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Sample records for effective potential calculation

  1. Ab initio effective core potentials for molecular calculations. Potentials for main group elements Na to Bi

    SciTech Connect

    Wadt, W.R.; Hay, P.J.

    1985-01-01

    A consistent set of ab initio effective core potentials (ECP) has been generated for the main group elements from Na to Bi using the procedure originally developed by Kahn. The ECP's are derived from all-electron numerical Hartree--Fock atomic wave functions and fit to analytical representations for use in molecular calculations. For Rb to Bi the ECP's are generated from the relativistic Hartree--Fock atomic wave functions of Cowan which incorporate the Darwin and mass--velocity terms. Energy-optimized valence basis sets of (3s3p) primitive Gaussians are presented for use with the ECP's. Comparisons between all-electron and valence-electron ECP calculations are presented for NaF, NaCl, Cl/sub 2/, Cl/sub 2//sup -/, Br/sub 2/, Br/sub 2//sup -/, and Xe/sub 2//sup +/. The results show that the average errors introduced by the ECP's are generally only a few percent.

  2. Sputtering yield calculations using an interatomic potential with the shell effect and a new local model

    NASA Astrophysics Data System (ADS)

    Li, Zhijie; Kenmotsu, Takahiro; Kawamura, Takaichi; Ono, Tadayoshi; Yamamura, Yasunori

    1999-06-01

    In order to test the availabilities of the theoretical screening lengths with the shell effect and the new local electronic-energy-loss model proposed by Yamamura et al., the sputtering yields due to various ion impacts on monatomic materials were calculated with the ACAT code. It is found that the sputtering yields calculated by the Molière potential with the present theoretical screening lengths are in reasonable good agreement with experimental data and Yamamura's empirical sputtering formula without free parameters.

  3. Calculating potential of mean force between like-charged nanoparticles: A comprehensive study on salt effects

    NASA Astrophysics Data System (ADS)

    Wu, Yuan-Yan; Wang, Feng-Hua; Tan, Zhi-Jie

    2013-10-01

    Ions are critical to the structure and stability of polyelectrolytes such as nucleic acids. In this work, we systematically calculated the potentials of mean force between two like-charged nanoparticles in salt solutions by Monte Carlo simulations. The pseudo-spring method is employed to calculate the potential of mean force and compared systematically with the inversed-Boltzmann method. An effective attraction is predicted between two like-charged nanoparticles in divalent/trivalent salt solution and such attraction becomes weakened at very high salt concentration. Our analysis reveals that for the system, the configuration of ion-bridging nanoparticles is responsible for the attraction, and the invasion of anions into the inter-nanoparticles region at high salt concentration would induce attraction weakening rather than the charge inversion effect. The present method would be useful for calculating effective interactions during nucleic acid folding.

  4. 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.

  5. 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.

  6. Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Sc to Hg

    SciTech Connect

    Hay, P.J.; Wadt, W.R.

    1985-01-01

    Ab initio effective core potentials (ECP's) have been generated to replace the Coulomb, exchange, and core-orthogonality effects of the chemically inert core electron in the transition metal atoms Sc to Hg. For the second and third transition series relative ECP's have been generated which also incorporate the mass--velocity and Darwin relativistic effects into the potential. The ab initio ECP's should facilitate valence electron calculations on molecules containing transition-metal atoms with accuracies approaching all-electron calculations at a fraction of the computational cost. Analytic fits to the potentials are presented for use in multicenter integral evaluation. Gaussian orbital valence basis sets are developed for the (3d,4s,4p), (4d,5s,5p), and (5d,6s,6p) orbitals of the first, second, and third transition series atoms, respectively. All-electron and valence-electron atomic excitation energies are also compared for the low-lying states of Sc--Hg, and the valence-electron calculations are found to reproduce the all-electron excitation energies (typically within a few tenths of an eV).

  7. Calculations of current densities for neutral and doubly charged persubstituted benzenes using effective core potentials.

    PubMed

    Rauhalahti, Markus; Taubert, Stefan; Sundholm, Dage; Liégeois, Vincent

    2017-03-08

    Magnetically induced current density susceptibilities and ring-current strengths have been calculated for neutral and doubly charged persubstituted benzenes C6X6 and C6X6(2+) with X = F, Cl, Br, I, At, SeH, SeMe, TeH, TeMe, and SbH2. The current densities have been calculated using the gauge-including magnetically induced current (GIMIC) method, which has been interfaced to the Gaussian electronic structure code rendering current density calculations using effective core potentials (ECP) feasible. Relativistic effects on the ring-current strengths have been assessed by employing ECP calculations of the current densities. Comparison of the ring-current strengths obtained in calculations on C6At6 and C6At6(2+) using relativistic and non-relativistic ECPs show that scalar relativistic effects have only a small influence on the ring-current strengths. Comparisons of the ring-current strengths and ring-current profiles show that the C6I6(2+), C6At6(2+), C6(SeH)6(2+), C6(SeMe)6(2+), C6(TeH)6(2+), C6(TeMe)6(2+), and C6(SbH2)6(2+) dications are doubly aromatic sustaining spatially separated ring currents in the carbon ring and in the exterior of the molecule. The C6I6(+) radical cation is also found to be doubly aromatic with a weaker ring current than obtained for the dication.

  8. Rotational g Tensors Calculated Using Hybrid Exchange-Correlation Functionals with the Optimized Effective Potential Approach.

    PubMed

    Teale, Andrew M; Helgaker, Trygve; Tozer, David J

    2006-05-01

    The calculation of rotational g tensors using density functional theory (DFT) with hybrid exchange-correlation functionals is considered. A total of 143 rotational g tensor elements in 58 molecules (67 isotopic combinations) are calculated using three standard hybrid functionals. Tensor elements determined using an uncoupled approach with orbitals and eigenvalues calculated from the multiplicative optimized effective potential (OEP) constitute a significant improvement over those determined in the conventional coupled manner with a nonmultiplicative exchange-correlation operator. Relative to experimental results, mean absolute errors are reduced by a factor of 2; mean errors and standard deviations are reduced by more than a factor of 3. The results are also an improvement over those determined using a generalized gradient-approximation functional optimized for magnetic response properties. The influence of orbital exchange is investigated for a representative subset of molecules, yielding an optimal amount near 0.3. Rotational g tensors are also determined from coupled-cluster electron densities using a combined DFT/wave-function approach. Being substantially more expensive, they do not offer a notable improvement on the pure DFT values from OEP-based hybrid calculations.

  9. 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.

  10. Ab initio effective core potentials for molecular calculations. Potentials for K to Au including the outermost core orbitals

    SciTech Connect

    Hay, P.J.; Wadt, W.R.

    1985-01-01

    Ab initio effective core potentials (ECP's) have been generated to replace the innermost core electron for third-row (K--Au), fourth-row (Rb--Ag), and fifth-row (Cs--Au) atoms. The outermost core orbitals: corresponding to the ns/sup 2/np/sup 6/ configuration for the three rows here: are not replaced by the ECP but are treated on an equal footing with the nd, (n+1)s and (n+1)p valence orbitals. These ECP's have been derived for use in molecular calculations where these outer core orbitals need to be treated explicitly rather than to be replaced by an ECP. The ECP's for the forth and fifth rows also incorporate the mass--velocity and Darwin relativistic effects into the potentials. Analytic fits to the potentials are presented for use in multicenter integral evaluation. Gaussian orbital valence basis sets are developed for the (3s, 3p, 3d, 4s, 4p), (4s, 4p, 4d, 5s, 5p), and (5s, 5p, 5d, 6s, 6p) ortibals of the three respective rows.

  11. CALCULATION OF POTENTIAL DEPRESSION IN KLYSTRON GAPS,

    DTIC Science & Technology

    A calculation in cylindrical geometry for the potential depression in klystron gaps is pre sented. The results of this calculation, which takes into...account the mutual effect of depressed potential and increased charge density, is in the form of a series involving Bessel functions of imaginary

  12. Calculation of Rydberg interaction potentials

    NASA Astrophysics Data System (ADS)

    Weber, Sebastian; Tresp, Christoph; Menke, Henri; Urvoy, Alban; Firstenberg, Ofer; Büchler, Hans Peter; Hofferberth, Sebastian

    2017-07-01

    The strong interaction between individual Rydberg atoms provides a powerful tool exploited in an ever-growing range of applications in quantum information science, quantum simulation and ultracold chemistry. One hallmark of the Rydberg interaction is that both its strength and angular dependence can be fine-tuned with great flexibility by choosing appropriate Rydberg states and applying external electric and magnetic fields. More and more experiments are probing this interaction at short atomic distances or with such high precision that perturbative calculations as well as restrictions to the leading dipole-dipole interaction term are no longer sufficient. In this tutorial, we review all relevant aspects of the full calculation of Rydberg interaction potentials. We discuss the derivation of the interaction Hamiltonian from the electrostatic multipole expansion, numerical and analytical methods for calculating the required electric multipole moments and the inclusion of electromagnetic fields with arbitrary direction. We focus specifically on symmetry arguments and selection rules, which greatly reduce the size of the Hamiltonian matrix, enabling the direct diagonalization of the Hamiltonian up to higher multipole orders on a desktop computer. Finally, we present example calculations showing the relevance of the full interaction calculation to current experiments. Our software for calculating Rydberg potentials including all features discussed in this tutorial is available as open source.

  13. Highly Efficient Free Energy Calculations of the Fe Equation of State Using Temperature-Dependent Effective Potential Method.

    PubMed

    Mosyagin, Igor; Hellman, Olle; Olovsson, Weine; Simak, Sergei I; Abrikosov, Igor A

    2016-11-03

    Free energy calculations at finite temperature based on ab initio molecular dynamics (AIMD) simulations have become possible, but they are still highly computationally demanding. Besides, achieving simultaneously high accuracy of the calculated results and efficiency of the computational algorithm is still a challenge. In this work we describe an efficient algorithm to determine accurate free energies of solids in simulations using the recently proposed temperature-dependent effective potential method (TDEP). We provide a detailed analysis of numerical approximations employed in the TDEP algorithm. We show that for a model system considered in this work, hcp Fe, the obtained thermal equation of state at 2000 K is in excellent agreement with the results of standard calculations within the quasiharmonic approximation.

  14. Highly Efficient Free Energy Calculations of the Fe Equation of State Using Temperature-Dependent Effective Potential Method

    PubMed Central

    2016-01-01

    Free energy calculations at finite temperature based on ab initio molecular dynamics (AIMD) simulations have become possible, but they are still highly computationally demanding. Besides, achieving simultaneously high accuracy of the calculated results and efficiency of the computational algorithm is still a challenge. In this work we describe an efficient algorithm to determine accurate free energies of solids in simulations using the recently proposed temperature-dependent effective potential method (TDEP). We provide a detailed analysis of numerical approximations employed in the TDEP algorithm. We show that for a model system considered in this work, hcp Fe, the obtained thermal equation of state at 2000 K is in excellent agreement with the results of standard calculations within the quasiharmonic approximation. PMID:27700093

  15. 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.

  16. 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.

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

    PubMed Central

    Mehler, E L; Guarnieri, F

    1999-01-01

    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

  18. 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.

  19. Development and testing of a compact basis set for use in effective core potential calculations on rhodium complexes.

    PubMed

    Roscioni, Otello M; Lee, Edmond P F; Dyke, John M

    2012-10-05

    We present a set of effective core potential (ECP) basis sets for rhodium atoms which are of reasonable size for use in electronic structure calculations. In these ECP basis sets, the Los Alamos ECP is used to simulate the effect of the core electrons while an optimized set of Gaussian functions, which includes polarization and diffuse functions, is used to describe the valence electrons. These basis sets were optimized to reproduce the ionization energy and electron affinity of atomic rhodium. They were also tested by computing the electronic ground state geometry and harmonic frequencies of [Rh(CO)(2) μ-Cl](2) , Rh(CO)(2) ClPy, and RhCO (neutral and its positive, and negative ions) as well as the enthalpy of the reaction of [Rh(CO)(2) μ-Cl](2) with pyridine (Py) to give Rh(CO)(2) ClPy, at different levels of theory. Good agreement with experimental values was obtained. Although the number of basis functions used in our ECP basis sets is smaller than those of other ECP basis sets of comparable quality, we show that the newly developed ECP basis sets provide the flexibility and precision required to reproduce a wide range of chemical and physical properties of rhodium compounds. Therefore, we recommend the use of these compact yet accurate ECP basis sets for electronic structure calculations on molecules involving rhodium atoms. Copyright © 2012 Wiley Periodicals, Inc.

  20. 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

  1. Density functional calculation of intermolecular potentials.

    PubMed

    Nyeland, Carl

    2011-06-30

    Calculations of intermolecular potentials following the density functional theory (DFT) turn out to be very complicated without using some appropriate approximations. Most often the following three approximations have been considered. In one approximation the disturbed charge distributions during collisions are reduced to sums of undisturbed charge distributions from the colliding species. In another approximation, the so-called local density approximation (LDA), one neglects the fact that the intermolecular potentials that depend on charge densities also depend on gradients in the densities. In a third approximation one assumes that the intermolecular potential can be considered as a sum of two terms: a term for the long-range geometry and a term for the short-range geometry. In this Article the three approximations mentioned will be discussed for numerical accuracy for calculations of potentials between inert gas atoms and for calculations of potentials between surfaces and inert gas atoms. In the discussion a few other approximations will be mentioned too.

  2. Calculation of effective dose.

    PubMed

    McCollough, C H; Schueler, B A

    2000-05-01

    The concept of "effective dose" was introduced in 1975 to provide a mechanism for assessing the radiation detriment from partial body irradiations in terms of data derived from whole body irradiations. The effective dose is the mean absorbed dose from a uniform whole-body irradiation that results in the same total radiation detriment as from the nonuniform, partial-body irradiation in question. The effective dose is calculated as the weighted average of the mean absorbed dose to the various body organs and tissues, where the weighting factor is the radiation detriment for a given organ (from a whole-body irradiation) as a fraction of the total radiation detriment. In this review, effective dose equivalent and effective dose, as established by the International Commission on Radiological Protection in 1977 and 1990, respectively, are defined and various methods of calculating these quantities are presented for radionuclides, radiography, fluoroscopy, computed tomography and mammography. In order to calculate either quantity, it is first necessary to estimate the radiation dose to individual organs. One common method of determining organ doses is through Monte Carlo simulations of photon interactions within a simplified mathematical model of the human body. Several groups have performed these calculations and published their results in the form of data tables of organ dose per unit activity or exposure. These data tables are specified according to particular examination parameters, such as radiopharmaceutical, x-ray projection, x-ray beam energy spectra or patient size. Sources of these organ dose conversion coefficients are presented and differences between them are examined. The estimates of effective dose equivalent or effective dose calculated using these data, although not intended to describe the dose to an individual, can be used as a relative measure of stochastic radiation detriment. The calculated values, in units of sievert (or rem), indicate the amount of

  3. 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.

  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. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. First Principles Structure Calculations Using the General Potential Lapw Method

    NASA Astrophysics Data System (ADS)

    Wei, Su-Huai

    We have developed a completely general first principles self-consistent full-potential linearized-augmented-plane -wave (LAPW) method program within the density functional formalism to calculate electronic band structure, total energy, pressure and other quantities. No symmetry assumptions are used for the crystal structure. Shape unrestricted charge densities and potentials are calculated inside muffin -tin (MT) spheres as well as in the interstitial regions. All contributions to the Hamiltonian matrix elements are completely taken into account. The core states are treated fully relativistically using the spherical part of the potential only. Scalar relativistic effects are included for the band-states, and spin-orbit coupling is included using a second variation procedure. Both core states and valence states are treated self-consistently, the frozen core approximation is not required. The fast Fourier transformation method is used wherever it is applicable, and this greatly improves the efficiency. This state-of-the-art program has been tested extensively to check the accuracy and convergence properties by comparing calculated electronic band structures, ground state properties, equations of state and cohesive energies for bulk W and GaAs with other theoretical calculations and experimental results. It has been successfully applied to calculate and predict structural and metal-insulator phase transitions for close-packed crystal BaSe and BaTe and the geometric structure of the d-band metal W(001) surface. The results are in generally good agreement with experiment.

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

    NASA Technical Reports Server (NTRS)

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

    1975-01-01

    Calculational procedure evolved in process of designing inlets. Douglas axisymmetric potential flow program called EOD calculates incompressible potential flow about arbitrary bodies. Program SCIRCL generates input for EOD from inlet components. Program COMBYN takes basic solutions output by EOD and combines them into solutions of interest and applied compressibility correction.

  12. 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.

  13. Spectral element discontinuous Galerkin simulations for wake potential calculations : NEKCEM.

    SciTech Connect

    Min, M.; Fischer, P. F.; Chae, Y.-C.

    2008-01-01

    In this paper we present high-order spectral element discontinuous Galerkin simulations for wake field and wake potential calculations. Numerical discretizations are based on body-conforming hexagonal meshes on Gauss-Lobatto-Legendre grids. We demonstrate wake potential profiles for cylindrically symmetric cavity structures in 3D, including the cases for linear and quadratic transitions between two cross sections. Wake potential calculations are carried out on 2D surfaces for various bunch sizes.

  14. 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

  15. Calculation of relativistic nucleon-nucleon potentials in three dimensions

    NASA Astrophysics Data System (ADS)

    Hadizadeh, M. R.; Radin, M.

    2017-02-01

    In this paper, we have applied a three-dimensional approach for the calculation of the relativistic nucleon-nucleon potential. The quadratic operator relation between the non-relativistic and the relativistic nucleon-nucleon interactions is formulated as a function of relative two-nucleon momentum vectors, which leads to a three-dimensional integral equation. The integral equation is solved by the iteration method, and the matrix elements of the relativistic potential are calculated from non-relativistic ones. The spin-independent Malfliet-Tjon potential is employed in the numerical calculations, and the numerical tests indicate that the two-nucleon observables calculated by the relativistic potential are preserved with high accuracy.

  16. 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.)

  17. 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.)

  18. 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.

  19. A new potential energy surface for H[sub 2]Br and its use to calculate branching ratios and kinetic isotope effects for the H + HBr reaction

    SciTech Connect

    Lynch, G.C.; Truhlar, D.G. ); Brown, F.B.; Zhao, J.G. )

    1995-01-05

    We have carried out multireference configuration interaction calculations with a large basis set for the H[sub 2]Br system at 104 geometries preselected for convenient use in fitting an analytic potential energy surface for the reactions H + HBr [yields] H[sub 2]Br and H + H[prime]Br [yields] H[prime] + HBr. The external part of the correlation energy is scaled (SEC method) to yield a 101 geometry data set which is fitted using the extended London -Eyring-Polanyi-Sato method with bond-distance- and internal-angle-dependent Sato parameters plus a three-center term localized at the colinear H-Br-H saddle point. The unweighted root-mean-square error for 88 points corresponding to collinear and bent H-H-Br geometries and collinear H-Br-H geometries is 0.55 kcal/mol, with larger deviations for bent H-Br-H geometries. Rate constants were calculated by combining the new analytic potential energy surface with improved canonical variational transition state theory and the least-action semiclassical tunneling approximation. For the abstraction reaction, H + HBr [yields] H[sub 2] + Br, and four deuterium and muonium isotopic analogs, agreement with experiment is very good. 87 refs., 11 figs., 30 tabs.

  20. POTENTIAL OF MEAN FORCE CALCULATION FOR THE PROTON AND HYDRIDE TRANSFER REACTIONS CATALYZED BY MEDIUM CHAIN ACYL-COA DEHYDROGENASE: THE EFFECT OF MUTATIONS ON ENZYME CATALYSISa

    PubMed Central

    Bhattacharyya, Sudeep; Ma, Shuhua; Stankovich, Marian T.; Truhlar, Donald G.; Gao, Jiali

    2008-01-01

    Potential of mean force calculations have been performed on the wild-type medium chain acyl-CoA dehydrogenase (MCAD) and two of its mutant forms. Initial simulation and analysis of the active site of the enzyme reveals that an arginine residue (Arg256), conserved in the substrate binding domain of this group of enzymes, exists in two alternate conformations, only one of which makes the enzyme active. This active conformation was used in subsequent computations of the enzymatic reactions. It is known that the catalytic α,β-dehydrogenation of fatty acyl-CoAs consists of two C-H bond dissociation processes: a proton abstraction and a hydride transfer. Energy profiles of the two reaction steps in the wild-type MCAD demonstrate that the reaction proceeds by a stepwise mechanism with a transient species. The activation barriers of the two steps differ by only ∼2 kcal/mol, indicating that both may contribute to the rate-limiting process. Thus this may be a stepwise dissociation mechanism whose relative barriers can be tuned by suitable alterations of the substrate and/or enzyme. Analysis of the structures along the reaction path reveals that Arg256 plays a key role in maintaining the reaction-center hydrogen-bonding network involving the thioester carbonyl group, which stabilizes transition states as well as the intervening transient species. Mutation of this arginine residue to glutamine increases the activation barrier of the hydride transfer reaction by ∼5 kcal/mol, and the present simulations predict a substantial loss of catalytic activity for this mutant. Structural analysis of this mutant reveals that the orientation of the thioester moiety of the substrate has been changed significantly as compared to that in the wild-type enzyme. In contrast, simulation of the active site of the Thr168Ala mutant shows no significant change in the relative orientation of the substrate and the cofactor in the active site; as a result, this mutation has very little effect on

  1. The effects of Co/N dopants on the electronic, redox potential, optical, and photocatalytic water-splitting properties of TiO2: First principles calculations

    NASA Astrophysics Data System (ADS)

    Zhao, Yafei; Wang, Wei; He, Liang

    2017-10-01

    The crystal structure, formation energy, electronic and optical properties of undoped, Co, N doped and co-doped TiO2 were investigated by first principles calculations. Considering the potential of water redox reaction of these systems indicate that only N-, Co-1N- and Co-2N co-doped TiO2 meet the requirement of the photosplitting water. Moreover, the optical absorption threshold and absorption area of Co-2N co-doped TiO2 are obviously enlarged compared with the undoped TiO2. Co-2N co-doped TiO2 has the highest light absorption efficiency and hydrogen production efficiency, due to the presence of curved and broad impurity levels that greatly improve the carriers' mobility and separation.

  2. Effect of interatomic potential on the calculated energy and structure of high-angle coincident site grain boundaries. I. (100) twist boundaries in aluminum

    SciTech Connect

    Wolf, D.

    1984-01-01

    A new computer code is described which permits the investigation of the energy and structure of coincident-site lattice (CSL) grain boundaries in metals. As an improvement over computer programs used by other workers, the full second-derivative (force-constant) matrix associated with a given interatomic potential is applied for the iterative energy minimization. Using this extremely efficient and reliable procedure the effect of the form of the interatomic potential and its truncation radius on the predicted grain-boundary energy and structure is investigated. Six different potentials for aluminum, ranging from a Morse potential to a pseudopotential, are applied to the simulation of the energy and structure (100) CSL twist boundaries with values of ..sigma.., the inverse density of CSL sites, ranging between ..sigma.. = 5 and ..sigma.. = 73. It is found that not only do both the energy and structure of a given boundary vary greatly from one potential to another, but also that the relative energies of different boundaries, i.e. the boundary-energy vs misfit-angle curves, depend on the potential. In contrast to recent claims of Brokman and Balluffi, no cusps in these curves are found for potentials which ignore the charge-density oscillations. The two basic assumptions of the Brokman-Balluffi cusp model are found to be valid only for extremely simple potentials with very short cutoff radii. It is suggested that (1) charge-density oscillations may be important for predicting grain-boundary properties, and (2) no obvious relationship exists between grain-boundary geometry (..sigma..) and the energy. 39 references, 18 figures, 1 table.

  3. Calculating potential fields using microchannel spatial light modulators

    NASA Technical Reports Server (NTRS)

    Reid, Max B.

    1993-01-01

    We describe and present experimental results of the optical calculation of potential field maps suitable for mobile robot navigation. The optical computation employs two write modes of a microchannel spatial light modulator (MSLM). In one mode, written patterns expand spatially, and this characteristic is used to create an extended two dimensional function representing the influence of the goal in a robot's workspace. Distinct obstacle patterns are written in a second, non-expanding, mode. A model of the mechanisms determining MSLM write mode characteristics is developed and used to derive the optical calculation time for full potential field maps. Field calculations at a few hertz are possible with current technology, and calculation time vs. map size scales favorably in comparison to digital electronic computation.

  4. 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.

  5. 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.

  6. Chemical potential calculations in dense liquids using metadynamics

    NASA Astrophysics Data System (ADS)

    Perego, C.; Giberti, F.; Parrinello, M.

    2016-10-01

    The calculation of chemical potential has traditionally been a challenge in atomistic simulations. One of the most used approaches is Widom's insertion method in which the chemical potential is calculated by periodically attempting to insert an extra particle in the system. In dense systems this method fails since the insertion probability is very low. In this paper we show that in a homogeneous fluid the insertion probability can be increased using metadynamics. We test our method on a supercooled high density binary Lennard-Jones fluid. We find that we can obtain efficiently converged results even when Widom's method fails.

  7. Green Function Calculation for Full-potential Multiple Scattering Methods

    NASA Astrophysics Data System (ADS)

    Wang, Yang; Stocks, G. Malcolm; Nicholson, Don

    2001-03-01

    The Green function in the multiple scattering theory of Korringa(J.Korringa, Physica) 13, 392 (1947)., Kohn and Rostoker(W.Kohn and N.Rostoker, Phys. Rev.) 94, 1111 (1954). provides a very convenient approach to the electronic structure calculation for solids. The Green function was originally developed for muffin-tin potentials(J.S. Faulkner and G.M. Stocks, Phys. Rev.) B 21, 3222 (1980)., but can be generalized to the full potential case in which the one-electron potential associated with each atom is of arbitrary geometric shape. In this talk, we present our numerical techniques for Green function calculation in our newly developed full potential multiple scattering method code. We test the calculated Green function against the analytical expression for the case of three dimensional space filling simple analytic potentials. We show how the surface integral technique is used for the calculation of the single site scattering matrices and irregular solutions. We also discuss the L-convergence properties of the Green function.

  8. 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.

  9. Ab initio calculation of the potential bubble nucleus 34Si

    NASA Astrophysics Data System (ADS)

    Duguet, T.; Somà, V.; Lecluse, S.; Barbieri, C.; Navrátil, P.

    2017-03-01

    Background: The possibility that an unconventional depletion (referred to as a "bubble") occurs in the center of the charge density distribution of certain nuclei due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. Based on a mean-field rationale, a correlation between the occurrence of such a semibubble and an anomalously weak splitting between low angular-momentum spin-orbit partners has been further conjectured. Energy density functional and valence-space shell model calculations have been performed to identify and characterize the best candidates, among which 34Si appears as a particularly interesting case. While the experimental determination of the charge density distribution of the unstable 34Si is currently out of reach, (d ,p ) experiments on this nucleus have been performed recently to test the correlation between the presence of a bubble and an anomalously weak 1 /2--3 /2- splitting in the spectrum of 35Si as compared to 37S. Purpose: We study the potential bubble structure of 34Si on the basis of the state-of-the-art ab initio self-consistent Green's function many-body method. Methods: We perform the first ab initio calculations of 34Si and 36S. In addition to binding energies, the first observables of interest are the charge density distribution and the charge root-mean-square radius for which experimental data exist in 36S. The next observable of interest is the low-lying spectroscopy of 35Si and 37S obtained from (d ,p ) experiments along with the spectroscopy of 33Al and 35P obtained from knock-out experiments. The interpretation in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input internucleon interactions. The convergence of the results with respect to the truncation of the many-body expansion, i.e., with respect to

  10. Kinetic Isotope Effects as a Probe for the Protonolysis Mechanism of Alkylmetal Complexes: VTST/MT Calculations Based on DFT Potential Energy Surfaces.

    PubMed

    Mai, Binh Khanh; Kim, Yongho

    2016-10-03

    Protonolysis by platinum or palladium complexes has been extensively studied because it is the microscopic reverse of the C-H bond activation reaction. The protonolysis of (COD)Pt(II)Me2, which exhibits abnormally large kinetic isotope effects (KIEs), is proposed to occur via a concerted pathway (SE2 mechanism) with large tunneling. However, further investigation of KIEs for the protonolysis of ZnMe2 and others led to a conclusion that there is no noticeable correlation between the mechanism and magnitude of KIE. In this study, we demonstrated that variational transition state theory including multidimensional tunneling (VTST/MT) could accurately predict KIEs and Arrhenius parameters of the protonolysis of alkylmetal complexes based on the potential energy surfaces generated by density functional theory. The predicted KIEs, Ea(D) - Ea(H) values, and AH/AD ratios for the protonolysis of (COD)Pt(II)Me2 and Zn(II)Me2 by TFA agreed very well with experimental values. The protonolysis of ZnMe2 with the concerted pathway has a very flat potential energy surface, which produces a very small tunneling effect and therefore a small KIE. The predicted KIE for the stepwise protonolysis (SE(ox) mechanism) of (COD)Pt(II)Me2 was much smaller than that of the concerted pathway, but greater than the KIE of the concerted protonolysis of ZnMe2. A large KIE, which entails a significant tunneling effect, could be used as an experimental probe of the concerted pathway. However, a normal or small KIE should not be used as an indicator of the stepwise mechanism, and the interplay between experiments and reliable theory including tunneling would be essential to uncover the mechanism correctly.

  11. Perturbation theory calculations of model pair potential systems

    SciTech Connect

    Gong, Jianwu

    2016-01-01

    Helmholtz free energy is one of the most important thermodynamic properties for condensed matter systems. It is closely related to other thermodynamic properties such as chemical potential and compressibility. It is also the starting point for studies of interfacial properties and phase coexistence if free energies of different phases can be obtained. In this thesis, we will use an approach based on the Weeks-Chandler-Anderson (WCA) perturbation theory to calculate the free energy of both solid and liquid phases of Lennard-Jones pair potential systems and the free energy of liquid states of Yukawa pair potentials. Our results indicate that the perturbation theory provides an accurate approach to the free energy calculations of liquid and solid phases based upon comparisons with results from molecular dynamics (MD) and Monte Carlo (MC) simulations.

  12. 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

  13. Thermal conductivity calculations of crystalline quartz from the BKS potential

    NASA Astrophysics Data System (ADS)

    Yoon, Young-Gui; Car, Roberto; Srolovitz, David J.; Scandolo, Sandro

    2003-03-01

    We present thermal conductivity calculations from the classical BKS potential[1]. Following a velocity rescaling method for a constant heat flux proposed by P. Jund and R. Jullien[2], thermal conductivity as a heat flux to temperature gradient ratio is directly calculated in periodic simulation cells. Our calculations in a wide temperature range at which crystalline quartz exists are consistent with the experimental trend[3]. The conductivity decreases with temperature in the alpha-quartz regime, and increases after the phase transition to beta-quartz. The temperature dependence is rather small in the beta-quartz regime. [1] B. W. H. van Beest, G. J. Kramer, and R. A. van Santen, Phy. Rev. Lett. 64, 1995 (1990). [2] P. Jund, and R. Jullien, Phy. Rev. B 59, 13707 (1999). [3] H. Kanamori, N. Fujii, and H. Mizutani, J. Geophys. Res. 73, 595 (1968).

  14. Calculating vibrational spectra using modified Shepard interpolated potential energy surfaces.

    PubMed

    Evenhuis, Christian R; Manthe, Uwe

    2008-07-14

    A potential energy interpolation approach based on modified Shepard interpolation and specifically designed for calculation of vibrational states is presented. The importance of the choice of coordinates for the rate of convergence is demonstrated. Studying the vibrational states of the water molecule as a test case, a coordinate system comprised of inverse bond distances and trigonometric functions of the bond angle is found to be particularly efficient. Different sampling schemes used to locate the reference points in the modified Shepard interpolation are investigated. A final scheme is recommended, which allows the construction of potential energy surfaces to sub-wave-number accuracy.

  15. 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.

  16. Calculation of potential flow past airship bodies in yaw

    NASA Technical Reports Server (NTRS)

    Lotz, I

    1932-01-01

    An outline of Von Karman's method of computing the potential flow of airships in yaw by means of partially constant dipolar superposition on the axis of the body is followed by several considerations for beginning and end of the superposition. Then this method is improved by postulating a continuous, in part linearly variable dipolar superposition on the axis. The second main part of the report brings the calculation of the potential flow by means of sources and sinks, arranged on the surface of the airship body. The integral equation which must satisfy this surface superposition is posed, and the core reduced to functions developed from whole elliptical normal integrals. The functions are shown diagrammatically. The integration is resolvable by iteration. The consequence of the method is good. The formulas for computing the velocity on the surface and of the potential for any point conclude the report.

  17. An inversion technique for the calculation of embedding potentials

    NASA Astrophysics Data System (ADS)

    Roncero, O.; de Lara-Castells, M. P.; Villarreal, P.; Flores, F.; Ortega, J.; Paniagua, M.; Aguado, A.

    2008-11-01

    A new embedding method to include local correlation in large systems is proposed. In this method the density of the whole system, calculated via density functional theory approaches, is partitioned in two pieces, one corresponding to the subsystem of interest and the rest to the environment. In the second step, an embedding potential is obtained iteratively using as a driving force the self-repulsion due to the density difference, in a similar form as proposed by Zhao et al. [Phys. Rev. A 50, 2138 (1994)], to obtain the "exact" exchange-correlation functional. Such potential is added to the Fock equation to build the localized molecular orbitals which are further used to include the local electronic correlation in the subsystem of interest. This method is an alternative to the previous DFT-based embedding methods first proposed by Wesolowski and Washell [J. Phys. Chem. 97, 8050 (1993)] and after enhanced by Govind et al. [J. Chem. Phys. 110, 7677 (1999)] and adapted to metal extended systems, which use density functionals to describe the kinetic energy contribution to the embedding potential, whose precise form has been largely treated in the literature and its crucial role is discussed here. The method is applied to hydrogen chains and its van der Waals interaction with H2. The results obtained are in very good agreement with exact calculations performed on the whole system, which demonstrates that the method proposed is a very promising route to introduce correlation in large systems.

  18. 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.

  19. Free energy calculations: an efficient adaptive biasing potential method.

    PubMed

    Dickson, Bradley M; Legoll, Frédéric; Lelièvre, Tony; Stoltz, Gabriel; Fleurat-Lessard, Paul

    2010-05-06

    We develop an efficient sampling and free energy calculation technique within the adaptive biasing potential (ABP) framework. By mollifying the density of states we obtain an approximate free energy and an adaptive bias potential that is computed directly from the population along the coordinates of the free energy. Because of the mollifier, the bias potential is "nonlocal", and its gradient admits a simple analytic expression. A single observation of the reaction coordinate can thus be used to update the approximate free energy at every point within a neighborhood of the observation. This greatly reduces the equilibration time of the adaptive bias potential. This approximation introduces two parameters: strength of mollification and the zero of energy of the bias potential. While we observe that the approximate free energy is a very good estimate of the actual free energy for a large range of mollification strength, we demonstrate that the errors associated with the mollification may be removed via deconvolution. The zero of energy of the bias potential, which is easy to choose, influences the speed of convergence but not the limiting accuracy. This method is simple to apply to free energy or mean force computation in multiple dimensions and does not involve second derivatives of the reaction coordinates, matrix manipulations nor on-the-fly adaptation of parameters. For the alanine dipeptide test case, the new method is found to gain as much as a factor of 10 in efficiency as compared to two basic implementations of the adaptive biasing force methods, and it is shown to be as efficient as well-tempered metadynamics with the postprocess deconvolution giving a clear advantage to the mollified density of states method.

  20. Footprinting molecular electrostatic potential surfaces for calculation of solvation energies.

    PubMed

    Calero, Christian Solis; Farwer, Jochen; Gardiner, Eleanor J; Hunter, Christopher A; Mackey, Mark; Scuderi, Serena; Thompson, Stuart; Vinter, Jeremy G

    2013-11-07

    A liquid is composed of an ensemble of molecules that populate a large number of different states, so calculation of the solvation energy of a molecule in solution requires a method for summing the interactions with the environment over all of these states. The surface site interaction model for the properties of liquids at equilibrium (SSIMPLE) simplifies the surface of a molecule to a discrete number of specific interaction sites (SSIPs). The thermodynamic properties of these interaction sites can be characterised experimentally, for example, through measurement of association constants for the formation of simple complexes that feature a single H-bonding interaction. Correlation of experimentally determined solution phase H-bond parameters with gas phase ab initio calculations of maxima and minima on molecular electrostatic potential surfaces (MEPS) provides a method for converting gas phase calculations on isolated molecules to parameters that can be used to estimate solution phase interaction free energies. This approach has been generalised using a footprinting technique that converts an MEPS into a discrete set of SSIPs (each described by a polar interaction parameter, εi). These SSIPs represent the molecular recognition properties of the entire surface of the molecule. For example, water is described by four SSIPs, two H-bond donor sites and two H-bond acceptor sites. A liquid mixture is described as an ensemble of SSIPs that represent the components of the mixture at appropriate concentrations. Individual SSIPs are assumed to be independent, so speciation of SSIP contacts can be calculated based on properties of the individual SSIP interactions, which are given by the sum of a polar (εiεj) and a non-polar (E(vdW)) interaction term. Results are presented for calculation the free energies of transfer of a range of organic molecules from the pure liquid into water, from the pure liquid into n-hexadecane, from n-hexadecane into water, from n-octanol into

  1. CO dimer: new potential energy surface and rovibrational calculations.

    PubMed

    Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker

    2013-08-15

    The spectrum of CO dimer was investigated by solving the rovibrational Schrödinger equation on a new potential energy surface constructed from coupled-cluster ab initio points. The Schrödinger equation was solved with a Lanczos algorithm. Several 4D (rigid monomer) global ab initio potential energy surfaces (PESs) were made using a previously reported interpolating moving least-squares (IMLS) fitting procedure specialized to describe the interaction of two linear fragments. The potential has two nonpolar minima giving rise to a complicated set of energy level stacks, which are very sensitive to the shapes and relative depths of the two wells. Although the CO dimer has defied previous attempts at an accurate purely ab initio description our best surface yields results in good agreement with experiment. Root-mean-square (rms) fitting errors of less than 0.1 cm(-1) were obtained for each of the fits using 2226 ab initio data at different levels. This allowed direct assessment of the quality of various levels of ab initio theory for prediction of spectra. Our tests indicate that standard CCSD(T) is slow to converge the interaction energy even when sextuple zeta bases as large as ACV6Z are used. The explicitly correlated CCSD(T)-F12b method was found to recover significantly more correlation energy (from singles and doubles) at the CBS limit. Correlation of the core-electrons was found to be important for this system. The best PES was obtained by extrapolation of calculations at the CCSD(T)(AE)-F12b/CVnZ-F12 (n = 3,4) levels. The calculated energy levels were compared to 105 J ≤ 10 levels from experiment. The rms error for 68 levels with J ≤ 6 is only 0.29 cm(-1). The calculated energy levels were assigned stack labels using several tools. New stacks were found. One of them, stack y1, has an energy lower than many previously known stacks and may be observable.

  2. Momentum-space optical potential SND elastic scattering calculations

    NASA Astrophysics Data System (ADS)

    Wolfe, D. H.; Hynes, M. V.; Picklesimer, A.; Tandy, P. C.; Thaler, R. M.

