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Sample records for calculated potential energy

  1. 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.

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

    SciTech Connect

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

    2014-12-15

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

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

    PubMed

    Tung, Wei-Cheng; Adamowicz, Ludwik

    2014-03-28

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

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

    NASA Astrophysics Data System (ADS)

    Tung, Wei-Cheng; Adamowicz, Ludwik

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Scheid, W.

    2016-01-01

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

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

    PubMed

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

    2010-10-12

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

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

    PubMed

    Rauhut, Guntram

    2004-11-15

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

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

    PubMed Central

    Wang, Jiyao; Deng, Yuqing; Roux, Benoît

    2006-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Rauhut, Guntram

    2004-11-01

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

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

    SciTech Connect

    Ho, T.; Rabitz, H.

    1996-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1988-06-01

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

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

    SciTech Connect

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

    1988-06-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

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

    PubMed

    Rashev, Svetoslav; Moule, David C

    2015-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  16. 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.

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

    NASA Astrophysics Data System (ADS)

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

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

  18. 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.

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

    NASA Astrophysics Data System (ADS)

    Buryak, Ilya; Vigasin, Andrey A.

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Akin-Ojo, Omololu; Szalewicz, Krzysztof

    2005-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

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

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

    PubMed

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

    2013-11-01

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

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

    PubMed

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

    2015-08-28

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

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

    PubMed

    Wierzchowski, S J; Monson, P A

    2007-06-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

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

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

    PubMed

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

    2012-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

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

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

    SciTech Connect

    Tung, Wei-Cheng; Adamowicz, Ludwik

    2014-03-28

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-08-01

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

  10. 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.

  11. 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).

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

    NASA Astrophysics Data System (ADS)

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

    2010-04-01

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

  13. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2005-02-01

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

  16. 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.

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

    PubMed

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

    2007-09-14

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

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

    SciTech Connect

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

    1998-08-01

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

  19. Calculate and Plot Complex Potential

    Energy Science and Technology Software Center (ESTSC)

    1998-05-05

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

  20. Ab initio calculations of accurate dissociation energy and analytic potential energy function for the second excited state B1Π of 7LiH

    NASA Astrophysics Data System (ADS)

    Shi, De-Heng; Liu, Yu-Fang; Sun, Jin-Feng; Zhu, Zun-Lue; Yang, Xiang-Dong

    2006-12-01

    The reasonable dissociation limit of the second excited singlet state B1Π of 7LiH molecule is obtained. The accurate dissociation energy and equilibrium geometry of the B1Π state are calculated using a symmetry-adapted-cluster configuration-interaction method in full active space. The whole potential energy curve for the B1Π state is obtained over the internuclear distance ranging from about 0.10 nm to 0.54 nm, and has a least-square fit to the analytic Murrell-Sorbie function form. The vertical excitation energy is calculated from the ground state to the B1Π state and compared with previous theoretical results. The equilibrium internuclear distance obtained by geometry optimization is found to be quite different from that obtained by single-point energy scanning under the same calculation condition. Based on the analytic potential energy function, the harmonic frequency value of the B1Π state is estimated. A comparison of the theoretical calculations of dissociation energies, equilibrium interatomic distances and the analytic potential energy function with those obtained by previous theoretical results clearly shows that the present work is more comprehensive and in better agreement with experiments than previous theories, thus it is an improvement on previous theories.

  1. An improved potential energy surface and multi-temperature quasiclassical trajectory calculations of N2 + N2 dissociation reactions.

    PubMed

    Bender, Jason D; Valentini, Paolo; Nompelis, Ioannis; Paukku, Yuliya; Varga, Zoltan; Truhlar, Donald G; Schwartzentruber, Thomas; Candler, Graham V

    2015-08-01

    Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration of collision-induced dissociation of molecular species and energy transfer between the translational and internal modes of the gas molecules. Here, we describe a study of the N2 + N2⟶N2 + 2N and N2 + N2⟶4N nitrogen dissociation reactions using the quasiclassical trajectory (QCT) method. The simulations used a new potential energy surface for the N4 system; the surface is an improved version of one that was presented previously. In the QCT calculations, initial conditions were determined based on a two-temperature model that approximately separates the translational-rotational temperature from the vibrational temperature of the N2 diatoms. Five values from 8000 K to 30,000 K were considered for each of the two temperatures. Over 2.4 × 10(9) trajectories were calculated. We present results for ensemble-averaged dissociation rate constants as functions of the translational-rotational temperature T and the vibrational temperature T(v). The rate constant depends more strongly on T when T(v) is low, and it depends more strongly on T(v) when T is low. Quasibound reactant states contribute significantly to the rate constants, as do exchange processes at higher temperatures. We discuss two sets of runs in detail: an equilibrium test set in which T = T(v) and a nonequilibrium test set in which T(v) < T. In the equilibrium test set, high-v and moderately-low-j molecules contribute most significantly to the overall dissociation rate, and this state specificity becomes stronger as the temperature decreases. Dissociating trajectories tend to result in a major loss of vibrational energy and a minor loss of rotational energy. In the nonequilibrium test set, as T(v) decreases while T is fixed, higher-j molecules contribute more significantly to the dissociation rate, dissociating trajectories tend to result in a greater rotational energy loss, and the dissociation probability

  2. 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

  3. 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.

  4. Ab initio calculation of accurate dissociation energy, potential energy curve and dipole moment function for the A1Σ+ state 7LiH molecule

    NASA Astrophysics Data System (ADS)

    Shi, De-Heng; Liu, Yu-Fang; Sun, Jin-Feng; Yang, Xiang-Dong; Zhu, Zun-Lue

    2006-05-01

    The reasonable dissociation limit of the A1Σ+ state 7LiH molecule is obtained. The accurate dissociation energy and the equilibrium geometry of this state are calculated using a symmetry-adapted-cluster configuration-interaction method in complete active space for the first time. The whole potential energy curve and the dipole moment function for the A1Σ+ state are calculated over a wide internuclear separation range from about 0.1 to 1.4 nm. The calculated equilibrium geometry and dissociation energy of this potential energy curve are of Re=0.2487 nm and De=1.064 eV, respectively. The unusual negative values of the anharmonicity constant and the vibration-rotational coupling constant are of ωeχe=-4.7158cm-1 and αe=-0.08649cm-1, respectively. The vertical excitation energy from the ground to the A1Σ+ state is calculated and the value is of 3.613 eV at 0.15875 nm (the equilibrium position of the ground state). The highly anomalous shape of this potential energy curve, which is exceptionally flat over a wide radial range around the equilibrium position, is discussed in detail. The harmonic frequency value of 502.47cm-1 about this state is approximately estimated. Careful comparison of the theoretical determinations with those obtained by previous theories about the A1Σ+ state dissociation energy clearly shows that the present calculations are much closer to the experiments than previous theories, thus represents an improvement.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

    Tarana, Michal; Čurík, Roman

    2016-05-01

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

  7. MULTIMODE quantum calculations of vibrational energies and IR spectrum of the NO{sup +}(H{sub 2}O) cluster using accurate potential energy and dipole moment surfaces

    SciTech Connect

    Homayoon, Zahra

    2014-09-28

    A new, full (nine)-dimensional potential energy surface and dipole moment surface to describe the NO{sup +}(H{sub 2}O) cluster is reported. The PES is based on fitting of roughly 32 000 CCSD(T)-F12/aug-cc-pVTZ electronic energies. The surface is a linear least-squares fit using a permutationally invariant basis with Morse-type variables. The PES is used in a Diffusion Monte Carlo study of the zero-point energy and wavefunction of the NO{sup +}(H{sub 2}O) and NO{sup +}(D{sub 2}O) complexes. Using the calculated ZPE the dissociation energies of the clusters are reported. Vibrational configuration interaction calculations of NO{sup +}(H{sub 2}O) and NO{sup +}(D{sub 2}O) using the MULTIMODE program are performed. The fundamental, a number of overtone, and combination states of the clusters are reported. The IR spectrum of the NO{sup +}(H{sub 2}O) cluster is calculated using 4, 5, 7, and 8 modes VSCF/CI calculations. The anharmonic, coupled vibrational calculations, and IR spectrum show very good agreement with experiment. Mode coupling of the water “antisymmetric” stretching mode with the low-frequency intermolecular modes results in intensity borrowing.

  8. Gas-phase reaction between calcium monocation and fluoromethane: Analysis of the potential energy hypersurface and kinetics calculations

    SciTech Connect

    Varela-Alvarez, Adrian; Sordo, Jose A.; Rayon, V. M.; Redondo, P.; Barrientos, C.

    2009-10-14

    The gas-phase reaction between calcium monocation and fluoromethane: Ca{sup +}+CH{sub 3}F{yields}CaF{sup +}+CH{sub 3} was theoretically analyzed. The potential energy hypersurface was explored by using density functional theory methodology with different functionals and Pople's, Dunning's, Ahlrichs', and Stuttgart-Dresden basis sets. Kinetics calculations (energy and total angular momentum resolved microcanonical variational/conventional theory) were accomplished. The theoretically predicted range for the global kinetic rate constant values at 295 K (7.2x10{sup -11}-5.9x10{sup -10} cm{sup 3} molecule{sup -1} s{sup -1}) agrees reasonably well with the experimental value at the same temperature [(2.6{+-}0.8)x10{sup -10} cm{sup 3} molecule{sup -1} s{sup -1}]. Explicit consideration of a two transition state model, where the formation of a weakly bounded prereactive complex is preceded by an outer transition state (entrance channel) and followed by an inner transition state connecting with a second intermediate that finally leads to products, is mandatory. Experimental observations on the correlation, or lack of correlation, between reaction rate constants and second ionization energies of the metal might well be rationalized in terms of this two transition state model.

  9. Collisional excitation of CH(X²Π) by He: new ab initio potential energy surfaces and scattering calculations.

    PubMed

    Marinakis, Sarantos; Dean, Indigo Lily; Kłos, Jacek; Lique, François

    2015-09-01

    We present a new set of potential energy surfaces (PESs) for the CH(X(2)Π)-He van der Waals system. Ab initio calculations of the CH-He PES were carried out using the open-shell single- and double-excitation coupled cluster approach with non-iterative perturbational treatment of triple excitations [RCCSD(T)]. The augmented correlation-consistent polarized valence quadruple-zeta (aug-cc-pVQZ) basis set was employed augmented by mid-bond functions. Integral cross sections for the rotational excitation in CH-He collisions were calculated using the new PES and compared with available experimental results. The newly constructed PES reproduces the available experimental results for CH(X(2)Π, v = 0)-He collisions better than any previously available PES. Differential cross sections (DCS) are presented for the first time for this system and discussed within the context of rotational rainbows. Finally, our work provides the first rate thermal coefficients for this system that are crucially needed for astrochemical modelling and future anticipated experiments in CH(X(2)Π)-He collisions. PMID:26220835

  10. Global analytical potential energy surface for the electronic ground state of NH3 from high level ab initio calculations.

    PubMed

    Marquardt, Roberto; Sagui, Kenneth; Zheng, Jingjing; Thiel, Walter; Luckhaus, David; Yurchenko, Sergey; Mariotti, Fabio; Quack, Martin

    2013-08-15

    The analytical, full-dimensional, and global representation of the potential energy surface of NH(3) in the lowest adiabatic electronic state developed previously (Marquardt, R.; et al. J. Phys. Chem. B 2005, 109, 8439–8451) is improved by adjustment of parameters to an enlarged set of electronic energies from ab initio calculations using the coupled cluster method with single and double substitutions and a perturbative treatment of connected triple excitations (CCSD(T)) and the method of multireference configuration interaction (MRCI). CCSD(T) data were obtained from an extrapolation of aug-cc-pVXZ results to the basis set limit (CBS), as described in a previous work (Yurchenko, S.N.; et al. J. Chem. Phys 2005, 123, 134308); they cover the region around the NH3 equilibrium structures up to 20,000 hc cm(–1). MRCI energies were computed using the aug-cc-pVQZ basis to describe both low lying singlet dissociation channels. Adjustment was performed simultaneously to energies obtained from the different ab initio methods using a merging strategy that includes 10,000 geometries at the CCSD(T) level and 500 geometries at the MRCI level. Characteristic features of this improved representation are NH3 equilibrium geometry r(eq)(NH(3)) ≈ 101.28 pm, α(eq)(NH(3)) ≈ 107.03°, the inversion barrier at r(inv)(NH(3)) ≈ 99.88 pm and 1774 hc cm(–1) above the NH(3) minimum, and dissociation channel energies 41,051 hc cm(–1) (for NH(3) → ((2)B(2))NH(2) + ((2)S(1/2))H) and 38,450 hc cm(–1) (for NH(3) → ((3)Σ(–))NH +((1)Σ(g)(+))H(2)); the average agreement between calculated and experimental vibrational line positions is 11 cm(–1) for (14)N(1)H(3) in the spectral region up to 5000 cm(–1). A survey of our current knowledge on the vibrational spectroscopy of ammonia and its isotopomers is also given. PMID:23688044

  11. Accurate high level ab initio-based global potential energy surface and dynamics calculations for ground state of CH{sub 2}{sup +}

    SciTech Connect

    Li, Y. Q.; Zhang, P. Y.; Han, K. L.

    2015-03-28

    A global many-body expansion potential energy surface is reported for the electronic ground state of CH{sub 2}{sup +} by fitting high level ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pV6Z basis set. The topographical features of the new global potential energy surface are examined in detail and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. In turn, in order to validate the potential energy surface, a test theoretical study of the reaction CH{sup +}(X{sup 1}Σ{sup +})+H({sup 2}S)→C{sup +}({sup 2}P)+H{sub 2}(X{sup 1}Σ{sub g}{sup +}) has been carried out with the method of time dependent wavepacket on the title potential energy surface. The total integral cross sections and the rate coefficients have been calculated; the results determined that the new potential energy surface can both be recommended for dynamics studies of any type and as building blocks for constructing the potential energy surfaces of larger C{sup +}/H containing systems.

  12. Simulation study on potential accuracy gains from dual energy CT tissue segmentation for low-energy brachytherapy Monte Carlo dose calculations

    NASA Astrophysics Data System (ADS)

    Landry, Guillaume; Granton, Patrick V.; Reniers, Brigitte; Öllers, Michel C.; Beaulieu, Luc; Wildberger, Joachim E.; Verhaegen, Frank

    2011-10-01

    This work compares Monte Carlo (MC) dose calculations for 125I and 103Pd low-dose rate (LDR) brachytherapy sources performed in virtual phantoms containing a series of human soft tissues of interest for brachytherapy. The geometries are segmented (tissue type and density assignment) based on simulated single energy computed tomography (SECT) and dual energy (DECT) images, as well as the all-water TG-43 approach. Accuracy is evaluated by comparison to a reference MC dose calculation performed in the same phantoms, where each voxel's material properties are assigned with exactly known values. The objective is to assess potential dose calculation accuracy gains from DECT. A CT imaging simulation package, ImaSim, is used to generate CT images of calibration and dose calculation phantoms at 80, 120, and 140 kVp. From the high and low energy images electron density ρe and atomic number Z are obtained using a DECT algorithm. Following a correction derived from scans of the calibration phantom, accuracy on Z and ρe of ±1% is obtained for all soft tissues with atomic number Z in [6,8] except lung. GEANT4 MC dose calculations based on DECT segmentation agreed with the reference within ±4% for 103Pd, the most sensitive source to tissue misassignments. SECT segmentation with three tissue bins as well as the TG-43 approach showed inferior accuracy with errors of up to 20%. Using seven tissue bins in our SECT segmentation brought errors within ±10% for 103Pd. In general 125I dose calculations showed higher accuracy than 103Pd. Simulated image noise was found to decrease DECT accuracy by 3-4%. Our findings suggest that DECT-based segmentation yields improved accuracy when compared to SECT segmentation with seven tissue bins in LDR brachytherapy dose calculation for the specific case of our non-anthropomorphic phantom. The validity of our conclusions for clinical geometry as well as the importance of image noise in the tissue segmentation procedure deserves further

  13. Simulation study on potential accuracy gains from dual energy CT tissue segmentation for low-energy brachytherapy Monte Carlo dose calculations.

    PubMed

    Landry, Guillaume; Granton, Patrick V; Reniers, Brigitte; Ollers, Michel C; Beaulieu, Luc; Wildberger, Joachim E; Verhaegen, Frank

    2011-10-01

    This work compares Monte Carlo (MC) dose calculations for (125)I and (103)Pd low-dose rate (LDR) brachytherapy sources performed in virtual phantoms containing a series of human soft tissues of interest for brachytherapy. The geometries are segmented (tissue type and density assignment) based on simulated single energy computed tomography (SECT) and dual energy (DECT) images, as well as the all-water TG-43 approach. Accuracy is evaluated by comparison to a reference MC dose calculation performed in the same phantoms, where each voxel's material properties are assigned with exactly known values. The objective is to assess potential dose calculation accuracy gains from DECT. A CT imaging simulation package, ImaSim, is used to generate CT images of calibration and dose calculation phantoms at 80, 120, and 140 kVp. From the high and low energy images electron density ρ(e) and atomic number Z are obtained using a DECT algorithm. Following a correction derived from scans of the calibration phantom, accuracy on Z and ρ(e) of ±1% is obtained for all soft tissues with atomic number Z ∊ [6,8] except lung. GEANT4 MC dose calculations based on DECT segmentation agreed with the reference within ±4% for (103)Pd, the most sensitive source to tissue misassignments. SECT segmentation with three tissue bins as well as the TG-43 approach showed inferior accuracy with errors of up to 20%. Using seven tissue bins in our SECT segmentation brought errors within ±10% for (103)Pd. In general (125)I dose calculations showed higher accuracy than (103)Pd. Simulated image noise was found to decrease DECT accuracy by 3-4%. Our findings suggest that DECT-based segmentation yields improved accuracy when compared to SECT segmentation with seven tissue bins in LDR brachytherapy dose calculation for the specific case of our non-anthropomorphic phantom. The validity of our conclusions for clinical geometry as well as the importance of image noise in the tissue segmentation procedure deserves

  14. CALCULATED MOLECULAR STRUCTURES AND POTENTIAL ENERGY FUNCTIONS OF PAHS WITH METHYL CROWDING IN THE BAY REGION AND THEIR METABOLITES: COMPARISON TO EXPERIMENTAL STRUCTURES

    EPA Science Inventory

    Calculated molecular structures and potential energy functions ofP AHs with methyl crowding in the bay region and their metabolites: Comparison to experimental structures

    PAHs with methyl group substitution near a bay region represent a class of chemicals associated with ...

  15. CALCULATED MOLECULAR STRUCTURES AND POTENTIAL ENERGY FUNCTIONS OF PAHS WITH METHYL CROWDING IN THE BAY REGION AND THEIR METABOLITES: COMPARISON TO EXPERIMENTAL STRUCTURES

    EPA Science Inventory

    Abstract Title: Calculated molecular structures and potential energy functions of P AHs with methyl crowding in the bay region and their metabolites: Comparison to experimental structures.

    Abstract:
    PAHs with methyl group substitution near a bay region represent a cl...

  16. 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.

  17. Transition energy and potential energy curves for ionized inner-shell states of CO, O2 and N 2 calculated by several inner-shell multiconfigurational approaches.

    PubMed

    Moura, Carlos E V de; Oliveira, Ricardo R; Rocha, Alexandre B

    2013-05-01

    Potential energy curves and inner-shell ionization energies of carbon monoxide, oxygen and nitrogen molecules were calculated using several forms of the inner-shell multiconfigurational self-consistent field (IS-MCSCF) method-a recently proposed protocol to obtain specifically converged inner-shell states at this level. The particular forms of the IS-MCSCF method designated IS-GVB-PP, IS-FVBL and IS-CASSCF stand for perfect pairing generalized valence bond, full valence bond-like MCSCF and complete active space self consistent field, respectively. A comparison of these different versions of the IS-MCSCF method was carried out for the first time. The results indicate that inner-shell states are described accurately even for the simplest version of the method (IS-GVB-PP). Dynamic correlation was recovered by multireference configuration interaction or multireference perturbation theory. For molecules not having equivalent atoms, all methods led to comparable and accurate transition energies. For molecules with equivalent atoms, the most accurate results were obtained by multireference perturbation theory. Scalar relativistic effects were accounted for using the Douglas-Kroll-Hess Hamiltonian. PMID:23070335

  18. Dielectric-dependent screened Hartree-Fock exchange potential and Slater-formula with Coulomb-hole interaction for energy band structure calculations.

    PubMed

    Shimazaki, Tomomi; Nakajima, Takahito

    2014-09-21

    We previously reported a screened Hartree-Fock (HF) exchange potential for energy band structure calculations [T. Shimazaki and Y. Asai, J. Chem. Phys. 130, 164702 (2009); T. Shimazaki and Y. Asai, J. Chem. Phys. 132, 224105 (2010)]. In this paper, we discuss the Coulomb-hole (COH) interaction and screened Slater-formula and determine the energy band diagrams of several semiconductors, such as diamond, silicon, AlAs, AlP, GaAs, GaP, and InP, based on the screened HF exchange potential and Slater-formula with COH interaction, to demonstrate the adequacy of those theoretical concepts. The screened HF exchange potential and Slater-formula are derived from a simplified dielectric function and, therefore, include the dielectric constant in their expressions. We also present a self-consistent calculation technique to automatically determine the dielectric constant, which is incorporated into each self-consistent field step. PMID:25240347

  19. Dielectric-dependent screened Hartree-Fock exchange potential and Slater-formula with Coulomb-hole interaction for energy band structure calculations

    NASA Astrophysics Data System (ADS)

    Shimazaki, Tomomi; Nakajima, Takahito

    2014-09-01

    We previously reported a screened Hartree-Fock (HF) exchange potential for energy band structure calculations [T. Shimazaki and Y. Asai, J. Chem. Phys. 130, 164702 (2009); T. Shimazaki and Y. Asai, J. Chem. Phys. 132, 224105 (2010)]. In this paper, we discuss the Coulomb-hole (COH) interaction and screened Slater-formula and determine the energy band diagrams of several semiconductors, such as diamond, silicon, AlAs, AlP, GaAs, GaP, and InP, based on the screened HF exchange potential and Slater-formula with COH interaction, to demonstrate the adequacy of those theoretical concepts. The screened HF exchange potential and Slater-formula are derived from a simplified dielectric function and, therefore, include the dielectric constant in their expressions. We also present a self-consistent calculation technique to automatically determine the dielectric constant, which is incorporated into each self-consistent field step.

  20. Parameterised local spin density exchange-correlation energies and potentials for electronic structure calculations I. Zero temperature formalism

    NASA Astrophysics Data System (ADS)

    MacLaren, J. M.; Clougherty, D. P.; McHenry, M. E.; Donovan, M. M.

    1991-09-01

    Commonly used approximate forms for the exchange-correlation energy and potential within the local density approximation are summarised, and FORTRAN code is included for the evaluation of these various forms. Included are the following: Xα, Kohn-Sham-Gaspàr, Hedin-Lundqvist-Wilkins, Janak-Moruzzi-Williams, Von Barth-Hedin, Ceperley-Alder (Perdew-Zunger), and Ceperley-Alder (Vosko-Wilk-Nusair). Both the Vosko-Wilk-Nusair and the Von Barth-Hedin expressions for spin interpolation between paramagnetic and ferromagnetic limits are also provided.

  1. Accurate double many-body expansion potential energy surface by extrapolation to the complete basis set limit and dynamics calculations for ground state of NH2.

    PubMed

    Li, Yongqing; Yuan, Jiuchuang; Chen, Maodu; Ma, Fengcai; Sun, Mengtao

    2013-07-15

    An accurate single-sheeted double many-body expansion potential energy surface is reported for the title system. A switching function formalism has been used to warrant the correct behavior at the H2(X1Σg+)+N(2D) and NH (X3Σ-)+H(2S) dissociation channels involving nitrogen in the ground N(4S) and first excited N(2D) states. The topographical features of the novel 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. The novel surface can be using to treat well the Renner-Teller degeneracy of the 12A″ and 12A' states of NH 2. Such a work can both be recommended for dynamics studies of the N(2D)+H2 reaction and as building blocks for constructing the double many-body expansion potential energy surface of larger nitrogen/hydrogen-containing systems. In turn, a test theoretical study of the reaction N(2D)+H2(X1Σg+)(ν=0,j=0)→NH (X3Σ-)+H(2S) has been carried out with the method of quantum wave packet on the new potential energy surface. Reaction probabilities, integral cross sections, and differential cross sections have been calculated. Threshold exists because of the energy barrier (68.5 meV) along the minimum energy path. On the curve of reaction probability for total angular momentum J = 0, there are two sharp peaks just above threshold. The value of integral cross section increases quickly from zero to maximum with the increase of collision energy, and then stays stable with small oscillations. The differential cross section result shows that the reaction is a typical forward and backward scatter in agreement with experimental measurement result. PMID:23666848

  2. 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.

  3. Communication: A new ab initio potential energy surface for HCl-H2O, diffusion Monte Carlo calculations of D0 and a delocalized zero-point wavefunction

    NASA Astrophysics Data System (ADS)

    Mancini, John S.; Bowman, Joel M.

    2013-03-01

    We report a global, full-dimensional, ab initio potential energy surface describing the HCl-H2O dimer. The potential is constructed from a permutationally invariant fit, using Morse-like variables, to over 44 000 CCSD(T)-F12b/aug-cc-pVTZ energies. The surface describes the complex and dissociated monomers with a total RMS fitting error of 24 cm-1. The normal modes of the minima, low-energy saddle point and separated monomers, the double minimum isomerization pathway and electronic dissociation energy are accurately described by the surface. Rigorous quantum mechanical diffusion Monte Carlo (DMC) calculations are performed to determine the zero-point energy and wavefunction of the complex and the separated fragments. The calculated zero-point energies together with a De value calculated from CCSD(T) with a complete basis set extrapolation gives a D0 value of 1348 ± 3 cm-1, in good agreement with the recent experimentally reported value of 1334 ± 10 cm-1 [B. E. Casterline, A. K. Mollner, L. C. Ch'ng, and H. Reisler, J. Phys. Chem. A 114, 9774 (2010), 10.1021/jp102532m]. Examination of the DMC wavefunction allows for confident characterization of the zero-point geometry to be dominant at the C2v double-well saddle point and not the Cs global minimum. Additional support for the delocalized zero-point geometry is given by numerical solutions to the 1D Schrödinger equation along the imaginary-frequency out-of-plane bending mode, where the zero-point energy is calculated to be 52 cm-1 above the isomerization barrier. The D0 of the fully deuterated isotopologue is calculated to be 1476 ± 3 cm-1, which we hope will stand as a benchmark for future experimental work.

  4. Full-dimensional quantum calculations of vibrational levels of NH4+ and isotopomers on an accurate ab initio potential energy surface

    DOE PAGESBeta

    Hua -Gen Yu; Han, Huixian; Guo, Hua

    2016-03-29

    Vibrational energy levels of the ammonium cation (NH4+) and its deuterated isotopomers are calculated using a numerically exact kinetic energy operator on a recently developed nine-dimensional permutation invariant semiglobal potential energy surface fitted to a large number of high-level ab initio points. Like CH4, the vibrational levels of NH4+ and ND4+ exhibit a polyad structure, characterized by a collective quantum number P = 2(v1 + v3) + v2 + v4. As a result, the low-lying vibrational levels of all isotopomers are assigned and the agreement with available experimental data is better than 1 cm–1.

  5. Free-energy calculations using classical molecular simulation: application to the determination of the melting point and chemical potential of a flexible RDX model.

    PubMed

    Sellers, Michael S; Lísal, Martin; Brennan, John K

    2016-03-21

    We present an extension of various free-energy methodologies to determine the chemical potential of the solid and liquid phases of a fully-flexible molecule using classical simulation. The methods are applied to the Smith-Bharadwaj atomistic potential representation of cyclotrimethylene trinitramine (RDX), a well-studied energetic material, to accurately determine the solid and liquid phase Gibbs free energies, and the melting point (Tm). We outline an efficient technique to find the absolute chemical potential and melting point of a fully-flexible molecule using one set of simulations to compute the solid absolute chemical potential and one set of simulations to compute the solid-liquid free energy difference. With this combination, only a handful of simulations are needed, whereby the absolute quantities of the chemical potentials are obtained, for use in other property calculations, such as the characterization of crystal polymorphs or the determination of the entropy. Using the LAMMPS molecular simulator, the Frenkel and Ladd and pseudo-supercritical path techniques are adapted to generate 3rd order fits of the solid and liquid chemical potentials. Results yield the thermodynamic melting point Tm = 488.75 K at 1.0 atm. We also validate these calculations and compare this melting point to one obtained from a typical superheated simulation technique. PMID:26661376

  6. Biogas - the calculable energy

    NASA Astrophysics Data System (ADS)

    Kith, Károly; Nagy, Orsolya; Balla, Zoltán; Tamás, András

    2015-04-01

    EU actions against climate change are rising energy prices, both have emphasized the use of renewable energy,increase investments and energy efficiency. A number of objectives formulated in the EC decree no. 29/2009 by 2020. This document is based on the share of renewable energies in energy consumption should be increased to 20% (EC, 2009). The EU average is 20% but the share of renewables vary from one member state to another. In Hungary in 2020, 14.65% renewable energy share is planned to be achieved. According to the latest Eurostat data, the share of renewable energy in energy consumption of the EU average was 14.1%, while in Hungary, this share was 9.6% in 2012. (EUROSTAT, 2014). The use of renewable energy plant level is influenced by several factors. The most important of these is the cost savings and efficiency gains. Hungarian investments in renewable energy production usually have high associated costs and the payback period is substantially more than five years, depending on the support rate. For example, the payback period is also influenced by the green electricity generated feed prices, which is one of the lowest in Hungary compared the Member States of the European Union. Consequently, it is important to increase the production of green energy. Nowadays, predictable biogas energy is an outstanding type of decentralized energy production. It follows directly that agricultural by-products can be used to produce energy and they also create jobs by the construction of a biogas plant. It is important to dispose of and destroy hazardous and noxious substances in energy production. It follows from this that the construction of biogas plants have a positive impact, in addition to green energy which is prepared to reduce the load on the environment. The production of biogas and green electricity is one of the most environment friendly forms of energy production. Biogas production also has other important ecological effects, such as the substitution of

  7. 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.

  8. Ab initio calculation of a global potential, vibrational energies, and wave functions for HCN/HNC, and a simulation of the (A-tilde)-(X-tilde) emission spectrum

    NASA Technical Reports Server (NTRS)

    Bowman, Joel M.; Gazdy, Bela; Bentley, Joseph A.; Lee, Timothy J.; Dateo, Christopher E.

    1993-01-01

    A potential energy surface for the HCN/HNC system which is a fit to extensive, high-quality ab initio, coupled-cluster calculations is presented. All HCN and HNC states with energies below the energy of the first delocalized state are reported and characterized. Vibrational transition energies are compared with all available experimental data on HCN and HNC, including high CH-overtone states up to 23,063/cm. A simulation of the (A-tilde)-(X-tilde) stimulated emission pumping (SEP) spectrum is also reported, and the results are compared to experiment. Franck-Condon factors are reported for odd bending states of HCN, with one quantum of vibrational angular momentum, in order to compare with the recent assignment by Jonas et al. (1992), on the basis of axis-switching arguments of a number of previously unassigned states in the SEP spectrum.

  9. New XDM-corrected potential energy surfaces for Ar–NO(X{sup 2}Π): A comparison with CCSD(T) calculations and experiments

    SciTech Connect

    Warehime, Michael; Johnson, Erin R.; Kłos, Jacek

    2015-01-14

    We report new potential energy surfaces for the ground state Ar–NO(X{sup 2}Π) van der Waals system calculated using the unrestricted Hartree-Fock (UHF) method with the addition of the Becke-Roussel correlation functional and exchange-hole dipole moment dispersion correction (XDM). We compare UHFBR-XDM surfaces and those previously reported by Alexander from coupled cluster CCSD(T) calculations [J. Chem. Phys. 111, 7426 (1999)]. The bound states of Ar–NO have been investigated with these new UHFBR-XDM surfaces, including relative energy-level spacing, adiabatic bender states and wave functions, and spectroscopic data. These results have been found to be in good agreement with calculations based on the CCSD(T) PESs. These new PESs are used to investigate the inelastic scattering of NO(X) by Ar. Full close-coupling integral cross sections at collision energies of 442 cm{sup −1}, 1774 cm{sup −1} and differential cross sections at collision energy of 530 cm{sup −1} were determined for transitions out of the lowest NO(X) rotational level (j = ω = 1/2,f). These cross sections are in good agreement with those calculated with CCSD(T) and accordingly in good agreement with the most recent initial and final state resolved experimental data. The UHFBR-XDM scheme yields high-quality potential surfaces with computational cost comparable to the Hartree-Fock method and our results may serve as a benchmark for application of this scheme to collisions between larger molecules.

  10. 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

  11. Calculation of total free energy yield as an alternative approach for predicting the importance of potential chemolithotrophic reactions in geothermal springs.

    PubMed

    Dodsworth, Jeremy A; McDonald, Austin I; Hedlund, Brian P

    2012-08-01

    To inform hypotheses regarding the relative importance of chemolithotrophic metabolisms in geothermal environments, we calculated free energy yields of 26 chemical reactions potentially supporting chemolithotrophy in two US Great Basin hot springs, taking into account the effects of changing reactant and product activities on the Gibbs free energy as each reaction progressed. Results ranged from 1.2 × 10(-5) to 3.6 J kg(-1) spring water, or 3.7 × 10(-5) to 11.5 J s(-1) based on measured flow rates, with aerobic oxidation of CH(4) or NH4 + giving the highest average yields. Energy yields calculated without constraining pH were similar to those at constant pH except for reactions where H(+) was consumed, which often had significantly lower yields when pH was unconstrained. In contrast to the commonly used normalization of reaction chemical affinities per mole of electrons transferred, reaction energy yields for a given oxidant varied by several orders of magnitude and were more sensitive to differences in the activities of products and reactants. The high energy yield of aerobic ammonia oxidation is consistent with previous observations of significant ammonia oxidation rates and abundant ammonia-oxidizing archaea in sediments of these springs. This approach offers an additional lens through which to view the thermodynamic landscape of geothermal springs. PMID:22443686

  12. Collisional excitation of NH(X{sup 3}Σ{sup −}) by Ne: Potential energy surface, scattering calculations, and comparison with experiments

    SciTech Connect

    Bouhafs, Nezha; Lique, François

    2015-11-14

    We present a new three-dimensional potential energy surface (PES) for the NH(X{sup 3}Σ{sup −})–Ne van der Waals system, which explicitly takes into account the NH vibrational motion. Ab initio calculations of the NH–Ne 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 quadruple zeta (aug-cc-pVQZ) basis set was employed. Mid-bond functions were also included in order to improve the accuracy in the van der Waals well. Using this new PES, we have studied the collisional excitation of NH(X{sup 3}Σ{sup −}) by Ne. Close-coupling calculations of the collisional excitation cross sections of the fine-structure levels of NH by Ne are performed for energies up to 3000 cm{sup −1}, which yield, after thermal average, rate coefficients up to 350 K. The propensity rules between fine-structure levels are reported, and it is found that F-conserving cross sections are larger than F-changing cross sections even if the propensity rules are not as strong as for the NH–He system. The calculated rate coefficients are compared with available experimental measurements at room temperature and a fairly good agreement is found between experimental and theoretical data, confirming the good quality of the scattering calculations and also the accuracy of the potential energy surface used in this work.

  13. 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.

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

    PubMed

    Zhang, Yan; Lin, Hai

    2009-10-29

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

  15. Distributed Gaussian basis sets: a comparison with finite difference Hartree Fock calculations for potential energy curves of H2, LiH and BH

    NASA Astrophysics Data System (ADS)

    Glushkov, V. N.; Kobus, J.; Wilson, S.

    2008-10-01

    Within the Hartree-Fock approximation, distributed basis sets of s-type Gaussian functions are used to compute those portions of the ground-state potential energy curves of the H2, LiH and BH molecules for which the model is appropriate. The exponents are generated using the even-tempered prescription and an anharmonic model is employed to distribute the basis functions. For few-electron diatomic systems, this approach is known to support sub-μHartree accuracy for electronic energies. For the molecules studied in the present work, matrix Hartree-Fock energy expectation values are compared with finite difference Hartree-Fock calculations carried out at the same geometries and using grids designed to support an accuracy of at least 1 nanoHartree. The distributed basis sets developed in this work support matrix Hartree-Fock energies which differ from the corresponding finite difference energies by 0.41, 0.58 and 0.68 μHartree, respectively, for the ground states of the H2, LiH and BH molecules at their equilibrium geometries. For each of these systems, a sub-μHartree level of accuracy is supported for a range of geometries.

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

    PubMed

    Chan, Karen; Nørskov, Jens K

    2016-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

  18. Ab initio calculations of stationary points on the benzene-Ar and p-difluorobenzene-Ar potential energy surfaces: barriers to bound orbiting states

    NASA Astrophysics Data System (ADS)

    Moulds, Rebecca J.; Buntine, Mark A.; Lawrance, Warren D.

    2004-09-01

    The potential energy surfaces of the van der Waals complexes benzene-Ar and p-difluorobenzene-Ar have been investigated at the second-order Møller-Plesset (MP2) level of theory with the aug-cc-pVDZ basis set. Calculations were performed with unconstrained geometry optimization for all stationary points. This study has been performed to elucidate the nature of a conflict between experimental results from dispersed fluorescence and velocity map imaging (VMI). The inconsistency is that spectra for levels of p-difluorobenzene-Ar and -Kr below the dissociation thresholds determined by VMI show bands where free p-difluorobenzene emits, suggesting that dissociation is occurring. We proposed that the bands observed in the dispersed fluorescence spectra are due to emission from states in which the rare gas atom orbits the aromatic chromophore; these states are populated by intramolecular vibrational redistribution from the initially excited level [S. M. Bellm, R. J. Moulds, and W. D. Lawrance, J. Chem. Phys. 115, 10709 (2001)]. To test this proposition, stationary points have been located on both the benzene-Ar and p-difluorobenzene-Ar potential energy surfaces (PESs) to determine the barriers to this orbiting motion. Comparison with previous single point CCSD(T) calculations of the benzene-Ar PES has been used to determine the amount by which the barriers are overestimated at the MP2 level. As there is little difference in the comparable regions of the benzene-Ar and p-difluorobenzene-Ar PESs, the overestimation is expected to be similar for p-difluorobenzene-Ar. Allowing for this overestimation gives the barrier to movement of the Ar atom around the pDFB ring via the valley between the H atoms as ⩽204 cm-1 in S0 (including zero point energy). From the estimated change upon electronic excitation, the corresponding barrier in S1 is estimated to be ⩽225 cm-1. This barrier is less than the 240 cm-1 energy of 302¯, the vibrational level for which the anomalous "free p

  19. Ab initio calculations on the excited states of Na3 cluster to explore beyond Born-Oppenheimer theories: adiabatic to diabatic potential energy surfaces and nuclear dynamics.

