatially varying model parameters. To account for the randomness of the calibration parameters over space and across specimens, the spatially varying parameter is represented as a random field. Based on this representation, Bayesian calibration of spatially varying parameter is investigated. To reduce the required computational effort during Bayesian calibration, the original computer simulation model is substituted with Kriging surrogate models based on the singular value decomposition (SVD) of the model response and the Karhunen-Loeve expansion (KLE) of the spatially varying parameters. A sensor placement optimization problem is then formulated based on the Bayesian calibration to maximize the expected information gain measured by the expected Kullback-Leibler (K-L) divergence. The optimization problem needs to evaluate the expected K-L divergence repeatedly which requires repeated calibration of the spatially varying parameter, and this significantly increases the computational effort of solving the optimization problem. To overcome this challenge, an approximation for the posterior distribution is employed within the optimization problem to facilitate the identification of the optimal sensor locations using the simulated annealing algorithm. A heat transfer problem with spatially varying thermal conductivity is used to demonstrate the effectiveness of the proposed method.
Identification of Neurofuzzy models using GTLS parameter estimation.
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.
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.
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
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…
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…
Multiple Model Parameter Adaptive Control for In-Flight Simulation.
1988-03-01
dynamics of an aircraft. The plant is control- lable by a proportional-plus-integral ( PI ) control law. This section describes two methods of calculating...adaptive model-following PI control law [20-24]. The control law bases its control gains upon the parameters of a linear difference equation model which
Hubble Expansion Parameter in a New Model of Dark Energy
NASA Astrophysics Data System (ADS)
Saadat, Hassan
2012-01-01
In this study, we consider new model of dark energy based on Taylor expansion of its density and calculate the Hubble expansion parameter for various parameterizations of equation of state. This model is useful to probe a possible evolving of dark energy component in comparison with current observational data.
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…
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…
Maximum likelihood estimation for distributed parameter models of flexible spacecraft
NASA Technical Reports Server (NTRS)
Taylor, L. W., Jr.; Williams, J. L.
1989-01-01
A distributed-parameter model of the NASA Solar Array Flight Experiment spacecraft structure is constructed on the basis of measurement data and analyzed to generate a priori estimates of modal frequencies and mode shapes. A Newton-Raphson maximum-likelihood algorithm is applied to determine the unknown parameters, using a truncated model for the estimation and the full model for the computation of the higher modes. Numerical results are presented in a series of graphs and briefly discussed, and the significant improvement in computation speed obtained by parallel implementation of the method on a supercomputer is noted.
Observation model and parameter partials for the JPL VLBI parameter estimation software MODEST, 1996
NASA Astrophysics Data System (ADS)
Sovers, O. J.; Jacobs, Christopher S.
1996-08-01
The current theoretical model of radio interferometric delays and delay rates observed in very long baseline interferometry experiments is discussed in detail. Modeling the time delay consists of a number of steps. First, the locations of the observing stations are expressed in an Earth fixed coordinate frame at the time that the incoming wave front reaches the reference station. These station coordinates are modified by Earth-fixed effects, such as tides and tectonic motion. Next, a transformation to a celestial coordinate system moving with the Earth accounts for the Earth's precession and nutation in inertial space. A relativistic transformation then brings these coordinates into a frame centered athlete center of mass of the Solar System. The time delays calculated in this Solar System Barycentric frame, including corrections to account for extended source structure of the source and gravitational delay of the signal. Finally, he delay is transformed back to the celestial geocentric frame, and corrected for additional delays of the signal by components of the Earth's atmosphere. Partial derivatives of the observables with respect to numerous parameters entering the model components are also given. This report is a revision of the document Observation Model and Parameter Partials for the JPL VLBI Parameter Estimation Software "MODEST" -1994 dated August 1994. It supersedes that document and its five previous versions (1983, 1985, 1986, 1987, and 1991). Numerous portions of the Very Long Baseline Interferometry (VLBI) model were improved in MODEST from 1994 to 1996. For various aspects of the geometric delay, improved expressions for the geodetic latitude and station altitude are now used, along with more recent values of the Earth's radius and rotation rate. The equation of equinoxes can now be selected to be the IERS-92 expression, plus its 1997 extension. Models for the tidal response of the Earth orientation now include Dickman's revision (UT1S) of Yoder et
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
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. Copyright © 2013 Wiley Periodicals, Inc.
A numerical model for atomization-spray coupling in liquid rocket thrust chambers
NASA Technical Reports Server (NTRS)
Giridharan, M. G.; Krishnan, Anantha; Lee, J. J.; Przekwas, A. J.; Gross, K.
