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Sample records for ab initio modelling

  1. Ab Initio Modeling of Molecular Radiation

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Schwenke, David

    2014-01-01

    Radiative emission from excited states of atoms and molecules can comprise a significant fraction of the total heat flux experienced by spacecraft during atmospheric entry at hypersonic speeds. For spacecraft with ablating heat shields, some of this radiative flux can be absorbed by molecular constituents in the boundary layer that are formed by the ablation process. Ab initio quantum mechanical calculations are carried out to predict the strengths of these emission and absorption processes. This talk will describe the methods used in these calculations using, as examples, the 4th positive emission bands of CO and the 1g+ 1u+ absorption in C3. The results of these calculations are being used as input to NASA radiation modeling codes like NeqAir, HARA and HyperRad.

  2. Ab initio derivation of model energy density functionals

    NASA Astrophysics Data System (ADS)

    Dobaczewski, Jacek

    2016-08-01

    I propose a simple and manageable method that allows for deriving coupling constants of model energy density functionals (EDFs) directly from ab initio calculations performed for finite fermion systems. A proof-of-principle application allows for linking properties of finite nuclei, determined by using the nuclear nonlocal Gogny functional, to the coupling constants of the quasilocal Skyrme functional. The method does not rely on properties of infinite fermion systems but on the ab initio calculations in finite systems. It also allows for quantifying merits of different model EDFs in describing the ab initio results.

  3. Ab Initio No-Core Shell Model

    SciTech Connect

    Barrett, B R; Navratil, P; Vary, J P

    2011-04-11

    A long-standing goal of nuclear theory is to determine the properties of atomic nuclei based on the fundamental interactions among the protons and neutrons (i.e., nucleons). By adopting nucleon-nucleon (NN), three-nucleon (NNN) and higher-nucleon interactions determined from either meson-exchange theory or QCD, with couplings fixed by few-body systems, we preserve the predictive power of nuclear theory. This foundation enables tests of nature's fundamental symmetries and offers new vistas for the full range of complex nuclear phenomena. Basic questions that drive our quest for a microscopic predictive theory of nuclear phenomena include: (1) What controls nuclear saturation; (2) How the nuclear shell model emerges from the underlying theory; (3) What are the properties of nuclei with extreme neutron/proton ratios; (4) Can we predict useful cross sections that cannot be measured; (5) Can nuclei provide precision tests of the fundamental laws of nature; and (6) Under what conditions do we need QCD to describe nuclear structure, among others. Along with other ab initio nuclear theory groups, we have pursued these questions with meson-theoretical NN interactions, such as CD-Bonn and Argonne V18, that were tuned to provide high-quality descriptions of the NN scattering phase shifts and deuteron properties. We then add meson-theoretic NNN interactions such as the Tucson-Melbourne or Urbana IX interactions. More recently, we have adopted realistic NN and NNN interactions with ties to QCD. Chiral perturbation theory within effective field theory ({chi}EFT) provides us with a promising bridge between QCD and hadronic systems. In this approach one works consistently with systems of increasing nucleon number and makes use of the explicit and spontaneous breaking of chiral symmetry to expand the strong interaction in terms of a dimensionless constant, the ratio of a generic small momentum divided by the chiral symmetry breaking scale taken to be about 1 GeV/c. The resulting NN

  4. Ab Initio Modelling of Steady Rotating Stars

    NASA Astrophysics Data System (ADS)

    Rieutord, Michel; Espinosa Lara, Francisco

    Modelling isolated rotating stars at any rotation rate is a challenge for the next generation of stellar models. These models will couple dynamical aspects of rotating stars, like angular momentum and chemicals transport, with classical chemical evolution, gravitational contraction or mass-loss. Such modelling needs to be achieved in two dimensions, combining the calculation of the structure of the star, its mean flows and the time-evolution of the whole. We present here a first step in this challenging programme. It leads to the first self-consistent two-dimensional models of rotating stars in a steady state generated by the ESTER code. In these models the structure (pressure, density and temperature) and the flow fields are computed in a self-consistent way allowing the prediction of the differential rotation and the associated meridian circulation of the stars. After a presentation of the physical properties of such models and the numerical methods at work, we give the first grid of such models describing massive and intermediate-mass stars for a selection of rotation rates up to 90 % of the breakup angular velocity.

  5. Student Modeling and Ab Initio Language Learning.

    ERIC Educational Resources Information Center

    Heift, Trude; Schulze, Mathias

    2003-01-01

    Provides examples of student modeling techniques that have been employed in computer-assisted language learning over the past decade. Describes two systems for learning German: "German Tutor" and "Geroline." Shows how a student model can support computerized adaptive language testing for diagnostic purposes in a Web-based language learning…

  6. Ab-Initio Shell Model with a Core

    SciTech Connect

    Lisetskiy, A F; Barrett, B R; Kruse, M; Navratil, P; Stetcu, I; Vary, J P

    2008-06-04

    We construct effective 2- and 3-body Hamiltonians for the p-shell by performing 12{h_bar}{Omega} ab initio no-core shell model (NCSM) calculations for A=6 and 7 nuclei and explicitly projecting the many-body Hamiltonians onto the 0{h_bar}{Omega} space. We then separate these effective Hamiltonians into 0-, 1- and 2-body contributions (also 3-body for A=7) and analyze the systematic behavior of these different parts as a function of the mass number A and size of the NCSM basis space. The role of effective 3- and higher-body interactions for A > 6 is investigated and discussed.

  7. Ab initio thermodynamic model for magnesium carbonates and hydrates.

    PubMed

    Chaka, Anne M; Felmy, Andrew R

    2014-09-01

    An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation. PMID:24679248

  8. Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates

    SciTech Connect

    Chaka, Anne M.; Felmy, Andrew R.

    2014-03-28

    An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogs of Ca-based hydrated carbonates monohydrocalcite and ikaite which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.

  9. Efficient Ab initio Modeling of Random Multicomponent Alloys

    NASA Astrophysics Data System (ADS)

    Jiang, Chao; Uberuaga, Blas P.

    2016-03-01

    We present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multicomponent alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high-entropy alloy chemistries. The SSOS method developed here can be broadly useful for the rapid computational design of multicomponent materials, especially those with a large number of alloying elements, a challenging problem for other approaches.

  10. Efficient Ab initio Modeling of Random Multicomponent Alloys.

    PubMed

    Jiang, Chao; Uberuaga, Blas P

    2016-03-11

    We present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multicomponent alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high-entropy alloy chemistries. The SSOS method developed here can be broadly useful for the rapid computational design of multicomponent materials, especially those with a large number of alloying elements, a challenging problem for other approaches. PMID:27015491

  11. TOPICAL REVIEW: Ab initio symplectic no-core shell model

    NASA Astrophysics Data System (ADS)

    Dytrych, T.; Sviratcheva, K. D.; Draayer, J. P.; Bahri, C.; Vary, J. P.

    2008-12-01

    The no-core shell model (NCSM) is a prominent ab initio method that yields a good description of the low-lying states in few-nucleon systems as well as in more complex p-shell nuclei. Nevertheless, its applicability is limited by the rapid growth of the many-body basis with larger model spaces and increasing number of nucleons. The symplectic no-core shell model (Sp-NCSM) aspires to extend the scope of the NCSM beyond the p-shell region by augmenting the conventional spherical harmonic oscillator basis with the physically relevant symplectic \\SpR{3} symmetry-adapted configurations of the symplectic shell model that describe naturally the monopole-quadrupole vibrational and rotational modes, and also partially incorporate α-cluster correlations. In this review, the models underpinning the Sp-NCSM approach, namely, the NCSM, the Elliott SU(3) model and the symplectic shell model, are discussed. Following this, a prescription for constructing translationally invariant symplectic configurations in the spherical harmonic oscillator basis is given. This prescription is utilized to unveil the extent to which symplectic configurations enter into low-lying states in 12C and 16O nuclei calculated within the framework of the NCSM with the JISP16 realistic nucleon-nucleon interaction. The outcomes of this proof-of-principle study are presented in detail.

  12. Thermochemical data for CVD modeling from ab initio calculations

    SciTech Connect

    Ho, P.; Melius, C.F.

    1993-12-31

    Ab initio electronic-structure calculations are combined with empirical bond-additivity corrections to yield thermochemical properties of gas-phase molecules. A self-consistent set of heats of formation for molecules in the Si-H, Si-H-Cl, Si-H-F, Si-N-H and Si-N-H-F systems is presented, along with preliminary values for some Si-O-C-H species.

  13. An investigation of ab initio shell-model interactions derived by no-core shell model

    NASA Astrophysics Data System (ADS)

    Wang, XiaoBao; Dong, GuoXiang; Li, QingFeng; Shen, CaiWan; Yu, ShaoYing

    2016-09-01

    The microscopic shell-model effective interactions are mainly based on the many-body perturbation theory (MBPT), the first work of which can be traced to Brown and Kuo's first attempt in 1966, derived from the Hamada-Johnston nucleon-nucleon potential. However, the convergence of the MBPT is still unclear. On the other hand, ab initio theories, such as Green's function Monte Carlo (GFMC), no-core shell model (NCSM), and coupled-cluster theory with single and double excitations (CCSD), have made many progress in recent years. However, due to the increasing demanding of computing resources, these ab initio applications are usually limited to nuclei with mass up to A = 16. Recently, people have realized the ab initio construction of valence-space effective interactions, which is obtained through a second-time renormalization, or to be more exactly, projecting the full-manybody Hamiltonian into core, one-body, and two-body cluster parts. In this paper, we present the investigation of such ab initio shell-model interactions, by the recent derived sd-shell effective interactions based on effective J-matrix Inverse Scattering Potential (JISP) and chiral effective-field theory (EFT) through NCSM. In this work, we have seen the similarity between the ab initio shellmodel interactions and the interactions obtained by MBPT or by empirical fitting. Without the inclusion of three-body (3-bd) force, the ab initio shell-model interactions still share similar defects with the microscopic interactions by MBPT, i.e., T = 1 channel is more attractive while T = 0 channel is more repulsive than empirical interactions. The progress to include more many-body correlations and 3-bd force is still badly needed, to see whether such efforts of ab initio shell-model interactions can reach similar precision as the interactions fitted to experimental data.

  14. AN AB INITIO MODEL FOR COSMIC-RAY MODULATION

    SciTech Connect

    Engelbrecht, N. E.; Burger, R. A.

    2013-07-20

    A proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays (CRs) is of vital importance for a better understanding of CR modulation in the heliosphere. This study presents an ab initio model for CR modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for solar minimum heliospheric conditions, utilizing boundary values chosen so that model results are in reasonable agreement with spacecraft observations of turbulence quantities in the solar ecliptic plane and along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modeled slab and two-dimensional (2D) turbulence energy spectra. The modeled 2D spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers. There currently exist no models or observations for the wavenumber where this drop-off occurs, and it is considered to be the only free parameter in this study. The modeled spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on CR drifts are modeled in a self-consistent way, also employing a recently developed model for wavy current sheet drift. The resulting diffusion and drift coefficients are applied to the study of galactic CR protons and antiprotons using a 3D, steady-state CR modulation code, and sample solutions in fair to good agreement with multiple spacecraft observations are presented.

  15. Ab initio modelling of methane hydrate thermophysical properties.

    PubMed

    Jendi, Z M; Servio, P; Rey, A D

    2016-04-21

    The key thermophysical properties of methane hydrate were determined using ab initio modelling. Using density functional theory, the second-order elastic constants, heat capacity, compressibility, and thermal expansion coefficient were calculated. A wide and relevant range of pressure-temperature conditions were considered, and the structures were assessed for stability using the mean square displacement and radial distribution functions. Methane hydrate was found to be elastically isotropic with a linear dependence of the bulk modulus on pressure. Equally significant, multi-body interactions were found to be important in hydrates, and water-water interactions appear to strongly influence compressibility like in ice Ih. While the heat capacity of hydrate was found to be higher than that of ice, the thermal expansion coefficient was significantly lower, most likely due to the lower rigidity of hydrates. The mean square displacement gave important insight into stability, heat capacity, and elastic moduli, and the radial distribution functions further confirmed stability. The presented results provide a much needed atomistic thermoelastic characterization of methane hydrates and are essential input for the large-scale applications of hydrate detection and production. PMID:27019976

  16. Ab initio no-core shell model with continuum

    NASA Astrophysics Data System (ADS)

    Navratil, Petr

    2008-04-01

    The ab initio no-core shell model (NCSM) is a many-body approach to nuclear structure of light nuclei. The NCSM adopts an effective interaction theory to transform fundamental inter-nucleon interactions into effective interactions for a specified nucleus in a selected harmonic oscillator basis space [1]. The method is capable of predicting nuclear structure from inter-nucleon forces derived from quantum chromodynamics by means of chiral effective field theory [2]. NCSM extensions to the microscopic description of nuclear reactions are now under development. In my talk, I will first discuss our recent calculations of the ^4He total photo-absorption cross section using two- and three-nucleon interactions from chiral effective field theory [3]. I will then outline our effort to augment the NCSM by the resonating group method (RGM) technique to develop a new method capable of describing simultaneously both bound states and nuclear reactions on light nuclei [4]. This approach, which preserves translational symmetry and the Pauli principle, will allow us to calculate cross sections of reactions important for astrophysics and describe weakly-bound systems from first principles. I will present our first phase shift results for neutron scattering off ^3H, ^4He and ^7Li and proton scattering off ^3He, ^4He and ^7Be using realistic nucleon-nucleon potentials. 3mm [1] P. Navr'atil, J. P. Vary and B. R. Barrett, Phys. Rev. C 62, 054311 (2000). [2] P. Navr'atil and V. G. Gueorguiev and J. P. Vary, W. E. Ormand and A. Nogga, Phys. Rev. Lett. 99, 042501 (2007). [3] S. Quaglioni and P. Navr'atil, Phys. Lett. B 652, 370 (2007). [4] S. Quaglioni and P. Navr'atil, arXiv:0712.0855.

  17. Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models

    SciTech Connect

    Keegan, Ronan M.; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D.; Rigden, Daniel J.

    2015-02-01

    Two ab initio modelling programs solve complementary sets of targets, enhancing the success of AMPLE with small proteins. AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

  18. Ab Initio and Phenomenological Modeling of the Phonon Spectrum of Superhard cp-BC2N

    NASA Astrophysics Data System (ADS)

    Basalaev, Yu. M.; Kopytov, A. V.; Pavlova, T. Yu.; Poplavnoi, A. S.

    2015-11-01

    The phonon spectrum of hypothetical superhard cp-BC2N is calculated based on ab initio method of density functional in the center of the Brillouin zone and interpolated over the entire Brillouin zone using the Keating phenomenological model. The interaction parameters are determined by optimization of the IR- and Ramanactive frequencies for a phenomenological model by their comparison with the results of ab initio calculations. Numerical values of short-range interaction constants and charges are in agreement with the characteristics of the chemical bond calculated ab initio. These parameters have transparent physical meaning and chemical nature and can further be used for both qualitative estimations of any physical and physico-chemical quantities and quantitative calculations of the phonon spectra of a number of isostructural compounds. The Keating phenomenological model is used to study the genesis of the phonon spectrum from the spectra of sublattices.

  19. Ab initio modeling of the motional Stark effect on MAST

    SciTech Connect

    De Bock, M. F. M.; Conway, N. J.; Walsh, M. J.; Carolan, P. G.; Hawkes, N. C.

    2008-10-15

    A multichord motional Stark effect (MSE) system has recently been built on the MAST tokamak. In MAST the {pi} and {sigma} lines of the MSE spectrum overlap due to the low magnetic field typical for present day spherical tokamaks. Also, the field curvature results in a large change in the pitch angle over the observation volume. The measured polarization angle does not relate to one local pitch angle but to an integration over all pitch angles in the observation volume. The velocity distribution of the neutral beam further complicates the measurement. To take into account volume effects and velocity distribution, an ab initio code was written that simulates the MSE spectrum on MAST. The code is modular and can easily be adjusted for other tokamaks. The code returns the intensity, polarized fraction, and polarization angle as a function of wavelength. Results of the code are presented, showing the effect on depolarization and wavelength dependence of the polarization angle. The code is used to optimize the design and calibration of the MSE diagnostic.

  20. Comparison of DFT and ab initio QM/MM methods for modelling reaction in chorismate synthase

    NASA Astrophysics Data System (ADS)

    Lawan, Narin; Ranaghan, Kara E.; Manby, Frederick R.; Mulholland, Adrian J.

    2014-07-01

    Quantum mechanics/molecular mechanics (QM/MM) methods are a popular tool in the investigation of enzyme reactions. Here, we compare B3LYP density functional theory (DFT) and ab initio QM/MM methods for modelling the conversion of 5-enolpyruvylshikimate-3-phosphate to chorismate in chorismate synthase. Good agreement with experimental data is only obtained at the SCS-MP2/CHARMM27 level for a reaction mechanism in which phosphate elimination precedes proton transfer. B3LYP predicts reaction energetics that are qualitatively wrong, stressing the need for ab initio QM/MM methods, and caution in interpretation of DFT results for this enzyme.

  1. Ab initio charge-carrier mobility model for amorphous molecular semiconductors

    NASA Astrophysics Data System (ADS)

    Massé, Andrea; Friederich, Pascal; Symalla, Franz; Liu, Feilong; Nitsche, Robert; Coehoorn, Reinder; Wenzel, Wolfgang; Bobbert, Peter A.

    2016-05-01

    Accurate charge-carrier mobility models of amorphous organic molecular semiconductors are essential to describe the electrical properties of devices based on these materials. The disordered nature of these semiconductors leads to percolative charge transport with a large characteristic length scale, posing a challenge to the development of such models from ab initio simulations. Here, we develop an ab initio mobility model using a four-step procedure. First, the amorphous morphology together with its energy disorder and intermolecular charge-transfer integrals are obtained from ab initio simulations in a small box. Next, the ab initio information is used to set up a stochastic model for the morphology and transfer integrals. This stochastic model is then employed to generate a large simulation box with modeled morphology and transfer integrals, which can fully capture the percolative charge transport. Finally, the charge-carrier mobility in this simulation box is calculated by solving a master equation, yielding a mobility function depending on temperature, carrier concentration, and electric field. We demonstrate the procedure for hole transport in two important molecular semiconductors, α -NPD and TCTA. In contrast to a previous study, we conclude that spatial correlations in the energy disorder are unimportant for α -NPD. We apply our mobility model to two types of hole-only α -NPD devices and find that the experimental temperature-dependent current density-voltage characteristics of all devices can be well described by only slightly decreasing the simulated energy disorder strength.

  2. Knockout reactions from p-shell nuclei : tests of ab initio structure models.

    SciTech Connect

    Grinyer, G. F.; Bazin, D.; Gade, A.; Tostevin, J. A.; Adrich, P.; Bowen, M. D.; Brown, B. A.; Campbell, C. M.; Cook, J. M.; Glasmacher, T.; McDaniel, S.; Navratil, P.; Obertelli, A.; Quaglioni, S.; Siwek, K.; Terry, J. R.; Weisshaar, D.; Wiringa, R. B.

    2011-04-22

    Absolute cross sections have been determined following single neutron knockout reactions from {sup 10}Be and {sup 10}C at intermediate energy. Nucleon density distributions and bound-state wave function overlaps obtained from both variational Monte Carlo (VMC) and no core shell model (NCSM) ab initio calculations have been incorporated into the theoretical description of knockout reactions. Comparison to experimental cross sections demonstrates that the VMC approach, with the inclusion of 3-body forces, provides the best overall agreement while the NCSM and conventional shell-model calculations both overpredict the cross sections by 20% to 30% for {sup 10}Be and by 40% to 50% for {sup 10}C, respectively. This study gains new insight into the importance of 3-body forces and continuum effects in light nuclei and provides a sensitive technique to assess the accuracy of ab initio calculations for describing these effects.

  3. Knockout Reactions from p-Shell Nuclei: Tests of Ab Initio Structure Models

    SciTech Connect

    Grinyer, G. F.; Bazin, D.; Adrich, P.; Obertelli, A.; Weisshaar, D.; Gade, A.; Bowen, M. D.; Brown, B. A.; Campbell, C. M.; Cook, J. M.; Glasmacher, T.; McDaniel, S.; Siwek, K.; Terry, J. R.; Tostevin, J. A.; Navratil, P.; Quaglioni, S.; Wiringa, R. B.

    2011-04-22

    Absolute cross sections have been determined following single neutron knockout reactions from {sup 10}Be and {sup 10}C at intermediate energy. Nucleon density distributions and bound-state wave function overlaps obtained from both variational Monte Carlo (VMC) and no core shell model (NCSM) ab initio calculations have been incorporated into the theoretical description of knockout reactions. Comparison to experimental cross sections demonstrates that the VMC approach, with the inclusion of 3-body forces, provides the best overall agreement while the NCSM and conventional shell-model calculations both overpredict the cross sections by 20% to 30% for {sup 10}Be and by 40% to 50% for {sup 10}C, respectively. This study gains new insight into the importance of 3-body forces and continuum effects in light nuclei and provides a sensitive technique to assess the accuracy of ab initio calculations for describing these effects.

  4. Point defect modeling in materials: Coupling ab initio and elasticity approaches

    NASA Astrophysics Data System (ADS)

    Varvenne, Céline; Bruneval, Fabien; Marinica, Mihai-Cosmin; Clouet, Emmanuel

    2013-10-01

    Modeling point defects at an atomic scale requires careful treatment of the long-range atomic relaxations. This elastic field can strongly affect point defect properties calculated in atomistic simulations because of the finite size of the system under study. This is an important restriction for ab initio methods which are limited to a few hundred atoms. We propose an original approach coupling ab initio calculations and linear elasticity theory to obtain the properties of an isolated point defect for reduced supercell sizes. The reliability and benefit of our approach are demonstrated for three problematic cases: the self-interstitial in zirconium, clusters of self-interstitials in iron, and the neutral vacancy in silicon.

  5. Ab Initio No-Core Shell Model Calculations Using Realistic Two- and Three-Body Interactions

    SciTech Connect

    Navratil, P; Ormand, W E; Forssen, C; Caurier, E

    2004-11-30

    There has been significant progress in the ab initio approaches to the structure of light nuclei. One such method is the ab initio no-core shell model (NCSM). Starting from realistic two- and three-nucleon interactions this method can predict low-lying levels in p-shell nuclei. In this contribution, we present a brief overview of the NCSM with examples of recent applications. We highlight our study of the parity inversion in {sup 11}Be, for which calculations were performed in basis spaces up to 9{Dirac_h}{Omega} (dimensions reaching 7 x 10{sup 8}). We also present our latest results for the p-shell nuclei using the Tucson-Melbourne TM three-nucleon interaction with several proposed parameter sets.

  6. Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions

    SciTech Connect

    Changlani, Hitesh J.; Zheng, Huihuo; Wagner, Lucas K.

    2015-09-14

    We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U{sup ∗}/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.

  7. Quantitative Comparison of a New Ab Initio Micrometeor Ablation Model with an Observationally Verifiable Standard Model

    NASA Astrophysics Data System (ADS)

    Meisel, David D.; Szasz, Csilla; Kero, Johan

    2008-06-01

    The Arecibo UHF radar is able to detect the head-echos of micron-sized meteoroids up to velocities of 75 km/s over a height range of 80 140 km. Because of their small size there are many uncertainties involved in calculating their above atmosphere properties as needed for orbit determination. An ab initio model of meteor ablation has been devised that should work over the mass range 10-16 kg to 10-7 kg, but the faint end of this range cannot be observed by any other method and so direct verification is not possible. On the other hand, the EISCAT UHF radar system detects micrometeors in the high mass part of this range and its observations can be fit to a “standard” ablation model and calibrated to optical observations (Szasz et al. 2007). In this paper, we present a preliminary comparison of the two models, one observationally confirmable. Among the features of the ab initio model that are different from the “standard” model are: (1) uses the experimentally based low pressure vaporization theory of O’Hanlon (A users’s guide to vacuum technology, 2003) for ablation, (2) uses velocity dependent functions fit from experimental data on heat transfer, luminosity and ionization efficiencies measured by Friichtenicht and Becker (NASA Special Publication 319: 53, 1973) for micron sized particles, (3) assumes a density and temperature dependence of the micrometeoroids and ablation product specific heats, (4) assumes a density and size dependent value for the thermal emissivity and (5) uses a unified synthesis of experimental data for the most important meteoroid elements and their oxides through least square fits (as functions of temperature, density, and/or melting point) of the tables of thermodynamic parameters given in Weast (CRC Handbook of Physics and Chemistry, 1984), Gray (American Institute of Physics Handbook, 1972), and Cox (Allen’s Astrophysical Quantities 2000). This utilization of mostly experimentally determined data is the main reason for

  8. Monte Carlo Shell Model for ab initio nuclear structure

    NASA Astrophysics Data System (ADS)

    Abe, T.; Maris, P.; Otsuka, T.; Shimizu, N.; Utsuno, Y.; Vary, J. P.

    2014-03-01

    We report on our recent application of the Monte Carlo Shell Model to no-core calculations. At the initial stage of the application, we have performed benchmark calculations in the p-shell region. Results are compared with those in the Full Configuration Interaction and No-Core Full Configuration methods. These are found to be consistent with each other within quoted uncertainties when they could be quantified. The preliminary results in Nshell = 5 reveal the onset of systematic convergence pattern.

  9. Ab initio electronic transport model with explicit solution to the linearized Boltzmann transport equation

    NASA Astrophysics Data System (ADS)

    Faghaninia, Alireza; Ager, Joel W.; Lo, Cynthia S.

    2015-06-01

    Accurate models of carrier transport are essential for describing the electronic properties of semiconductor materials. To the best of our knowledge, the current models following the framework of the Boltzmann transport equation (BTE) either rely heavily on experimental data (i.e., semiempirical), or utilize simplifying assumptions, such as the constant relaxation time approximation (BTE-cRTA). While these models offer valuable physical insights and accurate calculations of transport properties in some cases, they often lack sufficient accuracy—particularly in capturing the correct trends with temperature and carrier concentration. We present here a transport model for calculating low-field electrical drift mobility and Seebeck coefficient of n -type semiconductors, by explicitly considering relevant physical phenomena (i.e., elastic and inelastic scattering mechanisms). We first rewrite expressions for the rates of elastic scattering mechanisms, in terms of ab initio properties, such as the band structure, density of states, and polar optical phonon frequency. We then solve the linear BTE to obtain the perturbation to the electron distribution—resulting from the dominant scattering mechanisms—and use this to calculate the overall mobility and Seebeck coefficient. Therefore, we have developed an ab initio model for calculating mobility and Seebeck coefficient using the Boltzmann transport (aMoBT) equation. Using aMoBT, we accurately calculate electrical transport properties of the compound n -type semiconductors, GaAs and InN, over various ranges of temperature and carrier concentration. aMoBT is fully predictive and provides high accuracy when compared to experimental measurements on both GaAs and InN, and vastly outperforms both semiempirical models and the BTE-cRTA. Therefore, we assert that this approach represents a first step towards a fully ab initio carrier transport model that is valid in all compound semiconductors.

  10. Ab initio modeling of 2D layered organohalide lead perovskites.

    PubMed

    Fraccarollo, Alberto; Cantatore, Valentina; Boschetto, Gabriele; Marchese, Leonardo; Cossi, Maurizio

    2016-04-28

    A number of 2D layered perovskites A2PbI4 and BPbI4, with A and B mono- and divalent ammonium and imidazolium cations, have been modeled with different theoretical methods. The periodic structures have been optimized (both in monoclinic and in triclinic systems, corresponding to eclipsed and staggered arrangements of the inorganic layers) at the DFT level, with hybrid functionals, Gaussian-type orbitals and dispersion energy corrections. With the same methods, the various contributions to the solid stabilization energy have been discussed, separating electrostatic and dispersion energies, organic-organic intralayer interactions and H-bonding effects, when applicable. Then the electronic band gaps have been computed with plane waves, at the DFT level with scalar and full relativistic potentials, and including the correlation energy through the GW approximation. Spin orbit coupling and GW effects have been combined in an additive scheme, validated by comparing the computed gap with well known experimental and theoretical results for a model system. Finally, various contributions to the computed band gaps have been discussed on some of the studied systems, by varying some geometrical parameters and by substituting one cation in another's place. PMID:27131557

  11. Ab initio modeling of 2D layered organohalide lead perovskites

    NASA Astrophysics Data System (ADS)

    Fraccarollo, Alberto; Cantatore, Valentina; Boschetto, Gabriele; Marchese, Leonardo; Cossi, Maurizio

    2016-04-01

    A number of 2D layered perovskites A2PbI4 and BPbI4, with A and B mono- and divalent ammonium and imidazolium cations, have been modeled with different theoretical methods. The periodic structures have been optimized (both in monoclinic and in triclinic systems, corresponding to eclipsed and staggered arrangements of the inorganic layers) at the DFT level, with hybrid functionals, Gaussian-type orbitals and dispersion energy corrections. With the same methods, the various contributions to the solid stabilization energy have been discussed, separating electrostatic and dispersion energies, organic-organic intralayer interactions and H-bonding effects, when applicable. Then the electronic band gaps have been computed with plane waves, at the DFT level with scalar and full relativistic potentials, and including the correlation energy through the GW approximation. Spin orbit coupling and GW effects have been combined in an additive scheme, validated by comparing the computed gap with well known experimental and theoretical results for a model system. Finally, various contributions to the computed band gaps have been discussed on some of the studied systems, by varying some geometrical parameters and by substituting one cation in another's place.

  12. Converging sequences in the ab initio no-core shell model

    SciTech Connect

    Forssen, C.; Vary, J. P.; Caurier, E.; Navratil, P.

    2008-02-15

    We demonstrate the existence of multiple converging sequences in the ab initio no-core shell model. By examining the underlying theory of effective operators, we expose the physical foundations for the alternative pathways to convergence. This leads us to propose a revised strategy for evaluating effective interactions for A-body calculations in restricted model spaces. We suggest that this strategy is particularly useful for applications to nuclear processes in which states of both parities are used simultaneously, such as for transition rates. We demonstrate the utility of our strategy with large-scale calculations in light nuclei.

  13. Symmetry-Adapted Ab Initio Shell Model for Nuclear Structure Calculations

    NASA Astrophysics Data System (ADS)

    Draayer, J. P.; Dytrych, T.; Launey, K. D.; Langr, D.

    2012-05-01

    An innovative concept, the symmetry-adapted ab initio shell model, that capitalizes on partial as well as exact symmetries that underpin the structure of nuclei, is discussed. This framework is expected to inform the leading features of nuclear structure and reaction data for light and medium mass nuclei, which are currently inaccessible by theory and experiment and for which predictions of modern phenomenological models often diverge. We use powerful computational and group-theoretical algorithms to perform ab initio CI (configuration-interaction) calculations in a model space spanned by SU(3) symmetry-adapted many-body configurations with the JISP16 nucleon-nucleon interaction. We demonstrate that the results for the ground states of light nuclei up through A = 16 exhibit a strong dominance of low-spin and high-deformation configurations together with an evident symplectic structure. This, in turn, points to the importance of using a symmetry-adapted framework, one based on an LS coupling scheme with the associated spatial configurations organized according to deformation.

  14. An ab initio model for the modulation of galactic cosmic-ray electrons

    SciTech Connect

    Engelbrecht, N. E.; Burger, R. A.

    2013-12-20

    The modulation of galactic cosmic-ray electrons is studied using an ab initio three-dimensional steady state cosmic-ray modulation code in which the effects of turbulence on both the diffusion and drift of these cosmic-rays are treated as self-consistently as possible. A significant refinement is that a recent two-component turbulence transport model is used. This model yields results in reasonable agreement with observations of turbulence quantities throughout the heliosphere. The sensitivity of computed galactic electron intensities to choices of various turbulence parameters pertaining to the dissipation range of the slab turbulence spectrum, and to the choice of model of dynamical turbulence, is demonstrated using diffusion coefficients derived from the quasi-linear and extended nonlinear guiding center theories. Computed electron intensities and latitude gradients are also compared with spacecraft observations.

  15. Ab initio no core full configuration approach for light nuclei

    NASA Astrophysics Data System (ADS)

    Kim, Youngman; Shin, Ik Jae; Maris, Pieter; Vary, James P.; Forssén, Christian; Rotureau, Jimmy

    2014-07-01

    Comprehensive understanding of the structure and reactions of light nuclei poses theoretical and computational challenges. Still, a number of ab initio approaches have been developed to calculate the properties of atomic nuclei using fundamental interactions among nucleons. Among them, we work with the ab initio no core full configuration (NCFC) method and ab initio no core Gamow Shell Model (GSM). We first review these approaches and present some recent results.

  16. Ab initio no core full configuration approach for light nuclei

    NASA Astrophysics Data System (ADS)

    Kim, Youngman; Shin, Ik Jae; Maris, Pieter; Vary, James P.; Forssén, Christian; Rotureau, Jimmy

    2015-10-01

    Comprehensive understanding of the structure and reactions of light nuclei poses theoretical and computational challenges. Still, a number of ab initio approaches have been developed to calculate the properties of atomic nuclei using fundamental interactions among nucleons. Among them, we work with the ab initio no core full configuration (NCFC) method and ab initio no core Gamow Shell Model (GSM). We first review these approaches and present some recent results.

  17. Structure models: From shell model to ab initio methods. A brief introduction to microscopic theories for exotic nuclei

    NASA Astrophysics Data System (ADS)

    Bacca, Sonia

    2016-04-01

    A brief review of models to describe nuclear structure and reactions properties is presented, starting from the historical shell model picture and encompassing modern ab initio approaches. A selection of recent theoretical results on observables for exotic light and medium-mass nuclei is shown. Emphasis is given to the comparison with experiment and to what can be learned about three-body forces and continuum properties.

  18. Large basis ab initio shell model investigation of {sup 9}Be and {sup 11}Be

    SciTech Connect

    Forssen, C.; Navratil, P.; Ormand, W.E.; Caurier, E.

    2005-04-01

    We present the first ab initio structure investigation of the loosely bound {sup 11}Be nucleus, together with a study of the lighter isotope {sup 9}Be. The nuclear structure of these isotopes is particularly interesting because of the appearance of a parity-inverted ground state in {sup 11}Be. Our study is performed in the framework of the ab initio no-core shell model. Results obtained using four different, high-precision two-nucleon interactions, in model spaces up to 9({Dirac_h}/2{pi}){omega}, are shown. For both nuclei, and all potentials, we reach convergence in the level ordering of positive- and negative-parity spectra separately. Concerning their relative position, the positive-parity states are always too high in excitation energy, but a fast drop with respect to the negative-parity spectrum is observed when the model space is increased. This behavior is most dramatic for {sup 11}Be. In the largest model space we were able to reach, the 1/2{sup +} level has dropped down to become either the first or the second excited state, depending on which interaction we use. We also observe a contrasting behavior in the convergence patterns for different two-nucleon potentials and argue that a three-nucleon interaction is needed to explain the parity inversion. Furthermore, large-basis calculations of {sup 13}C and {sup 11}B are performed. This allows us to study the systematics of the position of the first unnatural-parity state in the N=7 isotone and the A=11 isobar. The {sup 11}B run in the 9({Dirac_h}/2{pi}){omega} model space involves a matrix with dimension exceeding 1.1x10{sup 9}, and is our largest calculation so far. We present results on binding energies, excitation spectra, level configurations, radii, electromagnetic observables, and {sup 10}Be+n overlap functions.

  19. Ab initio-based fracture toughness estimates and transgranular traction-separation modelling of zirconium hydrides

    NASA Astrophysics Data System (ADS)

    Olsson, P. A. T.; Kese, K.; Kroon, M.; Alvarez Holston, A.-M.

    2015-06-01

    In this work we report the results of an ab initio study of the transgranular fracture toughness and cleavage of brittle zirconium hydrides. We use the Griffith-Irwin relation to assess the fracture toughness using calculated surface energy and estimated isotropic Voigt-Reuss-Hill averages of the elastic constants. The calculated fracture toughness values are found to concur well with experimental data, which implies that fracture is dominated by cleavage failure. To investigate the cleavage energetics, we model the decohesion process. To describe the interplanar interaction we adopt Rose’s universal binding energy relation, which is found to reproduce the behaviour accurately. The modelling shows that the work of fracture and ductility decreases with increasing hydrogen content.

  20. Modeling and Ab initio Calculations of Thermal Transport in Si-Based Clathrates and Solar Perovskites

    NASA Astrophysics Data System (ADS)

    He, Yuping

    2015-03-01

    We present calculations of the thermal transport coefficients of Si-based clathrates and solar perovskites, as obtained from ab initio calculations and models, where all input parameters derived from first principles. We elucidated the physical mechanisms responsible for the measured low thermal conductivity in Si-based clatherates and predicted their electronic properties and mobilities, which were later confirmed experimentally. We also predicted that by appropriately tuning the carrier concentration, the thermoelectric figure of merit of Sn and Pb based perovskites may reach values ranging between 1 and 2, which could possibly be further increased by optimizing the lattice thermal conductivity through engineering perovskite superlattices. Work done in collaboration with Prof. G. Galli, and supported by DOE/BES Grant No. DE-FG0206ER46262.

  1. Ab initio nuclear structure theory

    NASA Astrophysics Data System (ADS)

    Negoita, Gianina Alina

    Ab initio no core methods have become major tools for understanding the properties of light nuclei based on realistic nucleon-nucleon (NN) and three-nucleon (NNN) interactions. A brief description is provided for the inter-nucleon interactions that fit two-body scattering and bound state data, as well as NNN interactions. Major new progress, including the goal of applying these interactions to solve for properties of nuclei, is limited by convergence issues. That is, with the goal of obtaining high precision solutions of the nuclear many-body Hamiltonian with no core methods (all nucleons treated on the same footing), one needs to proceed to very large basis spaces to achieve a convergence pattern suitable for extrapolation to the exact result. This thesis investigates (1) the similarity renormalization group (SRG) approach to soften the interaction, while preserving its phase shift properties, and (2) adoption of a realistic basis space using Woods-Saxon (WS) single-particle wavefunctions. Both have their advantages and limitations, discussed here. For (1), SRG was demonstrated by applying it to a realistic NN interaction, JISP16, in a harmonic oscillator (HO) representation. The degree of interaction softening achieved through a regulator parameter is examined. For (2), new results are obtained with the realistic JISP16 NN interaction in ab initio calculations of light nuclei 4He, 6He and 12C, using a WS basis optimized to minimize the ground-state energy within the truncated no core shell model. These are numerically-intensive many-body calculations. Finally, to gain insight into the potential for no core investigations of heavier nuclei, an initial investigation was obtained for the odd mass A = 47 - 49 region nuclei straddling 48Ca. The motivation for selecting these nuclei stems from the aim of preparing for nuclear double beta-decay studies of 48Ca. In these heavier systems, phenomenological additions to the realistic NN interaction determined by previous

  2. AB INITIO AND CALPHAD THERMODYNAMICS OF MATERIALS

    SciTech Connect

    Turchi, P A

    2004-04-14

    Ab initio electronic structure methods can supplement CALPHAD in two major ways for subsequent applications to stability in complex alloys. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics {acute a} la CALPHAD. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys.

  3. Ab initio RNA folding

    NASA Astrophysics Data System (ADS)

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-01

    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.

  4. Ab initio RNA folding.

    PubMed

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-17

    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding. PMID:25993396

  5. Ab initio derivation of multi-orbital extended Hubbard model for molecular crystals

    NASA Astrophysics Data System (ADS)

    Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu; Bonnet, Marie-Laure; Robert, Vincent

    2012-01-01

    From configuration interaction (CI) ab initio calculations, we derive an effective two-orbital extended Hubbard model based on the gerade (g) and ungerade (u) molecular orbitals (MOs) of the charge-transfer molecular conductor (TTM-TTP)I3 and the single-component molecular conductor [Au(tmdt)2]. First, by focusing on the isolated molecule, we determine the parameters for the model Hamiltonian so as to reproduce the CI Hamiltonian matrix. Next, we extend the analysis to two neighboring molecule pairs in the crystal and we perform similar calculations to evaluate the inter-molecular interactions. From the resulting tight-binding parameters, we analyze the band structure to confirm that two bands overlap and mix in together, supporting the multi-band feature. Furthermore, using a fragment decomposition, we derive the effective model based on the fragment MOs and show that the staking TTM-TTP molecules can be described by the zig-zag two-leg ladder with the inter-molecular transfer integral being larger than the intra-fragment transfer integral within the molecule. The inter-site interactions between the fragments follow a Coulomb law, supporting the fragment decomposition strategy.

  6. Ab Initio Enhanced calphad Modeling of Actinide-Rich Nuclear Fuels

    SciTech Connect

    Morgan, Dane; Yang, Yong Austin

    2013-10-28

    The process of fuel recycling is central to the Advanced Fuel Cycle Initiative (AFCI), where plutonium and the minor actinides (MA) Am, Np, and Cm are extracted from spent fuel and fabricated into new fuel for a fast reactor. Metallic alloys of U-Pu-Zr-MA are leading candidates for fast reactor fuels and are the current basis for fast spectrum metal fuels in a fully recycled closed fuel cycle. Safe and optimal use of these fuels will require knowledge of their multicomponent phase stability and thermodynamics (Gibbs free energies). In additional to their use as nuclear fuels, U-Pu-Zr-MA contain elements and alloy phases that pose fundamental questions about electronic structure and energetics at the forefront of modern many-body electron theory. This project will validate state-of-the-art electronic structure approaches for these alloys and use the resulting energetics to model U-Pu-Zr-MA phase stability. In order to keep the work scope practical, researchers will focus on only U-Pu-Zr-{Np,Am}, leaving Cm for later study. The overall objectives of this project are to: Provide a thermodynamic model for U-Pu-Zr-MA for improving and controlling reactor fuels; and, Develop and validate an ab initio approach for predicting actinide alloy energetics for thermodynamic modeling.

  7. Ab initio diffuse-interface model for lithiated electrode interface evolution

    NASA Astrophysics Data System (ADS)

    Stournara, Maria E.; Kumar, Ravi; Qi, Yue; Sheldon, Brian W.

    2016-07-01

    The study of chemical segregation at interfaces, and in particular the ability to predict the thickness of segregated layers via analytical expressions or computational modeling, is a fundamentally challenging topic in the design of novel heterostructured materials. This issue is particularly relevant for the phase-field (PF) methodology, which has become a prominent tool for describing phase transitions. These models rely on phenomenological parameters that pertain to the interfacial energy and thickness, quantities that cannot be experimentally measured. Instead of back-calculating these parameters from experimental data, here we combine a set of analytical expressions based on the Cahn-Hilliard approach with ab initio calculations to compute the gradient energy parameter κ and the thickness λ of the segregated Li layer at the LixSi-Cu interface. With this bottom-up approach we calculate the thickness λ of the Li diffuse interface to be on the order of a few nm, in agreement with prior experimental secondary ion mass spectrometry observations. Our analysis indicates that Li segregation is primarily driven by solution thermodynamics, while the strain contribution in this system is relatively small. This combined scheme provides an essential first step in the systematic evaluation of the thermodynamic parameters of the PF methodology, and we believe that it can serve as a framework for the development of quantitative interface models in the field of Li-ion batteries.

  8. Ab initio diffuse-interface model for lithiated electrode interface evolution.

    PubMed

    Stournara, Maria E; Kumar, Ravi; Qi, Yue; Sheldon, Brian W

    2016-07-01

    The study of chemical segregation at interfaces, and in particular the ability to predict the thickness of segregated layers via analytical expressions or computational modeling, is a fundamentally challenging topic in the design of novel heterostructured materials. This issue is particularly relevant for the phase-field (PF) methodology, which has become a prominent tool for describing phase transitions. These models rely on phenomenological parameters that pertain to the interfacial energy and thickness, quantities that cannot be experimentally measured. Instead of back-calculating these parameters from experimental data, here we combine a set of analytical expressions based on the Cahn-Hilliard approach with ab initio calculations to compute the gradient energy parameter κ and the thickness λ of the segregated Li layer at the Li_{x}Si-Cu interface. With this bottom-up approach we calculate the thickness λ of the Li diffuse interface to be on the order of a few nm, in agreement with prior experimental secondary ion mass spectrometry observations. Our analysis indicates that Li segregation is primarily driven by solution thermodynamics, while the strain contribution in this system is relatively small. This combined scheme provides an essential first step in the systematic evaluation of the thermodynamic parameters of the PF methodology, and we believe that it can serve as a framework for the development of quantitative interface models in the field of Li-ion batteries. PMID:27575197

  9. A Simple ab Initio Model for the Hydrated Electron That Matches Experiment.

    PubMed

    Kumar, Anil; Walker, Jonathan A; Bartels, David M; Sevilla, Michael D

    2015-08-27

    Since its discovery over 50 years ago, the "structure" and properties of the hydrated electron have been a subject for wonderment and also fierce debate. In the present work we seriously explore a minimal model for the aqueous electron, consisting of a small water anion cluster embedded in a polarized continuum, using several levels of ab initio calculation and basis set. The minimum energy "zero Kelvin" structure found for any 4-water (or larger) anion cluster, at any post-Hartree–Fock theory level, is very similar to a recently reported embedded-DFT-in-classical-water-MD simulation (Uhlig, Marsalek, and Jungwirth, J. Phys. Chem. Lett. 2012, 3, 3071−3075), with four OH bonds oriented toward the maximum charge density in a small central "void". The minimum calculation with just four water molecules does a remarkably good job of reproducing the resonance Raman properties, the radius of gyration derived from the optical spectrum, the vertical detachment energy, and the hydration free energy. For the first time we also successfully calculate the EPR g-factor and (low temperature ice) hyperfine couplings. The simple tetrahedral anion cluster model conforms very well to experiment, suggesting it does in fact represent the dominant structural motif of the hydrated electron. PMID:26275103

  10. Tunneling of electrons via rotor-stator molecular interfaces: Combined ab initio and model study

    NASA Astrophysics Data System (ADS)

    Petreska, Irina; Ohanesjan, Vladimir; Pejov, Ljupčo; Kocarev, Ljupčo

    2016-07-01

    Tunneling of electrons through rotor-stator anthracene aldehyde molecular interfaces is studied with a combined ab initio and model approach. Molecular electronic structure calculated from first principles is utilized to model different shapes of tunneling barriers. Together with a rectangular barrier, we also consider a sinusoidal shape that captures the effects of the molecular internal structure more realistically. Quasiclassical approach with the Simmons' formula for current density is implemented. Special attention is paid on conformational dependence of the tunneling current. Our results confirm that the presence of the side aldehyde group enhances the interesting electronic properties of the pure anthracene molecule, making it a bistable system with geometry dependent transport properties. We also investigate the transition voltage and we show that conformation-dependent field emission could be observed in these molecular interfaces at realistically low voltages. The present study accompanies our previous work where we investigated the coherent transport via strongly coupled delocalized orbital by application of Non-equilibrium Green's Function Formalism.

  11. Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations.

    PubMed

    Köster, Andreas; Spura, Thomas; Rutkai, Gábor; Kessler, Jan; Wiebeler, Hendrik; Vrabec, Jadran; Kühne, Thomas D

    2016-07-15

    The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force-matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force-matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc. PMID:27232117

  12. Beyond Born-Mayer: Improved Models for Short-Range Repulsion in ab Initio Force Fields.

    PubMed

    Van Vleet, Mary J; Misquitta, Alston J; Stone, Anthony J; Schmidt, J R

    2016-08-01

    Short-range repulsion within intermolecular force fields is conventionally described by either Lennard-Jones (A/r(12)) or Born-Mayer (A exp(-Br)) forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of intermolecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, and robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Finally, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach. PMID:27337546

  13. Ab Initio Dynamical Correlations from Auxiliary-field quantum Monte Carlo: applications in the Hubbard model

    NASA Astrophysics Data System (ADS)

    Vitali, Ettore; Shi, Hao; Qin, Mingpu; Zhang, Shiwei

    The possibility of calculating dynamical correlation functions from first principles provides a unique opportunity to explore the manifold of the excited states of a quantum many-body system. Such calculations allow us to predict interesting physical properties like spectral functions, excitation spectra and charge and spin gaps, which are more difficult to access from usual equilibrium calculations. We address the ab-initio calculation of dynamical Green functions and two-body correlation functions in the Auxiliary-field Quantum Monte Carlo method, using the two-dimensional Hubbard model as an example. When the sign problem is not present, an unbiased estimation of imaginary time correlation functions is obtained. We discuss in detail the complexity and the stability of the calculations. Moreover, we propose a new approach which is expected to be very useful when dealing with dilute systems, e.g. for cold gases, allowing calculations with a very favorable complexity in the system size. Supported by NSF, DOE SciDAC, and Simons Foundation.

  14. Molecular dynamics modeling using ab initio interatomic potentials for thermal properties of Ni-rich alloys

    SciTech Connect

    Mei, J.; Cooper, B.R.; Hao, Y.G.; Scoy, F.L. Van

    1994-12-31

    Molecular dynamics simulations have been performed to study thermal expansions of Ni-rich (fcc structure) Ni/Cr alloys (which serve as the basis for practical superalloy systems). This has been done using ab initio interatomic potentials with no experimental input. The coefficient of thermal expansion (CTE) as a function of temperature has been calculated. By admixing Re and Me atoms into fee Ni and the fee alloy system Ni/Cr, additive effects on the thermal expansion have been predicted. While addition of Cr lowers the CTE of Ni, and moderate addition of Mo lowers the CTE of Ni over a wide temperature range, moderate addition of Re raises the CTE of both Ni and Ni/Cr alloys over a significant temperature range. An explanation for the contrasting effect of additive Re on the CTE, based on a one-dimensional atomic chain model, is that the trade-off, between atomic volume effects increasing the CTE over that of pure Ni and pair-potential effects (exemplified by the Grueneisen parameter) decreasing the CTE from that of pure nickel, changes for Re compared to Cr and Mo.

  15. Ab initio molecular dynamics simulation of proton hopping in a model polymer membrane.

    PubMed

    Devanathan, Ram; Idupulapati, Nagesh; Baer, Marcel D; Mundy, Christopher J; Dupuis, Michel

    2013-12-27

    We report the results of ab initio molecular dynamics simulations of a model Nafion polymer membrane initially equilibrated using classical molecular dynamics simulations. We studied three hydration levels (λ) of 3, 9, and 15 H2O/SO3(-) corresponding to dry, hydrated, and saturated fuel cell membrane, respectively. The barrier for proton transfer from the SO3(-)-H3O(+) contact ion pair to a solvent-separated ion pair decreased from 2.3 kcal/mol for λ = 3 to 0.8 kcal/mol for λ = 15. The barrier for proton transfer between two water molecules was in the range from 0.7 to 0.8 kcal/mol for the λ values studied. The number of proton shuttling events between a pair of water molecules is an order of magnitude more than the number of proton hops across three distinct water molecules. The proton diffusion coefficient at λ = 15 is about 0.9 × 10(-5) cm(2)/s, which is in good agreement with experiment and our previous quantum hopping molecular dynamics simulations. PMID:24320080

  16. Beyond Born-Mayer: Improved models for short-range repulsion in ab initio force fields

    DOE PAGESBeta

    Van Vleet, Mary J.; Misquitta, Alston J.; Stone, Anthony J.; Schmidt, Jordan R.

    2016-06-23

    Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less

  17. 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.

  18. Ab-initio molecular modeling of interfaces in tantalum-carbon system

    SciTech Connect

    Balani, Kantesh; Mungole, Tarang; Bakshi, Srinivasa Rao; Agarwal, Arvind

    2012-03-15

    Processing of ultrahigh temperature TaC ceramic material with sintering additives of B{sub 4}C and reinforcement of carbon nanotubes (CNTs) gives rise to possible formation of several interfaces (Ta{sub 2}C-TaC, TaC-CNT, Ta{sub 2}C-CNT, TaB{sub 2}-TaC, and TaB{sub 2}-CNT) that could influence the resultant properties. Current work focuses on interfaces developed during spark plasma sintering of TaC-system and performing ab initio molecular modeling of the interfaces generated during processing of TaC-B{sub 4}C and TaC-CNT composites. The energy of the various interfaces has been evaluated and compared with TaC-Ta{sub 2}C interface. The iso-surface electronic contours are extracted from the calculations eliciting the enhanced stability of TaC-CNT interface by 72.2%. CNTs form stable interfaces with Ta{sub 2}C and TaB{sub 2} phases with a reduction in the energy by 35.8% and 40.4%, respectively. The computed Ta-C-B interfaces are also compared with experimentally observed interfaces in high resolution TEM images.

  19. A nonlocal, ab initio model of dissociative electron attachment and vibrational excitation of NO

    SciTech Connect

    Trevisan, Cynthia S.; Houfek, Karel; Zhang, Zhiyong; Orel, Ann E.; McCurdy, C. William; Rescigno, Thomas N.

    2005-02-01

    We present the results of an ab initio study of elastic scattering and vibrational excitation of NO by electron impact in the low-energy (0-2 eV) region where the cross sections are dominated by resonance contributions. The 3Sigma-, 1Delta and 1Sigma+ NO- resonance lifetimes are taken from our earlier study [Phys. Rev. A 69, 062711 (2004)], but the resonance energies used here are obtained from new configuration-interaction studies. Here we employ a more elaborate nonlocal treatment of the nuclear dynamics, which is found to remedy the principal deficiencies of the local complex potential model we employed in our earlier study, and gives cross sections in better agreement with the most recent experiments. We also present cross sections for dissociative electron attachment to NO leading to groundstate products. The calculations show that, while the peak cross sections starting from NO in its ground vibrational state are very small, the cross sections are extremely sensitive to vibrational excitation of the target and should be readily observable for target NO molecules excited to v = 10 and above.

  20. Cluster form factor calculation in the ab initio no-core shell model

    SciTech Connect

    Navratil, Petr

    2004-11-01

    We derive expressions for cluster overlap integrals or channel cluster form factors for ab initio no-core shell model (NCSM) wave functions. These are used to obtain the spectroscopic factors and can serve as a starting point for the description of low-energy nuclear reactions. We consider the composite system and the target nucleus to be described in the Slater determinant (SD) harmonic oscillator (HO) basis while the projectile eigenstate to be expanded in the Jacobi coordinate HO basis. This is the most practical case. The spurious center of mass components present in the SD bases are removed exactly. The calculated cluster overlap integrals are translationally invariant. As an illustration, we present results of cluster form factor calculations for <{sup 5}He vertical bar{sup 4}He+n>, <{sup 5}He vertical bar{sup 3}H+d>, <{sup 6}Li vertical bar{sup 4}He+d>, <{sup 6}Be vertical bar{sup 3}He+{sup 3}He>, <{sup 7}Li vertical bar{sup 4}He+{sup 3}H>, <{sup 7}Li vertical bar{sup 6}Li+n>, <{sup 8}Be vertical bar{sup 6}Li+d>, <{sup 8}Be vertical bar{sup 7}Li+p>, <{sup 9}Li vertical bar{sup 8}Li+n>, and <{sup 13}C vertical bar{sup 12}C+n>, with all the nuclei described by multi-({Dirac_h}/2{pi}){omega} NCSM wave functions.

  1. JUPITER MODELS WITH IMPROVED AB INITIO HYDROGEN EQUATION OF STATE (H-REOS.2)

    SciTech Connect

    Nettelmann, N.; Becker, A.; Redmer, R.; Holst, B.

    2012-05-01

    The amount and distribution of heavy elements in Jupiter gives indications on the process of its formation and evolution. Core mass and metallicity predictions, however, depend on the equations of state (EOSs) used and on model assumptions. We present an improved ab initio hydrogen EOS, H-REOS.2, and compute the internal structure and thermal evolution of Jupiter within the standard three-layer approach. The advance over our previous Jupiter models with H-REOS.1 by Nettelmann et al. is that the new models are also consistent with the observed {approx}> 2 times solar heavy element abundances in Jupiter's atmosphere. Such models have a rock core mass M{sub c} = 0-8 M{sub Circled-Plus }, total mass of heavy elements M{sub Z} = 28-32 M{sub Circled-Plus }, a deep internal layer boundary at {>=}4 Mbar, and a cooling time of 4.4-5.0 Gyr when assuming homogeneous evolution. We also calculate two-layer models in the manner of Militzer et al. and find a comparable large core of 16-21 M{sub Circled-Plus }, out of which {approx}11 M{sub Circled-Plus} is helium, but a significantly higher envelope metallicity of 4.5 times solar. According to our preferred three-layer models, neither the characteristic frequency ({nu}{sub 0} {approx} 156 {mu}Hz) nor the normalized moment of inertia ({lambda} {approx}0.276) is sensitive to the core mass but accurate measurements could well help to rule out some classes of models.

  2. Ab initio Based Modeling of Radiation Effects in Multi-Component Alloys: Final Scientific/Technical Report

    SciTech Connect

    Dane Morgan

    2010-06-10

    The project began March 13, 2006, allocated for three years, and received a one year extension from March 13, 2009 to March 12, 2010. It has now completed 48 of 48 total months. The project was focused on using ab initio methods to gain insights into radiation induced segregation (RIS) in Ni-Fe-Cr alloys. The project had the following key accomplishments • Development of a large database of ab initio energetics that can be used by many researchers in the future for increased understanding of this system. For example, we have the first calculations showing a dramatic stabilization effect of Cr-Cr interstitial dumbbells in Ni. • Prediction of both vacancy and interstitial diffusion constants for Ni-Cr and Ni-Fe for dilute Cr and Fe. This work included generalization of widely used multifrequency models to make use of ab initio derived energetics and thermodynamics. • Prediction of qualitative trends of RIS from vacancy and interstitial mechanisms, suggesting the two types of defect fluxes drive Cr RIS in opposite directions. • Detailed kinetic Monte Carlo modeling of diffusion by vacancy mechanism in Ni-Cr as a function of Cr concentration. The results demonstrate that Cr content can have a significant effect on RIS. • Development of a quantitative RIS transport model, including models for thermodynamic factors and boundary conditions.

