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Sample records for effective potential calculation

  1. {alpha}-decay calculations of heavy and superheavy nuclei using effective mean-field potentials

    SciTech Connect

    Pei, J. C.; Lin, Z. J.; Xu, F. R.; Zhao, E. G.

    2007-10-15

    Using an effective potential that is based on the Skyrme-Hartree-Fock mean-field model, systematic {alpha}-decay properties of even-even heavy and superheavy nuclei have been investigated. Calculations do not raise any adjustable parameter. The obtained {alpha}-decay half-lives agree reasonably well with experimental data. The characteristics of the effective potential and the deformation effect on the {alpha} decay are discussed.

  2. Use of Relativistic Effective Core Potentials in the Calculation of Electron-Impact Ionization Cross Sections

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.; Kim, Yong-Ki

    1999-01-01

    Based on the Binary-Encounter-Bethe (BEB) model, the advantage of using relativistic effective core potentials (RECP) in the calculation of total ionization cross sections of heavy atoms or molecules containing heavy atoms is discussed. Numerical examples for Ar, Kr, Xe, and WF6 are presented.

  3. Exchange-only optimized effective potential calculation of excited state spectra for He and Be atoms.

    SciTech Connect

    Desjarlais, Michael Paul; Muller, Richard Partain

    2006-02-01

    The optimized effective potential (OEP) method allows orbital-dependent functionals to be used in density functional theory (DFT), which, in particular, allows exact exchange formulations of the exchange energy to be used in DFT calculations. Because the exact exchange is inherently self-interaction correcting, the resulting OEP calculations have been found to yield superior band-gaps for condensed-phase systems. Here we apply these methods to the isolated atoms He and Be, and compare to high quality experiments and calculations to demonstrate that the orbital energies accurately reproduce the excited state spectrum for these species. These results suggest that coupling the exchange-only OEP calculations with proper (orbital-dependent or other) correlation functions might allow quantitative accuracy from DFT calculations.

  4. Effect of deformation on the calculated half-lives of cluster emission using a proximity potential

    NASA Astrophysics Data System (ADS)

    Nazarzadeh, P.; Mohebali, M.

    2016-06-01

    The half-lives of deformed cluster emission have been calculated by using the proximity potential Christensen-Winther potential form (1976) and compared to the experimental data and theoretical results of the liquid drop model. Also the calculated results have been compared to the results obtained by a universal form of the proximity potential for spherical cluster emission. The results show reasonable agreement with the experimental data.

  5. Temperature dependent effective potential method for accurate free energy calculations of solids

    NASA Astrophysics Data System (ADS)

    Hellman, Olle; Steneteg, Peter; Abrikosov, I. A.; Simak, S. I.

    2013-03-01

    We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on ab initio molecular dynamics followed by a mapping onto a model Hamiltonian that describes the lattice dynamics. The formalism and the numerical aspects of the technique are described in detail. A number of practical examples are given, and results are presented, which confirm the usefulness of TDEP within ab initio and classical molecular dynamics frameworks. In particular, we examine from first principles the behavior of force constants upon the dynamical stabilization of the body centered phase of Zr, and show that they become more localized. We also calculate the phase diagram for 4He modeled with the Aziz potential and obtain results which are in favorable agreement both with respect to experiment and established techniques.

  6. Nucleon-nucleon potential calculated for the cloudy bag and related to effective OBE parameters

    NASA Astrophysics Data System (ADS)

    Kahler, Richard

    1995-05-01

    The nucleon nucleon potential is calculated in the context of the cloudy bag model. The one pion exchange diagram is used to determine the pion quark coupling. Two pion exchange diagrams, box and crossed box, including the delta isobar, produce additional central, spin-spin, and tensor couplings. Using non-relativistic approximations to the OBE model potentials, the two pion exchange contributions are related to the masses and couplings of σ, ω, δ, and ρ mesons. It is found that the two pion exchange generates essentially all of the σ contribution required by the OBE model, that there is a large δ contribution at a lower mass than expected, and that the ω and ρ contributions, while significant, are not able to provide what is required by the OBE model.

  7. Properties of metastable alkaline-earth-metal atoms calculated using an accurate effective core potential

    SciTech Connect

    Santra, Robin; Christ, Kevin V.; Greene, Chris H.

    2004-04-01

    The first three electronically excited states in the alkaline-earth-metal atoms magnesium, calcium, and strontium comprise the (nsnp){sup 3}P{sub J}{sup o}(J=0,1,2) fine-structure manifold. All three states are metastable and are of interest for optical atomic clocks as well as for cold-collision physics. An efficient technique--based on a physically motivated potential that models the presence of the ionic core--is employed to solve the Schroedinger equation for the two-electron valence shell. In this way, radiative lifetimes, laser-induced clock shifts, and long-range interaction parameters are calculated for metastable Mg, Ca, and Sr.

  8. On the use of effective core potentials in the calculation of magnetic properties, such as magnetizabilites and magnetic shieldings.

    PubMed

    van Wüllen, Christoph

    2012-03-21

    State-of-the art effective core potentials (ECPs) that replace electrons of inner atomic cores involve non-local potentials. If such an effective core potential is added to the Hamiltonian of a system in a magnetic field, the resulting Hamiltonian is not gauge invariant. This means, magnetic properties such as magnetisabilities and magnetic shieldings (or magnetic susceptibilities and nuclear magnetic resonance chemical shifts) calculated with different gauge origins are different even for exact solutions of the Schrödinger equation. It is possible to restore gauge invariance of the Hamiltonian by adding magnetic field dependent terms arising from the effective core potential. Numerical calculations on atomic and diatomic model systems (potassium mono-cation and potassium dimer) clearly demonstrate that the standard effective core potential Hamiltonian violates gauge invariance, and this affects the calculation of magnetisabilities more strongly than the calculation of magnetic shieldings. The modified magnetic field dependent effective core potential Hamiltonian is gauge invariant, and therefore it is the correct starting point for distributed gauge origin methods. The formalism for gauge including atomic orbitals (GIAO) and individual gauge for localized orbitals methods is worked out. ECP GIAO results for the potassium dimer are presented. The new method performs much better than a previous ECP GIAO implementation that did not account for the non-locality of the potential. For magnetic shieldings, deviations are clearly seen, but they amount to few ppm only. For magnetisabilities, our new ECP GIAO implementation is a major improvement, as demonstrated by the comparison of all-electron and ECP results. PMID:22443751

  9. Calculate and Plot Complex Potential

    Energy Science and Technology Software Center (ESTSC)

    1998-05-05

    SOLUPLOT is a program designed to calculate and plot complex potential, pH diagrams and log oxygen activity, pH diagrams for aqueous chemical syatems, considering speciation of ligands, from free energy and thermodynamic activity data. These diagrams, commonly referred to as Eh-pH and ao2-pH diagrams, respectively, define areas of predominance in Eh-pH diagrams or ao2-pH space for chemical species of a chemical system at equilibrium. Over an area of predominance, one predominant species is at greatermore » activity than the other species of the system considered. The diagram axes, pH (a measure of hydrogen ion activity) and either Eh or log ao2 (measures of a tendency toward either oxidation or reduction) , are paremeters commonly applied in describing the chemistry of aqueous systems.« less

  10. Molecular wave function and effective adiabatic potentials calculated by extended multi-configuration time-dependent Hartree-Fock method

    NASA Astrophysics Data System (ADS)

    Kato, Tsuyoshi; Ide, Yoshihiro; Yamanouchi, Kaoru

    2015-12-01

    We first calculate the ground-state molecular wave function of 1D model H2 molecule by solving the coupled equations of motion formulated in the extended multi-configuration time-dependent Hartree-Fock (MCTDHF) method by the imaginary time propagation. From the comparisons with the results obtained by the Born-Huang (BH) expansion method as well as with the exact wave function, we observe that the memory size required in the extended MCTDHF method is about two orders of magnitude smaller than in the BH expansion method to achieve the same accuracy for the total energy. Second, in order to provide a theoretical means to understand dynamical behavior of the wave function, we propose to define effective adiabatic potential functions and compare them with the conventional adiabatic electronic potentials, although the notion of the adiabatic potentials is not used in the extended MCTDHF approach. From the comparison, we conclude that by calculating the effective potentials we may be able to predict the energy differences among electronic states even for a time-dependent system, e.g., time-dependent excitation energies, which would be difficult to be estimated within the BH expansion approach.

  11. Molecular wave function and effective adiabatic potentials calculated by extended multi-configuration time-dependent Hartree-Fock method

    SciTech Connect

    Kato, Tsuyoshi; Ide, Yoshihiro; Yamanouchi, Kaoru

    2015-12-31

    We first calculate the ground-state molecular wave function of 1D model H{sub 2} molecule by solving the coupled equations of motion formulated in the extended multi-configuration time-dependent Hartree-Fock (MCTDHF) method by the imaginary time propagation. From the comparisons with the results obtained by the Born-Huang (BH) expansion method as well as with the exact wave function, we observe that the memory size required in the extended MCTDHF method is about two orders of magnitude smaller than in the BH expansion method to achieve the same accuracy for the total energy. Second, in order to provide a theoretical means to understand dynamical behavior of the wave function, we propose to define effective adiabatic potential functions and compare them with the conventional adiabatic electronic potentials, although the notion of the adiabatic potentials is not used in the extended MCTDHF approach. From the comparison, we conclude that by calculating the effective potentials we may be able to predict the energy differences among electronic states even for a time-dependent system, e.g., time-dependent excitation energies, which would be difficult to be estimated within the BH expansion approach.

  12. Efficient methods for including quantum effects in Monte Carlo calculations of large systems: Extension of the displaced points path integral method and other effective potential methods to calculate properties and distributions

    NASA Astrophysics Data System (ADS)

    Mielke, Steven L.; Dinpajooh, Mohammadhasan; Siepmann, J. Ilja; Truhlar, Donald G.

    2013-01-01

    We present a procedure to calculate ensemble averages, thermodynamic derivatives, and coordinate distributions by effective classical potential methods. In particular, we consider the displaced-points path integral (DPPI) method, which yields exact quantal partition functions and ensemble averages for a harmonic potential and approximate quantal ones for general potentials, and we discuss the implementation of the new procedure in two Monte Carlo simulation codes, one that uses uncorrelated samples to calculate absolute free energies, and another that employs Metropolis sampling to calculate relative free energies. The results of the new DPPI method are compared to those from accurate path integral calculations as well as to results of two other effective classical potential schemes for the case of an isolated water molecule. In addition to the partition function, we consider the heat capacity and expectation values of the energy, the potential energy, the bond angle, and the OH distance. We also consider coordinate distributions. The DPPI scheme performs best among the three effective potential schemes considered and achieves very good accuracy for all of the properties considered. A key advantage of the effective potential schemes is that they display much lower statistical sampling variances than those for accurate path integral calculations. The method presented here shows great promise for including quantum effects in calculations on large systems.

  13. A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins.

    PubMed

    Mehler, E L; Guarnieri, F

    1999-07-01

    An improved approach is presented for calculating pH-dependent electrostatic effects in proteins using sigmoidally screened Coulomb potentials (SCP). It is hypothesized that a key determinant of seemingly aberrant behavior in pKa shifts is due to the properties of the unique microenvironment around each residue. To help demonstrate this proposal, an approach is developed to characterize the microenvironments using the local hydrophobicity/hydrophilicity around each residue of the protein. The quantitative characterization of the microenvironments shows that the protein is a complex mosaic of differing dielectric regions that provides a physical basis for modifying the dielectric screening functions: in more hydrophobic microenvironments the screening decreases whereas the converse applies to more hydrophilic regions. The approach was applied to seven proteins providing more than 100 measured pKa values and yielded a root mean square deviation of 0.5 between calculated and experimental values. The incorporation of the local hydrophobicity characteristics into the algorithm allowed the resolution of some of the more intractable problems in the calculation of pKa. Thus, the divergent shifts of the pKa of Glu-35 and Asp-66 in hen egg white lysozyme, which are both about 90% buried, was correctly predicted. Mechanistically, the divergence occurs because Glu-35 is in a hydrophobic microenvironment, while Asp-66 is in a hydrophilic microenvironment. Furthermore, because the calculation of the microenvironmental effects takes very little CPU time, the computational speed of the SCP formulation is conserved. Finally, results from different crystal structures of a given protein were compared, and it is shown that the reliability of the calculated pKa values is sufficient to allow identification of conformations that may be more relevant for the solution structure. PMID:10388736

  14. Towards a spectroscopically accurate set of potentials for heavy hydride laser cooling candidates: Effective core potential calculations of BaH

    NASA Astrophysics Data System (ADS)

    Moore, Keith; McLaughlin, Brendan M.; Lane, Ian C.

    2016-04-01

    BaH (and its isotopomers) is an attractive molecular candidate for laser cooling to ultracold temperatures and a potential precursor for the production of ultracold gases of hydrogen and deuterium. The theoretical challenge is to simulate the laser cooling cycle as reliably as possible and this paper addresses the generation of a highly accurate ab initio 2Σ+ potential for such studies. The performance of various basis sets within the multi-reference configuration-interaction (MRCI) approximation with the Davidson correction is tested and taken to the Complete Basis Set (CBS) limit. It is shown that the calculated molecular constants using a 46 electron effective core-potential and even-tempered augmented polarized core-valence basis sets (aug-pCVnZ-PP, n = 4 and 5) but only including three active electrons in the MRCI calculation are in excellent agreement with the available experimental values. The predicted dissociation energy De for the X2Σ+ state (extrapolated to the CBS limit) is 16 895.12 cm-1 (2.094 eV), which agrees within 0.1% of a revised experimental value of <16 910.6 cm-1, while the calculated re is within 0.03 pm of the experimental result.

  15. Model potential calculations of lithium transitions.

    NASA Technical Reports Server (NTRS)

    Caves, T. C.; Dalgarno, A.

    1972-01-01

    Semi-empirical potentials are constructed that have eigenvalues close in magnitude to the binding energies of the valence electron in lithium. The potentials include the long range polarization force between the electron and the core. The corresponding eigenfunctions are used to calculate dynamic polarizabilities, discrete oscillator strengths, photoionization cross sections and radiative recombination coefficients. A consistent application of the theory imposes a modification on the transition operator, but its effects are small for lithium. The method presented can be regarded as a numerical generalization of the widely used Coulomb approximation.

  16. Global Calculations Using Potential Functions and Effective Hamiltonian Models for Vibration-Rotation Spectroscopy and Dynamics of Small Polyatomic Molecules

    NASA Astrophysics Data System (ADS)

    Tuyterev, Vladimir

    2010-06-01

    It has become increasingly common to use accurate potential energy surfaces and dipole moment surfaces for predictions and assignment of high-resolution vibration-rotation molecular spectra. These surfaces are obtained either from high-level ab initio electronic structure calculations or from a direct fit to experimental spectroscopic data. The talk will continue a discussion of some recent advances in the domain of the "potentiology". The role of basis extrapolations, of the Born-Oppenheimer breakdown corrections , in particular for very highly excited vibration states will be considered. As effective polyad Hamiltonians and band transition moment operators are still widely used for data reductions in high-resolutions molecular spectroscopy, experimental spectra analyses invoke a need for accurate methods of building physically meaningful effective models from ab initio surfaces. This involves predictions for various spectroscopic constants, including vibration dependence of rotational and centrifugal distortion and resonance coupling parameters. Topics planned for discussion include: high-order Contact Transformations of rovibrational Hamiltonians and of the dipole moment for small polyatomic molecules; convergence issues; the role of the anharmonicity in a potential energy function and of resonance couplings on the normal mode mixing and on vib-rot assignments with application to high energy vibration levels of SO_2 and to ozone near the dissociation limit; intensity anomalies in H_2S / HDS / D_2S spectra, relation of the shape of ab initio dipole moment surfaces with a "mystery" of nearly vanishing symmetry allowed bands. A full account for symmetry properties requires efficient theoretical tools for transformations of molecular Hamiltonians such as irreducible tensor formalism, applications using phosphine and methane potentials will be discussed. Both potential functions and effective polyad Hamiltonians allow studying changes in quasi-classical vibration

  17. Effect of charge distribution over a chlorophyll dimer on the redox potential of P680 in photosystem II as studied by density functional theory calculations.

    PubMed

    Takahashi, Ryouta; Hasegawa, Koji; Noguchi, Takumi

    2008-06-17

    The effect of charge distribution over a chlorophyll dimer on the redox potential of P680 in photosystem II was studied by density functional theory calculations using the P680 coordinates in the X-ray structure. From the calculated ionization potentials of the dimer and the monomeric constituents, the decrease in the redox potential by charge delocalization over the dimer was estimated to be approximately 140 mV. Such charge delocalization was previously observed in the isolated D1-D2-Cyt b 559 complexes, whereas the charge was primarily localized on P D1 in the core complexes. The calculated potential decrease of approximately 140 mV can explain the inhibition of Y Z oxidation in the former complexes and in turn implies that the charge localization on P D1 upon formation of the core complex increases the P680 potential to the level necessary for water oxidation. PMID:18500822

  18. The effect of the time interval used to calculate mean wind velocity on the calculated drift potential, relative drift potential, and resultant drift direction for sands from three deserts in northern China

    NASA Astrophysics Data System (ADS)

    Zhang, Zhengcai; Dong, Zhibao; Zhao, Aiguo

    2016-01-01

    Wind is the power behind many erosion processes and is responsible for many of the characteristics of arid zone geomorphology. Wind velocity is a key factor in determining the potential sand transport, but the nature of the wind velocity data can strongly affect assessments of the risk of blowing sand. In this study, we obtained real-time wind velocity data in a region of the Tengger Desert with shifting sands, in the Badain Jaran Desert, and in the Madoi desertification land, with the data obtained at 1-min intervals, and used the data to determine the influence of how the wind velocity was calculated (mean versus mid-point values and the averaging time used to calculate these values) on sand drift potential. In the three regions, for both the mean and the mid-point wind velocities, the estimated drift potential decreased with increasing averaging time. The relationships between velocities calculated using the different averaging time intervals and the value calculated using a 1-min interval could be expressed as linear functions. The drift potential calculated using the mid-point wind velocity was larger than that calculated using the mean wind velocity.

  19. Relativistic density-functional theory with the optimized effective potential and self-interaction correction: Application to atomic structure calculations (Z=2-106)

    NASA Astrophysics Data System (ADS)

    Tong, Xiao-Min; Chu, Shih-I.

    1998-02-01

    We present a self-interaction-free relativistic density-functional theory (DFT). The theory is based on the extension of our recent nonrelativistic DFT treatment with optimized effective potential (OEP) and self-interaction correction (SIC) [Phys. Rev. A 55, 3406 (1997)] to the relativistic domain. Such a relativistic OEP-SIC procedure yields an orbital-independent single-particle local potential with proper long-range Coulombic (-1/r) behavior. The method is applied to the ground-state energy calculations for atoms with Z=2-106. A comparison with the corresponding nonrelativistic OEP-SIC calculations and other relativistic calculations is made. It is shown that the ionization potentials (obtained from the highest occupied orbital energies) and individual orbital binding energies determined by the present relativistic OEP-SIC method agree well with the experimental data across the Periodic Table.

  20. Relevance of Hydrodynamic Effects for the Calculation of Outer Surface Potential of Biological Membrane Using Electrophoretic Data.

    PubMed

    Silva, Izan M; Castro, Maria Clícia S; Silva, Dilson; Cortez, Célia M

    2016-06-01

    In this paper, we present the results of a study on the influence of hydrodynamic effects on the surface potentials of the erythrocyte membrane, comparing two different models formulated to simulate the electrophoretic movement of a biological cell: the classical Helmholtz-Smoluchowski model and a model presented by Hsu et al. (1996). This model considers hydrodynamic effects to describe the distribution of the fluid velocity. The electric potential equation was obtained from the non-linear Poisson-Boltzmann equation, considering the spatial distribution of electrical charges fixed in glycocalyx and cytoplasmic proteins, as well as electrolyte charges and ones fixed on the surfaces of lipidic bilayer. Our results show that the Helmholtz-Smoluchowski model is not able to reflect the real forces responsible to the electrophoretic behavior of cell, because it does not take account the hydrodynamic effects of glycocalyx. This charged network that covers cellular surface constitutes a complex physical system whose electromechanical characteristics cannot be neglected. Then, supporting the hypothesis of other authors, we suggest that, in electrophoretic motion analyses of cells, the classical model represents a limiting case of models that take into account hydrodynamic effects to describe the velocity distribution of fluid. PMID:27276378

  1. Recommended improvements to the DS02 dosimetry system's calculation of organ doses and their potential advantages for the Radiation Effects Research Foundation.

    PubMed

    Cullings, Harry M

    2012-03-01

    The Radiation Effects Research Foundation (RERF) uses a dosimetry system to calculate radiation doses received by the Japanese atomic bomb survivors based on their reported location and shielding at the time of exposure. The current system, DS02, completed in 2003, calculates detailed doses to 15 particular organs of the body from neutrons and gamma rays, using new source terms and transport calculations as well as some other improvements in the calculation of terrain and structural shielding, but continues to use methods from an older system, DS86, to account for body self-shielding. Although recent developments in models of the human body from medical imaging, along with contemporary computer speed and software, allow for improvement of the calculated organ doses, before undertaking changes to the organ dose calculations, it is important to evaluate the improvements that can be made and their potential contribution to RERF's research. The analysis provided here suggests that the most important improvements can be made by providing calculations for more organs or tissues and by providing a larger series of age- and sex-specific models of the human body from birth to adulthood, as well as fetal models. PMID:22262817

  2. Rotational excitation of symmetric top molecules by collisions with atoms: Close coupling, coupled states, and effective potential calculations for NH3-He

    NASA Technical Reports Server (NTRS)

    Green, S.

    1976-01-01

    The formalism for describing rotational excitation in collisions between symmetric top rigid rotors and spherical atoms is presented both within the accurate quantum close coupling framework and also the coupled states approximation of McGuire and Kouri and the effective potential approximation of Rabitz. Calculations are reported for thermal energy NH3-He collisions, treating NH3 as a rigid rotor and employing a uniform electron gas (Gordon-Kim) approximation for the intermolecular potential. Coupled states are found to be in nearly quantitative agreement with close coupling results while the effective potential method is found to be at least qualitatively correct. Modifications necessary to treat the inversion motion in NH3 are discussed.

  3. Calculating the potential to emit particulate matter

    SciTech Connect

    Vaart, D.R. van der

    1996-09-01

    As the implementation of the 1990 amendments to the Clean Air Act, and Title V in particular, continues, questions regarding the calculation of a facility`s potential to emit continue to surface. The US Environmental Protection Agency (EPA) has provided limited guidance decisions, although many are still being made during Title V implementation. This paper discusses what is meant by PM-10 and the validity of using sieve analysis in estimating particulate emissions. Title V of the Clean Air Amendments of 1990, and the accompanying regulations in 40 CFR Part 70, defines a major source subject to Title V by calculating its potential emissions of all regulated pollutants, both criteria and hazardous air pollutants. For PM, the threshold emission rate is 100 tons per year (tpy) for applicability to Title V. Much discussion has ensued regarding a definition of PM for the purpose of determining a facility`s potential to emit. Recently, EPA provided guidance which indicated that only PM-10 should be considered for making this determination although many states regulate larger particles through their state implementation plan (SIP) as a surrogate for PM-10.

  4. On calculating the potential vorticity flux

    SciTech Connect

    Hsu, Pei-Chun; Diamond, P. H.

    2015-03-15

    We discuss and compare different approaches to calculating the dynamics of anisotropic flow structure formation in quasi two-dimensional turbulence based on potential vorticity (PV) transport in real space. The general structure of the PV flux in the relaxation processes is deduced non-perturbatively. The transport coefficients of the PV flux are then systematically calculated using perturbation theory. We develop two non-perturbative relaxation models: the first is a mean field theory for the dynamics of minimum enstrophy relaxation based on the requirement that the mean flux of PV dissipates total potential enstrophy but conserves total fluid kinetic energy. The results show that the structure of PV flux has the form of a sum of a positive definite hyper-viscous and a negative or positive viscous flux of PV. Turbulence spreading is shown to be related to PV mixing via the link of turbulence energy flux to PV flux. In the relaxed state, the ratio of the PV gradient to zonal flow velocity is homogenized. This homogenized quantity sets a constraint on the amplitudes of PV and zonal flow in the relaxed state. The second relaxation model is derived from symmetry principles alone. The form of PV flux contains a nonlinear convective term in addition to viscous and hyper-viscous terms. For both cases, the transport coefficients are calculated using perturbation theory. For a broad turbulence spectrum, a modulational calculation of the PV flux gives both a negative viscosity and a positive hyper-viscosity. For a narrow turbulence spectrum, the result of a parametric instability analysis shows that PV transport is also convective. In both relaxation and perturbative analyses, it is shown that turbulent PV transport is sensitive to flow structure, and the transport coefficients are nonlinear functions of flow shear.

  5. Singularity embedding method in potential flow calculations

    NASA Technical Reports Server (NTRS)

    Jou, W. H.; Huynh, H.

    1982-01-01

    The so-called H-type mesh is used in a finite-element (or finite-volume) calculation of the potential flow past an airfoil. Due to coordinate singularity at the leading edge, a special singular trial function is used for the elements neighboring the leading edge. The results using the special singular elements are compared to those using the regular elements. It is found that the unreasonable pressure distribution obtained by the latter is removed by the embedding of the singular element. Suggestions to extend the present method to transonic cases are given.

  6. Effective one-body potential fitted for many-body interactions associated with a Jastrow function: application to the quantum Monte Carlo calculations

    NASA Astrophysics Data System (ADS)

    Umezawa, Naoto; Austin, Brian; Lester, William A., Jr.

    2009-03-01

    An efficient method of optimizing a Slater determinant, D, in the Jastrow-Slater-type wave function, FD, is suggested. Here, the so-called transcorrelated Hamiltonian, 1F H F, which is a similarity transformation of the usual Hamiltonian of an electronic system with respect to a Jastrow function F, is fitted to an effective Hamiltonian, Heff= ∑i^N ( -12 2̂i+ v(ri) ), in which all the electron-electron and electron-neucleus interactions are represented by a one-body potential, v(r). A single-particle Schr"odinger equation is then solved by using v(r) to determine the orbitals, of which the Slater determinant consists. The obtained orbitals improve the atomic total energies in the variational Monte Carlo calculations compared to those given by the density-functional-based orbitals. Advantages of using the optimized orbitals in the diffusion Monte Carlo calculations are also discussed.

  7. Relativistic Density Functional Theory with Optimized Effective Potential and Self-Interaction Correction : Application to Atomic Structure Calculations ( Z = 2 to 106)

    NASA Astrophysics Data System (ADS)

    Tong, X. M.; Chu, S. I.

    1998-05-01

    We introduce a self-interaction-free relativistic density functional theory (DFT) for the treatment of both the static and dynamical properties of many-electron atoms (X.M. Tong and S.I. Chu, Phys. Rev. A57), 855 (1998).. The theory is based on the extension of our recent development of non-relativistic DFT treatment (X.M. Tong and S.I. Chu, Phys. Rev. A55), 3406 (1997). with optimized effective potential (OEP) and self-interaction-corrction (SIC) to the relativistic domain. The relativistic OEP/SIC procedure yields orbital-independent single- particle local potential with proper long-range Coulombic (-1/r) behavior and is capable of providing accurate description of the ground, excited, and autoionizing states. The method is applied to the atomic structure calculations of atoms with Z = 2 to 106. Good agreement with the experimental data for both the ionization potentials (obtained from the highest occupied orbital energies) and individual orbital binding energies is obtained across the periodic table. To our knowledage, this is the first DFT calculation that has achieved such a quantitative accuracy. Detailed results will be presented.

  8. Ground-state properties of alkali dimers and their cations (including the elements Li, Na, and K) from ab initio calculations with effective core polarization potentials

    NASA Astrophysics Data System (ADS)

    Müller, Wolfgang; Meyer, Wilfried

    1984-04-01

    Extensive all-electron SCF and valence CI calculations are presented for alkali dimer systems with consideration of intershell correlation effects by use of an effective core polarization potential (CPP), which contains only a single adjustable atomic parameter. High accuracy is obtained for the ground-state spectroscopic constants of the studied molecules. The maximum deviations from accurate experimental data are as follows: 1% or 0.03 Å for Re, 2% or 100 cm-1 for De, 0.5% or 1 cm-1 for ωe, and 0.2% or 100 cm-1 for ionization energies. For experimentally uncertain or unknown values reliable predictions can thus be made. The calculated dipole moments for LiK and NaK agree with experiment to within 0.1%, but for LiNa we obtain a deviation of 8% or 0.036 D. An analysis of molecular core polarization contributions reveals the reasons for some systematic defects in previous pseudopotential calculations.

  9. Relativistically corrected nuclear magnetic resonance chemical shifts calculated with the normalized elimination of the small component using an effective potential-NMR chemical shifts of molybdenum and tungsten

    NASA Astrophysics Data System (ADS)

    Filatov, Michael; Cremer, Dieter

    2003-07-01

    A new method for relativistically corrected nuclear magnetic resonance (NMR) chemical shifts is developed by combining the individual gauge for the localized orbital approach for density functional theory with the normalized elimination of a small component using an effective potential. The new method is used for the calculation of the NMR chemical shifts of 95Mo and 183W in various molybdenum and tungsten compounds. It is shown that quasirelativistic corrections lead to an average improvement of calculated NMR chemical shift values by 300 and 120 ppm in the case of 95Mo and 183W, respectively, which is mainly due to improvements in the paramagnetic contributions. The relationship between electronic structure of a molecule and the relativistic paramagnetic corrections is discussed. Relativistic effects for the diamagnetic part of the magnetic shielding caused by a relativistic contraction of the s,p orbitals in the core region concern only the shielding values, however, have little consequence for the shift values because of the large independence from electronic structure and a cancellation of these effects in the shift values. It is shown that the relativistic corrections can be improved by level shift operators and a B3LYP hybrid functional, for which Hartree-Fock exchange is reduced to 15%.

  10. Two-component relativistic density-functional calculations of the dimers of the halogens from bromine through element 117 using effective core potential and all-electron methods.

    PubMed

    Mitin, Alexander V; van Wüllen, Christoph

    2006-02-14

    A two-component quasirelativistic Hamiltonian based on spin-dependent effective core potentials is used to calculate ionization energies and electron affinities of the heavy halogen atom bromine through the superheavy element 117 (eka-astatine) as well as spectroscopic constants of the homonuclear dimers of these atoms. We describe a two-component Hartree-Fock and density-functional program that treats spin-orbit coupling self-consistently within the orbital optimization procedure. A comparison with results from high-order Douglas-Kroll calculations--for the superheavy systems also with zeroth-order regular approximation and four-component Dirac results--demonstrates the validity of the pseudopotential approximation. The density-functional (but not the Hartree-Fock) results show very satisfactory agreement with theoretical coupled cluster as well as experimental data where available, such that the theoretical results can serve as an estimate for the hitherto unknown properties of astatine, element 117, and their dimers. PMID:16483205

  11. Extreme tunnelling in methylamine dehydrogenase revealed by hybrid QM/MM calculations: potential energy surface profile for methylamine and ethanolamine substrates and kinetic isotope effect values

    NASA Astrophysics Data System (ADS)

    Tresadern, Gary; Wang, Hong; Faulder, Paul F.; Burton, Neil A.; Hillier, Ian H.

    The rate-determining proton transfer step in the amine reduction reaction catalysed by the enzyme methylamine dehydrogenase has been studied using a hybrid quantum mechanical/molecular mechanical (QM/MM) model. Variational transition state theory, combined with multidimensional tunnelling corrections, has been employed to calculate reaction rate constants, and hence deuterium kinetic isotope effects (KIE). To render these calculations computationally feasible, the electronic structure was described using a PM3 method with specific reaction parameters obtained by a fit to energetics obtained at a high level for a small model system. Compared to the use of standard parameters, these revised parameters result in a considerable improvement in the predicted KIE values and activation energy. For both methylamine and ethanolamine substrates, through-barrier, rather than over-barrier, motion is found to dominate with KIE values that are large and close to the experimental values. A major difference between the two substrates is that, for ethanolamine, different hydrogen bonding structures involving the substrate hydroxyl are possible, leading to very different potential energy surfaces with KIE values covering a considerable range. We speculate that this is the origin of the differing temperature behaviour observed for the KIEs of the two substrates.

  12. Calculations of 21 Λ-S and 42 Ω states of BC molecule: Potential energy curves, spectroscopic parameters and spin-orbit coupling effect.

    PubMed

    Xing, Wei; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue

    2016-01-15

    The potential energy curves (PECs) were calculated for the 42 Ω states generated from the 21 Λ-S states (X(4)Σ(-), A(4)Π, B(4)Σ(-), a(2)Π, b(2)Σ(-), c(2)Δ, d(2)Σ(+), e(2)Π, 3(2)Π, 4(2)Π, 5(2)Π, 2(2)Σ(-), 3(2)Σ(-), 2(2)Σ(+), 3(2)Σ(+), 2(2)Δ, 3(2)Δ, 1(4)Σ(+), 2(4)Π, 1(4)Δ and 1(2)Φ), which originated from the lowest two dissociation channels, B((2)Pu)+C((3)Pg) and B((2)Pu)+C((1)Dg), of the BC molecule. The PECs were calculated for internuclear separations from 0.08 to 1.10 nm using the CASSCF method, which was followed by the icMRCI approach with the aug-cc-pV6Z basis set. Of these 21 Λ-S states, the e(2)Π, 2(2)Δ, 2(2)Σ(-), 4(2)Π, 1(2)Φ and 3(2)Δ possess the double wells. The A(4)Π, a(2)Π, c(2)Δ, 2(4)Π, 4(2)Π, 5(2)Π, 1(4)Δ and 1(2)Φ states are inverted with the spin-orbit coupling (SOC) effect taken into account. The first well of e(2)Π state and the second well of 4(2)Π and 2(2)Δ states do not have any vibrational states whether with or without the SOC effect included. All the Λ-S and Ω states involved in this paper are bound states. Scalar relativistic correction was included by the third-order Douglas-Kroll Hamiltonian approximation at the level of an aug-cc-pV5Z basis set. Core-valence correlation correction was included at the level of an aug-cc-pCV5Z basis set. The SOC effect was accounted for by the state interaction method with the Breit-Pauli Hamiltonian and the all-electron cc-pCV5Z basis set. The PECs of all the states were extrapolated to the complete basis set limit. The spectroscopic parameters were obtained. The vibrational properties of several Λ-S and Ω states with the relatively shallow wells were evaluated. The SOC effect on the spectroscopic parameters is not obvious for almost all the states. The spectroscopic properties reported in this paper can be expected to be reliably predicted ones. PMID:26476070

  13. An assessment of a modified potential flow code for calculating the effect of small geometric change on the pressure and forces of supercritical airfoils

    NASA Technical Reports Server (NTRS)

    Hicks, R. M.

    1982-01-01

    Wind-tunnel test data for two closely related supercritical airfoils were compared with calculations obtained from a nonconservative, potential flow code over a Mach number range from 0.20 to 0.80. The potential flow code includes an iterated, integral boundary-layer correction. The theoretical pressure distributions correlated more closely with the experimental pressure distributions when the flow was entirely subsonic or subsonic with a small supersonic zone than when the flow contained a large supersonic zone. The predicted drag level was below the experimental values at nearly all test conditions and the difference in drag level for the two airfoils was not accurately predicted.

  14. Design and development of a new micro-beam treatment planning system: effectiveness of algorithms of optimization and dose calculations and potential of micro-beam treatment.

    PubMed

    Tachibana, Hidenobu; Kojima, Hiroyuki; Yusa, Noritaka; Miyajima, Satoshi; Tsuda, Akihisa; Yamashita, Takashi

    2012-07-01

    A new treatment planning system (TPS) was designed and developed for a new treatment system, which consisted of a micro-beam-enabled linac with robotics and a real-time tracking system. We also evaluated the effectiveness of the implemented algorithms of optimization and dose calculations in the TPS for the new treatment system. In the TPS, the optimization procedure consisted of the pseudo Beam's-Eye-View method for finding the optimized beam directions and the steepest-descent method for determination of beam intensities. We used the superposition-/convolution-based (SC-based) algorithm and Monte Carlo-based (MC-based) algorithm to calculate dose distributions using CT image data sets. In the SC-based algorithm, dose density scaling was applied for the calculation of inhomogeneous corrections. The MC-based algorithm was implemented with Geant4 toolkit and a phase-based approach using a network-parallel computing. From the evaluation of the TPS, the system can optimize the direction and intensity of individual beams. The accuracy of the dose calculated by the SC-based algorithm was less than 1% on average with the calculation time of 15 s for one beam. However, the MC-based algorithm needed 72 min for one beam using the phase-based approach, even though the MC-based algorithm with the parallel computing could decrease multiple beam calculations and had 18.4 times faster calculation speed using the parallel computing. The SC-based algorithm could be practically acceptable for the dose calculation in terms of the accuracy and computation time. Additionally, we have found a dosimetric advantage of proton Bragg peak-like dose distribution in micro-beam treatment. PMID:22544809

  15. Sequence and conformation effects on ionization potential and charge distribution of homo-nucleobase stacks using M06-2X hybrid density functional theory calculations.

    PubMed

    Rooman, Marianne; Wintjens, René

    2014-04-01

    DNA is subject to oxidative damage due to radiation or by-products of cellular metabolism, thereby creating electron holes that migrate along the DNA stacks. A systematic computational analysis of the dependence of the electronic properties of nucleobase stacks on sequence and conformation was performed here, on the basis of single- and double-stranded homo-nucleobase stacks of 1-10 bases or 1-8 base pairs in standard A-, B-, and Z-conformation. First, several levels of theory were tested for calculating the vertical ionization potentials of individual nucleobases; the M06-2X/6-31G* hybrid density functional theory method was selected by comparison with experimental data. Next, the vertical ionization potential, and the Mulliken charge and spin density distributions were calculated and considered on all nucleobase stacks. We found that (1) the ionization potential decreases with the number of bases, the lowest being reached by Gua≡Cyt tracts; (2) the association of two single strands into a double-stranded tract lowers the ionization potential significantly (3) differences in ionization potential due to sequence variation are roughly three times larger than those due to conformational modifications. The charge and spin density distributions were found (1) to be located toward the 5'-end for single-stranded Gua-stacks and toward the 3'-end for Cyt-stacks and basically delocalized over all bases for Ade- and Thy-stacks; (2) the association into double-stranded tracts empties the Cyt- and Thy-strands of most of the charge and all the spin density and concentrates them on the Gua- and Ade-strands. The possible biological implications of these results for transcription are discussed. PMID:23582046

  16. Sequence and conformation effects on ionization potential and charge distribution of homo-nucleobase stacks using M06-2X hybrid density functional theory calculations

    PubMed Central

    Rooman, Marianne; Wintjens, René

    2013-01-01

    DNA is subject to oxidative damage due to radiation or by-products of cellular metabolism, thereby creating electron holes that migrate along the DNA stacks. A systematic computational analysis of the dependence of the electronic properties of nucleobase stacks on sequence and conformation was performed here, on the basis of single- and double-stranded homo-nucleobase stacks of 1–10 bases or 1–8 base pairs in standard A-, B-, and Z-conformation. First, several levels of theory were tested for calculating the vertical ionization potentials of individual nucleobases; the M06-2X/6-31G* hybrid density functional theory method was selected by comparison with experimental data. Next, the vertical ionization potential, and the Mulliken charge and spin density distributions were calculated and considered on all nucleobase stacks. We found that (1) the ionization potential decreases with the number of bases, the lowest being reached by Gua≡Cyt tracts; (2) the association of two single strands into a double-stranded tract lowers the ionization potential significantly (3) differences in ionization potential due to sequence variation are roughly three times larger than those due to conformational modifications. The charge and spin density distributions were found (1) to be located toward the 5′-end for single-stranded Gua-stacks and toward the 3′-end for Cyt-stacks and basically delocalized over all bases for Ade- and Thy-stacks; (2) the association into double-stranded tracts empties the Cyt- and Thy-strands of most of the charge and all the spin density and concentrates them on the Gua- and Ade-strands. The possible biological implications of these results for transcription are discussed. PMID:23582046

  17. Surface potentials and the calculated selectivity of ion channels.

    PubMed Central

    Miedema, Henk

    2002-01-01

    Ion channels catalyze the transport of ions across biological membranes. A proper understanding of ion-channel functioning is essential to our knowledge of cell physiology, and, in this context, ion-channel selectivity is a key concept. The extent to which a channel permeates two ion species, a and b, is expressed by the permeability ratio, P(a)/P(b). This paper addresses a complication in the calculation of P(a)/P(b) that is related to the existence of surface potentials (psi) and that so far has not been fully appreciated. This paper shows the rather surprising effect of psi on the calculated P(a)/P(b) of a channel that is permeable to two ion species of different valence. If we ignore psi, we conclude, for instance, P(a) > P(b). If we implement psi in the calculation of P(a)/P(b), we may, however, conclude exactly the reverse, i.e., P(a) < P(b). Because electrostatic potentials arise at the surface of essentially all biological membranes, this paper argues for a more critical evaluation of ion channel selectivity measurements. PMID:11751304

  18. The Calculation of the Electrostatic Potential of Infinite Charge Distributions

    ERIC Educational Resources Information Center

    Redzic, Dragan V.

    2012-01-01

    We discuss some interesting aspects in the calculation of the electrostatic potential of charge distributions extending to infinity. The presentation is suitable for the advanced undergraduate level. (Contains 3 footnotes.)

  19. Potential Dependence of Electrochemical Barriers from ab Initio Calculations.

    PubMed

    Chan, Karen; Nørskov, Jens K

    2016-05-01

    We present a simple and computationally efficient method to determine the potential dependence of the activation energies for proton-electron transfer from a single ab initio barrier calculation. We show that the potential dependence of the activation energy is given by the partial charge transferred at the transition state. The method is evaluated against the potential dependence determined explicitly through multiple calculations at varying potential. We show that the transfer coefficient is given by the charge transferred from the initial to transition state, which has significant implications for electrochemical kinetics. PMID:27088442

  20. Calculation of molecular free energies in classical potentials

    NASA Astrophysics Data System (ADS)

    Farhi, Asaf; Singh, Bipin

    2016-02-01

    Free energies of molecules can be calculated by quantum chemistry computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic dynamics. We present a novel, accurate and complete calculation of molecular free energies in standard classical potentials. In this method we transform the molecule by relaxing potential terms which depend on the coordinates of a group of atoms in that molecule and calculate the free energy difference associated with the transformation. Then, since the transformed molecule can be treated as non-interacting systems, the free energy associated with these atoms is analytically or numerically calculated. This two-step calculation can be applied to calculate free energies of molecules or free energy difference between (possibly large) molecules in a general environment. We demonstrate the method in free energy calculations for methanethiol and butane molecules in vacuum and solvent. We suggest the potential application of free energy calculation of chemical reactions in classical molecular simulations.

  1. Comparison of the Effective Fragment Potential Method with Symmetry-Adapted Perturbation Theory in the Calculation of Intermolecular Energies for Ionic Liquids.

    PubMed

    Tan, Samuel Y S; Izgorodina, Ekaterina I

    2016-06-14

    The effective fragment potential (EFP) method that decomposes the interaction energy as a sum of the five fundamental forces-electrostatic, exchange-repulsion, polarization, dispersion, and charge transfer-was applied to a large test set of ionic liquid ion pairs and compared against the state-of-the-art method, Symmetry-Adapted Perturbation Theory (SAPT). The ion pairs include imidazolium and pyrrolidinium cations combined with anions that are routinely used in the field of ionic liquids. The aug-cc-pVDZ, aug-cc-pVTZ, and 6-311++G(d,p) basis sets were used for EFP, while SAPT2+3/aug-cc-pVDZ provided the benchmark energies. Differences between the two methods were found to be large, and strongly dependent on the anion type. For the aug-cc-pVTZ basis set, which produced the least errors, average relative errors were between 2.3% and 18.4% for pyrrolidinium ion pairs and between 2.1% and 27.7% for imidazolium ion pairs for each individual energetic component (excluding charge transfer), as well as the total interaction energy. Charge transfer gave the largest relative errors: 56% and 63% on average for pyrrolidinium- and imidazolium-based ion pairs, respectively. Scaling of the EFP components against SAPT2+3 showed improvement for polarization (induction) and dispersion terms, thus indicating potential for the development of cost-effective alternatives for intermolecular induction and dispersion potentials for ionic liquids. PMID:27116302

  2. Accurate ionization potential of semiconductors from efficient density functional calculations

    NASA Astrophysics Data System (ADS)

    Ye, Lin-Hui

    2016-07-01

    Despite its huge successes in total-energy-related applications, the Kohn-Sham scheme of density functional theory cannot get reliable single-particle excitation energies for solids. In particular, it has not been able to calculate the ionization potential (IP), one of the most important material parameters, for semiconductors. We illustrate that an approximate exact-exchange optimized effective potential (EXX-OEP), the Becke-Johnson exchange, can be used to largely solve this long-standing problem. For a group of 17 semiconductors, we have obtained the IPs to an accuracy similar to that of the much more sophisticated G W approximation (GWA), with the computational cost of only local-density approximation/generalized gradient approximation. The EXX-OEP, therefore, is likely as useful for solids as for finite systems. For solid surfaces, the asymptotic behavior of the vx c has effects similar to those of finite systems which, when neglected, typically cause the semiconductor IPs to be underestimated. This may partially explain why standard GWA systematically underestimates the IPs and why using the same GWA procedures has not been able to get an accurate IP and band gap at the same time.

  3. Generalized transition state theory calculations for the reactions D+H2 and H+D2 using an accurate potential energy surface: Explanation of the kinetic isotope effect

    NASA Astrophysics Data System (ADS)

    Garrett, Bruce C.; Truhlar, Donald G.

    1980-03-01

    Rate constants are calculated for the reactions D+H2→DH+H and H+D2→HD+D and compared to measured values. An accurate potential energy surface, based on the ab initio calculations of Liu and Siegbahn, was used. Rates were calculated using both conventional transition state theory and canonical variational theory. In the former, the generalized transition state dividing surface is located at the saddle point; in the latter it is located to maximize the generalized free energy of activation. We show that, in the absence of tunneling corrections, locating the generalized-transition-state dividing surface variationally has an important quantitative effect on the predicted rate constants for these systems and that, when tunneling is included, most of the effect of using a better dividing surface can be included in conventional transition state theory for these systems by using a consistent transmission coefficient for quantal scattering by the vibrationally adiabatic potential energy curve. Tunneling effects are important for these reactions even for temperatures larger than 400 K. We show how to separate classical recrossing effects from quantal corrections on reaction-coordinate motion in both the transmission coefficients and the kinetic isotope effects. Our most complete calculations are in excellent agreement with most of the measured rate constants and kinetic isotope effects.

  4. Calculation of the potentials and 3D electric fields in a proton decay detector

    SciTech Connect

    Lari, R.J.; Dawson, J.W.; Turner, L.R.

    1987-01-01

    An electrostatic detector for measuring the lifetime of the proton has been modeled in three dimensions. Linear hexahedral finite elements were used and the potential obtained at all nodes. The three components of the electric field were calculated and used to determine field lines, calculate drift fields and drift times. Effective aperture calculations agreed with the measurements.

  5. Calculating Standard Reduction Potentials of [4Fe–4S] Proteins

    SciTech Connect

    Perrin, Bradley S.; Niu, Shuqiang; Ichiye, Toshiko

    2013-03-15

    The oxidation–reduction potentials of electron transfer proteins determine the driving forces for their electron transfer reactions. Although the type of redox site determines the intrinsic energy required to add or remove an electron, the electrostatic interaction energy between the redox site and its surrounding environment can greatly shift the redox potentials. Here, a method for calculating the reduction potential versus the standard hydrogen electrode, E°, of a metalloprotein using a combinatio of density functional theory and continuum electrostatics is presented. This work focuses on the methodology for the continuum electrostatics calculations, including various factors that may affect the accuracy. The calculations are demonstrated using crystal structures of six homologous HiPIPs, which give E° that are in excellent agreement with experimental results.

  6. New approach to calculating the potential energy of colliding nuclei

    SciTech Connect

    Kurmanov, R. S.; Kosenko, G. I.

    2014-12-15

    The differential method proposed by the present authors earlier for the reduction of volume integrals in calculating the potential energy of a compound nucleus is generalized to the case of two interacting nuclei. The Coulomb interaction energy is obtained for the cases of a sharp and a diffuse boundary of nuclei, while the nuclear interaction energy is found only for nuclei with a sharp boundary, the finiteness of the nuclear-force range being taken into account. The present method of calculations permits reducing the time it takes to compute the potential energy at least by two orders of magnitude.

  7. Computer programs for calculating potential flow in propulsion system inlets

    NASA Technical Reports Server (NTRS)

    Stockman, N. O.; Button, S. L.

    1973-01-01

    In the course of designing inlets, particularly for VTOL and STOL propulsion systems, a calculational procedure utilizing three computer programs evolved. The chief program is the Douglas axisymmetric potential flow program called EOD which calculates the incompressible potential flow about arbitrary axisymmetric bodies. The other two programs, original with Lewis, are called SCIRCL AND COMBYN. Program SCIRCL generates input for EOD from various specified analytic shapes for the inlet components. Program COMBYN takes basic solutions output by EOD and combines them into solutions of interest, and applies a compressibility correction.

  8. Assessment of the accuracy of shape-consistent relativistic effective core potentials using multireference spin-orbit configuration interaction singles and doubles calculations of the ground and low-lying excited states of U(4+) and U(5+).

    PubMed

    Beck, Eric V; Brozell, Scott R; Blaudeau, Jean-Philippe; Burggraf, Larry W; Pitzer, Russell M

    2009-11-12

    Multireference spin-orbit configuration interaction calculations were used to determine the accuracy of 60-, 68-, and 78-electron shape-consistent relativistic effective core potentials (RECPs) for uranium V and VI ground and low-lying excited states. Both 5f(n) and (5f6d)(n), (n = 1, 2) reference spaces were investigated using correlation-consistent double-zeta quality basis sets. Accuracy was assessed against gas-phase experimental spectra. The 68-electron RECP calculations yielded low relative and rms errors and predicted the empirical ordering of states most consistently. PMID:19888778

  9. Fully relativistic multiple scattering calculations for general potentials

    NASA Astrophysics Data System (ADS)

    Ebert, H.; Braun, J.; Ködderitzsch, D.; Mankovsky, S.

    2016-02-01

    The formal basis for fully relativistic Korringa-Kohn-Rostoker (KKR) or multiple scattering calculations for the electronic Green function in case of a general potential is discussed. Simple criteria are given to identify situations that require to distinguish between right- and left-hand-side solutions to the Dirac equation when setting up the electronic Green function. In addition, various technical aspects of an implementation of the relativistic KKR for general local and nonlocal potentials will be discussed.

  10. Effect of soil type patterns on the variability of bare soil evaporation within a field: comparison of eddy covariance measurements with potential and actual evaporation calculations

    NASA Astrophysics Data System (ADS)

    Vanderborght, J.; Graf, A.; Steenpass, C.; Scharnagl, B.; Prolingheuer, N.; Herbst, M.; Vereecken, H.

    2009-12-01

    Bare soil evaporation was measured with the eddy-covariance method at the Selhausen field site. The site has a distinct gradient in soil texture with a considerably higher stone content at the upper part of the field. Because of this gradient, a spatial variation in evaporation fluxes in the field is expected. Because of the higher stone content at the upper part of the field, it is expected that the water that is stored in the soil surface layer and can be evaporated at a maximal evaporation rate, which is determined by the energy that is available for evaporation, is considerable smaller in the upper than in the lower part of the field. We investigated whether this hypothesis is supported by eddy covariance (EC) measurements of the evaporation fluxes at the field site. The EC measurements were combined with a footprint model that predicts the location of the soil surface that contributes to the measured evaporation flux. In this way, evaporation measurements of the two parts of the field site could be distinguished. However, since only one EC station was available, simultaneous evaporation measurements for the two field parts were not available. As a consequence, the datasets of measurements had to be interpreted and put into context of the meteorological and soil hydrological conditions. The potential evapotranspiration was calculated using the FAO method (Allen et al., 1998) to represent the meteorological conditions whereas a simple soil evaporation model (Boesten and Stroosnijder, 1986) was used to represent the influence of the precipitation and soil hydrological conditions on the actual evaporation rate. Since different soil parameters were required to describe the evaporation measurements for the upper and lower part of the plot, our starting hypothesis that more water is evaporated in the lower part of the field could be confirmed. Allen, R. G., L. S. Pereira, D. Raes, and M. Smith (1998), Crop evapotranspiration: Guidelines for computing crop water

  11. Calculation of interaction-induced spectra using complex absorbing potentials

    SciTech Connect

    Gustafsson, Magnus; Antipov, Sergey V.

    2010-10-29

    A complex absorbing potential method is implemented for calculation of collision-induced spectra. The scheme provides a way to avoid the integration of the Schroedinger equation to very large separations of the collisional pair. The method is tested by reproducing a previously computed absorption spectrum for H-He at two different temperatures.

  12. Numerical Green's functions in optical potential calculations for positron scattering from argon and neon

    NASA Technical Reports Server (NTRS)

    Bartschat, K.; Mceachran, R. P.; Stauffer, A. D.

    1990-01-01

    An optical potential method was applied to the calculation of positron scattering from the noble gases in order to determine the effect of open excitation channels on the shape of differential scattering cross sections.

  13. Off disk-center potential field calculations using vector magnetograms

    NASA Technical Reports Server (NTRS)

    Venkatakrishnan, P.; Gary, G. Allen

    1989-01-01

    A potential field calculation for off disk-center vector magnetograms that uses all the three components of the measured field is investigated. There is neither any need for interpolation of grid points between the image plane and the heliographic plane nor for an extension or a truncation to a heliographic rectangle. Hence, the method provides the maximum information content from the photospheric field as well as the most consistent potential field independent of the viewing angle. The introduction of polarimetric noise produces a less tolerant extrapolation procedure than using the line-of-sight extrapolation, but the resultant standard deviation is still small enough for the practical utility of this method.

  14. Misfit effects in adhesion calculations

    NASA Astrophysics Data System (ADS)

    Schnitker, Jurgen; Srolovitz, David J.

    1998-03-01

    The work of adhesion of bimaterial interfaces is commonly computed using quantum mechanical methods in which the two materials are strained into coherency. There is no relaxation of the coherency by the formation of an array of interfacial misfit dislocations, contrary to what is commonly observed for essentially all systems other than very thin films. In this paper, we investigate the errors introduced into the work of adhesion associated with the assumption of coherency. Series of atomistic simulations in two and three dimensions are performed using a simple Lennard-Jones-type model potential. We demonstrate that the assumption of coherency introduces errors that increase rapidly with misfit (for small misfit) and can easily be of the order of several tens of percent. We trace the source of these errors to the neglect of the elastic fields of misfit dislocations and to the variation in the number of bonds per unit interfacial area with misfit when coherency is assumed. Suggestions are made to minimize and/or correct for this error.

  15. Proliferation Potential of Accelerator-Drive Systems: Feasibility Calculations

    SciTech Connect

    Riendeau, C.D.; Moses, D.L.; Olson, A.P.

    1998-11-01

    Accelerator-driven systems for fissile materials production have been proposed and studied since the early 1950s. Recent advances in beam power levels for small accelerators have raised the possibility that such use could be feasible for a potential proliferator. The objective of this study is to review the state of technology development for accelerator-driven spallation neutron sources and subcritical reactors. Energy and power requirements were calculated for a proton accelerator-driven neutron spallation source and subcritical reactors to produce a significant amount of fissile material--plutonium.

  16. Accurate potential energy curve of the LiH+ molecule calculated with explicitly correlated Gaussian functions.

    PubMed

    Tung, Wei-Cheng; Adamowicz, Ludwik

    2014-03-28

    Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH(+) ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations. PMID:24697449

  17. Accurate potential energy curve of the LiH+ molecule calculated with explicitly correlated Gaussian functions

    NASA Astrophysics Data System (ADS)

    Tung, Wei-Cheng; Adamowicz, Ludwik

    2014-03-01

    Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH+ ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations.

  18. Modified method of aerodynamic resistance calculation and its application to potential evapotranspiration estimation

    NASA Astrophysics Data System (ADS)

    Rodný, Marek; Nolz, Reinhard; Novák, Viliam; Hlaváčiková, Hana; Loiskandl, Willibald; Himmelbauer, Margarita

    2016-04-01

    The aim of this study was to present and validate an alternative evapotranspiration calculation procedure that includes specific expression for the aerodynamic resistance. Calculated daily potential evapotranspiration totals were compared to the results of FAO56 procedure application and to the results of measurements taken with a precision weighing lysimeter permanently grown with irrigated, short grass. For the examination period from March 17 through October 31, 2011, it was found that daily potential evapotranspiration estimates obtained by both calculation procedures fitted well to the lysimeter measurements. Potential evapotranspiration daily totals calculated with the use of the proposed aerodynamic resistance calculation procedure gave better results for days with higher evapotranspiration, compared to the FAO56 method. The most important is that the approach based on the proposed alternative aerodynamic resistance could be effectively used even for a wide variety of crops, because it is not limited to any particular crop.

  19. Surface calculations with asymptotically long-ranged potentials in the full-potential linearized augmented plane-wave method

    NASA Astrophysics Data System (ADS)

    Ye, Lin-Hui

    2015-09-01

    Although the supercell method has been widely used for surface calculations, it only works well with short-ranged potentials, but meets difficulty when the potential decays very slowly into the vacuum. Unfortunately, the exact exchange-correlation potential of the density functional theory is asymptotically long ranged, and therefore is not easily handled by use of supercells. This paper illustrates that the authentic slab geometry, another technique for surface calculations, is not affected by this issue: It works equally well with both short- and long-ranged potentials, with the computational cost and the convergence speed being essentially the same. Using the asymptotically long-ranged Becke-Roussel'89 exchange potential as an example, we have calculated six surfaces of various types. We found that accurate potential values can be obtained even in extremely low density regions of more than 100 Å away from the surface. This high performance allows us to explore the asymptotic region, and prove with clean numerical evidence that the Becke-Roussel'89 potential satisfies the correct asymptotic behavior for slab surfaces, as it does for finite systems. Our finding further implies that the Slater component of the exact exchange optimized effective potential is responsible for the asymptotic behavior, not only for jellium slabs, but for slabs of any type. The Becke-Roussel'89 potential may therefore be used to build asymptotically correct model exchange potentials applicable to both finite systems and slab surfaces.

  20. Efficient calculation of potential energy surfaces for the generation of vibrational wave functions.

    PubMed

    Rauhut, Guntram

    2004-11-15

    An automatic procedure for the generation of potential energy surfaces based on high level ab initio calculations is described. It allows us to determine the vibrational wave functions for molecules of up to ten atoms. Speedups in computer time of about four orders of magnitude in comparison to standard implementations were achieved. Effects due to introduced approximations--within the computation of the potential--on fundamental modes obtained from vibrational self-consistent field and vibrational configuration interaction calculations are discussed. Benchmark calculations are provided for formaldehyde and 1,2,5-oxadiazole (furazan). PMID:15538851

  1. A Molecular Full-Potential LMTO Calculation for Copper Clusters

    NASA Astrophysics Data System (ADS)

    Datta, Radhika Prosad; Banerjea, Amitava; Mookerjee, Abhijit; Bhattacharyya, A. K.

    We study the electronic properties of small (10-20 atoms) copper clusters using the newly-developed molecular full-potential linearized muffin-tin orbital two-centre-fit (TCF) method of Methfessel and van Schilfgaarde. The geometric structures of the clusters had earlier been determined by us through simulated annealing using the Equivalent Crystal Theory to compute total energies. We report the variation of the binding energy, as obtained from the TCF calculations, with cluster size and compare these to the binding energies determined, for the same structures, from the ECT. We also show the variation of the HOMO-LUMO gap with cluster size, and the pseudo-density of states for select cluster sizes.

  2. Electronic structure calculations toward new potentially AChE inhibitors

    NASA Astrophysics Data System (ADS)

    de Paula, A. A. N.; Martins, J. B. L.; Gargano, R.; dos Santos, M. L.; Romeiro, L. A. S.

    2007-10-01

    The main purpose of this study was the use of natural non-isoprenoid phenolic lipid of cashew nut shell liquid from Anacardium occidentale as lead material for generating new potentially candidates of acetylcholinesterase inhibitors. Therefore, we studied the electronic structure of 15 molecules derivatives from the cardanol using the following groups: methyl, acetyl, N, N-dimethylcarbamoyl, N, N-dimethylamine, N, N-diethylamine, piperidine, pyrrolidine, and N-benzylamine. The calculations were performed at RHF level using 6-31G, 6-31G(d), 6-31+G(d) and 6-311G(d,p) basis functions. Among the proposed compounds we found that the structures with substitution by acetyl, N, N-dimethylcarbamoyl, N, N-dimethylamine, and pyrrolidine groups were better correlated to rivastigmine indicating possible activity.

  3. Multi-grid calculation of transonic potential flows

    NASA Technical Reports Server (NTRS)

    Caughey, D. A.; Shmilovich, A.

    1985-01-01

    The finite-volume method discussed by Jameson and Caughey (1977), and Caughey and Jameson (1979, 1980) has made it possible to calculate the transonic potential flow past any configuration for which a suitable boundary-conforming coordinate grid can be constructed. However, computations for practical three-dimensional problems have remained quite expensive in terms of the required computer time. The reason for this is primarily related to the large number of grid cells necessary for adequate resolution in these complex three-dimensional problems, taking into account the large number of iterations required to achieve even modest convergence on these fine grids. The present chapter provides a description of work directed at removing this latter difficulty by making use of the multigrid method. Attention is given to finite-volume formulation, multigrid iteration, geometrical aspects, and computed results.

  4. A submerged singularity method for calculating potential flow velocities at arbitrary near-field points

    NASA Technical Reports Server (NTRS)

    Maskew, B.

    1976-01-01

    A discrete singularity method has been developed for calculating the potential flow around two-dimensional airfoils. The objective was to calculate velocities at any arbitrary point in the flow field, including points that approach the airfoil surface. That objective was achieved and is demonstrated here on a Joukowski airfoil. The method used combined vortices and sources ''submerged'' a small distance below the airfoil surface and incorporated a near-field subvortex technique developed earlier. When a velocity calculation point approached the airfoil surface, the number of discrete singularities effectively increased (but only locally) to keep the point just outside the error region of the submerged singularity discretization. The method could be extended to three dimensions, and should improve nonlinear methods, which calculate interference effects between multiple wings, and which include the effects of force-free trailing vortex sheets. The capability demonstrated here would extend the scope of such calculations to allow the close approach of wings and vortex sheets (or vortices).

  5. Efficient calculation of potential energy surfaces for the generation of vibrational wave functions

    NASA Astrophysics Data System (ADS)

    Rauhut, Guntram

    2004-11-01

    An automatic procedure for the generation of potential energy surfaces based on high level ab initio calculations is described. It allows us to determine the vibrational wave functions for molecules of up to ten atoms. Speedups in computer time of about four orders of magnitude in comparison to standard implementations were achieved. Effects due to introduced approximations—within the computation of the potential—on fundamental modes obtained from vibrational self-consistent field and vibrational configuration interaction calculations are discussed. Benchmark calculations are provided for formaldehyde and 1,2,5-oxadiazole (furazan).

  6. Helium-surface interaction potential of Sb(111) from scattering experiments and close-coupling calculations

    NASA Astrophysics Data System (ADS)

    Mayrhofer-Reinhartshuber, M.; Kraus, P.; Tamtögl, A.; Miret-Artés, S.; Ernst, W. E.

    2013-11-01

    Helium atom scattering (HAS) was used to study the antimony Sb(111) surface beyond the hard-wall model. HAS angular distributions and drift spectra show a number of selective adsorption resonance features, which correspond to five bound-state energies for He atoms trapped in the surface-averaged He-Sb(111) potential. As their best representation, a 9-3 potential with a depth of 4.4±0.1 meV was determined. Furthermore, the charge density corrugation of the surface was analyzed using close-coupling calculations. By using a hybrid potential, consisting of a corrugated Morse potential (short range) and a 9-3 potential (long range), a peak-to-peak corrugation of 17% was obtained. The kinematic focusing effects that occurred were in good agreement with surface phonon dispersion curves from already published density functional perturbation theory calculations.

  7. Electron-N/sub 2/ scattering calculations with a parameter-free model polarization potential

    SciTech Connect

    Morrison, M.A.; Saha, B.C.; Gibson, T.L.