    1983-03-01

    Initial results are presented for proton-nucleus elastic scattering observables calculated with a newly developed microscopic momentum-space code. This is the first phase of a program to treat elastic and inelastic scatterig consistently via an integral equation approach. A number of microscopic features which are often approximated or ignored are quite amenable to exact treatment within this approach, e.g. non-local effectss in elastic scattering, and inelastic effects which are non-linear in the NN t-matrix and target densities but nevertheless confined to one participating nucleon.

  3. 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.

  4. Osmotic potential calculations of inorganic and organic aqueous solutions over wide solute concentration levels and temperatures.

    PubMed

    Cochrane, T T; Cochrane, T A

    2016-01-01

    subsequently used to estimate Nf values at temperatures up to and excess of body temperatures. Those values, together with t values at temperatures up to and in excess of body temperatures recorded in the literature, were substituted in the authors' equation for the provisional calculation of osmotic potentials. The calculations indicated that solution temperatures and solute concentrations have a marked effect on osmotic potentials. Following work to measure the relative densities of aqueous solutions for the calculation of Nf values and the determination of definitive t values up to and beyond bodily temperatures, the authors' equation would enable the accurate estimations of the osmotic potentials of wide concentrations of aqueous solutions of inorganic and organic solutes over the temperature range. The study illustrates that not only solute concentrations but also temperatures have a marked effect on osmotic potentials, an observation of medical and biological significance.

  5. Categorical versus continuous risk factors and the calculation of potential impact fractions.

    PubMed

    Barendregt, Jan J; Veerman, J Lennert

    2010-03-01

    The potential impact fraction is a measure of effect that calculates the proportional change in disease risk after a change in the exposure of a related risk factor. Potential impact fractions are increasingly used to calculate attributable fractions when the lowest exposure is non-zero. Risk-factor exposure can be expressed as a categorical or a continuous variable. For a categorical risk factor, a change in risk-factor exposure can be expressed as a change in the proportion of the population in each category ('proportions shift'). For a continuous risk factor, the change is expressed as a change in its parameters ('distribution shift'). A third method ('RR shift') takes elements of both the categorical and the continuous approach. We compare the three calculation methods using hypothetical data on BMI and an intervention that affects the obese category. The 'proportion shift' calculation produces non-linear artefacts and is best avoided. The 'RR shift' and 'distribution shift' calculation require the estimation of an RR function to describe excess risk, but perform much better. The 'proportion shift' calculation is best avoided. The 'RR shift' and 'distribution shift' calculation produce virtually the same results. For evaluating high-risk strategies, the 'RR shift' calculation is the simplest and therefore preferred. The 'distribution shift' is best suited for evaluating population strategies.

  6. Theoretical calculation of polarizability isotope effects.

    PubMed

    Moncada, Félix; Flores-Moreno, Roberto; Reyes, Andrés

    2017-03-01

    We propose a scheme to estimate hydrogen isotope effects on molecular polarizabilities. This approach combines the any-particle molecular orbital method, in which both electrons and H/D nuclei are described as quantum waves, with the auxiliary density perturbation theory, to calculate analytically the polarizability tensor. We assess the performance of method by calculating the polarizability isotope effect for 20 molecules. A good correlation between theoretical and experimental data is found. Further analysis of the results reveals that the change in the polarizability of a X-H bond upon deuteration decreases as the electronegativity of X increases. Our investigation also reveals that the molecular polarizability isotope effect presents an additive character. Therefore, it can be computed by counting the number of deuterated bonds in the molecule.

  7. Calculation of action potential propagation in nerve fiber.

    PubMed

    Bogatov, N M; Grigoryan, L R; Ponetaeva, E G; Sinisyn, A S

    2014-05-01

    This article introduces generalization of the action potential spreading model which considers generation of the action potential in each segment of the nerve fiber. Behavior of the impulse signal waveform during the propagation process was analyzed. A mechanism of distributed generation of the charge in nerve fiber results in decrease of phase velocity of signal spreading rate. Amplitude of the action potential decreases and pulse width increases in the action potential propagation process. Copyright © 2014 Elsevier Ltd. All rights reserved.

  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. Photoelectron spectroscopy of quinoline derivatives. Correlation of experimental ionization potentials with calculated molecular energies

    NASA Astrophysics Data System (ADS)

    Ahmed, A. A.; Julliard, M.; Chanon, F.; Chanon, M.; Gracian, F.; Pfister-Guillouzo, G.

    1997-03-01

    Experimental ionization potentials of quinoline 1 and substituted quinolines: 6-methylquinoline 2, 2,6-dimethylquinoline 3, 6-methoxyquinoline 4, 3-bromoquinoline 5, 2-chloro-4-methylquinoline 6, 4-hydroxyquinoline 7, 4-hydroxy-2-methylquinoline 8, 2-hydroxy-4-methylquinoline 9, 4-methoxyquinoline 10, 4- methoxy-2-methylquinoline 11, 2-methoxy-4-methylquinoline 12, were measured by photoelectron spectroscopy. Molecular orbital energies of the same derivatives were calculated by the Austin Method 1. The assignments of the bands of the photoelectron spectra were done with the aid of the theoretical calculations and on the basis of the substituent effects. For quinolines 1-6 a good agreement was found between the experimental ionization potentials and the calculated orbital energies.

  10. Osmotic potential calculations of inorganic and organic aqueous solutions over wide solute concentration levels and temperatures

    SciTech Connect

    Cochrane, T. T.; Cochrane, T. A.

    2016-01-15

    } using recorded relative density data at 20 °C. They were subsequently used to estimate N{sub f} values at temperatures up to and excess of body temperatures. Those values, together with t values at temperatures up to and in excess of body temperatures recorded in the literature, were substituted in the authors’ equation for the provisional calculation of osmotic potentials. The calculations indicated that solution temperatures and solute concentrations have a marked effect on osmotic potentials. Conclusions: Following work to measure the relative densities of aqueous solutions for the calculation of N{sub f} values and the determination of definitive t values up to and beyond bodily temperatures, the authors’ equation would enable the accurate estimations of the osmotic potentials of wide concentrations of aqueous solutions of inorganic and organic solutes over the temperature range. The study illustrates that not only solute concentrations but also temperatures have a marked effect on osmotic potentials, an observation of medical and biological significance.

  11. Self-consistent calculations of rare-gas-transition-metal interaction potentials

    NASA Astrophysics Data System (ADS)

    Drakova, D.; Doyen, G.; v. Trentini, F.

    1985-11-01

    A model Hamiltonian is used to calculate potential-energy surfaces for He and Ne on the (110) faces of Ni, Cu, Pd, and Ag. The calculations are nonperturbative, self-consistent, and contain no parameters which are fittable with respect to the gas-solid interaction. Static image-force effects are included. The theory represents the first quantum-mechanical approach to rare-gas-transition-metal potentials which includes the interaction of the rare-gas orbitals with the d electrons in a consistent way. Corrugation is found to be approximately proportional to the d-electron charge density. The sp band is represented by a Sommerfeld model with hybridization gap, which does not contribute to the corrugation. Part of the potential arises through the hybridization of the rare-gas orbitals with the unoccupied metal states. This interference energy is roughly a factor of 2 larger for neon than for helium, leading to larger corrugations of the neon potentials as compared with the helium potentials. This is in agreement with recent experiments, but in contrast to earlier theoretical predictions. The theoretically calculated corrugations and well depths compare reasonably to the experimental data where available. The computed values of corrugation for He increase in the order Ni, Cu, Ag, and Pd. This agrees with experiments where soft potentials have been fitted to the scattering data, although the predicted He/Ni(110) corrugation is overly large by more than a factor of 2. With increasing energy, the He corrugation increases slightly in the calculations. The dependence is nearly constant for Ni and strongest for Pd. For Ne/Ni(110) and Ne/Pd(110) corrugation decreases with energy. Image-force effects are found to be important for the corrugation and softness of the neon potentials.

  12. Quantum scattering calculation for reaction Br + H2 on two potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Quan, Wei-Long; Tang, Ping-Ying; Tang, Bi-Yu

    Three-dimensional time-dependent quantum wave packet calculations have been carried out for Br + H2 on a new global ab initio and a semi-empirical extended London-Eyring-Polanyi-Sato potential energy surface. It is shown that on the ab initio surface, the threshold energy is much lower, and the reaction probabilities, cross sections, and rate constants are much larger. The effects of the initial rovibrational excitation have also been studied. Comparison of rate constants with experimental measurement implies that the ab initio surface is more suitable for quantum dynamic calculation. The possible reasons and mechanism for the dynamical difference on the two PES are analyzed and discussed.

  13. Many-Body Potentials for Aqueous Be(2+) Derived from ab Initio Calculations.

    PubMed

    Winter, Nicolas D

    2016-12-08

    An effective three-body potential for the aqueous Be(2+) ion has been constructed from a large number of high-level ab initio cluster calculations. The new potential was validated in subsequent molecular dynamics simulations of both gas phase ion-water clusters and bulk liquid. The structures of the first and second solvation shells were studied using radial distribution functions and angular distribution functions. The vibrational spectrum of Be(2+) and first shell waters was examined by computing power spectra from the molecular dynamics simulations. The observed bands showed reasonable agreement with experimental spectroscopic frequencies. The potential of mean force for water exchange between the first and second solvation shells was calculated and the energy barrier for exchange was found to have improved agreement with experiment relative to two-body force fields. Examination of the solvation structure near the transition state yielded results consistent with an associative mechanism.

  14. Potential infrared relaxation channels calculated for CO2 clathrate hydrates

    NASA Astrophysics Data System (ADS)

    Lakhlifi, Azzedine; Dahoo, Pierre Richard; Chassefière, Eric

    2017-01-01

    The infrared bar-spectrum of a single carbon dioxide molecule encapsulated in nano-cage clathrate hydrate is determined using the LD (Lakhlifi-Dahoo) extended site inclusion model successfully applied to analyze the spectra of CO2 isotopologues isolated in rare gas matrices. Trapping is energetically more favorable in clathrate structure of type sI than sII. CO2 exhibits hindered orientational motions (librational motions) around its equilibrium configurations in the small and large nano-cages. The orientation transitions are weak, and the spectra are purely vibrational. In the static field inside the cage, the doubly degenerate bending mode ν2 is blue shifted and split. From the scheme of the calculated energy levels for the different degrees of freedom, which is comparable to that of CO2 in rare gas matrices, it is conjectured that infrared excited CO2 will rather relax radiatively. Non-radiative channels can be analyzed by binary collision model.

  15. 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.

  16. Fully Relativistic Calculations on the Potential Energy Surfaces of the Lowest 23 States of Molecular Chlorine

    SciTech Connect

    Luiz Guilherme M. de Macedo; de Jong, Wibe A.

    2008-01-24

    The electronic structure and spectroscopic properties (Re, ωexe, βe, Te ) of the ground state and the 22 lowest excited states of chlorine molecule were studied within a four component relativistic framework using the MOLFDIR program package. The potential energy curves of all possible 23 covalent states were calculated using relativistic complete open shell configuration interaction (COSCI) approach. In addition, four component multi-reference configuration interaction with singles and doubles excitations (MRCISD) calculations were performed in order to infer the effects due to dynamical correlation in vertical excitations. The calculated properties are in good agreement with the available experimental data.

  17. [Hyponatremia: effective treatment based on calculated outcomes].

    PubMed

    Vervoort, G; Wetzels, J F M

    2006-09-30

    A 78-year-old man was treated for symptomatic hyponatremia. Despite administration of an isotonic NaCl 0.9% solution, plasma sodium remained unchanged due to high concentrations of sodium and potassium in the urine. After infusion of a hypertonic NaCl solution, a satisfactory increase in plasma sodium was reached and symptoms resolved gradually. The hyponatremia was found to be caused by hypothyroidism, which was treated. A 70-year-old female was admitted to the hospital with loss of consciousness and hyponatremia. She was treated initially with a hypertonic NaCl 2.5% solution, which resulted in a steady increase in plasma sodium and a resolution of symptoms. Treatment was changed to an isotonic NaCl 0.9% infusion to attenuate the rise of serum sodium. Nevertheless plasma sodium increased too rapidly due to increased diuresis and reduced urinary sodium and potassium excretion. A slower increase in plasma sodium was achieved by administering a glucose 5% infusion. Hyponatremia is frequently observed in hospitalised patients. It should be treated effectively, and the rate of correction should be adapted to the clinical situation. Effective treatment is determined by calculating changes in effective osmoles and the resulting changes in the distribution of water over extra- and intracellular spaces. Changes in urine production and urinary excretion of sodium and potassium should be taken into account.

  18. 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.

  19. Derivation of enhanced potentials for cerium brannerite and the calculation of lattice and intrinsic defect properties

    NASA Astrophysics Data System (ADS)

    Bird, Rebecca A.; Read, Mark S. D.

    2017-02-01

    A new potential has been derived for ceria and used to calculate its lattice and defect properties. The Ce4+ ⋯O2- potential is obtained via a combination of empirical fitting to crystal structural data and parametric fitting to additional physical properties, while the O2- ⋯O2- potential is transferred from earlier publications on UO2 and PuO2 . The overall potential is subsequently verified and validated by calculation of elastic and dielectric constants, whose values agree favourably with those measured experimentally. The potential is then employed to calculate intrinsic defect formation energies and predict the most favourable type of intrinsic disorder.

  20. Neural network approach for the calculation of potential coefficients in quantum mechanics

    NASA Astrophysics Data System (ADS)

    Ossandón, Sebastián; Reyes, Camilo; Cumsille, Patricio; Reyes, Carlos M.

    2017-05-01

    A numerical method based on artificial neural networks is used to solve the inverse Schrödinger equation for a multi-parameter class of potentials. First, the finite element method was used to solve repeatedly the direct problem for different parametrizations of the chosen potential function. Then, using the attainable eigenvalues as a training set of the direct radial basis neural network a map of new eigenvalues was obtained. This relationship was later inverted and refined by training an inverse radial basis neural network, allowing the calculation of the unknown parameters and therefore estimating the potential function. Three numerical examples are presented in order to prove the effectiveness of the method. The results show that the method proposed has the advantage to use less computational resources without a significant accuracy loss.

  1. Calculation of the Helmholtz potential of an elastic strand in an external electric field.

    PubMed

    Khaliullin, Renat N; Schieber, Jay D

    2011-02-14

    We derive from statistical mechanics the Gibbs free energy of an elastic random-walk chain affected by the presence of an external electric field. Intrachain charge interactions are ignored. In addition, we find two approximations of the Helmholtz potential for this system analogous to the gaussian and Cohen-Padé approximations for an elastic strand without the presence of an electric field. Our expressions agree well with exact numerical calculations of the potential in a wide range of conditions. Our analog of the gaussian approximation exhibits distortion of the monomer density due to the presence of the electric field, and our analog of the Cohen-Padé approximation additionally includes finite chain extensibility effects. The Helmholtz potential may be used in modeling the dynamics of electrophoresis experiments.

  2. Calculation of chemical potentials of chain molecules by the incremental gauge cell method.

    PubMed

    Rasmussen, Christopher J; Vishnyakov, Aleksey; Neimark, Alexander V

    2011-12-07

    The gauge cell Monte Carlo method is extended to calculations of the incremental chemical potentials and free energies of linear chain molecules. The method was applied to chains of Lennard-Jones beads with stiff harmonic bonds up to 500 monomers in length. We show that the suggested method quantitatively reproduces the modified Widom particle insertion method of Kumar et al. [S. K. Kumar, I. Szleifer, and A. Z. Panagiotopoulos, Phys. Rev. Lett. 66(22), 2935 (1991)], and is by an order of magnitude more efficient for long chains in terms of the computational time required for the same accuracy of chemical potential calculations. The chain increment ansatz, which suggests that the incremental chemical potential is independent of the chain length, was tested at different temperatures. We confirmed that the ansatz holds only for coils above the θ temperature. Special attention is paid to the effects of the magnitude of adsorption potential and temperature on the behavior of single chains in confinements that are comparable in size with the free chain radius of gyration. At sufficiently low temperatures, the dependence of the incremental chemical potential on the chain length in wetting pores is superficially similar to a capillary condensation isotherm, reflecting monolayer formation following by pore volume filling, as the chain length increases. We find that the incremental gauge cell method is an accurate and efficient technique for calculations of the free energies of chain molecules in bulk systems and nanoconfinements alike. The suggested method may find practical applications, such as modeling polymer partitioning on porous substrates and dynamics of chain translocation into nanopores.

  3. Calculation of chemical potentials of chain molecules by the incremental gauge cell method

    NASA Astrophysics Data System (ADS)

    Rasmussen, Christopher J.; Vishnyakov, Aleksey; Neimark, Alexander V.

    2011-12-01

    The gauge cell Monte Carlo method is extended to calculations of the incremental chemical potentials and free energies of linear chain molecules. The method was applied to chains of Lennard-Jones beads with stiff harmonic bonds up to 500 monomers in length. We show that the suggested method quantitatively reproduces the modified Widom particle insertion method of Kumar et al. [S. K. Kumar, I. Szleifer, and A. Z. Panagiotopoulos, Phys. Rev. Lett. 66(22), 2935 (1991)], 10.1103/PhysRevLett.66.2935, and is by an order of magnitude more efficient for long chains in terms of the computational time required for the same accuracy of chemical potential calculations. The chain increment ansatz, which suggests that the incremental chemical potential is independent of the chain length, was tested at different temperatures. We confirmed that the ansatz holds only for coils above the θ temperature. Special attention is paid to the effects of the magnitude of adsorption potential and temperature on the behavior of single chains in confinements that are comparable in size with the free chain radius of gyration. At sufficiently low temperatures, the dependence of the incremental chemical potential on the chain length in wetting pores is superficially similar to a capillary condensation isotherm, reflecting monolayer formation following by pore volume filling, as the chain length increases. We find that the incremental gauge cell method is an accurate and efficient technique for calculations of the free energies of chain molecules in bulk systems and nanoconfinements alike. The suggested method may find practical applications, such as modeling polymer partitioning on porous substrates and dynamics of chain translocation into nanopores.

  4. 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.

  5. Accurate calculation of second virial coefficient of the Exp-6 potential and its application

    NASA Astrophysics Data System (ADS)

    Mamedov, B. A.; Somuncu, E.

    2015-02-01

    In this study, a new approach to calculate the second virial coefficient of the Exp-6 potential is proposed. Over a wide temperature range, the calculated results of the second virial coefficient determined from Exp-6 potential are comparable with the calculations of second virial coefficient over Lennard-Jones (12-6) potential. As an example of application, the formulas obtained for second virial coefficient are calculated for molecules Kr,Xe,N2,Hg,CH4 and C2H6. The obtained results are in good agreement with the data available in the literature.

  6. 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.

  7. Comparison of repulsive interatomic potentials calculated with an all-electron DFT approach with experimental data

    NASA Astrophysics Data System (ADS)

    Zinoviev, A. N.; Nordlund, K.

    2017-09-01

    The interatomic potential determines the nuclear stopping power in materials. Most ion irradiation simulation models are based on the universal Ziegler-Biersack-Littmark (ZBL) potential (Ziegler et al., 1983), which, however, is an average and hence may not describe the stopping of all ion-material combinations well. Here we consider pair-specific interatomic potentials determined experimentally and by density-functional theory simulations with DMol approach (DMol software, 1997) to choose basic wave functions. The interatomic potentials calculated using the DMol approach demonstrate an unexpectedly good agreement with experimental data. Differences are mainly observed for heavy atom systems, which suggests they can be improved by extending a basis set and more accurately considering the relativistic effects. Experimental data prove that the approach of determining interatomic potentials from quasielastic scattering can be successfully used for modeling collision cascades in ion-solids collisions. The data obtained clearly indicate that the use of any universal potential is limited to internuclear distances R < 7 af (af is the Firsov length).

  8. Influence of the intramolecular potential of adsorbed hydrogen on frequency shift calculations

    NASA Astrophysics Data System (ADS)

    Larin, Alexander V.

    1995-01-01

    The influence of the choice of the intramolecular potential on the resulting frequency shift of the fundamental vibrational transition in the dihydrogen molecule adsorbed on zeolite NaA is estimated. It is shown that an improved Morse potential and the potential calculated by Kołtsos and Wolniewicz lead to the same frequency shift value. Application of the Buckingham method for the frequency shift calculation to this case is discussed.

  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. Nudged elastic band calculation of the binding potential for liquids at interfaces.

    PubMed

    Buller, Oleg; Tewes, Walter; Archer, Andrew J; Heuer, Andreas; Thiele, Uwe; Gurevich, Svetlana V

    2017-07-14

    The wetting behavior of a liquid on solid substrates is governed by the nature of the effective interaction between the liquid-gas and the solid-liquid interfaces, which is described by the binding or wetting potential g(h) which is an excess free energy per unit area that depends on the liquid film height h. Given a microscopic theory for the liquid, to determine g(h), one must calculate the free energy for liquid films of any given value of h, i.e., one needs to create and analyze out-of-equilibrium states, since at equilibrium there is a unique value of h, specified by the temperature and chemical potential of the surrounding gas. Here we introduce a Nudged Elastic Band (NEB) approach to calculate g(h) and illustrate the method by applying it in conjunction with a microscopic lattice density functional theory for the liquid. We also show that the NEB results are identical to those obtained with an established method based on using a fictitious additional potential to stabilize the non-equilibrium states. The advantages of the NEB approach are discussed.

  11. Nudged elastic band calculation of the binding potential for liquids at interfaces

    NASA Astrophysics Data System (ADS)

    Buller, Oleg; Tewes, Walter; Archer, Andrew J.; Heuer, Andreas; Thiele, Uwe; Gurevich, Svetlana V.

    2017-07-01

    The wetting behavior of a liquid on solid substrates is governed by the nature of the effective interaction between the liquid-gas and the solid-liquid interfaces, which is described by the binding or wetting potential g(h) which is an excess free energy per unit area that depends on the liquid film height h. Given a microscopic theory for the liquid, to determine g(h), one must calculate the free energy for liquid films of any given value of h, i.e., one needs to create and analyze out-of-equilibrium states, since at equilibrium there is a unique value of h, specified by the temperature and chemical potential of the surrounding gas. Here we introduce a Nudged Elastic Band (NEB) approach to calculate g(h) and illustrate the method by applying it in conjunction with a microscopic lattice density functional theory for the liquid. We also show that the NEB results are identical to those obtained with an established method based on using a fictitious additional potential to stabilize the non-equilibrium states. The advantages of the NEB approach are discussed.

  12. 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.

  13. 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…

  14. Calculation of smooth potential energy surfaces using local electron correlation methods

    NASA Astrophysics Data System (ADS)

    Mata, Ricardo A.; Werner, Hans-Joachim

    2006-11-01

    The geometry dependence of excitation domains in local correlation methods can lead to noncontinuous potential energy surfaces. We propose a simple domain merging procedure which eliminates this problem in many situations. The method is applied to heterolytic bond dissociations of ketene and propadienone, to SN2 reactions of Cl- with alkylchlorides, and in a quantum mechanical/molecular mechanical study of the chorismate mutase enzyme. It is demonstrated that smooth potentials are obtained in all cases. Furthermore, basis set superposition error effects are reduced in local calculations, and it is found that this leads to better basis set convergence when computing barrier heights or weak interactions. When the electronic structure strongly changes between reactants or products and the transition state, the domain merging procedure leads to a balanced description of all structures and accurate barrier heights.

  15. Calculation of smooth potential energy surfaces using local electron correlation methods

    SciTech Connect

    Mata, Ricardo A.; Werner, Hans-Joachim

    2006-11-14

    The geometry dependence of excitation domains in local correlation methods can lead to noncontinuous potential energy surfaces. We propose a simple domain merging procedure which eliminates this problem in many situations. The method is applied to heterolytic bond dissociations of ketene and propadienone, to SN2 reactions of Cl{sup -} with alkylchlorides, and in a quantum mechanical/molecular mechanical study of the chorismate mutase enzyme. It is demonstrated that smooth potentials are obtained in all cases. Furthermore, basis set superposition error effects are reduced in local calculations, and it is found that this leads to better basis set convergence when computing barrier heights or weak interactions. When the electronic structure strongly changes between reactants or products and the transition state, the domain merging procedure leads to a balanced description of all structures and accurate barrier heights.

  16. An accurate potential energy curve for helium based on ab initio calculations

    NASA Astrophysics Data System (ADS)

    Janzen, A. R.; Aziz, R. A.

    1997-07-01

    Korona, Williams, Bukowski, Jeziorski, and Szalewicz [J. Chem. Phys. 106, 1 (1997)] constructed a completely ab initio potential for He2 by fitting their calculations using infinite order symmetry adapted perturbation theory at intermediate range, existing Green's function Monte Carlo calculations at short range and accurate dispersion coefficients at long range to a modified Tang-Toennies potential form. The potential with retardation added to the dipole-dipole dispersion is found to predict accurately a large set of microscopic and macroscopic experimental data. The potential with a significantly larger well depth than other recent potentials is judged to be the most accurate characterization of the helium interaction yet proposed.

  17. Tunable redox potential of nonmetal doped monolayer MoS2: First principle calculations

    NASA Astrophysics Data System (ADS)

    Lu, S.; Li, C.; Zhao, Y. F.; Gong, Y. Y.; Niu, L. Y.; Liu, X. J.

    2016-10-01

    Doping is an effective method to alter the electronic behavior of materials by forming new chemical bonds and bringing bond relaxation. With this aid of first principle calculations, the crystal configuration and electronic properties of monolayer MoS2 have been modulated by the nonmetal (NM) dopants (H, B, C, N, O, F, Si, P, Cl, As, Se, Br, Te and I), and the thermodynamic stability depending on the preparation conditions (Mo-rich and S-rich conditions) were discussed. Results shown that, the NM dopants substituted preferentially for S under Mo-rich condition, the electronic distribution around the dopants and the nearby Mo atoms are changed by the new formed Mo-NM bonds and bands relaxation. Compared to pristine monolayer MoS2, the NM ions with odd chemical valences enhance the oxidation potential and reduce the reduction potential of specimens, but the NM ions with even chemical valences have the opposite effects on the redox potentials. Compared to the NM ions with even chemical valences, the lone pair electrons in NM ions with odd chemical valences can extra interact with the Mo ions and reduces the ECBM and EVBM values of specimens. It offers a simple way to design various monolayer MoS2 based catalysts in order to catalyze different materials by chose the reasonable dopants for stronger oxidation or reduction potential.

  18. 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.

  19. 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 of...

  20. 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 of...

  1. 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...

  2. 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.

  3. CASSCF/CI calculations of low-lying states and potential energy surfaces of Au3

    NASA Astrophysics Data System (ADS)

    Balasubramanian, K.; Liao, M. Z.

    1987-05-01

    Complete active space MCSCF (CASSCF) and second-order configuration interaction (SOCI) calculations of low-lying electronic states [2B2,2A1] of Au3 as well as the 1Σ+g state of Au2 are carried out. The bending potential energy surfaces of 2A1 and 2B2 states are also presented. A barrier is found in the potential energy surface of the 2A1 state in moving from the linear to bent structure. Two nearly-degenerate structures are found for the ground state. The 2Σ+u state arising from the linear structure with an Au-Au bond length of 2.66 Å is only 3.2 kcal/mol below the 2A1 bent state. The equilibrium geometry of the 2A1 state is an isosceles triangle with an apex angle of 54°. The Au3 cluster is found to be more stable than the gold dimer. The effect of d correlation is studied on Au2 by carrying out MRSDCI (multireference singles and doubles CI) calculations on the 1Σ+g state of Au2 which include excitations from the d orbitals.

  4. Algorithms of the Potential Field Calculation in a Three-Dimensional Box

    NASA Astrophysics Data System (ADS)

    Rudenko, G. V.; Anfinogentov, S. A.

    2017-08-01

    The potential field inside a three-dimensional box with the normal magnetic field component given on all boundaries needs to be calculated to estimate important quantities related to the magnetic field, such as free energy and relative helicity. In this work we present an analysis of three methods for calculating the potential field inside a three-dimensional box. The accuracy and performance of the methods are tested on artificial models with a priori known solutions.

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

    DOE PAGES

    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.

  6. Accurate effective pair potentials for polymer solutions

    NASA Astrophysics Data System (ADS)

    Bolhuis, P. G.; Louis, A. A.; Hansen, J. P.; Meijer, E. J.

    2001-03-01

    Dilute or semidilute solutions of nonintersecting self-avoiding walk (SAW) polymer chains are mapped onto a fluid of "soft" particles interacting via an effective pair potential between their centers of mass. This mapping is achieved by inverting the pair distribution function of the centers of mass of the original polymer chains, using integral equation techniques from the theory of simple fluids. The resulting effective pair potential is finite at all distances, has a range of the order of the radius of gyration, and turns out to be only moderately concentration-dependent. The dependence of the effective potential on polymer length is analyzed in an effort to extract the scaling limit. The effective potential is used to derive the osmotic equation of state, which is compared to simulation data for the full SAW segment model, and to the predictions of renormalization group calculations. A similar inversion procedure is used to derive an effective wall-polymer potential from the center of mass density profiles near the wall, obtained from simulations of the full polymer segment model. The resulting wall-polymer potential turns out to depend strongly on bulk polymer concentration when polymer-polymer correlations are taken into account, leading to a considerable enhancement of the effective repulsion with increasing concentration. The effective polymer-polymer and wall-polymer potentials are combined to calculate the depletion interaction induced by SAW polymers between two walls. The calculated depletion interaction agrees well with the "exact" results from much more computer-intensive direct simulation of the full polymer-segment model, and clearly illustrates the inadequacy—in the semidilute regime—of the standard Asakura-Oosawa approximation based on the assumption of noninteracting polymer coils.

  7. 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.

  8. Investigation of segregation of silver at copper grain boundaries by first principles and empirical potential calculations

    NASA Astrophysics Data System (ADS)

    Kiyohara, Shin; Mizoguchi, Teruyasu

    2016-08-01

    Segregation of silver at copper grain boundaries was investigated using theoretical calculations. Empirical potentials for copper-silver alloys were generated to systematically investigate the segregation. The segregation energies of the [001]-axis symmetric tilt Σ5 (210) and Σ25 (430) grain boundaries were calculated, and the most stable segregation sites for silver at these copper grain boundaries were determined. The generated empirical potential was validated by comparing it with that obtained from the first principles calculation. The segregation of silver at copper grain boundaries strongly depends on the open space at the segregation site.

  9. Polarizable interaction potential for water from coupled cluster calculations. I. Analysis of dimer potential energy surface

    NASA Astrophysics Data System (ADS)

    Bukowski, Robert; Szalewicz, Krzysztof; Groenenboom, Gerrit C.; van der Avoird, Ad

    2008-03-01

    A six-dimensional interaction potential for the water dimer has been fitted to ab initio interaction energies computed at 2510 dimer configurations. These energies were obtained by combining the supermolecular second-order energies extrapolated to the complete basis set limit from up to quadruple-zeta quality basis sets with the contribution from the coupled-cluster method including single, double, and noniterative triple excitations computed in a triple-zeta quality basis set. All basis sets were augmented by diffuse functions and supplemented by midbond functions. The energies have been fitted using an analytic form with the induction component represented by a polarizable term, making the potential directly transferable to clusters and the bulk phase. Geometries and energies of stationary points on the potential surface agree well with the results of high-level ab initio geometry optimizations.

  10. CAS SCF/CI calculations of potential energy surfaces of He 3+ and He 2+

    NASA Astrophysics Data System (ADS)

    Balasubramanian, K.; Liao, M. Z.; Lin, S. H.

    1987-12-01

    Complete active space MC SCF (CAS SCF) calculations followed by second-order configuration interaction (SOCI) calculations are carried out on the potential energy surfaces (bending surface, linear surfaces) of the 2Σ g+ ground state of He 3+. The potential minimum for the 2Σ g+ state occurs at a linear geometry with HeHe bond length of 1.248 Å. The binding energy of He 3+ with respect to He + He + + He was calculated to be 2.47 eV at the SOCI level. The energy required to dissociate He 3+ ( 2Σ g+) into He 2+ ( 2Σ u+) and He( 1S) is calculated to be 0.14 eV. The same level of SOCI calculations of He 2+ yield a De value of 2.36 eV.

  11. Analysis of the quasi-static approximation for calculating potentials generated by neural stimulation.

    PubMed

    Bossetti, Chad A; Birdno, Merrill J; Grill, Warren M

    2008-03-01

    In models of electrical stimulation of the nervous system, the electric potential is typically calculated using the quasi-static approximation. The quasi-static approximation allows Maxwell's equations to be simplified by ignoring capacitive, inductive and wave propagation contributions to the potential. While this simplification has been validated for bioelectric sources, its application to rapid stimulation pulses, which contain more high-frequency power, may not be appropriate. We compared the potentials calculated using the quasi-static approximation with those calculated from the exact solution to the inhomogeneous Helmholtz equation. The mean absolute errors between the two potential calculations were limited to 5-13% for pulse widths commonly used for neural stimulation (25 micros-1 ms). We also quantified the excitation properties of extracellular point source stimulation of a myelinated nerve fiber model using potentials calculated from each method. Deviations between the strength-duration curves for potentials calculated using the quasi-static (sigma = 0.105 S m(-1)) and Helmholtz approaches ranged from 3 to 16%, with the minimal error occurring for 100 micros pulses. Differences in the threshold-distance curves for the two calculations ranged from 0 to 9%, for the same value of quasi-static conductivity. A sensitivity analysis of the material parameters revealed that the potential was much more strongly dependent on the conductivity than on the permittivity. These results indicate that for commonly used stimulus pulse parameters, the exact solution for the potential can be approximated by quasi-static simplifications only for appropriate values of conductivity.

  12. 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... Potential Electric Output Capacity The potential electrical output capacity is calculated from the maximum... boiler with a maximum design heat input capacity of 340 million Btu/hr. (2) One-third of the...

  13. 40 CFR Appendix D to Part 72 - Calculation of Potential Electric Output Capacity

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Output Capacity D Appendix D to Part 72 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Potential Electric Output Capacity The potential electrical output capacity is calculated from the maximum... boiler with a maximum design heat input capacity of 340 million Btu/hr. (2) One-third of the...

  14. Electronic structure calculations for alloys using the polymorphous coherent potential approximation

    NASA Astrophysics Data System (ADS)

    Pella, Silvia

    The Polymorphous Coherent Approximation (PCPA) plays the central role in this study. The PCPA represents an extension of the Coherent Potential Approximation (CPA) in the sense that it treats an alloy model in which all of the atoms are allowed to have distinct charges and potentials. It makes use of the supercells that contain hundreds of atoms. The Madelung potentials at all sites are calculated exactly. The present calculations demonstrate the advantages of the PCPA over the CPA in explaining experiments that depend critically on the charge transfer in an alloy.

  15. Accurate calculation of absolute one-electron redox potentials of some para-quinone derivatives in acetonitrile.

    PubMed

    Namazian, Mansoor; Coote, Michelle L

    2007-08-02

    Standard ab initio molecular orbital theory and density functional theory calculations have been used to calculate absolute one-electron reduction potentials of several para-quinones in acetonitrile. The high-level composite method of G3(MP2)-RAD is used for the gas-phase calculations and a continuum model of solvation, CPCM, has been employed to calculate solvation energies. To compare the theoretical reduction potentials with experiment, the reduction potentials relative to a standard calomel electrode (SCE) have also been calculated and compared to experimental values. The average error of the calculated reduction potentials using the proposed method is 0.07 V without any additional approximation. An ONIOM method in which the core is studied at G3(MP2)-RAD and the substituent effect of the rest of the molecule is studied at R(O)MP2/6-311+G(3df,2p) provides an accurate low-cost alternative to G3(MP2)-RAD for larger molecules.

  16. New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations.

    PubMed

    Gapsys, Vytautas; Seeliger, Daniel; de Groot, Bert L

    2012-07-10

    The fields of rational drug design and protein engineering benefit from accurate free energy calculations based on molecular dynamics simulations. A thermodynamic integration scheme is often used to calculate changes in the free energy of a system by integrating the change of the system's Hamiltonian with respect to a coupling parameter. These methods exploit nonphysical pathways over thermodynamic cycles involving particle introduction and annihilation. Such alchemical transitions require the modification of the classical nonbonded potential energy terms by applying soft-core potential functions to avoid singularity points. In this work, we propose a novel formulation for a soft-core potential to be applied in nonequilibrium free energy calculations that alleviates singularities, numerical instabilities, and additional minima in the potential energy for all combinations of nonbonded interactions at all intermediate alchemical states. The method was validated by application to (a) the free energy calculations of a closed thermodynamic cycle, (b) the mutation influence on protein thermostability, (c) calculations of small ligand solvation free energies, and (d) the estimation of binding free energies of trypsin inhibitors. The results show that the novel soft-core function provides a robust and accurate general purpose solution to alchemical free energy calculations.

  17. Characteristic potential method of noise calculation in semiconductor devices: calculation of 1/f noise in MOS transistors in the ohmic region

    NASA Astrophysics Data System (ADS)

    Hong, Sung-min; Kim, Yong-Seok; Min, Hong S.; Park, Young June

    2003-05-01

    The characteristic potential method(CPM), which has been successfully applied to calculate 1/f noise and thermal noise of multi-terminal homogeneous semiconductor resistors, is extended to calculate 1/f noise in inhomogeneous devices such as MOSFETs. The drain 1/f noise current of MOSFETs in the linear region is calculated using the CPM together with the well-known existing 1/f noise sources based on either Hooge's empirical model or McWhorter's model, and the calculated results are compared with the experimental results. It is shown that the difference of the 1/f noise behaviour between n-MOSFETs and p-MOSFETs in the linear region can be attributed to either the difference in their effective field dependence between the local electron mobility and the local hole mobility near the Si-SiO2 interface in the inversion layer or the difference in degree of Nt(oxide trap density)dependence between the effective electron mobility and the effective hole mobility.

  18. The strategy for numerical solving of PIES without explicit calculation of singular integrals in 2D potential problems

    NASA Astrophysics Data System (ADS)

    Szerszeń, Krzysztof; Zieniuk, Eugeniusz

    2016-06-01

    The paper presents a strategy for numerical solving of parametric integral equation system (PIES) for 2D potential problems without explicit calculation of singular integrals. The values of these integrals will be expressed indirectly in terms of easy to compute non-singular integrals. The effectiveness of the proposed strategy is investigated with the example of potential problem modeled by the Laplace equation. The strategy simplifies the structure of the program with good the accuracy of the obtained solutions.

  19. Calculation of electrical potentials on the surface of a realistic head model by finite differences.

    PubMed

    Lemieux, L; McBride, A; Hand, J W

    1996-07-01

    We present a method for the calculation of electrical potentials at the surface of realistic head models from a point dipole generator based on a 3D finite-difference algorithm. The model was validated by comparing calculated values with those obtained algebraically for a three-shell spherical model. For a 1.25 mm cubic grid size, the mean error was 4.9% for a superficial dipole (3.75 mm from the inner surface of the skull) pointing in the radial direction. The effect of generator discretization and node spacing on the accuracy of the model was studied. Three values of the node spacing were considered: 1, 1.25 and 1.5 mm. The mean relative errors were 4.2, 6.3 and 9.3% respectively. The quality of the approximation of a point dipole by an array of nodes in a spherical neighbourhood did not depend significantly on the number of nodes used. The application of the method to a conduction model derived from MRI data is demonstrated.

  20. 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.

  1. 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.

  2. 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...

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

    SciTech Connect

    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.

  4. Calculated viscous and scale effects on transonic aeroelasticity

    NASA Technical Reports Server (NTRS)

    Edwards, John W.