    PubMed

    Paul, Amit Kumar; Ray, Somrita; Mukhopadhyay, Debasis; Adhikari, Satrajit

    2011-07-21

    We perform ab initio calculation using quantum chemistry package (MOLPRO) on the excited states of Na(3) cluster and present the adiabatic PESs for the electronic states 2(2)E' and 1(2)A(1)', and the non-adiabatic coupling (NAC) terms among those states. Since the ab initio calculated NAC elements for the states 2(2)E' and 1(2)A(1)' demonstrate the numerical validity of so called "Curl Condition," such states closely form a sub-Hilbert space. For this subspace, we employ the NAC terms to solve the "adiabatic-diabatic transformation (ADT)" equations to obtain the functional form of the transformation angles and pave the way to construct the continuous and single valued diabatic potential energy surface matrix by exploiting the existing first principle based theoretical means on beyond Born-Oppenheimer treatment. Nuclear dynamics has been carried out on those diabatic surfaces to reproduce the experimental spectrum for system B of Na(3) cluster and thereby, to explore the numerical validity of the theoretical development on beyond Born-Oppenheimer approach for adiabatic to diabatic transformation. PMID:21786987

  20. Accurate calculations on 9 Λ-S and 28 Ω states of NSe radical in the gas phase: potential energy curves, spectroscopic parameters and spin-orbit couplings.

    PubMed

    Shi, Deheng; Li, Peiling; Sun, Jinfeng; Zhu, Zunlue

    2014-01-01

    The potential energy curves (PECs) of 28 Ω states generated from 9 Λ-S states (X(2)Π, 1(4)Π, 1(6)Π, 1(2)Σ(+), 1(4)Σ(+), 1(6)Σ(+), 1(4)Σ(-), 2(4)Π and 1(4)Δ) are studied for the first time using an ab initio quantum chemical method. All the 9 Λ-S states correlate to the first two dissociation limits, N((4)Su)+Se((3)Pg) and N((4)Su)+Se((3)Dg), of NSe radical. Of these Λ-S states, the 1(6)Σ(+), 1(4)Σ(+), 1(6)Π, 2(4)Π and 1(4)Δ are found to be rather weakly bound states. The 1(2)Σ(+) is found to be unstable and has double wells. And the 1(6)Σ(+), 1(4)Σ(+), 1(4)Π and 1(6)Π are found to be the inverted ones with the SO coupling included. The PEC calculations are made by the complete active space self-consistent field method, which is followed by the internally contracted multireference configuration interaction approach with the Davidson modification. The spin-orbit coupling is accounted for by the state interaction approach with the Breit-Pauli Hamiltonian. The convergence of the present calculations is discussed with respect to the basis set and the level of theory. Core-valence correlation corrections are included with a cc-pCVTZ basis set. Scalar relativistic corrections are calculated by the third-order Douglas-Kroll Hamiltonian approximation at the level of a cc-pV5Z basis set. All the PECs are extrapolated to the complete basis set limit. The variation with internuclear separation of spin-orbit coupling constants is discussed in brief for some Λ-S states with one shallow well on each PEC. The spectroscopic parameters of 9 Λ-S and 28 Ω states are determined by fitting the first ten vibrational levels whenever available, which are calculated by solving the rovibrational Schrödinger equation with Numerov's method. The splitting energy in the X(2)Π Λ-S state is determined to be about 864.92 cm(-1), which agrees favorably with the measurements of 891.80 cm(-1). Moreover, other spectroscopic parameters of Λ-S and Ω states involved here are

  1. Convergence of normal mode variational calculations of methane spectra: Theoretical linelist in the icosad range computed from potential energy and dipole moment surfaces

    NASA Astrophysics Data System (ADS)

    Rey, Michaël; Nikitin, Andrei V.; Tyuterev, Vladimir G.

    2015-10-01

    Accurate basis set convergence of first-principles predictions of rotationally resolved spectra at high energy range is a common challenging issue for variational methods. In this paper, a detailed convergence study for the methane spectra is presented both for vibrational and rotational degrees of freedom as well as for intensities. For this purpose, we use our previously reported nine-dimensional potential energy and dipole moment surfaces of the methane molecule [Nikitin et al. Chem Phys Lett 2011;501:179-86; 2013;565:5-11]. Vibration-rotation calculations were carried out using variational normal mode approach with a full account of the Td symmetry. The aim was to obtain accurate theoretical methane line lists for the wavenumber range beyond currently available spectra analyses. The focus of this paper is the complicated icosad range (6280-7900 cm-1) containing 20 bands and 134 sub-bands where over 90% of experimental lines still remain unassigned. We provide variational line lists converged to a "spectroscopic precision" for icosad transitions for T=80 K and T=296 K. The first one contains 70 300 lines and the second one 286 170 lines with the intensity cut-off 10-29cm-1 /(moleculecm-2) with Jmax=18. An average error in line positions of theoretical predictions up to J=15 is estimated as 0.2-0.5 cm-1 from the comparisons with currently analyzed bands. Ab initio line strength calculations give the integrated intensity 4.37 ×10-20cm-1 /(moleculecm-2) at T=80 K for the sum of all icosad bands. This is to be compared to the integrated intensity 4.36 ×10-20cm-1 /(moleculecm-2) of the experimental icosad line list recorded in Grenoble University [Campargue et al., J Mol Spectrosc 2013;291:16-22] using very sensitive laser techniques. The shapes of absorption bands are also in a good qualitative agreement with experimental spectra.

  2. Good Practices in Free-energy Calculations

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Jarzynski, Christopher; Chipot, Christopher

    2013-01-01

    As access to computational resources continues to increase, free-energy calculations have emerged as a powerful tool that can play a predictive role in drug design. Yet, in a number of instances, the reliability of these calculations can be improved significantly if a number of precepts, or good practices are followed. For the most part, the theory upon which these good practices rely has been known for many years, but often overlooked, or simply ignored. In other cases, the theoretical developments are too recent for their potential to be fully grasped and merged into popular platforms for the computation of free-energy differences. The current best practices for carrying out free-energy calculations will be reviewed demonstrating that, at little to no additional cost, free-energy estimates could be markedly improved and bounded by meaningful error estimates. In energy perturbation and nonequilibrium work methods, monitoring the probability distributions that underlie the transformation between the states of interest, performing the calculation bidirectionally, stratifying the reaction pathway and choosing the most appropriate paradigms and algorithms for transforming between states offer significant gains in both accuracy and precision. In thermodynamic integration and probability distribution (histogramming) methods, properly designed adaptive techniques yield nearly uniform sampling of the relevant degrees of freedom and, by doing so, could markedly improve efficiency and accuracy of free energy calculations without incurring any additional computational expense.

  3. On the accuracy of explicitly correlated methods to generate potential energy surfaces for scattering calculations and clustering: application to the HCl-He complex.

    PubMed

    Ajili, Yosra; Hammami, Kamel; Jaidane, Nejm Eddine; Lanza, Mathieu; Kalugina, Yulia N; Lique, François; Hochlaf, Majdi

    2013-07-01

    We closely compare the accuracy of multidimensional potential energy surfaces (PESs) generated by the recently developed explicitly correlated coupled cluster (CCSD(T)-F12) methods in connection with the cc-pVXZ-F12 (X = D, T) and aug-cc-pVTZ basis sets and those deduced using the well-established orbital-based coupled cluster techniques employing correlation consistent atomic basis sets (aug-cc-pVXZ, X = T, Q, 5) and extrapolated to the complete basis set (CBS) limit. This work is performed on the benchmark rare gas-hydrogen halide interaction (HCl-He) system. These PESs are then incorporated into quantum close-coupling scattering dynamical calculations in order to check the impact of the accuracy of the PES on the scattering calculations. For this system, we deduced inelastic collisional data including (de-)excitation collisional and pressure broadening cross sections. Our work shows that the CCSD(T)-F12/aug-cc-pVTZ PES describes correctly the repulsive wall, the van der Waals minimum and long range internuclear distances whereas cc-pVXZ-F12 (X = D,T) basis sets are not diffuse enough for that purposes. Interestingly, the collision cross sections deduced from the CCSD(T)-F12/aug-cc-pVTZ PES are in excellent agreement with those obtained with CCSD(T)/CBS methodology. The position of the resonances and the general shape of these cross sections almost coincide. Since the cost of the electronic structure computations is reduced by several orders of magnitude when using CCSD(T)-F12/aug-cc-pVTZ compared to CCSD(T)/CBS methodology, this approach can be recommended as an alternative for generation of PESs of molecular clusters and for the interpretation of accurate scattering experiments as well as for a wide production of collisional data to be included in astrophysical and atmospherical models. PMID:23443908

  4. The Chirped-Pulse Fourier Transform Microwave Cp-Ftmw Spectrum and Potential Energy Calculations for AN Aromatic Claisen Rearrangement Molecule, Allyl Phenyl Ether

    NASA Astrophysics Data System (ADS)

    Grubbs, G. S. Grubbs, Ii; Cooke, S. A.; Novick, Stewart E.

    2012-06-01

    Claisen rearrangement ethers are a fundamental organic, pericyclic rearrangement reaction reagent. In the mechanism of a Claisen rearrangement, a vinyl allyl ether is needed to provide the necessary Lewis acid/base sites on the molecule for the rearrangement and are simply heated. This rearrangement was first discovered by heating up the title molecule, allyl phenyl ether. However, much like the Diels-Alder, Cope, and other pericyclic reactions, conformation and coordination of chemical groups is key to the Claisen mechanism. In this study, the authors present some structural characteristics of allyl phenyl ether from an analysis of the microwave spectra in the 8-14 GHz region using a CP-FTMW spectrometer. This is, to the authors knowledge, the first known microwave region study of the title molecule. Three conformers have been observed and assigned to date and will be discussed. Along with the rotational spectra, geometry calculations and potential energy surfaces performed at the MP2/6-311G++(3d,2p) level will be discussed and compared to the experimental results. Modeling the Claisen aromatic rearrangement mechanism using CP-FTMW spectroscopy will also be discussed. L. Claisen Chemische Berichte 45, 3157, October 1912.

  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. Light Pipe Energy Savings Calculator

    NASA Astrophysics Data System (ADS)

    Owens, Erin; Behringer, Ernest R.

    2009-04-01

    Dependence on fossil fuels is unsustainable and therefore a shift to renewable energy sources such as sunlight is required. Light pipes provide a way to utilize sunlight for interior lighting, and can reduce the need for fossil fuel-generated electrical energy. Because consumers considering light pipe installation may be more strongly motivated by cost considerations than by sustainability arguments, an easy means to examine the corresponding costs and benefits is needed to facilitate informed decision-making. The purpose of this American Physical Society Physics and Society Fellowship project is to create a Web-based calculator to allow users to quantify the possible cost savings for their specific light pipe application. Initial calculations show that the illumination provided by light pipes can replace electric light use during the day, and in many cases can supply greater illumination levels than those typically given by electric lighting. While the installation cost of a light pipe is significantly greater than the avoided cost of electricity over the lifetime of the light pipe at current prices, savings may be realized if electricity prices increase.

  7. 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.

  8. A computational study of barium blockades in the KcsA potassium channel based on multi-ion potential of mean force calculations and free energy perturbation

    PubMed Central

    Rowley, Christopher N.

    2013-01-01

    Electrophysiological studies have established that the permeation of Ba2+ ions through the KcsA K+-channel is impeded by the presence of K+ ions in the external solution, while no effect is observed for external Na+ ions. This Ba2+ “lock-in” effect suggests that at least one of the external binding sites of the KcsA channel is thermodynamically selective for K+. We used molecular dynamics simulations to interpret these lock-in experiments in the context of the crystallographic structure of KcsA. Assuming that the Ba2+ is bound in site S2 in the dominant blocked state, we examine the conditions that could impede its translocation and cause the observed “lock-in” effect. Although the binding of a K+ ion to site S1 when site S2 is occupied by Ba2+ is prohibitively high in energy (>10 kcal/mol), binding to site S0 appears to be more plausible (ΔG > 4 kcal/mol). The 2D potential of mean force (PMF) for the simultaneous translocation of Ba2+ from site S2 to site S1 and of a K+ ion on the extracellular side shows a barrier that is consistent with the concept of external lock-in. The barrier opposing the movement of Ba2+ is very high when a cation is in site S0, and considerably smaller when the site is unoccupied. Furthermore, free energy perturbation calculations show that site S0 is selective for K+ by 1.8 kcal/mol when S2 is occupied by Ba2+. However, the same site S0 is nonselective when site S2 is occupied by K+, which shows that the presence of Ba2+ affects the selectivity of the pore. A theoretical framework within classical rate theory is presented to incorporate the concentration dependence of the external ions on the lock-in effect. PMID:24043859

  9. A computational study of barium blockades in the KcsA potassium channel based on multi-ion potential of mean force calculations and free energy perturbation.

    PubMed

    Rowley, Christopher N; Roux, Benoît

    2013-10-01

    Electrophysiological studies have established that the permeation of Ba(2+) ions through the KcsA K(+)-channel is impeded by the presence of K(+) ions in the external solution, while no effect is observed for external Na(+) ions. This Ba(2+) "lock-in" effect suggests that at least one of the external binding sites of the KcsA channel is thermodynamically selective for K(+). We used molecular dynamics simulations to interpret these lock-in experiments in the context of the crystallographic structure of KcsA. Assuming that the Ba(2+) is bound in site S(2) in the dominant blocked state, we examine the conditions that could impede its translocation and cause the observed "lock-in" effect. Although the binding of a K(+) ion to site S(1) when site S(2) is occupied by Ba(2+) is prohibitively high in energy (>10 kcal/mol), binding to site S0 appears to be more plausible (ΔG > 4 kcal/mol). The 2D potential of mean force (PMF) for the simultaneous translocation of Ba(2+) from site S(2) to site S(1) and of a K(+) ion on the extracellular side shows a barrier that is consistent with the concept of external lock-in. The barrier opposing the movement of Ba(2+) is very high when a cation is in site S(0), and considerably smaller when the site is unoccupied. Furthermore, free energy perturbation calculations show that site S(0) is selective for K(+) by 1.8 kcal/mol when S(2) is occupied by Ba(2+). However, the same site S(0) is nonselective when site S(2) is occupied by K(+), which shows that the presence of Ba(2+) affects the selectivity of the pore. A theoretical framework within classical rate theory is presented to incorporate the concentration dependence of the external ions on the lock-in effect. PMID:24043859

  10. Explicitly correlated MRCI-F12 potential energy surfaces for methane fit with several permutation invariant schemes and full-dimensional vibrational calculations

    NASA Astrophysics Data System (ADS)

    Majumder, Moumita; Hegger, Samuel E.; Dawes, Richard; Manzhos, Sergei; Wang, Xiao-Gang; Tucker, Carrington, Jr.; Li, Jun; Guo, Hua

    2015-07-01

    A data-set of nearly 100,000 symmetry unique multi-configurational ab initio points for methane were generated at the (AE)-MRCI-F12(Q)/CVQZ-F12 level, including energies beyond 30,000 cm-1 above the minimum and fit into potential energy surfaces (PESs) by several permutation invariant schemes. A multi-expansion interpolative fit combining interpolating moving least squares (IMLS) fitting and permutation invariant polynomials (PIP) was able to fit the complete data-set to a root-mean-square deviation of 1.0 cm-1 and thus was used to benchmark the other fitting methods. The other fitting methods include a single PIP expansion and two neural network (NN) based approaches, one of which combines NN with PIP. Full-dimensional variational vibrational calculations using a contracted-iterative method (and a Lanczos eigensolver) were used to assess the spectroscopic accuracy of the electronic structure method. The results show that the NN-based fitting approaches are able to fit the data-set remarkably accurately with the PIP-NN method producing levels in remarkably close agreement with the PIP-IMLS benchmark. The (AE)-MRCI-F12(Q)/CVQZ-F12 electronic structure method produces vibrational levels of near spectroscopic accuracy and a superb equilibrium geometry. The levels are systematically slightly too high, beginning at ∼ 1-2 cm-1 above the fundamentals and becoming correspondingly higher for overtones. The PES is therefore suitable for small ab initio or empirical corrections and since it is based on a multi-reference method, can be extended to represent dynamically relevant dissociation channels.

  11. 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.

  12. Accurate calculations on the 12 electronic states and 23 Ω states of the SiBr+ cation: potential energy curves, spectroscopic parameters and spin-orbit coupling

    NASA Astrophysics Data System (ADS)

    Shi, De-Heng; Liu, Qionglan; Yu, Wei; Sun, Jinfeng; Zhu, Zunlue

    2014-05-01

    The potential energy curves (PECs) of 23 Ω states generated from the 12 electronic states (X1 Σ +, 21 Σ +, 11 Σ -, 11 Π, 21 Π, 11 Δ, 13 Σ +, 23 Σ +, 13 Σ -, a3 Π, 23 Π and 13 Δ) are studied for the first time. All the states correlate to the first dissociation channel of the SiBr+ cation. Of these electronic states, the 23 Σ + is the repulsive one without the spin-orbit coupling, whereas it becomes the bound one with the spin-orbit coupling added. On the one hand, without the spin-orbit coupling, the 11 Π, 21 Π and 23 Π are the rather weakly bound states, and only the 11 Π state possesses the double well; on the other hand, with the spin-orbit coupling included, the a3 Π and 11 Π states possess the double well, and the 13 Σ + and 13 Σ - are the inverted states. The PECs are calculated by the CASSCF method, which is followed by the internally contracted MRCI approach with the Davidson modification. Scalar relativistic correction is calculated by the third-order Douglas-Kroll Hamiltonian approximation with a cc-pVTZ-DK basis set. Core-valence correlation correction is included with a cc-pCVTZ basis set. The spin-orbit coupling is accounted for by the state interaction method with the Breit-Pauli Hamiltonian using the all-electron aug-cc-pCVTZ basis set. All the PECs are extrapolated to the complete basis set limit. The variation with internuclear separation of the spin-orbit coupling constant is discussed in brief. The spectroscopic parameters are evaluated for the 11 bound electronic states and the 23 bound Ω states, and are compared with available measurements. Excellent agreement has been found between the present results and the experimental data. It demonstrates that the spectroscopic parameters reported here can be expected to be reliably predicted ones. The Franck-Condon factors and radiative lifetimes of the transitions from the a3 Π 0 + and a3 Π 1 states to the X1 Σ + 0+ state are calculated for several low vibrational levels, and

  13. Accurate calculations on 12 Λ-S and 28 Ω states of BN+ cation: potential energy curves, spectroscopic parameters and spin-orbit coupling.

    PubMed

    Shi, Deheng; Liu, Qionglan; Sun, Jinfeng; Zhu, Zunlue

    2014-03-25

    The potential energy curves (PECs) of 28 Ω states generated from the 12 states (X(4)Σ(-), 1(2)Π, 1(2)Σ(-), 1(2)Δ, 1(2)Σ(+), 2(2)Π, A(4)Π, B(4)Σ(-), 3(2)Π, 1(6)Σ(-), 2(2)Σ(-) and 1(6)Π) of the BN(+) cation are studied for the first time for internuclear separations from about 0.1 to 1.0 nm using an ab initio quantum chemical method. All the Λ-S states correlate to the first four dissociation channels. The 1(6)Σ(-), 3(2)Π and A(4)Π states are found to be the inverted ones. The 1(2)Σ(+), 2(2)Π, 3(2)Π and 2(2)Σ(-) states are found to possess the double well. The PECs are calculated by the complete active space self-consistent field method, which is followed by the internally contracted multireference configuration interaction approach with the Davidson correction. Core-valence correlation correction is included by a cc-pCV5Z basis set. Scalar relativistic correction is calculated by the third-order Douglas-Kroll Hamiltonian approximation at the level of a cc-pV5Z basis set. The convergent behavior of present calculations is discussed with respect to the basis set and level of theory. The spin-orbit coupling is accounted for by the state interaction approach with the Breit-Pauli Hamiltonian using the all-electron cc-pCV5Z basis set. All the PECs are extrapolated to the complete basis set limit. The spectroscopic parameters are obtained, and the vibrational properties of 1(2)Σ(+), 2(2)Π, 3(2)Π and 2(2)Σ(-) states are evaluated. Analyses demonstrate that the spectroscopic parameters reported here can be expected to be reliably predicted ones. The conclusion is gained that the effect of spin-orbit coupling on the spectroscopic parameters are not obvious almost for all the Λ-S states involved in the present paper. PMID:24334021

  14. Potential energy of a dinuclear system

    SciTech Connect

    Adamyan, G.G.; Antonenko, N.V.; Jolos, R.V.; Ivanova, S.P.; Mel`nikova, O.I.

    1994-11-01

    An effective method for calculating the potential energy of a dinuclear system is proposed. Analytic expressions for calculating the nuclear part of the nucleus-nucleus potential in the double-folding form are obtained. A relationship between this potential and the proximity potential is found. Effects of deformation and mutual orientation of nuclei on the interaction potential are studied. It follows from a comparison of calculated potential energies with nuclear binding energies that excited states of some nuclei can be treated as dinuclear or trinuclear systems. 27 refs., 7 figs.

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

    PubMed

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

    2016-01-15

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

  16. Accurate calculations on the 22 electronic states and 54 spin-orbit states of the O2 molecule: potential energy curves, spectroscopic parameters and spin-orbit coupling.

    PubMed

    Liu, Hui; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue; Shulin, Zhang

    2014-04-24

    The potential energy curves (PECs) of 54 spin-orbit states generated from the 22 electronic states of O2 molecule are investigated for the first time for internuclear separations from about 0.1 to 1.0nm. Of the 22 electronic states, the X(3)Σg(-), A(')(3)Δu, A(3)Σu(+), B(3)Σu(-), C(3)Πg, a(1)Δg, b(1)Σg(+), c(1)Σu(-), d(1)Πg, f(1)Σu(+), 1(5)Πg, 1(3)Πu, 2(3)Σg(-), 1(5)Σu(-), 2(1)Σu(-) and 2(1)Δg are found to be bound, whereas the 1(5)Σg(+), 2(5)Σg(+), 1(1)Πu, 1(5)Δg, 1(5)Πu and 2(1)Πu are found to be repulsive ones. The B(3)Σu(-) and d(1)Πg states possess the double well. And the 1(3)Πu, C(3)Πg, A'(3)Δu, 1(5)Δg and 2(5)Σg(+) states are the inverted ones when the spin-orbit coupling is included. The PEC calculations are done by the complete active space self-consistent field (CASSCF) method, which is followed by the internally contracted multireference configuration interaction (icMRCI) approach with the Davidson correction. Core-valence correlation and scalar relativistic corrections are taken into account. The convergence of present calculations is evaluated with respect to the basis set and level of theory. The vibrational properties are discussed for the 1(5)Πg, 1(3)Πu, d(1)Πg and 1(5)Σu(-) states and for the second well of the B(3)Σu(-) state. The spin-orbit coupling effect is accounted for by the state interaction method with the Breit-Pauli Hamiltonian. The PECs of all the electronic states and spin-orbit states are extrapolated to the complete basis set limit. The spectroscopic parameters are obtained, and compared with available experimental and other theoretical results. Analyses demonstrate that the spectroscopic parameters reported here can be expected to be reliably predicted ones. The conclusion is obtained that the effect of spin-orbit coupling on the spectroscopic parameters are small almost for all the electronic states involved in this paper except for the 1(5)Σu(-), 1(5)Πg and 1(3)Πu. PMID:24486866

  17. Ultraviolet Absorption Spectra, AB Initio Calculations, and Carbonyl Wagging Potential Energy Functions of Cyclobutanone, Cyclopentanone, BICYCLO[3.1.0]HEXAN-3-ONE, and TETRAHYDROFURAN-3-ONE

    NASA Astrophysics Data System (ADS)

    Lee, Soono; Dakkouri, Marwan; Choo, Jaebum; Laane, Jaan

    2000-03-01

    The electronic absorption spectra of cyclobutanone, cyclopentanone, bicyclo[3.1.0]hexan-3-one, and tetrahydrofuran-3-one were recorded and analyzed in the 28,000 - 44,000 cm-1 region. Several dozen absorption bands were assigned for each molecule. These arise from combinations of the ring vibrations and the C=O wagging vibrations. Assigned bands were compared with previously recorded jet-cooled fluorescence excitation spectra. Additional C=O out-of-plane wagging bands were found for cyclopentanone and tetrahydrofuran-3-one, and the potential energy functions for this vibration in these molecules were recalculated. These potential energy functions have barriers to inversion reflecting the fact that the carbonyl group is bent out of the ring plane in the S1(n, π*) excited electronic state.

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

    PubMed

    Tan, Samuel Y S; Izgorodina, Ekaterina I

    2016-06-14

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

  19. Benchmark Calculations with Correlated Molecular Wave Functions. XIII. Potential Energy Curves for He-2, Ne-2, and Ar-2 Using Correlation Consistent Basis Sets Through Augmented Sextuple Zeta.

    SciTech Connect

    Mourik, Van Tonja; Wilson, Angela K.; Dunning, Thomas H.

    1999-02-20

    The potential energy curves of the rare gas dimers He2, Ne2, and Ar2 have been computed using correlation consistent basis sets ranging from singly augmented aug-cc-pVDZ sets through triply augmented t-aug-cc-pV6Z sets, with the augmented sextuple basis sets being reported herein. Several methods for including electron correlation were investigated, namely Moller Plesset perturbation theory (MP2, MP3 and MP4) and coupled cluster theory [CCSD and CCSD(T)].

  20. Interquark potential calculation from Dirac brackets

    NASA Astrophysics Data System (ADS)

    Gaete, Patricio

    2001-08-01

    We obtain the binding energy of an infinitely heavy quark-antiquark pair from Dirac brackets by computing the expectation value of the pure QCD Hamiltonian. This procedure exploits the rich structure of the dressing around static fermions. Some subtle points related to exhibing explicitly the interquark energy are considered.

  1. Renewable energy potential in Colombia

    NASA Astrophysics Data System (ADS)

    Correa Guzman, Jose Luis

    2008-12-01

    Renewable energy flows are very large in comparison with humankind's use of energy. In principle, all our energy needs, both now and into the future, can be met by energy from renewable sources. After many years trying to develop the alternative energy potential of Colombia, a major effort is principally being made since 2000 to explore and assess the renewable resources of the entire country. Until 2000, the availability of conventional energy sources in Colombia prevented renewable energy exploration from reaching a higher level. However, the extreme energy crisis of 1992 - 1993 alerted the authorities and the community to the necessity for exploring alternative energy sources. This energy study is a general approach to the current and future renewable energy scenario of Colombia. It was prepared in response to the increased interest around the world and in particular in Colombia to develop its non-fossil energy prospective. It, therefore, represents a working document giving an initial impression of the possible scale of the main renewables sources as a response to the concern about energy security and fossil fuel dependence problems. The assumptions made and calculations reported may therefore be subject to revision as more information becomes available. The aim of this dissertation is not only to improve the public understanding and discussion of renewable energy matters in Colombia but also to stimulate the development and application of renewable energy, wherever they have prospects of economic viability and environmental acceptability. To achieve such goal this paper reviews several renewable technologies, their availability, contribution and feasibility in Colombia.

  2. First-principles energy band calculation of Ruddlesden-Popper compound Sr3Sn2O7 using modified Becke-Johnson exchange potential

    NASA Astrophysics Data System (ADS)

    Kamimura, Sunao; Obukuro, Yuki; Matsushima, Shigenori; Nakamura, Hiroyuki; Arai, Masao; Xu, Chao-Nan

    2015-12-01

    The electronic structure of Sr3Sn2O7 is evaluated by the scalar-relativistic full potential linearized augmented plane wave (FLAPW+lo) method using the modified Becke-Johnson potential (Tran-Blaha potential) combined with the local density approximation correlation (MBJ-LDA). The fundamental gap between the valence band (VB) and conduction band (CB) is estimated to be 3.96 eV, which is close to the experimental value. Sn 5s states and Sr 4d states are predominant in the lower and upper CB, respectively. On the other hand, the lower VB is mainly composed of Sn 5s, 5p, and O 2p states, while the upper VB mainly consists of O 2p states. These features of the DOS are well reflected by the optical transition between the upper VB and lower CB, as seen in the energy dependence of the dielectric function. Furthermore, the absorption coefficient estimated from the MBJ-LDA is similar to the experimental result.

  3. Calibrating transition-metal energy levels and oxygen bands in first-principles calculations: Accurate prediction of redox potentials and charge transfer in lithium transition-metal oxides

    NASA Astrophysics Data System (ADS)

    Seo, Dong-Hwa; Urban, Alexander; Ceder, Gerbrand

    2015-09-01

    Transition-metal (TM) oxides play an increasingly important role in technology today, including applications such as catalysis, solar energy harvesting, and energy storage. In many of these applications, the details of their electronic structure near the Fermi level are critically important for their properties. We propose a first-principles-based computational methodology for the accurate prediction of oxygen charge transfer in TM oxides and lithium TM (Li-TM) oxides. To obtain accurate electronic structures, the Heyd-Scuseria-Ernzerhof (HSE06) hybrid functional is adopted, and the amount of exact Hartree-Fock exchange (mixing parameter) is adjusted to reproduce reference band gaps. We show that the HSE06 functional with optimal mixing parameter yields not only improved electronic densities of states, but also better energetics (Li-intercalation voltages) for LiCo O2 and LiNi O2 as compared to the generalized gradient approximation (GGA), Hubbard U corrected GGA (GGA +U ), and standard HSE06. We find that the optimal mixing parameters for TM oxides are system specific and correlate with the covalency (ionicity) of the TM species. The strong covalent (ionic) nature of TM-O bonding leads to lower (higher) optimal mixing parameters. We find that optimized HSE06 functionals predict stronger hybridization of the Co 3 d and O 2 p orbitals as compared to GGA, resulting in a greater contribution from oxygen states to charge compensation upon delithiation in LiCo O2 . We also find that the band gaps of Li-TM oxides increase linearly with the mixing parameter, enabling the straightforward determination of optimal mixing parameters based on GGA (α =0.0 ) and HSE06 (α =0.25 ) calculations. Our results also show that G0W0@GGA +U band gaps of TM oxides (M O ,M =Mn ,Co ,Ni ) and LiCo O2 agree well with experimental references, suggesting that G0W0 calculations can be used as a reference for the calibration of the mixing parameter in cases when no experimental band gap has been

  4. An approach to optimised calculations of the potential energy surfaces for the case of electron transfer reactions at a metal/solution interface

    NASA Astrophysics Data System (ADS)

    Bronshtein, Michael D.; Nazmutdinov, Renat R.; Schmickler, Wolfgang

    2004-12-01

    An effective computational scheme to construct the adiabatic potential energy surfaces (APES) along the reaction coordinates for an electron transfer reaction occurring by two steps at a metal electrode is considered in the framework of the Anderson-Newns model. Two Theorems have been proved which predict the existence of all possible solutions of the Anderson-Newns equations at arbitrary values of the key parameters and point out the region for each solution. Asymptotic formulas for solutions near multiple roots have been derived and combined in an effective way with numerical routines. The analysis of some important properties of the APES, which can be of interest for modelling the electrochemical electron transfer processes, is presented as well. The APES describing the reduction of Zn(II) and In(III) aqua-complexes at a mercury electrode have been built and discussed.

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

    NASA Astrophysics Data System (ADS)

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

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

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

    NASA Astrophysics Data System (ADS)

    Garrett, Bruce C.; Truhlar, Donald G.

    1980-03-01

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

  7. 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.

  8. Wave Energy Potential in the Latvian EEZ

    NASA Astrophysics Data System (ADS)

    Beriņš, J.; Beriņš, J.; Kalnačs, J.; Kalnačs, A.

    2016-06-01

    The present article deals with one of the alternative forms of energy - sea wave energy potential in the Latvian Exclusice Economic Zone (EEZ). Results have been achieved using a new method - VEVPP. Calculations have been performed using the data on wave parameters over the past five years (2010-2014). We have also considered wave energy potential in the Gulf of Riga. The conclusions have been drawn on the recommended methodology for the sea wave potential and power calculations for wave-power plant pre-design stage.

  9. New ab initio adiabatic potential energy surfaces and bound state calculations for the singlet ground X˜ 1A1 and excited C˜ 1B2(21A') states of SO2

    NASA Astrophysics Data System (ADS)

    Kłos, Jacek; Alexander, Millard H.; Kumar, Praveen; Poirier, Bill; Jiang, Bin; Guo, Hua

    2016-05-01

    We report new and more accurate adiabatic potential energy surfaces (PESs) for the ground X˜ 1A1 and electronically excited C˜ 1B2(21A') states of the SO2 molecule. Ab initio points are calculated using the explicitly correlated internally contracted multi-reference configuration interaction (icMRCI-F12) method. A second less accurate PES for the ground X ˜ state is also calculated using an explicitly correlated single-reference coupled-cluster method with single, double, and non-iterative triple excitations [CCSD(T)-F12]. With these new three-dimensional PESs, we determine energies of the vibrational bound states and compare these values to existing literature data and experiment.

  10. Spectroscopically Accurate Calculations of the Rovibrational Energies of Diatomic Hydrogen

    NASA Astrophysics Data System (ADS)

    Perry, Jason

    2005-05-01

    The Born-Oppenheimer approximation has been used to calculate the rotational and vibrational states of diatomic hydrogen. Because it is an approximation, our group now wants to use a Born-Oppenheimer potential to calculate the electronic energy that has been corrected to match closely with spectroscopic results. We are using a code that has corrections for adiabatic, relativistic, radiative, and non-adiabatic effects. The rovibrational energies have now been calculated for both bound and quasi-bound states. We also want to compute quadrupole transition probabilities for diatomic hydrogen. These calculations aspire to investigate diatomic hydrogen in astrophysical environments.

  11. Calculation of Rydberg energy levels for the francium atom

    NASA Astrophysics Data System (ADS)

    Huang, Shi-Zhong; Chu, Jin-Min

    2010-06-01

    Based on the weakest bound electron potential model theory, the Rydberg energy levels and quantum defects of the np2Po1/2 (n = 7-50) and np2Po3/2 (n = 7-50) spectrum series for the francium atom are calculated. The calculated results are in excellent agreement with the 48 measured levels, and 40 energy levels for highly excited states are predicted.

  12. Off-Diagonal Self-Energy Terms and Partially Self-Consistency in GW Calculations for Single Molecules: Efficient Implementation and Quantitative Effects on Ionization Potentials.

    PubMed

    Kaplan, F; Weigend, F; Evers, F; van Setten, M J

    2015-11-10

    The GW method in its most widespread variant takes, as an input, Kohn-Sham (KS) single particle energies and single particle states and yields results for the single-particle excitation energies that are significantly improved over the bare KS estimates. Fundamental shortcomings of density functional theory (DFT) when applied to excitation energies as well as artifacts introduced by approximate exchange-correlation (XC) functionals are thus reduced. At its heart lies the quasi-particle (qp) equation, whose solution yields the corrected excitation energies and qp-wave functions. We propose an efficient approximation scheme to treat this equation based on second-order perturbation theory and self-consistent iteration schemes. We thus avoid solving (large) eigenvalue problems at the expense of a residual error that is comparable to the intrinsic uncertainty of the GW truncation scheme and is, in this sense, insignificant. PMID:26574312

  13. Alaska's renewable energy potential.

    SciTech Connect

    Not Available

    2009-02-01

    This paper delivers a brief survey of renewable energy technologies applicable to Alaska's climate, latitude, geography, and geology. We first identify Alaska's natural renewable energy resources and which renewable energy technologies would be most productive. e survey the current state of renewable energy technologies and research efforts within the U.S. and, where appropriate, internationally. We also present information on the current state of Alaska's renewable energy assets, incentives, and commercial enterprises. Finally, we escribe places where research efforts at Sandia National Laboratories could assist the state of Alaska with its renewable energy technology investment efforts.

  14. Theoretical studies of potential energy surfaces

    SciTech Connect

    Harding, L.B.

    1995-07-01

    MRCI (configuration interaction) calculations were used to examine possible pathways for the O{sub 2} + CCH reaction. The H{sub 2} + CN potential surface was examined. An initial survey was made of the HCl + CN potential energy surface at a low level of theory.

  15. Free-Energy Calculations. A Mathematical Perspective

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrzej

    2015-01-01

    conductance, defined as the ratio of ionic current through the channel to applied voltage, can be calculated in MD simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. If the current is small, a voltage significantly higher than the experimental one needs to be applied to collect sufficient statistics of ion crossing events. Then, the calculated conductance has to be extrapolated to the experimental voltage using procedures of unknown accuracy. Instead, we propose an alternative approach that applies if ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. Then, it is possible to test the assumptions of the equation, recover the full voltage/current dependence, determine the reliability of the calculated conductance and reconstruct the underlying (equilibrium) free energy profile, all from MD simulations at a single voltage. We will present the underlying theory, model calculations that test this theory and simulations on ion conductance through a channel that has been extensively studied experimentally. To our knowledge this is the first case in which the complete, experimentally measured dependence of the current on applied voltage has been reconstructed from MD simulations.

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

    NASA Astrophysics Data System (ADS)

    Ye, Lin-Hui

    2016-07-01

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

  17. Model of Odd N in the Terrestrial Thermosphere: 1. A First Principles Calculation of the NO2 Potential Energy Surfaces Relevant to the Production of NO via the N(2D)+O2 Reaction.

    NASA Astrophysics Data System (ADS)

    Dothe, H.; Braunstein, M.; Duff, J. W.; Sharma, R. D.

    2001-12-01

    The daytime observation of 5.3 μ m thermospheric emission from the NO fundamental vibration-rotation band by the interferometer aboard the cryogenic infrared radiance instrumentation for shuttle (CIRRIS 1A) has provided important insight into the phenomenology of NO formation. The four major mechanisms to the 5.3 μ m emission considered by previous modeling are solar pumping, inelastic collisions of O with NO(v=0), the reactions of N(2D) with O2, and the reactions of N(4S) with O2. It has previously been shown that the reaction of N(4S) with O2 is consistent with rotationally nonthermal 5.3 μ m emission, while the N(2D)+O2 reaction has been assumed to contribute to rotationally thermal emission. The assumption of a thermal rotational distribution from the N(2D)+O2 reaction cannot be confirmed by the CIRRIS 1A data. The existence of a significant fraction of nonthermal atoms in the tail of the N(2D) energy distribution function (EDF) in the daylit thermosphere was demonstrated earlier (AGU Spring 2001). Therefore the investigation of possible nonthermal behavior in NO formation via the N(2D)+O2 reaction in the daylit and aurorally dosed thermosphere requires energy dependent cross sections for the reaction between N(2D) and O2. To calculate the N(2D)+O2 cross sections, potential energy surfaces (PES) of the NO2 system are required. The output of these calculations include the energy dependent cross sections and the vibrational and rotational distribution of the nascent NO needed for accurate calculation of the cooling rates due to 5.3 μ m emission. This work concentrates on the first step towards the calculation of such cross sections, the ab initio calculations of the NO2 PES. Previous existing PES, using different basis sets and electron correlation levels, have shown disagreements in the magnitude of the barriers for the lowest lying doublet surfaces in the reaction entrance channel. Comparative results from our calculations are presented here, showing PES

  18. Calculating Free Energies Using Average Force

    NASA Technical Reports Server (NTRS)

    Darve, Eric; Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    A new, general formula that connects the derivatives of the free energy along the selected, generalized coordinates of the system with the instantaneous force acting on these coordinates is derived. The instantaneous force is defined as the force acting on the coordinate of interest so that when it is subtracted from the equations of motion the acceleration along this coordinate is zero. The formula applies to simulations in which the selected coordinates are either unconstrained or constrained to fixed values. It is shown that in the latter case the formula reduces to the expression previously derived by den Otter and Briels. If simulations are carried out without constraining the coordinates of interest, the formula leads to a new method for calculating the free energy changes along these coordinates. This method is tested in two examples - rotation around the C-C bond of 1,2-dichloroethane immersed in water and transfer of fluoromethane across the water-hexane interface. The calculated free energies are compared with those obtained by two commonly used methods. One of them relies on determining the probability density function of finding the system at different values of the selected coordinate and the other requires calculating the average force at discrete locations along this coordinate in a series of constrained simulations. The free energies calculated by these three methods are in excellent agreement. The relative advantages of each method are discussed.