    1987-10-15

    We have extended our variationally determined nonadiabatic polarization potential (Gibson and Morrison, Phys. Rev. A 29, 2497 (1984)) to the e-N/sub 2/ system and calculated elastic, total momentum transfer, and rotational excitation cross sections. This model potential, which requires no scaling and contains no adjustable parameters, is presented in tabular and analytic (fitted) form for possible use in future studies. We evaluated the static potential at the near-Hartree-Fock level of accuracy and included exchange effects exactly via the linear algebraic method of Collins and Schneider (Phys. Rev. A 24, 2387 (1981)). Diverse cross sections based on this model are in excellent agreement with existing experiment. We also compare various scattering quantities calculated with our model to prior theoretical results and to newly determined numbers using two other model potentials: a cutoff phenomenological form and the correlation-polarization potential of O'Connell and Lane (Phys. Rev. A 27, 1893 (1983)).

  8. Bonn potential and shell-model calculations for N=126 isotones

    SciTech Connect

    Coraggio, L.; Covello, A.; Gargano, A.; Itaco, N.; Kuo, T. T. S.

    1999-12-01

    We have performed shell-model calculations for the N=126 isotones {sup 210}Po, {sup 211}At, and {sup 212}Rn using a realistic effective interaction derived from the Bonn-A nucleon-nucleon potential by means of a G-matrix folded-diagram method. The calculated binding energies, energy spectra, and electromagnetic properties show remarkably good agreement with the experimental data. The results of this paper complement those of our previous study on neutron hole Pb isotopes, confirming that realistic effective interactions are now able to reproduce with quantitative accuracy the spectroscopic properties of complex nuclei. (c) 1999 The American Physical Society.

  9. NATIONAL EMISSION STANDARDS FOR HAZARDOUS AIR POLLUTANTS (NESHAP) SUBPART H RADIONUCLIDES POTENTIAL TO EMIT CALCULATIONS

    SciTech Connect

    EARLEY JN

    2008-07-23

    This document provides an update of the status of stacks on the Hanford Site and the potential radionuclide emissions, i.e., emissions that could occur with no control devices in place. This review shows the calculations that determined whether the total effective dose equivalent (TEDE) received by the maximum public receptor as a result of potential emissions from any one of these stacks would exceed 0.1 millirem/year. Such stacks require continuous monitoring of the effluent, or other monitoring, to meet the requirements of Washington Administrative code (WAC) 246-247-035(1)(a)(ii) and WAC 246-247-075(1), -(2), and -(6). This revised update reviews the potential-to-emit (PTE) calculations of 31 stacks for Fluor Hanford, Inc. Of those 31 stacks, 11 have the potential to cause a TEDE greater than 0.1 mrem/year.

  10. Effective Potential in Noncommutative BTZ Black Hole

    NASA Astrophysics Data System (ADS)

    Sadeghi, Jafar; Shajiee, Vahid Reza

    2016-02-01

    In this paper, we investigated the noncommutative rotating BTZ black hole and showed that such a space-time is not maximally symmetric. We calculated effective potential for the massive and the massless test particle by geodesic equations, also we showed effect of non-commutativity on the minimum mass of BTZ black hole.

  11. Analytical second derivatives for effective core potentials

    NASA Astrophysics Data System (ADS)

    Breidung, Jürgen; Thiel, Walter; Komornicki, Andrew

    1988-12-01

    Analytical first and second derivatives for effective core potentials are reported. The computational implementation of the derivative formulas makes use of new integral routines which take advantage of the shell concept. Test calculations for H 3SnBr and F 3AsS demonstrate the efficiency of the analytical determination of harmonic force fields using effective core potentials. The spectroscopic constants of the unknown molecule F 3AsS are predicted.

  12. Absolute Binding Free Energy Calculations Using Molecular Dynamics Simulations with Restraining Potentials

    PubMed Central

    Wang, Jiyao; Deng, Yuqing; Roux, Benoît

    2006-01-01

    The absolute (standard) binding free energy of eight FK506-related ligands to FKBP12 is calculated using free energy perturbation molecular dynamics (FEP/MD) simulations with explicit solvent. A number of features are implemented to improve the accuracy and enhance the convergence of the calculations. First, the absolute binding free energy is decomposed into sequential steps during which the ligand-surrounding interactions as well as various biasing potentials restraining the translation, orientation, and conformation of the ligand are turned “on” and “off.” Second, sampling of the ligand conformation is enforced by a restraining potential based on the root mean-square deviation relative to the bound state conformation. The effect of all the restraining potentials is rigorously unbiased, and it is shown explicitly that the final results are independent of all artificial restraints. Third, the repulsive and dispersive free energy contribution arising from the Lennard-Jones interactions of the ligand with its surrounding (protein and solvent) is calculated using the Weeks-Chandler-Andersen separation. This separation also improves convergence of the FEP/MD calculations. Fourth, to decrease the computational cost, only a small number of atoms in the vicinity of the binding site are simulated explicitly, while all the influence of the remaining atoms is incorporated implicitly using the generalized solvent boundary potential (GSBP) method. With GSBP, the size of the simulated FKBP12/ligand systems is significantly reduced, from ∼25,000 to 2500. The computations are very efficient and the statistical error is small (∼1 kcal/mol). The calculated binding free energies are generally in good agreement with available experimental data and previous calculations (within ∼2 kcal/mol). The present results indicate that a strategy based on FEP/MD simulations of a reduced GSBP atomic model sampled with conformational, translational, and orientational restraining

  13. Perturbation method to calculate the interaction potentials and electronic excitation spectra of atoms in He nanodroplets.

    PubMed

    Callegari, Carlo; Ancilotto, Francesco

    2011-06-30

    A method is proposed for the calculation of potential energy curves and related electronic excitation spectra of dopant atoms captured in/on He nanodroplets and is applied to alkali metal atoms. The method requires knowledge of the droplet density distribution at equilibrium (here calculated within a bosonic-He density functional approach) and of a set of valence electron orbitals of the bare dopant atom (here calculated by numeric solution of the Schrödinger equation in a suitably parametrized model potential). The electron-helium interaction is added as a perturbation, and potential energy curves are obtained by numeric diagonalization of the resulting Hamiltonian as a function of an effective coordinate z(A) (here the distance between the dopant atom and center of mass of the droplet, resulting in a pseudodiatomic potential). Excitation spectra are calculated for Na in the companion paper as the Franck-Condon factors between the v = 0 vibrational state in the ground electronic state and excited states of the pseudodiatomic molecule. They agree well with available experimental data, even for highly excited states where a more traditional approach fails. PMID:21434657

  14. Model potential calculation of the thermal donor energy spectrum in silicon

    NASA Astrophysics Data System (ADS)

    Chen, C. S.; Schroder, D. K.

    1988-06-01

    The two-parameter model potential originally proposed by Ning and Sah [Phys. Rev. B 4, 3468 (1971)] for calculating the ground-state energies of group V and group VI impurities in silicon is extended to the variational calculation of the thermal donor ionization energies. In the multivalley effective mass approximation, the theoretical results are in excellent agreement with the reported experimental data. This provides additional evidence for the assumption that thermal donors consist of five to thirteen oxygen atoms, as first proposed by Ourmazd, Schröter, and Bourret [J. Appl. Phys. 56, 1670 (1984)].

  15. Model potential calculation of the thermal donor energy spectrum in silicon

    SciTech Connect

    Chen, C.S.; Schroder, D.K.

    1988-06-15

    The two-parameter model potential originally proposed by Ning and Sah (Phys. Rev. B 4, 3468 (1971)) for calculating the ground-state energies of group V and group VI impurities in silicon is extended to the variational calculation of the thermal donor ionization energies. In the multivalley effective mass approximation, the theoretical results are in excellent agreement with the reported experimental data. This provides additional evidence for the assumption that thermal donors consist of five to thirteen oxygen atoms, as first proposed by Ourmazd, Schroeter, and Bourret (J. Appl. Phys. 56, 1670 (1984)).

  16. The use of model potentials in molecular calculations. II

    NASA Astrophysics Data System (ADS)

    Sakai, Y.; Huzinaga, S.

    1982-03-01

    The model potential method is applied to CO, HCl, P2, Cl2, SH2, Cu2, Br2, Ni(CO)4, and Pd(CO)4. The results are generally very satisfactory. Reduction of computing cost is substantial for molecules containing heavy atoms.

  17. Improved finite difference schemes for transonic potential calculations

    NASA Technical Reports Server (NTRS)

    Hafez, M.; Osher, S.; Whitlow, W., Jr.

    1984-01-01

    Engquist and Osher (1980) have introduced a finite difference scheme for solving the transonic small disturbance equation, taking into account cases in which only compression shocks are admitted. Osher et al. (1983) studied a class of schemes for the full potential equation. It is proved that these schemes satisfy a new discrete 'entropy inequality' which rules out expansion shocks. However, the conducted analysis is restricted to steady two-dimensional flows. The present investigation is concerned with the adoption of a heuristic approach. The full potential equation in conservation form is solved with the aid of a modified artificial density method, based on flux biasing. It is shown that, with the current scheme, expansion shocks are not possible.

  18. Comparison of Electron Elastic-Scattering Cross Sections Calculated from Two Commonly Used Atomic Potentials

    NASA Astrophysics Data System (ADS)

    Jablonski, A.; Salvat, F.; Powell, C. J.

    2004-06-01

    We have analyzed differential cross sections (DCSs) for the elastic scattering of electrons by neutral atoms that have been derived from two commonly used atomic potentials: the Thomas-Fermi-Dirac (TFD) potential and the Dirac-Hartree-Fock (DHF) potential. DCSs from the latter potential are believed to be more accurate. We compared DCSs for six atoms (H, Al, Ni, Ag, Au, and Cm) at four energies (100, 500, 1000, and 10 000 eV) from two databases issued by the National Institute of Standards and Technology in which DCSs had been obtained from the TFD and DHF potentials. While the DCSs from the two potentials had similar shapes and magnitudes, there can be pronounced deviations (up to 70%) for small scattering angles for Al, Ag, Au, and Cm. In addition, there were differences of up to 400% at scattering angles for which there were deep minima in the DCSs; at other angles, the differences were typically less than 20%. The DCS differences decreased with increasing electron energy. DCSs calculated from the two potentials were compared with measured DCSs for six atoms (He, Ne, Ar, Kr, Xe, and Hg) at energies between 50 eV and 3 keV. For Ar, the atom for which experimental data are available over the largest energy range there is good agreement between the measured DCSs and those calculated from the TFD and DHF potentials at 2 and 3 keV, but the experimental DCSs agree better with the DCSs from the DHF potential at lower energies. A similar trend is found for the other atoms. At energies less than about 1 keV, there are increasing differences between the measured DCSs and the DCSs calculated from the DHF potential. These differences were attributed to the neglect of absorption and polarizability effects in the calculations. We compare transport cross sections for H, Al, Ni, Ag, Au, and Cm obtained from the DCSs for each potential. For energies between 200 eV and 1 keV, the largest differences are about 20% (for H, Au, and Cm); at higher energies, the differences are

  19. Potential theoretic methods for far field sound radiation calculations

    NASA Technical Reports Server (NTRS)

    Hariharan, S. I.; Stenger, Edward J.; Scott, J. R.

    1995-01-01

    In the area of computational acoustics, procedures which accurately predict the far-field sound radiation are much sought after. A systematic development of such procedures are found in a sequence of papers by Atassi. The method presented here is an alternate approach to predicting far field sound based on simple layer potential theoretic methods. The main advantages of this method are: it requires only a simple free space Green's function, it can accommodate arbitrary shapes of Kirchoff surfaces, and is readily extendable to three-dimensional problems. Moreover, the procedure presented here, though tested for unsteady lifting airfoil problems, can easily be adapted to other areas of interest, such as jet noise radiation problems. Results are presented for lifting airfoil problems and comparisons are made with the results reported by Atassi. Direct comparisons are also made for the flat plate case.

  20. On the calculation of potential flow about a body in an unbounded fluid

    NASA Astrophysics Data System (ADS)

    Noblesse, F.; Triantafyllou, G.

    1980-09-01

    This study is concerned with the problem of calculating potential flow about a nonlifting body in an unbounded fluid. Several simple explicit approximations for the velocity potential are obtained and investigated numerically. Results of calculations are presented for the simple cases of potential flows due to translations of ellipsoids and ogives.

  1. Calculations supporting evaluation of potential environmental standards for Yucca Mountain

    SciTech Connect

    Duguid, J.O.; Andrews, R.W.; Brandstetter, E.; Dale, T.F.; Reeves, M.

    1994-04-01

    The Energy Policy Act of 1992, Section 801 (US Congress, 1992) provides for the US Environmental Protection Agency (EPA) to contract the National Academy of Sciences (NAS) to conduct a study and provide findings and recommendations on reasonable standards for the disposal of high-level wastes at the Yucca Mountain site. The NAS study is to provide findings and recommendations which include, among other things, whether a health-based standard based on dose to individual members of the public from releases to the accessible environment will provide a reasonable standard for the protection of the health and safety of the public. The EPA, based upon and consistent with the findings and recommendations of the NAS, is required to promulgate standards for protection of the public from releases from radioactive materials stored or disposed of in a repository at the Yucca Mountain site. This document presents a number of different ``simple`` analyses of undisturbed repository performance that are intended to provide input to those responsible for setting appropriate environmental standards for a potential repository at the Yucca Mountain site in Nevada. Each of the processes included in the analyses has been simplified to capture the primary significance of that process in containing or isolating the waste from the biosphere. In these simplified analyses, the complex waste package interactions were approximated by a simple waste package ``failure`` distribution which is defined by the initiation and rate of waste package ``failures``. Similarly, releases from the waste package and the engineered barrier system are controlled by the very near field environment and the presence and rate of advective and diffusive release processes. Release was approximated by either a simple alteration-controlled release for the high solubility radionuclides and either a diffusive or advective-controlled release for the solubility-limited radionuclides.

  2. Piezoelectric constants for ZnO calculated using classical polarizable core-shell potentials

    NASA Astrophysics Data System (ADS)

    Dai, Shuangxing; Dunn, Martin L.; Park, Harold S.

    2010-11-01

    We demonstrate the feasibility of using classical atomistic simulations, i.e. molecular dynamics and molecular statics, to study the piezoelectric properties of ZnO using core-shell interatomic potentials. We accomplish this by reporting the piezoelectric constants for ZnO as calculated using two different classical interatomic core-shell potentials: that originally proposed by Binks and Grimes (1994 Solid State Commun. 89 921-4), and that proposed by Nyberg et al (1996 J. Phys. Chem. 100 9054-63). We demonstrate that the classical core-shell potentials are able to qualitatively reproduce the piezoelectric constants as compared to benchmark ab initio calculations. We further demonstrate that while the presence of the shell is required to capture the electron polarization effects that control the clamped ion part of the piezoelectric constant, the major shortcoming of the classical potentials is a significant underprediction of the clamped ion term as compared to previous ab initio results. However, the present results suggest that overall, these classical core-shell potentials are sufficiently accurate to be utilized for large scale atomistic simulations of the piezoelectric response of ZnO nanostructures.

  3. Accurate potential energy curve of the LiH{sup +} molecule calculated with explicitly correlated Gaussian functions

    SciTech Connect

    Tung, Wei-Cheng; Adamowicz, Ludwik

    2014-03-28

    Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH{sup +} ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations.

  4. On the consistent definition of spin-orbit effects calculated by relativistic effective core potentials with one-electron spin-orbit operators: Comparison of spin-orbit effects for Tl, TlH, TlH3, PbH2, and PbH4

    NASA Astrophysics Data System (ADS)

    Han, Young-Kyu; Bae, Cheolbeom; Lee, Yoon Sup

    1999-05-01

    The spin-orbit effects for Tl, TlH, TlH3, PbH2, and PbH4 are evaluated by two-component calculations using several relativistic effective core potentials (RECP) with one-electron spin-orbit operators. The used RECPs are shape-consistent RECPs derived by Wildman et al. [J. Chem. Phys. 107, 9975 (1997)] and three sets of energy-consistent (or adjusted) RECPs published by Schwerdtfeger et al. [Phys. Scr. 36, 453 (1987); J. Chem. Phys. 90, 762 (1989)], Küchle et al. [Mol. Phys. 74, 1245 (1991)], and Leininger et al. [Chem. Phys. 217, 19 (1997)]. The shape-consistent RECP results are in very good agreement with the Küchle et al. energy-consistent RECP results for all the molecules studied here and all-electron results for TlH. The RECPs of Schwerdtfeger et al. and Leininger et al. seem to provide qualitatively different spin-orbit effects. If one defines spin-free RECP as the potential average of the corresponding two-component RECP, all RECPs give very similar spin-orbit effects for all the cases. Most of the discrepancies of molecular spin-orbit effects among various RECPs reported in the literature may originate from different definitions of RECPs with or without a spin-orbit term and not from the inherent difference in spin-orbit operators.

  5. Effect of orientation anisotropy on calculating effective electrical conductivities

    NASA Astrophysics Data System (ADS)

    Myles, Timothy D.; Peracchio, Aldo A.; Chiu, Wilson K. S.

    2014-05-01

    This paper develops an analytical effective medium theory (EMT) equation for calculating the effective conductivity of a mixture based on Maxwell's and Maxwell-Garnett's theories, extended to higher volume fractions using Bruggeman's unsymmetrical treatment (BUT), with a long term goal of extending the treatment to mixtures more representative of real materials in order to calculate their effective electrical conductivity. The development accounts for spheroid shaped inclusions of varying degrees of anisotropic orientation. The orientation is described by the introduction of a distribution function. Two methodologies valid for the inclusion dilute limit were used to evaluate the effective conductivity: one based on Maxwell's far field approach, and the other based on the Maxwell-Garnett in the matrix approach. It was found that while the dilute limit equations for the effective conductivity were different, the final EMT equations derived by applying BUT collapsed to the same formula which was generalized for anisotropic orientation based on the distribution function presented.

  6. Ab initio calculation of ionization potential and electron affinity in solid-state organic semiconductors

    NASA Astrophysics Data System (ADS)

    Kang, Youngho; Jeon, Sang Ho; Cho, Youngmi; Han, Seungwu

    2016-01-01

    We investigate the vertical ionization potential (IP) and electron affinity (EA) of organic semiconductors in the solid state that govern the optoelectrical property of organic devices using a fully ab initio way. The present method combines the density functional theory and many-body perturbation theory based on G W approximations. To demonstrate the accuracy of this approach, we carry out calculations on several prototypical organic molecules. Since IP and EA depend on the molecular orientation at the surface, the molecular geometry of the surface is explicitly considered through the slab model. The computed IP and EA are in reasonable and consistent agreements with spectroscopic data on organic surfaces with various molecular arrangements. However, the transport gaps are slightly underestimated in calculations, which can be explained by different screening effects between surface and bulk regions.

  7. Potential effects of gallium on cladding materials

    SciTech Connect

    Wilson, D.F.; Beahm, E.C.; Besmann, T.M.; DeVan, J.H.; DiStefano, J.R.; Gat, U.; Greene, S.R.; Rittenhouse, P.L.; Worley, B.A.

    1997-10-01

    This paper identifies and examines issues concerning the incorporation of gallium in weapons derived plutonium in light water reactor (LWR) MOX fuels. Particular attention is given to the more likely effects of the gallium on the behavior of the cladding material. The chemistry of weapons grade (WG) MOX, including possible consequences of gallium within plutonium agglomerates, was assessed. Based on the calculated oxidation potentials of MOX fuel, the effect that gallium may have on reactions involving fission products and possible impact on cladding performance were postulated. Gallium transport mechanisms are discussed. With an understanding of oxidation potentials and assumptions of mechanisms for gallium transport, possible effects of gallium on corrosion of cladding were evaluated. Potential and unresolved issues and suggested research and development (R and D) required to provide missing information are presented.

  8. Calculation of Water Drop Trajectories to and About Arbitrary Three-Dimensional Bodies in Potential Airflow

    NASA Technical Reports Server (NTRS)

    Norment, H. G.

    1980-01-01

    Calculations can be performed for any atmospheric conditions and for all water drop sizes, from the smallest cloud droplet to large raindrops. Any subsonic, external, non-lifting flow can be accommodated; flow into, but not through, inlets also can be simulated. Experimental water drop drag relations are used in the water drop equations of motion and effects of gravity settling are included. Seven codes are described: (1) a code used to debug and plot body surface description data; (2) a code that processes the body surface data to yield the potential flow field; (3) a code that computes flow velocities at arrays of points in space; (4) a code that computes water drop trajectories from an array of points in space; (5) a code that computes water drop trajectories and fluxes to arbitrary target points; (6) a code that computes water drop trajectories tangent to the body; and (7) a code that produces stereo pair plots which include both the body and trajectories. Code descriptions include operating instructions, card inputs and printouts for example problems, and listing of the FORTRAN codes. Accuracy of the calculations is discussed, and trajectory calculation results are compared with prior calculations and with experimental data.

  9. Interface effects on calculated defect levels for oxide defects

    NASA Astrophysics Data System (ADS)

    Edwards, Arthur; Barnaby, Hugh; Schultz, Peter; Pineda, Andrew

    2014-03-01

    Density functional theory (DFT) has had impressive recent success predicting defect levels in insulators and semiconductors [Schultz and von Lillienfeld, 2009]. Such success requires care in accounting for long-range electrostatic effects. Recently, Komsa and Pasquarello have started to address this problem in systems with interfaces. We report a multiscale technique for calculating electrostatic energies for charged defects in oxide of the metal-oxide-silicon (MOS) system, but where account is taken of substrate doping density, oxide thickness, and gate bias. We use device modeling to calculate electric fields for a point charge a fixed distance from the interface, and used the field to numerically calculate the long-range electrostatic interactions. We find, for example, that defect levels in the oxide do depend on both the magnitude and the polarity the substrate doping density. Furthermore, below 20 Å, oxide thickness also has significant effects. So, transferring results directly from bulk calculations leads to inaccuracies up to 0.5 eV- half of the silicon band gap. We will present trends in defect levels as a function of device parameters. We show that these results explain previous experimental results, and we comment on their potential impact on models for NBTI. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the United States Department of Energy's National Nuclear Security Administration under co.

  10. The ozone depletion potentials on halocarbons: Their dependence of calculation assumptions

    NASA Technical Reports Server (NTRS)

    Karol, Igor L.; Kiselev, Andrey A.

    1994-01-01

    The concept of Ozone Depletion Potential (ODP) is widely used in the evaluation of numerous halocarbons and of their replacement effects on ozone, but the methods, assumptions and conditions used in ODP calculations have not been analyzed adequately. In this paper a model study of effects on ozone of the instantaneous releases of various amounts of CH3CCl3 and of CHF2Cl (HCFC-22) for several compositions of the background atmosphere are presented, aimed at understanding connections of ODP values with the assumptions used in their calculations. To facilitate the ODP computation in numerous versions for the long time periods after their releases, the above rather short-lived gases and the one-dimensional radiative photochemical model of the global annually averaged atmospheric layer up to 50 km height are used. The variation of released gas global mass from 1 Mt to 1 Gt leads to ODP value increase with its stabilization close to the upper bound of this range in the contemporary atmosphere. The same variations are analyzed for conditions of the CFC-free atmosphere of 1960's and for the anthropogenically loaded atmosphere in the 21st century according to the known IPCC 'business as usual' scenario. Recommendations for proper ways of ODP calculations are proposed for practically important cases.

  11. Calculators in the Mathematics Curriculum: Effects and Changes.

    ERIC Educational Resources Information Center

    Rabe, Rebecca Moore

    The purpose of this paper was to determine the effects of calculators in mathematics classes and to assess proposed curriculum revisions related to calculators. Twenty-six calculator studies and other selected sources were reviewed and annotated. Major conclusions of the study include: (1) calculator use has produced significant gains in…

  12. Interference effects in potential wells

    NASA Astrophysics Data System (ADS)

    Mullin, W. J.; Laloë, F.

    2015-05-01

    We propose using an array of potential wells as an interferometer in which the beam splitters are provided by tunneling during an appropriate time through the barrier between wells. This arrangement allows demonstration of generalized Hong-Ou-Mandel effects with multiple particles traversing one or several beam splitters. Other interferometer effects can occur, including a violation of the Bell-Clauser-Horne-Shimony-Holt form of the Bell inequality. With interactions, one sees various effects, including so-called fermionization, collective tunneling, and self-trapping.

  13. Quantum-Mechanical Calculation of Ionization-Potential Lowering in Dense Plasmas

    NASA Astrophysics Data System (ADS)

    Son, Sang-Kil; Thiele, Robert; Jurek, Zoltan; Ziaja, Beata; Santra, Robin

    2014-07-01

    The charged environment within a dense plasma leads to the phenomenon of ionization-potential depression (IPD) for ions embedded in the plasma. Accurate predictions of the IPD effect are of crucial importance for modeling atomic processes occurring within dense plasmas. Several theoretical models have been developed to describe the IPD effect, with frequently discrepant predictions. Only recently, first experiments on IPD in Al plasma have been performed with an x-ray free-electron laser, where their results were found to be in disagreement with the widely used IPD model by Stewart and Pyatt. Another experiment on Al, at the Orion laser, showed disagreement with the model by Ecker and Kröll. This controversy shows a strong need for a rigorous and consistent theoretical approach to calculate the IPD effect. Here, we propose such an approach: a two-step Hartree-Fock-Slater model. With this parameter-free model, we can accurately and efficiently describe the experimental Al data and validate the accuracy of standard IPD models. Our model can be a useful tool for calculating atomic properties within dense plasmas with wide-ranging applications to studies on warm dense matter, shock experiments, planetary science, inertial confinement fusion, and nonequilibrium plasmas created with x-ray free-electron lasers.

  14. Interpolation effects in tabulated interatomic potentials

    NASA Astrophysics Data System (ADS)

    Wen, M.; Whalen, S. M.; Elliott, R. S.; Tadmor, E. B.

    2015-10-01

    Empirical interatomic potentials are widely used in atomistic simulations due to their ability to compute the total energy and interatomic forces quickly relative to more accurate quantum calculations. The functional forms in these potentials are sometimes stored in a tabulated format, as a collection of data points (argument-value pairs), and a suitable interpolation (often spline-based) is used to obtain the function value at an arbitrary point. We explore the effect of these interpolations on the potential predictions by calculating the quasi-harmonic thermal expansion and finite-temperature elastic constant of a one-dimensional chain compared with molecular dynamics simulations. Our results show that some predictions are affected by the choice of interpolation regardless of the number of tabulated data points. Our results clearly indicate that the interpolation must be considered part of the potential definition, especially for lattice dynamics properties that depend on higher-order derivatives of the potential. This is facilitated by the Knowledgebase of Interatomic Models (KIM) project, in which both the tabulated data (‘parameterized model’) and the code that interpolates them to compute energy and forces (‘model driver’) are stored and given unique citeable identifiers. We have developed cubic and quintic spline model drivers for pair functional type models (EAM, FS, EMT) and uploaded them to the OpenKIM repository (https://openkim.org).

  15. Finite volume calculation of three-dimensional potential flow around a propeller

    NASA Technical Reports Server (NTRS)

    Jou, W.-H.

    1982-01-01

    The finite volume scheme of Jameson (1977) is used to calculate potential flow around a propeller rotating at high speed. An H-type mesh is generated and used successfully in the calculations. A test calculation with a thick blade cross section shows that the present code is capable of computing the propeller flow at the advance Mach number 0.8. The possible physical mechanisms which may play an important role in the propeller aerodynamics are discussed.

  16. Phase-integral calculation of phase shifts for a heavy-ion optical potential

    SciTech Connect

    Linnaeus, S.

    1986-10-01

    Phase shifts for an optical potential representing the nuclear scattering of /sup 18/O by /sup 58/Ni at 60 MeV laboratory energy are calculated by means of an arbitrary-order phase-integral formula taking account of two turning points. The results are found to be in excellent agreement with previously published numerical calculations.

  17. 40 CFR Appendix D to Part 72 - Calculation of Potential Electric Output Capacity

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 16 2011-07-01 2011-07-01 false Calculation of Potential Electric Output Capacity D Appendix D to Part 72 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) PERMITS REGULATION Pt. 72, App. D Appendix D to Part 72—Calculation...

  18. 40 CFR Appendix D to Part 72 - Calculation of Potential Electric Output Capacity

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 16 2010-07-01 2010-07-01 false Calculation of Potential Electric Output Capacity D Appendix D to Part 72 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) PERMITS REGULATION Pt. 72, App. D Appendix D to Part 72—Calculation...

  19. 40 CFR Appendix D to Part 72 - Calculation of Potential Electric Output Capacity

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 17 2013-07-01 2013-07-01 false Calculation of Potential Electric Output Capacity D Appendix D to Part 72 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) PERMITS REGULATION Pt. 72, App. D Appendix D to Part 72—Calculation...

  20. Crystal-field calculations for transition-metal ions by application of an opposing potential

    DOE PAGESBeta

    Zhou, Fei; Aberg, Daniel

    2016-02-16

    We propose a fully ab initio method, the opposing crystal potential (OCP), to calculate the crystal-field parameters of transition-metal impurities in insulator hosts. Through constrained density functional calculations, OCP obtains the constraining Lagrange multipliers, which act as a cancellation potential against the crystal field and lead to spherical d-electron distribution. Furthermore, the method is applied to several insulators doped with Mn4+ and Mn2+ ions and shown to be in good agreement with experiment.

  1. Improved calculation of Si sputter yield via first principles derived interatomic potential

    NASA Astrophysics Data System (ADS)

    Hossain, M. Z.; Freund, J. B.; Johnson, H. T.

    2009-04-01

    Silicon sputter yield under medium energy Ar+ ion bombardment is calculated via molecular dynamics, using a highly accurate interatomic potential for Ar-Si interactions derived from first-principles calculations. Unlike the widely used universal repulsive potentials such as the Moliere or ZBL parameterizations, this new potential, referred to as DFT-ArSi, is developed via localized basis density functional theory. Sputter yields for Si obtained with the DFT-ArSi potential at 500 eV and 1 keV incident energies are found to be within 6% and 2% of experimental results, respectively, while errors using existing potentials are typically on the order of 11%. The DFT-ArSi potential differs from existing empirical potentials in the ˜1 Å interatomic separation range which is shown to be the most important range for modeling low-to-medium energy ion bombardment.

  2. Calculating Second-Order Effects in MOSFET's

    NASA Technical Reports Server (NTRS)

    Benumof, Reuben; Zoutendyk, John A.; Coss, James R.

    1990-01-01

    Collection of mathematical models includes second-order effects in n-channel, enhancement-mode, metal-oxide-semiconductor field-effect transistors (MOSFET's). When dimensions of circuit elements relatively large, effects neglected safely. However, as very-large-scale integration of microelectronic circuits leads to MOSFET's shorter or narrower than 2 micrometer, effects become significant in design and operation. Such computer programs as widely-used "Simulation Program With Integrated Circuit Emphasis, Version 2" (SPICE 2) include many of these effects. In second-order models of n-channel, enhancement-mode MOSFET, first-order gate-depletion region diminished by triangular-cross-section deletions on end and augmented by circular-wedge-cross-section bulges on sides.

  3. Effect of EMP fields on cell membrane potentials

    SciTech Connect

    Gailey, P.C.; Easterly, C.E.

    1993-06-01

    A simple model is presented for cell membrane potentials induced during exposure to electromagnetic pulse (EMP). Using calculated values of internal electric field strength induced during EMP exposure, the model predicts that cell membrane potentials of about 100 mV may be induced for time frames on the order of 10 ns. Possible biological effects of these potentials including electroporation area discussed.

  4. Large magnetocrystalline anisotropy in bilayer transition metal phases from first-principles full-potential calculations

    NASA Astrophysics Data System (ADS)

    Ravindran, P.; Kjekshus, A.; Fjellvåg, H.; James, P.; Nordström, L.; Johansson, B.; Eriksson, O.

    2001-04-01

    The computational framework of this study is based on the local-spin-density approximation with first-principles full-potential linear muffin-tin orbital calculations including orbital polarization (OP) correction. We have studied the magnetic anisotropy for a series of bilayer CuAu(I)-type materials such as FeX, MnX (X=Ni,Pd,Pt), CoPt, NiPt, MnHg, and MnRh in a ferromagnetic state using experimental structural parameters to understand the microscopic origin of magnetic-anisotropy energy (MAE) in magnetic multilayers. Except for MnRh and MnHg, all these phases show perpendicular magnetization. We have analyzed our results in terms of angular momentum-, spin- and site-projected density of states, magnetic-angular-momentum-projected density of states, orbital-moment density of states, and total density of states. The orbital-moment number of states and the orbital-moment anisotropy for FeX (X=Ni,Pd,Pt) are calculated as a function of band filling to study its effect on MAE. The total and site-projected spin and orbital moments for all these systems are calculated with and without OP when the magnetization is along or perpendicular to the plane. The results are compared with available experimental as well as theoretical results. Our calculations show that OP always enhances the orbital moment in these phases and brings them closer to experimental values. The changes in MAE are analyzed in terms of exchange splitting, spin-orbit splitting, and tetragonal distortion/crystal-field splitting. The calculated MAE is found to be in good agreement with experimental values when the OP correction is included. Some of the materials considered here show large magnetic anisotropy of the order of meV. In particular we found that MnPt will have a very large MAE if it could be stabilized in a ferromagnetic configuration. Our analysis indicates that apart from large spin-orbit interaction and exchange interaction from at least one of the constituents, a large crystal-field splitting

  5. Transonic flow analysis for rotors. Part 2: Three-dimensional, unsteady, full-potential calculation

    NASA Technical Reports Server (NTRS)

    Chang, I. C.

    1985-01-01

    A numerical method is presented for calculating the three-dimensional unsteady, transonic flow past a helicopter rotor blade of arbitrary geometry. The method solves the full-potential equations in a blade-fixed frame of reference by a time-marching implicit scheme. At the far-field, a set of first-order radiation conditions is imposed, thus minimizing the reflection of outgoing wavelets from computational boundaries. Computed results are presented to highlight radial flow effects in three dimensions, to compare surface pressure distributions to quasi-steady predictions, and to predict the flow field on a swept-tip blade. The results agree well with experimental data for both straight- and swept-tip blade geometries.

  6. FINITE EXPANSION METHOD FOR THE CALCULATION AND INTERPRETATION OF MOLECULAR ELECTROSTATIC POTENTIALS

    EPA Science Inventory

    Because it is useful to have the molecular electrostatic potential as an element in a complex scheme to assess the toxicity of large molecules, efficient and reliable methods are needed for the calculation and characterization of these potentials. A multicenter multipole expansio...

  7. Comparison of spin-orbit configuration interaction methods employing relativistic effective core potentials for the calculation of zero-field splittings of heavy atoms with a 2Po ground state

    NASA Astrophysics Data System (ADS)

    Buenker, Robert J.; Alekseyev, Aleksey B.; Liebermann, Heinz-Peter; Lingott, Rainer; Hirsch, Gerhard

    1998-03-01

    Computational strategies for the treatment of relativistic effects including spin-orbit coupling at a highly correlated level are compared for a number of heavy atoms: indium, iodine, thallium, and astatine. Initial tests with perturbation theory emphasize the importance of high-energy singly excited configurations which possess large spin-orbit matrix elements with the ground state. A contracted basis consisting of L-S CI eigenfunctions (LSC-SO-CI) is found to give an accurate representation of both spin-perturbed 2Po components as long as key np→pi* singly excited configurations are included. Comparison is made with a more extensive treatment in which all selected configurations of various L-S symmetries form the basis for the multireference-spin-orbit-configuration interaction (MR-SO-CI). Good agreement is obtained with experimental SO splittings for the In, I, and At atoms at a variety of levels of treatment, indicating that the L-S contracted SO-CI approach can be implemented quite effectively with relativistic effective core potentials (RECPs) for both very electronegative atoms and also for lighter electropositive elements up through the fifth row of the periodic table. The thallium atom SO splitting is more difficult to obtain accurately because of greater differences between its valence p1/2 and p3/2 spinors than in the other cases studied, but good results are also possible with the contracted SO-CI approach in this instance, provided proper care is given to the inclusion of key singly excited L-S states. The relationship between all-electron two-component SO-CI treatments and those employing RECPs is also analyzed, and it is concluded that triply excited configurations relative to the 2Po ground state are far less important than previously reported.

  8. PSOLV: a code for calculating the potentials and densities in MFTF-B

    SciTech Connect

    Colborn, J.A.

    1983-08-17

    Code PSOLV solves for potential and densities at the cardinal points of MFTF-B. The code is equipped to handle both the throttle-coil and the axicell geometries. For the throttle-coil case, the potential at point MXO is input, while the potentials and densities at points MAI, b, and A are calculated. For the axicell case, the code must additionally solve for the potentials and densities at points X and MXO. PSOLV is intended primarily for use as a subroutine in TREQ, a code being developed by Rensink that calculates the densities and potentials at the cardinal points of MFTF-B as a function of time. TREQ is to be used for modeling start-up behavior.

  9. 17 CFR 230.459 - Calculation of effective date.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 17 Commodity and Securities Exchanges 2 2010-04-01 2010-04-01 false Calculation of effective date. 230.459 Section 230.459 Commodity and Securities Exchanges SECURITIES AND EXCHANGE COMMISSION GENERAL RULES AND REGULATIONS, SECURITIES ACT OF 1933 Filings; Fees; Effective Date § 230.459 Calculation...

  10. Effect of grid system on finite element calculation

    NASA Technical Reports Server (NTRS)

    Lee, K. D.; Yen, S. M.

    1980-01-01

    Detailed parametric studies of the effect of grid system on finite element calculation for potential flows were made. These studies led to the formulation of a design criteria for optimum mesh system and the development of two methods to generate the optimum mesh system. The guidelines for optimum mesh system are: (1) the mesh structure should be regular; (2) the element should be as regular and equilateral as possible; (3) the distribution of size of element should be consistent with that of flow variables to insure maximum uniformity in error distribution; (4) for non-Dirichlet boundary conditions, smaller boundary elements or higher order interpolation functions should be used; and (5) the mesh should accommodate the boundary geometry as accurately as possible. The results of the parametric studies are presented.

  11. Calculation of the polarization potential for e-N2 collisions

    NASA Technical Reports Server (NTRS)

    Onda, K.; Temkin, A.

    1983-01-01

    A polarization potential V(pol) for e-N2 collisions is calculated by the generalization of the static part of the method of polarized orbitals to molecular targets. Partial differential equations (PDE) are derived for polarized orbitals, which are functions of the distance (r) from the molecular center and angle (theta) from the molecular axis. The equations are solved with the use of the noniterative PDE technique. From the polarized orbitals a polarization potential can be constructed whose r and theta dependence is found to be significantly different from the well-known phenomenological one. The two potentials are further compared by carrying out limited hybrid-theory scattering calculations. Only those scattering results based on the calculated V(pol) are in satisfactory accord with experiment.

  12. Potential energy curves of Li+2 from all-electron EA-EOM-CCSD calculations

    NASA Astrophysics Data System (ADS)

    Musiał, Monika; Medrek, Magdalena; Kucharski, Stanisław A.

    2015-10-01

    The electron attachment (EA) equation-of-motion coupled-cluster theory provides description of the states obtained by the attachment of an electron to the reference system. If the reference is assumed to be a doubly ionised cation, then the EA results relate to the singly ionised ion. In the current work, the above scheme is applied to the calculations of the potential energy curves (PECs) of the Li+2 cation adopting the doubly ionised Li2 +2 structure as the reference system. The advantage of such computational strategy relies on the fact that the closed-shell Li2 +2 reference dissociates into closed-shell fragments (Li2 +2 ⇒ Li+ + Li+), hence the RHF (restricted Hartree-Fock) function can be used as the reference in the whole range of interatomic distances. This scheme offers the first principle method without any model or effective potential parameters for the description of the bond-breaking processes. In this study, the PECs and selected spectroscopic constants for 18 electronic states of the Li+2 ion were computed and compared with experimental and other theoretical results. †In honour of Professor Sourav Pal on the occasion of an anniversary in his private and scientific life.

  13. Exact calculation of a microscopic nucleon spin-orbit potential: Reexamination of Brieva-Rook localization

    NASA Astrophysics Data System (ADS)

    Haider, W.; Rafi, Syed; Rook, J. R.; Gambhir, Y. K.

    2016-05-01

    Brieva-Rook approximations for calculating the equivalent local microscopic nucleon-nucleus spin-orbit potential has been examined in the energy region of 65 calculating both the direct and the exchange parts of the spin-orbit potential. It has been shown that the series expansion used earlier overestimates both the real and the imaginary parts by about 50 % . Our results show that the exchange contribution to the total spin-orbit potential at low energies is only 15 % (much smaller than earlier estimates) and becomes negligible around 200-MeV nucleon incident energy. Predictions of the new spin-orbit potential with minor scaling has been found to be in fair agreement with p -208Pb scattering observables from 65 to 500 MeV.

  14. Comparisons of measured and calculated potential magnetic fields. [in solar corona

    NASA Technical Reports Server (NTRS)

    Hagyard, M. J.; Teuber, D.

    1978-01-01

    Photospheric line-of-sight and transverse-magnetic-field data obtained, with a vector magnetograph system for an isolated sunspot are described. A study of the linear polarization patterns and of the calculated transverse field lines indicates that the magnetic field of the region is very nearly potential. The H-alpha fibril structures of this region as seen in high-resolution photographs corroborate this conclusion. Consequently, a potential-field calculation is described using the measured line-of-sight fields together with assumed Neumann boundary conditions; both are necessary and sufficient for a unique solution. The computed transverse fields are then compared with the measured transverse fields to verify the potential-field model and assumed boundary values. The implications of these comparisons for the validity of magnetic-field extrapolations using potential theory are discussed.

  15. A finite volume method for calculating transonic potential flow around wings from the pressure minimum integral

    NASA Technical Reports Server (NTRS)

    Eberle, A.

    1978-01-01

    Analysis of the pressure minimum integral in the calculation of three-dimensional potential flow around wings makes it possible to use non-rectangular mesh networks for distributing the three-dimensional potential into discrete points. The method is comparatively easily expanded to the treatment of realistic airplane configurations. Shock-pressure affected pressure distributions on any wings are determined with accuracy using this method.

  16. Self-consistent calculation of hyperfine fields and adiabatic potential of impurities in iron

    NASA Astrophysics Data System (ADS)

    Kanamori, Junjiro; Akai, Hisazumi; Akai, Masako

    1984-01-01

    Hyperfine fields of impurities of the atomic number Z=1 56 at the substitutional site and those of light impurities of Z=1 9 at the interstitial sites in ferromagnetic iron are calculated by the KKR method adapted to the system containing a single impurity atom. The potential of the impurity atom is determined self-consistently by use of the local spin density functional formalism. The results for nonmagnetic sp valence impurities agree with those of the previous nonself-consistent calculation by Katayama-Yoshida, Terakura and Kanamori except for a few cases, confirming their theory of the systematic variation of hyperfine fields. The calculation for magnetic impurities of transition elements is presented for the first time in this paper. The calculations mentioned so far assume that impurities are situated at the center of each site. For the purpose of discussing the stability of the impurity positions, the change of the adiabatic potential due to displacements from the center is calculated by carrying out similar self-consistent calculations for off-center impurity positions. It is concluded that positive muon and some light impurities including boron will be displaced from the center when trapped in a vacancy.

  17. Calculating solar photovoltaic potential on residential rooftops in Kailua Kona, Hawaii

    NASA Astrophysics Data System (ADS)

    Carl, Caroline

    As carbon based fossil fuels become increasingly scarce, renewable energy sources are coming to the forefront of policy discussions around the globe. As a result, the State of Hawaii has implemented aggressive goals to achieve energy independence by 2030. Renewable electricity generation using solar photovoltaic technologies plays an important role in these efforts. This study utilizes geographic information systems (GIS) and Light Detection and Ranging (LiDAR) data with statistical analysis to identify how much solar photovoltaic potential exists for residential rooftops in the town of Kailua Kona on Hawaii Island. This study helps to quantify the magnitude of possible solar photovoltaic (PV) potential for Solar World SW260 monocrystalline panels on residential rooftops within the study area. Three main areas were addressed in the execution of this research: (1) modeling solar radiation, (2) estimating available rooftop area, and (3) calculating PV potential from incoming solar radiation. High resolution LiDAR data and Esri's solar modeling tools and were utilized to calculate incoming solar radiation on a sample set of digitized rooftops. Photovoltaic potential for the sample set was then calculated with the equations developed by Suri et al. (2005). Sample set rooftops were analyzed using a statistical model to identify the correlation between rooftop area and lot size. Least squares multiple linear regression analysis was performed to identify the influence of slope, elevation, rooftop area, and lot size on the modeled PV potential values. The equations built from these statistical analyses of the sample set were applied to the entire study region to calculate total rooftop area and PV potential. The total study area statistical analysis findings estimate photovoltaic electric energy generation potential for rooftops is approximately 190,000,000 kWh annually. This is approximately 17 percent of the total electricity the utility provided to the entire island in

  18. Calculation of equation of state of QCD at zero temperature and finite chemical potential

    NASA Astrophysics Data System (ADS)

    Jiang, Yu; Li, Ning; Sun, Wei-Min; Zong, Hong-Shi

    2010-09-01

    In this paper we calculate the equation of state (EOS) of QCD at zero temperature and finite chemical potential by using several models of quark propagators including the Dyson-Schwinger equations (DSEs) model, the hard-dense-loop (HDL) approximation and the quasi-particle model. The results are analyzed and compared with the known results in the literature.

  19. Computer programs for calculating two-dimensional potential flow in and about propulsion system inlets

    NASA Technical Reports Server (NTRS)

    Hawk, J. D.; Stockman, N. O.; Farrell, C. A., Jr.

    1978-01-01

    Incompressible potential flow calculations are presented that were corrected for compressibility in two-dimensional inlets at arbitrary operating conditions. Included are a statement of the problem to be solved, a description of each of the computer programs, and sufficient documentation, including a test case, to enable a user to run the program.

  20. The Inversion Potential of Ammonia: An Intrinsic Reaction Coordinate Calculation for Student Investigation

    ERIC Educational Resources Information Center

    Halpern, Arthur M.; Ramachandran, B. R.; Glendening, Eric D.

    2007-01-01

    A report is presented to describe how students can be empowered to construct the full, double minimum inversion potential for ammonia by performing intrinsic reaction coordinate calculations. This work can be associated with the third year physical chemistry lecture laboratory or an upper level course in computational chemistry.

  1. Improved computer programs for calculating potential flow in propulsion system inlets

    NASA Technical Reports Server (NTRS)

    Stockman, N. O.; Farrell, C. A., Jr.

    1977-01-01

    Computer programs to calculate the incompressible potential flow corrected for compressibility in axisymmetric inlets at arbitrary operating conditions are presented. Included are a statement of the problem to be solved, a description of each of the programs and sufficient documentation, including a test case, to enable a user to run the programs.

  2. A web-based calculator for estimating the profit potential of grain segregation by protein concentration

    Technology Transfer Automated Retrieval System (TEKTRAN)

    By ignoring spatial variability in grain quality, conventional harvesting systems may increase the likelihood that growers will not capture price premiums for high quality grain found within fields. The Grain Segregation Profit Calculator was developed to demonstrate the profit potential of segregat...

  3. Computer programs for calculating two-dimensional potential flow through deflected nozzles

    NASA Technical Reports Server (NTRS)

    Hawk, J. D.; Stockman, N. O.

    1979-01-01

    Computer programs to calculate the incompressible potential flow, corrected for compressibility, in two-dimensional nozzles at arbitrary operating conditions are presented. A statement of the problem to be solved, a description of each of the computer programs, and sufficient documentation, including a test case, to enable a user to run the program are included.

  4. A consistent calculation of the chemical potential for dense simple fluids.

    PubMed

    Bomont, Jean-Marc

    2006-05-28

    A general method to calculate the excess chemical potential betamuex, that is based on the Kirkwood coupling parameter's dependence of the correlation functions, is presented. The expression for the one particle bridge function B(1)r is derived for simple fluids with spherical interactions. Only the knowledge of the bridge function B(2)r is required. The accuracy of our approach is illustrated for a dense hard sphere fluid. As far as B(2)r is considered as exact, B(1)r is found to be, at high densities, the normalized bridge function -B(2)rB(2)(r=0). This expression ensures a consistent calculation of the excess chemical potential by satisfying implicitly the Gibbs-Duhem constraint. Only the pressure-consistency condition is necessary to calculate the structural and thermodynamic properties of the fluid. PMID:16774388

  5. Carbon dioxide hydrate phase equilibrium and cage occupancy calculations using ab initio intermolecular potentials.

    PubMed

    Velaga, Srinath C; Anderson, Brian J

    2014-01-16

    Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest–host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the “VAS” model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site–site ab initio intermolecular potentials) as Δμ(w)(0) = 1206 ± 2 J/mol and ΔH(w)(0) = 1260 ± 12 J/mol. With these reference parameters and the VAS model, pure CO2 hydrate equilibrium pressure was predicted with an average absolute deviation of less than 3.2% from the experimental data. Predictions of the small cage occupancy ranged from 32 to 51%, and the large cage is more than 98% occupied. The intermolecular potentials were also tested by calculating the pure CO2 density and diffusion of CO2 in water using molecular dynamics simulations. PMID:24328234

  6. The Effect of Calculator Use on College Students' Mathematical Performance

    ERIC Educational Resources Information Center

    Boyle, Robert W.; Farreras, Ingrid G.

    2015-01-01

    This experiment tested the effect that calculator use had on 200 randomly assigned college students' mathematical performance. The purposes of the current experiment were twofold: to measure the level of mathematical preparation of current college students, and to test whether calculators improve mathematical performance in such students as it…

  7. A study of potential numerical pitfalls in GPU-based Monte Carlo dose calculation

    NASA Astrophysics Data System (ADS)

    Magnoux, Vincent; Ozell, Benoît; Bonenfant, Éric; Després, Philippe

    2015-07-01

    The purpose of this study was to evaluate the impact of numerical errors caused by the floating point representation of real numbers in a GPU-based Monte Carlo code used for dose calculation in radiation oncology, and to identify situations where this type of error arises. The program used as a benchmark was bGPUMCD. Three tests were performed on the code, which was divided into three functional components: energy accumulation, particle tracking and physical interactions. First, the impact of single-precision calculations was assessed for each functional component. Second, a GPU-specific compilation option that reduces execution time as well as precision was examined. Third, a specific function used for tracking and potentially more sensitive to precision errors was tested by comparing it to a very high-precision implementation. Numerical errors were found in two components of the program. Because of the energy accumulation process, a few voxels surrounding a radiation source end up with a lower computed dose than they should. The tracking system contained a series of operations that abnormally amplify rounding errors in some situations. This resulted in some rare instances (less than 0.1%) of computed distances that are exceedingly far from what they should have been. Most errors detected had no significant effects on the result of a simulation due to its random nature, either because they cancel each other out or because they only affect a small fraction of particles. The results of this work can be extended to other types of GPU-based programs and be used as guidelines to avoid numerical errors on the GPU computing platform.

  8. Calculation of transient potential rise on the wind turbine struck by lightning.

    PubMed

    Xiaoqing, Zhang

    2014-01-01

    A circuit model is proposed in this paper for calculating the transient potential rise on the wind turbine struck by lightning. The model integrates the blade, sliding contact site, and tower and grounding system of the wind turbine into an equivalent circuit. The lightning current path from the attachment point to the ground can be fully described by the equivalent circuit. The transient potential responses are obtained in the different positions on the wind turbine by solving the circuit equations. In order to check the validity of the model, the laboratory measurement is made with a reduced-scale wind turbine. The measured potential waveform is compared with the calculated one and a better agreement is shown between them. The practical applicability of the model is also examined by a numerical example of a 2 MW Chinese-built wind turbine. PMID:25254231

  9. Calculation of Transient Potential Rise on the Wind Turbine Struck by Lightning

    PubMed Central

    Xiaoqing, Zhang

    2014-01-01

    A circuit model is proposed in this paper for calculating the transient potential rise on the wind turbine struck by lightning. The model integrates the blade, sliding contact site, and tower and grounding system of the wind turbine into an equivalent circuit. The lightning current path from the attachment point to the ground can be fully described by the equivalent circuit. The transient potential responses are obtained in the different positions on the wind turbine by solving the circuit equations. In order to check the validity of the model, the laboratory measurement is made with a reduced-scale wind turbine. The measured potential waveform is compared with the calculated one and a better agreement is shown between them. The practical applicability of the model is also examined by a numerical example of a 2 MW Chinese-built wind turbine. PMID:25254231

  10. Full dimension Rb2He ground triplet potential energy surface and quantum scattering calculations.

    PubMed

    Guillon, Grégoire; Viel, Alexandra; Launay, Jean-Michel

    2012-05-01

    We have developed a three-dimensional potential energy surface for the lowest triplet state of the Rb(2)He complex. A global analytic fit is provided as in the supplementary material [see supplementary material at http://dx.doi.org/10.1063/1.4709433 for the corresponding Fortran code]. This surface is used to perform quantum scattering calculations of (4)He and (3)He colliding with (87)Rb(2) in the partial wave J = 0 at low and ultralow energies. For the heavier helium isotope, the computed vibrational relaxation probabilities show a broad and strong shape resonance for a collisional energy of 0.15 K and a narrow Feshbach resonance at about 17 K for all initial Rb(2) vibrational states studied. The broad resonance corresponds to an efficient relaxation mechanism that does not occur when (3)He is the colliding partner. The Feshbach resonance observed at higher collisional energy is robust with respect to the isotopic substitution. However, its effect on the vibrational relaxation mechanism is faint for both isotopes. PMID:22583230

  11. Full dimension Rb2He ground triplet potential energy surface and quantum scattering calculations

    NASA Astrophysics Data System (ADS)

    Guillon, Grégoire; Viel, Alexandra; Launay, Jean-Michel

    2012-05-01

    We have developed a three-dimensional potential energy surface for the lowest triplet state of the Rb2He complex. A global analytic fit is provided as in the supplementary material [see supplementary material at http://dx.doi.org/10.1063/1.4709433E-JCPSA6-136-034218 for the corresponding Fortran code]. This surface is used to perform quantum scattering calculations of 4He and 3He colliding with 87Rb2 in the partial wave J = 0 at low and ultralow energies. For the heavier helium isotope, the computed vibrational relaxation probabilities show a broad and strong shape resonance for a collisional energy of 0.15 K and a narrow Feshbach resonance at about 17 K for all initial Rb2 vibrational states studied. The broad resonance corresponds to an efficient relaxation mechanism that does not occur when 3He is the colliding partner. The Feshbach resonance observed at higher collisional energy is robust with respect to the isotopic substitution. However, its effect on the vibrational relaxation mechanism is faint for both isotopes.

  12. An exploratory study of a finite difference method for calculating unsteady transonic potential flow

    NASA Technical Reports Server (NTRS)

    Bennett, R. M.; Bland, S. R.

    1979-01-01

    A method for calculating transonic flow over steady and oscillating airfoils was developed by Isogai. The full potential equation is solved with a semi-implicit, time-marching, finite difference technique. Steady flow solutions are obtained from time asymptotic solutions for a steady airfoil. Corresponding oscillatory solutions are obtained by initiating an oscillation and marching in time for several cycles until a converged periodic solution is achieved. The method is described in general terms and results for the case of an airfoil with an oscillating flap are presented for Mach numbers 0.500 and 0.875. Although satisfactory results are obtained for some reduced frequencies, it is found that the numerical technique generates spurious oscillations in the indicial response functions and in the variation of the aerodynamic coefficients with reduced frequency. These oscillations are examined with a dynamic data reduction method to evaluate their effects and trends with reduced frequency and Mach number. Further development of the numerical method is needed to eliminate these oscillations.

  13. Calculation procedures for potential and viscous flow solutions for engine inlets

    NASA Technical Reports Server (NTRS)

    Albers, J. A.; Stockman, N. O.

    1973-01-01

    The method and basic elements of computer solutions for both potential flow and viscous flow calculations for engine inlets are described. The procedure is applicable to subsonic conventional (CTOL), short-haul (STOL), and vertical takeoff (VTOL) aircraft engine nacelles operating in a compressible viscous flow. The calculated results compare well with measured surface pressure distributions for a number of model inlets. The paper discusses the uses of the program in both the design and analysis of engine inlets, with several examples given for VTOL lift fans, acoustic splitters, and for STOL engine nacelles. Several test support applications are also given.

  14. Exploring the MRCI method for calculating interaction energies: application to the HeNe potential curve

    NASA Astrophysics Data System (ADS)

    van de Bovenkamp, J.; van Mourik, T.; van Duijneveldt, F. B.

    A multi-reference configuration interaction (MRCI) method is described, which is devised for the calculation of interaction energies of van der Waals complexes and applied to calculating the HeNe potential energy curve. The MRCI calculations make use of a generalized Poplecorrection in order to account for the lack of size consistency. The orbital space is partitioned into three subspaces: the first active space (AS1), which contains the strongly occupied orbitals; the second active space (AS2), which contains the main intra-correlating orbitals; and the external space (ES). It is shown that, to keep the error below 0.2K in the excitation scheme and the active orbital space it is sufficient to include only sigma-orbitals in AS2 and to use an excitation scheme (labelled Qq-MRCI) that encompasses only up to quadruply excited configurations. The final active orbital space (AS2) turned out to be 2s(He), 2psigma(He), 3s(Ne), 3psigma(Ne) and 3dsigma(Ne). Other MRCI variants, in which most or all quadruply excited configurations were deleted from the CI expansion (Qt- and Tt-MRCI), were found to be inadequate. Using the Qq-MRCI scheme together with a 197-orbital 'interaction optimized' basis set (IO197), the MRCI interaction energy at R = 5.7 a0 was calculated to be-21.12K. The corresponding values at the MP4 and CCSD(T) levels of theory are-20.06K and-20.99K, respectively, indicating that the MP4 method is inappropriate for highly accurate calculations on this system. Fitting the calculated data using a generalized Morse function, including an additional C6/R6 term to account for a correct long-range behaviour of the potential, the MRCI well depth was calculated to be-21.16K at Req = 5.73 a0. The MRCI and CCSD(T) potentials have the same quality and are found to be in good agreement with the HartreeFock dispersion (HFD-B) potential of Keil, M., Danielson, L. J., and Dunlop, P. J., 1991, J. Chem. Phys., 94, 296. It is concluded that, for basis IO197, the CCSD(T) method is

  15. A refined quartic potential energy surface and large scale vibrational calculations for S0 thiophosgene.

    PubMed

    Rashev, Svetoslav; Moule, David C

    2015-04-01

    In this work we present a full 6D quartic potential energy surface (PES) for S0 thiophosgene in curvilinear symmetrized bond-angle coordinates. The PES was refined starting from an ab initio field derived from acc-pVTZ basis set with CCSD(T) corrections for electron correlation. In the present calculations we used our variational method that was recently tested on formaldehyde and some of its isotopomers, along with additional improvements. The lower experimentally known vibrational levels for 35Cl2CS were reproduced quite well in the calculations, which can be regarded as a test for the feasibility of the obtained quartic PES. PMID:25615683

  16. A general method for constructing multidimensional molecular potential energy surfaces from {ital ab} {ital initio} calculations

    SciTech Connect

    Ho, T.; Rabitz, H.

    1996-02-01

    A general interpolation method for constructing smooth molecular potential energy surfaces (PES{close_quote}s) from {ital ab} {ital initio} data are proposed within the framework of the reproducing kernel Hilbert space and the inverse problem theory. The general expression for an {ital a} {ital posteriori} error bound of the constructed PES is derived. It is shown that the method yields globally smooth potential energy surfaces that are continuous and possess derivatives up to second order or higher. Moreover, the method is amenable to correct symmetry properties and asymptotic behavior of the molecular system. Finally, the method is generic and can be easily extended from low dimensional problems involving two and three atoms to high dimensional problems involving four or more atoms. Basic properties of the method are illustrated by the construction of a one-dimensional potential energy curve of the He{endash}He van der Waals dimer using the exact quantum Monte Carlo calculations of Anderson {ital et} {ital al}. [J. Chem. Phys. {bold 99}, 345 (1993)], a two-dimensional potential energy surface of the HeCO van der Waals molecule using recent {ital ab} {ital initio} calculations by Tao {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 8680 (1994)], and a three-dimensional potential energy surface of the H{sup +}{sub 3} molecular ion using highly accurate {ital ab} {ital initio} calculations of R{umlt o}hse {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 2231 (1994)]. In the first two cases the constructed potentials clearly exhibit the correct asymptotic forms, while in the last case the constructed potential energy surface is in excellent agreement with that constructed by R{umlt o}hse {ital et} {ital al}. using a low order polynomial fitting procedure. {copyright} {ital 1996 American Institute of Physics.}

  17. A modified W-W interatomic potential based on ab initio calculations

    NASA Astrophysics Data System (ADS)

    Wang, J.; Zhou, Y. L.; Li, M.; Hou, Q.

    2014-01-01

    In this paper we have developed a Finnis-Sinclair-type interatomic potential for W-W interactions that is based on ab initio calculations. The modified potential is able to reproduce the correct formation energies of self-interstitial atom (SIA) defects in tungsten, offering a significant improvement over the Ackland-Thetford tungsten potential. Using the modified potential, the thermal expansion is calculated in a temperature range from 0 to 3500 K. The results are in reasonable agreement with the experimental data, thus overcoming the shortcomings of the negative thermal expansion using the Derlet-Nguyen-Manh-Dudarev tungsten potential. The W-W potential presented here is also applied to study in detail the diffusion of SIAs in tungsten. We reveal that the initial SIA initiates a sequence of tungsten atom displacements and replacements in the <1 1 1> direction. An Arrhenius fit to the diffusion data at temperatures below 550 K indicates a migration energy of 0.022 eV, which is in reasonable agreement with the experimental data.

  18. Comparison of molecular dynamics methods and interatomic potentials for calculating the thermal conductivity of silicon

    NASA Astrophysics Data System (ADS)

    Howell, P. C.

    2012-12-01

    We compare the molecular dynamics Green-Kubo and direct methods for calculating thermal conductivity κ, using as a test case crystalline silicon at temperatures T in the range 500-1000 K (classical regime). We pay careful attention to the convergence with respect to simulation size and duration and to the procedures used to fit the simulation data. We show that in the Green-Kubo method the heat current autocorrelation function is characterized by three decay processes, of which the slowest lasts several tens of picoseconds so that convergence requires several tens of nanoseconds of data. Using the Stillinger-Weber potential we find excellent agreement between the two methods. We also use the direct method to calculate κ(T) for the Tersoff potential and find that the magnitude and the temperature-dependence are different for the two potentials and that neither potential agrees with experimental data. We argue that this implies that using the Stillinger-Weber or Tersoff potentials to predict trends in kappa as some system parameter is varied may yield results which are specific to the potential but not intrinsic to Si.

  19. Comparison of molecular dynamics methods and interatomic potentials for calculating the thermal conductivity of silicon.

    PubMed

    Howell, P C

    2012-12-14

    We compare the molecular dynamics Green-Kubo and direct methods for calculating thermal conductivity κ, using as a test case crystalline silicon at temperatures T in the range 500-1000 K (classical regime). We pay careful attention to the convergence with respect to simulation size and duration and to the procedures used to fit the simulation data. We show that in the Green-Kubo method the heat current autocorrelation function is characterized by three decay processes, of which the slowest lasts several tens of picoseconds so that convergence requires several tens of nanoseconds of data. Using the Stillinger-Weber potential we find excellent agreement between the two methods. We also use the direct method to calculate κ(T) for the Tersoff potential and find that the magnitude and the temperature-dependence are different for the two potentials and that neither potential agrees with experimental data. We argue that this implies that using the Stillinger-Weber or Tersoff potentials to predict trends in kappa as some system parameter is varied may yield results which are specific to the potential but not intrinsic to Si. PMID:23248991

  20. Complex-scaling of screened Coulomb potentials for resonance calculations utilizing the modified Bessel functions

    NASA Astrophysics Data System (ADS)

    Jiao, Li-Guang; Ho, Yew Kam

    2014-05-01

    The screened Coulomb potential (SCP) has been extensively used in atomic physics, nuclear physics, quantum chemistry and plasma physics. However, an accurate calculation for atomic resonances under SCP is still a challenging task for various methods. Within the complex-scaling computational scheme, we have developed a method utilizing the modified Bessel functions to calculate doubly-excited resonances in two-electron atomic systems with configuration interaction-type basis. To test the validity of our method, we have calculated S- and P-wave resonance states of the helium atom with various screening strengths, and have found good agreement with earlier calculations using different methods. Our present method can be applied to calculate high-lying resonances associated with high excitation thresholds of the He+ ion, and with high-angular-momentum states. The derivation and calculation details of our present investigation together with new results of high-angular-momentum states will be presented at the meeting. Supported by NSC of Taiwan.