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

    SciTech Connect

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

    2015-05-21

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  5. The ab initio model potential method. Second series transition metal elements

    SciTech Connect

    Barandiaran, Z.; Seijo, L. ); Huzinaga, S. )

    1990-10-15

    The {ital ab} {ital initio} core method potential model (AIMP) has already been presented in its nonrelativistic version and applied to the main group and first series transition metal elements (J. Chem. Phys. {bold 86}, 2132 (1987); {bold 91}, 7011 (1989)). In this paper we extend the AIMP method to include relativistic effects within the Cowan--Griffin approximation and we present relativistic Zn-like core model potentials and valence basis sets, as well as their nonrelativistic Zn-like core and Kr-like core counterparts. The pilot molecular calculations on YO, TcO, AgO, and AgH reveal that the 4{ital p} orbital is indeed a core orbital only at the end part of the series, whereas the 4{ital s} orbital can be safely frozen from Y to Cd. The all-electron and model potential results agree in 0.01--0.02 A in {ital R}{sub {ital e}} and 25--50 cm{sup {minus}1} in {bar {nu}}{sub {ital e}} if the same type of valence part of the basis set is used. The comparison of the relativistic results on AgH with those of the all-electron Dirac--Fock calculations by Lee and McLean is satisfactory: the absolute value of {ital R}{sub {ital e}} is reproduced within the 0.01 A margin and the relativistic contraction of 0.077 A is also very well reproduced (0.075 A). Finally, the relative magnitude of the effects of the core orbital change, mass--velocity potential, and Darwin potential on the net relativistic effects are analyzed in the four molecules studied.

  6. The ab initio model potential method. Second series transition metal elements

    NASA Astrophysics Data System (ADS)

    Barandiarán, Zoila; Seijo, Luis; Huzinaga, Sigeru

    1990-10-01

    The ab initio core method potential model (AIMP) has already been presented in its nonrelativistic version and applied to the main group and first series transition metal elements [J. Chem. Phys. 86, 2132 (1987); 91, 7011 (1989)]. In this paper we extend the AIMP method to include relativistic effects within the Cowan-Griffin approximation and we present relativistic Zn-like core model potentials and valence basis sets, as well as their nonrelativistic Zn-like core and Kr-like core counterparts. The pilot molecular calculations on YO, TcO, AgO, and AgH reveal that the 4p orbital is indeed a core orbital only at the end part of the series, whereas the 4s orbital can be safely frozen from Y to Cd. The all-electron and model potential results agree in 0.01-0.02 Å in Re and 25-50 cm-1 in ν¯e if the same type of valence part of the basis set is used. The comparison of the relativistic results on AgH with those of the all-electron Dirac-Fock calculations by Lee and McLean is satisfactory: the absolute value of Re is reproduced within the 0.01 Å margin and the relativistic contraction of 0.077 Å is also very well reproduced (0.075 Å). Finally, the relative magnitude of the effects of the core orbital change, mass-velocity potential, and Darwin potential on the net relativistic effects are analyzed in the four molecules studied.

  7. Nonadiabatic ab initio dynamics of a model protonated Schiff base of 9-cis retinal.

    PubMed

    Chung, Wilfredo Credo; Nanbu, Shinkoh; Ishida, Toshimasa

    2010-08-19

    The dynamics of the photoisomerization of a model protonated Schiff base of 9-cis retinal in isorhodopsin is investigated using nonadiabatic molecular dynamics simulation combined with ab initio quantum chemical calculations on-the-fly. The quantum chemical part is treated at the complete-active space self-consistent field level for six electrons in six active pi orbitals with the 6-31G basis set (CASSCF(6,6)/6-31G). The probabilities of nonadiabatic transitions between the S(1) ((1)pipi*) and S(0) states are estimated in light of the Zhu-Nakamura theory. The photoinduced cis-trans isomerization of 9-cis retinal proceeds slower than that of its 11-cis analogue and at a lower quantum yield, confirming experimental observations. An energetic barrier in the excited state impedes the elongation and twist of the C(9)=C(10) stretch and torsion coordinates, respectively, resulting in the trapping of trajectories before transition. Consequently, the isomerization takes longer time and the transition more often occurs at smaller twist angle of =C(8)-C(9)=C(10)-C(11)=, which leads to regeneration of the 9-cis reactant. Thus, neither the smaller twist observed in the X-ray crystal nor the slower movement of nuclei in the transition region would be the main reason for the longer reaction time and lower yield. A well-known space-saving asynchronous bicycle pedal or crankshaft photoisomerization mechanism is found to be operational in 9-cis retinal. The simulation in vacuo suggests that the excited-state barrier and the photoisomerization itself are intrinsic properties of the visual chromophore and not triggered mainly by the protein environment that surrounds the chromophore. PMID:20666503

  8. Collective rotation from ab initio theory

    NASA Astrophysics Data System (ADS)

    Caprio, M. A.; Maris, P.; Vary, J. P.; Smith, R.

    2015-08-01

    Through ab initio approaches in nuclear theory, we may now seek to quantitatively understand the wealth of nuclear collective phenomena starting from the underlying internucleon interactions. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments and electromagnetic transitions. In this review, NCCI calculations of 7-9Be are used to illustrate and explore ab initio rotational structure, and the resulting predictions for rotational band properties are compared with experiment. We highlight the robustness of ab initio rotational predictions across different choices for the internucleon interaction.

  9. Time-domain ab initio modeling of photoinduced dynamics at nanoscale interfaces.

    PubMed

    Wang, Linjun; Long, Run; Prezhdo, Oleg V

    2015-04-01

    Nonequilibrium processes involving electronic and vibrational degrees of freedom in nanoscale materials are under active experimental investigation. Corresponding theoretical studies are much scarcer. The review starts with the basics of time-dependent density functional theory, recent developments in nonadiabatic molecular dynamics, and the fusion of the two techniques. Ab initio simulations of this kind allow us to directly mimic a great variety of time-resolved experiments performed with pump-probe laser spectroscopies. The focus is on the ultrafast photoinduced charge and exciton dynamics at interfaces formed by two complementary materials. We consider purely inorganic materials, inorganic-organic hybrids, and all organic interfaces, involving bulk semiconductors, metallic and semiconducting nanoclusters, graphene, carbon nanotubes, fullerenes, polymers, molecular crystals, molecules, and solvent. The detailed atomistic insights available from time-domain ab initio studies provide a unique description and a comprehensive understanding of the competition between electron transfer, thermal relaxation, energy transfer, and charge recombination processes. These advances now make it possible to directly guide the development of organic and hybrid solar cells, as well as photocatalytic, electronic, spintronic, and other devices relying on complex interfacial dynamics. PMID:25622188

  10. Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure

    DOE PAGESBeta

    Timoshenko, J.; Shivhare, A.; Scott, R. W.; Lu, D.; Frenkel, A. I.

    2016-06-30

    We adopted ab-initio X-ray Absorption Near Edge Structure (XANES) modelling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modelling, where the candidate structures are known, and the inverse modelling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by following the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.

  11. Ab initio phonon limited transport

    NASA Astrophysics Data System (ADS)

    Verstraete, Matthieu

    We revisit the thermoelectric (TE) transport properties of two champion materials, PbTe and SnSe, using fully first principles methods. In both cases the performance of the material is due to subtle combinations of structural effects, scattering, and phase space reduction. In PbTe anharmonic effects are completely opposite to the predicted quasiharmonic evolution of phonon frequencies and to frequently (and incorrectly) cited extrapolations of experiments. This stabilizes the material at high T, but also tends to enhance its thermal conductivity, in a non linear manner, above 600 Kelvin. This explains why PbTe is in practice limited to room temperature applications. SnSe has recently been shown to be the most efficient TE material in bulk form. This is mainly due to a strongly enhanced carrier concentration and electrical conductivity, after going through a phase transition from 600 to 800 K. We calculate the transport coefficients as well as the defect concentrations ab initio, showing excellent agreement with experiment, and elucidating the origin of the double phase transition as well as the new charge carriers. AH Romero, EKU Gross, MJ Verstraete, and O Hellman PRB 91, 214310 (2015) O. Hellman, IA Abrikosov, and SI Simak, PRB 84 180301 (2011)

  12. From Geometry Optimization to Time Dependent Molecular Structure Modeling: Method Developments, ab initio Theories and Applications

    NASA Astrophysics Data System (ADS)

    Liang, Wenkel

    This dissertation consists of two general parts: (I) developments of optimization algorithms (both nuclear and electronic degrees of freedom) for time-independent molecules and (II) novel methods, first-principle theories and applications in time dependent molecular structure modeling. In the first part, we discuss in specific two new algorithms for static geometry optimization, the eigenspace update (ESU) method in nonredundant internal coordinate that exhibits an enhanced performace with up to a factor of 3 savings in computational cost for large-sized molecular systems; the Car-Parrinello density matrix search (CP-DMS) method that enables direct minimization of the SCF energy as an effective alternative to conventional diagonalization approach. For the second part, we consider the time dependence and first presents two nonadiabatic dynamic studies that model laser controlled molecular photo-dissociation for qualitative understandings of intense laser-molecule interaction, using ab initio direct Ehrenfest dynamics scheme implemented with real-time time-dependent density functional theory (RT-TDDFT) approach developed in our group. Furthermore, we place our special interest on the nonadiabatic electronic dynamics in the ultrafast time scale, and presents (1) a novel technique that can not only obtain energies but also the electron densities of doubly excited states within a single determinant framework, by combining methods of CP-DMS with RT-TDDFT; (2) a solvated first-principles electronic dynamics method by incorporating the polarizable continuum solvation model (PCM) to RT-TDDFT, which is found to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution. (3) applications of the PCM-RT-TDDFT method to study the intramolecular charge-transfer (CT) dynamics in a C60 derivative. Such work provides insights into the

  13. Ab initio optimization principle for the ground states of translationally invariant strongly correlated quantum lattice models

    NASA Astrophysics Data System (ADS)

    Ran, Shi-Ju

    2016-05-01

    In this work, a simple and fundamental numeric scheme dubbed as ab initio optimization principle (AOP) is proposed for the ground states of translational invariant strongly correlated quantum lattice models. The idea is to transform a nondeterministic-polynomial-hard ground-state simulation with infinite degrees of freedom into a single optimization problem of a local function with finite number of physical and ancillary degrees of freedom. This work contributes mainly in the following aspects: (1) AOP provides a simple and efficient scheme to simulate the ground state by solving a local optimization problem. Its solution contains two kinds of boundary states, one of which play the role of the entanglement bath that mimics the interactions between a supercell and the infinite environment, and the other gives the ground state in a tensor network (TN) form. (2) In the sense of TN, a novel decomposition named as tensor ring decomposition (TRD) is proposed to implement AOP. Instead of following the contraction-truncation scheme used by many existing TN-based algorithms, TRD solves the contraction of a uniform TN in an opposite way by encoding the contraction in a set of self-consistent equations that automatically reconstruct the whole TN, making the simulation simple and unified; (3) AOP inherits and develops the ideas of different well-established methods, including the density matrix renormalization group (DMRG), infinite time-evolving block decimation (iTEBD), network contractor dynamics, density matrix embedding theory, etc., providing a unified perspective that is previously missing in this fields. (4) AOP as well as TRD give novel implications to existing TN-based algorithms: A modified iTEBD is suggested and the two-dimensional (2D) AOP is argued to be an intrinsic 2D extension of DMRG that is based on infinite projected entangled pair state. This paper is focused on one-dimensional quantum models to present AOP. The benchmark is given on a transverse Ising

  14. Combined electron beam imaging and ab initio modeling of T{sub 1} precipitates in Al-Li-Cu alloys

    SciTech Connect

    Dwyer, C.; Weyland, M.; Chang, L. Y.; Muddle, B. C.

    2011-05-16

    Among the many considerable challenges faced in developing a rational basis for advanced alloy design, establishing accurate atomistic models is one of the most fundamental. Here we demonstrate how advanced imaging techniques in a double-aberration-corrected transmission electron microscope, combined with ab initio modeling, have been used to determine the atomic structure of embedded 1 nm thick T{sub 1} precipitates in precipitation-hardened Al-Li-Cu aerospace alloys. The results provide an accurate determination of the controversial T{sub 1} structure, and demonstrate how next-generation techniques permit the characterization of embedded nanostructures in alloys and other nanostructured materials.

  15. AB INITIO Modeling of Thermomechanical Properties of Mo-Based Alloys for Fossil Energy Conversion

    SciTech Connect

    Ching, Wai-Yim

    2013-12-31

    In this final scientific/technical report covering the period of 3.5 years started on July 1, 2011, we report the accomplishments on the study of thermo-mechanical properties of Mo-based intermetallic compounds under NETL support. These include computational method development, physical properties investigation of Mo-based compounds and alloys. The main focus is on the mechanical and thermo mechanical properties at high temperature since these are the most crucial properties for their potential applications. In particular, recent development of applying ab initio molecular dynamic (AIMD) simulations to the T1 (Mo{sub 5}Si{sub 3}) and T2 (Mo{sub 5}SiB{sub 2}) phases are highlighted for alloy design in further improving their properties.

  16. Ab initio approach to model x-ray diffraction in warm dense matter.

    PubMed

    Vorberger, J; Gericke, D O

    2015-03-01

    It is demonstrated how the static electron-electron structure factor in warm dense matter can be obtained from density functional theory in combination with quantum Monte Carlo data. In contrast to theories assuming well-separated bound and free states, this ab initio approach yields also valid results for systems close to the Mott transition (pressure ionization), where bound states are strongly modified and merge with the continuum. The approach is applied to x-ray Thomson scattering and compared to predictions of the Chihara formula whereby we use the ion-ion and electron-ion structure from the same simulations. The results show significant deviations of the screening cloud from the often applied Debye-like form. PMID:25871229

  17. Precise Lifetime Measurements in Light Nuclei for Benchmarking Modern Ab-initio Nuclear Structure Models

    SciTech Connect

    Lister, C.J.; McCutchan, E.A.

    2014-06-15

    A new generation of ab-initio calculations, based on realistic two- and three-body forces, is having a profound impact on our view of how nuclei work. To improve the numerical methods, and the parameterization of 3-body forces, new precise data are needed. Electromagnetic transitions are very sensitive to the dynamics which drive mixing between configurations. We have made a series of precise (< 3%) measurements of electromagnetic transitions in the A=10 nuclei {sup 10}C and {sup 10}Be by using the Doppler Shift Attenuation method carefully. Many interesting features can be reproduced including the strong α clustering. New measurements on {sup 8}Be and {sup 12}Be highlight the interplay between the alpha clusters and their valence neutrons.

  18. Ab initio atomic recombination reaction energetics on model heat shield surfaces

    NASA Technical Reports Server (NTRS)

    Senese, Fredrick; Ake, Robert

    1992-01-01

    Ab initio quantum mechanical calculations on small hydration complexes involving the nitrate anion are reported. The self-consistent field method with accurate basis sets has been applied to compute completely optimized equilibrium geometries, vibrational frequencies, thermochemical parameters, and stable site labilities of complexes involving 1, 2, and 3 waters. The most stable geometries in the first hydration shell involve in-plane waters bridging pairs of nitrate oxygens with two equal and bent hydrogen bonds. A second extremely labile local minimum involves out-of-plane waters with a single hydrogen bond and lies about 2 kcal/mol higher. The potential in the region of the second minimum is extremely flat and qualitatively sensitive to changes in the basis set; it does not correspond to a true equilibrium structure.

  19. Ab Initio Study of Polonium

    SciTech Connect

    Zabidi, Noriza Ahmad; Kassim, Hasan Abu; Shrivastava, Keshav N.

    2008-05-20

    Polonium is the only element with a simple cubic (sc) crystal structure. Atoms in solid polonium sit at the corners of a simple cubic unit cell and no where else. Polonium has a valence electron configuration 6s{sup 2}6p{sup 4} (Z = 84). The low temperature {alpha}-phase transforms into the rhombohedral (trigonal) {beta} structure at {approx}348 K. The sc {alpha}-Po unit cell constant is a = 3.345 A. The beta form of polonium ({beta}-Po) has the lattice parameters, a{sub R} = 3.359 A and a rhombohedral angle 98 deg. 13'. We have performed an ab initio electronic structure calculation by using the density functional theory. We have performed the calculation with and without spin-orbit (SO) coupling by using both the LDA and the GGA for the exchange-correlations. The k-points in a simple cubic BZ are determined by R (0.5, 0.5, 0.5), {gamma} (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and {gamma} (0, 0, 0). Other directions of k-points are {gamma} (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and {gamma} (0, 0, 0). The SO splittings of p states at the {gamma} point in the GGA+SO scheme for {alpha}-Po are 0.04 eV and 0.02 eV while for the {beta}-Po these are 0.03 eV and 0.97 eV. We have also calculated the vibrational spectra for the unit cells in both the structures. We find that exchanging of a Po atom by Pb atom produces several more bands and destabilizes the {beta} phase.

  20. Validating a polarizable model for the glass-forming liquid Ca0.4K0.6(NO3)1.4 by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Ribeiro, Mauro C. C.; Almeida, Luiz C. J.

    2000-09-01

    Ab initio calculations have been performed in order to investigate a recently proposed polarizable model [M. C. C. Ribeiro, Phys. Rev. B 61, 3297 (2000)] for molecular dynamics (MD) simulation of the molten salt Ca0.4K0.6(NO3)1.4. On the basis of the electronegativity equalization method, polarization effects in the MD simulations have been introduced by a fluctuating charge (FC) model for the nitrate ion. Partial charges in the nitrate ion are obtained by ab initio calculations at several levels of theory, and compared with previously proposed models for MD simulations of nitrate melts. Charge fluctuation is achieved in the ab initio calculations by using positive probe charges placed around a nitrate ion. The parameters of the FC model are corroborated by comparison of the ab initio partial charges with the ones obtained directly by the electronegativity equalization method. Simulated annealing of a cluster including two double-charged cations and two nitrate ions shows that very different structures are obtained depending on whether the FC model or its nonpolarizable counterpart is considered. Ab initio calculations show that the structure of this cluster is strongly dependent on polarization effects in the nitrate ions.

  1. Ab initio non-relativistic spin dynamics

    SciTech Connect

    Ding, Feizhi; Goings, Joshua J.; Li, Xiaosong; Frisch, Michael J.

    2014-12-07

    Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li{sub 3} molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.

  2. Ab initio non-relativistic spin dynamics

    NASA Astrophysics Data System (ADS)

    Ding, Feizhi; Goings, Joshua J.; Frisch, Michael J.; Li, Xiaosong

    2014-12-01

    Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li3 molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.

  3. Ab Initio Neutron Drops with Chiral Hamiltonians

    NASA Astrophysics Data System (ADS)

    Potter, Hugh; Maris, Pieter; Vary, James

    2015-04-01

    Ab initio calculations for neutron drops are of interest for insights into neutron-rich nuclei and neutron star matter, and for examining the neutron-only sector of nucleon-nucleon and 3-nucleon interactions. I present ab initio results calculated using the no-core shell model with 2- and 3-body chiral Hamiltonians for neutron drops up to 20 neutrons confined in a 10 MeV harmonic trap. I discuss ground state energies, internal energies, radii, and evidence for pairing. In addition, excitation energies can be used to investigate the spin-orbit splittings in the p-shell and sd -shell. Prior Green's Function Monte Carlo calculations using the Argonne v8' potential with added 3-nucleon forces serve as a comparison. Supported by DOE Grants DESC0008485 (SciDAC/NUCLEI), DE-FG02-87ER40371, and NSF Grant 0904782; computational resources provided by the Oak Ridge Leadership Computing Facility (DOE Office of Science Contract DE-AC05-00OR22725) under an INCITE award.

  4. Conformational Characteristics of Poly(tetrafluoroethylene) (PTFE) Based Upon Ab Initio Electronic Structure Calculations on Model Molecules

    NASA Technical Reports Server (NTRS)

    Smith, Grant D.; Jaffe, R. L.; Yoon, D. Y.; Arnold, James O. (Technical Monitor)

    1994-01-01

    Conformational energy contours of perfluoroalkanes, determined from ab initio calculations, confirm the well-known spitting of trans states into two minima at plus or minus 17 degrees but also show that the gauche states split as well, with minima at plus or minus 124 degrees and plus or minus 84 in order to relieve steric crowding. The directions of such split distortions from the perfectly staggered states are strongly coupled for adjacent pairs of bonds in a manner identical to the intradyad pair for poly (isobutylene) chains. These conformational characteristics are fully represented by a six-state rotational isomeric state (RIS) model for PTFE comprised of t(+), t(-), g(sup +)+, g(sup +)-, g(sup -) + and g(sup -)-states, located at the split energy minima. The resultant 6 x 6 statistical weight matrix is described by first-order interaction parameters for the g+(+) (ca. 0.6 kcal/mol) and g+- (ca. 2.0 kcal/mol) states, and second order parameters for the g(sup +)+g(sup +)+ (ca 0.6 kcal/mol) and g(sup +)+g(sup -)+ (ca. 1.0 kcal/mol) states. This six-state RIS model, without adjustment of the geometric or energy parameters as determined from the ab initio calculations, predicts the unperturbed chain dimensions and the fraction of gauche bonds as a function of temperature for PTFE in good agreement with available experimental values.

  5. Surface electron density models for accurate ab initio molecular dynamics with electronic friction

    NASA Astrophysics Data System (ADS)

    Novko, D.; Blanco-Rey, M.; Alducin, M.; Juaristi, J. I.

    2016-06-01

    Ab initio molecular dynamics with electronic friction (AIMDEF) is a valuable methodology to study the interaction of atomic particles with metal surfaces. This method, in which the effect of low-energy electron-hole (e-h) pair excitations is treated within the local density friction approximation (LDFA) [Juaristi et al., Phys. Rev. Lett. 100, 116102 (2008), 10.1103/PhysRevLett.100.116102], can provide an accurate description of both e-h pair and phonon excitations. In practice, its applicability becomes a complicated task in those situations of substantial surface atoms displacements because the LDFA requires the knowledge at each integration step of the bare surface electron density. In this work, we propose three different methods of calculating on-the-fly the electron density of the distorted surface and we discuss their suitability under typical surface distortions. The investigated methods are used in AIMDEF simulations for three illustrative adsorption cases, namely, dissociated H2 on Pd(100), N on Ag(111), and N2 on Fe(110). Our AIMDEF calculations performed with the three approaches highlight the importance of going beyond the frozen surface density to accurately describe the energy released into e-h pair excitations in case of large surface atom displacements.

  6. Ab initio modeling of the optical properties in organometallic halide perovskites for photovoltaic applications

    NASA Astrophysics Data System (ADS)

    Neukirch, Amanda; Nei, Wanyi; Pedesseau, Laurent; Even, Jacky; Katan, Claudine; Mohite, Aditya; Tretiak, Segrei

    2015-03-01

    The need for an inexpensive, clean, and plentiful source of energy has generated large amounts of research in an assortment of solution processed organic and hybrid organic-inorganic solar cells. A relative newcomer to the field of solution processed photovoltaics is the lead halide perovskite solar cell. In the past 5 years, the efficiencies of devices made from this material have increased from 3.5% to nearly 20%. Despite the rapid development of organic-inorganic perovskite solar cells, a thorough understanding of the fundamental photophysical processes driving the high performance of these devices is not well understood. I am using state-of-the-art ab initio computational techniques in order to characterize the properties at the interface of perovskite devices in order to aide in materials design and device engineering. I will present an in-depth analysis of the electronic and optical properties of bulk and surface states of pure and mixed halide systems. The high-level static quantum mechanical calculations, including spin-orbit-coupling and the many body GW approach, identify the key electronic states involved in photoinduced dynamics. This knowledge provides important information on how the optical properties change with variations to the system. Supported by the DOE, the LANL LDRD program XW11, and CNLS.

  7. Predominance of the Kitaev interaction in a three-dimensional honeycomb iridate: From ab initio to spin model

    NASA Astrophysics Data System (ADS)

    Kim, Heung-Sik; Kin-Ho Lee, Eric; Kim, Yong Baek

    2015-12-01

    The recently discovered three-dimensional hyperhoneycomb iridate, β-Li2IrO3, has raised hopes for the realization of the dominant Kitaev interaction between spin-orbit entangled local moments due to its near-ideal lattice structure. If true, this material may lie close to the sought-after quantum spin-liquid phase in three dimensions. Utilizing ab initio electronic structure calculations, we first show that the spin-orbit entangled basis, j\\text{eff} = 1/2 , correctly captures the low-energy electronic structure. The effective spin model derived in the strong-coupling limit supplemented by the ab initio results is shown to be dominated by the Kitaev interaction. We demonstrated that the possible range of parameters is consistent with a non-coplanar spiral magnetic order found in a recent experiment. All of these analyses suggest that β-Li2IrO3 may be the closest among known materials to the Kitaev spin-liquid regime.

  8. Ab initio determination of light hadron masses.

    PubMed

    Dürr, S; Fodor, Z; Frison, J; Hoelbling, C; Hoffmann, R; Katz, S D; Krieg, S; Kurth, T; Lellouch, L; Lippert, T; Szabo, K K; Vulvert, G

    2008-11-21

    More than 99% of the mass of the visible universe is made up of protons and neutrons. Both particles are much heavier than their quark and gluon constituents, and the Standard Model of particle physics should explain this difference. We present a full ab initio calculation of the masses of protons, neutrons, and other light hadrons, using lattice quantum chromodynamics. Pion masses down to 190 mega-electron volts are used to extrapolate to the physical point, with lattice sizes of approximately four times the inverse pion mass. Three lattice spacings are used for a continuum extrapolation. Our results completely agree with experimental observations and represent a quantitative confirmation of this aspect of the Standard Model with fully controlled uncertainties. PMID:19023076

  9. Ab initio molar volumes and Gaussian radii.

    PubMed

    Parsons, Drew F; Ninham, Barry W

    2009-02-12

    Ab initio molar volumes are calculated and used to derive radii for ions and neutral molecules using a spatially diffuse model of the electron distribution with Gaussian spread. The Gaussian radii obtained can be used for computation of nonelectrostatic ion-ion dispersion forces that underlie Hofmeister specific ion effects. Equivalent hard-sphere radii are also derived, and these are in reasonable agreement with crystalline ionic radii. The Born electrostatic self-energy is derived for a Gaussian model of the electronic charge distribution. It is shown that the ionic volumes used in electrostatic calculations of strongly hydrated cosmotropic ions ought best to include the first hydration shell. Ionic volumes for weakly hydrated chaotropic metal cations should exclude electron overlap (in electrostatic calculations). Spherical radii are calculated as well as nonisotropic ellipsoidal radii for nonspherical ions, via their nonisotropic static polarizability tensors. PMID:19140766

  10. Discovering chemistry with an ab initio nanoreactor

    NASA Astrophysics Data System (ADS)

    Martinez, Todd

    Traditional approaches for modeling chemical reaction networks such as those involved in combustion have focused on identifying individual reactions and using theoretical approaches to explore the underlying mechanisms. Recent advances involving graphical processing units (GPUs), commodity products developed for the videogaming industry, have made it possible to consider a distinct approach wherein one attempts to discover chemical reactions and mechanisms. We provide a brief summary of these developments and then discuss the concept behind the ``ab initio nanoreactor'' which explores the space of possible chemical reactions and molecular species for a given stoichiometry. The nanoreactor concept is exemplified with an example to the Urey-Miller reaction network which has been previously advanced as a potential model for prebiotic chemistry. We briefly discuss some of the future directions envisioned for the development of this nanoreactor concept.

  11. Ab initio alpha-alpha scattering

    NASA Astrophysics Data System (ADS)

    Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A.; Luu, Thomas; Meißner, Ulf-G.

    2015-12-01

    Processes such as the scattering of alpha particles (4He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei—nuclei with even and equal numbers of protons and neutrons—is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the ‘adiabatic projection method’ to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of

  12. Ab initio alpha-alpha scattering.

    PubMed

    Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G

    2015-12-01

    Processes such as the scattering of alpha particles ((4)He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei--nuclei with even and equal numbers of protons and neutrons--is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the 'adiabatic projection method' to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of

  13. Charge radii and electromagnetic moments of Li and Be isotopes from the ab initio no-core shell model

    SciTech Connect

    Forssen, C.; Caurier, E.; Navratil, P.

    2009-02-15

    Recently, charge radii and ground-state electromagnetic moments of Li and Be isotopes were measured precisely. We have performed large-scale ab initio no-core shell model calculations for these isotopes using high-precision nucleon-nucleon potentials. The isotopic trends of our computed charge radii and quadrupole and magnetic-dipole moments are in good agreement with experimental results with the exception of the {sup 11}Li charge radius. The magnetic moments are in particular well described, whereas the absolute magnitudes of the quadrupole moments are about 10% too small. The small magnitude of the {sup 6}Li quadrupole moment is reproduced, and with the CD-Bonn NN potential, also its correct sign.

  14. Phase constitution and interface structure of nano-sized Ag-Cu/AlN multilayers: Experiment and ab initio modeling

    SciTech Connect

    Pigozzi, Giancarlo; Janczak-Rusch, Jolanta; Passerone, Daniele; Antonio Pignedoli, Carlo; Patscheider, Joerg; Jeurgens, Lars P. H.; Antusek, Andrej; Parlinska-Wojtan, Magdalena; Bissig, Vinzenz

    2012-10-29

    Nano-sized Ag-Cu{sub 8nm}/AlN{sub 10nm} multilayers were deposited by reactive DC sputtering on {alpha}-Al{sub 2}O{sub 3}(0001) substrates. Investigation of the phase constitution and interface structure of the multilayers evidences a phase separation of the alloy sublayers into nanosized grains of Ag and Cu. The interfaces between the Ag grains and the quasi-single-crystalline AlN sublayers are semi-coherent, whereas the corresponding Cu/AlN interfaces are incoherent. The orientation relationship between Ag and AlN is constant throughout the entire multilayer stack. These observations are consistent with atomistic models of the interfaces as obtained by ab initio calculations.

  15. Charge Radii and Electromagnetic Moments of Li and Be Isotopes from the Ab Initio No-Core Shell Model

    SciTech Connect

    Forssen, C; Caurier, E; Navratil, P

    2008-12-23

    Recently, charge radii and ground-state electromagnetic moments of Li and Be isotopes were measured precisely. We have performed large-scale ab initio no-core shell model calculations for these isotopes using high-precision nucleon-nucleon potentials. Our computed charge radii, quadrupole and magnetic-dipole moments are in a good agreement with the measurements with the exception of the {sup 11}Li charge radius. The overall trends of all observables are well reproduced. The magnetic moments are in particular well described. Also, we are able to reproduce the small magnitude of the {sup 6}Li quadrupole moment and with the CD-Bonn NN potential also its correct sign.

  16. Ab initio simulation of transport phenomena in rarefied gases.

    PubMed

    Sharipov, Felix; Strapasson, José L

    2012-09-01

    Ab initio potentials are implemented into the direct simulation Monte Carlo (DSMC) method. Such an implementation allows us to model transport phenomena in rarefied gases without any fitting parameter of intermolecular collisions usually extracted from experimental data. Applying the method proposed by Sharipov and Strapasson [Phys. Fluids 24, 011703 (2012)], the use of ab initio potentials in the DSMC requires the same computational efforts as the widely used potentials such as hard spheres, variable hard sphere, variable soft spheres, etc. At the same time, the ab initio potentials provide more reliable results than any other one. As an example, the transport coefficients of a binary mixture He-Ar, viz., viscosity, thermal conductivity, and thermal diffusion factor, have been calculated for several values of the mole fraction. PMID:23030889

  17. Ab initio joint density-functional theory of solvated electrodes, with model and explicit solvation

    NASA Astrophysics Data System (ADS)

    Arias, Tomas

    2015-03-01

    First-principles guided design of improved electrochemical systems has the potential for great societal impact by making non-fossil-fuel systems economically viable. Potential applications include improvements in fuel-cells, solar-fuel systems (``artificial photosynthesis''), supercapacitors and batteries. Economical fuel-cell systems would enable zero-carbon footprint transportation, solar-fuel systems would directly convert sunlight and water into hydrogen fuel for such fuel-cell vehicles, supercapacitors would enable nearly full recovery of energy lost during vehicle braking thus extending electric vehicle range and acceptance, and economical high-capacity batteries would be central to mitigating the indeterminacy of renewable resources such as wind and solar. Central to the operation of all of the above electrochemical systems is the electrode-electrolyte interface, whose underlying physics is quite rich, yet remains remarkably poorly understood. The essential underlying technical challenge to the first principles studies which could explore this physics is the need to properly represent simultaneously both the interaction between electron-transfer events at the electrode, which demand a quantum mechanical description, and multiscale phenomena in the liquid environment such as the electrochemical double layer (ECDL) and its associated shielding, which demand a statistical description. A direct ab initio approach to this challenge would, in principle, require statistical sampling and thousands of repetitions of already computationally demanding quantum mechanical calculations. This talk will begin with a brief review of a recent advance, joint density-functional theory (JDFT), which allows for a fully rigorous and, in principle, exact representation of the thermodynamic equilibrium between a system described at the quantum-mechanical level and a liquid environment, but without the need for costly sampling. We then shall demonstrate how this approach applies in

  18. Ab initio infrared and Raman spectra

    NASA Astrophysics Data System (ADS)

    Fredkin, Donald R.; Komornicki, Andrew; White, Steven R.; Wilson, Kent R.

    1983-06-01

    We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schrödinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules. Then the curse of dimensionality prevents mapping out in advance the complete potential, dipole moment, and polarizability functions over the whole space of nuclear positions of all atoms, and a solution in which the electronic and nuclear parts of the Born-Oppenheimer approximation are simultaneously solved is needed. A quantum force classical trajectory (QFCT) molecular dynamic method, based on linear response theory, is described, in which the forces, dipole moment, and polarizability are computed quantum

  19. Towards SiC Surface Functionalization: An Ab Initio Study

    SciTech Connect

    Cicero, G; Catellani, A

    2005-01-28

    We present a microscopic model of the interaction and adsorption mechanism of simple organic molecules on SiC surfaces as obtained from ab initio molecular dynamics simulations. Our results open the way to functionalization of silicon carbide, a leading candidate material for bio-compatible devices.

  20. Collective rotation from ab initio theory

    NASA Astrophysics Data System (ADS)

    Caprio, Mark A.; Maris, Pieter; Vary, James P.

    2015-10-01

    The challenge of ab initio nuclear theory is to quantitatively predict the complex and highly-correlated behavior of the nuclear many-body system, starting from the underlying internucleon interactions. We may now seek to understand the wealth of nuclear collective phenomena through ab initio approaches. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments, and electromagnetic transitions. In this talk, the intrinsic structure of these bands is discussed, and the predicted rotational bands are compared to experiment. Supported by the US DOE under Award Nos. DE-FG02-95ER-40934, DESC0008485 (SciDAC/NUCLEI), and DE-FG02-87ER40371 and the US NSF under Award No. 0904782. Computational resources provided by NERSC (US DOE Contract No. DE-AC02-05CH11231).

  1. Ab initio infrared and Raman spectra

    NASA Technical Reports Server (NTRS)

    Fredkin, D. R.; White, S. R.; Wilson, K. R.; Komornicki, A.

    1983-01-01

    It is pointed out that with increased computer power and improved computational techniques, such as the gradients developed in recent years, it is becoming practical to compute spectra ab initio, from the fundamental constants of nature, for systems of increasing complexity. The present investigation has the objective to explore several possible ab initio approaches to spectra, giving particular attention to infrared and nonresonance Raman. Two approaches are discussed. The sequential approach, in which first the electronic part and then later the nuclear part of the Born-Oppenheimer approximation is solved, is appropriate for small systems. The simultaneous approach, in which the electronic and nuclear parts are solved at the same time, is more appropriate for many-atom systems. A review of the newer quantum gradient techniques is provided, and the infrared and Raman spectral band contours for the water molecule are computed.

  2. Dissociative chemisorption of methane on metal surfaces: tests of dynamical assumptions using quantum models and ab initio molecular dynamics.

    PubMed

    Jackson, Bret; Nattino, Francesco; Kroes, Geert-Jan

    2014-08-01

    The dissociative chemisorption of methane on metal surfaces is of great practical and fundamental importance. Not only is it the rate-limiting step in the steam reforming of natural gas, the reaction exhibits interesting mode-selective behavior and a strong dependence on the temperature of the metal. We present a quantum model for this reaction on Ni(100) and Ni(111) surfaces based on the reaction path Hamiltonian. The dissociative sticking probabilities computed using this model agree well with available experimental data with regard to variation with incident energy, substrate temperature, and the vibrational state of the incident molecule. We significantly expand the vibrational basis set relative to earlier studies, which allows reaction probabilities to be calculated for doubly excited initial vibrational states, though it does not lead to appreciable changes in the reaction probabilities for singly excited initial states. Sudden models used to treat the center of mass motion parallel to the surface are compared with results from ab initio molecular dynamics and found to be reasonable. Similar comparisons for molecular rotation suggest that our rotationally adiabatic model is incorrect, and that sudden behavior is closer to reality. Such a model is proposed and tested. A model for predicting mode-selective behavior is tested, with mixed results, though we find it is consistent with experimental studies of normal vs. total (kinetic) energy scaling. Models for energy transfer into lattice vibrations are also examined. PMID:25106565

  3. Dissociative chemisorption of methane on metal surfaces: Tests of dynamical assumptions using quantum models and ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Jackson, Bret; Nattino, Francesco; Kroes, Geert-Jan

    2014-08-01

    The dissociative chemisorption of methane on metal surfaces is of great practical and fundamental importance. Not only is it the rate-limiting step in the steam reforming of natural gas, the reaction exhibits interesting mode-selective behavior and a strong dependence on the temperature of the metal. We present a quantum model for this reaction on Ni(100) and Ni(111) surfaces based on the reaction path Hamiltonian. The dissociative sticking probabilities computed using this model agree well with available experimental data with regard to variation with incident energy, substrate temperature, and the vibrational state of the incident molecule. We significantly expand the vibrational basis set relative to earlier studies, which allows reaction probabilities to be calculated for doubly excited initial vibrational states, though it does not lead to appreciable changes in the reaction probabilities for singly excited initial states. Sudden models used to treat the center of mass motion parallel to the surface are compared with results from ab initio molecular dynamics and found to be reasonable. Similar comparisons for molecular rotation suggest that our rotationally adiabatic model is incorrect, and that sudden behavior is closer to reality. Such a model is proposed and tested. A model for predicting mode-selective behavior is tested, with mixed results, though we find it is consistent with experimental studies of normal vs. total (kinetic) energy scaling. Models for energy transfer into lattice vibrations are also examined.

  4. Dissociative chemisorption of methane on metal surfaces: Tests of dynamical assumptions using quantum models and ab initio molecular dynamics

    SciTech Connect

    Jackson, Bret; Nattino, Francesco; Kroes, Geert-Jan

    2014-08-07

    The dissociative chemisorption of methane on metal surfaces is of great practical and fundamental importance. Not only is it the rate-limiting step in the steam reforming of natural gas, the reaction exhibits interesting mode-selective behavior and a strong dependence on the temperature of the metal. We present a quantum model for this reaction on Ni(100) and Ni(111) surfaces based on the reaction path Hamiltonian. The dissociative sticking probabilities computed using this model agree well with available experimental data with regard to variation with incident energy, substrate temperature, and the vibrational state of the incident molecule. We significantly expand the vibrational basis set relative to earlier studies, which allows reaction probabilities to be calculated for doubly excited initial vibrational states, though it does not lead to appreciable changes in the reaction probabilities for singly excited initial states. Sudden models used to treat the center of mass motion parallel to the surface are compared with results from ab initio molecular dynamics and found to be reasonable. Similar comparisons for molecular rotation suggest that our rotationally adiabatic model is incorrect, and that sudden behavior is closer to reality. Such a model is proposed and tested. A model for predicting mode-selective behavior is tested, with mixed results, though we find it is consistent with experimental studies of normal vs. total (kinetic) energy scaling. Models for energy transfer into lattice vibrations are also examined.

  5. Ab initio vel ex eventu. II

    NASA Astrophysics Data System (ADS)

    Thiessen, P. A.; Treder, H.-J.

    Jedes initium wird durch experimenta crucis zum eventus. Jedes theoretisch interpretierbare ex-eventu-Resultat führt auf ein neues Initium. Gerade dies ist die gemeinsame Aussage von Atomistik, Quantenmechanik und Relativitätstheorie.Translated AbstractAb initio vel ex eventu. IIEvery initium becomes an eventus by experimenta crucis. Every theoretically interpretable ex-eventu result leads to a new initium. Right this is the joint assertion of atomism, quantum mechanics, and relativity.

  6. Ab initio Bogoliubov coupled cluster theory

    NASA Astrophysics Data System (ADS)

    Signoracci, Angelo; Hagen, Gaute; Duguet, Thomas

    2014-09-01

    Coupled cluster (CC) theory has become a standard method in nuclear theory for realistic ab initio calculations of medium mass nuclei, but remains limited by its requirement of a Slater determinant reference state which reasonably approximates the nuclear system of interest. Extensions of the method, such as equation-of-motion CC, permit the calculation of nuclei with one or two nucleons added or removed from a doubly magic core, yet still only a few dozen nuclei are accessible with modern computational restrictions. In order to extend the applicability of ab initio methods to open-shell systems, the superfluid nature of nuclei must be taken into account. By utilizing Bogoliubov algebra and employing spontaneous symmetry breaking with respect to particle number conservation, superfluid systems can be treated by a single reference state. An ab initio theory to include correlations on top of a Bogoliubov reference state has been developed in the guise of standard CC theory. The formalism and first results of this Bogoliubov coupled cluster theory will be presented to demonstrate the applicability of the method.

  7. Gravitational wave signatures of ab initio two-dimensional core collapse supernova explosion models for 12 -25 M⊙ stars

    NASA Astrophysics Data System (ADS)

    Yakunin, Konstantin N.; Mezzacappa, Anthony; Marronetti, Pedro; Yoshida, Shin'ichirou; Bruenn, Stephen W.; Hix, W. Raphael; Lentz, Eric J.; Bronson Messer, O. E.; Harris, J. Austin; Endeve, Eirik; Blondin, John M.; Lingerfelt, Eric J.

    2015-10-01

    We present the gravitational waveforms computed in ab initio two-dimensional core collapse supernova models evolved with the chimera code for progenitor masses between 12 and 25 M⊙ . All models employ multifrequency neutrino transport in the ray-by-ray approximation, state-of-the-art weak interaction physics, relativistic transport corrections such as the gravitational redshift of neutrinos, two-dimensional hydrodynamics with the commensurate relativistic corrections, Newtonian self-gravity with a general-relativistic monopole correction, and the Lattimer-Swesty equation of state with 220 MeV compressibility, and begin with the most recent Woosley-Heger nonrotating progenitors in this mass range. All of our models exhibit robust explosions. Therefore, our waveforms capture all stages of supernova development: 1) a relatively short and weak prompt signal, 2) a quiescent stage, 3) a strong signal due to convection and standing accretion shock instability activity, 4) termination of active accretion onto the proto-neutron star, and 5) a slowly increasing tail that reaches a saturation value. Fourier decomposition shows that the gravitational wave signals we predict should be observable by AdvLIGO for Galactic events across the range of progenitors considered here. The fundamental limitation of these models is in their imposition of axisymmetry. Further progress will require counterpart three-dimensional models, which are underway.

  8. Ab Initio and Model-Hamiltonian Study of the Torsional Variation of the Three CH Stretching Normal Modes in Methanol

    NASA Astrophysics Data System (ADS)

    Xu, Li-Hong; Lees, Ronald M.; Hougen, Jon T.

    2013-06-01

    The ν_{2}, ν_{3} and ν_{9} CH stretching modes of methanol in the 3μm region exhibit a significant amount of torsion-vibration interaction, as illustrated for ν_{9} by the facts that: (i) the three hydrogen atoms each pass through a plane of symmetry of the molecule twice during the course of one full internal rotation motion, once at a minimum and once at a maximum in the three-fold potential energy curve, (ii) the H atom in the plane of symmetry is nearly motionless for the ν_{9} mode, and therefore (iii) the property of remaining motionless must be transferred from one H to another six times during one full internal rotation motion. In this talk we examine quantitatively the general phenomenon of torsion-vibration interaction in the methyl top stretching modes in two ways. First, we present plots of normal modes produced in Gaussian projected frequency calculations that are expressed either in terms of several sets of internal coordinates, or in terms of Cartesian displacement vectors for the methyl hydrogen atoms. Some of these plots display a nearly three-fold sine or cosine behavior, where the sine or cosine behavior is dictated by group-theoretical symmetry arguments. Other plots display stunning features ranging from loss of simple three-fold oscillatory pattern to cusp-like peaks or dips. Somewhat surprisingly, none of our ab initio plots for methanol exhibit a sign change after a 2π internal rotation of the methyl top. Second, we present a relatively simple model for the three CH stretching motions, characterized by three parameters associated with: (i) a vibrational A/E energy difference, (ii) a Jahn-Teller-like torsion-vibration interaction term within the vibrational E state, and (iii) a Renner-Teller-like torsion-vibration interaction term within the E state. This model gives nearly quantitative agreement with both the regular and irregular features of the ab initio plots. The good agreement suggests that various aspects of the physics of the

  9. Uranus and Neptune structure models with ab initio EOS data for CH4, NH3, and H2O

    NASA Astrophysics Data System (ADS)

    Nettelmann, Nadine; Fortney, Jonathan; Hamel, Sebastien; Bethkenhagen, Mandy; Redmer, Ronald

    2014-05-01

    Uranus and Neptune are supposed to be rich in ices in their deep interiors as their mean density closely resembles that of liquid water. Moreover, highly super-solar abundances of CH4 and CO, indicative of internal water, have been observed in their atmospheres. We here compare ab initio equations of state for CH4, NH3, and H2O and apply them to compute ice-rich, adiabatic internal structure models of Uranus and Neptune. The explicit consideration of the light ices CH4 and NH3 allows us to put tighter constraints on the minimum H/He abundance in their deep interior, which was found to be non-zero in all previous Uranus and in most of the Neptune models that were based on water as a proxy for ices. In particular, we investigate if hydrogen in the deep interior can solely be a result of assumed Carbon sedimentation (diamond rain), as an alternative scenario to the early accretion of H/He containing material during the formation of the planets. We conclude by discussing the deep internal H/He abundance in light of rock-rich and warmer-than-adiabatic interiors, which has been suggested to explain Uranus' low intrinsic luminosity. Our models serve to better understand the formation and bulk composition of Neptune-sized planets.

  10. Ab Initio Studies of Calcium Carbonate Hydration.

    PubMed

    Lopez-Berganza, Josue A; Diao, Yijue; Pamidighantam, Sudhakar; Espinosa-Marzal, Rosa M

    2015-11-25

    Ab initio simulations of large hydrated calcium carbonate clusters are challenging due to the existence of multiple local energy minima. Extensive conformational searches around hydrated calcium carbonate clusters (CaCO3·nH2O for n = 1-18) were performed to find low-energy hydration structures using an efficient combination of Monte Carlo searches, density-functional tight binding (DFTB+) method, and density-functional theory (DFT) at the B3LYP level, or Møller-Plesset perturbation theory at the MP2 level. This multilevel optimization yields several low-energy structures for hydrated calcium carbonate. Structural and energetics analysis of the hydration of these clusters revealed a first hydration shell composed of 12 water molecules. Bond-length and charge densities were also determined for different cluster sizes. The solvation of calcium carbonate in bulk water was investigated by placing the explicitly solvated CaCO3·nH2O clusters in a polarizable continuum model (PCM). The findings of this study provide new insights into the energetics and structure of hydrated calcium carbonate and contribute to the understanding of mechanisms where calcium carbonate formation or dissolution is of relevance. PMID:26505205

  11. Different models for phosphate anion shielding in DNA duplexes: An elaboration with ab initio and molecular mechanics calculations

    NASA Astrophysics Data System (ADS)

    Buck, Henk

    In an effort to overcome a significant difference between high-level ab initio calculations and X-ray data of DNA duplexes, Fonseca Guerra et al. 9-11 studied a number of model systems for A-T and G-C basepairs at various levels of nonlocal Density Functional Theory. There was an excellent agreement with the gas-phase experimental bond enthalpies for the A-T and G-C basepairs. On the other hand the hydrogen bond lengths between the bases differ from the X-ray results. After introduction of a molecular environment as local water and Na+ ions, the agreement between theory and experiment was excellent. However, careful analysis shows that this picture is far from correct. In fact, the model was constructed as a backbone-modified DNA duplex in which the nonbonding oxygens of the phosphate linkages are completely shielded by proton addition. Experimental results with respect to backbone-modified DNAs clearly show that changes in the backbone focused on phosphate shielding result in DNA duplexes with a variety in conformational behavior. In addition to an analysis of the aforementioned contradiction, we also give molecular mechanics calculations which show that the A-T and G-C bond enthalpies are of the same order as the corresponding results of Fonseca Guerra et al. under the condition of complete anionic shielding of the nonbonded oxygens in the phosphate linkages.

  12. 7Be(p,(gamma))8B S-factor from Ab Initio No-Core Shell Model Wave Functions

    SciTech Connect

    Navratil, P; Bertulani, C A; Caurier, E

    2005-12-02

    Nuclear structure of {sup 7}Be, {sup 8}B and {sup 7,8}Li is studied within the ab initio no-core shell model (NCSM). Starting from high-precision nucleon-nucleon (NN) interactions, wave functions of {sup 7}Be and {sup 8}B bound states are obtained in basis spaces up to 10 h bar{Omega} and used to calculate channel cluster form factors (overlap integrals) of the {sup 8}B ground state with {sup 7}Be+p. Due to the use of the harmonic oscillator (HO) basis, the overlap integrals have incorrect asymptotic properties. We fix this problem in two alternative ways. First, by a Woods-Saxon (WS) potential solution fit to the interior of the NCSM overlap integrals. Second, by a direct matching with the Whittaker function. The corrected overlap integrals are then used for the {sup 7}Be(p,{gamma}){sup 8}B S-factor calculation. We study the convergence of the S-factor with respect to the NCSM HO frequency and the model space size. Our S-factor results are in agreement with recent direct measurement data. We also test the spectroscopic factors and the corrected overlap integrals from the NCSM in describing the momentum distributions in knockout reactions with {sup 8}B projectiles. A good agreement with the available experimental data is also found, attesting the overall consistency of the calculations.

  13. Kaolin polytypes revisited ab initio.

    PubMed

    Mercier, Patrick H J; Le Page, Yvon

    2008-04-01

    The well known 36 distinguishable transformations between adjacent kaolin layers are split into 20 energetically distinguishable transformations (EDT) and 16 enantiomorphic transformations, hereafter denoted EDT*. For infinitesimal energy contribution of interactions between non-adjacent layers, the lowest-energy models must result from either (a) repeated application of an EDT or (b) alternate application of an EDT and its EDT*. All modeling, quantum input preparation and interpretation was performed with Materials Toolkit, and quantum optimizations with VASP. Kaolinite and dickite are the lowest-energy models at zero temperature and pressure, whereas nacrite and HP-dickite are the lowest-enthalpy models under moderate pressures based on a rough enthalpy/pressure graph built from numbers given in the supplementary tables. Minor temperature dependence of this calculated 0 K graph would explain the bulk of the current observations regarding synthesis, diagenesis and transformation of kaolin minerals. Other stackings that we list have energies so competitive that they might crystallize at ambient pressure. A homometric pair of energetically distinguishable ideal models, one of them for nacrite, is exposed. The printed experimental structure of nacrite correctly corresponds to the stable member of the pair. In our opinion, all recent literature measurements of the free energy of bulk kaolinite are too negative by approximately 15 kJ mol(-1) for some unknown reason. PMID:18369284

  14. Ab initio-aided CALPHAD thermodynamic modeling of the Sn-Pb binary system under current stressing

    PubMed Central

    Lin, Shih-kang; Yeh, Chao-kuei; Xie, Wei; Liu, Yu-chen; Yoshimura, Masahiro

    2013-01-01

    Soldering is an ancient process, having been developed 5000 years ago. It remains a crucial process with many modern applications. In electronic devices, electric currents pass through solder joints. A new physical phenomenon – the supersaturation of solders under high electric currents – has recently been observed. It involves (1) un-expected supersaturation of the solder matrix phase, and (2) the formation of unusual “ring-shaped” grains. However, the origin of these phenomena is not yet understood. Here we provide a plausible explanation of these phenomena based on the changes in the phase stability of Pb-Sn solders. Ab initio-aided CALPHAD modeling is utilized to translate the electric current-induced effect into the excess Gibbs free energies of the phases. Hence, the phase equilibrium can be shifted by current stressing. The Pb-Sn phase diagrams with and without current stressing clearly demonstrate the change in the phase stabilities of Pb-Sn solders under current stressing. PMID:24060995

  15. The ab initio model potential method with the spin-free relativistic scheme by eliminating small components Hamiltonian

    NASA Astrophysics Data System (ADS)

    Motegi, Kyosuke; Nakajima, Takahito; Hirao, Kimihiko; Seijo, Luis

    2001-04-01

    A relativistic ab initio model potential (AIMP) for Pt, Au, and Hg atoms has been developed using a relativistic scheme by eliminating small components (RESC) in which the 5p, 5d, and 6s electrons are treated explicitly. The quality of new RESC-AIMP has been tested by calculating the spectroscopic properties of the hydrides of these elements using the Hartree-Fock and coupled cluster with singles and doubles (CCSD) methods. The agreement with reference all-electron RESC calculations is excellent. The RESC-AIMP method is applied successfully in the investigation of the spectroscopic constants of Au2 and Hg2 using the CCSD method with a perturbative estimate of the contributions of triples. The ground state of Pt2 is also determined by RESC-AIMP with the second-order complete active space perturbation method. The results show that scalar relativistic effects on the valence properties are well described by the RESC-AIMP method. The effect on the basis set superposition error on the spectroscopic constants is also examined.

  16. Ab initio long-range interaction and adiabatic channel capture model for ultracold reactions between the KRb molecules

    NASA Astrophysics Data System (ADS)

    Buchachenko, A. A.; Stolyarov, A. V.; Szczȩśniak, M. M.; Chałasiński, G.

    2012-09-01

    The coefficients at the lowest-order electrostatic, induction, and dispersion terms of the anisotropic long-range potential between the two KRb(1Σ+) molecules are evaluated through the static and dynamic molecular properties using the ab initio coupled cluster techniques. Adiabatic channel potentials for the ground-state molecules are obtained and used for the numerical quantum capture probability calculations in the spirit of the statistical adiabatic channel models. Capture rate coefficients for indistinguishable (polarized) and distinguishable (unpolarized) molecules at temperatures below 10 μK agree well with those computed with the simple isotropic dispersion R-6 potential, but underestimate the measured ones [Ospelkaus et al., Science 327, 853 (2010), 10.1126/science.1184121] up to a factor of 3. Preliminary assessment of the effects of higher-order long-range terms, retardation of dispersion forces, and magnetic dipole-dipole interaction does not offer any clear perspectives for drastic improvement of the capture approximation for the reactions studied.

  17. Ab initio-aided CALPHAD thermodynamic modeling of the Sn-Pb binary system under current stressing.

    PubMed

    Lin, Shih-kang; Yeh, Chao-kuei; Xie, Wei; Liu, Yu-chen; Yoshimura, Masahiro

    2013-01-01

    Soldering is an ancient process, having been developed 5000 years ago. It remains a crucial process with many modern applications. In electronic devices, electric currents pass through solder joints. A new physical phenomenon--the supersaturation of solders under high electric currents--has recently been observed. It involves (1) un-expected supersaturation of the solder matrix phase, and (2) the formation of unusual "ring-shaped" grains. However, the origin of these phenomena is not yet understood. Here we provide a plausible explanation of these phenomena based on the changes in the phase stability of Pb-Sn solders. Ab initio-aided CALPHAD modeling is utilized to translate the electric current-induced effect into the excess Gibbs free energies of the phases. Hence, the phase equilibrium can be shifted by current stressing. The Pb-Sn phase diagrams with and without current stressing clearly demonstrate the change in the phase stabilities of Pb-Sn solders under current stressing. PMID:24060995

  18. Ab initio model of salicylate adsorbed onto Al{sub 2}O{sub 3} and illite clay

    SciTech Connect

    Kubicki, J.D.; Itoh, M.J.; Apitz, S.E.

    1996-10-01

    Organic-mineral surface chemistry plays a significant role in numerous geochemical processes such as global carbon cycling, weathering, and contaminant fate and transport. Knowledge of bonding mechanisms between naturally-occurring organic matter (NOM) and minerals is necessary in environmental science. This research examines surface complexation of salicylic acid (which is often used as an analog for NOM) adsorbed onto Al{sub 2}O{sub 3} and illite. ATR-FTIR spectra of the adsorbed complexes were measured and compared to theoretical vibrational spectra of possible surface configurations derived form molecular orbital (MO) calculations. A variety of Al- and Si-salicylate complexes were modeled with ab initio MO calculations. The theoretical vibrational spectrum that best fits the observed spectra corresponds to a salicylate anion bonded to an octahedral Al{sup 3+} ion via a C-O-Al ester-type linkage. These results support the configuration proposed in Biber and Stumm for salicylate adsorbed onto Al{sub 2}O{sub 3}.

  19. Ab initio melting curve of osmium

    NASA Astrophysics Data System (ADS)

    Burakovsky, L.; Burakovsky, N.; Preston, D. L.

    2015-11-01

    The melting curve of osmium up to a pressure P of 500 GPa is obtained from an extensive suite of ab initio quantum molecular dynamics (QMD) simulations using the Z method. The ab initio P =0 melting point of Os is 3370 ±75 K; this range encompasses all of the available data in the literature and corroborates the conclusion of J. W. Arblaster [Platinum Metals Rev. 49, 166 (2005)], 10.1595/147106705X70264 that the melting temperature of pure Os is 3400 ±50 K and that the 3300 K typically quoted in the literature is the melting point of impure Os. The T =0 equation of state (EOS) of Os and the P dependence of the optimized c /a ratio for the hexagonal unit cell, both to pressures ˜900 GPa, are obtained in the ab initio approach as validation of its use. Although excellent agreement with the available experimental data (P ≲80 GPa) is found, it is the third-order Birch-Murnaghan EOS with B0'=5 rather than the more widely accepted B0'=4 that describes the QMD data to higher pressures, in agreement with the more recent experimental EOS by Godwal et al. The theoretical melting curve of Os obtained earlier by Joshi et al. is shown to be inconsistent with our QMD results, and the possible reason for this discrepancy is suggested. Regularities in the melting curves of Os and five other third-row transition metals (Ta, W, Re, Pt, Au) could be used to estimate the currently unknown melting curves of Hf and Ir.

  20. Ab initio quantum chemistry: Methodology and applications

    PubMed Central

    Friesner, Richard A.

    2005-01-01

    This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller–Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation over the past decade. Incorporation of a condensed-phase environment by means of mixed quantum mechanical/molecular mechanics or self-consistent reaction field techniques, is presented. A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly. PMID:15870212

  1. Spin-orbit decomposition of ab initio nuclear wave functions

    NASA Astrophysics Data System (ADS)

    Johnson, Calvin W.