  19. Protein thermostability calculations using alchemical free energy simulations.

    PubMed

    Seeliger, Daniel; de Groot, Bert L

    2010-05-19

    Thermal stability of proteins is crucial for both biotechnological and therapeutic applications. Rational protein engineering therefore frequently aims at increasing thermal stability by introducing stabilizing mutations. The accurate prediction of the thermodynamic consequences caused by mutations, however, is highly challenging as thermal stability changes are caused by alterations in the free energy of folding. Growing computational power, however, increasingly allows us to use alchemical free energy simulations, such as free energy perturbation or thermodynamic integration, to calculate free energy differences with relatively high accuracy. In this article, we present an automated protocol for setting up alchemical free energy calculations for mutations of naturally occurring amino acids (except for proline) that allows an unprecedented, automated screening of large mutant libraries. To validate the developed protocol, we calculated thermodynamic stability differences for 109 mutations in the microbial Ribonuclease Barnase. The obtained quantitative agreement with experimental data illustrates the potential of the approach in protein engineering and design. PMID:20483340

  20. Energy Band Calculations for Maximally Even Superlattices

    NASA Astrophysics Data System (ADS)

    Krantz, Richard; Byrd, Jason

    2007-03-01

    Superlattices are multiple-well, semiconductor heterostructures that can be described by one-dimensional potential wells separated by potential barriers. We refer to a distribution of wells and barriers based on the theory of maximally even sets as a maximally even superlattice. The prototypical example of a maximally even set is the distribution of white and black keys on a piano keyboard. Black keys may represent wells and the white keys represent barriers. As the number of wells and barriers increase, efficient and stable methods of calculation are necessary to study these structures. We have implemented a finite-element method using the discrete variable representation (FE-DVR) to calculate E versus k for these superlattices. Use of the FE-DVR method greatly reduces the amount of calculation necessary for the eigenvalue problem.

  1. 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.)

  2. Is ring breaking feasible in relative binding free energy calculations?

    PubMed

    Liu, Shuai; Wang, Lingle; Mobley, David L

    2015-04-27

    Our interest is relative binding free energy (RBFE) calculations based on molecular simulations. These are promising tools for lead optimization in drug discovery, computing changes in binding free energy due to modifications of a lead compound. However, in the "alchemical" framework for RBFE calculations, some types of mutations have the potential to introduce error into the computed binding free energies. Here we explore the magnitude of this error in several different model binding calculations. We find that some of the calculations involving ring breaking have significant errors, and these errors are especially large in bridged ring systems. Since the error is a function of ligand strain, which is unpredictable in advance, we believe that ring breaking should be avoided when possible. PMID:25835054

  3. Predicting proteinase specificities from free energy calculations.

    PubMed

    Mekonnen, Seble Merid; Olufsen, Magne; Smalås, Arne O; Brandsdal, Bjørn O

    2006-10-01

    The role of the primary binding residue (P1) in complexes between three different subtilases (subtilisin Carlsberg, thermitase and proteinase K) and their canonical protein inhibitor eglin c have been studied by free energy calculations. Based on the crystal structures of eglin c in complex with subtilisin Carlsberg and thermitase, and a homology model of the eglin c-proteinase K complex, a total of 57 mutants have been constructed and docked into their host proteins. The binding free energy was then calculated using molecular dynamics (MD) simulations combined with the linear interaction energy (LIE) method for all complexes differing only in the nature of the amino acid at the P1 position. LIE calculations for 19 different complexes for each subtilase were thus carried out excluding proline. The effects of substitutions at the P1 position on the binding free energies are found to be very large, and positively charged residues (Arg, Lys and His) are particularly deleterious for all three enzymes. The charged variants of the acidic side chains are found to bind more favorably as compared to their protonated states in all three subtilases. Furthermore, hydrophobic amino acids are accommodated most favorably at the S1-site in all three enzymes. Comparison of the three series of binding free energies shows only minor differences in the 19 computed relative binding free energies among these subtilases. This is further reflected in the correlation coefficient between the 23 relative binding free energies obtained, including the possible protonation states of ionizable side chains, but excluding the P1 Pro, for subtilisin Carlsberg versus thermitase (0.95), subtilisin versus proteinase K (0.94) and thermitase versus proteinase K (0.96). PMID:16386933

  4. High-level ab initio calculations for the four low-lying families of minima of (H2O)(20): 1. Estimates of MP2/CBS binding energies and comparison with empirical potentials

    SciTech Connect

    Fanourgakis, Georgios S.; Apra, Edoardo; Xantheas, Sotiris S.

    2004-08-08

    We report estimates of complete basis set (CBS) limits at the second-order Møller-Plesset perturbation level of theory (MP2) for the binding energies of the lowest lying isomers within each of the four major families of minima of (H2O)20. These were obtained by performing MP2 calculations with the family of correlation-consistent basis sets up to quadruple zeta quality, augmented with additional diffuse functions (aug-cc-pVnZ, n=D, T, Q). The MP2/CBS estimates are: -200.1 kcal/mol (dodecahedron, 30 hydrogen bonds), -212.6 kcal/mol (fused cubes, 36 hydrogen bonds), -215.0 (face-sharing pentagonal prisms, 35 hydrogen bonds) and –217.9 kcal/mol (edge-sharing pentagonal prisms, 34 hydrogen bonds). The energetic ordering of the various (H2O)20 isomers does not follow monotonically the number of hydrogen bonds as in the case of smaller clusters such as the different isomers of the water hexamer. The dodecahedron lies ca. 18 kcal/mol higher in energy than the most stable edge-sharing pentagonal prism isomer. The TIP4P, ASP-W4, TTM2-R, AMOEBA and TTM2-F empirical potentials also predict the energetic stabilization of the edge-sharing pentagonal prisms with respect to the dodecahedron, albeit they universally underestimate the cluster binding energies with respect to the MP2/CBS result. Among them, the TTM2-F potential was found to predict the absolute cluster binding energies to within < 1% from the corresponding MP2/CBS values, whereas the error for the rest of the potentials considered in this study ranges from 3-5%.

  5. Potential Energy Curves of Hydrogen Fluoride

    NASA Technical Reports Server (NTRS)

    Fallon, Robert J.; Vanderslice, Joseph T.; Mason, Edward A.

    1960-01-01

    Potential energy curves for the X(sup 1)sigma+ and V(sup 1)sigma+ states of HF and DF have been calculated by the Rydberg-Klein-Rees method. The results calculated from the different sets of data for HF and DF are found to be in very good agreement. The theoretical results of Karo are compared to the experimental results obtained here.

  6. Rate constant calculations of the GeH4 + OH/OD → GeH3 + H2O/HOD reactions using an ab initio based full-dimensional potential energy surface.

    PubMed

    Espinosa-Garcia, J; Rangel, C; Corchado, J C

    2016-06-22

    We report an analytical full-dimensional potential energy surface for the GeH4 + OH → GeH3 + H2O reaction based on ab initio calculations. It is a practically barrierless reaction with very high exothermicity and the presence of intermediate complexes in the entrance and exit channels, reproducing the experimental evidence. Using this surface, thermal rate constants for the GeH4 + OH/OD isotopic reactions were calculated using two approaches: variational transition state theory (VTST) and quasi-classical trajectory (QCT) calculations, in the temperature range 200-1000 K, and results were compared with the only experimental data at 298 K. Both methods showed similar values over the whole temperature range, with differences less than 30%; and the experimental data was reproduced at 298 K, with negative temperature dependence below 300 K, which is associated with the presence of an intermediate complex in the entrance channel. However, while the QCT approach reproduced the experimental kinetic isotope effect, the VTST approach underestimated it. We suggest that this difference is associated with the harmonic approximation used in the treatment of vibrational frequencies. PMID:27292879

  7. On the calculation of classical vibrational energy exchange

    NASA Astrophysics Data System (ADS)

    Gibbons, John P.; Stettler, John D.

    1982-07-01

    A three-dimensional, Monte Carlo classical model for the calculation of vibrational energy relaxation and transfer rates for both diatomic—monatomic and diatomic—diatomic systems was developed, analyzed and implemented. Mediation by internal angular momentum changes was demonstrated to be important in these energy transfer processes. This mechanism was incorporated into the model in order to achieve statistically significant results within reasonable computer running times. This made possible the extension of the model calculations to much lower temperatures than had been previously investigated. This calculational procedure was applied to Ar—O 2, to He—O 2 and to the near resonant CO—N 2 process at several temperatures between room temperature and 4000 K with the use of exponential repulsive intermolecular potential. Three different sets of potential parameters obtained from three independent sources were used. The results were compared to experiment.

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

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

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

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

    SciTech Connect

    Linnaeus, S.

    1986-10-01

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

  10. 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.

  11. Total-energy and pressure calculations for random substitutional alloys

    SciTech Connect

    Johnson, D.D. ); Nicholson, D.M. ); Pinski, F.J. ); Gyoerffy, B.L. ); Stocks, G.M. )

    1990-05-15

    We present the details and the derivation of density-functional-based expressions for the total energy and pressure for random substitutional alloys (RSA) using the Korringa-Kohn-Rostoker Green's-function approach in combination with the coherent-potential approximation (CPA) to treat the configurational averaging. This includes algebraic cancellation of various electronic core contributions to the total energy and pressure, as in ordered-solid muffin-tin-potential calculations. Thus, within the CPA, total-energy and pressure calculations for RSA have the same foundation and have been found to have the same accuracy as those obtained in similar calculations for ordered solids. Results of our calculations for the impurity formation energy, and for the bulk moduli, the lattice parameters, and the energy of mixing as a function of concentration in fcc Cu{sub {ital c}}Zn{sub 1{minus}{ital c}} alloys show that this generalized density-functional theory will be useful in studying alloy phase stability.

  12. Bond-Energy and Surface-Energy Calculations in Metals

    ERIC Educational Resources Information Center

    Eberhart, James G.; Horner, Steve

    2010-01-01

    A simple technique appropriate for introductory materials science courses is outlined for the calculation of bond energies in metals from lattice energies. The approach is applied to body-centered cubic (bcc), face-centered cubic (fcc), and hexagonal-closest-packed (hcp) metals. The strength of these bonds is tabulated for a variety metals and is…

  13. Fully relativistic multiple scattering calculations for general potentials

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  14. Potential energy studies on silane dimers

    NASA Astrophysics Data System (ADS)

    Mahlanen, Riina; Pakkanen, Tapani A.

    2011-04-01

    Intermolecular interactions and parameters for use in MD studies of large molecule systems have earlier been determined for hydrocarbons, carbon tetrahalides and sulfur. The paper reports a model representing nonbonding interactions between silane molecules, which were examined in the same way as hydrocarbons in an earlier (neopentane, isopropane, propane, and ethane) study. Intermolecular potentials were determined for 11 combinations of silane compound pairs (silane SiH 4, disilane Si 2H 6, trisilane Si 3H 8, isotetrasilane Si 4H 10 and neopentasilane Si 5H 12) with MP2/aug(df)-6-311G ∗ab initio calculations. The most stable dimer configurations were identified. With use of the modified Morse potential model to represent the interactions, 276 new potential energy surfaces were generated for silane dimers. Separate and generic pair potentials were calculated for the silanes. The pair potentials can be used in MD studies of silanes.

  15. 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.

  16. Zero energy scattering calculation in Euclidean space

    NASA Astrophysics Data System (ADS)

    Carbonell, J.; Karmanov, V. A.

    2016-03-01

    We show that the Bethe-Salpeter equation for the scattering amplitude in the limit of zero incident energy can be transformed into a purely Euclidean form, as it is the case for the bound states. The decoupling between Euclidean and Minkowski amplitudes is only possible for zero energy scattering observables and allows determining the scattering length from the Euclidean Bethe-Salpeter amplitude. Such a possibility strongly simplifies the numerical solution of the Bethe-Salpeter equation and suggests an alternative way to compute the scattering length in Lattice Euclidean calculations without using the Luscher formalism. The derivations contained in this work were performed for scalar particles and one-boson exchange kernel. They can be generalized to the fermion case and more involved interactions.

  17. Potential energy function for the hydroperoxyl radical

    SciTech Connect

    Lemon, W.J.; Hase, W.L.

    1987-03-12

    A switching function formalism is used to derive an analytic potential energy surface for the O + OH in equilibrium HO/sub 2/ in equilibrium H + O/sub 2/ reactive system. Both experimental and ab initio data are used to derive parameters for the potential energy surface. Trajectory calculations for highly excited HO/sub 2/ are performed on this surface. From these trajectories quasi-periodic eigentrajectories are found for vibrational levels near the HO/sub 2/ dissociation threshold with small amounts of quanta in the OH stretch mode and large amounts of quanta in the OO stretch mode.

  18. Lead Optimization Mapper: Automating free energy calculations for lead optimization

    PubMed Central

    Liu, Shuai; Wu, Yujie; Lin, Teng; Abel, Robert; Redmann, Jonathan P.; Summa, Christopher M.; Jaber, Vivian R.; Lim, Nathan M.; Mobley, David L.

    2013-01-01

    Alchemical free energy calculations hold increasing promise as an aid to drug discovery efforts. However, applications of these techniques in discovery projects have been relatively few, partly because of the difficulty of planning and setting up calculations. Here, we introduce Lead Optimization Mapper, LOMAP, an automated algorithm to plan efficient relative free energy calculations between potential ligands within a substantial library of perhaps hundreds of compounds. In this approach, ligands are first grouped by structural similarity primarily based on the size of a (loosely defined) maximal common substructure, and then calculations are planned within and between sets of structurally related compounds. An emphasis is placed on ensuring that relative free energies can be obtained between any pair of compounds without combining the results of too many different relative free energy calculations (to avoid accumulation of error) and by providing some redundancy to allow for the possibility of error and consistency checking and provide some insight into when results can be expected to be unreliable. The algorithm is discussed in detail and a Python implementation, based on both Schrödinger's and OpenEye's APIs, has been made available freely under the BSD license. PMID:24072356

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

    NASA Technical Reports Server (NTRS)

    Venkatakrishnan, P.; Gary, G. Allen

    1989-01-01

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

  20. Theoretical studies of potential energy surfaces.

    SciTech Connect

    Harding, L. B.

    2006-01-01

    The goal of this program is to calculate accurate potential energy surfaces for both reactive and nonreactive systems. To do this the electronic Schroedinger equation must be solved. Our approach starts with multiconfiguration self-consistent field (MCSCF) reference wave functions. These reference wavefunctions are designed to be sufficiently flexible to accurately describe changes in electronic structure over a broad range of geometries. Dynamical electron correlation effects are included via multireference, singles and doubles configuration interaction (MRCI) calculations. With this approach, we are able to provide chemically useful predictions of the energetics for many systems. A second aspect of this program is the development of techniques to fit multi-dimensional potential surfaces to convenient, global, analytic functions that can then be used in dynamics calculations.

  1. Eight-dimensional quantum reaction rate calculations for the H+CH{sub 4} and H{sub 2}+CH{sub 3} reactions on recent potential energy surfaces

    SciTech Connect

    Zhou, Yong; Zhang, Dong H.

    2014-11-21

    Eight-dimensional (8D) transition-state wave packet simulations have been performed on two latest potential energy surfaces (PES), the Zhou-Fu-Wang-Collins-Zhang (ZFWCZ) PES [Y. Zhou, B. Fu, C. Wang, M. A. Collins, and D. H. Zhang, J. Chem. Phys. 134, 064323 (2011)] and the Xu-Chen-Zhang (XCZ)-neural networks (NN) PES [X. Xu, J. Chen, and D. H. Zhang, Chin. J. Chem. Phys. 27, 373 (2014)]. Reaction rate constants for both the H+CH{sub 4} reaction and the H{sub 2}+CH{sub 3} reaction are calculated. Simulations of the H+CH{sub 4} reaction based on the XCZ-NN PES show that the ZFWCZ PES predicts rate constants with reasonable high accuracy for low temperatures while leads to slightly lower results for high temperatures, in line with the distribution of interpolation error associated with the ZFWCZ PES. The 8D H+CH{sub 4} rate constants derived on the ZFWCZ PES compare well with full-dimensional 12D results based on the equivalent m-ZFWCZ PES, with a maximum relative difference of no more than 20%. Additionally, very good agreement is shown by comparing the 8D XCZ-NN rate constants with the 12D results obtained on the ZFWCZ-WM PES, after considering the difference in static barrier height between these two PESs. The reaction rate constants calculated for the H{sub 2}+CH{sub 3} reaction are found to be in good consistency with experimental observations.

  2. Theoretical studies of potential energy surfaces

    SciTech Connect

    Harding, L.B.

    1993-12-01

    The goal of this program is to calculate accurate potential energy surfaces (PES) for both reactive and nonreactive systems. To do this the electronic Schrodinger equation must be solved. Our approach to this problem starts with multiconfiguration self-consistent field (MCSCF) reference wavefunctions. These reference wavefunctions are designed to be sufficiently flexible to accurately describe changes in electronic structure over a broad range of geometries. Electron correlation effects are included via multireference, singles and doubles configuration interaction (MRSDCI) calculations. With this approach, the authors are able to provide useful predictions of the energetics for a broad range of systems.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  4. Analytical potential energy functions and theoretical spectroscopic constants for MX/MX- (M dbond Ge, Sn, Pb; X dbond O, S, Se, Te, Po) and LuA (A dbond H, F) systems: Density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Jalbout, Abraham F.; Li, Xin-Hua; Abou-Rachid, Hakima

    The molecular spectroscopic constants for the chalcogenide complexes MX (M dbond Ge, Sn, Pb; X dbond O, S, Se, Te, Po) and their corresponding MX- anions are presented with the LSDA/SDD, B1LYP/SDD, and B3LYP/SDD methods. Although many methods were attempted, only the most promising results are reported. We show that the best results are obtained by LSDA/SDD calculations, and thus this method is emphasized as an illustrative example of our methodology. The potential energy curves and physical property characterizations for X1 ?+ state of LuH and LuF are presented with a variety of density functional theory (DFT) methods. Comparisons with wave function-based treatments (HF, MP2, CCSD, QCISD) are made in addition to experimental correlations. We show that the best results are obtained by the B3LYP/SDD method for LuH, and the MPW1PW91/SDD method for LuF.

  5. Reaction Dynamics of O((3)P) + Propyne: II. Primary Products, Branching Ratios, and Role of Intersystem Crossing from Ab Initio Coupled Triplet/Singlet Potential Energy Surfaces and Statistical Calculations.

    PubMed

    Gimondi, Ilaria; Cavallotti, Carlo; Vanuzzo, Gianmarco; Balucani, Nadia; Casavecchia, Piergiorgio

    2016-07-14

    The mechanism of the O((3)P) + CH3CCH reaction was investigated using a combined experimental/theoretical approach. Experimentally the reaction dynamics was studied using crossed molecular beams (CMB) with mass-spectrometric detection and time-of-flight analysis at 9.2 kcal/mol collision energy. Theoretically master equation (ME) simulations were performed on a potential energy surface (PES) determined using high-level ab initio electronic structure calculations. In this paper (II) the theoretical results are described and compared with experiments, while in paper (I) are reported and discussed the results of the experimental study. The PES was investigated by determining structures and vibrational frequencies of wells and transition states at the CASPT2/aug-cc-pVTZ level using a minimal active space. Energies were then determined at the CASPT2 level increasing systematically the active space and at the CCSD(T) level extrapolating to the complete basis set limit. Two separate portions of the triplet PES were investigated, as O((3)P) can add either on the terminal or the central carbon of the unsaturated propyne bond. Minimum energy crossing points (MECPs) between the triplet and singlet PESs were searched at the CASPT2 level. The calculated spin-orbit coupling constants between the T1 and S0 electronic surfaces were ∼25 cm(-1) for both PESs. The portions of the singlet PES that can be accessed from the MECPs were investigated at the same level of theory. The system reactivity was predicted integrating stochastically the one-dimensional ME using Rice-Ramsperger-Kassel-Marcus theory to determine rate constants on the full T1/S0 PESs, accounting explicitly for intersystem crossing (ISC) using the Landau-Zener model. The computational results are compared both with the branching ratios (BRs) determined experimentally in the companion paper (I) and with those estimated in a recent kinetic study at 298 K. The ME results allow to interpret the main system reactivity: CH

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

    PubMed Central

    Miedema, Henk

    2002-01-01

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

  7. 18 CFR 11.13 - Energy gains calculations.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY... FEDERAL POWER ACT Charges for Headwater Benefits § 11.13 Energy gains calculations. (a) Energy gains at a... not complex or in which headwater benefits are expected to be small, calculations will be made...

  8. Calculating Free Energy Changes in Continuum Solvation Models.

    PubMed

    Ho, Junming; Ertem, Mehmed Z

    2016-02-25

    We recently showed for a large data set of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents [ Phys. Chem. Chem. Phys. 2015 , 17 , 2859 ]. In this paper, we significantly expand the scope of our study to examine the suitability of this approach for calculating general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMD-M062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems. This includes cluster-continuum schemes for pKa calculations as well as various neutral, radical, and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar-the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 and 25 kJ mol(-1), respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment. PMID:26878566

  9. California Industrial Energy Efficiency Potential

    SciTech Connect

    Coito, Fred; Worrell, Ernst; Price, Lynn; Masanet, Eric; RafaelFriedmann; Rufo, Mike

    2005-06-01

    This paper presents an overview of the modeling approach andhighlights key findings of a California industrial energy efficiencypotential study. In addition to providing estimates of technical andeconomic potential, the study examines achievable program potential undervarious program-funding scenarios. The focus is on electricity andnatural gas savings for manufacturing in the service territories ofCalifornia's investor-owned utilities (IOUs). The assessment is conductedby industry type and by end use. Both crosscutting technologies andindustry-specific process measures are examined. Measure penetration intothe marketplace is modeled as a function of customer awareness, measurecost effectiveness, and perceived market barriers. Data for the studycomes from a variety of sources, including: utility billing records, theEnergy Information Association (EIA) Manufacturing Energy ConsumptionSurvey (MECS), state-sponsored avoided cost studies, energy efficiencyprogram filings, and technology savings and cost data developed throughLawrence Berkeley National Laboratory (LBNL). The study identifies 1,706GWh and 47 Mth (million therms) per year of achievable potential over thenext twelve years under recent levels of program expenditures, accountingfor 5.2 percent of industrial electricity consumption and 1.3 percent ofindustrial natural gas consumption. These estimates grow to 2,748 GWh and192 Mth per year if all cost-effective and achievable opportunities arepursued. Key industrial electricity end uses, in terms of energy savingspotential, include compressed air and pumping systems that combine toaccount for about half of the total achievable potential estimates. Fornatural gas, savings are concentrated in the boiler and process heatingend uses, accounting for over 99 percent to total achievablepotential.

  10. 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.

  11. Potential energy savings from aquifer thermal energy storage

    SciTech Connect

    Anderson, M.R.; Weijo, R.O.

    1988-07-01

    Pacific Northwest Laboratory researchers developed an aggregate-level model to estimate the short- and long-term potential energy savings from using aquifer thermal storage (ATES) in the United States. The objectives of this effort were to (1) develop a basis from which to recommend whether heat or chill ATES should receive future research focus and (2) determine which market sector (residential, commercial, or industrial) offers the largest potential energy savings from ATES. Information was collected on the proportion of US land area suitable for ATES applications. The economic feasibility of ATES applications was then evaluated. The potential energy savings from ATES applications was calculated. Characteristic energy use in the residential, commercial, and industrial sectors was examined, as was the relationship between waste heat production and consumption by industrial end-users. These analyses provided the basis for two main conclusions: heat ATES applications offer higher potential for energy savings than do chill ATES applications; and the industrial sector can achieve the highest potential energy savings for the large consumption markets. Based on these findings, it is recommended that future ATES research and development efforts be directed toward heat ATES applications in the industrial sector. 11 refs., 6 figs., 9 tabs.

  12. The potential of renewable energy

    SciTech Connect

    Not Available

    1990-03-01

    On June 27 and 28, 1989, the US Department of Energy (DOE) national laboratories were convened to discuss plans for the development of a National Energy Strategy (NES) and, in particular, the analytic needs in support of NES that could be addressed by the laboratories. As a result of that meeting, interlaboratory teams were formed to produce analytic white papers on key topics, and a lead laboratory was designated for each core laboratory team. The broad-ranging renewables assignment is summarized by the following issue statement from the Office of Policy, Planning and Analysis: to what extent can renewable energy technologies contribute to diversifying sources of energy supply What are the major barriers to greater renewable energy use and what is the potential timing of widespread commercialization for various categories of applications This report presents the results of the intensive activity initiated by the June 1989 meeting to produce a white paper on renewable energy. Scores of scientists, analysts, and engineers in the five core laboratories gave generously of their time over the past eight months to produce this document. Their generous, constructive efforts are hereby gratefully acknowledged. 126 refs., 44 figs., 32 tabs.

  13. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1988-01-01

    The minimum energy path for the addition of a hydrogen atom to N2 is characterized in CASSCF/CCI calculations using the (4s3p2d1f/3s2p1d) basis set, with additional single point calculations at the stationary points of the potential energy surface using the (5s4p3d2f/4s3p2d) basis set. These calculations represent the most extensive set of ab initio calculations completed to date, yielding a zero point corrected barrier for HN2 dissociation of approx. 8.5 kcal mol/1. The lifetime of the HN2 species is estimated from the calculated geometries and energetics using both conventional Transition State Theory and a method which utilizes an Eckart barrier to compute one dimensional quantum mechanical tunneling effects. It is concluded that the lifetime of the HN2 species is very short, greatly limiting its role in both termolecular recombination reactions and combustion processes.

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

    NASA Astrophysics Data System (ADS)

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

    2004-06-01

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

  15. Improved initial guess for minimum energy path calculations.

    PubMed

    Smidstrup, Søren; Pedersen, Andreas; Stokbro, Kurt; Jónsson, Hannes

    2014-06-01

    A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of pairwise distances at each discretization point along the path and the nudged elastic band method then used to find an optimal path on this image dependent pair potential (IDPP) surface. This provides an initial path for the more computationally intensive calculations of a minimum energy path on an energy surface obtained, for example, by ab initio or density functional theory. The optimal path on the IDPP surface is significantly closer to a minimum energy path than a linear interpolation of the Cartesian coordinates and, therefore, reduces the number of iterations needed to reach convergence and averts divergence in the electronic structure calculations when atoms are brought too close to each other in the initial path. The method is illustrated with three examples: (1) rotation of a methyl group in an ethane molecule, (2) an exchange of atoms in an island on a crystal surface, and (3) an exchange of two Si-atoms in amorphous silicon. In all three cases, the computational effort in finding the minimum energy path with DFT was reduced by a factor ranging from 50% to an order of magnitude by using an IDPP path as the initial path. The time required for parallel computations was reduced even more because of load imbalance when linear interpolation of Cartesian coordinates was used. PMID:24907989

  16. Improved initial guess for minimum energy path calculations

    SciTech Connect

    Smidstrup, Søren; Pedersen, Andreas; Stokbro, Kurt

    2014-06-07

    A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of pairwise distances at each discretization point along the path and the nudged elastic band method then used to find an optimal path on this image dependent pair potential (IDPP) surface. This provides an initial path for the more computationally intensive calculations of a minimum energy path on an energy surface obtained, for example, by ab initio or density functional theory. The optimal path on the IDPP surface is significantly closer to a minimum energy path than a linear interpolation of the Cartesian coordinates and, therefore, reduces the number of iterations needed to reach convergence and averts divergence in the electronic structure calculations when atoms are brought too close to each other in the initial path. The method is illustrated with three examples: (1) rotation of a methyl group in an ethane molecule, (2) an exchange of atoms in an island on a crystal surface, and (3) an exchange of two Si-atoms in amorphous silicon. In all three cases, the computational effort in finding the minimum energy path with DFT was reduced by a factor ranging from 50% to an order of magnitude by using an IDPP path as the initial path. The time required for parallel computations was reduced even more because of load imbalance when linear interpolation of Cartesian coordinates was used.

  17. Non-Equilibrium Properties from Equilibrium Free Energy Calculations

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; Wilson, Michael A.

    2012-01-01

    Calculating free energy in computer simulations is of central importance in statistical mechanics of condensed media and its applications to chemistry and biology not only because it is the most comprehensive and informative quantity that characterizes the eqUilibrium state, but also because it often provides an efficient route to access dynamic and kinetic properties of a system. Most of applications of equilibrium free energy calculations to non-equilibrium processes rely on a description in which a molecule or an ion diffuses in the potential of mean force. In general case this description is a simplification, but it might be satisfactorily accurate in many instances of practical interest. This hypothesis has been tested in the example of the electrodiffusion equation . Conductance of model ion channels has been calculated directly through counting the number of ion crossing events observed during long molecular dynamics simulations and has been compared with the conductance obtained from solving the generalized Nernst-Plank equation. It has been shown that under relatively modest conditions the agreement between these two approaches is excellent, thus demonstrating the assumptions underlying the diffusion equation are fulfilled. Under these conditions the electrodiffusion equation provides an efficient approach to calculating the full voltage-current dependence routinely measured in electrophysiological experiments.

  18. 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.

  19. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1994-01-01

    Quantum mechanical methods have been used to compute potential energy surfaces for chemical reactions. The reactions studied were among those believed to be important to the NASP and HSR programs and included the recombination of two H atoms with several different third bodies; the reactions in the thermal Zeldovich mechanism; the reactions of H atom with O2, N2, and NO; reactions involved in the thermal De-NO(x) process; and the reaction of CH(squared Pi) with N2 (leading to 'prompt NO'). These potential energy surfaces have been used to compute reaction rate constants and rates of unimolecular decomposition. An additional application was the calculation of transport properties of gases using a semiclassical approximation (and in the case of interactions involving hydrogen inclusion of quantum mechanical effects).

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

    NASA Astrophysics Data System (ADS)

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

    2013-11-01

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

  1. 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.

  2. Multi-grid calculation of transonic potential flows

    NASA Technical Reports Server (NTRS)

    Caughey, D. A.; Shmilovich, A.

    1985-01-01

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

  3. Probing the Adsorption Behavior of 4,5-Diazafluoren-9-one and Its Schiff Base Derivatives on SIlver and Gold Nanosurfaces Using Raman Spectroscopy, Density Functional Theory and Potential Energy Distribution Calculations

    NASA Astrophysics Data System (ADS)

    McCoy, Rhonda Patrice

    4,5-Diazafluoren-9-one (DAFO) is an aromatic ketone synthesized by oxidizing 1,10-phenanthroline with potassium permanganate. In this present study, the Raman spectra of DAFO in the solid and solution states were recorded in the 100-2000 cm-1 spectral region using 1064, 633, 532, and 514 nm excitation sources. A normal mode analysis of DAFO was performed using density functional theory; the BLYP and B3LYP functionals, each with the 6-31G(d) and 6-311(d) basis sets were employed. The fundamental modes on the Raman spectrum of DAFO were assigned with the appropriate symmetry element using the BLYP functional and 6-31G(d) basis set. The vibrational modes were described and quantified by potential energy distribution calculations. The Raman frequencies for the solid and solution spectra were compared; the observed frequency shifts are attributed to hydrogen bonding or dipole-dipole interactions occurring between the solvent and DAFO ligand. To further assess solute-solvent interactions the UV-vis spectra of DAFO was obtained in hydrogen bonding, polar aprotic, and non-polar solvents. The fine structure of the band observed at lambda max becomes more resolved as solvent polarity decreases, therefore confirming solute-solvent interactions in polar solvents. A silver complex of DAFO was synthesized with the intent of understanding how coordination affected the Raman frequencies. The bands assigned to pyridine ring bending, nu(C=N), and nu(C=O) were shifted because of coordination. These shifts have been attributed to the molecule being perturbed because of coordination. Therefore, the Ag-DAFO complex was analyzed by X-Ray diffraction and the molecular geometries of the free and coordinated ligand were compared. The resolved crystalline structure revealed the silver ion coordinated DAFO using the lone pairs of electrons from the nitrogens in the pyridine ring. Analysis of the molecular geometry revealed the C=O bond increases in double bond character and the C5-C14 bond

  4. Free-energy calculation via mean-force dynamics using a logarithmic energy landscape.

    PubMed

    Morishita, Tetsuya; Itoh, Satoru G; Okumura, Hisashi; Mikami, Masuhiro

    2012-06-01

    A method for free-energy calculation based on mean-force dynamics (fictitious dynamics on a potential of mean force) is presented. The method utilizes a logarithmic form of free energy to enhance crossing barriers on a free-energy landscape, which results in efficient sampling of "rare" events. Invoking a conserved quantity in mean-force dynamics, free energy can be estimated on-the-fly without postprocessing. This means that an estimate of the free-energy profile can be locally made in contrast to the other methods based on mean-force dynamics such as metadynamics. The method is benchmarked against conventional methods and its high efficiency is demonstrated in the free-energy calculation for a glycine dipeptide molecule. PMID:23005238

  5. Potential energy surfaces of Polonium isotopes

    NASA Astrophysics Data System (ADS)

    Nerlo-Pomorska, B.; Pomorski, K.; Schmitt, C.; Bartel, J.

    2015-11-01

    The evolution of the potential energy landscape is analysed in detail for ten even-even polonium isotopes in the mass range 188\\lt A\\lt 220 as obtained within the macroscopic-microscopic approach, relying on the Lublin-Strasbourg drop model and the Yukawa-folded single-particle energies for calculating the microscopic shell and pairing corrections. A variant of the modified Funny-Hills nuclear shape parametrization is used to efficiently map possible fission paths. The approach explains the main features of the fragment partition as measured in low-energy fission along the polonium chain. The latter lies in a transitional region of the nuclear chart, and will be essential to consistently understand the evolution of fission properties from neutron-deficient mercury to heavy actinides. The ability of our method to predict fission observables over such an extended region looks promising.

  6. 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)

  7. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  9. Convective Available Potential Energy of World Ocean

    NASA Astrophysics Data System (ADS)

    Su, Z.; Ingersoll, A. P.; Thompson, A. F.

    2012-12-01

    Here, for the first time, we propose the concept of Ocean Convective Available Potential Energy (OCAPE), which is the maximum kinetic energy (KE) per unit seawater mass achievable by ocean convection. OCAPE occurs through a different mechanism from atmospheric CAPE, and involves the interplay of temperature and salinity on the equation of state of seawater. The thermobaric effect, which arises because the thermal coefficient of expansion increases with depth, is an important ingredient of OCAPE. We develop an accurate algorithm to calculate the OCAPE for a given temperature and salinity profile. We then validate our calculation of OCAPE by comparing it with the conversion of OCAPE to KE in a 2-D numerical model. We propose that OCAPE is an important energy source of ocean deep convection and contributes to deep water formation. OCAPE, like Atmospheric CAPE, can help predict deep convection and may also provide a useful constraint for modelling deep convection in ocean GCMs. We plot the global distribution of OCAPE using data from the World Ocean Atlas 2009 (WOA09) and see many important features. These include large values of OCAPE in the Labrador, Greenland, Weddell and Mediterranean Seas, which are consistent with our present observations and understanding, but also identify some new features like the OCAPE pattern in the Antarctic Circumpolar Current (ACC). We propose that the diagnosis of OCAPE can improve our understanding of global patterns of ocean convection and deep water formation as well as ocean stratification, the meridional overturning circulation and mixed layer processes. The background of this work is briefly introduced as below. Open-ocean deep convection can significantly modify water properties both at the ocean surface and throughout the water column (Gordon 1982). Open-ocean convection is also an important mechanism for Ocean Deep Water formation and the transport of heat, freshwater and nutrient (Marshall and Schott 1999). Open

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

    PubMed

    Callegari, Carlo; Ancilotto, Francesco

    2011-06-30

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

  11. Low-energy calculations for nuclear photodisintegration

    NASA Astrophysics Data System (ADS)

    Deflorian, S.; Efros, V. D.; Leidemann, W.

    2016-03-01

    In the Standard Solar Model a central role in the nucleosynthesis is played by reactions of the kind {}{Z_1}{A_1}{X_1} + {}{Z_2}{A_2}{X_2} to {}{Z_1 + {Z_2}}{A_1 + {A_2}}Y + γ , which enter the proton-proton chains. These reactions can also be studied through the inverse photodisintegration reaction. One option is to use the Lorentz Integral Transform approach, which transforms the continuum problem into a bound state-like one. A way to check the reliability of such methods is a direct calculation, for example using the Kohn Variational Principle to obtain the scattering wave function and then directly calculate the response function of the reaction.

  12. Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics.

    PubMed

    Jia, Xiangyu; Wang, Meiting; Shao, Yihan; König, Gerhard; Brooks, Bernard R; Zhang, John Z H; Mei, Ye

    2016-02-01

    In this work, the solvation free energies of 20 organic molecules from the 4th Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The sampling of phase space is carried out at a molecular mechanical level, and the associated free energy changes are estimated using the Bennett Acceptance Ratio (BAR). Then the quantum mechanical (QM) corrections are computed through the indirect Non-Boltzmann Bennett's acceptance ratio (NBB) or the thermodynamics perturbation (TP) method. We show that BAR+TP gives a minimum analytic variance for the calculated solvation free energy at the Gaussian limit and performs slightly better than NBB in practice. Furthermore, the expense of the QM calculations in TP is only half of that in NBB. We also show that defining the biasing potential as the difference of the solute-solvent interaction energy, instead of the total energy, can converge the calculated solvation free energies much faster but possibly to different values. Based on the experimental solvation free energies which have been published before, it is discovered in this study that BLYP yields better results than MP2 and some other later functionals such as B3LYP, M06-2X, and ωB97X-D. PMID:26731197

  13. A Frontier orbital energy approach to redox potentials

    NASA Astrophysics Data System (ADS)

    Conradie, Jeanet

    2015-09-01

    The prediction of the oxidation and reduction potentials of molecules is important in many research areas. A review of relationships obtained between frontier orbital energies (eV), the calculated ionization potentials (IP in eV), or adiabatic electron affinities (EA in eV) with the experimental oxidation and reduction potentials is presented, for selected series of β- diketones, rhodium-β-diketonato complexes, as well as metal-tris-β-diketonato complexes, with the metal Fe or Mn. The good linear relationships obtained for related series of complexes show that the oxidation and reduction potentials of these complexes can be predicted by their DFT-calculated energies.

  14. Ab initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

    1993-01-01

    Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

  15. 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.

  16. Calculation of energy deposition distributions for simple geometries

    NASA Technical Reports Server (NTRS)

    Watts, J. W., Jr.

    1973-01-01

    When high-energy charged particles pass through a thin detector, the ionization energy loss in that detector is subject to fluctuations or straggling which must be considered in interpreting the data. Under many conditions, which depend upon the charge and energy of the incident particle and the detector geometry, the ionization energy lost by the particle is significantly different from the energy deposited in the detector. This problem divides naturally into a calculation of the energy loss that results in excitation and low-energy secondary electrons which do not travel far from their production points, and a calculation of energy loss that results in high-energy secondary electrons which can escape from the detector. The first calculation is performed using a modification of the Vavilov energy loss distribution. A cutoff energy is introduced above which all electrons are ignored and energy transferred to low energy particles is assumed to be equivalent to the energy deposited by them. For the second calculation, the trajectory of the primary particle is considered as a source of secondary high-energy electrons. The electrons from this source are transported using Monte Carlo techniques and multiple scattering theory, and the energy deposited by them in the detector is calculated. The results of the two calculations are then combined to predict the energy deposition distribution. The results of these calculations are used to predict the charge resolution of parallel-plate pulse ionization chambers that are being designed to measure the charge spectrum of heavy nuclei in the galactic cosmic-ray flux.