  1. Calculating excess chemical potentials using dynamic simulations in the fourth dimension

    SciTech Connect

    Pomes, R.; Eisenmesser, E.; Post, C.B.; Roux, B.

    1999-08-01

    A general method for computing excess chemical potentials is presented. The excess chemical potential of a solute or ligand molecule is estimated from the potential of mean-force (PMF) calculated along a nonphysical fourth spatial dimension, {ital w}, into which the molecule is gradually inserted or from which it is gradually abstracted. According to this {open_quotes}4D-PMF{close_quotes} (four dimensional) scheme, the free energy difference between two limiting states defines the excess chemical potential: At w={plus_minus}{infinity}, the molecule is not interacting with the rest of the system, whereas at w=0, it is fully interacting. Use of a fourth dimension avoids the numerical instability in the equations of motion encountered upon growing or shrinking solute atoms in conventional free energy perturbation simulations performed in three dimensions, while benefiting from the efficient sampling of configurational space afforded by PMF calculations. The applicability and usefulness of the method are illustrated with calculations of the hydration free energy of simple Lennard-Jones (LJ) solutes, a water molecule, and camphor, using molecular dynamics simulations and umbrella sampling. Physical insight into the nature of the PMF profiles is gained from a continuum treatment of short- and long-range interactions. The short-range barrier for dissolution of a LJ solute in the added dimension provides an apparent surface tension of the solute. An approximation to the long-range behavior of the PMF profiles is made in terms of a continuum treatment of LJ dispersion and electrostatic interactions. Such an analysis saves the need for configurational sampling in the long-range limit of the fourth dimension. The 4D-PMF method of calculating excess chemical potentials should be useful for neutral solute and ligand molecules with a wide range of sizes, shapes, and polarities. {copyright} {ital 1999 American Institute of Physics.}

  2. Ionization potential of {sup 9}Be calculated including nuclear motion and relativistic corrections

    SciTech Connect

    Stanke, Monika; Kedziera, Dariusz; Bubin, Sergiy; Adamowicz, Ludwik

    2007-05-15

    Variational calculations employing explicitly correlated Gaussian functions have been performed for the ground states of {sup 9}Be and {sup 9}Be{sup +} including the nuclear motion [i.e., without assuming the Born-Oppenheimer (BO) approximation]. An approach based on the analytical energy gradient calculated with respect to the Gaussian exponential parameters was employed, leading to energies of the two systems noticeably improved over those found in the recent paper of Pachucki and Komasa [Phys. Rev. A 73, 052502 (2006)]. The non-BO wave functions were used to calculate the {alpha}{sup 2} relativistic corrections ({alpha}=e{sup 2}/({Dirac_h}/2{pi})c). With those corrections and the {alpha}{sup 3} and {alpha}{sup 4} corrections taken from Pachucki and Komasa, a new value of the ionization potential (IP) of {sup 9}Be was determined. It agrees very well with the most recent experimental IP.

  3. Classical calculation of the equilibrium constants for true bound dimers using complete potential energy surface

    SciTech Connect

    Buryak, Ilya; Vigasin, Andrey A.

    2015-12-21

    The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.

  4. Regularizing the molecular potential in electronic structure calculations. II. Many-body methods

    SciTech Connect

    Bischoff, Florian A.

    2014-11-14

    In Paper I of this series [F. A. Bischoff, “Regularizing the molecular potential in electronic structure calculations. I. SCF methods,” J. Chem. Phys. 141, 184105 (2014)] a regularized molecular Hamilton operator for electronic structure calculations was derived and its properties in SCF calculations were studied. The regularization was achieved using a correlation factor that models the electron-nuclear cusp. In the present study we extend the regularization to correlated methods, in particular the exact solution of the two-electron problem, as well as second-order many body perturbation theory. The nuclear and electronic correlation factors lead to computations with a smaller memory footprint because the singularities are removed from the working equations, which allows coarser grid resolution while maintaining the precision. Numerical examples are given.

  5. Classical calculation of the equilibrium constants for true bound dimers using complete potential energy surface

    NASA Astrophysics Data System (ADS)

    Buryak, Ilya; Vigasin, Andrey A.

    2015-12-01

    The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.

  6. Shear-deformation-potential constant of the conduction-band minima of Si: Pseudopotential calculations

    NASA Astrophysics Data System (ADS)

    Li, Ming-Fu; Gu, Zong-Quan; Wang, Jian-Qing

    1990-09-01

    We have calculated the value of the shear-deformation-potential constant Ξu of the conduction-band minima of Si and its temperature coefficient dΞu/dT. The value of Ξu is 9.0 eV for an ab initio pseudopotential calculation and 10.8 eV by the empirical-pseudopotential method (EPM), in good agreement with our experiment. The EPM calculations of the temperature dependence of Ξu yield the values of (dΞu/dT)||DW=-0.04 meV/K due to the Debye-Waller contribution, and (dΞu/dT)||TE=-0.04 meV/K for thermal expansion. We suspect and suggest that the existing experimental value of dΞu/dT~=+3 meV/K is unreliable due to large experimental uncertainty.

  7. Calculation of high-order virial coefficients for the square-well potential.

    PubMed

    Do, Hainam; Feng, Chao; Schultz, Andrew J; Kofke, David A; Wheatley, Richard J

    2016-07-01

    Accurate virial coefficients B_{N}(λ,ɛ) (where ɛ is the well depth) for the three-dimensional square-well and square-step potentials are calculated for orders N=5-9 and well widths λ=1.1-2.0 using a very fast recursive method. The efficiency of the algorithm is enhanced significantly by exploiting permutation symmetry and by storing integrands for reuse during the calculation. For N=9 the storage requirements become sufficiently large that a parallel algorithm is developed. The methodology is general and is applicable to other discrete potentials. The computed coefficients are precise even near the critical temperature, and thus open up possibilities for analysis of criticality of the system, which is currently not accessible by any other means. PMID:27575230

  8. Microscopic calculation of {alpha}-decay half-lives with a deformed potential

    SciTech Connect

    Ni Dongdong; Ren Zhongzhou

    2009-11-15

    A new version of the generalized density-dependent cluster model is presented to describe an {alpha} particle tunneling through a deformed potential barrier. The microscopic deformed potential is numerically constructed in the double-folding model by the multipole expansion method. The decay width is computed using the coupled-channel Schroedinger equation with outgoing wave boundary conditions. We perform a systematic calculation on {alpha}-decay half-lives of even-even nuclei ranging from Z=52 to Z=104, including 65 well-deformed ones. The calculated {alpha}-decay half-lives are found to be in good agreement with the experimental values. There also exists good agreement with the available experimental branching ratios for well-deformed systems.

  9. The ground-state potential energy curve of the radium dimer from relativistic coupled cluster calculations

    NASA Astrophysics Data System (ADS)

    Teodoro, Tiago Quevedo; Haiduke, Roberto Luiz Andrade; Dammalapati, Umakanth; Knoop, Steven; Visscher, Lucas

    2015-08-01

    The potential energy curve for the ground-state of radium dimer (Ra2) is provided by means of atomic and molecular relativistic coupled cluster calculations. The short-range part of this curve is defined by an equilibrium bond length of 5.324 Å, a dissociation energy of 897 cm-1, and a harmonic vibrational frequency of 20.5 cm-1. The asymptotic behavior at large interatomic distances is characterized by the van der Waals coefficients C6 = 5.090 × 103, C8 = 6.978 × 105, and C10 = 8.786 × 107 atomic units. The two regions are matched in an analytical potential to provide a convenient representation for use in further calculations, for instance, to model cold collisions between radium atoms. This might become relevant in future experiments on ultracold, optically trapped, radioactive radium atoms that are used to search for a permanent electric dipole moment.

  10. Calculation of high-order virial coefficients for the square-well potential

    NASA Astrophysics Data System (ADS)

    Do, Hainam; Feng, Chao; Schultz, Andrew J.; Kofke, David A.; Wheatley, Richard J.

    2016-07-01

    Accurate virial coefficients BN(λ ,ɛ ) (where ɛ is the well depth) for the three-dimensional square-well and square-step potentials are calculated for orders N = 5 - 9 and well widths λ =1.1 -2.0 using a very fast recursive method. The efficiency of the algorithm is enhanced significantly by exploiting permutation symmetry and by storing integrands for reuse during the calculation. For N = 9 the storage requirements become sufficiently large that a parallel algorithm is developed. The methodology is general and is applicable to other discrete potentials. The computed coefficients are precise even near the critical temperature, and thus open up possibilities for analysis of criticality of the system, which is currently not accessible by any other means.

  11. Multireference configuration interaction calculations of the first six ionization potentials of the uranium atom

    SciTech Connect

    Bross, David H.; Parmar, Payal; Peterson, Kirk A.

    2015-11-14

    The first 6 ionization potentials (IPs) of the uranium atom have been calculated using multireference configuration interaction (MRCI+Q) with extrapolations to the complete basis set limit using new all-electron correlation consistent basis sets. The latter was carried out with the third-order Douglas-Kroll-Hess Hamiltonian. Correlation down through the 5s5p5d electrons has been taken into account, as well as contributions to the IPs due to the Lamb shift. Spin-orbit coupling contributions calculated at the 4-component Kramers restricted configuration interaction level, as well as the Gaunt term computed at the Dirac-Hartree-Fock level, were added to the best scalar relativistic results. The final ionization potentials are expected to be accurate to at least 5 kcal/mol (0.2 eV) and thus more reliable than the current experimental values of IP{sub 3} through IP{sub 6}.

  12. Artificial Bee Colony Optimization of Capping Potentials for Hybrid Quantum Mechanical/Molecular Mechanical Calculations.

    PubMed

    Schiffmann, Christoph; Sebastiani, Daniel

    2011-05-10

    We present an algorithmic extension of a numerical optimization scheme for analytic capping potentials for use in mixed quantum-classical (quantum mechanical/molecular mechanical, QM/MM) ab initio calculations. Our goal is to minimize bond-cleavage-induced perturbations in the electronic structure, measured by means of a suitable penalty functional. The optimization algorithm-a variant of the artificial bee colony (ABC) algorithm, which relies on swarm intelligence-couples deterministic (downhill gradient) and stochastic elements to avoid local minimum trapping. The ABC algorithm outperforms the conventional downhill gradient approach, if the penalty hypersurface exhibits wiggles that prevent a straight minimization pathway. We characterize the optimized capping potentials by computing NMR chemical shifts. This approach will increase the accuracy of QM/MM calculations of complex biomolecules. PMID:26610125

  13. Phenomenological calculation of nuclear binding energy and density with Yukawa-potentials

    NASA Astrophysics Data System (ADS)

    Scheid, W.

    2016-01-01

    In this paper, we study a phenomenological collective model for the calculation of the nuclear density and ground state binding energy of nuclei. The proton density is assumed proportional to the nuclear density. The total binding energy of the nuclear matter consists of the binding energy of infinite nuclear matter, of two Yukawa-potentials, of the Coulomb-energy and of the symmetry-energy. The parameters of the Yukawa-potential are fitted with the Bethe-Weizsäcker (BW) mass formula. The resulting binding energies and nuclear densities agree quite satisfying with known nuclear values.

  14. Thermal conductivity of silicene calculated using an optimized Stillinger-Weber potential

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoliang; Xie, Han; Hu, Ming; Bao, Hua; Yue, Shengying; Qin, Guangzhao; Su, Gang

    2014-02-01

    Silicene, the silicon-based counterpart of graphene with a two-dimensional honeycomb lattice, has attracted tremendous interest both theoretically and experimentally due to its significant potential industrial applications. From the aspect of theoretical study, the widely used classical molecular dynamics simulation is an appropriate way to investigate the transport phenomena and mechanisms in nanostructures such as silicene. Unfortunately, no available interatomic potential can precisely characterize the unique features of silicene. Here, we optimized the Stillinger-Weber potential parameters specifically for a single-layer Si sheet, which can accurately reproduce the low buckling structure of silicene and the full phonon dispersion curves obtained from ab initio calculations. By performing equilibrium and nonequilibrium molecular dynamics simulations and anharmonic lattice dynamics calculations with the new potential, we reveal that the three methods consistently yield an extremely low thermal conductivity of silicene and a short phonon mean-free path, suggesting silicene as a potential candidate for high-efficiency thermoelectric materials. Moreover, by qualifying the relative contributions of lattice vibrations in different directions, we found that the longitudinal phonon modes dominate the thermal transport in silicene, which is fundamentally different from graphene, despite the similarity of their two-dimensional honeycomb lattices.

  15. Three-body calculations for the K ‑ pp system within potential models

    NASA Astrophysics Data System (ADS)

    Kezerashvili, R. Ya; Tsiklauri, S. M.; Filikhin, I.; Suslov, V. M.; Vlahovic, B.

    2016-06-01

    We present three-body nonrelativistic calculations within the framework of a potential model for the kaonic cluster K ‑ pp using two methods: the method of hyperspherical harmonics in the momentum representation and the method of Faddeev equations in configuration space. To perform numerical calculations, different NN and antikaon–nucleon interactions are applied. The results of the calculations for the ground-state energy for the K ‑ pp system obtained by both methods are in reasonable agreement. Although the ground-state energy is not sensitive to the pp interaction, it shows very strong dependence on the K ‑ p potential. We show that the dominant clustering of the {K}-{pp} system in the configuration Λ (1405) + p allows us to calculate the binding energy to good accuracy within a simple cluster approach for the differential Faddeev equations. The theoretical discrepancies in the binding energy and width for the K ‑ pp system related to the different pp and K ‑ p interactions are addressed.

  16. Calculations of {sup 8}He+p elastic cross sections using a microscopic optical potential

    SciTech Connect

    Lukyanov, V. K.; Zemlyanaya, E. V.; Lukyanov, K. V.; Kadrev, D. N.; Antonov, A. N.; Gaidarov, M. K.; Massen, S. E.

    2009-08-15

    An approach to calculate microscopic optical potential with the real part obtained by a folding procedure and with the imaginary part inherent in the high-energy approximation is applied to study the {sup 8}He+p elastic-scattering data at energies of tens of MeV/nucleon. The neutron and proton density distributions obtained in different models for {sup 8}He are used in the calculations of the differential cross sections. The role of the spin-orbit potential is studied. Comparison of the calculations with the available experimental data on the elastic-scattering differential cross sections at beam energies of 15.7, 26.25, 32, 66, and 73 MeV/nucleon is performed. The problem of the ambiguities of the depths of each component of the optical potential is considered by means of the imposed physical criterion related to the known behavior of the volume integrals as functions of the incident energy. It is shown also that the role of the surface absorption is rather important, in particular for the lowest incident energies (e.g., 15.7 and 26.25 MeV/nucleon)

  17. Evaluation of uncertainty in gravity wave potential energy calculations through GPS radio occultation measurements

    NASA Astrophysics Data System (ADS)

    Luna, D.; Alexander, P.; de la Torre, A.

    2013-09-01

    The application of the Global Positioning System (GPS) radio occultation (RO) method to the atmosphere enables the determination of height profiles of temperature, among other variables. From these measurements, gravity wave activity is usually quantified by calculating the potential energy through the integration of the ratio of perturbation and background temperatures between two given altitudes in each profile. The uncertainty in the estimation of wave activity depends on the systematic biases and random errors of the measured temperature, but also on additional factors like the selected vertical integration layer and the separation method between background and perturbation temperatures. In this study, the contributions of different parameters and variables to the uncertainty in the calculation of gravity wave potential energy in the lower stratosphere are investigated and quantified. In particular, a Monte Carlo method is used to evaluate the uncertainty that results from different GPS RO temperature error distributions. In addition, our analysis shows that RO data above 30 km height becomes dubious for gravity waves potential energy calculations.

  18. Medication calculation: the potential role of digital game-based learning in nurse education.

    PubMed

    Foss, Brynjar; Mordt Ba, Petter; Oftedal, Bjørg F; Løkken, Atle

    2013-12-01

    Medication dose calculation is one of several medication-related activities that are conducted by nurses daily. However, medication calculation skills appear to be an area of global concern, possibly because of low numeracy skills, test anxiety, low self-confidence, and low self-efficacy among student nurses. Various didactic strategies have been developed for student nurses who still lack basic mathematical competence. However, we suggest that the critical nature of these skills demands the investigation of alternative and/or supplementary didactic approaches to improve medication calculation skills and to reduce failure rates. Digital game-based learning is a possible solution because of the following reasons. First, mathematical drills may improve medication calculation skills. Second, games are known to be useful during nursing education. Finally, mathematical drill games appear to improve the attitudes of students toward mathematics. The aim of this article was to discuss common challenges of medication calculation skills in nurse education, and we highlight the potential role of digital game-based learning in this area. PMID:24107685

  19. Calculation of water drop trajectories to and about arbitrary three-dimensional lifting and nonlifting bodies in potential airflow

    NASA Technical Reports Server (NTRS)

    Norment, H. G.

    1985-01-01

    Subsonic, external flow about nonlifting bodies, lifting bodies or combinations of lifting and nonlifting bodies is calculated by a modified version of the Hess lifting code. Trajectory calculations can be performed for any atmospheric conditions and for all water drop sizes, from the smallest cloud droplet to large raindrops. Experimental water drop drag relations are used in the water drop equations of motion and effects of gravity settling are included. Inlet flow can be accommodated, and high Mach number compressibility effects are corrected for approximately. Seven codes are described: (1) a code used to debug and plot body surface description data; (2) a code that processes the body surface data to yield the potential flow field; (3) a code that computes flow velocities at arrays of points in space; (4) a code that computes water drop trajectories from an array of points in space; (5) a code that computes water drop trajectories and fluxes to arbitrary target points; (6) a code that computes water drop trajectories tangent to the body; and (7) a code that produces stereo pair plots which include both the body and trajectories. Accuracy of the calculations is discussed, and trajectory calculation results are compared with prior calculations and with experimental data.

  20. Bounces and the calculation of quantum tunneling effects

    NASA Astrophysics Data System (ADS)

    Liang, Jiu-Qing; Müller-Kirsten, H. J. W.

    1992-04-01

    The imaginary part of the energy of the metastable ground state for the inverted double-well potential is calculated by using the path-integral method. The tunneling process is dominated by bounces. It is shown that the evaluation of the determinant of the second variation of the action at the bounce can be avoided, and that the imaginary part of the energy results directly from characteristic properties of the bounce itself, namely, the antisymmetry of its first time derivative under time reversal. The imaginary part of the result is in exact agreement with that of the well-known WKB calculation of Bender and Wu.

  1. Electronic Structure Calculations of Inter-Ring Torsional Potentials of Regioregular Poly (3-METHYL Thiophene) Oligomers

    NASA Astrophysics Data System (ADS)

    Bhatta, Ram S.; Perry, David S.

    2010-06-01

    The inter-ring torsional potentials of poly (3-methyl thiophene) (P3MT) oligomers are investigated by means of electronic structure calculations. Single layer and ONIOM calculations were performed at B3LYP level with 6-31++G(d,p) basis on the partially optimized geometries of dimer, tetramer and hexamer of P3MT oligomers. Potential energy surfaces are computed as a function of the multiple inter-ring torsional angles involved. The following conclusions are reached: (i) A mixture of cis and trans geometries can be expected in a disordered polymer. (ii) The cis-trans barrier is low enough to allow cis-trans conversion at room temperature. (iii) In the dimer, the potential energy minima are about 30^0 from the cis and trans planar geometries, but planar geometries are stabilized as the chain length increases. (iv) The extended conjugation causes the torsional potential about one inter-ring bond to be coupled to other torsions along the oligomer chain.

  2. Quantum Calculations on Salt Bridges with Water: Potentials, Structure, and Properties

    SciTech Connect

    Liao, Sing; Green, Michael E.

    2011-01-01

    Salt bridges are electrostatic links between acidic and basic amino acids in a protein; quantum calculations are used here to determine the energetics and other properties of one form of these species, in the presence of water molecules. The acidic groups are carboxylic acids (aspartic and glutamic acids); proteins have two bases with pK above physiological pH: one, arginine, with a guanidinium basic group, the other lysine, which is a primary amine. Only arginine is modeled here, by ethyl guanidinium, while propionic acid is used as a model for either carboxylic acid. The salt bridges are accompanied by 0-12 water molecules; for each of the 13 systems, the energy-bond distance relation, natural bond orbitals (NBO), frequency calculations allowing thermodynamic corrections to room temperature, and dielectric constant dependence, were all calculated. The water molecules were found to arrange themselves in hydrogen bonded rings anchored to the oxygens of the salt bridge components. This was not surprising in itself, but it was found that the rings lead to a periodicity in the energy, and to a 'water addition' rule. The latter shows that the initial rings, with four oxygen atoms, become five member rings when an additional water molecule becomes available, with the additional water filling in at the bond with the lowest Wiberg index, as calculated using NBO. The dielectric constant dependence is the expected hyperbola, and the fit of the energy to the inverse dielectric constant is determined. There is an energy periodicity related to ring formation upon addition of water molecules. When 10 water molecules have been added, all spaces near the salt bridge are filled, completing the first hydration shell, and a second shell starts to form. The potentials associated with salt bridges depend on their hydration, and potentials assigned without regard to local hydration are likely to cause errors as large as or larger than kBT, thus suggesting a serious problem if these

  3. Regularizing the molecular potential in electronic structure calculations. I. SCF methods

    SciTech Connect

    Bischoff, Florian A.

    2014-11-14

    We present a method to remove the singular nuclear potential in a molecule and replace it with a regularized potential that is more amenable to be represented numerically. The singular nuclear potential is canceled by the similarity-transformed kinetic energy operator giving rise to an effective nuclear potential that contains derivative operators acting on the wave function. The method is fully equivalent to the non-similarity-transformed version. We give numerical examples within the framework of multi-resolution analysis for medium-sized molecules.

  4. Effective UV radiation from model calculations and measurements

    NASA Technical Reports Server (NTRS)

    Feister, Uwe; Grewe, Rolf

    1994-01-01

    Model calculations have been made to simulate the effect of atmospheric ozone and geographical as well as meteorological parameters on solar UV radiation reaching the ground. Total ozone values as measured by Dobson spectrophotometer and Brewer spectrometer as well as turbidity were used as input to the model calculation. The performance of the model was tested by spectroradiometric measurements of solar global UV radiation at Potsdam. There are small differences that can be explained by the uncertainty of the measurements, by the uncertainty of input data to the model and by the uncertainty of the radiative transfer algorithms of the model itself. Some effects of solar radiation to the biosphere and to air chemistry are discussed. Model calculations and spectroradiometric measurements can be used to study variations of the effective radiation in space in space time. The comparability of action spectra and their uncertainties are also addressed.

  5. Potential Ergogenic Effects of Saffron.

    PubMed

    Meamarbashi, Abbas; Rajabi, Ali

    2016-01-01

    Crocus sativus, commonly known as saffron, is a rich source of carotenoids with many health benefits. The muscular strength, pulmonary function, and reaction time are vital to the athlete's performance, and this study aimed to investigate an ergogenic effect of saffron. Twenty-eight nonactive and healthy male university students were randomly assigned into the saffron (n = 14) and control (n = 15) groups. The experimental group received dried saffron stigma (300 mg/day for 10 days) and the control group received a placebo. After one session, familiarization with the tests, anthropometric parameters, visual and audio reaction times, and the maximum isometric and isotonic forces on a leg press machine were measured accordingly, 1 day before and after the supplementation period. This study shows that 10 days of supplementation with saffron significantly increased (10.1%) the isometric force (p < .0001; effect size (EF) = 0.432) and increased 6.1% the isotonic force (p < .0001; effect size = 0.662), as well as effecting faster visual (p < .05; EF = 0.217) and audio (p < .05; EF = 0.214) reaction times. The ergogenic effect of saffron (increase in the forces) may contribute to increase in the muscle mitochondrial biogenesis and positive effect on the motor cortex, both of which may explain faster audio and visual reaction times. Saffron supplementation was also possibly responsible for improvement of muscle blood perfusion and facilitation in the oxygen transport. PMID:26811090

  6. The effect of dose calculation accuracy on inverse treatment planning

    NASA Astrophysics Data System (ADS)

    Jeraj, Robert; Keall, Paul J.; Siebers, Jeffrey V.

    2002-02-01

    The effect of dose calculation accuracy during inverse treatment planning for intensity modulated radiotherapy (IMRT) was studied in this work. Three dose calculation methods were compared: Monte Carlo, superposition and pencil beam. These algorithms were used to calculate beamlets, which were subsequently used by a simulated annealing algorithm to determine beamlet weights which comprised the optimal solution to the objective function. Three different cases (lung, prostate and head and neck) were investigated and several different objective functions were tested for their effect on inverse treatment planning. It is shown that the use of inaccurate dose calculation introduces two errors in a treatment plan, a systematic error and a convergence error. The systematic error is present because of the inaccuracy of the dose calculation algorithm. The convergence error appears because the optimal intensity distribution for inaccurate beamlets differs from the optimal solution for the accurate beamlets. While the systematic error for superposition was found to be ~1% of Dmax in the tumour and slightly larger outside, the error for the pencil beam method is typically ~5% of Dmax and is rather insensitive to the given objectives. On the other hand, the convergence error was found to be very sensitive to the objective function, is only slightly correlated to the systematic error and should be determined for each case individually. Our results suggest that because of the large systematic and convergence errors, inverse treatment planning systems based on pencil beam algorithms alone should be upgraded either to superposition or Monte Carlo based dose calculations.

  7. Theoretical calculations and vibrational potential energy surface of 4-silaspiro(3,3)heptane

    SciTech Connect

    Ocola, Esther J.; Medders, Cross; Laane, Jaan; Meinander, Niklas

    2014-04-28

    Theoretical computations have been carried out on 4-silaspiro(3,3)heptane (SSH) in order to calculate its molecular structure and conformational energies. The molecule has two puckered four-membered rings with dihedral angles of 34.2° and a tilt angle of 9.4° between the two rings. Energy calculations were carried out for different conformations of SSH. These results allowed the generation of a two-dimensional ring-puckering potential energy surface (PES) of the form V = a(x{sub 1}{sup 4} + x{sub 2}{sup 4}) – b(x{sub 1}{sup 2} + x{sub 2}{sup 2}) + cx{sub 1}{sup 2}x{sub 2}{sup 2}, where x{sub 1} and x{sub 2} are the ring-puckering coordinates for the two rings. The presence of sufficiently high potential energy barriers prevents the molecule from undergoing pseudorotation. The quantum states, wave functions, and predicted spectra resulting from the PESs were calculated.

  8. Application of a sitting MIRD phantom for effective dose calculations.

    PubMed

    Olsher, Richard H; Van Riper, Kenneth A

    2005-01-01

    In typical realistic scenarios, dose factors due to 60Co contaminated steel, used in consumer products, cannot be approximated by standard exposure geometries. It is then necessary to calculate the effective dose using an appropriate anthropomorphic phantom. MCNP calculations were performed using a MIRD human model in two settings. In the first, a male office worker is sitting in a chair containing contaminated steel, surrounded by contaminated furniture. In the second, a male driver is seated inside an automobile, the steel of which is uniformly contaminated. To accurately calculate the dose to lower body organs, especially the gonads, it was essential to modify the MIRD model to simulate two sitting postures: chair and driving position. The phantom modifications are described, and the results of the calculations are presented. In the case of the automobile scenarios, results are compared to those obtained using an isotropic fluence-to-dose conversion function. PMID:16604666

  9. Electronic coupling calculations with transition charges, dipoles, and quadrupoles derived from electrostatic potential fitting.

    PubMed

    Fujimoto, Kazuhiro J

    2014-12-01

    A transition charge, dipole, and quadrupole from electrostatic potential (TrESP-CDQ) method for electronic coupling calculations is proposed. The TrESP method is based on the classical description of electronic Coulomb interaction between transition densities for individual molecules. In the original TrESP method, only the transition charge interactions were considered as the electronic coupling. In the present study, the TrESP method is extended to include the contributions from the transition dipoles and quadrupoles as well as the transition charges. Hence, the self-consistent transition density is employed in the ESP fitting procedure. To check the accuracy of the present approach, several test calculations are performed to a helium dimer, a methane dimer, and an ethylene dimer. As a result, the TrESP-CDQ method gives a much improved description of the electronic coupling, compared with the original TrESP method. The calculated results also show that the self-consistent treatment to the transition densities contributes significantly to the accuracy of the electronic coupling calculations. Based on the successful description of the electronic coupling, the contributions to the electronic coupling are also analyzed. This analysis clearly shows a negligible contribution of the transition charge interaction to the electronic coupling. Hence, the distribution of the transition density is found to strongly influence the magnitudes of the transition charges, dipoles, and quadrupoles. The present approach is useful for analyzing and understanding the mechanism of excitation-energy transfer. PMID:25481127

  10. Calculation of subsonic and supersonic steady and unsteady aerodynamic forces using velocity potential aerodynamic elements

    NASA Technical Reports Server (NTRS)

    Haviland, J. K.; Yoo, Y. S.

    1976-01-01

    Expressions for calculation of subsonic and supersonic, steady and unsteady aerodynamic forces are derived, using the concept of aerodynamic elements applied to the downwash velocity potential method. Aerodynamic elements can be of arbitrary out of plane polygon shape, although numerical calculations are restricted to rectangular elements, and to the steady state case in the supersonic examples. It is suggested that the use of conforming, in place of rectangular elements, would give better results. Agreement with results for subsonic oscillating T tails is fair, but results do not converge as the number of collocation points is increased. This appears to be due to the form of expression used in the calculations. The methods derived are expected to facilitate automated flutter analysis on the computer. In particular, the aerodynamic element concept is consistent with finite element methods already used for structural analysis. The method is universal for the complete Mach number range, and, finally, the calculations can be arranged so that they do not have to be repeated completely for every reduced frequency.

  11. Electronic coupling calculations with transition charges, dipoles, and quadrupoles derived from electrostatic potential fitting

    SciTech Connect

    Fujimoto, Kazuhiro J.

    2014-12-07

    A transition charge, dipole, and quadrupole from electrostatic potential (TrESP-CDQ) method for electronic coupling calculations is proposed. The TrESP method is based on the classical description of electronic Coulomb interaction between transition densities for individual molecules. In the original TrESP method, only the transition charge interactions were considered as the electronic coupling. In the present study, the TrESP method is extended to include the contributions from the transition dipoles and quadrupoles as well as the transition charges. Hence, the self-consistent transition density is employed in the ESP fitting procedure. To check the accuracy of the present approach, several test calculations are performed to a helium dimer, a methane dimer, and an ethylene dimer. As a result, the TrESP-CDQ method gives a much improved description of the electronic coupling, compared with the original TrESP method. The calculated results also show that the self-consistent treatment to the transition densities contributes significantly to the accuracy of the electronic coupling calculations. Based on the successful description of the electronic coupling, the contributions to the electronic coupling are also analyzed. This analysis clearly shows a negligible contribution of the transition charge interaction to the electronic coupling. Hence, the distribution of the transition density is found to strongly influence the magnitudes of the transition charges, dipoles, and quadrupoles. The present approach is useful for analyzing and understanding the mechanism of excitation-energy transfer.

  12. Mesh size and code option effects of strength calculations

    SciTech Connect

    Kaul, Ann M

    2010-12-10

    Modern Lagrangian hydrodynamics codes include numerical methods which allow calculations to proceed past the point obtainable by a purely Lagrangian scheme. These options can be employed as the user deems necessary to 'complete' a calculation. While one could argue that any calculation is better than none, to truly understand the calculated results and their relationship to physical reality, the user needs to understand how their runtime choices affect the calculated results. One step toward this goal is to understand the effect of each runtime choice on particular pieces of the code physics. This paper will present simulation results for some experiments typically used for strength model validation. Topics to be covered include effect of mesh size, use of various ALE schemes for mesh detangling, and use of anti-hour-glassing schemes. Experiments to be modeled include the lower strain rate ({approx} 10{sup 4} s{sup -1}) gas gun driven Taylor impact experiments and the higher strain rate ({approx} 10{sup 5}-10{sup 6} s{sup -1}) HE products driven perturbed plate experiments. The necessary mesh resolution and the effect of the code runtime options are highly dependent on the amount of localization of strain and stress in each experiment. In turn, this localization is dependent on the geometry of the experimental setup and the drive conditions.

  13. Determination of a silane intermolecular force field potential model from an ab initio calculation

    SciTech Connect

    Li, Arvin Huang-Te; Chao, Sheng D.; Chang, Chien-Cheng

    2010-12-15

    Intermolecular interaction potentials of the silane dimer in 12 orientations have been calculated by using the Hartree-Fock (HF) self-consistent theory and the second-order Moeller-Plesset (MP2) perturbation theory. We employed basis sets from Pople's medium-size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (up to the triply augmented correlation-consistent polarized valence quadruple-zeta basis set). We found that the minimum energy orientations were the G and H conformers. We have suggested that the Si-H attractions, the central silicon atom size, and electronegativity play essential roles in weakly binding of a silane dimer. The calculated MP2 potential data were employed to parametrize a five-site force field for molecular simulations. The Si-Si, Si-H, and H-H interaction parameters in a pairwise-additive, site-site potential model for silane molecules were regressed from the ab initio energies.

  14. Calculations of the ionization potentials of the halogens by the relativistic Hartree-Rock-Dirac method taking account of superposition of configurations

    SciTech Connect

    Tupitsyn, I.I.

    1988-03-01

    The ionization potentials of the halogen group have been calculated. The calculations were carried out using the relativistic Hartree-Fock method taking into account correlation effects. Comparison of theoretical results with experimental data for the elements F, Cl, Br, and I allows an estimation of the accuracy and reliability of the method. The theoretical values of the ionization potential of astatine obtained here may be of definite interest for the chemistry of astatine.

  15. Semi-continuum electrostatic calculations of redox potentials in photosystem I.

    PubMed

    Ptushenko, Vasily V; Cherepanov, Dmitry A; Krishtalik, Lev I; Semenov, Alexey Yu

    2008-07-01

    The midpoint redox potentials (E(m)) of all cofactors in photosystem I from Synechococcus elongatus as well as of the iron-sulfur (Fe(4)S(4)) clusters in two soluble ferredoxins from Azotobacter vinelandii and Clostridium acidiurici were calculated within the framework of a semi-continuum dielectric approach. The widely used treatment of proteins as uniform media with single dielectric permittivity is oversimplified, particularly, because permanent charges are considered both as a source for intraprotein electric field and as a part of dielectric polarizability. Our approach overcomes this inconsistency by using two dielectric constants: optical epsilon(o)=2.5 for permanent charges pre-existing in crystal structure, and static epsilon(s) for newly formed charges. We also take into account a substantial dielectric heterogeneity of photosystem I revealed by photoelectric measurements and a liquid junction potential correction for E(m) values of relevant redox cofactors measured in aprotic solvents. We show that calculations based on a single permittivity have the discrepancy with experimental data larger than 0.7 V, whereas E(m) values calculated within our approach fall in the range of experimental estimates. The electrostatic analysis combined with quantum chemistry calculations shows that (i) the energy decrease upon chlorophyll dimerization is essential for the downhill mode of primary charge separation between the special pair P(700) and the primary acceptor A(0); (ii) the primary donor is apparently P(700) but not a pair of accessory chlorophylls; (iii) the electron transfer from the A branch quinone Q(A) to the iron-sulfur cluster F(X) is most probably downhill, whereas that from the B branch quinone Q(B) to F(X) is essentially downhill. PMID:18483776

  16. Using Electronic Energy Derivative Information in Automated Potential Energy Surface Construction for Vibrational Calculations.

    PubMed

    Sparta, Manuel; Hansen, Mikkel B; Matito, Eduard; Toffoli, Daniele; Christiansen, Ove

    2010-10-12

    The availability of an accurate representation of the potential energy surface (PES) is an essential prerequisite in an anharmonic vibrational calculation. At the same time, the high dimensionality of the fully coupled PES and the adverse scaling properties with respect to the molecular size make the construction of an accurate PES a computationally demanding task. In the past few years, our group tested and developed a series of tools and techniques aimed at defining computationally efficient, black-box protocols for the construction of PESs for use in vibrational calculations. This includes the definition of an adaptive density-guided approach (ADGA) for the construction of PESs from an automatically generated set of evaluation points. Another separate aspect has been the exploration of the use of derivative information through modified Shepard (MS) interpolation/extrapolation procedures. With this article, we present an assembled machinery where these methods are embedded in an efficient way to provide both a general machinery as well as concrete computational protocols. In this framework we introduce and discuss the accuracy and computational efficiency of two methods, called ADGA[2gx3M] and ADGA[2hx3M], where the ADGA recipe is used (with MS interpolation) to automatically define modest sized grids for up to two-mode couplings, while MS extrapolation based on, respectively, gradients only and gradients and Hessians from the ADGA determined points provides access to sufficiently accurate three-mode couplings. The performance of the resulting potentials is investigated in vibrational coupled cluster (VCC) calculations. Three molecular systems serve as benchmarks: a trisubstituted methane (CHFClBr), methanimine (CH2NH), and oxazole (C3H3NO). Furthermore, methanimine and oxazole are addressed in accurate calculations aiming to reproduce experimental results. PMID:26616778

  17. Intrinsic Defect Properties in GaN Calculated By Ab Initio and Empirical Potential Methods

    SciTech Connect

    Gao, Fei; Bylaska, Eric J.; Weber, William J.

    2004-12-13

    Density functional theory (DFT) has been used to investigate the formation, properties, and atomic configurations of vacancies, antisite defects and interstitials in GaN, and the DFT results are compared with those calculated by molecular dynamics (MD) simulations using two representative potentials. The DFT calculations reveal that the relaxation of vacancies is generally small, but the relaxation around antisite defects is large, especially for the Ga antisite that is not stable and converts to a N+-N<0001> split interstitial plus a Ga vacancy at the original site. The N interstitials, starting from all possible sites, eventually relax into a N+-N<11-20> split interstitial. In the case of Ga interstitials, the most stable configuration is a Ga octahedral interstitial, but the energy difference among all the interstitials is small. The Ga+-Ga<11-20> split interstitial can bridge the gap between non-bonded Ga atoms, thereby leading to a chain of four Ga atoms along the <11-20> direction in GaN. The formation energies of vacancies and antisite defects obtained using the Stillinger-Weber potential (SW) are in reasonable agreement with those obtained by DFT calculations, whereas the Tersoff-Brenner (TB) potential better describes the behavior of N interstitials. In the case of Ga interstitials, the most stable configuration predicted by the TB-model is a Ga+-N<11-20> split interstitial; while for the SW-model the Ga tetrahedral configuration is more stable, which is in contrast to DFT results.

  18. Effect size estimates: current use, calculations, and interpretation.

    PubMed

    Fritz, Catherine O; Morris, Peter E; Richler, Jennifer J

    2012-02-01

    The Publication Manual of the American Psychological Association (American Psychological Association, 2001, American Psychological Association, 2010) calls for the reporting of effect sizes and their confidence intervals. Estimates of effect size are useful for determining the practical or theoretical importance of an effect, the relative contributions of factors, and the power of an analysis. We surveyed articles published in 2009 and 2010 in the Journal of Experimental Psychology: General, noting the statistical analyses reported and the associated reporting of effect size estimates. Effect sizes were reported for fewer than half of the analyses; no article reported a confidence interval for an effect size. The most often reported analysis was analysis of variance, and almost half of these reports were not accompanied by effect sizes. Partial η2 was the most commonly reported effect size estimate for analysis of variance. For t tests, 2/3 of the articles did not report an associated effect size estimate; Cohen's d was the most often reported. We provide a straightforward guide to understanding, selecting, calculating, and interpreting effect sizes for many types of data and to methods for calculating effect size confidence intervals and power analysis. PMID:21823805

  19. Ab initio calculation of thermodynamic potentials and entropies for superionic water

    DOE PAGESBeta

    French, Martin; Desjarlais, Michael P.; Redmer, Ronald

    2016-02-25

    We construct thermodynamic potentials for two superionic phases of water [with body-centered cubic (bcc) and face-centered cubic (fcc) oxygen lattice] using a combination of density functional theory (DFT) and molecular dynamics simulations (MD). For this purpose, a generic expression for the free energy of warm dense matter is developed and parametrized with equation of state data from the DFT-MD simulations. A second central aspect is the accurate determination of the entropy, which is done using an approximate two-phase method based on the frequency spectra of the nuclear motion. The boundary between the bcc superionic phase and the ices VII andmore » X calculated with thermodynamic potentials from DFT-MD is consistent with that directly derived from the simulations. As a result, differences in the physical properties of the bcc and fcc superionic phases and their impact on interior modeling of water-rich giant planets are discussed.« less

  20. Ab initio calculation of thermodynamic potentials and entropies for superionic water

    NASA Astrophysics Data System (ADS)

    French, Martin; Desjarlais, Michael P.; Redmer, Ronald

    2016-02-01

    We construct thermodynamic potentials for two superionic phases of water [with body-centered cubic (bcc) and face-centered cubic (fcc) oxygen lattice] using a combination of density functional theory (DFT) and molecular dynamics simulations (MD). For this purpose, a generic expression for the free energy of warm dense matter is developed and parametrized with equation of state data from the DFT-MD simulations. A second central aspect is the accurate determination of the entropy, which is done using an approximate two-phase method based on the frequency spectra of the nuclear motion. The boundary between the bcc superionic phase and the ices VII and X calculated with thermodynamic potentials from DFT-MD is consistent with that directly derived from the simulations. Differences in the physical properties of the bcc and fcc superionic phases and their impact on interior modeling of water-rich giant planets are discussed.

  1. Ab initio calculation of thermodynamic potentials and entropies for superionic water.

    PubMed

    French, Martin; Desjarlais, Michael P; Redmer, Ronald

    2016-02-01

    We construct thermodynamic potentials for two superionic phases of water [with body-centered cubic (bcc) and face-centered cubic (fcc) oxygen lattice] using a combination of density functional theory (DFT) and molecular dynamics simulations (MD). For this purpose, a generic expression for the free energy of warm dense matter is developed and parametrized with equation of state data from the DFT-MD simulations. A second central aspect is the accurate determination of the entropy, which is done using an approximate two-phase method based on the frequency spectra of the nuclear motion. The boundary between the bcc superionic phase and the ices VII and X calculated with thermodynamic potentials from DFT-MD is consistent with that directly derived from the simulations. Differences in the physical properties of the bcc and fcc superionic phases and their impact on interior modeling of water-rich giant planets are discussed. PMID:26986321

  2. Ranking protein-protein docking results using steered molecular dynamics and potential of mean force calculations.

    PubMed

    Kingsley, Laura J; Esquivel-Rodríguez, Juan; Yang, Ying; Kihara, Daisuke; Lill, Markus A

    2016-07-01

    Crystallization of protein-protein complexes can often be problematic and therefore computational structural models are often relied on. Such models are often generated using protein-protein docking algorithms, where one of the main challenges is selecting which of several thousand potential predictions represents the most near-native complex. We have developed a novel technique that involves the use of steered molecular dynamics (sMD) and umbrella sampling to identify near-native complexes among protein-protein docking predictions. Using this technique, we have found a strong correlation between our predictions and the interface RMSD (iRMSD) in ten diverse test systems. On two of the systems, we investigated if the prediction results could be further improved using potential of mean force calculations. We demonstrated that a near-native (<2.0 Å iRMSD) structure could be identified in the top-1 ranked position for both systems. © 2016 Wiley Periodicals, Inc. PMID:27232548

  3. Potential energy surface and second virial coefficient of methane-water from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Akin-Ojo, Omololu; Szalewicz, Krzysztof

    2005-10-01

    Six-dimensional intermolecular potential energy surfaces (PESs) for the interaction of CH4 with H2O are presented, obtained from ab initio calculations using symmetry-adapted perturbation theory (SAPT) at two different levels of intramonomer correlation and the supermolecular approach at three different levels of electron correlation. Both CH4 and H2O are assumed to be rigid molecules with interatomic distances and angles fixed at the average values in the ground-state vibration. A physically motivated analytical expression for each PES has been developed as a sum of site-site functions. The PES of the CH4-H2O dimer has only two symmetry-distinct minima. From the SAPT calculations, the global minimum has an energy of -1.03kcal /mol at a geometry where H2O is the proton donor, HO -H⋯CH4, with the O-H-C angle of 165°, while the secondary minimum, with an energy of -0.72kcal/mol, has CH4 in the role of the proton donor (H3C -H⋯OH2). We estimated the complete basis set limit of the SAPT interaction energy at the global minimum to be -1.06kcal/mol. The classical cross second virial coefficient B12(T) has been calculated for the temperature range 298-653K. Our best results agree well with some experiments, allowing an evaluation of the quality of experimental results.

  4. Modeling intermolecular interactions of physisorbed organic molecules using pair potential calculations

    SciTech Connect

    Kroeger, Ingo; Stadtmueller, Benjamin; Wagner, Christian; Weiss, Christian; Temirov, Ruslan; Tautz, F. Stefan; Kumpf, Christian

    2011-12-21

    The understanding and control of epitaxial growth of organic thin films is of crucial importance in order to optimize the performance of future electronic devices. In particular, the start of the submonolayer growth plays an important role since it often determines the structure of the first layer and subsequently of the entire molecular film. We have investigated the structure formation of 3,4,9,10-perylene-tetracarboxylic dianhydride and copper-phthalocyanine molecules on Au(111) using pair-potential calculations based on van der Waals and electrostatic intermolecular interactions. The results are compared with the fundamental lateral structures known from experiment and an excellent agreement was found for these weakly interacting systems. Furthermore, the calculations are even suitable for chemisorptive adsorption as demonstrated for copper-phthalocyanine/Cu(111), if the influence of charge transfer between substrate and molecules is known and the corresponding charge redistribution in the molecules can be estimated. The calculations are of general applicability for molecular adsorbate systems which are dominated by electrostatic and van der Waals interaction.

  5. Potential energy curves via double electron-attachment calculations: Dissociation of alkali metal dimers

    NASA Astrophysics Data System (ADS)

    Musiał, Monika; Kowalska-Szojda, Katarzyna; Lyakh, Dmitry I.; Bartlett, Rodney J.

    2013-05-01

    The recently developed method [M. Musiał, J. Chem. Phys. 136, 134111 (2012), 10.1063/1.3700438] to study double electron attached states has been applied to the description of the ground and excited state potential energy curves of the alkali metal dimers. The method is based on the multireference coupled cluster scheme formulated within the Fock space formalism for the (2,0) sector. Due to the use of the efficient intermediate Hamiltonian formulation, the approach is free from the intruder states problem. The description of the neutral alkali metal dimers is accomplished via attaching two electrons to the corresponding doubly ionized system. This way is particularly advantageous when a closed shell molecule dissociates into open shell subunits while its doubly positive cation generates the closed shell fragments. In the current work, we generate the potential energy curves for the ground and multiple excited states of the Li2 and Na2 molecules. In all cases the potential energy curves are smooth for the entire range of interatomic distances (from the equilibrium point to the dissociation limit). Based on the calculated potential energy curves, we are able to compute spectroscopic parameters of the systems studied.

  6. The ground-state potential energy curve of the radium dimer from relativistic coupled cluster calculations.

    PubMed

    Teodoro, Tiago Quevedo; Haiduke, Roberto Luiz Andrade; Dammalapati, Umakanth; Knoop, Steven; Visscher, Lucas

    2015-08-28

    The potential energy curve for the ground-state of radium dimer (Ra2) is provided by means of atomic and molecular relativistic coupled cluster calculations. The short-range part of this curve is defined by an equilibrium bond length of 5.324 Å, a dissociation energy of 897 cm(-1), and a harmonic vibrational frequency of 20.5 cm(-1). The asymptotic behavior at large interatomic distances is characterized by the van der Waals coefficients C6 = 5.090 × 10(3), C8 = 6.978 × 10(5), and C10 = 8.786 × 10(7) atomic units. The two regions are matched in an analytical potential to provide a convenient representation for use in further calculations, for instance, to model cold collisions between radium atoms. This might become relevant in future experiments on ultracold, optically trapped, radioactive radium atoms that are used to search for a permanent electric dipole moment. PMID:26328843

  7. Multireference configuration interaction calculations of the first six ionization potentials of the uranium atom

    SciTech Connect

    Bross, David H.; Parmar, Payal; Peterson, Kirk A.

    2015-11-12

    The first 6 ionization potentials (IPs) of the uranium atom have been calculated using multireference configuration interaction (MRCI+Q) with extrapolations to the complete basis set (CBS) limit using new all-electron correlation consistent basis sets. The latter were carried out with the third-order Douglas-Kroll-Hess Hamiltonian. Correlation down through the 5s5p5d electrons have been taken into account, as well as contributions to the IPs due to the Lamb shift. Spin-orbit coupling contributions calculated at the 4-component Kramers restricted configuration interaction level, as well as the Gaunt term computed at the Dirac-Hartree-Fock level, were added to the best scalar relativistic results. As a result, the final ionization potentials are expected to be accurate to at least 5 kcal/mol (0.2 eV), and thus more reliable than the current experimental values of IP3 through IP6.

  8. Multireference configuration interaction calculations of the first six ionization potentials of the uranium atom

    DOE PAGESBeta

    Bross, David H.; Parmar, Payal; Peterson, Kirk A.

    2015-11-12

    The first 6 ionization potentials (IPs) of the uranium atom have been calculated using multireference configuration interaction (MRCI+Q) with extrapolations to the complete basis set (CBS) limit using new all-electron correlation consistent basis sets. The latter were carried out with the third-order Douglas-Kroll-Hess Hamiltonian. Correlation down through the 5s5p5d electrons have been taken into account, as well as contributions to the IPs due to the Lamb shift. Spin-orbit coupling contributions calculated at the 4-component Kramers restricted configuration interaction level, as well as the Gaunt term computed at the Dirac-Hartree-Fock level, were added to the best scalar relativistic results. As amore » result, the final ionization potentials are expected to be accurate to at least 5 kcal/mol (0.2 eV), and thus more reliable than the current experimental values of IP3 through IP6.« less

  9. Calculation of free energies and chemical potentials for gas hydrates using Monte Carlo simulations.

    PubMed

    Wierzchowski, S J; Monson, P A

    2007-06-28

    We describe a method for calculating free energies and chemical potentials for molecular models of gas hydrate systems using Monte Carlo simulations. The method has two components: (i) thermodynamic integration to obtain the water and guest molecule chemical potentials as functions of the hydrate occupancy; (ii) calculation of the free energy of the zero-occupancy hydrate system using thermodynamic integration from an Einstein crystal reference state. The approach is applicable to any classical molecular model of a hydrate. We illustrate the methodology with an application to the structure-I methane hydrate using two molecular models. Results from the method are also used to assess approximations in the van der Waals-Platteeuw theory and some of its extensions. It is shown that the success of the van der Waals-Platteeuw theory is in part due to a cancellation of the error arising from the assumption of a fixed configuration of water molecules in the hydrate framework with that arising from the neglect of methane-methane interactions. PMID:17530795

  10. Calculation of turbulence effects in an upward-refracting atmosphere

    NASA Astrophysics Data System (ADS)

    Gilbert, Kenneth E.; di, Xiao; Raspet, Richard

    1990-06-01

    The effect of atmospheric turbulence on sound propagation was investigated for both nonrefractive and refractive atmospheres, using the parabolic equation method of Gilbert and White (1989) in conjunction with a two-dimensional atmospheric turbulence model. The calculations for a nonrefractive atmosphere gave good agreement with experimental data and with Daigle's (1979) theory, while calculations for an upward-refractive atmosphere gave reasonable agreement with the data of Weiner and Keast (1959). It is concluded that, for a receiver deep in a shadow zone and for frequencies greater than a few hundred hertz, the measured sound-pressure level is due almost entirely to the sound scattered into the shadow zone by atmospheric turbulence. Consequently, for upward refraction and frequencies above a few hundred hertz, turbulence must be included in long-range propagation calculations.

  11. Seasonal variation of redox species and redox potentials in shallow groundwater: A comparison of measured and calculated redox potentials

    NASA Astrophysics Data System (ADS)

    Ramesh Kumar, A.; Riyazuddin, P.

    2012-06-01

    SummaryThe seasonal variation of redox potential (Eh) and redox species such as As(V)/As(III), Cr(VI)/Cr(III), Fe(III)/Fe(II), NO3-/NO2-, and Se(VI)/Se(IV) were studied in a shallow groundwater for a period of three years (May, 2004-January, 2007). The study area was Chrompet area of Chennai city, India. Groundwater samples from 65 wells were monitored for pH, electrical conductivity, dissolved oxygen (DO), and major ions during pre-(May) and post-monsoon (January) seasons. The objective of the study was to gain insight into the temporal variation of the redox species due to groundwater recharge and to identify the redox reactions controlling the measured Eh of the groundwater. The study revealed that the shallow groundwater was "oxic" with DO ranging between 0.25 and 5.00 mg L-1, and between 0.38 and 5.05 mg L-1 during pre-(May, 2004) and post-monsoon (January, 2005) seasons, respectively. The measured Eh (with respect to standard hydrogen electrode, SHE) ranged between 65 and 322 mV, and between 110 and 330 mV during pre- and post-monsoon seasons, respectively. During post-monsoon seasons, DO and Eh increased in most of the wells due to groundwater recharge. The calculated Eh using the redox couples As(V)/As(III), NO3-/NO2-, O2/H2O and Se(VI)/Se(IV) neither agreed among themselves nor with the measured Eh during all the seasons. It shows that in the shallow groundwater, the various redox couples are in disequilibrium among themselves and with the Pt electrode. However, 41% (n = 122) of the Eh values calculated from Fe(III)/Fe(II) couple agreed with the measured Eh within ±30 mV, the uncertainty of Pt-electrode measurement. The post-monsoon seasons showed higher values of As(V)/As(III) and Se(VI)/Se(IV) compared to the pre-monsoon seasons, whereas Fe(III)/Fe(II) behaved in the opposite manner. This pattern of variation is consistent with the increased oxidizing nature, as shown by the higher DO and Eh values observed during post-monsoon seasons. The results

  12. Hybrid MP2/MP4 potential surfaces in VSCF calculations of IR spectra: applications for organic molecules.

    PubMed

    Knaanie, Roie; Šebek, Jiří; Kalinowski, Jaroslaw; Benny Gerber, R

    2014-02-01

    This study introduces an improved hybrid MP2/MP4 ab initio potential for vibrational spectroscopy calculations which is very accurate, yet without high computational demands. The method uses harmonic vibrational calculations with the MP4(SDQ) potential to construct an improved MP2 potential by coordinate scaling. This improved MP2 potential is used for the anharmonic VSCF calculation. The method was tested spectroscopically for four molecules: butane, acetone, ethylene and glycine. Very good agreement with experiment was found. For most of the systems, the more accurate harmonic treatment considerably improved the MP2 anharmonic results. PMID:23838574

  13. Effective Connectivity Reveals Strategy Differences in an Expert Calculator

    PubMed Central

    Minati, Ludovico; Sigala, Natasha

    2013-01-01

    Mathematical reasoning is a core component of cognition and the study of experts defines the upper limits of human cognitive abilities, which is why we are fascinated by peak performers, such as chess masters and mental calculators. Here, we investigated the neural bases of calendrical skills, i.e. the ability to rapidly identify the weekday of a particular date, in a gifted mental calculator who does not fall in the autistic spectrum, using functional MRI. Graph-based mapping of effective connectivity, but not univariate analysis, revealed distinct anatomical location of “cortical hubs” supporting the processing of well-practiced close dates and less-practiced remote dates: the former engaged predominantly occipital and medial temporal areas, whereas the latter were associated mainly with prefrontal, orbitofrontal and anterior cingulate connectivity. These results point to the effect of extensive practice on the development of expertise and long term working memory, and demonstrate the role of frontal networks in supporting performance on less practiced calculations, which incur additional processing demands. Through the example of calendrical skills, our results demonstrate that the ability to perform complex calculations is initially supported by extensive attentional and strategic resources, which, as expertise develops, are gradually replaced by access to long term working memory for familiar material. PMID:24086291

  14. Absorbed Dose and Dose Equivalent Calculations for Modeling Effective Dose

    NASA Technical Reports Server (NTRS)

    Welton, Andrew; Lee, Kerry

    2010-01-01

    While in orbit, Astronauts are exposed to a much higher dose of ionizing radiation than when on the ground. It is important to model how shielding designs on spacecraft reduce radiation effective dose pre-flight, and determine whether or not a danger to humans is presented. However, in order to calculate effective dose, dose equivalent calculations are needed. Dose equivalent takes into account an absorbed dose of radiation and the biological effectiveness of ionizing radiation. This is important in preventing long-term, stochastic radiation effects in humans spending time in space. Monte carlo simulations run with the particle transport code FLUKA, give absorbed and equivalent dose data for relevant shielding. The shielding geometry used in the dose calculations is a layered slab design, consisting of aluminum, polyethylene, and water. Water is used to simulate the soft tissues that compose the human body. The results obtained will provide information on how the shielding performs with many thicknesses of each material in the slab. This allows them to be directly applicable to modern spacecraft shielding geometries.

  15. Infrared lens thermal effect: equivalent focal shift and calculating model

    NASA Astrophysics Data System (ADS)

    Zhang, Cheng-shuo; Shi, Zelin; Feng, Bin; Xu, Bao-shu

    2014-11-01

    It's well-know that the focal shift of infrared lens is the major factor in degeneration of imaging quality when temperature change. In order to figure out the connection between temperature change and focal shift, partial differential equations of thermal effect on light path are obtained by raytrace method, to begin with. The approximately solution of the PDEs show that focal shift is proportional to temperature change. And a formula to compute the proportional factor is given. In order to understand infrared lens thermal effect deeply, we use defocus by image plane shift at constant temperature to equivalently represent thermal effect on infrared lens. So equivalent focal shift (EFS) is defined and its calculating model is proposed at last. In order to verify EFS and its calculating model, Physical experimental platform including a motorized linear stage with built-in controller, blackbody, target, collimator, IR detector, computer and other devices is developed. The experimental results indicate that EFS make the image plane shift at constant temperature have the same influence on infrared lens as thermal effect and its calculating model is correct.

  16. Hybrid Density Functional Calculations of Redox Potentials of Transition Metal Compounds

    NASA Astrophysics Data System (ADS)

    Armiento, Rickard; Chevrier, Vincent; Ong, Shyue Ping; Ceder, Gerbrand

    2010-03-01

    Prior works have shown that density functional theory (DFT) with the DFT+U method resolves the underestimation of redox potentials calculated by conventional functionals for a number of transition metal compounds relevant for battery applications, including the olivine LixMPO4 (M = Fe, Mn, Co, Ni), layered LixMO2 (M = Co, Ni) and spinel-like LixMn2O4. We show that the redox potentials of these compounds are also well reproduced by the hybrid density functional by Heyd-Scuseria-Ernzerhof (HSE06). Hybrid functionals combine a conventional DFT functional with a part of Hartree-Fock (HF) exchange. While the HF part increases the computational expense by at least one order of magnitude, it provides, in contrast to DFT+U, a correction for the self-interaction error that does not rely on special treatment of the occupancies of the orbital states of ions or species-specific parameters. We compare the accuracy of regular DFT, DFT+U and HSE06 for the redox potentials, lattice constants, and other properties. Examples of electron delocalization problems connected to the self-interaction error in the systems are discussed, and shown to be resolved both by the hybrid functional and DFT+U methods. Comments are made on the possibility to approach the delocalization problem with a semi-local functional.

  17. Calculation of the Lightning Potential Index and electric field in numerical weather prediction models

    NASA Astrophysics Data System (ADS)

    Dementyeva, S. O.; Ilin, N. V.; Mareev, E. A.

    2015-03-01

    Modern methods for predicting thunderstorms and lightnings with the use of high-resolution numerical models are considered. An analysis of the Lightning Potential Index (LPI) is performed for various microphysics parameterizations with the use of the Weather Research and Forecasting (WRF) model. The maximum index values are shown to depend significantly on the type of parameterization. This makes it impossible to specify a single threshold LPI for various parameterizations as a criterion for the occurrence of lightning flashes. The topographic LPI maps underestimate the sizes of regions of likely thunderstorm-hazard events. Calculating the electric field under the assumption that ice and graupel are the main charge carriers is considered a new algorithm of lightning prediction. The model shows that the potential difference (between the ground and cloud layer at a given altitude) sufficient to generate a discharge is retained in a larger region than is predicted by the LPI. The main features of the spatial distribution of the electric field and potential agree with observed data.

  18. Calculation of Steady-state Evaporation for an Arbitrary Matrix Potential at Ground Surface

    NASA Astrophysics Data System (ADS)

    Liu, X.; Zhan, H.

    2014-12-01

    The water loss from soil by evaporation and the amount of ground water available to plants due to the upward movement of water from a water table is an important topic in many disciplines such as soil science, hydrology, and plant physiology. Although water evaporation in actual field setting is a highly complex process, a nearly steady upward flow from a water table to a bare soil surface may be established if the daily evaporative demand is reasonably uniform for a long period of time. While the maximum potential rate of evaporation from the ground surface depends on atmospheric conditions, the actual flux across the soil surface is limited by the ability of the porous medium for transmitting water from the unsaturated zone.The purpose of this study is to calculate the steady-state evaporation for an arbitrary matrix potential at bare soil surface above a shallow water table, while the unsaturated hydraulic conductivity is a nonlinear function of water content or matrix potential. The Haverkamp function and the Brooks-Corey function for the unsaturated hydraulic conductivity are used, and the study results are contrast among the solution developed from the two retention equation and HYDRUS simulation.

  19. A new Fe–He interatomic potential based on ab initio calculations in α-Fe

    SciTech Connect

    Gao, Fei; Deng, Huiqiu; Heinisch, Howard L.; Kurtz, Richard J.

    2011-11-01

    A new interatomic potential for Fe−He interactions has been developed by fitting to the results obtained from ab initio calculations. Based on the electronic hybridization between Fe d-electrons and He s-electrons, an s-band model, along with a repulsive pair potential, has been developed to describe the Fe−He interaction. The atomic configurations and formation energies of single He defects and small interstitial He clusters are utilized in the fitting process. The binding properties and relative stabilities of the He-vacancy and interstitial He clusters are studied. The present Fe−He potential is also applied to study the emission of self-interstitial atoms from small He clusters in alpha-Fe matrices. It is found that the di-He cluster dissociates when the temperature is higher than 400K, but the larger He clusters can create an interstitial Fe atom. The temperature for kicking out an interstitial Fe atom is found to decrease with increasing size of the He clusters.

  20. Comparative Study of Defect Properties in GaN: Ab initio and Empirical Potential Calculations

    SciTech Connect

    Gao, Fei; Bylaska, Eric J.; El-Azab, Anter; Weber, William J.; LM Wang, R Fromknecht, LL Snead, DF Downey and H Takahashi

    2004-04-05

    Density functional theory (DFT) is used to study the formation, properties and atomic configurations of monovacancies, antisite defects and possible interstitials in GaN. The relaxation around a vacancy is generally small, but the relaxation around antisite defects is large, particularly for a Ga antisite defect, which is not stable and converts to an N-N<0001> split interstitial. All N interstitials, starting from any possible sites, eventually transfer into the N-N split interstitials, forming N molecules. In the case of Ga interstitials, the most favorable configuration is the Ga octahedral interstitial. However, it is found that the Ga-Ga<> split interstitial can bridge the gap between non-bonded Ga atoms along the <11-2> direction, which leads to the formation of Ga atomic wires in GaN, with bond distance close to those noted in bulk Ga. In addition, two representative potentials, namely Stillinger-Weber and Tersoff-Brenner potentials, have been employed to deter mine the formation of defects using molecular dynamics (MD) method in GaN. The MD results are discussed and compared to DFT calculations. The present DFT and MD results provide guidelines for evaluating the quality and fit of empirical potentials for large-scale simulations of ion-solid interaction and thermal annealing of defects in GaN.