1992-01-01
The physical process of atomization is an important consideration in the stable operation of liquid rocket engines. Many spray combustion computational fluid dynamics (CFD) codes do not include an atomization sub-model but assume arbitrary drop size distributions, drop initial locations, and velocities. A method of coupling an atomization model with the spray model in a REFLEQS CFD code is presented. This method is based on a jet-embedding technique in which the equations governing the liquid jet core are solved separately using the surrounding gas phase conditions. The droplet initial conditions are calculated using a stability analysis appropriate for the atomization regime of liquid jet break-up.
Improving the realism of hydrologic model through multivariate parameter estimation
NASA Astrophysics Data System (ADS)
Rakovec, Oldrich; Kumar, Rohini; Attinger, Sabine; Samaniego, Luis
2017-04-01
Increased availability and quality of near real-time observations should improve understanding of predictive skills of hydrological models. Recent studies have shown the limited capability of river discharge data alone to adequately constrain different components of distributed model parameterizations. In this study, the GRACE satellite-based total water storage (TWS) anomaly is used to complement the discharge data with an aim to improve the fidelity of mesoscale hydrologic model (mHM) through multivariate parameter estimation. The study is conducted in 83 European basins covering a wide range of hydro-climatic regimes. The model parameterization complemented with the TWS anomalies leads to statistically significant improvements in (1) discharge simulations during low-flow period, and (2) evapotranspiration estimates which are evaluated against independent (FLUXNET) data. Overall, there is no significant deterioration in model performance for the discharge simulations when complemented by information from the TWS anomalies. However, considerable changes in the partitioning of precipitation into runoff components are noticed by in-/exclusion of TWS during the parameter estimation. A cross-validation test carried out to assess the transferability and robustness of the calibrated parameters to other locations further confirms the benefit of complementary TWS data. In particular, the evapotranspiration estimates show more robust performance when TWS data are incorporated during the parameter estimation, in comparison with the benchmark model constrained against discharge only. This study highlights the value for incorporating multiple data sources during parameter estimation to improve the overall realism of hydrologic model and its applications over large domains. Rakovec, O., Kumar, R., Attinger, S. and Samaniego, L. (2016): Improving the realism of hydrologic model functioning through multivariate parameter estimation. Water Resour. Res., 52, http://dx.doi.org/10
Modeling non-local thermodynamic equilibrium plasma using the Flexible Atomic Code data
NASA Astrophysics Data System (ADS)
Han, Bo; Wang, Feilu; Salzmann, David; Zhao, Gang
2015-04-01
We present a new code, RCF ("Radiative-Collisional code based on FAC"), which is used to simulate steady-state plasmas under non-local thermodynamic equilibrium condition, especially photoinization-dominated plasmas. RCF takes almost all of the radiative and collisional atomic processes into a rate equation to interpret the plasmas systematically. The Flexible Atomic Code (FAC) supplies all the atomic data needed for RCF, which insures calculating completeness and consistency of atomic data. With four input parameters relating to the radiation source and target plasma, RCF calculates the population of levels and charge states, as well as potential emission spectrum. In a preliminary application, RCF successfully reproduced the results of a photoionization experiment with reliable atomic data. The effects of the most important atomic processes on the charge state distribution are also discussed.
A Bayesian approach for parameter estimation and prediction using a computationally intensive model
Higdon, Dave; McDonnell, Jordan D.; Schunck, Nicolas; ...
2015-02-05
Bayesian methods have been successful in quantifying uncertainty in physics-based problems in parameter estimation and prediction. In these cases, physical measurements y are modeled as the best fit of a physics-based modelmore » $$\\eta (\\theta )$$, where θ denotes the uncertain, best input setting. Hence the statistical model is of the form $$y=\\eta (\\theta )+\\epsilon ,$$ where $$\\epsilon $$ accounts for measurement, and possibly other, error sources. When nonlinearity is present in $$\\eta (\\cdot )$$, the resulting posterior distribution for the unknown parameters in the Bayesian formulation is typically complex and nonstandard, requiring computationally demanding computational approaches such as Markov chain Monte Carlo (MCMC) to produce multivariate draws from the posterior. Although generally applicable, MCMC requires thousands (or even millions) of evaluations of the physics model $$\\eta (\\cdot )$$. This requirement is problematic if the model takes hours or days to evaluate. To overcome this computational bottleneck, we present an approach adapted from Bayesian model calibration. This approach combines output from an ensemble of computational model runs with physical measurements, within a statistical formulation, to carry out inference. A key component of this approach is a statistical response surface, or emulator, estimated from the ensemble of model runs. We demonstrate this approach with a case study in estimating parameters for a density functional theory model, using experimental mass/binding energy measurements from a collection of atomic nuclei. Lastly, we also demonstrate how this approach produces uncertainties in predictions for recent mass measurements obtained at Argonne National Laboratory.« less
Bayesian methods for characterizing unknown parameters of material models
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 to characterize unknown parameters of material properties for laser welds from measurements of peak forces sustained by these welds.
