WorldWideScience

Sample records for ab initio x-ray

  1. Ab initio theory and calculations of X-ray spectra

    International Nuclear Information System (INIS)

    Rehr, J.J.; Kas, J.J.; Prange, M.P.; Sorini, A.P.; Takimoto, Y.; Vila, F.

    2009-01-01

    There has been dramatic progress in recent years both in the calculation and interpretation of various x-ray spectroscopies. However, current theoretical calculations often use a number of simplified models to account for many-body effects, in lieu of first principles calculations. In an effort to overcome these limitations we describe in this article a number of recent advances in theory and in theoretical codes which offer the prospect of parameter free calculations that include the dominant many-body effects. These advances are based on ab initio calculations of the dielectric and vibrational response of a system. Calculations of the dielectric function over a broad spectrum yield system dependent self-energies and mean-free paths, as well as intrinsic losses due to multielectron excitations. Calculations of the dynamical matrix yield vibrational damping in terms of multiple-scattering Debye-Waller factors. Our ab initio methods for determining these many-body effects have led to new, improved, and broadly applicable x-ray and electron spectroscopy codes. (authors)

  2. X-ray spectroscopy at the Mn K edge in LaMnO3 : An ab initio study

    NARCIS (Netherlands)

    Hozoi, L.; Vries, A.H. de; Broer, R.

    2001-01-01

    We present ab initio quantum chemical embedded cluster calculations of Mn core-valence and d-d transitions in LaMnO3. The results are also important for the analysis of recent x-ray absorption and x-ray scattering experiments at the Mn K edge in LaMnO3. We find that the first two peaks of the

  3. Structural investigation of water-acetonitrile mixtures: An ab initio, molecular dynamics and X-ray diffraction study

    International Nuclear Information System (INIS)

    Bako, Imre; Megyes, Tuende; Palinkas, Gabor

    2005-01-01

    In this work, we present a study on water-acetonitrile (AN) mixtures by molecular dynamics ab initio and X-ray diffraction techniques. Comparison of the experimental total G(r) functions of the mixtures with the results of molecular dynamics simulation shows an overall good agreement. The properties of hydrogen bonded clusters (water clusters, and water-AN clusters) in these mixtures have been determined. Two different types of AN-water dimers were identified by ab initio quantum chemical calculation. One of these structures proved to be a true H-bonded dimer and the other a dipole bound dimer

  4. The T2 phase in the Nb–Si–B system studied by ab initio calculations and synchrotron X-ray diffraction

    International Nuclear Information System (INIS)

    Joubert, J.-M.; Colinet, C.; Rodrigues, G.; Suzuki, P.A.; Nunes, C.A.; Coelho, G.C.; Tedenac, J.-C.

    2012-01-01

    The solid solution based on Nb 5 Si 3 (Cr 5 B 3 structure type, D8 l , tI32, I4/mcm, No140, a=6.5767 Å, c=11.8967 Å) in the Nb–Si–B system was studied from the structural and thermodynamic point of view both experimentally and by ab initio calculations. Rietveld refinement of powder X-ray synchrotron data allowed to determine the boron to silicon substitution mechanism and the structural parameters. Ab initio calculations of different ordered compounds and selected disordered alloys allowed to obtain in addition to the enthalpy of formation of the solution, substitution mechanism and structural parameters which are in excellent agreement with the experimental data. The stability of the phase is discussed. - Graphial abstract: Valence-charge electron localization function in the z=0 plane of the D8 l structure for the ordered compound Nb 5 SiB 2 . Highlights: ► Coupling between ab initio data and experimental results from synchrotron powder diffraction. ► Excellent agreement between the two techniques for the site occupancies and internal coordinates. ► Explanation of the phase stability up to Nb 5 SiB 2 .

  5. X-ray magnetic scattering in SDW Cr - ab initio study

    International Nuclear Information System (INIS)

    Takahashi, M.; Igarashi, J.-I.; Hirai, K.

    2004-01-01

    Full text: Resonant x-ray scattering at the K-edge of transition metal atom has attracted much attention as a powerful tool for obtaining information on magnetic or orbital properties of 3d electrons. Recently Mannix et al. performed the x-ray magnetic scattering experiment in SDW Chromium and observed the finite scattering intensity with resonant enhancement at Cr K-edge on the SDW magnetic spot (0, 0, 1 ±δ). Applying ab-initio band structure calculation based on the local spin density approximation, we analyze the scattering spectra and elucidate the mechanism of the resonant enhancement in connection with the electronic structure. We assumed the bcc structure with the lattice constant a = 5.45a 0 and the SDW wavelength λ SDW = 20a, which are nearly equilibrium value at the spin-flip temperature T SF = 122K. The K-edge x-ray absorption and scattering spectra are calculated using Fermi's golden rule. We evaluate the non-resonant scattering amplitude within the spherical and dipolar approximations for spin and orbital moment contributions, respectively. The calculated absorption spectra are in good agreement with the experiment. This may assure the validity of the calculation. We obtained finite scattering amplitude with resonant enhancement at the K-edge. The calculated photon energy dependence of the scattering intensity shows good agreement with the experiment. The contribution of the 3d and 4p orbital moments to the non-resonant scattering amplitude is negligible in consequence of the smallness of their values, which are l max d ∼ 0.006ℎ and l max p ∼ 0.00007ℎ. On the other hand, although the 3d and 4p orbital moments are infinitesimal, they play important role on the resonant enhancement, which occurs through the 1s - 4p dipole transition and reflects the 4p orbital polarization. The 4p orbital polarization is caused by the on-site spin-orbit interaction in 4p orbital itself and the hybridization of the 4p orbital with the 3d orbital at neighboring

  6. State-dependent electron delocalization dynamics at the solute-solvent interface: soft-x-ray absorption spectroscopy and ab initio calculations.

    Science.gov (United States)

    Bokarev, Sergey I; Dantz, Marcus; Suljoti, Edlira; Kühn, Oliver; Aziz, Emad F

    2013-08-23

    Nonradiative decay channels in the L-edge fluorescence yield spectra from transition-metal-aqueous solutions give rise to spectral distortions with respect to x-ray transmission spectra. Their origin is unraveled here using partial and inverse partial fluorescence yields on the microjet combined with multireference ab initio electronic structure calculations. Comparing Fe2+, Fe3+, and Co2+ systems we demonstrate and quantify unequivocally the state-dependent electron delocalization within the manifold of d orbitals as one origin of this observation.

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

    Energy Technology Data Exchange (ETDEWEB)

    Draayer, Jerry P. [Louisiana State Univ., Baton Rouge, LA (United States)

    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).

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

    International Nuclear Information System (INIS)

    Draayer, Jerry P.

    2014-01-01

    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).

  9. Supplementary Material for Finding the Stable Structures of N1-xWX with an Ab-initio High-Throughput Approach

    Science.gov (United States)

    2015-05-08

    Supplementary material for “Finding the stable structures of N1−xWX with an ab - initio high-throughput approach” Michael J. Mehl∗ Center for...AND SUBTITLE Supplementary Material for ’Finding the Stable Structures of N1-xWX with an ab - initio High-throughput Approach’ 5a. CONTRACT NUMBER 5b...and J. Hafner, Ab initio molecular dynamics for open-shell transition metals, Phys. Rev. B 48, 13115–13118 (1993). 2 G. Kresse and J. Hafner, Ab initio

  10. Ab-initio calculations of Co-based diluted magnetic semiconductors Cd 1-xCoxX (X=S, Se, Te)

    KAUST Repository

    Saeed, Yasir; Nazir, Safdar; Shaukat, Ali; Reshak, A. H.

    2010-01-01

    Ab-initio calculations are performed to investigate the structural, electronic and magnetic properties of spin-polarized diluted magnetic semiconductors composed of IIVI compounds Cd1-xCoxX (X=S, Se, Te) at x=0.25. From the calculated results

  11. Electronic structure of polycrystalline cadmium dichloride studied by X-ray spectroscopies and ab initio calculations

    International Nuclear Information System (INIS)

    Demchenko, I.N.; Chernyshova, M.; Stolte, W.C.; Speaks, D.T.; Derkachova, A.

    2012-01-01

    The electronic structure of cadmium dichloride has been studied by X-ray absorption near edge structure (XANES) and, for the first time, by resonant inelastic X-ray scattering (RIXS) at the Cl K edge. Good agreement was obtained between the non-resonant X-ray emission (XES) along with XANES experimental spectra and the calculated Cl 3p local partial density of states (DOS). The calculations were performed using the full-potential linearized-augmented-plane-wave with the local orbitals (FP-(L)APW l o) method utilized in the WIEN2k code. It was shown that the position of the RIXS band in CdCl 2 follows a linear dispersion according to the Raman–Stokes law if the excitation energy is tuned below the absorption threshold. The situation changes for core excitation above the photoabsorption threshold where the dispersion relation is split into two branches. The position of the resonant contribution does not depend on the excitation energy, while the excitonic sideband follows the Raman–Stoke law. Combined XANES and RIXS measurements compared to calculated band structure allowed us to determine the direct band gap of CdCl 2 to be at 5.7 ± 0.05 eV. -- Highlights: ► XANES at the K edge of Cl and related emission KV band interpreted within the ab initio DFT formalism. ► Two dominant contributions observed in RIXS data: the resonant and the excitonic ones. ► The dispersion relation below the absorption threshold follows Raman–Stokes law. ► Dispersion above the threshold splits into two qualitatively different relations. ► Overlapping of XAS spectrum with RIXS one makes possible to estimate direct band gap value to be 5.7 eV.

  12. Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory.

    Science.gov (United States)

    Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

    2009-10-29

    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.

  13. Ab initio pseudopotential theory

    International Nuclear Information System (INIS)

    Yin, M.T.; Cohen, M.L.

    1982-01-01

    The ab initio norm-conserving pseudopotential is generated from a reference atomic configuration in which the pseudoatomic eigenvalues and wave functions outside the core region agree with the corresponding ab initio all-electron results within the density-functional formalism. This paper explains why such pseudopotentials accurately reproduce the all-electron results in both atoms and in multiatomic systems. In particular, a theorem is derived to demonstrate the energy- and perturbation-independent properties of ab initio pseudopotentials

  14. Conformational analysis of an acyclic tetrapeptide: ab-initio structure determination from X-ray powder diffraction, Hirshfeld surface analysis and electronic structure.

    Science.gov (United States)

    Das, Uday; Naskar, Jishu; Mukherjee, Alok Kumar

    2015-12-01

    A terminally protected acyclic tetrapeptide has been synthesized, and the crystal structure of its hydrated form, Boc-Tyr-Aib-Tyr-Ile-OMe·2H2O (1), has been determined directly from powder X-ray diffraction data. The backbone conformation of tetrapeptide (1) exhibiting two consecutive β-turns is stabilized by two 4 → 1 intramolecular N-H · · · O hydrogen bonds. In the crystalline state, the tetrapeptide molecules are assembled through water-mediated O-H · · · O hydrogen bonds to form two-dimensional molecular sheets, which are further linked by intermolecular C-H · · · O hydrogen bonds into a three-dimensional supramolecular framework. The molecular electrostatic potential (MEP) surface of (1) has been used to supplement the crystallographic observations. The nature of intermolecular interactions in (1) has been analyzed quantitatively through the Hirshfeld surface and two-dimensional fingerprint plot. The DFT optimized molecular geometry of (1) agrees closely with that obtained from the X-ray structure analysis. The present structure analysis of Boc-Tyr-Aib-Tyr-Ile-OMe·2H2 O (1) represents a case where ab-initio crystal structure of an acyclic tetrapeptide with considerable molecular flexibility has been accomplished from laboratory X-ray powder diffraction data. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.

  15. Ab initio vel ex eventu

    Science.gov (United States)

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

    Der gegenwärtige Stand der physikalischen Erkenntnis, in Sonderheit die Atomistik und die Quantentheorie, ermöglicht (in wohldefinierten Energie-Bereichen) eine ab initio-Berechnung aller physikalischen und chemischen Prozesse und Strukturen. Die Schrödinger-Gleichung erlaubt zusammen mit den Prinzipien der Quantenstatistik (Pauli-Prinzip) aus dem Planckschen Wirkungsquantum h und den atomischen Konstanten die Berechnung aller Energieumsätze, Zeitabläufe etc., die insbesondere die chemische Physik bestimmen. Die Rechenresultate gelten auch quantitativ bis auf die unvermeidliche Stochastik.Die ab initio-Berechnungen korrespondieren einerseits und sind andererseits komplementär zu den auf den Methoden der theoretischen Chemie und der klassischen Thermodynamik beruhenden Ergebnissen ex eventu. Die theoretische Behandlung ab initio führt zu mathematischen Experimenten, die die Laboratoriums-Experimente ergänzen oder auch substituieren.Translated AbstractAb initio vel ex eventuThe present state of physical knowledge, in peculiar atomistic and quantum theory, makes an ab initio calculation of all physical and chemical processes and structures possible (in well defined reaches of energy). The Schrödinger equation together with the principles of quantum statistics (Pauli principle) permits from the Planck and atomistic constants to calculate all exchanges of energy, courses of time, etc. which govern chemical physics. The calculated results are valid even quantitatively apart from the unavoidable stochastics.These ab initio calculations on the one hand correspond and are on the other complimentary to results ex eventu based on the methods of theoretical chemistry and classical thermodynamics. Theoretical treatment ab initio leads to mathematical experiments which add to or even substitute experiments in the laboratory.