  1. Chemically transferable coarse-grained potentials from conditional reversible work calculations.

    PubMed

    Brini, E; van der Vegt, N F A

    2012-10-21

    The representability and transferability of effective pair potentials used in multiscale simulations of soft matter systems is ill understood. In this paper, we study liquid state systems composed of n-alkanes, the coarse-grained (CG) potential of which may be assumed pairwise additive and has been obtained using the conditional reversible work (CRW) method. The CRW method is a free-energy-based coarse-graining procedure, which, by means of performing the coarse graining at pair level, rigorously provides a pair potential that describes the interaction free energy between two mapped atom groups (beads) embedded in their respective chemical environments. The pairwise nature of the interactions combined with their dependence on the chemically bonded environment makes CRW potentials ideally suited in studies of chemical transferability. We report CRW potentials for hexane using a mapping scheme that merges two heavy atoms in one CG bead. It is shown that the model is chemically and thermodynamically transferable to alkanes of different chain lengths in the liquid phase at temperatures between the melting and the boiling point under atmospheric (1 atm) pressure conditions. It is further shown that CRW-CG potentials may be readily obtained from a single simulation of the liquid state using the free energy perturbation method, thereby providing a fast and versatile molecular coarse graining method for aliphatic molecules. PMID:23083154

  2. Coaxial electromagnetic launcher calculations using FE-BE method and hybrid potentials

    NASA Astrophysics Data System (ADS)

    Chang, J. H.; Becker, E. B.; Driga, M. D.

    1993-01-01

    In this paper, a hybrid method combining finite and boundary elements (the FE-BE method) is presented to analyze the transient electromagnetic/mechanical behavior of coaxial induction launchers (i.e., the coilgun). The corresponding initial/boundary value problem is formulated in terms of the hybrid potentials, which mixes the vector and scalar magnetic potential functions. The problem is assumed to be axisymmetric and the forcing currents are circumferential. Thermal effect due to ohmic losses is considered during the launching processes.

  3. Consistent use of the standard model effective potential.

    PubMed

    Andreassen, Anders; Frost, William; Schwartz, Matthew D

    2014-12-12

    The stability of the standard model is determined by the true minimum of the effective Higgs potential. We show that the potential at its minimum when computed by the traditional method is strongly dependent on the gauge parameter. It moreover depends on the scale where the potential is calculated. We provide a consistent method for determining absolute stability independent of both gauge and calculation scale, order by order in perturbation theory. This leads to a revised stability bounds m(h)(pole)>(129.4±2.3)  GeV and m(t)(pole)<(171.2±0.3)  GeV. We also show how to evaluate the effect of new physics on the stability bound without resorting to unphysical field values. PMID:25541764

  4. Reduced neutron spectroscopic factors when using potential geometries constrained by Hartree-Fock calculations

    SciTech Connect

    Lee, Jenny; Brown, B.A.; Delaunay, F.; Lynch, W.G.; Saelim, M. J.; Tsang, M.B.; Tostevin, J.A.

    2006-04-15

    We carry out a systematic analysis of angular distribution measurements for selected ground-state to ground-state (d,p) and (p,d) neutron transfer reactions, including the calcium isotopes. We propose a consistent three-body model reaction methodology in which we constrain the transferred-neutron bound state and nucleon-target optical potential geometries using modern Hartree-Fock calculations. Our deduced neutron spectroscopic factors are found to be suppressed by {approx}30% relative to independent-particle shell-model values, from {sup 40}Ca through {sup 49}Ca. The other nuclei studied, ranging from B to Ti, show similar average suppressions with respect to large-basis shell-model expectations. Our results are consistent with deduced spectroscopic strengths for neutrons and protons from intermediate-energy nucleon knockout reactions and for protons from (e,e{sup '}p) reactions on well-bound nuclei.

  5. Spectroscopic studies, potential energy surface and molecular orbital calculations of pramipexole.

    PubMed

    Muthu, S; Uma Maheswari, J; Srinivasan, S; Isac paulraj, E

    2013-11-01

    A systematic vibrational spectroscopic assignment and analysis of pramipexole [(S)-N(6)-propyl-4,5,6,7-tetrahydro-1,3-benzothiazole-2,6-diamine] has been carried out using FT-IR and FT-Raman spectral data. The vibrational analysis was aided by an electronic structure calculation based on the hybrid density functional method B3LYP using a 6-311G(d, p) and cc-pVTZ basis sets. Molecular equilibrium geometries, electronic energies, IR and Raman intensities, harmonic vibrational frequencies have been computed. The assignments are based on the experimental IR and Raman spectra, and a complete assignment of the observed spectra has been proposed. The UV-visible spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies and the maximum absorption λmax were determined by time-dependent DFT (TD-DFT) method. The geometrical parameters, vibrational frequencies and absorption wavelengths were compared with the experimental data. The complete vibrational assignments are performed on the basis of the potential energy distributions (PEDs) of the vibrational modes in terms of natural internal coordinates. The simulated FT-IR, FT-Raman, and UV spectra of the title compound have been constructed. In addition, the potential energy surface, HOMO and LUMO energies, the molecular electrostatic potential and the first-order hyperpolarizability have been computed. The magnitude of the first-order hyperpolarizability is 5 times larger than that of urea and the title compound may be a potential applicant for the development of NLO materials. PMID:23831980

  6. Full potential calculation of electronics and thermoelectric properties of doped Mg{sub 2}Si

    SciTech Connect

    Poopanya, P.; Yangthaisong, A.

    2013-12-04

    We present the calculations of the electronic structure and transport properties on the anti-fluorite Mg{sub 2}Si using the full potential linearized augmented plane-wave (FP-LAPW) method and the semi-classical Boltzmann theory. The modified Becke-Johnson (mBJ) exchange potentials are used to derive energy gaps and correct band gaps according to experimental values. It is found that Mg{sub 2}Si is an indirect band gap (Γ→X) material with the gap of 0.56 eV which is in good agreement with the experimental observation. Note that the band structure of Mg{sub 2}Si is directly used in combination with the semi-classical Boltzmann theory to obtain the transport coefficients. It is found that the material is the n-type semiconductor with the lowest electron concentration of 3.03×10{sup 14} cm{sup −3} at 300 K. We have also calculated the thermoelectric properties of Mg{sub 2}Si based on the rigid band approximation by varying the p-type and n-type doping levels. At room temperature, the highest power factor for p-type and n-type dopants are obtained at the hole and electron concentration of 1.63×10{sup 20} cm{sup −3} and 1.15×1021 cm{sup −3}, respectively. From the electronic states, we also found that the n-type doping region is dominated by the Mg−2p{sup 6} 3s{sup 2} and Si−3p{sup 2} states, while the Mg−2p{sup 6} and Si−3p{sup 2} states are important in the p-type doped Mg{sub 2}Si.

  7. Potential Health Effects from Groundwater Pollution.

    ERIC Educational Resources Information Center

    Goyer, Robert A.

    1985-01-01

    Discusses the growing awareness of potential toxicological effects of synthetic organic chemicals contaminating groundwater. Problems concerning pesticides, chlorination, epidemiologic studies, cancer, nephrotoxicity, and considerations of risk are addressed. Additional research in this area is advocated. (DH)

  8. Calculation of the transport properties of carbon dioxide. II. Thermal conductivity and thermomagnetic effects.

    PubMed

    Bock, Steffen; Bich, Eckard; Vogel, Eckhard; Dickinson, Alan S; Vesovic, Velisa

    2004-05-01

    The transport properties of pure carbon dioxide have been calculated from the intermolecular potential using the classical trajectory method. Results are reported in the dilute-gas limit for thermal conductivity and thermomagnetic coefficients for temperatures ranging from 200 K to 1000 K. Three recent carbon dioxide potential energy hypersurfaces have been investigated. Since thermal conductivity is influenced by vibrational degrees of freedom, not included in the rigid-rotor classical trajectory calculation, a correction for vibration has also been employed. The calculations indicate that the second-order thermal conductivity corrections due to the angular momentum polarization (< 2%) and velocity polarization (< 1%) are both small. Thermal conductivity values calculated using the potential energy hypersurface by Bukowski et al. (1999) are in good agreement with the available experimental data. They underestimate the best experimental data at room temperature by 1% and in the range up to 470 K by 1%-3%, depending on the data source. Outside this range the calculated values, we believe, may be more reliable than the currently available experimental data. Our results are consistent with measurements of the thermomagnetic effect at 300 K only when the vibrational degrees of freedom are considered fully. This excellent agreement for these properties indicates that particularly the potential surface of Bukowski et al. provides a realistic description of the anisotropy of the surface. PMID:15267716

  9. High speed inlet calculations with real gas effects

    NASA Technical Reports Server (NTRS)

    Coirier, William J.

    1988-01-01

    A 2-D steady-state Navier-Stokes solver has been upgraded to include the effects of frozen and equilibrium air chemistry for applications to high speed flight vehicles. To provide a computationally economical first order approximation to the high temperature physics, variable thermodynamic data is used for the chemically frozen mode to allow for a variation with temperature of the air specific heats and enthalpy. For calculations involving air in chemical equilibrium, a specially modified version of the NASA Lewis Chemical Equilibrium Code, CEC, is used to compute the chemical composition and resultant thermochemical properties. The upgraded solver is demonstrated by comparing results from calorically perfect (C sub p=constant), thermally perfect (frozen) and equilibrium air calculations for a variety of geometries, and flight Mach numbers.

  10. Ab initio molecular orbital calculations of DNA radical ions. 5. Scaling of calculated electron affinities and ionization potentials to experimental values

    SciTech Connect

    Sevilla, M.D.; Colson, A.O. ); Besler, B. )

    1995-01-19

    Ab initio molecular orbital calculations of the electron affinities (EAs) and ionization potentials (IPs) of the DNA bases are presented in this work. Comparisons of calculated and experimental values are made for a series of compounds of size and/or structure similar to the DNA bases. Excellent correlations between calculated and experimental values are found for both Koopmans EAs at the 6-31G[sup *] and D95v levels and calculated vertical EAs of the model compounds. Several basis sets are considered: 6-31G[sup *], 6-31+G(d), and D95v. Calculations at 6-31G[sup *] and 6-31+G(d) using both ROHF and ROMP2 theories show a consistent difference between calculated vertical and adiabatic EAs. This allows for a good estimate of DNA base adiabatic EAs. i.e., -0.7, -0.3, 0.2, 0.3, and 0.4 eV; from the vertical EAs -1.23, -0.74, -0.40, -0.32, and -0.19 eV for G, A, C, T, and U respectively. While EAs must be scaled, we find that Koopmans IPs calculated at the simple 3-21G level predict vertical IPs of the DNA bases with only a 0.15 eV average absolute deviation from the experimentally reported values and calculations at MP2/6-31+G(d)//6-31G[sup *] for the adiabatic ionization potentials of the DNA bases are all within 0.1 eV of experiment. 41 refs., 2 figs., 5 tabs.

  11. Perturbative Calculation of Quasi-Potential in Non-equilibrium Diffusions: A Mean-Field Example

    NASA Astrophysics Data System (ADS)

    Bouchet, Freddy; Gawȩdzki, Krzysztof; Nardini, Cesare

    2016-06-01

    In stochastic systems with weak noise, the logarithm of the stationary distribution becomes proportional to a large deviation rate function called the quasi-potential. The quasi-potential, and its characterization through a variational problem, lies at the core of the Freidlin-Wentzell large deviations theory (Freidlin and Wentzell, Random perturbations of dynamical systems, 2012). In many interacting particle systems, the particle density is described by fluctuating hydrodynamics governed by Macroscopic Fluctuation Theory (Bertini et al., arXiv:1404.6466 , 2014), which formally fits within Freidlin-Wentzell's framework with a weak noise proportional to 1/√{N}, where N is the number of particles. The quasi-potential then appears as a natural generalization of the equilibrium free energy to non-equilibrium particle systems. A key physical and practical issue is to actually compute quasi-potentials from their variational characterization for non-equilibrium systems for which detailed balance does not hold. We discuss how to perform such a computation perturbatively in an external parameter λ , starting from a known quasi-potential for λ =0. In a general setup, explicit iterative formulae for all terms of the power-series expansion of the quasi-potential are given for the first time. The key point is a proof of solvability conditions that assure the existence of the perturbation expansion to all orders. We apply the perturbative approach to diffusive particles interacting through a mean-field potential. For such systems, the variational characterization of the quasi-potential was proven by Dawson and Gartner (Stochastics 20:247-308, 1987; Stochastic differential systems, vol 96, pp 1-10, 1987). Our perturbative analysis provides new explicit results about the quasi-potential and about fluctuations of one-particle observables in a simple example

  12. Perturbative Calculation of Quasi-Potential in Non-equilibrium Diffusions: A Mean-Field Example

    NASA Astrophysics Data System (ADS)

    Bouchet, Freddy; Gawȩdzki, Krzysztof; Nardini, Cesare

    2016-04-01

    In stochastic systems with weak noise, the logarithm of the stationary distribution becomes proportional to a large deviation rate function called the quasi-potential. The quasi-potential, and its characterization through a variational problem, lies at the core of the Freidlin-Wentzell large deviations theory (Freidlin and Wentzell, Random perturbations of dynamical systems, 2012). In many interacting particle systems, the particle density is described by fluctuating hydrodynamics governed by Macroscopic Fluctuation Theory (Bertini et al., arXiv:1404.6466, 2014), which formally fits within Freidlin-Wentzell's framework with a weak noise proportional to 1/√{N} , where N is the number of particles. The quasi-potential then appears as a natural generalization of the equilibrium free energy to non-equilibrium particle systems. A key physical and practical issue is to actually compute quasi-potentials from their variational characterization for non-equilibrium systems for which detailed balance does not hold. We discuss how to perform such a computation perturbatively in an external parameter λ , starting from a known quasi-potential for λ =0 . In a general setup, explicit iterative formulae for all terms of the power-series expansion of the quasi-potential are given for the first time. The key point is a proof of solvability conditions that assure the existence of the perturbation expansion to all orders. We apply the perturbative approach to diffusive particles interacting through a mean-field potential. For such systems, the variational characterization of the quasi-potential was proven by Dawson and Gartner (Stochastics 20:247-308, 1987; Stochastic differential systems, vol 96, pp 1-10, 1987). Our perturbative analysis provides new explicit results about the quasi-potential and about fluctuations of one-particle observables in a simple example of mean field diffusions: the Shinomoto-Kuramoto model of coupled rotators (Prog Theoret Phys 75:1105-1110, [74]). This

  13. Radion effective potential in brane gas cosmology

    SciTech Connect

    Kim, Jin Young

    2008-09-15

    We consider a cosmological solution which can explain anisotropic evolution of spatial dimensions and the stabilization of extra dimensions in brane gas formalism. We evaluate the effective potentials, induced by brane gas, bulk flux and supergravity particles, which govern the sizes of the observed three and the extra dimensions. It is possible that the wrapped internal volume can oscillate between two turning points or sit at the minimum of the potential while the unwrapped three-dimensional volume can expand monotonically. Including the supergravity particles makes the effective potential steeper as the internal volume shrinks.

  14. A comparison of estimated and calculated effective porosity

    NASA Astrophysics Data System (ADS)

    Stephens, Daniel B.; Hsu, Kuo-Chin; Prieksat, Mark A.; Ankeny, Mark D.; Blandford, Neil; Roth, Tracy L.; Kelsey, James A.; Whitworth, Julia R.

    Effective porosity in solute-transport analyses is usually estimated rather than calculated from tracer tests in the field or laboratory. Calculated values of effective porosity in the laboratory on three different textured samples were compared to estimates derived from particle-size distributions and soil-water characteristic curves. The agreement was poor and it seems that no clear relationships exist between effective porosity calculated from laboratory tracer tests and effective porosity estimated from particle-size distributions and soil-water characteristic curves. A field tracer test in a sand-and-gravel aquifer produced a calculated effective porosity of approximately 0.17. By comparison, estimates of effective porosity from textural data, moisture retention, and published values were approximately 50-90% greater than the field calibrated value. Thus, estimation of effective porosity for chemical transport is highly dependent on the chosen transport model and is best obtained by laboratory or field tracer tests. Résumé La porosité effective dans les analyses de transport de soluté est habituellement estimée, plutôt que calculée à partir d'expériences de traçage sur le terrain ou au laboratoire. Les valeurs calculées de la porosité effective au laboratoire sur trois échantillons de textures différentes ont été comparées aux estimations provenant de distributions de taille de particules et de courbes caractéristiques sol-eau. La concordance était plutôt faible et il semble qu'il n'existe aucune relation claire entre la porosité effective calculée à partir des expériences de traçage au laboratoire et la porosité effective estimée à partir des distributions de taille de particules et de courbes caractéristiques sol-eau. Une expérience de traçage de terrain dans un aquifère de sables et de graviers a fourni une porosité effective calculée d'environ 0,17. En comparaison, les estimations de porosité effective de données de

  15. Electron Affinity Calculations for Atoms: Sensitive Probe of Many-Body Effects

    NASA Astrophysics Data System (ADS)

    Felfli, Z.; Msezane, A. Z.

    2016-05-01

    Electron-electron correlations and core-polarization interactions are crucial for the existence and stability of most negative ions. Therefore, they can be used as a sensitive probe of many-body effects in the calculation of the electron affinities (EAs) of atoms. The importance of relativistic effects in the calculation of the EAs of atoms has recently been assessed to be insignificant up to Z of 85. Here we use the complex angular momentum (CAM) methodology wherein is embedded fully the electron-electron correlations, to investigate core-polarization interactions in low-energy electron elastic scattering from the atoms In, Sn, Eu, Au and At through the calculation of their EAs. For the core-polarization interaction we use the rational function approximation of the Thomas-Fermi potential, which can be analytically continued into the complex plane. The EAs are extracted from the large resonance peaks in the CAM calculated low-energy electron-atom scattering total cross sections and compared with those from measurements and sophisticated theoretical methods. It is concluded that when the electron-electron correlations and core polarization interactions (both major many-body effects) are accounted for adequately the importance of relativity on the calculation of the EAs of atoms can be assessed. Even for the high Z (85) At atom relativistic effects are estimated to contribute a maximum of 3.6% to its EA calculation.

  16. Dynamics study of the OH + NH3 hydrogen abstraction reaction using QCT calculations based on an analytical potential energy surface

    NASA Astrophysics Data System (ADS)

    Monge-Palacios, M.; Corchado, J. C.; Espinosa-Garcia, J.

    2013-06-01

    To understand the reactivity and mechanism of the OH + NH3 → H2O + NH2 gas-phase reaction, which evolves through wells in the entrance and exit channels, a detailed dynamics study was carried out using quasi-classical trajectory calculations. The calculations were performed on an analytical potential energy surface (PES) recently developed by our group, PES-2012 [Monge-Palacios et al. J. Chem. Phys. 138, 084305 (2013)], 10.1063/1.4792719. Most of the available energy appeared as H2O product vibrational energy (54%), reproducing the only experimental evidence, while only the 21% of this energy appeared as NH2 co-product vibrational energy. Both products appeared with cold and broad rotational distributions. The excitation function (constant collision energy in the range 1.0-14.0 kcal mol-1) increases smoothly with energy, contrasting with the only theoretical information (reduced-dimensional quantum scattering calculations based on a simplified PES), which presented a peak at low collision energies, related to quantized states. Analysis of the individual reactive trajectories showed that different mechanisms operate depending on the collision energy. Thus, while at high energies (Ecoll ≥ 6 kcal mol-1) all trajectories are direct, at low energies about 20%-30% of trajectories are indirect, i.e., with the mediation of a trapping complex, mainly in the product well. Finally, the effect of the zero-point energy constraint on the dynamics properties was analyzed.

  17. Accelerating quantum instanton calculations of the kinetic isotope effects.

    PubMed

    Karandashev, Konstantin; Vaníček, Jiří

    2015-11-21

    Path integral implementation of the quantum instanton approximation currently belongs among the most accurate methods for computing quantum rate constants and kinetic isotope effects, but its use has been limited due to the rather high computational cost. Here, we demonstrate that the efficiency of quantum instanton calculations of the kinetic isotope effects can be increased by orders of magnitude by combining two approaches: The convergence to the quantum limit is accelerated by employing high-order path integral factorizations of the Boltzmann operator, while the statistical convergence is improved by implementing virial estimators for relevant quantities. After deriving several new virial estimators for the high-order factorization and evaluating the resulting increase in efficiency, using ⋅Hα + HβHγ → HαHβ + ⋅ Hγ reaction as an example, we apply the proposed method to obtain several kinetic isotope effects on CH4 + ⋅ H ⇌ ⋅ CH3 + H2 forward and backward reactions. PMID:26590524

  18. Effect of hemodialysis on intraocular lens power calculation.

    PubMed

    Çalışkan, Sinan; Çelikay, Osman; Biçer, Tolga; Aylı, Mehmet Deniz; Gürdal, Canan

    2016-03-01

    Background To evaluate changes in ocular biometric parameters after hemodialysis (HD) in patients with end-stage renal disease (ESRD). Methods Forty eyes of 40 patients undergoing HD were included in this cross-sectional study. Keratometry (K) readings, white-to-white (WTW) distance, central corneal thickness (CCT), anterior chamber depth (ACD), pupil diameter, lens thickness (LT), axial length (AL), and intraocular lens (IOL) power calculation were measured with Lenstar LS 900 (Haag Streit AG, Koeniz, Switzerland) before and after hemodialysis. Intraocular pressure (IOP) was measured with a non-contact tonometer (Tonopachy NT-530P, Nidek Co., LTD, Tokyo, Japan). Main outcomes were changes in biometric parameters after HD. Reliability of the measurements (intraclass correlation coefficients (ICCs)) and the effect size (Cohen's d) were also calculated. Results Mean difference in AL before and after HD was -0.041 ± 0.022 mm with ICCs > 0.90 (p < 0.001 and Cohen's d = 0.06). Pupil diameter was also significantly different before (4.28 ± 0.81 mm) and after (4.44 ± 0.79 mm) HD with ICCs > 0.90 (p = 0.041 and Cohen's d = 0.20). Hemodialysis had no significant effect on K readings, WTW distance, CCT, ACD, LT, or IOP. Conclusion Axial length and pupil diameter increase after HD with small effect size, while HD does not significantly affect IOL power calculations. PMID:26707804

  19. Calculating effective resistances on underlying networks of association schemes

    NASA Astrophysics Data System (ADS)

    Jafarizadeh, M. A.; Sufiani, R.; Jafarizadeh, S.

    2008-07-01

    Recently, in the work of Jafarizadeh et al. [J. Phys, A: Math. Theor. 40, 4949 (2007); e-print arXiv:0705.2480], calculation of effective resistances on distance-regular networks was investigated, where in the first paper, the calculation was based on stratification and Stieltjes functions associated with the network, whereas in the latter one a recursive formula for effective resistances was given based on the Christoffel-Darboux identity. In this paper, evaluation of effective resistances on more general networks that are underlying networks of association schemes is considered, where by using the algebraic combinatoric structures of association schemes such as stratification and Bose-Mesner algebras, an explicit formula for effective resistances on these networks is given in terms of the parameters of the corresponding association schemes. Moreover, we show that for particular underlying networks of association schemes with diameter d such that the adjacency matrix A possesses d +1 distinct eigenvalues, all of the other adjacency matrices Ai, i ≠0, 1 can be written as polynomials of A, i.e., Ai=Pi(A), where Pi is not necessarily of degree i. Then, we use this property for these particular networks and assume that all of the conductances except for one of them, say, c ≡c1=1, are zero to give a procedure for evfor a galuating effective resistances on these networks. The preference of this procedure is that one can evaluate effective resistances by using the structure of their Bose-Mesner algebra without any need to know the spectrum of the adjacency matrices.

  20. SUSY Spectrum Calculator Effects on Dark Matter Observables

    NASA Astrophysics Data System (ADS)

    Bergeron, Paul

    2016-03-01

    Due to questions like the dark matter and hierarchy problem, searches for physics beyond the Standard Model (SM) have not only moved beyond the simplest extensions but the LHC has offered the first tantalizing hints of a new particle at 750 GeV. But as we move into new regimes beyond the minimal extensions to the SM, we need to ask ourselves how accurate are our existing simulations of theory therein? In my talk I will explore the effects of different supersymmetric, spectrum calculators (e.g. ISAJET and SPheno) on predictions for dark matter and Higgs sector observables.

  1. Full potential calculations on the electron bandstructures of Sphalerite, Pyrite and Chalcopyrite

    NASA Astrophysics Data System (ADS)

    Edelbro, R.; Sandström, Å.; Paul, J.

    2003-02-01

    The bulk electronic structures of Sphalerite, Pyrite and Chalcopyrite have been calculated within an ab initio, full potential, density functional approach. The exchange term was approximated with the Dirac exchange functional, the Vosko-Wilk-Nusair parameterization of the Cepler-Alder free electron gas was used for correlation and linear combinations of Gaussian type orbitals were used as basis functions. The Sphalerite (zinc blende) band gap was calculated to be direct with a width of 2.23 eV. The Sphalerite valence band was 5.2 eV wide and composed of a mixture of sulfur and zinc orbitals. The band below the valence band located around -6.2 eV was mainly composed of Zn 3d orbitals. The S 3s orbitals gave rise to a band located around -12.3 eV. Pyrite was calculated to be a semiconductor with an indirect band gap of 0.51 eV, and a direct gap of 0.55 eV. The valence band was 1.25 eV wide and mainly composed of non-bonding Fe 3d orbitals. The band below the valence band was 4.9 eV wide and composed of a mixture of sulfur and iron orbitals. Due to the short inter-atomic distance between the sulfur dumbbells, the S 3s orbitals in Pyrite were split into a bonding and an anti-bonding range. Chalcopyrite was predicted to be a conductor, with no band-crossings at the Fermi level. The bands at -13.2 eV originate from the sulfur 3s orbitals and were quite similar to the sulfur 3s bands in Sphalerite, though somewhat shifted to lower energy. The top of the valence band consisted of a mixture of orbitals from all the atoms. The lower part of the same band showed metal character. Computational modeling as a tool for illuminating the flotation and leaching processes of Pyrite and Chalcopyrite, in connection with surface science experiments, is discussed.

  2. Calculations of the Triton Binding Energy with a Lorentz Boosted Nucleon-Nucleon Potential

    NASA Astrophysics Data System (ADS)

    Kamada, H.; Glöckle, W.; Witała, H.; Golak, J.; Skibiński, R.; Polyzou, W. N.; Elster, Ch.

    2010-04-01

    We study the binding energy of the three-nucleon system in relativistic models that use two different relativistic treatments of the potential that are phase equivalent to realistic NN interactions. One is based on a unitary scale transformation that relates the non-relativistic center-of-mass Hamiltonian to the relativistic mass (rest energy) operator and the other uses a non-linear equation that relates the interaction in the relativistic mass operator to the non-relativistic interaction. In both cases Lorentz-boosted interactions are used in the relativistic Faddeev equation to solve for the three-nucleon binding energy. Using the same realistic NN potentials as input, the solution of the relativistic three-nucleon Faddeev equation for 3H shows slightly less binding energy than the corresponding nonrelativistic result. The effect of the Wigner spin rotation on the binding is very small.

  3. Dechanneling of Positrons in Disordered Lattices Effect of Anharmonic Potential

    NASA Astrophysics Data System (ADS)

    Abu-Assy, M. K.; El-Ashry, M. Y.; Mohamed, A. A.

    2005-01-01

    Dechanneling of positrons due to lattice disorder has been investigated for two stable configurations of the disordered face-centered cubic(fcc) lattices, Dumb-bell configuration (DBC) and Body-centered interstitial (BCI) for channeled positrons with incident energy (10 200) MeV in Cu single crystal in the planar direction (100). The effects of anharmonic terms in the channeling potential have been considered in the calculations. The calculations covered the transition-channeling probability, dechanneling probability, transmission and dechanneling coefficients. It has been found that the transition-channeling probability from the normal into the disordered region occurs only for the transitions n (normal) → n (disordered). Also the dependence of the transmission and dechanneling coefficients on the incident beam position has been studied by using a planar potential function based on shell structure model and compared with the results of a planar potential based on Lindhard's model.

  4. Hybrid density functional calculations of redox potentials and formation energies of transition metal compounds

    NASA Astrophysics Data System (ADS)

    Chevrier, V. L.; Ong, S. P.; Armiento, R.; Chan, M. K. Y.; Ceder, G.

    2010-08-01

    We compare the accuracy of conventional semilocal density functional theory (DFT), the DFT+U method, and the Heyd-Scuseria-Ernzerhof (HSE06) hybrid functional for structural parameters, redox reaction energies, and formation energies of transition metal compounds. Conventional DFT functionals significantly underestimate redox potentials for these compounds. Zhou [Phys. Rev. B 70, 235121 (2004)]10.1103/PhysRevB.70.235121 addressed this issue with DFT+U and a linear-response scheme for calculating U values. We show that the Li intercalation potentials of prominent Li-ion intercalation battery materials, such as the layered LixMO2 ( M=Co and Ni), LixTiS2 ; olivine LixMPO4 ( M=Mn , Fe, Co, and Ni); and spinel-like LixMn2O4 , LixTi2O4 , are also well reproduced by HSE06, due to the self-interaction error correction from the partial inclusion of Hartree-Fock exchange. For formation energies, HSE06 performs well for transition metal compounds, which typically are not well reproduced by conventional DFT functionals but does not significantly improve the results of nontransition metal oxides. Hence, we find that hybrid functionals provide a good alternative to DFT+U for transition metal applications when the large extra computational effort is compensated by the benefits of (i) avoiding species-specific adjustable parameters and (ii) a more universal treatment of the self-interaction error that is not exclusive to specific atomic orbital projections on selected ions.

  5. Calculation of effective doses for broad parallel photon beams.

    PubMed

    Kim, C H; Reece, W D; Poston, J W

    1999-02-01

    Values of effective dose (E) were calculated for the entire range of incident directions of broad parallel photon beams for selected photon energies using the Monte Carlo N-Particle (MCNP) transport code with a hermaphroditic phantom. The calculated results are presented in terms of conversion coefficients transforming air kerma to effective dose. This study also compared the numerical values of E and H(E) over the entire range of incident beam directions. E was always less than H(E) considering all beam directions and photon energies, but the differences were not significant except when a photon beam approaches some specific directions (overhead and underfoot). This result suggests that the current H(E) values can be directly interpreted as E or, at least, as a conservative value of E without knowing the details of irradiation geometries. Finally, based on the distributions of H(E) and E over the beam directions, this study proposes ideal angular response factors for personal dosimeters that can be used to improve the angular response properties of personal dosimeters for off-normal incident photons. PMID:9929126

  6. Analysis of water flow paths: methodology and example calculations for a potential geological repository in Sweden.

    PubMed

    Werner, Kent; Bosson, Emma; Berglund, Sten

    2006-12-01

    Safety assessment related to the siting of a geological repository for spent nuclear fuel deep in the bedrock requires identification of potential flow paths and the associated travel times for radionuclides originating at repository depth. Using the Laxemar candidate site in Sweden as a case study, this paper describes modeling methodology, data integration, and the resulting water flow models, focusing on the Quaternary deposits and the upper 150 m of the bedrock. Example simulations identify flow paths to groundwater discharge areas and flow paths in the surface system. The majority of the simulated groundwater flow paths end up in the main surface waters and along the coastline, even though the particles used to trace the flow paths are introduced with a uniform spatial distribution at a relatively shallow depth. The calculated groundwater travel time, determining the time available for decay and retention of radionuclides, is on average longer to the coastal bays than to other biosphere objects at the site. Further, it is demonstrated how GIS-based modeling can be used to limit the number of surface flow paths that need to be characterized for safety assessment. Based on the results, the paper discusses an approach for coupling the present models to a model for groundwater flow in the deep bedrock. PMID:17334050

  7. Molecular electrostatic potential at the atomic sites in the effective core potential approximation.

    PubMed

    Lesiuk, Michał; Zachara, Janusz

    2013-02-21

    Considering calculations of the molecular electrostatic potential at the atomic sites (MEP@AS) in the presence of effective core potentials (ECP), we found that the consequent use of the definition of MEP@AS based on the energy derivative with respect to nuclear charge leads to a formula that differs by one term from the result of simple application of Coulomb's law. We have developed a general method to analytically treat derivatives of ECP with respect to nuclear charge. Benchmarking calculations performed on a set of simple molecules show that our formula leads to a systematic decrease in the error connected with the introduction of ECP when compared to all-electron results. Because of a straightforward implementation and relatively low costs of the developed procedure we suggest to use it by default. PMID:23444997

  8. Molecular electrostatic potential at the atomic sites in the effective core potential approximation

    NASA Astrophysics Data System (ADS)

    Lesiuk, Michał; Zachara, Janusz

    2013-02-01

    Considering calculations of the molecular electrostatic potential at the atomic sites (MEP@AS) in the presence of effective core potentials (ECP), we found that the consequent use of the definition of MEP@AS based on the energy derivative with respect to nuclear charge leads to a formula that differs by one term from the result of simple application of Coulomb's law. We have developed a general method to analytically treat derivatives of ECP with respect to nuclear charge. Benchmarking calculations performed on a set of simple molecules show that our formula leads to a systematic decrease in the error connected with the introduction of ECP when compared to all-electron results. Because of a straightforward implementation and relatively low costs of the developed procedure we suggest to use it by default.

  9. Numerical calculation of steady inviscid full potential compressible flow about wind turbine blades

    NASA Technical Reports Server (NTRS)

    Dulikravich, D. S.

    1980-01-01

    The air flow through a propeller-type wind turbine rotor is characterized by three-dimensional rotating cascade effects about the inner portions of the rotor blades and compressibility effects about the tip regions of the blades. In the case of large rotor diameter and/or increased rotor angular speed, the existence of small supersonic zones terminated by weak shocks is possible. An exact nonlinear mathematical model (called a steady Full Potential Equation - FPE) that accounts for the above phenomena has been rederived. An artificially time dependent version of FPE was iteratively solved by a finite volume technique involving an artificial viscosity and a three-level consecutive mesh refinement. The exact boundary conditions were applied by generating a boundary conforming periodic computation mesh.

  10. VORSTAB: A computer program for calculating lateral-directional stability derivatives with vortex flow effect

    NASA Technical Reports Server (NTRS)

    Lan, C. Edward

    1985-01-01

    A computer program based on the Quasi-Vortex-Lattice Method of Lan is presented for calculating longitudinal and lateral-directional aerodynamic characteristics of nonplanar wing-body combination. The method is based on the assumption of inviscid subsonic flow. Both attached and vortex-separated flows are treated. For the vortex-separated flow, the calculation is based on the method of suction analogy. The effect of vortex breakdown is accounted for by an empirical method. A summary of the theoretical method, program capabilities, input format, output variables and program job control set-up are described. Three test cases are presented as guides for potential users of the code.

  11. Effects of potential functions on stochastic resonance

    NASA Astrophysics Data System (ADS)

    Li, Jian-Long; Zeng, Ling-Zao

    2011-01-01

    In this paper, the effects of a bistable potential function U(x) = —ax2/2 + b|x|2γ/(2γ) on stochastic resonance (SR) is discussed. We investigate the effects of index γ on the performance of the SR system with fixed parameters a and b, and with fixed potential barriers, respectively. To measure the performance of the SR system in the presence of an aperiodic input, the bit error rate is employed, as is commonly used in binary communications. The numerical simulations strongly support the theoretical results. The goal of this investigation is to explore the effects of the shape of potential functions on SR and give a guidance of nonlinear systems in the application of information processing.

  12. A new hydrocarbon empirical potential in angle bending calculation for the molecular dynamics simulation

    SciTech Connect

    Ping, Tan Ai; Hoe, Yeak Su

    2014-07-10

    Typically, short range potential only depends on neighbouring atoms and its parameters function can be categorized into bond stretching, angle bending and bond rotation potential. In this paper, we present our work called Angle Bending (AB) potential, whereas AB potential is the extension of our previous work namely Bond Stretching (BS) potential. Basically, potential will tend to zero after truncated region, potential in specific region can be represented by different piecewise polynomial. We proposed the AB piecewise potential which is possible to solve a system involving three atoms. AB potential able to handle the potential of covalent bonds for three atoms as well as two atoms cases due to its degeneracy properties. Continuity for the piecewise polynomial has been enforced by coupling with penalty methods. There are still plenty of improvement spaces for this AB potential. The improvement for three atoms AB potential will be studied and further modified into torsional potential which are the ongoing current research.

  13. Environmental Perchlorate Exposure: Potential Adverse Thyroid Effects

    PubMed Central

    Leung, Angela M.; Pearce, Elizabeth N.; Braverman, Lewis E.

    2014-01-01

    Purpose of review This review will present a general overview of the sources, human studies, and proposed regulatory action regarding environmental perchlorate exposure. Recent findings Some recent studies have reported significant associations between urinary perchlorate concentrations, thyroid dysfunction, and decreased infant IQ in groups who would be particularly susceptible to perchlorate effects. An update regarding the recent proposed regulatory actions and potential costs surrounding amelioration of perchlorate contamination is provided. Summary The potential adverse thyroidal effects of environmental perchlorate exposure remain controversial, and further research is needed to further define its relationship to human health among pregnant and lactating women and their infants. PMID:25106002

  14. Electron structure of molecules with very heavy atoms using effective core potentials

    SciTech Connect

    Pitzer, K.S.

    1982-01-01

    Topics covered include effective potential, Hamiltonian for valence-electron motion, molecular calculations, spin-spin coupling, L-S coupling, numerical results of molecular calculations, and results of configuration-interaction Slater-orbital calculations in L-S coupling. (GHT)

  15. The Effects of Relativity on First-Principles Calculations

    NASA Astrophysics Data System (ADS)

    Semi, T.; Mattsson, A. E.; Wills, J. M.

    2011-06-01

    The construction of the equation of state for a given material is of central importance to its characterization. Hugoniots can be calculated using Density Functional Theory (DFT), and DFT points compared to available experimental results. By evaluating the accuracy in a relevant phase space, confidence is gained in the DFT method. This bolsters the dependability of DFT data in phase spaces in which experiment may be difficult or impossible to perform, and verifies its usefulness. The equation of state is comprised of the cold curve and thermal electronic and ionic terms. We discuss differences in the cold curve of Ce produced by first principles calculations using the Scalar Dirac equation with variational spin-orbit coupling treatment and that generated by the full relativistic formulation, both with the same DFT functionals. The relativistic effects of f-electrons in systems like Ce are expected to be of a magnitude substantial enough to be consequential to the description of these structures. ``Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.''

  16. Dynamical properties of non-ideal plasma on the basis of effective potentials

    SciTech Connect

    Ramazanov, T. S.; Kodanova, S. K.; Moldabekov, Zh. A.; Issanova, M. K.

    2013-11-15

    In this work, stopping power has been calculated on the basis of the Coulomb logarithm using the effective potentials. Calculations of the Coulomb logarithm and stopping power for different interaction potentials and degrees of ionization are compared. The comparison with the data of other theoretical and experimental works was carried out.

  17. Full Dimensional Vibrational Calculations for Methane Using AN Accurate New AB Initio Based Potential Energy Surface

    NASA Astrophysics Data System (ADS)

    Majumder, Moumita; Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker; Li, Jun; Guo, Hua; Manzhos, Sergei

    2014-06-01

    New potential energy surfaces for methane were constructed, represented as analytic fits to about 100,000 individual high-level ab initio data. Explicitly-correlated multireference data (MRCI-F12(AE)/CVQZ-F12) were computed using Molpro [1] and fit using multiple strategies. Fits with small to negligible errors were obtained using adaptations of the permutation-invariant-polynomials (PIP) approach [2,3] based on neural-networks (PIP-NN) [4,5] and the interpolative moving least squares (IMLS) fitting method [6] (PIP-IMLS). The PESs were used in full-dimensional vibrational calculations with an exact kinetic energy operator by representing the Hamiltonian in a basis of products of contracted bend and stretch functions and using a symmetry adapted Lanczos method to obtain eigenvalues and eigenvectors. Very close agreement with experiment was produced from the purely ab initio PESs. References 1- H.-J. Werner, P. J. Knowles, G. Knizia, 2012.1 ed. 2012, MOLPRO, a package of ab initio programs. see http://www.molpro.net. 2- Z. Xie and J. M. Bowman, J. Chem. Theory Comput 6, 26, 2010. 3- B. J. Braams and J. M. Bowman, Int. Rev. Phys. Chem. 28, 577, 2009. 4- J. Li, B. Jiang and Hua Guo, J. Chem. Phys. 139, 204103 (2013). 5- S Manzhos, X Wang, R Dawes and T Carrington, JPC A 110, 5295 (2006). 6- R. Dawes, X-G Wang, A.W. Jasper and T. Carrington Jr., J. Chem. Phys. 133, 134304 (2010).

  18. Calculation of the piezoelectric and flexoelectric effects in nanowires using a decoupled finite element analysis method

    NASA Astrophysics Data System (ADS)

    Zhang, Zhiqiang; Geng, Dalong; Wang, Xudong

    2016-04-01

    A simple and effective decoupled finite element analysis method was developed for simulating both the piezoelectric and flexoelectric effects of zinc oxide (ZnO) and barium titanate (BTO) nanowires (NWs). The piezoelectric potential distribution on a ZnO NW was calculated under three deformation conditions (cantilever, three-point, and four-point bending) and compared to the conventional fully coupled method. The discrepancies of the electric potential maximums from these two methods were found very small, validating the accuracy and effectiveness of the decoupled method. Both ZnO and BTO NWs yielded very similar potential distributions. Comparing the potential distributions induced by the piezoelectric and flexoelectric effects, we identified that the middle segment of a four-point bending NW beam is the ideal place for measuring the flexoelectric coefficient, because the uniform parallel plate capacitor-like potential distribution in this region is exclusively induced by the flexoelectric effect. This decoupled method could provide a valuable guideline for experimental measurements of the piezoelectric effects and flexoelectric effects in the nanometer scale.

  19. Effective potential in density matrix functional theory.

    PubMed

    Nagy, A; Amovilli, C

    2004-10-01

    In the previous paper it was shown that in the ground state the diagonal of the spin independent second-order density matrix n can be determined by solving a single auxiliary equation of a two-particle problem. Thus the problem of an arbitrary system with even electrons can be reduced to a two-particle problem. The effective potential of the two-particle equation contains a term v(p) of completely kinetic origin. Virial theorem and hierarchy of equations are derived for v(p) and simple approximations are proposed. A relationship between the effective potential u(p) of the shape function equation and the potential v(p) is established. PMID:15473719

  20. Coupled generator and combustor performance calculations for potential early commercial MHD power plants

    NASA Technical Reports Server (NTRS)

    Dellinger, T. C.; Hnat, J. G.; Marston, C. H.

    1979-01-01

    A parametric study of the performance of the MHD generator and combustor components of potential early commercial open-cycle MHD/steam power plants is presented. Consideration is given to the effects of air heater system concept, MHD combustor type, coal type, thermal input power, oxygen enrichment of the combustion, subsonic and supersonic generator flow and magnetic field strength on coupled generator and combustor performance. The best performance is found to be attained with a 3000 F, indirectly fired air heater, no oxygen enrichment, Illinois no. 6 coal, a two-stage cyclone combustor with 85% slag rejection, a subsonic generator, and a magnetic field configuration yielding a constant transverse electric field of 4 kV/m. Results indicate that optimum net MHD generator power is generally compressor-power-limited rather than electric-stress-limited, with optimum net power a relatively weak function of operating pressure.

  1. WIND: Computer program for calculation of three dimensional potential compressible flow about wind turbine rotor blades

    NASA Technical Reports Server (NTRS)

    Dulikravich, D. S.

    1980-01-01

    A computer program is presented which numerically solves an exact, full potential equation (FPE) for three dimensional, steady, inviscid flow through an isolated wind turbine rotor. The program automatically generates a three dimensional, boundary conforming grid and iteratively solves the FPE while fully accounting for both the rotating cascade and Coriolis effects. The numerical techniques incorporated involve rotated, type dependent finite differencing, a finite volume method, artificial viscosity in conservative form, and a successive line overrelaxation combined with the sequential grid refinement procedure to accelerate the iterative convergence rate. Consequently, the WIND program is capable of accurately analyzing incompressible and compressible flows, including those that are locally transonic and terminated by weak shocks. The program can also be used to analyze the flow around isolated aircraft propellers and helicopter rotors in hover as long as the total relative Mach number of the oncoming flow is subsonic.

  2. Calculations of effective recombination coefficients for nebular astrophysics

    NASA Astrophysics Data System (ADS)

    Fang, Xuan; Liu, Xiaowei; Storey, Pete J.

    2015-08-01

    In the seemingly well established field of nebular astrophysics, there has been a long-standing dichotomy in plasma diagnostics and heavy elemental abundance determinations using the traditional method based on collisionally excited lines on the one hand, and optical recombination lines/continua, on the other. Several mechanisms have been proposed to explain this fundamental problem. Deep spectroscopy and recombination line analysis of emission line nebulae (planetary nebulae and H II regions) in the past decade have pointed to the existence of another previously unknown component of cold, H-deficient material as the culprit. Better constraints are needed on the physical conditions (electron temperature and density), chemical composition, mass, and spatial distribution of the postulated H-deficient inclusions in order to unravel their astrophysical origins. This requires knowledge of the relevant atomic parameters, most importantly the effective recombination coefficients of abundant heavy element ions, such as C II, O II, N II, and Ne II, appropriate for the physical conditions prevailing in those cold inclusions (e.g., electron temperature Te < 1000 K).In this contribution, I will introduce the creation of new effective recombination coefficients for the heavy element optical recombination lines, and review the recent progress in nebular astrophysics since the availability of new and high-quality atomic data. I will also present our new calculations of the effective recombination coefficients for the Ne II recombination line spectrum.

  3. Accelerating quantum instanton calculations of the kinetic isotope effects

    SciTech Connect

    Karandashev, Konstantin; Vaníček, Jiří

    2015-11-21

    Path integral implementation of the quantum instanton approximation currently belongs among the most accurate methods for computing quantum rate constants and kinetic isotope effects, but its use has been limited due to the rather high computational cost. Here, we demonstrate that the efficiency of quantum instanton calculations of the kinetic isotope effects can be increased by orders of magnitude by combining two approaches: The convergence to the quantum limit is accelerated by employing high-order path integral factorizations of the Boltzmann operator, while the statistical convergence is improved by implementing virial estimators for relevant quantities. After deriving several new virial estimators for the high-order factorization and evaluating the resulting increase in efficiency, using ⋅H{sub α} + H{sub β}H{sub γ} → H{sub α}H{sub β} + ⋅ H{sub γ} reaction as an example, we apply the proposed method to obtain several kinetic isotope effects on CH{sub 4} + ⋅ H ⇌ ⋅ CH{sub 3} + H{sub 2} forward and backward reactions.

  4. Electrode contamination effects of retarding potential analyzer.

    PubMed

    Fang, H K; Oyama, K-I; Cheng, C Z

    2014-01-01

    The electrode contamination in electrostatic analyzers such as Langmuir probes and retarding potential analyzers (RPA) is a serious problem for space measurements. The contamination layer acts as extra capacitance and resistance and leads to distortion in the measured I-V curve, which leads to erroneous measurement results. There are two main effects of the contamination layer: one is the impedance effect and the other is the charge attachment and accumulation due to the capacitance. The impedance effect can be reduced or eliminated by choosing the proper sweeping frequency. However, for RPA the charge accumulation effect becomes serious because the capacitance of the contamination layer is much larger than that of the Langmuir probe of similar dimension. The charge accumulation on the retarding potential grid causes the effective potential, that ions experience, to be changed from the applied voltage. Then, the number of ions that can pass through the retarding potential grid to reach the collector and, thus, the measured ion current are changed. This effect causes the measured ion drift velocity and ion temperature to be changed from the actual values. The error caused by the RPA electrode contamination is expected to be significant for sounding rocket measurements with low rocket velocity (1-2 km/s) and low ion temperature of 200-300 K in the height range of 100-300 km. In this paper we discuss the effects associated with the RPA contaminated electrodes based on theoretical analysis and experiments performed in a space plasma operation chamber. Finally, the development of a contamination-free RPA for sounding rocket missions is presented. PMID:24517809

  5. Symmetry preserving optimised effective potential theory (application to atoms)

    NASA Astrophysics Data System (ADS)

    Theophilou, Andreas K.; Papaconstantinou, Petros G.; Glushkov, Vitaly

    2006-02-01

    In this paper, general symmetry properties of physical systems are used in order to produce a mapping of the external potential of a many electron system to its optimized effective potential (OEP). The so derived effective potential is used to calculate the OEP ground state energies and spin orbitals. Applications are made to atoms and ions and the results are compared to those of the exact Hartree-Fock approximation. The relative deviations from the exact HF theory (triangleE/E) are of the order of 10-4. The same holds for molecules. One of the features of the present theory is that the many electron wave functions derived by the present method, transform according to the irreducible representations of the exact states.

  6. Potential effects on health of global warming

    SciTech Connect

    Haines, A. . Whittington Hospital); Parry, M. . Environmental Change Unit)

    1993-12-01

    Prediction of the impacts of global climate change on health is complicated by a number of factors. These include: the difficulty in predicting regional changes in climate, the capacity for adaptation to climate change, the interactions between the effects of global climate change and a number of other key determinants of health, including population growth and poverty, and the availability of adequate preventive and curative facilities for diseases that may be effected by climate change. Nevertheless, it is of importance to consider the potential health impacts of global climate change for a number of reasons. It is also important to monitor diseases which could be effected by climate change in order to detect changes in incidence as early as possible and study possible interactions with other factors. It seems likely that the possible impacts on health of climate change will be a major determinant of the degree to which policies aimed at reducing global warming are followed, as perceptions of the effect of climate change to human health and well-being are particularly likely to influence public opinion. The potential health impacts of climate change can be divided into direct (primary) and indirect (secondary and tertiary) effects. Primary effects are those related to the effect of temperature on human well-being and disease. Secondary effects include the impacts on health of changes in food production, availability of water and of sea level rise. A tertiary level of impacts can also be hypothesized.

  7. An effective algorithm for calculating the Chandrasekhar function

    NASA Astrophysics Data System (ADS)

    Jablonski, A.

    2012-08-01

    Numerical values of the Chandrasekhar function are needed with high accuracy in evaluations of theoretical models describing electron transport in condensed matter. An algorithm for such calculations should be possibly fast and also accurate, e.g. an accuracy of 10 decimal digits is needed for some applications. Two of the integral representations of the Chandrasekhar function are prospective for constructing such an algorithm, but suitable transformations are needed to obtain a rapidly converging quadrature. A mixed algorithm is proposed in which the Chandrasekhar function is calculated from two algorithms, depending on the value of one of the arguments. Catalogue identifier: AEMC_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 567 No. of bytes in distributed program, including test data, etc.: 4444 Distribution format: tar.gz Programming language: Fortran 90 Computer: Any computer with a FORTRAN 90 compiler Operating system: Linux, Windows 7, Windows XP RAM: 0.6 Mb Classification: 2.4, 7.2 Nature of problem: An attempt has been made to develop a subroutine that calculates the Chandrasekhar function with high accuracy, of at least 10 decimal places. Simultaneously, this subroutine should be very fast. Both requirements stem from the theory of electron transport in condensed matter. Solution method: Two algorithms were developed, each based on a different integral representation of the Chandrasekhar function. The final algorithm is edited by mixing these two algorithms and by selecting ranges of the argument ω in which performance is the fastest. Restrictions: Two input parameters for the Chandrasekhar function, x and ω (notation used in the code), are restricted to the range: 0⩽x⩽1 and 0⩽ω⩽1

  8. Effects of Fast Simple Numerical Calculation Training on Neural Systems

    PubMed Central

    Takeuchi, Hikaru; Nagase, Tomomi; Taki, Yasuyuki; Sassa, Yuko; Hashizume, Hiroshi; Nouchi, Rui; Kawashima, Ryuta

    2016-01-01

    Cognitive training, including fast simple numerical calculation (FSNC), has been shown to improve performance on untrained processing speed and executive function tasks in the elderly. However, the effects of FSNC training on cognitive functions in the young and on neural mechanisms remain unknown. We investigated the effects of 1-week intensive FSNC training on cognitive function, regional gray matter volume (rGMV), and regional cerebral blood flow at rest (resting rCBF) in healthy young adults. FSNC training was associated with improvements in performance on simple processing speed, speeded executive functioning, and simple and complex arithmetic tasks. FSNC training was associated with a reduction in rGMV and an increase in resting rCBF in the frontopolar areas and a weak but widespread increase in resting rCBF in an anatomical cluster in the posterior region. These results provide direct evidence that FSNC training alone can improve performance on processing speed and executive function tasks as well as plasticity of brain structures and perfusion. Our results also indicate that changes in neural systems in the frontopolar areas may underlie these cognitive improvements. PMID:26881117

  9. Effect of composition on antiphase boundary energy in Ni3Al based alloys: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Gorbatov, O. I.; Lomaev, I. L.; Gornostyrev, Yu. N.; Ruban, A. V.; Furrer, D.; Venkatesh, V.; Novikov, D. L.; Burlatsky, S. F.

    2016-06-01

    The effect of composition on the antiphase boundary (APB) energy of Ni-based L 12-ordered alloys is investigated by ab initio calculations employing the coherent potential approximation. The calculated APB energies for the {111} and {001} planes reproduce experimental values of the APB energy. The APB energies for the nonstoichiometric γ' phase increase with Al concentration and are in line with the experiment. The magnitude of the alloying effect on the APB energy correlates with the variation of the ordering energy of the alloy according to the alloying element's position in the 3 d row. The elements from the left side of the 3 d row increase the APB energy of the Ni-based L 12-ordered alloys, while the elements from the right side slightly affect it except Ni. The way to predict the effect of an addition on the {111} APB energy in a multicomponent alloy is discussed.

  10. On Effective Potential in Tortoise Coordinate

    NASA Astrophysics Data System (ADS)

    Ganjali, M. A.

    2012-08-01

    In this paper, we study the field dynamics in Tortoise coordinate where the equation of motion of a scalar can be written as Schrodinger-like form. We obtain a general form for effective potential by finding the Schrodinger equation for scalar and spinor fields and study its global behavior in some black hole backgrounds in three dimension such as BTZ black holes, new type black holes and black holes with no horizon. Especially, we study the asymptotic behavior of potential at infinity, horizons and origin and find that its asymptotic in BTZ and new type solution is completely different from that of vanishing horizon solution. In fact, potential for vanishing horizon goes to a fixed quantity at infinity, while in BTZ and new type black hole we have an infinite barrier.

  11. Potential health effects of space radiation

    NASA Technical Reports Server (NTRS)

    Yang, Chui-Hsu; Craise, Laurie M.

    1993-01-01

    Crewmembers on missions to the Moon or Mars will be exposed to radiation belts, galactic cosmic rays, and possibly solar particle events. The potential health hazards due to these space radiations must be considered carefully to ensure the success of space exploration. Because there is no human radioepidemiological data for acute and late effects of high-LET (Linear-Energy-Transfer) radiation, the biological risks of energetic charged particles have to be estimated from experimental results on animals and cultured cells. Experimental data obtained to date indicate that charged particle radiation can be much more effective than photons in causing chromosome aberrations, cell killing, mutation, and tumor induction. The relative biological effectiveness (RBE) varies with biological endpoints and depends on the LET of heavy ions. Most lesions induced by low-LET radiation can be repaired in mammalian cells. Energetic heavy ions, however, can produce large complex DNA damages, which may lead to large deletions and are irreparable. For high-LET radiation, therefore, there are less or no dose rate effects. Physical shielding may not be effective in minimizing the biological effects on energetic heavy ions, since fragments of the primary particles can be effective in causing biological effects. At present the uncertainty of biological effects of heavy particles is still very large. With further understanding of the biological effects of space radiation, the career doses can be kept at acceptable levels so that the space radiation environment need not be a barrier to the exploitation of the promise of space.

  12. Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

    SciTech Connect

    Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

    2015-05-21

    The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H{sub 2}O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0–4000 cm{sup −1} is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

  13. Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

    NASA Astrophysics Data System (ADS)

    Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

    2015-05-01

    The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm-1 is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

  14. Potential human health effects of acid rain

    SciTech Connect

    Not Available

    1984-01-01

    Adverse human health effects, namely acute and chronic respiratory effects, can occur from the pre-deposition phase of the acid rain phenomenon due to inhalation of acidic particles and gases. State-of-the-art methodology to evaluate these effects is just now being applied to this question. The major post-deposition effect of the acid rain phenomenon is to acidify water, increasing solubility and subsequent human exposure to mercury, lead, cadmium, and aluminum. Acidification increases bioconversion of mercury to methylmercury, a highly toxic compound, which accumulates in fish, increasing the risk to toxicity in people who eat fish. Increase in water and soil content of lead and cadmium increases human exposure to these metals which become additive to other sources presently under regulatory control. The potential adverse health effects of increased human exposure to aluminum is not known at the present time. Deficiencies in the identification of the contribution of pre-deposition of air pollutants and post-deposition mobilization of toxic metals to the recognized potential health effects of the involved toxic substances is due to the fact that scientists have not addressed these specific questions. 113 references, 4 figures, 2 tables.

  15. Effective Inflow Conditions for Turbulence Models in Aerodynamic Calculations

    NASA Technical Reports Server (NTRS)

    Spalart, Philippe R.; Rumsey, Christopher L.

    2007-01-01

    The selection of inflow values at boundaries far upstream of an aircraft is considered, for one- and two-equation turbulence models. Inflow values are distinguished from the ambient values near the aircraft, which may be much smaller. Ambient values should be selected first, and inflow values that will lead to them after the decay second; this is not always possible, especially for the time scale. The two-equation decay during the approach to the aircraft is shown; often, the time scale has been set too short for this decay to be calculated accurately on typical grids. A simple remedy for both issues is to impose floor values for the turbulence variables, outside the viscous sublayer, and it is argued that overriding the equations in this manner is physically justified. Selecting laminar ambient values is easy, if the boundary layers are to be tripped, but a more common practice is to seek ambient values that will cause immediate transition in boundary layers. This opens up a wide range of values, and selection criteria are discussed. The turbulent Reynolds number, or ratio of eddy viscosity to laminar viscosity has a huge dynamic range that makes it unwieldy; it has been widely mis-used, particularly by codes that set upper limits on it. The value of turbulent kinetic energy in a wind tunnel or the atmosphere is also of dubious value as an input to the model. Concretely, the ambient eddy viscosity must be small enough to preserve potential cores in small geometry features, such as flap gaps. The ambient frequency scale should also be small enough, compared with shear rates in the boundary layer. Specific values are recommended and demonstrated for airfoil flows

  16. Calculation of the effective permeability of saturated random porous media

    NASA Astrophysics Data System (ADS)

    Ostvar, S.; Wood, B. D.; Apte, S.; Liburdy, J.

    2014-12-01

    Estimation of the effective permeability tensor is an essential part of Darcy-scale representations of flow in porous media. The permeability tensor itself is a property of the medium, and depends only on the microscale geometry of the system. Determining the functional relationships between effective permeability (or conductivity in the general sense) and the structure of the medium is an old problem, with the earliest results for ordered porous media dating the 1920's. In this presentation, we report on the results of (1) detailed theory development, and (2) computations for the effective permeability tensor in fully-saturated random sphere packs, with a focus on the computational results. The theory is developed by volume averaging the Stokes equations, and using developing appropriate closures via potential theory, and has been reported on previously. For the computations, we have adopted an immersed boundary method to fully resolve the pore-scale velocity field. From our results, we compute the hydraulic permeability for both ordered and random media, and we compare these results with existing analytical solutions for the hydraulic conductivity in periodic arrays.

  17. Interpreting the Paramagnetic NMR Spectra of Potential Ru(III) Metallodrugs: Synergy between Experiment and Relativistic DFT Calculations.

    PubMed

    Novotný, Jan; Sojka, Martin; Komorovsky, Stanislav; Nečas, Marek; Marek, Radek

    2016-07-13

    Ruthenium-based compounds are potential candidates for use as anticancer metallodrugs. The central ruthenium atom can be in the oxidation state +2 (e.g., RAPTA, RAED) or +3 (e.g., NAMI, KP). In this study we focus on paramagnetic NAMI analogs of a general structure [4-R-pyH](+)trans-[Ru(III)Cl4(DMSO)(4-R-py)](-), where 4-R-py stands for a 4-substituted pyridine. As paramagnetic systems are generally considered difficult to characterize in detail by NMR spectroscopy, we performed a systematic structural and methodological NMR study of complexes containing variously substituted pyridines. The effect of the paramagnetic nature of these complexes on the (1)H and (13)C NMR chemical shifts was systematically investigated by temperature-dependent NMR experiments and density-functional theory (DFT) calculations. To understand the electronic factors influencing the orbital (δ(orb), temperature-independent) and paramagnetic (δ(para), temperature-dependent) contributions to the total NMR chemical shifts, a relativistic two-component DFT approach was used. The paramagnetic contributions to the (13)C NMR chemical shifts are correlated with the distribution of spin density in the ligand moiety and the (13)C isotropic hyperfine coupling constants, Aiso((13)C), for the individual carbon atoms. To analyze the mechanism of spin distribution in the ligand, the contributions of molecular spin-orbitals (MSOs) to the hyperfine coupling constants and the spatial distribution of the z-component of the spin density in the MSOs calculated at the relativistic four-component DFT level are discussed and rationalized. The significant effects of the substituent and the solvent on δ(para), particularly the contact contribution, are demonstrated. This work should contribute to further understanding of the link between the electronic structure and the NMR chemical shifts in open-shell systems, including the ruthenium-based metallodrugs investigated in this account. PMID:27312929

  18. The Stark Effect in Linear Potentials

    ERIC Educational Resources Information Center

    Robinett, R. W.

    2010-01-01

    We examine the Stark effect (the second-order shifts in the energy spectrum due to an external constant force) for two one-dimensional model quantum mechanical systems described by linear potentials, the so-called quantum bouncer (defined by V(z) = Fz for z greater than 0 and V(z) = [infinity] for z less than 0) and the symmetric linear potential…

  19. Effects of nonlocal potentials on (p ,d ) transfer reactions

    NASA Astrophysics Data System (ADS)

    Ross, A.; Titus, L. J.; Nunes, F. M.; Mahzoon, M. H.; Dickhoff, W. H.; Charity, R. J.

    2015-10-01

    Background: Although local phenomenological optical potentials have been standardly used to interpret nuclear reactions, recent studies suggest the effects of nonlocality should not be neglected. Purpose: In this work we investigate the effects of nonlocality in (p ,d ) transfer reactions using nonlocal optical potentials. We compare results obtained with the dispersive optical model to those obtained using the Perey-Buck interaction. Method: We solve the scattering and bound-state equations for the nonlocal version of the dispersive optical model. Then, using the distorted-wave Born approximation, we calculate the transfer cross section for (p ,d ) on 40Ca at Ep=20 , 35, and 50 MeV. Results: The inclusion of nonlocality in the bound state has a larger effect than that in the scattering states. The overall effect on the transfer cross section is very significant. We found an increase due to nonlocality in the transfer cross section of ≈30 - 50 % when using the Perey-Buck interaction and of ≈15 - 50 % when using the dispersive optical potential. Conclusions: Although the details of the nonlocal interaction can change the magnitude of the effects, our study shows that qualitatively the results obtained using the dispersive optical potential and the Perey-Buck interaction are consistent, in both cases the transfer cross sections are significantly increased.

  20. Effect of molecular models on viscosity and thermal conductivity calculations

    NASA Astrophysics Data System (ADS)

    Weaver, Andrew B.; Alexeenko, Alina A.

    2014-12-01

    The effect of molecular models on viscosity and thermal conductivity calculations is investigated. The Direct Simulation Monte Carlo (DSMC) method for rarefied gas flows is used to simulate Couette and Fourier flows as a means of obtaining the transport coefficients. Experimental measurements for argon (Ar) provide a baseline for comparison over a wide temperature range of 100-1,500 K. The variable hard sphere (VHS), variable soft sphere (VSS), and Lennard-Jones (L-J) molecular models have been implemented into a parallel version of Bird's one-dimensional DSMC code, DSMC1, and the model parameters have been recalibrated to the current experimental data set. While the VHS and VSS models only consider the short-range, repulsive forces, the L-J model also includes constributions from the long-range, dispersion forces. Theoretical results for viscosity and thermal conductivity indicate the L-J model is more accurate than the VSS model; with maximum errors of 1.4% and 3.0% in the range 300-1,500 K for L-J and VSS models, respectively. The range of validity of the VSS model is extended to 1,650 K through appropriate choices for the model parameters.

  1. Nonperturbative calculation of phonon effects on spin squeezing

    NASA Astrophysics Data System (ADS)

    Dylewsky, D.; Freericks, J. K.; Wall, M. L.; Rey, A. M.; Foss-Feig, M.