Bayesian methods for characterizing unknown parameters of material models
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
Kinetic model of the bichromatic dark trap for atoms
NASA Astrophysics Data System (ADS)
Krasnov, I. V.
2017-08-01
A kinetic model of atom confinement in a bichromatic dark trap (BDT) is developed with the goal of describing its dissipative properties. The operating principle of the deep BDT is based on using the combination of multiple bichromatic cosine-Gaussian optical beams (CGBs) for creating high-potential barriers, which is described in our previous work (Krasnov 2016 Laser Phys. 26 105501). In the indicated work, particle motion in the BDT is described in terms of classical trajectories. In the present study, particle motion is analyzed by means of the Wigner function (phase-space distribution function (DF)), which allows one to properly take into account the quantum fluctuations of optical forces. Besides, we consider an improved scheme of the BDT, where CGBs create, apart from plane potential barriers, a narrow cooling layer. We find an asymptotic solution of the Fokker-Planck equation for the DF and show that the DF of particles deeply trapped in a BDT with a cooling layer is the Tsallis distribution with the effective temperature, which can be considerably lower than in a BDT without a cooling layer. Moreover, it can be adjusted by slightly changing the CGBs’ radii. We also study the effect of particle escape from the trap due to the scattering of resonant photons and show that the particle lifetime in a BDT can exceed several tens of hours when it is limited by photon scattering.
Soil-related Input Parameters for the Biosphere Model
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
Parameter Estimation for Single Diode Models of Photovoltaic Modules
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.
The parameter landscape of a mammalian circadian clock model
NASA Astrophysics Data System (ADS)
Jolley, Craig; Ueda, Hiroki
2013-03-01
In mammals, an intricate system of feedback loops enables autonomous, robust oscillations synchronized with the daily light/dark cycle. Based on recent experimental evidence, we have developed a simplified dynamical model and parameterized it by compiling experimental data on the amplitude, phase, and average baseline of clock gene oscillations. Rather than identifying a single ``optimal'' parameter set, we used Monte Carlo sampling to explore the fitting landscape. The resulting ensemble of model parameter sets is highly anisotropic, with very large variances along some (non-trivial) linear combinations of parameters and very small variances along others. This suggests that our model exhibits ``sloppy'' features that have previously been identified in various multi-parameter fitting problems. We will discuss the implications of this model fitting behavior for the reliability of both individual parameter estimates and systems-level predictions of oscillator characteristics, as well as the impact of experimental constraints. The results of this study are likely to be important both for improved understanding of the mammalian circadian oscillator and as a test case for more general questions about the features of systems biology models.
Automatic Determination of the Conic Coronal Mass Ejection Model Parameters
NASA Technical Reports Server (NTRS)
Pulkkinen, A.; Oates, T.; Taktakishvili, A.
2009-01-01
Characterization of the three-dimensional structure of solar transients using incomplete plane of sky data is a difficult problem whose solutions have potential for societal benefit in terms of space weather applications. In this paper transients are characterized in three dimensions by means of conic coronal mass ejection (CME) approximation. A novel method for the automatic determination of cone model parameters from observed halo CMEs is introduced. The method uses both standard image processing techniques to extract the CME mass from white-light coronagraph images and a novel inversion routine providing the final cone parameters. A bootstrap technique is used to provide model parameter distributions. When combined with heliospheric modeling, the cone model parameter distributions will provide direct means for ensemble predictions of transient propagation in the heliosphere. An initial validation of the automatic method is carried by comparison to manually determined cone model parameters. It is shown using 14 halo CME events that there is reasonable agreement, especially between the heliocentric locations of the cones derived with the two methods. It is argued that both the heliocentric locations and the opening half-angles of the automatically determined cones may be more realistic than those obtained from the manual analysis
Automatic Determination of the Conic Coronal Mass Ejection Model Parameters
NASA Technical Reports Server (NTRS)
Pulkkinen, A.; Oates, T.; Taktakishvili, A.