  16. Cosmic-ray modulation: an ab initio approach

    Energy Technology Data Exchange (ETDEWEB)

    Engelbrecht, N.E.; Burger, R.A., E-mail: 12580996@nwu.ac.za [Center for Space Research, North-West University, Potchefstroom (South Africa)

    2014-07-01

    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. (author)

  17. Cosmic-ray modulation: an ab initio approach

    International Nuclear Information System (INIS)

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

    2014-01-01

    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. (author)

  18. Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo

    International Nuclear Information System (INIS)

    Zen, Andrea; Luo, Ye; Mazzola, Guglielmo; Sorella, Sandro; Guidoni, Leonardo

    2015-01-01

    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

  19. Lattice dynamics at high pressure: application of inelastic X-ray scattering and ab-initio calculations -MgO at 35 GPa

    International Nuclear Information System (INIS)

    Ghose, Subrata

    2006-01-01

    Full text: Until recently, inelastic neutron scattering (INS) has been extensively used to study the phonon dispersion throughout the Brillouin zone and phonon density of states in crystalline materials. The weak interaction of neutrons with matter and the typical size of the neutron beams require the use of cm-size single crystals that puts an upper limit to the measurement of phonon dispersion at high pressure to about 10-15 Gpa by INS. Inelastic X-ray scattering (IXS) using third generation synchrotron sources now makes it possible to measure the phonon dispersion at high pressures up to 50 GP A in crystals tens of microns in size mounted in a diamond-anvil cell, usually using He as the pressure transmitting medium. We have used this technique to measure the longitudinal acoustic and optic phonon branches of MgO along the Γ-X direction at 35 Gpa. The experimentally observed phonon-branches are in remarkable agreement with ab-initio quantum mechanical calculations using the density-functional perturbation theory. The derived thermodynamic properties, such as specific heat and the entropy are in very good agreement with values obtained from a thermodynamically assessed data set

  20. Multiple time step integrators in ab initio molecular dynamics

    International Nuclear Information System (INIS)

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

    2014-01-01

    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

  1. Structural, magnetic and electronic properties of FexCoyIrz (x + y + z = 5, 6) clusters: an ab initio study

    KAUST Repository

    Devi, Assa Aravindh Sasikala

    2014-01-01

    Investigations on freestanding binary and ternary clusters of Fe (x) Co (y) Ir (z) (x + y + z = 5, 6) are carried out using ab initio density functional theory techniques. The geometry, chemical order, binding energy, magnetic moment and electronic

  2. Collective rotation from ab initio theory

    International Nuclear Information System (INIS)

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

    2015-01-01

    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 7–9 Be 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. (author)

  3. Ab Initio Description of Disordered Sr1−xKxFe2As2 Using the Coherent Potential Approximation

    KAUST Repository

    Pulikkotil, J. J.; Schwingenschlö gl, Udo

    2010-01-01

    The electronic structure of disordered Sr1−xKxFe2As2 is studied by ab initio density functional theory. As no superstructure and/or atomic short range ordering is reported for Sr1−xKxFe2As2, the coherent potential approximation can be used

  4. Molecular form factors in X-ray crystallography

    NARCIS (Netherlands)

    Groenewegen, P.P.M.; Feil, D.

    1969-01-01

    The calculation of molecular form factors from ab initio molecular electronic wavefunctions is discussed, and a scheme for application to X-ray diffraction structure analysis is given. The method is used to calculate the form factor of the NH+4 molecular ion from three accurate molecular

  5. Oxide nanostructures on a Nb surface and related systems: experiments and ab initio calculations

    International Nuclear Information System (INIS)

    Kuznetsov, Mikhail V; Razinkin, A S; Ivanovskii, Alexander L

    2011-01-01

    This review discusses the state of the art in two related research areas: the surfaces of niobium and of its related group IV-VI transition metals, and surface (primarily oxide) nanostructures that form on niobium (and group IV-VI d-metals) due to gas adsorption or impurity diffusion from the bulk. Experimental (X-ray photoelectron spectroscopy, photoelectron diffraction, scanning tunneling microscopy) and theoretical (ab initio simulation) results on d-metal surfaces are summarized and reviewed. (reviews of topical problems)

  6. Ab initio model of porous periclase

    International Nuclear Information System (INIS)

    Drummond, Neil D.; Swift, Damian C.; Ackland, Graeme J.

    2004-01-01

    A two-phase equilibrium equation of state (EOS) for periclase (MgO) was constructed using ab initio quantum mechanics, including a rigorous calculation of quasiharmonic phonon modes. Much of the shock wave data reported for periclase is on porous material. We compared the theoretical EOS with porous data using a simple 'snowplough' treatment and also a model using finite equilibration rates suitable for continuum mechanics simulations. (This model has been applied previously to various heterogeneous explosives as well as other porous materials.) The results were consistent and matched the data well at pressures above the regime affected by strength - and ramp-wave formation - during compaction. Ab initio predictions of the response of porous material have been cited recently as a novel and advanced capability; we feel that this is a fairly routine extension to established ab initio techniques

  7. Development of materials science by Ab initio powder diffraction analysis

    International Nuclear Information System (INIS)

    Fujii, Kotaro

    2015-01-01

    Crystal structure is most important information to understand properties and behavior of target materials. Technique to analyze unknown crystal structures from powder diffraction data (ab initio powder diffraction analysis) enables us to reveal crystal structures of target materials even we cannot obtain a single crystal. In the present article, three examples are introduced to show the power of this technique in the field of materials sciences. The first example is dehydration/hydration of the pharmaceutically relevant material erythrocycin A. In this example, crystal structures of two anhydrous phases were determined from synchrotron X-ray powder diffraction data and their different dehydration/hydration properties were understood from the crystal structures. In the second example, a crystal structure of a three dimensional metal-organic-framework prepared by a mechanochemical reaction was determined from laboratory X-ray powder diffraction data and the reaction scheme has been revealed. In the third example, a crystal structure of a novel oxide-ion conductor of a new structure family was determined from synchrotron X-ray and neutron powder diffraction data which gave an important information to understand the mechanism of the oxide-ion conduction. (author)

  8. Ab initio derivation of model energy density functionals

    International Nuclear Information System (INIS)

    Dobaczewski, Jacek

    2016-01-01

    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. (letter)

  9. An ab initio molecular

    Indian Academy of Sciences (India)

    mechanisms of two molecular crystals: An ab initio molecular dynamics ... for Computation in Molecular and Materials Science and Department of Chemistry, School of ..... NSAF Foundation of National Natural Science Foun- ... Matter 14 2717.

  10. Ab initio study of phase equilibria in TiCx

    DEFF Research Database (Denmark)

    Korzhavyi, P.A.; Pourovskii, L.V.; Hugosson, H.W.

    2002-01-01

    The phase diagram for the vacancy-ordered structures in the substoichiometric TiCx (x = 0.5-1.0) has been established from Monte Carlo simulations with the long-range pair and multisite effective interactions obtained from ab initio calculations. Three ordered superstructures of vacancies (Ti2C, Ti...

  11. Speed-up of ab initio hybrid Monte Carlo and ab initio path integral hybrid Monte Carlo simulations by using an auxiliary potential energy surface

    International Nuclear Information System (INIS)

    Nakayama, Akira; Taketsugu, Tetsuya; Shiga, Motoyuki

    2009-01-01

    Efficiency of the ab initio hybrid Monte Carlo and ab initio path integral hybrid Monte Carlo methods is enhanced by employing an auxiliary potential energy surface that is used to update the system configuration via molecular dynamics scheme. As a simple illustration of this method, a dual-level approach is introduced where potential energy gradients are evaluated by computationally less expensive ab initio electronic structure methods. (author)

  12. Molecular structure determination of cyclootane by ab initio and electron diffraction methods in the gas phase

    OpenAIRE

    De Almeida, Wagner B.

    2000-01-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can ma...

  13. Ab initio R-matrix/Multi-channel Quantum Defect Theory applied to Molecular Core Excitation and Ionization

    International Nuclear Information System (INIS)

    Hiyama, M.; Kosugi, N.

    2004-01-01

    Full text: Ab initio R-matrix/MQDT approach, which is a combination of ab initio R-matrix techniques and the multi channel quantum defect theory (MQDT), has recently been developed by one of the present authors (MH) and Child, to successfully obtain the potential energy curves of Rydberg states converging to not only the lowest but also the higher ionized states. This approach is also applied to estimate the valence state interaction with Rydberg and continuum (ionization) channels. Very recently we have made an original ab initio polyatomic R-matrix/MQDT program package, GSCF4R based on Gaussian type basis functions for the bound and continuum states, to extensively study molecular excitation and ionization in the X-ray region as well as in the VUV region. We are going to report the results for core excitation and ionization of diatomic molecules such as NO and O 2 to show that the R-matrix/MQDT method is indispensable to describe the core-to-Rydberg states with the higher quantum number and the continuum states. These results lead us to the conclusion that the close-coupling approximation augmented with the correlation term within the R-matrix/MQDT formalism is powerful to calculate the Rydberg-valence mixing and the interchannel coupling between several core-ionized states

  14. Simple synthesis, structure and ab initio study of 1,4-benzodiazepine-2,5-diones

    Science.gov (United States)

    Jadidi, Khosrow; Aryan, Reza; Mehrdad, Morteza; Lügger, Thomas; Ekkehardt Hahn, F.; Ng, Seik Weng

    2004-04-01

    A simple procedure for the synthesis of pyrido[2,1-c][1,4] benzodiazepine-6,12-dione ( 1) and 1,4-benzodiazepine-2,5-diones ( 2a- 2d), using microwave irradiation and/or conventional heating is reported. The configuration of 1 was determined by single-crystal X-ray diffraction. A detailed ab initio B3LYP/6-31G* calculation of structural parameters and substituent effects on ring inversion barriers (Δ G#) and also free energy differences (Δ G0) for benzodiazepines are reported.

  15. Ab-initio calculations of Co-based diluted magnetic semiconductors Cd 1-xCoxX (X=S, Se, Te)

    KAUST Repository

    Saeed, Yasir

    2010-10-01

    Ab-initio calculations are performed to investigate the structural, electronic and magnetic properties of spin-polarized diluted magnetic semiconductors composed of IIVI compounds Cd1-xCoxX (X=S, Se, Te) at x=0.25. From the calculated results of band structure and density of states, the half-metallic character and stability of ferromagnetic state for Cd1-xCoxS, Cd1-xCoxSe and Cd 1-xCoxTe alloys are determined. It is found that the tetrahedral crystal field gives rise to triple degeneracy t2g and double degeneracy eg. Furthermore, we predict the values of spin-exchange splitting energies Δx(d) and Δ x(p-d) and exchange constants N0α and N 0β produced by the Co 3d states. Calculated total magnetic moments and the robustness of half-metallicity of Cd1-xCo xX (X=S, Se, Te) with respect to the variation in lattice parameters are also discussed. We also extend our calculations to x=0.50, 0.75 for S compounds in order to observe the change due to increase in Co. © 2010 Elsevier B.V.

  16. Ab initio valence calculations in chemistry

    CERN Document Server

    Cook, D B

    1974-01-01

    Ab Initio Valence Calculations in Chemistry describes the theory and practice of ab initio valence calculations in chemistry and applies the ideas to a specific example, linear BeH2. Topics covered include the Schrödinger equation and the orbital approximation to atomic orbitals; molecular orbital and valence bond methods; practical molecular wave functions; and molecular integrals. Open shell systems, molecular symmetry, and localized descriptions of electronic structure are also discussed. This book is comprised of 13 chapters and begins by introducing the reader to the use of the Schrödinge

  17. Experimental and ab initio investigations on textured Li–Mn–O spinel thin film cathodes

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, J., E-mail: Julian.Fischer@kit.edu [Karlsruhe Institute of Technology (KIT), Institute for Applied Materials (IAM), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany); Music, D. [RWTH Aachen University, Materials Chemistry, Kopernikusstrasse 10, 52074 Aachen (Germany); Bergfeldt, T.; Ziebert, C.; Ulrich, S.; Seifert, H.J. [Karlsruhe Institute of Technology (KIT), Institute for Applied Materials (IAM), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany)

    2014-12-01

    This paper describes the tailored preparation of nearly identical lithium–manganese–oxide thin film cathodes with different global grain orientations. The thin films were synthesized by rf magnetron sputtering from a LiMn{sub 2}O{sub 4}-target in a pure argon plasma. Under appropriate processing conditions, thin films with a cubic spinel structure and a nearly similar density and surface topography but different grain orientation, i.e. (111)- and (440)-textured films, were achieved. The chemical composition was determined by inductively coupled plasma optical emission spectroscopy and carrier gas hot extraction. The constitution- and microstructure were evaluated by X-ray diffraction and Raman spectroscopy. The surface morphology and roughness were investigated by scanning electron and atomic force microscopy. The differently textured films represent an ideal model system for studying potential effects of grain orientation on the lithium ion diffusion and electrochemical behavior in LiMn{sub 2}O{sub 4}-based thin films. They are nearly identical in their chemical composition, atomic bonding behavior, surface-roughness, morphology and thickness. Our initial ab initio molecular dynamics data indicate that Li ion transport is faster in (111)-textured structure than in (440)-textured one. - Highlights: • Thin film model system of differently textured cubic Li–Mn–O spinels. • Investigation of the Li–Mn–O thin film mass density by X-ray reflectivity. • Ab initio molecular dynamics simulation on Li ion diffusion in LiMn{sub 2}O{sub 4}.

  18. Experimental and ab initio investigations on textured Li–Mn–O spinel thin film cathodes

    International Nuclear Information System (INIS)

    Fischer, J.; Music, D.; Bergfeldt, T.; Ziebert, C.; Ulrich, S.; Seifert, H.J.

    2014-01-01

    This paper describes the tailored preparation of nearly identical lithium–manganese–oxide thin film cathodes with different global grain orientations. The thin films were synthesized by rf magnetron sputtering from a LiMn 2 O 4 -target in a pure argon plasma. Under appropriate processing conditions, thin films with a cubic spinel structure and a nearly similar density and surface topography but different grain orientation, i.e. (111)- and (440)-textured films, were achieved. The chemical composition was determined by inductively coupled plasma optical emission spectroscopy and carrier gas hot extraction. The constitution- and microstructure were evaluated by X-ray diffraction and Raman spectroscopy. The surface morphology and roughness were investigated by scanning electron and atomic force microscopy. The differently textured films represent an ideal model system for studying potential effects of grain orientation on the lithium ion diffusion and electrochemical behavior in LiMn 2 O 4 -based thin films. They are nearly identical in their chemical composition, atomic bonding behavior, surface-roughness, morphology and thickness. Our initial ab initio molecular dynamics data indicate that Li ion transport is faster in (111)-textured structure than in (440)-textured one. - Highlights: • Thin film model system of differently textured cubic Li–Mn–O spinels. • Investigation of the Li–Mn–O thin film mass density by X-ray reflectivity. • Ab initio molecular dynamics simulation on Li ion diffusion in LiMn 2 O 4

  19. Ab initio and Gordon--Kim intermolecular potentials for two nitrogen molecules

    International Nuclear Information System (INIS)

    Ree, F.H.; Winter, N.W.