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

    PubMed

    Velaga, Srinath C; Anderson, Brian J

    2014-01-16

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

  18. Investigation of Multipole Electrostatics in Hydration Free Energy Calculations

    PubMed Central

    Shi, Yue; Wu, Chuanjie; Ponder, Jay W.; Ren, Pengyu

    2010-01-01

    Hydration free energy (HFE) is generally used for evaluating molecular solubility, which is an important property for pharmaceutical and chemical engineering processes. Accurately predicting HFE is also recognized as one fundamental capability of molecular mechanics force field. Here we present a systematic investigation on HFE calculations with AMOEBA polarizable force field at various parameterization and simulation conditions. The HFEs of seven small organic molecules have been obtained alchemically using the Bennett Acceptance Ratio (BAR) method. We have compared two approaches to derive the atomic multipoles from quantum mechanical (QM) calculations: one directly from the new distributed multipole analysis (DMA) and the other involving fitting to the electrostatic potential around the molecules. Wave functions solved at the MP2 level with four basis sets (6-311G*, 6-311++G(2d,2p), cc-pVTZ, and aug-cc-pVTZ) are used to derive the atomic multipoles. HFEs from all four basis sets show a reasonable agreement with experimental data (root mean square error 0.63 kcal/mol for aug-ccpVTZ). We conclude that aug-cc-pVTZ gives the best performance when used with AMOEBA, and 6-311++G(2d,2p) is comparable but more efficient for larger systems. The results suggest that the inclusion of diffuse basis functions is important for capturing intermolecular interactions. The effect of long-range correction to van der Waals interaction on the hydration free energies is about 0.1 kcal/mol when the cutoff is 12Å, and increases linearly with the number of atoms in the solute/ligand. In addition, we also discussed the results from a hybrid approach that combines polarizable solute with fixed-charge water in the hydration free energy calculation. PMID:20925089

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

    SciTech Connect

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

    1999-08-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  1. Theoretical characterization of the potential energy surface for NH + NO

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1993-01-01

    The potential energy surface for NH + NO was characterized using complete active space self-consistent field (CASSCF) gradient calculation to determine the stationary point geometries and frequencies followed by CASSCF/internally contracted configuration interaction calculations to refine the energetics. The present results are in qualitative accord with the BAC-MP4 calculations, but there are differences as large as 8 kcal/mol in the detailed energetics.

  2. MCSCF potential energy surface for photodissociation of formaldehyde

    NASA Technical Reports Server (NTRS)

    Jaffe, R. L.; Morokuma, K.

    1976-01-01

    The ground state potential energy surface for the dissociation of formaldehyde (H2CO to H2 and CO) is calculated with the ab initio MCSCF method with an extended (4-31G) basis set. The location, barrier height, and force constants of the transition state are determined, and the normal coordinate analysis is carried out. The calculated barrier height is 4.5 eV. Based on the calculated quantities, the detailed mechanism of the photochemical dissociation is discussed.

  3. The Wind Energy Potential of Iceland

    NASA Astrophysics Data System (ADS)

    Nawri, Nikolai; Nína Petersen, Guðrún; Bjornsson, Halldór; Hahmann, Andrea N.; Jónasson, Kristján; Bay Hasager, Charlotte; Clausen, Niels-Erik

    2014-05-01

    infrastructure and the power grid, as well as due to the harsh winter climate. However, even in easily accessible regions, wind energy potential in Iceland, as measured by annual average power density, is among the highest in Western Europe. Based on these results, 14 test sites were selected for more detailed analyses using the Wind Atlas Analysis and Application Program (WAsP). These calculations show that a modest wind farm of ten medium size turbines would produce more energy throughout the year than a small hydro power plant, making wind energy a viable additional option.

  4. 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

  5. Semiclassical calculation of scars for a smooth potential

    SciTech Connect

    Provost, D.; Baranger, M. )

    1993-08-02

    Bogomolny's formula for energy-smoothed scars is applied to a nonspecific, nonscalable Hamiltonian, a two-dimensional anharmonic oscillator. The semiclassical theory reproduces well the exact quantal results over a large spatial and energy range.

  6. 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.

  7. Guidelines for the analysis of free energy calculations.

    PubMed

    Klimovich, Pavel V; Shirts, Michael R; Mobley, David L

    2015-05-01

    Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, alchemical-analysis.py, freely available on GitHub as part of the pymbar package (located at http://github.com/choderalab/pymbar), that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope this tool and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations. PMID:25808134

  8. Guidelines for the analysis of free energy calculations

    PubMed Central

    Klimovich, Pavel V.; Shirts, Michael R.; Mobley, David L.

    2015-01-01

    Free energy calculations based on molecular dynamics (MD) simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, alchemical–analysis.py, freely available on GitHub at https://github.com/choderalab/pymbar–examples, that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope these tools and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations. PMID:25808134

  9. Geothermal Energy: Tapping the Potential

    ERIC Educational Resources Information Center

    Johnson, Bill

    2008-01-01

    Ground source geothermal energy enables one to tap into the earth's stored renewable energy for heating and cooling facilities. Proper application of ground-source geothermal technology can have a dramatic impact on the efficiency and financial performance of building energy utilization (30%+). At the same time, using this alternative energy…

  10. 18 CFR 11.13 - Energy gains calculations.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...

  11. 18 CFR 11.13 - Energy gains calculations.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...

  12. 18 CFR 11.13 - Energy gains calculations.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...

  13. 18 CFR 11.13 - Energy gains calculations.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...

  14. Potential of renewable and alternative energy sources

    NASA Astrophysics Data System (ADS)

    Konovalov, V.; Pogharnitskaya, O.; Rostovshchikova, A.; Matveenko, I.

    2015-11-01

    The article deals with application potential of clean alternative renewable energy sources. By means of system analysis the forecast for consumption of electrical energy in Tomsk Oblast as well as main energy sources of existing energy system have been studied up to 2018. Engineering potential of renewable and alternative energy sources is evaluated. Besides, ranking in the order of their efficiency descending is performed. It is concluded that Tomsk Oblast has high potential of alternative and renewable energy sources, among which the most promising development perspective is implementation of gasification stations to save fuel consumed by diesel power stations as well as building wind-power plants.

  15. 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.

  16. Potential function and dissociation energy of alkali halide

    NASA Astrophysics Data System (ADS)

    Srivastava, Abhay P.; Pandey, Anjani K.; Pandey, Brijesh K.

    2016-05-01

    Dissociation energy of some alkali halides have been calculated by using different interaction potential function such as Born-Mayer, Varshani-Shukla and L5 potential model. The theoretical calculation is compared with experimental values. The Result shows that the values of dissociation energy as calculated by using different potential models have an equal amount of deviation with experimental values. The above said deviation with experimental values can be explained by consideration of rotational-vibrational coupling between the constituents of molecules in the limelight of molecular spectroscopy. Findings of present work suggest that the existing potential model need to be reviewed in view of the correction factors solely depending on the rotational, vibrational and electronic coupling between the constituents of molecules.

  17. Assessment of wind energy potential in Poland

    NASA Astrophysics Data System (ADS)

    Starosta, Katarzyna; Linkowska, Joanna; Mazur, Andrzej

    2014-05-01

    The aim of the presentation is to show the suitability of using numerical model wind speed forecasts for the wind power industry applications in Poland. In accordance with the guidelines of the European Union, the consumption of wind energy in Poland is rapidly increasing. According to the report of Energy Regulatory Office from 30 March 2013, the installed capacity of wind power in Poland was 2807MW from 765 wind power stations. Wind energy is strongly dependent on the meteorological conditions. Based on the climatological wind speed data, potential energy zones within the area of Poland have been developed (H. Lorenc). They are the first criterion for assessing the location of the wind farm. However, for exact monitoring of a given wind farm location the prognostic data from numerical model forecasts are necessary. For the practical interpretation and further post-processing, the verification of the model data is very important. Polish Institute Meteorology and Water Management - National Research Institute (IMWM-NRI) runs an operational model COSMO (Consortium for Small-scale Modelling, version 4.8) using two nested domains at horizontal resolutions of 7 km and 2.8 km. The model produces 36 hour and 78 hour forecasts from 00 UTC, for 2.8 km and 7 km domain resolutions respectively. Numerical forecasts were compared with the observation of 60 SYNOP and 3 TEMP stations in Poland, using VERSUS2 (Unified System Verification Survey 2) and R package. For every zone the set of statistical indices (ME, MAE, RMSE) was calculated. Forecast errors for aerological profiles are shown for Polish TEMP stations at Wrocław, Legionowo and Łeba. The current studies are connected with a topic of the COST ES1002 WIRE-Weather Intelligence for Renewable Energies.

  18. Ab Initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

    Patridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

    1993-01-01

    Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- 3 micro E(h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces (25-70 kcal/mol above the H-H2 asymptote) at small interatomic separations; the Boothroyd, Keogh, Martin, and Peterson (BKMP) potential energy surface is found to agree with results of the present calculations within the expected uncertainty (+/- 1 kcal/mol) of the fit. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(0)) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

  19. Exam Question Exchange: Potential Energy Surfaces.

    ERIC Educational Resources Information Center

    Alexander, John J., Ed.

    1988-01-01

    Presents three examination questions, graded in difficulty, that explore the topic of potential energy surfaces using a diagrammatic approach. Provides and discusses acceptable solutions including diagrams. (CW)

  20. Wind Energy Finance (WEF): An Online Calculator for Economic Analysis of Wind Projects

    SciTech Connect

    Not Available

    2004-02-01

    This brochure provides an overview of Wind Energy Finance (WEF), a free online cost of energy calculator developed by the National Renewable Energy Laboratory that provides quick, detailed economic evaluation of potential utility-scale wind energy projects. The brochure lists the features of the tool, the inputs and outputs that a user can expect, visuals of the screens and a Cash Flow Results table, and contact information.

  1. Sampling the potential energy surface of a DNA duplex damaged by a food carcinogen: Force field parameterization by ab initio quantum calculations and conformational searching using molecular mechanics computations

    NASA Astrophysics Data System (ADS)

    Wu, Xiangyang

    1999-07-01

    The heterocyclic amine 2-amino-3-methylimidazo (4, 5-f) quinoline (IQ) is one of a number of carcinogens found in barbecued meat and fish. It induces tumors in mammals and is probably involved in human carcinogenesis, because of great exposure to such food carcinogens. IQ is biochemically activated to a derivative which reacts with DNA to form a covalent adduct. This adduct may deform the DNA and consequently cause a mutation. which may initiate carcinogenesis. To understand this cancer initiating event, it is necessary to obtain atomic resolution structures of the damaged DNA. No such structures are available experimentally due to synthesis difficulties. Therefore, we employ extensive molecular mechanics and dynamics calculations for this purpose. The major IQ-DNA adduct in the specific DNA sequence d(5'G1G2C G3CCA3') - d(5'TGGCGCC3') with IQ modified at G3 is studied. The d(5'G1G2C G3CC3') sequence has recently been shown to be a hot-spot for mutations when IQ modification is at G3. Although this sequence is prone to -2 deletions via a ``slippage mechanism'' even when unmodified, a key question is why IQ increases the mutation frequency of the unmodified DNA by about 104 fold. Is there a structural feature imposed by IQ that is responsible? The molecular mechanics and dynamics program AMBER for nucleic acids with the latest force field was chosen for this work. This force field has been demonstrated to reproduce well the B-DNA structure. However, some parameters, the partial charges, bond lengths and angles, dihedral parameters of the modified residue, are not available in the AMBER database. We parameterized the force field using high level ab initio quantum calculations. We created 800 starting conformations which uniformly sampled in combination at 18° intervals three torsion angles that govern the IQ-DNA orientations, and energy minimized them. The most important structures are abnormal; the IQ damaged guanine is rotated out of its standard B

  2. An adaptive interpolation scheme for molecular potential energy surfaces.

    PubMed

    Kowalewski, Markus; Larsson, Elisabeth; Heryudono, Alfa

    2016-08-28

    The calculation of potential energy surfaces for quantum dynamics can be a time consuming task-especially when a high level of theory for the electronic structure calculation is required. We propose an adaptive interpolation algorithm based on polyharmonic splines combined with a partition of unity approach. The adaptive node refinement allows to greatly reduce the number of sample points by employing a local error estimate. The algorithm and its scaling behavior are evaluated for a model function in 2, 3, and 4 dimensions. The developed algorithm allows for a more rapid and reliable interpolation of a potential energy surface within a given accuracy compared to the non-adaptive version. PMID:27586901

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

    NASA Astrophysics Data System (ADS)

    Sakai, Y.; Huzinaga, S.

    1982-03-01

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

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

    SciTech Connect

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

    2010-12-15

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

  5. Semi-infinite jellium: Thermodynamic potential, chemical potential, and surface energy

    NASA Astrophysics Data System (ADS)

    Kostrobij, P. P.; Markovych, B. M.

    2015-08-01

    A general expression for the thermodynamic potential of the model of semi-infinite jellium is obtained. By using this expression, the surface energy for the infinite barrier model is calculated. The behavior of the surface energy and of the chemical potential as functions of the Wigner-Seitz radius and the influence of the Coulomb interaction between electrons on the calculated values is studied. It is shown that taking into account the Coulomb interaction between electrons leads to growth of the surface energy. The surface energy is positive in the entire area of the Wigner-Seitz radius. It is shown that taking into account the Coulomb interaction between electrons leads to a decrease of the chemical potential.

  6. Improved finite difference schemes for transonic potential calculations

    NASA Technical Reports Server (NTRS)

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

    1984-01-01

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

  7. The calculation of electrostatic potentials for periodic charge distributions

    SciTech Connect

    Johnson, E.

    1996-10-01

    A method for obtaining the Coulomb energy of a lattice of charges is presented. The method is used here to find the Madelung constant of a number of crystals. The method is simpler than the Ewald summation method. It is based on the use of a basis set of lattices. Any lattice may be represented by a linear combination of these basis lattices. {copyright} {ital 1996 American Institute of Physics.}

  8. Free energy calculations for molecular solids using GROMACS

    NASA Astrophysics Data System (ADS)

    Aragones, J. L.; Noya, E. G.; Valeriani, C.; Vega, C.

    2013-07-01

    In this work, we describe a procedure to evaluate the free energy of molecular solids with the GROMACS molecular dynamics package. The free energy is calculated using the Einstein molecule method that can be regarded as a small modification of the Einstein crystal method. Here, the position and orientation of the molecules is fixed by using an Einstein field that binds with harmonic springs at least three non-collinear atoms (or points of the molecule) to their reference positions. The validity of the Einstein field is tested by performing free-energy calculations of methanol, water (ice), and patchy colloids molecular solids. The free energies calculated with GROMACS show a very good agreement with those obtained using Monte Carlo and with previously published results.

  9. Periodic discrete energy for long-range potentials

    NASA Astrophysics Data System (ADS)

    Hardin, D. P.; Saff, E. B.; Simanek, B.

    2014-12-01

    We consider periodic energy problems in Euclidean space with a special emphasis on long-range potentials that cannot be defined through the usual infinite sum. One of our main results builds on more recent developments of Ewald summation to define the periodic energy corresponding to a large class of long-range potentials. Two particularly interesting examples are the logarithmic potential and the Riesz potential when the Riesz parameter is smaller than the dimension of the space. For these examples, we use analytic continuation methods to provide concise formulas for the periodic kernel in terms of the Epstein Hurwitz Zeta function. We apply our energy definition to deduce several properties of the minimal energy including the asymptotic order of growth and the distribution of points in energy minimizing configurations as the number of points becomes large. We conclude with some detailed calculations in the case of one dimension, which shows the utility of this approach.

  10. S-matrix calculations of energy levels of alkalilike ions

    NASA Astrophysics Data System (ADS)

    Sapirstein, Jonathan; Cheng, K. T.

    2013-05-01

    A recent S-matrix based QED calculation of energy levels of the lithium isoelectronic sequence is extended to the general case of a valence electron outside an arbitrary filled core. Formulas are presented that allow calculation of the energy levels of valence ns , np1 / 2 , np3 / 2 , nd3 / 2 , and nd5 / 2 states. Emphasis is placed on modifications of the lithiumlike formulas required because more than one core state is present, and a discussion of an unusual feature of the two-photon exchange contribution involving autoiononizing states is given. The method is illustrated with a calculation of energy levels of the sodium isoelectronic sequence, with results for 3s1 / 2 , 3p1 / 2 , and 3p3 / 2 energies tabulated for the range Z = 20 - 100 . A detailed breakdown of the calculation is given for Z = 74 . Comparison with experiment and other calculations is given, and prospects for extension of the method to ions with more complex electronic structure discussed. The work of JS was supported in part by NSF Grant No. PHY-1068065. The work of KTC was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  11. Contrastive studies of potential energy functions of some diatomic molecules

    NASA Astrophysics Data System (ADS)

    Abdallah, Hassan H.; Abdullah, Hewa Y.

    2016-03-01

    It was proposed that iron hydride, FeH, would be formed only on grains at the clouds through the reaction of the adsorbed H atoms or H2 molecules with the adsorbed Fe atoms on the grains. The importance of FeH in Astrophysics presents an additional motivation to study its energetic, spectroscopic constants and Potential Energy Curves. The structural optimization for ground state of FeH was calculated by different theoretical methods, namely, Hartree-Fock (HF), the density functional theory (DFT), B3LYP, MP2 method and QCISD(T) methods and compared with available data from the literature. The single ionized forms, cation and anion, were also obtained at the same level of calculations. Charges, dipole moment, geometrical parameters, molecular orbital energies and spectroscopic parameters were calculated and reported. In addition, the molecular ionization potential, electron affinity and dissociation energy were investigated.

  12. Performance calculation and simulation system of high energy laser weapon

    NASA Astrophysics Data System (ADS)

    Wang, Pei; Liu, Min; Su, Yu; Zhang, Ke

    2014-12-01

    High energy laser weapons are ready for some of today's most challenging military applications. Based on the analysis of the main tactical/technical index and combating process of high energy laser weapon, a performance calculation and simulation system of high energy laser weapon was established. Firstly, the index decomposition and workflow of high energy laser weapon was proposed. The entire system was composed of six parts, including classical target, platform of laser weapon, detect sensor, tracking and pointing control, laser atmosphere propagation and damage assessment module. Then, the index calculation modules were designed. Finally, anti-missile interception simulation was performed. The system can provide reference and basis for the analysis and evaluation of high energy laser weapon efficiency.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Noblesse, F.; Triantafyllou, G.

    1980-09-01

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

  15. Energy potential of modern landfills

    SciTech Connect

    Bogner, J.E.

    1990-01-01

    Methane produced by refuse decomposition in a sanitary landfill can be recovered for commercial use. Landfill methane is currently under-utilized, with commercial recovery at only a small percentage of US landfills. New federal regulations mandating control of landfill gas migration and atmospheric emissions are providing impetus to methane recovery schemes as a means of recovering costs for increased environmental control. The benefits of landfill methane recovery include utilization of an inexpensive renewable energy resource, removal of explosive gas mixtures from the subsurface, and mitigation of observed historic increases in atmospheric methane. Increased commercial interest in landfill methane recovery is dependent on the final form of Clean Air Act amendments pertaining to gaseous emissions from landfills; market shifts in natural gas prices; financial incentives for development of renewable energy resources; and support for applied research and development to develop techniques for increased control of the gas generation process in situ. This paper will discuss the controls on methane generation in landfills. In addition, it will address how landfill regulations affect landfill design and site management practices which, in turn, influence decomposition rates. Finally, future trends in landfilling, and their relationship to gas production, will be examined. 19 refs., 2 figs., 3 tabs.

  16. Calculating fusion neutron energy spectra from arbitrary reactant distributions

    NASA Astrophysics Data System (ADS)

    Eriksson, J.; Conroy, S.; Andersson Sundén, E.; Hellesen, C.

    2016-02-01

    The Directional Relativistic Spectrum Simulator (DRESS) code can perform Monte-Carlo calculations of reaction product spectra from arbitrary reactant distributions, using fully relativistic kinematics. The code is set up to calculate energy spectra from neutrons and alpha particles produced in the D(d, n)3He and T(d, n)4He fusion reactions, but any two-body reaction can be simulated by including the corresponding cross section. The code has been thoroughly tested. The kinematics calculations have been benchmarked against the kinematics module of the ROOT Data Analysis Framework. Calculated neutron energy spectra have been validated against tabulated fusion reactivities and against an exact analytical expression for the thermonuclear fusion neutron spectrum, with good agreement. The DRESS code will be used as the core of a detailed synthetic diagnostic framework for neutron measurements at the JET and MAST tokamaks.

  17. Geothermal Energy Potential in Western United States

    ERIC Educational Resources Information Center

    Pryde, Philip R.

    1977-01-01

    Reviews types of geothermal energy sources in the western states, including hot brine systems and dry steam systems. Conversion to electrical energy is a major potential use of geothermal energy, although it creates environmental disruptions such as noise, corrosion, and scaling of equipment. (AV)

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

    SciTech Connect

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

    2004-12-13

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

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

    PubMed

    Fujimoto, Kazuhiro J

    2014-12-01

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

  1. 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.

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

    DOE PAGESBeta

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

    2016-02-25

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

  3. 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.

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

    PubMed

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

    2016-02-01

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

  5. Ion beam energy spectrum calculation via dosimetry data deconvolution.

    SciTech Connect

    Harper-Slaboszewicz, Victor Jozef; Sharp, Andrew Clinton

    2010-10-01

    The energy spectrum of a H{sup +} beam generated within the HERMES III accelerator is calculated from dosimetry data to refine future experiments. Multiple layers of radiochromic film are exposed to the beam. A graphic user interface was written in MATLAB to align the film images and calculate the beam's dose depth profile. Singular value regularization is used to stabilize the unfolding and provide the H{sup +} beam's energy spectrum. The beam was found to have major contributions from 1 MeV and 8.5 MeV protons. The HERMES III accelerator is typically used as a pulsed photon source to experimentally obtain photon impulse response of systems due to high energy photons. A series of experiments were performed to explore the use of Hermes III to generate an intense pulsed proton beam. Knowing the beam energy spectrum allows for greater precision in experiment predictions and beam model verification.

  6. Calculation of exchange energies using algebraic perturbation theory

    SciTech Connect

    Burrows, B. L.; Dalgarno, A.; Cohen, M.

    2010-04-15

    An algebraic perturbation theory is presented for efficient calculations of localized states and hence of exchange energies, which are the differences between low-lying states of the valence electron of a molecule, formed by the collision of an ion Y{sup +} with an atom X. For the case of a homonuclear molecule these are the gerade and ungerade states and the exchange energy is an exponentially decreasing function of the internuclear distance. For such homonuclear systems the theory is used in conjunction with the Herring-Holstein technique to give accurate exchange energies for a range of intermolecular separations R. Since the perturbation parameter is essentially 1/R, this method is suitable for large R. In particular, exchange energies are calculated for X{sub 2}{sup +} systems, where X is H, Li, Na, K, Rb, or Cs.

  7. Trypsin-Ligand Binding Free Energy Calculation with AMOEBA

    PubMed Central

    Shi, Yue; Jiao, Dian; Schnieders, Michael J.; Ren, Pengyu

    2010-01-01

    The binding free energies of several benzamidine-like inhibitors to trypsin were examined using a polarizable potential. All the computed binding free energies are in good agreement with the experimental data. From free energy decomposition, electrostatic interaction was found to be the driving force for the binding. Structural analysis shows that the ligands form hydrogen bonds with residues and water molecules nearby in a competitive fashion. The dependence of binding free energy on molecular dipole moment and polarizability was also studied. While the binding free energy is independent on the dipole moment, it shows a negative correlation with the polarizability. PMID:19965178

  8. Determination of Multidimensional Intermolecular Potential Energy Surfaces

    NASA Astrophysics Data System (ADS)

    Cohen, Ronald Carl

    High resolution spectroscopy of the low frequency van der Waals vibrations (also referred to as Vibration -Rotation-Tunneling (VRT) spectroscopy) in weakly bound complexes provides the means to probe intermolecular forces with unprecedented detail and precision. We present an overview of the experimental information on intermolecular forces and intermolecular dynamics which has been obtained by far infrared VRT spectroscopy of 18 complexes. We then turn to a detailed examination of the Ar-H_2O complex, a simple prototype for the study of intermolecular forces. The measurement and analysis of 9 VRT bands is described. These data are first used to obtain a qualitative description of the intermolecular potential energy surface (IPS). A new simple and efficient method for calculating the eigenvalues of the multidimensional intermolecular dynamics on the IPS has been developed. This algorithm (an adaptation of the Collocation Method) was then used in a direct fit to obtain an accurate and detailed description of the intermolecular forces acting within the Ar-H_2O complex.

  9. Saint Paul Energy Park: the potential for district heating

    SciTech Connect

    Lee, C.; Kron, R.; Davis, H.

    1980-03-01

    The results of ANL's study of the energy and economic aspects of using district heating in the St. Paul Energy Park are summarized. The Energy Park is a 6 million ft/sup 2/ residential, commercial office, and light industrial complex to be built in the midway area of St. Paul, Minnesota. Space heating and cooling design loads for the park were calculated assuming that the ASHRAE's 90-75 energy-conserving construction standards would be used in constructing the park's buildings. Based in part on this assumption, ANL estimated the costs and energy use characteristics of six possible energy system options for supplying Energy Park's space heating, space cooling, and domestic hot water heating needs. The results indicate that in today's economy, a central heating and cooling plant with natural gas boilers and electrically driven centrifugal chillers with thermal storage has good potential for energy and economic savings and clearly merits further consideration.

  10. The Calculation of Accurate Metal-Ligand Bond Energies

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W.; Partridge, Harry, III; Ricca, Alessandra; Arnold, James O. (Technical Monitor)

    1997-01-01

    The optimization of the geometry and calculation of zero-point energies are carried out at the B3LYP level of theory. The bond energies are determined at this level, as well as at the CCSD(T) level using very large basis sets. The successive OH bond energies to the first row transition metal cations are reported. For most systems there has been an experimental determination of the first OH. In general, the CCSD(T) values are in good agreement with experiment. The bonding changes from mostly covalent for the early metals to mostly electrostatic for the late transition metal systems.

  11. Accurate calculation of diffraction-limited encircled and ensquared energy.

    PubMed

    Andersen, Torben B

    2015-09-01

    Mathematical properties of the encircled and ensquared energy functions for the diffraction-limited point-spread function (PSF) are presented. These include power series and a set of linear differential equations that facilitate the accurate calculation of these functions. Asymptotic expressions are derived that provide very accurate estimates for the relative amount of energy in the diffraction PSF that fall outside a square or rectangular large detector. Tables with accurate values of the encircled and ensquared energy functions are also presented. PMID:26368873

  12. Calculation of Mg(+)-ligand relative binding energies

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Bauschlicher, Charles W., Jr.

    1992-01-01

    The calculated relative binding energies of 16 organic molecules to Mg(+) are compared with experimental results where available. The geometries of the ligands and the Mg(+)-ligand complexes arc optimized at the self-consistent field level using a 6-31G* basis set. The Mg(+) binding energies are evaluated using second-order perturbation theory and basis sets of triple-sigma quality augmented with two sets of polarization functions. This level of theory is calibrated against higher levels of theory for selected systems. The computed binding energies are accurate to about 2 kcal/mol.

  13. Investigating Energy-Saving Potentials in the Cloud

    PubMed Central

    Lee, Da-Sheng

    2014-01-01

    Collecting webpage messages can serve as a sensor for investigating the energy-saving potential of buildings. Focusing on stores, a cloud sensor system is developed to collect data and determine their energy-saving potential. The owner of a store under investigation must register online, report the store address, area, and the customer ID number on the electric meter. The cloud sensor system automatically surveys the energy usage records by connecting to the power company website and calculating the energy use index (EUI) of the store. Other data includes the chain store check, company capital, location price, and the influence of weather conditions on the store; even the exposure frequency of store under investigation may impact the energy usage collected online. After collecting data from numerous stores, a multi-dimensional data array is constructed to determine energy-saving potential by identifying stores with similarity conditions. Similarity conditions refer to analyzed results that indicate that two stores have similar capital, business scale, weather conditions, and exposure frequency on web. Calculating the EUI difference or pure technical efficiency of stores, the energy-saving potential is determined. In this study, a real case study is performed. An 8-dimensional (8D) data array is constructed by surveying web data related to 67 stores. Then, this study investigated the savings potential of the 33 stores, using a site visit, and employed the cloud sensor system to determine the saving potential. The case study results show good agreement between the data obtained by the site visit and the cloud investigation, with errors within 4.17%. Among 33 the samples, eight stores have low saving potentials of less than 5%. The developed sensor on the cloud successfully identifies them as having low saving potential and avoids wasting money on the site visit. PMID:24561405

  14. Investigating energy-saving potentials in the cloud.

    PubMed

    Lee, Da-Sheng

    2014-01-01

    Collecting webpage messages can serve as a sensor for investigating the energy-saving potential of buildings. Focusing on stores, a cloud sensor system is developed to collect data and determine their energy-saving potential. The owner of a store under investigation must register online, report the store address, area, and the customer ID number on the electric meter. The cloud sensor system automatically surveys the energy usage records by connecting to the power company website and calculating the energy use index (EUI) of the store. Other data includes the chain store check, company capital, location price, and the influence of weather conditions on the store; even the exposure frequency of store under investigation may impact the energy usage collected online. After collecting data from numerous stores, a multi-dimensional data array is constructed to determine energy-saving potential by identifying stores with similarity conditions. Similarity conditions refer to analyzed results that indicate that two stores have similar capital, business scale, weather conditions, and exposure frequency on web. Calculating the EUI difference or pure technical efficiency of stores, the energy-saving potential is determined. In this study, a real case study is performed. An 8-dimensional (8D) data array is constructed by surveying web data related to 67 stores. Then, this study investigated the savings potential of the 33 stores, using a site visit, and employed the cloud sensor system to determine the saving potential. The case study results show good agreement between the data obtained by the site visit and the cloud investigation, with errors within 4.17%. Among 33 the samples, eight stores have low saving potentials of less than 5%. The developed sensor on the cloud successfully identifies them as having low saving potential and avoids wasting money on the site visit. PMID:24561405

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

    PubMed

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

    2008-07-01

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

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

    SciTech Connect

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

    1987-01-01

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

  17. Pseudospectral Gaussian quantum dynamics: Efficient sampling of potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Heaps, Charles W.; Mazziotti, David A.

    2016-04-01

    Trajectory-based Gaussian basis sets have been tremendously successful in describing high-dimensional quantum molecular dynamics. In this paper, we introduce a pseudospectral Gaussian-based method that achieves accurate quantum dynamics using efficient, real-space sampling of the time-dependent basis set. As in other Gaussian basis methods, we begin with a basis set expansion using time-dependent Gaussian basis functions guided by classical mechanics. Unlike other Gaussian methods but characteristic of the pseudospectral and collocation methods, the basis set is tested with N Dirac delta functions, where N is the number of basis functions, rather than using the basis function as test functions. As a result, the integration for matrix elements is reduced to function evaluation. Pseudospectral Gaussian dynamics only requires O ( N ) potential energy calculations, in contrast to O ( N 2 ) evaluations in a variational calculation. The classical trajectories allow small basis sets to sample high-dimensional potentials. Applications are made to diatomic oscillations in a Morse potential and a generalized version of the Henon-Heiles potential in two, four, and six dimensions. Comparisons are drawn to full analytical evaluation of potential energy integrals (variational) and the bra-ket averaged Taylor (BAT) expansion, an O ( N ) approximation used in Gaussian-based dynamics. In all cases, the pseudospectral Gaussian method is competitive with full variational calculations that require a global, analytical, and integrable potential energy surface. Additionally, the BAT breaks down when quantum mechanical coherence is particularly strong (i.e., barrier reflection in the Morse oscillator). The ability to obtain variational accuracy using only the potential energy at discrete points makes the pseudospectral Gaussian method a promising avenue for on-the-fly dynamics, where electronic structure calculations become computationally significant.

  18. Pseudospectral Gaussian quantum dynamics: Efficient sampling of potential energy surfaces.

    PubMed

    Heaps, Charles W; Mazziotti, David A

    2016-04-28

    Trajectory-based Gaussian basis sets have been tremendously successful in describing high-dimensional quantum molecular dynamics. In this paper, we introduce a pseudospectral Gaussian-based method that achieves accurate quantum dynamics using efficient, real-space sampling of the time-dependent basis set. As in other Gaussian basis methods, we begin with a basis set expansion using time-dependent Gaussian basis functions guided by classical mechanics. Unlike other Gaussian methods but characteristic of the pseudospectral and collocation methods, the basis set is tested with N Dirac delta functions, where N is the number of basis functions, rather than using the basis function as test functions. As a result, the integration for matrix elements is reduced to function evaluation. Pseudospectral Gaussian dynamics only requires O(N) potential energy calculations, in contrast to O(N(2)) evaluations in a variational calculation. The classical trajectories allow small basis sets to sample high-dimensional potentials. Applications are made to diatomic oscillations in a Morse potential and a generalized version of the Henon-Heiles potential in two, four, and six dimensions. Comparisons are drawn to full analytical evaluation of potential energy integrals (variational) and the bra-ket averaged Taylor (BAT) expansion, an O(N) approximation used in Gaussian-based dynamics. In all cases, the pseudospectral Gaussian method is competitive with full variational calculations that require a global, analytical, and integrable potential energy surface. Additionally, the BAT breaks down when quantum mechanical coherence is particularly strong (i.e., barrier reflection in the Morse oscillator). The ability to obtain variational accuracy using only the potential energy at discrete points makes the pseudospectral Gaussian method a promising avenue for on-the-fly dynamics, where electronic structure calculations become computationally significant. PMID:27131532

  19. Three dimensional calculation of flux of low energy atmospheric neutrinos

    NASA Technical Reports Server (NTRS)

    Lee, H.; Bludman, S. A.

    1985-01-01

    Results of three-dimensional Monte Carlo calculation of low energy flux of atmospheric neutrinos are presented and compared with earlier one-dimensional calculations 1,2 valid at higher neutrino energies. These low energy neutrinos are the atmospheric background in searching for neutrinos from astrophysical sources. Primary cosmic rays produce the neutrino flux peaking at near E sub=40 MeV and neutrino intensity peaking near E sub v=100 MeV. Because such neutrinos typically deviate by 20 approximately 30 from the primary cosmic ray direction, three-dimensional effects are important for the search of atmospheric neutrinos. Nevertheless, the background of these atmospheric neutrinos is negligible for the detection of solar and supernova neutrinos.

  20. Variational calculation of highly excited rovibrational energy levels of H2O2.

    PubMed

    Polyansky, Oleg L; Kozin, Igor N; Ovsyannikov, Roman I; Małyszek, Paweł; Koput, Jacek; Tennyson, Jonathan; Yurchenko, Sergei N

    2013-08-15

    Results are presented for highly accurate ab initio variational calculation of the rotation-vibration energy levels of H2O2 in its electronic ground state. These results use a recently computed potential energy surface and the variational nuclear-motion programs WARV4, which uses an exact kinetic energy operator, and TROVE, which uses a numerical expansion for the kinetic energy. The TROVE calculations are performed for levels with high values of rotational excitation, J up to 35. The purely ab initio calculations of the rovibrational energy levels reproduce the observed levels with a standard deviation of about 1 cm(-1), similar to that of the J = 0 calculation, because the discrepancy between theory and experiment for rotational energies within a given vibrational state is substantially determined by the error in the vibrational band origin. Minor adjustments are made to the ab initio equilibrium geometry and to the height of the torsional barrier. Using these and correcting the band origins using the error in J = 0 states lowers the standard deviation of the observed-calculated energies to only 0.002 cm(-1) for levels up to J = 10 and 0.02 cm(-1) for all experimentally known energy levels, which extend up to J = 35. PMID:23611762

  1. Wind energy in China: Estimating the potential

    NASA Astrophysics Data System (ADS)

    Yuan, Jiahai

    2016-07-01

    Persistent and significant curtailment has cast concern over the prospects of wind power in China. A comprehensive assessment of the production of energy from wind has identified grid-integrated wind generation potential at 11.9–14% of China's projected energy demand by 2030.

  2. Potential of energy production from conserved forages

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Forages have a potential role in meeting the demand for energy. Perennial forages are attractive for various reasons. One, both the monetary and energy cost of planting is spread over many years. Two, we already have the equipment for harvesting, storing and transporting this source of biomass. Thre...

  3. Composite electron propagator methods for calculating ionization energies

    NASA Astrophysics Data System (ADS)

    Díaz-Tinoco, Manuel; Dolgounitcheva, O.; Zakrzewski, V. G.; Ortiz, J. V.

    2016-06-01

    Accurate ionization energies of molecules may be determined efficiently with composite electron-propagator (CEP) techniques. These methods estimate the results of a calculation with an advanced correlation method and a large basis set by performing a series of more tractable calculations in which large basis sets are used with simpler approximations and small basis sets are paired with more demanding correlation techniques. The performance of several CEP methods, in which diagonal, second-order electron propagator results with large basis sets are combined with higher-order results obtained with smaller basis sets, has been tested for the ionization energies of closed-shell molecules from the G2 set. Useful compromises of accuracy and computational efficiency employ complete-basis-set extrapolation for second-order results and small basis sets in third-order, partial third-order, renormalized partial-third order, or outer valence Green's function calculations. Analysis of results for vertical as well as adiabatic ionization energies leads to specific recommendations on the best use of regular and composite methods. Results for 22 organic molecules of interest in the design of photovoltaic devices, benzo[a]pyrene, Mg-octaethylporphyrin, and C60 illustrate the capabilities of CEP methods for calculations on large molecules.

  4. Composite electron propagator methods for calculating ionization energies.

    PubMed

    Díaz-Tinoco, Manuel; Dolgounitcheva, O; Zakrzewski, V G; Ortiz, J V

    2016-06-14

    Accurate ionization energies of molecules may be determined efficiently with composite electron-propagator (CEP) techniques. These methods estimate the results of a calculation with an advanced correlation method and a large basis set by performing a series of more tractable calculations in which large basis sets are used with simpler approximations and small basis sets are paired with more demanding correlation techniques. The performance of several CEP methods, in which diagonal, second-order electron propagator results with large basis sets are combined with higher-order results obtained with smaller basis sets, has been tested for the ionization energies of closed-shell molecules from the G2 set. Useful compromises of accuracy and computational efficiency employ complete-basis-set extrapolation for second-order results and small basis sets in third-order, partial third-order, renormalized partial-third order, or outer valence Green's function calculations. Analysis of results for vertical as well as adiabatic ionization energies leads to specific recommendations on the best use of regular and composite methods. Results for 22 organic molecules of interest in the design of photovoltaic devices, benzo[a]pyrene, Mg-octaethylporphyrin, and C60 illustrate the capabilities of CEP methods for calculations on large molecules. PMID:27305999

  5. Three-dimensional potential energy surface of Ar–CO

    SciTech Connect

    Sumiyoshi, Yoshihiro; Endo, Yasuki

    2015-01-14

    A three-dimensional intermolecular potential energy surface of the Ar–CO complex has been determined by fitting most of the previously reported spectroscopic data, where observed transition frequencies by microwave, millimeter-wave, submillimeter-wave, and infrared spectroscopy were reproduced simultaneously within their experimental accuracies. A free rotor model Hamiltonian considering all the freedom of motions for an atom-diatom system was applied to calculate vibration-rotation energies. A three-dimensional potential energy surface obtained by ab initio calculations at the CCSD(T)-F12b/aug-cc-pV5Z level of theory was parameterized by a model function consisting of 46 parameters. They were used as initial values for the least-squares analysis of the experimental data. A total of 20 parameters were optimized to reproduce all the spectroscopic data.