    1998-01-01

    A viscous-inviscid interactive coupling method is used for the computation of unsteady transonic flows. A lagextrainment integral boundary layer method is used with a transonic small disturbance potential code to compute the transonic aeroelastic response for two wing flutter models. By varying the modeled length scale, viscous effects may be studied as the Reynolds number per reference chordlength varies. Appropriate variation of modeled frequencies and generalized masses then allows comparison of responses for varying scales or Reynolds number. Two wing planforms are studied: one a four percent thick swept wing and the other a typical business jet wing. Calculations for both wings show limit cycle oscillations at transonic speeds in the vicinity of minimum flutter speed indices.

  5. 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.

  6. Calculations of partial cross sections for photofragmentation processes using complex absorbing potentials

    SciTech Connect

    Grozdanov, T.P.; Andric, L.; McCarroll, R.

    2006-03-07

    We investigate the use of complex absorbing potentials for the calculation of partial cross sections in multichannel photofragmentation processes. An exactly solvable, coupled-two-channel problem involving square-well potentials is used to compare the performance of various types of absorbing potentials. Special emphasis is given to the near-threshold regions and the conditions under which the numerical results are able to reproduce the Wigner threshold laws. It was found that singular, transmission-free absorbing potentials perform better than those of power or polynomial form.

  7. Potential of pin-by-pin SPN calculations as an industrial reference

    SciTech Connect

    Fliscounakis, M.; Girardi, E.; Courau, T.; Couyras, D.

    2012-07-01

    This paper aims at analysing the potential of pin-by-pin SP{sub n} calculations to compute the neutronic flux in PWR cores as an alternative to the diffusion approximation. As far as pin-by-pin calculations are concerned, a SPH equivalence is used to preserve the reactions rates. The use of SPH equivalence is a common practice in core diffusion calculations. In this paper, a methodology to generalize the equivalence procedure in the SP{sub n} equations context is presented. In order to verify and validate the equivalence procedure, SP{sub n} calculations are compared to 2D transport reference results obtained with the APOLL02 code. The validation cases consist in 3x3 analytical assembly color sets involving burn-up heterogeneities, UOX/MOX interfaces, and control rods. Considering various energy discretizations (up to 26 groups) and flux development orders (up to 7) for the SP{sub n} equations, results show that 26-group SP{sub 3} calculations are very close to the transport reference (with pin production rates discrepancies < 1%). This proves the high interest of pin-by-pin SP{sub n} calculations as an industrial reference when relying on 26 energy groups combined with SP{sub 3} flux development order. Additionally, the SP{sub n} results are compared to diffusion pin-by-pin calculations, in order to evaluate the potential benefit of using a SP{sub n} solver as an alternative to diffusion. Discrepancies on pin-production rates are less than 1.6% for 6-group SP{sub 3} calculations against 3.2% for 2-group diffusion calculations. This shows that SP{sub n} solvers may be considered as an alternative to multigroup diffusion. (authors)

  8. Relativistic (Dirac equation) effects in microscopic elastic scattering calculations

    NASA Astrophysics Data System (ADS)

    Hynes, M. V.; Picklesimer, A.; Tandy, P. C.; Thaler, R. M.

    1985-04-01

    A simple relativistic extension of the first-order multiple scattering mechanism for the optical potential is employed within the context of a Dirac equation description of elastic nucleon-nucleus scattering. A formulation of this problem in terms of a momentum-space integral equation displaying an identifiable nonrelativistic sector is described and applied. Extensive calculations are presented for proton scattering from 40Ca and 16O at energies between 100 and 500 MeV. Effects arising from the relativistic description of the propagation of the projectile are isolated and are shown to be responsible for most of the departures from typical nonrelativistic (Schrödinger) results. Off-shell and nonlocal effects are included and these, together with uncertainties in the nuclear densities, are shown not to compromise the characteristic improvement of forward angle spin observable predictions provided by the relativistic approach. The sensitivity to ambiguities in the Lorentz scalar and vector composition of the optical potential is displayed and discussed.

  9. 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.

  10. On the accuracy of calculating the exchange part of the real heavy ion potential

    NASA Astrophysics Data System (ADS)

    Ismail, M.; Osman, M. M.; Salah, F.

    1996-02-01

    In the present work, we test the validity of replacing the non-diagonal density matrix appearing in the exchange part of the nucleus-nucleus optical potential by an approximation based on the density matrix expansion used frequently in the nuclear structure calculations. We have found that for the recently derived BDM3Y nucleon-nucleon force the DME may produce a maximum error more than 20% in the nucleus-nucleus potential.

  11. Accuracy of calculating the exchange part of the real alpha-nucleus potential

    NASA Astrophysics Data System (ADS)

    Ismail, M.; Salah, F.; Osman, M. M.

    1996-12-01

    In the present work, we test the validity of replacing the nondiagonal matrix ρ(r-->,r-->') appearing in the exchange part of the α-nucleus optical potential by an approximation based on the density matrix expansion (DME) used frequently in nuclear structure calculations. We have found that for the recently derived BDM3Y nucleon-nucleon force the DME may produce a maximum error more than 29% in the α-nucleus potential.

  12. 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.

  13. Effective one-electron approaches to calculate high harmonic generation

    NASA Astrophysics Data System (ADS)

    Rohringer, Nina; Santra, Robin

    2006-05-01

    The single-active electron approach (SAE) is frequently applied to calculate high harmonic generation in atoms and consists in solving a one-particle Schr"odinger equation in an appropriate model potential. As an ad hoc approach it is difficult to be systematically improved. Starting with the time-dependent configuration interaction singles (TDCIS) technique we derive a new class of effective one-electron approaches. The resulting one-electron equations are in general non-local and non-unitary. A local approximation to TDCIS can be derived by restricting the total many-body Hamiltonian to a local mean-field Hamiltonian (those usually used in SAE calculations). The resulting equations are similar to traditional SAE approaches but include an additional term which destroys the unitarity of the time-evolution. We show that this correction term is essential and improves on traditional SAE approaches. Numerical tests show that this improved SAE method gives dipole-moments in better agreement with exact results than time-dependent Hartree Fock. The test system is a one-dimensional model of helium which allows for a straightforward numerical solution and therefore provides a benchmark to assess the quality of the different approximations.

  14. 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

  15. 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.

  16. The Calculation of Potential Energy Curves of Diatomic Molecules: The RKR Method.

    ERIC Educational Resources Information Center

    Castano, F.; And Others

    1983-01-01

    The RKR method for determining accurate potential energy curves is described. Advantages of using the method (compared to Morse procedure) and a TRS-80 computer program which calculates the classical turning points by an RKR method are also described. The computer program is available from the author upon request. (Author/JN)

  17. 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.

  18. 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.

  19. The Calculation of Potential Energy Curves of Diatomic Molecules: The RKR Method.

    ERIC Educational Resources Information Center

    Castano, F.; And Others

    1983-01-01

    The RKR method for determining accurate potential energy curves is described. Advantages of using the method (compared to Morse procedure) and a TRS-80 computer program which calculates the classical turning points by an RKR method are also described. The computer program is available from the author upon request. (Author/JN)

  20. 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.

  1. 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.

  2. Improved Boundary Element Methods for Poisson-Boltzmann Electrostatic Potential and Force Calculations.

    PubMed

    Lu, Benzhuo; McCammon, J Andrew

    2007-05-01

    A patch representation differing from the traditional treatments in the boundary element method (BEM) is presented, which we call the constant "node patch" method. Its application to solving the Poisson-Boltzmann equation (PBE) demonstrates considerable improvement in speed compared with the constant element and linear element methods. In addition, for the node-based BEMs, we propose an efficient interpolation method for the calculation of the electrostatic stress tensor and PB force on the solvated molecular surface. This force calculation is simply an O(N) algorithm (N is the number of elements). Moreover, our calculations also show that the geometric factor correction in the boundary integral equations significantly increases the accuracy of the potential solution on the boundary, and thereby the PB force calculation.

  3. Nonperturbative calculation of the London-van der Waals interaction potential

    NASA Astrophysics Data System (ADS)

    Berman, P. R.; Ford, G. W.; Milonni, P. W.

    2014-02-01

    The so-called remarkable formula [G. W. Ford, J. T. Lewis, and R. F. O'Connell, Phys. Rev. Lett. 55, 2273 (1985), 10.1103/PhysRevLett.55.2273] for the Helmholtz free energy is applied to the problem of determining the interaction potential to all orders in the coupling strength of a pair of oscillator dipoles interacting through the familiar dipole-dipole interaction of electrodynamics. Simple, straightforward calculations lead to expressions for (1) the London short-range potential, (2) the Casimir-Polder long-range potential, and (3) the potential at high temperature. Explicit results are shown for both the temperature dependence of the interaction potential and its deviation from the weak-coupling limit. It is stressed that the interaction potential is a change in free energy, not the energy; in particular, in the high temperature case, the change of energy is zero.

  4. 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.

  5. 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…

  6. 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.

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

    PubMed

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

    2015-07-07

    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. Gaussian effective potential: Quantum mechanics

    NASA Astrophysics Data System (ADS)

    Stevenson, P. M.

    1984-10-01

    We advertise the virtues of the Gaussian effective potential (GEP) as a guide to the behavior of quantum field theories. Much superior to the usual one-loop effective potential, the GEP is a natural extension of intuitive notions familiar from quantum mechanics. A variety of quantum-mechanical examples are studied here, with an eye to field-theoretic analogies. Quantum restoration of symmetry, dynamical mass generation, and "quantum-mechanical resuscitation" are among the phenomena discussed. We suggest how the GEP could become the basis of a systematic approximation procedure. A companion paper will deal with scalar field theory.

  9. Quantum calculations of vibrational energies of H3O2- on an ab initio potential.

    PubMed

    Huang, Xinchuan; Braams, Bastiaan J; Carter, Stuart; Bowman, Joel M

    2004-04-28

    We report a full-dimensional potential energy surface for H3O2-, based on fitting 66,965 ab initio electronic energies. A major feature of this potential is a barrier of roughly 200 cm-1 to internal rotation of the two hydroxyl groups about a line connecting the two oxygen atoms and the bridging hydrogen atom. The potential is used in calculations of vibrational energies, performed with the "Reaction Path" version of the code "MULTIMODE". The results are compared to recent infrared messenger experiments and are used to propose interpretations of the experimental results.

  10. Aqueous Hydricity from Calculations of Reduction Potential and Acidity in Water.

    PubMed

    Brereton, Kelsey R; Bellows, Sarina M; Fallah, Hengameh; Lopez, Antonio A; Adams, Robert M; Miller, Alexander J M; Jones, William D; Cundari, Thomas R

    2016-12-22

    Hydricity, or hydride donating ability, is a thermodynamic value that helps define the reactivity of transition metal hydrides. To avoid some of the challenges of experimental hydricity measurements in water, a computational method for the determination of aqueous hydricity values has been developed. With a thermochemical cycle involving deprotonation of the metal hydride (pKa), 2e(-) oxidation of the metal (E°), and 2e(-) reduction of the proton, hydricity values are provided along with other valuable thermodynamic information. The impact of empirical corrections (for example, calibrating reduction potentials with 2e(-) organic versus 1e(-) inorganic potentials) was assessed in the calculation of the reduction potentials, acidities, and hydricities of a series of iridium hydride complexes. Calculated hydricities are consistent with electronic trends and agree well with experimental values.

  11. 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

  12. 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.

  13. Defect Properties in GaN: Ab Initio and Empirical Potential Calculations

    SciTech Connect

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

    2005-01-03

    The defect properties and atomic configurations in GaN have been comparatively investigated using density functional theory (DFT) and molecular dynamics method with two representative potentials. The DFT calculations show that the relaxation of vacancies is generally small, but the relaxation around antisite defects is large. The N interstitials, starting from any possible configurations, 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 Ga+-Ga<11-20 > split interstitial can bridge the gap between non-bounded Ga atoms. 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.

  14. Ab initio calculation of anion proton affinity and ionization potential for energetic ionic liquids.

    PubMed

    Carlin, Caleb; Gordon, Mark S

    2015-04-05

    Developing a better understanding of the bulk properties of ionic liquids requires accurate measurements of the underlying molecular properties that help to determine the bulk behavior. Two computational methods are used in this work: second-order perturbation theory (MP2) and completely renormalized coupled cluster theory [CR-CC(2,3)], to calculate the proton affinity and ionization potential of a set of anions that are of interest for use in protic, energetic ionic liquids. Compared with experimental values, both methods predict similarly accurate proton affinities, but CR-CC(2,3) predicts significantly more accurate ionization potentials. It is concluded that more time intensive methods like CR-CC(2,3) are required in calculations involving open shell states like the ionization potential.

  15. 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.

  16. Transformation of potential energy surfaces for estimating isotopic shifts in anharmonic vibrational frequency calculations

    SciTech Connect

    Meier, Patrick; Oschetzki, Dominik; Rauhut, Guntram; Berger, Robert

    2014-05-14

    A transformation of potential energy surfaces (PES) being represented by multi-mode expansions is introduced, which allows for the calculation of anharmonic vibrational spectra of any isotopologue from a single PES. This simplifies the analysis of infrared spectra due to significant CPU-time savings. An investigation of remaining deviations due to truncations and the so-called multi-level approximation is provided. The importance of vibrational-rotational couplings for small molecules is discussed in detail. In addition, an analysis is proposed, which provides information about the quality of the transformation prior to its execution. Benchmark calculations are provided for a set of small molecules.

  17. Volume 1: Calculating potential to emit releases and doses for FEMP's and NOCs

    SciTech Connect

    HILL, J.S.

    1999-07-27

    The purpose of this document is to provide Hanford Site facilities a handbook for estimating potential emissions and the subsequent offsite doses. General guidelines and information are provided to assist personnel in estimating emissions for use with U.S. Department of Energy (DOE) facility effluent monitoring plans (FEMPs) and regulatory notices of construction (NOCs), per 40 Code of Federal Regulations (CFR) Part 61, Subpart H, and Washington Administrative Code (WAC) Chapter 246-247 requirements. This document replaces Unit Dose Calculation Methods and Summary of Facility Effluent Monitoring Plan Determinations (WHC-EP-0498). Meteorological data from 1983 through 1996, 13-year data set, was used to develop the unit dose factors provided by this document, with the exception of two meteorological stations. Meteorological stations 23 and 24, located at Gable Mountain and the 100-F Area, only have data from 1986 through 1996, 10-year data set. The scope of this document includes the following: Estimating emissions and resulting effective dose equivalents (EDE) to a facility's nearest offsite receptor (NOR) for use with NOCs under 40 CFR Part 61, Subpart H, requirements Estimating emissions and resulting EDEs to a facility's or emission unit's NOR for use with NOCs under the WAC Chapter 246-247 requirements Estimating emissions and resulting EDEs to a facility's or emission unit's NOR for use with FEMPs and FEMP determinations under DOE Orders 5400.1 and 5400.5 requirements.

  18. Effective boson number calculations in Mo and Cd isotopes

    NASA Astrophysics Data System (ADS)

    Cata, G.; Bucurescu, D.; Cutoiu, D.; Ivaşcu, M.; Zamfir, N. V.

    1990-09-01

    The effects of the neutron-proton interaction on the low-lying levels of Mo and Cd isotopes have been considered in the frame of the IBA-1 model by taking into account an effective boson number ( N eff). Both an empirical procedure based on previous IBA-2 mixing calculations and the N p N n scheme provide comparable N eff values. Level spectra and electromagnetic transitions are investigated. The results support the idea that IBA-1 calculations with a suitable N eff can largely simulate IBA-2 mixing calculations, taking advantage of simplicity and a smaller number of parameters.

  19. 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).

  20. 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.

  1. 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.

  2. 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.

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

    PubMed

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

    NASA Astrophysics Data System (ADS)

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

    2015-11-01

    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 IP3 through IP6.

  5. 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}.

  6. Quantum Monte Carlo calculations with chiral effective field theory interactions.

    PubMed

    Gezerlis, A; Tews, I; Epelbaum, E; Gandolfi, S; Hebeler, K; Nogga, A; Schwenk, A

    2013-07-19

    We present the first quantum Monte Carlo (QMC) calculations with chiral effective field theory (EFT) interactions. To achieve this, we remove all sources of nonlocality, which hamper the inclusion in QMC calculations, in nuclear forces to next-to-next-to-leading order. We perform auxiliary-field diffusion Monte Carlo (AFDMC) calculations for the neutron matter energy up to saturation density based on local leading-order, next-to-leading order, and next-to-next-to-leading order nucleon-nucleon interactions. Our results exhibit a systematic order-by-order convergence in chiral EFT and provide nonperturbative benchmarks with theoretical uncertainties. For the softer interactions, perturbative calculations are in excellent agreement with the AFDMC results. This work paves the way for QMC calculations with systematic chiral EFT interactions for nuclei and nuclear matter, for testing the perturbativeness of different orders, and allows for matching to lattice QCD results by varying the pion mass.

  7. Effect size calculations for the clinician: methods and comparability.

    PubMed

    Seidel, Jason A; Miller, Scott D; Chow, Daryl L

    2014-01-01

    The measurement of clinical change via single-group pre-post effect size has become increasingly common in psychotherapy settings that collect practice-based evidence and engage in feedback-informed treatment. Different methods of calculating effect size for the same sample of clients and the same measure can lead to wide-ranging results, reducing interpretability. Effect sizes from therapists-including those drawn from a large web-based database of practicing clinicians-were calculated using nine different methods. The resulting effect sizes varied significantly depending on the method employed. Differences between measurement methods routinely exceeded 0.40 for individual therapists. Three methods for calculating effect sizes are recommended for moderating these differences, including two equations that show promise as valid and practical methods for use by clinicians in professional practice.

  8. The significance of rolling friction and nuclear potentials in classical trajectory calculations

    NASA Astrophysics Data System (ADS)

    Bangert, D.; Freiesleben, H.

    1980-05-01

    The influence of various conservative nuclear potentials (proximity, modified proximity, and Woods-Saxon potential) on the properties of damped reactions and heavy-ion induced fusion have been studied for a light and a heavy system by means of trajectory calculations. The equations of motion are numerically solved taking into account friction against rolling, whose strength is treated as free parameter to demonstrate its importance for the dynamics of the reaction. It is found that the amount of dissipated angular momentum as well as the fusion cross section sensitively depends on this friction term, which should not be neglected, in particular for asymmetric systems.

  9. 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.

  10. Native Defect Properties in Beta-SiC: Ab Initio and Empirical Potential Calculations

    SciTech Connect

    Gao, Fei; Bylaska, Eric J.; Weber, William J.; Corrales, Louis R.

    2001-06-25

    There is considerable ambiguity about the formation of native defects and their clusters in SiC, since different empirical potential gives different results, particular related to the stability of interstitial configurations. Ab intio pseudopotential methods are used to study the formation and properties of native defects in beta-SiC. The results are compared with those calculated by molecular dynamics (MD) using a Tersoff potential, where the various cut-off distances found in the literature are employed. The formation energy of vacancies and antisite defects obtained by ab initio calculations are in good agreement with those given by the Tersoff potential, regardless of the cut-off distances, but there is a disparity for interstitials between the two methods, depending on the cut-off distances used in the Tersoff potential. The present results, however, provide guidelines for evaluating the quality and fit of empirical potentials for large-scale simulations of irradiation damage (displacement cascades) and point defect migration (recombination or annealing) in SiC.

  11. 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.

  12. 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)

  13. A terrain-dependent reference atmosphere determination method for available potential energy calculations

    NASA Technical Reports Server (NTRS)

    Koehler, T. L.

    1986-01-01

    An iterative technique that determines the reference atmosphere which incorporates the effects of uneven surface topography is presented. This method has been successfully applied in several available potential energy studies. An alternative method due to Taylor is also evaluated. While Taylor presented excellent continuous formulations of the available potential energy that include topography, his method for determining the reference atmosphere distributions failed to provide the accuracy needed to produce reliable available potential energy estimates. Since topography has a significant influence on the general circulation, it is important to employ techniques that incorporate its effects in the determination of available potential energy.

  14. Radial nodalization effects on BWR (boiling water reactor) stability calculations

    SciTech Connect

    March-Leuba, J.

    1990-01-01

    Computer simulations have shown that stability calculations in boiling water reactors (BWRs) are very sensitive to a number of input parameters and modeling assumptions. In particular, the number of thermohydraulic regions (i.e., channels) used in the calculation can affect the results of decay ratio calculations by as much as 30%. This paper presents the background theory behind the observed effects of radial nodalization in BWR stability calculations. The theory of how a radial power distribution can be simulated in time or frequency domain codes by using representative'' regions is developed. The approximations involved in this method of solution are reviewed, and some examples of the effect of radial nodalization are presented based on LAPUR code solutions. 2 refs., 4 figs., 2 tabs.

  15. 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.

  16. Short range effective potentials for ionic fluids

    NASA Astrophysics Data System (ADS)

    Clarke, J. H. R.; Smith, W.; Woodcock, L. V.

    1986-02-01

    It is shown that the structure of a simple ionic liquid, potassium chloride, can be reproduced in computer simulations using short range effective pair (SHREP) potentials of a simple form. Aside from the balance between like and unlike particle interactions, the important parameters determining the structure are the depth ɛ and the position r0 of the unlike particle pair energy minimum. The results demonstrate that the long range ordering characteristic of ionic liquids is not a consequence of the long range of Coulomb interactions. It is further shown that first order perturbation theory can be used accurately to calculate the thermodynamic properties of an ionic liquid from a corresponding reference liquid generated using a SHREP potential. These results can be generalized to explain deviations from the Reiss-Mayer-Katz corresponding states law for alkali halides and suggest an alternative scheme, effective depth reduction (EDR), based on values of ɛ for the gas phase ion pairs.

  17. 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

  18. 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.

  19. 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.

  20. Spin-orbit configuration interaction calculation of the potential energy curves of iodine oxide

    SciTech Connect

    Roszak, S.; Krauss, M.; Alekseyev, A.B.; Liebermann, H.P.; Buenker, R.J.

    2000-04-06

    An ab initio configuration interaction (CI) study including spin-orbit coupling is carried out for the ground and excited states of the IO radical by employing relativistic effective core potentials. The computed spectroscopic constants are in good agreement with available experimental data, with some tendency to underestimate the strength of bonding. The first excited state, a{sup 4}{Sigma}{sup {minus}}, which has not yet been observed experimentally, is predicted to be bound by 30.1 kJ/mol and to have a significantly larger equilibrium distance than the ground state. It is split by spin-orbit interaction into 1/2 and 3/2 components, with the 1/2 component being the lower one with a calculated spin-orbit splitting of 210 cm{sup {minus}1}. The most interesting state in the low-energy IO spectrum, A{sub 1}{sup 2}{Pi}{sub 3/2}, is shown to be predissociated due to interaction with a number of repulsive electronic states. Predissociation of the A{sup 1}, {nu}{prime} = 0, 1 vibrational levels is attributed to a fairly weak spin-orbit coupling with the {sup 2}{Delta}{sub 3/2} state, while rotationally dependent predissociation of the {nu}{prime} = 2 level is explained by the coupling with the 1/2(III) state having mainly {sup 2}{Sigma}{sup {minus}} character. Strong predissociation of the {nu}{prime} {ge} 4 levels is attributed to interaction with the higher-lying {Omega} = 3/2 states, with predominantly {sup 4}{Sigma}{sup +} and {sup 4}{Delta} origin.

  1. Selected new developments in vibrational structure theory: potential construction and vibrational wave function calculations.

    PubMed

    Christiansen, Ove

    2012-05-21

    This perspective addresses selected recent developments in the theoretical calculation of vibrational spectra, energies, wave functions and properties. The theoretical foundation and recently developed computational protocols for constructing hierarchies of vibrational Hamiltonian operators are reviewed. A many-mode second quantization (SQ) formulation is discussed prior to the discussion of anharmonic wave functions. Emphasis is put on vibrational self-consistent field (VSCF) based methods and in particular vibrational coupled cluster (VCC) theory. Other issues are also reviewed briefly, such as inclusion of thermal effects, response theoretical calculation of spectra, and the difficulty in treating dense spectra.

  2. Calculation of Inductive Electric Fields in Pulsed Coaxial Devices Using Electric Vector Potentials

    DTIC Science & Technology

    2001-06-01

    formalism applies. The calculation tool we use to obtain the solution for both the vector potential and inductive electric field is FlexPDE �, a generalized...5.736917e-18 23:02:44 6/11/01 FlexPDE 2.20e Z 0. 0.2 0.4 0.6 0.8 1. R 0. 0.2 0.4 0.6 0.8 ab cd e f gh i j k lm n o p qr s t t Electric Vector Potential...Electric Vector Potential Evp004: Grid#7 p2 Nodes=3200 Cells=1525 RMS Err= 2.e-6 Vol_Integral= -1.352900e-17 23:02:44 6/11/01 FlexPDE 2.20e Z 0. 0.2

  3. Dissociative electron transfer in polychlorinated aromatics. Reduction potentials from convolution analysis and quantum chemical calculations.

    PubMed

    Romańczyk, Piotr P; Rotko, Grzegorz; Kurek, Stefan S

    2016-08-10

    Formal potentials of the first reduction leading to dechlorination in dimethylformamide were obtained from convolution analysis of voltammetric data and confirmed by quantum chemical calculations for a series of polychlorinated benzenes: hexachlorobenzene (-2.02 V vs. Fc(+)/Fc), pentachloroanisole (-2.14 V), and 2,4-dichlorophenoxy- and 2,4,5-trichlorophenoxyacetic acids (-2.35 V and -2.34 V, respectively). The key parameters required to calculate the reduction potential, electron affinity and/or C-Cl bond dissociation energy, were computed at both DFT-D and CCSD(T)-F12 levels. Comparison of the obtained gas-phase energies and redox potentials with experiment enabled us to verify the relative energetics and the performance of various implicit solvent models. Good agreement with the experiment was achieved for redox potentials computed at the DFT-D level, but only for the stepwise mechanism owing to the error compensation. For the concerted electron transfer/C-Cl bond cleavage process, the application of a high level coupled cluster method is required. Quantum chemical calculations have also demonstrated the significant role of the π*ring and σ*C-Cl orbital mixing. It brings about the stabilisation of the non-planar, C2v-symmetric C6Cl6˙(-) radical anion, explains the experimentally observed low energy barrier and the transfer coefficient close to 0.5 for C6Cl5OCH3 in an electron transfer process followed by immediate C-Cl bond cleavage in solution, and an increase in the probability of dechlorination of di- and trichlorophenoxyacetic acids due to substantial population of the vibrational excited states corresponding to the out-of-plane C-Cl bending at ambient temperatures.

  4. 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.

  5. Age difference in numeral recognition and calculation: an event-related potential study.

    PubMed

    Xuan, Dong; Wang, Suhong; Yang, Yilin; Meng, Ping; Xu, Feng; Yang, Wen; Sheng, Wei; Yang, Yuxia

    2007-01-01

    In this study, we investigated the age difference in numeral recognition and calculation in one group of school-aged children (n = 38) and one of undergraduate students (n = 26) using the event-related potential (ERP) methods. Consistent with previous reports, the age difference was significant in behavioral results. Both numeral recognition and calculation elicited a negativity peaking at about 170-280 ms (N2) and a positivity peaking at 200-470 ms (pSW) in raw ERPs, and a difference potential (dN3) between 360 and 450 ms. The difference between the two age groups indicated that more attention resources were devoted to arithmetical tasks in school-aged children, and that school-aged children and undergraduate students appear to use different strategies to solve arithmetical problems. The analysis of frontal negativity suggested that numeral recognition and mental calculation impose greater load on working memory and executive function in schoolchildren than in undergraduate students. The topography data determined that the parietal regions were responsible for arithmetical function in humans, and there was an age-related difference in the area of cerebral activation.

  6. 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.

  7. Comparison of methods used to calculate typical threshold values for potentially toxic elements in soil.

    PubMed

    McIlwaine, Rebekka; Cox, Siobhan F; Doherty, Rory; Palmer, Sherry; Ofterdinger, Ulrich; McKinley, Jennifer M

    2014-10-01

    The environmental quality of land can be assessed by calculating relevant threshold values, which differentiate between concentrations of elements resulting from geogenic and diffuse anthropogenic sources and concentrations generated by point sources of elements. A simple process allowing the calculation of these typical threshold values (TTVs) was applied across a region of highly complex geology (Northern Ireland) to six elements of interest; arsenic, chromium, copper, lead, nickel and vanadium. Three methods for identifying domains (areas where a readily identifiable factor can be shown to control the concentration of an element) were used: k-means cluster analysis, boxplots and empirical cumulative distribution functions (ECDF). The ECDF method was most efficient at determining areas of both elevated and reduced concentrations and was used to identify domains in this investigation. Two statistical methods for calculating normal background concentrations (NBCs) and upper limits of geochemical baseline variation (ULBLs), currently used in conjunction with legislative regimes in the UK and Finland respectively, were applied within each domain. The NBC methodology was constructed to run within a specific legislative framework, and its use on this soil geochemical data set was influenced by the presence of skewed distributions and outliers. In contrast, the ULBL methodology was found to calculate more appropriate TTVs that were generally more conservative than the NBCs. TTVs indicate what a "typical" concentration of an element would be within a defined geographical area and should be considered alongside the risk that each of the elements pose in these areas to determine potential risk to receptors.

  8. 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.

  9. The calculated ionization potential and electron affinity of cationic cyanine dyes.

    PubMed

    Delgado, Juan C; Ishikawa, Yasuyuki; Selsby, Ronald G

    2009-01-01

    The ionization potential (IP) and electron affinity (EA) of the isolated single dye molecule and a hypothetical isolated J-aggregated dimer are calculated as an energy difference between separately minimized ground and ionized states. Three quantum methods are employed: density functional theory (DFT) Gaussian03 B3LYP/6-311G** (++G**); DFT using Dmol(3); and a modification of CNDO/S, called CNDO/S-Deltazeta, which is developed for rapid calculation of the IP and EA. Results indicate that for the monomer, 1,1'-dimethyl-2,2'carbocyanine chloride, the vertical IP and EA are 6.2 +/- 0.1 and 1.90 +/- 0.05 eV, respectively. This is consistent with the threshold IP and EA predicted by the Yianoulis and Nelson "Statistical Model" of spectral sensitization. For the isolated J-aggregated dimer, whose configuration is consistent with being adsorbed on a dielectric substrate, the calculations predict a value of 5.2 +/- 0.2 and 2.35 +/- 0.05 eV for the IP and EA, respectively. Significant charge density is removed from the halide anion in the ionization process. The HOMO of the dye molecule is an MO associated with the halide anion. Calculation of the isolated entities is a necessary preliminary step in the study of the IP and EA of the adsorbed dye monomer and aggregate.

  10. 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.

  11. Uncertainties in Properties Calculated from Fitted Potential Functions and Determining Potential Functions from FITS to Bound to Continuum Intensity Data

    NASA Astrophysics Data System (ADS)

    Le Roy, Robert J.

    2013-06-01

    In recent years it has become increasingly common to analyse spectroscopic data by using ``direct potential fits" of simulated data generated from analytic potential energy functions to experiment to optimize the parameters defining that potential energy function. This has the advantages of circumventing use of the semiclassical approximations associated with traditional methodologies, and of directly yielding a closed-form expression that is the most compact and comprehensive way to summarize what we know about a molecule. A question which then arises is: What are the uncertainties in properties computed using this potential? It turns out that this question is very closely related to the question of how to apply this simulation/fitting method efficiently to the analysis of bound to continuum intensity data. Both depend upon being able to answer the question: What are the partial derivatives of a wavefunction with respect to the parameters defining the potential energy function from which it is generated? It will be shown that such partial derivatives may be obtained readily as the `particular' solutions of linear inhomogeneous differential equations of a type that is routinely solved in another context for calculating the centrifugal distortion constants of diatomic molecules. Applications of this technique have been incorporated into the publicly available bound-state data analysis and simulation program DPotFit and the distributed bound to continuum simulation/fitting program BCONT. J.M. Hutson, J. Phys. B (At. Mol. Phys) {14}, 851 (1981). J. Tellinghuisen, J. Mol. Spectrosc. {122}, 455 (1987). See http://leroy.uwaterloo.ca/programs/

  12. 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.

  13. Approximate first-principles anharmonic calculations of polyatomic spectra using MP2 and B3LYP potentials: comparisons with experiment.

    PubMed

    Roy, Tapta Kanchan; Carrington, Tucker; Gerber, R Benny

    2014-08-21

    Anharmonic vibrational spectroscopy calculations using MP2 and B3LYP computed potential surfaces are carried out for a series of molecules, and frequencies and intensities are compared with those from experiment. The vibrational self-consistent field with second-order perturbation correction (VSCF-PT2) is used in computing the spectra. The test calculations have been performed for the molecules HNO3, C2H4, C2H4O, H2SO4, CH3COOH, glycine, and alanine. Both MP2 and B3LYP give results in good accord with experimental frequencies, though, on the whole, MP2 gives very slightly better agreement. A statistical analysis of deviations in frequencies from experiment is carried out that gives interesting insights. The most probable percentage deviation from experimental frequencies is about -2% (to the red of the experiment) for B3LYP and +2% (to the blue of the experiment) for MP2. There is a higher probability for relatively large percentage deviations when B3LYP is used. The calculated intensities are also found to be in good accord with experiment, but the percentage deviations are much larger than those for frequencies. The results show that both MP2 and B3LYP potentials, used in VSCF-PT2 calculations, account well for anharmonic effects in the spectroscopy of molecules of the types considered.

  14. 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.

  15. 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.

  16. Accelerating equilibrium isotope effect calculations. I. Stochastic thermodynamic integration with respect to mass

    NASA Astrophysics Data System (ADS)

    Karandashev, Konstantin; Vaníček, Jiří

    2017-05-01

    Accurate path integral Monte Carlo or molecular dynamics calculations of isotope effects have until recently been expensive because of the necessity to reduce three types of errors present in such calculations: statistical errors due to sampling, path integral discretization errors, and thermodynamic integration errors. While the statistical errors can be reduced with virial estimators and path integral discretization errors with high-order factorization of the Boltzmann operator, here we propose a method for accelerating isotope effect calculations by eliminating the integration error. We show that the integration error can be removed entirely by changing particle masses stochastically during the calculation and by using a piecewise linear umbrella biasing potential. Moreover, we demonstrate numerically that this approach does not increase the statistical error. The resulting acceleration of isotope effect calculations is demonstrated on a model harmonic system and on deuterated species of methane.

  17. The critical role of logarithmic transformation in Nernstian equilibrium potential calculations.

    PubMed

    Sawyer, Jemima E R; Hennebry, James E; Revill, Alexander; Brown, Angus M

    2017-06-01

    The membrane potential, arising from uneven distribution of ions across cell membranes containing selectively permeable ion channels, is of fundamental importance to cell signaling. The necessity of maintaining the membrane potential may be appreciated by expressing Ohm's law as current = voltage/resistance and recognizing that no current flows when voltage = 0, i.e., transmembrane voltage gradients, created by uneven transmembrane ion concentrations, are an absolute requirement for the generation of currents that precipitate the action and synaptic potentials that consume >80% of the brain's energy budget and underlie the electrical activity that defines brain function. The concept of the equilibrium potential is vital to understanding the origins of the membrane potential. The equilibrium potential defines a potential at which there is no net transmembrane ion flux, where the work created by the concentration gradient is balanced by the transmembrane voltage difference, and derives from a relationship describing the work done by the diffusion of ions down a concentration gradient. The Nernst equation predicts the equilibrium potential and, as such, is fundamental to understanding the interplay between transmembrane ion concentrations and equilibrium potentials. Logarithmic transformation of the ratio of internal and external ion concentrations lies at the heart of the Nernst equation, but most undergraduate neuroscience students have little understanding of the logarithmic function. To compound this, no current undergraduate neuroscience textbooks describe the effect of logarithmic transformation in appreciable detail, leaving the majority of students with little insight into how ion concentrations determine, or how ion perturbations alter, the membrane potential.

  18. Calculation of Potential Energy Surfaces for HCO and HNO Using Many-Body Methods.

    DTIC Science & Technology

    1986-06-01

    Additional copies of this report may be obtained from the National Technical Information Service, U. S. Department of Commerce , Springfield...ACCESSION N~ -C iCP ET TALG ME Technical Report BRL-TR-2737 )VA 6 C TITLE ’and Sttifl) e TYPE OF REPORT & PERIOD COVERED Final CALCULATION OF POTENTIAL...Report) 13 S’JPPMENTAR, NCTES *U1niversity of Connecticut Storrs, CT ’Q KEY WOR$ ), .’Cun’inue un over** side if rf. . e . r’ and identify 5, block nurmber

  19. Quantum dynamics studies of gas-surface reactions and use of complex absorbing potentials in wave-packet calculations

    NASA Astrophysics Data System (ADS)

    Ge, Jiuyuan

    1999-11-01

    In this thesis, quantum dynamics studies are conducted on gas-surface reactions and complex absorbing potentials. Through a three-dimensional model, dissociation probabilities for O2 on both (110) and (100) surfaces of copper are calculated for ground state as well as rovibrationally excited oxygen molecules. Specifically, the reason for the difference in calculated dissociation probabilities of oxygen on two surfaces is explained. Then the thermal effect of the surface on the dissociation probability is studied by a one dimensional fluctuating barrier. It is observed that the quantum mechanical tunneling probability exhibits a maximum as a function of the oscillating frequency between the low and the high frequency limits. The physical origin and process underlying this resonantlike phenomenon are proposed. In the second part of this thesis, the complex absorbing potential (CAP) is introduced and studied. Exact numerical calculation shows that use of optimized CAP significantly improves the efficiency of wavefunction absorption over that of negative imaginary potential (NIP) in scattering applications. The CAP is optimized by an efficient time-dependent propagation approach. Application to the prototype inelastic scattering of He + H2 demonstrates the accuracy and efficiency of the channel-dependent CAP for extracting state-to-state scattering information.

  20. Calculations of the quasi-geostrophic potential vorticity gradient from climatological data

    NASA Technical Reports Server (NTRS)

    Fullmer, J. W. A.

    1982-01-01

    Climatological data (5-year sets) are used in calculating the quasi-geostrophic potential vorticity meridional gradient between 10 and 1000 mb for latitudes from 25 to 65 deg N in the months of January, April, July, and October. The data comprise zonal and one-month averaged values of the zonal velocity and temperature and represent seasonal transitions and extremes. It is noted that previous papers have shown that zeros of the meridional gradient are important in determining the stability properties of the atmosphere. It is shown that the profiles of the meridional gradient generated from the climatological data possess zero in all seasons and at many latitudes and levels. In all seasons, therefore, the atmosphere is shown to have a wide variety of potential sources of baroclinic instability.

  1. 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.

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

    DOE PAGES

    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

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

    SciTech Connect

    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 and 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.

  4. Mie potentials for phase equilibria calculations: application to alkanes and perfluoroalkanes.

    PubMed

    Potoff, Jeffrey J; Bernard-Brunel, Damien A

    2009-11-05

    Transferable united-atom force fields, based on n - 6 Lennard-Jones potentials, are presented for normal alkanes and perfluorocarbons. It is shown that by varying the repulsive exponent the range of the potential can be altered, leading to improved predictions of vapor pressures while also reproducing saturated liquid densities to high accuracy. Histogram-reweighting Monte Carlo simulations in the grand canonical ensemble are used to determine the vapor liquid coexistence curves, vapor pressures, heats of vaporization, and critical points for normal alkanes methane through tetradecane, and perfluorocarbons perfluoromethane through perfluorooctane. For all molecules studied, saturated liquid densities are reproduced to within 1% of experiment. Vapor pressures for normal alkanes and perfluorocarbons were predicted to within 3% and 6% of experiment, respectively. Calculations performed for binary mixture vapor-liquid equilibria for propane + pentane show excellent agreement with experiment, while slight deviations are observed for the ethane + perfluoroethane mixture.