    1980-01-01

    Both ab initio MO--LCAO--SCF and the electron-gas (or Gordon--Kim) methods have been used to compute the intermolecular potential (Phi) of N 2 molecules for seven different N 2 --N 2 orientations. The ab initio calculations were carried out using a [4s3p] contracted Gaussian basis set with and without 3d polarization functions. The larger basis set provides adequate results for Phi>0.002 hartree or intermolecular separations less than 6.5--7 bohr. We use a convenient analytic expression to represent the ab initio data in terms of the intermolecular distance and three angles defining the orientations of the two N 2 molecules. The Gordon--Kim method with Rae's self-exchange correction yields Phi, which agrees reasonably well over a large repulsive range. However, a detailed comparison of the electron kinetic energy contributions shows a large difference between the ab initio and the Gordon--Kim calculations. Using the ab initio data we derive an atom--atom potential of the two N 2 molecules. Although this expression does not accurately fit the data at some orientations, its spherical average agrees with the corresponding average of the ab initio Phi remarkably well. The spherically averaged ab initio Phi is also compared with the corresponding quantities derived from experimental considerations. The approach of the ab initio Phi to the classical quadrupole--quadrupole interaction at large intermolecular separation is also discussed

  20. Unraveling the structure of the h-BN/Rh(111) nanomesh with ab initio calculations

    International Nuclear Information System (INIS)

    Laskowski, R; Blaha, P

    2008-01-01

    The properties of a single layer of h-BN on top of a Rh(111) surface are discussed in terms of an ab initio generated force field approach as well as by direct ab initio density-functional theory (DFT) calculations. A single-layer model for the h-BN/Rh(111) nanomesh, in contrast to a previously considered (incomplete) double-layer model of h-BN, can explain the experimental data. The main focus of this work is to compare a force field approach described earlier in (Laskowski et al 2007 Phys. Rev. Lett. 98 106802) with direct ab initio calculations. The calculated geometry of the h-BN layer is very similar to the structure predicted by the force field approach. The ab initio calculated density of states projected on N-p x,y of BN corresponding to 'low' and 'high' regions with respect to the Rh surface shows a 1 eV splitting and thus explains the observed σ-band splitting. Moreover, we find good agreement between calculated and experimental scanning tunneling microscope (STM) images of this system

  1. Bicanonical ab Initio Molecular Dynamics for Open Systems.

    Science.gov (United States)

    Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

    2017-08-08

    Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

  2. Strong influence of coadsorbate interaction on CO desorption dynamics on Ru(0001) probed by ultrafast x-ray spectroscopy and ab initio simulations

    Energy Technology Data Exchange (ETDEWEB)

    Xin, H. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); LaRue, J. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Oberg, H. [Stockholm Univ., Stockholm (Sweden); Beye, M. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Dell' Angela, M. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); Turner, J. J. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Gladh, J. [Stockholm Univ., Stockholm (Sweden); Ng, M. L. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Sellberg, J. A. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Kaya, S. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Mercurio, G. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); Hieke, F. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); Nordlund, D. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Schlotter, W. F. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Dakovski, G. L. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Minitti, M. P. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Fohlisch, A. [Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Univ. Potsdam, Potsdam (Germany); Wolf, M. [Fritz-Haber Institute of the Max-Planck-Society, Berlin (Germany); Wurth, W. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); DESY Photon Science, Hamburg (Germany); Ogasawara, H. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Norskov, J. K. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); Ostrom, H. [Stockholm Univ., Stockholm (Sweden); Pettersson, L. G. M. [Stockholm Univ., Stockholm (Sweden); Nilsson, A. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stockholm Univ., Stockholm (Sweden); Ablid-Pedersen, F. [SLAC National Accelerator Lab., Menlo Park, CA (United States)

    2015-04-16

    We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distribution and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.

  3. Elastic properties of fcc Fe-Mn-X (X = Cr, Co, Ni, Cu) alloys studied by the combinatorial thin film approach and ab initio calculations.

    Science.gov (United States)

    Reeh, S; Kasprzak, M; Klusmann, C D; Stalf, F; Music, D; Ekholm, M; Abrikosov, I A; Schneider, J M

    2013-06-19

    The elastic properties of fcc Fe-Mn-X (X = Cr, Co, Ni, Cu) alloys with additions of up to 8 at.% X were studied by combinatorial thin film growth and characterization and by ab initio calculations using the disordered local moments (DLM) approach. The lattice parameter and Young's modulus values change only marginally with X. The calculations and experiments are in good agreement. We demonstrate that the elastic properties of transition metal alloyed Fe-Mn can be predicted by the DLM model.

  4. X-ray absorption near-edge structure in alpha-quartz and stishovite: Ab initio calculation with core - hole interaction

    International Nuclear Information System (INIS)

    Mo, Shang-Di; Ching, W. Y.

    2001-01-01

    Ab initio calculation of the XANSE/ELNES spectra for α quartz and stishovite were carried out using a large-supercell approach that includes the electron - core - hole interaction. Excellent agreements with experimental spectra were obtained for Si - K, Si - L 2,3 , and O - K edges. The usual interpretation using orbital-resolved local density of states in the conduction band is unsatisfactory. [copyright] 2001 American Institute of Physics

  5. Molecular structure determination of cyclooctane by Ab Initio and electron diffraction methods in the gas phase; Determinacao da estrutura molecular do ciclooctano por metodos Ab Initio e difracao de eletrons na fase gasosa

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Wagner B. de [Minas Gerais Univ., Belo Horizonte, MG (Brazil). Dept. de Quimica

    2000-10-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase an initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions. (author)

  6. Elastic properties of fcc Fe–Mn–X (X = Cr, Co, Ni, Cu) alloys studied by the combinatorial thin film approach and ab initio calculations

    International Nuclear Information System (INIS)

    Reeh, S; Kasprzak, M; Klusmann, C D; Stalf, F; Music, D; Schneider, J M; Ekholm, M; Abrikosov, I A

    2013-01-01

    The elastic properties of fcc Fe–Mn–X (X = Cr, Co, Ni, Cu) alloys with additions of up to 8 at.% X were studied by combinatorial thin film growth and characterization and by ab initio calculations using the disordered local moments (DLM) approach. The lattice parameter and Young’s modulus values change only marginally with X. The calculations and experiments are in good agreement. We demonstrate that the elastic properties of transition metal alloyed Fe–Mn can be predicted by the DLM model. (paper)

  7. Raman spectroscopy, ab-initio model calculations, and conformational, equilibria in ionic liquids

    DEFF Research Database (Denmark)

    Berg, Rolf W.

    2009-01-01

    spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT- Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methyl-imidazolium ([C4C1Im]+X-) salts. The rotational isomerism of the [C4C1Im]+ cation is described: the presence of anti.......3 Brief introduction to ab-initio model calculations .... 312 12.4 Case study on Raman spectroscopy and structure of imidazolium-based ionic liquids ..... 312 12.5 Raman spectra and structure of [C4C1Im]+ liquids ..... 315 12.6 Normal mode analysis and rotational isomerism of the [C4C1Im]+ cation...

  8. Ab-initio ZORA calculations

    NARCIS (Netherlands)

    Faas, S.; Snijders, Jaap; van Lenthe, J.H.; HernandezLaguna, A; Maruani, J; McWeeny, R; Wilson, S

    2000-01-01

    In this paper we present the first application of the ZORA (Zeroth Order Regular Approximation of the Dirac Fock equation) formalism in Ab Initio electronic structure calculations. The ZORA method, which has been tested previously in the context of Density Functional Theory, has been implemented in

  9. Raman Spectroscopy and Ab-Initio Model Calculations on Ionic Liquids

    DEFF Research Database (Denmark)

    Berg, Rolf W.

    2007-01-01

    spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT-Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methylimidazolium ([C4mim][X]) salts. The rotational isomerism of the [C4mim]þ cation is described: the presence of anti...

  10. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit; Bajic, Vladimir B.; Kaushik, Dinesh

    2011-01-01

    We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

  11. AN AB INITIO MODEL FOR COSMIC-RAY MODULATION

    Energy Technology Data Exchange (ETDEWEB)

    Engelbrecht, N. E.; Burger, R. A. [Center for Space Research, North-West University, Potchefstroom 2520 (South Africa)

    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.

  12. Ab Initio Calculation of Hyperfine Interaction Parameters: Recent Evolutions, Recent Examples

    International Nuclear Information System (INIS)

    Cottenier, Stefaan; Vanhoof, Veerle; Torumba, Doru; Bellini, Valerio; Cakmak, Mehmet; Rots, Michel

    2004-01-01

    For some years already, ab initio calculations based on Density Functional Theory (DFT) belong to the toolbox of the field of hyperfine interaction studies. In this paper, the standard ab initio approach is schematically sketched. New features, methods and possibilities that broke through during the past few years are listed, and their relation to the standard approach is explained. All this is illustrated by some highlights of recent ab initio work done by the Nuclear Condensed Matter Group at the K.U.Leuven.

  13. Molecular structure determination of cyclooctane by Ab Initio and electron diffraction methods in the gas phase

    International Nuclear Information System (INIS)

    Almeida, Wagner B. de

    2000-01-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase an initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions. (author)

  14. Modeling Disordered Materials with a High Throughput ab-initio Approach

    Science.gov (United States)

    2015-11-13

    Modeling Disordered Materials with a High Throughput ab - initio Approach Kesong Yang,1 Corey Oses,2 and Stefano Curtarolo3, 4 1Department of...J. Furthmüller, Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set, Phys. Rev. B 54, 11169–11186 (1996

  15. Embedded atom approach for gold–silicon system from ab initio

    Indian Academy of Sciences (India)

    In the present paper, an empirical embedded atom method (EAM) potential for gold–silicon (Au–Si) is developed by fitting to ab initio force (the 'force matching' method) and experimental data. The force database is generated within ab initio molecular dynamics (AIMD). The database includes liquid phase at various ...

  16. Towards hydrogen metallization: an Ab initio approach; Vers la metallisation de l`hydrogene: approche AB initio

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, St

    1998-12-31

    The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H{sub 2}){sub 2} which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author) 109 refs.

  17. Towards hydrogen metallization: an Ab initio approach; Vers la metallisation de l`hydrogene: approche AB initio

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, St

    1999-12-31

    The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H{sub 2}){sub 2} which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author) 109 refs.

  18. Ab initio potential for solids

    DEFF Research Database (Denmark)

    Chetty, N.; Stokbro, Kurt; Jacobsen, Karsten Wedel

    1992-01-01

    . At the most approximate level, the theory is equivalent to the usual effective-medium theory. At all levels of approximation, every term in the total-energy expression is calculated ab initio, that is, without any fitting to experiment or to other calculations. Every step in the approximation procedure can...

  19. High pressure stability of lithium metatitanate and metazirconate: Insight from experiments & ab-initio calculations

    Science.gov (United States)

    Chitnis, Abhishek; Chakraborty, B.; Tripathi, B. M.; Tyagi, A. K.; Garg, Nandini

    2018-02-01

    Lithium metatitanate (LTO) and lithium metazirconate (LZO) are lithium rich ceramics which can be used as tritium breeder materials for thermonuclear reactors. In-situ x-ray diffraction and ab-initio studies at high pressure show that LTO has a higher bulk modulus than that of LZO. In fact these studies indicate that they are the least compressible of the known lithium rich ceramics like Li2O or Li4SiO4, which are potential candidates for blanket materials. These studies show that the TiO6 octahedra are responsible for the higher bulk modulus of LTO when compared to that of LZO. It has also been shown that the compressibility and distortion of the softer LiO6 octahedra can be controlled by altering the stacking sequence of the more rigid covalently bonded octahedra. This knowledge can be used by chemists to design new lithium based ceramics with higher bulk modulus. It was observed that LTO was stable upto 34 GPa. Ab initio DFT calculations helped to understand the anisotropy in compressibility of both LZO and LTO. This study also shows, that even though the empirical potentials developed by Vijaykumar et al. successfully determine the ambient pressure structure of lithium metatitanate, they cannot be used at non ambient conditions like high pressure [1].

  20. Ab initio studies of vacancies in (8,0) and (8,8) single-walled carbon and boron nitride nanotubes

    CSIR Research Space (South Africa)

    Mashapa, MG

    2012-09-01

    Full Text Available -1 Journal of Nanoscience and Nanotechnology Vol. 12, 7030?7036, 2012 Ab Initio Studies of Vacancies in (8,0) and (8,8) Single-Walled Carbon and Boron Nitride NanotubesAb M. G. Mashapa 1, 2, *, N. Chetty 2, and S. Sinha Ray 1, 3 1 DST...

  1. Summation of Parquet diagrams as an ab initio method in nuclear structure calculations

    International Nuclear Information System (INIS)

    Bergli, Elise; Hjorth-Jensen, Morten

    2011-01-01

    Research highlights: → We present a Green's function based approach for doing ab initio nuclear structure calculations. → In particular the sum the subset of so-called Parquet diagrams. → Applying the theory to a simple but realistic model, results in good agreement with other ab initio methods. → This opens up for ab initio calculations for medium-heavy nuclei. - Abstract: In this work we discuss the summation of the Parquet class of diagrams within Green's function theory as a possible framework for ab initio nuclear structure calculations. The theory is presented and some numerical details are discussed, in particular the approximations employed. We apply the Parquet method to a simple model, and compare our results with those from an exact solution. The main conclusion is that even at the level of approximation presented here, the results shows good agreement with other comparable ab initio approaches.