2009-01-01
Characterization of the three-dimensional structure of solar transients using incomplete plane of sky data is a difficult problem whose solutions have potential for societal benefit in terms of space weather applications. In this paper transients are characterized in three dimensions by means of conic coronal mass ejection (CME) approximation. A novel method for the automatic determination of cone model parameters from observed halo CMEs is introduced. The method uses both standard image processing techniques to extract the CME mass from white-light coronagraph images and a novel inversion routine providing the final cone parameters. A bootstrap technique is used to provide model parameter distributions. When combined with heliospheric modeling, the cone model parameter distributions will provide direct means for ensemble predictions of transient propagation in the heliosphere. An initial validation of the automatic method is carried by comparison to manually determined cone model parameters. It is shown using 14 halo CME events that there is reasonable agreement, especially between the heliocentric locations of the cones derived with the two methods. It is argued that both the heliocentric locations and the opening half-angles of the automatically determined cones may be more realistic than those obtained from the manual analysis
Evaluation of Personnel Parameters in Software Cost Estimating Models
2007-11-02
ACAP , 1.42; all other parameters would be set to the nominal value of one. The effort multiplier will be a fixed value if the model uses linear...data. The calculated multiplier values were the 45 Table 8. COSTAR Trials For Multiplier Calculation Run ACAP PCAP PCON APEX PLEX LTEX Effort...impact. Table 9. COCOMO II Personnel Parameters Effort Multipliers Driver Lowest Nominal Highest Analyst Capability ( ACAP ) 1.42 1.00 0.71
Parameters and variables appearing in repository design models
Curtis, R.H.; Wart, R.J.
1983-12-01
This report defines the parameters and variables appearing in repository design models and presents typical values and ranges of values of each. Areas covered by this report include thermal, geomechanical, and coupled stress and flow analyses in rock. Particular emphasis is given to conductivity, radiation, and convection parameters for thermal analysis and elastic constants, failure criteria, creep laws, and joint properties for geomechanical analysis. The data in this report were compiled to help guide the selection of values of parameters and variables to be used in code benchmarking. 102 references, 33 figures, 51 tables.
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.
Evaluation of experiments for estimation of dynamical crop model parameters.
Ioslovich, Ilya; Gutman, Per-Olof
2007-07-01
Planned experiments are usually expected to provide maximal benefits within limited costs. However, there are known difficulties in optimal design of experiments. They are related to the case when only limited number of parameters could be estimated, because available experiments are noninformative. The useful method for this case is considered based on the dominant parameters selection procedure (DPS). The methodology is illustrated here with data from five planned experiments related to the NICOLET lettuce growth model. The maximal number and the list of estimated parameters are determined while the conditional number of the information Fisher matrix (modified E-criterion) is kept below a given upper constraint.
Ramirez, J.E.; Bera, R.K.; Hanrahan, R.J.
1985-04-01
Parameters relevant to the operation of an electron-beam initiated atomic iodine laser, which would lase on the transition 5 /sup 2/P/sub 1//sub ///sub 2/ (I*)..-->..5 /sup 2/P/sub 3//sub ///sub 2/ (I), have been measured by pulse radiolysis. Kinetic data for the parent compound quenching of I* were obtained by variation of the parent compound pressure at constant buffer gas pressure and observing I* decay rates versus time. Deactivation rates for perfluoroalkyl iodides were found to be much lower than for the corresponding alkyl iodides. Values obtained (in cm/sup 3/ molec/sup -1/ s/sup -1/) are as follows: CH/sub 3/I, (2.0 +- 0.1) x 10/sup -13/; C/sub 2/H/sub 5/I, (5.0 +- 0.3) x 10/sup -13/; CF/sub 3/I, (8.8 +- 0.3) x 10/sup -16/; C/sub 2/F/sub 5/I, (9.7 +- 1.0) x 10/sup -15/; n-C/sub 3/F/sub 7/I, (2.5 +- 0.2) x 10/sup -15/; i-C/sub 3/F/sub 7/I, (1.7 +- 0.1) x 10/sup -15/; n-C/sub 4/F/sub 9/I, (1.8 +- 0.1) x 10/sup -14/. The extent of population inversion was investigated by measuring initial excited state and ground state atomic iodine concentrations, which gives the branching ratio (I*)/(I). Values obtained are as follows: CH/sub 3/I, 2.7; CF/sub 3/I, 3.8; C/sub 2/F/sub 5/I, 2.7; i-C/sub 3/F/sub 7/I, 3.2; n-C/sub 4/F/sub 9/I, 1.8. Comparing both branching ratios and lifetimes, it is seen that CF/sub 3/I is the most promising candidate for an electron beam initiated atomic iodine laser.
Parameter identifiability and estimation of HIV/AIDS dynamic models.