  6. Economic Energy Savings Potential in Federal Buildings

    SciTech Connect

    Brown, Daryl R.; Dirks, James A.; Hunt, Diane M.

    2000-09-04

    The primary objective of this study was to estimate the current life-cycle cost-effective (i.e., economic) energy savings potential in Federal buildings and the corresponding capital investment required to achieve these savings, with Federal financing. Estimates were developed for major categories of energy efficiency measures such as building envelope, heating system, cooling system, and lighting. The analysis was based on conditions (building stock and characteristics, retrofit technologies, interest rates, energy prices, etc.) existing in the late 1990s. The potential impact of changes to any of these factors in the future was not considered.

  7. Global calculations of microscopic energies and nuclear deformations: Isospin dependence of the spin-orbit coupling

    NASA Astrophysics Data System (ADS)

    Wu, Zhe-Ying; Qi, Chong; Wyss, Ramon; Liu, Hong-Liang

    2015-08-01

    Background: The deviation between different model calculations that may occur when one goes toward regions where the masses are unknown is getting increased attention. This is related to the uncertainties of the different models which may have not been fully understood. Purpose: To explore in detail the effect of the isospin dependence of the spin-orbital force in the Woods-Saxon potential on global binding energy and deformation calculations. Method: The microscopic energies and nuclear deformations of about 1850 even-even nuclei are calculated systematically within the macroscopic-microscopic framework using three Woods-Saxon parametrizations, with different isospin dependencies, which were constructed mainly for nuclear spectroscopy calculations. Calculations are performed in the deformation space (β2,γ ,β4) . Both the monopole and doubly stretched quadrupole interactions are considered for the pairing channel. Results: The ground-state deformations obtained by the three calculations are quite similar to each other. Large differences are seen mainly in neutron-rich nuclei and in superheavy nuclei. Systematic calculations on the shape-coexisting second minima are also presented. As for the microscopic energies of the ground states, the results are also very close to each other. Only in a few cases the difference is larger than 2 MeV. The total binding energy is estimated by adding the macroscopic energy provided by the usual liquid drop model with its parameters fitted through the least square root and minimax criteria. Calculations are also compared with the results of other macroscopic-microscopic mass models. Conclusions: All the three calculations give similar values for the deformations, microscopic energies, and binding energies of most nuclei. One may expect to have a better understanding of the isospin dependence of the spin-orbital force with more data on proton- and neutron-rich nuclei.

  8. Binding Energy Calculations for Novel Ternary Ionic Lattices

    NASA Astrophysics Data System (ADS)

    Rodríguez-Mijangos, Ricardo; Vazquez-Polo, Gustavo

    2002-03-01

    Theoretical calculations for the binding energy between metalic ions and negative ions on a novel ternary ionic lattice is carried out for several solid solutions prepared with different concentrations and characterized recently (1). The ternary lattices that reach a good miscibility are: KCl(x)KBr(y)RbCl(z) in three different concentrations: (x=y=z=0.33), (x=0.5, y=0.25, z=0.25) and (x=0.33, y=0.07, z=0.60). The binding energy for these novel structures is calculated from the lattice constants obtained by X ray diffractometry analysis performed on the samples and the Vegard law (2). For the repulsive force exponent m, an average of the m values was considered. The energy values obtained by the Born´expression are compared with corresponding energy values from the lattice with more complex expressions, such as the Born Mayer, Born-Van der Walls. There is a good aggreement between all these calculations. (1)R. R. Mijangos, A. Cordero-Borboa, E. Alvarez, M. Cervantes, Physics Letters A 282 (2001) 195-200. (2) G. Vazquez-Polo, R. R. Mijangos et al. Revista Mexicana de Fisica, 47, Diciembre 2001. In Press.

  9. Ultrasonic energy in liposome production: process modelling and size calculation.

    PubMed

    Barba, A A; Bochicchio, S; Lamberti, G; Dalmoro, A

    2014-04-21

    The use of liposomes in several fields of biotechnology, as well as in pharmaceutical and food sciences is continuously increasing. Liposomes can be used as carriers for drugs and other active molecules. Among other characteristics, one of the main features relevant to their target applications is the liposome size. The size of liposomes, which is determined during the production process, decreases due to the addition of energy. The energy is used to break the lipid bilayer into smaller pieces, then these pieces close themselves in spherical structures. In this work, the mechanisms of rupture of the lipid bilayer and the formation of spheres were modelled, accounting for how the energy, supplied by ultrasonic radiation, is stored within the layers, as the elastic energy due to the curvature and as the tension energy due to the edge, and to account for the kinetics of the bending phenomenon. An algorithm to solve the model equations was designed and the relative calculation code was written. A dedicated preparation protocol, which involves active periods during which the energy is supplied and passive periods during which the energy supply is set to zero, was defined and applied. The model predictions compare well with the experimental results, by using the energy supply rate and the time constant as fitting parameters. Working with liposomes of different sizes as the starting point of the experiments, the key parameter is the ratio between the energy supply rate and the initial surface area. PMID:24647821

  10. Calculation of the vacuum condensates of the trace of the energy-momentum tensor

    SciTech Connect

    Ksenzov, V. G.

    2008-04-15

    It is shown that a modification of the effective potential proposed by A.A. Migdal and Shifman makes it possible to calculate the vacuum condensates of the trace of the energy-momentum tensor in massless theories in various spacetime dimensions.

  11. 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.

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

    SciTech Connect

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

    2006-04-15

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

  13. Self-consistent calculations of alpha-decay energies

    SciTech Connect

    Tolokonnikov, S. V.; Lutostansky, Yu. S.; Saperstein, E. E.

    2013-06-15

    On the basis of the self-consistent theory of finite Fermi systems, the energies of alphadecay chains were calculated for several new superheavy nuclei discovered recently in experiments of the Dubna-Livermore Collaboration headed by Yu.Ts. Oganessian. The approach in question is implemented on the basis of the generalized method of the density functional proposed by Fayans and his coauthors. The version used here relies on the functional DF3-a proposed recently for describing a wide array of nuclear data, including data on superheavy nuclei. A detailed comparison of the results obtained on this basis with the predictions of different approaches, including the self-consistent Skyrme-Hartree-Fock method, the micro-macro method in the version developed by Sobiczewski and his coauthors, and the phenomenological method of Liran and his coauthors, is performed. The resulting alpha-decay energies are used to calculate respective lifetimes with the aid of the phenomenological Parkhomenko-Sobiczewski formula.

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

    NASA Astrophysics Data System (ADS)

    Ye, Lin-Hui

    2015-09-01

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

  15. Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm

    NASA Technical Reports Server (NTRS)

    Darve, Eric; Wilson, Micahel A.; Pohorille, Andrew

    2000-01-01

    One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous

  16. Energy savings potential in air conditioners and chiller systems

    SciTech Connect

    Kaya, Durmus; Alidrisi, Hisham

    2014-01-22

    In the current paper we quantified and evaluated the energy saving potential in air conditioners and chiller systems. Here, we also showed how to reduce the cost of air conditioners and chiller systems in existing facilities on the basis of payback periods. Among the measures investigated were: (1) installing higher efficiency air conditioners, (2) installing higher efficiency chillers, (3) duty cycling air conditioning units, and (4) utilizing existing economizers on air conditioning units. For each method, examples were provided from Arizona, USA. In these examples, the amount of saved energy, the financial evaluation of this energy, and the investment cost and pay back periods were calculated.

  17. Energy savings potential in air conditioners and chiller systems

    DOE PAGESBeta

    Kaya, Durmus; Alidrisi, Hisham

    2014-01-22

    In the current paper we quantified and evaluated the energy saving potential in air conditioners and chiller systems. Here, we also showed how to reduce the cost of air conditioners and chiller systems in existing facilities on the basis of payback periods. Among the measures investigated were: (1) installing higher efficiency air conditioners, (2) installing higher efficiency chillers, (3) duty cycling air conditioning units, and (4) utilizing existing economizers on air conditioning units. For each method, examples were provided from Arizona, USA. In these examples, the amount of saved energy, the financial evaluation of this energy, and the investment costmore » and pay back periods were calculated.« less

  18. Free energy calculations for a flexible water model.

    PubMed

    Habershon, Scott; Manolopoulos, David E

    2011-11-28

    In this work, we consider the problem of calculating the classical free energies of liquids and solids for molecular models with intramolecular flexibility. We show that thermodynamic integration from the fully-interacting solid of interest to a Debye crystal reference state, with anisotropic harmonic interactions derived from the Hessian of the original crystal, provides a straightforward route to calculating the Gibbs free energy of the solid. To calculate the molecular liquid free energy, it is essential to correctly account for contributions from both intermolecular and intramolecular motion; we employ thermodynamic integration to a Lennard-Jones reference fluid, coupled with direct evaluation of the molecular ro-vibrational partition function. These approaches are used to study the low-pressure classical phase diagram of the flexible q-TIP4P/F water model. We find that, while the experimental ice-I/liquid and ice-III/liquid coexistence lines are described reasonably well by this model, the ice-II phase is predicted to be metastable. In light of this finding, we go on to examine how the coupling between intramolecular flexibility and intermolecular interactions influences the computed phase diagram by comparing our results with those of the underlying rigid-body water model. PMID:21887423

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

    SciTech Connect

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

    2011-11-01

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

  20. Free energy calculation of permeation through aquaporin-5

    NASA Astrophysics Data System (ADS)

    Bastien, David

    The work of this paper continues upon the large area of research being done on aquaporins (AQPs). AQPs are proteins that take on the role of facilitating the transfer of substances, mainly water, across cell membranes. There are many different types of AQPs, with each of these highly selective proteins conducting only certain solutes, along with unique permeability rates. The permeation characteristics of aquaporins rely mostly on the residue hydrophobicity and steric restraints of the aromatic arginine (ar/R) region of the protein channel. The purpose of this paper is to analyze the structures of aquaporin-5 (AQP5) and aquaglycerolporin (Glpf), including a radius profile of the respective protein channels, and to compare them to permeation events using steered molecular dynamics (SMD) pulling simulations. Two in silico experiments are performed in order to achieve the free Energy landscape of a single water molecule permeating through the four channels of both Aqp5 and GlpF. The equilibrium free energy curves are calculated from the non-equilibrium, irreversible work measurements using the fluctuation-dissipation theorem (FDT) of Brownian dynamicis (BD). The free energy profiles are then compared and related to the structural profiles of AQP5 and GlpF. The change in free energy across the ar/R region in AQP5 is found to be reasonably larger than that of GlpF. The free energy profiles of AQP5 and GlpF agree with the diameter profile of the channels respectively. Furthermore, free energy calculations are computed for the permeation of Na+ and Cl- ions through the central pore of Aqp5, which provide some insight into the structural mechanisms of AQP5. The free energy barrier for ion transport through the central pore is found to be very large, peaking at around 11 Kcal/mol for chloride and 20 Kcal/mol for sodium.

  1. Communication: Fitting potential energy surfaces with fundamental invariant neural network.

    PubMed

    Shao, Kejie; Chen, Jun; Zhao, Zhiqiang; Zhang, Dong H

    2016-08-21

    A more flexible neural network (NN) method using the fundamental invariants (FIs) as the input vector is proposed in the construction of potential energy surfaces for molecular systems involving identical atoms. Mathematically, FIs finitely generate the permutation invariant polynomial (PIP) ring. In combination with NN, fundamental invariant neural network (FI-NN) can approximate any function to arbitrary accuracy. Because FI-NN minimizes the size of input permutation invariant polynomials, it can efficiently reduce the evaluation time of potential energy, in particular for polyatomic systems. In this work, we provide the FIs for all possible molecular systems up to five atoms. Potential energy surfaces for OH3 and CH4 were constructed with FI-NN, with the accuracy confirmed by full-dimensional quantum dynamic scattering and bound state calculations. PMID:27544080

  2. Calculation of quasiparticle energy spectrum of silicon using the correlated Hartree-Fock method

    NASA Astrophysics Data System (ADS)

    Ishihara, Takamitsu; Yamagami, Hiroshi; Matsuzawa, Kazuya; Yasuhara, Hiroshi

    1999-06-01

    We present quasiparticle energy spectrum calculations of silicon using the correlated Hartree-Fock method proposed by Yasuhara and Takada [Phys. Rev. B 43, 7200 (1991)], in which the information on the effective mass of an electron liquid is included in the form of a nonlocal spin-parallel potential in addition to a local potential. The calculated band gaps of silicon are much improved, compared with the local density approximation values. The minimum indirect band gap is evaluated to be 1.37 eV.

  3. Geothermal energy and its potential. [Utah

    SciTech Connect

    Berge, C.W.

    1980-06-01

    A brief review of geothermal energy and its potential as a future energy source is presented. The type of geothermal systems and their geologic occurrence is discussed, and the Phillips Petroleum Company's exploration and drilling programs in the Roosevelt Hot Springs area in parts of Iron, Beaver, and Millard Counties, Utah are detailed. A section on the rock behavior and mechanical properties of rocks in the Roosevelt Hot Springs area is included. (JMT)

  4. Nuclear binding energy and symmetry energy of nuclear matter with modern nucleon-nucleon potentials

    SciTech Connect

    Hassaneen, Kh.S.A.; Abo-Elsebaa, H.M.; Sultan, E.A.; Mansour, H.M.M.

    2011-03-15

    Research Highlights: > The nuclear matter is studied within the Brueckner-Hartree-Fock (BHF) approach employing the most recent accurate nucleon-nucleon potentials. > The results come out by approximating the single particle self-consistent potential with a parabolic form. > We discuss the current status of the Coester line, i.e., density and energy of the various saturation points being strongly linearly correlated. > The nuclear symmetry energy is calculated as the difference between the binding energy of pure neutron matter and that of symmetric nuclear matter. - Abstract: The binding energy of nuclear matter at zero temperature in the Brueckner-Hartree-Fock approximation with modern nucleon-nucleon potentials is studied. Both the standard and continuous choices of single particle energies are used. These modern nucleon-nucleon potentials fit the deuteron properties and are phase shifts equivalent. Comparison with other calculations is made. In addition we present results for the symmetry energy obtained with different potentials, which is of great importance in astrophysical calculation.

  5. Variational Approach to Enhanced Sampling and Free Energy Calculations

    NASA Astrophysics Data System (ADS)

    Valsson, Omar; Parrinello, Michele

    2014-08-01

    The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo simulations, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small number of collective variables. However constructing such a bias is not simple. Here we introduce a functional of the bias potential and an associated variational principle. The bias that minimizes the functional relates in a simple way to the free energy surface. This variational principle can be turned into a practical, efficient, and flexible sampling method. A number of numerical examples are presented which include the determination of a three-dimensional free energy surface. We argue that, beside being numerically advantageous, our variational approach provides a convenient and novel standpoint for looking at the sampling problem.

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

    NASA Astrophysics Data System (ADS)

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

    2001-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  8. Biomass resource potential using energy crops

    SciTech Connect

    Wright, L.L.; Cushman, J.H.; Martin, S.A.

    1993-09-01

    Biomass energy crops can provide a significant and environmentally beneficial source of renewable energy feedstocks for the future. They can revitalize the agricultural sector of the US economy by providing profitable uses for marginal cropland. Energy crops include fast-growing trees, perennial grasses, and annual grasses, all capable of collecting solar energy and storing it as cellulosic compounds for several months to several years. Once solar energy is thus captured, it can be converted by means of currently available technologies to a wide variety of energy products such as electricity, heat, liquid transportation fuels, and gases. Experimental results from field trials have generated optimism that selected and improved energy crops, established on cropland with moderate limitations for crop production, have the potential for producing high yields. Both trees and grasses, under very good growing conditions, have produced average annual yields of 20 to 40 dry Mg ha{sup {minus}1} year{sup {minus}1}. Sorghum has shown especially high yields in the Midwest. Hybrids between sugar cane and its wild relatives, called energy cane, have yielded as much as 50 dry Mg ha{sup {minus}1} year{sup {minus}1} in Florida. These experimental results demonstrate that some species have the genetic potential for very rapid growth rates. New wood energy crop systems developed by the Department of Energy`s Biofuels Feedstock Development Program offer, at a minimum, a 100% increase in biomass production rates over the 2 to 4 Mg ha{sup {minus}1} year{sup {minus}1} of dry leafless woody biomass produced by most natural forest systems. Experimental data indicate that short rotation wood crops established on cropland with moderate limitations are capable of producing biomass yields of 8--20 dry Mg ha{sup {minus}1} year{sup {minus}1} with a present average about 11 dry Mg ha{sup {minus}1} year{sup {minus}1} on typical cropland sites.

  9. Separable representation of energy-dependent optical potentials

    NASA Astrophysics Data System (ADS)

    Hlophe, L.; Elster, Ch.

    2016-03-01

    Background: One important ingredient for many applications of nuclear physics to astrophysics, nuclear energy, and stockpile stewardship are cross sections for reactions of neutrons with rare isotopes. Since direct measurements are often not feasible, indirect methods, e.g., (d ,p ) reactions, should be used. Those (d ,p ) reactions may be viewed as three-body reactions and described with Faddeev techniques. Purpose: Faddeev equations in momentum space have a long tradition of utilizing separable interactions in order to arrive at sets of coupled integral equations in one variable. Optical potentials representing the effective interactions in the neutron (proton) nucleus subsystem are usually non-Hermitian as well as energy dependent. Potential matrix elements as well as transition matrix elements calculated with them must fulfill the reciprocity theorem. The purpose of this paper is to introduce a separable, energy-dependent representation of complex, energy-dependent optical potentials that fulfill reciprocity exactly. Methods: Momentum space Lippmann-Schwinger integral equations are solved with standard techniques to obtain the form factors for the separable representation. Results: Starting from a separable, energy-independent representation of global optical potentials based on a generalization of the Ernst-Shakin-Thaler (EST) scheme, a further generalization is needed to take into account the energy dependence. Applications to n +48Ca ,n +208Pb , and p +208Pb are investigated for energies from 0 to 50 MeV with special emphasis on fulfilling reciprocity. Conclusions: We find that the energy-dependent separable representation of complex, energy-dependent phenomenological optical potentials fulfills reciprocity exactly. In addition, taking into account the explicit energy dependence slightly improves the description of the S matrix elements.

  10. Potential reduction of DSN uplink energy cost

    NASA Technical Reports Server (NTRS)

    Dolinsky, S.; Degroot, N. F.

    1982-01-01

    DSN Earth stations typically transmit more power than that required to meet minimum specifications for uplink performance. Energy and cost savings that could result from matching the uplink power to the amount required for specified performance are studied. The Galileo mission was selected as a case study. Although substantial reduction in transmitted energy is possible, potential savings in source energy (oil or electricity) savings are much less. This is because of the rising inefficiency in power conversion and radio frequency power generation that accompanies reduced power output.

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

    NASA Astrophysics Data System (ADS)

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

    2013-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1990-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Jou, W.-H.

    1982-01-01

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

  14. Free Energies of Redox Half-Reactions from First-Principles Calculations.

    PubMed

    Tazhigulov, Ruslan N; Bravaya, Ksenia B

    2016-07-01

    Quantitative prediction of the energetics of redox half-reactions is still a challenge for modern computational chemistry. Here, we propose a simple scheme for reliable calculations of vertical ionization and attachment energies, as well as of redox potentials of solvated molecules. The approach exploits linear response approximation in the context of explicit solvent simulations with spherical boundary conditions. It is shown that both vertical ionization energies and vertical electron affinities, and, consequently redox potentials, exhibit linear dependence on the inverse radius of the solvation sphere. The explanation of the linear dependence is provided, and an extrapolation scheme is suggested. The proposed approach accounts for the specific short-range interactions within hybrid DFT and effective fragment potential approach as well as for the asymptotic system-size effects. The computed vertical ionization energies and redox potentials are in excellent agreement with the experimental values. PMID:27295124

  15. 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...

  16. 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...

  17. 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...

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

    DOE PAGESBeta

    Zhou, Fei; Aberg, Daniel

    2016-02-16

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

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

    PubMed

    Kuś, Tomasz; Krylov, Anna I

    2011-08-28

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

  20. Variational calculations of the HT{sup +} rovibrational energies

    SciTech Connect

    Bekbaev, A. K.; Korobov, V. I.; Dineykhan, M.

    2011-04-15

    In this Brief Report, we use the exponential explicitly correlated variational basis set of the type exp(-{alpha}{sub n}R-{beta}{sub n}r{sub 1}-{gamma}{sub n}r{sub 2}) to calculate systematically the nonrelativistic bound-state energies for the hydrogen molecular ion HT{sup +}. We perform calculations for the states of the total orbital angular momentum L=0 and 1 with the complete set of vibrational quantum numbers v= 0-23, as well as for the states of L= 2-5 and v= 0-5. The E1 dipole transition moments, which are of importance for the planning of spectroscopic laser experiments, have been obtained as well.

  1. Prediction of Protein Solubility from Calculation of Transfer Free Energy

    PubMed Central

    Tjong, Harianto; Zhou, Huan-Xiang

    2008-01-01

    Solubility plays a major role in protein purification, and has serious implications in many diseases. We studied the effects of pH and mutations on protein solubility by calculating the transfer free energy from the condensed phase to the solution phase. The condensed phase was modeled as an implicit solvent, with a dielectric constant lower than that of water. To account for the effects of pH, the protonation states of titratable side chains were sampled by running constant-pH molecular dynamics simulations. Conformations were then selected for calculations of the electrostatic solvation energy: once for the condensed phase, and once for the solution phase. The average transfer free energy from the condensed phase to the solution phase was found to predict reasonably well the variations in solubility of ribonuclease Sa and insulin with pH. This treatment of electrostatic contributions combined with a similar approach for nonelectrostatic contributions led to a quantitative rationalization of the effects of point mutations on the solubility of ribonuclease Sa. This study provides valuable insights into the physical basis of protein solubility. PMID:18515380

  2. SCALE Continuous-Energy Eigenvalue Sensitivity Coefficient Calculations

    DOE PAGESBeta

    Perfetti, Christopher M.; Rearden, Bradley T.; Martin, William R.

    2016-02-25

    Sensitivity coefficients describe the fractional change in a system response that is induced by changes to system parameters and nuclear data. The Tools for Sensitivity and UNcertainty Analysis Methodology Implementation (TSUNAMI) code within the SCALE code system makes use of eigenvalue sensitivity coefficients for an extensive number of criticality safety applications, including quantifying the data-induced uncertainty in the eigenvalue of critical systems, assessing the neutronic similarity between different critical systems, and guiding nuclear data adjustment studies. The need to model geometrically complex systems with improved fidelity and the desire to extend TSUNAMI analysis to advanced applications has motivated the developmentmore » of a methodology for calculating sensitivity coefficients in continuous-energy (CE) Monte Carlo applications. The Contributon-Linked eigenvalue sensitivity/Uncertainty estimation via Tracklength importance CHaracterization (CLUTCH) and Iterated Fission Probability (IFP) eigenvalue sensitivity methods were recently implemented in the CE-KENO framework of the SCALE code system to enable TSUNAMI-3D to perform eigenvalue sensitivity calculations using continuous-energy Monte Carlo methods. This work provides a detailed description of the theory behind the CLUTCH method and describes in detail its implementation. This work explores the improvements in eigenvalue sensitivity coefficient accuracy that can be gained through the use of continuous-energy sensitivity methods and also compares several sensitivity methods in terms of computational efficiency and memory requirements.« less

  3. Exploiting the Properties of Aquaporin to Calculate Free Energy

    NASA Astrophysics Data System (ADS)

    Espejel, Hugo; Chen, Liao

    2010-03-01

    Aquaporins' (AQPs) main purpose is to facilitate the transfer of water molecules through a molecular membrane. We can calculate the free energy of the AQP system when water permeates through it. This is performed using the Visual Molecular Dynamics (VMD) and the Nanoscale Molecular Dynamics (NAMD) programs. In our first set of experiments, AQP is submerged in a body of water, in which case a water molecule near AQP is pulled through the protein. The data is then used to calculate the free energy using two different equations: the Jarzynski equality and the fluctuation-dissipation theorem. The values from both equations are then compared to examine their accuracy. The second set of experiments has the same set up, but now AQP is embedded in a lipid bilayer. We found that both equations give values that are much smaller than kT. This verifies that AQP is a channel for water molecules because the pulling of water gives constant values of free energy. We also found that the water molecules' negative poles were all pointing towards the center of the AQP channel. This means that the process of proton transport in AQP is overwhelmingly difficult.

  4. AlaScan: A Graphical User Interface for Alanine Scanning Free-Energy Calculations.

    PubMed

    Ramadoss, Vijayaraj; Dehez, François; Chipot, Christophe

    2016-06-27

    Computation of the free-energy changes that underlie molecular recognition and association has gained significant importance due to its considerable potential in drug discovery. The massive increase of computational power in recent years substantiates the application of more accurate theoretical methods for the calculation of binding free energies. The impact of such advances is the application of parent approaches, like computational alanine scanning, to investigate in silico the effect of amino-acid replacement in protein-ligand and protein-protein complexes, or probe the thermostability of individual proteins. Because human effort represents a significant cost that precludes the routine use of this form of free-energy calculations, minimizing manual intervention constitutes a stringent prerequisite for any such systematic computation. With this objective in mind, we propose a new plug-in, referred to as AlaScan, developed within the popular visualization program VMD to automate the major steps in alanine-scanning calculations, employing free-energy perturbation as implemented in the widely used molecular dynamics code NAMD. The AlaScan plug-in can be utilized upstream, to prepare input files for selected alanine mutations. It can also be utilized downstream to perform the analysis of different alanine-scanning calculations and to report the free-energy estimates in a user-friendly graphical user interface, allowing favorable mutations to be identified at a glance. The plug-in also assists the end-user in assessing the reliability of the calculation through rapid visual inspection. PMID:27214306

  5. Potential energy surface of triplet N2O2

    NASA Astrophysics Data System (ADS)

    Varga, Zoltan; Meana-Pañeda, Rubén; Song, Guoliang; Paukku, Yuliya; Truhlar, Donald G.

    2016-01-01

    We present a global ground-state triplet potential energy surface for the N2O2 system that is suitable for treating high-energy vibrational-rotational energy transfer and collision-induced dissociation. The surface is based on multi-state complete-active-space second-order perturbation theory/minimally augmented correlation-consistent polarized valence triple-zeta electronic structure calculations plus dynamically scaled external correlation. In the multireference calculations, the active space has 14 electrons in 12 orbitals. The calculations cover nine arrangements corresponding to dissociative diatom-diatom collisions of N2, O2, and nitric oxide (NO), the interaction of a triatomic molecule (N2O and NO2) with the fourth atom, and the interaction of a diatomic molecule with a single atom (i.e., the triatomic subsystems). The global ground-state potential energy surface was obtained by fitting the many-body interaction to 54 889 electronic structure data points with a fitting function that is a permutationally invariant polynomial in terms of bond-order functions of the six interatomic distances.

  6. Potential energy surface of triplet N2O2.

    PubMed

    Varga, Zoltan; Meana-Pañeda, Rubén; Song, Guoliang; Paukku, Yuliya; Truhlar, Donald G

    2016-01-14

    We present a global ground-state triplet potential energy surface for the N2O2 system that is suitable for treating high-energy vibrational-rotational energy transfer and collision-induced dissociation. The surface is based on multi-state complete-active-space second-order perturbation theory/minimally augmented correlation-consistent polarized valence triple-zeta electronic structure calculations plus dynamically scaled external correlation. In the multireference calculations, the active space has 14 electrons in 12 orbitals. The calculations cover nine arrangements corresponding to dissociative diatom-diatom collisions of N2, O2, and nitric oxide (NO), the interaction of a triatomic molecule (N2O and NO2) with the fourth atom, and the interaction of a diatomic molecule with a single atom (i.e., the triatomic subsystems). The global ground-state potential energy surface was obtained by fitting the many-body interaction to 54 889 electronic structure data points with a fitting function that is a permutationally invariant polynomial in terms of bond-order functions of the six interatomic distances. PMID:26772574

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

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  8. Parquet decomposition calculations of the electronic self-energy

    NASA Astrophysics Data System (ADS)

    Gunnarsson, O.; Schäfer, T.; LeBlanc, J. P. F.; Merino, J.; Sangiovanni, G.; Rohringer, G.; Toschi, A.

    2016-06-01

    The parquet decomposition of the self-energy into classes of diagrams, those associated with specific scattering processes, can be exploited for different scopes. In this work, the parquet decomposition is used to unravel the underlying physics of nonperturbative numerical calculations. We show the specific example of dynamical mean field theory and its cluster extensions [dynamical cluster approximation (DCA)] applied to the Hubbard model at half-filling and with hole doping: These techniques allow for a simultaneous determination of two-particle vertex functions and self-energies and, hence, for an essentially "exact" parquet decomposition at the single-site or at the cluster level. Our calculations show that the self-energies in the underdoped regime are dominated by spin-scattering processes, consistent with the conclusions obtained by means of the fluctuation diagnostics approach [O. Gunnarsson et al., Phys. Rev. Lett. 114, 236402 (2015), 10.1103/PhysRevLett.114.236402]. However, differently from the latter approach, the parquet procedure displays important changes with increasing interaction: Even for relatively moderate couplings, well before the Mott transition, singularities appear in different terms, with the notable exception of the predominant spin channel. We explain precisely how these singularities, which partly limit the utility of the parquet decomposition and, more generally, of parquet-based algorithms, are never found in the fluctuation diagnostics procedure. Finally, by a more refined analysis, we link the occurrence of the parquet singularities in our calculations to a progressive suppression of charge fluctuations and the formation of a resonance valence bond state, which are typical hallmarks of a pseudogap state in DCA.

  9. 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.

  10. 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.

  11. Empirically corrected HEAT method for calculating atomization energies

    SciTech Connect

    Brand, Holmann V

    2008-01-01

    We describe how to increase the accuracy ofthe most recent variants ofthe HEAT method for calculating atomization energies of molecules by means ofextremely simple empirical corrections that depend on stoichiometry and the number ofunpaired electrons in the molecule. Our corrections reduce the deviation from experiment for all the HEAT variants. In particular, our corrections reduce the average absolute deviation and the root-mean-square deviation ofthe 456-QP variant to 0.18 and 0.23 kJoule/mol (i.e., 0.04 and 0.05 kcallmol), respectively.

  12. Multiple scattering calculations of relativistic electron energy loss spectra

    NASA Astrophysics Data System (ADS)

    Jorissen, K.; Rehr, J. J.; Verbeeck, J.

    2010-04-01

    A generalization of the real-space Green’s-function approach is presented for ab initio calculations of relativistic electron energy loss spectra (EELS) which are particularly important in anisotropic materials. The approach incorporates relativistic effects in terms of the transition tensor within the dipole-selection rule. In particular, the method accounts for relativistic corrections to the magic angle in orientation resolved EELS experiments. The approach is validated by a study of the graphite CK edge, for which we present an accurate magic angle measurement consistent with the predicted value.

  13. Model for analytical calculation of nuclear photoabsorption at intermediate energies

    NASA Astrophysics Data System (ADS)

    Hütt, M.-Th.; Milstein, A. I.; Schumacher, M.

    1997-02-01

    The universal curve {σ}/{A} of nuclear photoabsorption is investigated within a Fermi gas model of nuclear matter. An energy range from pion threshold up to 400 MeV is considered. The interactions between nucleon, pion, Δ-isobar and photon are considered in the non-relativistic approximation with corrections of the order {1}/{M} taken into account with respect to proton mass. Analytical expressions are obtained, in which the influence of nuclear correlations and two-nucleon contributions is studied explicitly. The contributions of real and virtual pions are found to be sufficient to obtain agreement with experimental data in this energy range. An extension of the model calculation to nucleon knock-out reactions is discussed.

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

    EPA Science Inventory

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

  15. A global potential energy surface for ArH2

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Walch, Stephen P.; Taylor, Peter R.

    1992-01-01

    We describe a simple analytic representation of the ArH2 potential energy surface which well reproduces the results of extensive ab initio electronic structure calculations. The analytic representation smoothly interpolates between the dissociated H2 and strong bonding limits. In the fitting process, emphasis is made on accurately reproducing regions of the potential expected to be important for high temperature (ca. 3000 K) collision processes. Overall, the anisotropy and H2 bond length dependence of the analytic representation well reproduce the input data.

  16. A Variational Approach to Enhanced Sampling and Free Energy Calculations

    NASA Astrophysics Data System (ADS)

    Parrinello, Michele

    2015-03-01

    The presence of kinetic bottlenecks severely hampers the ability of widely used sampling methods like molecular dynamics or Monte Carlo to explore complex free energy landscapes. One of the most popular methods for addressing this problem is umbrella sampling which is based on the addition of an external bias which helps overcoming the kinetic barriers. The bias potential is usually taken to be a function of a restricted number of collective variables. However constructing the bias is not simple, especially when the number of collective variables increases. Here we introduce a functional of the bias which, when minimized, allows us to recover the free energy. We demonstrate the usefulness and the flexibility of this approach on a number of examples which include the determination of a six dimensional free energy surface. Besides the practical advantages, the existence of such a variational principle allows us to look at the enhanced sampling problem from a rather convenient vantage point.

  17. Calculated photoelectron pitch angle and energy spectra. [in upper atmosphere

    NASA Technical Reports Server (NTRS)

    Mantas, G. P.; Bowhill, S. A.

    1974-01-01

    Calculations of the steady-state photoelectron energy and angular distribution in the altitude region between 120 and 1000 km are presented. The distribution is found to be isotropic at all altitudes below 250 km, while above this altitude anisotropies in both pitch angle and energy are found. The isotropy found in the angular distribution below 250 km implies that photoelectron transport below 250 km is insignificant, while the angular anisotropy found above this altitude implies a net photoelectron current in the upward direction. The energy anisotropy above 500 km arises from the selective backscattering of the low energy photoelectron population of the upward flux component by Coulomb collisions with the ambient ions. The total photoelectron flux attains its maximum value between about 40 and 70 km above the altitude at which the photoelectron production rate is maximum. The displacement of the maximum of the equilibrium flux is attributed to an increasing (with altitude) photoelectron lifetime. Photoelectrons at altitudes above that where the flux is maximum are on the average more energetic than those below that altitude.

  18. Potential energy hypersurface and molecular flexibility

    NASA Astrophysics Data System (ADS)

    Koča, Jaroslav

    1993-02-01

    The molecular flexibility phenomenon is discussed from the conformational potential energy(hyper) surface (PES) point of view. Flexibility is considered as a product of three terms: thermodynamic, kinetic and geometrical. Several expressions characterizing absolute and relative molecular flexibility are introduced, depending on a subspace studied of the entire conformational space, energy level E of PES as well as absolute temperature. Results obtained by programs DAISY, CICADA and PANIC in conjunction with molecular mechanics program MMX for flexibility analysis of isopentane, 2,2-dimethylpentane and isohexane molecules are introduced.

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

    PubMed

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

    2011-08-28

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

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

    SciTech Connect

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

    1986-10-01

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

  1. Measurements and calculations of neutron scattering angular distributions over a wide mass and energy range

    SciTech Connect

    Hansen, L.F.

    1985-05-01

    Neutron elastic and inelastic differential cross sections for targets between /sup 9/Be and /sup 239/Pu at energies, E > 14 MeV have been measured using the Livermore and Ohio University neutron time-of-flight facilities. We review here the data and the analyses based on two local microscopic optical potentials: that of Jeukenne, Lejeune and Mahaux, and that of Brieva and Rook. The results are also compared with calculations using global potentials. Coupled channel formalism has been used in the analysis of targets with strong deformations, such as Be, C, Ta, and actinides. The value of the microscopic optical potentials as a tool to predict elastic and inelastic neutron cross sections over a wide mass and energy range is discussed. The need for neutron measurements up to higher energies and their analysis in conjunction with (p,p) and charge exchange (p,n) data is addressed. 17 refs.

  2. Variational calculations with explicit energy functionals for fermion systems at zero temperature

    NASA Astrophysics Data System (ADS)

    Takano, M.; Suzuki, T.; Sakumichi, N.

    2016-03-01

    The variational method with explicit energy functionals (EEFs) is applied to infinite neutron matter. Starting from the Argonne v8’ two-body potential and the repulsive part of the Urbana IX three-body potential, the energy per neutron is expressed explicitly with the spin-dependent central, tensor, and spin-orbit distribution functions. This EEF is constructed as an extension of the previously proposed one for the Argonne v6’ potential, including central and tensor forces. The Euler-Lagrange equations derived from this EEF are solved numerically. The obtained fully minimized energy with this EEF is in good agreement with that obtained from the auxiliary field diffusion Monte Carlo calculation.

  3. Measurements and Calculations of Neutron Scattering Angular Distributions over a Wide Mass and Energy Range

    NASA Astrophysics Data System (ADS)

    Hansen, L. F.

    Neutron elastic and inelastic differential cross sections for targets between (9)Be and (239)Pu at energies, E 14 MeV have been measured using the Livermore and Ohio University neutron time-of-flight facilities. We review here the data and the analyses based on two local microscopic optical potentials: that of Jeukenne, Lejeune and Mahaux, and that of Brieva and Rook. The results are also compared with calculations using global potentials. Coupled channel formalism has been used in the analysis of targets with strong deformations, such as Be, C, Ta, and actinides. The value of the microscopic optical potentials as a tool to predict elastic and inelastic neutron cross sections over a wide mass and energy range is discussed. The need for neutron measurements up to higher energies and their analysis in conjunction with (p,p) and charge exchange (p,n) data is addressed.

  4. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1990-01-01

    The objective was to obtain accurate potential energy surfaces (PES's) for a number of reactions which are important in the H/N/O combustion process. The interest in this is centered around the design of the SCRAM jet engine for the National Aerospace Plane (NASP), which was envisioned as an air-breathing hydrogen-burning vehicle capable of reaching velocities as large as Mach 25. Preliminary studies indicated that the supersonic flow in the combustor region of the scram jet engine required accurate reaction rate data for reactions in the H/N/O system, some of which was not readily available from experiment. The most important class of combustion reactions from the standpoint of the NASP project are radical recombinaton reactions, since these reactions result in most of the heat release in the combustion process. Theoretical characterizations of the potential energy surfaces for these reactions are presented and discussed.

  5. Energy Savings Potential of Radiative Cooling Technologies

    SciTech Connect

    Fernandez, Nicholas; Wang, Weimin; Alvine, Kyle J.; Katipamula, Srinivas

    2015-11-30

    Pacific Northwest National Laboratory (PNNL), with funding from the U.S. Department of Energy’s (DOE’s) Building Technologies Program (BTP), conducted a study to estimate, through simulation, the potential cooling energy savings that could be achieved through novel approaches to capturing free radiative cooling in buildings, particularly photonic ‘selective emittance’ materials. This report documents the results of that study.

  6. Hyperspherical hidden crossing calculation of Ps formation in low-energy e+-Na collisions

    NASA Astrophysics Data System (ADS)

    Ward, S. J.; Shertzer, J.