  2. Ab initio ro-vibronic spectroscopy of SiCCl (X{sup ~2}Π)

    Energy Technology Data Exchange (ETDEWEB)

    Brites, Vincent [Université d’Evry Val d’Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE CNRS UMR 8587, Boulevard F. Mitterrand, 91025 Evry Cedex (France); Mitrushchenkov, Alexander O.; Léonard, Céline, E-mail: celine.leonard@u-pem.fr [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée (France); Peterson, Kirk A. [Department of Chemistry, Washington State University, Pullman, Washington 99164 (United States)

    2014-07-21

    The full dimensional potential energy surfaces of the {sup 2}A{sup ′} and {sup 2}A{sup ′′} electronic components of X{sup ~2}Π SiCCl have been computed using the explicitly correlated coupled cluster method, UCCSD(T)-F12b, combined with a composite approach taking into account basis set incompleteness, core-valence correlation, scalar relativity, and higher order excitations. The spin-orbit and dipole moment surfaces have also been computed ab initio. The ro-vibronic energy levels and absorption spectrum at 5 K have been determined from variational calculations. The influence of each correction on the fundamental frequencies is discussed. An assignment is proposed for bands observed in the LIF experiment of Smith et al. [J. Chem. Phys. 117, 6446 (2002)]. The overall agreement between the experimental and calculated ro-vibronic levels is better than 7 cm{sup −1} which is comparable with the 10–20 cm{sup −1} resolution of the emission spectrum.

  3. Ab initio study of vibronic transitions between x2π and 12Σ+ electronic states of HCP+ ion

    Directory of Open Access Journals (Sweden)

    Stojanović Ljiljana

    2013-01-01

    Full Text Available The ground and low-lying excited doublet electronic states of the HCP+ ion were studied by means of multireference configuration interaction method. Vibronic energy levels of the X2Π state of Σ, Π, Δ, and Φ symmetry, up to the 2500 cm-1, have been calculated variationally, employing previously developed ab initio methods which take into account vibronic and spin-orbit interactions. Obtained vibronic wave functions were used to estimate transition moments between vibronic energy levels of the X2Π and 12Σ+ electronic states. Results were compared to available experimental and theoretical data. [Projekat Ministarstva nauke Republike Srbije, br. 172040

  4. A Simplified Ab Initio Cosmic-ray Modulation Model with Simulated Time Dependence and Predictive Capability

    Science.gov (United States)

    Moloto, K. D.; Engelbrecht, N. E.; Burger, R. A.

    2018-06-01

    A simplified ab initio approach is followed to model cosmic-ray proton modulation, using a steady-state three-dimensional stochastic solver of the Parker transport equation that simulates some effects of time dependence. Standard diffusion coefficients based on Quasilinear Theory and Nonlinear Guiding Center Theory are employed. The spatial and temporal dependences of the various turbulence quantities required as inputs for the diffusion, as well as the turbulence-reduced drift coefficients, follow from parametric fits to results from a turbulence transport model as well as from spacecraft observations of these turbulence quantities. Effective values are used for the solar wind speed, magnetic field magnitude, and tilt angle in the modulation model to simulate temporal effects due to changes in the large-scale heliospheric plasma. The unusually high cosmic-ray intensities observed during the 2009 solar minimum follow naturally from the current model for most of the energies considered. This demonstrates that changes in turbulence contribute significantly to the high intensities during that solar minimum. We also discuss and illustrate how this model can be used to predict future cosmic-ray intensities, and comment on the reliability of such predictions.

  5. Ultrafast X-Ray Spectroscopy of Conical Intersections

    Science.gov (United States)

    Neville, Simon P.; Chergui, Majed; Stolow, Albert; Schuurman, Michael S.

    2018-06-01

    Ongoing developments in ultrafast x-ray sources offer powerful new means of probing the complex nonadiabatically coupled structural and electronic dynamics of photoexcited molecules. These non-Born-Oppenheimer effects are governed by general electronic degeneracies termed conical intersections, which play a key role, analogous to that of a transition state, in the electronic-nuclear dynamics of excited molecules. Using high-level ab initio quantum dynamics simulations, we studied time-resolved x-ray absorption (TRXAS) and photoelectron spectroscopy (TRXPS) of the prototypical unsaturated organic chromophore, ethylene, following excitation to its S2(π π*) state. The TRXAS, in particular, is highly sensitive to all aspects of the ensuing dynamics. These x-ray spectroscopies provide a clear signature of the wave packet dynamics near conical intersections, related to charge localization effects driven by the nuclear dynamics. Given the ubiquity of charge localization in excited state dynamics, we believe that ultrafast x-ray spectroscopies offer a unique and powerful route to the direct observation of dynamics around conical intersections.

  6. Hydration structures of U(III) and U(IV) ions from ab initio molecular dynamics simulations

    International Nuclear Information System (INIS)

    Leung, Kevin; Nenoff, Tina M.

    2012-01-01

    We apply DFT+U-based ab initio molecular dynamics simulations to study the hydration structures of U(III) and U(IV) ions, pertinent to redox reactions associated with uranium salts in aqueous media. U(III) is predicted to be coordinated to 8 water molecules, while U(IV) has a hydration number between 7 and 8. At least one of the innershell water molecules of the hydrated U(IV) complex becomes spontaneously deprotonated. As a result, the U(IV)–O pair correlation function exhibits a satellite peak at 2.15 Å associated with the shorter U(IV)–(OH − ) bond. This feature is not accounted for in analysis of extended x-ray absorption fine structure and x-ray adsorption near edge structure measurements, which yield higher estimates of U(IV) hydration numbers. This suggests that it may be useful to include the effect of possible hydrolysis in future interpretation of experiments, especially when the experimental pH is close to the reported hydrolysis equilibrium constant value.

  7. Mn L2,3-edge X-ray absorption spectroscopic studies on charge-discharge mechanism of Li2MnO3

    International Nuclear Information System (INIS)

    Kubobuchi, Kei; Mogi, Masato; Imai, Hideto; Ikeno, Hidekazu; Tanaka, Isao; Mizoguchi, Teruyasu

    2014-01-01

    The redox reaction of Mn in Li 2 MnO 3 was studied by X-ray absorption spectroscopy and ab initio multiplet calculation. Associated with the de-intercalation of Li-ion, small but clear spectral changes were observed in Mn-L 2,3 X-ray absorption near edge structure (XANES). The systematic ab initio multiplet calculations of Mn-L 2,3 XANES revealed that the spectral changes in the experiment could not simply be ascribed to the change of the valency from Mn 4+ to Mn 5+ but can be explained well by the changes of local atomic structures around Mn 4+ due to the Li de-intercalation. Our results suggest that the electronic state of oxygen should change during charging in Li 2 MnO 3

  8. A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein

    Directory of Open Access Journals (Sweden)

    Mingyuan Xu

    2018-05-01

    Full Text Available A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA9-NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

  9. Many-body optimization using an ab initio monte carlo method.

    Science.gov (United States)

    Haubein, Ned C; McMillan, Scott A; Broadbelt, Linda J

    2003-01-01

    Advances in computing power have made it possible to study solvated molecules using ab initio quantum chemistry. Inclusion of discrete solvent molecules is required to determine geometric information about solute/solvent clusters. Monte Carlo methods are well suited to finding minima in many-body systems, and ab initio methods are applicable to the widest range of systems. A first principles Monte Carlo (FPMC) method was developed to find minima in many-body systems, and emphasis was placed on implementing moves that increase the likelihood of finding minimum energy structures. Partial optimization and molecular interchange moves aid in finding minima and overcome the incomplete sampling that is unavoidable when using ab initio methods. FPMC was validated by studying the boron trifluoride-water system, and then the method was used to examine the methyl carbenium ion in water to demonstrate its application to solvation problems.

  10. Towards hydrogen metallization: an Ab initio approach

    International Nuclear Information System (INIS)

    Bernard, St.

    1998-01-01

    The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H 2 ) 2 which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author)

  11. Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics.

    Science.gov (United States)

    Tanzi, Luana; Ramondo, Fabio; Caminiti, Ruggero; Campetella, Marco; Di Luca, Andrea; Gontrani, Lorenzo

    2015-09-21

    We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

  12. Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics

    International Nuclear Information System (INIS)

    Tanzi, Luana; Ramondo, Fabio; Caminiti, Ruggero; Campetella, Marco; Di Luca, Andrea; Gontrani, Lorenzo

    2015-01-01

    We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features

  13. Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Tanzi, Luana; Ramondo, Fabio, E-mail: fabio.ramondo@univaq.it [Department of Physical and Chemical Sciences, University of L’Aquila, Via Vetoio, L’Aquila I-67100 (Italy); Caminiti, Ruggero; Campetella, Marco; Di Luca, Andrea; Gontrani, Lorenzo, E-mail: lorenzo.gontrani@uniroma1.it [Department of Chemistry, University of Rome ‘La Sapienza’, P.le Aldo Moro 5, I-00185 Rome (Italy)

    2015-09-21

    We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

  14. Perspective: Ab initio force field methods derived from quantum mechanics

    Science.gov (United States)

    Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.

    2018-03-01

    It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.

  15. Orbital free ab initio molecular dynamics simulation study of some static and dynamic properties of liquid noble metals

    Directory of Open Access Journals (Sweden)

    G.M. Bhuiyan

    2012-10-01

    Full Text Available Several static and dynamic properties of liquid Cu, Ag and Au at thermodynamic states near their respective melting points, have been evaluated by means of the orbital free ab-initio molecular dynamics simulation method. The calculated static structure shows good agreement with the available X-ray and neutron diffraction data. As for the dynamic properties, the calculated dynamic structure factors point to the existence of collective density excitations along with a positive dispersion for l-Cu and l-Ag. Several transport coefficients have been obtained which show a reasonable agreement with the available experimental data.

  16. An ab initio and TD DFT

    Indian Academy of Sciences (India)

    The photophysical behaviour of N-(2-hydroxy benzylidene) aniline or most commonly known as salicylideneaniline (SA) has been investigated using the ab initio and DFT levels of theory. The quantum chemical calculations show that the optimized non planar enol (1) form of the SA molecule is the most stable conformer ...

  17. Single-ion 4f element magnetism: an ab-initio look at Ln(COT)2(-).

    Science.gov (United States)

    Gendron, Frédéric; Pritchard, Benjamin; Bolvin, Hélène; Autschbach, Jochen

    2015-12-14

    The electron densities associated with the Ln 4f shell, and spin and orbital magnetizations ('magnetic moment densities'), are investigated for the Ln(COT)2(-) series. The densities are obtained from ab-initio calculations including spin-orbit coupling. For Ln = Ce, Pr the magnetizations are also derived from crystal field models and shown to agree with the ab-initio results. Analysis of magnetizations from ab-initio calculations may be useful in assisting research on single molecule magnets.

  18. Ab initio calculations of 3H(d,n)4He fusion

    International Nuclear Information System (INIS)

    Navratil, Petr; Quaglioni, Sofia

    2012-01-01

    We build 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 ab initio no-core shell model. 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. We will present the first results of the d- 3 H and d- 3 He fusion calculation obtained within our ab initio approach. We will also discuss our d- 4 He, 3 H- 4 He and 3 H- 3 H scattering calculations and the outline of the extension of the formalism to include three-cluster final states with the goal to calculate the 3 H( 3 H,2n) 4 He cross section

  19. Experimental and theoretical study of X-ray absorption around the chlorine L edge in vinyl chloride

    International Nuclear Information System (INIS)

    Kawerk, Elie; Carniato, Stéphane; Iwayama, Hiroshi; Shigemasa, Eiji; Piancastelli, Maria Novella; Wassaf, Joseph; Khoury, Antonio; Simon, Marc

    2013-01-01

    Highlights: ► We measured the X-ray absorption spectrum of C 2 H 3 Cl around the chlorine L edge. ► Ab-initio calculations of the spectrum shed light on eventual electronic resonances. ► Vibrational substructures for particular core excited states are considered. ► The potential energy surfaces of the core excited electronic states are evaluated. ► Sharp or narrow spectral bands are associated to bound or dissociative surfaces. -- Abstract: We present a combined experimental and theoretical study of the high-resolution chlorine L edge X-ray absorption spectrum in gas-phase vinyl chloride (C 2 H 3 Cl). With the help of ab-initio calculations, we interpret the experimental spectrum and attribute each band to its corresponding electronic transitions terminating at states characterized by an either binding or dissociative potential energy surface (PES). Vibrational substructures in some specific core-excited electronic states are taken into account

  20. Experimental and theoretical study of X-ray absorption around the chlorine L edge in vinyl chloride

    Energy Technology Data Exchange (ETDEWEB)

    Kawerk, Elie, E-mail: elie.kawerk@etu.upmc.fr [Université Pierre et Marie Curie, Laboratoire de Chimie Physique-Matière et Rayonnement, UMR 7614, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); Université Libanaise, Faculté des Sciences II Fanar, Laboratoire de Physique Appliquée, 90656 Jdeidet el Metn (Lebanon); Carniato, Stéphane [Université Pierre et Marie Curie, Laboratoire de Chimie Physique-Matière et Rayonnement, UMR 7614, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); Iwayama, Hiroshi; Shigemasa, Eiji [Ultraviolet Synchrotron Orbital Radiation Facility, Institute for Molecular Science, Okazaki 444-8585 (Japan); Piancastelli, Maria Novella [Université Pierre et Marie Curie, Laboratoire de Chimie Physique-Matière et Rayonnement, UMR 7614, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); Wassaf, Joseph; Khoury, Antonio [Université Libanaise, Faculté des Sciences II Fanar, Laboratoire de Physique Appliquée, 90656 Jdeidet el Metn (Lebanon); Simon, Marc [Université Pierre et Marie Curie, Laboratoire de Chimie Physique-Matière et Rayonnement, UMR 7614, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France)

    2013-02-15

    Highlights: ► We measured the X-ray absorption spectrum of C{sub 2}H{sub 3}Cl around the chlorine L edge. ► Ab-initio calculations of the spectrum shed light on eventual electronic resonances. ► Vibrational substructures for particular core excited states are considered. ► The potential energy surfaces of the core excited electronic states are evaluated. ► Sharp or narrow spectral bands are associated to bound or dissociative surfaces. -- Abstract: We present a combined experimental and theoretical study of the high-resolution chlorine L edge X-ray absorption spectrum in gas-phase vinyl chloride (C{sub 2}H{sub 3}Cl). With the help of ab-initio calculations, we interpret the experimental spectrum and attribute each band to its corresponding electronic transitions terminating at states characterized by an either binding or dissociative potential energy surface (PES). Vibrational substructures in some specific core-excited electronic states are taken into account.