    2015-03-01

    Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum j , leading to j -j coupling, decades ago phenomenological models suggested that a simpler picture for 0 p -shell nuclides can be realized via coupling of the total spin S and total orbital angular momentum L . I revisit this idea with large-basis, no-core shell-model calculations using modern ab initio two-body interactions and dissect the resulting wave functions into their component L - and S -components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly 50 years and six orders of magnitude in basis dimensions. I suggest that L -S decomposition may be a useful tool for analyzing ab initio wave functions of light nuclei, for example, in the case of rotational bands.

  2. ParaDynamics: An Effective and Reliable Model for Ab Initio QM/MM Free Energy Calculations and Related Tasks

    PubMed Central

    Plotnikov, Nikolay; Kamerlin, Shina Caroline Lynn; Warshel, Arieh

    2011-01-01

    Recent years have seen tremendous effort in the development of approaches with which to obtain quantum mechanics/molecular mechanics (QM/MM) free energies for reactions in the condensed phase. Nevertheless, there remain significant challenges to address, particularly the high computational cost involved in performing proper configurational sampling and in particular in obtaining ab initio QM/MM (QM(ai)/MM) free energy surfaces. One increasingly popular approach that seems to offer an ideal way to progress in this direction is the elegant metadynamics (MTD) approach. However, in the current work we point out the subtle efficiency problems associated with this approach, and illustrate that we have at hand what is arguably a more powerful approach. More specifically, we demonstrate the effectiveness of an updated version of our original idea of using a classical reference potential for QM(ai)/MM calculations [J. Phys. Chem. B. 102 (1998), 2293)], which we refer to as “paradynamics” (PD). This approach is based on the use of an empirical valence bond (EVB) reference potential, which is already similar to the real ab initio potential. The reference potential is fitted to the ab initio potential by an iterative and, to a great degree, automated refinement procedure. The corresponding free energy profile is then constructed using the refined EVB potential, and the linear response approximation (LRA) is used to evaluate the QM(ai)/MM activation free energy barrier. The automated refinement of the EVB surface (and thus the reduction of the difference between the reference and ab initio potentials) is a key factor in accelerating the convergence of the LRA approach. We apply our PD approach to a test reaction, namely the SN2 reaction between chloride ion and methyl chloride, and demonstrate that, at present, this approach is far more powerful and cost effective than the metadynamics approach (at least in its current implementation). We also discuss the general features

  3. Surface Segregation Energies of BCC Binaries from Ab Initio and Quantum Approximate Calculations

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2003-01-01

    We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy method. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameterization. Quantum approximate segregation energies are computed with and without atomistic relaxation. The ab initio calculations are performed without relaxation for the most part, but predicted relaxations from quantum approximate calculations are used in selected cases to compute approximate relaxed ab initio segregation energies. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with other quantum approximate and ab initio theoretical work, and available experimental results.

  4. Towards Accurate Ab Initio Predictions of the Spectrum of Methane

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Kwak, Dochan (Technical Monitor)

    2001-01-01

    We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born- Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

  5. Ab Initio Path-Integral Calculations of Kinetic and Equilibrium Isotope Effects on Base-Catalyzed RNA Transphosphorylation Models

    PubMed Central

    Wong, Kin-Yiu; Yuqing, Xu; York, Darrin M.

    2014-01-01

    Detailed understandings of the reaction mechanisms of RNA catalysis in various environments can have profound importance for many applications, ranging from the design of new biotechnologies to the unraveling of the evolutionary origin of life. An integral step in the nucleolytic RNA catalysis is self-cleavage of RNA strands by 2′-O-transphosphorylation. Key to elucidating a reaction mechanism is determining the molecular structure and bonding characteristics of transition state. A direct and powerful probe of transition state is measuring isotope effects on biochemical reactions, particularly if we can reproduce isotope effect values from quantum calculations. This paper significantly extends the scope of our previous joint experimental and theoretical work in examining isotope effects on enzymatic and non-enzymatic 2′-O-transphosphorylation reaction models that mimic reactions catalyzed by RNA enzymes (ribozymes), and protein enzymes such as ribonuclease A (RNase A). Native reactions are studied, as well as reactions with thio substitutions representing chemical modifications often used in experiments to probe mechanism. Here, we report and compare results from eight levels of electronic-structure calculations for constructing the potential energy surfaces in kinetic and equilibrium isotope effects (KIE and EIE) computations, including a “gold-standard” coupled-cluster level of theory [CCSD(T)]. In addition to the widely-used Bigeleisen equation for estimating KIE and EIE values, internuclear anharmonicity and quantum tunneling effects were also computed using our recently-developed ab initio path-integral method, i.e., automated integration-free path-integral (AIF-PI) method. The results of this work establish an important set of benchmarks that serve to guide calculations of KIE and EIE for RNA catalysis. PMID:24841935

  6. Understanding phonon transport in thermoelectric materials using ab initio approaches

    NASA Astrophysics Data System (ADS)

    Broido, David

    Good thermoelectric materials have low phonon thermal conductivity, kph. Accurate theories to describe kph are important components in developing predictive models of thermoelectric efficiency that can help guide synthesis and measurement efforts. We have developed ab initio approaches to calculate kph, in which phonon modes and phonon scattering rates are computed using interatomic force constants determined from density functional theory, and a full solution of the Boltzmann transport equation for phonons is implemented. A recent approach to calculate interatomic force constants using ab initio molecular dynamics has yielded a good description of the thermal properties of Bi2Te3. But, the complexity of new promising candidate thermoelectric materials introduces computational challenges in assessing their thermal properties. An example is germanane, a germanium based hydrogen-terminated layered semiconductor, which we will discuss in this talk.

  7. Ab Initio Calculations Of Light-Ion Reactions

    SciTech Connect

    Navratil, P; Quaglioni, S; Roth, R; Horiuchi, W

    2012-03-12

    The exact treatment of nuclei starting from the constituent nucleons and the fundamental interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of nuclear forces, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD employing Hamiltonians constructed within chiral effective field theory. In this contribution, we present one of such promising techniques capable of describing simultaneously both bound and scattering states in light nuclei. By combining the resonating-group method (RGM) with the ab initio no-core shell model (NCSM), we complement a microscopic cluster approach with the use of realistic interactions and a microscopic and consistent description of the clusters. We discuss applications to light nuclei scattering, radiative capture and fusion reactions.

  8. Ab Initio Electronic Relaxation Times and Transport in Noble Metals

    NASA Astrophysics Data System (ADS)

    Mustafa, Jamal I.; Bernardi, Marco; Neaton, Jeffrey B.; Louie, Steven G.

    Relaxation times employed to study electron transport in metals are typically assumed to be constants and obtained empirically using the Drude model. Here, we employ ab initio calculations to compute the electron-phonon relaxation times of Cu, Ag, and Au, and find that they vary significantly on the Fermi surface, spanning ~15 -45 fs. We compute room temperature resistivities in excellent agreement with experiment by combining GW bandstructures, Wannier-interpolated band velocities, and ab initio relaxation times. Our calculations are compared to other approximations used for the relaxation times. Additionally, an importance sampling scheme is introduced to speed up the convergence of resistivity and transport calculations by sampling directly points on the Fermi surface. This work was supported by NSF Grant No. DMR15-1508412 and U.S. DOE under Contract No. DE-AC02-05CH11231. Computational resources have been provided by DOE at LBNL's NERSC facility.

  9. Influence of ab initio chemistry models on simulations of the Ionian atmosphere

    NASA Astrophysics Data System (ADS)

    Parsons, Neal; Levin, Deborah A.; Walker, Andrew C.; Moore, Chris H.; Goldstein, David B.; Varghese, Philip L.; Trafton, Laurence

    2014-09-01

    There is significant scientific interest in simulating the unique atmospheric conditions on the Jovian moon Io that range from cold surface temperatures to hyperthermal interactions which possibly supply the Jovian plasma torus. The Direct Simulation Monte Carlo (DSMC) method is well suited to model the rarefied, predominantly SO2, Ionian atmosphere. High speed collisions between SO2 and the hypervelocity O atoms and ions that compose the plasma torus are a significant mechanism in determining the composition of the atmosphere; therefore, high-fidelity modeling of their interactions is crucial to the accuracy of such simulations. Typically, the Total Collision Energy (TCE) model is used to determine molecular dissociation probabilities and the Variable Hard Sphere (VHS) model is used to determine collision cross sections. However, the parameters for each of these baseline models are based on low-temperature experimental data and thus have unknown reliability for the hyperthermal conditions in the Ionian atmosphere. Recently, Molecular Dynamics/Quasi-Classical Trajectory (MD/QCT) studies have been conducted to generate accurate collision and chemistry models for the SO2-O collision pair in order to replace the baseline models. However, the influence of MD/QCT models on Ionian simulations compared to the previously used models is not well understood. In this work, 1D simulations are conducted using both the MD/QCT-based and baseline models in order to determine the effect of MD/QCT models on Ionian simulations. It is found that atmospheric structure predictions are highly sensitive to the chemistry and collision models. Specifically, the MD/QCT model predicts approximately half the SO2 atmospheric dissociation due to O and O+ bombardment compared to TCE models, and also predicts a temperature rise due to plasma heating further from the Ionian surface than the existing baseline methodologies. These findings indicate that the accurate MD/QCT chemistry and collision

  10. Phenylalanine ab initio models for the simulation of skin natural moisturizing factor

    NASA Astrophysics Data System (ADS)

    Carvalho, B. G.; Raniero, L. J.; Martin, A. A.; Favero, P. P.

    2013-04-01

    In this study, we evaluated models that can be used to simulate amino acids in biological environments via density functional theory (DFT). The goal was to obtain realistic representations that combine computational economy and result quality when compared to experimental data. We increased the complexity of the models by using a model of an amino acid in a vacuum, followed by a water-solvated amino acid model. To consider pH variation, we simulated zwitterionic and nonionic amino acid configurations. The amino acid chosen for testing was phenylalanine, an aromatic amino acid present in high concentrations in the natural moisturizing factor of skin that plays a fundamental role in ultraviolet protection and vitiligo disease. To validate the models, vibrational modes and electronic properties were calculated and compared to experimental results.

  11. Symplectic Symmetry and the Ab Initio No-Core Shell Model

    SciTech Connect

    Draayer, Jerry P.; Dytrych, Tomas; Sviratcheva, Kristina D.; Bahri, Chairul; Vary, James P.; /Iowa State U. /LLNL, Livermore /SLAC

    2007-03-14

    The symplectic symmetry of eigenstates for the 0{sub gs}{sup +} in {sup 16}O and the 0{sub gs}{sup +} and lowest 2{sup +} and 4{sup +} configurations of {sup 12}C that are well-converged within the framework of the no-core shell model with the JISP16 realistic interaction is examined. These states are found to project at the 85-90% level onto very few symplectic representations including the most deformed configuration, which confirms the importance of a symplectic no-core shell model and reaffirms the relevance of the Elliott SU(3) model upon which the symplectic scheme is built.

  12. Evidence for Symplectic Symmetry in Ab Initio No-Core Shell Model Results for Light Nuclei

    SciTech Connect

    Dytrych, Tomas; Sviratcheva, Kristina D.; Bahri, Chairul; Draayer, Jerry P.; Vary, James P.; /Iowa State U. /LLNL, Livermore /SLAC

    2007-04-24

    Clear evidence for symplectic symmetry in low-lying states of {sup 12}C and {sup 16}O is reported. Eigenstates of {sup 12}C and {sup 16}O, determined within the framework of the no-core shell model using the JISP16 NN realistic interaction, typically project at the 85-90% level onto a few of the most deformed symplectic basis states that span only a small fraction of the full model space. The results are nearly independent of whether the bare or renormalized effective interactions are used in the analysis. The outcome confirms Elliott's SU(3) model which underpins the symplectic scheme, and above all, points to the relevance of a symplectic no-core shell model that can reproduce experimental B(E2) values without effective charges as well as deformed spatial modes associated with clustering phenomena in nuclei.

  13. Ab Initio Study of 40Ca with an Importance Truncated No-Core Shell Model

    SciTech Connect

    Roth, R; Navratil, P

    2007-05-22

    We propose an importance truncation scheme for the no-core shell model, which enables converged calculations for nuclei well beyond the p-shell. It is based on an a priori measure for the importance of individual basis states constructed by means of many-body perturbation theory. Only the physically relevant states of the no-core model space are considered, which leads to a dramatic reduction of the basis dimension. We analyze the validity and efficiency of this truncation scheme using different realistic nucleon-nucleon interactions and compare to conventional no-core shell model calculations for {sup 4}He and {sup 16}O. Then, we present the first converged calculations for the ground state of {sup 40}Ca within no-core model spaces including up to 16{h_bar}{Omega}-excitations using realistic low-momentum interactions. The scheme is universal and can be easily applied to other quantum many-body problems.

  14. High throughput ab initio modeling of charge transport for bio-molecular-electronics

    NASA Astrophysics Data System (ADS)

    Bruque, Nicolas Alexander

    2009-12-01

    Self-assembled nanostructures, composed of inorganic and organic materials, have multiple applications in the fields of engineering and nanotechnology. Experimental research using nanoscaled materials, such as semiconductor/metallic nanocrystals, nanowires (NW), and carbon nanotube (CNT)-molecular systems have potential applications in next generation nano electronic devices. Many of these molecular systems exhibit electronic device functionality. However, experimental analytical techniques to determine how the chemistry and geometry affects electron transport through these devices does not yet exist. Using theory and modeling, one can approximate the chemistry and geometry at the atomic level and also determine how the chemistry and geometry governs electron current. Nanoelectronic devices however, contain several thousand atoms which makes quantum modeling difficult. Popular atomistic modeling approaches are capable of handling small molecular systems, which are of scientific interest, but have little engineering value. The lack of large scale modeling tools has left the scientific and engineering community with a limited ability to understand, explore, and design complex systems of engineering interest. To address these issues, I have developed a high performance general quantum charge transport model based on the non-equilibrium Green function (NEGF) formalism using density functional theory (DFT) as implemented in the FIREBALL software. FIREBALL is a quantum molecular dynamics code which has demonstrated the ability to model large molecular systems. This dissertation project of integrating NEGF into FIREBALL provides researchers with a modeling tool capable of simulating charge current in large inorganic/organic systems. To provide theoretical support for experimental efforts, this project focused on CNT-molecular systems, which includes the discovery of a CNT-molecular resonant tunneling diode (RTD) for electronic circuit applications. This research also

  15. Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes

    SciTech Connect

    Draayer, Jerry P.

    2014-09-28

    We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).

  16. Ab initio calculations of reactions with light nuclei

    NASA Astrophysics Data System (ADS)

    Quaglioni, Sofia; Hupin, Guillaume; Calci, Angelo; Navrátil, Petr; Roth, Robert

    2016-03-01

    An ab initio (i.e., from first principles) theoretical framework capable of providing a unified description of the structure and low-energy reaction properties of light nuclei is desirable to further our understanding of the fundamental interactions among nucleons, and provide accurate predictions of crucial reaction rates for nuclear astrophysics, fusion-energy research, and other applications. In this contribution we review ab initio calculations for nucleon and deuterium scattering on light nuclei starting from chiral two- and three-body Hamiltonians, obtained within the framework of the ab initio no-core shell model with continuum. This is a unified approach to nuclear bound and scattering states, in which square-integrable energy eigenstates of the A-nucleon system are coupled to (A-a)+a target-plus-projectile wave functions in the spirit of the resonating group method to obtain an efficient description of the many-body nuclear dynamics both at short and medium distances and at long ranges.

  17. Guiding ab initio calculations by alchemical derivatives.

    PubMed

    to Baben, M; Achenbach, J O; von Lilienfeld, O A

    2016-03-14

    We assess the concept of alchemical transformations for predicting how a further and not-tested change in composition would change materials properties. This might help to guide ab initio calculations through multidimensional property-composition spaces. Equilibrium volumes, bulk moduli, and relative lattice stability of fcc and bcc 4d transition metals Zr, Nb, Mo, Tc, Ru, Rh, Pd, and Ag are calculated using density functional theory. Alchemical derivatives predict qualitative trends in lattice stability while equilibrium volumes and bulk moduli are predicted with less than 9% and 28% deviation, respectively. Predicted changes in equilibrium volume and bulk moduli for binary and ternary mixtures of Rh-Pd-Ag are in qualitative agreement even for predicted bulk modulus changes as large as +100% or -50%. Based on these results, it is suggested that alchemical transformations could be meaningful for enhanced sampling in the context of virtual high-throughput materials screening projects. PMID:26979677

  18. Discovering chemistry with an ab initio nanoreactor

    DOE PAGESBeta

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.

    2014-11-02

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis frommore » primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.« less

  19. Discovering chemistry with an ab initio nanoreactor

    PubMed Central

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.

    2014-01-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings. PMID:25411881

  20. Guiding ab initio calculations by alchemical derivatives

    NASA Astrophysics Data System (ADS)

    to Baben, M.; Achenbach, J. O.; von Lilienfeld, O. A.

    2016-03-01

    We assess the concept of alchemical transformations for predicting how a further and not-tested change in composition would change materials properties. This might help to guide ab initio calculations through multidimensional property-composition spaces. Equilibrium volumes, bulk moduli, and relative lattice stability of fcc and bcc 4d transition metals Zr, Nb, Mo, Tc, Ru, Rh, Pd, and Ag are calculated using density functional theory. Alchemical derivatives predict qualitative trends in lattice stability while equilibrium volumes and bulk moduli are predicted with less than 9% and 28% deviation, respectively. Predicted changes in equilibrium volume and bulk moduli for binary and ternary mixtures of Rh-Pd-Ag are in qualitative agreement even for predicted bulk modulus changes as large as +100% or -50%. Based on these results, it is suggested that alchemical transformations could be meaningful for enhanced sampling in the context of virtual high-throughput materials screening projects.

  1. Discovering chemistry with an ab initio nanoreactor.

    PubMed

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S; Martínez, Todd J

    2014-12-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor--a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings. PMID:25411881

  2. Discovering chemistry with an ab initio nanoreactor

    NASA Astrophysics Data System (ADS)

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.

    2014-12-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor—a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.

  3. Discovering chemistry with an ab initio nanoreactor

    SciTech Connect

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.

    2014-11-02

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.

  4. Ab Initio Calculation of the Hoyle State

    SciTech Connect

    Epelbaum, Evgeny; Krebs, Hermann; Lee, Dean; Meissner, Ulf-G.

    2011-05-13

    The Hoyle state plays a crucial role in the helium burning of stars heavier than our Sun and in the production of carbon and other elements necessary for life. This excited state of the carbon-12 nucleus was postulated by Hoyle as a necessary ingredient for the fusion of three alpha particles to produce carbon at stellar temperatures. Although the Hoyle state was seen experimentally more than a half century ago nuclear theorists have not yet uncovered the nature of this state from first principles. In this Letter we report the first ab initio calculation of the low-lying states of carbon-12 using supercomputer lattice simulations and a theoretical framework known as effective field theory. In addition to the ground state and excited spin-2 state, we find a resonance at -85(3) MeV with all of the properties of the Hoyle state and in agreement with the experimentally observed energy.

  5. Effective Operators Within the Ab Initio No-Core Shell Model

    SciTech Connect

    Stetcu, I; Barrett, B R; Navratil, P; Vary, J P

    2004-11-30

    We implement an effective operator formalism for general one- and two-body operators, obtaining results consistent with the no-core shell model (NCSM) wave functions. The Argonne V8' nucleon-nucleon potential was used in order to obtain realistic wave functions for {sup 4}He, {sup 6}Li and {sup 12}C. In the NCSM formalism, we compute electromagnetic properties using the two-body cluster approximation for the effective operators and obtain results which are sensitive to the range of the bare operator. To illuminate the dependence on the range, we employ a Gaussian two-body operator of variable range, finding weak renormalization of long range operators (e.g., quadrupole) in a fixed model space. This is understood in terms of the two-body cluster approximation which accounts mainly for short-range correlations. Consequently, short range operators, such as the relative kinetic energy, will be well renormalized in the two-body cluster approximation.

  6. SurfKin: an ab initio kinetic code for modeling surface reactions.

    PubMed

    Le, Thong Nguyen-Minh; Liu, Bin; Huynh, Lam K

    2014-10-01

    In this article, we describe a C/C++ program called SurfKin (Surface Kinetics) to construct microkinetic mechanisms for modeling gas-surface reactions. Thermodynamic properties of reaction species are estimated based on density functional theory calculations and statistical mechanics. Rate constants for elementary steps (including adsorption, desorption, and chemical reactions on surfaces) are calculated using the classical collision theory and transition state theory. Methane decomposition and water-gas shift reaction on Ni(111) surface were chosen as test cases to validate the code implementations. The good agreement with literature data suggests this is a powerful tool to facilitate the analysis of complex reactions on surfaces, and thus it helps to effectively construct detailed microkinetic mechanisms for such surface reactions. SurfKin also opens a possibility for designing nanoscale model catalysts. PMID:25111729

  7. Ab initio transport coefficients of Ar⁺ ions in Ar for cold plasma jet modeling.

    PubMed

    Chicheportiche, A; Lepetit, B; Gadéa, F X; Benhenni, M; Yousfi, M; Kalus, R

    2014-06-01

    Collision cross sections and transport coefficients are calculated for Ar{+} ions, in the ground state {2}P_{3/2} and in the metastable state {2}P_{1/2}, colliding with their parent gas. Differential and integral collision cross sections are obtained using a numerical integration of the nuclear Schrödinger equation for several published interaction potentials. The Cohen-Schneider semi-empirical model is used for the inclusion of the spin-orbit interaction. The corresponding differential collision cross sections are then used in an optimized Monte Carlo code to calculate the ion transport coefficients for each initial ion state over a wide range of reduced electric field. Ion swarm data results are then compared with available experimental data for different proportions of ions in each state. This allows us to identify the most reliable interaction potential which reproduces ion transport coefficients falling within the experimental error bars. Such ion transport data will be used in electrohydrodynamic and chemical kinetic models of the low temperature plasma jet to quantify and to tune the active species production for a better use in biomedical applications. PMID:25019899

  8. Ab initio cluster model study of the chemisorptions of CO on low-index platinum surfaces

    SciTech Connect

    Curulla, D.; Clotet, A.; Ricart, J.M.; Illas, F.

    1999-06-24

    A systematic theoretical study of the adsorption of CO on the Pt{l_brace}100{r_brace}, Pt{l_brace}110{r_brace}, and Pt{l_brace}111{r_brace} surfaces is presented. The calculated equilibrium geometries and vibrational frequencies have been found to be rather independent of the cluster model chosen to represent the surface. However, calculated interaction energies are found to be very sensitive to the surface cluster model. The analysis of the chemisorption bond has been carried out by means of the constrained space orbital variation, CSOV, and of projection operator techniques. These analysis reveal that the bonding interactions are dominated by the {pi}-back-donation although {sigma}-donation plays a significant role. It is also clearly shown that all bonding mechanisms, other than Pauli repulsion, but specially {pi}-back-donation, contribute to the observed red shift. However, the {pi}-back-donation contribution to the red shift is very similar for CO on different sites. Hence, {pi}-back-donation cannot be the mechanism responsible for the observed difference for the CO vibrational frequency on on-top and bridge sites. The CSOV decomposition reveals that the leading term contributing to this difference in vibrational frequency of chemisorbed CO is the initial Pauli repulsion or wall effect; this is a new, important and unexpected conclusion.

  9. Mo;ecular Modeling of Biogenic Manganese Oxides Using ab Initio Density Functional Theory

    NASA Astrophysics Data System (ADS)

    Oconnor, M.; Sposito, G.; Refson, K.

    2003-12-01

    Layer type manganese oxides with short-range crystalline order (birnessites) are produced by many species of bacteria.Deposits of these oxides form a highly reactive catalytic surface that plays a major role in the destruction and sequestration of organic compounds and metals.Biogenic oxides also contain vacant Mn(IV)sites;these sites,with their associated negative charge, are the probable main cause of the high sorptive reactivity of the oxide surfaces. In order to acquire a deeper understanding of the molecular mechanisms involved in these processes, a model of a biogenic oxide was built and its structure was optimized using the CASTEP three-dimensional periodic system computational package. The resulting crystal structure shows good agreement with EXAFS data from crystals formed by a strain of the common soil and freshwater bacterium, Pseudomonas putida. The greatest challenge in modeling Mn oxides (like other transition metal oxides)comes in dealing with the electronic factors that lead to their magnetic and catalytic properties: they are highly correlated systems where the spin must be taken into account in order to obtain accurate predictions of their properties.

  10. Ab initio transport coefficients of Ar+ ions in Ar for cold plasma jet modeling

    NASA Astrophysics Data System (ADS)

    Chicheportiche, A.; Lepetit, B.; Gadéa, F. X.; Benhenni, M.; Yousfi, M.; Kalus, R.

    2014-06-01

    Collision cross sections and transport coefficients are calculated for Ar+ ions, in the ground state 2P3/2 and in the metastable state 2P1/2, colliding with their parent gas. Differential and integral collision cross sections are obtained using a numerical integration of the nuclear Schrödinger equation for several published interaction potentials. The Cohen-Schneider semi-empirical model is used for the inclusion of the spin-orbit interaction. The corresponding differential collision cross sections are then used in an optimized Monte Carlo code to calculate the ion transport coefficients for each initial ion state over a wide range of reduced electric field. Ion swarm data results are then compared with available experimental data for different proportions of ions in each state. This allows us to identify the most reliable interaction potential which reproduces ion transport coefficients falling within the experimental error bars. Such ion transport data will be used in electrohydrodynamic and chemical kinetic models of the low temperature plasma jet to quantify and to tune the active species production for a better use in biomedical applications.

  11. Ab initio approach to the non-perturbative scalar Yukawa model

    NASA Astrophysics Data System (ADS)

    Li, Yang; Karmanov, V. A.; Maris, P.; Vary, J. P.

    2015-09-01

    We report on the first non-perturbative calculation of the scalar Yukawa model in the single-nucleon sector up to four-body Fock sector truncation (one "scalar nucleon" and three "scalar pions"). The light-front Hamiltonian approach with a systematic non-perturbative renormalization is applied. We study the n-body norms and the electromagnetic form factor. We find that the one- and two-body contributions dominate up to coupling α ≈ 1.7. As we approach the coupling α ≈ 2.2, we discover that the four-body contribution rises rapidly and overtakes the two- and three-body contributions. By comparing with lower sector truncations, we show that the form factor converges with respect to the Fock sector expansion.

  12. Ab initio electronic structure study of a model water splitting dimer complex.

    PubMed

    Fernando, Amendra; Aikens, Christine M

    2015-12-28

    A model manganese dimer electrocatalyst bridged by μ-OH ligands is used to investigate changes in spin states that may occur during water oxidation. We have employed restricted open-shell Hartree-Fock (ROHF), second-order Møller-Plesset perturbation theory (MP2), complete active space self-consistent field (CASSCF), and multireference second-order Møller-Plesset perturbation theory (MRMP2) calculations to investigate this system. Multiconfigurational methods like CASSCF and MRMP2 are appropriate methods to study these systems with antiferromagnetically-coupled electrons. Orbital occupations and distributions have been closely analyzed to understand the electronic details and contributions to the water splitting from manganese and oxygen atoms. The presence of Mn(IV)O˙ radical moieties has been observed in this catalytic pathway. Multiple nearly degenerate excited states were found close to the ground state in all structures. This suggests competing potential energy landscapes near the ground state may influence the reactivity of manganese complexes such as the dimers studied in this work. PMID:26593689

  13. Ab Initio Modeling of Bulk and Intragranular Diffusion in Ni Alloys

    SciTech Connect

    Alexandrov, Vitali Y.; Sushko, Maria L.; Schreiber, Daniel K.; Bruemmer, Stephen M.; Rosso, Kevin M.

    2015-05-07

    importance for understanding mechanisms of grain boundary (GB) oxidation causing environmental degradation and cracking of Ni-base structural alloys. In this study, first-principles calculations of vacancy-mediated diffusion are performed across a wide series of alloying elements commonly used in Ni-based superalloys, as well as interstitial diffusion of atomic oxygen and sulfur in the bulk, at the (111) surface, <110> symmetric tilt GBs of Ni corresponding to model low- (Σ=3/(111)) and high-energy (Σ=9/(221)) GBs. A substantial enhancement of diffusion is found for all species at the high-energy GB as compared to the bulk and the low-energy GB, with Cr, Mn and Ti exhibiting remarkably small activation barriers (<0.1 eV; ~10 times lower than in the bulk). Calculations also show that the bulk diffusion mechanism and kinetics differ for oxygen and sulfur, with oxygen having a faster mobility and preferentially diffusing through the tetrahedral interstitial sites in Ni matrix where it can be trapped in a local minimum.

  14. Ab Initio Modeling of Bulk and Intragranular Diffusion in Ni Alloys.

    PubMed

    Alexandrov, Vitaly; Sushko, Maria L; Schreiber, Daniel K; Bruemmer, Stephen M; Rosso, Kevin M

    2015-05-01

    Knowledge of solid-state and interfacial species diffusion kinetics is of paramount importance for understanding mechanisms of grain boundary (GB) oxidation causing environmental degradation and cracking of Ni-base structural alloys. In this study, first-principles calculations of vacancy-mediated diffusion are performed across a wide series of alloying elements commonly used in Ni-based superalloys, as well as interstitial diffusion of atomic oxygen and sulfur in the bulk, at the (111) surface, ⟨110⟩ symmetric tilt GBs of Ni corresponding to model low- (Σ = 3/(111)) and high-energy (Σ = 9/(221)) GBs. A substantial enhancement of diffusion is found for all species at the high-energy GB as compared with the bulk and the low-energy GB, with Cr, Mn, and Ti exhibiting remarkably small activation barriers (<0.1 eV; ~10 times lower than in the bulk). Calculations also show that the bulk diffusion mechanism and kinetics differ for oxygen and sulfur, with oxygen having a faster mobility and preferentially diffusing through the tetrahedral interstitial sites in Ni matrix, where it can be trapped in a local minimum. PMID:26263324

  15. Obtaining model parameters for real materials from ab-initio calculations: Heisenberg exchange

    NASA Astrophysics Data System (ADS)

    Korotin, Dmitry; Mazurenko, Vladimir; Anisimov, Vladimir; Streltsov, Sergey

    An approach to compute exchange parameters of the Heisenberg model in plane-wave based methods is presented. This calculation scheme is based on the Green's function method and Wannier function projection technique. It was implemented in the framework of the pseudopotential method and tested on such materials as NiO, FeO, Li2MnO3, and KCuF3. The obtained exchange constants are in a good agreement with both the total energy calculations and experimental estimations for NiO and KCuF3. In the case of FeO our calculations explain the pressure dependence of the Néel temperature. Li2MnO3 turns out to be a Slater insulator with antiferromagnetic nearest neighbor exchange defined by the spin splitting. The proposed approach provides a unique way to analyze magnetic interactions, since it allows one to calculate orbital contributions to the total exchange coupling and study the mechanism of the exchange coupling. The work was supported by a grant from the Russian Scientific Foundation (Project No. 14-22-00004).

  16. Ab initio continuum model for the influence of local stress on cross-slip of screw dislocations in fcc metals

    NASA Astrophysics Data System (ADS)

    Ramírez, Benjamín R.; Ghoniem, Nasr; Po, Giacomo

    2012-09-01

    We develop a model of cross-slip in face-centered cubic (fcc) metals based on an extension of the Peierls-Nabarro representation of the dislocation core. The dissociated core is described by a group of parametric fractional Volterra dislocations, subject to their mutual elastic interaction and a lattice-restoring force. The elastic interaction between them is computed from a nonsingular expression, while the lattice force is derived from the γ surface obtained directly from ab initio calculations. Using a network-based formulation of dislocation dynamics, the dislocation core structure is not restricted to be planar, and the activation energy is determined for a path where the core has three-dimensional equilibrium configurations. We show that the activation energy for cross-slip in Cu is 1.9eV when the core is represented by only two Shockley partials, while this value converges to 1.43eV when the core is distributed over a bundle of 20 Volterra partial fractional dislocations. The results of the model compare favorably with the experimental value of 1.15±0.37eV [J. Bonneville and B. Escaig, Acta Metall.AMETAR0001-616010.1016/0001-6160(79)90170-6 27, 1477 (1979)]. We also show that the cross-slip activation energy decreases significantly when the core is in a particular local stress field. Results are given for a representative uniform “Escaig” stress and for the nonuniform stress field at the head of a dislocation pileup. A local homogeneous stress field is found to result in a significant reduction of the cross-slip energy. Additionally, for a nonhomogeneous stress field at the head of a five-dislocation pileup compressed against a Lomer-Cottrell junction, the cross-slip energy is found to decrease to 0.62eV. The relatively low values of the activation energy in local stress fields predicted by the proposed model suggest that cross-slip events are energetically more favorable in strained fcc crystals.

  17. Magnetism in Sr2CrMoO6 : A combined ab initio and model study

    NASA Astrophysics Data System (ADS)

    Sanyal, Prabuddha; Halder, Anita; Si, Liang; Wallerberger, Markus; Held, Karsten; Saha-Dasgupta, Tanusri

    2016-07-01

    Using a combination of first-principles density functional theory (DFT) calculations and exact diagonalization studies of a first-principles derived model, we carry out a microscopic analysis of the magnetic properties of the half-metallic double perovskite compound Sr2CrMoO6 , a sister compound of the much discussed material Sr2FeMoO6 . The electronic structure of Sr2CrMoO6 , though appearing similar to Sr2FeMoO6 at first glance, shows nontrivial differences with that of Sr2FeMoO6 on closer examination. In this context, our study highlights the importance of charge transfer energy between the two transition metal sites. The change in charge transfer energy due to a shift of Cr d states in Sr2CrMoO6 compared to Fe d in Sr2FeMoO6 suppresses the hybridization between Cr t2 g and Mo t2 g. This strongly weakens the hybridization-driven mechanism of magnetism discussed for Sr2FeMoO6 . Our study reveals that, nonetheless, the magnetic transition temperature of Sr2CrMoO6 remains high since an additional superexchange contribution to magnetism arises with a finite intrinsic moment developed at the Mo site. We further discuss the situation in comparison to another related double perovskite compound, Sr2CrWO6 . We also examine the effect of correlation beyond DFT, using dynamical mean field theory.

  18. Zinc complexation in chloride-rich hydrothermal fluids (25-600 °C): A thermodynamic model derived from ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Mei, Yuan; Sherman, David M.; Liu, Weihua; Etschmann, Barbara; Testemale, Denis; Brugger, Joël

    2015-02-01

    The solubility of zinc minerals in hydrothermal fluids is enhanced by chloride complexation of Zn2+. Thermodynamic models of these complexation reactions are central to models of Zn transport and ore formation. However, existing thermodynamic models, derived from solubility measurements, are inconsistent with spectroscopic measurements of Zn speciation. Here, we used ab initio molecular dynamics simulations (with the PBE exchange-correlation functional) to predict the speciation of Zn-Cl complexes from 25 to 600 °C. We also obtained in situ XAS measurements of Zn-Cl solutions at 30-600 °C. Qualitatively, the simulations reproduced the main features derived from in situ XANES and EXAFS measurements: octahedral to tetrahedral transition with increasing temperature and salinity, stability of ZnCl42- at high chloride concentration up to ⩾500 °C, and increasing stability of the trigonal planar [ZnCl3]- complex at high temperature. Having confirmed the dominant species, we directly determined the stability constants for the Zn-Cl complexes using thermodynamic integration along constrained Zn-Cl distances in a series of MD simulations. We corrected our stability constants to infinite dilution using the b-dot model for the activity coefficients of the solute species. In order to compare the ab initio results with experiments, we need to re-model the existing solubility data using the species we identified in our MD simulations. The stability constants derived from refitting published experimental data are in reasonable agreement with those we obtained using ab initio MD simulations. Our new thermodynamic model accurately predicts the experimentally observed changes in ZnO(s) and ZnCO3(s) solubility as a function of chloride concentration from 200 (Psat) to 600 °C (2000 bar). This study demonstrates that metal speciation and geologically useful stability constants can be derived for species in hydrothermal fluids from ab initio MD simulations even at the generalized

  19. Heats of Segregation of BCC Binaries from ab Initio and Quantum Approximate Calculations

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2004-01-01

    We compare dilute-limit heats of segregation for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent LMTO-based parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation, while the ab initio calculations are performed without relaxation. Results are discussed within the context of a segregation model driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

  20. Reply to Comment on "Ab Initio Study of 40Ca with an Importance Truncated No-Core Shell Model"

    SciTech Connect

    Roth, R; Navratil, P

    2008-01-04

    In their comment on our recent Letter [1] Dean et al. [2] criticize the calculations for the ground-state energy of {sup 40}Ca within the importance truncated no-core shell model (NCSM). In particular they address the role of configurations beyond the 3p3h level, which have not been included in the {sup 40}Ca calculations for large N{sub max} {h_bar}{Omega} model spaces. Before responding to this point, the following general statements are in order. For the atomic nucleus as a self-bound system, translational invariance is an important symmetry. The only possibility to preserve translational invariance when working with a Slater determinant basis is to use the harmonic oscillator (HO) basis in conjunction with a basis truncation according to the total HO excitation energy, i.e. N{sub max} {h_bar}{Omega}, as done in the ab initio NCSM. This is important not only for obtaining proper binding or excitation energies, but also for a correct extraction of physical wavefunctions. The spurious center-of-mass components can be exactly removed only if the HO basis and the N{sub max} {h_bar}{Omega} truncation are employed. The minimal violation of the translational invariance was one of the main motivations for developing the importance-truncation scheme introduced in the Letter. In this scheme, we start with the complete N{sub max} {h_bar}{Omega} HO basis space and select important configurations via perturbation theory. All symmetries are under control and our importance-truncated NCSM calculations are completely variational and provide an upper bound of the ground-state energy of the system. The restriction to the 3p3h level, made for computational reasons in the N{sub max} > 8 calculations for {sup 40}Ca, is not inherent to the importance truncation scheme. The explicit inclusion of 4p4h configurations--though computationally more demanding--is straight-forward, even for the largest N{sub max} {h_bar}{Omega} model spaces discussed. To demonstrate this fact we have

  1. Nonlinear effects in evolution - an ab initio study: A model in which the classical theory of evolution occurs as a special case.

    PubMed

    Clerc, Daryl G

    2016-07-21

    An ab initio approach was used to study the molecular-level interactions that connect gene-mutation to changes in an organism׳s phenotype. The study provides new insights into the evolutionary process and presents a simplification whereby changes in phenotypic properties may be studied in terms of the binding affinities of the chemical interactions affected by mutation, rather than by correlation to the genes. The study also reports the role that nonlinear effects play in the progression of organs, and how those effects relate to the classical theory of evolution. Results indicate that the classical theory of evolution occurs as a special case within the ab initio model - a case having two attributes. The first attribute: proteins and promoter regions are not shared among organs. The second attribute: continuous limiting behavior exists in the physical properties of organs as well as in the binding affinity of the associated chemical interactions, with respect to displacements in the chemical properties of proteins and promoter regions induced by mutation. Outside of the special case, second-order coupling contributions are significant and nonlinear effects play an important role, a result corroborated by analyses of published activity levels in binding and transactivation assays. Further, gradations in the state of perfection of an organ may be small or large depending on the type of mutation, and not necessarily closely-separated as maintained by the classical theory. Results also indicate that organs progress with varying degrees of interdependence, the likelihood of successful mutation decreases with increasing complexity of the affected chemical system, and differences between the ab initio model and the classical theory increase with increasing complexity of the organism. PMID:27029513

  2. Ab Initio: And a New Era of Airline Pilot Training.

    ERIC Educational Resources Information Center

    Gesell, Laurence E.

    1995-01-01

    Expansion of air transportation and decreasing numbers seeking pilot training point to a shortage of qualified pilots. Ab initio training, in which candidates with no flight time are trained to air transport proficiency, could resolve the problem. (SK)

  3. Phonocatalysis. An ab initio simulation experiment

    NASA Astrophysics Data System (ADS)

    Kim, Kwangnam; Kaviany, Massoud

    2016-06-01

    Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF6 on h-BN surface leads to formation of XeF4 and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon) energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent) requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.

  4. Ab initio two-component Ehrenfest dynamics

    NASA Astrophysics Data System (ADS)

    Ding, Feizhi; Goings, Joshua J.; Liu, Hongbin; Lingerfelt, David B.; Li, Xiaosong

    2015-09-01

    We present an ab initio two-component Ehrenfest-based mixed quantum/classical molecular dynamics method to describe the effect of nuclear motion on the electron spin dynamics (and vice versa) in molecular systems. The two-component time-dependent non-collinear density functional theory is used for the propagation of spin-polarized electrons while the nuclei are treated classically. We use a three-time-step algorithm for the numerical integration of the coupled equations of motion, namely, the velocity Verlet for nuclear motion, the nuclear-position-dependent midpoint Fock update, and the modified midpoint and unitary transformation method for electronic propagation. As a test case, the method is applied to the dissociation of H2 and O2. In contrast to conventional Ehrenfest dynamics, this two-component approach provides a first principles description of the dynamics of non-collinear (e.g., spin-frustrated) magnetic materials, as well as the proper description of spin-state crossover, spin-rotation, and spin-flip dynamics by relaxing the constraint on spin configuration. This method also holds potential for applications to spin transport in molecular or even nanoscale magnetic devices.

  5. Ab initio two-component Ehrenfest dynamics

    SciTech Connect

    Ding, Feizhi; Goings, Joshua J.; Liu, Hongbin; Lingerfelt, David B.; Li, Xiaosong

    2015-09-21

    We present an ab initio two-component Ehrenfest-based mixed quantum/classical molecular dynamics method to describe the effect of nuclear motion on the electron spin dynamics (and vice versa) in molecular systems. The two-component time-dependent non-collinear density functional theory is used for the propagation of spin-polarized electrons while the nuclei are treated classically. We use a three-time-step algorithm for the numerical integration of the coupled equations of motion, namely, the velocity Verlet for nuclear motion, the nuclear-position-dependent midpoint Fock update, and the modified midpoint and unitary transformation method for electronic propagation. As a test case, the method is applied to the dissociation of H{sub 2} and O{sub 2}. In contrast to conventional Ehrenfest dynamics, this two-component approach provides a first principles description of the dynamics of non-collinear (e.g., spin-frustrated) magnetic materials, as well as the proper description of spin-state crossover, spin-rotation, and spin-flip dynamics by relaxing the constraint on spin configuration. This method also holds potential for applications to spin transport in molecular or even nanoscale magnetic devices.

  6. Ab initio Study of He Stability in hcp-Ti

    SciTech Connect

    Dai, Yunya; Yang, Li; Peng, SM; Long, XG; Gao, Fei; Zu, Xiaotao T.

    2010-12-20

    The stability of He in hcp-Ti was studied using ab initio method based on density functional theory. The results indicate that a single He atom prefers to occupy the tetrahedral site rather than the octahedral site. The interaction of He defects with Ti atoms has been used to explain the relative stabilities of He point defects in hcp-Ti. The relative stability of He defects in hcp-Ti is useful for He clustering and bubble nucleation in metal tritides, which provides the basis for development of improved atomistic models.

  7. Ab initio study of neutron drops with chiral Hamiltonians

    NASA Astrophysics Data System (ADS)

    Potter, H. D.; Fischer, S.; Maris, P.; Vary, J. P.; Binder, S.; Calci, A.; Langhammer, J.; Roth, R.

    2014-12-01

    We report ab initio calculations for neutron drops in a 10 MeV external harmonic-oscillator trap using chiral nucleon-nucleon plus three-nucleon interactions. We present total binding energies, internal energies, radii and odd-even energy differences for neutron numbers N = 2- 18 using the no-core shell model with and without importance truncation. Furthermore, we present total binding energies for N = 8 , 16 , 20 , 28 , 40 , 50 obtained in a coupled-cluster approach. Comparisons with quantum Monte Carlo results, where available, using Argonne v8‧ with three-nucleon interactions reveal important dependences on the chosen Hamiltonian.

  8. Macromolecular ab initio phasing enforcing secondary and tertiary structure

    PubMed Central

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

    Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors’ approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a ‘still-life’, but some are correct enough for density modification and main-chain tracing to reveal the protein’s true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases. PMID:25610631

  9. Atomistic and Ab initio modeling of CaAl2O4 high-pressure polymorphs under Earth's mantle conditions

    NASA Astrophysics Data System (ADS)

    Eremin, N. N.; Grechanovsky, A. E.; Marchenko, E. I.

    2016-05-01

    Semi-empirical and ab initio theoretical investigation of crystal structure geometry, interatomic distances, phase densities and elastic properties for some CaAl2O4 phases under pressures up to 200 GPa was performed. Two independent simulation methods predicted the appearance of a still unknown super-dense CaAl2O4 modification. In this structure, the Al coordination polyhedron might be described as distorted one with seven vertices. Ca atoms were situated inside polyhedra with ten vertices and Ca-O distances from 1.96 to 2.49 Å. It became the densest modification under pressures of 170 GPa (density functional theory prediction) or 150 GPa (semi-empirical prediction). Both approaches indicated that this super-dense CaAl2O4 modification with a "stuffed α-PbO2" type structure could be a probable candidate for mutual accumulation of Ca and Al in the lower mantle. The existence of this phase can be verified experimentally using high pressure techniques.

  10. Recombination centers in 4H-SiC investigated by electrically detected magnetic resonance and ab initio modeling

    NASA Astrophysics Data System (ADS)

    Cottom, J.; Gruber, G.; Hadley, P.; Koch, M.; Pobegen, G.; Aichinger, T.; Shluger, A.

    2016-05-01

    Electrically detected magnetic resonance (EDMR) is a powerful technique for the observation and categorization of paramagnetic defects within semiconductors. The interpretation of the recorded EDMR spectra has long proved to be challenging. Here, defect spectra are identified by comparing EDMR measurements with extensive ab initio calculations. The defect identification is based upon the defect symmetry and the form of the hyperfine (HF) structure. A full description is given of how an accurate spectrum can be generated from the theoretical data by considering some thousand individual HF contributions out of some billion possibilities. This approach is illustrated with a defect observed in nitrogen implanted silicon carbide (SiC). Nitrogen implantation is a high energy process that gives rise to a high defect concentration. The majority of these defects are removed during the dopant activation anneal, shifting the interstitial nitrogen to the desired substitutional lattice sites, where they act as shallow donors. EDMR shows that a deep-level defect persists after the dopant activation anneal. This defect is characterized as having a g c ∥ B = 2.0054 ( 4 ) and g c ⊥ B = 2.0006 ( 4 ) , with pronounced hyperfine shoulder peaks with a 13 G peak to peak separation. The nitrogen at a carbon site next to a silicon vacancy ( N C V Si ) center is identified as the persistent deep-level defect responsible for the observed EDMR signal and the associated dopant deactivation.

  11. Skutterudites under pressure: An ab initio study

    SciTech Connect

    Ram, Swetarekha; Kanchana, V.; Valsakumar, M. C.

    2014-03-07

    Ab initio results on the band structure, density of states, and Fermi surface (FS) properties of LaRu{sub 4}X{sub 12} (X = P, As, Sb) are presented at ambient pressure as well as under compression. The analysis of density of states reveals the major contribution at the Fermi level to be mainly from the Ru-d and X-p states. We have a complicated Fermi surface with both electron and hole characters for all the three compounds which is derived mainly from the Ru-d and X-p states. There is also a simpler FS with hole character derived from the P-p{sub z} orbital for LaRu{sub 4}P{sub 12} and Ru-d{sub z{sup 2}} orbital in the case of As and Sb containing compounds. More interestingly, Fermi surface nesting feature is observed only in the case of the LaRu{sub 4}P{sub 12}. Under compression, we observe the topology of the complicated FS sheet of LaRu{sub 4}As{sub 12} to change around V/V{sub 0} = 0.85, leading to a behaviour similar to that of a multiband superconductor, and in addition, we have two more hole pockets centered around Γ at V/V{sub 0} = 0.8 for the same compound. Apart from this, we find the hole pocket to vanish at V/V{sub 0} = 0.8 in the case of LaRu{sub 4}Sb{sub 12} and the opening of the complicated FS sheet gets reduced. The de Haas van Alphen calculation shows the number of extremal orbits in the complicated sheet to change in As and Sb containing compounds under compression, where we also observe the FS topology to change.

  12. Ab initio prediction of the critical thickness of a precipitate

    NASA Astrophysics Data System (ADS)

    Sampath, S.; Janisch, R.

    2013-09-01

    Segregation and precipitation of second phases in metals and metallic alloys is an important phenomenon that has a strong influence on the mechanical properties of the material. Models exist that describe the growth of coherent, semi-coherent and incoherent precipitates. One important parameter of these models is the energy of the interface between matrix and precipitate. In this work we apply ab initio density functional theory calculations to obtain this parameter and to understand how it depends on chemical composition and mechanical strain at the interface. Our example is a metastable Mo-C phase, the body-centred tetragonal structure, which exists as a semi-coherent precipitate in body-centred cubic molybdenum. The interface of this precipitate is supposed to change from coherent to semi-coherent during the growth of the precipitate. We predict the critical thickness of the precipitate by calculating the different contributions to a semi-coherent interface energy by means of ab initio density functional theory calculations. The parameters in our model include the elastic strain energy stored in the precipitate, as well as a misfit dislocation energy that depends on the dislocation core width and the dislocation spacing. Our predicted critical thickness agrees well with experimental observations.

  13. Modeling surface motion effects in N2 dissociation on W(110): Ab initio molecular dynamics calculations and generalized Langevin oscillator model

    NASA Astrophysics Data System (ADS)

    Nattino, Francesco; Galparsoro, Oihana; Costanzo, Francesca; Díez Muiño, Ricardo; Alducin, Maite; Kroes, Geert-Jan

    2016-06-01

    Accurately modeling surface temperature and surface motion effects is necessary to study molecule-surface reactions in which the energy dissipation to surface phonons can largely affect the observables of interest. We present here a critical comparison of two methods that allow to model such effects, namely, the ab initio molecular dynamics (AIMD) method and the generalized Langevin oscillator (GLO) model, using the dissociation of N2 on W(110) as a benchmark. AIMD is highly accurate as the surface atoms are explicitly part of the dynamics, but this advantage comes with a large computational cost. The GLO model is much more computationally convenient, but accounts for lattice motion effects in a very approximate way. Results show that, despite its simplicity, the GLO model is able to capture the physics of the system to a large extent, returning dissociation probabilities which are in better agreement with AIMD than static-surface results. Furthermore, the GLO model and the AIMD method predict very similar energy transfer to the lattice degrees of freedom in the non-reactive events, and similar dissociation dynamics.

  14. Three-cluster dynamics within an ab initio framework

    DOE PAGESBeta

    Quaglioni, Sofia; Romero-Redondo, Carolina; Navratil, Petr

    2013-09-26

    In this study, we introduce a fully antisymmetrized treatment of three-cluster dynamics within the ab initio framework of the no-core shell model/resonating-group method. Energy-independent nonlocal interactions among the three nuclear fragments are obtained from realistic nucleon-nucleon interactions and consistent ab initio many-body wave functions of the clusters. The three-cluster Schrödinger equation is solved with bound-state boundary conditions by means of the hyperspherical-harmonic method on a Lagrange mesh. We discuss the formalism in detail and give algebraic expressions for systems of two single nucleons plus a nucleus. Using a soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we apply the method to amore » 4He+n+n description of 6He and compare the results to experiment and to a six-body diagonalization of the Hamiltonian performed within the harmonic-oscillator expansions of the no-core shell model. Differences between the two calculations provide a measure of core (4He) polarization effects.« less

  15. Oxidation of GaN: An ab initio thermodynamic approach

    NASA Astrophysics Data System (ADS)

    Jackson, Adam J.; Walsh, Aron

    2013-10-01

    GaN is a wide-band-gap semiconductor used in high-efficiency light-emitting diodes and solar cells. The solid is produced industrially at high chemical purities by deposition from a vapor phase, and oxygen may be included at this stage. Oxidation represents a potential path for tuning its properties without introducing more exotic elements or extreme processing conditions. In this work, ab initio computational methods are used to examine the energy potentials and electronic properties of different extents of oxidation in GaN. Solid-state vibrational properties of Ga, GaN, Ga2O3, and a single substitutional oxygen defect have been studied using the harmonic approximation with supercells. A thermodynamic model is outlined which combines the results of ab initio calculations with data from experimental literature. This model allows free energies to be predicted for arbitrary reaction conditions within a wide process envelope. It is shown that complete oxidation is favorable for all industrially relevant conditions, while the formation of defects can be opposed by the use of high temperatures and a high N2:O2 ratio.

  16. AB INITIO SIMULATIONS FOR MATERIAL PROPERTIES ALONG THE JUPITER ADIABAT

    SciTech Connect

    French, Martin; Becker, Andreas; Lorenzen, Winfried; Nettelmann, Nadine; Bethkenhagen, Mandy; Redmer, Ronald; Wicht, Johannes

    2012-09-15

    We determine basic thermodynamic and transport properties of hydrogen-helium-water mixtures for the extreme conditions along Jupiter's adiabat via ab initio simulations, which are compiled in an accurate and consistent data set. In particular, we calculate the electrical and thermal conductivity, the shear and longitudinal viscosity, and diffusion coefficients of the nuclei. We present results for associated quantities like the magnetic and thermal diffusivity and the kinematic shear viscosity along an adiabat that is taken from a state-of-the-art interior structure model. Furthermore, the heat capacities, the thermal expansion coefficient, the isothermal compressibility, the Grueneisen parameter, and the speed of sound are calculated. We find that the onset of dissociation and ionization of hydrogen at about 0.9 Jupiter radii marks a region where the material properties change drastically. In the deep interior, where the electrons are degenerate, many of the material properties remain relatively constant. Our ab initio data will serve as a robust foundation for applications that require accurate knowledge of the material properties in Jupiter's interior, e.g., models for the dynamo generation.

  17. Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions

    NASA Astrophysics Data System (ADS)

    Liu, Haiyan; Lu, Zhenyu; Cisneros, G. Andrés; Yang, Weitao

    2004-07-01

    The determination of reaction paths for enzyme systems remains a great challenge for current computational methods. In this paper we present an efficient method for the determination of minimum energy reaction paths with the ab initio quantum mechanical/molecular mechanical approach. Our method is based on an adaptation of the path optimization procedure by Ayala and Schlegel for small molecules in gas phase, the iterative quantum mechanical/molecular mechanical (QM/MM) optimization method developed earlier in our laboratory and the introduction of a new metric defining the distance between different structures in the configuration space. In this method we represent the reaction path by a discrete set of structures. For each structure we partition the atoms into a core set that usually includes the QM subsystem and an environment set that usually includes the MM subsystem. These two sets are optimized iteratively: the core set is optimized to approximate the reaction path while the environment set is optimized to the corresponding energy minimum. In the optimization of the core set of atoms for the reaction path, we introduce a new metric to define the distances between the points on the reaction path, which excludes the soft degrees of freedom from the environment set and includes extra weights on coordinates describing chemical changes. Because the reaction path is represented by discrete structures and the optimization for each can be performed individually with very limited coupling, our method can be executed in a natural and efficient parallelization, with each processor handling one of the structures. We demonstrate the applicability and efficiency of our method by testing it on two systems previously studied by our group, triosephosphate isomerase and 4-oxalocrotonate tautomerase. In both cases the minimum energy paths for both enzymes agree with the previously reported paths.

  18. Ab Initio Modeling of Fe(II) Adsorption and Interfacial Electron Transfer at Goethite (α-FeOOH) Surfaces

    SciTech Connect

    Alexandrov, Vitali Y.; Rosso, Kevin M.

    2015-01-01

    Goethite (α-FeOOH) surfaces represent one of the most ubiquitous redox-active interfaces in the environment, playing an important role in biogeochemical metal cycling and contaminant residence in the subsurface. Fe(II)-catalyzed recrystallization of goethite is a fundamental process in this context, but the proposed Fe(II)aq-Fe(III)goethite electron and iron atom exchange mechanism of recrystallization remains poorly understood at the atomic level. We examine the adsorption of aqueous Fe(II) and subsequent interfacial electron transfer (ET) between adsorbed Fe(II) and structural Fe(III) at the (110) and (021) goethite surfaces using density functional theory calculations including Hubbard U corrections (DFT+U) aided by ab initio molecular dynamics simulations. We investigate various surface sites for the adsorption of Fe2+(H2O)6 in different coordination environments. Calculated energies for adsorbed complexes at both surfaces favor monodentate complexes with reduced 4- and 5-fold coordination over higher-dentate structures and 6- fold coordination. The hydrolysis of H2O ligands is observed for some pre-ET adsorbed Fe(II) configurations. ET from the adsorbed Fe(II) into the goethite lattice is calculated to be energetically uphill always, but simultaneous proton transfer from H2O ligands of the adsorbed complexes to the surface oxygen species stabilizes post-ET states. We find that surface defects such as oxygen vacancies near the adsorption site also can stabilize post-ET states, enabling the Fe(II)aq-Fe(III)goethite interfacial electron transfer reaction implied from experiments to proceed.

  19. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    PubMed Central

    Elenewski, Justin E.; Hackett, John C

    2015-01-01

    The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis. PMID:25681906

  20. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    NASA Astrophysics Data System (ADS)

    Elenewski, Justin E.; Hackett, John C.

    2015-02-01

    The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.

  1. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    SciTech Connect

    Elenewski, Justin E.; Hackett, John C

    2015-02-14

    The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.