    2011-05-01

    The hyperspherical hidden crossing method (HHCM) can provide important insight into scattering processes. Previously, we have used the HHCM to calculate the Ps(1s)-formation cross section in low-energy e+-H and e+-Li collisions. Here we apply the HHCM to low-energy e+-Na collisions. We use the Peach model potential and treat e+e-Na+ as an effective three-body system. We calculate the Ps(1s)-formation cross sections for 0 <= L <= 3 and compare our results with a hyperspherical close-coupling calculation. The HHCM provides an explanation for the small S-wave Ps(1s)-formation cross section. The S-wave Stückelberg phase is close to π for the three collision systems due to destructive interference between the two amplitudes that correspond to different paths leading to Ps(1s) formation.

  7. Parallel AFMPB solver with automatic surface meshing for calculation of molecular solvation free energy

    NASA Astrophysics Data System (ADS)

    Zhang, Bo; Peng, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai; Lu, Benzhuo

    2015-05-01

    We present PAFMPB, an updated and parallel version of the AFMPB software package for fast calculation of molecular solvation-free energy. The new version has the following new features: (1) The adaptive fast multipole method and the boundary element methods are parallelized; (2) A tool is embedded for automatic molecular VDW/SAS surface mesh generation, leaving the requirement for a mesh file at input optional; (3) The package provides fast calculation of the total solvation-free energy, including the PB electrostatic and nonpolar interaction contributions. PAFMPB is implemented in C and Fortran programming languages, with the Cilk Plus extension to harness the computing power of both multicore and vector processing. Computational experiments demonstrate the successful application of PAFMPB to the calculation of the PB potential on a dengue virus system with more than one million atoms and a mesh with approximately 20 million triangles.

  8. Calculation of converged rovibrational energies and partition function for methane using vibrational-rotational configuration interaction.

    PubMed

    Chakraborty, Arindam; Truhlar, Donald G; Bowman, Joel M; Carter, Stuart

    2004-08-01

    The rovibration partition function of CH4 was calculated in the temperature range of 100-1000 K using well-converged energy levels that were calculated by vibrational-rotational configuration interaction using the Watson Hamiltonian for total angular momenta J = 0-50 and the MULTIMODE computer program. The configuration state functions are products of ground-state occupied and virtual modals obtained using the vibrational self-consistent field method. The Gilbert and Jordan potential energy surface was used for the calculations. The resulting partition function was used to test the harmonic oscillator approximation and the separable-rotation approximation. The harmonic oscillator, rigid-rotator approximation is in error by a factor of 2.3 at 300 K, but we also propose a separable-rotation approximation that is accurate within 2% from 100 to 1000 K. PMID:15260761

  9. Calculation of energy barriers for magnetic vortices in sub-100 nm dots

    NASA Astrophysics Data System (ADS)

    Lapa, Pavel; King, Andrew; Roshchin, Igor V.

    2012-10-01

    In a magnetic vortex, the magnetization is curling in plane everywhere except the ``core,'' where it is out of plane. Interest in switching of magnetic vortices in nanodots is stimulated by their potential application for magnetic memories and nano-oscillators. By combining analytical and micromagnetic techniques, we calculated energy barriers for vortex switching in 20 nm-thick iron dots as a function of applied in-plane field and dot diameter. Using analytical formula for magnetization distribution in the vortex,footnotetextN. A. Usov and S. E. Peschany, J. Magn. Magn. Mater. 118, 290 (1992). we performed micromagnetic calculations of the dot energy for different vortex core positions. In contrast to the ``rigid body approximation,'' the core size and core shape in our calculations were varied to achieve the energy minimum for every core displacement. The energy barriers required for vortex nucleation and annihilation were calculated as a function of magnetic field. By comparing these barriers to the thermal energy kBT we obtained the temperature dependences of the vortex nucleation and annihilation fields in good agreement with the experiment.footnotetextR. K. Dumas et al., Appl. Phys. Lett. 91, 202501 (2007).

  10. The Potential For Energy Efficiency In The State of Iowa

    SciTech Connect

    Hadley, SW

    2001-12-05

    The purpose of this study was to do an initial estimate of the potential for energy savings in the state of Iowa. Several methods for determining savings were examined, including existing programs, surveys, savings calculators, and economic simulation. Each method has advantages and disadvantages, trading off between detail of information, accuracy of results, and scope. This paper concentrated on using economic simulation (the NEMS model (EIA 2000a)) to determine market potential for energy savings for the residential and commercial sectors. The results of surveys were used to calculate the economic potential for savings in the industrial sector. The NEMS model is used by the Energy Information Administration to calculate twenty-year projections of energy use for every region of the country. The results of the Annual Energy Outlook 2000 were used as the Base case (EIA 1999a). Two alternative cases were created to simulate energy savings policies. Voluntary, market-related programs were simulated by lowering the effective discount rates that end-users use when making decisions on equipment purchases. Standards programs in the residential sector were simulated by eliminating the availability of low efficiency equipment in future years. The parameters for these programs were based on the Moderate scenario from the DOE Clean Energy Futures study (Interlaboratory Working Group 2000), which assumed increased concern by society on energy efficiency but not to the point of fiscal policies such as taxes or direct subsidies. The study only considered a subset of the various programs, policies, and technologies that could reduce energy use. The major end-uses in the residential sector affected by the policies were space cooling (20% savings by 2020) and water heating (14% savings by 2020.) Figure S-1 shows the space cooling savings when voluntary programs and minimum efficiency standards were implemented. Refrigerators, freezers, and clothes dryers saw slight improvements

  11. Ab initio molecular dynamics calculations of ion hydration free energies

    SciTech Connect

    Leung, Kevin; Rempe, Susan B.; Lilienfeld, O. Anatole von

    2009-05-28

    We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or '{lambda}-path' technique to compute the intrinsic hydration free energies of Li{sup +}, Cl{sup -}, and Ag{sup +} ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential ({phi}) contributions, we obtain absolute AIMD hydration free energies ({Delta}G{sub hyd}) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model {phi} predictions. The sums of Li{sup +}/Cl{sup -} and Ag{sup +}/Cl{sup -} AIMD {Delta}G{sub hyd}, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag{sup +}+Ni{sup +}{yields}Ag+Ni{sup 2+} in water. The predictions for this reaction suggest that existing estimates of {Delta}G{sub hyd} for unstable radiolysis intermediates such as Ni{sup +} may need to be extensively revised.

  12. Scattering Theory Calculations of Casimir Energies at High Curvature

    NASA Astrophysics Data System (ADS)

    Graham, Noah; Emig, Thorsten; Forrow, Aden; Jaffe, Robert; Kardar, Mehran; Maghrebi, Mohammad; Rahi, Jamal; Shpunt, Alex

    2013-03-01

    Scattering theory provides a powerful tool for capturing the response of an object to electromagnetic charge and field fluctuations. Techniques based on scattering theory have made possible a wide range of new calculations of Casimir energies. In this approach, the Casimir interaction energy for a collection of objects can be expressed in terms of the scattering T-matrices for each object individually, combined with universal translation matrices describing the objects' relative positions and orientations. These translation matrices are derived from an expansion of the free Green's function in an appropriate coordinate system, independent of the details of the objects themselves. This method proves particularly valuable for geometries involving high curvature, such as edges and tips. I will describe this approach in general terms and then give results from several problems to which it has been applied successfully. I will also discuss new developments in scattering theory that have been motivated by these problems. I would like to request that this abstract be part of a session on Casimir physics. Supported by the National Science Foundation, the US Department of Energy, the Defense Advanced Research Projects Agency, and the Deutsche Forschungsgemeinschaft

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

    SciTech Connect

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

    1987-10-15

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

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

    SciTech Connect

    Colborn, J.A.

    1983-08-17

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

  15. Potential energy surfaces and reaction dynamics of polyatomic molecules

    SciTech Connect

    Chang, Yan-Tyng.

    1991-11-01

    A simple empirical valence bond (EVB) model approach is suggested for constructing global potential energy surfaces for reactions of polyatomic molecular systems. This approach produces smooth and continuous potential surfaces which can be directly utilized in a dynamical study. Two types of reactions are of special interest, the unimolecular dissociation and the unimolecular isomerization. For the first type, the molecular dissociation dynamics of formaldehyde on the ground electronic surface is investigated through classical trajectory calculations on EVB surfaces. The product state distributions and vector correlations obtained from this study suggest very similar behaviors seen in the experiments. The intramolecular hydrogen atom transfer in the formic acid dimer is an example of the isomerization reaction. High level ab initio quantum chemistry calculations are performed to obtain optimized equilibrium and transition state dimer geometries and also the harmonic frequencies.

  16. Global Expression for Representing Diatomic Potential-Energy Curves

    NASA Technical Reports Server (NTRS)

    Ferrante, John; Schlosser, Herbert; Smith, John R.

    1991-01-01

    A three-parameter expression that gives an accurate fit to diatomic potential curves over the entire range of separation for charge transfers between 0 and 1. It is based on a generalization of the universal binding-energy relation of Smith et al. (1989) with a modification that describes the crossover from a partially ionic state to the neutral state at large separations. The expression is tested by comparison with first-principles calculations of the potential curves ranging from covalently bonded to ionically bonded. The expression is also used to calculate spectroscopic constants form a curve fit to the first-principles curves. A comparison is made with experimental values of the spectroscopic constants.

  17. 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.

  18. 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.

  19. 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.

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

    NASA Technical Reports Server (NTRS)

    Maskew, B.

    1976-01-01

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

  1. 3DRISM Multigrid Algorithm for Fast Solvation Free Energy Calculations.

    PubMed

    Sergiievskyi, Volodymyr P; Fedorov, Maxim V

    2012-06-12

    In this paper we present a fast and accurate method for modeling solvation properties of organic molecules in water with a main focus on predicting solvation (hydration) free energies of small organic compounds. The method is based on a combination of (i) a molecular theory, three-dimensional reference interaction sites model (3DRISM); (ii) a fast multigrid algorithm for solving the high-dimensional 3DRISM integral equations; and (iii) a recently introduced universal correction (UC) for the 3DRISM solvation free energies by properly scaled molecular partial volume (3DRISM-UC, Palmer et al., J. Phys.: Condens. Matter2010, 22, 492101). A fast multigrid algorithm is the core of the method because it helps to reduce the high computational costs associated with solving the 3DRISM equations. To facilitate future applications of the method, we performed benchmarking of the algorithm on a set of several model solutes in order to find optimal grid parameters and to test the performance and accuracy of the algorithm. We have shown that the proposed new multigrid algorithm is on average 24 times faster than the simple Picard method and at least 3.5 times faster than the MDIIS method which is currently actively used by the 3DRISM community (e.g., the MDIIS method has been recently implemented in a new 3DRISM implicit solvent routine in the recent release of the AmberTools 1.4 molecular modeling package (Luchko et al. J. Chem. Theory Comput. 2010, 6, 607-624). Then we have benchmarked the multigrid algorithm with chosen optimal parameters on a set of 99 organic compounds. We show that average computational time required for one 3DRISM calculation is 3.5 min per a small organic molecule (10-20 atoms) on a standard personal computer. We also benchmarked predicted solvation free energy values for all of the compounds in the set against the corresponding experimental data. We show that by using the proposed multigrid algorithm and the 3DRISM-UC model, it is possible to obtain good

  2. Calculations of molecular ionization energies using a self-consistent-charge Hartree-Fock-Slater method

    NASA Technical Reports Server (NTRS)

    Rosen, A.; Ellis, D. E.; Adachi, H.; Averill, F. W.

    1976-01-01

    A numerical-variational method for performing self-consistent molecular calculations in the Hartree-Fock-Slater (HFS) model is presented. Molecular wavefunctions are expanded in terms of basis sets constructed from numerical HFS solutions of selected one-center atomlike problems. Binding energies and wavefunctions for the molecules are generated using a discrete variational method for a given molecular potential. In the self-consistent-charge (SCC) approximation to the complete self-consistent-field (SCF) method, results of a Mulliken population analysis of the molecular eigenfunctions are used in each iteration to produce 'atomic' occupation numbers. The simplest SCC potential is then obtained from overlapping spherical atomlike charge distributions. Molecular ionization energies are calculated using the transition-state procedure; results are given for CO, H2O, H2S, AlCl, InCl, and the Ni5O surface complex. Agreement between experimental and theoretical ionization energies for the free-molecule valence levels is generally within 1 eV. The simple SCC procedure gives a reasonably good approximation to the molecular potential, as shown by comparison with experiment, and with complete SCF calculations for CO, H2O, and H2S.

  3. Valence calculations of lanthanide anion binding energies: a comprehensive study

    NASA Astrophysics Data System (ADS)

    O'Malley, Steven M.; Beck, Donald R.

    2009-05-01

    We have applied a methodology of universal jls restrictions on the 4f^n subgroup of relativistic configuration-interaction calculations of progressively more complex lanthanide anionsootnotetextS. M. O'Malley and D. R. Beck, Phys. Rev. A 77, 012505 (2008).^,ootnotetextS. M. O'Malley and D. R. Beck, Phys. Rev. A 78, 012510 (2008).^,ootnotetextS. M. O'Malley and D. R. Beck, Phys. Rev. A, in press.. Our completed study of the row predicts bound 6p attachments to all lanthanide ground state configurations except Yb, additional 6p attachments to excited opposite parity configurations in Tb and Lu, and 6s attachments to excited open-6s thresholds in La, Ce, Pr, and Gd. In total we predict more than 100 bound states for the lanthanide anions, and we hope this comprehensive study encourages further experimentalootnotetexte.g. V. T. Davis et al., Nucl. Instrum. Methods Phys. Res. B 241, 118 (2005).^,ootnotetexte.g. C. W. Walter et al., Phys. Rev. A 76, 052702 (2007). interest in these anions. Such measurements will be useful in ``fine tuning'' these ab initio binding energies to account for missing core-valence correlation and the approximations that were necessary in these complex calculations.

  4. 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

  5. Metadyn View: Fast web-based viewer of free energy surfaces calculated by metadynamics

    NASA Astrophysics Data System (ADS)

    Hošek, Petr; Spiwok, Vojtěch

    2016-01-01

    Metadynamics is a highly successful enhanced sampling technique for simulation of molecular processes and prediction of their free energy surfaces. An in-depth analysis of data obtained by this method is as important as the simulation itself. Although there are several tools to compute free energy surfaces from metadynamics data, they usually lack user friendliness and a build-in visualization part. Here we introduce Metadyn View as a fast and user friendly viewer of bias potential/free energy surfaces calculated by metadynamics in Plumed package. It is based on modern web technologies including HTML5, JavaScript and Cascade Style Sheets (CSS). It can be used by visiting the web site and uploading a HILLS file. It calculates the bias potential/free energy surface on the client-side, so it can run online or offline without necessity to install additional web engines. Moreover, it includes tools for measurement of free energies and free energy differences and data/image export.

  6. Calculating the free energy of nearly jammed hard-particle packings using molecular dynamics

    NASA Astrophysics Data System (ADS)

    Donev, Aleksandar; Stillinger, Frank H.; Torquato, Salvatore

    2007-07-01

    We present a new event-driven molecular dynamics (MD) algorithm for measuring the free energy of nearly jammed packings of spherical and non-spherical hard particles. This Bounding Cell Molecular Dynamics (BCMD) algorithm exactly calculates the free-energy of a single-occupancy cell (SOC) model in which each particle is restricted to a neighborhood of its initial position using a hard-wall bounding cell. Our MD algorithm generalizes previous ones in the literature by enabling us to study non-spherical particles as well as to measure the free-energy change during continuous irreversible transformations. Moreover, we make connections to the well-studied problem of computing the volume of convex bodies in high dimensions using random walks. We test and verify the numerical accuracy of the method by comparing against rigorous asymptotic results for the free energy of jammed and isostatic disordered packings of both hard spheres and ellipsoids, for which the free energy can be calculated directly as the volume of a high-dimensional simplex. We also compare our results to previously published Monte Carlo results for hard-sphere crystals near melting and jamming and find excellent agreement. We have successfully used the BCMD algorithm to determine the configurational and free-volume contributions to the free energy of glassy states of binary hard disks [A. Donev, F.H. Stillinger, S. Torquato, Do binary hard disks exhibit an ideal glass transition? Phys. Rev. Lett. 96 (22) (2006) 225502]. The algorithm can also be used to determine phases with locally- or globally-minimal free energy, to calculate the free-energy cost of point and extended crystal defects, or to calculate the elastic moduli of glassy or crystalline solids, among other potential applications.

  7. The ratios of partition functions at different temperatures - Sensitivity to potential energy shape II

    NASA Astrophysics Data System (ADS)

    Buchowiecki, Marcin

    2016-05-01

    The ratios of partition functions at different temperatures are calculated and its dependence on potential energy shape is analyzed. The role of anharmonicity and non-rigidity of rotations is discussed in the context of the angular frequency and the shape of potential energy curve. A role of inflection point of potential energy curve for the quality of rigid rotor harmonic oscillator and rigid rotor Morse oscillator is elucidated.

  8. Improved methods for Feynman path integral calculations and their application to calculate converged vibrational–rotational partition functions, free energies, enthalpies, entropies, and heat capacities for methane

    SciTech Connect

    Mielke, Steven L. E-mail: truhlar@umn.edu; Truhlar, Donald G. E-mail: truhlar@umn.edu

    2015-01-28

    We present an improved version of our “path-by-path” enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P{sup −6}) to O(P{sup −12}), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational–rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan–Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ∼1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300–3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities.

  9. Improved methods for Feynman path integral calculations and their application to calculate converged vibrational-rotational partition functions, free energies, enthalpies, entropies, and heat capacities for methane

    NASA Astrophysics Data System (ADS)

    Mielke, Steven L.; Truhlar, Donald G.

    2015-01-01

    We present an improved version of our "path-by-path" enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P-6) to O(P-12), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational-rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan-Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ˜1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300-3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities.

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2003-02-01

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

  12. An efficient method for energy levels calculation using full symmetry and exact kinetic energy operator: Tetrahedral molecules

    SciTech Connect

    Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.

    2015-03-07

    A simultaneous use of the full molecular symmetry and of an exact kinetic energy operator (KEO) is of key importance for accurate predictions of vibrational levels at a high energy range from a potential energy surface (PES). An efficient method that permits a fast convergence of variational calculations would allow iterative optimization of the PES parameters using experimental data. In this work, we propose such a method applied to tetrahedral AB{sub 4} molecules for which a use of high symmetry is crucial for vibrational calculations. A symmetry-adapted contracted angular basis set for six redundant angles is introduced. Simple formulas using this basis set for explicit calculation of the angular matrix elements of KEO and PES are reported. The symmetric form (six redundant angles) of vibrational KEO without the sin(q){sup −2} type singularity is derived. The efficient recursive algorithm based on the tensorial formalism is used for the calculation of vibrational matrix elements. A good basis set convergence for the calculations of vibrational levels of the CH{sub 4} molecule is demonstrated.

  13. An efficient method for energy levels calculation using full symmetry and exact kinetic energy operator: Tetrahedral molecules

    NASA Astrophysics Data System (ADS)

    Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.

    2015-03-01

    A simultaneous use of the full molecular symmetry and of an exact kinetic energy operator (KEO) is of key importance for accurate predictions of vibrational levels at a high energy range from a potential energy surface (PES). An efficient method that permits a fast convergence of variational calculations would allow iterative optimization of the PES parameters using experimental data. In this work, we propose such a method applied to tetrahedral AB4 molecules for which a use of high symmetry is crucial for vibrational calculations. A symmetry-adapted contracted angular basis set for six redundant angles is introduced. Simple formulas using this basis set for explicit calculation of the angular matrix elements of KEO and PES are reported. The symmetric form (six redundant angles) of vibrational KEO without the sin(q)-2 type singularity is derived. The efficient recursive algorithm based on the tensorial formalism is used for the calculation of vibrational matrix elements. A good basis set convergence for the calculations of vibrational levels of the CH4 molecule is demonstrated.

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

    NASA Technical Reports Server (NTRS)

    Hagyard, M. J.; Teuber, D.

    1978-01-01

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

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

    SciTech Connect

    EARLEY JN

    2008-07-23

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

  16. Semi-empirical method for calculating the activation energies of the unimolecular thermal decomposition of vinyl ethers

    NASA Astrophysics Data System (ADS)

    Sargsyan, G. N.; Shakhrokh, B.; Harutyunyan, A. B.

    2015-02-01

    A semi-empirical method is proposed for calculating the activation energy of the unimolecular decomposition of complex compounds using the example of vinyl (ethyl, propyl, and butyl) ethers. The method is based on the concept of the formation of intramolecular hydrogen bonds and the possibility of calculating the energy of deformation of ether molecules upon activation, resulting in the potential surface of the transition state undergoing distortion and the transfer of a hydrogen atom from an alkyl group to a vinyl group. The energy of deformation is calculated using the Mathcad 2001i and MM2 computer programs.

  17. INDIVIDUALISED CALCULATION OF TISSUE IMPARTED ENERGY IN BREAST TOMOSYNTHESIS.

    PubMed

    Geeraert, N; Klausz, R; Muller, S; Bloch, I; Bosmans, H

    2016-06-01

    The imparted energy to the glandular tissue in the breast (glandular imparted energy, GIE) is proposed for an improved assessment of the individual radiation-induced risk resulting from X-ray breast imaging. GIE is computed from an estimation of the quantity and localisation of glandular tissue in the breast. After a digital breast tomosynthesis (DBT) acquisition, the volumetric glandular content (volumetric breast density, VBD) is computed from the central X-ray projection. The glandular tissue distribution is determined by labelling the DBT voxels to ensure the conservation of the VBD. Finally, the GIE is calculated by Monte Carlo computation on the resulting tissue-labelled DBT volume. For verification, the method was applied to 10 breast-shaped digital phantoms made of different glandular spheres in an adipose background, and to a digital anthropomorphic phantom. Results were compared to direct GIE computations on the phantoms considered as 'ground-truth'. The major limitations in accuracy are those of DBT, in particular the limited z-resolution. However, for most phantoms, the results can be considered as acceptable. PMID:27127209

  18. Correlation energy and dispersion interaction in the ab initio potential energy curve of the neon dimer

    SciTech Connect

    Bytautas, L.; Ruedenberg, K.

    2008-06-06

    A close approximation to the empirical potential energy curve of the neon dimer is obtained by coupled-cluster singles plus doubles plus noniterative triples calculations by using nonaugmented correlation-consistent basis sets without counterpoise corrections and complementing them by three-term extrapolations to the complete basis set limit. The potential energy is resolved into a self-consistent-field Hartree-Fock contribution and a correlation contribution. The latter is shown to decay in the long-range region in accordance with the empirical dispersion expansion.

  19. Correlation energy and dispersion interaction in the ab initio potential energy curve of the neon dimer.

    PubMed

    Bytautas, Laimutis; Ruedenberg, Klaus

    2008-06-01

    A close approximation to the empirical potential energy curve of the neon dimer is obtained by coupled-cluster singles plus doubles plus noniterative triples calculations by using nonaugmented correlation-consistent basis sets without counterpoise corrections and complementing them by three-term extrapolations to the complete basis set limit. The potential energy is resolved into a self-consistent-field Hartree-Fock contribution and a correlation contribution. The latter is shown to decay in the long-range region in accordance with the empirical dispersion expansion. PMID:18537423

  20. Geothermal Energy Potential of Turkey: Inferred from the Aeromagnetic data

    NASA Astrophysics Data System (ADS)

    Ates, Abdullah; Bilim, Funda; Buyuksarac, Aydin; Bektas, Ozcan

    2010-05-01

    Geothermal energy potential of Turkey is well known. There are lots of hot springs with over 30° C water temperatures. However, the significance of these geothermal energy potential of Turkey is not adequately understood. We believe that the main reason for this; is the lack of exploration methods and tools in a wide area as large as Turkey. We exploited a well known physical property of rocks to estimate the geothermal energy potential. Physically, substances lose their magnetization above a temperature known as the Curie that is the 580° C for magnetite. Properties of the Curie temperature have been exploited to observe the bottom depth of the magnetization. That is the depth where the heat reaches to 580° C. In another word, there is no magnetization below this depth. In normal crust this depth is about 22-24 km. Thus, investigation of the bottom depth of magnetization by using aeromagnetic anomalies can lead to information that if there are any anomalous regions well above the normal crust. The aeromagnetic anomalies of whole of Turkey were surveyed by the Mineral Research and Exploration (MTA) of Turkey. The survey was completed during late 1980's. Five kilometers grid data were available and used for regional exploration purposes. Exploration of the geothermal energy potential of Turkey was done from west to east in the similar way to search for shallow high temperature regions. These are from west to east; i.) Western Turkey: Two major shallow depth regions were determined at the west of Kutahya and the north-east of Denizli. The Curie Point Depths (CPDs) were calculated as about 7 km and about 9 km in Kutahya and Denizli, respectively. Also, high heat flow values and crustal thinning (about 32 km from gravity anomalies of western Turkey) were calculated for western Turkey. ii.) Central Turkey: A CPD depth of 8 km was calculated. This gives us a temperature gradient of 0.073° C/m. Geothermal energy potential was studied using water chemistry and isotopic

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

    SciTech Connect

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

    2007-10-15

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

  2. 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.

  3. The wind energy potential of western Greece

    SciTech Connect

    Katsoulis, B.D.; Metaxas, D.A. )

    1992-12-01

    In this study wind data were used to determine the monthly and annual variations of the wind at 13 meterological stations in western Greece. An analysis of the available wind data for the Ionian Sea islands and the western coasts of Greece is carried out to ascertain its potential for wind energy development. The effect of the limited number of daily observations available on the accuracy of the mean wind speed and annual wind energy estimates is ascertained. The wind speed and direction distributions are represented with Weibull functions. Besides, a mass-consistent numerical mesoscale model was used to give an overview of the wind prospecting and siting problem, and an example of its use for Corfu (Kerkira), an island in the Ionian Sea, is given. The comparison of the accuracy of the stimulation results versus measured wind at an available site is quite encouraging even though it cannot be conclusive since only one station is available.

  4. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.; Levin, Eugene

    1993-01-01

    A new global potential energy surface (PES) is being generated for O(P-3) + H2 yields OH + H. This surface is being fit using the rotated Morse oscillator method, which was used to fit the previous POL-CI surface. The new surface is expected to be more accurate and also includes a much more complete sampling of bent geometries. A new study has been undertaken of the reaction N + O2 yields NO + O. The new studies have focused on the region of the surface near a possible minimum corresponding to the peroxy form of NOO. A large portion of the PES for this second reaction has been mapped out. Since state to state cross sections for the reaction are important in the chemistry of high temperature air, these studies will probably be extended to permit generation of a new global potential for reaction.

  5. A calculation of the diffusion energies for adatoms on surfaces of F.C.C. metals

    NASA Technical Reports Server (NTRS)

    Halicioglu, T.; Pound, G. M.

    1979-01-01

    The activation energies for diffusion were determined for gold, platinum and iridium adatoms on plane and plane PT surfaces and were found to be in good agreement with the measurements reported by Bassett and Webber. The Lennard-Jones pair potentials were used to model the interatomic forces, and relaxation of the substrate atoms in near proximity to the adatom was considered in detail. The present calculations clarify the mechanism of the observed two-dimensional diffusion of platinum and iridium atoms on a plane PT surface. The results are compared with those obtained using Morse potential functions and different relaxation techniques.

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

    PubMed

    Ghoufi, Aziz; Malfreyt, Patrice

    2006-12-14

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

  7. Free energy dependence of pure phase iron doped bismuth titanate from first principles calculations.

    PubMed

    Mayfield, Cedric L; Subramanian, Vaidyanathan Ravi; Huda, Muhammad N

    2015-08-12

    A density functional theory study of Fe substitutions in Bi2Ti2O7 photocatalyst (Fe-BTO) is presented. It models an experiment where H2 production of Fe-BTO peaked for samples loaded with 1% Fe concentration then decreased for samples with heavier loadings. The total energy calculations were used to determine defect formation energies and the chemical potential landscape that suggests the observed formation of Fe2O3 (in samples at 2% Fe concentration) was detrimental to H2 production. Doping configurations as a function of oxygen chemical potential are discussed, and the chemical potential ranges that avoid formation of the Fe2O3 phase in Fe-BTO are predicted. PMID:26199200

  8. Free energy dependence of pure phase iron doped bismuth titanate from first principles calculations

    NASA Astrophysics Data System (ADS)

    Mayfield, Cedric L.; (Ravi Subramanian, Vaidyanathan; Huda, Muhammad N.

    2015-08-01

    A density functional theory study of Fe substitutions in Bi2Ti2O7 photocatalyst (Fe-BTO) is presented. It models an experiment where H2 production of Fe-BTO peaked for samples loaded with 1% Fe concentration then decreased for samples with heavier loadings. The total energy calculations were used to determine defect formation energies and the chemical potential landscape that suggests the observed formation of Fe2O3 (in samples at 2% Fe concentration) was detrimental to H2 production. Doping configurations as a function of oxygen chemical potential are discussed, and the chemical potential ranges that avoid formation of the Fe2O3 phase in Fe-BTO are predicted.

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

    NASA Astrophysics Data System (ADS)

    Kanamori, Junjiro; Akai, Hisazumi; Akai, Masako

    1984-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-09-01

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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  16. 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.

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

    PubMed

    Bomont, Jean-Marc

    2006-05-28

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

  18. Intermolecular potential energy surface and thermophysical properties of ethylene oxide

    SciTech Connect

    Crusius, Johann-Philipp Hassel, Egon; Hellmann, Robert; Bich, Eckard

    2014-10-28

    A six-dimensional potential energy hypersurface (PES) for two interacting rigid ethylene oxide (C{sub 2}H{sub 4}O) molecules was determined from high-level quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the MP2 and CCSD(T) levels of theory was utilized to determine interaction energies for 10178 configurations of two molecules. An analytical site-site potential function with 19 sites per ethylene oxide molecule was fitted to the interaction energies and fine tuned to agree with data for the second acoustic virial coefficient from accurate speed of sound measurements. The PES was validated by computing the second virial coefficient, shear viscosity, and thermal conductivity. The values of these properties are substantiated by the best experimental data as they tend to fall within the uncertainty intervals and also obey the experimental temperature functions, except for viscosity, where experimental data are insufficient. Due to the lack of reliable data, especially for the transport properties, our calculated values are currently the most accurate estimates for these properties of ethylene oxide.

  19. Intermolecular potential energy surface and thermophysical properties of ethylene oxide.

    PubMed

    Crusius, Johann-Philipp; Hellmann, Robert; Hassel, Egon; Bich, Eckard

    2014-10-28

    A six-dimensional potential energy hypersurface (PES) for two interacting rigid ethylene oxide (C2H4O) molecules was determined from high-level quantum-chemical ab initio calculations. The counterpoise-corrected supermolecular approach at the MP2 and CCSD(T) levels of theory was utilized to determine interaction energies for 10178 configurations of two molecules. An analytical site-site potential function with 19 sites per ethylene oxide molecule was fitted to the interaction energies and fine tuned to agree with data for the second acoustic virial coefficient from accurate speed of sound measurements. The PES was validated by computing the second virial coefficient, shear viscosity, and thermal conductivity. The values of these properties are substantiated by the best experimental data as they tend to fall within the uncertainty intervals and also obey the experimental temperature functions, except for viscosity, where experimental data are insufficient. Due to the lack of reliable data, especially for the transport properties, our calculated values are currently the most accurate estimates for these properties of ethylene oxide. PMID:25362314

  20. 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.

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

    PubMed

    Xiaoqing, Zhang

    2014-01-01

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

  2. 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

  3. Residential energy efficiency: Progress since 1973 and future potential

    NASA Astrophysics Data System (ADS)

    Rosenfeld, Arthur H.

    1985-11-01

    Today's 85 million U.S. homes use 100 billion of fuel and electricity (1150/home). If their energy intensity (resource energy/ft2) were still frozen at 1973 levels, they would use 18% more. With well-insulated houses, need for space heat is vanishing. Superinsulated Saskatchewan homes spend annually only 270 for space heat, 150 for water heat, and 400 for appliances, yet they cost only 2000±1000 more than conventional new homes. The concept of Cost of Conserved Energy (CCE) is used to rank conservation technologies for existing and new homes and appliances, and to develop supply curves of conserved energy and a least cost scenario. Calculations are calibrated with the BECA and other data bases. By limiting investments in efficiency to those whose CCE is less than current fuel and electricity prices, the potential residential plus commercial energy use in 2000 AD drops to half of that estimated by DOE, and the number of power plants needed drops by 200. For the whole buildings sector, potential savings by 2000 are 8 Mbod (worth 50B/year), at an average CCE of 10/barrel.

  4. Evaluation of global onshore wind energy potential and generation costs.

    PubMed

    Zhou, Yuyu; Luckow, Patrick; Smith, Steven J; Clarke, Leon

    2012-07-17

    In this study, we develop an updated global estimate of onshore wind energy potential using reanalysis wind speed data, along with updated wind turbine technology performance, land suitability factors, cost assumptions, and explicit consideration of transmission distance in the calculation of transmission costs. We find that wind has the potential to supply a significant portion of the world energy needs, although this potential varies substantially by region and with assumptions such as on what types of land can be used to site wind farms. Total global economic wind potential under central assumptions, that is, intermediate between optimistic and pessimistic, is estimated to be approximately 119.5 petawatt hours per year (13.6 TW) at less than 9 cents/kWh. A sensitivity analysis of eight key parameters is presented. Wind potential is sensitive to a number of input parameters, particularly wind speed (varying by -70% to +450% at less than 9 cents/kWh), land suitability (by -55% to +25%), turbine density (by -60% to +80%), and cost and financing options (by -20% to +200%), many of which have important policy implications. As a result of sensitivities studied here we suggest that further research intended to inform wind supply curve development focus not purely on physical science, such as better resolved wind maps, but also on these less well-defined factors, such as land-suitability, that will also have an impact on the long-term role of wind power. PMID:22715929

  5. Energy potential of sugarcane and sweet sorghum

    SciTech Connect

    Elawad, S.H.; Gascho, G.J.; Shih, S.F.

    1980-01-01

    The potential of sugarcane and sweet sorghum as raw materials for the production of ethanol and petrochemical substitutes is discussed. Both crops belong to the grass family and are classified as C/sub 4/ malateformers which have the highest rate of photosynthesis among terrestrial plants. Large amounts of biomass are required to supply a significant fraction of US energy consumption. Biomass production could be substantially increased by including tops and leaves, adopting narrow row spacing and improving cultural practices. This presents challenges for cultivating, harvesting, and hauling the biomass to processing centers. Large plants and heavy capital investment are essential for energy production. Ethanol and ammonia are the most promising candidates of a biomass program. If sugarcane were to be used for biomass production, breeding programs should be directed for more fermentable sugars and fiber. Energy research on sweet sorghum should be done with syrup varieties. Sweet sorghum needs to be incorporated with other crops because of its short growing season. The disposal of stillage from an extensive ethanol industry may pose environmental problems.

  6. Identification of HIV Inhibitors Guided by Free Energy Perturbation Calculations

    PubMed Central

    Acevedo, Orlando; Ambrose, Zandrea; Flaherty, Patrick T.; Aamer, Hadega; Jain, Prashi; Sambasivarao, Somisetti V.

    2013-01-01

    Free energy perturbation (FEP) theory coupled to molecular dynamics (MD) or Monte Carlo (MC) statistical mechanics offers a theoretically precise method for determining the free energy differences of related biological inhibitors. Traditionally requiring extensive computational resources and expertise, it is only recently that its impact is being felt in drug discovery. A review of computer-aided anti-HIV efforts employing FEP calculations is provided here that describes early and recent successes in the design of human immunodeficiency virus type 1 (HIV-1) protease and non-nucleoside reverse transcriptase inhibitors. In addition, our ongoing work developing and optimizing leads for small molecule inhibitors of cyclophilin A (CypA) is highlighted as an update on the current capabilities of the field. CypA has been shown to aid HIV-1 replication by catalyzing the cis/trans isomerization of a conserved Gly-Pro motif in the N-terminal domain of HIV-1 capsid (CA) protein. In the absence of a functional CypA, e.g., by the addition of an inhibitor such as cyclosporine A (CsA), HIV-1 has reduced infectivity. Our simulations of acylurea-based and 1-indanylketone-based CypA inhibitors have determined that their nanomolar and micromolar binding affinities, respectively, are tied to their ability to stabilize Arg55 and Asn102. A structurally novel 1-(2,6-dichlorobenzamido) indole core was proposed to maximize these interactions. FEP-guided optimization, experimental synthesis, and biological testing of lead compounds for toxicity and inhibition of wild-type HIV-1 and CA mutants have demonstrated a dose-dependent inhibition of HIV-1 infection in two cell lines. While the inhibition is modest compared to CsA, the results are encouraging. PMID:22316150

  7. 5 CFR 591.220 - How does OPM calculate energy utility cost indexes?

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 5 Administrative Personnel 1 2011-01-01 2011-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...

  8. 5 CFR 591.220 - How does OPM calculate energy utility cost indexes?

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 5 Administrative Personnel 1 2014-01-01 2014-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...

  9. 5 CFR 591.220 - How does OPM calculate energy utility cost indexes?

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 5 Administrative Personnel 1 2013-01-01 2013-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...

  10. 5 CFR 591.220 - How does OPM calculate energy utility cost indexes?

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 5 Administrative Personnel 1 2012-01-01 2012-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...

  11. 5 CFR 591.220 - How does OPM calculate energy utility cost indexes?

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 1 2010-01-01 2010-01-01 false How does OPM calculate energy utility... Areas Cost-Of-Living Allowances § 591.220 How does OPM calculate energy utility cost indexes? (a) OPM calculates energy utility cost indexes based on the relative cost of maintaining a standard size dwelling...

  12. Calculations of planar defect energies in substitutional alloys using the special-quasirandom-structure approach

    NASA Astrophysics Data System (ADS)

    de Jong, Maarten; Qi, Liang; Olmsted, David L.; van de Walle, Axel; Asta, Mark

    2016-03-01

    A method is described for calculating the energetics of planar defects in alloys based on the special-quasirandom-structure (SQS) approach. We examine the accuracy of the approach employing atomistic calculations based on a classical embedded-atom-method (EAM) interatomic potential for hexagonal close packed (hcp) alloys, for which benchmark results can be obtained by direct configurational averaging. The results of these calculations demonstrate that the SQS-based approach can be employed to derive the concentration dependence of the energies of twin boundaries, unstable stacking faults, and surfaces to within an accuracy of approximately 10%. The SQS considered in this study contain up to 72 atoms and hence are small enough to be considered in first-principles density-functional-theory (DFT) based calculations. The application of the SQS-based approach in direct DFT-based calculations is demonstrated in a study of the concentration dependence of interfacial energies for {11 2 ¯1 } twins in hcp Ti-Al alloys.