  1. X-ray refractive index of laser-dressed atoms

    OpenAIRE

    Buth, Christian; Santra, Robin

    2008-01-01

    We investigated the complex index of refraction in the x-ray regime of atoms in laser light. The laser (intensity up to 10^13 W/cm^2, wavelength 800nm) modifies the atomic states but, by assumption, does not excite or ionize the atoms in their electronic ground state. Using quantum electrodynamics, we devise an ab initio theory to calculate the dynamic dipole polarizability and the photoabsorption cross section, which are subsequently used to determine the real and imaginary part, respectivel...

  2. In search of the X{sub 2}BO and X{sub 2}BS (X = H, F) free radicals: Ab initio studies of their spectroscopic signatures

    Energy Technology Data Exchange (ETDEWEB)

    Clouthier, Dennis J., E-mail: dclaser@uky.edu [Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055 (United States)

    2014-12-28

    The F{sub 2}BO free radical is a known, although little studied, species but similar X{sub 2}BY (X = H, D, F; Y = O, S) molecules are largely unknown. High level ab initio methods have been used to predict the molecular structures, vibrational frequencies (in cm{sup −1}), and relative energies of the ground and first two excited electronic states of these free radicals, as an aid to their eventual spectroscopic identification. The chosen theoretical methods and basis sets were tested on F{sub 2}BO and found to give good agreement with the known experimental quantities. In particular, complete basis set extrapolations of coupled-cluster single and doubles with perturbative triple excitations/aug-cc-pVXZ (X = 3, 4, 5) energies gave excellent electronic term values, due to small changes in geometry between states and the lack of significant multireference character in the wavefunctions. The radicals are found to have planar C{sub 2v} geometries in the X{sup ~2}B{sub 2} ground state, the low-lying A{sup ~2}B{sub 1} first excited state, and the higher B{sup ~2}A{sub 1} state. Some of these radicals have very small ground state dipole moments hindering microwave measurements. Infrared studies in matrices or in the gas phase may be possible although the fundamentals of H{sub 2}BO and H{sub 2}BS are quite weak. The most promising method of identifying these species in the gas phase appears to be absorption or laser-induced fluorescence spectroscopy through the allowed B{sup ~}-X{sup ~} transitions which occur in the visible-near UV region of the electromagnetic spectrum. The ab initio results have been used to calculate the Franck-Condon profiles of the absorption and emission spectra, and the rotational structure of the B{sup ~}-X{sup ~}0{sub 0}{sup 0} bands has been simulated. The calculated single vibronic level emission spectra provide a unique, readily recognizable fingerprint of each particular radical, facilitating the experimental identification of new X{sub 2}BY

  3. Investigation on electronic and magnetic properties of Mn2NiAl by ab initio calculations and Monte Carlo simulations

    International Nuclear Information System (INIS)

    Masrour, R.; Jabar, A.; Hlil, E.K.; Hamedoun, M.; Benyoussef, A.; Hourmatallah, A.; Rezzouk, A.; Bouslykhane, K.; Benzakour, N.

    2017-01-01

    Self-consistent ab initio calculations, based on Density Functional Theory (DFT) approach and using Full potential Linear Augmented Plane Wave (FLAPW) method, are performed to investigate both electronic and magnetic properties of the Mn 2 NiAl. Magnetic moment considered to lie along (001) axes are computed. Obtained data from ab initio calculations are used as input for Monte Carlo simulations to compute other magnetic parameters. Also, the magnetic properties of Mn 2 NiAl are studied using the Monte Carlo simulations. The variation of magnetization and magnetic susceptibility with the reduced temperature of Mn 2 NiAl are investigated. The transition temperature of this system is deduced for different values exchange interaction and crystal field. The thermal total magnetization has been obtained, and the magnetic hysteresis cycle is established. The total magnetic moment is superior to those obtained by the other method and is mainly determined by the antiparallel aligned Mn I , Mn II and Ni spin moments. The superparamagnetic phase is found at the neighborhood of transition temperature. - Highlights: • Ab initio calculations are used to study magnetic and electronic properties of Mn 2 NiX. • The transition temperature of Mn 2 NiX is established. • The magnetic hysteresis cycle of M n2 NiX (X = Al, Ga, In, Sn) is deduced. • The magnetic coercive field of Mn 2 NiX (X = Al, Ga, In, Sn) is given.

  4. Quantitative spectroscopy of X-ray lines and continua in tokamaks

    International Nuclear Information System (INIS)

    Peacock, N.J.; Lawson, K.D.; Patel, A.; Barnsley, R.; Melnick, I.M.; O'Mullane, M.G.; Singleton, M.A.

    1996-10-01

    Crystal and synthetic multilayer diffractors, deployed either as flat Bragg reflectors, or curved, as in the Johann configuration, are used to study the spectrum of COMPASS-D and other tokamaks in the wavelength region 1-100 A. In this paper we concentrate on the measurement of absolute photon fluxes and the derivation of volume emissivities of the lines and continua in the X-ray region. The sensitivities of these instruments to absolute photon flux have been constructed ab initio from the individual component efficiencies, including published values of the diffractor reflectivities, which have been checked or supplemented by measurements using a double-axis goniometer or from line branching ratios. For these tokamak plasmas where the elemental abundances and effective ion charge are documented, the X-ray continuum intensity itself has been used as a calibration source to derive absolute instrument sensitivity, in reasonable agreement with the ab initio method. In the COMPASS-D tokamak, changes in the effective ion charge state, Z eff , have been derived for different operating conditions, from the absolute intensity of the continuum at ∼4 A. From the irradiances of the line emission, changes in the absolute level of impurities following ''boronisation'' of the vacuum vessel have also been documented. (UK)

  5. Ab Initio molecular dynamics with excited electrons

    NARCIS (Netherlands)

    Alavi, A.; Kohanoff, J.; Parrinello, M.; Frenkel, D.

    1994-01-01

    A method to do ab initio molecular dynamics suitable for metallic and electronically hot systems is described. It is based on a density functional which is costationary with the finite-temperature functional of Mermin, with state being included with possibly fractional occupation numbers.

  6. Progress towards an ab initio real-time treatment of warm dense matter

    Science.gov (United States)

    Baczewski, Andrew; Cangi, Attila; Hansen, Stephanie; Jensen, Daniel

    2017-10-01

    Time-dependent density functional theory (TDDFT) provides an accurate description of equilibrium properties of warm dense matter, such as the dynamic structure factor (Baczewski et al., Phys. Rev. Lett., 116(11), 2016). While non-equilibrium properties, such as stopping power, have also been demonstrated to be within the grasp of TDDFT, the ultrafast isochoric heating of condensed matter into the warm dense state, enabled by recent advances in XFELs, remains beyond its capabilities. In this talk, we will describe the successes of and continuing challenges for TDDFT for warm dense matter, and present progress towards a more complete ab initio treatment of isochoric x-ray heating. Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International, Inc., for the DOE's National Nuclear Security Administration under contract DE-NA0003525.

  7. Ab Initio Calculations Of Light-Ion Reactions

    International Nuclear Information System (INIS)

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

    2012-01-01

    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. Use of ab initio quantum chemical methods in battery technology

    Energy Technology Data Exchange (ETDEWEB)

    Deiss, E [Paul Scherrer Inst. (PSI), Villigen (Switzerland)

    1997-06-01

    Ab initio quantum chemistry can nowadays predict physical and chemical properties of molecules and solids. An attempt should be made to use this tool more widely for predicting technologically favourable materials. To demonstrate the use of ab initio quantum chemistry in battery technology, the theoretical energy density (energy per volume of active electrode material) and specific energy (energy per mass of active electrode material) of a rechargeable lithium-ion battery consisting of a graphite electrode and a nickel oxide electrode has been calculated with this method. (author) 1 fig., 1 tab., 7 refs.

  9. Ab-initio calculations of superconducting properties of YBa2Cu3O7

    International Nuclear Information System (INIS)

    Zhao, G.L.; Bagayoko, D.

    1999-01-01

    The authors present ab-initio calculations for the electronic structure and superconducting properties of YBa 2 Cu 3 O 7 (YBCO). The electronic structure was calculated using a self-consistent ab-initio LCAO method. They solved the anisotropic Eliashberg gap equation numerically. The strong coupling of the high energy optical phonons around 60--73 meV, with the electrons at the Fermi surface, leads to a high Tc in YBCO. The calculated Tc is about 89 K for μ* = 0.1. The good agreement of the calculated results with experimental measurements and the ab-initio nature of the calculations support the scenario of an anisotropic s-wave superconductor for YBCO

  10. Theory-restricted resonant x-ray reflectometry of quantum materials

    Science.gov (United States)

    Fürsich, Katrin; Zabolotnyy, Volodymyr B.; Schierle, Enrico; Dudy, Lenart; Kirilmaz, Ozan; Sing, Michael; Claessen, Ralph; Green, Robert J.; Haverkort, Maurits W.; Hinkov, Vladimir

    2018-04-01

    The delicate interplay of competing phases in quantum materials is dominated by parameters such as the crystal field potential, the spin-orbit coupling, and, in particular, the electronic correlation strength. Whereas small quantitative variations of the parameter values can thus qualitatively change the material, these values can hitherto hardly be obtained with reasonable precision, be it theoretically or experimentally. Here we propose a solution combining resonant x-ray reflectivity (RXR) with multiplet ligand field theory (MLFT). We first perform ab initio DFT calculations within the MLFT framework to get initial parameter values, which we then use in a fit of the theoretical model to RXR. To validate our method, we apply it to NiO and SrTiO3 and obtain parameter values, which are amended by as much as 20 % compared to the ab initio results. Our approach is particularly useful to investigate topologically trivial and nontrivial correlated insulators, staggered moments in magnetically or orbitally ordered materials, and reconstructed interfaces.

  11. Ab initio nuclear structure - the large sparse matrix eigenvalue problem

    Energy Technology Data Exchange (ETDEWEB)

    Vary, James P; Maris, Pieter [Department of Physics, Iowa State University, Ames, IA, 50011 (United States); Ng, Esmond; Yang, Chao [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Sosonkina, Masha, E-mail: jvary@iastate.ed [Scalable Computing Laboratory, Ames Laboratory, Iowa State University, Ames, IA, 50011 (United States)

    2009-07-01

    The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several ab initio methods have now emerged that provide nearly exact solutions for some nuclear properties. The ab initio no core shell model (NCSM) and the no core full configuration (NCFC) method, frame this quantum many-particle problem as a large sparse matrix eigenvalue problem where one evaluates the Hamiltonian matrix in a basis space consisting of many-fermion Slater determinants and then solves for a set of the lowest eigenvalues and their associated eigenvectors. The resulting eigenvectors are employed to evaluate a set of experimental quantities to test the underlying potential. For fundamental problems of interest, the matrix dimension often exceeds 10{sup 10} and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. We survey recent results and advances in solving this large sparse matrix eigenvalue problem. We also outline the challenges that lie ahead for achieving further breakthroughs in fundamental nuclear theory using these ab initio approaches.

  12. Ab initio nuclear structure - the large sparse matrix eigenvalue problem

    International Nuclear Information System (INIS)

    Vary, James P; Maris, Pieter; Ng, Esmond; Yang, Chao; Sosonkina, Masha

    2009-01-01

    The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several ab initio methods have now emerged that provide nearly exact solutions for some nuclear properties. The ab initio no core shell model (NCSM) and the no core full configuration (NCFC) method, frame this quantum many-particle problem as a large sparse matrix eigenvalue problem where one evaluates the Hamiltonian matrix in a basis space consisting of many-fermion Slater determinants and then solves for a set of the lowest eigenvalues and their associated eigenvectors. The resulting eigenvectors are employed to evaluate a set of experimental quantities to test the underlying potential. For fundamental problems of interest, the matrix dimension often exceeds 10 10 and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. We survey recent results and advances in solving this large sparse matrix eigenvalue problem. We also outline the challenges that lie ahead for achieving further breakthroughs in fundamental nuclear theory using these ab initio approaches.