    2016-01-01

    Theoretical models of spins coupled to bosons provide a simple setting for studying a broad range of important phenomena in many-body physics, from virtually mediated interactions to decoherence and thermalization. In many atomic, molecular, and optical systems, such models also underlie the most successful attempts to engineer strong, long-ranged interactions for the purpose of entanglement generation. Especially when the coupling between the spins and bosons is strong, such that it cannot be treated perturbatively, the properties of such models are extremely challenging to calculate theoretically. Here, exact analytical expressions for nonequilibrium spin-spin correlation functions are derived for a specific model of spins coupled to bosons. The spatial structure of the coupling between spins and bosons is completely arbitrary, and thus the solution can be applied to systems in any number of dimensions. The explicit and nonperturbative inclusion of the bosons enables the study of entanglement generation (in the form of spin squeezing) even when the bosons are driven strongly and near resonantly, and thus provides a quantitative view of the breakdown of adiabatic elimination that inevitably occurs as one pushes towards the fastest entanglement generation possible. The solution also helps elucidate the effect of finite temperature on spin squeezing. The model considered is relevant to a variety of atomic, molecular, and optical systems, such as atoms in cavities or trapped ions. As an explicit example, the results are used to quantify phonon effects in trapped ion quantum simulators, which are expected to become increasingly important as these experiments push towards larger numbers of ions.

  2. The Effect of Using Graphing Calculators in Complex Function Graphs

    ERIC Educational Resources Information Center

    Ocak, Mehmet Akif

    2008-01-01

    This study investigates the role of graphing calculators in multiple representations for knowledge transfer and the omission of oversimplification in complex function graphs. The main aim is to examine whether graphing calculators were used efficiently to see different cases and multiple perspectives among complex function graphs, or whether…

  3. Confusing Aspects in the Calculation of the Electrostatic Potential of an Infinite Line of Charge

    ERIC Educational Resources Information Center

    Jimenez, J. L.; Campos, I.; Roa-Neri, J. A. E.

    2012-01-01

    In this work we discuss the trick of eliminating infinite potential of reference arguing that it corresponds to a constant of integration, in the problem of determining the electrostatic potential of an infinite line of charge with uniform density, and show how the problem must be tackled properly. The usual procedure is confusing for most…

  4. 40 CFR Appendix D to Part 72 - Calculation of Potential Electric Output Capacity

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Output Capacity D Appendix D to Part 72 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) PERMITS REGULATION Pt. 72, App. D Appendix D to Part 72—Calculation of... design heat input from the boiler by the following equation: EC10NO91.003 For example: (1) Assume...

  5. Surface heterogeneity of C{sub 60} as studied by infrared spectroscopy of adsorbed CO and adsorption potential calculations

    SciTech Connect

    Folman, M.; Fastow, M.; Kozirovski, Y.

    1997-03-05

    In our recent investigation of the IR spectrum of CO physically adsorbed on C{sub 60} films, two well-resolved absorption bands at 2135 and 2128 cm{sup -1} were found, suggesting that the molecule is adsorbed on two different sites. To determine the nature of these adsorption sites, calculations of adsorption potentials and spectral shifts for the CO/C{sub 60} system were performed. The calculations were done for the fcc (100), fcc (111) hcp (001), and hcp (111) surface planes. In the calculations the 6-exponential and the Lennard-Jones potentials were used. A number of adsorption sites were chosen. These included the void space between four, three, and two neighboring C{sub 60} molecules and the center of the hexagon and the pentagon on the C{sub 60} surface. The calculated potentials and spectral shifts clearly indicate that adsorption sites in the voids between the C{sub 60} molecules are energetically preferred over sites on top of single C{sub 60} molecules. Comparison is made between results obtained with the two potentials and with results obtained previously with the two other carbon allotropes: graphite and diamond. 11 refs., 4 figs., 3 tabs.

  6. Calculations of the ionization potentials and electron affinities of bacteriochlorophyll and bacteriopheophytin via ab initio quantum chemistry

    SciTech Connect

    Crystal, J.; Friesner, R.A.

    2000-03-23

    Ionization potentials (IP) and electron affinities (EA) are calculated for bacteriopheophytin (BPh) and bacteriochlorophyll (BChl) in the photosynthetic reaction center utilizing density functional methods implemented in a parallel version of the JAGUAR electronic structure code. These quantities are studied as a function of basis set size and molecular geometry. The results indicate the necessity of using large basis sets with diffuse functions in order to obtain reliable IP and EA in the gas phase. The relative reduction potentials of BChl and BPh in dimethylformamide solution are also calculated and compared with experimental results. Excellent agreement between theory and experiment is obtained when ligand binding of solvent molecules to the central Mg atom of BNhl is incorporated in the calculations.

  7. Calculation of pK(a) in proteins with the microenvironment modulated-screened coulomb potential.

    PubMed

    Shan, Jufang; Mehler, Ernest L

    2011-12-01

    The MM-SCP has been applied to predict pK(a) values of titratable residues in wild type and mutants of staphylococcal nuclease (SNase). The calculations were based on crystal structures made available by the Garcia-Moreno Laboratory. In the mutants, mostly deeply buried hydrophobic residues were replaced with ionizable residues, and thus their pK(a) values could be measured and calculated using various methods. The data set used here consisted of a set of WT SNase for which His pK(a) at several ionic strengths had been measured, a set of mutants for which measured pK(a) were available and a set of 11 mutants for which the measured pK(a) were not known at the time of calculation. For this latter set, blind predictions were submitted to the protein pK(a) cooperative, 2009 workshop at Telluride, where the results of the blind predictions were discussed (the RMSD of the submitted set was 1.10 pH units). The calculations on the structures with known pK(a) indicated that in addition to weaknesses of the method, structural issues were observed that led to larger errors (>1) in pK(a) predictions. For example, different crystallographic conditions or steric clashes can lead to differences in the local environment around the titratable residue, which can produce large differences in the calculated pK(a) . To gain further insight into the reliability of the MM-SCP, pK(a) of an extended set of 54 proteins belonging to several structural classes were carried out. Here some initial results from this study are reported to help place the SNase results in the appropriate context. PMID:21748803

  8. Garlic: a review of potential therapeutic effects

    PubMed Central

    Bayan, Leyla; Koulivand, Peir Hossain; Gorji, Ali

    2014-01-01

    Throughout history, many different cultures have recognized the potential use of garlic for prevention and treatment of different diseases. Recent studies support the effects of garlic and its extracts in a wide range of applications. These studies raised the possibility of revival of garlic therapeutic values in different diseases. Different compounds in garlic are thought to reduce the risk for cardiovascular diseases, have anti-tumor and anti-microbial effects, and show benefit on high blood glucose concentration. However, the exact mechanism of all ingredients and their long-term effects are not fully understood. Further studies are needed to elucidate the pathophysiological mechanisms of action of garlic as well as its efficacy and safety in treatment of various diseases. PMID:25050296

  9. On the calculation of the absolute grand potential of confined smectic-A phases

    NASA Astrophysics Data System (ADS)

    Huang, Chien-Cheng; Baus, Marc; Ryckaert, Jean-Paul

    2015-09-01

    We determine the absolute grand potential Λ along a confined smectic-A branch of a calamitic liquid crystal system enclosed in a slit pore of transverse area A and width L, using the rod-rod Gay-Berne potential and a rod-wall potential favouring perpendicular orientation at the walls. For a confined phase with an integer number of smectic layers sandwiched between the opposite walls, we obtain the excess properties (excess grand potential Λexc, solvation force fs and adsorption Γ) with respect to the bulk phase at the same μ (chemical potential) and T (temperature) state point. While usual thermodynamic integration methods are used along the confined smectic branch to estimate the grand potential difference as μ is varied at fixed L, T, the absolute grand potential at one reference state point is obtained via the evaluation of the absolute Helmholtz free energy in the (N, L, A, T) canonical ensemble. It proceeds via a sequence of free energy difference estimations involving successively the cost of localising rods on layers and the switching on of a one-dimensional harmonic field to keep layers integrity coupled to the elimination of inter-layers and wall interactions. The absolute free energy of the resulting set of fully independent layers of interacting rods is finally estimated via the existing procedures. This work opens the way to the computer simulation study of phase transitions implying confined layered phases.

  10. Full-dimensional vibrational calculations for H5O2+ using an ab initio potential energy surface

    NASA Astrophysics Data System (ADS)

    McCoy, Anne B.; Huang, Xinchuan; Carter, Stuart; Landeweer, Marc Y.; Bowman, Joel M.

    2005-02-01

    We report quantum diffusion Monte Carlo (DMC) and variational calculations in full dimensionality for selected vibrational states of H5O2+ using a new ab initio potential energy surface [X. Huang, B. Braams, and J. M. Bowman, J. Chem. Phys. 122, 044308 (2005)]. The energy and properties of the zero-point state are focused on in the rigorous DMC calculations. OH-stretch fundamentals are also calculated using "fixed-node" DMC calculations and variationally using two versions of the code MULTIMODE. These results are compared with infrared multiphoton dissociation measurements of Yeh et al. [L. I. Yeh, M. Okumura, J. D. Myers, J. M. Price, and Y. T. Lee, J. Chem. Phys. 91, 7319 (1989)]. Some preliminary results for the energies of several modes of the shared hydrogen are also reported.

  11. Could piracetam potentiate behavioural effects of psychostimulants?

    PubMed

    Slais, Karel; Machalova, Alena; Landa, Leos; Vrskova, Dagmar; Sulcova, Alexandra

    2012-08-01

    Press and internet reports mention abuse of nootropic drug piracetam (PIR) in combination with psychostimulants methamphetamine (MET) or 4-methylenedioxymethamphetamine (MDMA). These combinations are believed to produce more profound desirable effects, while decreasing hangover. However, there is a lack of valid experimental studies on such drug-drug interactions in the scientific literature available. Our hypothesis proposes that a functional interaction exists between PIR and amphetamine psychostimulants (MET and MDMA) which can potentiate psychostimulant behavioural effects. Our hypothesis is supported by the results of our pilot experiment testing acute effects of drugs given to mice intraperitoneally (Vehicle, n=12; MET 2.5mg/kg, n=10; MDMA 2.5mg/kg, n=11; PIR 300 mg/kg, n=12; PIR+MET, n=12; PIR+MDMA, n=11) in the Open Field Test (Actitrack, Panlab, Spain). PIR given alone caused no significant changes in mouse locomotor/exploratory behaviour, whereas the same dose combined with either MET or MDMA significantly enhanced their stimulatory effects. Different possible neurobiological mechanism underlying drug-drug interaction of PIR with MET or MDMA are discussed, as modulation of dopaminergic, glutamatergic or cholinergic brain systems. However, the interaction with membrane phospholipids seems as the most plausible mechanism explaining PIR action on activities of neurotransmitter systems. Despite that our behavioural experiment cannot serve for explanation of the pharmacological mechanisms of these functional interactions, it shows that PIR effects can increase behavioural stimulation of amphetamine drugs. Thus, the reported combining of PIR with MET or MDMA by human abusers is not perhaps a coincidental phenomenon and may be based on existing PIR potential to intensify acute psychostimulant effects of these drugs of abuse. PMID:22607774

  12. The Role of Molecular Dynamics Potential of Mean Force Calculations in the Investigation of Enzyme Catalysis.

    PubMed

    Yang, Y; Pan, L; Lightstone, F C; Merz, K M

    2016-01-01

    The potential of mean force simulations, widely applied in Monte Carlo or molecular dynamics simulations, are useful tools to examine the free energy variation as a function of one or more specific reaction coordinate(s) for a given system. Implementation of the potential of mean force in the simulations of biological processes, such as enzyme catalysis, can help overcome the difficulties of sampling specific regions on the energy landscape and provide useful insights to understand the catalytic mechanism. The potential of mean force simulations usually require many, possibly parallelizable, short simulations instead of a few extremely long simulations and, therefore, are fairly manageable for most research facilities. In this chapter, we provide detailed protocols for applying the potential of mean force simulations to investigate enzymatic mechanisms for several different enzyme systems. PMID:27498632

  13. MULTIPOLE EXPANSION TECHNIQUES FOR THE CALCULATION AND CHARACTERIZATION OF MOLECULAR ELECTROSTATIC POTENTIALS

    EPA Science Inventory

    The electrostatic interaction between a chemical and its site of biological action is often important in determining biological activity. In order to include this interaction in methods to assess the potential biological activity of large molecules, rapid and reliable techniques ...

  14. Scoping Calculations for Potential Groundwater Impacts from Operation of the APT Facility at SRS

    SciTech Connect

    Thibault, J.J.

    1999-10-07

    The purpose of this study was to determine the potential travel times and paths of the postulated activated groundwater beneath the facility and to examine the fate and transport of this activated groundwater.

  15. Potential Flow Analysis of Dynamic Ground Effect

    NASA Technical Reports Server (NTRS)

    Feifel, W. M.

    1999-01-01

    Interpretation of some flight test data suggests the presence of a 'dynamic ground effect'. The lift of an aircraft approaching the ground depends on the rate of descent and is lower than the aircraft steady state lift at a same height above the ground. Such a lift deficiency under dynamic conditions could have a serious impact on the overall aircraft layout. For example, the increased pitch angle needed to compensate for the temporary loss in lift would reduce the tail strike margin or require an increase in landing gear length. Under HSR2 an effort is under way to clarify the dynamic ground effect issue using a multi-pronged approach. A dynamic ground effect test has been run in the NASA Langley 14x22 ft wind tunnel. Northup-Grumman is conducting time accurate CFD (Computational Fluid Dynamics) Euler analyses on the National Aerodynamic Simulator facility. Boeing has been using linear potential flow methodology which are thought to provide much needed insight in, physics of this very complex problem. The present report summarizes the results of these potential flow studies.

  16. He-atom scattering from MgO(100): calculating diffraction peak intensities with a semi ab initio potential.

    PubMed

    Martinez-Casado, R; Mallia, G; Usvyat, D; Maschio, L; Casassa, S; Schütz, M; Harrison, N M

    2011-08-28

    An efficient model describing the He-atom scattering process is presented. The He-surface interaction potential is calculated from first principles by exploiting second-order Rayleigh-Schrödinger many-body perturbation theory and fitted by using a variety of pairwise interaction potentials. The attractive part of the fitted analytical form has been upscaled to compensate the underestimation of the well depth for this system in the perturbation theory description. The improved potential has been introduced in the close-coupling method to calculate the diffraction pattern. Quantitative agreement between the computed and observed binding energy and diffraction intensities for the He-MgO(100) system is achieved. It is expected that the utility of He scattering for probing dynamical processes at surfaces will be significantly enhanced by this quantitative description. PMID:21748190

  17. Investigation of parameter-free model polarization potentials for electron-molecule scattering calculations including the nuclear motion

    SciTech Connect

    Morrison, M.A.; Saha, B.C.

    1986-10-01

    A correlation-polarization potential originally introduced by O'Connell and Lane (Phys. Rev. A 27, 1893 (1983)) is used in e-H/sub 2/ scattering calculations in which the vibrational motion of the target is taken into account. Eigenphase sums (as a function of internuclear separation) and cross sections for elastic scattering and for rovibrational excitations are compared to their counterparts calculated using the ab initio nonadiabatic model polarization potential of Gibson and Morrison (Phys. Rev. A 29, 2497 (1984)). At low energies, these scattering quantities are found to be quite sensitive to the treatment of polarization. To assess these model potentials, theoretical total, momentum transfer, and rotational- and vibrational-excitation cross sections are compared to experimental data.

  18. Study of interatomic potentials in ZnS -- Crystal-GRID experiments versus ab initio calculations

    SciTech Connect

    Koch, T.; Heinig, K.H.; Jentschel, M.; Boerner, H.G.

    2000-02-01

    Crystal-GRID measurements have been performed with ZnS single crystals. For the first time, an asymmetric Crystal-GRID line shape could be observed. The preliminary data evaluation indicates that the reported lifetime of the 3221 keV level in {sup 33}S is too short. A value of about 60 fs has been found. Due to this long lifetime the line shape is much less structured than calculated with the reported lifetime.

  19. The potential, limitations, and challenges of divide and conquer quantum electronic structure calculations on energetic materials.

    SciTech Connect

    Tucker, Jon R.; Magyar, Rudolph J.

    2012-02-01

    High explosives are an important class of energetic materials used in many weapons applications. Even with modern computers, the simulation of the dynamic chemical reactions and energy release is exceedingly challenging. While the scale of the detonation process may be macroscopic, the dynamic bond breaking responsible for the explosive release of energy is fundamentally quantum mechanical. Thus, any method that does not adequately describe bonding is destined to lack predictive capability on some level. Performing quantum mechanics calculations on systems with more than dozens of atoms is a gargantuan task, and severe approximation schemes must be employed in practical calculations. We have developed and tested a divide and conquer (DnC) scheme to obtain total energies, forces, and harmonic frequencies within semi-empirical quantum mechanics. The method is intended as an approximate but faster solution to the full problem and is possible due to the sparsity of the density matrix in many applications. The resulting total energy calculation scales linearly as the number of subsystems, and the method provides a path-forward to quantum mechanical simulations of millions of atoms.

  20. Calculation of the thermoneutral potential of NiCd and NiH2 cells

    NASA Technical Reports Server (NTRS)

    Zimmerman, Albert H.

    1994-01-01

    The thermoneutral potential of a nickel cadmium or nickel hydrogen cell is the potential at which the cell charge or discharge process puts out zero heat, and thus is the potential corresponding to the enthalpy change of the charge/discharge reaction, delta H. A relatively straightforward method for obtaining the thermoneutral potential E(sub tn), is based on the measured potential and temperature derivative of the cell reactions, which are related to the free energy change delta G, and entropy change delta S, respectively. Particularly in the nickel hydrogen cell, the pressure of hydrogen can often vary over an order of magnitude or more during the course of a charge or discharge. In a nickel cadmium cell, although significant changes in oxygen pressure can occur during charge or discharge, since oxygen does not enter into the charge/discharge reaction, these pressure changes are related to the heat generated from oxygen evolution and recombination. However, the entropy changes due to changes in hydrogen pressure relative to the 1 atm standard state must be included to apply this method to the nickel hydrogen cell.

  1. Potential and effective meaning in therapeutic ritual.

    PubMed

    McCreery, J L

    1979-03-01

    Anthropologists who accept the functionalist dogma that everything in a culture is related to everything else can easily demonstrate from their own point of view that any ritual is richly meaningful. If, then, the healing power of therapeutic ritual depends on making illness meaningful, any ritual, if seen from this perspective, should be efficacious. We must distinguish, however, between potential and effective meaning, i.e. what a ritual might mean and what it does mean to participants in it who generally lack an anthropologist's global view of their culture. Effective meaning can be assessed by examining a ritual's relevance to the situation in which it occurs and factors which facilitate or hinder communication of what it might mean to particular persons. This argument is illustrated by analyzing the meaning of a Chinese healing ritual in two different situations in which it occurs. PMID:498802

  2. Potential adverse health effects of wood smoke.

    PubMed

    Pierson, W E; Koenig, J Q; Bardana, E J

    1989-09-01

    The use of wood stoves has increased greatly in the past decade, causing concern in many communities about the health effects of wood smoke. Wood smoke is known to contain such compounds as carbon monoxide, nitrogen oxides, sulfur oxides, aldehydes, polycyclic aromatic hydrocarbons, and fine respirable particulate matter. All of these have been shown to cause deleterious physiologic responses in laboratory studies in humans. Some compounds found in wood smoke--benzo[a]pyrene and formaldehyde--are possible human carcinogens. Fine particulate matter has been associated with decreased pulmonary function in children and with increased chronic lung disease in Nepal, where exposure to very high amounts of wood smoke occurs in residences. Wood smoke fumes, taken from both outdoor and indoor samples, have shown mutagenic activity in short-term bioassay tests. Because of the potential health effects of wood smoke, exposure to this source of air pollution should be minimal. PMID:2686171

  3. Potential adverse health effects of wood smoke.

    PubMed Central

    Pierson, W E; Koenig, J Q; Bardana, E J

    1989-01-01

    The use of wood stoves has increased greatly in the past decade, causing concern in many communities about the health effects of wood smoke. Wood smoke is known to contain such compounds as carbon monoxide, nitrogen oxides, sulfur oxides, aldehydes, polycyclic aromatic hydrocarbons, and fine respirable particulate matter. All of these have been shown to cause deleterious physiologic responses in laboratory studies in humans. Some compounds found in wood smoke--benzo[a]pyrene and formaldehyde--are possible human carcinogens. Fine particulate matter has been associated with decreased pulmonary function in children and with increased chronic lung disease in Nepal, where exposure to very high amounts of wood smoke occurs in residences. Wood smoke fumes, taken from both outdoor and indoor samples, have shown mutagenic activity in short-term bioassay tests. Because of the potential health effects of wood smoke, exposure to this source of air pollution should be minimal. PMID:2686171

  4. Calculating Non-Potentiality in Solar Active Regions Using SDO/HMI Vector Magnetic Field Data

    NASA Astrophysics Data System (ADS)

    Bobra, M.; Hoeksema, J. T.

    2010-12-01

    Non-potential magnetic fields in solar active regions are thought to be associated with flare occurrence. In this study, we parametrize the non-potentiality of several active regions, using data from the Helioseismic and Magnetic Imager (HMI) aboard the Solar Dynamics Observatory (SDO), and correlate these parameters with flare occurrence. In particular, we focus on a parameter that we call the Gradient-Weighted Inversion Line Length (GWILL). Using data from SOHO/MDI, Mason et al. found that GWILL generally tends to increase before a solar flare. We investigate whether extending the analysis of Mason et. al. to a three-dimensional field enables us to derive better near real-time indicators of flare occurrence. Before HMI, the availability of vector magnetograms was sparse at best. HMI provides continuous vector magnetogram data at a 12-minute cadence. As such, this study represents the first parametrization of non-potentiality in solar active regions using continuous vector magnetic field data.

  5. Calculating broad neutron resonances in a cut-off Woods-Saxon potential

    NASA Astrophysics Data System (ADS)

    Baran, Á.; Noszály, Cs.; Salamon, P.; Vertse, T.

    2015-07-01

    In a cut-off Woods-Saxon (CWS) potential with realistic depth S -matrix poles being far from the imaginary wave number axis form a sequence where the distances of the consecutive resonances are inversely proportional with the cut-off radius value, which is an unphysical parameter. Other poles lying closer to the imaginary wave number axis might have trajectories with irregular shapes as the depth of the potential increases. Poles being close repel each other, and their repulsion is responsible for the changes of the directions of the corresponding trajectories. The repulsion might cause that certain resonances become antibound and later resonances again when they collide on the imaginary axis. The interaction is extremely sensitive to the cut-off radius value, which is an apparent handicap of the CWS potential.

  6. A method for trap factor calculation and its effect

    SciTech Connect

    Xinguo, Z. )

    1992-01-01

    The accumulations and distributions of oil and gas in fault-block oil field are greatly controlled by various faults. Such oil field is characterized by complicated structure, multiple reservoirs, complex contact between oil and water, and big oil abundance difference among the reservoirs. The properties bring many troubles to the exploration and development of such oil and gas fields. There is no uniform statistical calculation standard that is special for multitudinous fault block traps. Common trap factor calculation methods are suitable for anticlinal trap, but they are not applicable to complicated fault block traps. In this paper, a new factor calculation method for fault traps in which there are quite thick reservoir and overlying formation is presented on the basis of fault trap property and interrelations among the factors which influence trap characteristics. Quite accurate closing areas of oil traps have been obtained by using the method in Dongpu seg.

  7. Reduced Osmotic Potential Effects on Photosynthesis 1

    PubMed Central

    Berkowitz, Gerald A.; Gibbs, Martin

    1983-01-01

    Addition of sorbitol, which facilitated reductions in reaction medium osmotic potential from standard (0.33 molar sorbitol, −10 bars) isotonic conditions to a stress level of 0.67 molar sorbitol (−20 bars), inhibited the photosynthetic capacity of isolated spinach (Spinacia oleracea) chloroplasts. This inhibition, which ranged from 64 to 74% under otherwise standard reaction conditions, was dependent on reaction medium inorganic phosphate concentration, with the phosphate optimum for photosynthesis reduced to 0.05 millimolar at the low osmotic potential stress treatment from a value of 0.25 millimolar under control conditions. Stromal alkalating agents such as NH4Cl (0.75 millimolar) and KCl (35 millimolar) were also found to affect the degree of low osmotic potential inhibition of photosynthesis. Both agents doubled the rate of NaHCO3-supported O2 evolution under the stress treatment, while hardly affecting the control rate at optimal concentrations. These agents also reduced the length of the lag phase of photosynthetic O2 evolution under the stress treatment to a much greater degree. The rate-enhancement effect of these agents under the stress treatment was reversed by sodium acetate, which is known to facilitate stromal acidification. The reaction medium pH optimum for photosynthesis under the stress treatment was higher than under control conditions. In the presence of optimal NH4Cl, this shift was no longer evident. Internal pH measurements indicated that the stress treatment caused a 0.43 and 0.24 unit reduction in the stromal and intrathylakoid pH, respectively, under illumination. This osmotically induced acidification was not evident in the dark. The presence of 0.75 millimolar NH4Cl partially reversed the osmotically induced reduction in the illuminated stromal pH. It was concluded that stromal acidification is a mediating mechanism of the most severe site of low osmotic potential inhibition of the photosynthetic process. PMID:16662927

  8. Excited State Effects in Nucleon Matrix Element Calculations

    SciTech Connect

    Constantia Alexandrou, Martha Constantinou, Simon Dinter, Vincent Drach, Karl Jansen, Theodoros Leontiou, Dru B Renner

    2011-12-01

    We perform a high-statistics precision calculation of nucleon matrix elements using an open sink method allowing us to explore a wide range of sink-source time separations. In this way the influence of excited states of nucleon matrix elements can be studied. As particular examples we present results for the nucleon axial charge g{sub A} and for the first moment of the isovector unpolarized parton distribution x{sub u-d}. In addition, we report on preliminary results using the generalized eigenvalue method for nucleon matrix elements. All calculations are performed using N{sub f} = 2+1+1 maximally twisted mass Wilson fermions.

  9. Microscopic calculation of interacting boson model parameters by potential-energy surface mapping

    SciTech Connect

    Bentley, I.; Frauendorf, S.

    2011-06-15

    A coherent state technique is used to generate an interacting boson model (IBM) Hamiltonian energy surface which is adjusted to match a mean-field energy surface. This technique allows the calculation of IBM Hamiltonian parameters, prediction of properties of low-lying collective states, as well as the generation of probability distributions of various shapes in the ground state of transitional nuclei, the last two of which are of astrophysical interest. The results for krypton, molybdenum, palladium, cadmium, gadolinium, dysprosium, and erbium nuclei are compared with experiment.

  10. On a new method for calculating the potential flow past a body of revolution

    NASA Technical Reports Server (NTRS)

    Kaplan, Carl

    1943-01-01

    A new method is presented for obtaining the velocity potential of the flow about a body of revolution moving uniformly in the direction of its axis of symmetry in a fluid otherwise at rest. This method is based essentially on the fact that the form of the differential equation for the velocity potential is invariant with regard to conformal transformation of the meridian plane. By means of the conformal transformation of the meridian profile into a circle a system of orthogonal curvilinear coordinates is obtained, the main feature of which is that one of the coordinate lines is the meridian profile itself. The use of this type of coordinate system yields a simple expression of the boundary condition at the surface of the solid and leads to a rational process of iteration for the solution of the differential equation for the velocity potential. It is shown that the velocity potential for an arbitrary body of revolution may be expressed in terms of universal functions which, although not normal, are obtainable by means of simple quadratures. The general results are applied to a body of revolution obtained by revolving a symmetrical Joukowski profile about its axis of symmetry. A numerical example further serves to illustrate the theory.

  11. Calculation of the refractive index of metal on the basis of nonlocal potential theory

    NASA Astrophysics Data System (ADS)

    Chrzanowski, Janusz

    2008-12-01

    In this paper a quantative discussion upon the frequency dependence of the refractive index of metal, in wide range of frequency, is performed on the basis of nonlocal potential theory connected with the concept of quasiparticles. Obtained results, for chosen metals, have been compared to evidence.

  12. Rapidly calculated density functional theory (DFT) relaxed Iso-potential Phi Si Maps: Beta-cellobiose

    Technology Transfer Automated Retrieval System (TEKTRAN)

    New cellobiose Phi-H/Si-H maps are rapidly generated using a mixed basis set DFT method, found to achieve a high level of confidence while reducing computer resources dramatically. Relaxed iso-potential maps are made for different conformational states of cellobiose, showing how glycosidic bond dihe...

  13. Theory of finite size effects for electronic quantum Monte Carlo calculations of liquids and solids

    NASA Astrophysics Data System (ADS)

    Holzmann, Markus; Clay, Raymond C.; Morales, Miguel A.; Tubman, Norm M.; Ceperley, David M.; Pierleoni, Carlo

    2016-07-01

    Concentrating on zero temperature quantum Monte Carlo calculations of electronic systems, we give a general description of the theory of finite size extrapolations of energies to the thermodynamic limit based on one- and two-body correlation functions. We introduce effective procedures, such as using the potential and wave function split up into long and short range functions to simplify the method, and we discuss how to treat backflow wave functions. Then we explicitly test the accuracy of our method to correct finite size errors on example hydrogen and helium many-body systems and show that the finite size bias can be drastically reduced for even small systems.

  14. EFFECTS OF ACID PRECIPITATION ON SOIL LEACHATE QUALITY: COMPUTER CALCULATIONS

    EPA Science Inventory

    The multipurpose computer program GEOCHEM was employed to calculate the equilibrium speciation in twenty-three examples of acid precipitation from New Hampshire, New York, and Maine, and in the same number of mixtures of acid precipitation with minerals characteristic of soils in...

  15. JCZS: An Intermolecular Potential Database for Performing Accurate Detonation and Expansion Calculations

    SciTech Connect

    Baer, M.R.; Hobbs, M.L.; McGee, B.C.

    1998-11-03

    Exponential-13,6 (EXP-13,6) potential pammeters for 750 gases composed of 48 elements were determined and assembled in a database, referred to as the JCZS database, for use with the Jacobs Cowperthwaite Zwisler equation of state (JCZ3-EOS)~l) The EXP- 13,6 force constants were obtained by using literature values of Lennard-Jones (LJ) potential functions, by using corresponding states (CS) theory, by matching pure liquid shock Hugoniot data, and by using molecular volume to determine the approach radii with the well depth estimated from high-pressure isen- tropes. The JCZS database was used to accurately predict detonation velocity, pressure, and temperature for 50 dif- 3 Accurate predictions were also ferent explosives with initial densities ranging from 0.25 glcm3 to 1.97 g/cm . obtained for pure liquid shock Hugoniots, static properties of nitrogen, and gas detonations at high initial pressures.

  16. Using corresponding state theory to obtain intermolecular potentials to calculate pure liquid shock Hugoniots

    SciTech Connect

    Hobbs, M.L.

    1997-12-01

    Determination of product species, equations-of-state (EOS) and thermochemical properties of high explosives and pyrotechnics remains a major unsolved problem. Although, empirical EOS models may be calibrated to replicate detonation conditions within experimental variability (5--10%), different states, e.g. expansion, may produce significant discrepancy with data if the basic form of the EOS model is incorrect. A more physically realistic EOS model based on intermolecular potentials, such as the Jacobs Cowperthwaite Zwisler (JCZ3) EOS, is needed to predict detonation states as well as expanded states. Predictive capability for any EOS requires a large species data base composed of a wide variety of elements. Unfortunately, only 20 species have known JCZ3 molecular force constants. Of these 20 species, only 10 have been adequately compared to experimental data such as molecular scattering or shock Hugoniot data. Since data in the strongly repulsive region of the molecular potential is limited, alternative methods must be found to deduce force constants for a larger number of species. The objective of the present study is to determine JCZ3 product species force constants by using a corresponding states theory. Intermolecular potential parameters were obtained for a variety of gas species using a simple corresponding states technique with critical volume and critical temperature. A more complex, four parameter corresponding state method with shape and polarity corrections was also used to obtain intermolecular potential parameters. Both corresponding state methods were used to predict shock Hugoniot data obtained from pure liquids. The simple corresponding state method is shown to give adequate agreement with shock Hugoniot data.

  17. Intercomparison of methods for calculating potential evaporation in regional and global water balance models

    NASA Astrophysics Data System (ADS)

    Federer, C. A.; Vörösmarty, C.; Fekete, B.

    Five methods (Thornthwaite, Hamon, Jensen-Haise, Turc, and Penman) for estimating potential evaporation for a reference surface (PEr) were compared to four methods (Priestley-Taylor, McNaughton-Black, Penman-Monteith, and Shuttleworth-Wallace) for estimating surface-dependent potential evaporation (PEs) using three cover types at each of seven locations from Fairbanks, Alaska, to San Juan, Puerto Rico. For annual PE the PEs methods generally agreed with the PEr methods, but for many locations, differences among methods were hundreds of millimeters per year. No methods were consistently low or high. Three of the PEs methods depend strongly on maximum leaf conductance, for which Körner [1994] provided satisfactory values by cover type. Potential interception (PEi) can only be estimated appropriately for all cover types by the Shuttleworth-Wallace method. Use of 5-day or monthly input data did not greatly degrade results, so use of monthly data to generate PE estimates appears warranted in global water balance models.

  18. Calculated potential surfaces for the reactions: O + N2 yields NO + N and N + O2 yields NO + O

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.; Jaffe, Richard J.

    1986-01-01

    Complete Active Space SCF/Contracted CI (CASSCF/CCI) calculations, using large Gaussian basis sets, are presented for selected portions of the potential surfaces for the reactions in the Zeldovich mechanism for the conversion of N2 to NO. The N + O2 reaction is exoergic by 32 kcal/mole and is computed to have an early barrier of 10.2 kcal/mole for the (sup 2)A(sup prime) surface and 18.0 kcal/mole for the (sup 4)A(sup prime) surface. The O + N2 reaction is endoergic by 75 kcal/mole. The (sup 3)A(sup double prime) surface is calculated to have a late barrier of 0.5 kcal/mole, while the (sup 3)A(sup prime) surface is calculated to have a late barrier of 14.4 kcal/mole.

  19. Nuclear shell model calculations of the effective interaction and other effective operators

    NASA Astrophysics Data System (ADS)

    Thoresen, Michael Joseph

    1997-12-01

    Recent breakthroughs in effective interaction and effective operator techniques allow us to take a new look at this field that has seen limited progress in the past twenty years. A comparison of the old and new techniques will shed some new light on the use of effective interactions and effective operators in shell model calculations of light nuclei. Three different methods of calculating the effective interaction and effective operators are described and compared. A large model-space no-core shell-model calculation for 6Li is used as the basis for comparison. In the no-core calculation all nucleons are active in a model space involving all configurations with energies up to 8/hbar/Omega. The second method is a perturbation expansion for the effective interaction and effective operators, using an inert 4He core and two valence particles. In particular, the electric quadrupole and magnetic dipole operators are studied to determine the effective charges to be used in connection with one- body operators in this shell-model space. The third method is a model-space truncation scheme, which maps operators in a large model space into operators in smaller, truncated model spaces. The effect of going to larger excitation spaces will be examined as well as the convergence trends regarding increases in the excitation space. The results from these three approaches are compared in order to gain new insight into the nature of effective interactions and operators in truncated model spaces. We find that by going to energies of 8/hbar/Omega we can accurately reproduce the experimental values for the binding energy, excitation spectrum, electric quadrupole moment and magnetic dipole moment of 6Li and that there is a definite model-space dependence for these operators. To obtain results similar to the 8/hbar/Omega ones in a truncated 2/hbar/Omega model space we use effective operators and effective charges. Effective charges of approximately 1.1e for the effective proton charge and 0

  20. Angle-resolved effective potentials for disk-shaped molecules

    SciTech Connect

    Heinemann, Thomas Klapp, Sabine H. L.; Palczynski, Karol Dzubiella, Joachim

    2014-12-07

    We present an approach for calculating coarse-grained angle-resolved effective pair potentials for uniaxial molecules. For integrating out the intramolecular degrees of freedom we apply umbrella sampling and steered dynamics techniques in atomistically-resolved molecular dynamics (MD) computer simulations. Throughout this study we focus on disk-like molecules such as coronene. To develop the methods we focus on integrating out the van der Waals and intramolecular interactions, while electrostatic charge contributions are neglected. The resulting coarse-grained pair potential reveals a strong temperature and angle dependence. In the next step we fit the numerical data with various Gay-Berne-like potentials to be used in more efficient simulations on larger scales. The quality of the resulting coarse-grained results is evaluated by comparing their pair and many-body structure as well as some thermodynamic quantities self-consistently to the outcome of atomistic MD simulations of many-particle systems. We find that angle-resolved potentials are essential not only to accurately describe crystal structures but also for fluid systems where simple isotropic potentials start to fail already for low to moderate packing fractions. Further, in describing these states it is crucial to take into account the pronounced temperature dependence arising in selected pair configurations due to bending fluctuations.

  1. Angle-resolved effective potentials for disk-shaped molecules

    NASA Astrophysics Data System (ADS)

    Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H. L.

    2014-12-01

    We present an approach for calculating coarse-grained angle-resolved effective pair potentials for uniaxial molecules. For integrating out the intramolecular degrees of freedom we apply umbrella sampling and steered dynamics techniques in atomistically-resolved molecular dynamics (MD) computer simulations. Throughout this study we focus on disk-like molecules such as coronene. To develop the methods we focus on integrating out the van der Waals and intramolecular interactions, while electrostatic charge contributions are neglected. The resulting coarse-grained pair potential reveals a strong temperature and angle dependence. In the next step we fit the numerical data with various Gay-Berne-like potentials to be used in more efficient simulations on larger scales. The quality of the resulting coarse-grained results is evaluated by comparing their pair and many-body structure as well as some thermodynamic quantities self-consistently to the outcome of atomistic MD simulations of many-particle systems. We find that angle-resolved potentials are essential not only to accurately describe crystal structures but also for fluid systems where simple isotropic potentials start to fail already for low to moderate packing fractions. Further, in describing these states it is crucial to take into account the pronounced temperature dependence arising in selected pair configurations due to bending fluctuations.

  2. Angle-resolved effective potentials for disk-shaped molecules.

    PubMed

    Heinemann, Thomas; Palczynski, Karol; Dzubiella, Joachim; Klapp, Sabine H L

    2014-12-01

    We present an approach for calculating coarse-grained angle-resolved effective pair potentials for uniaxial molecules. For integrating out the intramolecular degrees of freedom we apply umbrella sampling and steered dynamics techniques in atomistically-resolved molecular dynamics (MD) computer simulations. Throughout this study we focus on disk-like molecules such as coronene. To develop the methods we focus on integrating out the van der Waals and intramolecular interactions, while electrostatic charge contributions are neglected. The resulting coarse-grained pair potential reveals a strong temperature and angle dependence. In the next step we fit the numerical data with various Gay-Berne-like potentials to be used in more efficient simulations on larger scales. The quality of the resulting coarse-grained results is evaluated by comparing their pair and many-body structure as well as some thermodynamic quantities self-consistently to the outcome of atomistic MD simulations of many-particle systems. We find that angle-resolved potentials are essential not only to accurately describe crystal structures but also for fluid systems where simple isotropic potentials start to fail already for low to moderate packing fractions. Further, in describing these states it is crucial to take into account the pronounced temperature dependence arising in selected pair configurations due to bending fluctuations. PMID:25481132

  3. Effective medium approximation for effective propagation constant calculation in a dense random medium. [electromagnetic wave scattering

    NASA Technical Reports Server (NTRS)

    Zhu, P. Y.; Fung, A. K.

    1986-01-01

    The effective medium approximation (EMA) formalism developed for scalar wave calculations in solid state physics is generalized to electromagnetic wave scattering in a dense random medium. Results are applied to compute the effective propagation constant in a dense medium involving discrete spherical scatterers. When compared with a common quasicrystalline approximation (QCA), it is found that EMA accounts for backward scattering and the effect of correlation among three scatterers which are not available in QCA. It is also found that there is not much difference in the calculated normalized phase velocity between the use of these two approximations. However, there is a significant difference in the computed effective loss tangent in a nonabsorptive random medium. The computed effective loss tangent using EMA and measurements from a snow medium are compared, showing good agreement.

  4. An evaluation of calculation parameters in the EGSnrc/BEAMnrc Monte Carlo codes and their effect on surface dose calculation

    NASA Astrophysics Data System (ADS)

    Kim, Jung-Ha; Hill, Robin; Kuncic, Zdenka

    2012-07-01

    The Monte Carlo (MC) method has proven invaluable for radiation transport simulations to accurately determine radiation doses and is widely considered a reliable computational measure that can substitute a physical experiment where direct measurements are not possible or feasible. In the EGSnrc/BEAMnrc MC codes, there are several user-specified parameters and customized transport algorithms, which may affect the calculation results. In order to fully utilize the MC methods available in these codes, it is essential to understand all these options and to use them appropriately. In this study, the effects of the electron transport algorithms in EGSnrc/BEAMnrc, which are often a trade-off between calculation accuracy and efficiency, were investigated in the buildup region of a homogeneous water phantom and also in a heterogeneous phantom using the DOSRZnrc user code. The algorithms and parameters investigated include: boundary crossing algorithm (BCA), skin depth, electron step algorithm (ESA), global electron cutoff energy (ECUT) and electron production cutoff energy (AE). The variations in calculated buildup doses were found to be larger than 10% for different user-specified transport parameters. We found that using BCA = EXACT gave the best results in terms of accuracy and efficiency in calculating buildup doses using DOSRZnrc. In addition, using the ESA = PRESTA-I option was found to be the best way of reducing the total calculation time without losing accuracy in the results at high energies (few keV ∼ MeV). We also found that although choosing a higher ECUT/AE value in the beam modelling can dramatically improve computation efficiency, there is a significant trade-off in surface dose uncertainty. Our study demonstrates that a careful choice of user-specified transport parameters is required when conducting similar MC calculations.

  5. Ab Initio Potential Energy Surfaces and the Calculation of Accurate Vibrational Frequencies

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Dateo, Christopher E.; Martin, Jan M. L.; Taylor, Peter R.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within plus or minus 8 cm(exp -1) on average, and molecular bond distances are accurate to within plus or minus 0.001-0.003 Angstroms, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as vibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy will be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.

  6. Potential neurotoxic effects of polymethylmethacrylate during cranioplasty.

    PubMed

    Pikis, Stylianos; Goldstein, Jacob; Spektor, Sergey

    2015-01-01

    Cranioplasty for the surgical correction of cranial defects is often performed using polymethyl methacrylate (PMMA), or bone cement. Immediately prior to PMMA application, a liquid monomer form (methylacrylate) and a benzoyl peroxide accelerator are mixed resulting in polymerization, an exothermic reaction during which monomer linking and subsequent formation of solid polymer occur. The potential side effects of residual methylacrylate monomer toxicity and thermal damage of neural tissue during PMMA hardening have been described in various in vitro, animal, and cadaveric studies; however, clinically documented in vivo neurotoxicity in humans attributed to either of the above two mechanisms during PMMA cranioplasty is lacking. We present a series of four patients operated for removal of cerebellopontine angle lesions and two operated for the excision of parieto-occipital tumors who sustained cranial neuropathies and encephalopathies with transient or permanent neurological deficits that could not be attributed to surgical manipulation. We hypothesize that these complications most likely occurred due to thermal damage and/or chemical toxicity from exposure to PMMA during cranioplasty. Our case series indicates that even small volumes of PMMA used for cranioplasty may cause severe side effects related to thermal damage or to exposure of neural tissue to methylacrylate monomer. PMID:25085727

  7. Large impurity effects in rubrene crystals: First-principles calculations

    SciTech Connect

    Tsetseris, L.; Pantelides, Sokrates T.

    2008-01-01

    Carrier mobilities of rubrene films are among the highest values reported for any organic semiconductor. Here, we probe with first-principles calculations the sensitivity of rubrene crystals on impurities. We find that isolated oxygen impurities create distinct peaks in the electronic density of states consistent with observations of defect levels in rubrene and that increased O content changes the position and shape of rubrene energy bands significantly. We also establish a dual role of hydrogen as individual H species and H impurity pairs create and annihilate deep carrier traps, respectively. The results are relevant to the performance and reliability of rubrene-based devices.

  8. Numerical calculation of the transonic potential flow past a cranked wing

    NASA Technical Reports Server (NTRS)

    Chang, I. C.; Tauber, M.

    1983-01-01

    The widely transonic swept-wing code, FL022, was found to have an error in the transformed flow equation in the computational domain. The revised version of the code correctly accounted for the non-straight leading edge geometry and its effect on the pressure distribution.

  9. Basis set effects on the intermolecular interaction energies of methane dimers obtained by the Moeller-Plesset perturbation theory calculation

    SciTech Connect

    Tsuzuki, Seiji; Tanabe, Kazutoshi )

    1991-03-21

    Intermolecular interaction energies of methane dimer were calculated by using several basis sets up to 6-311G(3d,4p) with electron correlation energy correction by the Moeller-Plesset perturbation method and basis set superposition error (BSSE) correction by the counterpoise method to evaluate the basis set effect. The calculated interaction energies depended on the basis set considerably. Whereas the interaction energies of repulsive component calculated at HF level were not affected by the change of basis set, the dispersion energy component dependent greatly on the basis set used. The dispersion energies calculated with the Moeller-Plesset second- and third-order perturbation by using 6-311G(2d,2p) basis set were 0-10% and 4-6% smaller than those obtained with the fourth-order (MP4(SDTQ)) perturbation, respectively. The BSSE's calculated by the counterpoise method were still about 30% of the calculated intermolecular interaction energies for the conformers of energy minima event at the MP4(SDTQ)/6-311G(2d,2p) level. The calculated interaction potentials of dimers at the MP4(SDTQ)/6-311G(2d,2p) level were considerably shallower than those obtained by MM2 force fields but were close to the potentials given by the Williams potential and by the recently reported MM3 force field.

  10. Predicting Reduction Rates of Energetic Nitroaromatic Compounds Using Calculated One-Electron Reduction Potentials

    DOE PAGESBeta

    Salter-Blanc, Alexandra; Bylaska, Eric J.; Johnston, Hayley; Tratnyek, Paul G.

    2015-02-11

    The evaluation of new energetic nitroaromatic compounds (NACs) for use in green munitions formulations requires models that can predict their environmental fate. The susceptibility of energetic NACs to nitro reduction might be predicted from correlations between rate constants (k) for this reaction and one-electron reduction potentials (E1NAC) / 0.059 V, but the mechanistic implications of such correlations are inconsistent with evidence from other methods. To address this inconsistency, we have reevaluated existing kinetic data using a (non-linear) free-energy relationship (FER) based on the Marcus theory of outer-sphere electron transfer. For most reductants, the results are inconsistent with rate limitation bymore » an initial, outer-sphere electron transfer, suggesting that the strong correlation between k and E1NAC is justified only as an empirical model. This empirical correlation was used to calibrate a new quantitative structure-activity relationship (QSAR) using previously reported values of k for non-energetic NAC reduction by Fe(II) porphyrin and newly reported values of E1NAC determined using density functional theory at the B3LYP/6-311++G(2d,2p) level with the COSMO solvation model. The QSAR was then validated for energetic NACs using newly measured kinetic data for 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), and 2,4-dinitroanisole (DNAN). The data show close agreement with the QSAR, supporting its applicability to energetic NACs.« less

  11. Predicting reduction rates of energetic nitroaromatic compounds using calculated one-electron reduction potentials.

    PubMed

    Salter-Blanc, Alexandra J; Bylaska, Eric J; Johnston, Hayley J; Tratnyek, Paul G

    2015-03-17

    The evaluation of new energetic nitroaromatic compounds (NACs) for use in green munitions formulations requires models that can predict their environmental fate. Previously invoked linear free energy relationships (LFER) relating the log of the rate constant for this reaction (log(k)) and one-electron reduction potentials for the NAC (E1NAC) normalized to 0.059 V have been re-evaluated and compared to a new analysis using a (nonlinear) free-energy relationship (FER) based on the Marcus theory of outer-sphere electron transfer. For most reductants, the results are inconsistent with simple rate limitation by an initial, outer-sphere electron transfer, suggesting that the linear correlation between log(k) and E1NAC is best regarded as an empirical model. This correlation was used to calibrate a new quantitative structure-activity relationship (QSAR) using previously reported values of log(k) for nonenergetic NAC reduction by Fe(II) porphyrin and newly reported values of E1NAC determined using density functional theory at the M06-2X/6-311++G(2d,2p) level with the COSMO solvation model. The QSAR was then validated for energetic NACs using newly measured kinetic data for 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), and 2,4-dinitroanisole (DNAN). The data show close agreement with the QSAR, supporting its applicability to other energetic NACs. PMID:25671710

  12. Predicting Reduction Rates of Energetic Nitroaromatic Compounds Using Calculated One-Electron Reduction Potentials

    SciTech Connect

    Salter-Blanc, Alexandra; Bylaska, Eric J.; Johnston, Hayley; Tratnyek, Paul G.

    2015-02-11

    The evaluation of new energetic nitroaromatic compounds (NACs) for use in green munitions formulations requires models that can predict their environmental fate. The susceptibility of energetic NACs to nitro reduction might be predicted from correlations between rate constants (k) for this reaction and one-electron reduction potentials (E1NAC) / 0.059 V, but the mechanistic implications of such correlations are inconsistent with evidence from other methods. To address this inconsistency, we have reevaluated existing kinetic data using a (non-linear) free-energy relationship (FER) based on the Marcus theory of outer-sphere electron transfer. For most reductants, the results are inconsistent with rate limitation by an initial, outer-sphere electron transfer, suggesting that the strong correlation between k and E1NAC is justified only as an empirical model. This empirical correlation was used to calibrate a new quantitative structure-activity relationship (QSAR) using previously reported values of k for non-energetic NAC reduction by Fe(II) porphyrin and newly reported values of E1NAC determined using density functional theory at the B3LYP/6-311++G(2d,2p) level with the COSMO solvation model. The QSAR was then validated for energetic NACs using newly measured kinetic data for 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), and 2,4-dinitroanisole (DNAN). The data show close agreement with the QSAR, supporting its applicability to energetic NACs.

  13. Global Pattern of Potential Evaporation Calculated from the Penman-Monteith Equation Using Satellite and Assimilated Data

    NASA Technical Reports Server (NTRS)

    Choudhury, Bhaskar J.

    1997-01-01

    Potential evaporation (E(0)) has been found to be useful in many practical applications and in research for setting a reference level for actual evaporation. All previous estimates of regional or global E(0) are based upon empirical formulae using climatologic meteorologic measurements at isolated stations (i.e., point data). However, the Penman-Monteith equation provides a physically based approach for computing E(0), and by comparing 20 different methods of estimating E(0), Jensen et al. (1990) showed that the Penman-Monteith equation provides the most accurate estimate of monthly E(0) from well-watered grass or alfalfa. In the present study, monthly total E(0) for 24 months (January 1987 to December 1988) was calculated from the Penman-Monteith equation, with prescribed albedo of 0.23 and surface resistance of 70 s/m, which are considered to be representative of actively growing well-watered grass covering the ground. These calculations have been done using spatially representative data derived from satellite observations and data assimilation results. Satellite observations were used to obtain solar radiation, fractional cloud cover, air temperature, and vapor pressure, while four-dimensional data assimilation results were used to calculate the aerodynamic resistance. Meteorologic data derived from satellite observations were compared with the surface measurements to provide a measure of accuracy. The accuracy of the calculated E(0) values was assessed by comparing with lysimeter observations for evaporation from well-watered grass at 35 widely distributed locations, while recognizing that the period of present calculations was not concurrent with the lysimeter measurements and the spatial scales of these measurements and calculations are vastly different. These comparisons suggest that the error in the calculated E(0) values may not be exceeded, on average, 20% for any month or location, but are more likely to be about 15%. These uncertainties are difficult to

  14. A first-principle protocol for calculating ionization energies and redox potentials of solvated molecules and ions: Theory and application to aqueous phenol and phenolate

    PubMed Central

    Ghosh, Debashree; Roy, Anirban; Seidel, Robert; Winter, Bernd; Bradforth, Stephen; Krylov, Anna I.

    2012-01-01

    The effect of hydration on the lowest vertical ionization energy (VIE) of phenol and phenolate solvated in bulk water was characterized using the equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods (referred to as EOM/EFP), and determined experimentally by valence photo-emission measurements using microjets and synchrotron radiation. The computed solvent-induced shifts in VIEs (ΔVIE) are −0.66 eV and +5.72 eV for phenol and phenolate, respectively. Our best estimates of the absolute values of VIEs (7.9 and 7.7 eV for phenol and phenolate) agree reasonably well with the respective experimental values (7.8±0.1 eV and 7.1±0.1 eV). The EOM/EFP scheme was benchmarked against full EOM-IP-CCSD using micro-solvated phenol and phenolate clusters. A protocol for calculating redox potentials with EOM/EFP was developed based on linear response approximation (LRA) of free energy determination. The oxidation potentials of phenol and phenolate calculated using LRA and EOM/EFP are 1.32 V and 0.89 V, respectively; they agree well with experimental values. PMID:22497288

  15. Semiclassical calculations of tunneling using interpolating moving least-squares potentials

    NASA Astrophysics Data System (ADS)

    Pham, Phong

    The interpolating moving least-squares (IMLS) and Local-IMLS methods are incorporated into semiclassical trajectory simulation. Issues related to the implementation are investigated. Potential energy surface (PES) constructed by the IMLS/L-IMLS methods is used to study tunneling in polyatomic systems HONO and malonaldehyde, where direct dynamics becomes prohibitively expensive at high ab initio levels. To study cis--trans isomerization in HONO, the PES is constructed by L-IMLS fitting at the MP4(SDQ)/6-31++G(d,p) level with the HDMR(5,3,3) basis set. Results obtained can be compared with the others in the literature. Semiclassical rates are close to the referenced quantum mechanical ones. The isomerization is governed by energy transfer into the reaction coordinate---the torsional mode; the rate is strongly mode-selective, and much faster for the cis--trans direction than for the opposite one. To study the ground-state splitting of malonaldehyde, the PES is first constructed by single-level L-IMLS fitting at the MP2/6-31G(d,p) level with the HDMR(3,2) basis set. The dual-level method is then employed for increasing accuracy of the PES and reducing computational cost using MP4/6-31G(d,p) as the high level method. Results obtained can be compared with the others in the literature. For 0.5 kcal/mol fitting tolerance the splitting is 38.7 and 8.8 cm-1 at MP2 single-level, and 29.6 and 5.5 cm-1 at MP4 dual-level for H9 and D5D9 isotopomers respectively, compared to the experiment of 21.6 and 2.884 cm-1 . Splitting is within two times of the experiment and agrees with other quantum mechanical and semiclassical studies.

  16. Landauer's blow-torch effect in systems with entropic potential.

    PubMed

    Das, Moupriya; Ray, Deb Shankar

    2015-11-01

    We consider local heating of a part of a two-dimensional bilobal enclosure of a varying cross section confining a system of overdamped Brownian particles. Since varying cross section in higher dimension results in an entropic potential in lower dimension, local heating alters the relative stability of the entropic states. We show that this blow-torch effect modifies the entropic potential in a significant way so that the resultant effective entropic potential carries both the features of variation of width of the confinement and variation of temperature along the direction of transport. The reduced probability distribution along the direction of transport calculated by full numerical simulations in two dimensions agrees well with our analytical findings. The extent of population transfer in the steady state quantified in terms of the integrated probability of residence of the particles in either of the two lobes exhibits interesting variation with the mean position of the heated region. Our study reveals that heating around two particular zones of a given lobe maximizes population transfer to the other. PMID:26651672

  17. Landauer's blow-torch effect in systems with entropic potential

    NASA Astrophysics Data System (ADS)

    Das, Moupriya; Ray, Deb Shankar

    2015-11-01

    We consider local heating of a part of a two-dimensional bilobal enclosure of a varying cross section confining a system of overdamped Brownian particles. Since varying cross section in higher dimension results in an entropic potential in lower dimension, local heating alters the relative stability of the entropic states. We show that this blow-torch effect modifies the entropic potential in a significant way so that the resultant effective entropic potential carries both the features of variation of width of the confinement and variation of temperature along the direction of transport. The reduced probability distribution along the direction of transport calculated by full numerical simulations in two dimensions agrees well with our analytical findings. The extent of population transfer in the steady state quantified in terms of the integrated probability of residence of the particles in either of the two lobes exhibits interesting variation with the mean position of the heated region. Our study reveals that heating around two particular zones of a given lobe maximizes population transfer to the other.

  18. Effective Semi-empirical Interaction Potential for Dusty Particles

    SciTech Connect

    Ramazanov, T. S.; Dzhumagulova, K. N.; Omarbakiyeva, Y. A.; Dosbolayev, M. K.; Jumabekov, A. N.

    2008-09-07

    The Poisson equation was numerically solved on the basis of the experimental correlation functions of dusty particles. Calculations were performed with real parameters of dusty plasma. Reconstructed potential has oscillated character; the minimums coincide to maximums of correlation functions.

  19. Calculation of Molecular Shape Resonances Using Grid Based Exterior Complex Scaling and N2-Term Separable Potentials

    NASA Astrophysics Data System (ADS)

    Abeln, Brant; Rescigno, Thomas N.; McCurdy, C. William

    2015-05-01

    A novel approach employing Exterior Complex Scaling (ECS) and discrete grid methods is used to calculate molecular resonance energies and widths for the 2Πg shape resonance state of N2-and 2Πu shape resonance of CO2-.These calculations are performed using a Finite Element Discrete Variable Representation (FE-DVR) in prolate spheroidal coordinates with an atomic center placed at each of the foci of the coordinate system, thereby preserving the cusp condition at those sites. A separable approximation to the interaction potential is made from the matrices of the nuclear attraction, direct and exchange operators generated by an existing quantum chemistry structure code in a Gaussian basis. These potentials are then represented on our ECS FE-DVR grid allowing the calculation of complex-valued resonance energies. The method is demonstrated here in the static-exchange approximation. Work supported by NSFGRF DGE1148897, USDOE, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division.

  20. Accurate and Efficient Calculation of van der Waals Interactions Within Density Functional Theory by Local Atomic Potential Approach

    SciTech Connect

    Sun, Y. Y.; Kim, Y. H.; Lee, K.; Zhang, S. B.

    2008-01-01

    Density functional theory (DFT) in the commonly used local density or generalized gradient approximation fails to describe van der Waals (vdW) interactions that are vital to organic, biological, and other molecular systems. Here, we propose a simple, efficient, yet accurate local atomic potential (LAP) approach, named DFT+LAP, for including vdW interactions in the framework of DFT. The LAPs for H, C, N, and O are generated by fitting the DFT+LAP potential energy curves of small molecule dimers to those obtained from coupled cluster calculations with single, double, and perturbatively treated triple excitations, CCSD(T). Excellent transferability of the LAPs is demonstrated by remarkable agreement with the JSCH-2005 benchmark database [P. Jurecka et al. Phys. Chem. Chem. Phys. 8, 1985 (2006)], which provides the interaction energies of CCSD(T) quality for 165 vdW and hydrogen-bonded complexes. For over 100 vdW dominant complexes in this database, our DFT+LAP calculations give a mean absolute deviation from the benchmark results less than 0.5 kcal/mol. The DFT+LAP approach involves no extra computational cost other than standard DFT calculations and no modification of existing DFT codes, which enables straightforward quantum simulations, such as ab initio molecular dynamics, on biomolecular systems, as well as on other organic systems.

  1. The Potential Cardiotoxic Effects of Exercise.

    PubMed

    La Gerche, André

    2016-04-01

    The emerging controversy related to the potential cardiotoxic effects of high doses of intense exercise need to be considered among the much stronger evidence that supports the pleomorphic benefits of exercise as a whole. However, there is fairly compelling evidence to support the association between long-term sport practice and an increased prevalence of atrial fibrillation and the fact that this relates to a chronic altered atrial substrate. This article was designed to challenge the reader with speculative science that suggests that exercise might promote permanent structural changes in the myocardium which can, in some individuals, predispose to arrhythmias. In terms of long-term health outcomes, it would seem that these small risks are outweighed by the many other benefits of exercise, including a likely decrease in atherosclerotic vascular events, although some recent results have brought into question whether the protective benefits of exercise on vascular events also extends to high-intensity exercise training. Above all else, in this article we sought to highlight current controversies to stimulate research on the many unanswered questions. In particular, there is a lack of adequately powered prospective studies from which we can measure health outcomes and their relationship to exercise-induced cardiac remodelling. PMID:26922291

  2. Quantum Tunneling in Testosterone 6β-Hydroxylation by Cytochrome P450: Reaction Dynamics Calculations Employing Multiconfiguration Molecular-Mechanical Potential Energy Surfaces

    NASA Astrophysics Data System (ADS)

    Zhang, Yan; Lin, Hai

    2009-05-01

    Testosterone hydroxylation is a prototypical reaction of human cytochrome P450 3A4, which metabolizes about 50% of oral drugs on the market. Reaction dynamics calculations were carried out for the testosterone 6β-hydrogen abstraction and the 6β-d1-testosterone 6β-duterium abstraction employing a model that consists of the substrate and the active oxidant compound I. The calculations were performed at the level of canonical variational transition state theory with multidimensional tunneling and were based on a semiglobal full-dimensional potential energy surface generated by the multiconfiguration molecular mechanics technique. The tunneling coefficients were found to be around 3, indicating substantial contributions by quantum tunneling. However, the tunneling made only modest contributions to the kinetic isotope effects. The kinetic isotope effects were computed to be about 2 in the doublet spin state and about 5 in the quartet spin state.

  3. Quantum tunneling in testosterone 6beta-hydroxylation by cytochrome P450: reaction dynamics calculations employing multiconfiguration molecular-mechanical potential energy surfaces.

    PubMed

    Zhang, Yan; Lin, Hai

    2009-10-29

    Testosterone hydroxylation is a prototypical reaction of human cytochrome P450 3A4, which metabolizes about 50% of oral drugs on the market. Reaction dynamics calculations were carried out for the testosterone 6beta-hydrogen abstraction and the 6beta-d(1)-testosterone 6beta-duterium abstraction employing a model that consists of the substrate and the active oxidant compound I. The calculations were performed at the level of canonical variational transition state theory with multidimensional tunneling and were based on a semiglobal full-dimensional potential energy surface generated by the multiconfiguration molecular mechanics technique. The tunneling coefficients were found to be around 3, indicating substantial contributions by quantum tunneling. However, the tunneling made only modest contributions to the kinetic isotope effects. The kinetic isotope effects were computed to be about 2 in the doublet spin state and about 5 in the quartet spin state. PMID:19480428

  4. Quasiclassical trajectory calculations of the OH+NO2 association reaction on a global potential energy surface.

    PubMed

    Chen, Chao; Shepler, Benjamin C; Braams, Bastiaan J; Bowman, Joel M

    2007-09-14

    We report a full-dimensional potential energy surface (PES) for the OH+NO(2) reaction based on fitting more than 55,000 energies obtained with density functional theory-B3LYP6-311G(d,p) calculations. The PES is invariant with respect to permutation of like nuclei and describes all isomers of HOONO, HONO(2), and the fragments OH+NO(2) and HO(2)+NO. Detailed comparison of the structures, energies, and harmonic frequencies of various stationary points on the PES are made with previous and present high-level ab initio calculations. Two hydrogen-bond complexes are found on the PES and confirmed by new ab initio CASPT2 calculations. Quasiclassical trajectory calculations of the cross sections for ground rovibrational OH+NO(2) association reactions to form HOONO and HONO(2) are done using this PES. The cross section to form HOONO is larger than the one to form HONO(2) at low collision energies but the reverse is found at higher energies. The enhancement of the HOONO complex at low collision energies is shown to be due, in large part, to the transient formation of a H-bond complex, which decays preferentially to HOONO. The association cross sections are used to obtain rate constants for formation of HOONO and HONO(2) for the ground rovibrational states in the high-pressure limit. PMID:17867750

  5. Methodology for the calculation of the potential of mean force for a cation-pi complex in water.

    PubMed

    Ghoufi, Aziz; Archirel, Pierre; Morel, Jean-Pierre; Morel-Desrosiers, Nicole; Boutin, Anne; Malfreyt, Patrice

    2007-08-01

    We report potential of mean force (PMF) calculations on the interaction between the p-sulfonatocalix[4]arene and a monovalent cation (Cs(+)). It has been recently shown from microcalorimetry and (133)Cs NMR experiments that the association with Cs(+) is governed by favourable cation-pi interactions and is characterized by the insertion of the cation into the cavity of the macrocycle. We show that the PMF calculation based upon a classical model is not able to reproduce both the thermodynamic properties of association and the insertion of the cation. In order to take into account the different contributions of the cation-pi interactions, we develop a new methodology consisting of changing the standard PMF by an additional contribution resulting from quantum calculations. The calculated thermodynamic properties of association are thus in line with the microcalorimetry and (133)Cs NMR experiments and the structure of the complex at the Gibbs free-energy minimum shows the insertion of the cation into the cavity of the calixarene. PMID:17583904

  6. Effective Potential Energies and Transport Cross Sections for Atom-Molecule Interactions of Nitrogen and Nitrogen

    NASA Technical Reports Server (NTRS)

    Stallcop, James R.; Partridge, Harry; Levin, Eugene; Arnold, Jim (Technical Monitor)

    2001-01-01

    The potential energy surfaces for H2-N and N2-N interactions are calculated by accurate ab initio methods and applied to determine transport data. The results confirm that an effective potential energy for accurately determining transport properties can be calculated using a single orientation. A simple method is developed to determine the dispersion coefficients of effective potential energies Effective potential energies required for O2-O collisions are determ=ined. The H2-N, N2-N, O2-H, and O2-O collision integrals are calculated and tabulated for a large range of temperatures. The theoretical values of the N2-N and O2-O diffusion coefficients compare well with measured data available at room temperature.