Wu, Hulin; Zhu, Haihong; Miao, Hongyu; Perelson, Alan S
2008-04-01
We use a technique from engineering (Xia and Moog, in IEEE Trans. Autom. Contr. 48(2):330-336, 2003; Jeffrey and Xia, in Tan, W.Y., Wu, H. (Eds.), Deterministic and Stochastic Models of AIDS Epidemics and HIV Infections with Intervention, 2005) to investigate the algebraic identifiability of a popular three-dimensional HIV/AIDS dynamic model containing six unknown parameters. We find that not all six parameters in the model can be identified if only the viral load is measured, instead only four parameters and the product of two parameters (N and lambda) are identifiable. We introduce the concepts of an identification function and an identification equation and propose the multiple time point (MTP) method to form the identification function which is an alternative to the previously developed higher-order derivative (HOD) method (Xia and Moog, in IEEE Trans. Autom. Contr. 48(2):330-336, 2003; Jeffrey and Xia, in Tan, W.Y., Wu, H. (Eds.), Deterministic and Stochastic Models of AIDS Epidemics and HIV Infections with Intervention, 2005). We show that the newly proposed MTP method has advantages over the HOD method in the practical implementation. We also discuss the effect of the initial values of state variables on the identifiability of unknown parameters. We conclude that the initial values of output (observable) variables are part of the data that can be used to estimate the unknown parameters, but the identifiability of unknown parameters is not affected by these initial values if the exact initial values are measured with error. These noisy initial values only increase the estimation error of the unknown parameters. However, having the initial values of the latent (unobservable) state variables exactly known may help to identify more parameters. In order to validate the identifiability results, simulation studies are performed to estimate the unknown parameters and initial values from simulated noisy data. We also apply the proposed methods to a clinical data set
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.
Parameter Estimation for a crop model: separate and joint calibration of soil and plant parameters
NASA Astrophysics Data System (ADS)
Hildebrandt, A.; Jackisch, C.; Luis, S.
2008-12-01
Vegetation plays a major role both in the atmospheric and terrestrial water cycle. A great deal of vegetation cover in the developed world consists of agricultural used land (i.e. 44 % of the territory of the EU). Therefore, crop models have become increasingly prominent for studying the impact of Global Change both on economic welfare as well as on influence of vegetation on climate, and feedbacks with hydrological processes. By doing so, it is implied that crop models properly reflect the soil water balance and vertical exchange with the atmosphere. Although crop models can be incorporated in Surface Vegetation Atmosphere Transfer Schemes for that purpose, their main focus has traditionally not been on predicting water and energy fluxes, but yield. In this research we use data from two lysimeters in Brandis (Saxony, Germany), which have been planted with the crops of the surrounding farm, to test the capability of the crop model in SWAP. The lysimeters contain different natural soil cores, leading to substantially different yield. This experiment gives the opportunity to test, if the crop model is portable - that is if a calibrated crop can be moved between different locations. When using the default parameters for the respective environment, the model does neither quantitatively nor qualitatively reproduce the difference in yield and LAI for the different lysimeters. The separate calibration of soil and plant parameter was poor compared to the joint calibration of plant and soil parameters. This suggests that the model is not portable, but needs to be calibrated for individual locations, based on measurements or expert knowledge.
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.
Control of the SCOLE configuration using distributed parameter models
NASA Astrophysics Data System (ADS)
Hsiao, Min-Hung; Huang, Jen-Kuang
1994-06-01
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.
Moment structures of parameter-driven count time series models
NASA Astrophysics Data System (ADS)
Bukhari, Nawwal Ahmad; Beng, Koh You; Mohamed, Ibrahim
2017-05-01
This paper focuses on a parameter-driven count time series model with three different distributions. We provide a brief description of the first order autoregressive, AR(1) latent process. We consider the first four central moments of each models that are mean, variance, skewness and kurtosis. Next, the autocovariance and autocorrelation functions for each models are derived. We outline and discuss the possible directions of future research.
Chen, Jianhan
2010-09-14
The generalized Born (GB) theory is a prime choice for implicit treatment of solvent that provides a favorable balance between efficiency and accuracy for reliable simulation of protein conformational equilibria. In GB, the dielectric boundary is a key physical property that needs to be properly described. While it is widely accepted that the molecular surface (MS) should provide the most physical description, most existing GB models are based on van der Waals (vdW)-like surfaces for computational simplicity and efficiency. A simple and effective approximation to molecular volume is explored here using atom-centered dielectric functions within the context of a generalized Born model with simple switching (GBSW). The new model, termed GBSW/MS2, is as efficient as the original vdW-like-surface-based GBSW model, but is able to reproduce the Born radii calculated from the "exact" Poisson-Boltzmann theory with a correlation of 0.95. More importantly, examination of the potentials of mean force of hydrogen-bonding and charge-charge interactions demonstrates that GBSW/MS2 correctly captures the first desolvation peaks, a key signature of true MS. Physical parameters including atomic input radii and peptide backbone torsion were subsequently optimized on the basis of solvation free energies of model compounds, potentials of mean force of their interactions, and conformational equilibria of a set of helical and β-hairpin model peptides. The resulting GBSW/MS2 protein force field reasonably recapitulates the structures and stabilities of these model peptides. Several remaining limitations and possible future developments are also discussed.