  2. Entropy of Liquid Water from Ab Initio Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Spanu, Leonardo; Zhang, Cui; Galli, Giulia

    2012-02-01

    The debate on the structural properties of water has been mostly based on the calculation of pair correlation functions. However, the simulation of thermodynamic and spectroscopic quantities may be of great relevance for the characterization of liquid water properties. We have computed the entropy of liquid water using a two-phase thermodynamic model and trajectories generated by ab initio molecular dynamics simulations [1]. In an attempt to better understand the performance of several density functionals in simulating liquid water, we have performed ab initio molecular dynamics using semilocal, hybrid [2] and van der Waals density functionals [3]. We show that in all cases, at the experimental equilibrium density and at temperatures in the vicinity of 300 K, the computed entropies are underestimated, with respect to experiment, and the liquid exhibits a degree of tetrahedral order higher than in experiments. We also discuss computational strategies to simulate spectroscopic properties of water, including infrared and Raman spectra.[4pt] [1] C.Zhang, L.Spanu and G.Galli, J.Phys.Chem. B 2011 (in press)[0pt] [2] C.Zhang, D.Donadio, F.Gygi and G.Galli, J. Chem. Theory Comput. 7, 1443 (2011)[0pt] [3] C.Zhang, J.Wu, G.Galli and F.Gygi, J. Chem. Theory Comput. 7, 3061 (2011)

  3. Ab initio tight-binding Hamiltonian for transition metal dichalcogenides

    NASA Astrophysics Data System (ADS)

    Fang, Shiang; Kuate Defo, Rodrick; Shirodkar, Sharmila N.; Lieu, Simon; Tritsaris, Georgios A.; Kaxiras, Efthimios

    2015-11-01

    We present an accurate ab initio tight-binding Hamiltonian for the transition metal dichalcogenides, MoS2, MoSe2, WS2, WSe2, with a minimal basis (the d orbitals for the metal atoms and p orbitals for the chalcogen atoms) based on a transformation of the Kohn-Sham density functional theory Hamiltonian to a basis of maximally localized Wannier functions. The truncated tight-binding Hamiltonian, with only on-site, first, and partial second neighbor interactions, including spin-orbit coupling, provides a simple physical picture and the symmetry of the main band-structure features. Interlayer interactions between adjacent layers are modeled by transferable hopping terms between the chalcogen p orbitals. The full-range tight-binding Hamiltonian can be reduced to hybrid-orbital k .p effective Hamiltonians near the band extrema that capture important low-energy excitations. These ab initio Hamiltonians can serve as the starting point for applications to interacting many-body physics including optical transitions and Berry curvature of bands, of which we give some examples.

  4. Atomic kinetic Monte Carlo model based on ab initio data: Simulation of microstructural evolution under irradiation of dilute Fe CuNiMnSi alloys

    NASA Astrophysics Data System (ADS)

    Vincent, E.; Becquart, C. S.; Domain, C.

    2007-02-01

    The embrittlement of pressure vessel steels under radiation has been long ago correlated with the presence of Cu solutes. Other solutes such as Ni, Mn and Si are now suspected to contribute also to the embrittlement. The interactions of these solutes with radiation induced point defects thus need to be characterized properly in order to understand the elementary mechanisms behind the formation of the clusters formed upon radiation. Ab initio calculations based on the density functional theory have been performed to determine the interactions of point defects with solute atoms in dilute FeX alloys (X = Cu, Mn, Ni or Si) in order to build a database used to parameterise an atomic kinetic Monte Carlo model. Some results of irradiation damage in dilute Fe-CuNiMnSi alloys obtained with this model are presented.

  5. Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    An overview of the current understanding of ozone depletion chemistry, particularly with regards the formation of the so-called Antarctic ozone hole, will be presented together with an outline as to how ab initio quantum chemistry can be used to further our understanding of stratospheric chemistry. The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results will be shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

  6. THERMODYNAMICS OF MATERIALS: FROM AB INITIO TO PHENOMENOLOGY

    SciTech Connect

    Turchi, P A

    2004-09-24

    Quantum mechanical-based (or ab initio) methods are used to predict the stability properties of materials although their application is limited to relatively simple systems in terms of structures and number of alloy components. However thermodynamics of complex multi-component alloys requires a more versatile approach afforded within the CALPHAD formalism. Despite its success, the lack of experimental data very often prevents the design of robust thermodynamic databases. After a brief survey of ab initio methodologies and CALPHAD, it will be shown how ab initio electronic structure methods can supplement in two ways CALPHAD for subsequent applications. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics '{acute a} la CALPHAD'. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys. Finally, comments will be made on challenges and future prospects.

  7. Dynamical correlation effects on photoisomerization: Ab initio multiple spawning dynamics with MS-CASPT2 for a model trans-protonated Schiff base

    DOE PAGESBeta

    Liu, Lihong; Liu, Jian; Martinez, Todd J.

    2015-12-17

    Here, we investigate the photoisomerization of a model retinal protonated Schiff base (trans-PSB3) using ab initio multiple spawning (AIMS) based on multi-state second order perturbation theory (MSPT2). Discrepancies between the photodynamical mechanism computed with three-root state-averaged complete active space self-consistent field (SA-3-CASSCF, which does not include dynamic electron correlation effects) and MSPT2 show that dynamic correlation is critical in this photoisomerization reaction. Furthermore, we show that the photodynamics of trans-PSB3 is not well described by predictions based on minimum energy conical intersections (MECIs) or minimum energy conical intersection (CI) seam paths. Instead, most of the CIs involved in the photoisomerizationmore » are far from MECIs and minimum energy CI seam paths. Thus, both dynamical nuclear effects and dynamic electron correlation are critical to understanding the photochemical mechanism.« less

  8. Dynamical correlation effects on photoisomerization: Ab initio multiple spawning dynamics with MS-CASPT2 for a model trans-protonated Schiff base

    SciTech Connect

    Liu, Lihong; Liu, Jian; Martinez, Todd J.

    2015-12-17

    Here, we investigate the photoisomerization of a model retinal protonated Schiff base (trans-PSB3) using ab initio multiple spawning (AIMS) based on multi-state second order perturbation theory (MSPT2). Discrepancies between the photodynamical mechanism computed with three-root state-averaged complete active space self-consistent field (SA-3-CASSCF, which does not include dynamic electron correlation effects) and MSPT2 show that dynamic correlation is critical in this photoisomerization reaction. Furthermore, we show that the photodynamics of trans-PSB3 is not well described by predictions based on minimum energy conical intersections (MECIs) or minimum energy conical intersection (CI) seam paths. Instead, most of the CIs involved in the photoisomerization are far from MECIs and minimum energy CI seam paths. Thus, both dynamical nuclear effects and dynamic electron correlation are critical to understanding the photochemical mechanism.

  9. Bulk-phase thermodynamic properties and dielectric constant of ethanol: an ab initio quantum mechanical approach combined with a statistical model

    NASA Astrophysics Data System (ADS)

    Pandey, Prasenjit; Chakraborty, Tanmoy; Mukherjee, Asok K.

    2013-10-01

    Ab initio theory at the HF/6-311G(d,p) level has been used to compute the hydrogen bonding thermodynamics in bulk liquid ethanol. Inter-cluster hydrogen bonding is assumed to mimic the H-bonding in bulk ethanol. Rotation of the clusters has been neglected, but translational and vibrational motions are taken into account for calculating bulk thermodynamic parameters. Results are well in agreement with an earlier report [J. Chem. Phys. 116, 4212 (2002)]. For a more accurate dipole moment of monomer, MP2/6-311++G(d,p) calculation was done. Use of the computed thermodynamic data in a statistical model yields the Kirkwood-Frohlich correlation factor and the dielectric constant of ethanol (21.0) close to the experimental value, 24.3 at 298 K.

  10. Ab initio correlated calculations of rare-gas dimer quadrupoles

    NASA Astrophysics Data System (ADS)

    Donchev, Alexander G.

    2007-10-01

    This paper reports ab initio calculations of rare gas ( RG=Kr , Ar, Ne, and He) dimer quadrupoles at the second order of Møller-Plesset perturbation theory (MP2). The study reveals the crucial role of the dispersion contribution to the RG2 quadrupole in the neighborhood of the equilibrium dimer separation. The magnitude of the dispersion quadrupole is found to be much larger than that predicted by the approximate model of Hunt. As a result, the total MP2 quadrupole moment is significantly smaller than was assumed in virtually all previous related studies. An analytical model for the distance dependence of the RG2 quadrupole is proposed. The model is based on the effective-electron approach of Jansen, but replaces the original Gaussian approximation to the electron density in an RG atom by an exponential one. The role of the nonadditive contribution in RG3 quadrupoles is discussed.

  11. Ab initio computations of photodissociation products of CFC alternatives

    SciTech Connect

    Tai, S.; Illinger, K.H.; Kenny, J.E.

    1995-12-31

    Ab initio computations, have already been used to examine the energetics of the photodissociation of stratospheric chlorofluorocarbons. Our awn research has investigated the ab initio computation of vibrational frequencies and infrared intensities of CF{sub 3}CH{sub 2}F, CF{sub 3}CF{sub 2}H, and CF{sub 3}CH{sub 3}; continuing research will attempt to expand these computations to the energetics of the photodissociation of these molecules, since sane of the most common types of chlorofluorocarbon substitutes are hydrofluoroethanes.

  12. Ab Initio Structure Analysis Using Laboratory Powder Diffraction Data

    NASA Astrophysics Data System (ADS)

    Sasaki, Akito

    Today, laboratory X-ray diffractometers are seeing increasingly wide use in the ab initio crystal structure analysis of organic powder samples. This is because optics and optical devices have been improved, making it possible to obtain precise integrated intensities of reflections in high 2-theta ranges. Another reason is that one can use direct-space methods, which do not require “high-resolution diffraction data”, much more easily than before. Described here are some key points to remember when performig ab initio crystal structure analysis using powder diffraction data from organic compounds.

  13. High-throughput ab-initio dilute solute diffusion database

    PubMed Central

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-01-01

    We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world. PMID:27434308

  14. High-throughput ab-initio dilute solute diffusion database.

    PubMed

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-01-01

    We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world. PMID:27434308

  15. Electron Transport through Polyene Junctions in between Carbon Nanotubes: an Ab Initio Realization

    NASA Astrophysics Data System (ADS)

    Chen, Yiing-Rei; Chen, Kai-Yu; Dou, Kun-Peng; Tai, Jung-Shen; Lee, Hsin-Han; Kaun, Chao-Cheng

    With both ab initio and tight-binding model calculations, we study a system of polyene bridged armchair carbon nanotube electrodes, considering one-polyene and two-polyene cases, to address aspects of quantum transport through junctions with multiple conjugated molecules. The ab initio results of the two-polyene cases not only show the interference effect in transmission, but also the sensitive dependence of such effect on the combination of relative contact sites, which agrees nicely with the tight-binding model. Moreover, we show that the discrepancy mainly brought by ab initio relaxation provides an insight into the influence upon transmission spectra, from the junction's geometry, bonding and effective potential. This work was supported by the Ministry of Science and Technology of the Republic of China under Grant Nos. 99-2112-M-003-012-MY2 and 103-2622-E-002-031, and the National Center for Theoretical Sciences of Taiwan.

  16. Motif based Hessian matrixfor ab initio geometry optimization ofnanostructures

    SciTech Connect

    Zhao, Zhengji; Wang, Lin-Wang; Meza, Juan

    2006-04-05

    A simple method to estimate the atomic degree Hessian matrixof a nanosystem is presented. The estimated Hessian matrix, based on themotif decomposition of the nanosystem, can be used to accelerate abinitio atomic relaxations with speedups of 2 to 4 depending on the sizeof the system. In addition, the programing implementation for using thismethod in a standard ab initio package is trivial.

  17. Ab initio pseudopotential band calculation of organic conductors

    SciTech Connect

    Ishibashi, Shoji; Kohyama, Masanori

    1999-12-01

    The authors have calculated the band structures of organic conductors TTF-TCNQ and {beta}-(BEDT-TTF){sub 2}I{sub 3} using the ab initio plane-wave pseudopotential method within the local-density approximation (LDA). The Fermi-surface shape and the origin of bands near the Fermi level are investigated for each compound.

  18. Multiple time step integrators in ab initio molecular dynamics

    SciTech Connect

    Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

    2014-02-28

    Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

  19. Dialkylimidazolium chloroaluminates: Ab initio calculations, Raman and neutron scattering measurements

    SciTech Connect

    Takahasi, S. ); Curtiss, L.A.; Gosztola, D.; Koura, N. ); Loong, C.K.; Saboungi, M.L. . Materials Science Div.)

    1993-04-01

    The Raman and neutron scattering spectra of 46 mol% AlCl[sub 3] -54 mol% 1-ethyl-3-methyl imidazolium chloride (EMIC) and 67 mol% AlCl[sub 3] - 33 mol% EMIC melts are presented. Ab initio molecular orbital calculations have been carried out on structures of chloroaluminate anion and EMI cation and the interaction between anion and cation.

  20. An ab initio-based Er–He interatomic potential in hcp Er

    SciTech Connect

    Yang, Li; ye, Yeting; Fan, K. M.; Shen, Huahai; Peng, Shuming; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei

    2014-09-01

    We have developed an empirical erbium-helium (Er-He) potential by fitting to the results calculated from ab initio method. Based on the electronic hybridization between Er and He atoms, an s-band model, along with a repulsive pair potential, has been derived to describe the Er-He interaction. The atomic configurations and the formation energies of single He defects, small He interstitial clusters (Hen) and He-vacancy (HenV ) clusters obtained by ab initio calculations are used as the fitting database. The binding energies and relative stabilities of the HnVm clusters are studied by the present potential and compared with the ab initio calculations. The Er-He potential is also applied to study the migration of He in hcp-Er at different temperatures, and He clustering is found to occur at 600 K in hcp Er crystal, which may be due to the anisotropic migration behavior of He interstitials.

  1. Gravitational wave signatures of ab initio two-dimensional core collapse supernova explosion models for 12–25M⊙ stars

    DOE PAGESBeta

    Yakunin, Konstantin N.; Mezzacappa, Anthony; Marronetti, Pedro; Yoshida, Shin’ichirou; Bruenn, Stephen W.; Hix, W. Raphael; Lentz, Eric J.; Bronson Messer, O. E.; Harris, J. Austin; Endeve, Eirik; et al

    2015-10-19

    Here, we present the gravitational waveforms computed in ab initio two-dimensional core collapse supernova models evolved with the chimera code for progenitor masses between 12 and 25 M. For all models employ multifrequency neutrino transport in the ray-by-ray approximation, state-of-the-art weak interaction physics, relativistic transport corrections such as the gravitational redshift of neutrinos, two-dimensional hydrodynamics with the commensurate relativistic corrections, Newtonian self-gravity with a general-relativistic monopole correction, and the Lattimer-Swesty equation of state with 220 MeV compressibility, and begin with the most recent Woosley-Heger nonrotating progenitors in this mass range. All of our models exhibit robust explosions. Moreover, our waveformsmore » capture all stages of supernova development: 1) a relatively short and weak prompt signal, 2) a quiescent stage, 3) a strong signal due to convection and standing accretion shock instability activity, 4) termination of active accretion onto the proto-neutron star, and 5) a slowly increasing tail that reaches a saturation value. Fourier decomposition shows that the gravitational wave signals we predict should be observable by AdvLIGO for Galactic events across the range of progenitors considered here. The fundamental limitation of these models is in their imposition of axisymmetry. Further progress will require counterpart three-dimensional models, which are underway.« less

  2. Exploring the ab initio/classical free energy perturbation method: The hydration free energy of water

    SciTech Connect

    Sakane, Shinichi; Yezdimer, Eric M.; Liu, Wenbin; Barriocanal, Jose A.; Doren, Douglas J.; Wood, Robert H.

    2000-08-15

    The ab initio/classical free energy perturbation (ABC-FEP) method proposed previously by Wood et al. [J. Chem. Phys. 110, 1329 (1999)] uses classical simulations to calculate solvation free energies within an empirical potential model, then applies free energy perturbation theory to determine the effect of changing the empirical solute-solvent interactions to corresponding interactions calculated from ab initio methods. This approach allows accurate calculation of solvation free energies using an atomistic description of the solvent and solute, with interactions calculated from first principles. Results can be obtained at a feasible computational cost without making use of approximations such as a continuum solvent or an empirical cavity formation energy. As such, the method can be used far from ambient conditions, where the empirical parameters needed for approximate theories of solvation may not be available. The sources of error in the ABC-FEP method are the approximations in the ab initio method, the finite sample of configurations, and the classical solvent model. This article explores the accuracy of various approximations used in the ABC-FEP method by comparing to the experimentally well-known free energy of hydration of water at two state points (ambient conditions, and 973.15 K and 600 kg/m3). The TIP4P-FQ model [J. Chem. Phys. 101, 6141 (1994)] is found to be a reliable solvent model for use with this method, even at supercritical conditions. Results depend strongly on the ab initio method used: a gradient-corrected density functional theory is not adequate, but a localized MP2 method yields excellent agreement with experiment. Computational costs are reduced by using a cluster approximation, in which ab initio pair interaction energies are calculated between the solute and up to 60 solvent molecules, while multi-body interactions are calculated with only a small cluster (5 to 12 solvent molecules). Sampling errors for the ab initio contribution to

  3. Amorphous SiO2 surface models: energetics of the dehydroxylation process, strain, ab initio atomistic thermodynamics and IR spectroscopic signatures.

    PubMed

    Comas-Vives, Aleix

    2016-03-14

    In this contribution, realistic amorphous SiO2 models of 2.1 × 2.1 nm with silanol densities ranging 1.1-7.2 OH per nm(2) are obtained by means of ab initio calculations via the dehydroxylation of a fully hydroxylated silica surface. The dehydroxyation process is considered to take place via direct condensation of adjacent silanol groups and silica migration steps. The latter reconstructions are needed in order to obtain highly dehydroxylated silica surfaces with favorable energetics and without the formation of defects. The obtained surface phase diagram of different silica models as a function of temperature and PH2O is able to correctly describe the silanol density under different conditions, and the IR spectroscopic signatures of the silanols are in qualitative agreement with the experiment. The amorphous silica models presented here have a high degree of heterogeneity as found from the big variability obtained in the energetics of the dehydroxylation steps. It was also found that the resulting average Si-O distance of the newly formed siloxane bridges serves as a descriptor of the strain introduced in the silica surface. All these factors can be crucial in order to simulate the activity of catalysts grafted onto silica with different silanol densities, especially the one containing ca. 1 OH per nm(2), which can serve as a model for the SiO2 surface pretreated under high vacuum and at 700 °C. PMID:26898649

  4. Heats of Segregation of BCC Binaries from Ab Initio and Quantum Approximate Calculations

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2003-01-01

    We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

  5. Operator evolution for ab initio theory of light nuclei

    NASA Astrophysics Data System (ADS)

    Schuster, Micah; Quaglioni, Sofia; Johnson, Calvin; Jurgenson, Eric; Navrátil, Petr

    2014-09-01

    The past two decades have seen a revolution in ab initio calculations of nuclear properties. One key element has been the development of a rigorous effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence as a function of the model space size. For consistency, however, one ought to apply the same transformation to other operators when calculating transitions and mean values from the eigenstates of the renormalized Hamiltonian. Working in a translationally invariant harmonic oscillator basis for the two- and three-nucleon systems, we evolve the Hamiltonian, square radius, and total dipole strength operators by the similarity renormalization group (SRG). The inclusion of up to three-body matrix elements in the 4He nucleus all but completely restores the invariance of the expectation values under the transformation. We also consider a Gaussian operator with adjustable range; short ranges have the largest absolute renormalization when including two- and three-body induced terms, while at long ranges the induced three-body contribution takes on increased relative importance. The past two decades have seen a revolution in ab initio calculations of nuclear properties. One key element has been the development of a rigorous effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence as a function of the model space size. For consistency, however, one ought to apply the same transformation to other operators when calculating transitions and mean values from the eigenstates of the renormalized Hamiltonian. Working in a translationally invariant harmonic oscillator basis for the two- and three-nucleon systems, we evolve the Hamiltonian, square radius, and total dipole strength operators by the similarity renormalization group (SRG). The inclusion of up to three-body matrix elements in the 4He nucleus all but completely restores

  6. Ab initio effective interactions for s d -shell valence nucleons

    NASA Astrophysics Data System (ADS)

    Dikmen, E.; Lisetskiy, A. F.; Barrett, B. R.; Maris, P.; Shirokov, A. M.; Vary, J. P.

    2015-06-01

    We perform ab initio no-core shell-model calculations for A =18 and 19 nuclei in a 4 ℏ Ω , or Nmax=4 , model space by using the effective JISP16 and chiral N3LO nucleon-nucleon potentials and transform the many-body effective Hamiltonians into the 0 ℏ Ω model space to construct the A -body effective Hamiltonians in the s d shell. We separate the A -body effective Hamiltonians with A =18 and A =19 into inert core, one-, and two-body components. Then we use these core, one-, and two-body components to perform standard shell-model calculations for the A =18 and A =19 systems with valence nucleons restricted to the s d shell. Finally, we compare the standard shell-model results in the 0 ℏ Ω model space with the exact no-core shell-model results in the 4 ℏ Ω model space for the A =18 and A =19 systems and find good agreement.

  7. Unified ab initio approach to bound and unbound states: No-core shell model with continuum and its application to 7He

    DOE PAGESBeta

    Baroni, Simone; Navratil, Petr; Quaglioni, Sofia

    2013-03-26

    In this study, we introduce a unified approach to nuclear bound and continuum states based on the coupling of the no-core shell model (NCSM), a bound-state technique, with the no-core shell model/resonating group method (NCSM/RGM), a nuclear scattering technique. This new ab initio method, no-core shell model with continuum (NCSMC), leads to convergence properties superior to either NCSM or NCSM/RGM while providing a balanced approach to different classes of states. In the NCSMC, the ansatz for the many-nucleon wave function includes (i) a square-integrable A-nucleon component expanded in a complete harmonic oscillator basis and (ii) a binary-cluster component with asymptoticmore » boundary conditions that can properly describe weakly bound states, resonances, and scattering. The Schrödinger equation is transformed into a system of coupled-channel integral-differential equations that we solve using a modified microscopic R-matrix formalism within a Lagrange mesh basis. We demonstrate the usefulness of the approach by investigating the unbound 7He nucleus.« less

  8. {sup 7}Be(p,{gamma}){sup 8}B S factor from ab initio no-core shell model wave functions

    SciTech Connect

    Navratil, P.; Bertulani, C.A.; Caurier, E.

    2006-06-15

    Nuclear structure of {sup 7}Be, {sup 8}B, and {sup 7,8}Li is studied within the ab initio no-core shell model (NCSM). Starting from high-precision nucleon-nucleon (NN) interactions, wave functions of {sup 7}Be and {sup 8}B bound states are obtained in basis spaces up to 10({Dirac_h}/2{pi}){omega} and used to calculate channel cluster form factors (overlap integrals) of the {sup 8}B ground state with {sup 7}Be+p. Due to the use of the harmonic oscillator (HO) basis, the overlap integrals have incorrect asymptotic properties. We fix this problem in two alternative ways. First, by a Woods-Saxon potential solution fit to the interior of the NCSM overlap integrals. Second, by a direct matching with the Whittaker function. The corrected overlap integrals are then used for the {sup 7}Be(p,{gamma}){sup 8}B S-factor calculation. We study the convergence of the S factor with respect to the NCSM HO frequency and the model space size. Our S factor results agree with recent direct measurement data. We also test the spectroscopic factors and the corrected overlap integrals from the NCSM in describing the momentum distributions in knockout reactions with {sup 8}B projectiles. A good agreement with the available experimental data is also found, attesting to the overall consistency of the calculations.

  9. Absolute solvation free energy of Li{sup +} and Na{sup +} ions in dimethyl sulfoxide solution: A theoretical ab initio and cluster-continuum model study

    SciTech Connect

    Westphal, Eduard; Pliego, Josefredo R. Jr.

    2005-08-15

    The solvation of the lithium and sodium ions in dimethyl sulfoxide solution was theoretically investigated using ab initio calculations coupled with the hybrid cluster-continuum model, a quasichemical theory of solvation. We have investigated clusters of ions with up to five dimethyl sulfoxide (DMSO) molecules, and the bulk solvent was described by a dielectric continuum model. Our results show that the lithium and sodium ions have four and five DMSO molecules into the first coordination shell, and the calculated solvation free energies are -135.5 and -108.6 kcal mol{sup -1}, respectively. These data suggest a solvation free energy value of -273.2 kcal mol{sup -1} for the proton in dimethyl sulfoxide solution, a value that is more negative than the present uncertain experimental value. This and previous studies on the solvation of ions in water solution indicate that the tetraphenylarsonium tetraphenylborate assumption is flawed and the absolute value of the free energy of transfer of ions from water to DMSO solution is higher than the present experimental values.

  10. i-TTM Model for Ab Initio-Based Ion-Water Interaction Potentials. 1. Halide-Water Potential Energy Functions.

    PubMed

    Arismendi-Arrieta, Daniel J; Riera, Marc; Bajaj, Pushp; Prosmiti, Rita; Paesani, Francesco

    2016-03-01

    New potential energy functions (i-TTM) describing the interactions between halide ions and water molecules are reported. The i-TTM potentials are derived from fits to electronic structure data and include an explicit treatment of two-body repulsion, electrostatics, and dispersion energy. Many-body effects are represented through classical polarization within an extended Thole-type model. By construction, the i-TTM potentials are compatible with the flexible and fully ab initio MB-pol potential, which has recently been shown to accurately predict the properties of water from the gas to the condensed phase. The accuracy of the i-TTM potentials is assessed through extensive comparisons with CCSD(T)-F12, DF-MP2, and DFT data as well as with results obtained with common polarizable force fields for X(-)(H2O)n clusters with X(-) = F(-), Cl(-), Br(-), and I(-), and n = 1-8. By construction, the new i-TTM potentials will enable direct simulations of vibrational spectra of halide-water systems from clusters to bulk and interfaces. PMID:26560189

  11. Ab-initio calculations on melting of thorium

    NASA Astrophysics Data System (ADS)

    Mukherjee, D.; Sahoo, B. D.; Joshi, K. D.; Kaushik, T. C.; Gupta, Satish C.

    2016-05-01

    Ab-initio molecular dynamics study has been performed on face centered cubic structured thorium to determine its melting temperature at room pressure. The ion-electron interaction potential energy calculated as a function of temperature for three volumes (a0)3 and (1.02a0)3 and (1.04a0)3 increases gradually with temperature and undergoes a sharp jump at ~2200 K, ~2100 K and ~1800 K, respectively. Here, a0 = 5.043 Å is the equilibrium lattice parameter at 0 K obtained from ab-initio calculations. These jumps in interaction energy are treated as due to the onset of melting and corresponding temperatures as melting point. The melting point of 2100 K is close to the experimental value of 2023K. Further, the same has been verified by plotting the atomic arrangement evolved at various temperatures and corresponding pair correlation functions.

  12. Ab initio molecular dynamics: concepts, recent developments, and future trends.

    PubMed

    Iftimie, Radu; Minary, Peter; Tuckerman, Mark E

    2005-05-10

    The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed "on the fly" from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and testable predictions of new phenomena. The purpose of this work is to give a brief introduction to the technique and to review several important recent developments in the field. Several illustrative examples showing the power of the technique have been chosen. Perspectives on future directions in the field also will be given. PMID:15870204

  13. Recent progress in ab initio density matrix renormalization group methodology

    NASA Astrophysics Data System (ADS)

    Hachmann, Johannes; Dorando, Jonathan J.; Kin-Lic Chan, Garnet

    2008-03-01

    We present some recent developments in the ab initio density matrix renormalization group (DMRG) method for quantum chemical problems, in particular our local, quadratic scaling algorithm [1] for low dimensional systems. This method is particularly suited for the description of strong nondynamic correlation, and allows us to compute numerically exact (FCI) correlated energies for large active spaces, up to one order of magnitude larger then can be done by conventional CASCI techniques. Other features of this method are its inherent multireference nature, compactness, variational results, size-consistency and size-extensivity. In addition we will review the problems (predominantly organic electronic materials) on which we applied the ab initio DMRG: 1) metal-insulator transition in hydrogen chains [1] 2) all-trans polyacetylene [1] 3) acenes [2] 4) polydiacetylenes [3]. References [1] Hachmann, Cardoen, Chan, JCP 125 (2006), 144101. [2] Hachmann, Dorando, Avil'es, Chan, JCP 127 (2007), 134309. [3] unpublished.

  14. Exploring complex chemical reactions by ab-initio simulation

    NASA Astrophysics Data System (ADS)

    Parrinello, Michele

    1998-03-01

    Recent progress in the ab-initio molecular dynamics method and the power of parallel computing, allow the detailed study of complex chemical reaction of great industrial relevance. We illustrate this unprecedented capability by investigating the second generation Ziegler-Natta catalytic process. In this inhomogeneous catalyst, a polymerization reaction is induced by TiCl4 molecules deposited on an MgCl2 solid support. A density functional based ab-initio molecular dynamics calculation conducted with a minimum of initial assumption allows to understand the nature of the catalytic center and to determine the reaction path with the associated free energy barrier. Furthermore our calculation can explain in a nontrivial way the stereo-selectivity of the process.

  15. Ab initio Monte Carlo investigation of small lithium clusters.

    SciTech Connect

    Srinivas, S.

    1999-06-16

    Structural and thermal properties of small lithium clusters are studied using ab initio-based Monte Carlo simulations. The ab initio scheme uses a Hartree-Fock/density functional treatment of the electronic structure combined with a jump-walking Monte Carlo sampling of nuclear configurations. Structural forms of Li{sub 8} and Li{sub 9}{sup +} clusters are obtained and their thermal properties analyzed in terms of probability distributions of the cluster potential energy, average potential energy and configurational heat capacity all considered as a function of the cluster temperature. Details of the gradual evolution with temperature of the structural forms sampled are examined. Temperatures characterizing the onset of structural changes and isomer coexistence are identified for both clusters.

  16. Towards AB Initio Calculation of the Circular Dichroism of Peptides

    NASA Astrophysics Data System (ADS)

    Molteni, E.; Onida, G.; Tiana, G.

    2012-08-01

    In this work we plan to use ab initio spectroscopy calculations to compute circular dichroism (CD) spectra of peptides. CD provides information on protein secondary structure content; peptides, instead, remain difficult to address, due to their tendency to adopt multiple conformations in equilibrium. Therefore peptides are an interesting test-case for ab initio calculation of CD spectra. As a first application, we focus on the (83-92) fragment of HIV-1 protease, which is known to be involved in the folding and dimerization of this protein. As a preliminary step, we performed classical molecular dynamics (MD) simulations, in order to obtain a set of representative conformers of the peptide. Then, on some of the obtained conformations, we calculated absorption spectra at the independent particle, RPA and TDLDA levels, showing the presence of charge transfer excitations, and their influence on spectral features.

  17. Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes

    SciTech Connect

    Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott

    2012-02-13

    Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-{angstrom} C{alpha} root mean square deviation [RMSD]) the high-resolution (1.8-{angstrom}) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur.

  18. GAUSSIAN 76: An ab initio Molecular Orbital Program

    DOE R&D Accomplishments Database

    Binkley, J. S.; Whiteside, R.; Hariharan, P. C.; Seeger, R.; Hehre, W. J.; Lathan, W. A.; Newton, M. D.; Ditchfield, R.; Pople, J. A.

    1978-01-01

    Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type Gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans.

  19. The study of molecular spectroscopy by ab initio methods

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

    1991-01-01

    This review illustrates the potential of theory for solving spectroscopic problems. The accuracy of approximate techniques for including electron correlation have been calibrated by comparison with full configuration-interaction calculations. Examples of the application of ab initio calculations to vibrational, rotational, and electronic spectroscopy are given. It is shown that the state-averaged, complete active space self-consistent field, multireference configuration-interaction procedure provides a good approach for treating several electronic states accurately in a common molecular orbital basis.

  20. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

    SciTech Connect

    Makhov, Dmitry V.; Shalashilin, Dmitrii V.; Glover, William J.; Martinez, Todd J.

    2014-08-07

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  1. Ab Initio Study of Defect Properties in YPO4

    SciTech Connect

    Gao, Fei; Xiao, Haiyan Y.; Zhou, Yungang; Devanathan, Ramaswami; Hu, Shenyang Y.; Li, Yulan; Sun, Xin; Khaleel, Mohammad A.

    2012-03-01

    Ab initio methods based on density functional theory have been used to calculate the formation energies of intrinsic defects, including vacancies, interstitials, antisites and Frenkel pairs in YPO4 under the O-rich and Y2O3-rich, and the O-rich and Y-rich conditions. The larger size of the yttrium atom may give rise to higher formation energy of the phosphorus antisite defect. In general, the formation energies of anion interstitials are much smaller than those of cation interstitials for both conditions considered. It is of greatly interest to find that the relative stabilities among the same types of interstitials are independent of the reference states. The most stable configuration for oxygen interstitials is an O-O split interstitial near the Ta site, while the most stable configuration for cation interstitials is a tetrahedral interstitial near the Ta site. The cation split interstitials are unfavorable in YPO4, with much higher formation energies. Furthermore, the properties of Frenkel pairs are compared with those calculated using empirical potentials. The results reveal that both ab initio and empirical potential calculations show a similar trend in the formation energies of Frenkel pairs, but the formation energies obtained by empirical potentials are much larger than those calculated by ab initio method.

  2. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

    NASA Astrophysics Data System (ADS)

    Makhov, Dmitry V.; Glover, William J.; Martinez, Todd J.; Shalashilin, Dmitrii V.

    2014-08-01

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  3. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.

    PubMed

    Makhov, Dmitry V; Glover, William J; Martinez, Todd J; Shalashilin, Dmitrii V

    2014-08-01

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions. PMID:25106573

  4. A Complete and Accurate Ab Initio Repeat Finding Algorithm.

    PubMed

    Lian, Shuaibin; Chen, Xinwu; Wang, Peng; Zhang, Xiaoli; Dai, Xianhua

    2016-03-01

    It has become clear that repetitive sequences have played multiple roles in eukaryotic genome evolution including increasing genetic diversity through mutation, changes in gene expression and facilitating generation of novel genes. However, identification of repetitive elements can be difficult in the ab initio manner. Currently, some classical ab initio tools of finding repeats have already presented and compared. The completeness and accuracy of detecting repeats of them are little pool. To this end, we proposed a new ab initio repeat finding tool, named HashRepeatFinder, which is based on hash index and word counting. Furthermore, we assessed the performances of HashRepeatFinder with other two famous tools, such as RepeatScout and Repeatfinder, in human genome data hg19. The results indicated the following three conclusions: (1) The completeness of HashRepeatFinder is the best one among these three compared tools in almost all chromosomes, especially in chr9 (8 times of RepeatScout, 10 times of Repeatfinder); (2) in terms of detecting large repeats, HashRepeatFinder also performed best in all chromosomes, especially in chr3 (24 times of RepeatScout and 250 times of Repeatfinder) and chr19 (12 times of RepeatScout and 60 times of Repeatfinder); (3) in terms of accuracy, HashRepeatFinder can merge the abundant repeats with high accuracy. PMID:26272474

  5. Towards an ab initio description of correlated materials

    NASA Astrophysics Data System (ADS)

    Yee, Chuck-Hou

    Strongly-correlated materials are a rich playground for physical phenomena, exhibiting complex phase diagrams with many competing orders. Ab initio insights into materials combined with physical ideas provide the ability to identify the organizing principles driving the correlated electronic behavior and pursue first-principles design of new compounds. Realistic modeling of correlated materials is an active area of research, especially with the recent merger of density functional theory (DFT) with dynamical mean-field theory (DMFT). This thesis is structured in two parts. The first describes the methods and algorithmic developments which drive advances in DFT+DMFT. In Ch. 2 and 3, we provide an overview of the two foundational theories, DMFT and DFT. In the second half of Ch. 3, we describe some of the principles guiding the combination of the two theories to form DFT+DMFT. In Ch. 4, we describe the algorithm lying at the heart of modern DFT+DMFT implementations, the hybridization expansion formulation of continuous-time quantum monte carlo (CTQMC) for the general Anderson impurity problem, as well as a fast rejection algorithm for speeding-up the local trace evaluation. The final chapter in the methods section describes an algorithm for direct sampling of the partition function, and thus the free energy and entropy, of simple Anderson impurity models within CTQMC. The second part of the thesis is a collection of applications of our ab initio approach to key correlated materials. We first apply our method to plutonium binary alloys (Ch. 6), which when supplemented with slave-boson mean-field theory, allows us to understand the observed photoemission spectra. Ch. 7 describes the computation of spectra and optical conductivity for rare-earth nickelates grown as epitaxial thin films. In the final two chapters, we turn our attention to the high-temperature superconductors. In the first, we show that the charge-transfer energy is a key chemical variable which controls

  6. Ab initio-informed maximum entropy modeling of rovibrational relaxation and state-specific dissociation with application to the O2 + O system

    NASA Astrophysics Data System (ADS)

    Kulakhmetov, Marat; Gallis, Michael; Alexeenko, Alina

    2016-05-01

    Quasi-classical trajectory (QCT) calculations are used to study state-specific ro-vibrational energy exchange and dissociation in the O2 + O system. Atom-diatom collisions with energy between 0.1 and 20 eV are calculated with a double many body expansion potential energy surface by Varandas and Pais [Mol. Phys. 65, 843 (1988)]. Inelastic collisions favor mono-quantum vibrational transitions at translational energies above 1.3 eV although multi-quantum transitions are also important. Post-collision vibrational favoring decreases first exponentially and then linearly as Δv increases. Vibrationally elastic collisions (Δv = 0) favor small ΔJ transitions while vibrationally inelastic collisions have equilibrium post-collision rotational distributions. Dissociation exhibits both vibrational and rotational favoring. New vibrational-translational (VT), vibrational-rotational-translational (VRT) energy exchange, and dissociation models are developed based on QCT observations and maximum entropy considerations. Full set of parameters for state-to-state modeling of oxygen is presented. The VT energy exchange model describes 22 000 state-to-state vibrational cross sections using 11 parameters and reproduces vibrational relaxation rates within 30% in the 2500-20 000 K temperature range. The VRT model captures 80 × 106 state-to-state ro-vibrational cross sections using 19 parameters and reproduces vibrational relaxation rates within 60% in the 5000-15 000 K temperature range. The developed dissociation model reproduces state-specific and equilibrium dissociation rates within 25% using just 48 parameters. The maximum entropy framework makes it feasible to upscale ab initio simulation to full nonequilibrium flow calculations.

  7. Ab initio-informed maximum entropy modeling of rovibrational relaxation and state-specific dissociation with application to the O2 + O system.

    PubMed

    Kulakhmetov, Marat; Gallis, Michael; Alexeenko, Alina

    2016-05-01

    Quasi-classical trajectory (QCT) calculations are used to study state-specific ro-vibrational energy exchange and dissociation in the O2 + O system. Atom-diatom collisions with energy between 0.1 and 20 eV are calculated with a double many body expansion potential energy surface by Varandas and Pais [Mol. Phys. 65, 843 (1988)]. Inelastic collisions favor mono-quantum vibrational transitions at translational energies above 1.3 eV although multi-quantum transitions are also important. Post-collision vibrational favoring decreases first exponentially and then linearly as Δv increases. Vibrationally elastic collisions (Δv = 0) favor small ΔJ transitions while vibrationally inelastic collisions have equilibrium post-collision rotational distributions. Dissociation exhibits both vibrational and rotational favoring. New vibrational-translational (VT), vibrational-rotational-translational (VRT) energy exchange, and dissociation models are developed based on QCT observations and maximum entropy considerations. Full set of parameters for state-to-state modeling of oxygen is presented. The VT energy exchange model describes 22 000 state-to-state vibrational cross sections using 11 parameters and reproduces vibrational relaxation rates within 30% in the 2500-20 000 K temperature range. The VRT model captures 80 × 10(6) state-to-state ro-vibrational cross sections using 19 parameters and reproduces vibrational relaxation rates within 60% in the 5000-15 000 K temperature range. The developed dissociation model reproduces state-specific and equilibrium dissociation rates within 25% using just 48 parameters. The maximum entropy framework makes it feasible to upscale ab initio simulation to full nonequilibrium flow calculations. PMID:27155635

  8. Ab initio description of the exotic unbound 7He nucleus

    DOE PAGESBeta

    Baroni, Simone; Navratil, Petr; Quaglioni, Sofia

    2013-01-11

    In this study, the neutron-rich unbound 7He nucleus has been the subject of many experimental investigations. While the ground-state 3/2– resonance is well established, there is a controversy concerning the excited 1/2– resonance reported in some experiments as low lying and narrow (ER~1 MeV, Γ≤1 MeV) while in others as very broad and located at a higher energy. This issue cannot be addressed by ab initio theoretical calculations based on traditional bound-state methods. We introduce a new unified approach to nuclear bound and continuum states based on the coupling of the no-core shell model, a bound-state technique, with the no-coremore » shell model combined with the resonating-group method, a nuclear scattering technique. Our calculations describe the ground-state resonance in agreement with experiment and, at the same time, predict a broad 1/2– resonance above 2 MeV.« less

  9. Ab Initio Simulation of the Photoelectron Spectrum for Methoxy Radical

    NASA Astrophysics Data System (ADS)

    Cheng, Lan; Weichman, Marissa L.; Kim, Jongjin B.; Ichino, Takatoshi; Neumark, Daniel; Stanton, John F.

    2015-06-01

    A theoretical simulation of the photoelectron spectrum for the ground state of methoxy radical is reported based on the quasidiabatic model Hamiltonian originally proposed by Köppel, Domcke, and Cederbaum. The parameters in the model Hamiltonian have been obtained from ab initio coupled-cluster calculations. The linear and quadratic force constants have been calculated using equation-of-motion coupled-cluster ionization potential method with the singles, doubles, and triples (EOMIP-CCSDT) truncation scheme together with atomic natural orbital basis sets of triple-zeta quality (ANO1). The cubic and quartic force constants have been obtained from EOMIP-CCSD calculations with ANO basis sets of double-zeta quality (ANO0), and the spin-orbit coupling constant has been computed at the EOMIP-CCSD/pCVTZ level. The nuclear Schroedinger equation has been solved using the Lanzcos algorithm to obtain vibronic energy levels as well as the corresponding intensities. The simulated spectrum compares favorably with the recent high-resolution slow electron velocity-map imaging experiment for vibronic levels up to 2000 cm-1.

  10. Ab initio description of p-shell hypernuclei.

    PubMed

    Wirth, Roland; Gazda, Daniel; Navrátil, Petr; Calci, Angelo; Langhammer, Joachim; Roth, Robert

    2014-11-01

    We present the first ab initio calculations for p-shell single-Λ hypernuclei. For the solution of the many-baryon problem, we develop two variants of the no-core shell model with explicit Λ and Σ(+),Σ(0),Σ(-) hyperons including Λ-Σ conversion, optionally supplemented by a similarity renormalization group transformation to accelerate model-space convergence. In addition to state-of-the-art chiral two- and three-nucleon interactions, we use leading-order chiral hyperon-nucleon interactions and a recent meson-exchange hyperon-nucleon interaction. We validate the approach for s-shell hypernuclei and apply it to p-shell hypernuclei, in particular to (Λ)(7)Li, (Λ)(9)Be, and (Λ)(13)C. We show that the chiral hyperon-nucleon interactions provide ground-state and excitation energies that generally agree with experiment within the cutoff dependence. At the same time we demonstrate that hypernuclear spectroscopy provides tight constraints on the hyperon-nucleon interactions. PMID:25415901

  11. Ab initio Raman spectroscopy of water under extreme conditions

    NASA Astrophysics Data System (ADS)

    Rozsa, Viktor; Pan, Ding; Wan, Quan; Galli, Giulia

    Water exhibits one of the most complex phase diagrams of any binary compound. Despite extensive studies, the melting lines of high-pressure ice phases remain very controversial, with reports differing by hundreds of Kelvin. The boundary between ice VII and liquid phase is particularly disputed, with recent work exploring plasticity and amorphization mediating the transition. Raman measurements are often used to fingerprint melting, yet their interpretation is difficult without atomistic modeling. Here, we report a study of high P/T water where we computed Raman spectra using a method combining ab initio molecular dynamics and density functional perturbation theory, as implemented in the Qbox code. Spectra were computed for the liquid at 10 and 20 GPa, both at 1000 K, and for solid ice VII (20 GPa, 500 K). Decomposing the spectra into inter and intra molecular contributions provided insight into the dynamics of the hydrogen-bonded network at extreme conditions. The relevance of our simulation results for models of water in Earth, Uranus, and Neptune will be discussed, and an interpretation of existing experiments at high pressure will be presented.

  12. Cosmic-Ray Modulation: an Ab Initio Approach

    NASA Astrophysics Data System (ADS)

    Engelbrecht, N. E.; Burger, R. A.

    2014-10-01

    A better understanding of cosmic-ray modulation in the heliosphere can only be gained through a proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays. We present an ab initio model for cosmic-ray modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for periods of minimum solar activity, utilizing boundary values chosen so that model results are in fair to good agreement with spacecraft observations of turbulence quantities, not only in the solar ecliptic plane but also along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modelled slab and 2D turbulence energy spectra. The latter spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers commencing at the 2D outerscale. There currently exist no models or observations for this quantity, and it is the only free parameter in this study. The modelled turbulence spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on cosmic-ray drifts are modelled in a self-consistent way, employing a recently developed model for drift along the wavy current sheet. The resulting diffusion coefficients and drift expressions are applied to the study of galactic cosmic-ray protons and antiprotons using a three-dimensional, steady-state cosmic-ray modulation code, and sample solutions in fair agreement with multiple spacecraft observations are presented.

  13. Ab initio investigation of grain boundary cohesion in Al alloys

    NASA Astrophysics Data System (ADS)

    Zhang, Shengjun; Kontsevoi, Oleg Y.; Freeman, A. J.; Olson, G. B.

    2010-03-01

    Strength and hardness of aluminum alloys can be substantially increased by alloying with Mg, Zn, Cu, Si, and other elements. The main drawback of Al alloys is their susceptibility to stress corrosion cracking, which is caused by alloying impurities segregated at grain boundaries. We investigated the embrittling and cohesion-enhancing effects of impurities on a σ5(012)[100] grain boundary in Al by means of the full-potential linearized augmented plane-wave (FLAPW) method within the framework of the Rice-Wang thermodynamic model and within the ab initio tensile test approach. We calculated segregation energies, analyzed local atomic configurations, electronic structures and spatial charge density distributions around segregated impurities, and identified the roles of atomic size and the bonding behavior of the impurity with the surrounding Al atoms. The results show that He, H and Na are strong embrittlers, Zn is a weak embrittler, while Sc, B, Cu and Mg are cohesion enhancers. We further evaluated the effect of co-alloying with two or more elements on grain boundary strength. This work provides a fundamental basis for the design of high strength Al alloys.

  14. Microsolvation of methyl hydrogen peroxide: Ab initio quantum chemical approach

    NASA Astrophysics Data System (ADS)

    Kulkarni, Anant D.; Rai, Dhurba; Bartolotti, Libero J.; Pathak, Rajeev K.

    2009-08-01

    Methyl hydrogen peroxide (MHP), one of the simplest organic hydroperoxides, is a strong oxidant, with enhanced activity in aqueous ambience. The present study investigates, at the molecular level, the role of hydrogen bonding that is conducive to cluster formation of MHP with water molecules from its peroxide end, with the methyl group remaining hydrophobic for up to five water molecules. Ab initio quantum chemical computations on MHP⋯(H2O)n, [n =1-5] are performed at second order Møller-Plesset (MP2) perturbation theory employing the basis sets 6-31G(d,p) and 6-311++G(2d,2p) to study the cluster formation of MHP with water molecules from its peroxide end and hydrophobic hydration due to the methyl group. Successive addition of water molecules alters the hydrogen bonding pattern, which leads to changes in overall cluster geometry and in turn to IR vibrational frequency shifts. Molecular co-operativity in these clusters is gauged directly through a detailed many-body interaction energy analysis. Molecular electrostatic potential maps are shown to have a bearing on predicting further growth of these clusters, which is duly corroborated through sample calculations for MHP⋯(H2O)8. Further, a continuum solvation model calculation for energetically stable clusters suggests that this study should serve as a precursor for pathways to aqueous solvation of MHP.

  15. Engineering Room-temperature Superconductors Via ab-initio Calculations

    NASA Astrophysics Data System (ADS)

    Gulian, Mamikon; Melkonyan, Gurgen; Gulian, Armen

    The BCS, or bosonic model of superconductivity, as Little and Ginzburg have first argued, can bring in superconductivity at room temperatures in the case of high-enough frequency of bosonic mode. It was further elucidated by Kirzhnitset al., that the condition for existence of high-temperature superconductivity is closely related to negative values of the real part of the dielectric function at finite values of the reciprocal lattice vectors. In view of these findings, the task is to calculate the dielectric function for real materials. Then the poles of this function will indicate the existence of bosonic excitations which can serve as a "glue" for Cooper pairing, and if the frequency is high enough, and the dielectric matrix is simultaneously negative, this material is a good candidate for very high-Tc superconductivity. Thus, our approach is to elaborate a methodology of ab-initio calculation of the dielectric function of various materials, and then point out appropriate candidates. We used the powerful codes (TDDF with the DP package in conjunction with ABINIT) for computing dielectric responses at finite values of the wave vectors in the reciprocal lattice space. Though our report is concerned with the particular problem of superconductivity, the application range of the data processing methodology is much wider. The ability to compute the dielectric function of existing and still non-existing (though being predicted!) materials will have many more repercussions not only in fundamental sciences but also in technology and industry.

  16. Ab Initio Investigation of NH_3-O_2 Exciplex

    NASA Astrophysics Data System (ADS)

    Haupert, L. M.; Simpson, G.; Slipchenko, L. V.

    2010-06-01

    In their recent investigation of fluorescence from poly(amido amine) (PAMAM) dendrimers, Chu and Imae suggested an exciplex composed of tertiary amine and oxygen molecules might be responsible for fluorescence in PAMAM dendrimers. In this work, we present an ab initio investigation of the electronic structure of a possible ammonia-oxygen exciplex model system using equation-of-motion coupled cluster techniques. Geometry optimization of the triplet ground state produced a weakly bound state with an equilibrium separation of ˜ 3.5 Å, and an excited state geometry scan revealed a bound, excited triplet state with an equilibrium separation of 2.02 Å, consistent with results of earlier PM3 work by Juranic et al. The energy gap between the triplet ground state and first triplet excited state of the exciplex at 2.02 Å is 412.8 nm, lending support to the exciplex hypothesis. C.-C. Chu, and T. Imae, Macromol. Rapid. Commun., 30, 89-93 (2009). I. Juranic, H. S. Rzepa, and Y. MinYan, J. Chem. Soc. Perkin Trans., 2 (1990)

  17. Ab initio simulations of peptide-mineral interactions

    NASA Astrophysics Data System (ADS)

    Hug, Susanna; Hunter, Graeme K.; Goldberg, Harvey; Karttunen, Mikko

    We performed Car-Parrinello Molecular Dynamics (CPMD) simulations of two amino acids, aspartic acid (Asp) and phophoserine (pSer), on a calcium oxalate monohydrate (COM) surface as a model of the interactions of phosphoproteins with biominerals. In our earlier work using in vitro experiments and classical Molecular Dynamics (MD) simulations we have demonstrated the importance of phosphorylation of serine on the interactions of osteopontin (OPN) with COM. We used configurations from our previous classical MD simulations as a starting point for the ab initio simulations. In the case of Asp we found that the α-carboxyl and amine groups form temporary close contacts with the surface. For the dipeptide Asp-pSer the carboxyl groups form permanent close contacts with the surface and the distances of its other functional groups do not vary much. We show how the interaction of carboxyl groups with COM crystal is established and confirm the importance of phosphorylation in mediating the interactions between COM surfaces and OPN.

  18. Ab initio simulations on rutile-based titania nanowires

    NASA Astrophysics Data System (ADS)

    Zhukovskii, Yu F.; Evarestov, R. A.

    2012-08-01

    The rod symmetry groups for monoperiodic (1D) nanostructures have been applied for construction of models for bulk-like TiO2 nanowires (NWs) cut from a rutile-based 3D crystal along the chosen [001] and [110] directions of crystallographic axes. In this study, we have considered nanowires described by both the Ti-atom centered rotation axes as well as the hollow site centered axes passing through the interstitial positions between the Ti and O atoms closest to the axes. The most stable [001]-oriented TiO2 NWs with rhombic cross sections are found to display the energetically preferable {110} facets only while the nanowires with quasi-square sections across the [110] axis are formed by the alternating { 1bar 10 } and {001} facets. For simulations on rutile-based nanowires possessing different diameters for each NW type, we have performed large-scale ab initio Density Functional Theory (DFT) and hybrid DFT-Hartree Fock (DFT-HF) calculations with total geometry optimization within the Generalized Gradient Approximation (GGA) in the form of the Perdew-Becke-Ernzenhof (PBE) exchange-correlation functionals (PBE and PBE0, respectively), using the formalism of linear combination of localized atomic functions (LCAO). We have simulated both structural and electronic properties of TiO2 NWs depending both on orientation and position of symmetry axes as well as on diameter and morphology of nanowires.

  19. 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.

  20. Ab initio study of ice catalyzation of HOCl + HCl reaction

    SciTech Connect

    Zhou, Y.F.; Liu, C.B.

    2000-06-15

    The observations by Farman et al. revealed remarkable depletions in the total atmospheric ozone content in Antarctica. The observed total ozone decreased smoothing during the spring season from about 1975. Satellite observations have proved Antarctic ozone depletions over a very extended region, in general agreement with the local ground-based data of Farman et al. It was suggested that heterogeneous reactions occurring on particles in polar stratospheric clouds (PSCs) play a central role in the depletion of stratospheric ozone. Experiments proved that the reaction of HOCl + HCl was very slow in the gas phase, but on ice surface it was rapid. In this work the ice catalysis of HOCl + HCl reaction was investigated by using ab initio molecular orbital theory. The authors applied the Hartree-Fock self-consistent field and the second-order Moeller-Plesset perturbation theory with the basis sets of 6-31G* to the model system. The complexes and transition state were obtained along the reaction with and without the presence of ice surface. By comparing the results, a possible catalyzation mechanism of ice on the reaction is proposed.

  1. Ab initio study of the influence of structural parameters on the potential energy surfaces of spin-crossover Fe(II) model compounds

    NASA Astrophysics Data System (ADS)

    Boilleau, Corentin; Suaud, Nicolas; Guihéry, Nathalie

    2012-12-01

    In spin-crossover (SCO) compounds exhibiting a light induced excited spin state trapping (LIESST) effect, the thermodynamic T1/2 and kinetic T(LIESST) temperature values depend on the features of the potential energy surfaces (PES) of the two lowest singlet and quintet states but also on vibrational contributions, collective effects, such as electrostatics, for instance, spin-orbit couplings to a lesser extent, etc. In this work, the question of the link between the shape of the PES of SCO compounds exhibiting a LIESST effect and their first coordination sphere structure is addressed from wave function theory based ab initio calculations. Fe(II) complexes based on model ligands suited to reproduce the main characteristics of the PES of such compounds are distorted to emphasize selectively the role played by the metal-ligand distances and the ligand-metal-ligand angles. The studied angular deformations are those usually observed in many Fe(L)2(NCS)2 complexes. It is shown that the larger the deformation between the low spin and high spin equilibrium geometries, the higher the energy barrier from the high spin state and the weaker the energy difference between the bottom of the wells. These results corroborate observations made by experimentalists on a large number of complexes. While the PES features only constitutes one of the contributions to these temperatures, it is worth noticing that, relating T1/2 to the energy difference between the bottoms of the singlet and quintet wells and the T(LIESST) to the energy barrier from the quintet bottom well, the same slope of the empirical law T(LIESST) = -0.3T1/2+T0 is observed.

  2. Ab initio cluster study of crystalline NaF

    SciTech Connect

    Temple, D.K.

    1992-01-01

    A highly-accurate ab initio cluster model of crystalline NaF has been constructed to explore the limits of cluster methods in the treatment of ionic solids. The focus of this model was the characterization of the lattice environment and its influence on the easily-polarizable fluorine anion. The model consisted of a central all-electron fluorine anion coordinated by pseudopotentials, to represent the nearest-neighbor sodium cations, and a finite array of point charges chosen to generate the correct crystal field from the surrounding infinite ionic lattice. The wavefunction and properties of the anion were calculated using the restricted Hartree-Fock and configuration interaction techniques from quantum chemistry. An extensive analysis of basis set incompleteness errors in the anion wavefunction was performed. Important features were identified in the embedded anion, such as its distortion under the influence of the lattice compressions, its stabilization from the Madelung potential, and its changes in size due to electron correlations. Bulk properties of the rocksalt-structure (B1) NaF crystal were derived from the total mode energies, calculated as a function of the crystal volume. The properties included the zero-pressure lattice constant, cohesive energy, and bulk modulus, and the pressure-volume equation-of-state. A series of test calculations explored the relationships, and their underlying physical mechanisms, between the features of the embedded anion and the bulk properties of the crystal. These features often produced opposing changes in the properties, demonstrating the importance of a thorough and systematic treatment of the embedded anion. The most thorough test calculation gave bulk properties that were within 1% of experiment. Using an embedded anion model for the high-pressure cesium-chloride (B2) phase of NaF, the B1-to-B2 structural transition was correctly predicted at 25 GPa, in excellent agreement with the experimental values of 23 to 27 GPa.

  3. Ab initio yield curve dynamics [rapid communication

    NASA Astrophysics Data System (ADS)

    Hawkins, Raymond J.; Roy Frieden, B.; D'Anna, Joseph L.

    2005-09-01

    We derive an equation of motion for interest-rate yield curves by applying a minimum Fisher information variational approach to the implied probability density. By construction, solutions to the equation of motion recover observed bond prices. More significantly, the form of the resulting equation explains the success of the Nelson Siegel approach to fitting static yield curves and the empirically observed modal structure of yield curves. A practical numerical implementation of this equation of motion is found by using the Karhunen Lòeve expansion and Galerkin's method to formulate a reduced-order model of yield curve dynamics.

  4. Efficient conformational space exploration in ab initio protein folding simulation.

    PubMed

    Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A Z M Dayem; Rahman, M Sohel

    2015-08-01

    Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic-polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency. PMID:26361554

  5. Efficient conformational space exploration in ab initio protein folding simulation

    PubMed Central

    Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A. Z. M. Dayem; Rahman, M. Sohel

    2015-01-01

    Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic–polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency. PMID:26361554

  6. Ab Initio Computation of the Energies of Circular Quantum Dots

    SciTech Connect

    Lohne, M. Pedersen; Hagen, Gaute; Hjorth-Jensen, M.; Kvaal, S.; Pederiva, F.

    2011-01-01

    We perform coupled-cluster and diffusion Monte Carlo calculations of the energies of circular quantum dots up to 20 electrons. The coupled-cluster calculations include triples corrections and a renormalized Coulomb interaction defined for a given number of low-lying oscillator shells. Using such a renormalized Coulomb interaction brings the coupled-cluster calculations with triples correlations in excellent agreement with the diffusion Monte Carlo calculations. This opens up perspectives for doing ab initio calculations for much larger systems of electrons.