  7. STREAM MODELS FOR CALCULATING POLLUTIONAL EFFECTS OF STORMWATER RUNOFF

    EPA Science Inventory

    Three related studies are described which provide the means to quantify the pollutional and hydraulic effects on flowing streams caused by stormwater runoff. Mathematical stream models were developed to simulate the biological, physical, chemical, and hydraulic reactions which oc...

  8. Calculation of the absolute thermodynamic properties of association of host-guest systems from the intermolecular potential of mean force.

    PubMed

    Ghoufi, Aziz; Malfreyt, Patrice

    2006-12-14

    The authors report calculations of the intermolecular potential of mean force (PMF) in the case of the host-guest interaction. The host-guest system is defined by a water soluble calixarene and a cation. With an organic cation such as the tetramethylammonium cation, the calixarene forms an insertion complex, whereas with the Lanthane cation, the supramolecular assembly is an outer-sphere complex. The authors apply a modified free energy perturbation method and the force constraint technique to establish the PMF profiles as a function of the separation distance between the host and guest. They use the PMF profile for the calculation of the absolute thermodynamic properties of association that they compare to the experimental values previously determined. They finish by giving some structural features of the insertion and outer-sphere complexes at the Gibbs free energy minimum. PMID:17176145

  9. An analytical model for the calculation of the change in transmembrane potential produced by an ultrawideband electromagnetic pulse.

    PubMed

    Hart, Francis X; Easterly, Clay E

    2004-05-01

    The electric field pulse shape and change in transmembrane potential produced at various points within a sphere by an intense, ultrawideband pulse are calculated in a four stage, analytical procedure. Spheres of two sizes are used to represent the head of a human and the head of a rat. In the first stage, the pulse is decomposed into its Fourier components. In the second stage, Mie scattering analysis (MSA) is performed for a particular point in the sphere on each of the Fourier components, and the resulting electric field pulse shape is obtained for that point. In the third stage, the long wavelength approximation (LWA) is used to obtain the change in transmembrane potential in a cell at that point. In the final stage, an energy analysis is performed. These calculations are performed at 45 points within each sphere. Large electric fields and transmembrane potential changes on the order of a millivolt are produced within the brain, but on a time scale on the order of nanoseconds. The pulse shape within the brain differs considerably from that of the incident pulse. Comparison of the results for spheres of different sizes indicates that scaling of such pulses across species is complicated. PMID:15114634

  10. Using the charge-stabilization technique in the double ionization potential equation-of-motion calculations with dianion references.

    PubMed

    Kuś, Tomasz; Krylov, Anna I

    2011-08-28

    The charge-stabilization method is applied to double ionization potential equation-of-motion (EOM-DIP) calculations to stabilize unstable dianion reference functions. The auto-ionizing character of the dianionic reference states spoils the numeric performance of EOM-DIP limiting applications of this method. We demonstrate that reliable excitation energies can be computed by EOM-DIP using a stabilized resonance wave function instead of the lowest energy solution corresponding to the neutral + free electron(s) state of the system. The details of charge-stabilization procedure are discussed and illustrated by examples. The choice of optimal stabilizing Coulomb potential, which is strong enough to stabilize the dianion reference, yet, minimally perturbs the target states of the neutral, is the crux of the approach. Two algorithms of choosing optimal parameters of the stabilization potential are presented. One is based on the orbital energies, and another--on the basis set dependence of the total Hartree-Fock energy of the reference. Our benchmark calculations of the singlet-triplet energy gaps in several diradicals show a remarkable improvement of the EOM-DIP accuracy in problematic cases. Overall, the excitation energies in diradicals computed using the stabilized EOM-DIP are within 0.2 eV from the reference EOM spin-flip values. PMID:21895161

  11. An improved fast multipole method for electrostatic potential calculations in a class of coarse-grained molecular simulations

    SciTech Connect

    Poursina, Mohammad; Anderson, Kurt S.

    2014-08-01

    This paper presents a novel algorithm to approximate the long-range electrostatic potential field in the Cartesian coordinates applicable to 3D coarse-grained simulations of biopolymers. In such models, coarse-grained clusters are formed via treating groups of atoms as rigid and/or flexible bodies connected together via kinematic joints. Therefore, multibody dynamic techniques are used to form and solve the equations of motion of such coarse-grained systems. In this article, the approximations for the potential fields due to the interaction between a highly negatively/positively charged pseudo-atom and charged particles, as well as the interaction between clusters of charged particles, are presented. These approximations are expressed in terms of physical and geometrical properties of the bodies such as the entire charge, the location of the center of charge, and the pseudo-inertia tensor about the center of charge of the clusters. Further, a novel substructuring scheme is introduced to implement the presented far-field potential evaluations in a binary tree framework as opposed to the existing quadtree and octree strategies of implementing fast multipole method. Using the presented Lagrangian grids, the electrostatic potential is recursively calculated via sweeping two passes: assembly and disassembly. In the assembly pass, adjacent charged bodies are combined together to form new clusters. Then, the potential field of each cluster due to its interaction with faraway resulting clusters is recursively calculated in the disassembly pass. The method is highly compatible with multibody dynamic schemes to model coarse-grained biopolymers. Since the proposed method takes advantage of constant physical and geometrical properties of rigid clusters, improvement in the overall computational cost is observed comparing to the tradition application of fast multipole method.

  12. A review of back-calculation techniques and their potential to inform mitigation strategies with application to non-transmissible acute infectious diseases

    PubMed Central

    Egan, Joseph R.; Hall, Ian M.

    2015-01-01

    Back-calculation is a process whereby generally unobservable features of an event leading to a disease outbreak can be inferred either in real-time or shortly after the end of the outbreak. These features might include the time when persons were exposed and the source of the outbreak. Such inferences are important as they can help to guide the targeting of mitigation strategies and to evaluate the potential effectiveness of such strategies. This article reviews the process of back-calculation with a particular emphasis on more recent applications concerning deliberate and naturally occurring aerosolized releases. The techniques can be broadly split into two themes: the simpler temporal models and the more sophisticated spatio-temporal models. The former require input data in the form of cases' symptom onset times, whereas the latter require additional spatial information such as the cases' home and work locations. A key aspect in the back-calculation process is the incubation period distribution, which forms the initial topic for consideration. Links between atmospheric dispersion modelling, within-host dynamics and back-calculation are outlined in detail. An example of how back-calculation can inform mitigation strategies completes the review by providing improved estimates of the duration of antibiotic prophylaxis that would be required in the response to an inhalational anthrax outbreak. PMID:25977955

  13. An update on the circuit approach to calculate shielding effectiveness

    NASA Astrophysics Data System (ADS)

    Bridges, Jack E.

    1988-08-01

    The shielding effectiveness of an enclosure at low frequencies can be computed using a circuit approach. Not only does this technique include the effects of the properties of the shield material, but it also includes the details of the geometry of the enclosure. This approach allows a nonempirical consideration of mesh enclosures and the effects of resistive seams in enclosure walls. By working with the circuit analog, penetration by transient fields can be computed. Essentially the enclosure is viewed as an antenna. In the case of magnetic shielding effectiveness, the enclosure is viewed as a short-circuited loop antenna. In the case of electric-field penetration, the enclosure is viewed as a fat electric dipole. Using this characterization and exact solutions where available, the current distribution on the outside of the enclosure is determined. Based on the current distribution, the penetrating fields are computed. The equations are developed in such a way as to preserve a lumped circuit analog for the low-frequency region. The basic circuit equations for magnetic-field penetration are rederived from a rigorous solution. Rules to estimate the rise time, fall time, and peak magnitudes of transient penetrating fields are developed. The electric shielding effectiveness is developed in a similar manner.

  14. Probing calculated O 2 + potential curves with an XUV-IR pump-probe experiment

    NASA Astrophysics Data System (ADS)

    Coerlin, Philipp; Fischer, Andreas; Schoenwald, Michael; Sperl, Alexander; Mizuno, Tomoya; Pfeifer, Thomas; Moshammer, Robert; Thumm, Uwe

    2015-05-01

    We study dissociative photo-ionization of O2 in a kinematically complete XUV-IR pump-probe experiment, preparing a vibrational wave packet in the potential of the binding O2+(a4Πu)state by ionization with a single XUV photon. After a variable time-delay the wave packet is promoted to the repulsive O2+(f4Πg)state by a weak IR probe pulse. Comparing the results of a coupled-channel simulation with the experimental kinetic-energy-release and quantum-beat spectra, we are able to discriminate between the adiabatic O2+potential-energy curves (PECs) calculated by. The overall agreement between simulated and experimental results is good; however, not all features of the experimental spectra could be reproduced using these PECs. Using a Morse potential adjusted to the experimental data instead, most features of the experimental spectra are well reproduced by our simulation. This optimized Morse potential is remarkably similar to the theoretically predicted PECs, demonstrating the sensitivity of our experimental method to small changes in the shape of the binding potential. Supported by the DoE, NSF, and Alexander von Humboldt foundation.

  15. Numerical calculation of thermal effect on cavitation in cryogenic fluids

    NASA Astrophysics Data System (ADS)

    Shi, Suguo; Wang, Guoyu

    2012-11-01

    A key design issue related to the turbopump of the rocket engine is that cavitation occurs in cryogenic fluids when the fluid pressure is lower than the vapor pressure at a local thermodynamic state. Cavitation in cryogenic fluids generates substantial thermal effects and strong variations in fluid properties, which in turn alter the cavity characteristics. To date, fewer investigate the thermal effect on cavitation in cryogenic fluids clearly by the numerical methods due to the difficulty of the heat transfer in the phase change process. In order to study the thermal effect on cavitation in cryogenic fluid, computations are conducted around a 2D quarter caliber hydrofoil in liquid nitrogen and hydrogen respectively by implementing modified Merkle cavitation model, which accounts for the energy balance and variable thermodynamic properties of the fluid. The numerical results show that with the thermal effect, the vapour content in constant location decreases, the cavity becomes more porous and the interface becomes less distinct which shows increased spreading while getting shorter in length. In the cavity region, the temperature around the cavity depresses due to absorb the evaporation latent heat and the saturation pressure drops. When the vapour volume fraction is higher, the temperature depression and pressure depression becomes larger. It is also observed that a slight temperature rise is found above the reference fluid temperature at the cavity rear end attributed to the release of latent heat during the condensation process. When the fluid is operating close to its critical temperature, thermal effects on cavitation are more obviously in both the liquid nitrogen and hydrogen. The thermal effect on cavitation in liquid hydrogen is more distinctly compared with that in liquid nitrogen due to the density ratio, vapour pressure and other variable properties of the fluid. The investigation provides aid for the design of the cryogenic pump of the liquid rocket.

  16. Calculation of three-body resonances using slow-variable discretization coupled with a complex absorbing potential

    NASA Astrophysics Data System (ADS)

    Blandon, Juan; Kokoouline, Viatcheslav; Masnou-Seeuws, Françoise

    2007-04-01

    We developed a method to calculate positions and widths of three-body resonances. The method combines the hyperspherical adiabatic approach, slow variable discretization method [O. I. Tolstikhin , J. Phys. B 29, L389 (1996)], and a complex absorbing potential. The method can be used to obtain resonances having short-range or long-range wave functions. In particular, we have applied the method to obtain very shallow three-body Efimov resonances for a model system [E. Nielsen , Phys. Rev. A 66, 012705 (2002)].

  17. Assessing the effect of electron density in photon dose calculations

    SciTech Connect

    Seco, J.; Evans, P. M.

    2006-02-15

    Photon dose calculation algorithms (such as the pencil beam and collapsed cone, CC) model the attenuation of a primary photon beam in media other than water, by using pathlength scaling based on the relative mass density of the media to water. In this study, we assess if differences in the electron density between the water and media, with different atomic composition, can influence the accuracy of conventional photon dose calculations algorithms. A comparison is performed between an electron-density scaling method and the standard mass-density scaling method for (i) tissues present in the human body (such as bone, muscle, etc.), and for (ii) water-equivalent plastics, used in radiotherapy dosimetry and quality assurance. We demonstrate that the important material property that should be taken into account by photon dose algorithms is the electron density, and not the mass density. The mass-density scaling method is shown to overestimate, relative to electron-density predictions, the primary photon fluence for tissues in the human body and water-equivalent plastics, where 6%-7% and 10% differences were observed respectively for bone and air. However, in the case of patients, differences are expected to be smaller due to the large complexity of a treatment plan and of the patient anatomy and atomic composition and of the smaller thickness of bone/air that incident photon beams of a treatment plan may have to traverse. Differences have also been observed for conventional dose algorithms, such as CC, where an overestimate of the lung dose occurs, when irradiating lung tumors. The incorrect lung dose can be attributed to the incorrect modeling of the photon beam attenuation through the rib cage (thickness of 2-3 cm in bone upstream of the lung tumor) and through the lung and the oversimplified modeling of electron transport in convolution algorithms. In the present study, the overestimation of the primary photon fluence, using the mass-density scaling method, was shown

  18. Risk calculations for hereditary effects of ionizing radiation in humans.

    PubMed

    Vogel, F

    1992-05-01

    A prediction of the extent to which an additional dose of ionizing radiation increases the natural germ cell mutation rate, and how much such an increase will affect the health status of future human populations is part of the service that human geneticists are expected to offer to human society. However, more detailed scrutiny of the difficulties involved reveals an extremely complex set of problems. A large number of questions arises before such a prediction can be given with confidence; many such questions cannot be answered at our present state of knowledge. However, such predictions have recently been attempted. The 1988 report of the United Nations Scientific Committee for the Effects of Atomic Radiation and the fifth report of the Committee on Biological Effects of Ionizing Radiation of the US National Research Council have presented a discussion of the human genetics problems involved. Empirical data from studies on children of highly radiation-exposed parents, e.g. parents exposed to the atomic bombs of Hiroshima and Nagasaki, or parents belonging to populations living on soil with high background radiation, have been mentioned in this context. Whereas precise predictions are impossible as yet because of deficiencies in our knowledge of medical genetics at various levels, the bulk of the existing evidence points to only small effects of low or moderate radiation doses, effects that will probably be buried in the "background noise" of changing patterns of human morbidity and mortality. PMID:1587523

  19. Thermodynamic calculation and interatomic potential to predict the favored composition region for the Cu-Zr-Al metallic glass formation.

    PubMed

    Cui, Y Y; Wang, T L; Li, J H; Dai, Y; Liu, B X

    2011-03-01

    For the Cu-Zr-Al system, the glass forming compositions were firstly calculated based on the extended Miedema's model, suggesting that the amorphous phase could be thermodynamically favored over a large composition region. An n-body potential was then constructed under the smoothed and long-range second-moment-approximation of tight-binding formulism. Applying the constructed Cu-Zr-Al potential, molecular dynamics simulations were conducted using solid solution models to compare relative stability of crystalline solid solution versus its disordered counterpart. Simulations reveal that the physical origin of metallic glass formation is crystalline lattice collapsing while solute concentration exceeding the critical value, thus predicting a hexagonal composition region, within which the Cu-Zr-Al ternary metallic glass formation is energetically favored. The molecular dynamics simulations predicted composition region is defined as the quantitative glass-forming-ability or glass-forming-region of the Cu-Zr-Al system. PMID:21229150

  20. Calculated Effects of Nitric Oxide Flow Contamination on Scramjet Performance

    NASA Technical Reports Server (NTRS)

    Fischer, Karen E.; Rock, Kenneth E.

    1995-01-01

    The level of nitric oxide contamination in the test gas of the NASA Langley Research Center Arc-Heated Scramjet Test Facility and the effect of the contamination on scramjet test engine performance were investigated analytically. The study was conducted for standard facility conditions corresponding to Mach 6, 7, and 8 flight simulations. The analytically determined levels of nitric oxide produced in the facility are compared with experimentally measured levels. Results of the analysis indicate that nitric oxide levels range from one to three mole percent, which corroborates the measured levels. A three-stream combustor code with finite rate chemistry was used to investigate how nitric oxide affects scramjet performance in terms of combustor pressure rise, heat release, and thrust performance. Results indicate minimal effects on engine performance for the test conditions of this investigation.

  1. Calculation of Tip Clearance Effects in a Transonic Compressor Rotor

    NASA Technical Reports Server (NTRS)

    Chima, R. V.

    1998-01-01

    The flow through the tip clearance region of a transonic compressor rotor (NASA rotor 37) was computed and compared to aerodynamic probe and laser anemometer data. Tip clearance effects were modeled both by gridding the clearance gap and by using a simple periodicity model across the ungridded gap. The simple model was run with both the full gap height, and with half the gap height to simulate a vena-contracta effect. Comparisons between computed and measured performance maps and downstream profiles were used to validate the models and to assess the effects of gap height on the simple clearance model. Recommendations were made concern- ing the use of the simple clearance model Detailed comparisons were made between the gridded clearance gap solution and the laser anemometer data near the tip at two operating points. The computed results agreed fairly well with the data but overpredicted the extent of the casing separation and underpredicted the wake decay rate. The computations were then used to describe the interaction of the tip vortex, the passage shock, and the casing boundary layer.

  2. Relatedness calculations for linked loci incorporating subpopulation effects.

    PubMed

    Bright, Jo-Anne; Curran, James M; Buckleton, John S

    2013-05-01

    Often the loci in forensic multiplexes are selected to avoid linked loci. However linked loci have occurred in some recent commercially available multiplexes. Previously formulae have been given for both joint and conditional match probabilities for some relationships that did not account for subpopulation effects. In this paper we extend these works to include a subpopulation correction of the form first suggested by Balding and Nichols. We extend the work to grandparent/grandchild, first cousin, uncle/nephew and half uncle/nephew relationships and apply these to two different populations and STR multiplexes. Our model assumes that the two people have no relationship other that the one specified. That is, we assume their parents are neither related nor themselves inbred. The multiplications inherent in these formulae also assume that there is no linkage disequilibrium at the subpopulation level for these loci. We found that when taking into account linkage the match statistic decreases for all relationships, with siblings having the greatest effect. However, the effect was less than a factor of two decrease in match statistic. PMID:23537755

  3. Calculation of tip clearance effects in a transonic compressor rotor

    NASA Technical Reports Server (NTRS)

    Chima, R. V.

    1996-01-01

    The flow through the tip clearance region of a transonic compressor rotor (NASA rotor 37) was computed and compared to aerodynamic probe and laser anemometer data. Tip clearance effects were modeled both by gridding the clearance gap and by using a simple periodicity model across the ungridded gap. The simple model was run with both the full gap height, and with half the gap height to simulate a vena-contracta effect. Comparisons between computed and measured performance maps and downstream profiles were used to validate the models and to assess the effects of gap height on the simple clearance model. Recommendations were made concerning the use of the simple clearance model. Detailed comparisons were made between the gridded clearance gap solution and the laser anemometer data near the tip at two operating points. The computer results agreed fairly well with the data but overpredicted the extent of the casing separation and underpredicted the wake decay rate. The computations were then used to describe the interaction of the tip vortex, the passage shock, and the casing boundary layer.

  4. Analysing collimator structure effects in head-scatter calculations for IMRT class fields using scatter raytracing.

    PubMed

    Naqvi, S A; Sarfaraz, M; Holmes, T; Yu, C X; Li, X A

    2001-07-01

    The frequent blocking of the irradiated volume in intensity modulated radiation therapy (IMRT) makes the head-scatter fraction of the incident photon fluence more significant than that in conventional therapy with open fields. On the other hand. certain collimator configurations block scatter photons directed to a given observation point while allowing primary photons to be transmitted. The 'anomalous blocking' makes the primary field a poor indicator of the scatter fluence. Since large MU-to-cGy ratios in IMRT can magnify head-scatter uncertainties, it becomes necessary to accurately model both the effective scatter source and the collimator structure that limits the scatter reaching the irradiated volume. First we obtain a dual-source model, using a Taylor series expansion to derive the effective scatter source distribution from the data measured for the Elekta SL20 linac equipped with a multi-leaf collimator (MLC). Then, using a raytracing algorithm, we calculate the transmission of scatter rays from the effective scatter source plane to points in the patient plane. The method can account for the anomalous blocking of scatter by the MLC leaves and the backup diaphragms. For a variety of collimator settings tested, the calculations agree with measurements to an accuracy of 0.002psi10 x 10, where psi10 x 10 is the total (primary + scatter) photon fluence of an open 10 x 10 cm2 field for the same MU delivered. Although the significance of collimator structure in IMRT depends strongly on fields shapes employed for the delivery, potential cumulative errors on the order of a few per cent can be avoided in fluence calculations if the proposed method is used. PMID:11474941

  5. MCSCF-CI calculations of the ground state potential curves of LiH, Li2, and F2

    NASA Astrophysics Data System (ADS)

    Jönsson, Bo; Roos, Björn O.; Taylor, Peter R.; Siegbahn, Per E. M.

    1981-04-01

    The potential curves for LiH(X 1Σ+), Li2(X 1Σ+g), and F2(X 1Σ+g) have been calculated using a wave function comprising all single and double replacements from an MCSCF reference state. It is shown that in order to obtain satisfactory results, the reference function should describe properly not only the dissociation of the molecule, but also the united atom limit. This implies that for Li2, 1πu, and for F2,2πu orbitals should be included in the reference state. Calculated dissociation energies are 2.48 (2.52) eV for LiH, and 1.00 (1.05) eV for Li2 (experimental values within parentheses). For F2 only 1.31 (1.66) eV is obtained with 2πu excluded from the reference orbital space. A calculation including this orbital yields 1.40 eV even at the MCSCF level.

  6. Two-electron R-matrix approach to calculations of potential-energy curves of long-range Rydberg molecules

    NASA Astrophysics Data System (ADS)

    Tarana, Michal; Čurík, Roman

    2016-05-01

    We introduce a computational method developed for study of long-range molecular Rydberg states of such systems that can be approximated by two electrons in a model potential of the atomic cores. The method is based on a two-electron R-matrix approach inside a sphere centered on one of the atoms. The wave function is then connected to a Coulomb region outside the sphere via a multichannel version of the Coulomb Green's function. This approach is applied to a study of Rydberg states of Rb2 for internuclear separations R from 40 to 320 bohrs and energies corresponding to n from 7 to 30. We report bound states associated with the low-lying 3Po resonance and with the virtual state of the rubidium atom that turn into ion-pair-like bound states in the Coulomb potential of the atomic Rydberg core. The results are compared with previous calculations based on single-electron models employing a zero-range contact-potential and short-range modele potential. Czech Science Foundation (Project No. P208/14-15989P).

  7. An accurate {ital ab initio} HOCl potential energy surface, vibrational and rotational calculations, and comparison with experiment

    SciTech Connect

    Skokov, S.; Peterson, K.A.; Bowman, J.M.

    1998-08-01

    Accurate {ital ab initio} multireference configuration interaction (CI) calculations with large correlation-consistent basis sets are performed for HOCl. After extrapolation to the complete basis set limit, the {ital ab initio} data are precisely fit to give a semiglobal three-dimensional potential energy surface to describe HOCl{r_arrow}Cl+OH from high overtone excitation of the OH-stretch. The average absolute deviation between the {ital ab initio} and fitted energies is 4.2thinspcm{sup {minus}1} for energies up to 60 kcal/mol relative to the HOCl minimum. Vibrational energies of HOCl including the six overtones of the OH-stretch are computed using a vibrational-Cl method on the fitted potential and also on a slightly adjusted potential. Near-spectroscopic accuracy is obtained using the adjusted potential; the average absolute deviation between theory and experiment for 19 experimentally reported states is 4.8thinspcm{sup {minus}1}. Very good agreement with experiment is also obtained for numerous rotational energies for the ground vibrational state, the ClO-stretch fundamental, and the fifth overtone of the OH-stretch. {copyright} {ital 1998 American Institute of Physics.}

  8. Density functional theory calculations of the redox potentials of actinide(VI)/actinide(V) couple in water.

    PubMed

    Steele, Helen M; Guillaumont, Dominique; Moisy, Philippe

    2013-05-30

    The measured redox potential of an actinide at an electrode surface involves the transfer of a single electron from the electrode surface on to the actinide center. Before electron transfer takes place, the complexing ligands and molecules of solvation need to become structurally arranged such that the electron transfer is at its most favorable. Following the electron transfer, there is further rearrangement to obtain the minimum energy structure for the reduced state. As such, there are three parts to the total energy cycle required to take the complex from its ground state oxidized form to its ground state reduced form. The first part of the energy comes from the structural rearrangement and solvation energies of the actinide species before the electron transfer or charge transfer process; the second part, the energy of the electron transfer; the third part, the energy required to reorganize the ligands and molecules of solvation around the reduced species. The time resolution of electrochemical techniques such as cyclic voltammetry is inadequate to determine to what extent bond and solvation rearrangement occurs before or after electron transfer; only for a couple to be classed as reversible is it fast in terms of the experimental time. Consequently, the partitioning of the energy theoretically is of importance to obtain good experimental agreement. Here we investigate the magnitude of the instantaneous charge transfer through calculating the fast one electron reduction energies of AnO2(H2O)n(2+), where An = U, Np, and Pu, for n = 4-6, in solution without inclusion of the structural optimization energy of the reduced form. These calculations have been performed using a number of DFT functionals, including the recently developed functionals of Zhao and Truhlar. The results obtained for calculated electron affinities in the aqueous phase for the AnO2(H2O)5(2+/+) couples are within 0.04 V of accepted experimental redox potentials, nearly an order of magnitude

  9. The impact of site factors and climate variability on the calculation of potential evaporation at Moel Cynnedd, Plynlimon

    NASA Astrophysics Data System (ADS)

    Crane, S. B.; Hudson, J. A.

    The meteorological record from the manual Moel Cynnedd climate station at Plynlimon in the Welsh Uplands has been supplemented with solar radiation data, initially from the Institute of Hydrology's Dolydd Office, and later from an adjacent automatic weather station, in order to calculate Penman potential evapotranspiration for the entire 27 year data set, 1969-1995. The methods of data capture are consistent with Meteorological Office criteria throughout the entire record, establishing an unbiased and probably unique indicator of climatic variability and change for this type of environment. Values of Penman Et calculated from these data provides an independent index of atmospheric demand for moisture as an adjunct to the hydrological studies being carried out in the Plynlimon and neighbouring catchments. Analysis of the long term data indicates considerable year-to year variability in the component variables, including some cyclical changes and possible long term trends in measured temperature. Annual variability in Et is less than in the component variables, and there is an indication of a possible long term cycle, but no evidence of an overall trend in Et during this particular study period. The results indicate that some of the observed variability can be explained by inevitable changes in exposure within this forest clearing site rather than changes in regional or global climatic patterns. A single meteorological station sited in a forest clearing at a relatively low altitude may underestimate potential evaporation across the catchment, as this will also include areas of exposed hillside and forest canopy.

  10. Spectroscopic and electronic structure calculation of a potential antibacterial agent incorporating pyrido-dipyrimidine-dione moiety using first principles

    NASA Astrophysics Data System (ADS)

    Fatma, Shaheen; Bishnoi, Abha; Singh, Vineeta; Al-Omary, Fatmah A. M.; El-Emam, Ali A.; Pathak, Shilendra; Srivastava, Ruchi; Prasad, Onkar; Sinha, Leena

    2016-04-01

    Quantum chemical calculations of geometrical structure, energy and vibrational wavenumbers of a novel functionalized pyrido-pyrimidine compound (a prospective antibacterial agent), chemically known as 6-Methyl,13,14,15-Trihydro-14-(4-Nitrophenyl)pyrido[1,2-a:1‧,2‧-a‧] pyrido[2″,3″-d:6″,5″-d‧]dipyrimidine-13,15-dione (C24H16N6O4), were carried out, using B3LYP/6311++G(d,p) method. Comprehensive interpretation of the infrared and Raman spectra of the compound under study is based on potential energy distribution. A good coherence between experimental and theoretical wavenumbers shows the preciseness of the assignments. NLO properties like the dipole moment, polarizability, first static hyperpolarizability and molecular electrostatic potential surface have been calculated to get a better cognizance of the properties of the title compound. Molecular docking results reveal that the title compound exhibit inhibitory activity against Staphylococcus aureus.

  11. Calculation of the effective dose from natural radioactivity in soil using MCNP code.

    PubMed

    Krstic, D; Nikezic, D

    2010-01-01

    Effective dose delivered by photon emitted from natural radioactivity in soil was calculated in this work. Calculations have been done for the most common natural radionuclides in soil (238)U, (232)Th series and (40)K. A ORNL human phantoms and the Monte Carlo transport code MCNP-4B were employed to calculate the energy deposited in all organs. The effective dose was calculated according to ICRP 74 recommendations. Conversion factors of effective dose per air kerma were determined. Results obtained here were compared with other authors. PMID:20045343

  12. Fourier domain calculation of terrain effects in marine MT

    NASA Astrophysics Data System (ADS)

    Parker, Robert L.; Wheelock, Brent

    2012-04-01

    Magnetotelluric surveys on the seafloor have become an important part of marine geophysics in recent years. The distorting effects of topographic relief on the electromagnetic fields can be far-reaching, but local terrain is also important. Thus, computational techniques that can treat a large area containing fine-scale topography could find widespread application. We describe a new solution to the problem based on a well-established theory of electromagnetic induction in thin sheets. The procedure requires taking the Fourier transform of the integral equations derived by Dawson and Weaver in 1979, and by McKirdy, Weaver and Dawson in 1985. The equations in the transformed electric field are solved iteratively by a new technique. We prove the new iterative procedure is always convergent, whereas the original scheme diverges when the grid spacing of the discretization is small. We also give a means of correcting for distant features that need not be specified in as great detail. Preliminary tests confirm the new process is very efficient and that topographic data sets of several million points will be handled with ease.

  13. Using BRDFs for accurate albedo calculations and adjacency effect corrections

    SciTech Connect

    Borel, C.C.; Gerstl, S.A.W.

    1996-09-01

    In this paper the authors discuss two uses of BRDFs in remote sensing: (1) in determining the clear sky top of the atmosphere (TOA) albedo, (2) in quantifying the effect of the BRDF on the adjacency point-spread function and on atmospheric corrections. The TOA spectral albedo is an important parameter retrieved by the Multi-angle Imaging Spectro-Radiometer (MISR). Its accuracy depends mainly on how well one can model the surface BRDF for many different situations. The authors present results from an algorithm which matches several semi-empirical functions to the nine MISR measured BRFs that are then numerically integrated to yield the clear sky TOA spectral albedo in four spectral channels. They show that absolute accuracies in the albedo of better than 1% are possible for the visible and better than 2% in the near infrared channels. Using a simplified extensive radiosity model, the authors show that the shape of the adjacency point-spread function (PSF) depends on the underlying surface BRDFs. The adjacency point-spread function at a given offset (x,y) from the center pixel is given by the integral of transmission-weighted products of BRDF and scattering phase function along the line of sight.

  14. Band-structure calculations of noble-gas and alkali halide solids using accurate Kohn-Sham potentials with self-interaction correction

    SciTech Connect

    Li, Y.; Krieger, J.B. ); Norman, M.R. ); Iafrate, G.J. )

    1991-11-15

    The optimized-effective-potential (OEP) method and a method developed recently by Krieger, Li, and Iafrate (KLI) are applied to the band-structure calculations of noble-gas and alkali halide solids employing the self-interaction-corrected (SIC) local-spin-density (LSD) approximation for the exchange-correlation energy functional. The resulting band gaps from both calculations are found to be in fair agreement with the experimental values. The discrepancies are typically within a few percent with results that are nearly the same as those of previously published orbital-dependent multipotential SIC calculations, whereas the LSD results underestimate the band gaps by as much as 40%. As in the LSD---and it is believed to be the case even for the exact Kohn-Sham potential---both the OEP and KLI predict valence-band widths which are narrower than those of experiment. In all cases, the KLI method yields essentially the same results as the OEP.

  15. Effects of electron emission on sheath potential

    NASA Astrophysics Data System (ADS)

    Dow, Ansel; Khrabrov, Alexander; Kaganovich, Igor; Schamis, Hanna

    2015-11-01

    We investigate the potential profile of a sheath under the influence of surface electron emission. The plasma and sheath profiles are simulated using the Large Scale Plasma (LSP) particle-in-cell code. Using one dimensional models we corroborate the analytical relationship between sheath potential and plasma electron and emitted electron temperatures derived earlier. This work was made possible by funding from the Department of Energy for the Summer Undergraduate Laboratory Internship (SULI) program. This work is supported by the US DOE Contract No. DE-AC02-09CH11466.

  16. Single particle calculations for a Woods-Saxon potential with triaxial deformations, and large Cartesian oscillator basis

    NASA Astrophysics Data System (ADS)

    Mohammed-Azizi, B.; Medjadi, D. E.

    2004-01-01

    We present a computer program which solves the Schrodinger equation of the stationary states for an average nuclear potential of Woods-Saxon type. In this work, we take specifically into account triaxial (i.e. ellipsoidal) nuclear surfaces. The deformation is specified by the usual Bohr parameters. The calculations are carried out in two stages. In the first, one calculates the representative matrix of the Hamiltonian in the Cartesian oscillator basis. In the second stage one diagonalizes this matrix with the help of subroutines of the Eispack library. If it is wished, one can calculate all eigenvalues, or only the part of the eigenvalues that are contained in a fixed interval defined in advance. In this latter case the eigenvectors are given conjointly. The program is very rapid, and the run-time is mainly used for the diagonalization. Thus, it is possible to use a significant number of the basis states in order to insure a best convergence of the results. Program summaryProgram obtainable from:CPC Program Library, Queen's University of Belfast, N. Ireland Title of program:Triaxial Catalogue number:ADSK Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSK Licensing provisions:None Computer:PC. AMD Athlon 1000 MHz Hard disk:40 Go Ram:256 Mo Swap file:4 Go Operating system:WINDOWS XP Software used:Microsoft Visual Fortran 5.0A (with full optimizations in the settings project options) Programming language:Fortran 77/90 (double precision) Number of bits in a word:32 Number of lines:7662 No. of bytes in distributed program, including test data, etc.:174 601 Distribution format:tar gzip file Nature of the problem: The single particle energies and the single particle wave functions are calculated from one-body Hamiltonian including a central field of Woods-Saxon type, a spin-orbit interaction, and the Coulomb potential for the protons. We consider only ellipsoidal (triaxial) shapes. The deformation of the nuclear shape is fixed by the usual Bohr parameters ( β,

  17. Single particle calculations for a Woods Saxon potential with triaxial deformations, and large Cartesian oscillator basis (new version code)

    NASA Astrophysics Data System (ADS)

    Mohammed-Azizi, B.; Medjadi, D. E.

    2007-05-01

    We present a new version of the computer program which solves the Schrödinger equation of the stationary states for an average nuclear potential of Woods-Saxon type. In this work, we take specifically into account triaxial (i.e. ellipsoidal) nuclear surfaces. The deformation is specified by the usual Bohr parameters. The calculations are carried out in two stages. In the first, one calculates the representative matrix of the Hamiltonian in the Cartesian oscillator basis. In the second stage one diagonalizes this matrix with the help of subroutines of the EISPACK library. This new version calculates all the eigenvalues up to a given cutoff energy, and gives the components of the corresponding eigenfunctions. For a more convenient handling, these results are stored simultaneously in the computer memory, and on a files. Program summaryTitle of program:Triaxial2007 Catalogue identifier:ADSK_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSK_v2_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Summary of revision:One input file instead two. Reduced number of input parameters. Storage of eigenvalues and eigenvectors in memory in a very simple way which makes the code very convenient to the user. Reasons for the new version: More convenient handling of the eigenvectors Catalogue number old version: ADSK Catalogue number new version:ADSK_v2_0 Journal: Computer Physics Commun. 156 (2004) 241-282 Licensing provisions: none Computer: PC Pentium 4, 2600 MHz Hard disk: 40 Gb RAM: 256 Mb Swap file: 4 Gb Operating system: WINDOWS XP Software used: Compaq Visual FORTRAN (with full optimizations in the settings project options) Programming language used:Fortran 77/90 (double precision) Number of bits in a word: 32 No. of lines in distributed program, including test data, etc.:4058 No. of bytes in distributed program, including test data, etc.:75 590 Distribution format:tar.gz Nature of the problem: The single particle energies

  18. Effects of subpopulation structure on probability calculations of DNA profiles from forensic PCR analysis.

    PubMed

    Gallo, J C; Thomas, E; Novick, G E; Herrera, R J

    1997-01-01

    DNA typing for forensic identification is a two-step process. The first step involves determining the profiles of samples collected at the crime scene and comparing them with the profiles obtained from suspects and the victims. In the case of a match that includes the suspect as the potential source of the material collected at the crime scene, the last step in the process is to answer the question, what is the likelihood that someone in addition to the suspect could match the profile of the sample studied? This likelihood is calculated by determining the frequency of the suspect's profile in the relevant population databases. The design of forensic databases and the criteria for comparison has been addressed by the NRC report of 1996 (National Research Council, 1996). However, the fact that geographical proximity, migrational patterns, and even cultural and social practices have effects on subpopulation structure establishes the grounds for further study into its effects on the calculation of probability of occurrence values. The issue becomes more relevant in the case of discrete polymorphic markers that show higher probability of occurrence in the reference populations, where several orders of magnitude difference between the databases may have an impact on the jury. In this study, we calculated G values for all possible pairwise comparisons of allelic frequencies in the different databases from the races or subpopulations examined. In addition, we analyzed a set of 24 unrelated Caucasian, 37 unrelated African-American, and 96 unrelated Sioux/Chippewa individuals for seven polymorphic loci (DQA1, LDLR, GYPA, HBGG, D7S8, GC, and D1S80). All three sets of individuals where sampled from Minnesota. The probability of occurrence for all seven loci were calculated with respect to nine different databases: Caucasian, Arabic, Korean, Sioux/Chippewa, Navajo, Pueblo, African American, Southeastern Hispanic, and Southwestern Hispanic. Analysis of the results demonstrated

  19. Probing calculated O2+ potential-energy curves with an XUV-IR pump-probe experiment

    NASA Astrophysics Data System (ADS)

    Cörlin, Philipp; Fischer, Andreas; Schönwald, Michael; Sperl, Alexander; Mizuno, Tomoya; Thumm, Uwe; Pfeifer, Thomas; Moshammer, Robert

    2015-04-01

    We study dissociative photoionization of molecular oxygen in a kinematically complete XUV-IR pump-probe experiment. Detecting charged fragments and photoelectrons in coincidence using a reaction microscope, we observe a pump-probe delay-dependent yield of very low energetic O+ ions which oscillates with a period of 40 fs . This feature is caused by a time-dependent vibrational wave packet in the potential of the binding O2+(a Π4u) state, which is probed by resonant absorption of a single infrared photon to the weakly repulsive O2+(f Π4g) state. By quantitative comparison of the experimental kinetic-energy-release (KER) and quantum-beat (QB) spectra with the results of a coupled-channel simulation, we are able to discriminate between the calculated adiabatic O2+ potential-energy curves (PECs) of Marian et al. [Marian, Marian, Peyerimhoff, Hess, Buenker, and Seger, Mol. Phys. 46, 779 (1982), 10.1080/00268978200101591] and Magrakvelidze et al. [Magrakvelidze, Aikens, and Thumm, Phys. Rev. A 86, 023402 (2012), 10.1103/PhysRevA.86.023402]. In general, we find a good agreement between experimental and simulated KER and QB spectra. However, we could not reproduce all features of the experimental data with these PECs. In contrast, adjusting a Morse potential to the experimental data, most features of the experimental spectra are well reproduced by our simulation. By comparing this Morse potential to theoretically predicted PECs, we demonstrate the sensitivity of our experimental method to small changes in the shape of the binding potential.

  20. Calculation of total effective dose equivalent and collective dose in the event of a LOCA in Bushehr Nuclear Power Plant.

    PubMed

    Raisali, G; Davilu, H; Haghighishad, A; Khodadadi, R; Sabet, M

    2006-01-01

    In this research, total effective dose equivalent (TEDE) and collective dose (CD) are calculated for the most adverse potential accident in Bushehr Nuclear Power Plant from the viewpoint of radionuclides release to the environment. Calculations are performed using a Gaussian diffusion model and a slightly modified version of AIREM computer code to adopt for conditions in Bushehr. The results are comparable with the final safety analysis report which used DOZAM code. Results of our calculations show no excessive dose in populated regions. Maximum TEDE is determined to be in the WSW direction. CD in the area around the nuclear power plant by a distance of 30 km (138 man Sv) is far below the accepted limits. Thyroid equivalent dose is also calculated for the WSW direction (maximum 25.6 mSv) and is below the limits at various distances from the reactor stack. PMID:16785243

  1. Potential negative ecological effects of corridors.

    PubMed

    Haddad, Nick M; Brudvig, Lars A; Damschen, Ellen I; Evans, Daniel M; Johnson, Brenda L; Levey, Douglas J; Orrock, John L; Resasco, Julian; Sullivan, Lauren L; Tewksbury, Josh J; Wagner, Stephanie A; Weldon, Aimee J

    2014-10-01

    Despite many studies showing that landscape corridors increase dispersal and species richness for disparate taxa, concerns persist that corridors can have unintended negative effects. In particular, some of the same mechanisms that underlie positive effects of corridors on species of conservation interest may also increase the spread and impact of antagonistic species (e.g., predators and pathogens), foster negative effects of edges, increase invasion by exotic species, increase the spread of unwanted disturbances such as fire, or increase population synchrony and thus reduce persistence. We conducted a literature review and meta-analysis to evaluate the prevalence of each of these negative effects. We found no evidence that corridors increase unwanted disturbance or non-native species invasion; however, these have not been well-studied concerns (1 and 6 studies, respectively). Other effects of corridors were more often studied and yielded inconsistent results; mean effect sizes were indistinguishable from zero. The effect of edges on abundances of target species was as likely to be positive as negative. Corridors were as likely to have no effect on antagonists or population synchrony as they were to increase those negative effects. We found 3 deficiencies in the literature. First, despite studies on how corridors affect predators, there are few studies of related consequences for prey population size and persistence. Second, properly designed studies of negative corridor effects are needed in natural corridors at scales larger than those achievable in experimental systems. Third, studies are needed to test more targeted hypotheses about when corridor-mediated effects on invasive species or disturbance may be negative for species of management concern. Overall, we found no overarching support for concerns that construction and maintenance of habitat corridors may result in unintended negative consequences. Negative edge effects may be mitigated by widening

  2. Why can water cages adsorb aqueous methane? A potential of mean force calculation on hydrate nucleation mechanisms.

    PubMed

    Guo, Guang-Jun; Li, Meng; Zhang, Yi-Gang; Wu, Chang-Hua

    2009-11-28

    By performing constrained molecular dynamics simulations in the methane-water system, we successfully calculated the potential of mean force (PMF) between a dodecahedral water cage (DWC) and dissolved methane for the first time. As a function of the distance between DWC and methane, this is characterized by a deep well at approximately 6.2 A and a shallow well at approximately 10.2 A, separated by a potential barrier at approximately 8.8 A. We investigated how the guest molecule, cage rigidity and the cage orientation affected the PMF. The most important finding is that the DWC itself strongly adsorbs methane and the adsorption interaction is independent of the guests. Moreover, the activation energy of the DWC adsorbing methane is comparable to that of hydrogen bonds, despite differing by a factor of approximately 10% when considering different water-methane interaction potentials. We explain that the cage-methane adsorption interaction is a special case of the hydrophobic interaction between methane molecules. The strong net attraction in the DWC shell with radii between 6.2 and 8.8 A may act as the inherent driving force that controls hydrate formation. A cage adsorption hypothesis for hydrate nucleation is thus proposed and discussed. PMID:19890529

  3. Dose Calculations for [131I] Meta-Iodobenzylguanidine-Induced Bystander Effects

    PubMed Central

    Gow, M. D.; Seymour, C. B.; Boyd, M.; Mairs, R. J.; Prestiwch, W. V.; Mothersill, C. E.

    2014-01-01

    Targeted radiotherapy is a potentially useful treatment for some cancers and may be potentiated by bystander effects. However, without estimation of absorbed dose, it is difficult to compare the effects with conventional external radiation treatment. Methods: Using the Vynckier – Wambersie dose point kernel, a model for dose rate evaluation was created allowing for calculation of absorbed dose values to two cell lines transfected with the noradrenaline transporter (NAT) gene and treated with [131I]MIBG. Results: The mean doses required to decrease surviving fractions of UVW/NAT and EJ138/NAT cells, which received medium from [131I]MIBG-treated cells, to 25 – 30% were 1.6 and 1.7 Gy respectively. The maximum mean dose rates achieved during [131I]MIBG treatment were 0.09 – 0.75 Gy/h for UVW/NAT and 0.07 – 0.78 Gy/h for EJ138/NAT. These were significantly lower than the external beam gamma radiation dose rate of 15 Gy/h. In the case of control lines which were incapable of [131I]MIBG uptake the mean absorbed doses following radiopharmaceutical were 0.03 – 0.23 Gy for UVW and 0.03 – 0.32 Gy for EJ138. Conclusion: [131I]MIBG treatment for ICCM production elicited a bystander dose-response profile similar to that generated by external beam gamma irradiation but with significantly greater cell death. PMID:24659931

  4. Gaussian effective potential for the standard model SU(2)xU(1) electroweak theory

    SciTech Connect

    Siringo, Fabio; Marotta, Luca

    2008-07-01

    The Gaussian effective potential is derived for the non-Abelian SU(2)xU(1) gauge theory of electroweak interactions. At variance with naive derivations, the Gaussian effective potential is proven to be a genuine variational tool in any gauge. The role of ghosts is discussed and the unitarity gauge is shown to be the only choice which allows calculability without insertion of further approximations. The full non-Abelian calculation confirms the existence of a light Higgs boson in the nonperturbative strong coupling regime of the Higgs sector.

  5. POTENTIAL DEVELOPMENTAL EFFECTS OF ATRAZINE ON AMPHIBIANS

    EPA Science Inventory

    Recent research has generated conflicting results on the effects of atrazine on gonadal developmental (e.g., male hermaphroditism) in amphibians and how these effects influence secondary sexual characteristics (e.g., laryngeal muscle mass). The SAP is being asked to consider the...

  6. The calculation of electron chemical potential and ion charge state and their influence on plasma conductivity in electrical explosion of metal wire

    SciTech Connect

    Shi, Zongqian; Wang, Kun; Li, Yao; Shi, Yuanjie; Wu, Jian; Jia, Shenli

    2014-03-15

    The electron chemical potential and ion charge state (average ion charge and ion distribution) are important parameters in calculating plasma conductivity in electrical explosion of metal wire. In this paper, the calculating method of electron chemical potential and ion charge state is discussed at first. For the calculation of electron chemical potential, the ideal free electron gas model and Thomas-Fermi model are compared and analyzed in terms of the coupling constant of plasma. The Thomas-Fermi ionization model, which is used to calculate ion charge state, is compared with the method based on Saha equation. Furthermore, the influence of electron degenerated energy levels and ion excited states in Saha equation on the ion charge state is also analyzed. Then the influence of different calculating methods of electron chemical potential and ion charge state on plasma conductivity is discussed by applying them in the Lee-More conductivity model.

  7. Computer program for calculating full potential transonic, quasi-three-dimensional flow through a rotating turbomachinery blade row

    NASA Technical Reports Server (NTRS)

    Farrell, C. A.

    1982-01-01

    A fast, reliable computer code is described for calculating the flow field about a cascade of arbitrary two dimensional airfoils. The method approximates the three dimensional flow in a turbomachinery blade row by correcting for stream tube convergence and radius change in the throughflow direction. A fully conservative solution of the full potential equation is combined with the finite volume technique on a body-fitted periodic mesh, with an artificial density imposed in the transonic region to insure stability and the capture of shock waves. The instructions required to set up and use the code are included. The name of the code is QSONIC. A numerical example is also given to illustrate the output of the program.

  8. Second-Order Perturbation Theory for Fractional Occupation Systems: Applications to Ionization Potential and Electron Affinity Calculations.

    PubMed

    Su, Neil Qiang; Xu, Xin

    2016-05-10

    Recently, we have developed an integration approach for the calculations of ionization potentials (IPs) and electron affinities (EAs) of molecular systems at the level of second-order Møller-Plesset (MP2) (Su, N. Q.; Xu, X. J. Chem. Theory Comput. 11, 4677, 2015), where the full MP2 energy gradient with respect to the orbital occupation numbers was derived but only at integer occupations. The theory is completed here to cover the fractional occupation systems, such that Slater's transition state concept can be used to have accurate predictions of IPs and EAs. Antisymmetrized Goldstone diagrams have been employed for interpretations and better understanding of the derived equations, where two additional rules were introduced in the present work specifically for hole or particle lines with fractional occupation numbers. PMID:27010405

  9. Anharmonic rovibrational calculations of singlet cyclic C4 using a new ab initio potential and a quartic force field.

    PubMed

    Wang, Xiaohong; Huang, Xinchuan; Bowman, Joel M; Lee, Timothy J

    2013-12-14

    We report a CCSD(T)/cc-pCV5Z quartic force field (QFF) and a semi-global CCSD(T)-F12b/aug-cc-pVTZ potential energy surface (PES) for singlet, cyclic C4. Vibrational fundamentals, combinations, and overtones are obtained using vibrational second-order perturbation theory (VPT2) and the vibrational configuration-interaction (VCI) approach. Agreement is within 10 cm(-1) between the VCI calculated fundamentals on the QFF and PES using the MULTIMODE (MM) program, and VPT2 and VCI results agree for the fundamentals. The agreement between VPT2-QFF and MM-QFF results is also good for the C4 combinations and overtones. The J = 1 and J = 2 rovibrational energies are reported from both VCI (MM) on the PES and VPT2 on the QFF calculations. The spectroscopic constants of (12)C4 and two C2v-symmetry, single (13)C-substituted isotopologues are presented, which may help identification of cyclic C4 in future experimental analyses or astronomical observations. PMID:24329063

  10. Potential of mean force calculation of the free energy of adsorption of Type I winter flounder antifreeze protein on ice

    NASA Astrophysics Data System (ADS)

    Battle, Keith; Alan Salter, E.; Wesley Edmunds, R.; Wierzbicki, Andrzej

    2010-04-01

    Antifreeze proteins (AFPs) are a unique class of proteins that inhibit ice growth without changing the melting point of ice. In this work, we study the detailed molecular mechanism of interactions between the hydrophobic side of the winter flounder (WF) AFP and two mutants, AAAA and SSSS, in which threonine residues are substituted by serines and alanines, respectively. Umbrella sampling molecular dynamics simulations of the separation of the proteins from the (2 0 1) surface in an explicit water box is carried out to calculate the potential of mean force free energies of adsorption using AMBER10i. We estimate wild-type WF's free energy of adsorption to ice to be about -12.0 kcal/mol. Gas-phase pseudopotential plane-wave calculations of methane adsorption onto select surfaces of ice are also carried out under periodic boundary conditions to address the possible enthalpic role of WF's methyl groups in binding. The contributions of hydrophobic residues to the free energy of adsorption are discussed.

  11. Anharmonic Rovibrational Calculations of Singlet Cyclic C4 Using a New Ab Initio Potential and a Quartic Force

    NASA Technical Reports Server (NTRS)

    Wang, Xiaohong; Huang, Xinchuan; Bowman, Joel M.; Lee, Timothy J.

    2013-01-01

    We report a CCSD(T)/cc-pCV5Z quartic force field (QFF) and a semi-global CCSD(T)-F12b/aug-cc-pVTZ potential energy surface (PES) for singlet, cyclic C4. Vibrational fundamentals, combinations and overtones are obtained using vibrational second-order perturbation theory (VPT2) and the vibrational configurationinteraction (VCI) approach. Agreement is within 10 cm(exp -1) between the VCI calculated fundamentals on the QFF and PES using the MULTIMODE (MM) program, and VPT2 and VCI results agree for the fundamentals. The agreement between VPT2- QFF and MM-QFF results is also good for the C4 combinations and overtones. The J = 1 and J = 2 rovibrational energies are reported from both VCI (MM) on the PES and VPT2 on the QFF calculations. The spectroscopic constants of (12)C4 and two C(sub 2v)-symmetry, single (13)C-substituted isotopologues are presented, which may help identification of cyclic C4 in future experimental analyses or astronomical observations.

  12. Collisional excitation of CH(X²Π) by He: new ab initio potential energy surfaces and scattering calculations.

    PubMed

    Marinakis, Sarantos; Dean, Indigo Lily; Kłos, Jacek; Lique, François

    2015-09-01

    We present a new set of potential energy surfaces (PESs) for the CH(X(2)Π)-He van der Waals system. Ab initio calculations of the CH-He PES were carried out using the open-shell single- and double-excitation coupled cluster approach with non-iterative perturbational treatment of triple excitations [RCCSD(T)]. The augmented correlation-consistent polarized valence quadruple-zeta (aug-cc-pVQZ) basis set was employed augmented by mid-bond functions. Integral cross sections for the rotational excitation in CH-He collisions were calculated using the new PES and compared with available experimental results. The newly constructed PES reproduces the available experimental results for CH(X(2)Π, v = 0)-He collisions better than any previously available PES. Differential cross sections (DCS) are presented for the first time for this system and discussed within the context of rotational rainbows. Finally, our work provides the first rate thermal coefficients for this system that are crucially needed for astrochemical modelling and future anticipated experiments in CH(X(2)Π)-He collisions. PMID:26220835

  13. [Potentially beneficial effects of climate changes].

    PubMed

    Hitz, Mette Friberg; Jensen, Jens Erik Beck

    2009-10-26

    Climate changes have many unbeneficial effects on human health, but may also have beneficial effects. An increased mean temperature reduces the incidence of death due to hypothermia and cardiovascular disease and may increase exercise frequency. As the ozone layer decreases, the synthesis of vitamin D in the organism will also increase. An increased level of plasma vitamin D has beneficial effects on bone- and muscle health, seems to reduce cancer incidence and mortality and reduces the prevalence of autoimmune- and cardiovascular disease. PMID:19857402

  14. Measurement effects on the calculation of in-flight thrust for an F404 turbofan engine

    NASA Technical Reports Server (NTRS)

    Conners, Timothy R.

    1989-01-01

    A study was performed that investigates parameter measurement effects on calculated in-flight thrust for the General Electric F404-GE-400 afterburning turbofan engine which powered the X-29A forward-swept wing research aircraft. Net-thrust uncertainty and influence coefficients were calculated and are presented. Six flight conditions were analyzed at five engine power settings each. Results were obtained using the mass flow-temperature and area-pressure thrust calculation methods, both based on the commonly used gas generator technique. Thrust uncertainty was determined using a common procedure based on the use of measurement uncertainty and influence coefficients. The effects of data nonlinearity on the uncertainty calculation procedure were studied and results are presented. The advantages and disadvantages of using this particular uncertainty procedure are discussed. A brief description of the thrust-calculation technique along with the uncertainty calculation procedure is included.

  15. Measurement effects on the calculation of in-flight thrust for an F404 turbofan engine

    NASA Technical Reports Server (NTRS)

    Conners, Timothy R.

    1989-01-01

    A study has been performed that investigates parameter measurement effects on calculated in-flight thrust for the General Electric F404-GE-400 afterburning turbofan engine which powered the X-29A forward-swept wing research aircraft. Net-thrust uncertainty and influence coefficients were calculated and are presented. Six flight conditions were analyzed at five engine power settings each. Results were obtained using the mass flow-temperature and area-pressure thrust calculation methods, both based on the commonly used gas generator technique. Thrust uncertainty was determined using a common procedure based on the use of measurement uncertainty and influence coefficients. The effects of data nonlinearity on the uncertainty calculation procedure were studied and results are presented. The advantages and disadvantages of using this particular uncertainty procedure are discussed. A brief description of the thrust-calculation technique along with the uncertainty calculation procedure is included.

  16. An isotopic mass effect on the intermolecular potential

    NASA Astrophysics Data System (ADS)

    Herman, Michael F.; Currier, Robert P.; Clegg, Samuel M.

    2015-10-01

    The impact of isotopic variation on the electronic energy and intermolecular potentials is often suppressed when calculating isotopologue thermodynamics. Intramolecular potential energy surfaces for distinct isotopologues are in fact equivalent under the Born-Oppenheimer approximation, which is sometimes used to imply that the intermolecular interactions are independent of isotopic mass. In this communication, the intermolecular dipole-dipole interaction between hetero-nuclear diatomic molecules is considered. It is shown that the intermolecular potential contains mass-dependent terms even though each nucleus moves on a Born-Oppenheimer surface. The analysis suggests that mass dependent variations in intermolecular potentials should be included in comprehensive descriptions of isotopologue thermodynamics.

  17. Calculation of Dilational and Uniaxial Shear Potentials of Ge by a State-Independent Many-Body Projection Technique

    NASA Astrophysics Data System (ADS)

    Kang, Nam; Ryu, Jai; Choi, Sang

    1998-07-01

    Utilizing state-independent projection operators, we present a new optical conductivity formula for cyclotron transition in the system of electrons interacting anisotropically with phonons. The line-shape factor appearing in the conductivity tensor contains the many body effects for electrons and phonons. Applying this formula, we determine the two deformation potentials (dilation potential Ξd and uniaxial shear potential Ξu) of Ge in the quantum limit. By fitting the present theoretical values with the experimental data of Murase, Enjouji and Otsuka [J. Phys. Soc. Jpn. 29 (1970) 1248] and Kobori, Ohyama and Otsuka [J. Phys. Soc. Jpn. 59 (1990) 2141], we obtain Ξu=17.0±0.6 eV and Ξd=-10.88±0.47 eV.

  18. Performance of Density Functional Theory and Relativistic Effective Core Potential for Ru-Based Organometallic Complexes.

    PubMed

    Paranthaman, Selvarengan; Moon, Jiwon; Kim, Joonghan; Kim, Dong Eon; Kim, Tae Kyu

    2016-04-01

    Herein a performance assessment of density functionals used for calculating the structural and energetic parameters of bi- and trimetallic Ru-containing organometallic complexes has been performed. The performance of four popular relativistic effective core potentials (RECPs) has also been assessed. On the basis of the calculated results, the MN12-SX (range-separated hybrid functional) demonstrates good performance for calculating the molecular structures, while MN12-L (local functional) performs well for calculating the energetics, including that of the Ru-Ru bond breaking process. The choice of appropriate density functional is a crucial factor for calculating the energetics. The LANL08 demonstrates the lowest performance of the RECPs for calculating the molecular structures, especially the Ru-Ru bond length. PMID:26986051

  19. An Effective Method to Accurately Calculate the Phase Space Factors for β - β - Decay

    DOE PAGESBeta

    Neacsu, Andrei; Horoi, Mihai

    2016-01-01

    Accurate calculations of the electron phase space factors are necessary for reliable predictions of double-beta decay rates and for the analysis of the associated electron angular and energy distributions. We present an effective method to calculate these phase space factors that takes into account the distorted Coulomb field of the daughter nucleus, yet it allows one to easily calculate the phase space factors with good accuracy relative to the most exact methods available in the recent literature.

  20. Relativistic calculations of the nuclear recoil effect in highly charged Li-like ions

    NASA Astrophysics Data System (ADS)

    Zubova, N. A.; Shabaev, V. M.; Tupitsyn, I. I.; Plunien, G.

    2013-09-01

    Relativistic theory of the nuclear recoil effect in highly charged Li-like ions is considered within the Breit approximation. The normal mass shift (NMS) and the relativistic NMS (RNMS) are calculated by perturbation theory to zeroth and first orders in the parameter 1/Z. The calculations are performed using the dual kinetic balance method with the basis functions constructed from B-splines. The results of the calculations are compared with the theoretical values obtained by other methods.

  1. Full potential unsteady computations including aeroelastic effects

    NASA Technical Reports Server (NTRS)

    Shankar, Vijaya; Ide, Hiroshi

    1989-01-01

    A unified formulation is presented based on the full potential framework coupled with an appropriate structural model to compute steady and unsteady flows over rigid and flexible configurations across the Mach number range. The unsteady form of the full potential equation in conservation form is solved using an implicit scheme maintaining time accuracy through internal Newton iterations. A flux biasing procedure based on the unsteady sonic reference conditions is implemented to compute hyperbolic regions with moving sonic and shock surfaces. The wake behind a trailing edge is modeled using a mathematical cut across which the pressure is satisfied to be continuous by solving an appropriate vorticity convection equation. An aeroelastic model based on the generalized modal deflection approach interacts with the nonlinear aerodynamics and includes both static as well as dynamic structural analyses capability. Results are presented for rigid and flexible configurations at different Mach numbers ranging from subsonic to supersonic conditions. The dynamic response of a flexible wing below and above its flutter point is demonstrated.

  2. On orthogonality constrained multiple core-hole states and optimized effective potential method.

    PubMed

    Glushkov, V N; Assfeld, X

    2012-10-01

    An attempt to construct a multiple core-hole state within the optimized effective potential (OEP) methodology is presented. In contrast to the conventional Δ-self-consistent field method for hole states, the effects of removing an electron is achieved using some orthogonality constraints imposed on the orbitals so that a Slater determinant describing a hole state is constrained to be orthogonal to that of a neutral system. It is shown that single, double, and multiple core-hole states can be treated within a unified framework and can be easily implemented for atoms and molecules. For this purpose, a constrained OEP method proposed earlier for excited states (Glushkov and Levy, J. Chem. Phys. 2007, 126, 174106) is further developed to calculate single and double core ionization energies using a local effective potential expressed as a direct mapping of the external potential. The corresponding equations, determining core-hole orbitals from a one-particle Schrödinger equation with a local potential as well as correlation corrections derived from the second-order many-body perturbation theory are given. One of the advantages of the present direct mapping formulation is that the effective potential, which plays the role of the Kohn-Sham potential, has the symmetry of the external potential. Single and double core ionization potentials computed with the presented scheme were found to be in agreement with data available from experiment and other calculations. We also discuss core-hole state local potentials for the systems studied. PMID:22696265

  3. Potential of mean force calculations of the stacking-unstacking process in single-stranded deoxyribodinucleoside monophosphates.

    PubMed Central

    Norberg, J; Nilsson, L

    1995-01-01

    The free energy of the stacking-unstacking process of deoxyribodinucleoside monophosphates in aqueous solution has been investigated by potential of mean force calculations along a reaction coordinate, defined by the distance between the glycosidic nitrogen atoms of the bases. The stacking-unstacking process of a ribodinucleoside monophosphate was observed to be well characterized by this coordinate, which has the advantage that it allows for a dynamical backbone and flexible bases. All 16 naturally occurring DNA dimers composed of the adenine, cytosine, guanine, or thymine bases in both the 5' and the 3' positions were studied. From the free-energy profiles we observed the deepest minima for the stacked states of the purine-purine dimers, but good stacking was also observed for the purine-pyrimidine and pyrimidine-purine dimers. Substantial stacking ability was found for the dimers composed of a thymine base and a purine base and also for the deoxythymidylyl-3',5'-deoxythymidine dimer. Very poor stacking was observed for the dCpdC dimer. Conformational properties and solvent accessibility are discussed for the stacked and unstacked dimers. The potential of mean force profiles of the stacking-unstacking process for the DNA dimers are compared with the RNA dimers. PMID:8599635

  4. Calculation of 29Si NMR shifts of silicate complexes with carbohydrates, amino acids, and muhicarboxylic acids: potential role in biological silica utilization

    NASA Astrophysics Data System (ADS)

    Sahai, Nita

    2004-01-01

    The existence of ether or ester-like complexes of silicate with organic compounds has long been debated in the literature on biological utilization of silicon. Comparison of theoretically calculated 29Si NMR chemical shifts for such complexes with experimentally measured values in biological systems could provide a diagnostic tool for identifying which, if any of these molecules exist under physiological conditions. Results are presented here for ab initio molecular orbital calculations of 29Si NMR shifts and formation energies of silicate complexes with polyalcohols, sugar-acids, pyranose sugars, amino acids and multicarboxylic acids. The effects of functional group and molecular structure including ligand size, denticity, ring size, silicon polymerization and coordination number on calculated 29Si shifts were considered. The potential role of such compounds in biological silica utilization pathways is discussed. 29Si NMR shifts and energies were calculated at the HF/6-311+G(2d,p)//HF/6-31G* level. The main result is that only five-membered rings containing penta- and hexa-coordinated Si can explain experimentally observed resonances at ˜ -101 and -141 ppm. Further, the heptet observed in 1H- 29Si coupled spectra can only be explained by structures where Si bonds to oxygens atoms in H-C-O-Si linkages with six symmetrically equivalent H atoms. While compounds containing quadra-coordinated silicon may exist in intracellular silicon storage pools within diatoms, calculated reaction energies suggest that the organism has no thermodynamic advantage in taking up extracellular organ-silicate compounds, instead of silicic acid, from the ambient aqueous environment. Hyper-coordinated complexes are deemed unlikely for transport and storage, though they may exist as transient reactive intermediates or activated complexes during enzymatically- catalyzed silica polymerization, as known previously from sol-gel silica synthesis studies.