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.
Modeling precursor diffusion and reaction of atomic layer deposition in porous structures
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.
Utilizing Soize's Approach to Identify Parameter and Model Uncertainties
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.
QCD-inspired determination of NJL model parameters
NASA Astrophysics Data System (ADS)
Springer, Paul; Braun, Jens; Rechenberger, Stefan; Rennecke, Fabian
2017-03-01
The QCD phase diagram at finite temperature and density has attracted considerable interest over many decades now, not least because of its relevance for a better understanding of heavy-ion collision experiments. Models provide some insight into the QCD phase structure but usually rely on various parameters. Based on renormalization group arguments, we discuss how the parameters of QCD low-energy models can be determined from the fundamental theory of the strong interaction. We particularly focus on a determination of the temperature dependence of these parameters in this work and comment on the effect of a finite quark chemical potential. We present first results and argue that our findings can be used to improve the predictive power of future model calculations.
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.
Improving the Ni I atomic model for solar and stellar atmospheric models
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.
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
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.
Dynamic Factor Analysis Models With Time-Varying Parameters.
Chow, Sy-Miin; Zu, Jiyun; Shifren, Kim; Zhang, Guangjian
2011-04-11
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 with vector autoregressive relations and time-varying cross-regression parameters at the factor level. Using techniques drawn from the state-space literature, the model was fitted to a set of daily affect data (over 71 days) from 10 participants who had been diagnosed with Parkinson's disease. Our empirical results lend partial support and some potential refinement to the Dynamic Model of Activation with regard to how the time dependencies between positive and negative affects change over time. A simulation study is conducted to examine the performance of the proposed techniques when (a) changes in the time-varying parameters are represented using the true model of change, (b) supposedly time-invariant parameters are represented as time-varying, and
Modelling of intermittent microwave convective drying: parameter sensitivity
NASA Astrophysics Data System (ADS)
Zhang, Zhijun; Qin, Wenchao; Shi, Bin; Gao, Jingxin; Zhang, Shiwei
2017-06-01
The reliability of the predictions of a mathematical model is a prerequisite to its utilization. A multiphase porous media model of intermittent microwave convective drying is developed based on the literature. The model considers the liquid water, gas and solid matrix inside of food. The model is simulated by COMSOL software. Its sensitivity parameter is analysed by changing the parameter values by ±20%, with the exception of several parameters. The sensitivity analysis of the process of the microwave power level shows that each parameter: ambient temperature, effective gas diffusivity, and evaporation rate constant, has significant effects on the process. However, the surface mass, heat transfer coefficient, relative and intrinsic permeability of the gas, and capillary diffusivity of water do not have a considerable effect. The evaporation rate constant has minimal parameter sensitivity with a ±20% value change, until it is changed 10-fold. In all results, the temperature and vapour pressure curves show the same trends as the moisture content curve. However, the water saturation at the medium surface and in the centre show different results. Vapour transfer is the major mass transfer phenomenon that affects the drying process.
[Parameter uncertainty analysis for urban rainfall runoff modelling].
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.
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.
Classical-field model of the hydrogen atom
NASA Astrophysics Data System (ADS)
Rashkovskiy, Sergey A.
2017-06-01
It is shown that all of the basic properties of the hydrogen atom can be consistently described in terms of classical electrodynamics if instead of considering the electron to be a particle, we consider an electrically charged classical wave field—an "electron wave"—which is held by the electrostatic field of the proton. It is shown that quantum mechanics must be considered not as a theory of particles but as a classical field theory in the spirit of classical electrodynamics. In this case, we are not faced with difficulties in interpreting the results of the theory. In the framework of classical electrodynamics, all of the well-known regularities of the spontaneous emission of the hydrogen atom are obtained, which is usually derived in the framework of quantum electrodynamics. It is shown that there are no discrete states and discrete energy levels of the atom: the energy of the atom and its states change continuously. An explanation of the conventional corpuscular-statistical interpretation of atomic phenomena is given. It is shown that this explanation is only a misinterpretation of continuous deterministic processes. In the framework of classical electrodynamics, the nonlinear Schrödinger equation is obtained, which accounts for the inverse action of self-electromagnetic radiation of the electron wave and completely describes the spontaneous emissions of an atom.
Classical-field model of the hydrogen atom
NASA Astrophysics Data System (ADS)
Rashkovskiy, Sergey A.