  7. The implementation of ab initio quantum chemistry calculations on transporters.

    PubMed

    Cooper, M D; Hillier, I H

    1991-06-01

    The RHF and geometry optimization sections of the ab initio quantum chemistry code, GAMESS, have been optimized for a network of parallel microprocessors, Inmos T800-20 transputers, using both indirect and direct SCF techniques. The results indicate great scope for implementation of such codes on small parallel computer systems, very high efficiencies having been achieved, particularly in the cases of direct SCF and geometry optimization with large basis sets. The work, although performed upon one particular parallel system, the Meiko Computing Surface, is applicable to a wide range of parallel systems with both shared and distributed memory. PMID:1919615

  8. Ab initio electronic properties of dual phosphorus monolayers in silicon

    PubMed Central

    2014-01-01

    In the midst of the epitaxial circuitry revolution in silicon technology, we look ahead to the next paradigm shift: effective use of the third dimension - in particular, its combination with epitaxial technology. We perform ab initio calculations of atomically thin epitaxial bilayers in silicon, investigating the fundamental electronic properties of monolayer pairs. Quantitative band splittings and the electronic density are presented, along with effects of the layers’ relative alignment and comments on disordered systems, and for the first time, the effective electronic widths of such device components are calculated. PMID:25246862

  9. Ab initio vibrational and dielectric properties of Y V O

    NASA Astrophysics Data System (ADS)

    Vali, R.

    2009-10-01

    For the yttrium orthovanadate Y V O with a tetragonal zircon-type structure, the first complete set of Raman-active and IR-active phonon modes has been calculated using ab initio density functional perturbation theory. The calculated IR reflectivity spectra are in good agreement with available experimental data. We report the calculated frequencies of three Raman-active modes that could not be detected experimentally and a new assignment of the experimental Raman data. The contributions of each IR-active phonon modes to static dielectric tensor have been determined.

  10. 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

  11. Ab Initio Calculations Applied to Problems in Metal Ion Chemistry

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Partridge, Harry; Arnold, James O. (Technical Monitor)

    1994-01-01

    Electronic structure calculations can provide accurate spectroscopic data (such as molecular structures) vibrational frequencies, binding energies, etc.) that have been very useful in explaining trends in experimental data and in identifying incorrect experimental measurements. In addition, ab initio calculations. have given considerable insight into the many interactions that make the chemistry of transition metal systems so diverse. In this review we focus on cases where calculations and experiment have been used to solve interesting chemical problems involving metal ions. The examples include cases where theory was used to differentiate between disparate experimental values and cases where theory was used to explain unexpected experimental results.

  12. Ab initio study of hydrogen on beryllium surfaces

    NASA Astrophysics Data System (ADS)

    Bachurin, D. V.; Vladimirov, P. V.

    2015-11-01

    Static ab initio calculations were performed for five principal hexagonal close-packed beryllium surfaces: basal, prismatic (type I and II) and pyramidal (type I and II). The basal plane was found to be the most energetically favorable, while the energies of the prismatic (type I) and pyramidal (type I) planes were slightly higher followed by the type II planes. Beryllium is known to show extreme interlayer distance relaxation near the surface. Up to five outermost atomic layers were involved in surface relaxation. The presence of hydrogen on the beryllium surfaces led to a noticeable reduction of the surface energy.

  13. An improved ab initio structure for fluorine peroxide (FOOF)

    NASA Astrophysics Data System (ADS)

    Mack, Hans-Georg; Oberhammer, Heinz

    1988-03-01

    Ab initio calculations with the 6-31G* and Dunning (9s5p/4s2p) basis sets augmented with p and d functions at various levels of theory (RHF, MP2, MP3, and MP4) were carried out on F 2O 2. The best result was obtained at the MP2 level with the Dunning basis plus one set of d functions on fluorine and two sets of d functions on oxygen. These calculations reproduce the experimental bond lengths to within 0.01 Å and the angles to within the experimental uncertainties.

  14. Ab-initio study of transition metal hydrides

    SciTech Connect

    Sharma, Ramesh; Shukla, Seema Dwivedi, Shalini Sharma, Yamini

    2014-04-24

    We have performed ab initio self consistent calculations based on Full potential linearized augmented plane wave (FP-LAPW) method to investigate the optical and thermal properties of yttrium hydrides. From the band structure and density of states, the optical absorption spectra and specific heats have been calculated. The band structure of Yttrium metal changes dramatically due to hybridization of Y sp orbitals with H s orbitals and there is a net charge transfer from metal to hydrogen site. The electrical resistivity and specific heats of yttrium hydrides are lowered but the thermal conductivity is slightly enhanced due to increase in scattering from hydrogen sites.

  15. On limits of ab initio calculations of pairing gap in nuclei

    SciTech Connect

    Saperstein, E. E.; Baldo, M.; Lombardo, U.; Pankratov, S. S.; Zverev, M. V.

    2011-11-15

    A brief review of recent microscopic calculations of nuclear pairing gap is given. A semi-microscopic model is suggested in which the ab initio effective pairing interaction is supplemented with a small phenomenological addendum. It involves a parameter which is universal for all medium and heavy nuclei. Calculations for several isotopic and isotonic chains of semi-magic nuclei confirm the relevance of the model.

  16. Ab initio molecular dynamics study of liquid sodium and cesium up to critical point

    SciTech Connect

    Yuryev, Anatoly A.; Gelchinski, Boris R.

    2015-08-17

    Ab initio modeling of liquid metals Na and K is carried out using the program SIESTA. We have determined the parameters of the model (the optimal step, the number of particles, the initial state etc) and calculated a wide range of properties: the total energy, pair correlation function, coefficient of self-diffusion, heat capacity, statistics of Voronoi polyhedra, the density of electronic states up to the critical temperature.

  17. Trajectory and Model Studies of Collisions of Highly Excited Methane with Water Using an ab Initio Potential.

    PubMed

    Conte, Riccardo; Houston, Paul L; Bowman, Joel M

    2015-12-17

    Quasi-classical trajectory studies have been performed for the collision of internally excited methane with water using an accurate methane-water potential based on a full-dimensional, permutationally invariant analytical representation of energies calculated at a high level of theory. The results suggest that most energy transfer takes place at impact parameters smaller than about 8 Bohr; collisions at higher impact parameters are mostly elastic. Overall, energy transfer is fairly facile, with values for ⟨ΔEdown⟩ and ⟨ΔEup⟩ approaching almost 2% of the total excitation energy. A classical model previously developed for the collision of internally excited molecules with atoms (Houston, P. L.; Conte, R.; Bowman, J. M. J. Phys. Chem. A 2015, 119, 4695-4710) has been extended to cover collisions of internally excited molecules with other molecules. For high initial rotational levels, the agreement with the trajectory results is quite good (R(2) ≈ 0.9), whereas for low initial rotational levels it is only fair (R(2) ≈ 0.7). Both the model and the trajectories can be characterized by a four-dimensional joint probability distribution, P(J1,f,ΔE1,J2,f,ΔE2), where J1,f and J2,f are the final rotational levels of molecules 1 and 2 and ΔE1 and ΔE2 are the respective changes in internal energy. A strong anticorrelation between ΔE1 and ΔE2 is observed in both the model and trajectory results and can be explained by the model. There is evidence in the trajectory results for a small amount of V ↔ V energy transfer from the water, which has low internal energy, to the methane, which has substantial internal energy. This observation suggests that V ↔ V energy transfer in the other direction also occurs. PMID:26299678

  18. The electronic excited states of a model organic endoperoxide: A comparison of TD-DFT and ab initio methods

    NASA Astrophysics Data System (ADS)

    Corral, Inés; González, Leticia

    2007-10-01

    The vertical excited spectrum of a model endoperoxide (cyclohexadieneendoperoxide) has been calculated using time dependent density functional theory (TD-DFT), resolution of the identity second order approximate coupled-cluster theory (RI-CC2), multiconfigurational complete active space self consistent field (CASSCF) and second order multi-state perturbation theory (MS-CASPT2). All theoretical methods predict the charge transfer πOO∗→πCC∗, and the πOO∗→σOO∗ excitation to be the lowest absorbing excited states. CASSCF optimized geometries for these states provide some hints about the photodissociation mechanisms as well as the emission spectrum of the molecule.

  19. Ab Initio Modeling and Experimental Assessment of Janus Kinase 2 (JAK2) Kinase-Pseudokinase Complex Structure

    PubMed Central

    McClendon, Christopher L.; Huang, Lily Jun-shen; Huang, Niu

    2013-01-01

    The Janus Kinase 2 (JAK2) plays essential roles in transmitting signals from multiple cytokine receptors, and constitutive activation of JAK2 results in hematopoietic disorders and oncogenesis. JAK2 kinase activity is negatively regulated by its pseudokinase domain (JH2), where the gain-of-function mutation V617F that causes myeloproliferative neoplasms resides. In the absence of a crystal structure of full-length JAK2, how JH2 inhibits the kinase domain (JH1), and how V617F hyperactivates JAK2 remain elusive. We modeled the JAK2 JH1–JH2 complex structure using a novel informatics-guided protein-protein docking strategy. A detailed JAK2 JH2-mediated auto-inhibition mechanism is proposed, where JH2 traps the activation loop of JH1 in an inactive conformation and blocks the movement of kinase αC helix through critical hydrophobic contacts and extensive electrostatic interactions. These stabilizing interactions are less favorable in JAK2-V617F. Notably, several predicted binding interfacial residues in JH2 were confirmed to hyperactivate JAK2 kinase activity in site-directed mutagenesis and BaF3/EpoR cell transformation studies. Although there may exist other JH2-mediated mechanisms to control JH1, our JH1–JH2 structural model represents a verifiable working hypothesis for further experimental studies to elucidate the role of JH2 in regulating JAK2 in both normal and pathological settings. PMID:23592968

  20. Serious Gaming for Test & Evaluation of Clean-Slate (Ab Initio) National Airspace System (NAS) Designs

    NASA Technical Reports Server (NTRS)

    Allen, B. Danette; Alexandrov, Natalia

    2016-01-01

    Incremental approaches to air transportation system development inherit current architectural constraints, which, in turn, place hard bounds on system capacity, efficiency of performance, and complexity. To enable airspace operations of the future, a clean-slate (ab initio) airspace design(s) must be considered. This ab initio National Airspace System (NAS) must be capable of accommodating increased traffic density, a broader diversity of aircraft, and on-demand mobility. System and subsystem designs should scale to accommodate the inevitable demand for airspace services that include large numbers of autonomous Unmanned Aerial Vehicles and a paradigm shift in general aviation (e.g., personal air vehicles) in addition to more traditional aerial vehicles such as commercial jetliners and weather balloons. The complex and adaptive nature of ab initio designs for the future NAS requires new approaches to validation, adding a significant physical experimentation component to analytical and simulation tools. In addition to software modeling and simulation, the ability to exercise system solutions in a flight environment will be an essential aspect of validation. The NASA Langley Research Center (LaRC) Autonomy Incubator seeks to develop a flight simulation infrastructure for ab initio modeling and simulation that assumes no specific NAS architecture and models vehicle-to-vehicle behavior to examine interactions and emergent behaviors among hundreds of intelligent aerial agents exhibiting collaborative, cooperative, coordinative, selfish, and malicious behaviors. The air transportation system of the future will be a complex adaptive system (CAS) characterized by complex and sometimes unpredictable (or unpredicted) behaviors that result from temporal and spatial interactions among large numbers of participants. A CAS not only evolves with a changing environment and adapts to it, it is closely coupled to all systems that constitute the environment. Thus, the ecosystem that

  1. Strontium complexation in aqueous solutions and silicate glasses: Insights from high energy-resolution fluorescence detection X-ray spectroscopy and ab-initio modeling

    NASA Astrophysics Data System (ADS)

    Borchert, Manuela; Wilke, Max; Schmidt, Christian; Kvashnina, Kristina; Jahn, Sandro

    2014-10-01

    Although fluid-melt partitioning of trace elements like Sr, Ba, La, and Y is known to be strongly influenced by the fluid and melt chemical composition, their speciation in silicate-saturated fluids is studied insufficiently at high temperatures and pressures. Here, high energy-resolution fluorescence detection-X-ray absorption spectroscopy (HERFD-XAS) has been applied to investigate the local environment of strontium in crystalline model compounds, silicate glasses, and aqueous solutions. Acquisition of Sr K-edge HERFD-XAS spectra of aqueous solutions of SrCl2 and Sr(OH)2, and three aqueous fluids with dissolved silicate components was done in situ at temperatures to 780 °C and pressures to ∼800 MPa using hydrothermal diamond-anvil cells. Experiments were complemented by theoretical spectroscopy calculations using the finite difference method near edge structure (FDMNES) code. This approach was validated for a number of crystalline model compounds. For the silicate glasses and aqueous solutions (SrCl2 and Sr(OH)2), small clusters were examined. Either symmetric or distorted SrO6 clusters were found to describe Sr complexation in peraluminous or peralkaline glasses. However, small ‘static’ clusters seem not to be fully suited to account for the dynamically changing atomic arrangements in aqueous solutions at high temperature. Therefore, ab-initio molecular dynamics simulations were performed and used as input for modeling of X-ray absorption spectra. Analyses of these simulations indicated [SrCl(H2O)6]+ and Sr(OH)2(H2O)4 as the most likely complexes in the chloride and hydroxide solutions, respectively. Analysis of the spectra of the silicate-rich fluids shows that both melt and fluid composition strongly influence Sr complexation. For the silicate-rich fluids, formation of Sr-Cl complexes occurs at low (Na + K)/Cl and (Si + Al)/(Na + K) ratios in the fluid, whereas Sr hydroxide and possibly silicate complexes (similar to those in the silicate glass) are

  2. Chiroptical properties of unsubstituted carbohydrates: Ab initio and semiempirical studies

    NASA Astrophysics Data System (ADS)

    Parra C., Alejandro

    Ab initio calculations support assignment of the vacuum ultraviolet circular dichroism (CD) of simple saccharides to 11A 1 --> 21B1 and 11A 1 --> 11A2 transitions centered on the oxygen atoms of the acetal group treated as two weakly coupled ether chromophores. The calculations are consistent with assignments previously made on the basis of a deconvolution of CD spectra. Estimates of the oxygen centered contributions to magnetic transition dipole moments were made. Semiempirical calculations were performed to model the NaD molar optical rotation of 1,6- and 3,6- anhydrosugars. For 1,6-anhydrosugars, current parameters produce reasonable agreement with experimental values. For 3,6-anhydrosugars, modifications to the ether parameters had to be introduced. The most relevant included a reorientation of the bond-centered s-->s* transition dipole charges in the ether chromophore to a C2v orientation, and a shift from prolate polarizability ellipsoids to general ellipsoids. These changes result in good agreement with experimental Na D molar rotations for 3,6-anhydrosugars. A low energy CD band arises in 3,6- and 1,6-anhydrosugars when agreement with the experimental NaD molar rotations is achieved. It is proposed that this band is a real feature in the spectrum. The origin of the band is primarily the interaction between b1 symmetry- oriented transition dipoles in the COC groups with other transition dipoles in the molecule. Comparison with experimental spectra leads to an assignment of this band to 11A1 --> 21B1 transitions centered on the COC groups.

  3. Ab initio study of hot electrons in GaAs.

    PubMed

    Bernardi, Marco; Vigil-Fowler, Derek; Ong, Chin Shen; Neaton, Jeffrey B; Louie, Steven G

    2015-04-28

    Hot carrier dynamics critically impacts the performance of electronic, optoelectronic, photovoltaic, and plasmonic devices. Hot carriers lose energy over nanometer lengths and picosecond timescales and thus are challenging to study experimentally, whereas calculations of hot carrier dynamics are cumbersome and dominated by empirical approaches. In this work, we present ab initio calculations of hot electrons in gallium arsenide (GaAs) using density functional theory and many-body perturbation theory. Our computed electron-phonon relaxation times at the onset of the Γ, L, and X valleys are in excellent agreement with ultrafast optical experiments and show that the ultrafast (tens of femtoseconds) hot electron decay times observed experimentally arise from electron-phonon scattering. This result is an important advance to resolve a controversy on hot electron cooling in GaAs. We further find that, contrary to common notions, all optical and acoustic modes contribute substantially to electron-phonon scattering, with a dominant contribution from transverse acoustic modes. This work provides definitive microscopic insight into hot electrons in GaAs and enables accurate ab initio computation of hot carriers in advanced materials. PMID:25870287

  4. Unified ab initio approaches to nuclear structure and reactions

    NASA Astrophysics Data System (ADS)

    Navrátil, Petr; Quaglioni, Sofia; Hupin, Guillaume; Romero-Redondo, Carolina; Calci, Angelo

    2016-05-01

    The description of nuclei starting from the constituent nucleons and the realistic interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of the nuclear forces, with two-, three- and possibly higher many-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD-employing Hamiltonians constructed within chiral effective field theory. After a brief overview of the field, we focus on ab initio many-body approaches—built upon the no-core shell model—that are capable of simultaneously describing both bound and scattering nuclear states, and present results for resonances in light nuclei, reactions important for astrophysics and fusion research. In particular, we review recent calculations of resonances in the 6He halo nucleus, of five- and six-nucleon scattering, and an investigation of the role of chiral three-nucleon interactions in the structure of 9Be. Further, we discuss applications to the 7Be {({{p}},γ )}8{{B}} radiative capture. Finally, we highlight our efforts to describe transfer reactions including the 3H{({{d}},{{n}})}4He fusion.

  5. Ab initio calculation of valley splitting in monolayer δ-doped phosphorus in silicon.

    PubMed

    Drumm, Daniel W; Budi, Akin; Per, Manolo C; Russo, Salvy P; L Hollenberg, Lloyd C

    2013-01-01

    : The differences in energy between electronic bands due to valley splitting are of paramount importance in interpreting transport spectroscopy experiments on state-of-the-art quantum devices defined by scanning tunnelling microscope lithography. Using vasp, we develop a plane-wave density functional theory description of systems which is size limited due to computational tractability. Nonetheless, we provide valuable data for the benchmarking of empirical modelling techniques more capable of extending this discussion to confined disordered systems or actual devices. We then develop a less resource-intensive alternative via localised basis functions in siesta, retaining the physics of the plane-wave description, and extend this model beyond the capability of plane-wave methods to determine the ab initio valley splitting of well-isolated δ-layers. In obtaining an agreement between plane-wave and localised methods, we show that valley splitting has been overestimated in previous ab initio calculations by more than 50%. PMID:23445785

  6. Ab initio calculation of valley splitting in monolayer δ-doped phosphorus in silicon

    PubMed Central

    2013-01-01

    The differences in energy between electronic bands due to valley splitting are of paramount importance in interpreting transport spectroscopy experiments on state-of-the-art quantum devices defined by scanning tunnelling microscope lithography. Using vasp, we develop a plane-wave density functional theory description of systems which is size limited due to computational tractability. Nonetheless, we provide valuable data for the benchmarking of empirical modelling techniques more capable of extending this discussion to confined disordered systems or actual devices. We then develop a less resource-intensive alternative via localised basis functions in siesta, retaining the physics of the plane-wave description, and extend this model beyond the capability of plane-wave methods to determine the ab initio valley splitting of well-isolated δ-layers. In obtaining an agreement between plane-wave and localised methods, we show that valley splitting has been overestimated in previous ab initio calculations by more than 50%. PMID:23445785

  7. Characterization of the Aqueous Uranyl-Silicate Complex Using X-Ray Absorption Spectroscopy and Ab Initio Modeling

    NASA Astrophysics Data System (ADS)

    Vu, M.; Massey, M.; Huang, P.

    2015-12-01

    The speciation of aqueous uranium ions is an important factor in predicting its mobility and fate in the environment. Two major controls on speciation are pH and the presence of complexing ligands. For the case of aqueous uranyl, UO22+(aq), some common complexes include uranyl-hydroxy, uranyl-carbonato, and uranyl-calcium-carbonato complexes, all of which differ in chemical reactivity and mobility. Uranyl-silicate complexes are also known but remain poorly characterized. In this work, we studied uranyl speciation in a series of aqueous solutions of 0.1 mM uranyl and 2 mM silicate with pH ranging from 4 to 7. Extended X-Ray Absorption Fine Structure (EXAFS) spectra of these samples were recorded at the Stanford Synchrotron Radiation Lightsource (SLAC National Accelerator Laboratory). Of particular note are the uranyl and silicate concentrations employed in our experiments, which are lower than conditions in previously reported EXAFS studies and approach conditions in natural groundwater systems. Preliminary analyses of EXAFS data indicate that uranyl speciation changes across the pH range, consistent with published thermodynamic data that suggest uranyl-silicate complexes may be important for pH ~ 5 and below, while uranyl-carbonato complexes become dominant at circumneutral pH. To guide the interpretation of the EXAFS data, molecular-scale simulations were carried out using density functional theory. We considered two classes of models: (i) hydrated clusters, and (ii) ab initio molecular dynamics simulations of 3D-periodic models involving uranyl and silicate in water. These calculations reveal that at pH ~ 5, the uranyl speciation is the [UO2(H2O)4H3SiO4]+ complex formed by the substitution of an equatorial uranyl water with a monodentate silicate ligand. The evidence from experiments and simulations provide a consistent picture for the uranyl-silicate complex, which may be important in the transport of uranyl in acidic, silicate-rich waters.

  8. Dzyaloshinskii-Moriya interaction and chiral magnetism in 3d-5d zigzag chains: Tight-binding model and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Kashid, Vikas; Schena, Timo; Zimmermann, Bernd; Mokrousov, Yuriy; Blügel, Stefan; Shah, Vaishali; Salunke, H. G.

    2014-08-01

    We investigate the chiral magnetic order in freestanding planar 3d-5d biatomic metallic chains (3d: Fe, Co; 5d: Ir, Pt, Au) using first-principles calculations based on density functional theory. We find that the antisymmetric exchange interaction, commonly known as the Dzyaloshinskii-Moriya interaction (DMI), contributes significantly to the energetics of the magnetic structure. For the Fe-Pt and Co-Pt chains, the DMI can compete with the isotropic Heisenberg-type exchange interaction and the magnetocrystalline anisotropy energy, and for both cases a homogeneous left-rotating cycloidal chiral spin-spiral with a wavelength of 51 Å and 36 Å, respectively, was found. The sign of the DMI, which determines the handedness of the magnetic structure, changes in the sequence of the 5d atoms Ir(+), Pt(-), Au(+). We use the full-potential linearized augmented plane wave method and perform self-consistent calculations of homogeneous spin spirals, calculating the DMI by treating the effect of spin-orbit interaction in the basis of the spin-spiral states in first-order perturbation theory. To gain insight into the DMI results of our ab initio calculations, we develop a minimal tight-binding model of three atoms and four orbitals that contains all essential features: the spin canting between the magnetic 3d atoms, the spin-orbit interaction at the 5d atoms, and the structure inversion asymmetry facilitated by the triangular geometry. We find that spin canting can lead to spin-orbit active eigenstates that split in energy due to the spin-orbit interaction at the 5d atom. We show that the sign and strength of the hybridization, the bonding or antibonding character between d orbitals of the magnetic and nonmagnetic sites, the bandwidth, and the energy difference between occupied and unoccupied states of different spin projection determine the sign and strength of the DMI. The key features observed in the trimer model are also found in the first-principles results.

  9. Optical and other material properties of SiO2 from ab initio studies

    NASA Astrophysics Data System (ADS)

    Warmbier, Robert; Mohammed, Faris; Quandt, Alexander

    2014-07-01

    The optical properties of photonic devices largely depend on the dielectric properties of the underlying materials. We apply modern ab initio methods to study crystalline SiO2 phases, which serve as toy models for amorphous glass. We discuss the dielectric response from the infrared to the VIS/UV, which is crucial for glass based photonic applications. Low density silica, like cristobalite, may provide a good basis for high transmission optical devices.

  10. Ab initio study of the ν(CO 2) mode in EDA complexes

    NASA Astrophysics Data System (ADS)

    Jamróz, M. H.; Dobrowolski, J. Cz.; Bajdor, K.; Borowiak, M. A.

    1995-04-01

    Stabilization energy, geometry and ν2 mode of CO 2 molecule in EDA complexes with organic electron donors are ab initio modeled using SPARTAN program. We prove that the splitting of ν2 mode, observed previously in IR spectra, is an effect of removing the double degeneracy of this mode in the complex resulted from the deformation of CO 2 moiety. The dependence of the deformation on complex stabilization energy is discussed.

  11. Ab Initio Studies of Shock-Induced Chemical Reactions of Inter-Metallics

    NASA Astrophysics Data System (ADS)

    Zaharieva, Roussislava; Hanagud, Sathya

    2009-06-01

    Shock-induced and shock assisted chemical reactions of intermetallic mixtures are studied by many researchers, using both experimental and theoretical techniques. The theoretical studies are primarily at continuum scales. The model frameworks include mixture theories and meso-scale models of grains of porous mixtures. The reaction models vary from equilibrium thermodynamic model to several non-equilibrium thermodynamic models. The shock-effects are primarily studied using appropriate conservation equations and numerical techniques to integrate the equations. All these models require material constants from experiments and estimates of transition states. Thus, the objective of this paper is to present studies based on ab initio techniques. The ab inito studies, to date, use ab inito molecular dynamics. This paper presents a study that uses shock pressures, and associated temperatures as starting variables. Then intermetallic mixtures are modeled as slabs. The required shock stresses are created by straining the lattice. Then, ab initio binding energy calculations are used to examine the stability of the reactions. Binding energies are obtained for different strain components super imposed on uniform compression and finite temperatures. Then, vibrational frequencies and nudge elastic band techniques are used to study reactivity and transition states. Examples include Ni and Al.

  12. Development of Novel Analytical Method for Ab Initio Powder Structural Analysis

    NASA Astrophysics Data System (ADS)

    Sakata, Makoto; Nishibori, Eiji; Sawa, Hiroshi

    Genetic Algorithm (GA) applied to ab initio structure determination from synchrotron powder diffraction is described. It seems to have an advantage over other real space methods for ab initio structure determination because of the existence of schema theorem. As an example, the case of Prednisolone Succinate is shown in some detail. Future development of GA in crystallography is briefly described.

  13. Dominant Modes in Light Nuclei - Ab Initio View of Emergent Symmetries

    NASA Astrophysics Data System (ADS)

    Draayer, J. P.; Dytrych, T.; Launey, K. D.; Dreyfuss, A. C.; Langr, D.

    2015-01-01

    An innovative symmetry-guided concept is discussed with a focus on emergent symmetry patterns in complex nuclei. In particular, the ab initio symmetry-adapted no-core shell model (SA-NCSM), which capitalizes on exact as well as partial symmetries that underpin the structure of nuclei, provides remarkable insight into how simple symmetry patterns emerge in the many-body nuclear dynamics from first principles. This ab initio view is complemented by a fully microscopic no-core symplectic shell-model framework (NCSpM), which, in turn, informs key features of the primary physics responsible for the emergent phenomena of large deformation and alpha-cluster substructures in studies of the challenging Hoyle state in Carbon-12 and enhanced collectivity in intermediate-mass nuclei. Furthermore, by recognizing that deformed configurations often dominate the low-energy regime, the SA-NCSM provides a strategy for determining the nature of bound states of nuclei in terms of a relatively small subspace of the symmetry-reorganized complete model space, which opens new domains of nuclei for ab initio investigations, namely, the intermediate-mass region, including isotopes of Ne, Mg, and Si.

  14. Ab initio calculations on the magnetic properties of transition metal complexes

    SciTech Connect

    Bodenstein, Tilmann; Fink, Karin

    2015-12-31

    We present a protocol for the ab initio determination of the magnetic properties of mono- and polynuclear transition metal compounds. First, we obtain the low lying electronic states by multireference methods. Then, we include spin-orbit coupling and an external magnetic field for the determination of zero-field splitting and g-tensors. For the polynuclear complexes the magnetic exchange coupling constants are determined by a modified complete active space self consistent field method. Based on the results of the ab initio calculations, magnetic data such as magnetic susceptibility or magnetization are simulated and compared to experimental data. The results obtained for the polynuclear complexes are further analysed by calculations on model complexes where part of the magnetic centers are substituted by diamagnetic ions. The methods are applied to different Co and Ni containing transition metal complexes.

  15. Evaluating high-throughput ab initio gene finders to discover proteins encoded in eukaryotic pathogen genomes missed by laboratory techniques.

    PubMed

    Goodswen, Stephen J; Kennedy, Paul J; Ellis, John T

    2012-01-01

    Next generation sequencing technology is advancing genome sequencing at an unprecedented level. By unravelling the code within a pathogen's genome, every possible protein (prior to post-translational modifications) can theoretically be discovered, irrespective of life cycle stages and environmental stimuli. Now more than ever there is a great need for high-throughput ab initio gene finding. Ab initio gene finders use statistical models to predict genes and their exon-intron structures from the genome sequence alone. This paper evaluates whether existing ab initio gene finders can effectively predict genes to deduce proteins that have presently missed capture by laboratory techniques. An aim here is to identify possible patterns of prediction inaccuracies for gene finders as a whole irrespective of the target pathogen. All currently available ab initio gene finders are considered in the evaluation but only four fulfil high-throughput capability: AUGUSTUS, GeneMark_hmm, GlimmerHMM, and SNAP. These gene finders require training data specific to a target pathogen and consequently the evaluation results are inextricably linked to the availability and quality of the data. The pathogen, Toxoplasma gondii, is used to illustrate the evaluation methods. The results support current opinion that predicted exons by ab initio gene finders are inaccurate in the absence of experimental evidence. However, the results reveal some patterns of inaccuracy that are common to all gene finders and these inaccuracies may provide a focus area for future gene finder developers. PMID:23226328

  16. Ab initio based thermal property predictions at a low cost: An error analysis

    NASA Astrophysics Data System (ADS)

    Lejaeghere, Kurt; Jaeken, Jan; Van Speybroeck, Veronique; Cottenier, Stefaan

    2014-01-01

    Ab initio calculations often do not straightforwardly yield the thermal properties of a material yet. It requires considerable computational efforts, for example, to predict the volumetric thermal expansion coefficient αV or the melting temperature Tm from first principles. An alternative is to use semiempirical approaches. They relate the experimental values to first-principles predictors via fits or approximative models. Before applying such methods, however, it is of paramount importance to be aware of the expected errors. We therefore quantify these errors at the density-functional theory level using the Perdew-Burke-Ernzerhof functional for several semiempirical approximations of αV and Tm, and compare them to the errors from fully ab initio methods, which are computationally more intensive. We base our conclusions on a benchmark set of 71 ground-state elemental crystals. For the thermal expansion coefficient, it appears that simple quasiharmonic theory, in combination with different approximations to the Grüneisen parameter, provides a similar overall accuracy as exhaustive first-principles phonon calculations. For the melting temperature, expensive ab initio molecular-dynamics simulations still outperform semiempirical methods.

  17. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    NASA Astrophysics Data System (ADS)

    Geng, Hua Y.

    2015-02-01

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model-the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of rs = 0.912.

  18. The ab-initio density matrix renormalization group in practice

    SciTech Connect

    Olivares-Amaya, Roberto; Hu, Weifeng; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic; Nakatani, Naoki

    2015-01-21

    The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.

  19. Ab initio engineering of materials with stacked hexagonal tin frameworks.

    PubMed

    Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N

    2016-01-01

    The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator. PMID:27387140

  20. Ab Initio Calculations of Excited Carrier Dynamics in Gallium Nitride

    NASA Astrophysics Data System (ADS)

    Jhalani, Vatsal; Bernardi, Marco

    Bulk wurtzite GaN is the primary material for blue light-emission technology. The radiative processes in GaN are regulated by the dynamics of excited (or so-called ``hot'') carriers, through microscopic processes not yet completely understood. We present ab initio calculations of electron-phonon (e-ph) scattering rates for hot carriers in GaN. Our work combines density functional theory to compute the electronic states, and density functional perturbation theory to obtain the phonon dispersions and e-ph coupling matrix elements. These quantities are interpolated on fine Brillouin zone grids with maximally localized Wannier functions, to converge the e-ph scattering rates within 5 eV of the band edges. We resolve the contribution of the different phonon modes to the total scattering rate, and study the impact on the relaxation times of the long-range Fröhlich interaction due to the longitudinal-optical phonon modes.

  1. Highly anisotropic thermal conductivity of arsenene: An ab initio study

    NASA Astrophysics Data System (ADS)

    Zeraati, Majid; Vaez Allaei, S. Mehdi; Abdolhosseini Sarsari, I.; Pourfath, Mahdi; Donadio, Davide

    2016-02-01

    Elemental two-dimensional (2D) materials exhibit intriguing heat transport and phononic properties. Here we have investigated the lattice thermal conductivity of newly proposed arsenene, the 2D honeycomb structure of arsenic, using ab initio calculations. Solving the Boltzmann transport equation for phonons, we predict a highly anisotropic thermal conductivity of 30.4 and 7.8 W/mK along the zigzag and armchair directions, respectively, at room temperature. Our calculations reveal that phonons with mean free paths between 20 nm and 1 μ m provide the main contribution to the large thermal conductivity in the zigzag direction; mean free paths of phonons contributing to heat transport in the armchair directions range between 20 and 100 nm. The obtained anisotropic thermal conductivity and feasibility of synthesis, in addition to high electron mobility reported elsewhere, make arsenene a promising material for nanoelectronic applications and thermal management.

  2. Ab initio study of II-(VI)2 dichalcogenides.

    PubMed

    Olsson, P; Vidal, J; Lincot, D

    2011-10-12

    The structural stabilities of the (Zn,Cd)(S,Se,Te)(2) dichalcogenides have been determined ab initio. These compounds are shown to be stable in the pyrite phase, in agreement with available experiments. Structural parameters for the ZnTe(2) pyrite semiconductor compound proposed here are presented. The opto-electronic properties of these dichalcogenide compounds have been calculated using quasiparticle GW theory. Bandgaps, band structures and effective masses are proposed as well as absorption coefficients and refraction indices. The compounds are all indirect semiconductors with very flat conduction band dispersion and high absorption coefficients. The work functions and surface properties are predicted. The Te and Se based compounds could be of interest as absorber materials in photovoltaic applications. PMID:21937783

  3. Ab initio study of guanine damage by hydroxyl radical.

    PubMed

    Chaban, Galina M; Wang, Dunyou; Huo, Winifred M

    2015-01-15

    Multiconfigurational ab initio methods are used in this study to examine two initial reactions that take place during the OH radical attack of the DNA base guanine: a ring opening reaction and a hydrogen transfer reaction. The same reactions are also studied in the presence of a single water molecule. The ring opening reaction has a moderate barrier height of ∼20-25 kcal/mol that is relatively insensitive to the presence of water. The barrier of the H-transfer reaction, on the other hand, is lowered from ∼50 to ∼22 kcal/mol when one water molecule is added, thus becoming comparable to the barrier height of the ring opening reaction. PMID:25517252

  4. Vibrational and ab initio molecular dynamics studies of bradykinin

    NASA Astrophysics Data System (ADS)

    Święch, Dominika; Kubisiak, Piotr; Andrzejak, Marcin; Borowski, Piotr; Proniewicz, Edyta

    2016-07-01

    In this study, the comprehensive theoretical and experimental investigations of Raman (RS) and infrared absorption (IR) spectra of bradykinin (BK) are presented. The ab initio Born-Oppenheimer molecular dynamics (BOMD) calculations, in the presence of water molecules that form the first coordination sphere, were used for conformational analysis of the BK structure. Based on the Density Functional Theory (DFT) calculations at the B3LYP/6-311G(d) level the vibrational spectra were interpreted. The calculated frequencies were scaled by means of the effective scaling frequency factor (ESFF) method. The theoretical data, which confirm the compact structure of BK in the presence of the water molecules revealed the remarkable effect of the intermolecular hydrogen bonding on the BK structural properties.

  5. Ab initio water pair potential with flexible monomers.

    PubMed

    Jankowski, Piotr; Murdachaew, Garold; Bukowski, Robert; Akin-Ojo, Omololu; Leforestier, Claude; Szalewicz, Krzysztof

    2015-03-26

    A potential energy surface for the water dimer with explicit dependence on monomer coordinates is presented. The surface was fitted to a set of previously published interaction energies computed on a grid of over a quarter million points in the 12-dimensional configurational space using symmetry-adapted perturbation theory and coupled-cluster methods. The present fit removes small errors in published fits, and its accuracy is critically evaluated. The minimum and saddle-point structures of the potential surface were found to be very close to predictions from direct ab initio optimizations. The computed second virial coefficients agreed well with experimental values. At low temperatures, the effects of monomer flexibility in the virial coefficients were found to be much smaller than the quantum effects. PMID:25687650

  6. Reactive Monte Carlo sampling with an ab initio potential

    NASA Astrophysics Data System (ADS)

    Leiding, Jeff; Coe, Joshua D.

    2016-05-01

    We present the first application of reactive Monte Carlo in a first-principles context. The algorithm samples in a modified NVT ensemble in which the volume, temperature, and total number of atoms of a given type are held fixed, but molecular composition is allowed to evolve through stochastic variation of chemical connectivity. We discuss general features of the method, as well as techniques needed to enhance the efficiency of Boltzmann sampling. Finally, we compare the results of simulation of NH3 to those of ab initio molecular dynamics (AIMD). We find that there are regions of state space for which RxMC sampling is much more efficient than AIMD due to the "rare-event" character of chemical reactions.

  7. Ab initio H2O in realistic hydrophilic confinement.

    PubMed

    Allolio, Christoph; Klameth, Felix; Vogel, Michael; Sebastiani, Daniel

    2014-12-15

    A protocol for the ab initio construction of a realistic cylindrical pore in amorphous silica, serving as a geometric nanoscale confinement for liquids and solutions, is presented. Upon filling the pore with liquid water at different densities, the structure and dynamics of the liquid inside the confinement can be characterized. At high density, the pore introduces long-range oscillations into the water density profile, which makes the water structure unlike that of the bulk across the entire pore. The tetrahedral structure of water is also affected up to the second solvation shell of the pore wall. Furthermore, the effects of the confinement on hydrogen bonding and diffusion, resulting in a weakening and distortion of the water structure at the pore walls and a slowdown in diffusion, are characterized. PMID:25208765

  8. Ab initio engineering of materials with stacked hexagonal tin frameworks

    PubMed Central

    Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.

    2016-01-01

    The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator. PMID:27387140

  9. Ab initio calculation of the shock Hugoniot of bulk silicon

    NASA Astrophysics Data System (ADS)

    Strickson, Oliver; Artacho, Emilio

    2016-03-01

    We describe how ab initio molecular dynamics can be used to determine the Hugoniot locus (states accessible by a shock wave) for materials with a number of stable phases, and with an approximate treatment of plasticity and yield, without having to simulate these phenomena directly. We consider the case of bulk silicon, with forces from density-functional theory, up to 70 GPa. The fact that shock waves can split into multiple waves due to phase transitions or yielding is taken into account here by specifying the strength of any preceding waves explicitly based on their yield strain. Points corresponding to uniaxial elastic compression along three crystal axes and a number of postshock phases are given, including a plastically yielded state, approximated by an isotropic stress configuration following an elastic wave of predetermined strength. The results compare well to existing experimental data for shocked silicon.

  10. Interatomic Coulombic decay widths of helium trimer: Ab initio calculations

    SciTech Connect

    Kolorenč, Přemysl; Sisourat, Nicolas

    2015-12-14

    We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green’s function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states.

  11. Interatomic Coulombic decay widths of helium trimer: Ab initio calculations.

    PubMed

    Kolorenč, Přemysl; Sisourat, Nicolas

    2015-12-14

    We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green's function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states. PMID:26671378

  12. Ab initio calculation of thermodynamic properties of silicon

    NASA Astrophysics Data System (ADS)

    Wei, Siqing; Li, Changlin; Chou, M. Y.

    1994-11-01

    We present a fully ab initio calculation of the thermodynamic properties for silicon within the quasiharmonic approximation, making use of volume-dependent phonon frequencies obtained from pseudopotential local-density calculations. The temperature dependence of the thermal-expansion coefficient, specific heat (at constant volume), and other related quantities are studied. We confirm that the thermal-expansion coefficient behaves differently in three temperature regions: positive for temperature below 15 K, negative between 15 and 125 K, and positive again above 125 K. This finding agrees with experiment. The abnormal (negative) thermal-expansion coefficient at low temperatures is explained through a detailed study of mode Grüneisen parameters. Both specific-heat and thermal-expansion-coefficient values calculated are in excellent agreement with experiment up to a few hundred kelvin.

  13. XMVB: a program for ab initio nonorthogonal valence bond computations.

    PubMed

    Song, Lingchun; Mo, Yirong; Zhang, Qianer; Wu, Wei

    2005-04-15

    An ab initio nonorthogonal valence bond program, called XMVB, is described in this article. The XMVB package uses Heitler-London-Slater-Pauling (HLSP) functions as state functions, and calculations can be performed with either all independent state functions for a molecule or preferably a few selected important state functions. Both our proposed paired-permanent-determinant approach and conventional Slater determinant expansion algorithm are implemented for the evaluation of the Hamiltonian and overlap matrix elements among VB functions. XMVB contains the capabilities of valence bond self-consistent field (VBSCF), breathing orbital valence bond (BOVB), and valence bond configuration interaction (VBCI) computations. The VB orbitals, used to construct VB functions, can be defined flexibly in the calculations depending on particular applications and focused problems, and they may be strictly localized, delocalized, or bonded-distorted (semidelocalized). The parallel version of XMVB based on MPI (Message Passing Interface) is also available. PMID:15704237

  14. Ab initio theory of NMR chemical shifts in solids

    SciTech Connect

    Louie, S.G. |

    1997-12-31

    A new formalism for ab initio calculation of the orbital magnetic susceptibility and the NMR chemical shifts in solids and liquids is presented. The approach can be applied to periodic systems such as crystals, surfaces or polymers, and with a supercell technique, to nonperiodic systems such as amorphous materials, liquids, or solids with defects. The formalism is based on the density functional theory in the local density approximation and makes use of a generalized f-sum rule to eliminate the divergent terms that plagued previous theories. Calculations have been successfully carried out for the diamagnetic susceptibility of a number of insulators and for the NMR chemical shifts of a variety of systems including free molecules, ionic crystals, hydrogen-bonded materials and amorphous carbon.

  15. 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.

  16. Ab initio calculations of grain boundaries in bcc metals

    NASA Astrophysics Data System (ADS)

    Scheiber, Daniel; Pippan, Reinhard; Puschnig, Peter; Romaner, Lorenz

    2016-03-01

    In this study, we compute grain boundary (GB) properties for a large set of GBs in bcc transition metals with a special focus on W, Mo and Fe using ab initio density functional theory (DFT) and semi-empirical second nearest neighbour modified embedded atom method (2NN-MEAM) potentials. The GB properties include GB energies, surface energies, GB excess volume and work of separation, which we analyse and then compare to experimental data. We find that the used 2NN-MEAM potentials can predict general trends of GB properties, but do not always reproduce the GB ground state structure and energy found with DFT. In particular, our results explain the experimental finding that W and Mo prefer intergranular fracture, while other bcc metals prefer transgranular cleavage.

  17. Transport coefficients in diamond from ab-initio calculations

    NASA Astrophysics Data System (ADS)

    Löfâs, Henrik; Grigoriev, Anton; Isberg, Jan; Ahuja, Rajeev

    2013-03-01

    By combining the Boltzmann transport equation with ab-initio electronic structure calculations, we obtain transport coefficients for boron-doped diamond. We find the temperature dependence of the resistivity and the hall coefficients in good agreement with experimental measurements. Doping in the samples is treated via the rigid band approximation and scattering is treated in the relaxation time approximation. In contrast to previous results, the acoustic phonon scattering is the dominating scattering mechanism for the considered doping range. At room temperature, we find the thermopower, S, in the range 1-1.6 mV/K and the power factor, S2σ, in the range 0.004-0.16 μW /cm K2.

  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. Ab initio engineering of materials with stacked hexagonal tin frameworks

    NASA Astrophysics Data System (ADS)

    Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.

    2016-07-01

    The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator.

  20. Ab initio electronic stopping power of protons in bulk materials

    NASA Astrophysics Data System (ADS)

    Shukri, Abdullah Atef; Bruneval, Fabien; Reining, Lucia

    2016-01-01

    The electronic stopping power is a crucial quantity for ion irradiation: it governs the deposited heat, the damage profile, and the implantation depth. Whereas experimental data are readily available for elemental solids, the data are much more scarce for compounds. Here we develop a fully ab initio computational scheme based on linear response time-dependent density-functional theory to predict the random electronic stopping power (RESP) of materials without any empirical fitting. We show that the calculated RESP compares well with experimental data, when at full convergence, with the inclusion of the core states and of the exchange correlation. We evaluate the unexpectedly limited magnitude of the nonlinear terms in the RESP by comparing with other approaches based on the time propagation of time-dependent density-functional theory. Finally, we check the validity of a few empirical rules of thumbs that are commonly used to estimate the electronic stopping power.

  1. Isofulminic acid, HONC: Ab initio theory and microwave spectroscopy.

    PubMed

    Mladenović, Mirjana; Lewerenz, Marius; McCarthy, Michael C; Thaddeus, Patrick

    2009-11-01

    Isofulminic acid, HONC, the most energetic stable isomer of isocyanic acid HNCO, higher in energy by 84 kcal/mol, has been detected spectroscopically by rotational spectroscopy supported by coupled cluster electronic structure calculations. The fundamental rotational transitions of the normal, carbon-13, oxygen-18, and deuterium isotopic species have been detected in the centimeter band in a molecular beam by Fourier transform microwave spectroscopy, and rotational constants and nitrogen and deuterium quadrupole coupling constants have been derived. The measured constants agree well with those predicted by ab initio calculations. A number of other electronic and spectroscopic parameters of isofulminic acid, including the dipole moment, vibrational frequencies, infrared intensities, and centrifugal distortion constants have been calculated at a high level of theory. Isofulminic acid is a good candidate for astronomical detection with radio telescopes because it is highly polar and its more stable isomers (HNCO, HOCN, and HCNO) have all been identified in space. PMID:19895013

  2. Ab initio study of helium behavior in titanium tritides

    SciTech Connect

    Liang, J. H.; Dai, Yunya; Yang, Li; Peng, SM; Fan, K. M.; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei

    2013-03-01

    Ab initio calculations based on density functional theory have been performed to investigate the relative stability of titanium tritides and the helium behavior in stable titanium tritides. The results show that the β-phase TiT1.5 without two tritium along the [100] direction (TiT1.5[100]) is more stable than other possible structures. The stability of titanium tritides decrease with the increased generation of helium in TiT1.5[100]. In addition, helium generated by tritium decay prefers locating at a tetrahedral site, and favorably migrates between two neighbor vacant tetrahedral sites through an intermediate octahedral site in titanium tritides, with a migration energy of 0.23 eV. Furthermore, helium is easily accumulated on a (100) plane in β-phase TiT1.5[100].

  3. Ab initio quantum dynamics using coupled-cluster.

    PubMed

    Kvaal, Simen

    2012-05-21

    The curse of dimensionality (COD) limits the current state-of-the-art ab initio propagation methods for non-relativistic quantum mechanics to relatively few particles. For stationary structure calculations, the coupled-cluster (CC) method overcomes the COD in the sense that the method scales polynomially with the number of particles while still being size-consistent and extensive. We generalize the CC method to the time domain while allowing the single-particle functions to vary in an adaptive fashion as well, thereby creating a highly flexible, polynomially scaling approximation to the time-dependent Schrödinger equation. The method inherits size-consistency and extensivity from the CC method. The method is dubbed orbital-adaptive time-dependent coupled-cluster, and is a hierarchy of approximations to the now standard multi-configurational time-dependent Hartree method for fermions. A numerical experiment is also given. PMID:22612082

  4. Ab Initio Screening of CO2-philic Groups.

    PubMed

    Tian, Ziqi; Saito, Tomonori; Jiang, De-En

    2015-04-23

    Ab initio calculations were used to identify CO2-philic groups. Over 55 neutral molecules were screened for CO2 affinity via binding energetics. It is found that poly(ethylene oxide)s (PEO) oligomers with more than three repeating units are good CO2-binding groups, consistent with the high-performance of PEO-based materials for CO2/N2 separation. More interestingly, two triazole groups linked with a methylene chain are also excellent for CO2 binding with a favorable interaction of more than 28 kJ/mol, indicating that polymers or covalent-organic frameworks (COFs) with triazoles may be utilized for CO2 capture. This work provides a useful guide to introduce promising organic groups into polymeric membranes and COFs for CO2/N2 separation media. PMID:25825811

  5. Ab initio methods for nuclear properties - a computational physics approach

    NASA Astrophysics Data System (ADS)

    Maris, Pieter

    2011-04-01

    A microscopic theory for the structure and reactions of light nuclei poses formidable challenges for high-performance computing. Several ab-initio methods have now emerged that provide nearly exact solutions for some nuclear properties. The ab-initio no-core full configuration (NCFC) approach is based on basis space expansion methods and uses Slater determinants of single-nucleon basis functions to express the nuclear wave function. In this approach, the quantum many-particle problem becomes a large sparse matrix eigenvalue problem. The eigenvalues of this matrix give us the binding energies, and the corresponding eigenvectors the nuclear wave functions. These wave functions can be employed to evaluate experimental quantities. In order to reach numerical convergence for fundamental problems of interest, the matrix dimension often exceeds 1 billion, and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. I discuss different strategies for distributing and solving this large sparse matrix on current multicore computer architectures, including methods to deal with with memory bottleneck. Several of these strategies have been implemented in the code MFDn, which is a parallel fortran code for nuclear structure calculations. I will show scaling behavior and compare the performance of the pure MPI version with the hybrid MPI/OpenMP code on Cray XT4 and XT5 platforms. For large core counts (typically 5,000 and above), the hybrid version is more efficient than pure MPI. With this code, we have been able to predict properties of the unstable nucleus 14F, which have since been confirmed by experiments. I will also give an overview of other recent results for nuclei in the A = 6 to 16 range with 2- and 3-body interactions. Supported in part by US DOE Grant DE-FC02-09ER41582.

  6. 4He Thermophysical Properties: New Ab Initio Calculations

    PubMed Central

    Hurly, John J.; Mehl, James B.

    2007-01-01

    Since 2000, atomic physicists have reduced the uncertainty of the helium-helium “ab initio” potential; for example, from approximately 0.6 % to 0.1 % at 4 bohr, and from 0.8 % to 0.1 % at 5.6 bohr. These results led us to: (1) construct a new inter-atomic potential ϕ07, (2) recalculate values of the second virial coefficient, the viscosity, and the thermal conductivity of 4He from 1 K to 10,000 K, and (3), analyze the uncertainties of the thermophysical properties that propagate from the uncertainty of ϕ07 and from the Born-Oppenheimer approximation of the electron-nucleon quantum mechanical system. We correct minor errors in a previous publication [J. J. Hurly and M. R. Moldover, J. Res. Nat. Inst. Standards Technol. 105, 667 (2000)] and compare our results with selected data published after 2000. The ab initio results tabulated here can serve as standards for the measurement of thermophysical properties. PMID:27110456

  7. Avoiding fractional electrons in subsystem DFT based ab-initio molecular dynamics yields accurate models for liquid water and solvated OH radical

    NASA Astrophysics Data System (ADS)

    Genova, Alessandro; Ceresoli, Davide; Pavanello, Michele

    2016-06-01

    In this work we achieve three milestones: (1) we present a subsystem DFT method capable of running ab-initio molecular dynamics simulations accurately and efficiently. (2) In order to rid the simulations of inter-molecular self-interaction error, we exploit the ability of semilocal frozen density embedding formulation of subsystem DFT to represent the total electron density as a sum of localized subsystem electron densities that are constrained to integrate to a preset, constant number of electrons; the success of the method relies on the fact that employed semilocal nonadditive kinetic energy functionals effectively cancel out errors in semilocal exchange-correlation potentials that are linked to static correlation effects and self-interaction. (3) We demonstrate this concept by simulating liquid water and solvated OH• radical. While the bulk of our simulations have been performed on a periodic box containing 64 independent water molecules for 52 ps, we also simulated a box containing 256 water molecules for 22 ps. The results show that, provided one employs an accurate nonadditive kinetic energy functional, the dynamics of liquid water and OH• radical are in semiquantitative agreement with experimental results or higher-level electronic structure calculations. Our assessments are based upon comparisons of radial and angular distribution functions as well as the diffusion coefficient of the liquid.

  8. Ab initio study of hypervalent sulfur hydrides as model intermediates in the interconversion reactions of compounds containing sulfur-sulfur bonds

    SciTech Connect

    Laitinen, R.S.; Pakkanen, T.A.; Steudel, R.

    1987-02-04

    Ab initio MO calculations involving the 4-31G* basis set have been used to predict the equilibrium geometries of the hypervalent sulfur hydrides H/sub 2/SS, (HS)/sub 2/SS, H/sub 2/S(SH)/sub 2/, H/sub 2/S(SSH)/sub 2/, and the cyclic H/sub 4/S/sub 4/. The energy changes in their formation from appropriate sulfanes H/sub 2/S/sub n/ (n = 1-4) have been studied with the 6-31G* basis set including the correction for the electron correlation by the second- and third-order Moeller-Plesset perturbation theory. The results are used to discuss the possible pathways in the interconversion reactions between various sulfur compounds containing cumulated SS bonds, for example, the formation of S/sub 7/ from S/sub 8/ for which hypervalent intermediates have been proposed recently. Comparison with experimental evidence is made whenever possible.

  9. Electronic Structures of Anti-Ferromagnetic Tetraradicals: Ab Initio and Semi-Empirical Studies.

    PubMed

    Zhang, Dawei; Liu, Chungen

    2016-04-12

    The energy relationships and electronic structures of the lowest-lying spin states in several anti-ferromagnetic tetraradical model systems are studied with high-level ab initio and semi-empirical methods. The Full-CI method (FCI), the complete active space second-order perturbation theory (CASPT2), and the n-electron valence state perturbation theory (NEVPT2) are employed to obtain reference results. By comparing the energy relationships predicted from the Heisenberg and Hubbard models with ab initio benchmarks, the accuracy of the widely used Heisenberg model for anti-ferromagnetic spin-coupling in low-spin polyradicals is cautiously tested in this work. It is found that the strength of electron correlation (|U/t|) concerning anti-ferromagnetically coupled radical centers could range widely from strong to moderate correlation regimes and could become another degree of freedom besides the spin multiplicity. Accordingly, the Heisenberg-type model works well in the regime of strong correlation, which reproduces well the energy relationships along with the wave functions of all the spin states. In moderately spin-correlated tetraradicals, the results of the prototype Heisenberg model deviate severely from those of multi-reference electron correlation ab initio methods, while the extended Heisenberg model, containing four-body terms, can introduce reasonable corrections and maintains its accuracy in this condition. In the weak correlation regime, both the prototype Heisenberg model and its extended forms containing higher-order correction terms will encounter difficulties. Meanwhile, the Hubbard model shows balanced accuracy from strong to weak correlation cases and can reproduce qualitatively correct electronic structures, which makes it more suitable for the study of anti-ferromagnetic coupling in polyradical systems. PMID:26963572

  10. Ab initio calculation and anharmonic force field of hypochlorous acid, HOCl

    NASA Astrophysics Data System (ADS)

    Halonen, L.; Ha, T.-K.

    1988-03-01

    Ab initio calculations on HOCl have been performed at the third-order Møller-Plesset perturbation theory level to determine the equilibrium structure and the anharmonic force field. An empirical anharmonic force field based on the ab initio results is obtained using available experimental vibration-rotation data. Four of the six harmonic and six of the ten cubic force constants have been determined experimentally, the remaining values being fixed at the ab initio values. A good fit to the experimental vibration-rotation data of four isotopic species is obtained.

  11. Ab initio molecular crystal structures, spectra, and phase diagrams.

    PubMed

    Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

  12. 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

  13. Ab Initio Studies of Halogen and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

  14. Ab initio studies of niobium defects in uranium

    SciTech Connect

    Xiang, S; Huang, H; Hsiung, L

    2007-06-01

    Uranium (U), with the addition of small amount of niobium (Nb), is stainless. The Nb is fully miscible with the high temperature phase of U and tends to segregate upon cooling below 647 C. The starting point of segregation is the configuration of Nb substitutional or interstitial defects. Using density-functional-theory based ab initio calculations, the authors find that the formation energy of a single vacancy is 1.08 eV, that of Nb substitution is 0.59 eV, that of Nb interstitial at octahedral site is 1.58 eV, and that of Nb interstitial at tetrahedral site is 2.35 eV; all with reference to a reservoir of {gamma} phase U and pure Nb. The formation energy of Nb defects correlates with the local perturbation of electron distribution; higher formation energy to larger perturbation. Based on this study, Nb atoms thermodynamically prefer to occupy substitutional sites in {gamma} phase U, and they prefer to be in individual substitutional defects than clusters.

  15. Melting curves of metals by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Minakov, Dmitry; Levashov, Pavel

    2015-06-01

    In this work we used several ab initio approaches to reproduce melting curves and discussed their abilities, advantages and drawbacks. We used quasiharmonic appoximation and Lindemann criterion to build melting curves in wide region of pressures. This approach allows to calculate the total free energy of electrons and phonons, so it is possible to obtain all thermodynamic properties in the crystalline state. We also used quantum molecular dynamics simulations to investigate melting at various pressures. We explored the size-effect of the heat until it melts (HUM) method in detail. Special attention was paid to resolve the boundaries of the melting region on density. All calculations were performed for aluminum, copper and gold. Results were in good agreement with available experimental data. Also we studied the influence of electronic temperature on melting curves. It turned out that the melting temperature increased with the rise of electron temperature at normal density and had non-monotonic behavior at higher densities. This work is supported by the Ministry of Education and Science of the Russian Federation (Project No. 3.522.2014/K).

  16. Ab initio simulation of gap discrete breathers in strained graphene

    NASA Astrophysics Data System (ADS)

    Lobzenko, I. P.; Chechin, G. M.; Bezuglova, G. S.; Baimova, Yu. A.; Korznikova, E. A.; Dmitriev, S. V.

    2016-03-01

    The methods of the density functional theory were used for the first time for the simulation of discrete breathers in graphene. It is demonstrated that breathers can exist with frequencies lying in the gap of the phonon spectrum, induced by uniaxial tension of a monolayer graphene sheet in the "zigzag" direction (axis X), polarized in the "armchair" direction (axis Y). The found gap breathers are highly localized dynamic objects, the core of which is formed by two adjacent carbon atoms located on the Y axis. The atoms surrounding the core vibrate at much lower amplitudes along both the axes ( X and Y). The dependence of the frequency of these breathers on amplitude is found, which shows a soft type of nonlinearity. No breathers of this type were detected in the gap induced by stretching along the Y axis. It is shown that the breather vibrations may be approximated by the Morse oscillators, the parameters of which are determined from ab initio calculations. The results are of fundamental importance, as molecular dynamics calculations based on empirical potentials cannot serve as a reliable proof of the existence of breathers in crystals.