  5. Renormalization effects on the MSSM from a calculable model of a strongly coupled hidden sector

    SciTech Connect

    Arai, Masato; Okada, Nobuchika

    2011-10-01

    We investigate possible renormalization effects on the low-energy mass spectrum of the minimal supersymmetric standard model (MSSM), using a calculable model of strongly coupled hidden sector. We model the hidden sector by N=2 supersymmetric quantum chromodynamics with gauge group SU(2)xU(1) and N{sub f}=2 matter hypermultiplets, perturbed by a Fayet-Iliopoulos term which breaks the supersymmetry down to N=0 on a metastable vacuum. In the hidden sector the Kaehler potential is renormalized. Upon identifying a hidden sector modulus with the renormalization scale, and extrapolating to the strongly coupled regime using the Seiberg-Witten solution, the contribution from the hidden sector to the MSSM renormalization group flows is computed. For concreteness, we consider a model in which the renormalization effects are communicated to the MSSM sector via gauge mediation. In contrast to the perturbative toy examples of hidden sector renormalization studied in the literature, we find that our strongly coupled model exhibits rather intricate effects on the MSSM soft scalar mass spectrum, depending on how the hidden sector fields are coupled to the messenger fields. This model provides a concrete example in which the low-energy spectrum of MSSM particles that are expected to be accessible in collider experiments is obtained using strongly coupled hidden sector dynamics.

  6. Incorporation of solvation effects into the fragment molecular orbital calculations with the Poisson-Boltzmann equation

    NASA Astrophysics Data System (ADS)

    Watanabe, Hirofumi; Okiyama, Yoshio; Nakano, Tatsuya; Tanaka, Shigenori

    2010-11-01

    We developed FMO-PB method, which incorporates solvation effects into the Fragment Molecular Orbital calculation with the Poisson-Boltzmann equation. This method retains good accuracy in energy calculations with reduced computational time. We calculated the solvation free energies for polyalanines, Alpha-1 peptide, tryptophan cage, and complex of estrogen receptor and 17 β-estradiol to show the applicability of this method for practical systems. From the calculated results, it has been confirmed that the FMO-PB method is useful for large biomolecules in solution. We also discussed the electric charges which are used in solving the Poisson-Boltzmann equation.

  7. Alternative time-dependent optimized effective potential

    NASA Astrophysics Data System (ADS)

    Nazarov, Vladimir

    2013-03-01

    The OEP is known as a single-particle potential minimizing the expectation value of a many-body Hamiltonian on the set of eigen-functions of a single-particle Hamiltonian. The time-dependent (TD) OEP can be constructed with the TD quantum stationary-action principle. Very useful conceptually in DFT and TDDFT, both OEPs are not practicable due to the complexity of their implementations. Here we report a TDOEP by minimizing the difference of LHS and RHS of the TD Schrödinger equation. If the orbitals are varied, then the TD Hartree-Fock equations are reproduced. Similarly, we now find the OEP. New OMP does not involve the inversion of the density-response function χs, which greatly facilitates implementations. Accordingly, the exchange-correlation kernel fxc involves of χs- 1 only, not its quadratic counterpart. To show the power of this method, we work out the fxch (q , ω) of the homogeneous electron gas to be used with the nearly-free electrons theory, where fxch is the main input. Partial support from National Science Council, Taiwan, Grant No. 100-2112-M-001-025-MY3 is acknowledged.

  8. Potential effect of ultrasound on carbohydrates.

    PubMed

    Bera, Smritilekha; Mondal, Dhananjoy; Martin, Jacob T; Singh, Man

    2015-06-17

    The use of ultrasound has emerged as one of the most useful alternative energy sources for the synthesis of carbohydrate-derived biologically and pharmaceutically potential compounds. Spectacular advances have been made in the field of sonication-assisted organic reactions, which are known for producing superior yields, enhanced reactivity of the reactant, improved stereoselectivity, and shortened reaction times. Orthogonal protection-deprotection reactions and/or modification and manipulation of functional groups in carbohydrates are common synthetic steps in carbohydrate chemistry. These reaction steps can be driven by the ultrasonic energy generated by acoustic cavitation via the formation and subsequent collapse of ultrasound-induced bubbles. The ultrasound-assisted synthesis of differently functionalised monosaccharides is useful in a wide variety of applications of carbohydrate chemistry such as the glycosylation of oligosaccharides, one pot domino reactions, thioglycoside syntheses, azidoglycoside syntheses, 1,3-dipolar cycloaddition reactions, and syntheses of natural products. This review article covers ultrasound-mediated reactions on carbohydrates that have been described in the literature since 2000. PMID:25954862

  9. Extension of the Effective Fragment Potential Method to Macromolecules.

    PubMed

    Gurunathan, Pradeep Kumar; Acharya, Atanu; Ghosh, Debashree; Kosenkov, Dmytro; Kaliman, Ilya; Shao, Yihan; Krylov, Anna I; Slipchenko, Lyudmila V

    2016-07-14

    The effective fragment potential (EFP) approach, which can be described as a nonempirical polarizable force field, affords an accurate first-principles treatment of noncovalent interactions in extended systems. EFP can also describe the effect of the environment on the electronic properties (e.g., electronic excitation energies and ionization and electron-attachment energies) of a subsystem via the QM/EFP (quantum mechanics/EFP) polarizable embedding scheme. The original formulation of the method assumes that the system can be separated, without breaking covalent bonds, into closed-shell fragments, such as solvent and solute molecules. Here, we present an extension of the EFP method to macromolecules (mEFP). Several schemes for breaking a large molecule into small fragments described by EFP are presented and benchmarked. We focus on the electronic properties of molecules embedded into a protein environment and consider ionization, electron-attachment, and excitation energies (single-point calculations only). The model systems include chromophores of green and red fluorescent proteins surrounded by several nearby amino acid residues and phenolate bound to the T4 lysozyme. All mEFP schemes show robust performance and accurately reproduce the reference full QM calculations. For further applications of mEFP, we recommend either the scheme in which the peptide is cut along the Cα-C bond, giving rise to one fragment per amino acid, or the scheme with two cuts per amino acid, along the Cα-C and Cα-N bonds. While using these fragmentation schemes, the errors in solvatochromic shifts in electronic energy differences (excitation, ionization, electron detachment, or electron-attachment) do not exceed 0.1 eV. The largest error of QM/mEFP against QM/EFP (no fragmentation of the EFP part) is 0.06 eV (in most cases, the errors are 0.01-0.02 eV). The errors in the QM/molecular mechanics calculations with standard point charges can be as large as 0.3 eV. PMID:27314461

  10. Microscopic Calculation of 240Pu Scission with a Finite-Range Effective Force

    SciTech Connect

    Younes, W; Gogny, D

    2009-05-04

    Hartree-Fock-Bogoliubov calculations of hot fission in {sup 240}Pu have been performed with a newly-implemented code that uses the D1S finite-range effective interaction. The hot-scission line is identified in the quadrupole-octupole-moment coordinate space. Fission-fragment shapes are extracted from the calculations. A benchmark calculation for {sup 226}Th is obtained and compared to results in the literature. In addition, technical aspects of the use of HFB calculations for fission studies are examined in detail. In particular, the identification of scission configurations, the sensitivity of near-scission calculations to the choice of collective coordinates in the HFB iterations, and the formalism for the adjustment of collective-variable constraints are discussed. The power of the constraint-adjustment algorithm is illustrated with calculations near the critical scission configurations with up to seven simultaneous constraints.

  11. A comparison of methods used to calculate normal background concentrations of potentially toxic elements for urban soil.

    PubMed

    Rothwell, Katherine A; Cooke, Martin P

    2015-11-01

    To meet the requirements of regulation and to provide realistic remedial targets there is a need for the background concentration of potentially toxic elements (PTEs) in soils to be considered when assessing contaminated land. In England, normal background concentrations (NBCs) have been published for several priority contaminants for a number of spatial domains however updated regulatory guidance places the responsibility on Local Authorities to set NBCs for their jurisdiction. Due to the unique geochemical nature of urban areas, Local Authorities need to define NBC values specific to their area, which the national data is unable to provide. This study aims to calculate NBC levels for Gateshead, an urban Metropolitan Borough in the North East of England, using freely available data. The 'median + 2MAD', boxplot upper whisker and English NBC (according to the method adopted by the British Geological Survey) methods were compared for test PTEs lead, arsenic and cadmium. Due to the lack of systematically collected data for Gateshead in the national soil chemistry database, the use of site investigation (SI) data collected during the planning process was investigated. 12,087 SI soil chemistry data points were incorporated into a database and 27 comparison samples were taken from undisturbed locations across Gateshead. The SI data gave high resolution coverage of the area and Mann-Whitney tests confirmed statistical similarity for the undisturbed comparison samples and the SI data. SI data was successfully used to calculate NBCs for Gateshead and the median+2MAD method was selected as most appropriate by the Local Authority according to the precautionary principle as it consistently provided the most conservative NBC values. The use of this data set provides a freely available, high resolution source of data that can be used for a range of environmental applications. PMID:26119377

  12. X-ray absorption spectra of graphene and graphene oxide by full-potential multiple scattering calculations with self-consistent charge density

    NASA Astrophysics Data System (ADS)

    Xu, Junqing; Krüger, Peter; Natoli, Calogero R.; Hayakawa, Kuniko; Wu, Ziyu; Hatada, Keisuke

    2015-09-01

    The x-ray absorption near-edge structure of graphene, graphene oxide, and diamond is studied by the recently developed real-space full potential multiple scattering (FPMS) theory with space-filling cells. It is shown how accurate potentials for FPMS can be generated from self-consistent charge densities obtained with other schemes, especially the projector augmented wave method. Compared to standard multiple scattering calculations in the muffin-tin approximation, FPMS gives much better agreement with experiment. The effects of various structural modifications on the graphene spectra are well reproduced. (1) Stacking of graphene layers increases the peak intensity in the higher energy region. (2) The spectrum of the C atom located at the edge of a graphene sheet shows a prominent pre-edge structure. (3) Adsorption of oxygen gives rise to the so-called interlayer-state peak. Moreover, O K-edge spectra of graphene oxide are calculated for three types of bonding, C-OH, C-O-C, and C-O, and the proportions of these bondings at 800 ∘C are deduced by fitting them to the experimental spectrum.

  13. Prebiotic Atmospheric Chemistry on Titan: Formation Kinetics via Ab Initio Calculations for Potential Energy Surface (PES) Mapping

    NASA Astrophysics Data System (ADS)

    Gonzalez, Dayana; Mebel, Alexander

    2016-03-01

    It has been recently shown that Titan provides a unique perspective in our solar system: its atmosphere is comparable to a model of prebiotic Earth's. Provided the organic cationic and anionic molecular species identified by the Cassini spacecraft, this research characterizes reaction pathways for the reactions of methyl derivatives of the cyclopropenyl cation, the methyl cation with methyl- and dimethyl-acetylene, and reactions of resonance structures of protonated acrylonitrile with CH2NH. Isomerization and dissociation reactions involving methyl-cyclopropenyl cations, the perinaphthenyl cation and anion, and cations of pyrimidine and purine precursors of nucleobases will be examined to locate reaction pathways, intermediates, transition states, and products of the reactions. Gaussian '09 software is used for ab initio calculations to map out the PES. Geometry optimizations and vibrational frequency computations are preformed via the double-hybrid density functional B2PLYP-D3. Single-point energies are refined by use of the explicitly-correlated coupled-cluster CCSD(T)-F12 method. Rate constants are calculated using microcanonical RRKM theory, and pressure effects evaluated used the Master Equation approach; these allow for prediction of absolute rate constants and product branching ratios at different pressures and temperatures.

  14. Calculated K-effectives using ENDF/B-V data for U + Pu solution critical experiments

    SciTech Connect

    Primm, R.T. III; Mincey, J.F.

    1981-01-01

    Effective multiplication factors for 12 critical experiments have been calculated using multigroup cross sections derived from the ENDF/B-V library. All 12 experiments contained mixed plutonium and uranium nitrate solutions. The range of hydrogen-to-fissile plutonium atom ratios spanned by these experiments was 200 to 2200. A comparison with K-effectives calculated with ENDF/B-IV data is presented.

  15. An improved potential energy surface and multi-temperature quasiclassical trajectory calculations of N2 + N2 dissociation reactions.

    PubMed

    Bender, Jason D; Valentini, Paolo; Nompelis, Ioannis; Paukku, Yuliya; Varga, Zoltan; Truhlar, Donald G; Schwartzentruber, Thomas; Candler, Graham V

    2015-08-01

    Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration of collision-induced dissociation of molecular species and energy transfer between the translational and internal modes of the gas molecules. Here, we describe a study of the N2 + N2⟶N2 + 2N and N2 + N2⟶4N nitrogen dissociation reactions using the quasiclassical trajectory (QCT) method. The simulations used a new potential energy surface for the N4 system; the surface is an improved version of one that was presented previously. In the QCT calculations, initial conditions were determined based on a two-temperature model that approximately separates the translational-rotational temperature from the vibrational temperature of the N2 diatoms. Five values from 8000 K to 30,000 K were considered for each of the two temperatures. Over 2.4 × 10(9) trajectories were calculated. We present results for ensemble-averaged dissociation rate constants as functions of the translational-rotational temperature T and the vibrational temperature T(v). The rate constant depends more strongly on T when T(v) is low, and it depends more strongly on T(v) when T is low. Quasibound reactant states contribute significantly to the rate constants, as do exchange processes at higher temperatures. We discuss two sets of runs in detail: an equilibrium test set in which T = T(v) and a nonequilibrium test set in which T(v) < T. In the equilibrium test set, high-v and moderately-low-j molecules contribute most significantly to the overall dissociation rate, and this state specificity becomes stronger as the temperature decreases. Dissociating trajectories tend to result in a major loss of vibrational energy and a minor loss of rotational energy. In the nonequilibrium test set, as T(v) decreases while T is fixed, higher-j molecules contribute more significantly to the dissociation rate, dissociating trajectories tend to result in a greater rotational energy loss, and the dissociation probability

  16. An improved potential energy surface and multi-temperature quasiclassical trajectory calculations of N2 + N2 dissociation reactions

    NASA Astrophysics Data System (ADS)

    Bender, Jason D.; Valentini, Paolo; Nompelis, Ioannis; Paukku, Yuliya; Varga, Zoltan; Truhlar, Donald G.; Schwartzentruber, Thomas; Candler, Graham V.

    2015-08-01

    Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration of collision-induced dissociation of molecular species and energy transfer between the translational and internal modes of the gas molecules. Here, we describe a study of the N2 + N2⟶N2 + 2N and N2 + N2⟶4N nitrogen dissociation reactions using the quasiclassical trajectory (QCT) method. The simulations used a new potential energy surface for the N4 system; the surface is an improved version of one that was presented previously. In the QCT calculations, initial conditions were determined based on a two-temperature model that approximately separates the translational-rotational temperature from the vibrational temperature of the N2 diatoms. Five values from 8000 K to 30 000 K were considered for each of the two temperatures. Over 2.4 × 109 trajectories were calculated. We present results for ensemble-averaged dissociation rate constants as functions of the translational-rotational temperature T and the vibrational temperature Tv. The rate constant depends more strongly on T when Tv is low, and it depends more strongly on Tv when T is low. Quasibound reactant states contribute significantly to the rate constants, as do exchange processes at higher temperatures. We discuss two sets of runs in detail: an equilibrium test set in which T = Tv and a nonequilibrium test set in which Tv < T. In the equilibrium test set, high-v and moderately-low-j molecules contribute most significantly to the overall dissociation rate, and this state specificity becomes stronger as the temperature decreases. Dissociating trajectories tend to result in a major loss of vibrational energy and a minor loss of rotational energy. In the nonequilibrium test set, as Tv decreases while T is fixed, higher-j molecules contribute more significantly to the dissociation rate, dissociating trajectories tend to result in a greater rotational energy loss, and the dissociation probability's dependence on v

  17. Scattering and Bound States of Klein-Gordon Particle with Hylleraas Potential Within Effective Mass Formalism

    NASA Astrophysics Data System (ADS)

    Onyeaju, M. C.; Ikot, A. N.; Chukwuocha, E. O.; Obong, H. P.; Zare, S.; Hassanabadi, H.

    2016-06-01

    Scattering and bound states solution for the one-dimensional Klein-Gordon particle with Hylleraas potential is presented within the frame work of position dependent effective mass formalism. We calculate in detail the reflection and transmission coefficients using the properties of hypergeometric functions and the equation of continuity of the wave functions.

  18. The exterior tidal potential acting on a satellite. [satellite orbits/satellite perturbation - gravitation effects

    NASA Technical Reports Server (NTRS)

    Musen, P.

    1975-01-01

    A theory is presented that points out the existence of several long period and 'cross effects' in the coefficients in the expansion of the geopotential and in the motion of satellites. The tidal potential, defined as small periodic variations in the geopotential, was calculated. The influence of these geopotential variations on satellite perturbation is examined. Spherical harmonics were employed.

  19. Calculated k-effectives for light water reactor typical, U + Pu nitrate solution critical experiments

    SciTech Connect

    Primm, R.T. III; Mincey, J.F.

    1982-01-01

    The Department of Energy's Consolidated Fuel Reprocessing Program has as a goal the design of nuclear fuel reprocessing equipment. In order to validate computer codes used for criticality analyses in the design of such equipment, k-effectives have been calculated for several U + Pu nitrate solution critical experiments. As of January 1981, descriptions of 45 unpoisoned, U + Pu solution experiments were available in the open literature. Twelve of these experiments were performed with solutions which have physical characteristics typical of dissolved, light water reactor fuel. This paper contains a discussion of these twelve experiments, a review of the calculational procedure used to determine k-effectives, and the results of the calculations.

  20. A rate equation approach to gain saturation effects in laser mode calculations

    NASA Technical Reports Server (NTRS)

    Roberts, Lila F.

    1990-01-01

    Space exploration and research require large amounts of power. Solar pumped laser systems have been shown to have the potential for meeting the performance requirements necessary for power transmission in space. The successful design of laser systems for these applications will depend, in part, on having a clear understanding of the development of the dynamical processes in the laser cavity and on the effects that changes in physical and design parameters have on laser performance. In particular, it is necessary to know the amplitude and phase distributions of the laser beam at the output aperture when steady state operation is achieved in order to determine the far-field power distribution. The output from the laser will depend on the active medium, the optical environment of the active material and on the gain distribution in the active region as laser action builds up and reaches steady state. An important component in the design process will be a realistic model of the active laser cavity. A computer model of the laser cavity, based on Huygens' principle was developed. The code calculates the amplitude and phase of an optical wave reflected back and forth between the mirrors of a laser cavity. The original code assumes a gain distribution which does not change with the buildup of oscillations in the cavity. A step in the direction of realism is the inclusion of a saturable gain medium in the cavity. The objective is to incorporate saturation effects into the existing computer model.

  1. Charge-correlation effects in calculations of atomic short-range order in metallic alloys

    NASA Astrophysics Data System (ADS)

    Pinski, F. J.; Staunton, J. B.; Johnson, D. D.

    1998-06-01

    The ``local'' chemical environment that surrounds an atom directly influences its electronic charge density. These atomic charge correlations play an important role in describing the Coulomb and total energies for random substitutional alloys. Although the electronic structure may be well represented by a single-site theory, such as the coherent potential approximation, the electrostatic energy is not as well represented when these charge correlations are ignored. For metals, including the average effect from the charge correlation coming from only the nearest-neighbor shell has been shown to be sufficient to determine accurately the energy of formation. In this paper, we incorporate such charge correlations into the concentration-wave approach for calculating the atomic short-range order in random (substitutional) alloys. We present changes within the formalism, and apply the resulting equations to equiatomic nickel platinum. By including these effects, we obtain significantly better agreement with experimental data. In fact, particular to NiPt, a consequence of the charge correlation is a screening which cancels much of the electrostatic contribution to the energy and thus to the atomic short-range order, resulting in agreement with a picture originally outlined using only ``band-energy'' contributions.

  2. An illustration of the effect of various sources of uncertainty on DNA likelihood ratio calculations.

    PubMed

    Taylor, D; Bright, J-A; Buckleton, J; Curran, J

    2014-07-01

    A typical assessment of the strength of forensic DNA evidence is based on a population genetic model and estimated allele frequencies determined from a population database. Some experts provide a confidence or credible interval which takes into account the sampling variation inherent in deriving these estimates from only a sample of a total population. This interval is given in conjunction with the statistic of interest, be it a likelihood ratio (LR), match probability, or cumulative probability of inclusion. Bayesian methods of addressing database sampling variation produce a distribution for the statistic from which the bound(s) of the desired interval can be determined. Population database sampling uncertainty represents only one of the sources of uncertainty that affects estimation of the strength of DNA evidence. There are other uncertainties which can potentially have a much larger effect on the statistic such as, those inherent in the value of Fst, the weights given to genotype combinations in a continuous interpretation model, and the composition of the relevant population. In this paper we model the effect of each of these sources of uncertainty on a likelihood ratio (LR) calculation and demonstrate how changes in the distribution of these parameters affect the reported value. In addition, we illustrate the impact the different approaches of accounting for sampling uncertainties has on the LR for a four person mixture. PMID:24667729

  3. Quantum Calculations on Hydrogen Bonds in Certain Water Clusters Show Cooperative Effects

    SciTech Connect

    Znamenskiy, Vasiliy S.; Green, Michael E.

    2007-01-09

    Water molecules in clefts and small clusters are in a significantly different environment than those in bulk water. We have carried out ab initio calculations that demonstrate this in a series of clusters, showing that cooperative effects must be taken into account in the treatment of hydrogen bonds and water clusters in such bounded systems. Hydrogen bonds between water molecules in simulations are treated most frequently by using point-charge water potentials, such as TIP3P or SPC, sometimes with a polarizable extension. These produce excellent results in bulk water, for which they are calibrated. Clefts are different from bulk; it is necessary to look at smaller systems and investigate the effect of limited numbers of neighbors. We start with a study of isolated clusters of water with varying numbers of neighbors of a hydrogen-bonded pair of water molecules. The cluster as a whole is in a vacuum. The clusters are defined so as to provide the possible arrangements of nearest neighbors of a central hydrogen-bonded pair of water molecules. We then scan the length and angles of the central hydrogen bond of the clusters, using density functional theory, for each possible arrangement of donor and acceptor hydrogen bonds on the central hydrogen-bonding pair; the potential of interaction of two water molecules varies with the number of donor and acceptor neighbors. This also involves changes in charge on the water molecules as a function of bond length and changes in energy and length as a function of the number of neighboring donor and acceptor molecules. The energy varies by approximately 6 kBT near room temperature from the highest to the lowest energy when bond length alone is varied, enough to seriously affect simulations.

  4. Quantum Calculations on Hydrogen Bonds in Certain Water Clusters Show Cooperative Effects.

    SciTech Connect

    Znamenskiy, Vasiliy S.; Green, Michael E.

    2006-12-08

    The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. Water molecules in clefts and small clusters are in a significantly different environment than those in bulk water. We have carried out ab initio calculations that demonstrate this in a series of clusters, showing that cooperative effects must be taken into account in the treatment of hydrogen bonds and water clusters in such bounded systems. Hydrogen bonds between water molecules in simulations are treated most frequently by using point-charge water potentials, such as TIP3P or SPC, sometimes with a polarizable extension. These produce excellent results in bulk water, for which they are calibrated. Clefts are different from bulk; it is necessary to look at smaller systems and investigate the effect of limited numbers of neighbors. We start with a study of isolated clusters of water with varying numbers of neighbors of a hydrogen-bonded pair of water molecules. The cluster as a whole is in a vacuum. The clusters are defined so as to provide the possible arrangements of nearest neighbors of a central hydrogen-bonded pair of water molecules. We then scan the length and angles of the central hydrogen bond of the clusters, using density functional theory, for each possible arrangement of donor and acceptor hydrogen bonds on the central hydrogen-bonding pair; the potential of interaction of two water molecules varies with the number of donor and acceptor neighbors. This also involves changes in charge on the water molecules as a function of bond length and changes in energy and length as a function of the number of neighboring donor and acceptor molecules. The energy varies by approximately 6 kBT near room temperature from the highest to the lowest energy when bond length alone is

  5. Gas-phase reaction between calcium monocation and fluoromethane: Analysis of the potential energy hypersurface and kinetics calculations

    SciTech Connect

    Varela-Alvarez, Adrian; Sordo, Jose A.; Rayon, V. M.; Redondo, P.; Barrientos, C.

    2009-10-14

    The gas-phase reaction between calcium monocation and fluoromethane: Ca{sup +}+CH{sub 3}F{yields}CaF{sup +}+CH{sub 3} was theoretically analyzed. The potential energy hypersurface was explored by using density functional theory methodology with different functionals and Pople's, Dunning's, Ahlrichs', and Stuttgart-Dresden basis sets. Kinetics calculations (energy and total angular momentum resolved microcanonical variational/conventional theory) were accomplished. The theoretically predicted range for the global kinetic rate constant values at 295 K (7.2x10{sup -11}-5.9x10{sup -10} cm{sup 3} molecule{sup -1} s{sup -1}) agrees reasonably well with the experimental value at the same temperature [(2.6{+-}0.8)x10{sup -10} cm{sup 3} molecule{sup -1} s{sup -1}]. Explicit consideration of a two transition state model, where the formation of a weakly bounded prereactive complex is preceded by an outer transition state (entrance channel) and followed by an inner transition state connecting with a second intermediate that finally leads to products, is mandatory. Experimental observations on the correlation, or lack of correlation, between reaction rate constants and second ionization energies of the metal might well be rationalized in terms of this two transition state model.

  6. Performance of heterogeneous computing with graphics processing unit and many integrated core for hartree potential calculations on a numerical grid.

    PubMed

    Choi, Sunghwan; Kwon, Oh-Kyoung; Kim, Jaewook; Kim, Woo Youn

    2016-09-15

    We investigated the performance of heterogeneous computing with graphics processing units (GPUs) and many integrated core (MIC) with 20 CPU cores (20×CPU). As a practical example toward large scale electronic structure calculations using grid-based methods, we evaluated the Hartree potentials of silver nanoparticles with various sizes (3.1, 3.7, 4.9, 6.1, and 6.9 nm) via a direct integral method supported by the sinc basis set. The so-called work stealing scheduler was used for efficient heterogeneous computing via the balanced dynamic distribution of workloads between all processors on a given architecture without any prior information on their individual performances. 20×CPU + 1GPU was up to ∼1.5 and ∼3.1 times faster than 1GPU and 20×CPU, respectively. 20×CPU + 2GPU was ∼4.3 times faster than 20×CPU. The performance enhancement by CPU + MIC was considerably lower than expected because of the large initialization overhead of MIC, although its theoretical performance is similar with that of CPU + GPU. © 2016 Wiley Periodicals, Inc. PMID:27431905

  7. The effect of statistical uncertainty on inverse treatment planning based on Monte Carlo dose calculation

    NASA Astrophysics Data System (ADS)

    Jeraj, Robert; Keall, Paul

    2000-12-01

    The effect of the statistical uncertainty, or noise, in inverse treatment planning for intensity modulated radiotherapy (IMRT) based on Monte Carlo dose calculation was studied. Sets of Monte Carlo beamlets were calculated to give uncertainties at Dmax ranging from 0.2% to 4% for a lung tumour plan. The weights of these beamlets were optimized using a previously described procedure based on a simulated annealing optimization algorithm. Several different objective functions were used. It was determined that the use of Monte Carlo dose calculation in inverse treatment planning introduces two errors in the calculated plan. In addition to the statistical error due to the statistical uncertainty of the Monte Carlo calculation, a noise convergence error also appears. For the statistical error it was determined that apparently successfully optimized plans with a noisy dose calculation (3% 1σ at Dmax ), which satisfied the required uniformity of the dose within the tumour, showed as much as 7% underdose when recalculated with a noise-free dose calculation. The statistical error is larger towards the tumour and is only weakly dependent on the choice of objective function. The noise convergence error appears because the optimum weights are determined using a noisy calculation, which is different from the optimum weights determined for a noise-free calculation. Unlike the statistical error, the noise convergence error is generally larger outside the tumour, is case dependent and strongly depends on the required objectives.

  8. Potential estrogenic effects of phosphorus-containing flame retardants.

    PubMed

    Zhang, Quan; Lu, Meiya; Dong, Xiaowu; Wang, Cui; Zhang, Chunlong; Liu, Weiping; Zhao, Meirong

    2014-06-17

    As the substitute of polybrominated diphenyl ethers (PBDEs), further assessments about the potential ecological safety and health risks of phosphorus-containing flame retardants (PFRs) are required because the worldwide demand for PFRs has been increasing every year. In this study, we examined the agonistic/antagonistic activity of a group of PFRs by three in vitro models (luciferase reporter gene assay, yeast two-hybrid assay, and E-screen assay). Molecule docking was used to further explain the interactions between ERα and PFRs. Data from luciferase reporter gene analysis showed three members of the nine tested PFRs significantly induced estrogenic effects, with the order of TPP > TCP > TDCPP, while TCEP and TEHP have remarkable antiestrogenic properties with calculated REC20 and RIC20 values of 10(-6) M or lower. Results from the luciferase reporter gene method are generally consistent with results obtained from the yeast two-hybrid assay and E-screen, except for the positive estrogenic activity of TBP in E-screen testing. Docking results showed that binding between ligands and ERα was stabilized by hydrophobic interactions. As a proposed alternative for brominated flame retardant, PFRs may have anti/estrogenic activity via ERα at the low dose typical of residue in environmental matrix or animals. PFRs with a short chain, halogen, and benzene ring in the substituent group tend to be estrogenic. Our research suggests that comprehensive evaluations, including health and ecological assessments, are required in determining whether PFRs are preferable as an emerging industrial substitute. PMID:24844797

  9. Future aircraft and potential effects on stratospheric ozone and climate

    SciTech Connect

    Kinnison, D.E.; Wuebbles, D.J.

    1991-10-01

    The purpose of this study is to extend the recent research examining the global environmental effects from potential fleets of subsonic and supersonic commercial aircraft. Initial studies with LLNL models of global atmospheric chemical, radiative, and transport processes have indicated that substantial decreases in stratospheric ozone concentrations could result from emissions of NO{sub x} from aircraft flying in the stratosphere, depending on fleet size and magnitude of the engine emissions. These studies used homogeneous chemical reaction rates (e.g. gas-phase chemistry). Recent evidence indicates that reactions on particles in the stratosphere may be important. Heterogeneous chemical reactions, for instance, N{sub 2}O{sub 5}and ClONO{sub 2} on background sulfuric acid aerosols, convert NO{sub x}(NO and NO{sub 2}) molecules to HNO{sub 3}. This decreases the odd oxygen loss from the NO{sub x} catalytic cycle and increases the odd oxygen loss from the Cl{sub x} catalytic cycle. By including these heterogeneous reactions in the LLNL model, the relative partitioning of odd oxygen loss between these two families changes, with the result that emissions of NO{sub x} from proposed aircraft fleets flying in the stratosphere now increase zone. Having these heterogeneous processes present also increases ozone concentration in the troposphere relative to gas-phase only chemistry calculations for emissions of NO{sub x} from subsonic aircraft. 26 refs., 5 figs., 3 tabs.

  10. Training software using virtual-reality technology and pre-calculated effective dose data.

    PubMed

    Ding, Aiping; Zhang, Di; Xu, X George

    2009-05-01

    This paper describes the development of a software package, called VR Dose Simulator, which aims to provide interactive radiation safety and ALARA training to radiation workers using virtual-reality (VR) simulations. Combined with a pre-calculated effective dose equivalent (EDE) database, a virtual radiation environment was constructed in VR authoring software, EON Studio, using 3-D models of a real nuclear power plant building. Models of avatars representing two workers were adopted with arms and legs of the avatar being controlled in the software to simulate walking and other postures. Collision detection algorithms were developed for various parts of the 3-D power plant building and avatars to confine the avatars to certain regions of the virtual environment. Ten different camera viewpoints were assigned to conveniently cover the entire virtual scenery in different viewing angles. A user can control the avatar to carry out radiological engineering tasks using two modes of avatar navigation. A user can also specify two types of radiation source: Cs and Co. The location of the avatar inside the virtual environment during the course of the avatar's movement is linked to the EDE database. The accumulative dose is calculated and displayed on the screen in real-time. Based on the final accumulated dose and the completion status of all virtual tasks, a score is given to evaluate the performance of the user. The paper concludes that VR-based simulation technologies are interactive and engaging, thus potentially useful in improving the quality of radiation safety training. The paper also summarizes several challenges: more streamlined data conversion, realistic avatar movement and posture, more intuitive implementation of the data communication between EON Studio and VB.NET, and more versatile utilization of EDE data such as a source near the body, etc., all of which needs to be addressed in future efforts to develop this type of software. PMID:19359853

  11. Global analytical potential energy surface for the electronic ground state of NH3 from high level ab initio calculations.

    PubMed

    Marquardt, Roberto; Sagui, Kenneth; Zheng, Jingjing; Thiel, Walter; Luckhaus, David; Yurchenko, Sergey; Mariotti, Fabio; Quack, Martin

    2013-08-15

    The analytical, full-dimensional, and global representation of the potential energy surface of NH(3) in the lowest adiabatic electronic state developed previously (Marquardt, R.; et al. J. Phys. Chem. B 2005, 109, 8439–8451) is improved by adjustment of parameters to an enlarged set of electronic energies from ab initio calculations using the coupled cluster method with single and double substitutions and a perturbative treatment of connected triple excitations (CCSD(T)) and the method of multireference configuration interaction (MRCI). CCSD(T) data were obtained from an extrapolation of aug-cc-pVXZ results to the basis set limit (CBS), as described in a previous work (Yurchenko, S.N.; et al. J. Chem. Phys 2005, 123, 134308); they cover the region around the NH3 equilibrium structures up to 20,000 hc cm(–1). MRCI energies were computed using the aug-cc-pVQZ basis to describe both low lying singlet dissociation channels. Adjustment was performed simultaneously to energies obtained from the different ab initio methods using a merging strategy that includes 10,000 geometries at the CCSD(T) level and 500 geometries at the MRCI level. Characteristic features of this improved representation are NH3 equilibrium geometry r(eq)(NH(3)) ≈ 101.28 pm, α(eq)(NH(3)) ≈ 107.03°, the inversion barrier at r(inv)(NH(3)) ≈ 99.88 pm and 1774 hc cm(–1) above the NH(3) minimum, and dissociation channel energies 41,051 hc cm(–1) (for NH(3) → ((2)B(2))NH(2) + ((2)S(1/2))H) and 38,450 hc cm(–1) (for NH(3) → ((3)Σ(–))NH +((1)Σ(g)(+))H(2)); the average agreement between calculated and experimental vibrational line positions is 11 cm(–1) for (14)N(1)H(3) in the spectral region up to 5000 cm(–1). A survey of our current knowledge on the vibrational spectroscopy of ammonia and its isotopomers is also given. PMID:23688044

  12. Accounting for strong localized heterogeneities and local transport effect in core calculations

    SciTech Connect

    Ruggieri, J.M.; Doriath, J.Y.; Finck, P.J.; Boyer, R.

    1996-09-01

    Two methods based on the variational nodal transport method have been developed to account for localized heterogeneities and local transport effects in full core calculations. A local mesh refinement technique relies on using the projected partial ingoing surface currents produced during coarse-mesh iterations as boundary conditions for fine-mesh calculations embedded within the coarse-mesh calculations. The outgoing fine-mesh partial currents are averaged to serve in the coarse-mesh iterations. Then, a mixed transport-diffusion method using two levels of angular approximations for the surface partial currents depending on the node considered has been implemented to account for local transport effects in full core diffusion calculations. These methods have been tested for a model of the Superphenix complementary shutdown rods.

  13. The effects of digital elevation model resolution on the calculation and predictions of topographic wetness indices.

    SciTech Connect

    Drover, Damion, Ryan

    2011-12-01

    One of the largest exports in the Southeast U.S. is forest products. Interest in biofuels using forest biomass has increased recently, leading to more research into better forest management BMPs. The USDA Forest Service, along with the Oak Ridge National Laboratory, University of Georgia and Oregon State University are researching the impacts of intensive forest management for biofuels on water quality and quantity at the Savannah River Site in South Carolina. Surface runoff of saturated areas, transporting excess nutrients and contaminants, is a potential water quality issue under investigation. Detailed maps of variable source areas and soil characteristics would therefore be helpful prior to treatment. The availability of remotely sensed and computed digital elevation models (DEMs) and spatial analysis tools make it easy to calculate terrain attributes. These terrain attributes can be used in models to predict saturated areas or other attributes in the landscape. With laser altimetry, an area can be flown to produce very high resolution data, and the resulting data can be resampled into any resolution of DEM desired. Additionally, there exist many maps that are in various resolutions of DEM, such as those acquired from the U.S. Geological Survey. Problems arise when using maps derived from different resolution DEMs. For example, saturated areas can be under or overestimated depending on the resolution used. The purpose of this study was to examine the effects of DEM resolution on the calculation of topographic wetness indices used to predict variable source areas of saturation, and to find the best resolutions to produce prediction maps of soil attributes like nitrogen, carbon, bulk density and soil texture for low-relief, humid-temperate forested hillslopes. Topographic wetness indices were calculated based on the derived terrain attributes, slope and specific catchment area, from five different DEM resolutions. The DEMs were resampled from LiDAR, which is a

  14. Calculation of the biological effective dose for piecewise defined dose-rate fits

    SciTech Connect

    Hobbs, Robert F.; Sgouros, George

    2009-03-15

    An algorithmic solution to the biological effective dose (BED) calculation from the Lea-Catcheside formula for a piecewise defined function is presented. Data from patients treated for metastatic thyroid cancer were used to illustrate the solution. The Lea-Catcheside formula for the G-factor of the BED is integrated numerically using a large number of small trapezoidal fits to each integral. The algorithmically calculated BED is compatible with an analytic calculation for a similarly valued exponentially fitted dose-rate plot and is the only resolution for piecewise defined dose-rate functions.

  15. Estimation of Nuclear Reaction Effects in Proton-Tissue-Dose Calculations.

    Energy Science and Technology Software Center (ESTSC)

    1983-01-14

    Version 00 REPC reviews calculational methods for the estimation of dose from external proton exposure of arbitrary convex bodies and presents the necessary information for the estimation of dose in soft tissue. The effects of nuclear reactions, especially in relation to the dose equivalent, are retained. REPC subroutines can be used to convert existing computer programs which neglect nuclear reaction effects to include them.

  16. Implementation of the forward-reverse method for calculating the potential of mean force using a dynamic restraining protocol.

    PubMed

    Nategholeslam, Mostafa; Gray, C G; Tomberli, Bruno

    2014-12-11

    We present a new sampling and analysis scheme for calculating the potential of mean force (PMF) of systems studied by steered molecular dynamics simulations. This scheme, which we call the bin-passing method, is based on the forward-reverse (FR) method (due to I. Kosztin and co-workers, Kosztin et al. J. Chem. Phys. 2006, 124(6), 064106) and arguments based on the second law of thermodynamics. Applying the bin-passing method results in enhanced sampling, better separation of the reversible and irreversible work distributions, and faster convergence to the underlying PMF of the system under study. Post-simulation analysis is performed using a purpose-built software that we have made publicly available at https://github.com/1particle/bin-passing_analyzer under the terms of the GNU General Public License (version 3). Three examples are provided, for systems of varying sizes and complexities, to demonstrate the efficiency of this method and the quality of the results: for the dissociation PMF of NaCl in water, the bin-passing method obtains PMFs in excellent agreement with that obtained for the same system and using the same force-field through static (equilibrium) methods. The bin-passing method gives a very symmetric PMF for passage of a single water molecule through a DPPC bilayer, and the resultant PMF leads to permeability values in better agreement with experiments than those obtained through previous simulation studies. Finally, we consider the interaction of the antimicrobial peptide HHC-36 with two model membranes and employ the bin-passing method to obtain the PMFs for peptide adsorption to the membranes. The characteristics of these PMFs are consistent with the qualities established for the HHC-36 peptide through in vivo and in vitro experiments, as a non-toxic strong antimicrobial agent. PMID:25372312

  17. Radiative Convective Transfer Calculations for Effective Stellar Fluxes of Habitable and Life Supporting Zones

    NASA Astrophysics Data System (ADS)

    Ludwig, Wolfgang; Eggl, Siegfried; Neubauer, David; Leitner, Johannes; Firneis, Maria; Hitzenberger, Regina

    2014-05-01

    Recent fields of interest in exoplanetary research include studies of potentially habitable planets orbiting stars outside of our Solar System. Habitable Zones (HZs) are currently defined by calculating the inner and the outer limits of the mean distance between exoplanets and their central stars based on effective solar fluxes that allow for maintaining liquid water on the planet's surface. Kasting et al. (1993), Selsis et al. (2007), and recently Kopparapu et al. (2013) provided stellar flux limits for such scenarios. We compute effective solar fluxes for Earth-like planets using Earth-like and other atmospheric scenarios including atmospheres with high level and low level clouds. Furthermore we provide habitability limits for solvents other than water, i.e. limits for the so called Life Supporting Zone, introduced by Leitner et al. (2010). The Life Supporting Zone (LSZ) encompasses many habitable zones based on a variety of liquid solvents. Solvents like ammonia and sulfuric acid have been identified for instance by Leitner et al (2012) as possibly life supporting. Assuming planets on circular orbits, the extent of the individual HZ is then calculated via the following equation, d(i,o) = [L/Lsun*1/S(i,o)]**0.5 au, where L is the star's luminosity, and d(i,o) and S(i,o) are the distances to the central star for the inner and the outer edge and effective insolation for inner and the outer edge of the HZ, respectively. After generating S(i,o) values for a selection of solvents, we provide the means to determine LSZ boundaries for main sequence stars. Effective flux calculations are done using a one dimensional radiative convective model (Neubauer et al. 2011) based on a modified version of the open source radiative transfer software Streamer (Key and Schweiger, 1998). Modifications include convective adjustments, additional gases for absorption and the use of an offline cloud model, which allow us to observe the influence of clouds on effective stellar fluxes

  18. Local-spin-density calculations for iron: Effect of spin interpolation on ground-state properties

    NASA Astrophysics Data System (ADS)

    MacLaren, J. M.; Clougherty, D. P.; Albers, R. C.

    1990-08-01

    Scalar-relativistic self-consistent linear muffin-tin orbital (LMTO) calculations for bcc and fcc Fe have been performed with several different local approximations to the exchange and correlation energy density and potential. Overall, in contrast to the conclusions of previous studies, we find that the local-spin-density approximation to exchange and correlation can provide an adequate description of bulk Fe provided that a proper parametrization of the correlation energy density and potential of the homogeneous electron gas over both spin and density is used. Lattice constants, found from the position of the minimum of the total energy as a function of Wigner-Seitz radius, agree to within 1% (for s,p,d LMTO's only) and within 1-2% (for s,p,d,f LMTO's) of the experimental lattice constants for all forms used for the local correlation. The best agreement, however, was obtained using a local correlation potential derived from the Vosko-Wilk-Nusair form for the spin dependence of the correlation energy density. The calculation performed with this correlation potential was also the only calculation to correctly predict a bcc ferromagnetic ground state.

  19. Real-space electronic structure calculations with full-potential all-electron precision for transition metals

    NASA Astrophysics Data System (ADS)

    Ono, Tomoya; Heide, Marcus; Atodiresei, Nicolae; Baumeister, Paul; Tsukamoto, Shigeru; Blügel, Stefan

    2010-11-01

    We have developed an efficient computational scheme utilizing the real-space finite-difference formalism and the projector augmented-wave (PAW) method to perform precise first-principles electronic-structure simulations based on the density-functional theory for systems containing transition metals with a modest computational effort. By combining the advantages of the time-saving double-grid technique and the Fourier-filtering procedure for the projectors of pseudopotentials, we can overcome the egg box effect in the computations even for first-row elements and transition metals, which is a problem of the real-space finite-difference formalism. In order to demonstrate the potential power in terms of precision and applicability of the present scheme, we have carried out simulations to examine several bulk properties and structural energy differences between different bulk phases of transition metals and have obtained excellent agreement with the results of other precise first-principles methods such as a plane-wave-based PAW method and an all-electron full-potential linearized augmented plane-wave (FLAPW) method.

  20. Enzymatic Kinetic Isotope Effects from First-Principles Path Sampling Calculations.

    PubMed

    Varga, Matthew J; Schwartz, Steven D

    2016-04-12

    In this study, we develop and test a method to determine the rate of particle transfer and kinetic isotope effects in enzymatic reactions, specifically yeast alcohol dehydrogenase (YADH), from first-principles. Transition path sampling (TPS) and normal mode centroid dynamics (CMD) are used to simulate these enzymatic reactions without knowledge of their reaction coordinates and with the inclusion of quantum effects, such as zero-point energy and tunneling, on the transferring particle. Though previous studies have used TPS to calculate reaction rate constants in various model and real systems, it has not been applied to a system as large as YADH. The calculated primary H/D kinetic isotope effect agrees with previously reported experimental results, within experimental error. The kinetic isotope effects calculated with this method correspond to the kinetic isotope effect of the transfer event itself. The results reported here show that the kinetic isotope effects calculated from first-principles, purely for barrier passage, can be used to predict experimental kinetic isotope effects in enzymatic systems. PMID:26949835

  1. Variational transition state theory calculations of tunneling effects on concerted hydrogen motion in water clusters and formaldehyde/water clusters

    SciTech Connect

    Garrett, B.C. ); Melius, C.F. )

    1990-08-01

    The direct participation of water molecules in aqueous phase reaction processes has been postulated to occur via both single-step mechanisms as well as concerted hydrogen atom or proton shifts. In the present work, simple prototypes of concerted hydrogen atom transfer processes are examined for small hydrogen-bonded water clusters -- cyclic trimers and tetramers -- and hydrogen-bonded clusters of formaldehyde with one and two water molecules. Rate constants for the rearrangement processes are computed using variational transition state theory, accounting for quantum mechanical tunneling effects by semiclassical ground-state adiabatic transmission coefficients. The variational transition state theory calculations directly utilize selected information about the potential energy surface along the minimum energy path as parameters of the reaction path Hamiltonian. The potential energy information is obtained from ab ignite electronic structure calculations with an empirical bond additivity correction (the BAC-MP4 method). Tunneling is found to be very important for these concerted rearrangement processes -- the semiclassical ground-state adiabatic transmission coefficients are estimated to be as high as four order of magnitude at room temperature. Effects of the size of the cluster (number of water molecules in the cyclic complex) are also dramatic -- addition of a water molecule is seen to change the calculated rates by orders of magnitude. 36 refs., 10 figs.

  2. Calculation of total free energy yield as an alternative approach for predicting the importance of potential chemolithotrophic reactions in geothermal springs.

    PubMed

    Dodsworth, Jeremy A; McDonald, Austin I; Hedlund, Brian P

    2012-08-01

    To inform hypotheses regarding the relative importance of chemolithotrophic metabolisms in geothermal environments, we calculated free energy yields of 26 chemical reactions potentially supporting chemolithotrophy in two US Great Basin hot springs, taking into account the effects of changing reactant and product activities on the Gibbs free energy as each reaction progressed. Results ranged from 1.2 × 10(-5) to 3.6 J kg(-1) spring water, or 3.7 × 10(-5) to 11.5 J s(-1) based on measured flow rates, with aerobic oxidation of CH(4) or NH4 + giving the highest average yields. Energy yields calculated without constraining pH were similar to those at constant pH except for reactions where H(+) was consumed, which often had significantly lower yields when pH was unconstrained. In contrast to the commonly used normalization of reaction chemical affinities per mole of electrons transferred, reaction energy yields for a given oxidant varied by several orders of magnitude and were more sensitive to differences in the activities of products and reactants. The high energy yield of aerobic ammonia oxidation is consistent with previous observations of significant ammonia oxidation rates and abundant ammonia-oxidizing archaea in sediments of these springs. This approach offers an additional lens through which to view the thermodynamic landscape of geothermal springs. PMID:22443686

  3. Bernoulli effect and contact potential difference in superconductors

    SciTech Connect

    Omel'yanchuk, A.N.; Beloborod'ko, S.I.

    1983-10-01

    An expression is derived for the Bernoulli potential that arises in superconductors with an inhomogeneous current distribution. The expression is valid for arbitrary temperatures and superfluid velocities. In the superconductor--dielectric--superconductor system we consider the Bernoulli effect, which manifests itself in a contact potential difference between the superconductors. The potential difference is determined by the currents flowing through one plate of the contact and can be measured with a voltmeter in the quasi-stationary regime.

  4. Study of electronic effects in a catalytic diode: DFT calculations and MEIRAS experiments

    NASA Astrophysics Data System (ADS)

    Deshlahra, Prashant

    The role of electron transfer between metal catalyst and its oxide support in modifying the binding of the molecules adsorbed on the catalyst surface is investigated using Pt/TiO2 catalytic diode as a novel model catalyst system. The effect of electron transfer is interpreted and demonstrated as that of creating an electric field at the metal-support interface. The effect of such electric fields is studied by using Density Functional Theory (DFT) calculations to simulate adsorption of different molecules under a uniform external electric field. Experimentally, the charge transfer at metal support junction and the resulting electric field is controlled by applying an external bias voltage to the catalytic diode. The effect of controlling the charge transfer on CO molecules used as probe adsorbates is studied using a multilayer enhanced reflection adsorption spectroscopy (MEIRAS) technique developed in this work. DFT calculations show that the sensitivity of adsorption energy of a molecule on a metal surface to the external electric field depends on its dipole moment and polarizability. The dipole moment varies significantly from one molecule to another, and changes with the surface adsorbate coverage due to the electrostatic interaction from neighboring adsorbates on the surface. Vibrational frequency of molecules shifting linearly with external electric field is shown to be a key experimental observable useful in the study of these effects. MEIRAS is a new form of the Fourier Transform Infrared (FTIR) spectroscopy performed in reflection mode, in which, the multilayer structure of the sample and its interaction with the incident infrared causes a large enhancement in the sensitivity. The mechanism of sensitivity enhancement is elucidated through experimental measurement of wavelength dependent reflectance of multilayer structures and theoretical optical analysis of infrared reflection on such structures. An experimental setup is developed for MEIRAS measurements

  5. The Effect of Measurement Bias on Nuclear Criticality Safety Calculations for WIPP TRUPACT-II Shipments

    SciTech Connect

    Blackwood, Larry G.; Harker, Yale D.

    2000-12-15

    Current nuclear criticality safety limit requirements for transporting TRUPACT-II waste containers to the U.S. Department of Energy's Waste Isolation Pilot Plant (WIPP) specify that the {sup 239}Pu fissile gram equivalent (FGE) plus two times its measurement error must be {<=}325 g for a payload of fourteen 55-gal drums. The authorized method for calculating a TRUPACT-II FGE measurement error value is to take the square root of the sum of the squared error values for the individual containers (often called root-sum-squares or simply RSS). However, to the extent that the individual drum measurements contain common bias effects (e.g., due to common calibration or other adjustment factors), the corresponding measurement errors are correlated, and simple RSS calculations will underestimate the true error in the TRUPACT-II FGE value.The RSS calculations assume independence, while common bias effects can induce strong correlations between the errors in measurements. Significant bias effects can occur when the matrix characteristics for a particular waste type are not fully accounted for in the measurement process. Depending on the relative size of the bias error compared to precision error, the true measurement error can be greater than twice that calculated by RSS. In such cases, the FGE shipping requirement may not be met. To avoid underestimating the error, bias components should be estimated and propagated separately (combined only at the final step in the TRUPACT-II FGE calculation), or the effect of bias on covariance between measurements must be calculated. These covariance terms then need to be included in the final uncertainty calculations.

  6. Unfolding and effective bandstructure calculations as discrete real- and reciprocal-space operations

    NASA Astrophysics Data System (ADS)

    Boykin, Timothy B.; Ajoy, Arvind; Ilatikhameneh, Hesameddin; Povolotskyi, Michael; Klimeck, Gerhard

    2016-06-01

    In recent years, alloy electronic structure calculations based on supercell Brillouin zone unfolding have become popular. There are a number of formulations of the method which on the surface might appear different. Here we show that a discrete real-space description, based on discrete Fourier transforms, is fully general. Furthermore, such an approach can more easily show the effects of alloy scattering. We present such a method for treating the random alloy problem. This treatment features straightforward mathematics and a transparent physical interpretation of the calculated effective (i.e., approximate) energy bands.

  7. Solvent effects in time-dependent self-consistent field methods. I. Optical response calculations.

    PubMed

    Bjorgaard, J A; Kuzmenko, V; Velizhanin, K A; Tretiak, S

    2015-01-28

    We implement and examine three excited state solvent models in time-dependent self-consistent field methods using a consistent formalism which unambiguously shows their relationship. These are the linear response, state specific, and vertical excitation solvent models. Their effects on energies calculated with the equivalent of COSMO/CIS/AM1 are given for a set of test molecules with varying excited state charge transfer character. The resulting solvent effects are explained qualitatively using a dipole approximation. It is shown that the fundamental differences between these solvent models are reflected by the character of the calculated excitations. PMID:25637965

  8. Solvent effects in time-dependent self-consistent field methods. I. Optical response calculations

    SciTech Connect

    Bjorgaard, J. A.; Kuzmenko, V.; Velizhanin, K. A.; Tretiak, S.

    2015-01-22

    In this study, we implement and examine three excited state solvent models in time-dependent self-consistent field methods using a consistent formalism which unambiguously shows their relationship. These are the linear response, state specific, and vertical excitation solvent models. Their effects on energies calculated with the equivalent of COSMO/CIS/AM1 are given for a set of test molecules with varying excited state charge transfer character. The resulting solvent effects are explained qualitatively using a dipole approximation. It is shown that the fundamental differences between these solvent models are reflected by the character of the calculated excitations.

  9. Calculations of the IR spectra of bend fundamentals of (H2O)n=3,4,5 using the WHBB_2 potential and dipole moment surfaces.

    PubMed

    Wang, Yimin; Bowman, Joel M

    2016-09-14

    Stimulated by new experiments from the Havenith group, we report IR spectra of the bend fundamentals of (H2O)n=3,4,5, using anharmonic, coupled-mode VSCF/VCI calculations, done in a subspace of modes consisting of all the monomer bends plus the hydrogen-bonded OH stretches. Double-harmonic spectra are also reported. All calculations employ a faster version of the ab initio WHBB potential and also a more accurate representation of the dipole moment surface, reported previously. Comparisons at the harmonic level are made with previous high-level ab initio calculations, notably those of Howard and Tschumper and also with harmonic frequencies from the semi-empirical TTM3-F potential, which have been reported previously by Howard and Tschumper. The calculations provide energies and intensities of the hydrogen-bonded OH stretches and these are also presented and briefly discussed. PMID:27523256

  10. Percolation temperature and the ''instability'' of the effective potential

    SciTech Connect

    Arago de Carvalho, C.; Bazeia, D.; Eboli, O.J.P.; Marques, G.C.; da Silva, A.J.; Ventura, I.

    1985-03-15

    We show that in spontaneously broken lambdaphi/sup 4/ theory the percolation temperature coincides with the temperature at which the semiclassical (loop) expansion of the effective potential (free energy) of the system around a uniform field configuration fails. This allows us to extract the percolation temperature directly from the effective potential. The addition of fermions or gauge fields does not alter the result as long as they are weakly coupled to the scalars. The coincidence holds in the high-temperature limit.

  11. Accurate high level ab initio-based global potential energy surface and dynamics calculations for ground state of CH{sub 2}{sup +}

    SciTech Connect

    Li, Y. Q.; Zhang, P. Y.; Han, K. L.

    2015-03-28

    A global many-body expansion potential energy surface is reported for the electronic ground state of CH{sub 2}{sup +} by fitting high level ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pV6Z basis set. The topographical features of the new global potential energy surface are examined in detail and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. In turn, in order to validate the potential energy surface, a test theoretical study of the reaction CH{sup +}(X{sup 1}Σ{sup +})+H({sup 2}S)→C{sup +}({sup 2}P)+H{sub 2}(X{sup 1}Σ{sub g}{sup +}) has been carried out with the method of time dependent wavepacket on the title potential energy surface. The total integral cross sections and the rate coefficients have been calculated; the results determined that the new potential energy surface can both be recommended for dynamics studies of any type and as building blocks for constructing the potential energy surfaces of larger C{sup +}/H containing systems.

  12. Application of Analytical Model of the Electric Potential Distribution for Calculation of Charged Particle Dynamics in a Near-Wall Layer and Sputtering of the Plasma Facing Surfaces

    NASA Astrophysics Data System (ADS)

    Borodkina, I. E.; Komm, M.; Tsvetkov, I. V.

    2015-08-01

    Simple analytical formulas are derived for calculation of the electric field potential distribution in the magnetic pre-layer and the Debye layer near the plasma facing surfaces. It is shown that the calculated potential profiles are in good agreement with the dependences of the potential distribution on the magnetic field inclination obtained by solving the magnetic hydrodynamic (MHD) equations and modeling using the PIC code SPICE2. Dependences of the angular distribution of ions incident on the surface of plasma facing elements on the magnetic field inclination are obtained. Results of calculations demonstrate that the surface areas, on which the magnetic field is incident at sliding angles, are critical from the viewpoint of the increase of sputtering.

  13. Ab initio calculations of vibrational frequencies and infrared intensities for global warning potential of CFC substitutes. CF{sub 3}CH{sub 2}F (HFC-134a)

    SciTech Connect

    Papasavva, S.; Tai, S.; Esslinger, A.; Illinger, K.H.; Kenny, J.E.

    1995-03-16

    We have investigated the feasibility of using ab initio molecular orbital methods for predicting the global warming potential of the proposed chlorofluorocarbon (CFC) substitute CF{sub 3}CH{sub 2}F, HFC-134a. Various levels of theory and basis sets were used to optimize geometry and calculate harmonic vibrational frequencies and infrared intensities for the molecule using the GAUSSIAN 92 software package. In attempting to assess the quality of the computations, we found it necessary to reconsider the vibrational assignments available in the literature. On the basis of the current assignment, we find that for the highest level calculation, MP2/6-31G{sup **}, the calculated harmonic frequencies agree extremely well with the experimentally observed ones at frequencies below 800 cm{sup {minus}1}, with a systematic error toward higher calculated frequencies becoming apparent above 800 cm{sup {minus}1}. At lower levels of theory, the systematic error is apparent at all frequencies. The regularity of the deviation between calculated and observed frequencies makes ab initio calculations of vibrational frequencies much more useful than semiempirical calculations, which tend to show random deviations, as demonstrated with a PM3-UHF calculation in this work. The calculated absolute intensities are in good agreement with the limited experimental measurements previously reported. 23 refs., 3 figs., 5 tabs.

  14. Transuranic Transmutation and Criticality Calculation Sensitivity to Heterogeneous Lattice Effects - 12391

    SciTech Connect

    Barbaras, Sean A.; Knight, Travis W.

    2012-07-01

    Using Mixed Oxide (MOX) fuel in traditional Pressurized Water Reactor (PWR) assemblies has been researched at length and has shown to provide the benefit of transmutation and targets the amount and toxicity of high level waste needed to be managed. Advanced MOX concepts using enriched Uranium Dioxide (UO{sub 2}) are required for multiple recycling of plutonium. The use of MOX and ordinary UO{sub 2} fuel in the same assembly as well as unfueled rods and assembly edge effects contrasts with the unit cell computational assumption of a uniform infinite array of rods. While a deterministic method of calculating the Dancoff factor has traditionally been employed in fuel assembly analysis due to the lighter computational and modeling requirements, this research seeks to determine the validity of the uniform, infinite lattice assumption with respect to Dancoff factor and determine the magnitude of the impact of nonuniform lattice effects on fuel assembly criticality calculations as well as transuranic isotope production and transmutation. This research explored the pin-to-pin interaction in a non-uniform lattice of MOX fuel rods and UO{sub 2} fuel rods through the impact of the calculated Dancoff factors from the deterministic method used in SCALE versus the Monte Carlo method used in the code DANCOFF-MC. Using the Monte Carlo method takes into account the non-uniform lattice effects of having neighboring fuel rods with different cross-sectional spectra whereas the Dancoff factor calculated by SCALE assumes a uniform, infinite lattice of one fuel rod type. Differences in eigenvalue calculations as a function of burnup are present between the two methods of Dancoff factor calculation. The percent difference is greatest at low burnup and then becomes smaller throughout the cycle. Differences in the transmutation rate of transuranic isotopes in the MOX fuel are also present between the Dancoff factor calculation methods. The largest difference is in Pu-239, Pu-242, and Am-241

  15. Chemical potential effects on neutrino diffusion in supernovae

    NASA Technical Reports Server (NTRS)

    Mazurek, T. J.

    1975-01-01

    The validity of imposing a zero chemical potential for neutrinos in hydrodynamic calculations of collapsing supernovae is investigated in the diffusion approximation of neutrino transport. A coupled system of equations is solved for neutrino and energy diffusion fluxes as well as lepton diffusion in a collapsing supernovae ambient medium, and the results indicate a substantial growth in the neutrino chemical potential for densities greater than 10 to the 12th power gm/cu cm. The rate of energy transport is shown to be significantly affected by increases in Fermi integrals and chemical-potential gradients accompanied by decreases in temperature, and the extent of neutrino particle/antiparticle reactions is found also to affect energy diffusion rates. It is concluded that the photon-like behavior usually assumed for neutrinos may be incorrect and that an extension of the Sn transport approximation to include lepton characteristics is necessary for a definitive answer to the question of neutrino transport in supernovae.

  16. Magnetoconductance of a hybrid quantum ring: Effects of antidot potentials

    NASA Astrophysics Data System (ADS)

    Kim, Nammee; Park, Dae-Han; Kim, Heesang

    2016-05-01

    The electronic structures and two-terminal magnetoconductance of a hybrid quantum ring are studied. The backscattering due to energy-resonance is considered in the conductance calculation. The hybrid magnetic-electric quantum ring is fabricated by applying an antidot electrostatic potential in the middle of a magnetic quantum dot. Electrons are both magnetically and electrically confined in the plane. The antidot potential repelling electrons from the center of the dot plays a critical role in the energy spectra and magnetoconductance. The angular momentum transition in the energy dispersion and the magnetoconductance behavior are investigated in consideration of the antidot potential variation. Results are shown using a comparison of the results of the conventional magnetic quantum dot.

  17. Alternative to the effective transmittance approach for the calculation of polychromatic transmittances in rapid transmittance models

    NASA Astrophysics Data System (ADS)

    Xiong, Xiaozhen; McMillin, Larry M.

    2005-01-01

    Many current rapid transmittance algorithms, specifically the Optical Path Transmittance (OPTRAN), are based on use of effective transmittances to account for the effects of polychromatic radiation on the transmittance calculations. We document how OPTRAN was modified by replacing the effective transmittance concept with a correction term. Use of the correction term solves some numerical problems that were associated with use of effective transmittances, greatly reduces the line-by-line computational burden, and allows for the efficient inclusion of more gases. This correction method can easily be applied to any other fast models that use the effective transmittance approach.