  5. Effective source approach to self-force calculations

    NASA Astrophysics Data System (ADS)

    Vega, Ian; Wardell, Barry; Diener, Peter

    2011-07-01

    Numerical evaluation of the self-force on a point particle is made difficult by the use of delta functions as sources. Recent methods for self-force calculations avoid delta functions altogether, using instead a finite and extended 'effective source' for a point particle. We provide a review of the general principles underlying this strategy, using the specific example of a scalar point charge moving in a black hole spacetime. We also report on two new developments: (i) the construction and evaluation of an effective source for a scalar charge moving along a generic orbit of an arbitrary spacetime, and (ii) the successful implementation of hyperboloidal slicing that significantly improves on previous treatments of boundary conditions used for effective-source-based self-force calculations. Finally, we identify some of the key issues related to the effective source approach that will need to be addressed by future work.

  6. A simulation method for the calculation of chemical potentials in small, inhomogeneous, and dense systems.

    PubMed

    Neimark, Alexander V; Vishnyakov, Aleksey

    2005-06-15

    We present a modification of the gauge cell Monte Carlo simulation method [A. V. Neimark and A. Vishnyakov, Phys. Rev. E 62, 4611 (2000)] designed for chemical potential calculations in small confined inhomogeneous systems. To measure the chemical potential, the system under study is set in chemical equilibrium with the gauge cell, which represents a finite volume reservoir of ideal particles. The system and the gauge cell are immersed into the thermal bath of a given temperature. The size of the gauge cell controls the level of density fluctuations in the system. The chemical potential is rigorously calculated from the equilibrium distribution of particles between the system cell and the gauge cell and does not depend on the gauge cell size. This scheme, which we call a mesoscopic canonical ensemble, bridges the gap between the canonical and the grand canonical ensembles, which are known to be inconsistent for small systems. The ideal gas gauge cell method is illustrated with Monte Carlo simulations of Lennard-Jones fluid confined to spherical pores of different sizes. Special attention is paid to the case of extreme confinement of several molecular diameters in cross section where the inconsistency between the canonical ensemble and the grand canonical ensemble is most pronounced. For sufficiently large systems, the chemical potential can be reliably determined from the mean density in the gauge cell as it was implied in the original gauge cell method. The method is applied to study the transition from supercritical adsorption to subcritical capillary condensation, which is observed in nanoporous materials as the pore size increases.

  7. Electrostatic calculations for an ion channel. I. Energy and potential profiles and interactions between ions.

    PubMed Central

    Levitt, D G

    1978-01-01

    The electrostatic energy profile of one, two, or three ions in an aqueous channel through a lipid membrane is calculated. It is shown that the previous solution to this problem (based on the assumption that the channel is infinitely long) significantly overestimates the electrostatic energy barrier. For example, for a 3-A radius pore, the energy is 16 kT for the infinite channel and 6.7 kT for an ion in the center of a channel 25 A long. The energy as a function of the position of the ion is also determined. With this energy profile, the rate of crossing the membrane (using the Nernst-Planck equation) was estimated and found to be compatible with the maximum conductance observed for the gramicidin A channel. The total electrostatic energy (as a function of position) required to place two or three ions in the channel is also calculated. The electrostatic interaction is small for two ions at opposite ends of the channel and large for any positioning of the three ions. Finally, the gradient through the channel of an applied potential is calculated. The solution to these problems is based on solving an equivalent problem in which an appropriate surface charge is placed on the boundary between the lipid and aqueous regions. The magnitude of the surface charge is obtained from the numerical solution for a system of coupled integral equations. PMID:656542

  8. First-principles study of terpyrrole as a potential hydrogen cyanide sensor: DFT calculations.

    PubMed

    Shokuhi Rad, Ali; Zardoost, Mohammad Reza; Abedini, Ehsan

    2015-10-01

    The sensitivity of terpyrrole (TPy; used as a polypyrrole model) to toxic hydrogen cyanide (HCN) adsorption was studied by using DFT to perform geometry optimization and to calculate the adsorption energy of HCN on TPy as well as orbital properties. The interaction of terpyrrole with HCN was studied for different relative orientations of the molecules. The adsorption energy, charge analysis, and the density of states were used to evaluate the ability of TPy to sense HCN in these different relative orientations. The adsorption energy was calculated to be -3.9 and -3.1 kcal mol(-1) for two possible relative orientations. Frontier molecular orbitals and energies indicated that some hybridization occurs during the adsorption of HCN on TPy when the molecules have appropriate relative orientations, resulting in an increase in conductivity. Considering the changes in the HOMO-LUMO energy gap that were calculated to occur during HCN adsorption, it is clear that TPy is sensitive to HCN adsorption, suggesting that TPy has the potential to act as an HCN sensor. Graphical abstract HCN adsorption on TPy.

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

    PubMed

    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 -1.03 kcal/mol at a geometry where H2O is the proton donor, HO-H...CH4, with the O-H-C angle of 165 degrees, while the secondary minimum, with an energy of -0.72 kcal/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 -1.06 kcal/mol. The classical cross second virial coefficient B12(T) has been calculated for the temperature range 298-653 K. Our best results agree well with some experiments, allowing an evaluation of the quality of experimental results.

  10. Calculated ground state potential surface and excitation energies for the copper trimer

    NASA Technical Reports Server (NTRS)

    Walch, S. P.; Laskowski, B. C.

    1986-01-01

    In the context of their relevance to catalysis and to materials science problems, transition metals and transition metal (TM) compounds are currently of considerable interest, and studies have been conducted of the copper trimer, Cu3. The present investigation is concerned with a study of the ground state surface and several groups of excited states in order to improve the understanding of the spectroscopy of Cu3. Differences of the current study from previous investigations are related to an employment of larger basis sets and a more extensive electron correlation. This was done with the objective to obtain a more accurate definition of the ground state surface. Features of the bonding in the copper dimer are considered to obtain a basis for an understanding of the copper trimer. Attention is given to calculational details, the ground state surface, and calculated vertical excitation energies. The results of SCF/SDCI calculations are reported for portions of the ground surface, for two groups of excited states, and for the ionization potential of Cu3.

  11. General theory for calculating disorder-averaged Green's function correlators within the coherent potential approximation

    NASA Astrophysics Data System (ADS)

    Zhou, Chenyi; Guo, Hong

    2017-01-01

    We report a diagrammatic method to solve the general problem of calculating configurationally averaged Green's function correlators that appear in quantum transport theory for nanostructures containing disorder. The theory treats both equilibrium and nonequilibrium quantum statistics on an equal footing. Since random impurity scattering is a problem that cannot be solved exactly in a perturbative approach, we combine our diagrammatic method with the coherent potential approximation (CPA) so that a reliable closed-form solution can be obtained. Our theory not only ensures the internal consistency of the diagrams derived at different levels of the correlators but also satisfies a set of Ward-like identities that corroborate the conserving consistency of transport calculations within the formalism. The theory is applied to calculate the quantum transport properties such as average ac conductance and transmission moments of a disordered tight-binding model, and results are numerically verified to high precision by comparing to the exact solutions obtained from enumerating all possible disorder configurations. Our formalism can be employed to predict transport properties of a wide variety of physical systems where disorder scattering is important.

  12. 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.

  13. 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.

  14. Algorithms of electro-optical effect calculation in nanodisperse systems

    NASA Astrophysics Data System (ADS)

    Bregman, A. M.; Petrov, M. P.; Trusov, A. A.; Voitylov, A. V.; Vojtylov, V. V.

    2017-07-01

    Electro-optical techniques are widely used to study nanodisperse systems and obtain geometrical, electrical, and optical characteristics of particles in the suspension. The theory that describes electro-optical effects in nanodisperse systems employs several generic relations which could benefit from fast numerical calculations. The presented Taylor series expansion and differential equations allow to perform such numerical calculations fast and with a pre-defined accuracy. To take into account the polydispersity of the particles in the solution the optical properties of particles need to be taken into account. The theory that allows to do this is presented.

  15. 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.

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

    DOE PAGES

    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

  17. A contribution to improve the calculation of the acid generating potential of mining wastes.

    PubMed

    Chopard, Aurélie; Benzaazoua, Mostafa; Bouzahzah, Hassan; Plante, Benoît; Marion, Philippe

    2017-05-01

    Mine wastes from sulfide-bearing ore extraction and processing are often stored at the surface of mine sites and could generate mine drainage. Prediction tests are completed to predict the water quality associated with the deposition of mining wastes. Static tests can quickly assess the acid-generating potential (AP) and the neutralization potential (NP). Whereas some studies recommend to take into account a mineral reactivity factor for the NP determination, the reactivity rates of acidifying minerals are not considered in the AP calculation. The aim of this study is to bring contribution to the improvement of the static test determination by adding kinetic factors in the AP determination. Eight sulfides (pyrite, Ni-pyrite, pyrrhotite, Ni-pyrrhotite, chalcopyrite, galena, sphalerite, arsenopyrite) and a sulfosalt (gersdorffite) were separately submitted to kinetic tests in modified weathering cells. This test was selected for its rapidity of results and for the low amount of material used, as it is somewhat difficult to obtain pure minerals samples. Five synthetic tailings were composed by mixing pure sulfides in various proportions and submitted to the same kinetic tests. The oxidation rates of synthetic tailings were compared with the weighted combined oxidation rates of individual pure sulfides. The oxidation rates of the synthetic tailings calculated from those of pure sulfides are within the same order of magnitude than those obtained through the kinetic experiments. The AP of synthetic tailings were calculated according to standard equations of the literature and compared with the new method. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. An analytical ab initio potential surface and the calculated tunneling energies for the HCl dimer

    NASA Astrophysics Data System (ADS)

    Bunker, P. R.; Epa, V. C.; Jensen, Per; Karpfen, Alfred

    1991-03-01

    The six-dimensional potential energy surface of the HCl dimer has been calculated ab initio at 1654 nuclear geometries [A. Karpfen, P. R. Bunker and P. Jensen, Chem. Phys., in press]. In the present paper we have fitted an analytical function to these points; the analytical function is similar to that used previously by us for the potential surface of the HF dimer. The fitted function has 38 adjustable parameters and the standard deviation of the weighted fit is 19.0 cm -1. We have determined the minimum energy path for the trans-bending tunneling motion on this surface, and have calculated the tunneling and K-rotation energies and wavefunctions. Around equilibrium the path is qualitatively similar to that for the HF dimer in that there are two equivalent hydrogen-bonded structures of Cs symmetry (which are approximately L-shaped with a "bound" and a "free" H-atom) that can tunnel through a C2 h saddle point (the "closed" C2 h saddle point). However, away from equilibrium the path is qualitatively different from that found for the HF dimer since the HCl dimer never becomes linear along the path; in fact it passes through a second C2 h saddle point (the "open" C2 h saddle point). As a result the A-rotational constant only varies slightly along the path, and this explains the experimental observation that the tunneling splitting varies little with K-type rotation for the HCl dimer, in contrast to the situation for the HF dimer. Quantitatively it is clear that errors in the ab initio calculation, errors in the fitting of an analytic function to the points, the correction to the path that is caused by the zero point motion in the other vibrations, and the coupling between the four low-frequency modes, will all be relatively more significant than they were for the HF dimer because the full six-dimensional potential is much flatter; the ab initio dissociation energy is only ˜600 cm -1, and the ab initio tunneling barrier is only ˜70 cm -1. Therefore, we modify the

  19. Calculation of binary magnetic properties and potential energy curve in xenon dimer: second virial coefficient of (129)Xe nuclear shielding.

    PubMed

    Hanni, Matti; Lantto, Perttu; Runeberg, Nino; Jokisaari, Jukka; Vaara, Juha

    2004-09-22

    Quantum chemical calculations of the nuclear shielding tensor, the nuclear quadrupole coupling tensor, and the spin-rotation tensor are reported for the Xe dimer using ab initio quantum chemical methods. The binary chemical shift delta, the anisotropy of the shielding tensor Delta sigma, the nuclear quadrupole coupling tensor component along the internuclear axis chi( parallel ), and the spin-rotation constant C( perpendicular ) are presented as a function of internuclear distance. The basis set superposition error is approximately corrected for by using the counterpoise correction (CP) method. Electron correlation effects are systematically studied via the Hartree-Fock, complete active space self-consistent field, second-order Møller-Plesset many-body perturbation, and coupled-cluster singles and doubles (CCSD) theories, the last one without and with noniterative triples, at the nonrelativistic all-electron level. We also report a high-quality theoretical interatomic potential for the Xe dimer, gained using the relativistic effective potential/core polarization potential scheme. These calculations used valence basis set of cc-pVQZ quality supplemented with a set of midbond functions. The second virial coefficient of Xe nuclear shielding, which is probably the experimentally best-characterized intermolecular interaction effect in nuclear magnetic resonance spectroscopy, is computed as a function of temperature, and compared to experiment and earlier theoretical results. The best results for the second virial coefficient, obtained using the CCSD(CP) binary chemical shift curve and either our best theoretical potential or the empirical potentials from the literature, are in good agreement with experiment. Zero-point vibrational corrections of delta, Delta sigma, chi (parallel), and C (perpendicular) in the nu=0, J=0 rovibrational ground state of the xenon dimer are also reported.

  20. Balanced Basis Sets in the Calculation of Potential Energy Curves for Diatomic Molecules.

    NASA Astrophysics Data System (ADS)

    Barclay, V. J.

    "Balanced" basis sets, which describe the internuclear region as well as the nuclear region, are examined in the context of an ab initio selection-extrapolation configuration -interaction method (MRD-CI). The sets are balanced by adding bond functions (BF's), which are s, p and d-type orbitals at the bond mid-point, to atomic-centred molecular basis sets, which have double and triple sets of valence -shell orbitals (DZ and TZ) and one or two sets of polarization functions (PF's). Potential energy curves and spectroscopic constants were calculated for the ground states of the hydrides H _2, OH, NaH, MgH, MH, SiH, PH, SH, HCl, and for the ionized species OH^+ and OH^{++}, and for the A^3Sigma_{u}, w^3Delta_{u} and B^3Pi_{g} excited states of N_2. The basis sets containing bond functions gave curves and constants superior to the DZP and (where calculated) TZPP results, and of quality similar to large basis set calculations in the literature. The single and double ionization potentials of OH, and the term energies of the N_2 excited states had error at the atomic asymptotes for all basis sets. The dissociation energies of the ground states of ten first-row diatomics (C_2, N_2, O_2, F_2, CN, CO, CF, NO, NF, and FO) were studied using balanced basis sets. A correlation was found to exist between the actual bond order of a species, and the number and kinds of orbitals which comprise the optimum BF. For MRD-CI diatomic calculations, the following BF's should be added to a DZP basis set (sp) (for a bond order of 1); 2(sp) (B. O. 1.5); (spd) (B. O. 2); 3(sp) (B. O. 2.5); 2(spd) (B. O. 3). The prescribed BF basis method was tested on the 26 second-row congeners Si _2, P_2, S _2, Cl_2, SiP, SiS, SiCl, PS, PCl, and ClS, and mixed-row congeners SiN, SiO, SiF, PO, PF, SF, SiC, PN, SO, ClF, CP, CS, CCl, NS, NCl, and ClO. An average error of 6% and a maximum error of 10% relative to known experimental D_{e }'s was found: compared to an average error of 18% for TZPP calculations

  1. 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

  2. Potential adverse effects of phytoestrogens.

    PubMed

    Whitten, P L; Lewis, C; Russell, E; Naftolin, F

    1995-03-01

    Evaluation of the potential benefits and risks offered by naturally occurring plant estrogens requires investigation of their potency and sites of action when consumed at natural dietary concentrations. Our investigations have examined the effects of a range of natural dietary concentrations of the most potent plant isoflavonoid, coumestrol, using a rat model and a variety of estrogen-dependent tissues and endpoints. Treatments of immature females demonstrated agonistic action in the reproductive tract, brain, and pituitary at natural dietary concentrations. Experiments designed to test for estrogen antagonism demonstrated that coumestrol did not conform to the picture of a classic antiestrogen. However, coumestrol did suppress estrous cycles in adult females. Developmental actions were examined by neonatal exposure of pups through milk of rat dams fed a coumestrol, control, or commercial soy-based diet during the critical period of the first 10 postnatal days or throughout the 21 days of lactation. The 10-day treatment did not significantly alter adult estrous cyclicity, but the 21-day treatment produced in a persistent estrus state in coumestrol-treated females by 132 days of age. In contrast, the 10-day coumestrol treatments produced significant deficits in the sexual behavior of male offspring. These findings illustrate the broad range of actions of these natural estrogens and the variability in potency across endpoints. This variability argues for the importance of fully characterizing each phytoestrogen in terms of its sites of action, balance of agonistic and antagonistic properties, natural potency, and short-term and long-term effects.

  3. 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

  4. 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

    2014-02-05

    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.

  5. 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.

  6. Interatomic potentials via the effective-action formalism

    SciTech Connect

    Rasamny, M.; Valiev, M. |; Fernando, G.W. |

    1998-10-01

    We present a method for generating interatomic potentials from first-principles calculations. Using the effective-action formalism we describe a classical system of interacting atoms in terms of the expectation value of the pair density operator. Such a description naturally leads to the concept of the effective two-body interatomic potential. This is similar in spirit to the Kohn-Sham potential that arises in density-functional theory; however, in this case, the system is reduced from a fully interacting many-body system to an auxiliary system that interacts via a renormalized two-body potential. This potential contains the effects of three- and higher-body correlations and can be calculated via a systematic self-consistent procedure. This method can be trivially extended to the generation of higher-order interatomic potentials. {copyright} {ital 1998} {ital The American Physical Society}

  7. Redox potentials of protein disulfide bonds from free-energy calculations.

    PubMed

    Li, Wenjin; Baldus, Ilona B; Gräter, Frauke

    2015-04-30

    Thiol/disulfide exchange in proteins is a vital process in all organisms. To ensure specificity, the involved thermodynamics and kinetics are believed to be tailored by the structure and dynamics of the protein hosting the thiol/disulfide pair. We here aim at predicting the thermodynamics of thiol/disulfide pairs in proteins. We devise a free-energy calculation scheme, which makes use of the Crooks Gaussian intersection method to estimate the redox potential of thiol/disulfide pairs in 12 proteins belonging to the thioredoxin superfamily, namely, thioredoxins, glutaredoxins, and thiol-disulfide oxidoreductases in disulfide bond formation systems. We obtained a satisfying correlation of computed with experimental redox potentials (varying by 160 mV), with a residual error of ∼40 mV (8 kJ/mol), which drastically reduces when considering a less diverse set of only thioredoxins. Our simple and transferrable approach provides a route toward estimating redox potentials of any disulfide-containing protein given that its (reduced or oxidized) structure is known and thereby represents a step toward a rational design of redox proteins.

  8. Effect of neglecting geothermal gradient on calculated oil recovery

    NASA Astrophysics Data System (ADS)

    Safari, Mehdi; Mohammadi, Majid; Sedighi, Mehdi

    2017-03-01

    Reduced recovery rate with time is a common challenge for most of the oil producing reservoirs. Water flooding is one of the most common methods used for enhanced oil recovery. Simulating water-flooding process is sometimes carried out without considering the effect of geothermal gradient, and an average temperature is assumed for all the grid blocks. However, the gradient plays a significant role on the reservoir fluid properties. So neglecting its effect might result in a large error in the calculated oil recovery results, especially for the thick reservoirs, which in theory can show significant variations in temperature with depth. In this paper, first, advancing the waterfront during injection into a geothermal oil reservoir is discussed. Then, the performance of considering either an average temperature or gradient temperature, are considered and compared with each other. The results suggest that assuming a fixed average reservoir temperature with no geothermal gradient, can lead to a pronounced error for calculated oil recovery.

  9. Variational calculation of 4He tetramer ground and excited states using a realistic pair potential

    NASA Astrophysics Data System (ADS)

    Hiyama, E.; Kamimura, M.

    2012-02-01

    We calculated the 4He trimer and tetramer ground and excited states with the LM2M2 potential using our Gaussian expansion method for ab initio variational calculations of few-body systems. The method has been extensively used for a variety of three-, four-, and five-body systems in nuclear physics and exotic atomic and molecular physics. The trimer (tetramer) wave function is expanded in terms of symmetric three- (four-) body Gaussian basis functions, ranging from very compact to very diffuse, without assumption of any pair correlation function. The calculated results for the trimer ground and excited states are in excellent agreement with values reported in the literature. The binding energies of the tetramer ground and excited states are obtained as 558.98 and 127.33 mK (0.93 mK below the trimer ground state), respectively. We found that precisely the same shape of the short-range correlation (rij≲4 Å) in the dimer appears in the ground and excited states of the trimer and tetramer. The overlap function between the trimer excited state and the dimer ground state and that between the tetramer excited state and the trimer ground state are almost proportional to the dimer wave function in the asymptotic region (up to ˜1000 Å). Also, the pair correlation functions of trimer and tetramer excited states are almost proportional to the squared dimer wave function. We then propose a model which predicts the binding energy of the first excited state of 4HeN (N≥3) measured from the 4HeN-1 ground state to be nearly (N)/(2(N-1))B2 where B2 is the dimer binding energy.

  10. Software Tools for Measuring and Calculating Electromagnetic Shielding Effectiveness

    DTIC Science & Technology

    2005-09-01

    ARMY RSRCH LAB ATTN AMSRD- ARL -CI-OK-T TECHL PUB (2 COPIES) ATTN AMSRD- ARL -CI-OK-TL TECHL LIB (2 COPIES) ATTN AMSRD- ARL -D J M MILLER ATTN...Software Tools for Measuring and Calculating Electromagnetic Shielding Effectiveness by Neal Tesny ARL -TR-3645 September 2005...report when it is no longer needed. Do not return it to the originator. Army Research Laboratory Adelphi, MD 20783-1197 ARL -TR-3645 September

  11. Some calculations of transonic potential flow for the NACA 64A006 airfoil with oscillating flap

    NASA Technical Reports Server (NTRS)

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

    1978-01-01

    A method for calculating the transonic flow over steady and oscillating airfoils was developed by Isogai. It solves the full potential equation 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. In this paper the method is described in general terms, and results are compared with experimental data for both steady flow and for oscillations at several values of reduced frequency. Good agreement for static pressures is shown for subcritical speeds, with increasing deviation as Mach number is increased into the supercritical speed range. Fair agreement with experiment was obtained at high reduced frequencies with larger deviations at low reduced frequencies.

  12. Some calculations of transonic potential flow for the NACA 64A006 airfoil with oscillating flap

    NASA Technical Reports Server (NTRS)

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

    1978-01-01

    A method for calculating the transonic flow over steady and oscillating airfoils was developed by Isogai. It solves the full potential equation 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. In this paper the method is described in general terms, and results are compared with experimental data for both steady flow and for oscillations at several values of reduced frequency. Good agreement for static pressures is shown for subcritical speeds, with increasing deviation as Mach number is increased into the supercritical speed range. Fair agreement with experiment was obtained at high reduced frequencies with larger deviations at low reduced frequencies.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

    A systematic vibrational spectroscopic assignment and analysis of pramipexole [(S)-N6-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.

  15. Calculation of real-gas effects on airfoil aerodynamic characteristics

    NASA Technical Reports Server (NTRS)

    Park, Chul; Yoon, Seokkwan

    1990-01-01

    The effects of high temperature thermochemical phenomena on the aerodynamic characteristics at hypersonic speeds are calculated for two-dimensional airfoils in air. The calculations are performed on an airfoil similar to that used for the Space Shuttle Orbiter, and ellipses of thickness ratios varying between 5 and 15 percent. For the airfoil, one flight condition is considered. For the ellipses, the calculations are carried out over a range of chord lengths, flight velocities, flight altitudes, and angles of attack. It is shown that the lift and drag coefficients are consistently reduced by the thermochemical phenomena, and that the behavior can be represented by a specific heat ratio value less than 1.4. The center of pressure shifts forward due to the thermochemical phenomena, but its extent is sensitively affected by the geometry and angle of attack and cannot be represented by a fixed specific heat ratio. The calculated results are in qualitative agreement with the data obtained during the entry flights of the Space Shuttle vehicle.

  16. The screened pseudo-charge repulsive potential in perturbed orbitals for band calculations by DFT+U.

    PubMed

    Huang, Bolong

    2017-03-06

    The conventional linear response overestimates the U in DFT+U calculations for solids with fully occupied orbitals. Here, we demonstrate that the challenge arises from the incomplete cancellation of the electron-electron Coulomb repulsion energy under external perturbation. We applied the second charge response, denoted as the "pseudo-charge" model, to offset such residue effects. Counteracting between these two charge response-induced Coulomb potentials, the U parameters are self-consistently obtained by fulfilling the conditions for minimizing the non-Koopmans energy. Moreover, the pseudo-charge-induced repulsive potential shows a screening behavior related to the orbital occupation and is potentially in compliance with the screened exact exchange-correlation of electrons. The resultant U parameters are self-consistent solutions for improved band structure calculations by the DFT+U method. This work extends the validity of the linear response method to both partially and fully occupied orbitals and gives a reference for estimating the Hubbard U parameter prior to other advanced methods. The U parameters were determined in a transferability test using both PBE and hybrid density functional methods, and the results showed that this method is independent of the functional. The electronic structures determined from the hybrid-DFT+U(hybrid) approach are provided. Comparisons are also made with the recently developed self-consistent hybrid-DFT+Uw method.

  17. Effects of internal gain assumptions in building energy calculations

    NASA Astrophysics Data System (ADS)

    Christensen, C.; Perkins, R.

    1981-01-01

    The utilization of direct solar gains in buildings can be affected by operating profiles, such as schedules for internal gains, thermostat controls, and ventilation rates. Building energy analysis methods use various assumptions about these profiles. The effects of typical internal gain assumptions in energy calculations are described. Heating and cooling loads from simulations using the DOE 2.1 computer code are compared for various internal gain inputs: typical hourly profiles, constant average profiles, and zero gain profiles. Prototype single-family-detached and multifamily-attached residential units are studied with various levels of insulation and infiltration. Small detached commercial buildings and attached zones in large commercial buildings are studied with various levels of internal gains. The results indicate that calculations of annual heating and cooling loads are sensitive to internal gains, but in most cases are relatively insensitive to hourly variations in internal gains.

  18. Effects of internal gain assumptions in building energy calculations

    NASA Astrophysics Data System (ADS)

    Christensen, C.; Perkins, R.

    The utilization of direct solar gains in buildings can be affected by operating profiles, such as schedules for internal gains, thermostat controls, and ventilation rates. Building energy analysis methods use various assumptions about these profiles. The effects of typical internal gain assumptions in energy calculations. Heating and cooling loads from simulations using the Department of Energy 2.1 computer code are compared for various internal-gain inputs: typical hourly profiles, constant average profiles, and zero gain profiles. Prototype single-family-detached and multi-family-attached residential units are studied with various levels of insulation and infiltration. Small detached commercial buildings and attached zones in large commercial buildings are studied with various levels of internal gains. The results indicate that calculations of annual heating and cooling loads are sensitive to internal gains, but in most cases are relatively insensitive to hourly variations in internal gains.

  19. Effects of internal gain assumptions in building energy calculations

    SciTech Connect

    Christensen, C.; Perkins, R.

    1981-01-01

    The utilization of direct solar gains in buildings can be affected by operating profiles, such as schedules for internal gains, thermostat controls, and ventilation rates. Building energy analysis methods use various assumptions about these profiles. The effects of typical internal gain assumptions in energy calculations are described. Heating and cooling loads from simulations using the DOE 2.1 computer code are compared for various internal-gain inputs: typical hourly profiles, constant average profiles, and zero gain profiles. Prototype single-family-detached and multi-family-attached residential units are studied with various levels of insulation and infiltration. Small detached commercial buildings and attached zones in large commercial buildings are studied with various levels of internal gains. The results of this study indicate that calculations of annual heating and cooling loads are sensitive to internal gains, but in most cases are relatively insensitive to hourly variations in internal gains.

  20. 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.

  1. Calculations of multiquark functions in effective models of strong interaction

    SciTech Connect

    Jafarov, R. G.; Rochev, V. E.

    2013-09-15

    In this paper we present our results of the investigation of multiquark equations in the Nambu-Jona-Lasinio model with chiral symmetry of SU(2) group in the mean-field expansion. To formulate the mean-field expansion we have used an iteration scheme of solution of the Schwinger-Dyson equations with the fermion bilocal source. We have considered the equations for Green functions of the Nambu-Jona-Lasinio model up to third step for this iteration scheme. To calculate the high-order corrections to the mean-field approximation, we propose the method of the Legendre transformation with respect to the bilocal source, which allows effectively to take into account the symmetry constraints related with the chiral Ward identity. We discuss also the problem of calculating the multiquark functions in the mean-field expansion for Nambu-Jona-Lasinio-type models with other types of the multifermion sources.

  2. Symmetry-adapted perturbation theory calculation of the He-HF intermolecular potential energy surface

    NASA Astrophysics Data System (ADS)

    Moszynski, Robert; Wormer, Paul E. S.; Jeziorski, Bogumil; van der Avoird, Ad

    1994-08-01

    Symmetry-adapted perturbation theory has been applied to compute the HeHF intermolecular potential energy surface for three internuclear distances in the HF subunit. The interaction energy is found to be dominated by the first-order exchange contribution and by the dispersion energy (including the intramonomer correlation effects). However, smaller corrections as the electrostatics, induction, and second-order exchange are found to be nonnegligible, and the final shape of the potential results from a delicate balance of attractive and repulsive contributions due to the four fundamental intermolecular interactions: electrostatics, exchange, induction, and dispersion. For a broad range of He-HF configurations the theoretical potential agrees very well with the empirical potential of Lovejoy and Nesbitt [C. M. Lovejoy and D. J. Nesbitt, J. Chem. Phys. 93, 5387 (1990)], which was adjusted to reproduce the near-infrared spectrum of the complex. Our potential has a global minimum of ɛm=-39.68 cm-1 for the linear He-HF geometry at Rm=6.16 bohr, and a secondary minimum of ɛm=-36.13 cm-1 for the linear He-FH geometry at Rm=5.59 bohr. These values are in very good agreement with the corresponding empirical results: ɛm=-39.20 cm-1 and Rm=6.17 bohr for the global minimum, and ɛm=-35.12 cm-1 and Rm=5.67 bohr for the secondary minimum.

  3. Calculation of effective diffusivities for biofilms and tissues.

    PubMed

    Wood, Brian D; Quintard, Michel; Whitaker, Stephen

    2002-03-05

    In this study we describe a scheme for numerically calculating the effective diffusivity of cellular systems such as biofilms and tissues. This work extends previous studies in which we developed the macroscale representations of the transport equations for cellular systems based on the subcellular-scale transport and reaction processes. A finite-difference model is used to predict the effective diffusivity of a cellular system on the basis of the subcellular-scale geometry and transport parameters. The effective diffusivity is predicted for a complex three-dimensional structure that is based on laboratory observations of a biofilm, and these numerical predictions are compared with predictions from a simple analytical solution and with experimental data. Our results indicate that, under many practical circumstances, the simple analytical solution can be used to provide reasonable estimates of the effective diffusivity.

  4. Calculation of alloying effect on formation enthalpy of TiCu intermetallics from first-principles calculations for designing Ti-Cu-system metallic glasses

    NASA Astrophysics Data System (ADS)

    Shirasawa, Naoya; Takigawa, Yorinobu; Uesugi, Tokuteru; Higashi, Kenji

    2016-01-01

    The effect of alloying on the formation enthalpy of TiCu intermetallics was investigated via first-principles calculations to propose a new design method for Ti-Cu-system metallic glasses. The calculation results showed good agreement with the reported experimental results that Ni, Pd, Sn and Zr improve this system's glass-forming ability. According to the calculation results, a Ti-Zr-Cu-Ga system was designed as a potential new bulk Ti-based metallic glass, and a bulk sample with a 2-mm diameter was fabricated.

  5. Ground- and excited-state properties of inorganic solids from full-potential density-functional calculations

    NASA Astrophysics Data System (ADS)

    Ravindran, P.; Vidya, R.; Vajeeston, P.; Kjekshus, A.; Fjellvåg, H.

    2003-12-01

    The development in theoretical condensed-matter science based on density-functional theory (DFT) has reached a level where it is possible, from "parameter-free" quantum mechanical calculations to obtain total energies, forces, vibrational frequencies, magnetic moments, mechanical and optical properties and so forth. The calculation of such properties are important in the analyses of experimental data and they can be predicted with a precision that is sufficient for comparison with experiments. It is almost impossible to do justice to all developments achieved by DFT because of its rapid growth. Hence, it has here been focused on a few advances, primarily from our laboratory. Unusual bonding behaviors in complex materials are conveniently explored using the combination of charge density, charge transfer, and electron-localization function along with crystal-orbital Hamilton-population analyses. It is indicated that the elastic properties of materials can reliably be predicted from DFT calculations if one takes into account the structural relaxations along with gradient corrections in the calculations. Experimental techniques have their limitations in studies of the structural stability and pressure-induced structural transitions in hydride materials whereas the present theoretical approach can be applied to reliably predict properties under extreme pressures. From the spin-polarized, relativistic full-potential calculations one can study novel materials such as ruthenates, quasi-one-dimensional oxides, and spin-, charge-, and orbital-ordering in magnetic perovskite-like oxides. The importance of orbital-polarization correction to the DFT to predict the magnetic anisotropy in transition-metal compounds and magnetic moments in lanthanides and actinides are emphasized. Apart from the full-potential treatment, proper magnetic ordering as well as structural distortions have to be taken into account to predict correctly the insulating behavior of transition-metal oxides

  6. Simple, accurate electrostatics-based formulas for calculating ionization potentials, electron affinities, and capacitances of fullerenes

    NASA Astrophysics Data System (ADS)

    Atanasov, Alexander B.; Ellenbogen, James C.

    2017-03-01

    A set of simple analytic formulas is derived via electrostatics-based methods to accurately calculate the values of electron affinities An and ionization potentials In for n -carbon icosahedral fullerene molecules as a function of their average radii Rn. These formulas reproduce with accuracy the values of An, In, and their scalings with 1 /Rn that were determined previously in detailed, computationally intensive density functional theory calculations. The formula for An is derived from an enhanced image-charge model that treats the valence region of the icosahedral system as a quasispherical conductor of radius (Rn+δ ) , where δ =1 /4 W∞ is a small constant distance determined from the work function W∞ of graphene. Using this model, though, a formula for In that includes only electrostatics-like terms does not exhibit accuracy similar to the analogous formula for An. To make it accurate, a term must be added to account for the large symmetry-induced quantum energy gap in the valence energy levels (i.e., the HOMO-LUMO gap). An elementary two-state model based upon a quantum rotor succeeds in producing a simple expression that evaluates the energy gap as an explicit function of An. Adding this to the electrostatics-like formula for In gives a simple quantum equation that yields accurate values for In and expresses them as a function of An. Further, the simple equations for An and In yield significant insight into both the physics of electron detachment in the fullerenes and the scaling with Rn of their quantum capacitances Cn=1 /(In-An) .

  7. Theoretical study of ignition reactions of linear symmetrical monoethers as potential diesel fuel additives: DFT calculations

    NASA Astrophysics Data System (ADS)

    Marrouni, Karim El; Abou-Rachid, Hakima; Kaliaguine, Serge

    This work investigates the chemical reactivity of four linear symmetrical monoethers with molecular oxygen. Such oxygenated compounds may be considered as potential diesel fuel additives in order to reduce the ignition delay in diesel fuel engines. For this purpose, a kinetic study is proposed to clarify the relation between the molecular structure of the fuel molecule and its ignition properties. To this end, DFT calculations were performed for these reactions using B3LYP/6-311G(d,p) and BH&HLYP/6-311G(d,p) to determine structures, energies, and vibrational frequencies of stationary points as well as activated complexes involved in each gas-phase combustion initiation reaction of the monoethers CH3OCH3, C2H5OC2H5, C3H7OC3H7, or C4H9OC4H9 with molecular oxygen. This theoretical kinetic study was carried out using electronic structure results and the transition state theory, to assess the rate constants for all studied combustion reactions. As it has been shown in our previous work [Abou-Rachid et al., J Mol Struct (Theochem) 2003, 621, 293], the cetane number (CN) of a pure organic molecule depends on the initiation rate of its homogeneous gas-phase reaction with molecular oxygen. Indeed, the calculated initiation rate constants of the H-abstraction process of linear monoethers with O2 show a very good correlation with experimental CN data of these pure compounds at T D 1,000 K. This temperature is representative of the operating conditions of a diesel fuel engine.0

  8. 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

  9. 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

  10. Selecting the optimal method to calculate daily global reference potential evaporation from CFSR reanalysis data

    NASA Astrophysics Data System (ADS)

    Sperna Weiland, F. C.; Tisseuil, C.; Dürr, H. H.; Vrac, M.; van Beek, L. P. H.

    2011-07-01

    Potential evaporation (PET) is one of the main inputs of hydrological models. Yet, there is limited consensus on which PET equation is most applicable in hydrological climate impact assessments. In this study six different methods to derive global scale reference PET time series from CFSR reanalysis data are compared: Penman-Monteith, Priestley-Taylor and original and modified versions of the Hargreaves and Blaney-Criddle method. The calculated PET time series are (1) evaluated against global monthly Penman-Monteith PET time series calculated from CRU data and (2) tested on their usability for modeling of global discharge cycles. The lowest root mean squared differences and the least significant deviations (95 % significance level) between monthly CFSR derived PET time series and CRU derived PET were obtained for the cell specific modified Blaney-Criddle equation. However, results show that this modified form is likely to be unstable under changing climate conditions and less reliable for the calculation of daily time series. Although often recommended, the Penman-Monteith equation did not outperform the other methods. In arid regions (e.g., Sahara, central Australia, US deserts), the equation resulted in relatively low PET values and, consequently, led to relatively high discharge values for dry basins (e.g., Orange, Murray and Zambezi). Furthermore, the Penman-Monteith equation has a high data demand and the equation is sensitive to input data inaccuracy. Therefore, we preferred the modified form of the Hargreaves equation, which globally gave reference PET values comparable to CRU derived values. Although it is a relative efficient empirical equation, like Blaney-Criddle, the equation considers multiple spatial varying meteorological variables and consequently performs well for different climate conditions. In the modified form of the Hargreaves equation the multiplication factor is uniformly increased from 0.0023 to 0.0031 to overcome the global underestimation

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2013-06-07

    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)]. 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 (E(coll) ≥ 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.