  17. Volumic omit maps in ab initio dual-space phasing.

    PubMed

    Oszlányi, Gábor; Sütő, András

    2016-07-01

    Alternating-projection-type dual-space algorithms have a clear construction, but are susceptible to stagnation and, thus, inefficient for solving the phase problem ab initio. To improve this behaviour new omit maps are introduced, which are real-space perturbations applied periodically during the iteration process. The omit maps are called volumic, because they delete some predetermined subvolume of the unit cell without searching for atomic regions or analysing the electron density in any other way. The basic algorithms of positivity, histogram matching and low-density elimination are tested by their solution statistics. It is concluded that, while all these algorithms based on weak constraints are practically useless in their pure forms, appropriate volumic omit maps can transform them to practically useful methods. In addition, the efficiency of the already useful reflector-type charge-flipping algorithm can be further improved. It is important that these results are obtained by using non-sharpened structure factors and without any weighting scheme or reciprocal-space perturbation. The mathematical background of volumic omit maps and their expected applications are also discussed. PMID:27357850

  18. Ab initio study of optical excitations in VO2

    NASA Astrophysics Data System (ADS)

    Coulter, John; Gali, Adam; Manousakis, Efstratios

    2014-03-01

    Motivated by recent experimental efforts to fabricate p-n junctions from transition metal oxides (TMOs) and a recent theoretical study claiming TMOs to be good absorbers and promising materials for efficient carrier multiplication, we study the optical properties of a prototypical TMO, the insulator M1 phase of vanadium dioxide (VO2), by ab initio methods. We applied the Bethe-Salpeter equations (BSE) to calculate the optical properties, starting from self-consistent GW quasi-particle energy levels and states. In contrast to expectations, the exciton binding energy obtained by BSE is in good agreement with the experiment. We find that the electron-electron interaction is very strong which makes this material promising for efficient carrier multiplication that might lead to an enhanced efficiency in photo-voltaics applications. To illustrate this more quantitatively, we calculated the impact ionization rate within the independent quasiparticle approximation, and find that the rate is significantly higher than silicon in the region of highest solar intensity, due to the strong multiple carrier excitations.

  19. Ab initio studies of phoshorene island single electron transistor.

    PubMed

    Ray, S J; Venkata Kamalakar, M; Chowdhury, R

    2016-05-18

    Phosphorene is a newly unveiled two-dimensional crystal with immense potential for nanoelectronic and optoelectronic applications. Its unique electronic structure and two dimensionality also present opportunities for single electron devices. Here we report the behaviour of a single electron transistor (SET) made of a phosphorene island, explored for the first time using ab initio calculations. We find that the band gap and the charging energy decrease monotonically with increasing layer numbers due to weak quantum confinement. When compared to two other novel 2D crystals such as graphene and MoS2, our investigation reveals larger adsorption energies of gas molecules on phosphorene, which indicates better a sensing ability. The calculated charge stability diagrams show distinct changes in the presence of an individual molecule which can be applied to detect the presence of different molecules with sensitivity at a single molecular level. The higher charging energies of the molecules within the SET display operational viability at room temperature, which is promising for possible ultra sensitive detection applications. PMID:27093536

  20. Ab initio studies of phosphorene island single electron transistor

    NASA Astrophysics Data System (ADS)

    Ray, S. J.; Venkata Kamalakar, M.; Chowdhury, R.

    2016-05-01

    Phosphorene is a newly unveiled two-dimensional crystal with immense potential for nanoelectronic and optoelectronic applications. Its unique electronic structure and two dimensionality also present opportunities for single electron devices. Here we report the behaviour of a single electron transistor (SET) made of a phosphorene island, explored for the first time using ab initio calculations. We find that the band gap and the charging energy decrease monotonically with increasing layer numbers due to weak quantum confinement. When compared to two other novel 2D crystals such as graphene and MoS2, our investigation reveals larger adsorption energies of gas molecules on phosphorene, which indicates better a sensing ability. The calculated charge stability diagrams show distinct changes in the presence of an individual molecule which can be applied to detect the presence of different molecules with sensitivity at a single molecular level. The higher charging energies of the molecules within the SET display operational viability at room temperature, which is promising for possible ultra sensitive detection applications.

  1. An Ab Initio Based Potential Energy Surface for Water

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Schwenke, David W.; Langhoff, Stephen R. (Technical Monitor)

    1996-01-01

    We report a new determination of the water potential energy surface. A high quality ab initio potential energy surface (PES) and dipole moment function of water have been computed. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base. The adjustment is small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with experiment. Of the 27,245 assigned transitions in the HITRAN 92 data base for H2(O-16), the overall root mean square (rms) deviation between the computed and observed line positions is 0.125/cm. However the deviations do not correspond to a normal distribution: 69% of the lines have errors less than 0.05/cm. Overall, the agreement between the line intensities computed in the present work and those contained in the data base is quite good, however there are a significant number of line strengths which differ greatly.

  2. Exploring the free energy surface using ab initio molecular dynamics.

    PubMed

    Samanta, Amit; Morales, Miguel A; Schwegler, Eric

    2016-04-28

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti. PMID:27131525

  3. Ab initio study of MoS2 nanotube bundles

    NASA Astrophysics Data System (ADS)

    Verstraete, Matthieu; Charlier, Jean-Christophe

    2003-07-01

    Recently, the synthesis of a new phase of MoS2I1/3 stoichiometry was reported [M. Remskar, A. Mrzel, Z. Skraba, A. Jesih, M. Ceh, J. Demšar, P. Stadelmann, F. Lévy, and D. Mihailovic, Science 292, 479 (2001)]. Electron microscope images and diffraction data were interpreted to indicate bundles of sub-nanometer-diameter single-wall MoS2 nanotubes. After experimental characterization, the structure was attributed to an assembly of “armchair” nanotubes with interstitial iodine. Using first-principles total-energy calculations, bundles of MoS2 nanotubes with different topologies and stoichiometries are investigated. All of the systems are strongly metallic. Configurations with “zigzag” structures are found to be more stable energetically than the “armchair” ones, though all of the structures have similar stabilities. After relaxation, there remain several candidates which give a lattice parameter in relative agreement with experiment. Further, spin-polarized calculations indicate that a structure with armchair tubes iodine atoms in their center acquires a very large spontaneous magnetic moment of 12μB, while the other structures are nonmagnetic. Our ab initio calculations show that in most of the other structures, the tubes are very strongly bound together, and that the compounds should be considered as a crystal, rather than as a bundle of tubes in the habitual sense.

  4. Ab initio simulations of pseudomorphic silicene and germanene bidimensional heterostructures

    NASA Astrophysics Data System (ADS)

    Debernardi, Alberto; Marchetti, Luigi

    2016-06-01

    Among the novel two-dimensional (2D) materials, silicene and germanene, which are two honeycomb crystal structures composed of a monolayer of Si and Ge, respectively, have attracted the attention of material scientists because they combine the advantages of the new 2D ultimate-scaled electronics with their compatibility with industrial processes presently based on Si and Ge. We envisage pseudomorphic lateral heterostructures based on ribbons of silicene and germanene, which are the 2D analogs of conventional 3D Si/Ge superlattices and quantum wells. In spite of the considerable lattice mismatch (˜4 % ) between free-standing silicene and germanene, our ab initio simulations predict that, considering striped 2D lateral heterostructures made by alternating silicene and germanene ribbons of constant width, the silicene/germanene junction remains pseudomorphic—i.e., it maintains lattice-matched edges—up to critical ribbon widths that can reach some tens of nanometers. Such critical widths are one order of magnitude larger than the critical thickness measured in 3D pseudomorphic Si/Ge heterostructures and the resolution of state-of-the-art lithography, thus enabling the possibility of lithography patterned silicene/germanene junctions. We computed how the strain produced by the pseudomorphic growth modifies the crystal structure and electronic bands of the ribbons, providing a mechanism for band-structure engineering. Our results pave the way for lithography patterned lateral heterostructures that can serve as the building blocks of novel 2D electronics.

  5. Exploring the free energy surface using ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

    2016-04-01

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.

  6. Accurate ab initio vibrational energies of methyl chloride

    SciTech Connect

    Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    2015-06-28

    Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH{sub 3}{sup 35}Cl and CH{sub 3}{sup 37}Cl. The respective PESs, CBS-35{sup  HL}, and CBS-37{sup  HL}, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY {sub 3}Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35{sup  HL} and CBS-37{sup  HL} PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm{sup −1}, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH{sub 3}Cl without empirical refinement of the respective PESs.

  7. 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.

  8. Ab initio SCF calculations on hydrogen bonded cresol isomers

    NASA Astrophysics Data System (ADS)

    Pohl, M.; Kleinermanns, K.

    1988-12-01

    Ab initio GAUSSIAN 80 calculations with two different basis sets (STO-3G and 4 31 G*) were performed on hydrogen bonded cresol isomers for comparison with experimental data from free jet fluorescence excitation spectroscopy. For m-cresol, the calculated barriers for hindered internal rotation of the OH-group and the CH3-group are in good agreement with experiment. The calculations show the trans-linear configuration of p-cresol· B-clusters ( B = H2O, CH3OH) to be more stable than the all-planar configuration. This agrees with CI calculations and microwave spectroscopic investigations of the water dimer. Calculations of both the intermolecular stretch and bend frequencies of p-cresol· B-clusters show little dependence on the all-planar or trans-linear configuration but a strong dependence on the choice of the basis set. With the minimal basis set STO-3G, the vibrational energies are generally too high. The agreement between the calculated vibrational frequencies from the 4 31 G* basis set and the experimental values is fair.

  9. Predicting lattice thermal conductivity with help from ab initio methods

    NASA Astrophysics Data System (ADS)

    Broido, David

    2015-03-01

    The lattice thermal conductivity is a fundamental transport parameter that determines the utility a material for specific thermal management applications. Materials with low thermal conductivity find applicability in thermoelectric cooling and energy harvesting. High thermal conductivity materials are urgently needed to help address the ever-growing heat dissipation problem in microelectronic devices. Predictive computational approaches can provide critical guidance in the search and development of new materials for such applications. Ab initio methods for calculating lattice thermal conductivity have demonstrated predictive capability, but while they are becoming increasingly efficient, they are still computationally expensive particularly for complex crystals with large unit cells . In this talk, I will review our work on first principles phonon transport for which the intrinsic lattice thermal conductivity is limited only by phonon-phonon scattering arising from anharmonicity. I will examine use of the phase space for anharmonic phonon scattering and the Grüneisen parameters as measures of the thermal conductivities for a range of materials and compare these to the widely used guidelines stemming from the theory of Liebfried and Schölmann. This research was supported primarily by the NSF under Grant CBET-1402949, and by the S3TEC, an Energy Frontier Research Center funded by the US DOE, office of Basic Energy Sciences under Award No. DE-SC0001299.

  10. Ab initio calculation of double ionization of atoms

    SciTech Connect

    Serov, V. V.

    2013-02-15

    The Solov'ev-Vinitsky method was used to perform an ab initio calculation of the triple-differential cross section for the double single-photon photoionization of helium for the case of equal emitted-electron energies. A Gaussian width {gamma} describing angular electron-electron correlations at the total electron energy E taking values in range between 0.1 and 100 eV was obtained for this cross section. The results agree with available experimental data, but they raise a doubt as to whether the well-known Wannier law {gamma} {proportional_to} E{sup 1/4} is applicable at experimentally accessible energies. The Gaussian width {gamma} was investigated as a function of the total emitted-electron energy for targets that have a strongly asymmetric configuration of the initial state-specifically, a negative atomic-hydrogen ion H{sup -} and heliumin the 1s2s{sup 1}S and 1s3s{sup 1}S excited states. It was found that this function, {gamma}(E), had a maximum at low energies. It was also shown that, at low energies, the dependence of the double-differential cross section on the angle between the emitted-electron momenta for the targets indicated above differed substantially from the Gaussian dependence, featuring maxima whose number was equal to the number of radial nodes in the initial state. This opens new possibilities for a qualitative analysis of the electron structure of targets.

  11. Ab initio calculation of infrared intensities for hydrogen peroxide

    NASA Technical Reports Server (NTRS)

    Rogers, J. D.; Hillman, J. J.

    1982-01-01

    Results of an ab initio SCF quantum mechanical study are used to derive estimates for the infrared intensities of the fundamental vibrations of hydrogen peroxide. Atomic polar tensors (APTs) were calculated on the basis of a 4-31G basis set, and used to derive absolute intensities for the vibrational transitions. Comparison of the APTs calculated for H2O2 with those previously obtained for H2O and CH3OH, and of the absolute intensities derived from the H2O2 APTs with those derived from APTs transferred from H2O and CH3OH, reveals the sets of values to differ by no more than a factor of two, supporting the validity of the theoretical calculation. Values of the infrared intensities obtained correspond to A1 = 14.5 km/mol, A2 = 0.91 km/mol, A3 = 0.058 km/mol, A4 = 123 km/mol, A5 = 46.2 km/mol, and A6 = 101 km/mol. Charge, charge flux and overlap contributions to the dipole moment derivatives are also computed.

  12. Ab initio study of the phenol-water cation radical

    NASA Astrophysics Data System (ADS)

    Hobza, Pavel; Burcl, Rudolf; Špirko, Vladimír; Dopfer, Otto; Müller-Dethlefs, Klaus; Schlag, Edward W.

    1994-07-01

    The phenol-water cation radical has been investigated by ab initio theory using the spin-restricted open-shell Hartree-Fock and spin-restricted open-shell second-order Møller-Plesset theories with 3-21G*(O) and 6-31G* basis sets. The full geometrical optimization was performed for several hydrogen-bonded structures and one hemibonded structure. Clearly, the most stable structure has been found for Cs symmetry with the linear hydrogen bond between the proton of the OH group of the phenol cation radical and the oxygen of the water, and the water hydrogens pointing away from the phenyl ring. For this structure harmonic (and for some intermolecular modes anharmonic) vibrational frequencies have been computed for various isotopic complexes. The computed shifts of phenol-localized intramolecular modes on complexation and on deuteration as well as the calculated intermolecular frequencies of the different isotopic complexes allow for an assignment of vibrational frequencies observed in the experimental zero-kinetic-energy (ZEKE) photoelectron spectra. Five out of a possible six intermolecular vibrations and several intramolecular modes have been assigned, including the 18b vibration which shows a strong blue shift in frequency upon complexation. Structure and properties of the phenol-water cation radical are compared with those of the corresponding neutral complex.

  13. An efficient approach to ab initio Monte Carlo simulation

    SciTech Connect

    Leiding, Jeff; Coe, Joshua D.

    2014-01-21

    We present a Nested Markov chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, was used to substantially decorrelate configurations at which the potential of interest was evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure was maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature β{sup 0}), which was otherwise unconstrained. Local density approximation results are presented for shocked states of argon at pressures from 4 to 60 GPa, where—depending on the quality of the reference system potential—acceptance probabilities were enhanced by factors of 1.2–28 relative to unoptimized NMC. The optimization procedure compensated strongly for reference potential shortcomings, as evidenced by significantly higher speedups when using a reference potential of lower quality. The efficiency of optimized NMC is shown to be competitive with that of standard ab initio molecular dynamics in the canonical ensemble.

  14. Accurate ab initio vibrational energies of methyl chloride.

    PubMed

    Owens, Alec; Yurchenko, Sergei N; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    2015-06-28

    Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH3 (35)Cl and CH3 (37)Cl. The respective PESs, CBS-35( HL), and CBS-37( HL), are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY 3Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35( HL) and CBS-37( HL) PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm(-1), respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH3Cl without empirical refinement of the respective PESs. PMID:26133427

  15. Accurate ab initio vibrational energies of methyl chloride

    NASA Astrophysics Data System (ADS)

    Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    2015-06-01

    Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH335Cl and CH337Cl. The respective PESs, CBS-35 HL, and CBS-37 HL, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY 3Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35 HL and CBS-37 HL PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm-1, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH3Cl without empirical refinement of the respective PESs.

  16. Ab initio study of the bonding in diatomic nickel

    SciTech Connect

    Noell, J.O.; Newton, M.D.; Hay, P.J.; Martin, R.L.; Bobrowicz, F.W.

    1980-09-01

    Hartree--Fock, GVB, and configuration interaction calculations were performed for diatomic nickel using an ab initio effective core potential. A basis set specifically optimized for the /sup 3/D state of atomic nickel is found to be far superior to the more common basis obtained from the /sup 3/F atomic state. Correlation effects are found to be significant in determining the bond energy. In particular, the two electrons of the s--s bond must be appropriately correlated. In addition, correlation effects which one would interpret as being principally intra-atomic in character are found to have a marked effect on the molecular properties. The theoretically predicted bond dissociation energy (D/sub e/) of 43.4 kcal/mol is significantly lower than the experimental estimate of 55 +- 5 kcal/mol. However, molecular partition functions calculated using the present results indicate that the experimental value should be revised downward to a value of approx.46 +- 5 kcal/mol, in good agreement with our calculations. An interatomic distance of 4.27 bohr is computed and compared with experimental estimates. Spectroscopic parameters for dipole-allowed transitions from the ground state were determined from SCF and GVB calculations and discussed in relation to the experimentally observed visible and ultraviolet spectra attributed to Ni/sub 2/.

  17. Lead-Chalcogenides Under Pressure: Ab-Initio Study

    NASA Astrophysics Data System (ADS)

    Gupta, Dinesh C.; Hamid, Idris

    ab-initio calculations using fully relativistic pseudo-potential have been performed to investigate the high pressure phase transition, elastic and electronic properties of lead-chalcogenides including the less known lead polonium. The calculated ground state parameters, for the rock-salt structure show good agreement with the experimental data. The enthalpy calculations show that these materials undergo a first-order phase transition from rock-salt to CsCl structure at 19.4, 15.5, 11.5 and 7.3 GPa for PbS, PbSe, PbTe and PbPo, respectively. Present calculations successfully predicted the location of the band gap at L-point of Brillouin zone as well as the value of the band gap in every case at ambient pressure. It is observed that unlike other lead-chalcogenides, PbPo is semi-metal at ambient pressure. The pressure variation of the energy gap indicates that these materials metalized under high pressures. For this purpose, the electronic structure of these materials has also been computed in parent as well as in high pressure phase.

  18. Amide N-oxides: an ab initio molecular orbital study

    NASA Astrophysics Data System (ADS)

    Greenberg, Arthur; DuBois, Thomas D.

    2001-06-01

    There are no known examples of amide N-oxides. The present study employs ab initio molecular orbital calculations at the 6-3G ∗ level to explore potential target molecules in this class. Bridgehead bicyclic lactams appear to be attractive targets for oxidation to form the corresponding N-oxides because they have reduced (or zero) amide resonance energy. The amide N-oxide linkage is predicted to have a ca. 9-10 kcal/mol rotational barrier due to eclipsing of nonbonded oxygen atoms in the transition state. The linkage has a nearly flat conformational ( ΦON-CO) profile in the range 120-240° and this suggests that a very sterically hindered acyclic amide N-oxide may be a practical synthetic target. The oxidation of strained amides is calculated to be highly exothermic if dimethyldioxirane is employed. This reagent is predicted to react appreciably exothermically with normal, stable amides such as N, N-dimethylacetamide, thus offering the potential for generating and studying such relatively unstable amide N-oxides at low temperatures.

  19. FTIR, Raman spectra and ab initio calculations of 2-mercaptobenzothiazole.

    PubMed

    Rai, Amareshwar K; Singh, Rachana; Singh, K N; Singh, V B

    2006-02-01

    FTIR and Raman spectra of a rubber vulcanization accelerator, 2-mercaptobenzothiazole (MBT), were recorded in the solid phase. The harmonic vibrational wavenumbers, for both the toutomeric forms of MBT, as well as for its dimeric complex, have been calculated, using ab initio RHF and density functional B3LYP methods invoking different basis sets upto RHF/6-31G** and B3LYP/6-31G** and the results were compared with the experimental values. Conformational studies have been also carried out regarding its toutomeric monomer forms and its dimer form. With all the basis sets the thione form of MBT (II) is predicted to be more stable than thiol form (I) and dimeric conformation (III) is predicted to be more stable with monomeric conformations (I) and (II). Vibrational assignments have been made, and it has been found that the calculated normal mode frequencies of dimeric conformation (III) are required for the analysis of IR and Raman bands of the MBT. The predicted shift in NH- stretching vibration towards the lower wave number side with the B3LYP/6-31G** calculations for the most stable dimer form (III), is in better agreement with experimental results. The intermolecular sulfur-nitrogen distance in N-H...S hydrogen bond was found to be 3.35 angstroms from these calculations, is also in agreement to the experimental value. PMID:16098806

  20. Electronic states of Zn2 - Ab initio calculations of a prototype for Hg2

    NASA Technical Reports Server (NTRS)

    Hay, P. J.; Dunning, T. H., Jr.; Raffenetti, R. C.

    1976-01-01

    The electronic states of Zn2 are investigated by ab initio polarization configuration-interaction calculations. Molecular states dissociating to Zn(1S) + Zn(1S, 3P, 1P) and Zn(3P) + Zn(3P) are treated. Important effects from states arising from Zn(+)(25) + Zn(-)(2P) are found in the potential-energy curves and electronic-transition moments. A model calculation for Hg2 based on the Zn2 curves and including spin-orbit coupling leads to a new interpretation of the emission bands in Hg vapor.

  1. Fully ab initio finite-size corrections for charged-defect supercell calculations.

    PubMed

    Freysoldt, Christoph; Neugebauer, Jörg; Van de Walle, Chris G

    2009-01-01

    In ab initio theory, defects are routinely modeled by supercells with periodic boundary conditions. Unfortunately, the supercell approximation introduces artificial interactions between charged defects. Despite numerous attempts, a general scheme to correct for these is not yet available. We propose a new and computationally efficient method that overcomes limitations of previous schemes and is based on a rigorous analysis of electrostatics in dielectric media. Its reliability and rapid convergence with respect to cell size is demonstrated for charged vacancies in diamond and GaAs. PMID:19257218

  2. Communication: GAIMS—Generalized Ab Initio Multiple Spawning for both internal conversion and intersystem crossing processes

    NASA Astrophysics Data System (ADS)

    Curchod, Basile F. E.; Rauer, Clemens; Marquetand, Philipp; González, Leticia; Martínez, Todd J.

    2016-03-01

    Full multiple spawning is a formally exact method to describe the excited-state dynamics of molecular systems beyond the Born-Oppenheimer approximation. However, it has been limited until now to the description of radiationless transitions taking place between electronic states with the same spin multiplicity. This Communication presents a generalization of the full and ab initio multiple spawning methods to both internal conversion (mediated by nonadiabatic coupling terms) and intersystem crossing events (triggered by spin-orbit coupling matrix elements) based on a spin-diabatic representation. The results of two numerical applications, a model system and the deactivation of thioformaldehyde, validate the presented formalism and its implementation.

  3. Charge carrier motion in disordered conjugated polymers: a multiscale ab-initio study

    SciTech Connect

    Vukmirovic, Nenad; Wang, Lin-Wang

    2009-11-10

    We developed an ab-initio multiscale method for simulation of carrier transport in large disordered systems, based on direct calculation of electronic states and electron-phonon coupling constants. It enabled us to obtain the never seen before rich microscopic details of carrier motion in conjugated polymers, which led us to question several assumptions of phenomenological models, widely used in such systems. The macroscopic mobility of disordered poly(3- hexylthiophene) (P3HT) polymer, extracted from our simulation, is in agreement with experimental results from the literature.

  4. Enhancing mechanical toughness of aluminum surfaces by nano-boron implantation: An ab initio study

    NASA Astrophysics Data System (ADS)

    Zhu, Zhen; Kwon, Dae-Gyeon; Kwon, Young-Kyun; Tománek, David

    2015-01-01

    Searching for ways to enhance surface hardness of aluminum, we study the equilibrium structure, stability, elastic properties and formation dynamics of a boron-enriched surface using ab initio density functional calculations. We used molecular dynamics simulations to model the implantation of energetic boron nanoparticles in Al and identify structural arrangements that optimize the formation of strong covalent Bsbnd Al bonds. Nano-indentation simulations based on constrained optimization suggest that presence of boron nanostructures in the subsurface region enhances significantly the mechanical hardness of aluminum surfaces.

  5. Ab Initio Simulations of Hydrogen in Crystalline and Amorphous Metal Membranes

    NASA Astrophysics Data System (ADS)

    Huhn, William; Widom, Mike

    2011-03-01

    Solid metallic membranes are used to separate hydrogen from other gases for clean energy applications. In order to create cheaper, more effective membranes for hydrogen separation, it is desirable to model hydrogen transport through the membrane. Amorphous metal membranes in particular have potential for this type of application due to low expense and high theoretical hydrogen capacity. We computationally model hydrogen absorption and transport through materials in order to find materials that can be used to construct effective membranes for hydrogen capture. In this talk, we will obtain hydrogen binding sites and diffusion barriers in order to model the hydrogen diffusion through various nickel-based amorphous alloys and compare them to associated crystalline structures as well as elemental palladium, which is favored for this application despite its high expense. Ab initio methods (specifically the Vienna Ab Initio Simulation Package, VASP) are used to develop the hydrogen binding energy spectrum, from which thermodynamic models can be constructed. Kinetic Monte Carlo methods are used to model the hydrogen transport through the bulk, from which we can obtain the permeability.

  6. Relevance of 4f-3d exchange to finite-temperature magnetism of rare-earth permanent magnets: An ab-initio-based spin model approach for NdFe12N

    NASA Astrophysics Data System (ADS)

    Matsumoto, Munehisa; Akai, Hisazumi; Harashima, Yosuke; Doi, Shotaro; Miyake, Takashi

    2016-06-01

    A classical spin model derived ab initio for rare-earth-based permanent magnet compounds is presented. Our target compound, NdFe12N, is a material that goes beyond today's champion magnet compound Nd2Fe14B in its intrinsic magnetic properties with a simpler crystal structure. Calculated temperature dependence of the magnetization and the anisotropy field agrees with the latest experimental results in the leading order. Having put the realistic observables under our numerical control, we propose that engineering 5d-electron-mediated indirect exchange coupling between 4f-electrons in Nd and 3d-electrons from Fe would most critically help enhance the material's utility over the operation-temperature range.

  7. On the use of speciation techniques and ab initio modelling to understand tetravalent actinide behavior in a biological medium: An(IV)DTPA case.

    PubMed

    Aupiais, J; Bonin, L; Den Auwer, C; Moisy, P; Siberchicot, B; Topin, S

    2016-03-01

    In the case of an accidental nuclear event, contamination of human bodies by actinide elements may occur. Such elements have the particularity to exhibit both radiological and chemical toxicities that may induce severe damages at several levels, depending on the biokinetics of the element. In order to eliminate the actinide elements before they are stored in target organs (liver, kidneys, or bone, depending on the element), sequestering agents must be quickly injected. However, to date, there is still no ideal sequestering agent, despite the recent interest in this topic due to contamination concerns. DTPA (diethylene triamine pentaacetic acid) is currently generating interest for the development of oral or alternative self-administrable forms. Although biokinetics data are mostly available, molecular scale characterization of actinide-DTPA complexes is still scarce. Nevertheless, strong interest is growing in the characterization of An(IV)DTPA(-) complexes at the molecular level because this opens the way for predicting the stability constants of unknown systems or even for developing new analytical strategies aimed at better and more selective decorporation. For this purpose, Extended X-ray Absorption Fine Structure (EXAFS) and Ab Initio Molecular Dynamics (AIMD) investigations were undertaken and compared with capillary electrophoresis (CE) used in a very unusual way. Indeed, it is commonly believed that CE is incapable of extracting structural information. In capillary electrophoresis, the electrophoretic mobility of an ion is a function of its charge and size. Despite very similar ratios, partial separations between An(IV)DTPA(-) species (An(IV) = Th, U, Np, Pu) were obtained. A linear relationship between the electrophoretic mobility and the actinide--oxygen distance calculated by AIMD was evidenced. As an example, the interpolated U-O distances in U(IV)DTPA(-) from CE-ICPMS experiments, EXAFS, AIMD, and the relationship between the stability constants and

  8. Ab initio quantum transport calculations using plane waves

    NASA Astrophysics Data System (ADS)

    Garcia-Lekue, A.; Vergniory, M. G.; Jiang, X. W.; Wang, L. W.

    2015-08-01

    We present an ab initio method to calculate elastic quantum transport at the nanoscale. The method is based on a combination of density functional theory using plane wave nonlocal pseudopotentials and the use of auxiliary periodic boundary conditions to obtain the scattering states. The method can be applied to any applied bias voltage and the charge density and potential profile can either be calculated self-consistently, or using an approximated self-consistent field (SCF) approach. Based on the scattering states one can straightforwardly calculate the transmission coefficients and the corresponding electronic current. The overall scheme allows us to obtain accurate and numerically stable solutions for the elastic transport, with a computational time similar to that of a ground state calculation. This method is particularly suitable for calculations of tunneling currents through vacuum, that some of the nonequilibrium Greens function (NEGF) approaches based on atomic basis sets might have difficulty to deal with. Several examples are provided using this method from electron tunneling, to molecular electronics, to electronic devices: (i) On a Au nanojunction, the tunneling current dependence on the electrode-electrode distance is investigated. (ii) The tunneling through field emission resonances (FERs) is studied via an accurate description of the surface vacuum states. (iii) Based on quantum transport calculations, we have designed a molecular conformational switch, which can turn on and off a molecular junction by applying a perpendicular electric field. (iv) Finally, we have used the method to simulate tunnel field-effect transistors (TFETs) based on two-dimensional transition-metal dichalcogenides (TMDCs), where we have studied the performance and scaling limits of such nanodevices and proposed atomic doping to enhance the transistor performance.

  9. Internal dynamics in azetidine: A microwave and ab initio study

    NASA Astrophysics Data System (ADS)

    López, Juan C.; Blanco, Susana; Lesarri, Alberto; Alonso, José L.

    2001-02-01

    The internal dynamics of interconversion between equivalent conformations due to the coupling between ring puckering and NH inversion in azetidine has been investigated by rotational spectroscopy and ab initio computations. Analysis of the rotational spectra in the 8-220 GHz region has been completed for the ground state and first four excited states of the ring-puckering vibration. Rotational transitions exhibit a characteristic doubling originated by tunneling between equivalent conformations through a C2v barrier, which is related to symmetric (A1) and antisymmetric (B1) inversion states. Additionally, nuclear quadrupole hyperfine structure arising from the N nucleus could be resolved for low-J transitions. Accurate rotational and centrifugal distortion parameters together with the energy difference between inversion states derived from μc-type inversion transitions have been derived for each ring-puckering state using a two-state Hamiltonian. An effective monodimensional reduced potential function for the ring-puckering vibration V(X)=10.82(X4+14.29X-8.93X2-0.28X3) has been found consistent with the observed experimental variation of the rotational and centrifugal distortion constants with ring-puckering. This asymmetric single minimum potential function supports the existence of only one stable equatorial form. The barrier to interconversion between equivalent equatorial conformers, related to the C2v conformation of azetidine in which the ring atoms and the NH group are coplanar, has been estimated to range between 1900 and 2600 cm-1. The strong dependence of the dipole moment and quadrupole coupling constants with ring-puckering vibrational state evidence structural changes that occur along the ring-puckering coordinate.

  10. Ab initio calculations of the optical properties of crystalline and liquid InSb

    NASA Astrophysics Data System (ADS)

    Sano, Haruyuki; Mizutani, Goro

    2015-11-01

    Ab initio calculations of the electronic and optical properties of InSb were performed for both the crystalline and liquid states. Two sets of atomic structure models for liquid InSb at 900 K were obtained by ab initio molecular dynamics simulations. To reduce the effect of structural peculiarities in the liquid models, an averaging of the two sets of the calculated electronic and optical properties corresponding to the two liquid models was performed. The calculated results indicate that, owing to the phase transition from crystal to liquid, the density of states around the Fermi level increases. As a result, the energy band gap opening near the Fermi level disappears. Consequently, the optical properties change from semiconductor to metallic behavior. Namely, owing to the melting of InSb, the interband transition peaks disappear and a Drude-like dispersion is observed in the optical dielectric functions. The optical absorption at a photon energy of 3.06 eV, which is used in Blu-ray Disc systems, increases owing to the melting of InSb. This increase in optical absorption is proposed to result from the increased optical transitions below 2 eV.

  11. Ab initio calculations of the optical properties of crystalline and liquid InSb

    SciTech Connect

    Sano, Haruyuki; Mizutani, Goro

    2015-11-15

    Ab initio calculations of the electronic and optical properties of InSb were performed for both the crystalline and liquid states. Two sets of atomic structure models for liquid InSb at 900 K were obtained by ab initio molecular dynamics simulations. To reduce the effect of structural peculiarities in the liquid models, an averaging of the two sets of the calculated electronic and optical properties corresponding to the two liquid models was performed. The calculated results indicate that, owing to the phase transition from crystal to liquid, the density of states around the Fermi level increases. As a result, the energy band gap opening near the Fermi level disappears. Consequently, the optical properties change from semiconductor to metallic behavior. Namely, owing to the melting of InSb, the interband transition peaks disappear and a Drude-like dispersion is observed in the optical dielectric functions. The optical absorption at a photon energy of 3.06 eV, which is used in Blu-ray Disc systems, increases owing to the melting of InSb. This increase in optical absorption is proposed to result from the increased optical transitions below 2 eV.

  12. Ab initio prediction of the critical thickness of a precipitate.

    PubMed

    Sampath, S; Janisch, R

    2013-09-01

    Segregation and precipitation of second phases in metals and metallic alloys is an important phenomenon that has a strong influence on the mechanical properties of the material. Models exist that describe the growth of coherent, semi-coherent and incoherent precipitates. One important parameter of these models is the energy of the interface between matrix and precipitate. In this work we apply ab initio density functional theory calculations to obtain this parameter and to understand how it depends on chemical composition and mechanical strain at the interface.Our example is a metastable Mo-C phase, the body-centred tetragonal structure, which exists as a semi-coherent precipitate in body-centred cubic molybdenum. The interface of this precipitate is supposed to change from coherent to semi-coherent during the growth of the precipitate. We predict the critical thickness of the precipitate by calculating the different contributions to a semi-coherent interface energy by means of ab initio density functional theory calculations. The parameters in our model include the elastic strain energy stored in the precipitate, as well as a misfit dislocation energy that depends on the dislocation core width and the dislocation spacing. Our predicted critical thickness agrees well with experimental observations. PMID:23896820

  13. Experimental and ab initio infrared study of chi-, kappa- and alpha-aluminas formed from gibbsite

    SciTech Connect

    Favaro, L.; Boumaza, A.; Roy, P.; Ledion, J.; Sattonnay, G.; Brubach, J.B.; Huntz, A.M.; Tetot, R.

    2010-04-15

    chi-, kappa- and alpha-alumina phases formed by dehydration of micro-grained gibbsite between 773 and 1573 K are studied using infrared spectroscopy (IR). The structural transitions evidenced by X-ray diffraction (XRD) were interpreted by comparing IR measurements with ab initio simulations (except for the chi form whose complexity does not allow a reliable simulation). For each phase, IR spectrum presents specific bands corresponding to transverse optical (TO) modes of Al-O stretching and bending under 900 cm{sup -1}. The very complex chi phase, obtained at 773 K, provides a distinctive XRD pattern in contrast with the IR absorbance appearing as a broad structure extending between 200 and 900 cm{sup -1} resembling the equivalent spectra for gamma-alumina phase. kappa-alumina is forming at 1173 K and its rich IR spectrum is in good qualitative agreement with ab initio simulations. This complexity reflects the large number of atoms in the kappa-alumina unit cell and the wide range of internuclear distances as well as the various coordinances of both Al and O atoms. Ab initio simulations suggest that this form of transition alumina demonstrates a strong departure from the simple pattern observed for other transition alumina. At 1573 K, the stable alpha-ALPHAl{sub 2}OMICRON{sub 3} develops. Its IR spectra extends in a narrower energy range as compared to transition alumina and presents characteristics features similar to model alpha-ALPHAl{sub 2}OMICRON{sub 3}. Ab initio calculations show again a very good general agreement with the observed IR spectra for this phase. In addition, for both kappa- and alpha-ALPHAl{sub 2}OMICRON{sub 3}, extra modes, measured at high energy (above 790 cm{sup -1} for kappa and above 650 cm{sup -1} for alpha), can originate from either remnant chi-alumina or from surface modes. - Graphical abstract: Infrared spectra of the sequence Gibbsite ->chi->kappa->alpha-Al{sub 2}O{sub 3} obtained from 24 h calcinations of Gibbsite at 773 K, 1173 K

  14. Ground state analytical ab initio intermolecular potential for the Cl{sub 2}-water system

    SciTech Connect

    Hormain, Laureline; Monnerville, Maurice Toubin, Céline; Duflot, Denis; Pouilly, Brigitte; Briquez, Stéphane; Bernal-Uruchurtu, Margarita I.; Hernández-Lamoneda, Ramón

    2015-04-14

    The chlorine/water interface is of crucial importance in the context of atmospheric chemistry. Modeling the structure and dynamics at this interface requires an accurate description of the interaction potential energy surfaces. We propose here an analytical intermolecular potential that reproduces the interaction between the Cl{sub 2} molecule and a water molecule. Our functional form is fitted to a set of high level ab initio data using the coupled-cluster single double (triple)/aug-cc-p-VTZ level of electronic structure theory for the Cl{sub 2} − H{sub 2}O complex. The potential fitted to reproduce the three minima structures of 1:1 complex is validated by the comparison of ab initio results of Cl{sub 2} interacting with an increasing number of water molecules. Finally, the model potential is used to study the physisorption of Cl{sub 2} on a perfectly ordered hexagonal ice slab. The calculated adsorption energy, in the range 0.27 eV, shows a good agreement with previous experimental results.

  15. Operator evolution for ab initio electric dipole transitions of 4He

    DOE PAGESBeta

    Schuster, Micah D.; Quaglioni, Sofia; Johnson, Calvin W.; Jurgenson, Eric D.; Navartil, Petr

    2015-07-24

    A goal of nuclear theory is to make quantitative predictions of low-energy nuclear observables starting from accurate microscopic internucleon forces. A major element of such an effort is applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence of ab initio calculations as a function of the model space size. The consistent simultaneous transformation of external operators, however, has been overlooked in applications of the theory, particularly for nonscalar transitions. We study the evolution of the electric dipole operator in the framework of the similarity renormalization group method and apply the renormalized matrix elements to the calculationmore » of the 4He total photoabsorption cross section and electric dipole polarizability. All observables are calculated within the ab initio no-core shell model. Furthermore, we find that, although seemingly small, the effects of evolved operators on the photoabsorption cross section are comparable in magnitude to the correction produced by including the chiral three-nucleon force and cannot be neglected.« less

  16. Operator evolution for ab initio electric dipole transitions of 4 He

    NASA Astrophysics Data System (ADS)

    Schuster, Micah; Quaglioni, Sofia; Johnson, Calvin; Jurgenson, Eric; Navratil, Petr

    2015-04-01

    A goal of nuclear theory is to make quantitative predictions of low-energy nuclear observables starting from accurate microscopicinternucleon forces. Modern effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence of ab initio calculations as a function of the model space size, is a major element of such an effort. The consistent simultaneous transformation of external operators, however, has been overlooked in applications of the theory, particularly for non-scalar transitions. We study the evolution of the electric dipole operator in the framework of the similarity-renormalization group method and apply the renormalized matrix elements to the calculation of the 4 He total photo absorption cross section and electric dipole polarizability. All observables are calculated within the ab initio no-core shell model. We find that, although seemingly small, the effects of induced operators on the photo absorption cross section are comparable in magnitude to the correction produced by including the three-nucleon force and cannot be neglected. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  17. Three-cluster dynamics within an ab initio framework

    SciTech Connect

    Quaglioni, Sofia; Romero-Redondo, Carolina; Navratil, Petr

    2013-09-26

    In this study, we introduce a fully antisymmetrized treatment of three-cluster dynamics within the ab initio framework of the no-core shell model/resonating-group method. Energy-independent nonlocal interactions among the three nuclear fragments are obtained from realistic nucleon-nucleon interactions and consistent ab initio many-body wave functions of the clusters. The three-cluster Schrödinger equation is solved with bound-state boundary conditions by means of the hyperspherical-harmonic method on a Lagrange mesh. We discuss the formalism in detail and give algebraic expressions for systems of two single nucleons plus a nucleus. Using a soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we apply the method to a 4He+n+n description of 6He and compare the results to experiment and to a six-body diagonalization of the Hamiltonian performed within the harmonic-oscillator expansions of the no-core shell model. Differences between the two calculations provide a measure of core (4He) polarization effects.

  18. Ab initio many-body calculations of nucleon scattering on ^16O

    NASA Astrophysics Data System (ADS)

    Navratil, Petr; Quaglioni, Sofia; Roth, Robert

    2008-10-01

    We develop a new ab initio many-body approachootnotetextS. Quaglioni and P. Navratil, arXiv:0804.1560. capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group methodootnotetextY. C. Tang et al., Phys. Rep. 47, 167 (1978); K. Langanke and H. Friedrich, Advances in Nuclear Physics, Plenum, New York, 1987. with the ab initio no-core shell model (NCSM).ootnotetextP. Navratil, J. P. Vary, and B. R. Barrett, Phys. Rev. Lett. 84, 5728 (2000); Phys. Rev. C 62, 054311 (2000). In this way, we complement a microscopic-cluster technique with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters, while preserving Pauli principle and translational symmetry. We will present results for low-energy nucleon scattering on ^16O and for A=17 bound states obtained using realistic nucleon-nucleon potentials. The ^16O wave functions are calculated within the importance-truncated NCSMootnotetextR. Roth and P. Navratil, Phys. Rev. Lett. 99, 092501 (2007). that allows the use of model spaces up to 18φ and ultimately enables to reach convergence of phase-shifts and other observables. Prepared by LLNL under Contract DE-AC52-07NA27344. Support from the U.S. DOE/SC/NP (Work Proposal No. SCW0498), and from the U. S. Department of Energy Grant DE-FC02-07ER41457 is acknowledged.

  19. Comparison between Gaussian-type orbitals and plane wave ab initio density functional theory modeling of layer silicates: Talc [Mg3Si4O10(OH)2] as model system

    NASA Astrophysics Data System (ADS)

    Ulian, Gianfranco; Tosoni, Sergio; Valdrè, Giovanni

    2013-11-01

    The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, and phonon properties of a model layer silicate, talc [Mg3Si4O10(OH)2], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO/B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum.

  20. Comparison between Gaussian-type orbitals and plane wave ab initio density functional theory modeling of layer silicates: talc [Mg3Si4O10(OH)2] as model system.

    PubMed

    Ulian, Gianfranco; Tosoni, Sergio; Valdrè, Giovanni

    2013-11-28

    The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, and phonon properties of a model layer silicate, talc [Mg3Si4O10(OH)2], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO∕B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum. PMID:24289338

  1. Comparison between Gaussian-type orbitals and plane wave ab initio density functional theory modeling of layer silicates: Talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}] as model system

    SciTech Connect

    Ulian, Gianfranco; Valdrè, Giovanni; Tosoni, Sergio

    2013-11-28

    The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, and phonon properties of a model layer silicate, talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO/B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum.

  2. An ab Initio Benchmark and DFT Validation Study on Gold(I)-Catalyzed Hydroamination of Alkynes.

    PubMed

    Ciancaleoni, Gianluca; Rampino, Sergio; Zuccaccia, Daniele; Tarantelli, Francesco; Belanzoni, Paola; Belpassi, Leonardo

    2014-03-11

    High level ab initio calculations have been carried out on an archetypal gold(I)-catalyzed reaction: hydroamination of ethyne. We studied up to 12 structures of possible gold(I)-coordinated species modeling different intermediates potentially present in a catalytic cycle for the addition of a protic nucleophile to an alkyne. The benchmark is used to evaluate the performances of some popular density functionals for describing geometries and relative energies of stationary points along the reaction profile. Most functionals (including hybrid or meta-hybrid) give accurate structures but large nonsystematic errors (4-12 kcal/mol) along the reaction energy profile. The double hybrid functional B2PLYP outperforms all considered functionals and compares very nicely with our reference ab initio benchmark energies. Moreover, we present an assessment of the accuracy of commonly used approaches to include relativistic effects, such as relativistic effective potentials and a scalar ZORA Hamiltonian, by a comparison with the results obtained using a relativistic all-electron four-component Dirac-Kohn-Sham method. The contribution of nonscalar relativistic effects in gold(I)-catalyzed reactions, as we investigated here, is expected to be on the order of 1 kcal/mol. PMID:26580180

  3. Ab initio quantum chemistry in parallel-portable tools and applications

    SciTech Connect

    Harrison, R.J.; Shepard, R. ); Kendall, R.A. )

    1991-01-01

    In common with many of the computational sciences, ab initio chemistry faces computational constraints to which a partial solution is offered by the prospect of highly parallel computers. Ab initio codes are large and complex (O(10{sup 5}) lines of FORTRAN), representing a significant investment of communal effort. The often conflicting requirements of portability and efficiency have been successfully resolved on vector computers by reliance on matrix oriented kernels. This proves inadequate even upon closely-coupled shared-memory parallel machines. We examine the algorithms employed during a typical sequence of calculations. Then we investigate how efficient portable parallel implementations may be derived, including the complex multi-reference singles and doubles configuration interaction algorithm. A portable toolkit, modeled after the Intel iPSC and the ANL-ACRF PARMACS, is developed, using shared memory and TCP/IP sockets. The toolkit is used as an initial platform for programs portable between LANS, Crays and true distributed-memory MIMD machines. Timings are presented. 53 refs., 4 tabs.

  4. Can an ab initio three-body virial equation describe the mercury gas phase?

    PubMed

    Wiebke, J; Wormit, M; Hellmann, R; Pahl, E; Schwerdtfeger, P

    2014-03-27

    We report a sixth-order ab initio virial equation of state (EOS) for mercury. The virial coefficients were determined in the temperature range from 500 to 7750 K using a three-body approximation to the N-body interaction potential. The underlying two-body and three-body potentials were fitted to highly accurate Coupled-Cluster interaction energies of Hg2 (Pahl, E.; Figgen, D.; Thierfelder, C.; Peterson, K. A.; Calvo, F.; Schwerdtfeger, P. J. Chem. Phys. 2010, 132, 114301-1) and equilateral-triangular configurations of Hg3. We find the virial coefficients of order four and higher to be negative and to have large absolute values over the entire temperature range considered. The validity of our three-body, sixth-order EOS seems to be limited to small densities of about 1.5 g cm(-3) and somewhat higher densities at higher temperatures. Termwise analysis and comparison to experimental gas-phase data suggest a small convergence radius of the virial EOS itself as well as a failure of the three-body interaction model (i.e., poor convergence of the many-body expansion for mercury). We conjecture that the nth-order term of the virial EOS is to be evaluated from the full n-body interaction potential for a quantitative picture. Consequently, an ab initio three-body virial equation cannot describe the mercury gas phase. PMID:24547987

  5. 4He+n+n continuum within an ab initio framework

    DOE PAGESBeta

    Romero-Redondo, Carolina; Quaglioni, Sofia; Navratil, Petr; Hupin, Guillaume

    2014-07-16

    In this study, the low-lying continuum spectrum of the 6He nucleus is investigated for the first time within an ab initio framework that encompasses the 4He+n+n three-cluster dynamics characterizing its lowest decay channel. This is achieved through an extension of the no-core shell model combined with the resonating-group method, in which energy-independent nonlocal interactions among three nuclear fragments can be calculated microscopically, starting from realistic nucleon-nucleon interactions and consistent ab initio many-body wave functions of the clusters. The three-cluster Schrödinger equation is solved with three-body scattering boundary conditions by means of the hyperspherical-harmonics method on a Lagrange mesh. Using amore » soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we find the known Jπ = 2+ resonance as well as a result consistent with a new low-lying second 2+ resonance recently observed at GANIL at ~2.6 MeV above the He6 ground state. We also find resonances in the 2–, 1+, and 0– channels, while no low-lying resonances are present in the 0+ and 1– channels.« less

  6. Ab initio many-body calculations of light nuclei neutron and proton scattering

    NASA Astrophysics Data System (ADS)

    Quaglioni, Sofia

    2008-10-01

    One of the greatest challenges of nuclear physics today is the development of a quantitative microscopic theory of low-energy reactions on light nuclei. At the same time, technical progress on the theoretical front is urgent to match the major experimental advances in the study of exotic nuclei at the radioactive beam facilities. We build a new ab initio many-body approachootnotetextS. Quaglioni and P. Navratil, arXiv:0804.1560. capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group methodootnotetextY. C. Tang et al., Phys. Rep. 47, 167 (1978); K. Langanke and H. Friedrich, Advances in Nuclear Physics, chapter 4., Plenum, New York, 1987. with the ab initio no-core shell model.ootnotetextP. Navratil, J. P. Vary, and B. R. Barrett, Phys. Rev. Lett. 84, 5728 (2000); Phys. Rev. C 62, 054311 (2000).. In this way, we complement a microscopic-cluster technique with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters, while preserving Pauli principle and translational symmetry. I will present results for neutron and proton scattering on light nuclei, including n- and p-^4He phase shifts, and low-lying states of one-neutron halo p-shell nuclei, obtained using realistic nucleon-nucleon potentials. In particular, I will address the parity inversion of the ^11Be ground state.

  7. Ab initio study of the structure and dynamics of bulk liquid Fe

    NASA Astrophysics Data System (ADS)

    Marqués, M.; González, L. E.; González, D. J.

    2015-10-01

    Several static and dynamic properties of bulk liquid Fe at a thermodynamic state near its triple point have been evaluated by ab initio molecular dynamics simulations. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak in the structure factor which underlines a substantial local icosahedral short-range order in the liquid. The dynamical structure reveals propagating density fluctuations, with an associated dispersion relation which closely follows the experimental data. The dynamic structure factors S (q ,ω ) show a good agreement with their experimental counterparts which have been recently measured by an inelastic x-ray scattering experiment. The dynamical processes behind the S (q ,ω ) have been analyzed by using a model with two decay channels (a fast and a slow) associated with the relaxations of the collective excitations. The recent finding of transverselike excitation modes in the IXS data is analyzed by using the present ab initio simulation results. Several transport coefficients have been evaluated and the results are compared with the available experimental data.

  8. Emergent properties of nuclei from ab initio coupled-cluster calculations

    NASA Astrophysics Data System (ADS)

    Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; Papenbrock, T.

    2016-06-01

    Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. This endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. This paper reviews some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO{}{{sat}} is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon–nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. The coupling to the continuum impacts the energies of the {J}π =1/{2}-,3/{2}-,7/{2}-,3/{2}+ states in {}{17,23,25}O, and—contrary to naive shell-model expectations—the level ordering of the {J}π =3/{2}+,5/{2}+,9/{2}+ states in {}{53,55,61}Ca. ).

  9. Structure and Raman spectra in cryolitic melts: simulations with an ab initio interaction potential.

    PubMed

    Cikit, Serpil; Akdeniz, Zehra; Madden, Paul A

    2014-01-30

    The Raman spectra of cryolitic melts have been calculated from molecular dynamics computer simulations using a polarizable ionic potential obtained by force-fitting to ab initio electronic structure calculations. Simulations which made use of this ab initio derived polarizable interaction potential reproduced the structure and dynamical properties of crystalline cryolite, Na3AlF6, rather well. The transferability of the potential model from solid state to the molten state is tested by comparing results for the Raman spectra of melts of various compositions with those previously obtained with empirically developed potentials and with experimental data. The shapes of the spectra and their evolution with composition in the mixtures conform quite well to those seen experimentally, and we discuss the relationship between the bands seen in the spectra and the vibrational modes of the AlFn((3–n)) coordination complexes which are found in the NaF/AlF3 mixtures. The simulations thus enable a link between the structure of the melt as derived through Raman spectroscopy and through diffraction experiments. We report results for quantities which relate to the degree of cross-linking between these coordination complexes and the diffusive properties of ions. PMID:24432905

  10. An Ab Initio Approach Towards Engineering Fischer-Tropsch Surface Chemistry

    SciTech Connect

    Matthew Neurock

    2005-06-13

    As petroleum prices continue to rise and the United States seeks to reduce its dependency on foreign oil, there is a renewed interest in the research and development of more efficient and alternative energy sources, such as fuel cells. One approach is to utilize processes that can produce long-chain hydrocarbons from other sources. One such reaction is Fischer-Tropsch synthesis. Fischer-Tropsch synthesis is a process by which syngas (CO and H{sub 2}) is converted to higher molecular weight hydrocarbons. The reaction involves a complex set of bond-breaking and bond-making reactions, such as CO and H{sub 2} activation, hydrocarbon hydrogenation reactions, and hydrocarbon coupling reactions. This report details our initial construction of an ab initio based kinetic Monte Carlo code that can be used to begin to simulate Fischer-Tropsch synthesis over model Co(0001) surfaces. The code is based on a stochastic kinetic formalism that allows us to explicitly track the transformation of all reactants, intermediates and products. The intrinsic kinetics for the simulations were derived from the ab initio results that we reported in previous year summaries.

  11. Mixed ab initio quantum mechanics/molecular mechanics methods using frozen orbitals with applications to peptides and proteins

    NASA Astrophysics Data System (ADS)

    Philipp, Dean Michael

    Methodology is discussed for mixed ab initio quantum mechanics/molecular mechanics modeling of systems where the quantum mechanics (QM) and molecular mechanics (MM) regions are within the same molecule. The ab initio QM calculations are at the restricted Hartree-Fock level using the pseudospectral method of the Jaguar program while the MM part is treated with the OPLS force fields implemented in the IMPACT program. The interface between the QM and MM regions, in particular, is elaborated upon, as it is dealt with by ``breaking'' bonds at the boundaries and using Boys-localized orbitals found from model molecules in place of the bonds. These orbitals are kept frozen during QM calculations. The mixed modeling presented here can be used for single point energy calculations and geometry optimizations. Results from tests of the method to find relative conformational energies and geometries of alanine tetrapeptides are presented along with comparisons to pure QM and pure MM calculations.

  12. Efficient ab initio free energy calculations by classically assisted trajectory sampling

    NASA Astrophysics Data System (ADS)

    Wilson, Hugh F.

    2015-12-01

    A method for efficiently performing ab initio free energy calculations based on coupling constant thermodynamic integration is demonstrated. By the use of Boltzmann-weighted sums over states generated from a classical ensemble, the free energy difference between the classical and ab initio ensembles is readily available without the need for time-consuming integration over molecular dynamics trajectories. Convergence and errors in this scheme are discussed and characterised in terms of a quantity representing the degree of misfit between the classical and ab initio systems. Smaller but still substantial efficiency gains over molecular dynamics are also demonstrated for the calculation of average properties such as pressure and total energy for systems in equilibrium.

  13. An Efficient Time-Stepping Scheme for Ab Initio Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Tsuchida, Eiji

    2016-08-01

    In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. We also propose several extensions of the algorithm required for use in ab initio molecular dynamics. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2× performance gain over the standard Verlet method for a given accuracy. We also show how to generate a canonical ensemble within this approach.

  14. On the role of hydrogen filled vacancies on the embrittlement of zirconium: An ab initio investigation

    NASA Astrophysics Data System (ADS)

    Olsson, Pär A. T.; Kese, Kwadwo; Alvarez Holston, Anna-Maria

    2015-12-01

    In this work we report the results of an ab initio study of the influence of hydrogen filled vacancies on the mechanical properties of zirconium. The modelling shows that hydrogen filled vacancies contribute to a lowering of the surface energy and an increase in the unstable stacking fault energy, which implies a reduction in ductility. The increase in unstable stacking fault energy suggests that the defects promote a change in the dislocation glide mechanism from prismatic to basal slip. To investigate the cleavage energetics, we model the decohesion process. For describing the interplanar interaction we adopt an extended version of Rose's universal binding energy relation, which is found to reproduce the behaviour accurately. The results of the modelling imply that the work of fracture and peak stress decrease as a result of the presence of hydrogen filled vacancies.

  15. Experimental and ab initio investigations of microscopic properties of laser-shocked Ge-doped ablator

    NASA Astrophysics Data System (ADS)

    Huser, G.; Recoules, V.; Ozaki, N.; Sano, T.; Sakawa, Y.; Salin, G.; Albertazzi, B.; Miyanishi, K.; Kodama, R.

    2015-12-01

    Plastic materials (CH) doped with mid-Z elements are used as ablators in inertial confinement fusion (ICF) capsules and in their surrogates. Hugoniot equation of state (EOS) and electronic properties of CH doped with germanium (at 2.5% and 13% dopant fractions) are investigated experimentally up to 7 Mbar using velocity and reflectivity measurements of shock fronts on the GEKKO laser at Osaka University. Reflectivity and temperature measurements were updated using a quartz standard. Shocked quartz reflectivity was measured at 532 and 1064 nm. Theoretical investigation of shock pressure and reflectivity was then carried out by ab initio simulations using the quantum molecular dynamics (QMD) code abinit and compared with tabulated average atom EOS models. We find that shock states calculated by QMD are in better agreement with experimental data than EOS models because of a more accurate description of ionic structure. We finally discuss electronic properties by comparing reflectivity data to a semiconductor gap closure model and to QMD simulations.

  16. Ab Initio Protein Structure Assembly Using Continuous Structure Fragments and Optimized Knowledge-based Force Field

    PubMed Central

    Xu, Dong; Zhang, Yang

    2012-01-01

    Ab initio protein folding is one of the major unsolved problems in computational biology due to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1–20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 non-homologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score (TM-score) >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in 1/3 cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction (CASP9) experiment, QUARK server outperformed the second and third best servers by 18% and 47% based on the cumulative Z-score of global distance test-total (GDT-TS) scores in the free modeling (FM) category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress towards the solution of the most important problem in the field. PMID:22411565

  17. A-dependence of the Spectra of the F Isotopes from ab initio Calculations

    NASA Astrophysics Data System (ADS)

    Barrett, Bruce R.; Dikmen, Erdal; Maris, Pieter; Vary, James P.; Shirokov, Andrey M.