  13. EnergyPlus Analysis Capabilities for Use in California Building Energy Efficiency Standards Development and Compliance Calculations

    SciTech Connect

    Hong, Tianzhen; Buhl, Fred; Haves, Philip

    2008-03-28

    California has been using DOE-2 as the main building energy analysis tool in the development of building energy efficiency standards (Title 24) and the code compliance calculations. However, DOE-2.1E is a mature program that is no longer supported by LBNL on contract to the USDOE, or by any other public or private entity. With no more significant updates in the modeling capabilities of DOE-2.1E during recent years, DOE-2.1E lacks the ability to model, with the necessary accuracy, a number of building technologies that have the potential to reduce significantly the energy consumption of buildings in California. DOE-2's legacy software code makes it difficult and time consuming to add new or enhance existing modeling features in DOE-2. Therefore the USDOE proposed to develop a new tool, EnergyPlus, which is intended to replace DOE-2 as the next generation building simulation tool. EnergyPlus inherited most of the useful features from DOE-2 and BLAST, and more significantly added new modeling capabilities far beyond DOE-2, BLAST, and other simulations tools currently available. With California's net zero energy goals for new residential buildings in 2020 and for new commercial buildings in 2030, California needs to evaluate and promote currently available best practice and emerging technologies to significantly reduce energy use of buildings for space cooling and heating, ventilating, refrigerating, lighting, and water heating. The California Energy Commission (CEC) needs to adopt a new building energy simulation program for developing and maintaining future versions of Title 24. Therefore, EnergyPlus became a good candidate to CEC for its use in developing and complying with future Title 24 upgrades. In 2004, the Pacific Gas and Electric Company contracted with ArchitecturalEnergy Corporation (AEC), Taylor Engineering, and GARD Analytics to evaluate EnergyPlus in its ability to model those energy efficiency measures specified in both the residential and

  14. Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach

    PubMed Central

    Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A

    2015-01-01

    Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange. PMID:26418190

  15. 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.

  16. Calculating activation energies for temperature compensation in circadian rhythms

    NASA Astrophysics Data System (ADS)

    Bodenstein, C.; Heiland, I.; Schuster, S.

    2011-10-01

    Many biological species possess a circadian clock, which helps them anticipate daily variations in the environment. In the absence of external stimuli, the rhythm persists autonomously with a period of approximately 24 h. However, single pulses of light, nutrients, chemicals or temperature can shift the clock phase. In the case of light- and temperature-cycles, this allows entrainment of the clock to cycles of exactly 24 h. Circadian clocks have the remarkable property of temperature compensation, that is, the period of the circadian rhythm remains relatively constant within a physiological range of temperatures. For several organisms, temperature-regulated processes within the circadian clock have been identified in recent years. However, how these processes contribute to temperature compensation is not fully understood. Here, we theoretically investigate temperature compensation in general oscillatory systems. It is known that every oscillator can be locally temperature compensated around a reference temperature, if reactions are appropriately balanced. A balancing is always possible if the control coefficient with respect to the oscillation period of at least one reaction in the oscillator network is positive. However, for global temperature compensation, the whole physiological temperature range is relevant. Here, we use an approach which leads to an optimization problem subject to the local balancing principle. We use this approach to analyse different circadian clock models proposed in the literature and calculate activation energies that lead to temperature compensation.

  17. Path-breaking schemes for nonequilibrium free energy calculations

    NASA Astrophysics Data System (ADS)

    Chelli, Riccardo; Gellini, Cristina; Pietraperzia, Giangaetano; Giovannelli, Edoardo; Cardini, Gianni

    2013-06-01

    We propose a path-breaking route to the enhancement of unidirectional nonequilibrium simulations for the calculation of free energy differences via Jarzynski's equality [C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)], 10.1103/PhysRevLett.78.2690. One of the most important limitations of unidirectional nonequilibrium simulations is the amount of realizations necessary to reach suitable convergence of the work exponential average featuring the Jarzynski's relationship. In this respect, a significant improvement of the performances could be obtained by finding a way of stopping trajectories with negligible contribution to the work exponential average, before their normal end. This is achieved using path-breaking schemes which are essentially based on periodic checks of the work dissipated during the pulling trajectories. Such schemes can be based either on breaking trajectories whose dissipated work exceeds a given threshold or on breaking trajectories with a probability increasing with the dissipated work. In both cases, the computer time needed to carry out a series of nonequilibrium trajectories is reduced up to a factor ranging from 2 to more than 10, at least for the processes under consideration in the present study. The efficiency depends on several aspects, such as the type of process, the number of check-points along the pathway and the pulling rate as well. The method is illustrated through radically different processes, i.e., the helix-coil transition of deca-alanine and the pulling of the distance between two methane molecules in water solution.

  18. Projection potentials and angular momentum convergence of total energies in the full-potential Korringa-Kohn-Rostoker method.

    PubMed

    Zeller, Rudolf

    2013-03-13

    Although the full-potential Korringa-Kohn-Rostoker Green function method yields accurate results for many physical properties, the convergence of calculated total energies with respect to the angular momentum cutoff is usually considered to be less satisfactory. This is surprising because accurate single-particle energies are expected if they are calculated by Lloyd's formula and because accurate densities and hence accurate double-counting energies should result from the total energy variational principle. It is shown how the concept of projection potentials can be used as a tool to analyse the convergence behaviour. The key factor blocking fast convergence is identified and it is illustrated how total energies can be improved with only a modest increase of computing time. PMID:23396831

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  20. S-matrix Calculations of Energy Levels of the Lithium Isoelectronic Sequence

    SciTech Connect

    sapirstein, J; Cheng, K T

    2010-11-02

    A QED approach to the calculation of the spectra of the lithium isoelectronic sequence is implemented. A modified Furry representation based on the Kohn-Sham potential is used to evaluate all one- and two-photon diagrams with the exception of the two-loop Lamb shift. Three-photon diagrams are estimated with Hamiltonian methods. After incorporating recent calculations of the two-loop Lamb shift and recoil corrections a comprehensive tabulation of the 2s, 2p{sub 1/2} and 2p{sub 3/2} energy levels as well as the 2s - 2p{sub 1/2} and 2s - 2p{sub 3/2} transition energies for Z = 10 - 100 is presented.

  1. Induced Seismicity Potential of Energy Technologies

    NASA Astrophysics Data System (ADS)

    Hitzman, Murray

    2013-03-01

    Earthquakes attributable to human activities-``induced seismic events''-have received heightened public attention in the United States over the past several years. Upon request from the U.S. Congress and the Department of Energy, the National Research Council was asked to assemble a committee of experts to examine the scale, scope, and consequences of seismicity induced during fluid injection and withdrawal associated with geothermal energy development, oil and gas development, and carbon capture and storage (CCS). The committee's report, publicly released in June 2012, indicates that induced seismicity associated with fluid injection or withdrawal is caused in most cases by change in pore fluid pressure and/or change in stress in the subsurface in the presence of faults with specific properties and orientations and a critical state of stress in the rocks. The factor that appears to have the most direct consequence in regard to induced seismicity is the net fluid balance (total balance of fluid introduced into or removed from the subsurface). Energy technology projects that are designed to maintain a balance between the amount of fluid being injected and withdrawn, such as most oil and gas development projects, appear to produce fewer seismic events than projects that do not maintain fluid balance. Major findings from the study include: (1) as presently implemented, the process of hydraulic fracturing for shale gas recovery does not pose a high risk for inducing felt seismic events; (2) injection for disposal of waste water derived from energy technologies does pose some risk for induced seismicity, but very few events have been documented over the past several decades relative to the large number of disposal wells in operation; and (3) CCS, due to the large net volumes of injected fluids suggested for future large-scale carbon storage projects, may have potential for inducing larger seismic events.

  2. 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.

  3. 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.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

    Howell, P. C.

    2012-12-01

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

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

    PubMed

    Howell, P C

    2012-12-14

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

  7. 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.

  8. Caveat Emptor: Calculating All the Costs of Energy.

    ERIC Educational Resources Information Center

    Zinberg, Dorothy S.

    This paper examines the energy problem. Specific topics discussed include the recent history of oil and gas consumption in the United States, conservation, coal, solar energy, and nuclear energy. While solutions to the energy problem differ, there is an urgent need for broad, public debate. Ultimately, the decisions made regarding energy will be…

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

    NASA Astrophysics Data System (ADS)

    Jiao, Li-Guang; Ho, Yew Kam

    2014-05-01

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

  10. Certification and the potential energy landscape

    SciTech Connect

    Mehta, Dhagash; Hauenstein, Jonathan D.; Wales, David J.

    2014-06-14

    Typically, there is no guarantee that a numerical approximation obtained using standard nonlinear equation solvers is indeed an actual solution, meaning that it lies in the quadratic convergence basin. Instead, it may lie only in the linear convergence basin, or even in a chaotic region, and hence not converge to the corresponding stationary point when further optimization is attempted. In some cases, these non-solutions could be misleading. Proving that a numerical approximation will quadratically converge to a stationary point is termed certification. In this report, we provide details of how Smale's α-theory can be used to certify numerically obtained stationary points of a potential energy landscape, providing a mathematical proof that the numerical approximation does indeed correspond to an actual stationary point, independent of the precision employed.

  11. An ab initio calculation of the rotational-vibrational energies in the electronic ground state of NH2

    NASA Astrophysics Data System (ADS)

    Jensen, Per; Buenker, Robert J.; Hirsch, Gerhard; Rai, Sachchida N.

    We have calculated ab initio the three-dimensional potential-energy surface of the NH2 molecule at 145 nuclear geometries spanning energy ranges of about 18 000 cm-1 for the NH stretch and 12 000 cm-1 for the bend. The ab initio configuration-interaction calculations were done using the multireference MRD-CI method. The calculated equilibrium configuration has NH bond length re = 1·0207 Å and bond angle α = 103·1°. The rotational-vibrational energies for 14NH2, 14NHD and 14ND2 were calculated variationally using the Morse-oscillator rigid-bender internal-dynamics Hamiltonian. For 14NH2 we calculate that υ1 = 3267 (3219) cm-1, υ2 = 1462 (1497) cm-1 and υ3 = 3283 (3301) cm-1, where experimental values are given in parentheses.

  12. Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

    NASA Astrophysics Data System (ADS)

    Zeng, Xiancheng; Hu, Hao; Hu, Xiangqian; Yang, Weitao

    2009-04-01

    A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids "on-the-fly" QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.

  13. Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

    SciTech Connect

    Zeng Xiancheng; Hu Hao; Hu Xiangqian; Yang Weitao

    2009-04-28

    A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids 'on-the-fly' QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.

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

    PubMed

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

    2016-01-01

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

  15. The Wind Energy Potential of Kurdistan, Iran.

    PubMed

    Arefi, Farzad; Moshtagh, Jamal; Moradi, Mohammad

    2014-01-01

    In the current work by using statistical methods and available software, the wind energy assessment of prone regions for installation of wind turbines in, Qorveh, has been investigated. Information was obtained from weather stations of Baneh, Bijar, Zarina, Saqez, Sanandaj, Qorveh, and Marivan. The monthly average and maximum of wind speed were investigated between the years 2000-2010 and the related curves were drawn. The Golobad curve (direction and percentage of dominant wind and calm wind as monthly rate) between the years 1997-2000 was analyzed and drawn with plot software. The ten-minute speed (at 10, 30, and 60 m height) and direction (at 37.5 and 10 m height) wind data were collected from weather stations of Iranian new energy organization. The wind speed distribution during one year was evaluated by using Weibull probability density function (two-parametrical), and the Weibull curve histograms were drawn by MATLAB software. According to the average wind speed of stations and technical specifications of the types of turbines, the suitable wind turbine for the station was selected. Finally, the Divandareh and Qorveh sites with favorable potential were considered for installation of wind turbines and construction of wind farms. PMID:27355042

  16. The Wind Energy Potential of Kurdistan, Iran

    PubMed Central

    Arefi, Farzad; Moshtagh, Jamal; Moradi, Mohammad

    2014-01-01

    In the current work by using statistical methods and available software, the wind energy assessment of prone regions for installation of wind turbines in, Qorveh, has been investigated. Information was obtained from weather stations of Baneh, Bijar, Zarina, Saqez, Sanandaj, Qorveh, and Marivan. The monthly average and maximum of wind speed were investigated between the years 2000–2010 and the related curves were drawn. The Golobad curve (direction and percentage of dominant wind and calm wind as monthly rate) between the years 1997–2000 was analyzed and drawn with plot software. The ten-minute speed (at 10, 30, and 60 m height) and direction (at 37.5 and 10 m height) wind data were collected from weather stations of Iranian new energy organization. The wind speed distribution during one year was evaluated by using Weibull probability density function (two-parametrical), and the Weibull curve histograms were drawn by MATLAB software. According to the average wind speed of stations and technical specifications of the types of turbines, the suitable wind turbine for the station was selected. Finally, the Divandareh and Qorveh sites with favorable potential were considered for installation of wind turbines and construction of wind farms. PMID:27355042

  17. Energy resource potential of natural gas hydrates

    USGS Publications Warehouse

    Collett, T.S.

    2002-01-01

    The discovery of large gas hydrate accumulations in terrestrial permafrost regions of the Arctic and beneath the sea along the outer continental margins of the world's oceans has heightened interest in gas hydrates as a possible energy resource. However, significant to potentially insurmountable technical issues must be resolved before gas hydrates can be considered a viable option for affordable supplies of natural gas. The combined information from Arctic gas hydrate studies shows that, in permafrost regions, gas hydrates may exist at subsurface depths ranging from about 130 to 2000 m. The presence of gas hydrates in offshore continental margins has been inferred mainly from anomalous seismic reflectors, known as bottom-simulating reflectors, that have been mapped at depths below the sea floor ranging from about 100 to 1100 m. Current estimates of the amount of gas in the world's marine and permafrost gas hydrate accumulations are in rough accord at about 20,000 trillion m3. Disagreements over fundamental issues such as the volume of gas stored within delineated gas hydrate accumulations and the concentration of gas hydrates within hydrate-bearing strata have demonstrated that we know little about gas hydrates. Recently, however, several countries, including Japan, India, and the United States, have launched ambitious national projects to further examine the resource potential of gas hydrates. These projects may help answer key questions dealing with the properties of gas hydrate reservoirs, the design of production systems, and, most important, the costs and economics of gas hydrate production.

  18. Molecular Multipole Potential Energy Functions for Water.

    PubMed

    Tan, Ming-Liang; Tran, Kelly N; Pickard, Frank C; Simmonett, Andrew C; Brooks, Bernard R; Ichiye, Toshiko

    2016-03-01

    Water is the most common liquid on this planet, with many unique properties that make it essential for life as we know it. These properties must arise from features in the charge distribution of a water molecule, so it is essential to capture these features in potential energy functions for water to reproduce its liquid state properties in computer simulations. Recently, models that utilize a multipole expansion located on a single site in the water molecule, or "molecular multipole models", have been shown to rival and even surpass site models with up to five sites in reproducing both the electrostatic potential around a molecule and a variety of liquid state properties in simulations. However, despite decades of work using multipoles, confusion still remains about how to truncate the multipole expansions efficiently and accurately. This is particularly important when using molecular multipole expansions to describe water molecules in the liquid state, where the short-range interactions must be accurate, because the higher order multipoles of a water molecule are large. Here, truncation schemes designed for a recent efficient algorithm for multipoles in molecular dynamics simulations are assessed for how well they reproduce results for a simple three-site model of water when the multipole moments and Lennard-Jones parameters of that model are used. In addition, the multipole analysis indicates that site models that do not account for out-of-plane electron density overestimate the stability of a non-hydrogen-bonded conformation, leading to serious consequences for the simulated liquid. PMID:26562223

  19. Enhanced ligand sampling for relative protein-ligand binding free energy calculations.

    PubMed

    Kaus, Joseph W; McCammon, J Andrew

    2015-05-21

    Free energy calculations are used to study how strongly potential drug molecules interact with their target receptors. The accuracy of these calculations depends on the accuracy of the molecular dynamics (MD) force field as well as proper sampling of the major conformations of each molecule. However, proper sampling of ligand conformations can be difficult when there are large barriers separating the major ligand conformations. An example of this is for ligands with an asymmetrically substituted phenyl ring, where the presence of protein loops hinders the proper sampling of the different ring conformations. These ring conformations become more difficult to sample when the size of the functional groups attached to the ring increases. The Adaptive Integration Method (AIM) has been developed, which adaptively changes the alchemical coupling parameter λ during the MD simulation so that conformations sampled at one λ can aid sampling at the other λ values. The Accelerated Adaptive Integration Method (AcclAIM) builds on AIM by lowering potential barriers for specific degrees of freedom at intermediate λ values. However, these methods may not work when there are very large barriers separating the major ligand conformations. In this work, we describe a modification to AIM that improves sampling of the different ring conformations, even when there is a very large barrier between them. This method combines AIM with conformational Monte Carlo sampling, giving improved convergence of ring populations and the resulting free energy. This method, called AIM/MC, is applied to study the relative binding free energy for a pair of ligands that bind to thrombin and a different pair of ligands that bind to aspartyl protease β-APP cleaving enzyme 1 (BACE1). These protein-ligand binding free energy calculations illustrate the improvements in conformational sampling and the convergence of the free energy compared to both AIM and AcclAIM. PMID:25906170

  20. Enhanced Ligand Sampling for Relative Protein–Ligand Binding Free Energy Calculations

    PubMed Central

    2016-01-01

    Free energy calculations are used to study how strongly potential drug molecules interact with their target receptors. The accuracy of these calculations depends on the accuracy of the molecular dynamics (MD) force field as well as proper sampling of the major conformations of each molecule. However, proper sampling of ligand conformations can be difficult when there are large barriers separating the major ligand conformations. An example of this is for ligands with an asymmetrically substituted phenyl ring, where the presence of protein loops hinders the proper sampling of the different ring conformations. These ring conformations become more difficult to sample when the size of the functional groups attached to the ring increases. The Adaptive Integration Method (AIM) has been developed, which adaptively changes the alchemical coupling parameter λ during the MD simulation so that conformations sampled at one λ can aid sampling at the other λ values. The Accelerated Adaptive Integration Method (AcclAIM) builds on AIM by lowering potential barriers for specific degrees of freedom at intermediate λ values. However, these methods may not work when there are very large barriers separating the major ligand conformations. In this work, we describe a modification to AIM that improves sampling of the different ring conformations, even when there is a very large barrier between them. This method combines AIM with conformational Monte Carlo sampling, giving improved convergence of ring populations and the resulting free energy. This method, called AIM/MC, is applied to study the relative binding free energy for a pair of ligands that bind to thrombin and a different pair of ligands that bind to aspartyl protease β-APP cleaving enzyme 1 (BACE1). These protein–ligand binding free energy calculations illustrate the improvements in conformational sampling and the convergence of the free energy compared to both AIM and AcclAIM. PMID:25906170

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

    NASA Astrophysics Data System (ADS)

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

    1998-02-01

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

  2. 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.

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

    NASA Astrophysics Data System (ADS)

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

    1990-09-01

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

  4. Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution.

    PubMed

    Rosta, Edina; Haranczyk, Maciej; Chu, Zhen T; Warshel, Arieh

    2008-05-01

    Reliable studies of enzymatic reactions by combined quantum mechanical/molecular mechanics (QM(ai)/MM) approaches with an ab initio description of the quantum region presents a major challenge to computational chemists. The main problem is the need for very large computer time to evaluate the QM energy, which in turn makes it extremely challenging to perform proper configurational sampling. One of the most obvious options for accelerating QM/MM simulations is the use of an average solvent potential. In fact, the idea of using an average solvent potential is rather obvious and has implicitly been used in Langevin dipole/QM calculations. However, in the case of explicit solvent models the practical implementations are more challenging, and the accuracy of the averaging approach has not been validated. The present study introduces the average effect of the fluctuating solvent charges by using equivalent charge distributions, which are updated every m steps. Several models are evaluated in terms of the resulting accuracy and efficiency. The most effective model divides the system into an inner region with N explicit solvent atoms and an external region with two effective charges. Different models are considered in terms of the division of the solvent system and the update frequency. Another key element of our approach is the use of the free energy perturbation (FEP) and/or linear response approximation treatments that guarantees the evaluation of the rigorous solvation free energy. Special attention is paid to the convergence of the calculated solvation free energies and the corresponding solute polarization. The performance of the method is examined by evaluating the solvation of a water molecule and a formate ion in water and also the dipole moment of water in water solution. Remarkably, it is found that different averaging procedures eventually converge to the same value but some protocols provide optimal ways of obtaining the final QM(ai)/MM converged results. The

  5. Accelerating QM/MM Free Energy Calculations: Representing the Surroundings by an Updated Mean Charge Distribution

    PubMed Central

    Rosta, Edina; Haranczyk, Maciej; Chu, Zhen T.; Warshel, Arieh

    2009-01-01

    Reliable studies of enzymatic reactions by combined quantum mechanical /molecular mechanics (QM(ai)/MM) approaches, with an ab initio description of the quantum region, presents a major challenge to computational chemists. The main problem is the need for very large computer time to evaluate the QM energy, which in turn makes it extremely challenging to perform proper configurational sampling. One of the most obvious options for accelerating QM/MM simulations is the use of an average solvent potential. In fact the idea of using an average solvent potential is rather obvious and has implicitly been used in Langevin dipole / QM calculations. However, in the case of explicit solvent models the practical implementations are more challenging and the accuracy of the averaging approach has not been validated. The present study introduces the average effect of the fluctuating solvent charges by using equivalent charge distributions, which are updated every m steps. Several models are evaluated in terms of the resulting accuracy and efficiency. The most effective model divides the system into an inner region with N explicit solvent atoms and an external region with two effective charges. Different models are considered in terms of the division of the solvent system and the update frequency. Another key element of our approach is the use of the free energy perturbation (FEP) and/or linear response approximation (LRA) treatments that guarantees the evaluation of the rigorous solvation free energy. Special attention is paid to the convergence of the calculated solvation free energies and the corresponding solute polarization. The performance of the method is examined by evaluating the solvation of a water molecule and a formate ion in water and also the dipole moment of water in water solution. Remarkably, it is found that different averaging procedures eventually converge to the same value but some protocols provide optimal ways of obtaining the final QM(ai)/MM converged

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

    NASA Technical Reports Server (NTRS)

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

    2001-01-01

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

  7. Microscopically derived potential energy surfaces from mostly structural considerations

    NASA Astrophysics Data System (ADS)

    Ermamatov, M. J.; Hess, Peter O.

    2016-08-01

    A simple procedure to estimate the quadrupole Potential-Energy-Surface (PES) is presented, using mainly structural information, namely the content of the shell model space and the Pauli exclusion principle. Further microscopic properties are implicitly contained through the use of results from the Möller and Nix tables or experimental information. A mapping to the geometric potential is performed yielding the PES. The General Collective Model is used in order to obtain an estimate on the spectrum and quadrupole transitions, adjusting only the mass parameter. First, we test the conjecture on known nuclei, deriving the PES and compare them to known data. We will see that the PES approximates very well the structure expected. Having acquired a certain confidence, we predict the PES of several chain of isotopes of heavy and super-heavy nuclei and at the end we investigate the structure of nuclei in the supposed island of stability. One of the main points to show is that simple assumptions can provide already important information on the structure of nuclei outside known regions and that spectra and electromagnetic transitions can be estimated without using involved calculations and assumptions. The procedure does not allow to calculate binding energies. The method presented can be viewed as a starting point for further improvements.

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

    PubMed

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

    2016-07-01

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

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

    SciTech Connect

    Ni Dongdong; Ren Zhongzhou

    2009-11-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

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

    SciTech Connect

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

    2015-11-14

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

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

    PubMed

    Schiffmann, Christoph; Sebastiani, Daniel

    2011-05-10

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

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

    PubMed

    Brini, E; van der Vegt, N F A

    2012-10-21

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2010-11-01

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

  16. Energy spectra of the hyperbolic and second Poeschl-Teller like potentials solved by new exact quantization rule

    SciTech Connect

    Dong Shihai Gonzalez-Cisneros, A.

    2008-05-15

    A new exact quantization rule simplifies the calculation of the energy levels for the exactly solvable quantum system. In this work we calculate the energy levels of the Schroedinger equation with the hyperbolic potential by this quantization rule. The corresponding eigenfunction is also derived for completeness. The second Poeschl-Teller like potential case is also carried out.

  17. 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.

  18. Ab initio potential energy surface and rovibrational states of HBO

    NASA Astrophysics Data System (ADS)

    Ha, Tae-Kyu; Makarewicz, Jan

    1999-01-01

    The potential energy surface describing the large-amplitude motion of H around the BO core in the HBO molecule has been determined from ab initio calculations. This surface has been sampled by a set of 170 grid points from a two-dimensional space defined by the stretching and the bending coordinates of the H nucleus. At each grid point, the BO bond length has been optimized using the second-order Møller-Plesset perturbation theory with the basis set aug-cc-pVTZ. The surface has a local minimum for the linear as well as the bent configuration of HBO. A low energy barrier to the linear configuration BOH causes a large-amplitude motion and a strong rovibrational interaction in the molecule. Its rovibrational dynamics is different from the dynamics in bent or quasilinear triatomic molecules.

  19. Finite field-energy and interparticle potential in logarithmic electrodynamics

    NASA Astrophysics Data System (ADS)

    Gaete, Patricio; Helayël-Neto, José

    2014-03-01

    We pursue an investigation of logarithmic electrodynamics, for which the field energy of a point-like charge is finite, as happens in the case of the usual Born-Infeld electrodynamics. We also show that, contrary to the latter, logarithmic electrodynamics exhibits the feature of birefringence. Next, we analyze the lowest-order modifications for both logarithmic electrodynamics and for its non-commutative version, within the framework of the gauge-invariant path-dependent variables formalism. The calculation shows a long-range correction (-type) to the Coulomb potential for logarithmic electrodynamics. Interestingly enough, for its non-commutative version, the interaction energy is ultraviolet finite. We highlight the role played by the new quantum of length in our analysis.

  20. Stabilized quasi-Newton optimization of noisy potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Schaefer, Bastian; Ghasemi, S. Alireza; Roy, Shantanu; Goedecker, Stefan; Goedecker Group Team

    Optimizations of atomic positions belong to the most frequently performed tasks in electronic structure calculations. Many simulations like global minimum searches or the identification of chemical reaction pathways can require the computation of hundreds or thousands of minimizations or saddle points. To automatize these tasks, optimization algorithms must not only be efficient but also very reliable. Unfortunately, computational noise in forces and energies is inherent to electronic structure codes. This computational noise poses a severe problem to the stability of efficient optimization methods like the limited-memory Broyden-Fletcher-Goldfarb-Shanno algorithm. In this talk a recently published technique that allows to obtain significant curvature information of noisy potential energy surfaces is presented. This technique was used to construct both, a stabilized quasi-Newton minimization method and a stabilized quasi-Newton saddle finding approach. With the help of benchmarks both the minimizer and the saddle finding approach were demonstrated to be superior to comparable existing methods.

  1. Potential energy curves and collision integrals of air components

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Stallcop, James R.; Levin, Eugene; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Collision integrals are fundamental quantities required to determine the transport properties of the environment surrounding aerospace vehicles in the upper atmosphere. These collision integrals can be determined as a function of temperature from the potential energy curves describing the atomic and molecular collisions. Ab initio calculations provide a practical method of computing the required interaction potentials. In this work we will discuss recent advances with an emphasis on the accuracy that is obtainable. Results for interactions, e.g. N+N, N+O, O+O, and H+N2 will be reviewed and their application to the determination of transport properties, such as diffusion and viscosity coefficients, will be examined.

  2. On the importance of full-dimensionality in low-energy molecular scattering calculations

    PubMed Central

    Faure, Alexandre; Jankowski, Piotr; Stoecklin, Thierry; Szalewicz, Krzysztof

    2016-01-01

    Scattering of H2 on CO is of great importance in astrophysics and also is a benchmark system for comparing theory to experiment. We present here a new 6-dimensional potential energy surface for the ground electronic state of H2-CO with an estimated uncertainty of about 0.6 cm−1 in the global minimum region, several times smaller than achieved earlier. This potential has been used in nearly exact 6-dimensional quantum scattering calculations to compute state-to-state cross-sections measured in low-energy crossed-beam experiments. Excellent agreement between theory and experiment has been achieved in all cases. We also show that the fully 6-dimensional approach is not needed with the current accuracy of experimental data since an equally good agreement with experiment was obtained using only a 4-dimensional treatment, which validates the rigid-rotor approach widely used in scattering calculations. This finding, which disagrees with some literature statements, is important since for larger systems full-dimensional scattering calculations are currently not possible. PMID:27333870

  3. On the importance of full-dimensionality in low-energy molecular scattering calculations.

    PubMed

    Faure, Alexandre; Jankowski, Piotr; Stoecklin, Thierry; Szalewicz, Krzysztof

    2016-01-01

    Scattering of H2 on CO is of great importance in astrophysics and also is a benchmark system for comparing theory to experiment. We present here a new 6-dimensional potential energy surface for the ground electronic state of H2-CO with an estimated uncertainty of about 0.6 cm(-1) in the global minimum region, several times smaller than achieved earlier. This potential has been used in nearly exact 6-dimensional quantum scattering calculations to compute state-to-state cross-sections measured in low-energy crossed-beam experiments. Excellent agreement between theory and experiment has been achieved in all cases. We also show that the fully 6-dimensional approach is not needed with the current accuracy of experimental data since an equally good agreement with experiment was obtained using only a 4-dimensional treatment, which validates the rigid-rotor approach widely used in scattering calculations. This finding, which disagrees with some literature statements, is important since for larger systems full-dimensional scattering calculations are currently not possible. PMID:27333870

  4. Direct computation of general chemical energy differences: Application to ionization potentials, excitation, and bond energies

    SciTech Connect

    Beste, Ariana; Harrison, Robert J; Yanai, Takeshi

    2006-01-01

    Chemists are mainly interested in energy differences. In contrast, most quantum chemical methods yield the total energy which is a large number compared to the difference and has therefore to be computed to a higher relative precision than would be necessary for the difference alone. Hence, it is desirable to compute energy differences directly, thereby avoiding the precision problem. Whenever it is possible to find a parameter which transforms smoothly from an initial to a final state, the energy difference can be obtained by integrating the energy derivative with respect to that parameter (c.f., thermodynamic integration or adiabatic connection methods). If the dependence on the parameter is predominantly linear, accurate results can be obtained by single-point integration. In density functional theory (DFT) and Hartree-Fock, we applied the formalism to ionization potentials, excitation energies, and chemical bond breaking. Example calculations for ionization potentials and excitation energies showed that accurate results could be obtained with a linear estimate. For breaking bonds, we introduce a non-geometrical parameter which gradually turns the interaction between two fragments of a molecule on. The interaction changes the potentials used to determine the orbitals as well as constraining the orbitals to be orthogonal.

  5. Direct computation of general chemical energy differences: Application to ionization potentials, excitation, and bond energies

    NASA Astrophysics Data System (ADS)

    Beste, A.; Harrison, R. J.; Yanai, T.

    2006-08-01

    Chemists are mainly interested in energy differences. In contrast, most quantum chemical methods yield the total energy which is a large number compared to the difference and has therefore to be computed to a higher relative precision than would be necessary for the difference alone. Hence, it is desirable to compute energy differences directly, thereby avoiding the precision problem. Whenever it is possible to find a parameter which transforms smoothly from an initial to a final state, the energy difference can be obtained by integrating the energy derivative with respect to that parameter (cf. thermodynamic integration or adiabatic connection methods). If the dependence on the parameter is predominantly linear, accurate results can be obtained by single-point integration. In density functional theory and Hartree-Fock, we applied the formalism to ionization potentials, excitation energies, and chemical bond breaking. Example calculations for ionization potentials and excitation energies showed that accurate results could be obtained with a linear estimate. For breaking bonds, we introduce a nongeometrical parameter which gradually turns the interaction between two fragments of a molecule on. The interaction changes the potentials used to determine the orbitals as well as the constraint on the orbitals to be orthogonal.

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

    PubMed

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

    2013-12-01

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

  7. Transition Metal Oxide Alloys as Potential Solar Energy Conversion Materials

    SciTech Connect

    Toroker, Maytal; Carter, Emily A.

    2013-02-21

    First-row transition metal oxides (TMOs) are inexpensive potentia alternative materials for solar energy conversion devices. However, some TMOs, such as manganese(II) oxide, have band gaps that are too large for efficiently absorbing solar energy. Other TMOs, such as iron(II) oxide, have conduction and valence band edges with the same orbital character that may lead to unfavorably high electron–hole recombination rates. Another limitation of iron(II) oxide is that the calculated valence band edge is not positioned well for oxidizing water. We predict that key properties, including band gaps, band edge positions, and possibly electron–hole recombination rates, may be improved by alloying TMOs that have different band alignments. A new metric, the band gap center offset, is introduced for simple screening of potential parent materials. The concept is illustrated by calculating the electronic structure of binary oxide alloys that contain manganese, nickel, iron, zinc, and/or magnesium, within density functional theory (DFT)+U and hybrid DFT theories. We conclude that alloys of iron(II) oxide are worth evaluating further as solar energy conversion materials.

  8. The Direct Calculation of Solid and Liquid Free Energies of Metals and Alloys Using the Embedded Atom Method

    NASA Astrophysics Data System (ADS)

    Song, Xueyu; Morris, James

    2003-03-01

    We present a method of directly and accurately calculating the free energy of metals and alloys, directly from models such as the Embedded Atom Method (EAM). An effective pair potential is defined, and used in an extended Weeks-Chandler-Andersen (WCA) approach. An effective hard-sphere density is defined, and perturbations from the hard-sphere limit are calculated using the pair correlation functions calculated from density functional theory. Calculations using the Mei and Davenport EAM potential for Al, with the modifications of Sturgeon and Laird, demonstrate the accuracy of the approach for both the liquid and solid phases by comparison with simulations. These results are the first step toward the direct calculation of the solid-liquid interfacial free energy for metallic systems, an important parameter for classical nucleation theory and for solidification dynamics. Our recent simulation results for the interfacial free energy provides an important test of the inhomogeneous theory. We also present preliminary results for binary systems, where the direct calculation of phase diagrams based upon the inter-atomic potentials will be compared with simulations. The approach will also allow for the direct calculation of the properties of under-cooled liquid metals and alloys.

  9. Recent advances in QM/MM free energy calculations using reference potentials☆

    PubMed Central

    Duarte, Fernanda; Amrein, Beat A.; Blaha-Nelson, David; Kamerlin, Shina C.L.

    2015-01-01

    Background Recent years have seen enormous progress in the development of methods for modeling (bio)molecular systems. This has allowed for the simulation of ever larger and more complex systems. However, as such complexity increases, the requirements needed for these models to be accurate and physically meaningful become more and more difficult to fulfill. The use of simplified models to describe complex biological systems has long been shown to be an effective way to overcome some of the limitations associated with this computational cost in a rational way. Scope of review Hybrid QM/MM approaches have rapidly become one of the most popular computational tools for studying chemical reactivity in biomolecular systems. However, the high cost involved in performing high-level QM calculations has limited the applicability of these approaches when calculating free energies of chemical processes. In this review, we present some of the advances in using reference potentials and mean field approximations to accelerate high-level QM/MM calculations. We present illustrative applications of these approaches and discuss challenges and future perspectives for the field. Major conclusions The use of physically-based simplifications has shown to effectively reduce the cost of high-level QM/MM calculations. In particular, lower-level reference potentials enable one to reduce the cost of expensive free energy calculations, thus expanding the scope of problems that can be addressed. General significance As was already demonstrated 40 years ago, the usage of simplified models still allows one to obtain cutting edge results with substantially reduced computational cost. This article is part of a Special Issue entitled Recent developments of molecular dynamics. PMID:25038480

  10. An ab initio method for locating potential energy minima

    SciTech Connect

    Bock, Nicolas; Peery, Travis; Venneri, Giulia; Chisolm, Eric; Wallace, Duane; Lizarraga, Raquel; Holmstrom, Erik

    2009-01-01

    We study the potential energy landscape underlying the motion of monatomic liquids by quenching from random initial configurations (stochastic configurations) to the nearest local minimum of the potential energy. We show that this procedure reveals the underlying potential energy surface directly. This is in contrast to the common technique of quenching from a molecular dynamics trajectory which does not allow a direct view of the underlying potential energy surface, but needs to be corrected for thermodynamic weighting factors.

  11. A program to calculate non-bonded interaction energy in biomolecular aggregates.

    PubMed

    Sundaram, K; Prasad, C V

    1982-02-01

    This paper describes a program to calculate intermolecular as well as intramolecular electronic potential energy resulting from non-bonded interactions. The underlying theory is obtained by the application of Rayleigh-Schroedinger perturbation theory to non-overlap regions of a molecular system. The rigorous theoretical expressions for the energy terms are simplified by approximations consistent with those commonly employed in semi-empirical molecular orbital theories. The program is particularly suited for the study of biomolecular assemblies, and in situations where insight into contributions to total energy from various component interaction types is desired. The inclusion of the non-additive dispersion effects in this approach makes it especially interesting for the study of cooperative phenomena in the light of a recent finding [1]. PMID:7067416

  12. Free energy calculations using dual-level Born-Oppenheimer molecular dynamics

    NASA Astrophysics Data System (ADS)

    Retegan, Marius; Martins-Costa, Marilia; Ruiz-López, Manuel F.

    2010-08-01

    We describe an efficient and accurate method to compute free energy changes in complex chemical systems that cannot be described through classical molecular dynamics simulations, examples of which are chemical and photochemical reactions in solution, enzymes, interfaces, etc. It is based on the use of dual-level Born-Oppenheimer molecular dynamics simulations. A low-level quantum mechanical method is employed to calculate the potential of mean force through the umbrella sampling technique. Then, a high-level quantum mechanical method is used to estimate a free energy correction on selected points of the reaction coordinate using perturbation theory. The precision of the results is comparable to that of ab initio molecular dynamics methods such as the Car-Parrinello approach but the computational cost is much lower, roughly by two to three orders of magnitude. The method is illustrated by discussing the association free energy of simple organometallic compounds, although the field of application is very broad.

  13. Energy Savings Calculations for Heat Island Reduction Strategies in Baton Rouge, Sacramento and Salt Lake City

    SciTech Connect

    Konopacki, S.; Akbari, H.

    2000-03-01

    In 1997, the US Environmental Protection Agency (EPA) established the ''Heat Island Reduction Initiative'', to quantify the potential benefits of Heat Island Reduction (HIR) strategies (i.e., shade trees, reflective roofs, reflective pavements and urban vegetation) to reduce cooling energy use in buildings, lower the ambient air temperature and improve urban air quality in cities, and reduce CO2 emissions from power plants. Under this initiative, the Urban Heat Island Pilot Project (UHIPP) was created with the objective to investigate the potential of HIR strategies in residential and commercial buildings in three initial UHIPP cities: Baton Rouge, Sacramento and Salt Lake City. This paper summarizes our efforts to calculate the annual energy savings, peak power avoidance and annual C02 reduction of HIR strategies in the three initial cities. In this analysis, we focused on three building types that offer most savings potential: single-family residence, office and retail store. Each building type was characterized in detail by old or new construction and with a gas furnace or an electric heat pump. We defined prototypical building characteristics for each building type and simulated the impact of HIR strategies on building cooling and heating energy use and peak power demand using the DOE-2.IE model. Our simulations included the impact of (1) strategically-placed shade trees near buildings [direct effect], (2) use of high-albedo roofing material on building [direct effect], (3) combined strategies I and 2 [direct effect], (4) urban reforestation with high-albedo pavements and building surfaces [indirect effect] and (5) combined strategies 1, 2 and 4 [direct and indirect effects]. We then estimated the total roof area of air-conditioned buildings in each city using readily obtainable data to calculate the metropolitan-wide impact of HIR strategies. The results show, that in Baton Rouge, potential annual energy savings of $15M could be realized by rate-payers from

  14. Ab initio based calculations of vacancy formation and clustering energies including lattice relaxation in Fe{sub 3}Al

    SciTech Connect

    Muratov, L.S.; Cooper, B.R.; Wills, J.M.