  13. Generic effective source for scalar self-force calculations

    NASA Astrophysics Data System (ADS)

    Wardell, Barry; Vega, Ian; Thornburg, Jonathan; Diener, Peter

    2012-05-01

    A leading approach to the modeling of extreme mass ratio inspirals involves the treatment of the smaller mass as a point particle and the computation of a regularized self-force acting on that particle. In turn, this computation requires knowledge of the regularized retarded field generated by the particle. A direct calculation of this regularized field may be achieved by replacing the point particle with an effective source and solving directly a wave equation for the regularized field. This has the advantage that all quantities are finite and require no further regularization. In this work, we present a method for computing an effective source which is finite and continuous everywhere, and which is valid for a scalar point particle in arbitrary geodesic motion in an arbitrary background spacetime. We explain in detail various technical and practical considerations that underlie its use in several numerical self-force calculations. We consider as examples the cases of a particle in a circular orbit about Schwarzschild and Kerr black holes, and also the case of a particle following a generic timelike geodesic about a highly spinning Kerr black hole. We provide numerical C code for computing an effective source for various orbital configurations about Schwarzschild and Kerr black holes.

  14. Nuclear Weapon Effects Calculations in the TACWAR Code

    DTIC Science & Technology

    1978-10-20

    DNA 4702F NUCLEAR WEAPON EFFECTS _" CALCULATIONS IN THE TACWAR CODE _ Systems, Science & Software, Inc. i t, The Atrium, Suite 202 277 S. Washington...FOR PUBLIC RELEASE; - DISTRIBUTION UNLIMITED.1 THIS WORK SPONSORED BY THE DEFENSE NUCLEAR AGENCY1 " UNDER RDT&E RMSS CODE 836407046 V990AXNL12258 H25M0...Prepared forDD Director " - ! P DEFENSE NUCLEAR AGENCY JUL 23 1979 Washington, D. C. 20305 L • _. ,, ; .,.. : = *- k - .. _i , m i z "D ’ - ’ ’F 3 m

  15. Full potential calculation of electronic properties of rutile RO 2 (R=Si, Ge, Sn and Pb) compounds via modified Becke Johnson potential

    NASA Astrophysics Data System (ADS)

    Singh, Hardev; Singh, Mukhtiyar; Kumar, Sarvesh; Kashyap, Manish K.

    2011-10-01

    The electronic properties of RO 2 (R=Si, Ge, Sn and Pb; a group IVA element) compounds in rutile structure have been calculated using WIEN2k implementation of full potential linearized augmented plane wave (FPLAPW) method. The exchange and correlation (XC) effects are taken into account by an orbital independent modified Becke Johnson (MBJ) potential as coupled with Local Density Approximation (LDA) for all the compounds except for PbO 2 where only Generalized Gradient Approximation (GGA) is considered for the same. We predict a direct band gap in all these compounds with continuous decrease as the atomic size of IVA element increases such that there is an appearance of semimetallic band structure for the last compound, PbO 2. The largest band gap (7.66 eV) has been found for SiO 2, which governs its insulating nature. We observe that MBJLDA results for band gaps of these compounds are far better than those obtained using GGA and Engel-Vosko's GGA (EV-GGA). A very good agreement is observed between MBJLDA band gaps with corresponding experimental values as compared to other calculations. The electronic band structures are also analyzed in terms of contributions from various electrons.

  16. Separable Representation of Nucleon-Nucleus Optical Potentials as Input to (d; p) Reaction Calculations

    NASA Astrophysics Data System (ADS)

    Hlophe, Linda D.

    The three-body description of deuteron-induced nuclear reactions requires the nucleon-nucleon (NN) and effective nucleon-nucleus interactions as input. The latter are given by Optical Model Potentials (OMPs), which are complex as well as energy-dependent. While a lot of effort has been dedicated to creating separable NN potentials, the same is not true for the nucleon-nucleus OMPs. In this work, separable representations of nucleon-nucleus OMPs are presented. To construct separable representations of neutron-nucleus OMPs, a scheme due to Ernst, Shakin, and Thaler (EST) is adopted as a starting point. It is shown that, by including both incoming and outgoing scattering states in the EST scheme, separable expansions for complex neutron-nucleus potentials that partially obey reciprocity are obtained. For the application to neutron-nucleus potentials that are complex as well as energy-dependent, a further generalization is carried out leading to an energy-dependent separable expansion that exactly fulfills reciprocity. By working exclusively with half-shell transition matrices in momentum space, the implementation of these separable representation schemes is straightforward. The proton-nucleus interaction consists of a short-ranged nuclear piece as well as the long-ranged point-Coulomb potential. After separating the point-Coulomb piece via the Gell-Mann-Goldberger relation, one is left with the short-ranged potential in the Coulomb basis. An extension of the separable representation schemes for neutron-nucleus OMPs to proton-nucleus systems thus requires scattering solutions in the Coulomb basis. This complicates a momentum space implementation of the aforementioned separable expansions. However, by employing the techniques first suggested by Elster, Liu, and Thaler, the separable representation schemes generalized for proton-nucleus OMPs are implemented in a similar manner to neutron-nucleus OMPs. Taking into account the internal structure of the nucleus leads to

  17. 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.

  18. Redox Potentials from Ab Initio Molecular Dynamics and Explicit Entropy Calculations: Application to Transition Metals in Aqueous Solution.

    PubMed

    Caro, Miguel A; Lopez-Acevedo, Olga; Laurila, Tomi

    2017-08-08

    We present a complete methodology to consistently estimate redox potentials strictly from first-principles, without any experimental input. The methodology is based on (i) ab initio molecular dynamics (MD) simulations, (ii) all-atom explicit solvation, (iii) the two-phase thermodynamic (2PT) model, and (iv) the use of electrostatic potentials as references for the absolute electrochemical scale. We apply the approach presented to compute reduction potentials of the following redox couples: Cr(2+/3+), V(2+/3+), Ru(NH3)6(2+/3+), Sn(2+/4+), Cu(1+/2+), FcMeOH(0/1+), and Fe(2+/3+) (in aqueous solution) and Fc(0/1+) (in acetonitrile). We argue that fully quantum-mechanical simulations are required to correctly model the intricate dynamical effects of the charged complexes on the surrounding solvent molecules within the solvation shell. Using the proposed methodology allows for a computationally efficient and statistically stable approach to compute free energy differences, yielding excellent agreement between our computed redox potentials and the experimental references. The root-mean-square deviation with respect to experiment for the aqueous test set and the two exchange-correlation density functionals used, PBE and PBE with van der Waals corrections, are 0.659 and 0.457 V, respectively. At this level of theory, depending on the functional employed, its ability to correctly describe each particular molecular complex seems to be the factor limiting the accuracy of the calculations.

  19. Configuration interaction calculations of potential curves and annihilation rates for positronic complexes of alkali monoxides.

    PubMed

    Buenker, Robert J; Liebermann, Heinz-Peter

    2009-09-21

    Ab initio multireference single- and double-excitation configuration interaction calculations have been carried out to compute the potential curves and annihilation rates (ARs) of positronic molecular complexes of a series of alkali monoxides. The dissociation limit for the lowest states of these systems consists of the positive alkali ion ground state (M(+)) and the OPs (e(+)O(-)) complex formed by attaching the positron to O(-), even though the ground state of the corresponding neutral molecule always correlates with uncharged fragments (M+O). The positron affinity of the neutral oxide (2)Pi state is greater than that of (2)Sigma(+) in each case, so that the e(+)MO ground state always has (3,1)Pi symmetry, despite the fact that both KO and RbO have (2)Sigma(+) ground states. The bonding in the positronic systems is highly ionic at all internuclear distances and this causes their ARs to decrease gradually as the positive alkali ion approaches the OPs fragment.

  20. 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.

  1. Effective method for calculating modes of multilayer waveguide

    NASA Astrophysics Data System (ADS)

    Ivanov, I. K.; Dimitrov, P. D.

    2017-01-01

    A fast and efficient numerical method for finding the modes of a multilayered waveguide is proposed. Using the complex vector of the Riemann-Silberstein has resulted in a reduction of the order of the differential equations describing the passage of light through the different layers, as well as a double reduction of the searched variables. The approximation of the differential equations is made by the method of Galyorkin by a suitable choice of the base functions. The calculation of the effective indices and their corresponding wave configurations is realized by the inverse-shifting power method with Rayleigh’s quantity. The method was successfully applied waveguide systems, generating values close in the effective indices.

  2. Electron phonon effects on the direct band gap in semiconductors: LCAO calculations

    NASA Astrophysics Data System (ADS)

    Olguín, D.; Cardona, M.; Cantarero, A.

    2002-06-01

    Using a perturbative treatment of the electron-phonon interaction, we have studied the effect of phonons on the direct band gap of conventional semiconductors. Our calculations are performed in the framework of the tight-binding linear combination of atomic orbitals (LCAO) approach. Within this scheme we have calculated the temperature and isotopic mass dependence of the lowest direct band gap of several semiconductors with diamond and zincblende structure. Our results reproduce the overall trend of available experimental data for the band gap as a function of temperature, as well as give correctly the mass dependence of the band gap on isotopic. A calculation of conduction band intervalley deformation potentials is also reported. Finally, calculated Debye-Waller factors are compared with X-ray and EXAFS experimental results.

  3. The calculation of the effective diamagnetic frequency using BOUT + + code

    NASA Astrophysics Data System (ADS)

    Wang, Y. M.; Xu, X. Q.; Snyder, P. B.; Osborne, T. H.

    2016-10-01

    The effective diamagnetic frequency of the peeling-ballooning modes is evaluated by the ideal MHD and the 2-fliud models. This effective diamagnetic frequency is used in the EPED code to predict the pedestal width and height. In the DIII-D detachment experiments, the difference of the measured pedestal height and predicted pedestal height become more significant for the higher density cases. In the higher gas puffing case, the bootstrap current is suppressed and the decrease of the pressure gradient will lead to less ion diamagnetic stabilization. A new effective diamagnetic model is needed to improve the accuracy of the pedestal parameters prediction. The effective diamagnetic frequency with different parameters is calculated by BOUT + + 3-field linear code using dbm19 equilibrium generated by TOQ code. The equilibriums are generated using sets of different fraction of bootstrap current, elongation, q95, pedestal width and height. A new formula of effective diamagnetic frequency with these parameters is generated by fitting the simulation results. Using the new formula, the comparison between the simulation results and the experimental measurements will be conducted. This work is supported by the National Natural Science Fonudation of China (Grant No. 11505221) and China Scholarship Council (Grant No. 201504910132).

  4. Study of Ray Effects in Discrete Ordinates Calculations.

    NASA Astrophysics Data System (ADS)

    Gomes, Luisa Maria Torres

    Ray effects, an inherent problem in the formulation of the discrete ordinates approximation to the transport equation, is studied in this research. In particular, the effectiveness of using Monte Carlo procedures to generate a first collision source or a second collision source is investigated. Monte Carlo procedures provide a general methodology that can be applied to the discrete ordinates solution of complex problems in either two- or three-dimensional geometries, for which ray effects are likely to occur. The Monte Carlo method, which is intrinsically free from ray effects, performs the transport of the source particle to the first collision site. The Monte Carlo estimated uncollided fluxes or first collided fluxes are used to compute the scattering sources in a format suitable for input into the DORT two-dimensional and the TORT three -dimensional discrete ordinates codes. The computational time and precision requirements of the Monte Carlo calculation are analyzed. Also, three procedures for estimating the second collision source with the modified version of MORSE are investigated. The results show that significant improvements are achieved in the solution of the test problems when using the first collision source and that virtual elimination of ray effects is realized when using the second collision source.

  5. 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.

  6. 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.

  7. A New Green's Function for the Wake Potential Calculation of the SLAC S-band Constant Gradient Accelerating Section

    SciTech Connect

    Novokhatski, A,; /SLAC

    2012-02-17

    The behavior of the longitudinal wake fields excited by a very short bunch in the SLAC S-band constant gradient accelerating structures has been studied. Wake potential calculations were performed for a bunch length of 10 microns using the author's code to obtain a numerical solution of Maxwell's equations in the time domain. We have calculated six accelerating sections in the series (60-ft) to find the stationary solution. While analyzing the computational results we have found a new formula for the Green's function. Wake potentials, which are calculated using this Green's function are in amazingly good agreement with numerical results over a wide range of bunch lengths. The Green's function simplifies the wake potential calculations and can be easily incorporated into the tracking codes. This is very useful for beam dynamics studies of the linear accelerators of LCLS and FACET.

  8. 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.

  9. 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.

  10. 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).

  11. Conformational evaluation of DNA-carcinogen adducts using semi-empirical potential energy calculations

    SciTech Connect

    Verna, L.K.

    1992-01-01

    The covalent attachment of an aromatic amine to guanine C8 can produce a conformational change within the DNA molecule. This conformational change is likely to influence the altered DNA's biological capacity. The author used semi-empirical potential energy calculations to evaluate conformational patterns of DNA-aromatic amine adducts using the series: aniline, 4-aminobiphenyl, 2-aminofluorene and 1-aminopyrene. An exhaustive search was made of the conformational space for carcinogen modified two-base sequences. Information was incorporated into single stranded modified trimers. Modified strands were incorporated in duplex trimers. Nine-base modified duplexes were constructed and evaluated. This procedure produced distinctly different patterns for each aromatic amine investigated. It was apparent that the base sequence in which the carcinogen modification was found was crucial to the conformational change produced. At the dimer level, aniline allows both syn and anti guanine orientations at the carcinogen modification site. There were base-base and base-carcinogen stacked states, suggesting a flexible adduct easily able to assume many conformations. 4-Aminobiphenyl attachment resulted in low energy base-carcinogen stacked states, and a guanine torsion predominantly in a low syn orientation. The flexibility of this adduct was greatly reduced from that of the aniline adduct. 2-Aminofluorene adducts assumed more of a conformational mix. The major portion was base-base stacked with modified guanine anti, with a portion with base-carcinogen stacking and guanine syn or low syn. 1-Aminopyrene adducts were inflexible. The majority assumed a base-carcinogen stack with guanine syn. The conformational profiles of large modified pieces provided details of a unique low energy wedge conformation, in which aminofluorene, particularly, was able to fit into the minor groove with very little helix distortion.

  12. Three oxime ether derivatives: Synthesis, crystallographic study, electronic structure and molecular electrostatic potential calculation

    NASA Astrophysics Data System (ADS)

    Dey, Tanusri; Praveena, Koduru Sri Shanthi; Pal, Sarbani; Mukherjee, Alok Kumar

    2017-06-01

    Three oxime ether derivatives, (E)-3-methoxy-4-(prop-2-ynyloxy)-benzaldehyde-O-prop-2-ynyl-oxime (C14H13NO3) (2), benzophenone-O-prop-2-ynyl-oxime (C16H13NO) (3) and (E)-2-chloro-6-methylquinoline-3-carbaldehyde-O-prop-2-ynyl-oxime (C14H11ClN2O) (4), have been synthesized and their crystal structures have been determined. The DFT optimized molecular geometries in 2-4 agree closely with those obtained from the crystallographic study. An interplay of intermolecular Csbnd H⋯O, Csbnd H⋯N, Csbnd H⋯Cl and Csbnd H···π(arene) hydrogen bonds and π···π interactions assembles molecules into a 2D columnar architecture in 2, a 1D molecular ribbon in 3 and a 3D framework in 4. Hirshfeld surface analysis showed that the structures of 2 and 3 are mainly characterized by H⋯H, H⋯C and H⋯O contacts but some contribution of H⋯N and H⋯Cl contacts is also observed in 4. Hydrogen-bond based interactions in 2-4 have been complemented by calculating molecular electrostatic potential (MEP) surfaces. The electronic structures of molecules reveal that the estimated band gap in 3, in which both aldehyde hydrogen atoms of formaldehyde-O-prop-2-ynyl-oxime (1) have been substituted by two benzene rings, is higher than that of 2 and 4 with only one aldehyde hydrogen atom replaced.

  13. New method for calculating comparative toxicity potential of cationic metals in freshwater: application to copper, nickel, and zinc.

    PubMed

    Gandhi, Nilima; Diamond, Miriam L; van de Meent, Dik; Huijbregts, Mark A J; Peijnenburg, Willie J G M; Guinée, Jeroen

    2010-07-01

    Current practice in chemical hazard ranking and toxic impact assessments is to estimate fate and toxicity assuming the chemical exists in dissolved and particulate phases and, for metals, that all dissolved species are equally bioavailable. This introduces significant error since metal effects are related to the truly dissolved phase and free metal ion within it, not the total dissolved phase. We introduce a Bioavailability Factor (BF) to the calculation of hazard or Comparative Toxicity Potentials (CTPs) (also known as Characterization Factors; CFs) for use in Life Cycle Impact Assessment (LCIA). The method uses for calculation (1) USEtox for environmental fate, (2) WHAM 6.0 for metal partitioning and speciation in aquatic systems, and (3) Biotic Ligand Model (BLM) for average toxicity. For 12 EU water-types, we calculated medians (range) of CTPs of 1.5 x 10(4) (1.5 x 10(2) to 1.2 x 10(5)), 5.6 x 10(4) (9.4 x 10(3) to 4.1 x 10(5)), and 2.1 x 10(4) (7 x 10(3) to 5.8 x 10(4)) day*m(3)/kg for Cu, Ni, and Zn, respectively, which are up to approximately 1000 times lower than previous values. The greatest contributor to variability in CTPs was the BF, followed by toxicity Effect Factor (EF). The importance of the choice of water-type is shown by changes in the relative ranking of CTPs, which are equally influenced by water chemistry and inherent metal-specific differences.

  14. Contribution of ghost and narcissus effects in MTF calculation

    NASA Astrophysics Data System (ADS)

    Arasa, Josep; Pizarro, Carlos; Tomas, Nuria; Diaz, Jose A.

    1999-08-01

    The MTF is a parameter used for quality analysis of a system in optical design. In optical design, this parameter is usually obtained without taking into account energy losses and ghost and narcissus effects. The proposed method to calculate MTF with this contribution has the same structure than traditional method. This one is based on ray tracing to obtain the PSF of the optical system, and then apply the Fourier transform to obtain MTF. The method we propose has three modifications from the traditional method: it uses a non-sequential ray tracing, it includes samples structures in the process to obtain the PSF and it also includes energy looses in the PSF function. In this work, we present the influence of and ghost and narcissus effects in MTF for a triplet system proposed by M. Laikin. We have obtained the traditional MTF with commercial available software Beam4, and our method without inclusion of ghost and narcissus effects. Also we have compared all results obtained with those that M. Laikin gives. Finally we have obtained the MTF with the contribution of ghost and narcissus effects using our proposed method.

  15. Effective pair potentials for spherical nanoparticles

    NASA Astrophysics Data System (ADS)

    van Zon, Ramses

    2009-02-01

    An effective description for rigid spherical nanoparticles in a fluid of point particles is presented. The points inside the nanoparticles and the point particles are assumed to interact via spherically symmetric additive pair potentials, while the distribution of points inside the nanoparticles is taken to be spherically symmetric and smooth. The resulting effective pair interactions between a nanoparticle and a point particle, as well as between two nanoparticles, are then given by spherically symmetric potentials. If overlap between particles is allowed, as can occur for some forms of the pair potentials, the effective potential generally has non-analytic points. It is shown that for each effective potential the expressions for different overlapping cases can be written in terms of one analytic auxiliary potential. Even when only non-overlapping situations are possible, the auxiliary potentials facilitate the formulation of the effective potentials. Effective potentials for hollow nanoparticles (appropriate e.g. for buckyballs) are also considered and shown to be related to those for solid nanoparticles. For hollow nanoparticles overlap is more physical, since this covers the case of a smaller particle embedded in a larger, hollow nanoparticle. Finally, explicit expressions are given for the effective potentials derived from basic pair potentials of power law and exponential form, as well as from the commonly used London-van der Waals, Morse, Buckingham, and Lennard-Jones potentials. The applicability of the latter is demonstrated by comparison with an atomic description of nanoparticles with an internal face centered cubic structure.

  16. 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.

  17. The effect of carbon defects on Cl anion diffusion in graphene based on first principles calculations

    NASA Astrophysics Data System (ADS)

    Zhang, Renhui; Zhao, Juan

    2017-07-01

    Generally, the role of carbon defects in the corrosion of graphene is investigated by the experimental methods. Defects and cracks are considered to be the major cause of corrosion. Thus far, the intrinsic corrosion mechanism at the nanoscale is still not understood. In this work, using a first principles method, the energy barriers and average potentials of Cl anion diffusion cross the defective graphene are calculated in order to better understand the role of carbon defects in the corrosion of graphene at the nanoscale. The calculated results show that the reconstructed nanopores have a significant effect on retaining the anticorrosion of graphene.

  18. Research for the calculation of the potential transfer energy on ±800kV DC Transmission Lines

    NASA Astrophysics Data System (ADS)

    Ren, Huisong; Wang, Hui; Gao, Liyuan; Li, Jinliang

    2017-07-01

    It would be hard to be repaired in the case of a power outage if the ±800kV ultra high voltage DC (UHVDC) transmission line was put into operation, so live working is the guarantee for its security and stability. It’s necessary to calculate potential transfer energy to ensure the safety of the live working personnel. The transfer energy can be calculated by establishing the equivalent model of the process of potential transfer. Potential differences and capacitance parameters can be calculated by the finite element method, thereby transfer energy in different transfer distances can be worked out. The results show that the transfer energy increases with the increase of the transfer distance and the transfer energy reaches to 1.0 J when the distance is 0.5 m. So the potential transfer rod is necessary for the security of the live working personnel on ±800kV DC transmission lines.

  19. Nonscaling calculation of the effective diffusion coefficient in periodic channels

    NASA Astrophysics Data System (ADS)

    Kalinay, Pavol

    2017-01-01

    An algorithm calculating the effective diffusion coefficient D(x) in 2D and 3D channels with periodically varying cross section along the longitudinal coordinate x is presented. Unlike other methods, it is not based on scaling of the transverse coordinates, or the smallness of the width of the channel. The result is expressed as an integral of specific contributions to D(x) coming from the positions neighboring to x. The method avoids the hierarchy of derivatives of the channel shaping function h(x), so it is also suitable for the channels with cusps or jumps of their width. The method describes correctly D(x) in wide channels, giving the expected behavior in the limit of infinite width (no confinement).

  20. Effect of blood activity on dosimetric calculations for radiopharmaceuticals

    NASA Astrophysics Data System (ADS)

    Zvereva, Alexandra; Petoussi-Henss, Nina; Li, Wei Bo; Schlattl, Helmut; Oeh, Uwe; Zankl, Maria; Graner, Frank Philipp; Hoeschen, Christoph; Nekolla, Stephan G.; Parodi, Katia; Schwaiger, Markus

    2016-11-01

    The objective of this work was to investigate the influence of the definition of blood as a distinct source on organ doses, associated with the administration of a novel radiopharmaceutical for positron emission tomography-computed tomography (PET/CT) imaging—(S)-4-(3-18F-fluoropropyl)-L-glutamic acid (18F-FSPG). Personalised pharmacokinetic models were constructed based on clinical PET/CT images from five healthy volunteers and blood samples from four of them. Following an identifiability analysis of the developed compartmental models, person-specific model parameters were estimated using the commercial program SAAM II. Organ doses were calculated in accordance to the formalism promulgated by the Committee on Medical Internal Radiation Dose (MIRD) and the International Commission on Radiological Protection (ICRP) using specific absorbed fractions for photons and electrons previously derived for the ICRP reference adult computational voxel phantoms. Organ doses for two concepts were compared: source organ activities in organs parenchyma with blood as a separate source (concept-1); aggregate activities in perfused source organs without blood as a distinct source (concept-2). Aggregate activities comprise the activities of organs parenchyma and the activity in the regional blood volumes (RBV). Concept-1 resulted in notably higher absorbed doses for most organs, especially non-source organs with substantial blood contents, e.g. lungs (92% maximum difference). Consequently, effective doses increased in concept-1 compared to concept-2 by 3-10%. Not considering the blood as a distinct source region leads to an underestimation of the organ absorbed doses and effective doses. The pronounced influence of the blood even for a radiopharmaceutical with a rapid clearance from the blood, such as 18F-FSPG, suggests that blood should be introduced as a separate compartment in most compartmental pharmacokinetic models and blood should be considered as a distinct source in

  1. Exploring Ce3+/Ce4+ cation ordering in reduced ceria nanoparticles using interionic-potential and density-functional calculations.

    PubMed

    Migani, Annapaola; Neyman, Konstantin M; Illas, Francesc; Bromley, Stefan T

    2009-08-14

    The performance of atomistic calculations using interionic potentials has been examined in detail with respect to the structures and energetic stabilities of ten configurational isomers (i.e., distinct Ce3+/Ce4+ cationic orderings) of a low energy octahedral ceria nanoparticle Ce19O32. The outcome of these calculations is compared with the results of corresponding density-functional (DF) calculations employing local and gradient corrected functionals with an additional corrective onsite Coulombic interaction applied to the f-electrons (i.e., LDA+U and GGA+U, respectively). Strikingly similar relative energy ordering of the isomers and atomic scale structural trends (e.g., cation-cation distances) are obtained in both the DF and interionic-potential calculations. The surprisingly good agreement between the DF electronic structure calculations and the relatively simple classical potentials is not found to be due to a single dominant interaction type but is due to a sensitive balance between long range electrostatics and local bonding contributions to the energy. Considering the relatively high computational cost and technical difficulty involved in obtaining charge-localized electronic solutions for reduced ceria using DF calculations, the use of interionic potentials for rapid and reliable preselection of the most stable Ce3+/Ce4+ cationic orderings is of considerable benefit.

  2. Effective core potentials for the cadmium and mercury atoms

    NASA Technical Reports Server (NTRS)

    Basch, H.; Newton, M. D.; Jafri, J.; Moskowitz, J. W.; Topiol, S.

    1978-01-01

    Ab initio effective core potentials have been obtained for the cadmium and mercury atoms by the methods of Kahn et al. (1976). Both two and twelve valence electron representations of Cd and Hg were tested for various atom state-configurations by comparison with all-electron calculations. The generated potentials were used to obtain the equilibrium bond distances and molecular binding energies for the dichloride and dimethyl compounds of both atoms from single and optimum-double configuration self-consistent field calculations.

  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. 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.

  5. 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.

  6. 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

  7. 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

  8. Accurate high level ab initio-based global potential energy surface and dynamics calculations for ground state of CH2(+).

    PubMed

    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 CH2 (+) 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(+)(X(1)Σ(+))+H((2)S)→C(+)((2)P)+H2(X(1)Σg (+)) 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(+)/H containing systems.

  9. Positron-electron correlation-polarization potentials for the calculation of positron collisions with atoms and molecules*

    NASA Astrophysics Data System (ADS)

    Franz, Jan

    2017-02-01

    We present correlation-polarization potentials for the calculation of scattering cross sections of positrons with atoms and molecules. The potentials are constructed from a short-range correlation term and a long-range polarization term. For the short-range correlation term we present four different potentials that are derived from multi-component density functionals. For the long-range polarization term we employ a multi-term expansion. Quantum scattering calculations are presented for low energy collisions of positrons with two atomic targets (argon and krypton) and two molecular targets (nitrogen and methane). For collision energies below the threshold for Positronium formation our calculations of scattering cross sections are in good agreement with recent data sets from experiments and theory. Contribution to the Topical Issue "Low-Energy Interactions related to Atmospheric and Extreme Conditions", edited by S. Ptasinska, M. Smialek-Telega, A. Milosavljevic and B. Sivaraman.

  10. Molecular calculations of excitation energies and (hyper)polarizabilities with a statistical average of orbital model exchange-correlation potentials

    NASA Astrophysics Data System (ADS)

    Schipper, P. R. T.; Gritsenko, O. V.; van Gisbergen, S. J. A.; Baerends, E. J.

    2000-01-01

    An approximate Kohn-Sham exchange-correlation potential νxcSAOP is developed with the method of statistical averaging of (model) orbital potentials (SAOP) and is applied to the calculation of excitation energies as well as of static and frequency-dependent multipole polarizabilities and hyperpolarizabilities within time-dependent density functional theory (TDDFT). νxcSAOP provides high quality results for all calculated response properties and a substantial improvement upon the local density approximation (LDA) and the van Leeuwen-Baerends (LB) potentials for the prototype molecules CO, N2, CH2O, and C2H4. For the first three molecules and the lower excitations of the C2H4 the average error of the vertical excitation energies calculated with νxcSAOP approaches the benchmark accuracy of 0.1 eV for the electronic spectra.

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

    SciTech Connect

    Zhang, Zhiqiang; Geng, Dalong; Wang, Xudong

    2016-04-21

    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.

  12. Potential Therapeutic Effects of Psilocybin.

    PubMed

    Johnson, Matthew W; Griffiths, Roland R

    2017-07-01

    Psilocybin and other 5-hydroxytryptamine2A agonist classic psychedelics have been used for centuries as sacraments within indigenous cultures. In the mid-twentieth century they were a focus within psychiatry as both probes of brain function and experimental therapeutics. By the late 1960s and early 1970s these scientific inquires fell out of favor because classic psychedelics were being used outside of medical research and in association with the emerging counter culture. However, in the twenty-first century, scientific interest in classic psychedelics has returned and grown as a result of several promising studies, validating earlier research. Here, we review therapeutic research on psilocybin, the classic psychedelic that has been the focus of most recent research. For mood and anxiety disorders, three controlled trials have suggested that psilocybin may decrease symptoms of depression and anxiety in the context of cancer-related psychiatric distress for at least 6 months following a single acute administration. A small, open-label study in patients with treatment-resistant depression showed reductions in depression and anxiety symptoms 3 months after two acute doses. For addiction, small, open-label pilot studies have shown promising success rates for both tobacco and alcohol addiction. Safety data from these various trials, which involve careful screening, preparation, monitoring, and follow-up, indicate the absence of severe drug-related adverse reactions. Modest drug-related adverse effects at the time of medication administration are readily managed. US federal funding has yet to support therapeutic psilocybin research, although such support will be important to thoroughly investigate efficacy, safety, and therapeutic mechanisms.

  13. 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

  14. 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…

  15. Advanced relativistic model potential approach to calculation of radiation transition parameters in spectra of multicharged ions

    NASA Astrophysics Data System (ADS)

    Svinarenko, A. A.; Ignatenko, A. V.; Ternovsky, V. B.; Nikola, V. V.; Seredenko, S. S.; Tkach, T. B.

    2014-11-01

    The combined relativistic energy approach and relativistic many-body perturbation theory with the zeroth order optimized one-particle approximation are used for calculation of the Li-like ions (Z=11-42,69,70) energies and oscillator strengths of radiative transitions from the ground state to the low-excited and Rydberg states, in particular, 2s1/2 - np1/2,3/2, np1/2,3/2- nd3/2,5/2 (n=2-12). A comparison of the calculated oscillator strengths with available theoretical and experimental data is performed.

  16. 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.

  17. Effect of cephalometer misalignment on calculations of facial asymmetry.

    PubMed

    Lee, Ki-Heon; Hwang, Hyeon-Shik; Curry, Sean; Boyd, Robert L; Norris, Kevin; Baumrind, Sheldon

    2007-07-01

    In this study, we evaluated errors introduced into the interpretation of facial asymmetry on posteroanterior (PA) cephalograms due to malpositioning of the x-ray emitter focal spot. We tested the hypothesis that horizontal displacements of the emitter from its ideal position would produce systematic displacements of skull landmarks that could be fully accounted for by the rules of projective geometry alone. A representative dry skull with 22 metal markers was used to generate a series of PA images from different emitter positions by using a fully calibrated stereo cephalometer. Empirical measurements of the resulting cephalograms were compared with mathematical predictions based solely on geometric rules. The empirical measurements matched the mathematical predictions within the limits of measurement error (x= 0.23 mm), thus supporting the hypothesis. Based upon this finding, we generated a completely symmetrical mathematical skull and calculated the expected errors for focal spots of several different magnitudes. Quantitative data were computed for focal spot displacements of different magnitudes. Misalignment of the x-ray emitter focal spot introduces systematic errors into the interpretation of facial asymmetry on PA cephalograms. For misalignments of less than 20 mm, the effect is small in individual cases. However, misalignments as small as 10 mm can introduce spurious statistical findings of significant asymmetry when mean values for large groups of PA images are evaluated.

  18. An event-related potential investigation of spatial attention orientation in children trained with mental abacus calculation

    PubMed Central

    Liu, Xiaoqin

    2017-01-01

    The objective of this study was to investigate the effects of long-term mental abacus calculation training (MACT) on children’s spatial attention orientation. Fifteen children with intensive MACT (MACT group) and 15 children without MACT (non-MACT group) were selected. The two groups of children were matched in age, sex, handedness, and academic grade. The participants were tested with a Posner spatial cueing task while their neural activities were recorded with a 32-channel electroencephalogram system. The participants’ behavior scores (reaction time and accuracy) as well as early components of event-related potential (ERP) during the tests were statistically analyzed. The behavioral scores showed no significant difference between the two groups of children, although the MACT group tended to have a shorter reaction time. The early ERP components showed that under valid cueing condition, the MACT group had significantly higher P1 amplitude [F(1, 28)=5.06, P<0.05, effective size=0.72] and lower N1 amplitude [F(1, 28)=6.05, P<0.05, effective size=0.82] in the occipital region compared with the non-MACT group. In the centrofrontal brain region, the MACT group had lower N1 amplitude [F(1, 28)=4.89, P<0.05, effect size=0.70] and longer N1 latency [F(1, 28)=6.26, P<0.05, effect size=0.80] than the non-MACT group. In particular, the MACT group also showed a higher centrofrontal P2 amplitude in the right hemisphere [F(1, 28)=4.82, P<0.05, effect size 0.81] compared with the left hemisphere and the middle location. MACT enhances the children’s spatial attention orientation, which can be detected in the early components of ERP. PMID:27831960

  19. 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.

  20. 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.

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

    PubMed

    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 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.

  2. 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.

  3. 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.

  4. 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…

  5. 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…

  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. Electronically Excited States in Poly(p-phenylenevinylene): Vertical Excitations and Torsional Potentials from High-Level Ab Initio Calculations

    PubMed Central

    2013-01-01

    Ab initio second-order algebraic diagrammatic construction (ADC(2)) calculations using the resolution of the identity (RI) method have been performed on poly-(p-phenylenevinylene) (PPV) oligomers with chain lengths up to eight phenyl rings. Vertical excitation energies for the four lowest π–π* excitations and geometry relaxation effects for the lowest excited state (S1) are reported. Extrapolation to infinite chain length shows good agreement with analogous data derived from experiment. Analysis of the bond length alternation (BLA) based on the optimized S1 geometry provides conclusive evidence for the localization of the defect in the center of the oligomer chain. Torsional potentials have been computed for the four excited states investigated and the transition densities divided into fragment contributions have been used to identify excitonic interactions. The present investigation provides benchmark results, which can be used (i) as reference for lower level methods and (ii) give the possibility to parametrize an effective Frenkel exciton Hamiltonian for quantum dynamical simulations of ultrafast exciton transfer dynamics in PPV type systems. PMID:23427902

  8. CEPA Calculations of potential energy surfaces for open-shell systems. II. The reaction of C + Ions with molecular hydrogen

    NASA Astrophysics Data System (ADS)

    Jaquet, Ralph; Staemmler, Volker

    1982-07-01

    Ab initio calculations including electron correlation effects (mainly on CEPA-PNO level) have been performed for the potential energy surface (PES) of the reaction of 2P carbon ions with molecular hydrogen. For the collinear abstraction reactions (C ∞v symmetry: 2σ +, 2Π-2) the minimum energy paths have been determined. The vertical insertion reaction (C 2v; 2A 1,B 1, 2B 2) has been investigated with particular emphasis (minimum energy path, barrier heights, intersystem crossing). The influence of the size of the orbital basis and of electron correlation has been studied in some detail. The interaction of the 2A 1, and 2B 2 surfaces has been analyzed, leading to the conclusion that close to C 2v symmetry a low energy path exists by which CH 2+( 2A 1)can be easily formed, with a barrier ( 2B 2 → 2A 1) ≈ 18 kcal/mol below the asymptote. The analysis of electron correlation effects reveals that it is compulsory to correlate the whole valence shell if one wants to obtain reliable surfaces. The influence of singly excited configurations for getting the correct behaviour of the PES is generally small.

  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. New Method for Calculating the Potential Energy of Deformed Nuclei within the Liquid-Drop Model

    SciTech Connect

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

    2004-11-01

    The method that we previously developed for going over from double volume integrals to double surface integrals in calculating the Coulomb energy of nuclei that have a sharp surface is generalized to the case of nuclei where the range of nuclear forces is finite and where the nuclear surface is diffuse. New formulas for calculating the Coulomb and the nuclear energy of deformed nuclei are obtained within this approach. For a spherically symmetric nucleus, in which case there is an analytic solution to the problem in question, the results are compared with those that are quoted in the literature, and it is shown that the respective results coincide identically. A differential formulation of the method developed previously by Krappe, Nix, and Sierk for going over from double volume integrals to double surface integrals is proposed here on the basis of the present approach.

  11. Relativistic semiempirical-core-potential calculations of Sr+ using Laguerre and Slater spinors

    NASA Astrophysics Data System (ADS)

    Jiang, Jun; Mitroy, J.; Cheng, Yongjun; Bromley, Michael W. J.

    2016-12-01

    A relativistic description of the structure of heavy alkali-metal atoms and alkali-like ions using S-spinors and L-spinors is developed. The core wave function is defined by a Dirac-Fock calculation using an S-spinor basis. The S-spinor basis is then supplemented with a large set of L-spinors for calculation of the valence wave function in a frozen-core model. The numerical stability of the L-spinor approach is demonstrated by computing the energies and decay rates of several low-lying hydrogen eigenstates, along with the polarizabilities of a Z =60 hydrogenic ion. The approach is then applied to calculate the dynamic polarizabilities of the 5 s , 4 d , and 5 p states of Sr+. The magic wavelengths at which the Stark shifts between different pairs of transitions are 0 are computed. Determination of the magic wavelengths for the 5 s →4 d3/2 and 5 s →4 d5/2 transitions near 417 nm (near the wavelength for the 5 s →5 pj transitions) would allow determination of the oscillator strength ratio for the 5 s →5 p1/2 and 5 s →5 p3/2 transitions.

  12. 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.

  13. Electronic structure of molecules using relativistic effective core potentials

    SciTech Connect

    Hay, P.J.

    1981-01-01

    Starting with one-component Cowan-Griffin relativistic Hartree-Fock orbitals, which successfully incorporate the mass-velocity and Darwin terms present in more complicated wavefunctions such as Dirac-Hartree-Fock, one can derive relativistic effective core potentials (RECP's) to carry out molecular calculations. These potentials implicitly include the dominant relativistic terms for molecules while allowing one to use the traditional quantum chemical techniques for studying the electronic structure of molecules. The effects of spin-orbit coupling can then be included using orbitals from such calculations using an effective 1-electron, 1-center spin-orbit operator. Applications to molecular systems involving heavy atoms, show good agreement with available spectroscopic data on molecular geometries and excitation energies.