    2016-03-01

    Using a succession of Okubo-Lee-Suzuki transformations within the No Core Shell Model (NCSM) formalism, we derive an ab initio, non-perturbative procedure for calculating the input for standard shell-model (SSM) calculations within one major shell. We have used this approach for calculating the spectra of the F isotopes from A=18 to A=25, so as to study the A-dependence of the results. In particular, we are interested in seeing if the theoretical input is weak enough, so that a single set of two-body effective interactions can be used for all of the F isotopes investigated. We will present results from SSM calculations based on input obtained with the JISP16 nucleon-nucleon interaction in an initial 4 ℏΩ NCSM basis space. This work supported in part by TUBITAK-BIDEB, the US DOE, the US NSF, NERSC, and the Russian Ministry of Education and Science.

  18. Ab initio determination of the instability growth rate of warm dense beryllium-deuterium interface

    NASA Astrophysics Data System (ADS)

    Wang, Cong; Li, Zi; Li, DaFang; Zhang, Ping

    2015-10-01

    Accurate knowledge about the interfacial unstable growth is of great importance in inertial confinement fusion. During implosions, the deuterium-tritium capsule is driven by laser beams or X-rays to access the strongly coupled and partially degenerated warm dense matter regime. At this stage, the effects of dissipative processes, such as diffusion and viscosity, have significant impact on the instability growth rates. Here, we present ab initio molecular dynamics simulations to determine the equations of state and the transport coefficients. Several models are used to estimate the reduction in the growth rate dispersion curves of Rayleigh-Taylor and Richtmyer-Meshkov instabilities with considering the presence of these dissipative effects. We show that these instability growth rates are effectively reduced when considering diffusion. The findings provide significant insights into the microscopic mechanism of the instability growth at the ablator-fuel interface and will refine the models used in the laser-driven hydrodynamic instability experiments.

  19. Ab initio determination of the instability growth rate of warm dense beryllium-deuterium interface

    SciTech Connect

    Wang, Cong; Zhang, Ping; Li, Zi; Li, DaFang

    2015-10-15

    Accurate knowledge about the interfacial unstable growth is of great importance in inertial confinement fusion. During implosions, the deuterium-tritium capsule is driven by laser beams or X-rays to access the strongly coupled and partially degenerated warm dense matter regime. At this stage, the effects of dissipative processes, such as diffusion and viscosity, have significant impact on the instability growth rates. Here, we present ab initio molecular dynamics simulations to determine the equations of state and the transport coefficients. Several models are used to estimate the reduction in the growth rate dispersion curves of Rayleigh-Taylor and Richtmyer-Meshkov instabilities with considering the presence of these dissipative effects. We show that these instability growth rates are effectively reduced when considering diffusion. The findings provide significant insights into the microscopic mechanism of the instability growth at the ablator-fuel interface and will refine the models used in the laser-driven hydrodynamic instability experiments.

  20. Ab initio determination of the proton affinities of small neutral and anionic molecules

    NASA Technical Reports Server (NTRS)

    DeFrees, D. J.; McLean, A. D.

    1986-01-01

    The proton affinity of a molecule in the gas phase is a fundamental measure of its basicity and is the factor controlling the course of many ion-molecule reactions. In this article, ab initio molecular orbital theory at the MP4/6-311 ++ G(3df, 3pd) level of theory is demonstrated to predict proton affinities (PA's) for small neutral and anionic bases to within 2 kcal mol-1. Furthermore, the errors are random, indicating that there are likely no systematic errors in either the experimental or theoretical PA's. Also, this level of theory is used to calibrate less sophisticated theoretical models which are suitable for larger molecules; the MP4/6-311 ++ G(2d, 2p) and MP2/6-311 ++ G(d, p) theoretical models should be particularly useful. A procedure for predicting the vibrational frequencies for anion is proposed and applied to CH3-, NH2-, OH-, and CN-.

  1. Dissipation of alignment in CO2 gas: A comparison between ab initio predictions and experiments

    NASA Astrophysics Data System (ADS)

    Hartmann, J.-M.; Boulet, C.; Vieillard, T.; Chaussard, F.; Billard, F.; Faucher, O.; Lavorel, B.

    2013-07-01

    We present comparisons between measurements and ab initio calculations of the dissipation of the nonadiabatic laser-induced alignment in pure CO2 and CO2-He gas mixtures. The experiments were made for pressures between 2 and 20 bars at 295 K by using short non-resonant linearly polarized laser pulses for alignment and probe. The calculations are carried, free of any adjusted parameter, using refined intermolecular potentials and a requantized Classical Molecular Dynamics Simulations approach presented previously but not yet confronted to experiments. The results demonstrate that the model accurately reproduces the decays with time of both the transient revivals and "permanent" component of the alignment. The significant differences observed between the behaviors resulting from CO2-CO2 and CO2-He collisions are also well predicted by the model.

  2. An ab initio approach to the anisotropic perpendicular diffusion of galactic cosmic rays

    NASA Astrophysics Data System (ADS)

    Engelbrecht, Nicholas; Richardson, John; Burger, Renier

    2016-07-01

    The assumption that cosmic-ray diffusion perpendicular to the background magnetic field is anisotropic has been made in many numerical modulation studies. This was done in order to reproduce spacecraft observations of, for example, lower than expected latitude gradients of galactic protons. This assumption is usually justified in terms of observations of non-axisymmetric turbulent magnetic fluctuations, but is often implemented in a completely ad hoc manner. This study implements anisotropic perpendicular diffusion coefficients in an ab initio cosmic ray modulation model in a self-consistent manner, employing perpendicular mean free path expressions derived for the case where transverse magnetic fluctuations are non-axisymmetric. Voyager magnetic field observations are analysed to ascertain the nature of this non-axisymmetry, and modulation model solutions for various assumptions as to the spatial dependence of this non-axisymmetry, also taking into account the Voyager observations, are presented.

  3. Ab Initio Dynamics of AN Electron Interacting with a Lattice Defect

    NASA Astrophysics Data System (ADS)

    Ivanov, Vsevolod; Bernardi, Marco

    We study the scattering process of a charge carrier with a defect in a range of bulk and 2D materials. The scattering potential is obtained using density functional theory, the carrier is represented by a gaussian wavepacket, and the dynamics is carried out with a split-operator technique. Our parallel code can model the electron-defect scattering processes in real space and time, with an electron wavepacket of realistic size (100 - 1000 unit cells) and an accuracy typical of ab initio calculations. We apply our approach to model a carrier scattering with a vacancy in silicon and an impurity in monolayer MoS2, obtaining angular dependent scattering cross sections and resonant states.

  4. STM and ab initio study of holmium nanowires on a Ge(111) surface

    NASA Astrophysics Data System (ADS)

    Eames, C.; Bonet, C.; Probert, M. I. J.; Tear, S. P.; Perkins, E. W.

    2006-11-01

    A nanorod structure has been observed on the Ho/Ge(111) surface using scanning tunneling microscopy (STM). The rods do not require patterning of the surface or defects such as step edges in order to grow as is the case for nanorods on Si(111). At low holmium coverage the nanorods exist as isolated nanostructures while at high coverage they form a periodic 5×1 structure. We propose a structural model for the 5×1 unit cell and show using an ab initio calculation that the STM profile of our model structure compares favorably to that obtained experimentally for both filled and empty states sampling. The calculated local density of states shows that the nanorod is metallic in character.

  5. Electron-scattering form factors for 6Li in the ab initio symmetry-guided framework

    NASA Astrophysics Data System (ADS)

    Dytrych, T.; Hayes, A. C.; Launey, K. D.; Draayer, J. P.; Maris, P.; Vary, J. P.; Langr, D.; Oberhuber, T.

    2015-02-01

    We present an ab initio symmetry-adapted no-core shell-model description for 6Li. We study the structure of the ground state of 6Li and the impact of the symmetry-guided space selection on the charge density components for this state in momentum space, including the effect of higher shells. We accomplish this by investigating the electron scattering charge form factor for momentum transfers up to q ˜4 fm-1 . We demonstrate that this symmetry-adapted framework can achieve significantly reduced dimensions for equivalent large shell-model spaces while retaining the accuracy of the form factor for any momentum transfer. These new results confirm the previous outcomes for selected spectroscopy observables in light nuclei, such as binding energies, excitation energies, electromagnetic moments, E 2 and M 1 reduced transition probabilities, as well as point-nucleon matter rms radii.

  6. reaxFF Reactive Force Field for Disulfide Mechanochemistry, Fitted to Multireference ab Initio Data.

    PubMed

    Müller, Julian; Hartke, Bernd

    2016-08-01

    Mechanochemistry, in particular in the form of single-molecule atomic force microscopy experiments, is difficult to model theoretically, for two reasons: Covalent bond breaking is not captured accurately by single-determinant, single-reference quantum chemistry methods, and experimental times of milliseconds or longer are hard to simulate with any approach. Reactive force fields have the potential to alleviate both problems, as demonstrated in this work: Using nondeterministic global parameter optimization by evolutionary algorithms, we have fitted a reaxFF force field to high-level multireference ab initio data for disulfides. The resulting force field can be used to reliably model large, multifunctional mechanochemistry units with disulfide bonds as designed breaking points. Explorative calculations show that a significant part of the time scale gap between AFM experiments and dynamical simulations can be bridged with this approach. PMID:27415976

  7. H 3SiOH and F 3SiOH as models for isolated hydroxyl groups of amorphous silica: an ab initio study of the adducts with dihydrogen and carbon monoxide

    NASA Astrophysics Data System (ADS)

    Senchenya, I. N.; Civalleri, B.; Ugliengo, P.; Garrone, E.

    1998-09-01

    Ab initio calculations have been performed at both the self-consistent field (SCF) and the second-order Møller-Plesset (MP2) levels of theory, using both double-zeta plus polarisation functions basis sets and augmented correlation-consistent valence-polarised (aug-cc-pVDZ and aug-cc-pVTZ) ones, to compare the acidic and vibration features and the geometry of H 3SiOH, the model usually adopted for the isolated hydroxyls of silica, with those of its fluorinated analogue, F 3SiOH. Their complexes with H 2 and CO have also been studied. Passing from the MP2/DZP level of computation to MP2/aug-cc-pVDZ and MP2/aug-cc-pVTZ levels results in a considerable improvement of calculated data for H 3SiOH and its complexes when compared with experimental data. H 3SiOH is, however, less acidic than isolated hyroxyls of silica. In contrast, the use of F 3SiOH as a model yields an overestimation of the acidic properties; e.g., the stretching O-H mode frequency shifts caused by hydrogen-bond interaction with the base molecules. The combined use of both models may provide guidelines for prediction of the adducts of the isolated hydroxyl of silica with small molecules.

  8. Unified ab initio approach to bound and unbound states: No-core shell model with continuum and its application to 7He

    SciTech Connect

    Baroni, Simone; Navratil, Petr; Quaglioni, Sofia

    2013-03-26

    In this study, we introduce a unified approach to nuclear bound and continuum states based on the coupling of the no-core shell model (NCSM), a bound-state technique, with the no-core shell model/resonating group method (NCSM/RGM), a nuclear scattering technique. This new ab initio method, no-core shell model with continuum (NCSMC), leads to convergence properties superior to either NCSM or NCSM/RGM while providing a balanced approach to different classes of states. In the NCSMC, the ansatz for the many-nucleon wave function includes (i) a square-integrable A-nucleon component expanded in a complete harmonic oscillator basis and (ii) a binary-cluster component with asymptotic boundary conditions that can properly describe weakly bound states, resonances, and scattering. The Schrödinger equation is transformed into a system of coupled-channel integral-differential equations that we solve using a modified microscopic R-matrix formalism within a Lagrange mesh basis. We demonstrate the usefulness of the approach by investigating the unbound 7He nucleus.

  9. Electronic aspects of the hydride transfer mechanism. Ab initio analytical gradient studies of the cyclopropenyl-cation/lithium hydride model reactant system

    NASA Astrophysics Data System (ADS)

    Tapia, O.; Andres, J.; Aullo, J. M.; Bränden, C.-I.

    1985-11-01

    The electronic mechanisms of a model hydride transfer reaction are theoretically studied with ab inito RHF and UHF SCF MO procedures at the 4-31G basis set level and analytical gradient methods. The model system describes the reduction of cyclopropenyl cation to cyclopropene by the oxidation of lithium hydride to lithium cation. The molecular fragments corresponding to the asymptotic reactive channels characterizing the stepwise mechanisms currently discussed in the literature have been characterized. The binding energy between the fragments is estimated within a simple electrostatic approximate scheme. The results show that a hydride-ion mechanism is a likely pathway for this particular system. The system is thereafter thoroughly studied from the supermolecule approach. Reaction paths for the ground and first triplet electronic states have been calculated. The hypersurface is explored from a geometrical disposition of the reactants that mimics the one found in several dehydrogenases (perpendicular configuration). A hydride ion is found to be the particle transferred on the unconstrained as well as the constrained reaction pathways in the ground electronic state. In the triplet state (perpendicular configuration) the mechanism is stepwise: electron transfer followed by a hydrogen atom transfer. It has been noticed that the perpendicular geometrical disposition of the reactants plays an important role by polarizing the susceptible cyclopropene C-H bond in the sense of increasing the electronic density at the hydrogen nucleus. This provides a clue to rationalize several dehydrogenase's active site structure and mechanism. The reactant molecular complex found in the inverted potential energy curves, namely the LiH---Cp+ association has an electronic distribution which can be described as a hydride ion cementing two electron deficient centers corresponding to the cyclopropenyl and the lithium cations. Direct CI calculations confirm the overall picture obtained above.

  10. Ab initio investigation of barium-scandium-oxygen coatings on tungsten for electron emitting cathodes

    NASA Astrophysics Data System (ADS)

    Vlahos, Vasilios; Booske, John H.; Morgan, Dane

    2010-02-01

    Microwave, x-ray, and radio-frequency radiation sources require a cathode emitting electrons into vacuum. Thermionic B-type dispenser cathodes consist of BaxOz coatings on tungsten (W), where the surface coatings lower the W work function and enhance electron emission. The new and promising class of scandate cathodes modifies the B-type surface through inclusion of Sc, and their superior emissive properties are also believed to stem from the formation of a low work function surface alloy. In order to better understand these cathode systems, density-functional theory (DFT)-based ab initio modeling is used to explore the stability and work function of BaxScyOz on W(001) monolayer-type surface structures. It is demonstrated how surface depolarization effects can be calculated easily using ab initio calculations and fitted to an analytic depolarization equation. This approach enables the rapid extraction of the complete depolarization curve (work function versus coverage relation) from relatively few DFT calculations, useful for understanding and characterizing the emitting properties of novel cathode materials. It is generally believed that the B-type cathode has some concentration of Ba-O dimers on the W surface, although their structure is not known. Calculations suggest that tilted Ba-O dimers are the stable dimer surface configuration and can explain the observed work function reduction corresponding to various dimer coverages. Tilted Ba-O dimers represent a new surface coating structure not previously proposed for the activated B-type cathode. The thermodynamically stable phase of Ba and O on the W surface was identified to be the Ba0.25O configuration, possessing a significantly lower Φ value than any of the Ba-O dimer configurations investigated. The identification of a more stable Ba0.25O phase implies that if Ba-O dimers cover the surface of emitting B-type cathodes, then a nonequilibrium steady state must dominate the emitting surface. The identification of

  11. Ab initio Ti-Zr-Ni phase diagram predicts stability of icosahedral TiZrNi quasicrystals

    NASA Astrophysics Data System (ADS)

    Hennig, R. G.; Carlsson, A. E.; Kelton, K. F.; Henley, C. L.

    2005-04-01

    The ab initio phase diagram determines the energetic stability of the icosahedral TiZrNi quasicrystal. The complete ab initio zero-temperature ternary phase diagram is constructed from the calculated energies of the elemental, binary and ternary Ti-Zr-Ni phases. For this, the icosahedral i -TiZrNi quasicrystal is approximated by periodic structures of up to 123 atoms/unit cell, based on a decorated-tiling model [R. G. Hennig, K. F. Kelton, A. E. Carlsson, and C. L. Henley, Phys. Rev. B 67, 134202 (2003)]. The approximant structures containing the 45-atom Bergman cluster are nearly degenerate in energy, and are all energetically stable against the competing phases. It is concluded that i -TiZrNi is a ground-state quasicrystal, as it is experimentally the low-temperature phase for its composition.

  12. Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

    PubMed Central

    Hu, Hao; Yang, Weitao

    2013-01-01

    Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes. PMID:24146439

  13. Ab initio and density functional theoretical design and screening of model crown ether based ligand (host) for extraction of lithium metal ion (guest): effect of donor and electronic induction.

    PubMed

    Boda, Anil; Ali, Sk Musharaf; Rao, Hanmanth; Ghosh, Sandip K

    2012-08-01

    The structures, energetic and thermodynamic parameters of model crown ethers with different donor, cavity and electron donating/ withdrawing functional group have been determined with ab initio MP2 and density functional theory in gas and solvent phase. The calculated values of binding energy/ enthalpy for lithium ion complexation are marginally higher for hard donor based aza and oxa crown compared to soft donor based thia and phospha crown. The calculated values of binding enthalpy for lithium metal ion with 12C4 at MP2 level of theory is in good agreement with the available experimental result. The binding energy is altered due to the inductive effect imparted by the electron donating/ withdrawing group in crown ether, which is well correlated with the values of electron transfer. The role of entropy for extraction of hydrated lithium metal ion by different donor and functional group based ligand has been demonstrated. The HOMO-LUMO gap is decreased and dipole moment of the ligand is increased from gas phase to organic phase because of the dielectric constant of the solvent. The gas phase binding energy is reduced in solvent phase as the solvent molecules weaken the metal-ligand binding. The theoretical values of extraction energy for LiCl salt from aqueous solution in different organic solvent is validated by the experimental trend. The study presented here should contribute to the design of model host ligand and screening of solvent for metal ion recognition and thus can contribute in planning the experiments. PMID:22318713

  14. Ab Initio and Analytic Intermolecular Potentials for Ar–CH3OH

    SciTech Connect

    Tasic, Uros; Alexeev, Yuri; Vayner, Grigoriy; Crawford, T Daniel; Windus, Theresa L.; Hase, William L.

    2006-09-20

    Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar–CH₃y6tOH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH₃OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar–C, Ar–O, Ar–H(C), and Ar–H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol¯¹, and adding an additional r¯¹n term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar–CH₃OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. The structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol¯¹ with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol¯¹ smaller than this value. The well depths of the other two minima are within 0.16 kcal mol¯¹ of the global minimum. The analytic Ar–CH₃OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol¯1 of the ab initio values. Combining this Ar–CH₃OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.

  15. i-PI: A Python interface for ab initio path integral molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

    2014-03-01

    Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic

  16. Predictive Nuclear Many-Body Theory with Ab Initio Methods: A Brief Survey and A Look Ahead

    NASA Astrophysics Data System (ADS)

    Hergert, Heiko

    2015-10-01

    The reach of ab initio many-body techniques has increased tremendously in recent years, owing to new developments in many-body theory as well as advances in their numerical implementation. Coupled Cluster, Self-Consistent Green's Function, and In-Medium Similarity Renormalization Group (IM-SRG) calculations are routinely performed for isotopes in the A ~ 100 region. Moreover, these techniques have been extended to tackle open-shell nuclei, either directly or through the auxiliary step of deriving valence-space interactions for use with existing Shell Model technology. One of the most powerful aspects of ab initio methods is their capability to provide results for energies and other observables with systematic uncertainties. Together with new accurate nuclear forces (and operators) derived from Chiral Effective Field Theory, they provide a consistent framework--and a road map--for a predictive description of nuclei. This will have a critical impact on the search for the limits of nuclear existence, tests of fundamental symmetries (e.g., the search for neutrinoless double beta decay), our understanding of quenching and effective charges in phenomenological Shell Model calculations etc. Using the Multi-Reference IM-SRG as a representative example, I will survey the current capabilities of ab initio methods with an emphasis on uncertainty quantification, highlight successes in the description of ground-state properties and spectra, and preview upcoming developments like the construction of consistent transition operators.

  17. Effect of electric field on the mechanical properties of bilayer boron nitride with AB stacking order: An ab initio study

    NASA Astrophysics Data System (ADS)

    Ansari, R.; Faghihnasiri, M.; Malakpour, S.; Sahmani, S.

    2015-07-01

    In the current investigation, ab initio calculations are performed to explore the influence of electric field on the mechanical properties of bilayer boron nitride with AB stacking order (AB-2LBN). To accomplish this, density functional theory (DFT) within the framework of generalized gradient approximation (GGA) is implemented. It is demonstrated that the electric field has significant effects on Young's modulus and Poisson's ratio of AB-2LBN when its magnitude is small. With increasing the magnitude of electric field, these effects diminish so that the mechanical properties with and without considering the electric field become approximately identical. Also, it is shown that the equilibrium strain energy decreases linearly by increasing the magnitude of applied electric field.

  18. Kinetics of reaction with water vapor and ab initio study of titanium beryllide

    NASA Astrophysics Data System (ADS)

    Munakata, K.; Kawamura, H.; Uchida, M.

    2007-08-01

    Beryllium is one of the candidate materials of the neutron multiplier in the tritium-breeding blanket. Titanium beryllides such as Be 12Ti are known to have advantages over beryllium from the perspectives of higher melting point, lower chemical reactivity, lower swelling and so forth. The reaction of titanium beryllides with water vapor was investigated. The sample disks of Be 12Ti were exposed to an argon gas with 10 000 ppm of water vapor, and the sample temperature was raised to 1000 °C. However, the chaotic breakaway reaction was not observed. The kinetics of oxidation on the surface of Be 12Ti by water vapor was investigated using a model differential equation, and the reaction constant was quantified. Furthermore, to know the electron state in Be 12Ti, ab initio calculations of quantum chemistry were performed using CRYSTAL 98. The structure optimization of Be 12Ti crystal was attempted, and an electron density map was generated.

  19. A room temperature CO2 line list with ab initio computed intensities

    NASA Astrophysics Data System (ADS)

    Zak, Emil; Tennyson, Jonathan; Polyansky, Oleg L.; Lodi, Lorenzo; Zobov, Nikolay F.; Tashkun, Sergey A.; Perevalov, Valery I.

    2016-07-01

    Atmospheric carbon dioxide concentrations are being closely monitored by remote sensing experiments which rely on knowing line intensities with an uncertainty of 0.5% or better. We report a theoretical study providing rotation-vibration line intensities substantially within the required accuracy based on the use of a highly accurate ab initio dipole moment surface (DMS). The theoretical model developed is used to compute CO2 intensities with uncertainty estimates informed by cross comparing line lists calculated using pairs of potential energy surfaces (PES) and DMS's of similar high quality. This yields lines sensitivities which are utilized in reliability analysis of our results. The final outcome is compared to recent accurate measurements as well as the HITRAN2012 database. Transition frequencies are obtained from effective Hamiltonian calculations to produce a comprehensive line list covering all 12C16O2 transitions below 8000cm-1 and stronger than 10-30 cm/molecule at T = 296 K.

  20. Ab Initio determination of Cu 3d orbital energies in layered copper oxides

    PubMed Central

    Hozoi, Liviu; Siurakshina, Liudmila; Fulde, Peter; van den Brink, Jeroen

    2011-01-01

    It has long been argued that the minimal model to describe the low-energy physics of the high Tc superconducting cuprates must include copper states of other symmetries besides the canonical one, in particular the orbital. Experimental and theoretical estimates of the energy splitting of these states vary widely. With a novel ab initio quantum chemical computational scheme we determine these energies for a range of copper-oxides and -oxychlorides, determine trends with the apical Cu–ligand distances and find excellent agreement with recent Resonant Inelastic X-ray Scattering measurements, available for La2CuO4, Sr2CuO2Cl2, and CaCuO2. PMID:22355584

  1. Ab initio determination of effective electron-phonon coupling factor in copper

    NASA Astrophysics Data System (ADS)

    Ji, Pengfei; Zhang, Yuwen

    2016-04-01

    The electron temperature Te dependent electron density of states g (ε), Fermi-Dirac distribution f (ε), and electron-phonon spectral function α2 F (Ω) are computed as prerequisites before achieving effective electron-phonon coupling factor Ge-ph. The obtained Ge-ph is implemented into a molecular dynamics (MD) and two-temperature model (TTM) coupled simulation of femtosecond laser heating. By monitoring temperature evolutions of electron and lattice subsystems, the result utilizing Ge-ph from ab initio calculation shows a faster decrease of Te and increase of Tl than those using Ge-ph from phenomenological treatment. The approach of calculating Ge-ph and its implementation into MD-TTM simulation is applicable to other metals.

  2. Ab initio based investigation of interstitial interactions and Snoek relaxation in Nb-O

    NASA Astrophysics Data System (ADS)

    Dmitriev, V. V.; Blanter, M. S.; Ruban, A. V.; Johansson, B.

    2012-02-01

    Chemical and strain-induced effective pair interactions of interstitial oxygen atoms in bcc Nb have been determined in supercell first-principles calculations using Vienna ab initio simulation package (VASP). The strain-induced interactions are in reasonable agreement with those obtained earlier within a phenomenological microscopic Krivoglaz-Kanzaki-Khachaturyan model (KKKM). At the same time, the chemical interactions, which have been considered to be small in earlier theoretical considerations, turned out to be dominating at the first several coordination shells. The obtained interactions have been used in calculations of the concentration- and temperature-dependence of the internal friction Snoek peak. The theoretical results are found to be in good agreement with the existing experimental data.

  3. Communication: GAIMS—generalized ab initio multiple spawning for both internal conversion and intersystem crossing processes

    DOE PAGESBeta

    Curchod, Basile F. E.; Rauer, Clemens; Marquetand, Philipp; Gonzalez, Leticia; Martinez, Todd J.

    2016-03-11

    Full Multiple Spawning is a formally exact method to describe the excited-state dynamics of molecular systems beyond the Born-Oppenheimer approximation. However, it has been limited until now to the description of radiationless transitions taking place between electronic states with the same spin multiplicity. This Communication presents a generalization of the full and ab initio Multiple Spawning methods to both internal conversion (mediated by nonadiabatic coupling terms) and intersystem crossing events (triggered by spin-orbit coupling matrix elements) based on a spin-diabatic representation. Lastly, the results of two numerical applications, a model system and the deactivation of thioformaldehyde, validate the presented formalismmore » and its implementation.« less

  4. Ab Initio Calculation of Structure and Thermodynamic Properties of Zintl Aluminide SrAl2

    NASA Astrophysics Data System (ADS)

    Fu, Zhi-Jian; Jia, Li-Jun; Xia, Ji-Hong; Tang, Ke; Li, Zhao-Hong; Sun, Xiao-Wei; Chen, Qi-Feng

    2015-12-01

    The structural and thermodynamic properties of the orthorhombic and cubic structure SrAl2 at pressure and temperature are investigated by using the ab initio plane-wave pseudopotential density functional theory methodwithin the generalised gradient approximation (GGA). The calculated lattice parameters are in agreement with the available experimental data and other theoretical results. The phase transition predicted takes place at 0.5 GPa from the orthorhombic to the cubic structure at zero temperature. The thermodynamic properties of the zinc-blende structure SrAl2 are calculated by the quasi-harmonic Debye model. The pressure-volume relationship and the variations inthe thermal expansion α are obtained systematically in the pressure and temperature ranges of 0-5 GPa and 0-500 K, respectively.

  5. Ab initio calculations of vacancy interactions with solute atoms in bcc Fe

    NASA Astrophysics Data System (ADS)

    Vincent, E.; Becquart, C. S.; Domain, C.

    2005-01-01

    Solute Cu plays a major role in the embrittlement of reactor pressure vessel (RPV) steels under radiation. In RPV steels and dilute FeCu alloys, the tomographic atom probe has revealed the formation of Cu atmospheres under neutron flux. More recently the role of other solutes such as Ni, Mn and Si which are also within the atmospheres has been put forward. It is thus very important to characterise the interactions of these solutes with radiation-induced point defects in order to understand the elementary mechanisms behind the formation of these atmospheres. We have investigated by ab initio calculations based on the density functional theory the interactions of point defects in dilute FeX alloys (X = Cu, Mn, Ni or Si). The structure of X-vacancy complexes has been determined, as well as their binding energies. Their relative stability is discussed and compared to experimental results obtained with model alloys.

  6. The C4H radical and the diffuse interstellar bands. An ab initio study

    NASA Technical Reports Server (NTRS)

    Kolbuszewski, Marcin

    1994-01-01

    An ab initio study of the low-lying electronic states of C4H has been presented where the species studied has a chi(2)sigma(+) ground state and two low lying pi states. Based on the vertical and adiabatic excitation energies between those states it is suggested that the 4428 A diffuse interstellar band is not carried by C4H. The application of the particle in a box model shows strong coincidences between the strong DIB's and predicted wavelengths of pi-pi transitions in C(2n)H series. Based on those coincidences, it is suggested the C(2n)H species as good candidates for carriers of diffuse interstellar bands.

  7. Quantum transition state dynamics of the cyclooctatetraene unimolecular reaction on ab initio potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Tokizaki, Chihiro; Yoshida, Takahiko; Takayanagi, Toshiyuki

    2016-05-01

    The cyclooctatetraene (COT) anion has a stable D4h structure that is similar to the transition state configurations of the neutral C-C bond-alternation (D4h ↔ D8h ↔ D4h) and ring-inversion (D2d ↔ D4h ↔ D2d) unimolecular reactions. The previously measured photodetachment spectrum of COT- revealed the reaction dynamics in the vicinity of the two transition states on the neutral potential energy surface. In this work, the photodetachment spectrum is calculated quantum mechanically on ab initio-level potential energy surfaces within a three degree-of-freedom reduced-dimensionality model. Very good agreement has been obtained between theory and experiment, providing reliable interpretations for the experimental spectrum. A detailed picture of the reactive molecular dynamics of the COT unimolecular reaction in the transition state region is also discussed.

  8. Ab initio cross sections for low-energy inelastic H+Na collisions

    NASA Astrophysics Data System (ADS)

    Belyaev, A. K.; Grosser, J.; Hahne, J.; Menzel, T.

    1999-09-01

    We report ab initio results for the integral cross section of the process H+Na(3s)-->H+Na(3p) for collision energies from the threshold (2.1 eV) to 600 eV. We achieve a reasonable agreement with the experimental data, which are available for energies above 10 eV. The main contributions to the cross section come from a rotational coupling mechanism in the NaH triplet molecular system and from a curve-crossing mechanism in the singlet system. At very low energy (2.1-2.4 eV), the process is governed by a centrifugal barrier in the exit channel leading to orbital resonances. The Landau-Zener model provides a reasonable qualitative description of the radial coupling mechanism at high energies, but fails below 10 eV.

  9. Iodine-polyphenylacetylene charge-transfer complex: an ab initio quantum-chemical assessment

    NASA Astrophysics Data System (ADS)

    Andreocci, M. V.; Bossa, M.; Furlani, A.; Polzonetti, G.; Russo, M. V.

    1991-07-01

    The ab initio MO-LCAO-HF method has been used to calculate the electronic structure of the iodine-polyphenylacetylene charge-transfer complex (PPAI 2). Two models have been considered for the PPA molecule: a simple one containing two phenyl groups and a more realistic one containing six phenyl groups. The calculations give automatically the charge separation between I 5 and the polymer, and show that the total charge separation can be less than 1 e at short distances. The computed charges at the energy minimum have been succesfully introduced into the curve fitting of the I-3d 5/2 core level spectrum of PPAI 2 films, giving good agreement between experimental and theoretical results.

  10. Quantum fluctuations and isotope effects in ab initio descriptions of water

    SciTech Connect

    Wang, Lu; Markland, Thomas E.; Ceriotti, Michele

    2014-09-14

    Isotope substitution is extensively used to investigate the microscopic behavior of hydrogen bonded systems such as liquid water. The changes in structure and stability of these systems upon isotope substitution arise entirely from the quantum mechanical nature of the nuclei. Here, we provide a fully ab initio determination of the isotope exchange free energy and fractionation ratio of hydrogen and deuterium in water treating exactly nuclear quantum effects and explicitly modeling the quantum nature of the electrons. This allows us to assess how quantum effects in water manifest as isotope effects, and unravel how the interplay between electronic exchange and correlation and nuclear quantum fluctuations determine the structure of the hydrogen bond in water.

  11. High-accuracy ab initio rotation-vibration transitions for water.

    PubMed

    Polyansky, Oleg L; Császár, Attila G; Shirin, Sergei V; Zobov, Nikolai F; Barletta, Paolo; Tennyson, Jonathan; Schwenke, David W; Knowles, Peter J

    2003-01-24

    The spectrum of water vapor is of fundamental importance for a variety of processes, including the absorption and retention of sunlight in Earth's atmosphere. Therefore, there has long been an urgent need for a robust and accurate predictive model for this spectrum. In our work on the high-resolution spectrum of water, we report first-principles calculations that approach experimental accuracy. To achieve this, we performed exceptionally large electronic structure calculations and considered a variety of effects, including quantum electrodynamics, which have routinely been neglected in studies of small many-electron molecules. The high accuracy of the resulting ab initio procedure is demonstrated for the main isotopomers of water. PMID:12543967

  12. Impact of oxygen on the 300-K isotherm of Laser Megajoule ablator using ab initio simulation

    NASA Astrophysics Data System (ADS)

    Colin-Lalu, P.; Recoules, V.; Salin, G.; Huser, G.

    2015-11-01

    The ablator material for inertial confinement fusion (ICF) capsules on the Laser Mégajoule is a glow-discharge polymer (GDP) plastic. Its equation of state (EOS) is of primary importance for the design of such capsules, since it has direct consequences on shock timing and is essential to mitigate hydrodynamic instabilities. Using ab initio molecular dynamics (AIMD), we have investigated the 300-K isotherm of amorphous CH1.37O0.08 plastic, whose structure is close to GDP plastic. The 300-K isotherm, which is often used as a cold curve within tabular EOS, is an important contribution of the EOS in the multimegabar pressure range. AIMD results are compared to analytic models within tabular EOS, pointing out large discrepancies. In addition, we show that the effect of oxygen decreases 300-K isotherm pressure by 10%-15%. The implication of these observations is the ability to improve ICF target performance, which is essential to achieve fusion ignition.

  13. Ab initio study of heterojunction discontinuities in the ZnO/Cu2O system

    NASA Astrophysics Data System (ADS)

    Zemzemi, M.; Alaya, S.; Ben Ayadi, Z.

    2014-06-01

    Solar cells based on transparent conductive oxides such as ZnO/Cu2O constitute a very advanced way to build high-performance cells. In this work, we are interested in the characterization of the interface through nanoscale modeling based on ab initio approaches (density functional theory, local density approximation, and pseudopotential). This work aims to build a supercell containing a heterojunction ZnO/Cu2O and study the structural properties and the discontinuity of the valence band (band offset) from a semiconducting to another phase. We build a zinc oxide in the wurtzite structure along [0001] on which we place the copper oxide in the hexagonal (CdI2-type) structure. We choose the method of Van de Walle and Martin to calculate the energy offset. This approach fits well the density functional theory. Our calculation of the band offset gives a value that corresponds to other experimental and theoretical values.

  14. Ab initio perspective on the Mollwo-Ivey relation for F centers in alkali halides

    NASA Astrophysics Data System (ADS)

    Tiwald, Paul; Karsai, Ferenc; Laskowski, Robert; Gräfe, Stefanie; Blaha, Peter; Burgdörfer, Joachim; Wirtz, Ludger

    2015-10-01

    We revisit the well-known Mollwo-Ivey relation that describes the "universal" dependence of the absorption energies of F-type color centers on the lattice constant a of alkali-halide crystals, Eabs∝a-n. We perform both state-of-the-art ab initio quantum chemistry and post-DFT calculations of F-center absorption spectra. By "tuning" independently the lattice constant and the atomic species we show that the scaling with the lattice constant alone (keeping the elements fixed) would yield n =2 in agreement with the "particle-in-the-box" model. Keeping the lattice constant fixed and changing the atomic species enables us to quantify the ion-size effects which are shown to be responsible for the exponent n ≈1.8 .

  15. Probing Defects and Correlations in the Hydrogen-Bond Network of ab Initio Water.

    PubMed

    Gasparotto, Piero; Hassanali, Ali A; Ceriotti, Michele

    2016-04-12

    The hydrogen-bond network of water is characterized by the presence of coordination defects relative to the ideal tetrahedral network of ice, whose fluctuations determine the static and time-dependent properties of the liquid. Because of topological constraints, such defects do not come alone but are highly correlated coming in a plethora of different pairs. Here we discuss in detail such correlations in the case of ab initio water models and show that they have interesting similarities to regular and defective solid phases of water. Although defect correlations involve deviations from idealized tetrahedrality, they can still be regarded as weaker hydrogen bonds that retain a high degree of directionality. We also investigate how the structure and population of coordination defects is affected by approximations to the interatomic potential, finding that, in most cases, the qualitative features of the hydrogen-bond network are remarkably robust. PMID:26881726

  16. HEAT: High accuracy extrapolated ab initio thermochemistry. III. Additional improvements and overview.

    SciTech Connect

    Harding, M. E.; Vazquez, J.; Ruscic, B.; Wilson, A. K.; Gauss, J.; Stanton, J. F.; Chemical Sciences and Engineering Division; Univ. t Mainz; The Univ. of Texas; Univ. of North Texas

    2008-01-01

    Effects of increased basis-set size as well as a correlated treatment of the diagonal Born-Oppenheimer approximation are studied within the context of the high-accuracy extrapolated ab initio thermochemistry (HEAT) theoretical model chemistry. It is found that the addition of these ostensible improvements does little to increase the overall accuracy of HEAT for the determination of molecular atomization energies. Fortuitous cancellation of high-level effects is shown to give the overall HEAT strategy an accuracy that is, in fact, higher than most of its individual components. In addition, the issue of core-valence electron correlation separation is explored; it is found that approximate additive treatments of the two effects have limitations that are significant in the realm of <1 kJ mol{sup -1} theoretical thermochemistry.

  17. Exploring the Photophysical Properties of Molecular Systems Using Excited State Accelerated ab Initio Molecular Dynamics

    PubMed Central

    2012-01-01

    In the present work, we employ excited state accelerated ab initio molecular dynamics (A-AIMD) to efficiently study the excited state energy landscape and photophysical topology of a variety of molecular systems. In particular, we focus on two important challenges for the modeling of excited electronic states: (i) the identification and characterization of conical intersections and crossing seams, in order to predict different and often competing radiationless decay mechanisms, and (ii) the description of the solvent effect on the absorption and emission spectra of chemical species in solution. In particular, using as examples the Schiff bases formaldimine and salicylidenaniline, we show that A-AIMD can be readily employed to explore the conformational space around crossing seams in molecular systems with very different photochemistry. Using acetone in water as an example, we demonstrate that the enhanced configurational space sampling may be used to accurately and efficiently describe both the prominent features and line-shapes of absorption and emission spectra. PMID:22904696

  18. The constrained space orbital variation analysis for periodic ab initio calculations

    SciTech Connect

    Cruz Hernandez, N.; Zicovich-Wilson, Claudio Marcelo; Fdez Sanz, Javier

    2006-05-21

    The constrained space orbital variation (CSOV) method for the analysis of the interaction energy has been implemented in the periodic ab initio CRYSTAL03 code. The method allows for the partition of the energy of two interacting chemical entities, represented in turn by periodic models, into contributions which account for electrostatic effects, mutual polarization and charge transfer. The implementation permits one to carry out the analysis both at the Hartree-Fock and density functional theory levels, where in the latter the most popular exchange-correlation functionals can be used. As an illustrating example, the analysis of the interaction between CO and the MgO (001) surface has been considered. As expected by the almost fully ionic character of the support, our periodic CSOV results, in general agree with those previously obtained using the embedded cluster approach, showing the reliability of the present implementation.

  19. Ab-initio study on crystal structure of α-RuCl3

    NASA Astrophysics Data System (ADS)

    Kee, Hae-Young; Kim, Heung-Sik

    α -RuCl3 was recently proposed as a candidate system for materialization of Kitaev model, but precise structural information of the compound has remained elusive. For the clarification of the full three-dimensional crystal structure of α-RuCl3, we performed ab-initio electronic structure calculations including effects of spin-orbit coupling (SOC) and electron correlations. We found that SOC prevents dimerization between Ru atoms, and keeps the system close to honeycomb lattice. The ground state crystal structure has monoclinic C 2 / m -type layer stacking, but trigonal P31 12 -and orthorhombic Cmc21 -type stacking orders are comparable to the C 2 / m structure in energy, so that stacking faults can be easily introduced. The electronic structure and the jeff=1/2 pseudospin exchange interactions and possible magnetic states in α-RuCl3 will be presented.

  20. An ab initio variationally computed room-temperature line list for (32)S(16)O3.

    PubMed

    Underwood, Daniel S; Tennyson, Jonathan; Yurchenko, Sergei N

    2013-07-01

    Ab initio potential energy and dipole moment surfaces are computed for sulfur trioxide (SO3) at the CCSD(T)-F12b level of theory with appropriate triple-zeta basis sets. The analytical representations of these surfaces are used, with a slight correction, to compute pure rotational and rotation-vibration spectra of (32)S(16)O3 using the variational nuclear motion program TROVE. The calculations considered transitions in the region 0-4000 cm(-1) with rotational states up to J = 85. The resulting line list of 174,674,257 transitions is appropriate for modelling room temperature (32)S(16)O3 spectra. Good agreement is found with the observed infrared absorption spectra and the calculations are used to place the measured relative intensities on an absolute scale. A list of 10,878 experimental transitions is provided in a form suitable for inclusion in standard atmospheric and planetary spectroscopic databases. PMID:23579443

  1. 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.

  2. Ab initio electron scattering cross-sections and transport in liquid xenon

    NASA Astrophysics Data System (ADS)

    Boyle, G. J.; McEachran, R. P.; Cocks, D. G.; Brunger, M. J.; Buckman, S. J.; Dujko, S.; White, R. D.

    2016-09-01

    Ab initio fully differential cross-sections for electron scattering in liquid xenon are developed from a solution of the Dirac–Fock scattering equations, using a recently developed framework (Boyle et al 2015 J. Chem. Phys. 142 154507) which considers multipole polarizabilities, a non-local treatment of exchange, and screening and coherent scattering effects. A multi-term solution of Boltzmann’s equation accounting for the full anisotropic nature of the differential cross-section is used to calculate transport properties of excess electrons in liquid xenon. The results were found to agree to within 25% of the measured mobilities and characteristic energies over the reduced field range of 10‑4–1 Td. The accuracies are comparable to those achieved in the gas phase. A simple model, informed by highly accurate gas-phase cross-sections, is presented to improve the liquid cross-sections, which was found to enhance the accuracy of the transport coefficient calculations.

  3. Electronic states of lithium passivated germanium nanowires: An ab-initio study

    SciTech Connect

    Trejo, A.; Carvajal, E.; Vázquez-Medina, R.; Cruz-Irisson, M.

    2014-05-15

    A study of the electronic and structural properties of germanium nanowires (GeNWs) was performed using the ab-initio Density Functional Theory within the generalized gradient approximation where electron-ion interactions are described by ultrasoft pseudopotentials. To study the effects of the lithium in the surface of the GeNWs we compare the electronic band structures of Hydrogen passivated GeNWs with those of partial and totally Li passivated GeNWs. The nanowires were constructed in the [001], [111] and [110] directions, using the supercell model to create different wire diameters. The results show that in the case of partial Li passivation there are localized orbitals near the valence band maximum, which would create a p-doped-kind of state. The total Li passivation created metallic states for all the wires.

  4. Equation of state and phase diagram of ammonia at high pressures from ab initio simulations.

    PubMed

    Bethkenhagen, Mandy; French, Martin; Redmer, Ronald

    2013-06-21

    We present an equation of state as well as a phase diagram of ammonia at high pressures and high temperatures derived from ab initio molecular dynamics simulations. The predicted phases of ammonia are characterized by analyzing diffusion coefficients and structural properties. Both the phase diagram and the subsequently computed Hugoniot curves are compared to experimental results. Furthermore, we discuss two methods that allow us to take into account nuclear quantum effects, which are of considerable importance in molecular fluids. Our data cover pressures up to 330 GPa and a temperature range from 500 K to 10,000 K. This regime is of great interest for interior models of the giant planets Uranus and Neptune, which contain, besides water and methane, significant amounts of ammonia. PMID:23802968

  5. Deuteron-induced nucleon transfer reactions within an ab initio framework: First application to p -shell nuclei

    NASA Astrophysics Data System (ADS)

    Raimondi, Francesco; Hupin, Guillaume; Navrátil, Petr; Quaglioni, Sofia

    2016-05-01

    Background: Low-energy transfer reactions in which a proton is stripped from a deuteron projectile and dropped into a target play a crucial role in the formation of nuclei in both primordial and stellar nucleosynthesis, as well as in the study of exotic nuclei using radioactive beam facilities and inverse kinematics. Ab initio approaches have been successfully applied to describe the 3H (d ,n )4He and 3He(d ,p )4He fusion processes. Purpose: An ab initio treatment of transfer reactions would also be desirable for heavier targets. In this work, we extend the ab initio description of (d ,p ) reactions to processes with light p -shell nuclei. As a first application, we study the elastic scattering of deuterium on 7Li and the 7Li(d ,p )8Li transfer reaction based on a two-body Hamiltonian. Methods: We use the no-core shell model to compute the wave functions of the nuclei involved in the reaction, and describe the dynamics between targets and projectiles with the help of microscopic-cluster states in the spirit of the resonating group method. Results: The shapes of the excitation functions for deuterons impinging on 7Li are qualitatively reproduced up to the deuteron breakup energy. The interplay between d -7Li and p -8Li particle-decay channels determines some features of the 9Be spectrum above the d +7Li threshold. Our prediction for the parity of the 17.298 MeV resonance is at odds with the experimental assignment. Conclusions: Deuteron stripping reactions with p -shell targets can now be computed ab initio, but calculations are very demanding. A quantitative description of the 7Li(d ,p )8Li reaction will require further work to include the effect of three-nucleon forces and additional decay channels and to improve the convergence rate of our calculations.

  6. Ab initio electronic structure study for TTF-TCNQ under uniaxial compression

    NASA Astrophysics Data System (ADS)

    Ishibashi, Shoji; Hashimoto, Tamotsu; Kohyama, Masanori; Terakura, Kiyoyuki

    2004-04-01

    We have investigated the electronic structure of TTF-TCNQ under uniaxial compression with ab initio plane-wave pseudopotential calculations within the local-density approximation and generalized gradient approximation. Depending on the compression direction, the constituent molecules are deformed in different ways. Along with these structural deformations, quasi-one-dimensional Fermi surfaces show dramatic changes in their shapes and sizes.

  7. Dispersion Interactions between Rare Gas Atoms: Testing the London Equation Using ab Initio Methods

    ERIC Educational Resources Information Center

    Halpern, Arthur M.

    2011-01-01

    A computational chemistry experiment is described in which students can use advanced ab initio quantum mechanical methods to test the ability of the London equation to account quantitatively for the attractive (dispersion) interactions between rare gas atoms. Using readily available electronic structure applications, students can calculate the…

  8. Ab Initio Studies of Chlorine Oxide and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of chlorine oxide and nitrogen oxide species will be demonstrated by presentation of some example studies. In particular the geometrical structures, vibrational spectra, and heats of formation Of ClNO2, CisClONO, and trans-ClONO are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the ab initio results are shown to fill in the gaps and to resolve the experimental controversy. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of ClONO2, HONO2, ClOOC17 ClOOH, and HOOH will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of the experimental studies.

  9. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms

    NASA Astrophysics Data System (ADS)

    Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R.

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

  10. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms.

    PubMed

    Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms. PMID:27394094

  11. Predicting materials for solar energy conversion: ab-initio spectroscopy of heterogeneous interfaces

    NASA Astrophysics Data System (ADS)

    Galli, Giulia

    We will discuss some progress in predicting materials for solar energy conversion using ab initio calculations, in particular we will focus on heterogeneous interfaces between photo-electrodes and water and between nanocomposites. We will also address the problem of building much needed tighter connections between computational and laboratory experiments.

  12. CVRQD ab initio ground-state adiabatic potential energy surfaces for the water molecule.

    PubMed

    Barletta, Paolo; Shirin, Sergei V; Zobov, Nikolai F; Polyansky, Oleg L; Tennyson, Jonathan; Valeev, Edward F; Császár, Attila G

    2006-11-28

    The high accuracy ab initio adiabatic potential energy surfaces (PESs) of the ground electronic state of the water molecule, determined originally by Polyansky et al. [Science 299, 539 (2003)] and called CVRQD, are extended and carefully characterized and analyzed. The CVRQD potential energy surfaces are obtained from extrapolation to the complete basis set of nearly full configuration interaction valence-only electronic structure computations, augmented by core, relativistic, quantum electrodynamics, and diagonal Born-Oppenheimer corrections. We also report ab initio calculations of several quantities characterizing the CVRQD PESs, including equilibrium and vibrationally averaged (0 K) structures, harmonic and anharmonic force fields, harmonic vibrational frequencies, vibrational fundamentals, and zero-point energies. They can be considered as the best ab initio estimates of these quantities available today. Results of first-principles computations on the rovibrational energy levels of several isotopologues of the water molecule are also presented, based on the CVRQD PESs and the use of variational nuclear motion calculations employing an exact kinetic energy operator given in orthogonal internal coordinates. The variational nuclear motion calculations also include a simplified treatment of nonadiabatic effects. This sophisticated procedure to compute rovibrational energy levels reproduces all the known rovibrational levels of the water isotopologues considered, H(2) (16)O, H(2) (17)O, H(2) (18)O, and D(2) (16)O, to better than 1 cm(-1) on average. Finally, prospects for further improvement of the ground-state adiabatic ab initio PESs of water are discussed. PMID:17144700

  13. Emergent properties of nuclei from ab initio coupled-cluster calculations

    DOE PAGESBeta

    Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; Papenbrock, T.

    2016-05-17

    Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. Our endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. We review some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLOmore » $${}_{{\\rm{sat}}}$$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon–nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. Finally, the coupling to the continuum impacts the energies of the $${J}^{\\pi }=1/{2}^{-},3/{2}^{-},7/{2}^{-},3/{2}^{+}$$ states in $${}^{\\mathrm{17,23,25}}$$O, and—contrary to naive shell-model expectations—the level ordering of the $${J}^{\\pi }=3/{2}^{+},5/{2}^{+},9/{2}^{+}$$ states in $${}^{\\mathrm{53,55,61}}$$Ca.« less

  14. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-01

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K+ ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K+ ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K+ ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K+ ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

  15. Coordination modes and bonding of sulfur oxides on transition metal surfaces: combined ab initio and BOC-MP results

    NASA Astrophysics Data System (ADS)

    Seller, Harrell; Shustorovich, Evgeny

    1996-02-01

    Binding energies for sulfur oxides, SO x, x = 1-3, have been determined for several coordination modes on silver, gold and palladium surfaces employing ab initio quantum chemical methods and the bond order conservation Morse potential (BOC-MP) method. SO 2 coordination was studied in the most detail. In general the agreement between the BOC-MP and ab initio binding energies is good for the (111) surfaces of silver and palladium with both methods predicting that, in the zero coverage limit, di-coordination via S,O and O,O will be more favorable energetically than mono-coordination via S. In the case of chemisorption on the Pd (110) surface the two methods agree well for the cases in which there are formulas for the BOC-MP binding energies. In going from the (111) surfaces to the (110) surfaces of silver and palladium the ab initio calculations predict that the preferred chemisorption site shifts from the bridge site to the hollow site. On the silver surfaces the net charge transferred to the adsorbate as judged from the Mulliken populations correlates roughly with the binding energy. No significant charge transfer was found on the palladium surfaces. Our SO 2 chemisorption calculations indicate that the work functions of the metal surfaces examined should increase upon mono-S adsorption, increase to a lesser extent upon di S,O adsorption and may even decrease upon di O,O adsorption. Ab initio calculations provide evidence of the existence of SO 2 surface dimers. The binding energy predicted by the BOC-MP model for SO 3 in the bridging site agrees well with the ab initio result for SO 3 di-coordinated in the long bridge of the Ag(110) surface. The methods yield similar predictions for the case of SO on silver. Our modeling provides a coherent picture consistent with many aspects of the experimental literature. We present some model predictions, particularly the di O,O coordination mode for SO 2, that require verification experimentally.

  16. Mechanism of alkane dehydrogenation catalyzed by acidic zeolites: Ab initio transition path sampling

    NASA Astrophysics Data System (ADS)

    Bučko, Tomáš; Benco, Lubomir; Dubay, Orest; Dellago, Christoph; Hafner, Jürgen

    2009-12-01

    The dehydrogenation of propane over acidic chabazite has been studied using ab initio density-functional simulations in combination with static transition-state searches and dynamic transition path sampling (TPS) methods at elevated temperatures. The acidic zeolite has been modeled both using a small cluster and a large periodic model consisting of two unit cells, the TPS simulations allow to account for the effect of temperature and entropy. In agreement with experimental observations we find propene as the dominant reaction product and that the barrier for the dehydrogenation of a methyl group is higher than that for a methylene group. However, whereas all studies based on small cluster models (including the present one) conclude that the reaction proceeds via the formation of an alkoxy intermediate, our TPS studies based on a large periodic model lead to the conclusion that propene formation occurs via the formation of various forms of propyl cations stabilized by entropy, while the formation of an alkoxy species is a relatively rare event. It was observed only in 15% of the reactive trajectories for methyl dehydrogenation and even in only 8% of the methylene dehydrogenation reactions. Our studies demonstrate the importance of entropic effects and the need to account for the structure and flexibility of the zeolitic framework by using large periodic models.

  17. Relating Ab Initio Mechanical Behavior of Intergranular Glassy Films in Γ-Si3N4 to Continuum Scales

    NASA Astrophysics Data System (ADS)

    Ouyang, L.; Chen, J.; Ching, W.; Misra, A.

    2006-05-01

    Nanometer thin intergranular glassy films (IGFs) form in polycrystalline ceramics during sintering at high temperatures. The structure and properties of these IGFs are significantly changed by doping with rare earth elements. We have performed highly accurate large-scale ab initio calculations of the mechanical properties of both undoped and Yittria doped (Y-IGF) model by theoretical uniaxial tensile experiments. Uniaxial strain was applied by incrementally stretching the super cell in one direction, while the other two dimensions were kept constant. At each strain, all atoms in the model were fully relaxed using Vienna Ab initio Simulation Package VASP. The relaxed model at a given strain serves as the starting position for the next increment of strain. This process is carried on until the total energy (TE) and stress data show that the "sample" is fully fractured. Interesting differences are seen between the stress-strain response of undoped and Y-doped models. For the undoped model, the stress-strain behavior indicates that the initial atomic structure of the IGF is such that there is negligible coupling between the x- and the y-z directions. However, once the behavior becomes non- linear the lateral stresses increase, indicating that the atomic structure evolves with loading [1]. To relate the ab initio calculations to the continuum scales we analyze the atomic-scale deformation field under this uniaxial loading [1]. The applied strain in the x-direction is mostly accommodated by the IGF part of the model and the crystalline part experiences almost negligible strain. As the overall strain on the sample is incrementally increased, the local strain field evolves such that locations proximal to the softer spots attract higher strains. As the load progresses, the strain concentration spots coalesce and eventually form persistent strain localization zone across the IGF. The deformation pattern obtained through ab initio calculations indicates that it is possible to

  18. Melting of sodium under high pressure. An ab-initio study

    SciTech Connect

    González, D. J.; González, L. E.

    2015-08-17

    We report ab-initio molecular dynamics simulations of dense liquid/solid sodium for a pressure range from 0 to 100 GPa. The simulations have been performed with the orbital free ab-initio molecular dynamics method which, by using the electron density as the basic variable, allows to perform simulations with large samples and for long runs. The calculated melting curve shows a maximum at a pressure ≈ 30 GPa and it is followed by a long, steep decrease. These features are in good agreement with the experimental data. For various pressures along the melting curve, we have calculated several liquid static properties (pair distribution functions, static structure factors and short-range order parameters) in order to analyze the structural effects of pressure.

  19. Polysiloxanes: ab initio force field and structural, conformational and thermophysical properties

    NASA Astrophysics Data System (ADS)

    Sun, Huai; Rigby, David

    1997-07-01

    Various levels of ab initio calculation have been performed to determine the optimum strategy for parameterization of the valence parameters of a CFF-type force field for siloxanes and polysiloxanes. Electrostatic nonbond parameters have been determined using scaled electrostatic potential (ESP) charges adjusted for known systematic differences between ab initio and experimental data, while van der Waals nonbond parameters have been determined using a classical approach involving fitting to experimental liquid density and cohesive energy density data measured at atmospheric pressure and a single temperature for a set of four small molecules. Simulations have been performed on molecular crystals, liquids and isolated molecules, yielding results which agree favorably with available experimental data. Properties calculated include unit cell parameters and crystal densities, liquid densities from 303-473 K and 0-1800 bar, dependence of oligomer density and solubility parameters on chain length and temperature, gas-phase geometries and vibrational frequencies, and gas and liquid-phase conformational behavior.

  20. Comparison between ab initio and semiempirical net atomic charges of some nicotinic acetylcholine receptor agonists

    SciTech Connect

    Yadav, J.S.; Hermsmeier, M.; Gund, T. )

    1989-01-01

    We have calculated the net atomic charges and molecular electrostatic potentials of two potent nicotinic acetylcholine receptor agonists, isoarecolone and acetylpiperazine, by three different methods to see how well they correlate and if the simplest method gives the same predictive results. The calculational methods involved calculating net atomic charges by semiempirical (MNDO from MOPAC) and ab initio (Mulliken) and ab initio (potential derived) at STO-3G basis set level. Some deviations were observed when comparisons were made atom by atom, but when group comparisons were made, good correlations were observed. When these partial charges were used to calculate the respective molecular electrostatic potentials on the van der Waals surface, very good correlations were obtained. This study shows that for routine electrostatic calculations, semiempirical MNDO Calculations give similar results and thus lead to similar predictions.

  1. Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo

    SciTech Connect

    Zen, Andrea; Luo, Ye Mazzola, Guglielmo Sorella, Sandro; Guidoni, Leonardo

    2015-04-14

    Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.

  2. B28: the smallest all-boron cage from an ab initio global search

    NASA Astrophysics Data System (ADS)

    Zhao, Jijun; Huang, Xiaoming; Shi, Ruili; Liu, Hongsheng; Su, Yan; King, R. Bruce

    2015-09-01

    Our ab initio global searches reveal the lowest-energy cage for B28, which is built from two B12 units and prevails over the competing structural isomers such as planar, bowl, and tube. This smallest boron cage extends the scope of all-boron fullerene and provides a new structural motif of boron clusters and nanostructures.Our ab initio global searches reveal the lowest-energy cage for B28, which is built from two B12 units and prevails over the competing structural isomers such as planar, bowl, and tube. This smallest boron cage extends the scope of all-boron fullerene and provides a new structural motif of boron clusters and nanostructures. Electronic supplementary information (ESI) available: Planar isomer structures of B28 and spatial distributions of front molecular orbitals. See DOI: 10.1039/c5nr04034e

  3. Ab initio investigation of light-induced relativistic spin-flip effects in magneto-optics

    NASA Astrophysics Data System (ADS)

    Mondal, Ritwik; Berritta, Marco; Carva, Karel; Oppeneer, Peter M.