2017-02-01
It is shown that all of the basic properties of the hydrogen atom can be consistently described in terms of classical electrodynamics if instead of considering the electron to be a particle, we consider an electrically charged classical wave field—an "electron wave"—which is held by the electrostatic field of the proton. It is shown that quantum mechanics must be considered not as a theory of particles but as a classical field theory in the spirit of classical electrodynamics. In this case, we are not faced with difficulties in interpreting the results of the theory. In the framework of classical electrodynamics, all of the well-known regularities of the spontaneous emission of the hydrogen atom are obtained, which is usually derived in the framework of quantum electrodynamics. It is shown that there are no discrete states and discrete energy levels of the atom: the energy of the atom and its states change continuously. An explanation of the conventional corpuscular-statistical interpretation of atomic phenomena is given. It is shown that this explanation is only a misinterpretation of continuous deterministic processes. In the framework of classical electrodynamics, the nonlinear Schrödinger equation is obtained, which accounts for the inverse action of self-electromagnetic radiation of the electron wave and completely describes the spontaneous emissions of an atom.
Comparing spatial and temporal transferability of hydrological model parameters
NASA Astrophysics Data System (ADS)
Patil, Sopan; Stieglitz, Marc
2015-04-01
Operational use of hydrological models requires the transfer of calibrated parameters either in time (for streamflow forecasting) or space (for prediction at ungauged catchments) or both. Although the effects of spatial and temporal parameter transfer on catchment streamflow predictions have been well studied individually, a direct comparison of these approaches is much less documented. In our view, such comparison is especially pertinent in the context of increasing appeal and popularity of the "trading space for time" approaches that are proposed for assessing the hydrological implications of anthropogenic climate change. Here, we compare three different schemes of parameter transfer, viz., temporal, spatial, and spatiotemporal, using a spatially lumped hydrological model called EXP-HYDRO at 294 catchments across the continental United States. Results show that the temporal parameter transfer scheme performs best, with lowest decline in prediction performance (median decline of 4.2%) as measured using the Kling-Gupta efficiency metric. More interestingly, negligible difference in prediction performance is observed between the spatial and spatiotemporal parameter transfer schemes (median decline of 12.4% and 13.9% respectively). We further demonstrate that the superiority of temporal parameter transfer scheme is preserved even when: (1) spatial distance between donor and receiver catchments is reduced, or (2) temporal lag between calibration and validation periods is increased. Nonetheless, increase in the temporal lag between calibration and validation periods reduces the overall performance gap between the three parameter transfer schemes. Results suggest that spatiotemporal transfer of hydrological model parameters has the potential to be a viable option for climate change related hydrological studies, as envisioned in the "trading space for time" framework. However, further research is still needed to explore the relationship between spatial and temporal
Coupling of an average-atom model with a collisional-radiative equilibrium model
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.
Estimation of dynamic stability parameters from drop model flight tests
NASA Technical Reports Server (NTRS)
Chambers, J. R.; Iliff, K. W.
1981-01-01
A recent NASA application of a remotely-piloted drop model to studies of the high angle-of-attack and spinning characteristics of a fighter configuration has provided an opportunity to evaluate and develop parameter estimation methods for the complex aerodynamic environment associated with high angles of attack. The paper discusses the overall drop model operation including descriptions of the model, instrumentation, launch and recovery operations, piloting concept, and parameter identification methods used. Static and dynamic stability derivatives were obtained for an angle-of-attack range from -20 deg to 53 deg. The results of the study indicated that the variations of the estimates with angle of attack were consistent for most of the static derivatives, and the effects of configuration modifications to the model (such as nose strakes) were apparent in the static derivative estimates. The dynamic derivatives exhibited greater uncertainty levels than the static derivatives, possibly due to nonlinear aerodynamics, model response characteristics, or additional derivatives.
Models wagging the dog: are circuits constructed with disparate parameters?
Nowotny, Thomas; Szücs, Attila; Levi, Rafael; Selverston, Allen I
2007-08-01
In a recent article, Prinz, Bucher, and Marder (2004) addressed the fundamental question of whether neural systems are built with a fixed blueprint of tightly controlled parameters or in a way in which properties can vary largely from one individual to another, using a database modeling approach. Here, we examine the main conclusion that neural circuits indeed are built with largely varying parameters in the light of our own experimental and modeling observations. We critically discuss the experimental and theoretical evidence, including the general adequacy of database approaches for questions of this kind, and come to the conclusion that the last word for this fundamental question has not yet been spoken.
Do land parameters matter in large-scale hydrological modelling?
NASA Astrophysics Data System (ADS)
Gudmundsson, Lukas; Seneviratne, Sonia I.