  14. Electric potential invariants and ions-in-molecules effective potentials for molecular Rydberg states.

    PubMed

    Coy, Stephen L; Grimes, David D; Zhou, Yan; Field, Robert W; Wong, Bryan M

    2016-12-21

    The dependence of multipole moments and polarizabilities on external fields appears in many applications including biomolecular molecular mechanics, optical non-linearity, nanomaterial calculations, and the perturbation of spectroscopic signatures in atomic clocks. Over a wide range of distances, distributed multipole and polarizability potentials can be applied to obtain the variation of atom-centered atoms-in-molecules electric properties like bonding-quenched polarizability. For cylindrically symmetric charge distributions, we examine single-center and atom-centered effective polarization potentials in a non-relativistic approximation for Rydberg states. For ions, the multipole expansion is strongly origin-dependent, but we note that origin-independent invariants can be defined. The several families of invariants correspond to optimized representations differing by origin and number of terms. Among them, a representation at the center of dipole polarizability optimizes the accuracy of the potential with terms through 1/r(4). We formulate the single-center expansion in terms of polarization-modified effective multipole moments, defining a form related to the source-multipole expansion of Brink and Satchler. Atom-centered potentials are an origin independent alternative but are limited both by the properties allowed at each center and by the neglected effects like bond polarizability and charge flow. To enable comparisons between single-center effective potentials in Cartesian or spherical form and two-center effective potentials with differing levels of mutual induction between atomic centers, we give analytical expressions for the bond-length and origin-dependence of multipole and polarizability terms projected in the multipole and polarizability expansion of Buckingham. The atom-centered potentials can then be used with experimental data and ab initio calculations to estimate atoms-in-molecules properties. Some results are given for BaF(+) and HF showing the

  15. Electric potential invariants and ions-in-molecules effective potentials for molecular Rydberg states

    NASA Astrophysics Data System (ADS)

    Coy, Stephen L.; Grimes, David D.; Zhou, Yan; Field, Robert W.; Wong, Bryan M.

    2016-12-01

    The dependence of multipole moments and polarizabilities on external fields appears in many applications including biomolecular molecular mechanics, optical non-linearity, nanomaterial calculations, and the perturbation of spectroscopic signatures in atomic clocks. Over a wide range of distances, distributed multipole and polarizability potentials can be applied to obtain the variation of atom-centered atoms-in-molecules electric properties like bonding-quenched polarizability. For cylindrically symmetric charge distributions, we examine single-center and atom-centered effective polarization potentials in a non-relativistic approximation for Rydberg states. For ions, the multipole expansion is strongly origin-dependent, but we note that origin-independent invariants can be defined. The several families of invariants correspond to optimized representations differing by origin and number of terms. Among them, a representation at the center of dipole polarizability optimizes the accuracy of the potential with terms through 1/r4. We formulate the single-center expansion in terms of polarization-modified effective multipole moments, defining a form related to the source-multipole expansion of Brink and Satchler. Atom-centered potentials are an origin independent alternative but are limited both by the properties allowed at each center and by the neglected effects like bond polarizability and charge flow. To enable comparisons between single-center effective potentials in Cartesian or spherical form and two-center effective potentials with differing levels of mutual induction between atomic centers, we give analytical expressions for the bond-length and origin-dependence of multipole and polarizability terms projected in the multipole and polarizability expansion of Buckingham. The atom-centered potentials can then be used with experimental data and ab initio calculations to estimate atoms-in-molecules properties. Some results are given for BaF+ and HF showing the

  16. 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.

  17. Electric potential calculation in molecular simulation of electric double layer capacitors

    NASA Astrophysics Data System (ADS)

    Wang, Zhenxing; Olmsted, David L.; Asta, Mark; Laird, Brian B.

    2016-11-01

    For the molecular simulation of electric double layer capacitors (EDLCs), a number of methods have been proposed and implemented to determine the one-dimensional electric potential profile between the two electrodes at a fixed potential difference. In this work, we compare several of these methods for a model LiClO4-acetonitrile/graphite EDLC simulated using both the traditional fixed-charged method (FCM), in which a fixed charge is assigned a priori to the electrode atoms, or the recently developed constant potential method (CPM) (2007 J. Chem. Phys. 126 084704), where the electrode charges are allowed to fluctuate to keep the potential fixed. Based on an analysis of the full three-dimensional electric potential field, we suggest a method for determining the averaged one-dimensional electric potential profile that can be applied to both the FCM and CPM simulations. Compared to traditional methods based on numerically solving the one-dimensional Poisson’s equation, this method yields better accuracy and no supplemental assumptions.

  18. Electric potential calculation in molecular simulation of electric double layer capacitors.

    PubMed

    Wang, Zhenxing; Olmsted, David L; Asta, Mark; Laird, Brian B

    2016-11-23

    For the molecular simulation of electric double layer capacitors (EDLCs), a number of methods have been proposed and implemented to determine the one-dimensional electric potential profile between the two electrodes at a fixed potential difference. In this work, we compare several of these methods for a model LiClO4-acetonitrile/graphite EDLC simulated using both the traditional fixed-charged method (FCM), in which a fixed charge is assigned a priori to the electrode atoms, or the recently developed constant potential method (CPM) (2007 J. Chem. Phys. 126 084704), where the electrode charges are allowed to fluctuate to keep the potential fixed. Based on an analysis of the full three-dimensional electric potential field, we suggest a method for determining the averaged one-dimensional electric potential profile that can be applied to both the FCM and CPM simulations. Compared to traditional methods based on numerically solving the one-dimensional Poisson's equation, this method yields better accuracy and no supplemental assumptions.

  19. Effect of the cluster integrals on three particles on the calculated electron density of a hydrogen plasma

    NASA Technical Reports Server (NTRS)

    Mcintyre, R. G.; Bruce, R. E.

    1974-01-01

    The effect of the calculation of the cluster integrals on three particles is analyzed and evaluated for a hydrogen plasma where a pairwise-additive hard sphere-Coulomb potential is assumed. The Mayer cluster integral method was used to calculate the Helmholtz free energy which was then applied to the calculation of the electron number density through an iterative technique using a corrected Saha equation. It is seen that the three particle integrals provide a substantial correction to the calculations in the low energy-high density region of the hydrogen plasma.

  20. Effect of the cluster integrals on three particles on the calculated electron density of a hydrogen plasma

    NASA Technical Reports Server (NTRS)

    Mcintyre, R. G.; Bruce, R. E.

    1974-01-01

    The effect of the calculation of the cluster integrals on three particles is analyzed and evaluated for a hydrogen plasma where a pairwise-additive hard sphere-Coulomb potential is assumed. The Mayer cluster integral method was used to calculate the Helmholtz free energy which was then applied to the calculation of the electron number density through an iterative technique using a corrected Saha equation. It is seen that the three particle integrals provide a substantial correction to the calculations in the low energy-high density region of the hydrogen plasma.

  1. Calculation of P, T-odd effects in 205TlF including electron correlation.

    PubMed

    Petrov, A N; Mosyagin, N S; Isaev, T A; Titov, A V; Ezhov, V F; Eliav, E; Kaldor, U

    2002-02-18

    A method and codes for two-step correlation calculations of heavy-atom molecules have been developed, employing the generalized relativistic effective core potential (GRECP) and relativistic coupled cluster (RCC) methods at the first step, followed by nonvariational one-center restoration of proper four-component spinors in the heavy cores. Electron correlation is included for the first time in an ab initio calculation of the interaction of the permanent P,T-odd proton electric dipole moments with the internal electromagnetic field in a molecule. Inclusion of electron correlation by GRECP/RCC has a major effect on the P,T-odd parameters of 205TlF, decreasing M by 17% and X by 22%.

  2. Effects of nonlinear aerodynamics and static aeroelasticity on mission performance calculations for a fighter aircraft

    NASA Technical Reports Server (NTRS)

    Giles, Gary L.; Tatum, Kenneth E.; Foss, Willard E., Jr.

    1989-01-01

    During conceptual design studies of advanced aircraft, the usual practice is to use linear theory to calculate the aerodynamic characteristics of candidate rigid (nonflexible) geometric external shapes. Recent developments and improvements in computational methods, especially computational fluid dynamics (CFD), provide significantly improved capability to generate detailed analysis data for the use of all disciplines involved in the evaluation of a proposed aircraft design. A multidisciplinary application of such analysis methods to calculate the effects of nonlinear aerodynamics and static aeroelasticity on the mission performance of a fighter aircraft concept is described. The aircraft configuration selected for study was defined in a previous study using linear aerodynamics and rigid geometry. The results from the previous study are used as a basis of comparison for the data generated herein. Aerodynamic characteristics are calculated using two different nonlinear theories, potential flow and rotational (Euler) flow. The aerodynamic calculations are performed in an iterative procedure with an equivalent plate structural analysis method to obtain lift and drag data for a flexible (nonrigid) aircraft. These static aeroelastic data are then used in calculating the combat and mission performance characteristics of the aircraft.

  3. 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.

  4. Elastocaloric effect on the piezoelectric potential of boron nitride nanotubes

    NASA Astrophysics Data System (ADS)

    Zhang, Jin

    2017-10-01

    In this paper, molecular dynamics (MD) simulations and analytical calculations are performed to study the influence of the elastocaloric effect (ECE) on the piezoelectric potential of hexagonal boron nitride (BN) nanotubes. To take into account the ECE in the simulations and calculations, the adiabatic condition is required. To reach this goal, the heat transfer between the BN nanotubes and their environment is excluded in the present study. In MD simulations, we find a large ECE in BN nanotubes, which will make the temperature of the BN nanotubes greatly change after external loads are applied on them. Moreover, the piezoelectric and dielectric properties of BN nanotubes calculated from MD simulations are found to be strongly dependent on the temperature. The temperature-dependent piezoelectric and dielectric properties together with the ECE are thus considered in the analytical calculations of the piezoelectric potential of BN nanotubes. The obtained analytical results reveal that the large ECE in BN nanotubes will make the piezoelectric potential of BN nanotubes strongly depend on the loading path of external loads. Specifically, stretching a BN nanotube is found to be more efficient than compressing the nanotube to generate the piezoelectric potential. These results are expected to significantly expand the knowledge of the electromechanical behaviours of piezoelectric nanomaterials and provide important guidelines for the optimum design of piezotronics nanodevices.

  5. 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.

  6. Calculation of the nd Scattering Lengths by a Realistic Nonlocal Gaussian Potential

    SciTech Connect

    Fukukawa, K.; Fujiwara, Y.

    2010-05-12

    We apply a quark-model nucleon-nucleon interaction to the neutron-deuteron (nd) scattering. We solve the Alt-Grassberger-Sandhas equation in the momentum space. The doublet and quartet nd scattering lengths ({sup 2}a{sub nd} and {sup 4}a{sub nd}) are calculated. We re-confirm the pole structure in the doublet scattering length. The experimental data are well reproduced without three-nucleon forces. This result seems to be related to the off-shell properties of the quark-model nucleon-nucleon interaction.

  7. Half-life calculation of one-proton emitters with a shell model potential

    SciTech Connect

    Rodrigues, M. M.; Duarte, S. B.

    2013-03-25

    The accumulated amount of data for half-lives of proton emitters still remains a challenge to the ability of nuclear models to reproduce them consistently. These nuclei are far from beta stability line in a region where the validity of current nuclear models is not guaranteed. A nuclear shell model is introduced to the calculation of the nuclear barrier of less deformed proton emitters. The predictions using the proposed model are in good agreement with the data, with the advantage of have used only a single parameter in the model.

  8. 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)

  9. 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)

  10. PT symmetric interpretation of effective potentials

    NASA Astrophysics Data System (ADS)

    Sarkar, Sarben

    2017-07-01

    Conventional systems in equilibrium should have convex effective potentials. PT symmetry applies to systems which are in between open and closed systems. A PT symmetric interpretation can allow some non-convex effective potentials to be entirely physical. The oneloop effective potentials of the Higgs field in the Standard Model and the gravitino condensate in dynamically broken supergravity are conventionally unstable at large field values. In the specially simple case of space-independent and time-independent fields, the effective potentials are governed by PT-symmetric quantum mechanics. The PT-symmetric reinterpretation of these models at a quantum-mechanical level eliminates these instabilities and involves unusual semi-classical analysis involving many Riemann sheets. This interpretation is based on a combination of numerical analysis and semi-classical asymptotics.

  11. 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.

  12. 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.

  13. 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.

  14. Self-consistent field calculations on diatomic hydrogen in a potential well

    SciTech Connect

    Bunch, K.J.; Grow, R.W. )

    1991-07-01

    The equilibrium behavior of diatomic hydrogen in a potential well is explored. The amount of squeezing experienced by hydrogen in the well is compared to that expected for hydrogen within palladium. Results show insufficient squeezing to account for the cold fusion phenomenon.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  16. Accelerating Electrostatic Surface Potential Calculation with Multiscale Approximation on Graphics Processing Units

    PubMed Central

    Anandakrishnan, Ramu; Scogland, Tom R. W.; Fenley, Andrew T.; Gordon, John C.; Feng, Wu-chun; Onufriev, Alexey V.

    2010-01-01

    Tools that compute and visualize biomolecular electrostatic surface potential have been used extensively for studying biomolecular function. However, determining the surface potential for large biomolecules on a typical desktop computer can take days or longer using currently available tools and methods. Two commonly used techniques to speed up these types of electrostatic computations are approximations based on multi-scale coarse-graining and parallelization across multiple processors. This paper demonstrates that for the computation of electrostatic surface potential, these two techniques can be combined to deliver significantly greater speed-up than either one separately, something that is in general not always possible. Specifically, the electrostatic potential computation, using an analytical linearized Poisson Boltzmann (ALPB) method, is approximated using the hierarchical charge partitioning (HCP) multiscale method, and parallelized on an ATI Radeon 4870 graphical processing unit (GPU). The implementation delivers a combined 934-fold speed-up for a 476,040 atom viral capsid, compared to an equivalent non-parallel implementation on an Intel E6550 CPU without the approximation. This speed-up is significantly greater than the 42-fold speed-up for the HCP approximation alone or the 182-fold speed-up for the GPU alone. PMID:20452792

  17. Potential and electron density calculated for freely expanding plasma by an electron beam

    SciTech Connect

    Ho, C. Y.; Tsai, Y. H.; Ma, C.; Wen, M. Y.

    2011-07-01

    This paper investigates the radial distributions of potential and electron density in free expansion plasma induced by an electron beam irradiating on the plate. The region of plasma production is assumed to be cylindrical, and the plasma expansion is assumed to be from a cylindrical source. Therefore, the one-dimensional model in cylindrical coordinates is employed in order to analyze the radial distributions of the potential and electron density. The Runge-Kutta method and the perturbation method are utilized in order to obtain the numerical and approximate solutions, respectively. The results reveal that the decrease in the initial ion energy makes most of the ions gather near the plasma production region and reduces the distribution of the average positive potential, electron, and ion density along the radial direction. The oscillation of steady-state plasma along the radial direction is also presented in this paper. The ions induce a larger amplitude of oscillation along the radial direction than do electrons because the electrons oscillate around slowly moving ions due to a far smaller electron mass than ion mass. The radial distributions of the positive potential and electron density predicted from this study are compared with the available experimental data.

  18. Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units.

    PubMed

    Anandakrishnan, Ramu; Scogland, Tom R W; Fenley, Andrew T; Gordon, John C; Feng, Wu-chun; Onufriev, Alexey V

    2010-06-01

    Tools that compute and visualize biomolecular electrostatic surface potential have been used extensively for studying biomolecular function. However, determining the surface potential for large biomolecules on a typical desktop computer can take days or longer using currently available tools and methods. Two commonly used techniques to speed-up these types of electrostatic computations are approximations based on multi-scale coarse-graining and parallelization across multiple processors. This paper demonstrates that for the computation of electrostatic surface potential, these two techniques can be combined to deliver significantly greater speed-up than either one separately, something that is in general not always possible. Specifically, the electrostatic potential computation, using an analytical linearized Poisson-Boltzmann (ALPB) method, is approximated using the hierarchical charge partitioning (HCP) multi-scale method, and parallelized on an ATI Radeon 4870 graphical processing unit (GPU). The implementation delivers a combined 934-fold speed-up for a 476,040 atom viral capsid, compared to an equivalent non-parallel implementation on an Intel E6550 CPU without the approximation. This speed-up is significantly greater than the 42-fold speed-up for the HCP approximation alone or the 182-fold speed-up for the GPU alone.

  19. QM/MM calculations of kinetic isotope effects in the chorismate mutase active site.

    PubMed

    Martí, Sergio; Moliner, Vincent; Tuñón, Iñaki; Williams, Ian H

    2003-02-07

    Kinetic isotope effects have been computed for the Claisen rearrangement of chorismate to prephenate in aqueous solution and in the active site of chorismate mutase from B. subtilus. These included primary 13C and 18O and secondary 3H effects for substitutions at the bond-making and bond-breaking positions. The initial structures of the putative stationary points on the potential energy surface, required for the calculations of isotope effects using the CAMVIB/CAMISO programs, have been selected from hybrid QM/MM molecular dynamical simulations using the DYNAMO program. Refinement of the reactant complex and transition-state structures has been carried out by means of AM1/CHARMM24/TIP3P calculations using the GRACE program, with full gradient relaxation of the position of > 5200 atoms for the enzymic simulations, and with a box containing 711 water molecules for the corresponding reaction in aqueous solution. Comparison of these results, and of gas phase calculations, with experimental data has shown that the chemical rearrangement is largely rate-determining for the enzyme mechanism. Inclusion of the chorismate conformational pre-equilibrium step in the modelled kinetic scheme leads to better agreement between recent experimental data and theoretical predictions. These results provide new information on an important enzymatic transformation, and the key factors responsible for the kinetics of its molecular mechanism are clarified. Treatment of the enzyme and/or solvent environment by means of a large and flexible model is absolutely essential for prediction of kinetic isotope effects.

  20. Chern-Simons potential in models of Casimir effect

    SciTech Connect

    Pis'mak, Yury M.; Pis'mak, Daria Yu.

    2014-07-23

    In the model constructed in the framework of the proposed by Symanzik approach for description of interaction of a macroscopic material body with quantum fields the interaction of thin material film with photon field is presented by the Chern-Simons potential. All the effects of this interaction with can by described in the framework of one model. In this way, the Casimir energy for two parallel infinite planes and sphere, the Casimir-Polder potential, and characteristics of other physical phenomena have been calculated for non-ideal conducting material of film. The specific of regularization and renormalization procedures used by calculations and the physical meaning of obtained results are discussed. In the limit of infinite coupling constant one obtains the known results of models with boundary conditions. By finite value of coupling constants the model predicts unusual effects which could be important for micro-mechanics, nano-photonics, constructing of new materials.

  1. Liquid junction potentials calculated from numerical solutions of the Nernst-Planck and Poisson equations.

    PubMed

    Riveros, O J; Croxton, T L; Armstrong, W M

    1989-09-22

    We present numerical solutions for the one-dimensional Nernst-Planck and Poisson system of equations for steady-state electrodiffusion. Commonly used approximate solutions to these equations invoke assumptions of local electroneutrality (Planck approximation) or constant electric field (Goldman approximation). Calculations were performed to test the ranges over which these approximate theories are valid. For a dilutional junction of a 1:1 electrolyte, separated from adjoining perfectly stirred solutions by sharp boundaries, the Planck approximation is valid for values of kappa dL greater than 10, where 1/kappa d is the Debye length of the more dilute solution. The Goldman approximation is valid for kappa cL less than 0.1 where 1/kappa c is the Debye length of the more concentrated solution. These results suggest that the modeling of electrodiffusive flows in and near membrane ion channels may require numerical solutions of this set of equations rather than the use of either limiting case.

  2. 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)

  3. [Cost-effectiveness analysis of prevention of reinfarction using low-dose acetylsalicylic acid; model calculation].

    PubMed

    Schädlich, P K; Brecht, J G

    1997-01-01

    The purpose of this study is to estimate the potential of savings which can be achieved by prophylaxis of myocardial reinfarction with low-dose acetylsalicylic acid (ASA) at 75 mg per day over a treatment period of two years. After secondary analysis of published data, the effectiveness of low-dose ASA is compared to placebo by a model calculation. The difference in the effectiveness between the prophylaxis with ASA and placebo is taken from an international meta-analysis. The economic valuation of this difference is carried out by a cost-effectiveness analysis applying disease costs per case. According to the model calculation, 5535 DM can be saved per patient with a history of myocardial infarction with 75 mg ASA a day over a treatment period of two years. In 1991 there were around 740,000 patients with a history of myocardial infarction in the age group of 25-64 in the Old Bundesländer of the Federal Republic of Germany. The application of the results of the model calculation would lead to considerable savings. Even in the sensitivity analysis with different assumptions regarding costs incurred by hospital treatment and costs incurred by premature retirement, the cost advantage of the ASA-prophylaxis remains. Due to the cautious and conservative assumptions in the model calculation the potential of savings is likely underestimated. Nevertheless, there is a distinct advantage for the prophylaxis with low-dose ASA which already occurs in direct costs thus leading to advantages also for cost carriers.

  4. Effective potentials from complex simulations: a potential-matching algorithm and remarks on coarse-grained potentials

    NASA Astrophysics Data System (ADS)

    Tóth, Gergely

    2007-08-01

    The projection of complex interactions onto simple distance-dependent or angle-dependent classical mechanical functions is a long-standing theoretical challenge in the field of computational sciences concerning biomolecules, colloids, aggregates and simple systems as well. The construction of an effective potential may be based on theoretical assumptions, on the application of fitting procedures on experimental data and on the simplification of complex molecular simulations. Recently, a force-matching method was elaborated to project the data of Car-Parrinello ab initio molecular dynamics simulations onto two-particle classical interactions (Izvekov et al 2004 J. Chem. Phys. 120 10896). We have developed a potential-matching algorithm as a practical analogue of this force-matching method. The algorithm requires a large number of configurations (particle positions) and a single value of the potential energy for each configuration. We show the details of the algorithm and the test calculations on simple systems. The test calculation on water showed an example in which a similar structure was obtained for qualitatively different pair interactions. The application of the algorithm on reverse Monte Carlo configurations was tried as well. We detected inconsistencies in a part of our calculations. We found that the coarse graining of potentials cannot be performed perfectly both for the structural and the thermodynamic data. For example, if one applies an inverse method with an input of the pair-correlation function, it provides energetics data for the configurations uniquely. These energetics data can be different from the desired ones obtained by all atom simulations, as occurred in the testing of our potential-matching method.

  5. 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.

  6. 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.

  7. Shielding requirements for constant-potential diagnostic x-ray beams determined by a Monte Carlo calculation.

    PubMed

    Simpkin, D J

    1989-02-01

    A Monte Carlo calculation has been performed to determine the transmission of broad constant-potential x-ray beams through Pb, concrete, gypsum wallboard, steel and plate glass. The EGS4 code system was used with a simple broad-beam geometric model to generate exposure transmission curves for published 70, 100, 120 and 140-kVcp x-ray spectra. These curves are compared to measured three-phase generated x-ray transmission data in the literature and found to be reasonable. For calculation ease the data are fit to an equation previously shown to describe such curves quite well. These calculated transmission data are then used to create three-phase shielding tables for Pb and concrete, as well as other materials not available in Report No. 49 of the NCRP.

  8. 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.

  9. Conceptual DFT Descriptors of Amino Acids with Potential Corrosion Inhibition Properties Calculated with the Latest Minnesota Density Functionals.

    PubMed

    Frau, Juan; Glossman-Mitnik, Daniel

    2017-01-01

    Amino acids and peptides have the potential to perform as corrosion inhibitors. The chemical reactivity descriptors that arise from Conceptual DFT for the twenty natural amino acids have been calculated by using the latest Minnesota family of density functionals. In order to verify the validity of the calculation of the descriptors directly from the HOMO and LUMO, a comparison has been performed with those obtained through ΔSCF results. Moreover, the active sites for nucleophilic and electrophilic attacks have been identified through Fukui function indices, the dual descriptor Δf(r) and the electrophilic and nucleophilic Parr functions. The results could be of interest as a starting point for the study of large peptides where the calculation of the radical cation and anion of each system may be computationally harder and costly.

  10. Conceptual DFT Descriptors of Amino Acids with Potential Corrosion Inhibition Properties Calculated with the Latest Minnesota Density Functionals

    NASA Astrophysics Data System (ADS)

    Frau, Juan; Glossman-Mitnik, Daniel

    2017-03-01

    It is well known that amino acids and peptides have the potential to perform as corrosion inhibitors. The chemical reactivity descriptors that arise from Conceptual DFT for the twenty natural amino acids have been calculated by using the latest Minnesota family of density functionals. In order to verify the validity of the calculation of the descriptors directly from the HOMO and LUMO, a comparison has been performed with those obtained through ∆SCF results. Moreover, the active sites for nucleophilic and electrophilic attacks have been identified through Fukui function indices, the dual descriptor ∆f(r) and the electrophilic and nucleophilic Parr functions. The results could be of interest as a starting point for the study of large peptides where the calculation of the radical cation and anion of each system may be computationally harder and costly.

  11. Conceptual DFT Descriptors of Amino Acids with Potential Corrosion Inhibition Properties Calculated with the Latest Minnesota Density Functionals

    PubMed Central

    Frau, Juan; Glossman-Mitnik, Daniel

    2017-01-01

    Amino acids and peptides have the potential to perform as corrosion inhibitors. The chemical reactivity descriptors that arise from Conceptual DFT for the twenty natural amino acids have been calculated by using the latest Minnesota family of density functionals. In order to verify the validity of the calculation of the descriptors directly from the HOMO and LUMO, a comparison has been performed with those obtained through ΔSCF results. Moreover, the active sites for nucleophilic and electrophilic attacks have been identified through Fukui function indices, the dual descriptor Δf(r) and the electrophilic and nucleophilic Parr functions. The results could be of interest as a starting point for the study of large peptides where the calculation of the radical cation and anion of each system may be computationally harder and costly. PMID:28361050

  12. Ab initio projected-unrestricted Hartree-Fock calculation of some potential energy curves for carbonyl fluoride

    NASA Technical Reports Server (NTRS)

    Brewer, D. A.; Schug, J. C.; Phillips, D. H.

    1980-01-01

    Some potential energy curves for CF2O were calculated using projected-unrestricted Hartree-Fock (PUHF) theory. The calculations employed a contracted (4s 3p) Gaussian-type atomic orbital basis set. Bound states were found for the X-tilde 1A1 and 1,3A2 states while the 1,3B1 and 1,3B2 states were repulsive in the valence representation. The merits of the PUHF treatment for excited states are discussed. The results are discussed in terms of available experimental information and previous calculations with particular emphasis on the question of the photolysis channels open in the solar spectral region.

  13. Merit functions for more effective thin film calculations.

    PubMed

    Dobrowolski, J A; Ho, F C; Belkind, A; Koss, V A

    1989-07-15

    This paper reviews the different types of merit functions that have been used in the past in optical thin film calculations. Attention is drawn to the power of merit functions which operate on complicated quantities that require one or more integral expressions for their definition. To prove this point, several thin film problems are solved in which the CIE coordinates, luminous transmittances or reflectances, solar absorptance, and blackbody emittances of a multilayer are specified.

  14. Quantum calculations of vibrational energies of H3O2(-) and H5O2(+) with new ab initio potentials

    NASA Astrophysics Data System (ADS)

    Huang, Xinchuan; Braams, Bastiaan J.; Carter, Stuart; Bowman, Joel M.

    2004-03-01

    We have performed quantum mechanical studies of the vibrations of H3O2(-) and H5O2(+) in full dimensionality and with sufficient accuracy to resolve important features of the measured spectra. The computational procedure starts with extensive electronic structure calculations (several 10K configurations) at the CCSD(T) level of theory with augmented VTZ basis set using MOLPRO 2002. Then a global fit to the potential energy surface is constructed, based on a functional form that respects the spatial and permutational symmetries of the system. This PES fit is employed in a "Reaction Path Hamiltonian" MULTIMODE [1] calculation to obtain the vibrational spectrum. We provide comparisons with experimental data [2]. [1] MULTIMODE: A code to calculate rovibrational energies of polyatomic molecules, J. M. Bowman, S. Carter, and X.-C. Huang, Int. Rev. Phys. Chem. 22, 533 (2003). [2] Quantum calculations of vibrational energies of H3O2(-) with a new ab initio potential reveal large tunneling splittings. Manuscript in preparation, Dec 2003.

  15. Transonic flow analysis for rotors. Part 1: Three-dimensional quasi-steady, full-potential calculation

    NASA Technical Reports Server (NTRS)

    Chang, I. C.

    1984-01-01

    A new computer program is presented for calculating the quasi-steady transonic flow past a helicopter rotor blade in hover as well as in forward flight. The program is based on the full potential equations in a blade attached frame of reference and is capable of treating a very general class of rotor blade geometries. Computed results show good agreement with available experimental data for both straight and swept tip blade geometries.

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

    NASA Technical Reports Server (NTRS)

    Dulikravich, D. S.

    1980-01-01

    An exact nonlinear mathematical model that accounts for three-dimensional cascade effects about the inner portions of the rotor blades and compressibility effects about the tip regions of the blades was derived. An artificially time dependent version 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.

  17. Ruthenium tetraoxide oxidations of alkanes: DFT calculations of barrier heights and kinetic isotope effects.

    PubMed

    Drees, Markus; Strassner, Thomas

    2006-03-03

    The oxidation of C-H and C-C bonds by metal-oxo compounds is of general interest. We studied the RuO4-mediated catalytic oxidation of several cycloalkanes such as adamantane and cis- and trans-decalin as well as methane. B3LYP/6-31G(d) calculations on the experimentally proposed (3+2) mechanism are in good agreement with known experimental results. Comparison of experimental and theoretical kinetic isotope effects confirms the proposed mechanism. Besides RuO4, we also looked at RuO4(OH)- as a potential active species to account for ruthenium tetraoxide oxidations under strong basic conditions.

  18. Potential-model calculation of an order-v2 nonrelativistic QCD matrix element

    NASA Astrophysics Data System (ADS)

    Bodwin, Geoffrey T.; Kang, Daekyoung; Lee, Jungil

    2006-07-01

    We present two methods for computing dimensionally regulated nonrelativistic QCD heavy-quarkonium matrix elements that are related to the second derivative of the heavy-quarkonium wave function at the origin. The first method makes use of a hard-cutoff regulator as an intermediate step and requires knowledge only of the heavy-quarkonium wave function. It involves a significant cancellation that is an obstacle to achieving high numerical accuracy. The second method is more direct and yields a result that is identical to the Gremm-Kapustin relation, but it is limited to use in potential models. It can be generalized to the computation of matrix elements of higher order in the heavy-quark velocity and can be used to resum the contributions to decay and production rates that are associated with those matrix elements. We apply these methods to the Cornell potential model and compute a matrix element for the J/ψ state that appears in the leading relativistic correction to the production and decay of that state through the color-singlet quark-antiquark channel.

  19. 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.

  20. 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.

  1. Drift-oscillatory steering with the forward-reverse method for calculating the potential of mean force

    NASA Astrophysics Data System (ADS)

    Nategholeslam, Mostafa; Holland, Bryan W.; Gray, C. G.; Tomberli, Bruno

    2011-02-01

    We present a method that enables the use of the forward-reverse (FR) method of Kosztin on a broader range of problems in soft matter physics. Our method, which we call the oscillating forward-reverse (OFR) method, adds an oscillatory steering potential to the constant velocity steering potential of the FR method. This enables the calculation of the potential of mean force (PMF) in a single unidirectional oscillatory drift, rather than multiple drifts in both directions as required by the FR method. By following small forward perturbations with small reverse perturbations, the OFR method is able to generate a piecewise reverse path that follows the piecewise forward path much more closely than any practical set of paths used in the FR method. We calculate the PMF for four different systems: a dragged Brownian oscillator, a pair of atoms in a Lennard-Jones liquid, a Na+-Cl- ion pair in an aqueous solution, and a deca-alanine molecule being stretched in an implicit solvent. In all cases, the PMF results are in good agreement with those published previously using various other methods, and, to our knowledge, we give for the first time PMFs calculated by nonequilibrium methods for the Lennard-Jones and Na+-Cl- systems.

  2. [Calculating the optimum size of a hemodialysis unit based on infrastructure potential].

    PubMed

    Avila-Palomares, Paula; López-Cervantes, Malaquías; Durán-Arenas, Luis

    2010-01-01

    To estimate the optimum size for hemodialysis units to maximize production given capital constraints. A national study in Mexico was conducted in 2009. Three possible methods for estimating a units optimum size were analyzed: hemodialysis services production under monopolistic market, under a perfect competitive market and production maximization given capital constraints. The third method was considered best based on the assumptions made in this paper; an optimal size unit should have 16 dialyzers (15 active and one back up dialyzer) and a purifier system able to supply all. It also requires one nephrologist, five nurses per shift, considering four shifts per day. Empirical evidence shows serious inefficiencies in the operation of units throughout the country. Most units fail to maximize production due to not fully utilizing equipment and personnel, particularly their water purifier potential which happens to be the most expensive asset for these units.

  3. 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.

  4. Using effective group potential methodology for predicting organometallic complex properties.

    PubMed

    Alary, Fabienne; Heully, Jean-Louis; Poteau, Romuald; Maron, Laurent; Trinquier, Georges; Daudey, Jean-Pierre

    2003-09-10

    Using the Effective Group Potentials (EGP) method, optimal geometries, harmonic vibrational frequencies, and relative energies of different sets of metal complexes are calculated. All of the systems under consideration contain the cyclopentadienyl (Cp) ligand. They are as follows: (i). Group V metal Atom complexes showing one Cp ligand, (ii). a tetrameric Al-Cp compound with four Cp ligands, (iii). homometallic lutetium hydrides containing six cyclopentadienyl rings. Various electron correlation treatments have been carried out. All of the results compare very satisfactorily with available experimental data and with all-electron ab initio calculations performed for this work or published in the literature. Furthermore, the performance of the EGP method was tested on a rather large complex for which experimental evidence exists, but no all-electron calculation has been reported so far.

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

    DOE PAGES

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

    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

  6. Extension of the Source-Sink Potential (SSP) approach for multi-channel conductance calculations

    NASA Astrophysics Data System (ADS)

    Rocheleau, Philippe; Ernzerhof, Matthias

    2010-03-01

    In molecular electronics, molecules are connected to macroscopic contacts and the current passing through is studied as a function of the applied voltage. We focus on modeling the transmission of electrons through such a molecular electronic device (MED). Based on a simple H"uckel Hamiltonian to describe the π electrons in conjugated systems, the SSP method [1,2,3] employs complex potentials to replace the wavefunction of the infinite contacts in a rigorous way. The initial SSP approach [4] was limited to two one-dimensional contacts, here we extend the approach to multiple channels, i.e., to two-dimensional contacts including transverse modes. We describe the development of the method and illustrate it with applications. References:[1] F. Goyer, M. Ernzerhof and M. Zhuang, J. Chem. Phys., 126, (2007) 144104.[2] M. Ernzerhof, J. Chem. Phys., 127, (2007) 204709.[3] B.T. Pickup and P.W. Fowler, Chem. Phys. Lett., 459, (2008) 198-202.[4] P. Rocheleau and M. Ernzerhof, J. Chem. Phys., 130 (17) (2009).

  7. 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.

  8. Resonance energies, lifetimes and complex energy potential curves from standard wave-packet calculations

    NASA Astrophysics Data System (ADS)

    Goldzak, Tamar; Gilary, Ido; Moiseyev, Nimrod

    2012-05-01

    We show here for a simple model system that the wavepacket dynamics in the interaction region can be described by a superposition of the non-Hermitian exponential divergent eigenfunctions of the physical Hamiltonian. We demonstrate how it is possible to obtain the complex eigenvalues and also the corresponding resonance eigenfunctions from the propagation of the wavepacket within the framework of the standard formalism of quantum mechanics. The general results demonstrated here for a simple model can lead to two different types of computational applications: (i) for systems where one can obtain the resonance energies and lifetimes as well as their corresponding eigenfunctions it is possible to study the evolution of the physical properties solely based on the initially populated resonance states without the need to propagate the wavepacket; (ii) for molecular systems where it is quite difficult to solve the non-Hermitian time-independent Schrödinger equation and obtain molecular resonance energies and functions. For this type of problem, the methods presented here enable one to evaluate the topology of complex potential energy surfaces from the wavepacket propagation and facilitate the study of the nuclear dynamics of ionizing molecular systems.

  9. Calculating potential energy curves with fixed-node diffusion Monte Carlo: CO and N2

    NASA Astrophysics Data System (ADS)

    Powell, Andrew D.; Dawes, Richard

    2016-12-01

    This study reports on the prospect for the routine use of Quantum Monte Carlo (QMC) for the electronic structure problem, applying fixed-node Diffusion Monte Carlo (DMC) to generate highly accurate Born-Oppenheimer potential energy curves (PECs) for small molecular systems. The singlet ground electronic states of CO and N2 were used as test cases. The PECs obtained by DMC employing multiconfigurational trial wavefunctions were compared with those obtained by conventional high-accuracy electronic structure methods such as multireference configuration interaction and/or the best available empirical spectroscopic curves. The goal was to test whether a straightforward procedure using available QMC codes could be applied robustly and reliably. Results obtained with DMC codes were found to be in close agreement with the benchmark PECs, and the n3 scaling with the number of electrons (compared with n7 or worse for conventional high-accuracy quantum chemistry) could be advantageous depending on the system size. Due to a large pre-factor in the scaling, for the small systems tested here, it is currently still much more computationally intensive to compute PECs with QMC. Nevertheless, QMC algorithms are particularly well-suited to large-scale parallelization and are therefore likely to become more relevant for future massively parallel hardware architectures.

  10. Efficient generation of Heisenberg Hamiltonian matrices for VB calculations of potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Tokmachev, A. M.; Robb, M. A.

    The spin-Hamiltonian valence bond theory relies upon covalent configurations formed by singly occupied orbitals differing by their spin counterparts. This theory has been proven to be successful in studying potential energy surfaces of the ground and lowest excited states in organic molecules when used as a part of the hybrid molecular mechanics - valence bond method. The method allows one to consider systems with large active spaces formed by n electrons in n orbitals and relies upon a specially proposed graphical unitary group approach. At the same time, the restriction of the equality of the numbers of electrons and orbitals in the active space is too severe: it excludes from the consideration a lot of interesting applications. We can mention here carbocations and systems with heteroatoms. Moreover, the structure of the method makes it difficult to study charge-transfer excited states because they are formed by ionic configurations. In the present work we tackle these problems by significant extension of the spin-Hamiltonian approach. We consider (i) more general active space formed by n ± m electrons in n orbitals and (ii) states with the charge transfer. The main problem addressed is the generation of Hamiltonian matrices for these general cases. We propose a scheme combining operators of electron exchange and hopping, generating all nonzero matrix elements step-by-step. This scheme provides a very efficient way to generate the Hamiltonians, thus extending the applicability of spin-Hamiltonian valence bond theory.

  11. 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

  12. Environmental perchlorate exposure: potential adverse thyroid effects.

    PubMed

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

    2014-10-01

    This review will present a general overview of the sources, human studies, and proposed regulatory action regarding environmental perchlorate exposure. Some recent studies have reported significant associations between urinary perchlorate concentrations, thyroid dysfunction, and decreased infant intelligence quotient in groups who would be particularly susceptible to perchlorate effects. An update regarding the recently proposed regulatory actions and potential costs surrounding amelioration of perchlorate contamination is provided. 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.

  13. An accurate and efficient empirical approach for calculating the dielectric self-energy and ion-ion pair potential in continuum models of biological ion channels.

    PubMed

    Cheng, Mary Hongying; Coalson, Rob D

    2005-01-13

    This paper presents empirical formulas for calculating the dielectric self-energy and ion-ion pair interactions in cylindrical ion channels. The proposed approach can be extended to more complex channel structures, for example, (i) a "straight" channel with variable radius and (ii) a "curved" channel with constant radius. For calibration purposes, we compare results obtained based on the approximate effective potentials developed herein to exact electrostatic calculations obtained via the algorithm of Graf et al.: the agreement is satisfactory. A dynamic lattice Monte Carlo (DLMC) technique is used to further assess the accuracy and efficiency of the proposed empirical potentials. The concentration profiles and current-voltage curves produced with our simple empirical energy formulas are in excellent agreement with numerical results obtained using the algorithm of Graf et al., which calculates all relevant electrostatic forces exactly. The use of effective ion-ion potentials greatly reduces the computer memory required to perform DLMC ion permeation simulations in dielectrically inhomogeneous environments, thus enabling treatment of larger systems than can be handled by numerically exact techniques.