    2015-05-01

    Excitation of a metallic ferromagnet such as Ni with an intensive femtosecond laser pulse causes an ultrafast demagnetization within approximately 300 fs. It was proposed that the ultrafast demagnetization measured in femtosecond magneto-optical experiments could be due to relativistic light-induced processes. We perform an ab initio investigation of the influence of relativistic effects on the magneto-optical response of Ni. To this end, first, we develop a response theory formulation of the additional appearing ultrarelativistic terms in the Foldy-Wouthuysen transformed Dirac Hamiltonian due to the electromagnetic field, and second, we compute the influence of relativistic light-induced spin-flip transitions on the magneto-optics. Our ab initio calculations of relativistic spin-flip optical excitations predict that these can give only a very small contribution (≤0.1 %) to the laser-induced magnetization change in Ni.

  4. DFT and ab initio quantum chemical studies on p-cyanobenzoic acid

    NASA Astrophysics Data System (ADS)

    Arjunan, V.; Rani, T.; Varalakshmy, L.; Mohan, S.; Tedlamelekot, F.

    2011-05-01

    The Fourier transform infrared (FTIR) and FT-Raman spectra of p-cyanobenzoic acid (CBA) have been recorded in the range 4000-400 and 4000-100 cm -1, respectively. The complete vibrational assignment and analysis of the fundamental modes of the compound were carried out using the observed FTIR and FT-Raman data. The vibrational frequencies determined experimentally were compared with theoretical wavenumbers obtained from ab initio HF and DFT-B3LYP gradient calculations employing 6-31G**, 6-311++G** and cc-pVTZ basis sets for the optimised geometry of the compound. The geometry and normal modes of vibration obtained from the HF and DFT methods are in good agreement with the experimental data. The normal coordinate analysis was also carried out with ab initio force fields utilising Wilson's FG matrix method. The interactions of cyano and carboxylic acid groups with the skeletal vibrational modes were investigated.

  5. Ab Initio Many-Body Calculations Of Nucleon-Nucleus Scattering

    SciTech Connect

    Quaglioni, S; Navratil, P

    2008-12-17

    We develop a new ab initio many-body approach capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group method with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters. This approach preserves translational symmetry and Pauli principle. We outline technical details and present phase shift results for neutron scattering on {sup 3}H, {sup 4}He and {sup 10}Be and proton scattering on {sup 3,4}He, using realistic nucleon-nucleon (NN) potentials. Our A = 4 scattering results are compared to earlier ab initio calculations. We find that the CD-Bonn NN potential in particular provides an excellent description of nucleon-{sup 4}He S-wave phase shifts. We demonstrate that a proper treatment of the coupling to the n-{sup 10}Be continuum is successful in explaining the parity-inverted ground state in {sup 11}Be.

  6. Hyperfine Parameters for Aluminum Hydride: An ab Initio Molecular Orbital Study

    NASA Astrophysics Data System (ADS)

    Gee, Myrlene; Wasylishen, Roderick E.

    2001-06-01

    An extensive ab initio molecular orbital study of the 27Al nuclear spin-rotation and nuclear quadrupolar coupling constants in aluminum hydride, AlH, has been performed. The 27Al nuclear spin-rotation constant (C⊥), calculated to be approximately 300 kHz, was neglected in a previous analysis of the hyperfine structure in the microwave spectrum (M. Goto and S. Saito, Astrophys. J.452, L147-148 (1995)). Unfortunately, the ab initio calculations do not provide a definitive value for the aluminum nuclear quadrupolar coupling constant, but suggest a value of -49±4 MHz. It is apparent that the microwave study of AlH should be repeated.

  7. Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

    SciTech Connect

    Sharma, Nalini; Ahluwalia, P. K.; Thakur, Anil

    2015-05-15

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.

  8. Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals

    NASA Astrophysics Data System (ADS)

    Pham, Cong-Huy; Kucukbenli, Emine; de Gironcoli, Stefano

    2015-03-01

    Ab initio crystal structure prediction of even small organic compounds is extremely challenging due to polymorphism, molecular flexibility and difficulties in addressing the dispersion interaction from first principles. We recently implemented vdW-aware density functionals and demonstrated their success in energy ordering of aminoacid crystals. In this work we combine this development with the evolutionary structure prediction method to study cholesterol polymorphs. Cholesterol crystals have paramount importance in various diseases, from cancer to atherosclerosis. The structure of some polymorphs (e.g. ChM, ChAl, ChAh) have already been resolved while some others, which display distinct NMR spectra and are involved in disease formation, are yet to be determined. Here we thoroughly assess the applicability of evolutionary structure prediction to address such real world problems. We validate the newly predicted structures with ab initio NMR chemical shift data using secondary referencing for an improved comparison with experiments.

  9. Properties of metals during the heating by intense laser irradiation using ab initio simulations

    NASA Astrophysics Data System (ADS)

    Holst, Bastian; Recoules, Vanina; Torrent, Marc; Mazevet, Stephane

    2011-10-01

    Ultrashort laser pulses irradiating a target heat the electrons to very high temperatures. In contrast, the ionic lattice is unaffected on the time scale of the laser pulse since the heat capacity of electrons is much smaller than that of the lattice. This non-equilibrium system can be described as a composition of two subsystems: one consisting of hot electrons and the other of an ionic lattice at low temperature. We studied the effect of this intense electronic excitations on the optical properties of gold using ab initio simulations. We additionally use ab initio linear response to compute the phonon spectrum and the electron-phonon coupling constant within Density Functional Theory for several electronic temperatures of few eV. LULI, Ecole Polytechnique, CNRS, CEA, UPMC, 91128 Palaiseau, France.

  10. Ab initio studies of equations of state and chemical reactions of reactive structural materials

    NASA Astrophysics Data System (ADS)

    Zaharieva, Roussislava

    subject of studies of the shock or thermally induced chemical reactions of the two solids comprising these reactive materials, from first principles, is a relatively new field of study. The published literature on ab initio techniques or quantum mechanics based approaches consists of the ab initio or ab initio-molecular dynamics studies in related fields that contain a solid and a gas. One such study in the literature involves a gas and a solid. This is an investigation of the adsorption of gasses such as carbon monoxide (CO) on Tungsten. The motivation for these studies is to synthesize alternate or synthetic fuel technology by Fischer-Tropsch process. In this thesis these studies are first to establish the procedure for solid-solid reaction and then to extend that to consider the effects of mechanical strain and temperature on the binding energy and chemisorptions of CO on tungsten. Then in this thesis, similar studies are also conducted on the effect of mechanical strain and temperature on the binding energies of Titanium and hydrogen. The motivations are again to understand the method and extend the method to such solid-solid reactions. A second motivation is to seek strained conditions that favor hydrogen storage and strain conditions that release hydrogen easily when needed. Following the establishment of ab initio and ab initio studies of chemical reactions between a solid and a gas, the next step of research is to study thermally induced chemical reaction between two solids (Ni+Al). Thus, specific new studies of the thesis are as follows: (1) Ab initio Studies of Binding energies associated with chemisorption of (a) CO on W surfaces (111, and 100) at elevated temperatures and strains and (b) adsorption of hydrogen in titanium base. (2) Equations of state of mixtures of reactive material structures from ab initio methods. (3) Ab initio studies of the reaction initiation, transition states and reaction products of intermetallic mixtures of (Ni+Al) at elevated

  11. Large-scale ab initio configuration interaction calculations for light nuclei

    NASA Astrophysics Data System (ADS)

    Maris, Pieter; Metin Aktulga, H.; Caprio, Mark A.; Çatalyürek, Ümit V.; Ng, Esmond G.; Oryspayev, Dossay; Potter, Hugh; Saule, Erik; Sosonkina, Masha; Vary, James P.; Yang, Chao; Zhou, Zheng

    2012-12-01

    In ab-initio Configuration Interaction calculations, the nuclear wavefunction is expanded in Slater determinants of single-nucleon wavefunctions and the many-body Schrodinger equation becomes a large sparse matrix problem. The challenge is to reach numerical convergence to within quantified numerical uncertainties for physical observables using finite truncations of the infinite-dimensional basis space. We discuss strategies for constructing and solving the resulting large sparse matrix eigenvalue problems on current multicore computer architectures. Several of these strategies have been implemented in the code MFDn, a hybrid MPI/OpenMP Fortran code for ab-initio nuclear structure calculations that can scale to 100,000 cores and more. Finally, we will conclude with some recent results for 12C including emerging collective phenomena such as rotational band structures using SRG evolved chiral N3LO interactions.

  12. Explicit Polarization (X-Pol) Potential Using ab Initio Molecular Orbital Theory and Density Functional Theory†

    PubMed Central

    Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

    2010-01-01

    The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree—Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations. PMID:19618944

  13. Ab initio calculations on twisted graphene/hBN: Electronic structure and STM image simulation

    NASA Astrophysics Data System (ADS)

    Correa, J. D.; Cisternas, E.

    2016-09-01

    By performing ab initio calculations we obtained theoretical scanning tunneling microscopy (STM) images and studied the electronic properties of graphene on a hexagonal boron-nitrite (hBN) layer. Three different stack configurations and four twisted angles were considered. All calculations were performed using density functional theory, including van der Waals interactions as implemented in the SIESTA ab initio package. Our results show that the electronic structure of graphene is preserved, although some small changes are induced by the interaction with the hBN layer, particularly in the total density of states at 1.5 eV under the Fermi level. When layers present a twisted angle, the density of states shows several van Hove singularities under the Fermi level, which are associated to moiré patterns observed in theoretical STM images.

  14. Liquid Be, Ca and Ba. An orbital-free ab-initio molecular dynamics study

    SciTech Connect

    Rio, B. G. del; González, L. E.

    2015-08-17

    Several static and dynamic properties of liquid beryllium (l-Be), liquid calcium (l-Ca) and liquid barium (l-Ba) near their triple point have been evaluated by the orbital-free ab initio molecular dynamics method (OF-AIMD), where the interaction between valence electrons and ions is described by means of local pseudopotentials. These local pseudopotentials used were constructed through a force-matching process with those obtained from a Kohn-Sham ab initio molecular dynamics study (KS-AIMD) of a reduced system with non-local pseudopotentials. The calculated static structures show good agreement with the available experimental data, including an asymmetric second peak in the structure factor which has been linked to the existence of a marked icosahedral short-range order in the liquid. As for the dynamic properties, we obtain collective density excitations whose associated dispersion relations exhibit a positive dispersion.

  15. Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.

    2016-05-01

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg10In90, Hg30In70,. Hg50In50, Hg70In30, and Hg90Pb10) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.

  16. Ultracold mixtures of metastable He and Rb: Scattering lengths from ab initio calculations and thermalization measurements

    NASA Astrophysics Data System (ADS)

    Knoop, S.; Żuchowski, P. S.; KÈ©dziera, D.; Mentel, Ł.; Puchalski, M.; Mishra, H. P.; Flores, A. S.; Vassen, W.

    2014-08-01

    We have investigated the ultracold interspecies scattering properties of metastable triplet He and Rb. We performed state-of-the-art ab initio calculations of the relevant interaction potential, and measured the interspecies elastic cross section for an ultracold mixture of metastable triplet He4 and Rb87 in a quadrupole magnetic trap at a temperature of 0.5 mK. Our combined theoretical and experimental study gives an interspecies scattering length a4+87=+17-4+1a0, which prior to this work was unknown. More general, our work shows the possibility of obtaining accurate scattering lengths using ab initio calculations for a system containing a heavy, many-electron atom, such as Rb.

  17. Implementation of a vector potential method in an ab initio Hartree-Fock code

    NASA Astrophysics Data System (ADS)

    Tevekeliyska, Violina; Springborg, Michael; Champagne, Benoît; Kirtman, Bernard

    2012-12-01

    For extended systems exposed to an external, electrostatic field, the presence of the field leads to an extra term (E⃗. P⃗) to the Hamiltonian, where E⃗ is the field vector and P⃗ is the polarization of the system of interest. In order to find out how a polymer chain responds to an external electric perturbation, a field with a charge and a current term for the polarization is added to an ab initio Hartree-Fock Hamiltonian. The polarization expression is taken from an efficient vector potential approach (VPA) [1] for calculating electronic and nuclear responses of infinite periodic systems to finite electric fields and is implemented in the ab initio LCAO-SCF algorithm [3], which computes band structure of regular or helical polymers, taking into account the one-dimensional translational symmetry. A smoothing procedure for numerical differentiation of the orbital coefficients is used in order to calculate self-consistently the charge flow contribution to the polarization.

  18. Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

    SciTech Connect

    Matsushita, Y. Murakawa, T. Shimamura, K. Oishi, M. Ohyama, T. Kurita, N.

    2015-02-27

    The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

  19. Ethanol decomposition on transition metal nanoparticles during carbon nanotube growth: ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Shibuta, Yasushi; Shimamura, Kohei; Oguri, Tomoya; Arifin, Rizal; Shimojo, Fuyuki; Yamaguchi, Shu

    2015-03-01

    The growth mechanism of carbon nanotubes (CNT) has been widely discussed both from experimental and computational studies. Regarding the computational studies, most of the studies focuses on the aggregation of isolate carbon atoms on the catalytic metal nanoparticle, whereas the initial dissociation of carbon source molecules should affect the yield and quality of the products. On the other hand, we have studied the dissociation process of carbon source molecules on the metal surface by the ab initio molecular dynamics simulation. In the study, we investigate the ethanol dissociation on Pt and Ni clusters by ab initio MD simulations to discuss the initial stage of CNT growth by alcohol CVD technique. Part of this research is supported by the Grant-in-Aid for Young Scientists (a) (No. 24686026) from MEXT, Japan.

  20. Ab initio calculations of the equations of state for hydrogen, helium, and water and the relevance to the giant planets

    NASA Astrophysics Data System (ADS)

    French, Martin

    2010-11-01

    Since the interior structure of giant planets inside or outside our solar system cannot be probed directly by experiments, planetary models have been developed to gain further insight. Such models require accurate equations of state (EOS) for the major components (H, He, and heavier compounds like water) up to extreme thermodynamic conditions (pressures of several ten megabars and temperatures of more than ten thousand degrees Kelvin) [1]. Ab initio methods that combine finite temperature density functional theory (FT-DFT) for the electrons with classical molecular dynamics (MD) for the ions have proven to be a powerful tool to calculate such accurate EOS data. In addition, the FT-DFT-MD also generates structural information, transport and optical properties and, most important, information on phase diagrams and demixing regions. Based on our recently calculated ab initio data for H, He, and water, we derive interior models of Saturn and Jupiter and discuss the role of H-He demixing [2] and of the plasma phase transition in hydrogen on the planetary interiors. We also present new models for Uranus and Neptune which offer conditions to allow the formation of the exotic superionic phase of water [3]. The ab initio data can also be applied in planetary evolution scenarios and dynamo simulations of solar and extrasolar planets.[4pt] [1] J. J. Fortney, N. Nettelmann, Space Sci. Rev. 152, 423 (2010)[0pt] [2] W. Lorenzen, B. Holst, R. Redmer, Phys. Rev. Lett. 102, 115701 (2009)[0pt] [3] M. French, T. R. Mattsson, N. Nettelmann, R. Redmer, Phys. Rev. B 79, 054107 (2009)

  1. Ab initio cluster studies of La sub 2 CuO sub 4

    SciTech Connect

    Martin, R.L.

    1991-01-01

    In this paper we examine the properties of small cluster models of La{sub 2}CuO{sub 4}. In Section 2, the Madelung/Pauli background potential used to imbed the primary cluster and the basis sets used to expand the cluster wavefunction are discussed. Section 3 presents the results of calculations on CuO{sub 6} in which the optical absorption and the photoemission spectrum are examined. The calculation on CuO{sub 6} and our earlier work on larger clusters suggest that a single-band Pariser-Parr-Pople (PPP) model be developed. Therefore, in Section 4 the PPP model and extensions which relax the zero-differential-overlap (ZDO) approximation upon which it is based are reviewed. Calculations on the states of Cu{sub 2}O{sub 7} necessary to parameterize the PPP model are presented in Section 5 and compared with analogous calculations for Cu{sub 2}O{sub 11}. Section 6 discusses the problems associated with the direct ab initio determination of the anti-ferromagnetic exchange interaction, examines the magnitudes of the occupation-dependent hopping and direct exchange interactions which arise when the ZDO approximation is relaxed, and provides estimates of the uncertainties in the parameters due to electron correlation and polarization effects not recoverable with the present basis sets and finite clusters. A comparison of the parameters with those extracted from constrained LDF theory concludes Section 6. Finally, Section 7 summarizes the conclusions of this research.

  2. Hydrogen adsorption in ZIF-7: A DFT and ab-initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Dixit, Mudit; Major, Dan Thomas; Pal, Sourav

    2016-05-01

    Primary H2 adsorption sites in a zeolitic imidazolate framework, ZIF-7, are identified using ab-initio density functional theory (DFT) based molecular dynamics annealing simulations. The simulations suggest several low energy adsorption sites. The effect of light transition metal decoration on hydrogen storage properties was studied. Our ab-intio DFT calculations illustrate that decorating the ZIF with Sc increases both the number of H2 molecules, as well as the H2 binding energy. The binding energy (∼25 kJ/mol per H2) at 8H2 loading in the pore, suggests that Sc-ZIFs can be potential candidates for hydrogen storage.

  3. Transport coefficients of helium-argon mixture based on ab initio potential

    NASA Astrophysics Data System (ADS)

    Sharipov, Felix; Benites, Victor J.

    2015-10-01

    The viscosity, thermal conductivity, diffusion coefficient, and thermal diffusion factor of helium-argon mixtures are calculated for a wide range of temperature and for various mole fractions up to the 12th order of the Sonine polynomial expansion with an ab initio intermolecular potential. The calculated values for these transport coefficients are compared with other data available in the open literature. The comparison shows that the obtained transport coefficients of helium-argon mixture have the best accuracy for the moment.

  4. Ab initio dipole moment and theoretical rovibrational intensities in the electronic ground state of PH 3

    NASA Astrophysics Data System (ADS)

    Yurchenko, Sergei N.; Carvajal, Miguel; Thiel, Walter; Jensen, Per

    2006-09-01

    We report a six-dimensional CCSD(T)/aug-cc-pVTZ dipole moment surface for the electronic ground state of PH 3 computed ab initio on a large grid of 10 080 molecular geometries. Parameterized, analytical functions are fitted through the ab initio data, and the resulting dipole moment functions are used, together with a potential energy function determined by refining an existing ab initio surface in fittings to experimental wavenumber data, for simulating absorption spectra of the first three polyads of PH 3, i.e., ( ν2, ν4), ( ν1, ν3, 2 ν2, 2 ν4, ν2 + ν4), and ( ν1 + ν2, ν3 + ν2, ν1 + ν4, ν3 + ν4, 2 ν2 + ν4, ν2 + 2 ν4, 3 ν2, 3 ν4). The resulting theoretical transition moments show excellent agreement with experiment. A line-by-line comparison of the simulated intensities of the ν2/ ν4 band system with 955 experimental intensity values reported by Brown et al. [L.R. Brown, R.L. Sams, I. Kleiner, C. Cottaz, L. Sagui, J. Mol. Spectrosc. 215 (2002) 178-203] gives an average absolute percentage deviation of 8.7% (and a root-mean-square deviation of 0.94 cm -1 for the transition wavenumbers). This is very remarkable since the calculations rely entirely on ab initio dipole moment surfaces and do not involve any adjustment of these surfaces to reproduce the experimental intensities. Finally, we predict the line strengths for transitions between so-called cluster levels (near-degenerate levels formed at high rotational excitation) for J up to 60.

  5. An ab initio MIA study of TIBO derivatives R79882 and R82913

    NASA Astrophysics Data System (ADS)

    Peeters, Anik; Van Alsenoy, C.

    1995-04-01

    The gas phase structure of two TIBO compounds (R79882 and R82913), potent inhibitors of the reverse transcriptase of HIV1, was studied with ab initio Hartree-Fock methods using the MIA approach. For compound R82913 the geometry of a dimer and of the respective monomers was fully optimized and compared with experiment. For compound R79882 a complete geometry optimization of 15 different conformers was performed.

  6. Ab initio calculation of positron distribution, ACAR and lifetime in TTF-TCNQ

    NASA Astrophysics Data System (ADS)

    Ishibashi, Shoji; Kohyama, Masanori

    2000-06-01

    We have performed ab initio calculations of positron distribution, ACAR and lifetime in the quasi-one-dimensional organic conductor TTF-TCNQ. The electronic structure is obtained within the LDA, while the positron state is calculated either with the LDA or with the GGA. Except the positron lifetime, differences between the LDA and GGA results are rather small. The obtained results are compared with our previous experiments and calculations.

  7. Methylchloride adsorbed on Si(0 0 1): an ab initio study

    NASA Astrophysics Data System (ADS)

    Preuss, M.; Schmidt, W. G.; Seino, K.; Bechstedt, F.

    2004-07-01

    We present ab initio calculations of the adsorption of methylchloride (CH 3Cl) on Si(0 0 1). Among multiple plausible adsorption geometries, we find five thermodynamically favorable configurations. These lead to strong geometrical changes in the Si surface structure as well as to significant charge transfer processes. The stability of the adsorption structures is discussed in terms of electrostatics. The results are compared to recent experimental and theoretical findings.

  8. Electron-ejection cross sections in electron- and ion impact ionization: ab initio and semiempirical calculations

    SciTech Connect

    Manson, S.T.; Miller, J.H.

    1987-01-01

    Ab initio calculations of single and double differential cross sections for ionization by fast, charged particles within the framework of the Born approximation are presented. In addition, a semi-empirical method based on the asymptotic Bethe-Born expansion is also discussed. Both are applied to ionization of helium by electrons and protons in an effort to assess their accuracy and validity. Agreement with experiment is quite good. The implications for other targets is discussed.

  9. Ab initio calculations in a uniform magnetic field using periodic supercells

    SciTech Connect

    Cai, W; Galli, G

    2003-10-21

    We present a formulation of ab initio electronic structure calculations in a finite magnetic field, which retains the simplicity and efficiency of techniques widely used in first principles molecular dynamics simulations, based on plane-wave basis sets and Fourier transforms. In addition we discuss results obtained with this method for the energy spectrum of interacting electrons in quantum wells, and for the electronic properties of dense fluid deuterium in a uniform magnetic field.

  10. Condensed-matter ab initio approach for strongly correlated electrons: Application to a quantum spin liquid candidate

    SciTech Connect

    Yamaji, Youhei

    2015-12-31

    Recently, condensed-matter ab initio approaches to strongly correlated electrons confined in crystalline solids have been developed and applied to transition-metal oxides and molecular conductors. In this paper, an ab initio scheme based on constrained random phase approximations and localized Wannier orbitals is applied to a spin liquid candidate Na{sub 2}IrO{sub 3} and is shown to reproduce experimentally observed specific heat.

  11. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    SciTech Connect

    Geng, Hua Y.

    2015-02-15

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.

  12. In pursuit of the ab initio limit for conformational energy prototypes

    NASA Astrophysics Data System (ADS)

    Császár, Attila G.; Allen, Wesley D.; Schaefer, Henry F.

    1998-06-01

    The convergence of ab initio predictions to the one- and n-particle limits has been systematically explored for several conformational energy prototypes: the inversion barriers of ammonia, water, and isocyanic acid, the torsional barrier of ethane, the E/Z rotamer separation of formic acid, and the barrier to linearity of silicon dicarbide. Explicit ab initio results were obtained with atomic-orbital basis sets as large as [7s6p5d4f3g2h1i/6s5p4d3f2g1h] and electron correlation treatments as extensive as fifth-order Møller-Plesset perturbation theory (MP5), the full coupled-cluster method through triple excitations (CCSDT), and Brueckner doubles theory including perturbational corrections for both triple and quadruple excitations [BD(TQ)]. Subsequently, basis set and electron correlation extrapolation schemes were invoked to gauge any further variations in arriving at the ab initio limit. Physical effects which are tacitly neglected in most theoretical work have also been quantified by computations of non-Born-Oppenheimer (BODC), relativistic, and core correlation shifts of relative energies. Instructive conclusions are drawn for the pursuit of spectroscopic accuracy in theoretical conformational analyses, and precise predictions for the key energetic quantities of the molecular prototypes are advanced.

  13. Experimental and ab initio investigations of microscopic properties of laser-shocked Ge-doped ablator.

    PubMed

    Huser, G; Recoules, V; Ozaki, N; Sano, T; Sakawa, Y; Salin, G; Albertazzi, B; Miyanishi, K; Kodama, R

    2015-12-01

    Plastic materials (CH) doped with mid-Z elements are used as ablators in inertial confinement fusion (ICF) capsules and in their surrogates. Hugoniot equation of state (EOS) and electronic properties of CH doped with germanium (at 2.5% and 13% dopant fractions) are investigated experimentally up to 7 Mbar using velocity and reflectivity measurements of shock fronts on the GEKKO laser at Osaka University. Reflectivity and temperature measurements were updated using a quartz standard. Shocked quartz reflectivity was measured at 532 and 1064 nm. Theoretical investigation of shock pressure and reflectivity was then carried out by ab initio simulations using the quantum molecular dynamics (QMD) code abinit and compared with tabulated average atom EOS models. We find that shock states calculated by QMD are in better agreement with experimental data than EOS models because of a more accurate description of ionic structure. We finally discuss electronic properties by comparing reflectivity data to a semiconductor gap closure model and to QMD simulations. PMID:26764839

  14. Ab initio study of hydrogen migration across n-alkyl radicals.

    PubMed

    Davis, Alexander C; Francisco, Joseph S

    2011-04-14

    A thorough ab initio investigation is conducted on all possible hydrogen migration pathways for the 1-ethyl, 1-propyl, 1-butyl, 1-pentyl, 1-hexyl, 1-heptyl, and 1-octyl radicals in order to determine underlying trends in reaction enthalpies, activation energies, Arrhenius A-factors, tunneling, and rate coefficients. The G4, G2, and CBS-Q composite methods are used to determine the enthalpy of reaction and activation energy barrier for each reaction. Each method shows excellent agreement with eight experimental enthalpy of reaction values, with root mean squared values of 0.8, 0.9, and 0.6 kcal mol(-1) for CBS-Q, G2, and G4, respectively. Differences in barrier heights, A-factors, tunneling, and rate coefficients are observed for axial and equatorial arrangements as well as between secondary hydrogen migration sites, depending on the location of the secondary site relative to the terminal carbon. The validity of using cycloalkane model systems to estimate rate parameters is also assessed. The failure of two key assumptions inherent to the cycloalkane models, resulting in a breakdown in the accuracy of these methods for larger transition states, is discussed. This study has significant ramifications for future theoretical, experimental, and modeling studies involving the decomposition of n-alkanes. PMID:21413772

  15. Solvation structure of glucosamine in aqueous solution as studied by Monte Carlo simulation using ab initio fitted potential

    NASA Astrophysics Data System (ADS)

    Siraleartmukul, Krisana; Siriwong, Khatcharin; Remsungnen, Tawun; Muangsin, Nongnuj; Udomkichdecha, Werasak; Hannongbua, Supot

    2004-09-01

    The solvation structure of glucosamine in aqueous solution was investigated using Monte Carlo simulation at 298 K. The MCY rigid water model and ab initio glucosamine-water fitted potential were applied. The first hydration shell appears at 4.6 Å from the center of glucosamine with a coordination number of seven water molecules where one water lies in the ligand's plane while two and four of them are about 2-4 Å above and below the plane, respectively. Furthermore, the mobility distribution and orientation of the water molecules around the ligand have been intensively investigated and reported.

  16. Conformations of 1,2-dimethoxypropane and 5-methoxy-1,3-dioxane: are ab initio quantum chemistry predictions accurate?

    NASA Astrophysics Data System (ADS)

    Smith, Grant D.; Jaffe, Richard L.; Yoon, Do. Y.

    1998-06-01

    High-level ab initio quantum chemistry calculations are shown to predict conformer populations of 1,2-dimethoxypropane and 5-methoxy-1,3-dioxane that are consistent with gas-phase NMR vicinal coupling constant measurements. The conformational energies of the cyclic ether 5-methoxy-1,3-dioxane are found to be consistent with those predicted by a rotational isomeric state (RIS) model based upon the acyclic analog 1,2-dimethoxypropane. The quantum chemistry and RIS calculations indicate the presence of strong attractive 1,5 C(H 3)⋯O electrostatic interactions in these molecules, similar to those found in 1,2-dimethoxyethane.

  17. Photoejection of electrons from pyrrole into an aqueous environment: ab initio results on pyrrole-water clusters

    NASA Astrophysics Data System (ADS)

    Sobolewski, Andrzej L.; Domcke, Wolfgang

    2000-05-01

    Ab initio (RHF, CASSCF and CASPT2) calculations in the ground and lowest excited singlet states have been performed on pyrrole and pyrrole-water clusters. Full geometry optimization in the 1πσ ∗ state, which is energetically accessible from the optically allowed 1ππ ∗ state, reveals the flow of the electronic charge from pyrrole towards the water molecules, i.e., the formation of a charge transfer-to-solvent state. The computational results indicate that pyrrole-water clusters are good models for the investigation of the mechanistic details of the electron solvation process occurring upon ultraviolet photoexcitation of organic chromophores in liquid water.

  18. Ab initio investigation of the surface properties of dispenser B-type and scandate thermionic emission cathodes

    NASA Astrophysics Data System (ADS)

    Vlahos, Vasilios; Lee, Yueh-Lin; Booske, John H.; Morgan, Dane; Turek, Ladislav; Kirshner, Mark; Kowalczyk, Richard; Wilsen, Craig

    2009-05-01

    Scandate cathodes (BaxScyOz on W) are important thermionic electron emission materials whose emission mechanism remains unclear. Ab initio modeling is used to investigate the surface properties of both scandate and traditional B-type (Ba-O on W) cathodes. We demonstrate that the Ba-O dipole surface structure believed to be present in active B-type cathodes is not thermodynamically stable, suggesting that a nonequilibrium steady state dominates the active cathode's surface structure. We identify a stable, low work function BaxScyOz surface structure, which may be responsible for some scandate cathode properties and demonstrate that multicomponent surface coatings can lower cathode work functions.

  19. SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models

    PubMed Central

    2014-01-01

    Background Locating the protein-coding genes in novel genomes is essential to understanding and exploiting the genomic information but it is still difficult to accurately predict all the genes. The recent availability of detailed information about transcript structure from high-throughput sequencing of messenger RNA (RNA-Seq) delineates many expressed genes and promises increased accuracy in gene prediction. Computational gene predictors have been intensively developed for and tested in well-studied animal genomes. Hundreds of fungal genomes are now or will soon be sequenced. The differences of fungal genomes from animal genomes and the phylogenetic sparsity of well-studied fungi call for gene-prediction tools tailored to them. Results SnowyOwl is a new gene prediction pipeline that uses RNA-Seq data to train and provide hints for the generation of Hidden Markov Model (HMM)-based gene predictions and to evaluate the resulting models. The pipeline has been developed and streamlined by comparing its predictions to manually curated gene models in three fungal genomes and validated against the high-quality gene annotation of Neurospora crassa; SnowyOwl predicted N. crassa genes with 83% sensitivity and 65% specificity. SnowyOwl gains sensitivity by repeatedly running the HMM gene predictor Augustus with varied input parameters and selectivity by choosing the models with best homology to known proteins and best agreement with the RNA-Seq data. Conclusions SnowyOwl efficiently uses RNA-Seq data to produce accurate gene models in both well-studied and novel fungal genomes. The source code for the SnowyOwl pipeline (in Python) and a web interface (in PHP) is freely available from http://sourceforge.net/projects/snowyowl/. PMID:24980894

  20. Semi-empirical and ab initio DFT modeling of the spin-Hamiltonian parameters for Fe6+: K2MO4 (M = S, Cr, Se)

    NASA Astrophysics Data System (ADS)

    Avram, N. M.; Brik, M. G.; Andreici, E.-L.

    2014-09-01

    In this paper we calculated the spin-Hamiltonian parameters (g factors {{g}||}, {{g}\\bot } and zero field splitting parameter D) for Fe6+ ions doped in K2MO4 (M = S, Cr, Se) crystals, taking into account the actual site symmetry of the Fe6+ impurity ion. The suggested method is based on the successful application of two different approaches: the crystal field theory (CFT) and density functional based (DFT). Within the CFT model we used the cluster approach and the perturbation theory method, based on the crystal field parameters, which were calculated in the superposition model. Within the DFT approach the calculations were done at the self-consistent field (SCF) by solving the coupled perturbed SCF equations. Comparison with experimental data shows that the obtained results are quite satisfactory, which proves applicability of the suggested calculating technique.

  1. Investigation of microstructure evolution during self-annealing in thin Cu films by combining mesoscale level set and ab initio modeling

    NASA Astrophysics Data System (ADS)

    Hallberg, Håkan; Olsson, Pär A. T.

    2016-05-01

    Microstructure evolution in thin Cu films during room temperature self-annealing is investigated by means of a mesoscale level set model. The model is formulated such that the relative, or collective, influence of anisotropic grain boundary energy, mobility and heterogeneously distributed stored energy can be investigated. Density functional theory (DFT) calculations are performed in the present work to provide the variation of grain boundary energy for different grain boundary configurations. The stability of the predominant (111) fiber texture in the as-deposited state is studied as well as the stability of some special low-Σ grain boundaries. Further, the numerical model allows tracing of the grain size distribution and occurrence of abnormal grain growth during self-annealing. It is found that abnormal grain growth depends mainly on the presence of stored energy variations, whereas anisotropic grain boundary energy or mobility is insufficient to trigger any abnormal growth in the model. However, texture dependent grain boundary properties, mobility in particular, contribute to an increased content of low-Σ boundaries in the annealed microstructure. The increased presence of such boundaries is also promoted by stored energy variations. In addition, if the stored energy variations are sufficient the coexisting (111) and (001) texture components in the as-deposited state will evolve into a (001) dominated texture during annealing. Further, it is found that whereas stored energy variations promote the stability of the (001) texture component, anisotropic grain boundary energy and mobility tend to work the other way and stabilize the (111) component at the expense of (001) grains.

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

    PubMed

    Misquitta, Alston J; Stone, Anthony J

    2016-09-13

    Creating accurate, analytic atom-atom potentials for small organic molecules from first principles can be a time-consuming and computationally intensive task, particularly if we also require them to include explicit polarization terms, which are essential in many systems. We describe how the CamCASP suite of programs can be used to generate such potentials using some of the most accurate electronic structure methods currently applicable. We derive the long-range terms from monomer properties and determine the short-range anisotropy parameters by a novel and robust method based on the iterated stockholder atom approach. Using these techniques, we develop distributed multipole models for the electrostatic, polarization, and dispersion interactions in the pyridine dimer and develop a series of many-body potentials for the pyridine system. Even the simplest of these potentials exhibits root mean square errors of only about 0.6 kJ mol(-1) for the low-energy pyridine dimers, significantly surpassing the best empirical potentials. Our best model is shown to support eight stable minima, four of which have not been reported before in the literature. Further, the functional form can be made systematically more elaborate so as to improve the accuracy without a significant increase in the human-time spent in their generation. We investigate the effects of anisotropy, rank of multipoles, and choice of polarizability and dispersion models. PMID:27467814

  3. Periodic Trends in Lanthanide Compounds through the Eyes of Multireference ab Initio Theory.

    PubMed

    Aravena, Daniel; Atanasov, Mihail; Neese, Frank

    2016-05-01

    Regularities among electronic configurations for common oxidation states in lanthanide complexes and the low involvement of f orbitals in bonding result in the appearance of several periodic trends along the lanthanide series. These trends can be observed on relatively different properties, such as bonding distances or ionization potentials. Well-known concepts like the lanthanide contraction, the double-double (tetrad) effect, and the similar chemistry along the lanthanide series stem from these regularities. Periodic trends on structural and spectroscopic properties are examined through complete active space self-consistent field (CASSCF) followed by second-order N-electron valence perturbation theory (NEVPT2) including both scalar relativistic and spin-orbit coupling effects. Energies and wave functions from electronic structure calculations are further analyzed in terms of ab initio ligand field theory (AILFT), which allows one to rigorously extract angular overlap model ligand field, Racah, and spin-orbit coupling parameters directly from high-level ab initio calculations. We investigated the elpasolite Cs2NaLn(III)Cl6 (Ln(III) = Ce-Nd, Sm-Eu, Tb-Yb) crystals because these compounds have been synthesized for most Ln(III) ions. Cs2NaLn(III)Cl6 elpasolites have been also thoroughly characterized with respect to their spectroscopic properties, providing an exceptionally vast and systematic experimental database allowing one to analyze the periodic trends across the lanthanide series. Particular attention was devoted to the apparent discrepancy in metal-ligand covalency trends between theory and spectroscopy described in the literature. Consistent with earlier studies, natural population analysis indicates an increase in covalency along the series, while a decrease in both the nephelauxetic (Racah) and relativistic nephelauxetic (spin-orbit coupling) reduction with increasing atomic number is calculated. These apparently conflicting results are discussed on the

  4. Time-domain ab initio studies of photoinduced electron dynamics in nanoscale semiconductors

    NASA Astrophysics Data System (ADS)

    Prezhdo, Oleg

    2010-03-01

    Design of novel materials for energy harvesting and storage requires an understanding of the dynamical response on the nanometer scale. We have developed state-of-the-art non-adiabatic molecular dynamics techniques and implemented them within time-dependent density functional theory in order to model the ultrafast processes in these materials at the atomistic level and in real time. Quantum dots (QD) are quasi-zero dimensional structures with a unique combination of molecular and bulk properties. As a result, QDs exhibit new physical phenomena such as the electron-phonon relaxation bottleneck and carrier multiplication, which have the potential to greatly increase solar cell efficiencies. Photoinduced charge separation across molecular/bulk interfaces drives the dye-sensitized semiconductor solar cell. A subject of active research, it creates many challenges due to the stark differences between the quantum states of molecular and periodic systems, as well as the different sets of theories and experimental tools used by physicists and chemists. Our time-domain atomistic simulations create a detailed picture of these materials. By comparing and contrasting their properties, we provide a unifying description of quantum dynamics on the nanometer scale, resolve several highly debated issues, and generate theoretical guidelines for development of novel systems for energy harvesting and storage. [4pt] [1] O. V. Prezhdo ``Photoinduced dynamics in semiconductor quantum-dots: insights from time-domain ab initio studies'', Acc. Chem. Res., available online.[0pt] [2] O. V. Prezhdo, W. R. Duncan, V. V. Prezhdo, ``Photoinduced electron dynamics at semiconductor interfaces: a time-domain ab initio prospective'', Prog. Surf. Science, 84, 39 (2009).[0pt] [3] O. V. Prezhdo, et al., ``Dynamics of the photoexcited electron at the chromophore-semiconductor interface'', Acc. Chem. Res., 41, 339 (2008).[0pt] [4] W. R. Duncan, O. V. Prezhdo, ``Theoretical studies of photoinduced electron

  5. Ab initio study of the magnetostructural properties of MnAs

    NASA Astrophysics Data System (ADS)

    Rungger, Ivan; Sanvito, Stefano

    2006-07-01

    The magnetic and structural properties of MnAs are studied with ab initio methods and by mapping total energies onto a Heisenberg model. The stability of the different phases is found to depend mainly on the volume and on the amount of magnetic order, confirming previous experimental findings and phenomenological models. It is generally found that for large lattice constants the ferromagnetic state is favored, whereas for small lattice constants different antiferromagnetic states can be stabilized. In the ferromagnetic state the structure with minimal energy is always hexagonal, whereas it becomes orthorhombically distorted if there is an antiferromagnetic alignment of the magnetic moments in the hexagonal plane. For the paramagnetic state the stable cell is found to be orthorhombic up to a critical lattice constant of about 3.7Å , above which it remains hexagonal. This leads to the second-order structural phase transition between paramagnetic states at about 400K , where the lattice parameter increases above this critical value with rising temperature due to the thermal expansion. We also evaluate the magnetic susceptibility as a function of temperature, from which a semiquantitative description of the MnAs phase diagram emerges.

  6. Amorphous Ge quantum dots embedded in crystalline Si: ab initio results.

    PubMed

    Laubscher, M; Küfner, S; Kroll, P; Bechstedt, F

    2015-10-14

    We study amorphous Ge quantum dots embedded in a crystalline Si matrix through structure modeling and simulation using ab initio density functional theory including spin-orbit interaction and quasiparticle effects. Three models are generated by replacing a spherical region within diamond Si by Ge atoms and creating a disordered bond network with appropriate density inside the Ge quantum dot. After total-energy optimisations of the atomic geometry we compute the electronic and optical properties. We find three major effects: (i) the resulting nanostructures adopt a type-I heterostructure character; (ii) the lowest optical transitions occur only within the Ge quantum dots, and do not involve or cross the Ge-Si interface. (iii) for larger amorphous Ge quantum dots, with diameters of about 2.0 and 2.7 nm, absorption peaks appear in the mid-infrared spectral region. These are promising candidates for intense luminescence at photon energies below the gap energy of bulk Ge. PMID:26402441

  7. Ab initio study of biphenyl chemisorption on Si(001): Configurational stability

    NASA Astrophysics Data System (ADS)

    Mamatkulov, M.; Stauffer, L.; Minot, C.; Sonnet, Ph.

    2006-01-01

    We present an ab initio energetical and structural study of the configurational stability of the biphenyl molecule adsorbed on the Si(001) surface. A number of models in biphenyl tight-bridge, butterfly, twisted, and tilted configurations are considered. For an undissociated biphenyl adsorption, the tight-bridge configuration is found to be the most stable one, slightly favored over the butterfly configuration. The effect on the stability of various parameters is investigated. The position with respect to the surface of the first phenyl ring atom (C1) on which the second ring is bound plays a determinant role. The tilted dimer under the second ring mainly acts in the biphenyl butterfly and tilted configurations, and a second ring location above a silicon down-atom favors stability. The effect of the second ring height above the surface is also discussed. Our results allow us to classify these different contributions by decreasing importance. By the hypothesis of a dissociative biphenyl adsorption, the calculated adsorption energies are clearly lower than in the corresponding undissociated model and the dissociated butterfly configuration is largely favored. Comparing our results to the experimental data, we propose some interpretations relative to the weakly and strongly chemisorbed biphenyl molecule observed in the scanning tunneling microscopy experiments.

  8. Ab initio Calculations of Charge Symmetry Breaking in the A =4 Hypernuclei

    NASA Astrophysics Data System (ADS)

    Gazda, Daniel; Gal, Avraham

    2016-03-01

    We report on ab initio no-core shell model calculations of the mirror Λ hypernuclei H4Λ and He4Λ , using the Bonn-Jülich leading-order chiral effective field theory hyperon-nucleon potentials plus a charge symmetry breaking Λ -Σ0 mixing vertex. In addition to reproducing rather well the 0g.s . + and 1exc+ binding energies, these four-body calculations demonstrate for the first time that the observed charge symmetry breaking splitting of mirror levels, reaching hundreds of keV for 0g.s . +, can be reproduced using realistic theoretical interaction models, although with a non-negligible momentum cutoff dependence. Our results are discussed in relation to recent measurements of the H4Λ(0g.s . +) binding energy at the Mainz Microtron [A. Esser et al. (A1 Collaboration), Phys. Rev. Lett. 114, 232501 (2015)] and the He4Λ(1exc+) excitation energy [T.O. Yamamoto et al. (J-PARC E13 Collaboration), Phys. Rev. Lett. 115, 222501 (2015)].

  9. Parametrization and Validation of Coarse Grained Force-Fields Derived from ab Initio Calculations.

    PubMed

    Prampolini, Giacomo

    2006-05-01

    A novel multisite interaction potential, suitable for computer simulations of complex materials as liquid crystals or polymers, is proposed and parametrized. Its validation is achieved through Monte Carlo numerical experiments at constant temperature and pressure, performed on the p-n-phenyls series and a typical mesogenic molecule (5CB). The model is constructed by connecting an array of anisotropic Gay-Berne sites and a collection of isotropic Lennard-Jones sites. The former mimics the rigid planar six-membered rings of the molecule, while the latter represents the flexible chain, if present. Such intermolecular potential, coupled with an intramolecular part to account for molecular flexibility, is parametrized from ab initio information only, obtained through the recently proposed Fragmentation-Reconstruction Method (FRM). Computer simulations are performed on all systems by exploring phase behavior at several temperatures and by comparing the resulting thermodynamic and structural properties with the relevant experimental data. Despite the simplicity of the present models, the good agreement with the experimental measures suggests the possibility of adopting such hybrid potentials for those systems with a large number of atoms, where high computational cost does not allow the use of more accurate atomistic potentials. PMID:26626663

  10. Microstructure from joint analysis of experimental data and ab initio interactions: Hydrogenated amorphous silicon

    SciTech Connect

    Biswas, Parthapratim; Drabold, D. A.; Atta-Fynn, Raymond

    2014-12-28

    A study of the formation of voids and molecular hydrogen in hydrogenated amorphous silicon is presented based upon a hybrid approach that involves inversion of experimental nuclear magnetic resonance data in conjunction with ab initio total-energy relaxations in an augmented solution space. The novelty of this approach is that the voids and molecular hydrogen appear naturally in the model networks unlike conventional approaches, where voids are created artificially by removing silicon atoms from the networks. Two representative models with 16 and 18 at. % of hydrogen are studied in this work. The result shows that the microstructure of the a-Si:H network consists of several microvoids and few molecular hydrogen for concentration above 15 at. % H. The microvoids are highly irregular in shape and size, and have a linear dimension of 5–7 Å. The internal surface of a microvoid is found to be decorated with 4–9 hydrogen atoms in the form of monohydride Si–H configurations as observed in nuclear magnetic resonance experiments. The microstructure consists of (0.9–1.4)% hydrogen molecules of total hydrogen in the networks. These observations are consistent with the outcome of infrared spectroscopy, nuclear magnetic resonance, and calorimetry experiments.

  11. Ab initio and analytical intermolecular potential for ClO-H2O

    SciTech Connect

    Du, Shiyu; Francisco, Joseph S.; Schenter, Gregory K.; Garrett, Bruce C.

    2007-03-19

    In recent years, the ClO free radical has been found to play an important role in the ozone removal processes in the atmosphere. In this work, we present a Potential Energy Surface (PES) Scan of the ClO•H2O system with high-level ab initio methods. Because of the existence of low-lying excited states of the ClO•H2O complex, and their potential impact on the chemical behavior of the ClO radical in the atmosphere, we perform a PES scan at CCSD(T)/aug-cc-pVTZ level of both the first excited and ground states in order to model the physics of the unpaired electron in the ClO radical. Analytical potentials for both ground and excited states, with internal molecular coordinates held fixed, were built based on a Thole Type Model. The two minima of the ClO•H2O complex are recovered by the analytical potential. This work was supported by the Office of Basic Energy Sciences of the Department of Energy, in part by the Chemical Sciences program and in part by the Engineering and Geosciences Division. The Pacific Northwest National Laboratory is operated by Battelle for the U.S. Department of Energy.

  12. Ab initio Mapping of Interlayer Coupling in Transition Metal Dichalcogenides and Graphene

    NASA Astrophysics Data System (ADS)

    Fang, Shiang; Kaxiras, Efthimios

    Two-dimensional layered materials cover a wide variety of physics phenomena, such as topological phases, superconductivity, magnetism and charge density waves. Owing to the layered geometry and the van der Waals interactions in between, stacks of these van der Waals layered materials provide a venue to create a heterostructure with various physics properties. The interaction between different physics properties is particular interesting to engineer the material with the desired properties. One of the crucial ingredient in understanding the heterostructure is the interlayer coupling in between. In the literature, such kind of coupling has been proposed in various empirical forms. However, a true ab initio coupling model is still lacking. For the first time, here we have derived such interlayer coupling model from the first principle calculations based on the Wannier transformation of graphene stacks. We further investigate the Fermi velocity renormalization, van Hove singularities and the moire pattern for electron localization. Such microscopic understanding of the interlayer coupling would shed light on orbital hybridization and transport in multilayer stacks. This work was supported by the STC Center for Integrated Quantum Materials, NSF Grant No. DMR-1231319, and by ARO MURI Award No. W911NF-14-0247.

  13. Ab initio investigation of the first hydration shell of protonated glycine

    SciTech Connect

    Wei, Zhichao; Chen, Dong E-mail: boliu@henu.edu.cn; Zhao, Huiling; Li, Yinli; Zhu, Jichun; Liu, Bo E-mail: boliu@henu.edu.cn

    2014-02-28

    The first hydration shell of the protonated glycine is built up using Monte Carlo multiple minimum conformational search analysis with the MMFFs force field. The potential energy surfaces of the protonated glycine and its hydration complexes with up to eight water molecules have been scanned and the energy-minimized structures are predicted using the ab initio calculations. First, three favorable structures of protonated glycine were determined, and the micro-hydration processes showed that water can significantly stabilize the unstable conformers, and then their first hydration shells were established. Finally, we found that seven water molecules are required to fully hydrate the first hydration shell for the most stable conformer of protonated glycine. In order to analyse the hydration process, the dominant hydration sites located around the ammonium and carboxyl groups are studied carefully and systemically. The results indicate that, water molecules hydrate the protonated glycine in an alternative dynamic hydration process which is driven by the competition between different hydration sites. The first three water molecules are strongly attached by the ammonium group, while only the fourth water molecule is attached by the carboxyl group in the ultimate first hydration shell of the protonated glycine. In addition, the first hydration shell model has predicted most identical structures and a reasonable accord in hydration energy and vibrational frequencies of the most stable conformer with the conductor-like polarizable continuum model.

  14. Nonlocal torque operators in ab initio theory of the Gilbert damping in random ferromagnetic alloys

    NASA Astrophysics Data System (ADS)

    Turek, I.; Kudrnovský, J.; Drchal, V.

    2015-12-01

    We present an ab initio theory of the Gilbert damping in substitutionally disordered ferromagnetic alloys. The theory rests on introduced nonlocal torques which replace traditional local torque operators in the well-known torque-correlation formula and which can be formulated within the atomic-sphere approximation. The formalism is sketched in a simple tight-binding model and worked out in detail in the relativistic tight-binding linear muffin-tin orbital method and the coherent potential approximation (CPA). The resulting nonlocal torques are represented by nonrandom, non-site-diagonal, and spin-independent matrices, which simplifies the configuration averaging. The CPA-vertex corrections play a crucial role for the internal consistency of the theory and for its exact equivalence to other first-principles approaches based on the random local torques. This equivalence is also illustrated by the calculated Gilbert damping parameters for binary NiFe and FeCo random alloys, for pure iron with a model atomic-level disorder, and for stoichiometric FePt alloys with a varying degree of L 10 atomic long-range order.

  15. Multiphase semiclassical approximation of an electron in a one-dimensional crystalline lattice - III. From ab initio models to WKB for Schroedinger-Poisson

    SciTech Connect

    Gosse, Laurent . E-mail: mauser@univie.ac.at

    2006-01-01

    This work is concerned with the semiclassical approximation of the Schroedinger-Poisson equation modeling ballistic transport in a 1D periodic potential by means of WKB techniques. It is derived by considering the mean-field limit of a N-body quantum problem, then K-multivalued solutions are adapted to the treatment of this weakly nonlinear system obtained after homogenization without taking into account for Pauli's exclusion principle. Numerical experiments display the behaviour of self-consistent wave packets and screening effects.

  16. Investigation of the Fe3+ centers in perovskite KMgF3 through a combination of ab initio (density functional theory) and semi-empirical (superposition model) calculations

    NASA Astrophysics Data System (ADS)

    Emül, Y.; Erbahar, D.; Açıkgöz, M.

    2015-08-01

    Analyses of the local crystal and electronic structure in the vicinity of Fe3+ centers in perovskite KMgF3 crystal have been carried out in a comprehensive manner. A combination of density functional theory (DFT) and a semi-empirical superposition model (SPM) is used for a complete analysis of all Fe3+ centers in this study for the first time. Some quantitative information has been derived from the DFT calculations on both the electronic structure and the local geometry around Fe3+ centers. All of the trigonal (K-vacancy case, K-Li substitution case, and normal trigonal Fe3+ center case), FeF5O cluster, and tetragonal (Mg-vacancy and Mg-Li substitution cases) centers have been taken into account based on the previously suggested experimental and theoretical inferences. The collaboration between the experimental data and the results of both DFT and SPM calculations provides us to understand most probable structural model for Fe3+ centers in KMgF3.

  17. Assessing the Accuracy of Various Ab Initio Methods for Geometries and Excitation Energies of Retinal Chromophore Minimal Model by Comparison with CASPT3 Results.

    PubMed

    Grabarek, Dawid; Walczak, Elżbieta; Andruniów, Tadeusz

    2016-05-10

    The effect of the quality of the ground-state geometry on excitation energies in the retinal chromophore minimal model (PSB3) was systematically investigated using various single- (within Møller-Plesset and coupled-cluster frameworks) and multiconfigurational [within complete active space self-consistent field (CASSCF) and CASSCF-based perturbative approaches: second-order CASPT2 and third-order CASPT3] methods. Among investigated methods, only CASPT3 provides geometry in nearly perfect agreement with the CCSD(T)-based equilibrium structure. The second goal of the present study was to assess the performance of the CASPT2 methodology, which is popular in computational spectroscopy of retinals, in describing the excitation energies of low-lying excited states of PSB3 relative to CASPT3 results. The resulting CASPT2 excitation energy error is up to 0.16 eV for the S0 → S1 transition but only up to 0.06 eV for the S0 → S2 transition. Furthermore, CASPT3 excitation energies practically do not depend on modification of the zeroth-order Hamiltonian (so-called IPEA shift parameter), which does dramatically and nonsystematically affect CASPT2 excitation energies. PMID:27049438

  18. Axisymmetric Ab Initio Core-Collapse Supernova Simulations of 12--25 Solar Mass Stars

    SciTech Connect

    Bruenn, S. W.; Mezzacappa, Anthony; Hix, William Raphael; Lentz, E. J.; Messer, Bronson; Lingerfelt, Eric J; Blondin, J. M.; Endeve, Eirik; Marronetti, Pedro; Yakunin, Konstantin

    2013-01-01

    We present an overview of four ab initio axisymmetric core-collapse supernova simulations employing detailed spectral neutrino transport computed with our CHIMERA code and initiated from Woosley & Heger (2007) progenitors of mass 12, 15, 20, and 25 M_sun. All four models exhibit shock revival over ~ 200 ms (leading to the possibility of explosion), driven by neutrino energy deposition. Hydrodynamic instabilities that impart substantial asymmetries to the shock aid these revivals, with convection appearing first in the 12 solar mass model and the standing accretion shock instability (SASI) appearing first in the 25 solar mass model. Three of the models have developed pronounced prolate morphologies (the 20 solar mass model has remained approximately spherical). By 500 ms after bounce the mean shock radii in all four models exceed 3,000 km and the diagnostic explosion energies are 0.33, 0.66, 0.65, and 0.70 Bethe (B=10^{51} ergs) for the 12, 15, 20, and 25 solar mass models, respectively, and are increasing. The three least massive of our models are already sufficiently energetic to completely unbind the envelopes of their progenitors (i.e., to explode), as evidenced by our best estimate of their explosion energies, which first become positive at 320, 380, and 440 ms after bounce. By 850 ms the 12 solar mass diagnostic explosion energy has saturated at 0.38 B, and our estimate for the final kinetic energy of the ejecta is ~ 0.3 B, which is comparable to observations for lower-mass progenitors.

  19. Precise Electromagnetic Tests of Ab Initio Calculations of Light Nuclei: States in {sup 10}Be

    SciTech Connect

    McCutchan, E. A.; Lister, C. J.; Wiringa, R. B.; Pieper, Steven C.; Seweryniak, D.; Greene, J. P.; Carpenter, M. P.; Janssens, R. V. F.; Khoo, T. L.; Lauritsen, T.; Zhu, S.; Chiara, C. J.; Stefanescu, I.

    2009-11-06

    In order to test ab initio calculations of light nuclei, we have remeasured lifetimes in {sup 10}Be using the Doppler shift attenuation method (DSAM) following the {sup 7}Li({sup 7}Li,alpha){sup 10}Be reaction at 8 and 10 MeV. The new experiments significantly reduce systematic uncertainties in the DSAM technique. The J{sup p}i=2{sub 1}{sup +} state at 3.37 MeV has tau=205+-(5){sub stat}+-(7){sub sys} fs corresponding to a B(E2arrow down) of 9.2(3)e{sup 2} fm{sup 4} in broad agreement with many calculations. The J{sup p}i=2{sub 2}{sup +} state at 5.96 MeV was found to have a B(E2arrow down) of 0.11(2)e{sup 2} fm{sup 4} and provides a more discriminating test of nuclear models. New Green's function Monte Carlo calculations for these states and transitions with a number of Hamiltonians are also reported and compared to experiment.

  20. Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions.

    PubMed

    Zhou, Y; Wang, S; Li, Y; Zhang, Y

    2016-01-01

    There are two key requirements for reliably simulating enzyme reactions: one is a reasonably accurate potential energy surface to describe the bond-forming/breaking process as well as to adequately model the heterogeneous enzyme environment; the other is to perform extensive sampling since an enzyme system consists of at least thousands of atoms and its energy landscape is very complex. One attractive approach to meet both daunting tasks is Born-Oppenheimer ab initio QM/MM molecular dynamics (aiQM/MM-MD) simulation with umbrella sampling. In this chapter, we describe our recently developed pseudobond Q-Chem-Amber interface, which employs a combined electrostatic-mechanical embedding scheme with periodic boundary condition and the particle mesh Ewald method for long-range electrostatics interactions. In our implementation, Q-Chem and the sander module of Amber are combined at the source code level without using system calls, and all necessary data communications between QM and MM calculations are achieved via computer memory. We demonstrate the applicability of this pseudobond Q-Chem-Amber interface by presenting two examples, one reaction in aqueous solution and one enzyme reaction. Finally, we describe our established aiQM/MM-MD enzyme simulation protocol, which has been successfully applied to study more than a dozen enzymes. PMID:27498636