  18. Finite-basis correction applied to the optimized effective potential within the FLAPW method

    NASA Astrophysics Data System (ADS)

    Friedrich, Christoph; Betzinger, Markus; Blügel, Stefan

    2011-03-01

    The optimized-effective-potential (OEP) method is a special technique to construct local exchange-correlation (xc) potentials from general orbital-dependent xc energy functionals for density-functional theory. Recently, we showed that particular care must be taken to construct local potentials within the all-electron full-potential augmented-plane-wave (FLAPW) approach. In fact, we found that the LAPW basis had to be converged to an accuracy that was far beyond that in calculations using conventional functionals, leading to a very high computational cost. This could be traced back to the convergence behavior of the density response function: only a highly converged basis lends the density enough flexibility to react adequately to changes of the potential. In this work we derive a numerical correction for the response function, which vanishes in the limit of an infinite, complete basis. It is constructed in the atomic spheres from the response of the basis functions themselves to changes of the potential. We show that such a finite-basis correction reduces the computational demand of OEP calculations considerably. We also discuss a similar correction scheme for GW calculations.

  19. Ab initio calculation of proton-coupled electron transfer rates using the external-potential representation: a ubiquinol complex in solution.

    PubMed

    Yamamoto, Takeshi; Kato, Shigeki

    2007-06-14

    In quantum-mechanical/molecular-mechanical (QM/MM) treatment of chemical reactions in condensed phases, one solves the electronic Schrodinger equation for the solute (or an active site) under the electrostatic field from the environment. This Schrodinger equation depends parametrically on the solute nuclear coordinates R and the external electrostatic potential V. This fact suggests that one may use R and V as natural collective coordinates for describing the entire system, where V plays the role of collective solvent variables. In this paper such an (R,V) representation of the QM/MM canonical ensemble is described, with particular focus on how to treat charge transfer processes in this representation. As an example, the above method is applied to the proton-coupled electron transfer of a ubiquinol analog with phenoxyl radical in acetonitrile solvent. Ab initio free-energy surfaces are calculated as functions of R and V using the reference interaction site model self-consistent field method, the equilibrium points and the minimum free-energy crossing point are located in the (R,V) space, and then the kinetic isotope effects (KIEs) are evaluated approximately. The results suggest that a stiffer proton potential at the transition state may be responsible for unusual KIEs observed experimentally for related systems. PMID:17581070

  20. Calculation of Radiofrequency Electromagnetic Fields and Their Effects in MRI of Human Subjects

    PubMed Central

    Collins, Christopher M.; Wang, Zhangwei

    2011-01-01

    Radiofrequency magnetic fields are critical to nuclear excitation and signal reception in Magnetic Resonance Imaging (MRI). The interactions between these fields and human tissues in anatomical geometries results in a variety of effects regarding image integrity and safety of the human subject. In recent decades numerical methods of calculation have been used increasingly to understand the effects of these interactions and aid in engineering better, faster, and safer equipment and methods. As MRI techniques and technology have evolved through the years, so too have the requirements for meaningful interpretation of calculation results. Here we review the basic physics of RF electromagnetics in MRI and discuss a variety of ways RF field calculations are used in MRI in engineering and safety assurance from simple systems and sequences through advanced methods of development for the future. PMID:21381106

  1. Multipole expansion in plasmas: Effective interaction potentials between compound particles

    NASA Astrophysics Data System (ADS)

    Ramazanov, T. S.; Moldabekov, Zh. A.; Gabdullin, M. T.

    2016-05-01

    In this paper, the multipole expansion method is used to determine effective interaction potentials between particles in both classical dusty plasma and dense quantum plasma. In particular, formulas for interactions of dipole-dipole and charge-dipole pairs in a classical nondegenerate plasma as well as in degenerate quantum and semiclassical plasmas were derived. The potentials describe interactions between atoms, atoms and charged particles, dust particles in the complex plasma, atoms and electrons in the degenerate plasma, and metals. Correctness of the results obtained from the multipole expansion is confirmed by their agreement with the results based on other methods of statistical physics and dielectric response function. It is shown that the method of multipole expansion can be used to derive effective interaction potentials of compound particles, if the effect of the medium on the potential of individual particles comprising compound particles is known.

  2. The effects of calculator-based laboratories on standardized test scores

    NASA Astrophysics Data System (ADS)

    Stevens, Charlotte Bethany Rains

    Nationwide, the goal of providing a productive science and math education to our youth in today's educational institutions is centering itself around the technology being utilized in these classrooms. In this age of digital technology, educational software and calculator-based laboratories (CBL) have become significant devices in the teaching of science and math for many states across the United States. Among the technology, the Texas Instruments graphing calculator and Vernier Labpro interface, are among some of the calculator-based laboratories becoming increasingly popular among middle and high school science and math teachers in many school districts across this country. In Tennessee, however, it is reported that this type of technology is not regularly utilized at the student level in most high school science classrooms, especially in the area of Physical Science (Vernier, 2006). This research explored the effect of calculator based laboratory instruction on standardized test scores. The purpose of this study was to determine the effect of traditional teaching methods versus graphing calculator teaching methods on the state mandated End-of-Course (EOC) Physical Science exam based on ability, gender, and ethnicity. The sample included 187 total tenth and eleventh grade physical science students, 101 of which belonged to a control group and 87 of which belonged to the experimental group. Physical Science End-of-Course scores obtained from the Tennessee Department of Education during the spring of 2005 and the spring of 2006 were used to examine the hypotheses. The findings of this research study suggested the type of teaching method, traditional or calculator based, did not have an effect on standardized test scores. However, the students' ability level, as demonstrated on the End-of-Course test, had a significant effect on End-of-Course test scores. This study focused on a limited population of high school physical science students in the middle Tennessee

  3. Effectiveness of a computer based medication calculation education and testing programme for nurses.

    PubMed

    Sherriff, Karen; Burston, Sarah; Wallis, Marianne

    2012-01-01

    The aim of the study was to evaluate the effect of an on-line, medication calculation education and testing programme. The outcome measures were medication calculation proficiency and self efficacy. This quasi-experimental study involved the administration of questionnaires before and after nurses completed annual medication calculation testing. The study was conducted in two hospitals in south-east Queensland, Australia, which provide a variety of clinical services including obstetrics, paediatrics, ambulatory, mental health, acute and critical care and community services. Participants were registered nurses (RNs) and enrolled nurses with a medication endorsement (EN(Med)) working as clinicians (n=107). Data pertaining to success rate, number of test attempts, self-efficacy, medication calculation error rates and nurses' satisfaction with the programme were collected. Medication calculation scores at first test attempt showed improvement following one year of access to the programme. Two of the self-efficacy subscales improved over time and nurses reported satisfaction with the online programme. Results of this study may facilitate the continuation and expansion of medication calculation and administration education to improve nursing knowledge, inform practise and directly improve patient safety. PMID:21345550

  4. Effect of voxel size when calculating patient specific radionuclide dosimetry estimates using direct Monte Carlo simulation.

    PubMed

    Hickson, Kevin J; O'Keefe, Graeme J

    2014-09-01

    The scalable XCAT voxelised phantom was used with the GATE Monte Carlo toolkit to investigate the effect of voxel size on dosimetry estimates of internally distributed radionuclide calculated using direct Monte Carlo simulation. A uniformly distributed Fluorine-18 source was simulated in the Kidneys of the XCAT phantom with the organ self dose (kidney ← kidney) and organ cross dose (liver ← kidney) being calculated for a number of organ and voxel sizes. Patient specific dose factors (DF) from a clinically acquired FDG PET/CT study have also been calculated for kidney self dose and liver ← kidney cross dose. Using the XCAT phantom it was found that significantly small voxel sizes are required to achieve accurate calculation of organ self dose. It has also been used to show that a voxel size of 2 mm or less is suitable for accurate calculations of organ cross dose. To compensate for insufficient voxel sampling a correction factor is proposed. This correction factor is applied to the patient specific dose factors calculated with the native voxel size of the PET/CT study. PMID:24859803

  5. 30 CFR 254.44 - Calculating response equipment effective daily recovery capacities.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ..., AND ENFORCEMENT, DEPARTMENT OF THE INTERIOR OFFSHORE OIL-SPILL RESPONSE REQUIREMENTS FOR FACILITIES... calculate the effective daily recovery capacity of the response equipment identified in your response plan... daily recovery capacity of the equipment by multiplying the manufacturer's rated throughput...

  6. 30 CFR 254.44 - Calculating response equipment effective daily recovery capacities.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... INTERIOR OFFSHORE OIL-SPILL RESPONSE REQUIREMENTS FOR FACILITIES LOCATED SEAWARD OF THE COAST LINE Related... capacity of the response equipment identified in your response plan that you would use to contain and recover your worst case discharge. You must calculate the effective daily recovery capacity of...

  7. The Effect of Calculator-Based Ranger Activities on Students' Graphing Ability.

    ERIC Educational Resources Information Center

    Kwon, Oh Nam

    2002-01-01

    Addresses three issues of Calculator-based Ranger (CBR) activities on graphing abilities: (a) the effect of CBR activities on graphing abilities; (b) the extent to which prior knowledge about graphing skills affects graphing ability; and (c) the influence of instructional styles on students' graphing abilities. Indicates that CBR activities are…

  8. Thermodynamic method of calculating the effect of alloying additives on interphase interaction in composite materials

    NASA Technical Reports Server (NTRS)

    Tuchinsky, L. I.

    1986-01-01

    The effect of alloying additives to the matrix of a composite on the high temperature solubility rate of a single component fiber was analyzed thermodynamically. With an example of binary Ni alloys, with Group IV-VI transition metals reinforced with W fibers, agreement between the calculated and experimental data was demonstrated.

  9. Calculation of Effective Gas Flux from Soil following Band Application of Manure or Fertilizer

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Greenhouse gases are emitted following application of manure and nitrogen-containing fertilizers to soil. Manure and fertilizers are often applied in subsurface bands in the soil, or in bands on the soil surface. This article presents a method that has been developed for calculating the effective ...

  10. The Effects of Statistical Analysis Software and Calculators on Statistics Achievement

    ERIC Educational Resources Information Center

    Christmann, Edwin P.

    2009-01-01

    This study compared the effects of microcomputer-based statistical software and hand-held calculators on the statistics achievement of university males and females. The subjects, 73 graduate students enrolled in univariate statistics classes at a public comprehensive university, were randomly assigned to groups that used either microcomputer-based…

  11. 40 CFR Appendix A to Part 197 - Calculation of Annual Committed Effective Dose Equivalent

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 25 2014-07-01 2014-07-01 false Calculation of Annual Committed Effective Dose Equivalent A Appendix A to Part 197 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) RADIATION PROTECTION PROGRAMS PUBLIC HEALTH AND ENVIRONMENTAL RADIATION PROTECTION STANDARDS FOR YUCCA MOUNTAIN, NEVADA Pt. 197, App....

  12. Event-Related Potentials and the Stroop Effect

    PubMed Central

    Sahinoglu, Babur; Dogan, Gamze

    2016-01-01

    In this manuscript, the researches on the Event-Related Potentials (ERP) elicited by the standard Stroop effect were reviewed. For the sake of clarity, only the parts of the manuscripts that reported the standard Stroop effect - ERPs relation were taken into consideration. PMID:27026765

  13. Event-Related Potentials and the Stroop Effect.

    PubMed

    Sahinoglu, Babur; Dogan, Gamze

    2016-02-01

    In this manuscript, the researches on the Event-Related Potentials (ERP) elicited by the standard Stroop effect were reviewed. For the sake of clarity, only the parts of the manuscripts that reported the standard Stroop effect - ERPs relation were taken into consideration. PMID:27026765

  14. Effects of ozone on transepithelial potential of mouse trachea

    SciTech Connect

    Takahashi, M.; Kleeberger, S.R.; Croxton, T.L. )

    1993-07-01

    The effects of ozone on tracheal electrical potential were investigated in inbred strains of mice that are differentially susceptible to ozone-induced inflammation. In male mice (9-13 wk), a tracheostomy was made under pentobarbital anesthesia for spontaneous breathing and tracheal potential was measured in the cephalad portion of the bisected trachea using Hanks' salt/agar-capped KCl bridges connected to a pair of calomel half cells. The mean tracheal potentials of five different strains of mice (C3H/HeJ, DBA/2J, C57BL/6J, BALB/cJ, and 129/J) were approximately 10 mV (lumen negative) with no significant interstrain difference. Amiloride reduced mouse tracheal potentials by approximately 70% in both C3H/HeJ and C57BL/6J mice, indicating that sodium absorption is the predominant ion transport across this tissue. Relative to air-exposed controls, acute ozone exposure (2 ppm for 3 h) significantly attenuated tracheal potential of inflammation-susceptible C57BL/6J mice by approximately 50% at 6 h and 40% at 24 h postexposure but had no effect immediately after exposure. The mean tracheal potential of C3H/HeJ mice was not changed by ozone. The differential effect of acute ozone exposure on tracheal potential in C57BL/6J and C3H/HeJ mice is consistent with differential susceptibility to ozone-induced increases in epithelial permeability in these strains.

  15. ParaDynamics: An Effective and Reliable Model for Ab Initio QM/MM Free Energy Calculations and Related Tasks

    PubMed Central

    Plotnikov, Nikolay; Kamerlin, Shina Caroline Lynn; Warshel, Arieh

    2011-01-01

    Recent years have seen tremendous effort in the development of approaches with which to obtain quantum mechanics/molecular mechanics (QM/MM) free energies for reactions in the condensed phase. Nevertheless, there remain significant challenges to address, particularly the high computational cost involved in performing proper configurational sampling and in particular in obtaining ab initio QM/MM (QM(ai)/MM) free energy surfaces. One increasingly popular approach that seems to offer an ideal way to progress in this direction is the elegant metadynamics (MTD) approach. However, in the current work we point out the subtle efficiency problems associated with this approach, and illustrate that we have at hand what is arguably a more powerful approach. More specifically, we demonstrate the effectiveness of an updated version of our original idea of using a classical reference potential for QM(ai)/MM calculations [J. Phys. Chem. B. 102 (1998), 2293)], which we refer to as “paradynamics” (PD). This approach is based on the use of an empirical valence bond (EVB) reference potential, which is already similar to the real ab initio potential. The reference potential is fitted to the ab initio potential by an iterative and, to a great degree, automated refinement procedure. The corresponding free energy profile is then constructed using the refined EVB potential, and the linear response approximation (LRA) is used to evaluate the QM(ai)/MM activation free energy barrier. The automated refinement of the EVB surface (and thus the reduction of the difference between the reference and ab initio potentials) is a key factor in accelerating the convergence of the LRA approach. We apply our PD approach to a test reaction, namely the SN2 reaction between chloride ion and methyl chloride, and demonstrate that, at present, this approach is far more powerful and cost effective than the metadynamics approach (at least in its current implementation). We also discuss the general features

  16. The effect of molecular dynamics sampling on the calculated observable gas-phase structures.

    PubMed

    Tikhonov, Denis S; Otlyotov, Arseniy A; Rybkin, Vladimir V

    2016-07-21

    In this study, we compare the performance of various ab initio molecular dynamics (MD) sampling methods for the calculation of the observable vibrationally-averaged gas-phase structures of benzene, naphthalene and anthracene molecules. Nose-Hoover (NH), canonical and quantum generalized-Langevin-equation (GLE) thermostats as well as the a posteriori quantum correction to the classical trajectories have been tested and compared to the accurate path-integral molecular dynamics (PIMD), static anharmonic vibrational calculations as well as to the experimental gas electron diffraction data. Classical sampling methods neglecting quantum effects (NH and canonical GLE thermostats) dramatically underestimate vibrational amplitudes for the bonded atom pairs, both C-H and C-C, the resulting radial distribution functions exhibit nonphysically narrow peaks. This deficiency is almost completely removed by taking the quantum effects on the nuclei into account. The quantum GLE thermostat and a posteriori correction to the canonical GLE and NH thermostatted trajectories capture most vibrational quantum effects and closely reproduce computationally expensive PIMD and experimental radial distribution functions. These methods are both computationally feasible and accurate and are therefore recommended for calculations of the observable gas-phase structures. A good performance of the quantum GLE thermostat for the gas-phase calculations is encouraging since its parameters have been originally fitted for the condensed-phase calculations. Very accurate molecular structures can be predicted by combining the equilibrium geometry obtained at a high level of electronic structure theory with vibrational amplitudes and corrections calculated using MD driven by a lower level of electronic structure theory. PMID:27331660

  17. Estimating Potential Effects of Hypothetical Oil Spills on Polar Bears

    USGS Publications Warehouse

    Amstrup, Steven C.; Durner, G.M.; McDonald, T.L.; Johnson, W.R.

    2006-01-01

    Much is known about the transport and fate of oil spilled into the sea and its toxicity to exposed wildlife. Previously, however, there has been no way to quantify the probability that wildlife dispersed over the seascape would be exposed to spilled oil. Polar bears, the apical predator of the arctic, are widely dispersed near the continental shelves of the Arctic Ocean, an area also undergoing considerable hydrocarbon exploration and development. We used 15,308 satellite locations from 194 radiocollared polar bears to estimate the probability that polar bears could be exposed to hypothetical oil spills. We used a true 2 dimensional Gausian kernel density estimator, to estimate the number of bears likely to occur in each 1.00 km2 cell of a grid superimposed over near shore areas surrounding 2 oil production facilities: the existing Northstar oil production facility, and the proposed offshore site for the Liberty production facility. We estimated the standard errors of bear numbers per cell with bootstrapping. Simulated oil spill footprints for September and October, the times during which we hypothesized effects of an oil-spill would be worst, were estimated using real wind and current data collected between 1980 and 1996. We used ARC/Info software to calculate overlap (numbers of bears oiled) between simulated oil-spill footprints and polar bear grid-cell values. Numbers of bears potentially oiled by a hypothetical 5912 barrel spill (the largest spill thought probable from a pipeline breach) ranged from 0 to 27 polar bears for September open water conditions, and from 0 to 74 polar bears in October mixed ice conditions. Median numbers oiled by the 5912 barrel hypothetical spill from the Liberty simulation in September and October were 1 and 3 bears, equivalent values for the Northstar simulation were 3 and 11 bears. In October, 75% of trajectories from the 5912 barrel simulated spill at Liberty oiled 9 or fewer bears while 75% of the trajectories affected 20 or

  18. Effect of the chiral chemical potential on the position of the critical endpoint

    NASA Astrophysics Data System (ADS)

    Wang, Bin; Wang, Yong-Long; Cui, Zhu-Fang; Zong, Hong-Shi

    2015-02-01

    The effect of chiral imbalance on the QCD phase structure is studied in a framework of Dyson-Schwinger equations. It is found that the chiral phase transition is always a crossover in the T -μ5 plane when μ is 0 MeV or small values. The trail of the critical endpoints (CEPs) along with the variation of the chiral chemical potential is given. We find that the effect of μ5 is somewhat different from the existing chiral model calculations; namely, the CEP first moves roughly along the phase boundary of T -μ plane in a smaller μ direction, as in the chiral model calculations, but turns in the opposite direction to move away from the small chemical potential region, which has never been observed before. In addition, we also discuss the possibility of whether the study at finite temperature and chiral chemical potential can provide some useful information for the detection of the CEP at finite temperature and baryon chemical potential, since the former can be calculated in lattice QCD without the sign problem.

  19. Adsorbed molecules in external fields: Effect of confining potential.

    PubMed

    Tyagi, Ashish; Silotia, Poonam; Maan, Anjali; Prasad, Vinod

    2016-12-01

    We study the rotational excitation of a molecule adsorbed on a surface. As is well known the interaction potential between the surface and the molecule can be modeled in number of ways, depending on the molecular structure and the geometry under which the molecule is being adsorbed by the surface. We explore the effect of change of confining potential on the excitation, which is largely controlled by the static electric fields and continuous wave laser fields. We focus on dipolar molecules and hence we restrict ourselves to the first order interaction in field-molecule interaction potential either through permanent dipole moment or/and the molecular polarizability parameter. It is shown that confining potential shapes, strength of the confinement, strongly affect the excitation. We compare our results for different confining potentials. PMID:27387127

  20. Selective effects of an octopus toxin on action potentials

    PubMed Central

    Dulhunty, Angela; Gage, Peter W.

    1971-01-01

    1. A lethal, water soluble toxin (Maculotoxin, MTX) with a molecular weight less than 540, can be extracted from the salivary glands of an octopus (Hapalochlaena maculosa). 2. MTX blocks action potentials in sartorius muscle fibres of toads without affecting the membrane potential. Delayed rectification is not inhibited by the toxin. 3. At low concentrations (10-6-10-5 g/ml.) MTX blocks action potentials only after a certain number have been elicited. The number of action potentials, which can be defined accurately, depends on the concentration of MTX and the concentration of sodium ions in the extracellular solution. 4. The toxin has no post-synaptic effect at the neuromuscular junction and it is concluded that it blocks neuromuscular transmission by inhibiting action potentials in motor nerve terminals. PMID:4330930

  1. Calculation of doublet capture rate for muon capture in deuterium within chiral effective field theory

    NASA Astrophysics Data System (ADS)

    Adam, J.; Tater, M.; Truhlík, E.; Epelbaum, E.; Machleidt, R.; Ricci, P.

    2012-03-01

    The doublet capture rate Λ1 / 2 of the negative muon capture in deuterium is calculated employing the nuclear wave functions generated from accurate nucleon-nucleon (NN) potentials constructed at next-to-next-to-next-to-leading order of heavy-baryon chiral perturbation theory and the weak meson exchange current operator derived within the same formalism. All but one of the low-energy constants that enter the calculation were fixed from pion-nucleon and nucleon-nucleon scattering data. The low-energy constant dˆR (cD), which cannot be determined from the purely two-nucleon data, was extracted recently from the triton β-decay and the binding energies of the three-nucleon systems. The calculated values of Λ1 / 2 show a rather large spread for the used values of the dˆR. Precise measurement of Λ1 / 2 in the future will not only help to constrain the value of dˆR, but also provide a highly nontrivial test of the nuclear chiral EFT framework. Besides, the precise knowledge of the constant dˆR will allow for consistent calculations of other two-nucleon weak processes, such as proton-proton fusion and solar neutrino scattering on deuterons, which are important for astrophysics.

  2. CALCULATED MOLECULAR STRUCTURES AND POTENTIAL ENERGY FUNCTIONS OF PAHS WITH METHYL CROWDING IN THE BAY REGION AND THEIR METABOLITES: COMPARISON TO EXPERIMENTAL STRUCTURES

    EPA Science Inventory

    Calculated molecular structures and potential energy functions ofP AHs with methyl crowding in the bay region and their metabolites: Comparison to experimental structures

    PAHs with methyl group substitution near a bay region represent a class of chemicals associated with ...

  3. CALCULATED MOLECULAR STRUCTURES AND POTENTIAL ENERGY FUNCTIONS OF PAHS WITH METHYL CROWDING IN THE BAY REGION AND THEIR METABOLITES: COMPARISON TO EXPERIMENTAL STRUCTURES

    EPA Science Inventory

    Abstract Title: Calculated molecular structures and potential energy functions of P AHs with methyl crowding in the bay region and their metabolites: Comparison to experimental structures.

    Abstract:
    PAHs with methyl group substitution near a bay region represent a cl...

  4. Effect of tensile strain on the electronic structure of Ge: A first-principles calculation

    SciTech Connect

    Liu, Li; Zhang, Miao; Di, Zengfeng E-mail: shijin.zhao@shu.edu.cn; Hu, Lijuan; Zhao, Shi-Jin E-mail: shijin.zhao@shu.edu.cn

    2014-09-21

    Taking the change of L-point conduction band valley degeneracy under strain into consideration, we investigate the effect of biaxially tensile strain (parallel to the (001), (110), and (111) planes) and uniaxially tensile strain (along the [001], [110], and [111] directions) on the electronic structure of Ge using density functional theory calculations. Our calculation shows that biaxial tension parallel to (001) is the most efficient way to transform Ge into a direct bandgap material among all tensile strains considered. [111]-tension is the best choice among all uniaxial approaches for an indirect- to direct-bandgap transition of Ge. The calculation results, which are further elaborated by bond-orbital approximation, provide a useful guidance on the optical applications of Ge through strain engineering.

  5. Turbine vane coolant flow variations and calculated effects on metal temperatures

    NASA Technical Reports Server (NTRS)

    Yeh, F. C.; Meitner, P. L.; Russell, L. M.

    1975-01-01

    Seventy-two air-cooled turbine vanes were tested to determine coolant flow variations among the vanes. Calculations were made to estimate the effect of measured coolant flow variations on local vane metal temperatures. The calculations were based on the following assumed operating conditions: turbine inlet temperature, 1700 K (2600 F); turbine inlet pressure, 31 N/sq cm (45 psia); coolant inlet temperature, 811 K (1000 F); and total coolant to gas flow ratio, 0.065. Variations of total coolant flow were not large (about 10 percent from the arithmetic mean) for all 72 vanes, but variations in local coolant flows were large. The local coolant flow variations ranged from 8 to 75 percent, and calculated metal temperature variations ranged from 8 to 60 K (15 to 180 F).

  6. Density functional theory based generalized effective fragment potential method

    SciTech Connect

    Nguyen, Kiet A. E-mail: ruth.pachter@wpafb.af.mil; Pachter, Ruth E-mail: ruth.pachter@wpafb.af.mil; Day, Paul N.

    2014-06-28

    We present a generalized Kohn-Sham (KS) density functional theory (DFT) based effective fragment potential (EFP2-DFT) method for the treatment of solvent effects. Similar to the original Hartree-Fock (HF) based potential with fitted parameters for water (EFP1) and the generalized HF based potential (EFP2-HF), EFP2-DFT includes electrostatic, exchange-repulsion, polarization, and dispersion potentials, which are generated for a chosen DFT functional for a given isolated molecule. The method does not have fitted parameters, except for implicit parameters within a chosen functional and the dispersion correction to the potential. The electrostatic potential is modeled with a multipolar expansion at each atomic center and bond midpoint using Stone's distributed multipolar analysis. The exchange-repulsion potential between two fragments is composed of the overlap and kinetic energy integrals and the nondiagonal KS matrices in the localized molecular orbital basis. The polarization potential is derived from the static molecular polarizability. The dispersion potential includes the intermolecular D3 dispersion correction of Grimme et al. [J. Chem. Phys. 132, 154104 (2010)]. The potential generated from the CAMB3LYP functional has mean unsigned errors (MUEs) with respect to results from coupled cluster singles, doubles, and perturbative triples with a complete basis set limit (CCSD(T)/CBS) extrapolation, of 1.7, 2.2, 2.0, and 0.5 kcal/mol, for the S22, water-benzene clusters, water clusters, and n-alkane dimers benchmark sets, respectively. The corresponding EFP2-HF errors for the respective benchmarks are 2.41, 3.1, 1.8, and 2.5 kcal/mol. Thus, the new EFP2-DFT-D3 method with the CAMB3LYP functional provides comparable or improved results at lower computational cost and, therefore, extends the range of applicability of EFP2 to larger system sizes.

  7. Density functional theory based generalized effective fragment potential method.

    PubMed

    Nguyen, Kiet A; Pachter, Ruth; Day, Paul N

    2014-06-28

    We present a generalized Kohn-Sham (KS) density functional theory (DFT) based effective fragment potential (EFP2-DFT) method for the treatment of solvent effects. Similar to the original Hartree-Fock (HF) based potential with fitted parameters for water (EFP1) and the generalized HF based potential (EFP2-HF), EFP2-DFT includes electrostatic, exchange-repulsion, polarization, and dispersion potentials, which are generated for a chosen DFT functional for a given isolated molecule. The method does not have fitted parameters, except for implicit parameters within a chosen functional and the dispersion correction to the potential. The electrostatic potential is modeled with a multipolar expansion at each atomic center and bond midpoint using Stone's distributed multipolar analysis. The exchange-repulsion potential between two fragments is composed of the overlap and kinetic energy integrals and the nondiagonal KS matrices in the localized molecular orbital basis. The polarization potential is derived from the static molecular polarizability. The dispersion potential includes the intermolecular D3 dispersion correction of Grimme et al. [J. Chem. Phys. 132, 154104 (2010)]. The potential generated from the CAMB3LYP functional has mean unsigned errors (MUEs) with respect to results from coupled cluster singles, doubles, and perturbative triples with a complete basis set limit (CCSD(T)/CBS) extrapolation, of 1.7, 2.2, 2.0, and 0.5 kcal/mol, for the S22, water-benzene clusters, water clusters, and n-alkane dimers benchmark sets, respectively. The corresponding EFP2-HF errors for the respective benchmarks are 2.41, 3.1, 1.8, and 2.5 kcal/mol. Thus, the new EFP2-DFT-D3 method with the CAMB3LYP functional provides comparable or improved results at lower computational cost and, therefore, extends the range of applicability of EFP2 to larger system sizes. PMID:24985612

  8. The effects of temperature on human compound action potentials.

    PubMed Central

    Bolton, C F; Sawa, G M; Carter, K

    1981-01-01

    The upper limbs of 10 healthy subjects were cooled and then warmed over physiological temperature ranges. The compound action potentials of median digital nerves, median sensory nerve at the wrist, radial sensory nerve at the wrist, and median thenar muscle, all showed progressive reduction in latency, amplitude, duration and area during rising temperature. Our studies suggest that the sensory compound action potential changes occur predominantly because of the summated effects of reduction in the duration of the action potentials of single myelinated fibres, although disproportionate increase in the conduction velocity of larger myelinated fibres also plays a role. Images PMID:7264687

  9. Effect of Several Drugs on Gastric Potential Difference in Man

    PubMed Central

    Murray, H. S.; Strottman, M. P.; Cooke, A. R.

    1974-01-01

    Measurement of gastric mucosal potential difference was used to study the effect on the gastric mucosal barrier in six volunteer subjects of several drugs known to provoke ulcers. Potential differences were also recorded in nine patients with rheumatoid arthritis being treated with long-term aspirin and five patients on long-term prednisone. Unbuffered aspirin and ethanol “broke” the barrier as shown by a rapid fall in potential difference. The effects of aspirin were dose related, with 600 mg causing a greater reduction than 300 mg. The effects of aspirin and ethanol given together were additive and caused the greatest fall in potential difference. Sodium acetylsalicylate did not alter the normal potential difference. Indomethacin, phenylbutazone, and prednisone all failed to cause any change in potential difference. The patients on long-term aspirin and prednisone had readings within the normal range and responded the same as normal subjects to an acute challenge. These studies show that aspirin and ethanol will damage the gastric mucosal barrier but that indomethacin, phenylbutazone, and prednisone do not. PMID:4808815

  10. CALCULATION OF pKa IN PROTEINS WITH THE MICROENVIRONMENT MODULATED-SCREENED COULOMB POTENTIAL (MM-SCP)

    PubMed Central

    Shan, Jufang; Mehler, Ernest L.

    2011-01-01

    The MM-SCP has been applied to predict pKa values of titratable residues in wild type and mutants of staphylococcal nuclease (SNase). The calculations were based on crystal structures made available by the Garcia-Moreno Laboratory. In the mutants, mostly deeply buried hydrophobic residues were replaced with ionizable residues, and thus their pKa values could be measured and calculated using various methods. The data set used here consisted of a set of WT SNase for which His pKa at several ionic strengths had been measured, a set of mutants for which measured pKa were available and a set of 11 mutants for which the measured pKa were not known at the time of calculation. For this latter set, blind predictions were submitted to the protein pKa cooperative, 2009 workshop at Telluride, where the results of the blind predictions were discussed (the RMSD of the submitted set was 1.10 pH units). The calculations on the structures with known pKa indicated that in addition to weaknesses of the method, structural issues were observed that led to larger errors (>1) in pKa predictions. For example, different crystallography conditions or steric clashes can lead to differences in the local environment around the titratable residue, which can produce large differences in the calculated pKa. To gain further insight into the reliability of the MM-SCP, pKa of an extended set of 54 proteins belonging to several structural classes were carried out. Here some initial results from this study are reported to help place the SNase results in the appropriate context. PMID:21748803

  11. A computational study of barium blockades in the KcsA potassium channel based on multi-ion potential of mean force calculations and free energy perturbation

    PubMed Central

    Rowley, Christopher N.

    2013-01-01

    Electrophysiological studies have established that the permeation of Ba2+ ions through the KcsA K+-channel is impeded by the presence of K+ ions in the external solution, while no effect is observed for external Na+ ions. This Ba2+ “lock-in” effect suggests that at least one of the external binding sites of the KcsA channel is thermodynamically selective for K+. We used molecular dynamics simulations to interpret these lock-in experiments in the context of the crystallographic structure of KcsA. Assuming that the Ba2+ is bound in site S2 in the dominant blocked state, we examine the conditions that could impede its translocation and cause the observed “lock-in” effect. Although the binding of a K+ ion to site S1 when site S2 is occupied by Ba2+ is prohibitively high in energy (>10 kcal/mol), binding to site S0 appears to be more plausible (ΔG > 4 kcal/mol). The 2D potential of mean force (PMF) for the simultaneous translocation of Ba2+ from site S2 to site S1 and of a K+ ion on the extracellular side shows a barrier that is consistent with the concept of external lock-in. The barrier opposing the movement of Ba2+ is very high when a cation is in site S0, and considerably smaller when the site is unoccupied. Furthermore, free energy perturbation calculations show that site S0 is selective for K+ by 1.8 kcal/mol when S2 is occupied by Ba2+. However, the same site S0 is nonselective when site S2 is occupied by K+, which shows that the presence of Ba2+ affects the selectivity of the pore. A theoretical framework within classical rate theory is presented to incorporate the concentration dependence of the external ions on the lock-in effect. PMID:24043859

  12. A computational study of barium blockades in the KcsA potassium channel based on multi-ion potential of mean force calculations and free energy perturbation.

    PubMed

    Rowley, Christopher N; Roux, Benoît

    2013-10-01

    Electrophysiological studies have established that the permeation of Ba(2+) ions through the KcsA K(+)-channel is impeded by the presence of K(+) ions in the external solution, while no effect is observed for external Na(+) ions. This Ba(2+) "lock-in" effect suggests that at least one of the external binding sites of the KcsA channel is thermodynamically selective for K(+). We used molecular dynamics simulations to interpret these lock-in experiments in the context of the crystallographic structure of KcsA. Assuming that the Ba(2+) is bound in site S(2) in the dominant blocked state, we examine the conditions that could impede its translocation and cause the observed "lock-in" effect. Although the binding of a K(+) ion to site S(1) when site S(2) is occupied by Ba(2+) is prohibitively high in energy (>10 kcal/mol), binding to site S0 appears to be more plausible (ΔG > 4 kcal/mol). The 2D potential of mean force (PMF) for the simultaneous translocation of Ba(2+) from site S(2) to site S(1) and of a K(+) ion on the extracellular side shows a barrier that is consistent with the concept of external lock-in. The barrier opposing the movement of Ba(2+) is very high when a cation is in site S(0), and considerably smaller when the site is unoccupied. Furthermore, free energy perturbation calculations show that site S(0) is selective for K(+) by 1.8 kcal/mol when S(2) is occupied by Ba(2+). However, the same site S(0) is nonselective when site S(2) is occupied by K(+), which shows that the presence of Ba(2+) affects the selectivity of the pore. A theoretical framework within classical rate theory is presented to incorporate the concentration dependence of the external ions on the lock-in effect. PMID:24043859

  13. Simple and effective calculations about spectral power distributions of outdoor light sources for computer vision.

    PubMed

    Tian, Jiandong; Duan, Zhigang; Ren, Weihong; Han, Zhi; Tang, Yandong

    2016-04-01

    The spectral power distributions (SPD) of outdoor light sources are not constant over time and atmospheric conditions, which causes the appearance variation of a scene and common natural illumination phenomena, such as twilight, shadow, and haze/fog. Calculating the SPD of outdoor light sources at different time (or zenith angles) and under different atmospheric conditions is of interest to physically-based vision. In this paper, for computer vision and its applications, we propose a feasible, simple, and effective SPD calculating method based on analyzing the transmittance functions of absorption and scattering along the path of solar radiation through the atmosphere in the visible spectrum. Compared with previous SPD calculation methods, our model has less parameters and is accurate enough to be directly applied in computer vision. It can be applied in computer vision tasks including spectral inverse calculation, lighting conversion, and shadowed image processing. The experimental results of the applications demonstrate that our calculation methods have practical values in computer vision. It establishes a bridge between image and physical environmental information, e.g., time, location, and weather conditions. PMID:27137018

  14. Effects of grid size and aggregation on regional scale landuse scenario calculations using SVAT schemes

    NASA Astrophysics Data System (ADS)

    Bormann, H.

    2006-09-01

    This paper analyses the effect of spatial input data resolution on the simulated effects of regional scale landuse scenarios using the TOPLATS model. A data set of 25 m resolution of the central German Dill catchment (693 km2) and three different landuse scenarios are used for the investigation. Landuse scenarios in this study are field size scenarios, and depending on a specific target field size (0.5 ha, 1.5 ha and 5.0 ha) landuse is determined by optimising economic outcome of agricultural used areas and forest. After an aggregation of digital elevation model, soil map, current landuse and landuse scenarios to 50 m, 75 m, 100 m, 150 m, 200 m, 300 m, 500 m, 1 km and 2 km, water balances and water flow components for a 20 years time period are calculated for the entire Dill catchment as well as for 3 subcatchments without any recalibration. Additionally water balances based on the three landuse scenarios as well as changes between current conditions and scenarios are calculated. The study reveals that both model performance measures (for current landuse) as well as water balances (for current landuse and landuse scenarios) almost remain constant for most of the aggregation steps for all investigated catchments. Small deviations are detected at the resolution of 50 m to 500 m, while significant differences occur at the resolution of 1 km and 2 km which can be explained by changes in the statistics of the input data. Calculating the scenario effects based on increasing grid sizes yields similar results. However, the change effects react more sensitive to data aggregation than simple water balance calculations. Increasing deviations between simulations based on small grid sizes and simulations using grid sizes of 300 m and more are observed. Summarizing, this study indicates that an aggregation of input data for the calculation of regional water balances using TOPLATS type models does not lead to significant errors up to a resolution of 500 m. Focusing on scenario

  15. Computer subroutines for the estimation of nuclear reaction effects in proton-tissue-dose calculations

    NASA Technical Reports Server (NTRS)

    Wilson, J. W.; Khandelwal, G. S.

    1976-01-01

    Calculational methods for estimation of dose from external proton exposure of arbitrary convex bodies are briefly reviewed. All the necessary information for the estimation of dose in soft tissue is presented. Special emphasis is placed on retaining the effects of nuclear reaction, especially in relation to the dose equivalent. Computer subroutines to evaluate all of the relevant functions are discussed. Nuclear reaction contributions for standard space radiations are in most cases found to be significant. Many of the existing computer programs for estimating dose in which nuclear reaction effects are neglected can be readily converted to include nuclear reaction effects by use of the subroutines described herein.

  16. The effect of gamma-ray transport on afterheat calculations for accident analysis

    SciTech Connect

    Reyes, S.; Latkowski, J.F.; Sanz, J.

    2000-05-01

    Radioactive afterheat is an important source term for the release of radionuclides in fusion systems under accident conditions. Heat transfer calculations are used to determine time-temperature histories in regions of interest, but the true source term needs to be the effective afterheat, which considers the transport of penetrating gamma rays. Without consideration of photon transport, accident temperatures may be overestimated in others. The importance of this effect is demonstrated for a simple, one-dimensional problem. The significance of this effect depends strongly on the accident scenario being analyzed.

  17. Effective Interaction Potentials and Physical Properties of Complex Plasmas

    SciTech Connect

    Ramazanov, T. S.; Dzhumagulova, K. N.; Gabdullin, M. T.; Omarbakiyeva, Y. A.

    2009-11-10

    Microscopic, thermodynamic and transport properties of complex plasmas are investigated on the basis of effective potentials of interparticle interaction. These potentials take into account correlation effects and quantum-mechanical diffraction. Plasma composition, thermodynamic functions of hydrogen and helium plasmas are obtained for a wide region of coupling parameter. Collision processes in partially ionized plasma are considered; some kinetic characteristics such as phase shift, scattering cross section, bremsstrahlung cross section and absorption coefficient are investigated. Dynamic and transport properties of dusty plasma are studied by computer simulation method of the Langevin dynamics.

  18. Potential effects of rational prescribing on national health care spending

    PubMed Central

    Littman, Jordan; Halil, Roland

    2016-01-01

    Abstract Objective To estimate the cost savings that could result from implementation of a rational prescribing model for drug classes that are equivalent in terms of efficacy, toxicity, and convenience. Design The top 10 drug classes based on annual spending were gathered from the Canadian Institute for Health Information. They were reviewed for potential inclusion in the study based on the ability to compare intraclass medications. When equivalence in efficacy, toxicity, and convenience was determined from a literature review, annual prescribing data were gathered from the National Prescription Drug Utilization Information Systems Database. The potential cost savings were then calculated by comparing current market shares with potential future market shares. Setting Canada. Main outcome measures Estimated differences in spending produced by a rational prescribing model. Results Statins, proton pump inhibitors, angiotensin-converting enzyme inhibitors, and selective serotonin reuptake inhibitors were determined to have class equivalence for efficacy, toxicity, and convenience. Total current annual spending on these classes is $856 million through public drug programs, and an estimated $1.97 billion nationally. Through rational prescribing, annual savings could reach $222 million for public drug programs, and $521 million nationally. Conclusion Most of the potential savings are derived from deprescribing the newest patent-protected medications in each class. Avoiding prescribing the newest intraclass drug, particularly in the absence of research to support its superiority in relevant clinical outcomes, could lead to considerable savings in health care expenditures and might push the pharmaceutical industry to innovate rather than imitate. PMID:26975917

  19. CFD-CAA Coupled Calculations of a Tandem Cylinder Configuration to Assess Facility Installation Effects

    NASA Technical Reports Server (NTRS)

    Redonnet, Stephane; Lockard, David P.; Khorrami, Mehdi R.; Choudhari, Meelan M.

    2011-01-01

    This paper presents a numerical assessment of acoustic installation effects in the tandem cylinder (TC) experiments conducted in the NASA Langley Quiet Flow Facility (QFF), an open-jet, anechoic wind tunnel. Calculations that couple the Computational Fluid Dynamics (CFD) and Computational Aeroacoustics (CAA) of the TC configuration within the QFF are conducted using the CFD simulation results previously obtained at NASA LaRC. The coupled simulations enable the assessment of installation effects associated with several specific features in the QFF facility that may have impacted the measured acoustic signature during the experiment. The CFD-CAA coupling is based on CFD data along a suitably chosen surface, and employs a technique that was recently improved to account for installed configurations involving acoustic backscatter into the CFD domain. First, a CFD-CAA calculation is conducted for an isolated TC configuration to assess the coupling approach, as well as to generate a reference solution for subsequent assessments of QFF installation effects. Direct comparisons between the CFD-CAA calculations associated with the various installed configurations allow the assessment of the effects of each component (nozzle, collector, etc.) or feature (confined vs. free jet flow, etc.) characterizing the NASA LaRC QFF facility.

  20. Dielectric-dependent screened Hartree-Fock exchange potential and Slater-formula with Coulomb-hole interaction for energy band structure calculations.

    PubMed

    Shimazaki, Tomomi; Nakajima, Takahito

    2014-09-21

    We previously reported a screened Hartree-Fock (HF) exchange potential for energy band structure calculations [T. Shimazaki and Y. Asai, J. Chem. Phys. 130, 164702 (2009); T. Shimazaki and Y. Asai, J. Chem. Phys. 132, 224105 (2010)]. In this paper, we discuss the Coulomb-hole (COH) interaction and screened Slater-formula and determine the energy band diagrams of several semiconductors, such as diamond, silicon, AlAs, AlP, GaAs, GaP, and InP, based on the screened HF exchange potential and Slater-formula with COH interaction, to demonstrate the adequacy of those theoretical concepts. The screened HF exchange potential and Slater-formula are derived from a simplified dielectric function and, therefore, include the dielectric constant in their expressions. We also present a self-consistent calculation technique to automatically determine the dielectric constant, which is incorporated into each self-consistent field step. PMID:25240347

  1. Dielectric-dependent screened Hartree-Fock exchange potential and Slater-formula with Coulomb-hole interaction for energy band structure calculations

    NASA Astrophysics Data System (ADS)

    Shimazaki, Tomomi; Nakajima, Takahito

    2014-09-01

    We previously reported a screened Hartree-Fock (HF) exchange potential for energy band structure calculations [T. Shimazaki and Y. Asai, J. Chem. Phys. 130, 164702 (2009); T. Shimazaki and Y. Asai, J. Chem. Phys. 132, 224105 (2010)]. In this paper, we discuss the Coulomb-hole (COH) interaction and screened Slater-formula and determine the energy band diagrams of several semiconductors, such as diamond, silicon, AlAs, AlP, GaAs, GaP, and InP, based on the screened HF exchange potential and Slater-formula with COH interaction, to demonstrate the adequacy of those theoretical concepts. The screened HF exchange potential and Slater-formula are derived from a simplified dielectric function and, therefore, include the dielectric constant in their expressions. We also present a self-consistent calculation technique to automatically determine the dielectric constant, which is incorporated into each self-consistent field step.

  2. A Comparison of Teacher Effectiveness Measures Calculated Using Three Multilevel Models for Raters Effects

    ERIC Educational Resources Information Center

    Murphy, Daniel L.; Beretvas, S. Natasha

    2015-01-01

    This study examines the use of cross-classified random effects models (CCrem) and cross-classified multiple membership random effects models (CCMMrem) to model rater bias and estimate teacher effectiveness. Effect estimates are compared using CTT versus item response theory (IRT) scaling methods and three models (i.e., conventional multilevel…

  3. CAR 88: A method to calculate subsonic and supersonic, steady and unsteady, potential flow about complex configurations

    NASA Astrophysics Data System (ADS)

    Hounjet, M. H. L.

    1988-10-01

    A description of the method CAR88 for the calculation of steady and time linearized unsteady subsonic and supersonic flow about complex two dimensional and three dimensional configurations is given. The method belongs to the category of the so called panel methods. Results of applications in supersonic flow made to a two dimensional oscillating flat plate, a two dimensional double and single edge airfoil, three dimensional cones, and to single and multiple interfering wing surface are shown.

  4. Ab Initio Path-Integral Calculations of Kinetic and Equilibrium Isotope Effects on Base-Catalyzed RNA Transphosphorylation Models

    PubMed Central

    Wong, Kin-Yiu; Yuqing, Xu; York, Darrin M.

    2014-01-01

    Detailed understandings of the reaction mechanisms of RNA catalysis in various environments can have profound importance for many applications, ranging from the design of new biotechnologies to the unraveling of the evolutionary origin of life. An integral step in the nucleolytic RNA catalysis is self-cleavage of RNA strands by 2′-O-transphosphorylation. Key to elucidating a reaction mechanism is determining the molecular structure and bonding characteristics of transition state. A direct and powerful probe of transition state is measuring isotope effects on biochemical reactions, particularly if we can reproduce isotope effect values from quantum calculations. This paper significantly extends the scope of our previous joint experimental and theoretical work in examining isotope effects on enzymatic and non-enzymatic 2′-O-transphosphorylation reaction models that mimic reactions catalyzed by RNA enzymes (ribozymes), and protein enzymes such as ribonuclease A (RNase A). Native reactions are studied, as well as reactions with thio substitutions representing chemical modifications often used in experiments to probe mechanism. Here, we report and compare results from eight levels of electronic-structure calculations for constructing the potential energy surfaces in kinetic and equilibrium isotope effects (KIE and EIE) computations, including a “gold-standard” coupled-cluster level of theory [CCSD(T)]. In addition to the widely-used Bigeleisen equation for estimating KIE and EIE values, internuclear anharmonicity and quantum tunneling effects were also computed using our recently-developed ab initio path-integral method, i.e., automated integration-free path-integral (AIF-PI) method. The results of this work establish an important set of benchmarks that serve to guide calculations of KIE and EIE for RNA catalysis. PMID:24841935

  5. Effect of dynamical polarization potentials on fusion radial potential barriers and on fusion cross sections for the proton-halo system 8B+58Ni

    NASA Astrophysics Data System (ADS)

    Gómez Camacho, A.

    2013-03-01

    Fusion radial potential (l = 0) barriers of 8B+58Ni are determined from a simultaneous optical model analysis of elastic scattering angular distributions and fusion data at energies around the Coulomb energy. Dynamical energy dependent Woods-Saxon polarization potentials, UF (volume) and UDR (surface) are used in the calculation of the barriers, where UF is a potential that accounts for polarization effects emerging from couplings to the fusion channel and UDR for effects due to direct reaction absorption couplings. Each of these potentials, UF and UDR are in turn, split into real and imaginary potentials VF, WF and VDR, WDR, which are related via the dispersion relation. The parameters of these potentials are determined during the simultaneous fitting process. The effect on fusion cross section from the competitive barrier lowering and rising produced respectively by VF and VDR, is investigated. Also, the net effect of breakup couplings on the fusion cross section is studied by analyzing the particular effect from both direct reaction polarization potentials VDR and WDR. Finally, it is shown that energy dependence of the total polarization potential U(E) = UF(E) + UDR(E) at the strong absorption radius Rsa is consistent with the Breakup Threshold Anomaly as expected for weakly bound nuclei.

  6. Effects of surface pressures and streamline metrics on the calculation of laminar heating rates

    NASA Technical Reports Server (NTRS)

    Riley, Christopher J.; Dejarnette, Fred R.; Zoby, Vincent

    1988-01-01

    The effect of streamline geometry and pressure distributions on surface heating rates is examined for slender, spherically blunted cones. The modifications to the approximate aeroheating code include a curve fit of pressures computed by an Euler solution over a range of Mach numbers and cone angles. The streamline geometry is then found using the surface pressures and inviscid surface properties. Previously, streamlines were determined using the inviscid properties at the edge of the boundary layer when accounting for the effects of entropy-layer swallowing. Streamline calculations are now based on inviscid surface conditions rather than boundary-layer edge properties. However, the heating rates are calculated using inviscid properties at the edge of the boundary layer. Resulting heating rates compare favorably with solutions from the viscous-shock-layer equations.

  7. Accurate calculations on 12 Λ-S and 28 Ω states of BN+ cation: potential energy curves, spectroscopic parameters and spin-orbit coupling.

    PubMed

    Shi, Deheng; Liu, Qionglan; Sun, Jinfeng; Zhu, Zunlue

    2014-03-25

    The potential energy curves (PECs) of 28 Ω states generated from the 12 states (X(4)Σ(-), 1(2)Π, 1(2)Σ(-), 1(2)Δ, 1(2)Σ(+), 2(2)Π, A(4)Π, B(4)Σ(-), 3(2)Π, 1(6)Σ(-), 2(2)Σ(-) and 1(6)Π) of the BN(+) cation are studied for the first time for internuclear separations from about 0.1 to 1.0 nm using an ab initio quantum chemical method. All the Λ-S states correlate to the first four dissociation channels. The 1(6)Σ(-), 3(2)Π and A(4)Π states are found to be the inverted ones. The 1(2)Σ(+), 2(2)Π, 3(2)Π and 2(2)Σ(-) states are found to possess the double well. The PECs are calculated by the complete active space self-consistent field method, which is followed by the internally contracted multireference configuration interaction approach with the Davidson correction. Core-valence correlation correction is included by a cc-pCV5Z basis set. Scalar relativistic correction is calculated by the third-order Douglas-Kroll Hamiltonian approximation at the level of a cc-pV5Z basis set. The convergent behavior of present calculations is discussed with respect to the basis set and level of theory. The spin-orbit coupling is accounted for by the state interaction approach with the Breit-Pauli Hamiltonian using the all-electron cc-pCV5Z basis set. All the PECs are extrapolated to the complete basis set limit. The spectroscopic parameters are obtained, and the vibrational properties of 1(2)Σ(+), 2(2)Π, 3(2)Π and 2(2)Σ(-) states are evaluated. Analyses demonstrate that the spectroscopic parameters reported here can be expected to be reliably predicted ones. The conclusion is gained that the effect of spin-orbit coupling on the spectroscopic parameters are not obvious almost for all the Λ-S states involved in the present paper. PMID:24334021

  8. On accurate calculation of the potential of mean force between antigen and antibody: A case of the HyHEL-10-hen egg white lysozyme system

    NASA Astrophysics Data System (ADS)

    Yamashita, Takefumi; Fujitani, Hideaki

    2014-08-01

    We study several free energy calculation methods in the dissociation process of lysozyme and its antibody. We introduce the multi-step targeted molecular dynamics (mTMD) method to determine the dissociation pathway. The dissociation free energy calculated along the mTMD dissociation pathway is significantly lower than that along the dissociation pathway determined by the steered molecular dynamics (SMD) method. This indicates that SMD leads to a meta-stable dissociation state. While the SMD restrains the distance between the two proteins, the mTMD restrains the internal structures additionally. We discuss the effect of fragility of the protein structures on the free energy calculations.

  9. Ab initio calculations of accurate dissociation energy and analytic potential energy function for the second excited state B1Π of 7LiH

    NASA Astrophysics Data System (ADS)

    Shi, De-Heng; Liu, Yu-Fang; Sun, Jin-Feng; Zhu, Zun-Lue; Yang, Xiang-Dong

    2006-12-01

    The reasonable dissociation limit of the second excited singlet state B1Π of 7LiH molecule is obtained. The accurate dissociation energy and equilibrium geometry of the B1Π state are calculated using a symmetry-adapted-cluster configuration-interaction method in full active space. The whole potential energy curve for the B1Π state is obtained over the internuclear distance ranging from about 0.10 nm to 0.54 nm, and has a least-square fit to the analytic Murrell-Sorbie function form. The vertical excitation energy is calculated from the ground state to the B1Π state and compared with previous theoretical results. The equilibrium internuclear distance obtained by geometry optimization is found to be quite different from that obtained by single-point energy scanning under the same calculation condition. Based on the analytic potential energy function, the harmonic frequency value of the B1Π state is estimated. A comparison of the theoretical calculations of dissociation energies, equilibrium interatomic distances and the analytic potential energy function with those obtained by previous theoretical results clearly shows that the present work is more comprehensive and in better agreement with experiments than previous theories, thus it is an improvement on previous theories.

  10. Calculation of wing response to gusts and blast waves with vortex lift effect

    NASA Technical Reports Server (NTRS)

    Chao, D. C.; Lan, C. E.

    1983-01-01

    A numerical study of the response of aircraft wings to atmospheric gusts and to nuclear explosions when flying at subsonic speeds is presented. The method is based upon unsteady quasi-vortex-lattice method, unsteady suction analogy, and Pade approximate. The calculated results, showing vortex lag effect, yield reasonable agreement with experimental data for incremental lift on wings in gust penetration and due to nuclear blast waves.

  11. Calculation of wing response to gusts and blast waves with vortex lift effect

    NASA Technical Reports Server (NTRS)

    Chao, D. C.; Lan, C. E.

    1983-01-01

    A numerical study of the response of aircraft wings to atmospheric gusts and to nuclear explosions when flying at subsonic speeds is presented. The method is based upon unsteady quasi-vortex lattice method, unsteady suction analogy and Pade approximant. The calculated results, showing vortex lag effect, yield reasonable agreement with experimental data for incremental lift on wings in gust penetration and due to nuclear blast waves.

  12. The effects of anatomic resolution, respiratory variations and dose calculation methods on lung dosimetry

    NASA Astrophysics Data System (ADS)

    Babcock, Kerry Kent Ronald

    2009-04-01

    The goal of this thesis was to explore the effects of dose resolution, respiratory variation and dose calculation method on dose accuracy. To achieve this, two models of lung were created. The first model, called TISSUE, approximated the connective alveolar tissues of the lung. The second model, called BRANCH, approximated the lungs bronchial, arterial and venous branching networks. Both models were varied to represent the full inhalation, full exhalation and midbreath phases of the respiration cycle. To explore the effects of dose resolution and respiratory variation on dose accuracy, each model was converted into a CT dataset and imported into a Monte Carlo simulation. The resulting dose distributions were compared and contrasted against dose distributions from Monte Carlo simulations which included the explicit model geometries. It was concluded that, regardless of respiratory phase, the exclusion of the connective tissue structures in the CT representation did not significantly effect the accuracy of dose calculations. However, the exclusion of the BRANCH structures resulted in dose underestimations as high as 14% local to the branching structures. As lung density decreased, the overall dose accuracy marginally decreased. To explore the effects of dose calculation method on dose accuracy, CT representations of the lung models were imported into the Pinnacle 3 treatment planning system. Dose distributions were calculated using the collapsed cone convolution method and compared to those derived using the Monte Carlo method. For both lung models, it was concluded that the accuracy of the collapsed cone algorithm decreased with decreasing density. At full inhalation lung density, the collapsed cone algorithm underestimated dose by as much as 15%. Also, the accuracy of the CCC method decreased with decreasing field size. Further work is needed to determine the source of the discrepancy.

  13. Transition energy and potential energy curves for ionized inner-shell states of CO, O2 and N 2 calculated by several inner-shell multiconfigurational approaches.

    PubMed

    Moura, Carlos E V de; Oliveira, Ricardo R; Rocha, Alexandre B

    2013-05-01

    Potential energy curves and inner-shell ionization energies of carbon monoxide, oxygen and nitrogen molecules were calculated using several forms of the inner-shell multiconfigurational self-consistent field (IS-MCSCF) method-a recently proposed protocol to obtain specifically converged inner-shell states at this level. The particular forms of the IS-MCSCF method designated IS-GVB-PP, IS-FVBL and IS-CASSCF stand for perfect pairing generalized valence bond, full valence bond-like MCSCF and complete active space self consistent field, respectively. A comparison of these different versions of the IS-MCSCF method was carried out for the first time. The results indicate that inner-shell states are described accurately even for the simplest version of the method (IS-GVB-PP). Dynamic correlation was recovered by multireference configuration interaction or multireference perturbation theory. For molecules not having equivalent atoms, all methods led to comparable and accurate transition energies. For molecules with equivalent atoms, the most accurate results were obtained by multireference perturbation theory. Scalar relativistic effects were accounted for using the Douglas-Kroll-Hess Hamiltonian. PMID:23070335

  14. Potential effects of environmental regulatory procedures on geothermal development

    SciTech Connect

    Beeland, G.V.; Boies, D.B.

    1981-01-01

    The potential effects of several types of applicable environmental regulatory procedures on geothermal development were assessed, and particular problem areas were identified. The possible impact of procedures adopted pursuant to the following Federal statutes were analyzed: Clean Air Act; Clean Water Act; Safe Drinking Water Act; and Resource Conservation and Recovery Act. State regulations applicable, or potentially applicable, to geothermal facilities were also reviewed to determine: permit information requirements; pre-permit air or water quality monitoring requirements; effect of mandated time frames for permit approval; and potential for exemption of small facilities. The regulations of the following states were covered in the review: Alaska; Arizona; California; Colorado; Hawaii; Idaho; Montana; Nevada; New Mexico; Oregon; Utah; Washington; and Wyoming. (MHR)

  15. Potentiators exert distinct effects on human, murine, and Xenopus CFTR.

    PubMed

    Cui, Guiying; Khazanov, Netaly; Stauffer, Brandon B; Infield, Daniel T; Imhoff, Barry R; Senderowitz, Hanoch; McCarty, Nael A

    2016-08-01

    VX-770 (Ivacaftor) has been approved for clinical usage in cystic fibrosis patients with several CFTR mutations. Yet the binding site(s) on CFTR for this compound and other small molecule potentiators are unknown. We hypothesize that insight into this question could be gained by comparing the effect of potentiators on CFTR channels from different origins, e.g., human, mouse, and Xenopus (frog). In the present study, we combined this comparative molecular pharmacology approach with that of computer-aided drug discovery to identify and characterize new potentiators of CFTR and to explore possible mechanism of action. Our results demonstrate that 1) VX-770, NPPB, GlyH-101, P1, P2, and P3 all exhibited ortholog-specific behavior in that they potentiated hCFTR, mCFTR, and xCFTR with different efficacies; 2) P1, P2, and P3 potentiated hCFTR in excised macropatches in a manner dependent on the degree of PKA-mediated stimulation; 3) P1 and P2 did not have additive effects, suggesting that these compounds might share binding sites. Also 4) using a pharmacophore modeling approach, we identified three new potentiators (IOWH-032, OSSK-2, and OSSK-3) that have structures similar to GlyH-101 and that also exhibit ortholog-specific potentiation of CFTR. These could potentially serve as lead compounds for development of new drugs for the treatment of cystic fibrosis. The ortholog-specific behavior of these compounds suggest that a comparative pharmacology approach, using cross-ortholog chimeras, may be useful for identification of binding sites on human CFTR. PMID:27288484

  16. Visualizing skin effects in conductors with MRI: (7)Li MRI experiments and calculations.

    PubMed

    Ilott, Andrew J; Chandrashekar, S; Klöckner, Andreas; Chang, Hee Jung; Trease, Nicole M; Grey, Clare P; Greengard, Leslie; Jerschow, Alexej

    2014-08-01

    While experiments on metals have been performed since the early days of NMR (and DNP), the use of bulk metal is normally avoided. Instead, often powders have been used in combination with low fields, so that skin depth effects could be neglected. Another complicating factor of acquiring NMR spectra or MRI images of bulk metal is the strong signal dependence on the orientation between the sample and the radio frequency (rf) coil, leading to non-intuitive image distortions and inaccurate quantification. Such factors are particularly important for NMR and MRI of batteries and other electrochemical devices. Here, we show results from a systematic study combining rf field calculations with experimental MRI of (7)Li metal to visualize skin depth effects directly and to analyze the rf field orientation effect on MRI of bulk metal. It is shown that a certain degree of selectivity can be achieved for particular faces of the metal, simply based on the orientation of the sample. By combining rf field calculations with bulk magnetic susceptibility calculations accurate NMR spectra can be obtained from first principles. Such analyses will become valuable in many applications involving battery systems, but also metals, in general. PMID:25036296

  17. Visualizing skin effects in conductors with MRI: 7Li MRI experiments and calculations

    NASA Astrophysics Data System (ADS)

    Ilott, Andrew J.; Chandrashekar, S.; Klöckner, Andreas; Chang, Hee Jung; Trease, Nicole M.; Grey, Clare P.; Greengard, Leslie; Jerschow, Alexej

    2014-08-01

    While experiments on metals have been performed since the early days of NMR (and DNP), the use of bulk metal is normally avoided. Instead, often powders have been used in combination with low fields, so that skin depth effects could be neglected. Another complicating factor of acquiring NMR spectra or MRI images of bulk metal is the strong signal dependence on the orientation between the sample and the radio frequency (rf) coil, leading to non-intuitive image distortions and inaccurate quantification. Such factors are particularly important for NMR and MRI of batteries and other electrochemical devices. Here, we show results from a systematic study combining rf field calculations with experimental MRI of 7Li metal to visualize skin depth effects directly and to analyze the rf field orientation effect on MRI of bulk metal. It is shown that a certain degree of selectivity can be achieved for particular faces of the metal, simply based on the orientation of the sample. By combining rf field calculations with bulk magnetic susceptibility calculations accurate NMR spectra can be obtained from first principles. Such analyses will become valuable in many applications involving battery systems, but also metals, in general.

  18. Neuroprotective effect of lidocaine: is there clinical potential?

    PubMed Central

    Leng, Tiandong; Gao, Xiuren; Dilger, James P; Lin, Jun

    2016-01-01

    Local anesthetic lidocaine has been shown to be protective in animal models of focal and global ischemia as well as in in vitro hypoxic models. Lidocaine has been tested in patients for its potential protective effect on postoperative cognitive dysfunction. This mini-review summarizes the laboratory and clinical evidences and discusses its clinical applications as neuroprotective agent. PMID:27186318

  19. Effective Electromagnetic Interaction Potential in Flat and Curved Spacetimes

    SciTech Connect

    Caicedo, Jose Alexander; Urrutia, Luis F.

    2010-07-12

    We present a summary of the main steps in the construction of the effective relativistic interaction potential between two charged Dirac particles in the presence of a background weak gravitational field, by extending a procedure previously used for electrodynamics in Minkowski space. We consider the full two-body problem and apply the method to the hydrogen atom.

  20. Examining triclosan-induced potentiation of the estrogen uterotrophic effect

    EPA Science Inventory

    Triclosan (TCS), a widely used antibacterial, has been shown to be an endocrine disruptor. We reported previously that TCS potentiated the estrogenic effect of ethinyl estradiol (EE) on uterine growth in rats orally administered 3 μg/kg EE and TCS (2 to 18 mg/kg) in the utero...