  14. 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

  15. 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

  16. 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.

  17. [Neural tube defects in Austria: Assumption and calculations on the prevention potential through folic acid enrichment and supplementation].

    PubMed

    Schiller-Frühwirth, I; Mittermayr, T; Wild, C

    2010-12-01

    Countries with obligatory fortification of food (USA, Canada) document a significant decrease of neural tube defects in newborns. In this study the Daly or, respectively, the Wald method was employed for calculating the potential of fortification/and supplementation for prevention in Austria. According to the EUROCAT study, in Austria the overall prevalence of neural tube defects (live birth, still births and induced abortions due to neural defect) is assumed to be 7.95 per 10,000 live and still births, and the prevalence of 3.9 per 10,000 live births - that is 62 or, respectively, 30 in absolute numbers per 78,000 births per year. In 2006, 26 live-born children with neural tube defects were actually reported in Austria by Statistik Austria. Different folic acid fortification and supplementation strategies can avoid 1.2-1.4 per 10,000 (9-11 cases) of neural tube defects (live and still births). Folic acid supplements are effective to decrease the amount of neural tube defects, however, only when pregnancies are planned. Thus, evidence-based neural tube defects are more common among lower social groups. An obligatory fortification of food could therefore reach unplanned pregnancies and women facing social problems. A reason to justify this population-based intervention where people need not decide for themselves could be the reduction of social imbalances. There are, of course, advantages and disadvantages of obligatory fortification of food and, therefore, all circumstances have to be taken into consideration. © Georg Thieme Verlag KG Stuttgart · New York.

  18. 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.

  19. 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.

  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. Accurate and efficient calculation of van der Waals interactions within density functional theory by local atomic potential approach.

    PubMed

    Sun, Y Y; Kim, Yong-Hyun; Lee, Kyuho; Zhang, S B

    2008-10-21

    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.

  2. 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.

  3. Incorporating Allee effects into the potential biological removal level

    USGS Publications Warehouse

    Hadier, Humza; Oldfield, Sarah; Tu, Tiffany; Moreno, Rosa; Diffendorfer, Jay E.; Eager, Eric A.; Erickson, Richard A.

    2017-01-01

    Potential biological removal (PBR) is an approach used to calculate sustainable harvest and “take” limits for populations. PBR was originally derived assuming logistic growth while ignoring the effects of small population size (i.e., an Allee effect). We derived a version of PBR that includes an Allee effect (i.e., small population size or densities limiting population growth rates). We found that PBR becomes less conservative when it fails to consider an Allee effect. Specifically, sustainable harvest and take levels based upon PBR with an Allee effect were between approximately 51% and 66% of levels based upon PBR without an Allee effect. Managers and biologists using PBR may need to consider the limitations if an Allee effect may be present in the species being modeled.

  4. 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

    2007-08-06

    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.

  5. Accelerating potential of mean force calculations for lipid membrane permeation: System size, reaction coordinate, solute-solute distance, and cutoffs

    NASA Astrophysics Data System (ADS)

    Nitschke, Naomi; Atkovska, Kalina; Hub, Jochen S.

    2016-09-01

    Molecular dynamics simulations are capable of predicting the permeability of lipid membranes for drug-like solutes, but the calculations have remained prohibitively expensive for high-throughput studies. Here, we analyze simple measures for accelerating potential of mean force (PMF) calculations of membrane permeation, namely, (i) using smaller simulation systems, (ii) simulating multiple solutes per system, and (iii) using shorter cutoffs for the Lennard-Jones interactions. We find that PMFs for membrane permeation are remarkably robust against alterations of such parameters, suggesting that accurate PMF calculations are possible at strongly reduced computational cost. In addition, we evaluated the influence of the definition of the membrane center of mass (COM), used to define the transmembrane reaction coordinate. Membrane-COM definitions based on all lipid atoms lead to artifacts due to undulations and, consequently, to PMFs dependent on membrane size. In contrast, COM definitions based on a cylinder around the solute lead to size-independent PMFs, down to systems of only 16 lipids per monolayer. In summary, compared to popular setups that simulate a single solute in a membrane of 128 lipids with a Lennard-Jones cutoff of 1.2 nm, the measures applied here yield a speedup in sampling by factor of ˜40, without reducing the accuracy of the calculated PMF.

  6. 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.

  7. New three-dimensional far-field potential repository thermomechanical calculations; Yucca Mountain Site Characterization Project

    SciTech Connect

    Hardy, M.P.; Bai, M.; Goodrich, R.R.; Lin, M.; Carlisle, S.; Bauer, S.J.

    1993-03-01

    The thermomechanical effect on the exploratory ramps, drifts, and shafts as a result of high-level nuclear waste disposal is examined using a three-dimensional thermo-elastic model. The repository layout modeled is based on the use of mechanical mining of all excavations with equivalent waste emplacement areal power densities of 57 and 80 kW/acre. Predicted temperatures and stress changes for the north and south access drifts, east main drift, east-west exploratory drift, the north and south Calico Hills access ramps, the Calico Hills north-south exploratory drift, and the optional exploratory studies facility and man and materials shafts are presented for times 10, 35, 50, 100, 300, 500, 1000, 2000, 5000, and 10,000 years after the start of waste emplacement. The study indicates that the east-west exploratory drift at the repository horizon is subject to the highest thermomechanical impact because it is located closest the buried waste canisters. For most exploratory openings, the thermally induced temperatures and stresses tend to reach the maximum magnitudes at approximately 1000 years after waste emplacement.

  8. Embedding Fragment ab Initio Model Potentials in CASSCF/CASPT2 Calculations of Doped Solids: Implementation and Applications.

    PubMed

    Swerts, Ben; Chibotaru, Liviu F; Lindh, Roland; Seijo, Luis; Barandiaran, Zoila; Clima, Sergiu; Pierloot, Kristin; Hendrickx, Marc F A

    2008-04-01

    In this article, we present a fragment model potential approach for the description of the crystalline environment as an extension of the use of embedding ab initio model potentials (AIMPs). The biggest limitation of the embedding AIMP method is the spherical nature of its model potentials. This poses problems as soon as the method is applied to crystals containing strongly covalently bonded structures with highly nonspherical electron densities. The newly proposed method addresses this problem by keeping the full electron density as its model potential, thus allowing one to group sets of covalently bonded atoms into fragments. The implementation in the MOLCAS 7.0 quantum chemistry package of the new method, which we call the embedding fragment ab inito model potential method (embedding FAIMP), is reported here, together with results of CASSCF/CASPT2 calculations. The developed methodology is applied for two test problems: (i) the investigation of the lowest ligand field states (2)A1 and (2)B1 of the Cr(V) defect in the YVO4 crystal and (ii) the investigation of the lowest ligand field and ligand-metal charge transfer (LMCT) states at the Mn(II) substitutional impurity doped into CaCO3. Comparison with similar calculations involving AIMPs for all environmental atoms, including those from covalently bounded units, shows that the FAIMP treatment of the YVO4 units surrounding the CrO4(3-) cluster increases the excitation energy (2)B1 → (2)A1 by ca. 1000 cm(-1) at the CASSCF level of calculation. In the case of the Mn(CO3)6(10-) cluster, the FAIMP treatment of the CO3(2-) units of the environment give smaller corrections, of ca. 100 cm(-1), for the ligand-field excitation energies, which is explained by the larger ligands of this cluster. However, the correction for the energy of the lowest LMCT transition is found to be ca. 600 cm(-1) for the CASSCF and ca. 1300 cm(-1) for the CASPT2 calculation.

  9. 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.

  10. Calculation of activities of ions in molten salts with potential application to the pyroprocessing of nuclear waste.

    PubMed

    Salanne, Mathieu; Simon, Christian; Turq, Pierre; Madden, Paul A

    2008-01-31

    The ability to separate fission products by electrodeposition from molten salts depends, in part, on differences between the interactions of the different fission product cations with the ions present in the molten salt "solvent". These differences may be expressed as ratios of activity coefficients, which depend on the identity of the solvent and other factors. Here, we demonstrate the ability to calculate these activity coefficient ratios using molecular dynamics simulations with sufficient precision to guide the choice of suitable solvent systems in practical applications. We use polarizable ion interaction potentials which have previously been shown to give excellent agreement with structural, transport, and spectroscopic information of the molten salts, and the activity coefficients calculated in this work agree well with experimental data. The activity coefficients are shown to vary systematically with cation size for a set of trivalent cations.

  11. The potential health effects of dietary phytoestrogens

    PubMed Central

    Louisse, Jochem; Beekmann, Karsten

    2016-01-01

    Phytoestrogens are plant‐derived dietary compounds with structural similarity to 17‐β‐oestradiol (E2), the primary female sex hormone. This structural similarity to E2 enables phytoestrogens to cause (anti)oestrogenic effects by binding to the oestrogen receptors. The aim of the present review is to present a state‐of‐the‐art overview of the potential health effects of dietary phytoestrogens. Various beneficial health effects have been ascribed to phytoestrogens, such as a lowered risk of menopausal symptoms like hot flushes and osteoporosis, lowered risks of cardiovascular disease, obesity, metabolic syndrome and type 2 diabetes, brain function disorders, breast cancer, prostate cancer, bowel cancer and other cancers. In contrast to these beneficial health claims, the (anti)oestrogenic properties of phytoestrogens have also raised concerns since they might act as endocrine disruptors, indicating a potential to cause adverse health effects. The literature overview presented in this paper illustrates that several potential health benefits of phytoestrogens have been reported but that, given the data on potential adverse health effects, the current evidence on these beneficial health effects is not so obvious that they clearly outweigh the possible health risks. Furthermore, the data currently available are not sufficient to support a more refined (semi) quantitative risk–benefit analysis. This implies that a definite conclusion on possible beneficial health effects of phytoestrogens cannot be made. Linked Articles This article is part of a themed section on Principles of Pharmacological Research of Nutraceuticals. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.11/issuetoc PMID:27723080

  12. 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.

  13. Probing the mechanism of hypoxia selectivity of copper bis(thiosemicarbazonato) complexes: DFT calculation of redox potentials and absolute acidities in solution.

    PubMed

    Holland, Jason P; Green, Jennifer C; Dilworth, Jonathan R

    2006-02-14

    Density functional theory (DFT) calculations have been performed using the uB3LYP/6-31++G(d,p) model to calculate the solution phase one-electron reduction potentials (E(calc)) and absolute pKa values of a series of copper bis(thiosemicarbazonato) complexes. The effects of solvation in water and dimethylsulfoxide (DMSO) are incorporated as a self-consistent reaction field (SCRF) using the integral equation formalism polarisable continuum model (IEFPCM) and are found to be essential for quantitative agreement with an average error in E(calc) of -0.02 V compared to experiment. The bonding and spin densities are examined through the use of Natural Bond Order analysis and the results used to rationalise the calculated and observed reduction potentials. Calculated estimates of pKa values of several copper(II) species are presented and their implications for the mechanisms of transport and trapping within hypoxic cells are considered. Reduction is found to be a prerequisite for protonation of the complexes which suggests their transport in the blood stream as neutral species, and the mechanistic sequence is identified as a sequential electrochemical-chemical (EC) process. The complex equilibria of protonation, reoxidation and dissociation are discussed and the copper(I) diprotonated, cationic complex of diacetyl bis(4-methyl-3-thiosemicarbazonato)copper(II), Cu(I)ATSMH2(+), is identified as a possible candidate for the initial species trapped in hypoxic cells.

  14. COME: a robust coding potential calculation tool for lncRNA identification and characterization based on multiple features

    PubMed Central

    Hu, Long; Xu, Zhiyu; Hu, Boqin; Lu, Zhi John

    2017-01-01

    Recent genomic studies suggest that novel long non-coding RNAs (lncRNAs) are specifically expressed and far outnumber annotated lncRNA sequences. To identify and characterize novel lncRNAs in RNA sequencing data from new samples, we have developed COME, a coding potential calculation tool based on multiple features. It integrates multiple sequence-derived and experiment-based features using a decompose–compose method, which makes it more accurate and robust than other well-known tools. We also showed that COME was able to substantially improve the consistency of predication results from other coding potential calculators. Moreover, COME annotates and characterizes each predicted lncRNA transcript with multiple lines of supporting evidence, which are not provided by other tools. Remarkably, we found that one subgroup of lncRNAs classified by such supporting features (i.e. conserved local RNA secondary structure) was highly enriched in a well-validated database (lncRNAdb). We further found that the conserved structural domains on lncRNAs had better chance than other RNA regions to interact with RNA binding proteins, based on the recent eCLIP-seq data in human, indicating their potential regulatory roles. Overall, we present COME as an accurate, robust and multiple-feature supported method for the identification and characterization of novel lncRNAs. The software implementation is available at https://github.com/lulab/COME. PMID:27608726

  15. 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.

  16. 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.

  17. Calculation of the surface potential and surface charge density by measurement of the three-phase contact angle.

    PubMed

    Horiuchi, H; Nikolov, A; Wasan, D T

    2012-11-01

    The silica/silicon wafer is widely used in the semiconductor industry in the manufacture of electronic devices, so it is essential to understand its physical chemistry and determine the surface potential at the silica wafer/water interface. However, it is difficult to measure the surface potential of a silica/silicon wafer directly due to its high electric resistance. In the present study, the three-phase contact angle (TPCA) on silica is measured as a function of the pH. The surface potential and surface charge density at the silica/water surface are calculated by a model based on the Young-Lippmann equation in conjunction with the Gouy-Chapman model for the electric double layer. In measurements of the TPCA on silica, two distinct regions were identified with a boundary at pH 9.5-showing a dominance of the surface ionization of silanol groups below pH 9.5 and a dominance of the dissolution of silica into the aqueous solution above pH 9.5. Since the surface chemistry changes above pH 9.5, the model is applied to solutions below pH 9.5 (ionization dominant) for the calculation of the surface potential and surface charge density at the silica/aqueous interface. In order to evaluate the model, a galvanic mica cell was made of a mica sheet and the surface potential was measured directly at the mica/water interface. The model results are also validated by experimental data from the literature, as well as the results obtained by the potentiometric titration method and the electro-kinetic measurements.

  18. 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.

  19. Dynamic polarization potential effects on vector analyzing powers of 6Li- 28Si elastic scattering from non-monotonic potentials

    NASA Astrophysics Data System (ADS)

    Basak, A. K.; Roy, P. K.; Hossain, S.; Abdullah, M. N. A.; Tariq, A. S. B.; Uddin, M. A.; Reichstein, I.; Malik, F. B.

    2010-08-01

    Experimental cross section (CS) and vector analyzing power (VAP) data of the 6Li-28Si elastic scattering at 22.8 MeV are analyzed in the coupled-channels (CC) and coupled discretized continuum channels (CDCC) methods. Non-monotonic (NM) 6Li and α potentials of microscopic origin are employed, respectively, in the CC calculations and to generate folding potentials for the CDCC calculations. The study demonstrates that the use of central NM potentials can generate an appropriate dynamic polarization potential (DPP) required to describe both the CS and VAP data without the necessity of renormalization. This also produces an effective spin-orbit (SO) potential to account for the iT11 data without the requirement of an additional static SO potential at the incident energy considered.

  20. 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

  1. 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

  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. 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

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

    PubMed

    Egan, Joseph R; Hall, Ian M

    2015-05-06

    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.

  5. Precision calculation for nucleon capture by deuteron with Effective Field Theory

    SciTech Connect

    Bayegan, S.; Sadeghi, H.

    2005-05-06

    We calculate the cross section for radiative capture of neutron by deuteron n + d {yields} 3H+{gamma} using Effective Field Theory (EFT). The calculation includes N2LO order and we compare our results with available calculated data below E = 0.2 MeV.

  6. 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.

  7. Calculation of effective parameters of thermoelectromagnetoelastic layered media

    NASA Astrophysics Data System (ADS)

    Starkov, A. S.; Kudryavtseva, I. V.; Starkov, K. A.; Korzenkov, K. V.

    2017-07-01

    A system of layered multiferroic materials is averaged with allowance for thermal properties of layers. Matrix averaging is used to obtain effective parameters of the system. Formulas that make it possible to characterize the effect of magnetoelectroelastic coefficients of layers on thermal parameters are derived. The presence of pyrocoefficients in the system is possible even in the absence of the coefficients for the layers. The heat capacity of the system ceases to be an additive quantity and becomes dependent on permittivity and permeability of the layers owing to the interaction of the fields.

  8. Path integral molecular dynamics calculations of the H6+ and D6+ clusters on an ab initio potential energy surface

    NASA Astrophysics Data System (ADS)

    Kakizaki, Akira; Takayanagi, Toshiyuki; Shiga, Motoyuki

    2007-11-01

    Path integral molecular dynamics simulations for the H6+ and D6+ cluster cations have been carried out in order to understand the floppy nature of their molecular structure due to quantum-mechanical fluctuation. A full-dimensional analytical potential energy surface for the ground electronic state of H6+ has been developed on the basis of accurate ab initio electronic structure calculations at the CCSD(T)/cc-pVTZ level. It is found that the outer H 2(D 2) nuclei rotate almost freely and that the probability density distributions of the central H 2(D 2) nuclei show strong spatial delocalization.

  9. Resonances in SN2 reactions: Two-mode quantum calculations for Cl-+CH3Br on a coupled-cluster potential energy surface

    NASA Astrophysics Data System (ADS)

    Schmatz, Stefan; Botschwina, Peter; Hauschildt, Jan; Schinke, Reinhard

    2002-12-01

    An effective two-dimensional potential energy surface has been constructed for the SN2 reaction Cl-+CH3Br→ClCH3+Br- from coupled-cluster calculations with a large basis set. In the quantum dynamics calculations Radau coordinates were employed to describe the Cl-C and C-Br stretching modes. Making use of the filter diagonalization method and an optical potential, bound states as well as resonance states up to energies far above the dissociation threshold have been calculated. The resonance widths fluctuate over several orders of magnitude. In addition to a majority of Feshbach-type resonances there are also exceedingly long-lived shape resonances, which can only decay by tunneling. Owing to a smaller width of the potential barrier and a larger density of states, tunneling through the barrier is more important for Cl-+CH3Br than for Cl-+CH3Cl despite the larger total mass of this system. Excitation of the C-Br stretching vibration enhances the tunneling probability of the entrance channel complex.

  10. 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.

  11. Gyroid Optical Metamaterials: Calculating the Effective Permittivity of Multidomain Samples.

    PubMed

    Dolan, James A; Saba, Matthias; Dehmel, Raphael; Gunkel, Ilja; Gu, Yibei; Wiesner, Ulrich; Hess, Ortwin; Wilkinson, Timothy D; Baumberg, Jeremy J; Steiner, Ullrich; Wilts, Bodo D

    2016-10-19

    Gold gyroid optical metamaterials are known to possess a reduced plasma frequency and linear dichroism imparted by their intricate subwavelength single gyroid morphology. The anisotropic optical properties are, however, only evident when a large individual gyroid domain is investigated. Multidomain gyroid metamaterials, fabricated using a polyisoprene-b-polystyrene-b-poly(ethylene oxide) triblock terpolymer and consisting of multiple small gyroid domains with random orientation and handedness, instead exhibit isotropic optical properties. Comparing three effective medium models, we here show that the specular reflectance spectra of such multidomain gyroid optical metamaterials can be accurately modeled over a broad range of incident angles by a Bruggeman effective medium consisting of a random wire array. This model accurately reproduces previously published results tracking the variation in normal incidence reflectance spectra of gold gyroid optical metamaterials as a function of host refractive index and volume fill fraction of gold. The effective permittivity derived from this theory confirms the change in sign of the real part of the permittivity in the visible spectral region (so, that gold gyroid metamaterials exhibit both dielectric and metallic behavior at optical wavelengths). That a Bruggeman effective medium can accurately model the experimental reflectance spectra implies that small multidomain gold gyroid optical metamaterials behave both qualitatively and quantitatively as an amorphous composite of gold and air (i.e., nanoporous gold) and that coherent electromagnetic contributions arising from the subwavelength gyroid symmetry are not dominant.

  12. Gyroid Optical Metamaterials: Calculating the Effective Permittivity of Multidomain Samples

    PubMed Central

    2016-01-01

    Gold gyroid optical metamaterials are known to possess a reduced plasma frequency and linear dichroism imparted by their intricate subwavelength single gyroid morphology. The anisotropic optical properties are, however, only evident when a large individual gyroid domain is investigated. Multidomain gyroid metamaterials, fabricated using a polyisoprene-b-polystyrene-b-poly(ethylene oxide) triblock terpolymer and consisting of multiple small gyroid domains with random orientation and handedness, instead exhibit isotropic optical properties. Comparing three effective medium models, we here show that the specular reflectance spectra of such multidomain gyroid optical metamaterials can be accurately modeled over a broad range of incident angles by a Bruggeman effective medium consisting of a random wire array. This model accurately reproduces previously published results tracking the variation in normal incidence reflectance spectra of gold gyroid optical metamaterials as a function of host refractive index and volume fill fraction of gold. The effective permittivity derived from this theory confirms the change in sign of the real part of the permittivity in the visible spectral region (so, that gold gyroid metamaterials exhibit both dielectric and metallic behavior at optical wavelengths). That a Bruggeman effective medium can accurately model the experimental reflectance spectra implies that small multidomain gold gyroid optical metamaterials behave both qualitatively and quantitatively as an amorphous composite of gold and air (i.e., nanoporous gold) and that coherent electromagnetic contributions arising from the subwavelength gyroid symmetry are not dominant. PMID:27785456

  13. Additive scales in degenerative disease - calculation of effect sizes and clinical judgment

    PubMed Central

    2011-01-01

    Background The therapeutic efficacy of an intervention is often assessed in clinical trials by scales measuring multiple diverse activities that are added to produce a cumulative global score. Medical communities and health care systems subsequently use these data to calculate pooled effect sizes to compare treatments. This is done because major doubt has been cast over the clinical relevance of statistically significant findings relying on p values with the potential to report chance findings. Hence in an aim to overcome this pooling the results of clinical studies into a meta-analyses with a statistical calculus has been assumed to be a more definitive way of deciding of efficacy. Methods We simulate the therapeutic effects as measured with additive scales in patient cohorts with different disease severity and assess the limitations of an effect size calculation of additive scales which are proven mathematically. Results We demonstrate that the major problem, which cannot be overcome by current numerical methods, is the complex nature and neurobiological foundation of clinical psychiatric endpoints in particular and additive scales in general. This is particularly relevant for endpoints used in dementia research. 'Cognition' is composed of functions such as memory, attention, orientation and many more. These individual functions decline in varied and non-linear ways. Here we demonstrate that with progressive diseases cumulative values from multidimensional scales are subject to distortion by the limitations of the additive scale. The non-linearity of the decline of function impedes the calculation of effect sizes based on cumulative values from these multidimensional scales. Conclusions Statistical analysis needs to be guided by boundaries of the biological condition. Alternatively, we suggest a different approach avoiding the error imposed by over-analysis of cumulative global scores from additive scales. PMID:22176535

  14. QuickPol: Fast calculation of effective beam matrices for CMB polarization

    NASA Astrophysics Data System (ADS)

    Hivon, Eric; Mottet, Sylvain; Ponthieu, Nicolas

    2017-01-01

    Current and planned observations of the cosmic microwave background (CMB) polarization anisotropies, with their ever increasing number of detectors, have reached a potential accuracy that requires a very demanding control of systematic effects. While some of these systematics can be reduced in the design of the instruments, others will have to be modeled and hopefully accounted for or corrected a posteriori. We propose QuickPol, a quick and accurate calculation of the full effective beam transfer function and of temperature to polarization leakage at the power spectra level, as induced by beam imperfections and mismatches between detector optical and electronic responses. All the observation details such as exact scanning strategy, imperfect polarization measurements, and flagged samples are accounted for. Our results are validated on Planck high frequency instrument (HFI) simulations. We show how the pipeline can be used to propagate instrumental uncertainties up to the final science products, and could be applied to experiments with rotating half-wave plates.

  15. Large vibrational effects upon calculated phase boundaries in Al-Sc.

    PubMed

    Ozoliņs, V; Asta, M

    2001-01-15

    The fcc portion of the Al-Sc phase diagram is calculated from first principles including contributions to alloy free energies associated with ionic vibrations. It is found that vibrational entropy accounts for a 27-fold increase in the calculated solubility limits for Sc in fcc Al at high temperatures, bringing calculated and measured values into very good agreement. The present work gives a clear example demonstrating a large effect of vibrational entropy upon calculated phase boundaries in substitutional alloys.

  16. The effective potential in nonconformal gauge theories

    NASA Astrophysics Data System (ADS)

    Brandt, F. T.; Chishtie, F. A.; McKeon, D. G. C.

    2017-01-01

    By using the renormalization group (RG) equation it has proved possible to sum logarithmic corrections to quantities that arise due to quantum effects in field theories. In particular, the effective potential V in the Standard Model in the limit that there are no massive parameters in the classical action (the “conformal limit”) has been subject to this analysis, as has the effective potential in a scalar theory with a quartic self-coupling and in massless scalar electrodynamics. Having multiple coupling constants and/or mass parameters in the initial action complicates this analysis, as then several mass scales arise. We show how to address this problem by considering the effective potential in a Yukawa model when the scalar field has a tree-level mass term. In addition to summing logarithmic corrections by using the RG equation, we also consider the consequences of the condition V‧(v) = 0 where v is the vacuum expectation value of the scalar. If V is expanded in powers of logarithms that arise, then it proves possible to show that either v is zero or that V is independent of the scalar. (That is, either there is no spontaneous symmetry breaking or the vacuum expectation value is not determined by minimizing V as V is “flat”.)

  17. 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.

  18. 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.

  19. Efficient calculation of the quasi-static electrical potential on a tetrahedral mesh and its implementation in STEPS

    PubMed Central

    Hepburn, Iain; Cannon, Robert; De Schutter, Erik

    2013-01-01

    We describe a novel method for calculating the quasi-static electrical potential on tetrahedral meshes, which we call E-Field. The E-Field method is implemented in STEPS, which performs stochastic spatial reaction-diffusion computations in tetrahedral-based cellular geometry reconstructions. This provides a level of integration between electrical excitability and spatial molecular dynamics in realistic cellular morphology not previously achievable. Deterministic solutions are also possible. By performing the Rallpack tests we demonstrate the accuracy of the E-Field method. Efficient node ordering is an important practical consideration, and we find that a breadth-first search provides the best solutions, although principal axis ordering suffices for some geometries. We discuss potential applications and possible future directions, and predict that the E-Field implementation in STEPS will play an important role in the future of multiscale neural simulations. PMID:24194715

  20. Synthesis, crystal structure, vibrational spectra and theoretical calculations of quantum chemistry of a potential antimicrobial Meldrum's acid derivative

    NASA Astrophysics Data System (ADS)

    Campelo, M. J. M.; Freire, P. T. C.; Mendes Filho, J.; de Toledo, T. A.; Teixeira, A. M. R.; da Silva, L. E.; Bento, R. R. F.; Faria, J. L. B.; Pizani, P. S.; Gusmão, G. O. M.; Coutinho, H. D. M.; Oliveira, M. T. A.

    2017-10-01

    A new derivative of Meldrum's acid 5-((5-chloropyridin-2-ylamino)methylene)-2,2-dimethyl-1,3-dioxane-4,6-dione (CYMM) of molecular formula C12H11ClN2O4 was synthesized and structurally characterized using single crystal X-ray diffraction technique. The vibrational properties of the crystal were studied by Fourier Transform infrared (FT-IR), Fourier Transform Raman (FT-Raman) techniques and theoretical calculations of quantum chemistry using Density functional theory (DFT) and Density functional perturbation theory (DFPT). A comparison with experimental spectra allowed the assignment of all the normal modes. The descriptions of the normal modes were carried by means of potential energy distribution (PED). Additionally, analysis of the antimicrobial activity and antibiotic resistance modulatory activity was carried out to evaluate the antibacterial potential of the CYMM.

  1. Efficient calculation of the quasi-static electrical potential on a tetrahedral mesh and its implementation in STEPS.

    PubMed

    Hepburn, Iain; Cannon, Robert; De Schutter, Erik

    2013-01-01

    We describe a novel method for calculating the quasi-static electrical potential on tetrahedral meshes, which we call E-Field. The E-Field method is implemented in STEPS, which performs stochastic spatial reaction-diffusion computations in tetrahedral-based cellular geometry reconstructions. This provides a level of integration between electrical excitability and spatial molecular dynamics in realistic cellular morphology not previously achievable. Deterministic solutions are also possible. By performing the Rallpack tests we demonstrate the accuracy of the E-Field method. Efficient node ordering is an important practical consideration, and we find that a breadth-first search provides the best solutions, although principal axis ordering suffices for some geometries. We discuss potential applications and possible future directions, and predict that the E-Field implementation in STEPS will play an important role in the future of multiscale neural simulations.

  2. An Effective Stress Model for Ground Motion Calculations

    DTIC Science & Technology

    1979-09-01

    which simulate, respectively, the drained and undrained stress-strain behavior of earth media, and whose coefficients can all be determined... BEHAVIOR OF SOIL 13 2.1 EFFECTIVE STRESS CONCEPT 13 2.2 MECHANICAL BEHAVIOR OF SOIL 15 CHAPTER 3 ELASTIC-PLASTIC CONSTITUTIVE MODEL 20 3.1...ELASTIC BEHAVIOR 20 3.2 PLASTIC BEHAVIOR 22 3.3 SUMMARY 2k CHAPTER U THE TREATMENT OF A MULTIPHASE SYSTEM 31 CHAPTER 5 BEHAVIOR OF THE MULTIPHASE

  3. 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.

  4. 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.

  5. Exact RG invariance and symmetry improved 2PI effective potential

    NASA Astrophysics Data System (ADS)

    Pilaftsis, Apostolos; Teresi, Daniele

    2017-07-01

    The Symmetry Improved Two-Particle-Irreducible (SI2PI) formalism is a powerful tool to calculate the effective potential beyond perturbation theory, whereby infinite sets of selective loop-graph topologies can be resummed in a systematic and consistent manner. In this paper we study the Renormalization-Group (RG) properties of this formalism, by proving for the first time a number of new field-theoretic results. First, the RG runnings of all proper 2PI couplings are found to be UV finite, in the Hartree-Fock and sunset approximations of the 2PI effective action. Second, the SI2PI effective potential is exactly RG invariant, in contrast to what happens in the ordinary One-Particle-Irreducible (1PI) perturbation theory, where the effective potential is RG invariant only up to higher orders. Finally, we show how the effective potential of an O (2) theory evaluated in the SI2PI framework, appropriately RG improved, can reach a higher level of accuracy, even up to one order of magnitude, with respect to the corresponding one obtained in the 1PI formalism.

  6. 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.

  7. The Stark effect in linear potentials

    NASA Astrophysics Data System (ADS)

    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 > 0 and V(z) = ∞ for z < 0) and the symmetric linear potential (given by V(z) = F|z|). We show how straightforward use of the most obvious properties of the Airy function solutions and simple Taylor expansions gives closed form results for the Stark shifts in both systems. These exact results are then compared to other approximation techniques, such as perturbation theory and WKB methods. These expressions add to the small number of closed-form descriptions available for the Stark effect in model quantum mechanical systems.

  8. Productivity cost calculations in health economic evaluations: correcting for compensation mechanisms and multiplier effects.

    PubMed

    Krol, Marieke; Brouwer, Werner B F; Severens, Johan L; Kaper, Janneke; Evers, Silvia M A A

    2012-12-01

    Productivity costs related to paid work are commonly calculated in economic evaluations of health technologies by multiplying the relevant number of work days lost with a wage rate estimate. It has been argued that actual productivity costs may either be lower or higher than current estimates due to compensation mechanisms and/or multiplier effects (related to team dependency and problems with finding good substitutes in cases of absenteeism). Empirical evidence on such mechanisms and their impact on productivity costs is scarce, however. This study aims to increase knowledge on how diminished productivity is compensated within firms. Moreover, it aims to explore how compensation and multiplier effects potentially affect productivity cost estimates. Absenteeism and compensation mechanisms were measured in a randomized trial among Dutch citizens examining the cost-effectiveness of reimbursement for smoking cessation treatment. Multiplier effects were extracted from published literature. Productivity costs were calculated applying the Friction Cost Approach. Regular estimates were subsequently adjusted for (i) compensation during regular working hours, (ii) job dependent multipliers and (iii) both compensation and multiplier effects. A total of 187 respondents included in the trial were useful for inclusion in this study, based on being in paid employment, having experienced absenteeism in the preceding six months and completing the questionnaire on absenteeism and compensation mechanisms. Over half of these respondents stated that their absenteeism was compensated during normal working hours by themselves or colleagues. Only counting productivity costs not compensated in regular working hours reduced the traditional estimate by 57%. Correcting for multiplier effects increased regular estimates by a quarter. Combining both impacts decreased traditional estimates by 29%. To conclude, large amounts of lost production are compensated in normal hours. Productivity costs

  9. 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

  10. 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…

  11. 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…

  12. Potential Radiation-Related Effects on Radiologists.

    PubMed

    Parikh, Jay R; Geise, Richard A; Bluth, Edward I; Bender, Claire E; Sze, Gordon; Jones, A Kyle

    2017-03-01

    The risk of injury associated with long-term occupational exposure to ionizing radiation is low for radiologists. The purpose of this article is to systematically review and inform radiologists about radiation-related effects to which they are potentially susceptible. Formal education and training on radiation safety and management, careful attention to good radiation protection habits, and continued emphasis on radiation management and the as low as reasonably achievable principle are recommended for all radiologists.

  13. 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.

  14. The surface tension of a solid at the solid-vacuum interface, an evaluation from adsorption and wall potential calculations.

    PubMed

    Jakubov, Tim S; Mainwaring, David E

    2007-03-15

    A method for the evaluation of quantities that are experimentally inaccessible such as the surface tension at the solid-vacuum interface and the superficial tension of the fluid in contact with the solid is presented. The approach is based on consideration of an equilibrium of a fluid in solid capillary wherein a balance between surface and capillary forces has been replaced by conceptual alternative interfacial and centrifugal forces. This approach involves the simultaneous numerical solution one the special forms of the Gibbs equation for solid-fluid interface and a generalized Kelvin equation derived earlier. The latter equation takes into account interactions between the solid thick cylindrical wall and confined fluid, this body-body interaction potential has been primarily calculated using the Lennard-Jones (6-12) expression for the atom-atom pair potentials and expressed by hypergeometrical functions having good convergences. All numerical calculations shown here have been performed for the model graphite-argon system at 90 K. Finally, an analysis of the accuracy of the proposed method is considered.

  15. 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).

  16. Calculation of Permeability Change Due to Coupled Thermal-Hydrological-Mechanical Effects

    SciTech Connect

    S. Blair

    2000-06-28

    The purpose of this calculation is to provide a bounding estimate of how thermal-hydrological-mechanical (THM) behavior of rock in the region surrounding an emplacement drift in a Monitored Geologic Repository subsurface facility may affect the permeability of fractures in the rock mass forming the region. The bounding estimate will provide essential input to performance assessment analysis of the potential repository system. This calculation also supports the Near Field Environment Process Model Report (NFE PMR) and will contribute to Site Recommendation. The geologic unit being considered as a potential repository horizon at Yucca Mountain, Nevada lies within a fractured, densely welded ash-flow tuff located in the Topopah Spring Tuff member of the Paintbrush Group. Fractures form the primary conduits for fluid flow in the rock mass. Considerable analysis has been performed to characterize the thermal-hydrologic (TH) behavior of this rock unit (e.g., CRWMS M&O 2000a, pp. 83-87), and recently the dual permeability model (DKM) has proved to be an effective tool for predicting TH behavior (CRWMS M&O 2000a). The DKM uses fracture permeability as a primary input parameter, and it is well known that fracture permeability is strongly dependent on fracture deformation (Brown. 1995). Consequently, one major unknown is how deformation during heating and cooling periods may change fracture permeability. Opening of fractures increases their permeability, whereas closing reduces permeability. More importantly, shear displacement on fractures increases their permeability, and fractures undergoing shear are likely to conduct fluids. This calculation provides a bounding estimate of how heating and cooling in the rock surrounding an emplacement drift and the resulting mechanical deformation may affect the fracture permeability of the rock.

  17. 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.

  18. Combining Slater-type orbitals and effective core potentials

    NASA Astrophysics Data System (ADS)

    Lesiuk, Michał; Tucholska, Aleksandra M.; Moszynski, Robert

    2017-05-01

    We present a general methodology to evaluate matrix elements of the effective core potentials (ECPs) within a one-electron basis set of Slater-type orbitals (STOs). The scheme is based on translation of individual STO distributions in the framework of the Barnett-Coulson method. We discuss different types of integrals which naturally appear and reduce them to a few basic quantities which can be calculated recursively or purely numerically. Additionally, we consider evaluation of the STOs matrix elements involving the core polarization potentials and effective spin-orbit potentials. Construction of the STOs basis sets designed specifically for use with ECPs is discussed and differences in comparison with all-electron basis sets are briefly summarized. We verify the validity of the present approach by calculating excitation energies, static dipole polarizabilities, and valence orbital energies for the alkaline-earth metals (Ca, Sr, and Ba). Finally, we evaluate interaction energies, permanent dipole moments, and ionization energies for barium and strontium hydrides, and compare them with the best available experimental and theoretical data.

  19. Conservatism in effective dose calculations for accident events involving fuel reprocessing waste tanks.

    PubMed

    Bevelacqua, J J

    2011-07-01

    Conservatism in the calculation of the effective dose following an airborne release from an accident involving a fuel reprocessing waste tank is examined. Within the regulatory constraints at the Hanford Site, deterministic effective dose calculations are conservative by at least an order of magnitude. Deterministic calculations should be used with caution in reaching decisions associated with required safety systems and mitigation philosophy related to the accidental release of airborne radioactive material to the environment.

  20. 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

  1. 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,

  2. Effects of exercise on visual evoked potentials.

    PubMed

    Ozmerdivenli, Recep; Bulut, Serpil; Bayar, Hale; Karacabey, Kursat; Ciloglu, Figen; Peker, Ismail; Tan, Uner

    2005-07-01

    The aim of this study was to investigate the effects of acute or habitual exercise on visual evoked potentials (VEP). The study group consisted of 9 female and 7 male volleyball players and the control group contained 9 female and 7 male students who were not involved in any sportive activity. The N75, P100, and N145 latency and amplitudes were measured before and after exercise. Intragroup comparison was made to evaluate the acute effects and intergroup comparison for the chronic effects of exercise. Significant differences were noted between athletes and the sedentary subjects in terms of pre-exercise left-N145 latencies and amplitudes and left -P100 amplitudes. Right-eye N145 latencies of inactive female subjects obtained before and after exercise were also statistically different. The results suggest that acute and habitual exercise affects the VEP responses independent from the body temperature and other physiological parameters. Small sized pre-exercise P100 amplitudes in the athletes can be attributed to the effect of rapid visual-activity-demanding sports on the central nervous system. Visual evoked potentials maybe used as neurophysiological criteria in defining the performance of an athlete.