    1999-07-01

    Vacancy formation and clustering significantly affect structural properties of transition-metal aluminides. Ab-initio quantum mechanical total-energy calculations using a full-potential linear combination of muffin-tin orbitals (LMTO) technique provide a convenient method of studying relevant characteristics such as changes in density of states, and charge redistribution around defects. Augmented with Hellmann-Feymann forces, LMTO allows calculations of relaxation geometries and relaxation energies. The authors have performed such calculations for vacancies and antisite substitutional point defects in Fe{sub 3}Al with DO{sub 3} crystallographic structure. There are two limiting factors complicating calculations of defect formation energies directly from ab-initio calculations. The first is that a single defect, due to the lattice periodicity necessitated by the use of ab-initio total energy techniques, cannot be considered as an isolated defect, even in the maximum computable simulation cell. The second complication is the fact that chemical potentials of elements cannot be directly extracted from the total energy calculations for the compound. To deal with this problem, the authors considered two possible approximations and compared results, which were found to be quite similar for iron vacancies.

  15. Calculation of positron binding energies using the generalized any particle propagator theory

    SciTech Connect

    Romero, Jonathan; Charry, Jorge A.; Flores-Moreno, Roberto; Varella, Márcio T. do N.; Reyes, Andrés

    2014-09-21

    We recently extended the electron propagator theory to any type of quantum species based in the framework of the Any-Particle Molecular Orbital (APMO) approach [J. Romero, E. Posada, R. Flores-Moreno, and A. Reyes, J. Chem. Phys. 137, 074105 (2012)]. The generalized any particle molecular orbital propagator theory (APMO/PT) was implemented in its quasiparticle second order version in the LOWDIN code and was applied to calculate nuclear quantum effects in electron binding energies and proton binding energies in molecular systems [M. Díaz-Tinoco, J. Romero, J. V. Ortiz, A. Reyes, and R. Flores-Moreno, J. Chem. Phys. 138, 194108 (2013)]. In this work, we present the derivation of third order quasiparticle APMO/PT methods and we apply them to calculate positron binding energies (PBEs) of atoms and molecules. We calculated the PBEs of anions and some diatomic molecules using the second order, third order, and renormalized third order quasiparticle APMO/PT approaches and compared our results with those previously calculated employing configuration interaction (CI), explicitly correlated and quantum Montecarlo methodologies. We found that renormalized APMO/PT methods can achieve accuracies of ∼0.35 eV for anionic systems, compared to Full-CI results, and provide a quantitative description of positron binding to anionic and highly polar species. Third order APMO/PT approaches display considerable potential to study positron binding to large molecules because of the fifth power scaling with respect to the number of basis sets. In this regard, we present additional PBE calculations of some small polar organic molecules, amino acids and DNA nucleobases. We complement our numerical assessment with formal and numerical analyses of the treatment of electron-positron correlation within the quasiparticle propagator approach.

  16. ASSESSMENT OF ENERGY RECOVERY POTENTIAL OF INDUSTRIAL COMBUSTION EQUIPMENT

    EPA Science Inventory

    An assessment was conducted to evaluate the waste heat content and energy recovery potential of flue gases from 30 industrial combustion devices. Pollution controls on nine of the devices were evaluated to estimate energy requirements and particulate reduction; energy requirement...

  17. Ab-initio based calculations of vacancy formation and clustering energies including lattice relaxation in Fe{sub 3}Al

    SciTech Connect

    Muratov, L.S.; Cooper, B.R.; Wills, J.M.

    1999-03-01

    Vacancy formation and clustering significantly affect structural properties of transition-metal aluminides. Ab-initio quantum mechanical total-energy calculations using a full-potential linear combination of muffin-tin orbitals (LMTO) technique provide a convenient method of studying relevant characteristics such as changes in density of states, and charge redistribution around defects. Augmented with Hellmann-Feymann forces, LMTO allows calculations of relaxation geometries and relaxation energies. The authors have performed such calculations for vacancies and antisite substitutional point defects in Fe{sub 3}Al with DO{sub 3} crystallographic structure. There are two limiting factors complicating calculations of defect formation energies directly from ab-initio calculations. The first is that a single defect, due to the lattice periodicity necessitated by the use of ab-initio total energy techniques, cannot be considered as an isolated defect, even in the maximum computable simulation cell. Unlike previous calculations, which did not find a dependency on the size of the simulation cell, the calculations have shown a significant difference in results for 32- and 16- atom cells. This difference provides information about vacancy clustering since it can be explained by a relatively small attractive interaction energy {approximately} 0.2 eV between two vacancies located in adjacent simulation cells and separated by the lattice constant distance (5.52 {angstrom}). By comparing the internal energies for two configurations of 30 atom cells (32 atom--2 vacancies), the authors were able to estimate that the attractive interaction between two vacancies could reach 1.2 eV. The second complication is the fact that chemical potentials of elements cannot be directly extracted from the total energy calculations for the compound. To deal with this problem, they considered two possible approximations and compared results, which were found to be quite similar for iron vacancies.

  18. Transportation Energy Use and Conservation Potential

    ERIC Educational Resources Information Center

    Hirst, Eric

    1973-01-01

    Analyzes transportation energy consumption and energy intensiveness for inter-city freight and passenger traffic and urban passenger traffic with the definition of energy intensiveness as Btu per ton-mile or per passenger-mile. Indicates that public education is one of three ways to achieve the goals of energy conservation. (CC)

  19. Locating all transition states and studying the reaction pathways of potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Westerberg, K. M.; Floudas, C. A.

    1999-05-01

    We propose a new method for calculating all stationary states, including saddle points of all orders, of a potential energy surface based on the αBB deterministic branch and bound global optimization algorithm. This method is based on rigorous optimization methods and offers a theoretical guarantee of enclosing all solutions to the equation ∇V=0. We apply this method to Murrel-Sorbie analytic potential energy surfaces of HCN, HSiN, HBO, and CS2, and to the Empirical Conformational Energy Program for Peptides (ECEPP/3) potential energy surfaces of alanine, alanine dipeptide, and tetra-alanine. For alanine, alanine dipeptide, and tetra-alanine, we proceed to analyze the topography of the potential energy surface by calculating reaction pathways, transition rate matrices, time-evolution of occupation probabilities, and rate disconnectivity graphs.

  20. Theoretical studies of potential energy surfaces and computational methods.

    SciTech Connect

    Shepard, R.

    2006-01-01

    This project involves the development, implementation, and application of theoretical methods for the calculation and characterization of potential energy surfaces (PES) involving molecular species that occur in hydrocarbon combustion. These potential energy surfaces require an accurate and balanced treatment of reactants, intermediates, and products. Most of our work focuses on general multiconfiguration self-consistent-field (MCSCF) and multireference single- and double-excitation configuration interaction (MRSDCI) methods. In contrast to the more common single-reference electronic structure methods, this approach is capable of describing accurately molecular systems that are highly distorted away from their equilibrium geometries, including reactant, fragment, and transition-state geometries, and of describing regions of the potential surface that are associated with electronic wave functions of widely varying nature. The MCSCF reference wave functions are designed to be sufficiently flexible to describe qualitatively the changes in the electronic structure over the broad range of molecular geometries of interest. The necessary mixing of ionic, covalent, and Rydberg contributions, along with the appropriate treatment of the different electron-spin components (e.g. closed shell, high-spin open-shell, low-spin open shell, radical, diradical, etc.) of the wave functions are treated correctly at this level. Further treatment of electron correlation effects is included using large scale multireference CI wave functions, particularly including the single and double excitations relative to the MCSCF reference space. This leads to the most flexible and accurate large-scale MRSDCI wave functions that have been used to date in global PES studies.

  1. Theoretical studies of potential energy surfaces and computational methods

    SciTech Connect

    Shepard, R.

    1993-12-01

    This project involves the development, implementation, and application of theoretical methods for the calculation and characterization of potential energy surfaces involving molecular species that occur in hydrocarbon combustion. These potential energy surfaces require an accurate and balanced treatment of reactants, intermediates, and products. This difficult challenge is met with general multiconfiguration self-consistent-field (MCSCF) and multireference single- and double-excitation configuration interaction (MRSDCI) methods. In contrast to the more common single-reference electronic structure methods, this approach is capable of describing accurately molecular systems that are highly distorted away from their equilibrium geometries, including reactant, fragment, and transition-state geometries, and of describing regions of the potential surface that are associated with electronic wave functions of widely varying nature. The MCSCF reference wave functions are designed to be sufficiently flexible to describe qualitatively the changes in the electronic structure over the broad range of geometries of interest. The necessary mixing of ionic, covalent, and Rydberg contributions, along with the appropriate treatment of the different electron-spin components (e.g. closed shell, high-spin open-shell, low-spin open shell, radical, diradical, etc.) of the wave functions, are treated correctly at this level. Further treatment of electron correlation effects is included using large scale multireference CI wave functions, particularly including the single and double excitations relative to the MCSCF reference space. This leads to the most flexible and accurate large-scale MRSDCI wave functions that have been used to date in global PES studies.

  2. 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.

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

    PubMed

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

    2007-08-01

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

  4. 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.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

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

    PubMed

    Hart, Francis X; Easterly, Clay E

    2004-05-01

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

  8. Rotational Energy Transfer of N2 Determined Using a New Ab Initio Potential Energy Surface

    NASA Technical Reports Server (NTRS)

    Huo, Winifred M.; Stallcop, James R.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    A new N2-N2 rigid-rotor surface has been determined using extensive Ab Initio quantum chemistry calculations together with recent experimental data for the second virial coefficient. Rotational energy transfer is studied using the new potential energy surface (PES) employing the close coupling method below 200 cm(exp -1) and coupled state approximation above that. Comparing with a previous calculation based on the PES of van der Avoird et al.,3 it is found that the new PES generally gives larger cross sections for large (delta)J transitions, but for small (delta)J transitions the cross sections are either comparable or smaller. Correlation between the differences in the cross sections and the two PES will be attempted. The computed cross sections will also be compared with available experimental data.

  9. Theoretical characterization of the potential energy surface for NH + NO

    NASA Technical Reports Server (NTRS)

    Walch, Stephen P.

    1992-01-01

    The potential energy surface (PES) for NH + NO was characterized using complete active space self-consistent field (CASSCF) gradient calculations to determine the stationary point geometries and frequencies followed by CASSCF/internally contracted configuration interaction (CCI) calculations to refine the energetics. The present results are in qualitative accord with the BAC-MP4 calculations, but there are differences as large as 8 kcal/mol in the detailed energetics. Addition of NH to NO on a (2)A' surface, which correlated with N2 + OH or H + N2O products, involves barriers of 3.2 kcal/mol (trans) and 6.3 kcal/mol (cis). Experimental evidence for these barriers is found in earlier works. The (2)A' surface has no barrier to addition, but does not correlate with products. Surface crossings between the barrierless (2)A' surface and the (2)A' surface may be important. Production of N2 + OH products is predicted to occur via a planar saddle point of (2)A' symmetry. This is in accord with the preferential formation of II(A') lambda doublet levels of OH in earlier experiments. Addition of NH (1)delta to NO is found to occur on an excited state surface and is predicted to lead to N2O product as observed in earlier works.

  10. Quantum Monte Carlo calculation of the binding energy of the beryllium dimer

    NASA Astrophysics Data System (ADS)

    Deible, Michael J.; Kessler, Melody; Gasperich, Kevin E.; Jordan, Kenneth D.

    2015-08-01

    The accurate calculation of the binding energy of the beryllium dimer is a challenging theoretical problem. In this study, the binding energy of Be2 is calculated using the diffusion Monte Carlo (DMC) method, using single Slater determinant and multiconfigurational trial functions. DMC calculations using single-determinant trial wave functions of orbitals obtained from density functional theory calculations overestimate the binding energy, while DMC calculations using Hartree-Fock or CAS(4,8), complete active space trial functions significantly underestimate the binding energy. In order to obtain an accurate value of the binding energy of Be2 from DMC calculations, it is necessary to employ trial functions that include excitations outside the valence space. Our best estimate DMC result for the binding energy of Be2, obtained by using configuration interaction trial functions and extrapolating in the threshold for the configurations retained in the trial function, is 908 cm-1, only slightly below the 935 cm-1 value derived from experiment.

  11. An Accurate Potential Energy Surface for H2O

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    We have carried out extensive high quality ab initio electronic structure calculations of the ground state potential energy surface (PES) and dipole moment function (DMF) for H2O. A small adjustment is made to the PES to improve the agreement of line positions from theory and experiment. The theoretical line positions are obtained from variational ro-vibrational calculations using the exact kinetic energy operator. For the lines being fitted, the root-mean-square error was reduced from 6.9 to 0.08 /cm. We were then able to match 30,092 of the 30,117 lines from the HITRAN 96 data base to theoretical lines, and 80% of the line positions differed less than 0.1 /cm. About 3% of the line positions in the experimental data base appear to be incorrect. Theory predicts the existence of many additional weak lines with intensities above the cutoff used in the data base. To obtain results of similar accuracy for HDO, a mass dependent correction to the PH is introduced and is parameterized by simultaneously fitting line positions for HDO and D2O. The mass dependent PH has good predictive value for T2O and HTO. Nonadiabatic effects are not explicitly included. Line strengths for vibrational bands summed over rotational levels usually agree well between theory and experiment, but individual line strengths can differ greatly. A high temperature line list containing about 380 million lines has been generated using the present PES and DMF

  12. A simplified confinement method for calculating absolute free energies and free energy and entropy differences.

    PubMed

    Ovchinnikov, Victor; Cecchini, Marco; Karplus, Martin

    2013-01-24

    A simple and robust formulation of the path-independent confinement method for the calculation of free energies is presented. The simplified confinement method (SCM) does not require matrix diagonalization or switching off the molecular force field, and has a simple convergence criterion. The method can be readily implemented in molecular dynamics programs with minimal or no code modifications. Because the confinement method is a special case of thermodynamic integration, it is trivially parallel over the integration variable. The accuracy of the method is demonstrated using a model diatomic molecule, for which exact results can be computed analytically. The method is then applied to the alanine dipeptide in vacuum, and to the α-helix ↔ β-sheet transition in a 16-residue peptide modeled in implicit solvent. The SCM requires less effort for the calculation of free energy differences than previous formulations because it does not require computing normal modes. The SCM has a diminished advantage for determining absolute free energy values, because it requires decreasing the MD integration step to obtain accurate results. An approximate confinement procedure is introduced, which can be used to estimate directly the configurational entropy difference between two macrostates, without the need for additional computation of the difference in the free energy or enthalpy. The approximation has convergence properties similar to those of the standard confinement method for the calculation of free energies. The use of the approximation requires about 5 times less wall-clock simulation time than that needed to compute enthalpy differences to similar precision from an MD trajectory. For the biomolecular systems considered in this study, the errors in the entropy approximation are under 10%. Practical applications of the methods to proteins are currently limited to implicit solvent simulations. PMID:23268557

  13. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP\\H-REMD) for absolute ligand binding free energy calculations.

    SciTech Connect

    Jiang, W.; Roux, B.

    2010-09-01

    Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a powerful strategy to improve the convergence of free energy computations. In particular, it has been shown previously that a FEP/REMD scheme allowing random moves within an extended replica ensemble of thermodynamic coupling parameters '{lambda}' can improve the statistical convergence in calculations of absolute binding free energy of ligands to proteins [J. Chem. Theory Comput. 2009, 5, 2583]. In the present study, FEP/REMD is extended and combined with an accelerated MD simulations method based on Hamiltonian replica-exchange MD (H-REMD) to overcome the additional problems arising from the existence of kinetically trapped conformations within the protein receptor. In the combined strategy, each system with a given thermodynamic coupling factor {lambda} in the extended ensemble is further coupled with a set of replicas evolving on a biased energy surface with boosting potentials used to accelerate the interconversion among different rotameric states of the side chains in the neighborhood of the binding site. Exchanges are allowed to occur alternatively along the axes corresponding to the thermodynamic coupling parameter {lambda} and the boosting potential, in an extended dual array of coupled {lambda}- and H-REMD simulations. The method is implemented on the basis of new extensions to the REPDSTR module of the biomolecular simulation program CHARMM. As an illustrative example, the absolute binding free energy of p-xylene to the nonpolar cavity of the L99A mutant of the T4 lysozyme was calculated. The tests demonstrate that the dual {lambda}-REMD and H-REMD simulation scheme greatly accelerates the configurational sampling of the rotameric states of the side chains around the binding pocket, thereby improving the convergence of the FEP computations.

  14. Computed potential energy surfaces for chemical reactions

    NASA Technical Reports Server (NTRS)

    Heinemann, K.; Walch, Stephen P.

    1992-01-01

    The work on the NH + NO system which was described in the last progress report was written up and a draft of the manuscript is included in the appendix. The appendix also contains a draft of a manuscript on an Ar + H + H surface. New work which was completed in the last six months includes the following: (1) calculations on the (1)CH2 + H2O, H2 + HCOH, and H2 + H2CO product channels in the CH3 + OH reaction; (2) calculations for the NH2 + O reaction; (3) calculations for the CH3 + O2 reaction; and (4) calculations for CH3O and the two decomposition channels--CH2OH and H + H2CO. Detailed descriptions of this work will be given in manuscripts; however, brief descriptions of the CH3 + OH and CH3 + O2 projects are given.

  15. Subtleties in Energy Calculations in the Image Method

    ERIC Educational Resources Information Center

    Taddei, M. M.; Mendes, T. N. C.; Farina, C.

    2009-01-01

    In this pedagogical work, we point out a subtle mistake that can be made by undergraduate or graduate students in the computation of the electrostatic energy of a system containing charges and perfect conductors if they naively use the image method. Specifically, we show that naive expressions for the electrostatic energy for these systems…

  16. Global potential energy hypersurface for dynamical studies of energy transfer in HF--HF collisions

    SciTech Connect

    Redmon, M.J.; Binkley, J.S.

    1987-07-15

    The interaction energy of two HF molecules at 1332 individual points has been calculated with Moeller--Plesset (many--body) perturbation theory at the MP4-SDTQ level using a 6-311G** basis set. 293 of the points correspond to stretching of one HF molecule from its equilibrium geometry. No attempt was made to use a sufficiently fine grid to accurately describe the well region corresponding to hydrogen bonding. However, the location and minimum energy are consistent with experiment and other accurate theoretical results. An extensive global fit (rms error of 1 kcal/mol) is reported of 1319 points (below 10 eV of potential energy) using a modified London potential with corrections obtained using polynomials through four-body interactions. A model electrostatic potential represents the long-range interaction. In addition, the use of an expansion in products of three Legendre functions is discussed. It is shown that the latter approach, although accurately fitting the ab initio data, has difficulties interpolating in regions of the surface exhibiting diverse magnitudes of potential energy, and therefore must be used with caution. This surface should be useful for studies of T--V--R processes in this system.

  17. Potential contribution of the wastewater sector to energy supply.

    PubMed

    Heubeck, S; de Vos, R M; Craggs, R

    2011-01-01

    The biological treatment of wastewater could yield high energy fuels such as methane and alcohols, however most conventional treatment systems do not recover this energy potential. with a simple model of the energy yields of various wastewater treatment technologies it is possible to demonstrate how minor shifts in technology selection can lead the industry from being identified as predominantly energy intensive, to being recognised as a source of energy resources. The future potential energy yield is estimated by applying energy yield factors to alternative use scenarios of the same wastewater loads. The method for identifying the energy potential of wastewater was demonstrated for the New Zealand wastewater sector, but can equally be applied to other countries or regions. The model suggests that by using technologies that maximise the recovery of energy from wastewater, the potential energy yield from this sector would be substantially increased (six fold for New Zealand). PMID:21866779

  18. Rovibrational energy transfer in the He-C3 collision: potential energy surface and bound states.

    PubMed

    Denis-Alpizar, Otoniel; Stoecklin, Thierry; Halvick, Philippe

    2014-02-28

    We present a four-dimensional potential energy surface (PES) for the collision of C3 with He. Ab initio calculations were carried out at the coupled-cluster level with single and double excitations and a perturbative treatment of triple excitations, using a quadruple-zeta basis set and mid-bond functions. The global minimum of the potential energy is found to be -26.9 cm(-1) and corresponds to an almost T-shaped structure of the van der Waals complex along with a slightly bent configuration of C3. This PES is used to determine the rovibrational energy levels of the He-C3 complex using the rigid monomer approximation (RMA) and the recently developed atom-rigid bender approach at the Close Coupling level (RB-CC). The calculated dissociation energies are -9.56 cm(-1) and -9.73 cm(-1), respectively at the RMA and RB-CC levels. This is the first theoretical prediction of the bound levels of the He-C3 complex with the bending motion. PMID:24588178

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

    PubMed

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

    2016-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Kahler, Richard

    1995-05-01

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

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

    SciTech Connect

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

    2011-12-21

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

  2. 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.

  3. Oxyfluoroborate host glass for upconversion application: phonon energy calculation

    NASA Astrophysics Data System (ADS)

    Abdel-Baki, Manal; El-Diasty, Fouad

    2016-04-01

    Reducing the glass phonon energy is an essential procedure to achieve high efficient radiative upconversion process. The degree of covalence of chemical bonds is responsible for the high oscillator strength of intracenter transitions in rare-earth ions. So, conversion covalent to ionic glass character is proposed as a structure-sensitive criterion that controls the phonon energy of the glasses. A series of oxyfluoro aluminum-borate host glasses used for upconversion application is prepared by the conventional melt-quenching technique. Through lithium oxide substitution by lithium fluoride, the ionic-covalent property of Li+ ion successes to regulate the band gap energies of the studied glasses. Furthermore, a new method to determine the glass phonon energy is offered.

  4. Improved DFT Potential Energy Surfaces via Improved Densities.

    PubMed

    Kim, Min-Cheol; Park, Hansol; Son, Suyeon; Sim, Eunji; Burke, Kieron

    2015-10-01

    Density-corrected DFT is a method that cures several failures of self-consistent semilocal DFT calculations by using a more accurate density instead. A novel procedure employs the Hartree-Fock density to bonds that are more severely stretched than ever before. This substantially increases the range of accurate potential energy surfaces obtainable from semilocal DFT for many heteronuclear molecules. We show that this works for both neutral and charged molecules. We explain why and explore more difficult cases, for example, CH(+), where density-corrected DFT results are even better than sophisticated methods like CCSD. We give a simple criterion for when DC-DFT should be more accurate than self-consistent DFT that can be applied for most cases. PMID:26722874

  5. Free energy calculations, enhanced by a Gaussian ansatz, for the "chemical work" distribution.

    PubMed

    Boulougouris, Georgios C

    2014-05-15

    The evaluation of the free energy is essential in molecular simulation because it is intimately related with the existence of multiphase equilibrium. Recently, it was demonstrated that it is possible to evaluate the Helmholtz free energy using a single statistical ensemble along an entire isotherm by accounting for the "chemical work" of transforming each molecule, from an interacting one, to an ideal gas. In this work, we show that it is possible to perform such a free energy perturbation over a liquid vapor phase transition. Furthermore, we investigate the link between a general free energy perturbation scheme and the novel nonequilibrium theories of Crook's and Jarzinsky. We find that for finite systems away from the thermodynamic limit the second law of thermodynamics will always be an inequality for isothermal free energy perturbations, resulting always to a dissipated work that may tend to zero only in the thermodynamic limit. The work, the heat, and the entropy produced during a thermodynamic free energy perturbation can be viewed in the context of the Crooks and Jarzinsky formalism, revealing that for a given value of the ensemble average of the "irreversible" work, the minimum entropy production corresponded to a Gaussian distribution for the histogram of the work. We propose the evaluation of the free energy difference in any free energy perturbation based scheme on the average irreversible "chemical work" minus the dissipated work that can be calculated from the variance of the distribution of the logarithm of the work histogram, within the Gaussian approximation. As a consequence, using the Gaussian ansatz for the distribution of the "chemical work," accurate estimates for the chemical potential and the free energy of the system can be performed using much shorter simulations and avoiding the necessity of sampling the computational costly tails of the "chemical work." For a more general free energy perturbation scheme that the Gaussian ansatz may not be

  6. 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.

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

    DOE PAGESBeta

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

    2015-11-12

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

  8. Alternative definitions of the frozen energy in energy decomposition analysis of density functional theory calculations.

    PubMed

    Horn, Paul R; Head-Gordon, Martin

    2016-02-28

    In energy decomposition analysis (EDA) of intermolecular interactions calculated via density functional theory, the initial supersystem wavefunction defines the so-called "frozen energy" including contributions such as permanent electrostatics, steric repulsions, and dispersion. This work explores the consequences of the choices that must be made to define the frozen energy. The critical choice is whether the energy should be minimized subject to the constraint of fixed density. Numerical results for Ne2, (H2O)2, BH3-NH3, and ethane dissociation show that there can be a large energy lowering associated with constant density orbital relaxation. By far the most important contribution is constant density inter-fragment relaxation, corresponding to charge transfer (CT). This is unwanted in an EDA that attempts to separate CT effects, but it may be useful in other contexts such as force field development. An algorithm is presented for minimizing single determinant energies at constant density both with and without CT by employing a penalty function that approximately enforces the density constraint. PMID:26931692

  9. Alternative definitions of the frozen energy in energy decomposition analysis of density functional theory calculations

    NASA Astrophysics Data System (ADS)

    Horn, Paul R.; Head-Gordon, Martin

    2016-02-01

    In energy decomposition analysis (EDA) of intermolecular interactions calculated via density functional theory, the initial supersystem wavefunction defines the so-called "frozen energy" including contributions such as permanent electrostatics, steric repulsions, and dispersion. This work explores the consequences of the choices that must be made to define the frozen energy. The critical choice is whether the energy should be minimized subject to the constraint of fixed density. Numerical results for Ne2, (H2O)2, BH3-NH3, and ethane dissociation show that there can be a large energy lowering associated with constant density orbital relaxation. By far the most important contribution is constant density inter-fragment relaxation, corresponding to charge transfer (CT). This is unwanted in an EDA that attempts to separate CT effects, but it may be useful in other contexts such as force field development. An algorithm is presented for minimizing single determinant energies at constant density both with and without CT by employing a penalty function that approximately enforces the density constraint.

  10. Energy levels of isoelectronic impurities by large scale LDA calculations

    SciTech Connect

    Li, Jingbo; Wang, Lin-Wang

    2002-11-22

    Isoelectronic impurity states are localized states induced by stoichiometric single atom substitution in bulk semiconductor. Photoluminescence spectra indicate deep impurity levels of 0.5 to 0.9eV above the top of valence band for systems like: GaN:As, GaN:P, CdS:Te, ZnS:Te. Previous calculations based on small supercells seemingly confirmed these experimental results. However, the current ab initio calculations based on thousand atom supercells indicate that the impurity levels of the above systems are actually much shallower(0.04 to 0.23 eV), and these impurity levels should be compared with photoluminescence excitation spectra, not photoluminescence spectra.

  11. Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design.

    PubMed

    Chen, Wei; Chang, Chia-En; Gilson, Michael K

    2004-11-01

    The second generation Mining Minima method yields binding affinities accurate to within 0.8 kcal/mol for the associations of alpha-, beta-, and gamma-cyclodextrin with benzene, resorcinol, flurbiprofen, naproxen, and nabumetone. These calculations require hours to a day on a commodity computer. The calculations also indicate that the changes in configurational entropy upon binding oppose association by as much as 24 kcal/mol and result primarily from a narrowing of energy wells in the bound versus the free state, rather than from a drop in the number of distinct low-energy conformations on binding. Also, the configurational entropy is found to vary substantially among the bound conformations of a given cyclodextrin-guest complex. This result suggests that the configurational entropy must be accounted for to reliably rank docked conformations in both host-guest and ligand-protein complexes. In close analogy with the common experimental observation of entropy-enthalpy compensation, the computed entropy changes show a near-linear relationship with the changes in mean potential plus solvation energy. PMID:15339804

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

    NASA Astrophysics Data System (ADS)

    Bouchet, Freddy; Gawȩdzki, Krzysztof; Nardini, Cesare

    2016-06-01

    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

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

    NASA Astrophysics Data System (ADS)

    Bouchet, Freddy; Gawȩdzki, Krzysztof; Nardini, Cesare

    2016-04-01

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

  14. 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

  15. HIGH ENERGY PHYSICS POTENTIAL AT MUON COLLIDERS

    SciTech Connect

    PARSA,Z.

    2000-04-07

    In this paper, high energy physics possibilities and future colliders are discussed. The {mu}{sup +} {mu}{sup {minus}} collider and experiments with high intensity muon beams as the stepping phase towards building Higher Energy Muon Colliders (HEMC) are briefly reviewed and encouraged.

  16. Energy in America: Progress and Potential.

    ERIC Educational Resources Information Center

    American Petroleum Inst., Washington, DC.

    An overview of America's energy situation is presented with emphasis on recent progress, the risk of depending upon foreign oil, and policy choices. Section one reviews the energy problems of the 1970s, issues of the 1980s, concerns for the future, and choices that if made today could alleviate future problems. Section two examines past problems,…

  17. The Potential Energy of an Autoencoder.

    PubMed

    Kamyshanska, Hanna; Memisevic, Roland

    2015-06-01

    Autoencoders are popular feature learning models, that are conceptually simple, easy to train and allow for efficient inference. Recent work has shown how certain autoencoders can be associated with an energy landscape, akin to negative log-probability in a probabilistic model, which measures how well the autoencoder can represent regions in the input space. The energy landscape has been commonly inferred heuristically, by using a training criterion that relates the autoencoder to a probabilistic model such as a Restricted Boltzmann Machine (RBM). In this paper we show how most common autoencoders are naturally associated with an energy function, independent of the training procedure, and that the energy landscape can be inferred analytically by integrating the reconstruction function of the autoencoder. For autoencoders with sigmoid hidden units, the energy function is identical to the free energy of an RBM, which helps shed light onto the relationship between these two types of model. We also show that the autoencoder energy function allows us to explain common regularization procedures, such as contractive training, from the perspective of dynamical systems. As a practical application of the energy function, a generative classifier based on class-specific autoencoders is presented. PMID:26357347

  18. Energy conservation potential of surface modification technologies

    SciTech Connect

    Le, H.K.; Horne, D.M.; Silberglitt, R.S.

    1985-09-01

    This report assesses the energy conservation impact of surface modification technologies on the metalworking industries. The energy conservation impact of surface modification technologies on the metalworking industries is assessed by estimating their friction and wear tribological sinks and the subsequent reduction in these sinks when surface modified tools are used. Ion implantation, coatings, and laser and electron beam surface modifications are considered.

  19. 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.

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

    NASA Astrophysics Data System (ADS)

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

    1981-04-01

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

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

    PubMed

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

    2014-02-01

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

  2. Anharmonic rovibrational calculations of singlet cyclic C4 using a new ab initio potential and a quartic force field.

    PubMed

    Wang, Xiaohong; Huang, Xinchuan; Bowman, Joel M; Lee, Timothy J

    2013-12-14

    We report a CCSD(T)/cc-pCV5Z quartic force field (QFF) and a semi-global CCSD(T)-F12b/aug-cc-pVTZ potential energy surface (PES) for singlet, cyclic C4. Vibrational fundamentals, combinations, and overtones are obtained using vibrational second-order perturbation theory (VPT2) and the vibrational configuration-interaction (VCI) approach. Agreement is within 10 cm(-1) between the VCI calculated fundamentals on the QFF and PES using the MULTIMODE (MM) program, and VPT2 and VCI results agree for the fundamentals. The agreement between VPT2-QFF and MM-QFF results is also good for the C4 combinations and overtones. The J = 1 and J = 2 rovibrational energies are reported from both VCI (MM) on the PES and VPT2 on the QFF calculations. The spectroscopic constants of (12)C4 and two C2v-symmetry, single (13)C-substituted isotopologues are presented, which may help identification of cyclic C4 in future experimental analyses or astronomical observations. PMID:24329063

  3. 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.

  4. Recent advances in electronic structure theory and their influence on the accuracy of ab initio potential energy surfaces

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1988-01-01

    Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F+H2 yields HF+H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.

  5. Recent advances in electronic structure theory and their influence on the accuracy of ab initio potential energy surfaces

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F + H2 yields HF + H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.

  6. Recent advances in electronic structure theory and their influence on the accuracy of ab initio potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F + H2 yields HF + H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.

  7. Recent advances in electronic structure theory and their influence on the accuracy of ab initio potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F+H2 yields HF+H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.

  8. Advancing QCD-based calculations of energy loss

    NASA Astrophysics Data System (ADS)

    Tywoniuk, Konrad

    2013-08-01

    We give a brief overview of the basics and current developments of QCD-based calculations of radiative processes in medium. We put an emphasis on the underlying physics concepts and discuss the theoretical uncertainties inherently associated with the fundamental parameters to be extracted from data. An important area of development is the study of the single-gluon emission in medium. Moreover, establishing the correct physical picture of multi-gluon emissions is imperative for comparison with data. We will report on progress made in both directions and discuss perspectives for the future.

  9. Turbulent energy exchange: Calculation and relevance for profile prediction

    SciTech Connect

    Candy, J.

    2013-08-15

    The anomalous heat production due to turbulence is neither routinely calculated in nonlinear gyrokinetic simulations nor routinely retained in profile prediction studies. In this work, we develop a symmetrized method to compute the exchange which dramatically reduces the intermittency in the time-dependent moment, thereby improving the accuracy of the time-average. We also examine the practical impact on transport-timescale simulations, and show that the exchange has only a minor impact on profile evolution for a well-studied DIII-D discharge.

  10. Permutation invariant polynomial neural network approach to fitting potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Jiang, Bin; Guo, Hua

    2013-08-01

    A simple, general, and rigorous scheme for adapting permutation symmetry in molecular systems is proposed and tested for fitting global potential energy surfaces using neural networks (NNs). The symmetry adaptation is realized by using low-order permutation invariant polynomials (PIPs) as inputs for the NNs. This so-called PIP-NN approach is applied to the H + H2 and Cl + H2 systems and the analytical potential energy surfaces for these two systems were accurately reproduced by PIP-NN. The accuracy of the NN potential energy surfaces was confirmed by quantum scattering calculations.

  11. Stretching the inflaton potential with kinetic energy

    SciTech Connect

    Lidsey, James E.

    2007-08-15

    Inflation near a maximum of the potential is studied when nonlocal derivative operators are included in the inflaton Lagrangian. Such terms can impose additional sources of friction on the field. For an arbitrary spacetime geometry, these effects can be quantified in terms of a local field theory with a potential whose curvature around the turning point is strongly suppressed. This implies that a prolonged phase of slow-roll inflation can be achieved with potentials that are otherwise too steep to drive quasiexponential expansion. We illustrate this mechanism within the context of p-adic string theory.

  12. Energy of Cohesion, Compressibility, and the Potential Energy Functions of the Graphite System

    NASA Technical Reports Server (NTRS)

    Girifalco, L. A.; Lad, R. A.

    1956-01-01

    The lattice summations of the potential energy of importance in the graphite system have been computed by direct summation assuming a Lennard-Jones 6-12 potential between carbon atoms. From these summations, potential energy curves were constructed for interactions between a carbon atom and a graphite monolayer, between a carbon atom and a graphite surface, between a graphite monolayer and a semi-infinite graphite crystal and between two graphite semi-infinite crystals. Using these curves, the equilibrium distance between two isolated physically interacting carbon atoms was found to be 2.70 a, where a is the carbon-carbon distance in a graphite sheet. The distance between a surface plane and the rest of the crystal was found to be 1.7% greater than the interlayer spacing. Theoretical values of the energy of cohesion and the compressibility were calculated from the potential curve for the interaction between two semi-infinite crystals. They were (delta)E(sub c) = -330 ergs/sq cm and beta =3.18x10(exp -12)sq cm/dyne, respectively. These compared favorably with the experimental values of (delta)E(sub c) = -260 ergs/sq cm and beta = 2.97 X 10(exp -2) sq cm/dyne.

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

    NASA Astrophysics Data System (ADS)

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

    2010-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Liu, X.; Zhan, H.

    2014-12-01

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

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

    SciTech Connect

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

    2004-04-05

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

  17. Energy functions for rubber from microscopic potentials

    NASA Astrophysics Data System (ADS)

    Johal, A. S.; Dunstan, D. J.

    2007-04-01

    The finite deformation theory of rubber and related materials is based on energy functions that describe the macroscopic response of these materials under deformation. Energy functions and elastic constants are here derived from a simple microscopic (ball-and-spring) model. Exact uniaxial force-extension relationships are given for Hooke's Law and for the thermodynamic entropy-based microscopic model using the Gaussian and the inverse Langevin statistical approximations. Methods are given for finding the energy functions as expansions of tensor invariants of deformation, with exact solutions for functions that can be expressed as expansions in even powers of the extension. Comparison with experiment shows good agreement with the neo-Hookean energy function and we show how this derives directly from the simple Gaussian statistical model with a small modification.

  18. Computed Potential Energy Surfaces for Chemical Reactions

    NASA Technical Reports Server (NTRS)

    Heinemann, K.; Walch, Stephen P.; Levin, Eugene

    1993-01-01

    A manuscript describing the calculations on the (1)CH2 + H2O, H2 + HCOH, and H2 + H2CO product channels in the CH3 + OH reaction, which were described in the last progress report, has been accepted for publication in J. Chem. Phys., and a copy of the manuscript is included in the appendix. The production of (1)CH2 in this reaction is important in hydrocarbon combustion since (1)CH2 is highly reactive and would be expected to insert into N2, possibly leading to a new source for prompt NO(x) (vide infra). During the last six months new calculations have been carried out for the NH2 + NO system, which is important in the thermal de-NO(x) process.

  19. The ab initio potential energy surface and spectroscopic constants of HOCl

    NASA Astrophysics Data System (ADS)

    Koput, Jacek; Peterson, Kirk A.

    1998-02-01

    The potential energy surface of hypochlorous acid, HOCl, has been determined from large-scale ab initio calculations using the coupled-cluster method CCSD(T), with basis sets of quadruple- and quintuple-zeta quality. The effect of core-electron correlation on the calculated structural parameters has been investigated. The vibrational-rotational energy levels of the three isotopic species of HOCl have then been calculated using the variational method and have been further characterized by the spectroscopic constants determined using the perturbational approach. The spectroscopic constants determined, are found to be in excellent agreement with experimental data.

  20. Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H.

    PubMed

    Rosta, Edina; Woodcock, H Lee; Brooks, Bernard R; Hummer, Gerhard

    2009-08-01

    We describe a method for the systematic improvement of reaction coordinates in quantum mechanical/molecular mechanical (QM/MM) calculations of reaction free-energy profiles. In umbrella-sampling free-energy calculations, a biasing potential acting on a chosen reaction coordinate is used to sample the system in reactant, product, and transition states. Sharp, nearly discontinuous changes along the resulting reaction path are used to identify coordinates that are relevant for the reaction but not properly sampled. These degrees of freedom are then included in an extended reaction coordinate. The general formalism is illustrated for the catalytic cleavage of the RNA backbone of an RNA/DNA hybrid duplex by the RNase H enzyme of Bacillus halodurans. We find that in the initial attack of the phosphate diester by water, the oxygen-phosphorus distances alone are not sufficient as reaction coordinates, resulting in substantial hysteresis in the proton degrees of freedom and a barrier that is too low (approximately 10 kcal/mol). If the proton degrees of freedom are included in an extended reaction coordinate, we obtain a barrier of 21.6 kcal/mol consistent with the experimental rates. As the barrier is approached, the attacking water molecule transfers one of its protons to the O1P oxygen of the phosphate group. At the barrier top, the resulting hydroxide ion forms a penta-coordinated phosphate intermediate. The method used to identify important degrees of freedom, and the procedure to optimize the reaction coordinate are general and should be useful both in classical and in QM/MM free-energy calculations. PMID:19462398