  13. Investigation on electronic and magnetic properties of Mn{sub 2}NiAl by ab initio calculations and Monte Carlo simulations

    Energy Technology Data Exchange (ETDEWEB)

    Masrour, R., E-mail: rachidmasrour@hotmail.com [Laboratory of Materials, Processes, Environment and Quality, Cady Ayyed University, National School of Applied Sciences, PB 63 46000 Safi (Morocco); Jabar, A. [Laboratory of Materials, Processes, Environment and Quality, Cady Ayyed University, National School of Applied Sciences, PB 63 46000 Safi (Morocco); Hlil, E.K. [Institut Néel, CNRS, Université Grenoble Alpes, BP 166, F-38042 Grenoble cedex 9 (France); Hamedoun, M. [Institute of Nanomaterials and Nanotechnologies, MAScIR, Rabat (Morocco); Benyoussef, A. [Institute of Nanomaterials and Nanotechnologies, MAScIR, Rabat (Morocco); Hassan II Academy of Science and Technology, Rabat (Morocco); Hourmatallah, A. [Equipe de Physique du Solide, Laboratoire LIPI, Ecole Normale Supérieure, BP 5206, Bensouda, Fes (Morocco); Rezzouk, A.; Bouslykhane, K.; Benzakour, N. [Laboratoire de Physique du Solide, Université Sidi Mohammed Ben Abdellah, Faculté des sciences DharMahraz, BP 1796, Fes (Morocco)

    2017-04-15

    Self-consistent ab initio calculations, based on Density Functional Theory (DFT) approach and using Full potential Linear Augmented Plane Wave (FLAPW) method, are performed to investigate both electronic and magnetic properties of the Mn{sub 2}NiAl. Magnetic moment considered to lie along (001) axes are computed. Obtained data from ab initio calculations are used as input for Monte Carlo simulations to compute other magnetic parameters. Also, the magnetic properties of Mn{sub 2}NiAl are studied using the Monte Carlo simulations. The variation of magnetization and magnetic susceptibility with the reduced temperature of Mn{sub 2}NiAl are investigated. The transition temperature of this system is deduced for different values exchange interaction and crystal field. The thermal total magnetization has been obtained, and the magnetic hysteresis cycle is established. The total magnetic moment is superior to those obtained by the other method and is mainly determined by the antiparallel aligned Mn{sub I}, Mn{sub II} and Ni spin moments. The superparamagnetic phase is found at the neighborhood of transition temperature. - Highlights: • Ab initio calculations are used to study magnetic and electronic properties of Mn{sub 2}NiX. • The transition temperature of Mn{sub 2}NiX is established. • The magnetic hysteresis cycle of M{sub n2}NiX (X = Al, Ga, In, Sn) is deduced. • The magnetic coercive field of Mn{sub 2}NiX (X = Al, Ga, In, Sn) is given.

  14. Structural, magnetic and electronic properties of FexCoyIrz (x + y + z = 5, 6) clusters: an ab initio study

    KAUST Repository

    Devi, Assa Aravindh Sasikala

    2014-05-01

    Investigations on freestanding binary and ternary clusters of Fe (x) Co (y) Ir (z) (x + y + z = 5, 6) are carried out using ab initio density functional theory techniques. The geometry, chemical order, binding energy, magnetic moment and electronic structure of the clusters are analyzed for the entire range of composition. Composition dependent structural transition is observed in the five atom clusters, while octahedral geometry prevailed in clusters with six atoms. Both the clusters show increment in binding energy with the increase in number of heterogeneous bonds. Analysis based on the chemical order parameter indicates that clusters favor mixing rather than segregation. The clusters exhibit ferromagnetic ordering and the inter-dependence of optimal cluster geometry to the magnetic moments and electronic structure is observed.

  15. Ab initio NMR parameters of BrCH3 and ICH3 with relativistic and vibrational corrections

    Science.gov (United States)

    Uhlíková, Tereza; Urban, Štěpán

    2018-05-01

    This study is focused on two effects identified when NMR parameters are calculated based on first principles. These effects are 1. vibrational correction of properties when using ab initio optimized equilibrium geometry; 2. relativistic effects and limits of using the Flygare equation. These effects have been investigated and determined for nuclear spin-rotation constants and nuclear magnetic shieldings for the CH3Br and CH3I molecules. The most significant result is the difference between chemical shieldings determined based on the ab initio relativistic four-component Dirac-Coulomb Hamiltonian and chemical shieldings calculated using experimental values and the Flygare equation. This difference is approximately 320 ppm and 1290 ppm for 79Br and 127I in the CH3X molecule, respectively.

  16. Ab initio structural and spectroscopic study of HPS{sup x} and HSP{sup x} (x = 0,+1,−1) in the gas phase

    Energy Technology Data Exchange (ETDEWEB)

    Yaghlane, Saida Ben [Laboratoire de Spectroscopie Atomique, Moléculaire et Applications – LSAMA, Université de Tunis, Tunis (Tunisia); Cotton, C. Eric; Francisco, Joseph S., E-mail: francisc@purdue.edu, E-mail: hochlaf@univ-mlv.fr [Department of Chemistry and Department of Earth and Atmospheric Science, Purdue University, West Lafayette, Indiana 49707 (United States); Linguerri, Roberto; Hochlaf, Majdi, E-mail: francisc@purdue.edu, E-mail: hochlaf@univ-mlv.fr [Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est, 5 bd Descartes, 77454 Marne-la-Vallée (France)

    2013-11-07

    Accurate ab initio computations of structural and spectroscopic parameters for the HPS/HSP molecules and corresponding cations and anions have been performed. For the electronic structure computations, standard and explicitly correlated coupled cluster techniques in conjunction with large basis sets have been adopted. In particular, we present equilibrium geometries, rotational constants, harmonic vibrational frequencies, adiabatic ionization energies, electron affinities, and, for the neutral species, singlet-triplet relative energies. Besides, the full-dimensional potential energy surfaces (PESs) for HPS{sup x} and HSP{sup x} (x = −1,0,1) systems have been generated at the standard coupled cluster level with a basis set of augmented quintuple-zeta quality. By applying perturbation theory to the calculated PESs, an extended set of spectroscopic constants, including τ, first-order centrifugal distortion and anharmonic vibrational constants has been obtained. In addition, the potentials have been used in a variational approach to deduce the whole pattern of vibrational levels up to 4000 cm{sup −1} above the minima of the corresponding PESs.

  17. Ab Initio Atomistic Thermodynamics for Surfaces: A Primer

    National Research Council Canada - National Science Library

    Rogal, Jutta; Reuter, Karsten

    2006-01-01

    .... These techniques are referred to as first-principles (or in latin: ab initio) to indicate that they do not rely on empirical or fitted parameters, which then makes them applicable for a wide range of realistic conditions...

  18. Ab initio study of lattice instabilities of zinc chalcogenides ZnX (X=O, S, Se, Te induced by ultrafast intense laser irradiation

    Directory of Open Access Journals (Sweden)

    Dahua Ren

    2017-09-01

    Full Text Available Ab initio calculations of lattice constants, lattice stabilities of ZnX (X=O, S, Se, Te at different electronic temperatures (Te have been performed using generalized gradient approximation (GGA pseudopotential method within the density functional theory (DFT. The calculated phonon frequencies of ZnX at Te = 0 eV accord well with the experimental and other theoretical values. Firstly, it is indicated that the lattice constants of ZnX increase and all the phonon frequencies reduce as Te increases. Additionally, the transverse-acoustic phonon frequencies of ZnX are imaginary with the elevation of Te, namely the lattices of ZnX become unstable under ultrafast intense laser irradiation. Moreover, the transverse optical mode-longitudinal optical mode (LO-TO splitting degree of ZnX (X=S, Se, Te gradually decreases as the electronic temperature increases, mainly due to the reason that the electronic excitation weakens the strength ionicity of ionic crystal ZnX under intense laser irradiation. However, the LO-TO splitting degree of ZnO firstly increases and then decreases with the increase of electronic temperature. After that, it can be helpful for understanding the mechanism of ultrafast intense laser induced semiconductors damage.

  19. Trends in magnetism of free Rh clusters via relativistic ab-initio calculations.

    Science.gov (United States)

    Šipr, O; Ebert, H; Minár, J

    2015-02-11

    A fully relativistic ab-initio study on free Rh clusters of 13-135 atoms is performed to identify general trends concerning their magnetism and to check whether concepts which proved to be useful in interpreting magnetism of 3d metals are applicable to magnetism of 4d systems. We found that there is no systematic relation between local magnetic moments and coordination numbers. On the other hand, the Stoner model appears well-suited both as a criterion for the onset of magnetism and as a guide for the dependence of local magnetic moments on the site-resolved density of states at the Fermi level. Large orbital magnetic moments antiparallel to spin magnetic moments were found for some sites. The intra-atomic magnetic dipole Tz term can be quite large at certain sites but as a whole it is unlikely to affect the interpretation of x-ray magnetic circular dichroism experiments based on the sum rules.

  20. In situ X-ray probing reveals fingerprints of surface platinum oxide.

    Science.gov (United States)

    Friebel, Daniel; Miller, Daniel J; O'Grady, Christopher P; Anniyev, Toyli; Bargar, John; Bergmann, Uwe; Ogasawara, Hirohito; Wikfeldt, Kjartan Thor; Pettersson, Lars G M; Nilsson, Anders

    2011-01-07

    In situ X-ray absorption spectroscopy (XAS) at the Pt L(3) edge is a useful probe for Pt-O interactions at polymer electrolyte membrane fuel cell (PEMFC) cathodes. We show that XAS using the high energy resolution fluorescence detection (HERFD) mode, applied to a well-defined monolayer Pt/Rh(111) sample where the bulk penetrating hard X-rays probe only surface Pt atoms, provides a unique sensitivity to structure and chemical bonding at the Pt-electrolyte interface. Ab initio multiple-scattering calculations using the FEFF code and complementary extended X-ray absorption fine structure (EXAFS) results indicate that the commonly observed large increase of the white-line at high electrochemical potentials on PEMFC cathodes originates from platinum oxide formation, whereas previously proposed chemisorbed oxygen-containing species merely give rise to subtle spectral changes.

  1. The Pu–U–Am system: An ab initio informed CALPHAD thermodynamic study

    International Nuclear Information System (INIS)

    Perron, A.; Turchi, P.E.A.; Landa, A.; Söderlind, P.; Ravat, B.; Oudot, B.; Delaunay, F.

    2015-01-01

    Highlights: • The ab initio informed CALPHAD assessment of the Am–U system has been realized. • A strong tendency toward phase separation across the whole composition range is predicted. • The ab initio informed Pu–U–Am thermodynamic database has been developed. • The solubility of Am and U in the liquid phase is improved by adding Pu. • The δ-Pu (fcc) phase is strongly stabilized by Am, on the contrary to the bcc phase. - Abstract: Phase diagram and thermodynamic properties of the Am–U system, that are experimentally unknown, are calculated using the CALPHAD method with input from ab initio electronic-structure calculations for the fcc and bcc phases. A strong tendency toward phase separation across the whole composition range is predicted. In addition, ab initio informed Pu–U and Am–Pu thermodynamic assessments are combined to build a Pu–U–Am thermodynamic database. Regarding the Pu-rich corner of the ternary system, predictions indicate that Am acts as a powerful δ-Pu (fcc) stabilizer. In the U-rich corner, similar predictions are made but to a lesser extent. In both cases, the bcc phase is destabilized and the fcc phase is enhanced. Finally, results and methodology are discussed and compared with previous assessments and guidelines are provided for further experimental studies

  2. The Pu–U–Am system: An ab initio informed CALPHAD thermodynamic study

    Energy Technology Data Exchange (ETDEWEB)

    Perron, A., E-mail: perron1@llnl.gov [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Turchi, P.E.A.; Landa, A.; Söderlind, P. [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Ravat, B.; Oudot, B.; Delaunay, F. [CEA-Centre de Valduc, 21120 Is sur Tille (France)

    2015-03-15

    Highlights: • The ab initio informed CALPHAD assessment of the Am–U system has been realized. • A strong tendency toward phase separation across the whole composition range is predicted. • The ab initio informed Pu–U–Am thermodynamic database has been developed. • The solubility of Am and U in the liquid phase is improved by adding Pu. • The δ-Pu (fcc) phase is strongly stabilized by Am, on the contrary to the bcc phase. - Abstract: Phase diagram and thermodynamic properties of the Am–U system, that are experimentally unknown, are calculated using the CALPHAD method with input from ab initio electronic-structure calculations for the fcc and bcc phases. A strong tendency toward phase separation across the whole composition range is predicted. In addition, ab initio informed Pu–U and Am–Pu thermodynamic assessments are combined to build a Pu–U–Am thermodynamic database. Regarding the Pu-rich corner of the ternary system, predictions indicate that Am acts as a powerful δ-Pu (fcc) stabilizer. In the U-rich corner, similar predictions are made but to a lesser extent. In both cases, the bcc phase is destabilized and the fcc phase is enhanced. Finally, results and methodology are discussed and compared with previous assessments and guidelines are provided for further experimental studies.

  3. Ab initio approach to the ion stopping power at the plasma-solid interface

    Science.gov (United States)

    Bonitz, Michael; Schlünzen, Niclas; Wulff, Lasse; Joost, Jan-Philip; Balzer, Karsten

    2016-10-01

    The energy loss of ions in solids is of key relevance for many applications of plasmas, ranging from plasma technology to fusion. Standard approaches are based on density functional theory or SRIM simulations, however, the applicability range and accuracy of these results are difficult to assess, in particular, for low energies. Here we present an independent approach that is based on ab initio nonequilibrium Green functions theory, e.g. that allows to incorporate electronic correlations effects of the solid. We present the first application of this method to low-temperature plasmas, concentrating on proton and alpha-particle stopping in a graphene layer. In addition to the stopping power we present time-dependent results for the local electron density, the spectral function and the photoemission spectrum that is directly accessible in optical, UV or x-ray diagnostics. http://www.itap.uni-kiel.de/theo-physik/bonitz/.

  4. Time-resolved photoelectron spectroscopy and ab initio multiple spawning studies of hexamethylcyclopentadiene

    DEFF Research Database (Denmark)

    Wolf, T. J. A.; Kuhlman, Thomas Scheby; Schalk, O.

    2014-01-01

    Time-resolved photoelectron spectroscopy and ab initio multiple spawning were applied to the ultrafast non-adiabatic dynamics of hexamethylcyclopentadiene. The high level of agreement between experiment and theory associates wavepacket motion with a distinct degree of freedom.......Time-resolved photoelectron spectroscopy and ab initio multiple spawning were applied to the ultrafast non-adiabatic dynamics of hexamethylcyclopentadiene. The high level of agreement between experiment and theory associates wavepacket motion with a distinct degree of freedom....