  3. Effective potential and interdiffusion in binary ionic mixtures.

    PubMed

    Beznogov, M V; Yakovlev, D G

    2014-09-01

    We calculate interdiffusion coefficients in a two-component, weakly or strongly coupled ion plasma (gas or liquid, composed of two ion species immersed into a neutralizing electron background). We use an effective potential method proposed recently by Baalrud and Daligaut [Phys. Rev. Lett. 110, 235001 (2013)]. It allows us to extend the standard Chapman-Enskog procedure of calculating the interdiffusion coefficients to the case of strong Coulomb coupling. We compute binary diffusion coefficients for several ionic mixtures and fit them by convenient expressions in terms of the generalized Coulomb logarithm. These fits cover a wide range of plasma parameters spanning from weak to strong Coulomb couplings. They can be used to simulate diffusion of ions in ordinary stars as well as in white dwarfs and neutron stars.

  4. 30 CFR 254.44 - Calculating response equipment effective daily recovery capacities.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... recovery capacities. 254.44 Section 254.44 Mineral Resources BUREAU OF OCEAN ENERGY MANAGEMENT, REGULATION... Calculating response equipment effective daily recovery capacities. (a) You are required by § 254.26(d)(1) to calculate the effective daily recovery capacity of the response equipment identified in your response...

  5. 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

  6. 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.

  7. 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.

  8. Force and heat current formulas for many-body potentials in molecular dynamics simulations with applications to thermal conductivity calculations

    NASA Astrophysics Data System (ADS)

    Fan, Zheyong; Pereira, Luiz Felipe C.; Wang, Hui-Qiong; Zheng, Jin-Cheng; Donadio, Davide; Harju, Ari

    2015-09-01

    We derive expressions of interatomic force and heat current for many-body potentials such as the Tersoff, the Brenner, and the Stillinger-Weber potential used extensively in molecular dynamics simulations of covalently bonded materials. Although these potentials have a many-body nature, a pairwise force expression that follows Newton's third law can be found without referring to any partition of the potential. Based on this force formula, a stress applicable for periodic systems can be unambiguously defined. The force formula can then be used to derive the heat current formulas using a natural potential partitioning. Our heat current formulation is found to be equivalent to most of the seemingly different heat current formulas used in the literature, but to deviate from the stress-based formula derived from two-body potential. We validate our formulation numerically on various systems described by the Tersoff potential, namely three-dimensional silicon and diamond, two-dimensional graphene, and quasi-one-dimensional carbon nanotube. The effects of cell size and production time used in the simulation are examined.

  9. 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. Copyright © 2012 Elsevier Ltd. All rights reserved.

  10. 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.

  11. A potential-flow/boundary-layer method for calculating subsonic and transonic airfoil flow with trailing-edge separation

    NASA Technical Reports Server (NTRS)

    Barnwell, R. W.

    1981-01-01

    The development of a potential-flow/boundary-layer method for calculating subsonic and transonic turbulent flow past airfoils with trailing-edge separation is reported. A moment-of-momentum integral boundary-layer method is used which employs the law-of-the-wall/law-of-the-wake velocity profile and a two-layer eddy-viscosity model and ignores the laminar sublayer. All integrals across the boundary layer are obtained in closed form. Separation is assumed to occur when the shearing-stress velocity vanishes. A closed-form solution is derived for separated-flow regions where the shearing stress is negligible. In the potential-flow method, the exact form of the airfoil boundary condition is used, but it is applied at the chord line rather than the airfoil surface. This allows the accurate computation of flow about airfoils at large angles of attack but permits the use of body-oriented Cartesian computational grids. The governing equation for the perturbation velocity potential contains several terms in addition to the classical small-disturbance terms.

  12. Pyridine adsorbed on H-Faujasite zeolite: Electrostatic effect of the infinite crystal lattice calculated from a point charge representation

    NASA Astrophysics Data System (ADS)

    Injan, Natcha; Pannorad, Narong; Probst, Michael; Limtrakul, Jumras

    Calculations on cluster models of infinite systems require less computational effort and are technically simpler than periodic calculations, but they neglect, among other contributions, the effect of long-range electrostatic interaction from the infinite crystal lattice. In the case of zeolites, such contributions can be important for adsorption processes and surface reactions. We test a simple method for including this effect into the calculation by generating a finite number of point charges placed on the lattice sites. These point charges reproduce the infinite electrostatic potential at the chemically important region of the zeolite. We apply this method to the adsorption of pyridine on H-Faujasite zeolite. The embedding method gives an adsorption energy of -42.8 kcal/mol, which agrees well with the experimental value of -43.1 ± 1 kcal/mol. Without the electrostatic effect of the crystal field, the value is ˜9 kcal/mol higher.

  13. 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.

  14. Bioconjugates: harnessing potential for effective therapeutics.

    PubMed

    Khare, Piush; Jain, Aviral; Gulbake, Arvind; Soni, Vandana; Jain, Nitin K; Jain, Sanjay K

    2009-01-01

    The accomplishment of selective delivery can be brought through efficient drug targeting in which the attack of drug moiety is visualized only by the diseased organ and not by the organs of the whole body. This, in turn, consequently minimizes the unwanted effects or side effects caused by the drug action on the other organs. Bioconjugation is a fascinating technique that explores new vistas of drug delivery, and at the same time opens new possibilities for safe and effective therapy. This review is dedicated to and describes the science of bioconjugation and its potential in the drug delivery field, including different bioconjugates and their use in various therapeutic strategies. These have been classified as polymer based, macromolecule based, carrier based, and novel bioconjugates. This review describes the utility of bioconjugates in major diseases like cancer and others, and discusses experiments and research on the same. Bioconjugates have immense potential and extend a promising future in the drug delivery field. The review can act as a quick reference for those actively engaged in drug delivery and drug research to help overcome the hurdles of therapeutics.

  15. 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.

  16. Calculating the Sachs-Wolfe Effect from Solutions of Null Geodesics in Perturbed FRW Spacetime

    NASA Astrophysics Data System (ADS)

    Arroyo-Cárdenas, C. A.; Muñoz-Cuartas, J. C.

    2017-07-01

    In the upcoming precision era in cosmology, fine grained effects will be measured accurately. In particular, the late integrated Sachs-Wolfe (ISW) effect measurements will be improved to levels of unprecedented precision. The ISW consists on temperature fluctuations in the CMB due to gravitational redshift induced by the evolving potential well of large scale structure in the Universe. Currently there is large controversy related to the actual observability of the ISW effect. In principle, it is expected that, as an effect of the late accelerated expansion of the universe motivated by the current amount of dark energy, large scale structures may evolve rapidly, inducing an observable signature in the CMB photons in the way of a ISW anisotropy in the CMB. Tension arises since using galaxy redshift surveys some works report a temperature fluctuations with amplitude smaller than predicted by the Lambda-CDM. We argue that these discrepancies may be originated in the approximation that one has to make to get the classic Sachs-Wolfe effect. In this work, we compare the classic Sachs-Wolfe approximation with an exact solution to the propagation of photons in a dynamical background. We solve numerically the null geodesics on a perturbed FRW spacetime in the Newtonian gauge. From null geodesics, temperature fluctuations in the CMB due to the evolving potential has been calculated. Since solving geodesics accounts for more terms than solving the Sachs-Wolfe (approximated) integral, our results are more accurate. We have been able to substract the background cosmological redshift with the information provided by null geodesics, which allows to get an estimate of the integrated Sachs-Wolfe effect contribution to the temperature of the CMB.

  17. Calculation of two-dimensional potential energy surfaces of CO on a rutile(110) surface: ground and excited states

    NASA Astrophysics Data System (ADS)

    Mehring, Matthias; Klüner, Thorsten

    2013-07-01

    Being one of the most important catalytically active metal oxide surfaces, the aim of this study was the description of the laser-induced photodesorption of the CO adsorbate from a TiO2(110) surface. As a first step, this paper presents two-dimensional potential energy surfaces of a CO molecule on a rutile TiO2(110) surface. Focussing on the desorption mechanism taking place in this adsorbate-substrate system, the quantum chemical and quantum dynamical calculations regarding the desorption coordinate Z and the polar angle θ allowed a first insight into the mechanistic processes in the CO-TiO2(110) system which are relevant for laser-induced photodesorption. For the electronic ground state X1A1 the adsorption minimum was found for the polar angle θ = 0°, which corresponds to a linear coordination of the CO adsorbate with the carbon atom down to the substrate surface. This is in contrast to the electronically excited state A3B2, where the adsorption minimum was found for the polar angle θ = 180°, which describes a linear coordination with the oxygen atom of the CO molecule on top of the rutile TiO2(110) surface. Moreover, this paper shows exemplary quantum dynamical calculations which simulate the laser-induced photodesorption as a first step to understand the desorption process in detail. Hence, higher dimensional calculations regarding more than 2 degrees of freedom of the CO molecule on the substrate surface are needed to get a complete description of this complex adsorbate-substrate system.

  18. Calculations of H2O microwave line broadening in collisions with He atoms - Sensitivity to potential energy surfaces

    NASA Technical Reports Server (NTRS)

    Green, Sheldon; Defrees, D. J.; Mclean, A. D.

    1991-01-01

    Theoretical computations of broadening parameters are reported for three microwave lines of H2O in a bath of He atoms. The potential-energy surfaces employed are corrected for basis-set superposition error, and their reliability is checked by repeating the calculations with a different basis set for orbital expansion. The results are presented in extensive tables and discussed in detail. The corrections applied are shown to have a significant impact on the accuracy of the room-temperature broadenings determined: 8.9 sq A for the 22.2-GHz line, 11.8 sq A for the 183,3-GHz line, and 10.0 sq A for the 380.2-GHz line, in good agreement with published experimental data. The importance of collisional broadening for the atmospheric transmission of radiation and for remote-sensing applications is indicated.

  19. 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.

  20. Calculations of H2O microwave line broadening in collisions with He atoms - Sensitivity to potential energy surfaces

    NASA Technical Reports Server (NTRS)

    Green, Sheldon; Defrees, D. J.; Mclean, A. D.

    1991-01-01

    Theoretical computations of broadening parameters are reported for three microwave lines of H2O in a bath of He atoms. The potential-energy surfaces employed are corrected for basis-set superposition error, and their reliability is checked by repeating the calculations with a different basis set for orbital expansion. The results are presented in extensive tables and discussed in detail. The corrections applied are shown to have a significant impact on the accuracy of the room-temperature broadenings determined: 8.9 sq A for the 22.2-GHz line, 11.8 sq A for the 183,3-GHz line, and 10.0 sq A for the 380.2-GHz line, in good agreement with published experimental data. The importance of collisional broadening for the atmospheric transmission of radiation and for remote-sensing applications is indicated.

  1. Theoretical Calculations on the Feasibility of Microalgal Biofuels: Utilization of Marine Resources Could Help Realizing the Potential of Microalgae

    PubMed Central

    Park, Hanwool

    2016-01-01

    Abstract Microalgae have long been considered as one of most promising feedstocks with better characteristics for biofuels production over conventional energy crops. There have been a wide range of estimations on the feasibility of microalgal biofuels based on various productivity assumptions and data from different scales. The theoretical maximum algal biofuel productivity, however, can be calculated by the amount of solar irradiance and photosynthetic efficiency (PE), assuming other conditions are within the optimal range. Using the actual surface solar irradiance data around the world and PE of algal culture systems, maximum algal biomass and biofuel productivities were calculated, and feasibility of algal biofuel were assessed with the estimation. The results revealed that biofuel production would not easily meet the economic break‐even point and may not be sustainable at a large‐scale with the current algal biotechnology. Substantial reductions in the production cost, improvements in lipid productivity, recycling of resources, and utilization of non‐conventional resources will be necessary for feasible mass production of algal biofuel. Among the emerging technologies, cultivation of microalgae in the ocean shows great potentials to meet the resource requirements and economic feasibility in algal biofuel production by utilizing various marine resources. PMID:27782372

  2. Ab initio calculations, potential representation and vibrational dynamics of He2Br2 van der Waals complex.

    PubMed

    Valdés, Alvaro; Prosmiti, Rita; Villarreal, Pablo; Delgado-Barrio, Gerardo

    2005-01-22

    An intermolecular potential energy surface for He(2)Br(2) complex in the ground state is calculated at the levels of fourth-order (MP4) Moller-Plesset and coupled-cluster [CCSD(T)] approximations, using large-core pseudopotential for Br atoms and the aug-cc-pV5Z basis set for He. The surface is characterized by three minima and the minimum energy pathways through them. The global minimum corresponds to a linear He-Br(2)-He configuration, while the two other ones to "police-nightstick" and tetrahedral structures. The corresponding well depths are -90.39/-89.18, -81.23/-80.78 and -74.40/-74.02 cm(-1), respectively, at MP4/CCSD(T) levels of theory. It is found that results obtained by summing three-body parametrized HeBr(2) interactions and the He-He interaction are in very good accord with the corresponding MP4/CSSD(T) configuration energies of the He(2)Br(2). Variational calculations using a sum of three-body interactions are presented to study the bound states of the vdW He(2)Br(2) complex. The binding energy D(0) and the corresponding vibrationally averaged structure are determined for different isomers of the cluster and their comparison with the available experimental data is discussed.

  3. Theoretical Calculations on the Feasibility of Microalgal Biofuels: Utilization of Marine Resources Could Help Realizing the Potential of Microalgae.

    PubMed

    Park, Hanwool; Lee, Choul-Gyun

    2016-11-01

    Microalgae have long been considered as one of most promising feedstocks with better characteristics for biofuels production over conventional energy crops. There have been a wide range of estimations on the feasibility of microalgal biofuels based on various productivity assumptions and data from different scales. The theoretical maximum algal biofuel productivity, however, can be calculated by the amount of solar irradiance and photosynthetic efficiency (PE), assuming other conditions are within the optimal range. Using the actual surface solar irradiance data around the world and PE of algal culture systems, maximum algal biomass and biofuel productivities were calculated, and feasibility of algal biofuel were assessed with the estimation. The results revealed that biofuel production would not easily meet the economic break-even point and may not be sustainable at a large-scale with the current algal biotechnology. Substantial reductions in the production cost, improvements in lipid productivity, recycling of resources, and utilization of non-conventional resources will be necessary for feasible mass production of algal biofuel. Among the emerging technologies, cultivation of microalgae in the ocean shows great potentials to meet the resource requirements and economic feasibility in algal biofuel production by utilizing various marine resources.

  4. Determination of lipophilicity of novel potential antituberculotic agents using HPLC on monolithic stationary phase and theoretical calculations.

    PubMed

    Mrkvicková, Z; Kovaríková, P; Balíková, S; Klimes, J

    2008-09-29

    The HPLC analyses on the monolithic stationary phase were employed for rapid determination of lipophilicity of the two sets of newly synthesized potential antituberculotic agents. The analyses utilized the mixture of methanol and phosphate buffer (pH 7.4) as a mobile phase and a flow rate of 4mL/min. Monolithic stationary phase enabled to significantly reduce the time of analyses, achieve appropriate peak shapes for all tested compounds as well as the separation of positional isomers. Furthermore, the theoretical lipophilic parameters (logP) for all compounds were calculated employing the chemical programs (e.g., ACD/logP, HyperChem, miLogP, AlogP, KOWWIN and COSMOFrag, etc.). The experimental data (logk) and calculated logP values were compared by linear regression analysis. The highest correlation for both series was obtained for KOWWIN and miLogP programs. However, capability of particular chemical software to precisely predict lipophilicity of a compound is structurally dependent. Thus the predictive power of the selected program should be verified using experimental method. The results of this study documented that experimental determination of lipophilicity using HPLC on monolithic stationary phase is practical and reasonable for this purpose.

  5. Ab initio calculations, potential representation and vibrational dynamics of He2Br2 van der Waals complex

    NASA Astrophysics Data System (ADS)

    Valdés, Álvaro; Prosmiti, Rita; Villarreal, Pablo; Delgado-Barrio, Gerardo

    2005-01-01

    An intermolecular potential energy surface for He2Br2 complex in the ground state is calculated at the levels of fourth-order (MP4) Møller-Plesset and coupled-cluster [CCSD(T)] approximations, using large-core pseudopotential for Br atoms and the aug-cc-pV5Z basis set for He. The surface is characterized by three minima and the minimum energy pathways through them. The global minimum corresponds to a linear He-Br2-He configuration, while the two other ones to "police-nightstick" and tetrahedral structures. The corresponding well depths are -90.39/-89.18, -81.23/-80.78 and -74.40/-74.02 cm-1, respectively, at MP4/CCSD(T) levels of theory. It is found that results obtained by summing three-body parametrized HeBr2 interactions and the He-He interaction are in very good accord with the corresponding MP4/CSSD(T) configuration energies of the He2Br2. Variational calculations using a sum of three-body interactions are presented to study the bound states of the vdW He2Br2 complex. The binding energy D0 and the corresponding vibrationally averaged structure are determined for different isomers of the cluster and their comparison with the available experimental data is discussed.

  6. 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.

  7. 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

    2015-09-07

    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.

  8. 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.

  9. 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.

  10. Potential adverse health effects of wood smoke

    SciTech Connect

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

    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.29 references.

  11. 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.

  12. Potential effects of global climate change

    SciTech Connect

    Gucinski, H.; Vance, E.; Reiners, W.A.

    1995-07-01

    The difficulties of detecting climatic changes do not diminish the need to examine the consequences of a changing global radiative energy balance. In part, detecting global changes is difficult (even though many, though by no means all, theoretical climatic processes are well understood) because the potential effects of changes on the unmanaged ecosystems of the globe, especially forests, which may have great human significance, involve tightly woven ecosystems, inextricably linked to global habitat. Coniferous forests are of particular interest because they dominate high-latitude forest systems, and potential effects of global climate change are likely to be greatest at high latitudes. The degree of projected climate change is a function of many likely scenarios of fossil fuel consumption, and the ratios of manmade effects to natural sources and sinks of CO{sub 2}. Because CO{sub 2}, like water vapor, CH{sub 4}, CFCs, and other gases, absorbs infrared energy, it will alter the radiation balance of the global atmosphere. The consequences of this alteration to the radiation balance cannot simply be translated into changing climate because (1) the existence of large energy reservoirs (the oceans) can introduce a lag in responses, (2) feedback loops between atmosphere, oceans, and biosphere can change the net rate of buildup of greenhouse gases in the atmosphere, (3) complex interactions in the atmospheric water balance can change the rate of cloud formation with their persistence, in turn, changing the global albedo and the energy balance, and (4) there is intrusion of other global effects, such as periodic volcanic gas injections to the stratosphere.

  13. Liquid drops on a surface: Using density functional theory to calculate the binding potential and drop profiles and comparing with results from mesoscopic modelling

    NASA Astrophysics Data System (ADS)

    Hughes, Adam P.; Thiele, Uwe; Archer, Andrew J.

    2015-02-01

    The contribution to the free energy for a film of liquid of thickness h on a solid surface due to the interactions between the solid-liquid and liquid-gas interfaces is given by the binding potential, g(h). The precise form of g(h) determines whether or not the liquid wets the surface. Note that differentiating g(h) gives the Derjaguin or disjoining pressure. We develop a microscopic density functional theory (DFT) based method for calculating g(h), allowing us to relate the form of g(h) to the nature of the molecular interactions in the system. We present results based on using a simple lattice gas model, to demonstrate the procedure. In order to describe the static and dynamic behaviour of non-uniform liquid films and drops on surfaces, a mesoscopic free energy based on g(h) is often used. We calculate such equilibrium film height profiles and also directly calculate using DFT the corresponding density profiles for liquid drops on surfaces. Comparing quantities such as the contact angle and also the shape of the drops, we find good agreement between the two methods. We also study in detail the effect on g(h) of truncating the range of the dispersion forces, both those between the fluid molecules and those between the fluid and wall. We find that truncating can have a significant effect on g(h) and the associated wetting behaviour of the fluid.

  14. Liquid drops on a surface: using density functional theory to calculate the binding potential and drop profiles and comparing with results from mesoscopic modelling.

    PubMed

    Hughes, Adam P; Thiele, Uwe; Archer, Andrew J

    2015-02-21

    The contribution to the free energy for a film of liquid of thickness h on a solid surface due to the interactions between the solid-liquid and liquid-gas interfaces is given by the binding potential, g(h). The precise form of g(h) determines whether or not the liquid wets the surface. Note that differentiating g(h) gives the Derjaguin or disjoining pressure. We develop a microscopic density functional theory (DFT) based method for calculating g(h), allowing us to relate the form of g(h) to the nature of the molecular interactions in the system. We present results based on using a simple lattice gas model, to demonstrate the procedure. In order to describe the static and dynamic behaviour of non-uniform liquid films and drops on surfaces, a mesoscopic free energy based on g(h) is often used. We calculate such equilibrium film height profiles and also directly calculate using DFT the corresponding density profiles for liquid drops on surfaces. Comparing quantities such as the contact angle and also the shape of the drops, we find good agreement between the two methods. We also study in detail the effect on g(h) of truncating the range of the dispersion forces, both those between the fluid molecules and those between the fluid and wall. We find that truncating can have a significant effect on g(h) and the associated wetting behaviour of the fluid.

  15. Advanced Quantum Mechanical Calculation of Superheavy Ions: Energy Levels, Radiation and Finite Nuclear Size Effects

    SciTech Connect

    Glushkov, Alexander V.; Gurnitskaya, E.P.; Loboda, A.V.

    2005-10-26

    Advanced quantum approach to calculation of spectra for superheavy ions with an account of relativistic, correlation, nuclear, radiative effects is developed and based on the gauge invariant quantum electrodynamics (QED) perturbation theory (PT). The Lamb shift polarization part is calculated in the Ueling approximation, self-energy part is defined within a new non-PT procedure of Ivanov-Ivanova. Calculation results for energy levels, hyperfine structure parameters of some heavy elements ions are presented.

  16. An effective method to accurately calculate the phase space factors for β-β- decay

    DOE PAGES

    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. Here, 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.

  17. Effects of (18)O isotopic substitution on the rotational spectra and potential splitting in the OH-OH2 complex: improved measurements for (16)OH-(16)OH2 and (18)OH-(18)OH2, new measurements for the mixed isotopic forms, and ab initio calculations of the (2)A'-(2)A" energy separation.

    PubMed

    Brauer, Carolyn S; Sedo, Galen; Dahlke, Erin; Wu, Shenghai; Grumstrup, Erik M; Leopold, Kenneth R; Marshall, Mark D; Leung, Helen O; Truhlar, Donald G

    2008-09-14

    Rotational spectra have been observed for (16)OH-(16)OH(2), (16)OH-(18)OH(2), (18)OH-(16)OH(2), and (18)OH-(18)OH(2) with complete resolution of the nuclear magnetic hyperfine structure from the OH and water protons. Transition frequencies have been analyzed for each isotopic form using the model of Marshall and Lester [J. Chem. Phys. 121, 3019 (2004)], which accounts for partial quenching of the OH orbital angular momentum and the decoupling of the electronic spin from the OH molecular axis. The analysis accounts for both the ground ((2)A(')) and first electronically excited ((2)A(")) states of the system, which correspond roughly to occupancy by the odd electron in the p(y) and p(x) orbitals, respectively (where p(y) is in the mirror plane of the complex and p(x) is perpendicular to p(y) and the OH bond axis). The spectroscopic measurements yield a parameter, rho, which is equal to the vibrationally averaged (2)A(')-(2)A(") energy separation that would be obtained if spin-orbit coupling and rotation were absent. For the parent species, rho = -146.560 27(9) cm(-1). (18)O substitution on the water increases /rho/ by 0.105 29(10) cm(-1), while substitution on the OH decreases /rho/ by 0.068 64(11) cm(-1). In the OH-OH(2) complex, the observed value of rho implies an energy spacing between the rotationless levels of the (2)A(') and (2)A(") states of 203.76 cm(-1). Ab initio calculations have been performed with quadratic configuration interaction with single and double excitations (QCISD), as well as multireference configuration interaction (MRCI), both with and without the inclusion of spin-orbit coupling. The MRCI calculations with spin-orbit coupling perform the best, giving a value of 171 cm(-1) for the (2)A(')-(2)A(") energy spacing at the equilibrium geometry. Calculations along the large-amplitude bending coordinates of the OH and OH(2) moieties within the complex are presented and are shown to be consistent with a vibrational averaging effect as the main

  18. Asymptotic correction approach to improving approximate exchange-correlation potentials: Time-dependent density-functional theory calculations of molecular excitation spectra

    NASA Astrophysics Data System (ADS)

    Casida, Mark E.; Salahub, Dennis R.

    2000-11-01

    The time-dependent density functional theory (TD-DFT) calculation of excitation spectra places certain demands on the DFT exchange-correlation potential, vxc, that are not met by the functionals normally used in molecular calculations. In particular, for high-lying excitations, it is crucial that the asymptotic behavior of vxc be correct. In a previous paper, we introduced a novel asymptotic-correction approach which we used with the local density approximation (LDA) to yield an asymptotically corrected LDA (AC-LDA) potential [Casida, Casida, and Salahub, Int. J. Quantum Chem. 70, 933 (1998)]. The present paper details the theory underlying this asymptotic correction approach, which involves a constant shift to incorporate the effect of the derivative discontinuity (DD) in the bulk region of finite systems, and a spliced asymptotic correction in the large r region. This is done without introducing any adjustable parameters. We emphasize that correcting the asymptotic behavior of vxc is not by itself sufficient to improve the overall form of the potential unless the effect of the derivative discontinuity is taken into account. The approach could be used to correct vxc from any of the commonly used gradient-corrected functionals. It is here applied to the LDA, using the asymptotically correct potential of van Leeuwen and Baerends (LB94) in the large r region. The performance of our AC-LDA vxc is assessed for the calculation of TD-DFT excitation energies for a large number of excitations, including both valence and Rydberg states, for each of four small molecules: N2, CO, CH2O, and C2H4. The results show a significant improvement over those from either the LB94 or the LDA functionals. This confirms that the DD is indeed an important element in the design of functionals. The quality of TDLDA/LB94 and TDLDA/AC-LDA oscillator strengths were also assessed in what we believe to be the first rigorous assessment of TD-DFT molecular oscillator strengths in comparison with

  19. DFT calculation of the potential energy landscape topology and Raman spectra of type I CH4 and CO2 hydrates.

    PubMed

    Vidal-Vidal, Ángel; Pérez-Rodríguez, Martín; Torré, Jean-Philippe; Piñeiro, Manuel M

    2015-03-14

    CO2 and CH4 clathrate hydrates of type I were studied by means of DFT and QTAIM, in order to better understand their properties at the molecular level. Sub-cells of type I hydrates were modeled as independent rigid cages, both empty and containing guest molecules. Interaction potentials of guest molecules inside each cage, and moving from a cell to the adjacent one, were calculated using the DFT approximation B3LYP/6-311+g(d,p), considering the cases with and without long range Coulombic corrections. The selected theory level was validated by comparison of the simulated Raman spectra with the experimental ones, for the case of type I lattice at full occupation of CO2 and CH4, respectively. For this comparison, Fermi resonances of CO2 were taken into account by transforming experimental bands to the corresponding theoretical non-mixed states. On the one hand, our results confirm the validity of the theory level selected for the model. We have shown the high anisotropy of the guest-cell interaction potential of the molecules analyzed, which has implications in the formulation and use of equations of state, and in the study of transport properties as well. On the other hand, our results suggest that the concentration of guest species inside type I hydrates could be computed from the comparison of experimental and predicted Raman spectra, although there are non-trivial experimental limitations to get over for that purpose.

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  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

    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.

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

    PubMed

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

    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.

  4. Spin-orbit effects in iridates via electronic structure calculations: effects of tension and dimensionality

    NASA Astrophysics Data System (ADS)

    Pardo, Victor; Lado, Jose L.

    2015-03-01

    Ab initio calculations have been performed in 5d5-electron-based oxides in the large spin-orbit coupling limit. Our work tries to analyze the effects of strain and dimensionality in the electronic structure properties of iridates with Ir4+:5d5 electronic configuration in order to understand the different set of properties these materials present: they can be either metals or insulators, e.g. We focus on studying how close to the fully ionic jeff=1/2 limit the system is by analyzing the Lz/Sz ratio. We observe that it varies continuously as a function of strain or pressure, changing drastically with relatively small variations. We also analyze what effects on the band structure accompany this variation. In order to do this, we needed to include a full non-collinearity in the calculation of spin-orbit interaction. We have explored SrIrO3, Sr2IrO4, Sr3Ir2O7, thin films of SrIrO3 so as to analyze the dimensionality effects and the structural implications. We acknowledge support of the MINECO through the Ramon y Cajal Program, Xunta de Galicia through Project No. EM2013/037 and the EU through the Marie-Curie ITN ``Spinograph''.

  5. 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.

  6. A method for the evaluation of dose-effect data utilizing a programmable calculator.

    PubMed

    Carmines, E L; Carchman, R A; Borzelleca, J F

    1980-08-01

    A program for the calculation of the median effective dose (ED50) and the slope of the dose-effect line was developed for a programmable calculator. The method employed approximated the solution described by Bliss. Experimental data were evaluated and compared to both hand calculated results and results of other computer methods. This method produced results which differed from other computer methods by less than 1 percent. This program provided information necessary for the test for parallelism and estimate of relative potency of two dose-effect lines.

  7. Theory for the semi-analytical calculation of oil recovery and effective relative permeabilities using streamtubes

    NASA Astrophysics Data System (ADS)

    Hewett, Thomas A.; Yamada, Tomomi

    A semi-analytical method has been developed for calculating oil recovery in two and three dimensions, and for calculating effective relative permeabilities for coarse grids. The calculations are based on the assumption that the effects of a changing mobility field can be accounted for by using fixed streamtube geometries with flowrates updated to account for the changing mobility distribution. The single-phase pressure distribution from a numerical solution of Laplace's equation is used to calculate the pressure distribution for a two-phase flow based on a mapping of the solution of the Buckley-Leverett equation onto the streamtubes derived from the single-phase solution. The displacement calculations for oil recovery are based on theory previously developed by Dykstra and Parsons, extended to include the effects of spatially varying permeability and continuously changing mobilities, as occurs in solutions of the Buckley-Leverett equation for typical values of the mobility ratio. This idea has also been extended to the calculation of effective relative permeabilities for coarse-grid simulation and finally establishes the proper rules for averaging the results of fine-grid numerical simulations of two-phase flow for the definition of effective two-phase flow properties on coarse grids. These calculations have been generalized to three-dimensional flows by the simple device of conceptually inserting a gridded plane across the flow and defining each streamtube at that location as those streamlines which pass through any one of the grid cells. When combined with time-of-flight calculations from the gridded plane to both the producer and injector, the distribution of pore volume along each streamtube can be calculated. This information, combined with a tabulation of the single-phase, steady-state pressure distribution along each streamtube, provides all of the information needed for the semi-analytical calculation of oil recovery and effective flow properties in three

  8. 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.

  9. Finding quantum effects in strong classical potentials

    NASA Astrophysics Data System (ADS)

    Hegelich, B. Manuel; Labun, Lance; Labun, Ou Z.

    2017-06-01

    The long-standing challenge to describing charged particle dynamics in strong classical electromagnetic fields is how to incorporate classical radiation, classical radiation reaction and quantized photon emission into a consistent unified framework. The current, semiclassical methods to describe the dynamics of quantum particles in strong classical fields also provide the theoretical framework for fundamental questions in gravity and hadron-hadron collisions, including Hawking radiation, cosmological particle production and thermalization of particles created in heavy-ion collisions. However, as we show, these methods break down for highly relativistic particles propagating in strong fields. They must therefore be improved and adapted for the description of laser-plasma experiments that typically involve the acceleration of electrons. Theory developed from quantum electrodynamics, together with dedicated experimental efforts, offer the best controllable context to establish a robust, experimentally validated foundation for the fundamental theory of quantum effects in strong classical potentials.

  10. 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.

  11. Structure-based sampling and self-correcting machine learning for accurate calculations of potential energy surfaces and vibrational levels.

    PubMed

    Dral, Pavlo O; Owens, Alec; Yurchenko, Sergei N; Thiel, Walter

    2017-06-28

    We present an efficient approach for generating highly accurate molecular potential energy surfaces (PESs) using self-correcting, kernel ridge regression (KRR) based machine learning (ML). We introduce structure-based sampling to automatically assign nuclear configurations from a pre-defined grid to the training and prediction sets, respectively. Accurate high-level ab initio energies are required only for the points in the training set, while the energies for the remaining points are provided by the ML model with negligible computational cost. The proposed sampling procedure is shown to be superior to random sampling and also eliminates the need for training several ML models. Self-correcting machine learning has been implemented such that each additional layer corrects errors from the previous layer. The performance of our approach is demonstrated in a case study on a published high-level ab initio PES of methyl chloride with 44 819 points. The ML model is trained on sets of different sizes and then used to predict the energies for tens of thousands of nuclear configurations within seconds. The resulting datasets are utilized in variational calculations of the vibrational energy levels of CH3Cl. By using both structure-based sampling and self-correction, the size of the training set can be kept small (e.g., 10% of the points) without any significant loss of accuracy. In ab initio rovibrational spectroscopy, it is thus possible to reduce the number of computationally costly electronic structure calculations through structure-based sampling and self-correcting KRR-based machine learning by up to 90%.

  12. Structure-based sampling and self-correcting machine learning for accurate calculations of potential energy surfaces and vibrational levels

    NASA Astrophysics Data System (ADS)

    Dral, Pavlo O.; Owens, Alec; Yurchenko, Sergei N.; Thiel, Walter

    2017-06-01

    We present an efficient approach for generating highly accurate molecular potential energy surfaces (PESs) using self-correcting, kernel ridge regression (KRR) based machine learning (ML). We introduce structure-based sampling to automatically assign nuclear configurations from a pre-defined grid to the training and prediction sets, respectively. Accurate high-level ab initio energies are required only for the points in the training set, while the energies for the remaining points are provided by the ML model with negligible computational cost. The proposed sampling procedure is shown to be superior to random sampling and also eliminates the need for training several ML models. Self-correcting machine learning has been implemented such that each additional layer corrects errors from the previous layer. The performance of our approach is demonstrated in a case study on a published high-level ab initio PES of methyl chloride with 44 819 points. The ML model is trained on sets of different sizes and then used to predict the energies for tens of thousands of nuclear configurations within seconds. The resulting datasets are utilized in variational calculations of the vibrational energy levels of CH3Cl. By using both structure-based sampling and self-correction, the size of the training set can be kept small (e.g., 10% of the points) without any significant loss of accuracy. In ab initio rovibrational spectroscopy, it is thus possible to reduce the number of computationally costly electronic structure calculations through structure-based sampling and self-correcting KRR-based machine learning by up to 90%.

  13. Prediction of Thermal Properties and Effect of OH Substituent for Poly(vinyl alcohol)s by Molecular Dynamics Calculations

    NASA Astrophysics Data System (ADS)

    Tsuchiya, Yooko; Yoshii, Noriyuki; Iwatsubo, Tetsushiro

    2004-08-01

    Since heat storage technology contributes greatly to the effective use of energy, we are attempting to develop latent heat storage materials. If computer simulations enable the estimation of material properties prior to experiments, they will provide us with very effective tools for the development of new materials. We use molecular dynamics calculations to predict the melting points and latent heats of fusion, which are crucial thermal properties for evaluating the suitability of heat-storage materials. As the object of calculation, poly(vinyl alcohol) (PVA) was chosen, because polymer materials are effective in that they can be made to cover all temperature ranges by changing the molecular weight. The melting points were determined from the volume change, and the latent heats of fusion were determined from the internal energy. As for these calculations, it was ascertained that these thermal properties were suitable values in comparison with the results of actual calorimetry. From the comparative calculation of the polymer consistent force field (PCFF) and optimized potentials for liquid simulations (OPLS) force field, it was shown that the intermolecular potential could be simplified. Moreover, the stability of the structural isomer of PVA and the state of the hydrogen bond were evaluated, because a strong intermolecular bond leads to structural stability and a high melting temperature.

  14. 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.

  15. 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

  16. 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

    2015-08-07

    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

  17. Effects of microscopic transport coefficients on fission observables calculated by Langevin equation and its systematics

    NASA Astrophysics Data System (ADS)

    Usang, Mark; Ivanyuk, Fedir; Ishizuka, Chikako; Chiba, Satoshi

    2017-09-01

    The Langevin dynamical description of fission observables is inspired by the random evolution of shape parameters across the potential surface. In these work, we shall use mass and friction tensors inspired from Linear Response Theory (microscopic transport coefficients) and obtain the fission observables associated with these calculations. We compare these microscopic results with calculations using hydrodynamical mass tensor and wall-window friction tensor (macroscopic transport coefficients). We are able to calculate the fission product yield, Coulomb kinetic energy and prescission kinetic energy from the Langevin calculation. This allows us to observe the systematic of average light and heavy mass fission product yield calculated using both microscopic and macroscopic calculations. We also compare the results of microscopic and macroscopic calculation total kinetic energy (TKE) with Viola's TKE systematics. In the case of 236,239U compound nucleus, we do the microscopic calculation for several excitation energy up to 30 MeV and afterwards compare it to the TKE of experimental data and corresponding macroscopic TKE. Reasonable agreement of microscopic TKE to experiment is obtained which shows decreasing TKE with increasing excitation energy. Macroscopic TKE however, is independent of excitation energy and thus contrary to experimental data.

  18. SULISO: The Bath suite of vibrational characterization and isotope effect calculation software

    NASA Astrophysics Data System (ADS)

    Williams, Ian H.; Wilson, Philippe B.

    Isotope effects are subtle but powerful probes of chemical reaction mechanisms and environmental conditions, with applications across chemical, biological and earth sciences. Their meaningful interpretation often relies on calculations based upon fundamental theories for their origin. The SULISO suite consists of four programs for the calculation of vibrational frequencies and isotope effects. CAMVIB is a broad vibrational characterization code developed for analysis of calculated harmonic frequencies and of normal modes in terms of internal coordinates. LIPFR calculates isotopic partition function ratios for pairs of isotopically substituted whole molecules, corresponding to conventional methodology, whereas UJISO is designed to perform similar calculations on subsets of atoms from very large systems. CUTOFF is a utility which truncates a force-constant matrix for a large system to obtain a smaller matrix appropriate for a specified subset of atoms.

  19. 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.

  20. Effects of aging on laser evoked potentials.

    PubMed

    Creac'H, Christelle; Bertholon, Alexandre; Convers, Philippe; Garcia-Larrea, Luis; Peyron, Roland

    2015-05-01

    Aging has been reported to reduce the amplitude of laser evoked potentials. However, it is unknown whether this effect depends on the length of the sensory fibers. This is an important issue, because most painful neuropathies are length-dependent. We conducted a study of 40 healthy subjects, half of whom were older than age 50 years. Nociceptive stimuli were delivered to the feet and thighs using a CO2 laser stimulator. Detection and pain perception thresholds did not correlate with age. Latencies of N1, N2, and P2 correlated positively with age on the feet but not on the thighs, whereas the amplitude of N2-P2 decreased with age for both areas. The effects of aging on latencies may reflect a distal loss of peripheral inputs and a length-dependent de-synchronization of the ascending nociceptive volley. Additional changes in peripheral and central processes may explain the diffuse decrease of N2-P2 amplitudes observed with aging. © 2014 Wiley Periodicals, Inc.