2013-04-01
Many of the most pending issues in large-scale hydrology are concerned with predicting hydrological variability at ungauged locations. However, current-generation hydrological and land surface models that are used for their estimation suffer from large uncertainties. These models rely on mathematical approximations of the physical system as well as on mapped values of land parameters (e.g. topography, soil types, land cover) to predict hydrological variables (e.g. evapotranspiration, soil moisture, stream flow) as a function of atmospheric forcing (e.g. precipitation, temperature, humidity). Despite considerable progress in recent years, it remains unclear whether better estimates of land parameters can improve predictions - or - if a refinement of model physics is necessary. To approach this question we suggest scrutinizing our perception of hydrological systems by confronting it with the radical assumption that hydrological variability at any location in space depends on past and present atmospheric forcing only, and not on location-specific land parameters. This so called "Constant Land Parameter Hypothesis (CLPH)" assumes that variables like runoff can be predicted without taking location specific factors such as topography or soil types into account. We demonstrate, using a modern statistical tool, that monthly runoff in Europe can be skilfully estimated using atmospheric forcing alone, without accounting for locally varying land parameters. The resulting runoff estimates are used to benchmark state-of-the-art process models. These are found to have inferior performance, despite their explicit process representation, which accounts for locally varying land parameters. This suggests that progress in the theory of hydrological systems is likely to yield larger improvements in model performance than more precise land parameter estimates. The results also question the current modelling paradigm that is dominated by the attempt to account for locally varying land
Estimation of the parameters of ETAS models by Simulated Annealing.
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.
Estimation of the parameters of ETAS models by Simulated Annealing
NASA Astrophysics Data System (ADS)
Lombardi, Anna Maria
2015-02-01
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.
Estimation of the parameters of ETAS models by Simulated Annealing
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
Climate change decision-making: Model & parameter uncertainties explored
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.
Fast and accurate modeling of molecular atomization energies with machine learning.
Rupp, Matthias; Tkatchenko, Alexandre; Müller, Klaus-Robert; von Lilienfeld, O Anatole
2012-02-03
We introduce a machine learning model to predict atomization energies of a diverse set of organic molecules, based on nuclear charges and atomic positions only. The problem of solving the molecular Schrödinger equation is mapped onto a nonlinear statistical regression problem of reduced complexity. Regression models are trained on and compared to atomization energies computed with hybrid density-functional theory. Cross validation over more than seven thousand organic molecules yields a mean absolute error of ∼10 kcal/mol. Applicability is demonstrated for the prediction of molecular atomization potential energy curves.
An information approach to regularization parameter selection under model misspecification
NASA Astrophysics Data System (ADS)
Urmanov, A. M.; Gribok, A. V.; Hines, J. W.; Uhrig, R. E.
2002-10-01
We review the information approach to regularization parameter selection and its information complexity extension for the solution of discrete ill posed problems. An information criterion for regularization parameter selection was first proposed by Shibata in the context of ridge regression as an extension of Takeuchi's information criterion. In the information approach, the regularization parameter value is chosen to maximize the mean expected log likelihood (MELL) of a model whose parameters are estimated using the maximum penalized likelihood method. Under the Gaussian noise assumption such a choice coincides with the minimum of mean predictive error choice. Maximization of the MELL corresponds to minimization of the mean Kullback-Leibler information, that measures the deviation of the approximating (model) distribution from the true one. The resulting regularization parameter selection methods can handle possible functional and distributional misspecifications when the usual assumptions of Gaussian noise and/or linear relationship have been made but not met. We also suggest that in engineering applications it is beneficial to find ways of lowering the risk of getting grossly under-regularized solutions and that the new information complexity regularization parameter selection method (RPSM) is one of the possibilities. Several examples of applying the reviewed RPSMs are given.
Macroscopic singlet oxygen model incorporating photobleaching as an input parameter
NASA Astrophysics Data System (ADS)
Kim, Michele M.; Finlay, Jarod C.; Zhu, Timothy C.
2015-03-01
A macroscopic singlet oxygen model for photodynamic therapy (PDT) has been used extensively to calculate the reacted singlet oxygen concentration for various photosensitizers. The four photophysical parameters (ξ, σ, β, δ) and threshold singlet oxygen dose ([1O2]r,sh) can be found for various drugs and drug-light intervals using a fitting algorithm. The input parameters for this model include the fluence, photosensitizer concentration, optical properties, and necrosis radius. An additional input variable of photobleaching was implemented in this study to optimize the results. Photobleaching was measured by using the pre-PDT and post-PDT sensitizer concentrations. Using the RIF model of murine fibrosarcoma, mice were treated with a linear source with fluence rates from 12 - 150 mW/cm and total fluences from 24 - 135 J/cm. The two main drugs investigated were benzoporphyrin derivative monoacid ring A (BPD) and 2-[1-hexyloxyethyl]-2-devinyl pyropheophorbide-a (HPPH). Previously published photophysical parameters were fine-tuned and verified using photobleaching as the additional fitting parameter. Furthermore, photobleaching can be used as an indicator of the robustness of the model for the particular mouse experiment by comparing the experimental and model-calculated photobleaching ratio.