  5. Ab Initio Molecular Dynamics Simulations of Furfural at the Liquid-Solid Interface

    OpenAIRE

    Sanwu Wang; Hongli Dang; Wenhua Xue; Darwin Shields; Xin Liu; Friederike C. Jentoft; Daniel E. Resasco

    2013-01-01

    The bonding configuration and the heat of adsorption of a furfural molecule on the Pd(111) surface were determined by ab initio density-functional-theory calculations. The dynamics of pure liquid water, the liquid-solid interface formed by liquid water and the Pd(111) surface, as well as furfural at the water-Pd interface, were investigated by ab initio molecular dynamics simulations at finite temperatures. Calculations and simulations suggest that the bonding configurati...

  6. AB INITIO calculations of magneto-optical effects

    Czech Academy of Sciences Publication Activity Database

    Kuneš, Jan; Oppeneer, P. M.

    2002-01-01

    Roč. 2, - (2002), s. 141-146 ISSN 1346-7948 R&D Projects: GA AV ČR IAA1010214 Institutional research plan: CEZ:AV0Z1010914 Keywords : electronic structure * ab initio calculation * polar magneto-optical Kerr effect * transitiom metal * uranium intermetallics * CrO 2 Subject RIV: BM - Solid Matter Physics ; Magnetism

  7. Augmented wave ab initio EFG calculations: some methodological warnings

    International Nuclear Information System (INIS)

    Errico, Leonardo A.; Renteria, Mario; Petrilli, Helena M.

    2007-01-01

    We discuss some accuracy aspects inherent to ab initio electronic structure calculations in the understanding of nuclear quadrupole interactions. We use the projector augmented wave method to study the electric-field gradient (EFG) at both Sn and O sites in the prototype cases SnO and SnO 2 . The term ab initio is used in the standard context of the also called first principles methods in the framework of the Density Functional Theory. As the main contributions of EFG calculations to problems in condensed matter physics are related to structural characterizations on the atomic scale, we discuss the 'state of the art' on theoretical EFG calculations and make a brief critical review on the subject, calling attention to some fundamental theoretical aspects

  8. Augmented wave ab initio EFG calculations: some methodological warnings

    Energy Technology Data Exchange (ETDEWEB)

    Errico, Leonardo A. [Departamento de Fisica-IFLP (CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC67 (1900) La Plata (Argentina); Renteria, Mario [Departamento de Fisica-IFLP (CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC67 (1900) La Plata (Argentina); Petrilli, Helena M. [Instituto de Fisica-DFMT, Universidade de Sao Paulo, C.P. 66318, 05315-970 Sao Paulo, SP (Brazil)]. E-mail: hmpetril@macbeth.if.usp.br

    2007-02-01

    We discuss some accuracy aspects inherent to ab initio electronic structure calculations in the understanding of nuclear quadrupole interactions. We use the projector augmented wave method to study the electric-field gradient (EFG) at both Sn and O sites in the prototype cases SnO and SnO{sub 2}. The term ab initio is used in the standard context of the also called first principles methods in the framework of the Density Functional Theory. As the main contributions of EFG calculations to problems in condensed matter physics are related to structural characterizations on the atomic scale, we discuss the 'state of the art' on theoretical EFG calculations and make a brief critical review on the subject, calling attention to some fundamental theoretical aspects.

  9. Determinação da estrutura molecular do ciclooctano por métodos ab initio e difração de elétrons na fase gasosa

    OpenAIRE

    De Almeida,Wagner B.

    2000-01-01

    The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can ma...

  10. The interaction of MnH(X 7Sigma+) with He: ab initio potential energy surface and bound states.

    Science.gov (United States)

    Turpin, Florence; Halvick, Philippe; Stoecklin, Thierry

    2010-06-07

    The potential energy surface of the ground state of the He-MnH(X (7)Sigma(+)) van der Waals complex is presented. Within the supermolecular approach of intermolecular energy calculations, a grid of ab initio points was computed at the multireference configuration interaction level using the aug-cc-pVQZ basis set for helium and hydrogen and the relativistic aug-cc-pVQZ-DK basis set for manganese. The potential energy surface was then fitted to a global analytical form which main features are discussed. As a first application of this potential energy surface, we present accurate calculations of bound energy levels of the (3)He-MnH and (4)He-MnH complexes.

  11. The interaction of MnH(X 7Σ+) with He: Ab initio potential energy surface and bound states

    Science.gov (United States)

    Turpin, Florence; Halvick, Philippe; Stoecklin, Thierry

    2010-06-01

    The potential energy surface of the ground state of the He-MnH(X Σ7+) van der Waals complex is presented. Within the supermolecular approach of intermolecular energy calculations, a grid of ab initio points was computed at the multireference configuration interaction level using the aug-cc-pVQZ basis set for helium and hydrogen and the relativistic aug-cc-pVQZ-DK basis set for manganese. The potential energy surface was then fitted to a global analytical form which main features are discussed. As a first application of this potential energy surface, we present accurate calculations of bound energy levels of the H3e-MnH and H4e-MnH complexes.

  12. Atomic carbon chains as spin-transmitters: An ab initio transport study

    DEFF Research Database (Denmark)

    Fürst, Joachim Alexander; Brandbyge, Mads; Jauho, Antti-Pekka

    2010-01-01

    An atomic carbon chain joining two graphene flakes was recently realized in a ground-breaking experiment by Jin et al. (Phys. Rev. Lett., 102 (2009) 205501). We present ab initio results for the electron transport properties of such chains and demonstrate complete spin-polarization of the transmi......An atomic carbon chain joining two graphene flakes was recently realized in a ground-breaking experiment by Jin et al. (Phys. Rev. Lett., 102 (2009) 205501). We present ab initio results for the electron transport properties of such chains and demonstrate complete spin...

  13. Ab initio transport across bismuth selenide surface barriers

    KAUST Repository

    Narayan, Awadhesh; Rungger, Ivan; Droghetti, Andrea; Sanvito, Stefano

    2014-01-01

    © 2014 American Physical Society. We investigate the effect of potential barriers in the form of step edges on the scattering properties of Bi2Se3(111) topological surface states by means of large-scale ab initio transport simulations. Our results

  14. Ab initio lattice dynamics of metal surfaces

    International Nuclear Information System (INIS)

    Heid, R.; Bohnen, K.-P.

    2003-01-01

    Dynamical properties of atoms on surfaces depend sensitively on their bonding environment and thus provide valuable insight into the local geometry and chemical binding at the boundary of a solid. Density-functional theory provides a unified approach to the calculation of structural and dynamical properties from first principles. Its high accuracy and predictive power for lattice dynamical properties of semiconductor surfaces has been demonstrated in a previous article by Fritsch and Schroeder (Phys. Rep. 309 (1999) 209). In this report, we review the state-of-the-art of these ab initio approaches to surface dynamical properties of metal surfaces. We give a brief introduction to the conceptual framework with focus on recent advances in computational procedures for the ab initio linear-response approach, which have been a prerequisite for an efficient treatment of surface dynamics of noble and transition metals. The discussed applications to clean and adsorbate-covered surfaces demonstrate the high accuracy and reliability of this approach in predicting detailed microscopic properties of the phonon dynamics for a wide range of metallic surfaces

  15. Mn L{sub 2,3}-edge X-ray absorption spectroscopic studies on charge-discharge mechanism of Li{sub 2}MnO{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Kubobuchi, Kei, E-mail: kubobuchi@nissan-arc.co.jp [NISSAN ARC Ltd., 1 Natsushima, Yokosuka 237-0061 (Japan); Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan. (Japan); Mogi, Masato; Imai, Hideto [NISSAN ARC Ltd., 1 Natsushima, Yokosuka 237-0061 (Japan); Ikeno, Hidekazu [Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8570 (Japan); Tanaka, Isao [Department of Materials Science and Engineering, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501 (Japan); Mizoguchi, Teruyasu, E-mail: teru@iis.u-tokyo.ac.jp [Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505, Japan. (Japan)

    2014-02-03

    The redox reaction of Mn in Li{sub 2}MnO{sub 3} was studied by X-ray absorption spectroscopy and ab initio multiplet calculation. Associated with the de-intercalation of Li-ion, small but clear spectral changes were observed in Mn-L{sub 2,3} X-ray absorption near edge structure (XANES). The systematic ab initio multiplet calculations of Mn-L{sub 2,3} XANES revealed that the spectral changes in the experiment could not simply be ascribed to the change of the valency from Mn{sup 4+} to Mn{sup 5+} but can be explained well by the changes of local atomic structures around Mn{sup 4+} due to the Li de-intercalation. Our results suggest that the electronic state of oxygen should change during charging in Li{sub 2}MnO{sub 3}.

  16. Evaluation of ABS resin disk certified reference materials for heavy metal analysis by x-ray fluorescence analysis

    International Nuclear Information System (INIS)

    Ohata, Masaki; Kidokoro, Toshihiro; Kurahashi, Masayasu; Hioki, Akiharu

    2010-01-01

    ABS resin disk certified reference materials (CRMs) for heavy-metal analysis (NMIJ CRM 8105-a, NMIJ CRM 8106-a, NMIJ CRM 8115-a and NMIJ CRM 8116-a) were evaluated using an energy dispersive X-ray fluorescence (ED-XRF) analysis. The homogeneities of elements for both among-disks and within-disk were evaluated by ED-XRF analysis without any sample pre-treatment, which were similar to those evaluated by ICP-MS analysis after a sample digenstion procedure. The normalized XRF sensitivities for Cd, Cr and Pb in different ABS resin disk CRMs were compared, and the differences among them for those ABS resin disks that have similar matrices were observed. Moreover, Hg in those ABS resin disk CRMs was stable for long-term X-ray irradiation during ED-XRF analysis. (author)

  17. Ab Initio Molecular Dynamics of Uranium Incorporated in Goethite (α-FeOOH): Interpretation of X-ray Absorption Spectroscopy of Trace Polyvalent Metals.

    Science.gov (United States)

    Kerisit, Sebastien; Bylaska, Eric J; Massey, Michael S; McBriarty, Martin E; Ilton, Eugene S

    2016-11-21

    Incorporation of economically or environmentally consequential polyvalent metals into iron (oxyhydr)oxides has applications in environmental chemistry, remediation, and materials science. A primary tool for characterizing the local coordination environment of such metals, and therefore building models to predict their behavior, is extended X-ray absorption fine structure spectroscopy (EXAFS). Accurate structural information can be lacking yet is required to constrain and inform data interpretation. In this regard, ab initio molecular dynamics (AIMD) was used to calculate the local coordination environment of minor amounts of U incorporated in the structure of goethite (α-FeOOH). U oxidation states (VI, V, and IV) and charge compensation schemes were varied. Simulated trajectories were used to calculate the U L III -edge EXAFS function and fit experimental EXAFS data for U incorporated into goethite under reducing conditions. Calculations that closely matched the U EXAFS of the well-characterized mineral uraninite (UO 2 ), and constrained the S 0 2 parameter to be 0.909, validated the approach. The results for the U-goethite system indicated that U(V) substituted for structural Fe(III) in octahedral uranate coordination. Charge balance was achieved by the loss of one structural proton coupled to addition of one electron into the solid (-1 H + , +1 e - ). The ability of AIMD to model higher energy states thermally accessible at room temperature is particularly relevant for protonated systems such as goethite, where proton transfers between adjacent octahedra had a dramatic effect on the calculated EXAFS. Vibrational effects as a function of temperature were also estimated using AIMD, allowing separate quantification of thermal and configurational disorder. In summary, coupling AIMD structural modeling and EXAFS experiments enables modeling of the redox behavior of polyvalent metals that are incorporated in conductive materials such as iron (oxyhydr)oxides, with

  18. Evaluation on the stability of Hg in ABS disk CRM during measurements by wavelength dispersive X-ray fluorescence spectrometry.

    Science.gov (United States)

    Ohata, Masaki; Kidokoro, Toshihiro; Hioki, Akiharu

    2012-01-01

    The stability of Hg in an acrylonitrile-butadiene-styrene disk certified reference material (ABS disk CRM, NMIJ CRM 8116-a) during measurements by wavelength dispersion X-ray fluorescence (WD-XRF) analysis was evaluated in this study. The XRF intensities of Hg (L(α)) and Pb (L(α)) as well as the XRF intensity ratios of Hg (L(α))/Pb (L(α)) observed under different X-ray tube current conditions as well as their irradiation time were examined to evaluate the stability of Hg in the ABS disk CRM. The observed XRF intensities and the XRF intensity ratios for up to 32 h of measurements under 80 mA of X-ray tube current condition were constant, even though the surface of the ABS disk CRM was charred by the X-ray irradiation with high current for a long time. Moreover, the measurements on Hg and Pb in the charred disks by an energy dispersive XRF (ED-XRF) spectrometer showed constant XRF intensity ratios of Hg (L(α))/Pb (L(α)). From these results, Hg in the ABS disk CRM was evaluated to be sufficiently stable for XRF analysis.

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

    International Nuclear Information System (INIS)

    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

  20. Ab initio study of alanine polypeptide chain twisting

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.

    2006-01-01

    chains. These particular degrees of freedom are essential for the characterization of the proteins folding process. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined...

  1. Ab initio simulation of dislocation cores in metals

    International Nuclear Information System (INIS)

    Ventelon, L.

    2008-01-01

    In the framework of the multi scale simulation of metals and alloys plasticity, the aim of this study is to develop a methodology of ab initio dislocations study and to apply it to the [111] screw dislocation in the bc iron. (A.L.B.)

  2. Realization of prediction of materials properties by ab initio ...

    Indian Academy of Sciences (India)

    Unknown

    alization of the results of ab initio molecular dynamics simulation on atom insertion process to C60 and to carbon nanotube ... micro-clusters to estimate absolute highest occupied mo- .... To analyse the observed properties theoretically,.

  3. Ab initio calculations of the electronic structure and bonding characteristics of LaB6

    International Nuclear Information System (INIS)

    Hossain, Faruque M.; Riley, Daniel P.; Murch, Graeme E.

    2005-01-01

    Lanthanum hexaboride (LaB 6 , NIST SRM-660a) is widely used as a standard reference material for calibrating the line position and line shape parameters of powder diffraction instruments. The accuracy of this calibration technique is highly dependent on how completely the reference material is characterized. Critical to x-ray diffraction, this understanding must include the valence of the La atomic position, which in turn will influence the x-ray form factor (f) and hence the diffracted intensities. The electronic structure and bonding properties of LaB 6 have been investigated using ab initio plane-wave pseudopotential total energy calculations. The electronic properties and atomic bonding characteristics were analyzed by estimating the energy band structure and the density of states around the Fermi energy level. The calculated energy band structure is consistent with previously reported experimental findings; de Haas-van Alphen and two-dimensional angular correlation of electron-positron annihilation radiation. In addition, the bond strengths and types of atomic bonds in the LaB 6 compound were estimated by analyzing the Mulliken charge density population. The calculated result revealed the coexistence of covalent, ionic, and metallic bonding in the LaB 6 system and partially explains its high efficiency as a thermionic emitter

  4. (4)He Thermophysical Properties: New Ab Initio Calculations.

    Science.gov (United States)

    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 ϕ 07, (2) recalculate values of the second virial coefficient, the viscosity, and the thermal conductivity of (4)He from 1 K to 10,000 K, and (3), analyze the uncertainties of the thermophysical properties that propagate from the uncertainty of ϕ 07 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.

  5. Ab initio study of weakly bound halogen complexes: RX⋯PH3.

    Science.gov (United States)

    Georg, Herbert C; Fileti, Eudes E; Malaspina, Thaciana

    2013-01-01

    Ab initio calculations were employed to study the role of ipso carbon hybridization in halogenated compounds RX (R=methyl, phenyl, acetyl, H and X=F, Cl, Br and I) and its interaction with a phosphorus atom, as occurs in the halogen bonded complex type RX⋯PH3. The analysis was performed using ab initio MP2, MP4 and CCSD(T) methods. Systematic energy analysis found that the interaction energies are in the range -4.14 to -11.92 kJ mol(-1) (at MP2 level without ZPE correction). Effects of electronic correlation levels were evaluated at MP4 and CCSD(T) levels and a reduction of up to 27% in interaction energy obtained in MP2 was observed. Analysis of the electrostatic maps confirms that the PhCl⋯PH3 and all MeX⋯PH3 complexes are unstable. NBO analysis suggested that the charge transfer between the moieties is bigger when using iodine than bromine and chlorine. The electrical properties of these complexes (dipole and polarizability) were determined and the most important observed aspect was the systematic increase at the dipole polarizability, given by the interaction polarizability. This increase is in the range of 0.7-6.7 u.a. (about 3-7%).

  6. Ab Initio Calculations of Transport in Titanium and Aluminum Mixtures

    Science.gov (United States)

    Walker, Nicholas; Novak, Brian; Tam, Ka Ming; Moldovan, Dorel; Jarrell, Mark

    In classical molecular dynamics simulations, the self-diffusion and shear viscosity of titanium about the melting point have fallen within the ranges provided by experimental data. However, the experimental data is difficult to collect and has been rather scattered, making it of limited value for the validation of these calculations. By using ab initio molecular dynamics simulations within the density functional theory framework, the classical molecular dynamics data can be validated. The dynamical data from the ab initio molecular dynamics can also be used to calculate new potentials for use in classical molecular dynamics, allowing for more accurate classical dynamics simulations for the liquid phase. For metallic materials such as titanium and aluminum alloys, these calculations are very valuable due to an increasing demand for the knowledge of their thermophysical properties that drive the development of new materials. For example, alongside knowledge of the surface tension, viscosity is an important input for modeling the additive manufacturing process at the continuum level. We are developing calculations of the viscosity along with the self-diffusion for aluminum, titanium, and titanium-aluminum alloys with ab initio molecular dynamics. Supported by the National Science Foundation through cooperative agreement OIA-1541079 and the Louisiana Board of Regents.

  7. Steel — ab Initio: Quantum Mechanics Guided Design of New Fe-Based Materials

    Science.gov (United States)

    Prahl, Ulrich; Bleck, Wolfgang; Saeed-Akbari, Alireza

    This contribution reports the results of the collaborative research unit SFB 761 "Steel — ab initio", a cooperative project between RWTH Aachen University and the Max-Planck-Institute for Iron Research in Düsseldorf (MPIE) financed by the German Research Foundation (DFG). For the first time, it is exploited how ab initio approaches may lead to a detailed understanding and thus to a specific improvement of material development. The challenge lies in the combination of abstract natural science theories with rather engineering-like established concepts. Aiming at the technological target of the development of a new type of structural materials based on Fe-Mn-C alloys, the combination of ab initio and engineering methods is new, but could be followed quite successfully. Three major topics are treated in this research unit: a) development of a new method for material- and process-development based on ab initio calculations; b) design of a new class of structural materials with extraordinary property combinations; c) acceleration of development time and reduction of experimental efforts and complexity for material- and process-development. In the present work, an overview of the results of the first five years as well as an outlook for the upcoming three-year period is given.

  8. Ab Initio Calculations and Raman and SERS Spectral Analyses of Amphetamine Species

    DEFF Research Database (Denmark)

    Berg, Rolf W.; Nørbygaard, Thomas; White, Peter C.

    2011-01-01

    For the first time, the differences between the spectra of amphetamine and amphetamine-H+ and between different conformers are thoroughly studied by ab initio model calculations, and Raman and surface-enhanced Raman spectroscopy (SERS) spectra are measured for different species of amphetamine....... The spectra of amphetamine and amphetamine-H+ sampleswere obtained and assigned according to a comparison of the experimental spectra and the ab initio MO calculations, performed using the Gaussian 03W program (Gaussian, Inc., Pittsburgh, PA). The analyses were based on complete geometry minimization...

  9. Ab Initio Description of Disordered Sr1−xKxFe2As2 Using the Coherent Potential Approximation

    KAUST Repository

    Pulikkotil, J. J.

    2010-04-29

    The electronic structure of disordered Sr1−xKxFe2As2 is studied by ab initio density functional theory. As no superstructure and/or atomic short range ordering is reported for Sr1−xKxFe2As2, the coherent potential approximation can be used to describe the effects of chemical disorder. We find clear deviations from the rigid band model characteristics. Nonmagnetic calculations show an enhancement of the density of states at the Fermi energy in the range 0.4≤x≤0.65, which coincides with the region where experiments observe an enhanced superconducting transition temperature, and antiferromagnetic calculations indicate a significant renormalization of states at Fermi energy. Analyzing the distribution of the Fe 3d states over the range 0≤x≤1 we propose an effective three band model.

  10. A Review of Solid-Solution Models of High-Entropy Alloys Based on Ab Initio Calculations

    Directory of Open Access Journals (Sweden)

    Fuyang Tian

    2017-11-01

    Full Text Available Similar to the importance of XRD in experiments, ab initio calculations, as a powerful tool, have been applied to predict the new potential materials and investigate the intrinsic properties of materials in theory. As a typical solid-solution material, the large degree of uncertainty of high-entropy alloys (HEAs results in the difficulty of ab initio calculations application to HEAs. The present review focuses on the available ab initio based solid-solution models (virtual lattice approximation, coherent potential approximation, special quasirandom structure, similar local atomic environment, maximum-entropy method, and hybrid Monte Carlo/molecular dynamics and their applications and limits in single phase HEAs.

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

    International Nuclear Information System (INIS)

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

    2000-01-01

    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

  12. Ab Initio Predictions of Structures and Densities of Energetic Solids

    National Research Council Canada - National Science Library

    Rice, Betsy M; Sorescu, Dan C

    2004-01-01

    We have applied a powerful simulation methodology known as ab initio crystal prediction to assess the ability of a generalized model of CHNO intermolecular interactions to predict accurately crystal...

  13. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms

    Science.gov (United States)

    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.

  14. Geometry optimization of supersymmetrical molecules in quantum chemical ab-initio calculations

    International Nuclear Information System (INIS)

    Gruenbichler, H.

    1985-01-01

    One-dimensional geometry optimizations in ab-initio SCF-calculations are investigated. It is shown, that the well known standard algorithms are sometimes too expensive and can be replaced or accompanied by more recent algorithms. Two alternatives were realized in the molecule calculating program GAUSSIAN 80, basing on the Fibonacci algorithm and Kryachco potential adjustment. The algorithms were compared in terms of accuracy of results, CPU-time used and reliability of the method. The results are presented in various tables, showing the efficiency of the various methods. A survey of the usual model potentials is given and the compatibility with ab-initio data is evaluated. (Author, shortened and translated by A.N.)

  15. Quantum chemistry interpretation of x-ray spectra

    International Nuclear Information System (INIS)

    Bocharov, D.; Kuzmin, A.

    2005-01-01

    Full text: In this study, we present the results of ab initio computer simulations on X-ray absorption spectra of some perovskite-type tungsten oxides. For our calculations, we combine a periodic bulk model with Hartree-Fock method including a posteriori electron correlation corrections, as implemented in CRYSTAL98 computer code [1]. First, we describe the results of calculations performed on some bulk properties of the tungsten oxides (lattice constant and bulk modulus), in order to achieve the necessary level of agreement with available experimental and theoretical data. Our calculations on the densities of oneelectron energy states (DOS) for models of tungsten oxides are verified by experimental X-ray absorption spectra, which allow us to make correct qualitative interpretation of the latter. The main difficulties appearing during our first principles simulations will be discussed. [1] V.R. Saunders, R. Dovesi, C. Roetti, M. Causi, N.M. Harrison, R. Orlando, and C.M. Zicovich-Wilson, CRYSTAL-98 User Manual, University of Turin, 1999

  16. Inelastic neutron scattering an ab-initio calculation of negative thermal expansion in Ag2O

    International Nuclear Information System (INIS)

    Gupta, M.K.; Mittal, R.; Rols, S.; Chaplot, S.L.

    2012-01-01

    The compound Ag 2 O undergoes large and isotropic negative thermal expansion over 0-500 K. We report temperature dependent inelastic neutron scattering measurements and ab-initio calculations of the phonon spectrum. The temperature dependence of the experimental phonon spectrum shows strong anharmonic nature of phonon modes of energy around 2.4 meV. The ab-initio calculations reveal that the maximum negative Grüneisen parameter, which is a measure of the relevant anharmonicity, occurs for the transverse phonon modes that involve bending motions of the Ag 4 O tetrahedra. The thermal expansion is evaluated from the ab-initio calculation of the pressure dependence of the phonon modes, and found in good agreement with available experimental data.

  17. Ab initio and relativistic DFT study of spin–rotation and NMR shielding constants in XF{sub 6} molecules, X = S, Se, Te, Mo, and W

    Energy Technology Data Exchange (ETDEWEB)

    Ruud, Kenneth [Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø—The Arctic University of Norway, N-9037 Tromsø (Norway); Demissie, Taye B. [Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø—The Arctic University of Norway, N-9037 Tromsø (Norway); Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warszawa, Kasprzaka 44 (Poland); Jaszuński, Michał, E-mail: michal.jaszunski@icho.edu.pl [Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warszawa, Kasprzaka 44 (Poland)

    2014-05-21

    We present an analysis of the spin–rotation and absolute shielding constants of XF{sub 6} molecules (X = S, Se, Te, Mo, W) based on ab initio coupled cluster and four-component relativistic density-functional theory (DFT) calculations. The results show that the relativistic contributions to the spin–rotation and shielding constants are large both for the heavy elements as well as for the fluorine nuclei. In most cases, incorporating the computed relativistic corrections significantly improves the agreement between our results and the well-established experimental values for the isotropic spin–rotation constants and their anisotropic components. This suggests that also for the other molecules, for which accurate and reliable experimental data are not available, reliable values of spin–rotation and absolute shielding constants were determined combining ab initio and relativistic DFT calculations. For the heavy nuclei, the breakdown of the relationship between the spin–rotation constant and the paramagnetic contribution to the shielding constant, due to relativistic effects, causes a significant error in the total absolute shielding constants.

  18. Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.

    Science.gov (United States)

    Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian; Deane, Charlotte M

    2017-05-01

    Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. deane@stats.ox.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

  19. Computational methods for ab initio detection of microRNAs

    Directory of Open Access Journals (Sweden)

    Malik eYousef

    2012-10-01

    Full Text Available MicroRNAs are small RNA sequences of 18-24 nucleotides in length, which serve as templates to drive post transcriptional gene silencing. The canonical microRNA pathway starts with transcription from DNA and is followed by processing via the Microprocessor complex, yielding a hairpin structure. Which is then exported into the cytosol where it is processed by Dicer and then incorporated into the RNA induced silencing complex. All of these biogenesis steps add to the overall specificity of miRNA production and effect. Unfortunately, their modes of action are just beginning to be elucidated and therefore computational prediction algorithms cannot model the process but are usually forced to employ machine learning approaches. This work focuses on ab initio prediction methods throughout; and therefore homology-based miRNA detection methods are not discussed. Current ab initio prediction algorithms, their ties to data mining, and their prediction accuracy are detailed.

  20. Sensitivity of core-level spectroscopy to electrostatic environments of nitrile groups: An ab initio study

    Directory of Open Access Journals (Sweden)

    Abid Hussain

    2017-09-01

    Full Text Available Ab initio quantum chemistry calculations have been performed to probe the influence of hydrogen bonding on the electronic structure of hydrogen cyanide (HCN. Our calculations determine the origin of nitrogen-specific Raman spectral features from resonant inelastic X-ray scattering occurring in the presence of a water molecule and an electric dipole field. The similarity of the two interactions in altering the electronic structure of the nitrogen atom differs only in the covalent contributions from the water molecule. The CN stretching mode as a structural probe was also investigated to study the electronic origin of the anomalous frequency shift of the nitrile group when subjected to hydrogen bonding and an electrostatic dipole field. The major changes in the electronic structure of HCN are electrostatic in nature and originate from dipole-dipole interactions. The relative shifts of the CN stretching frequency are in good agreement with those experimentally observed.

  1. Shear stiffness in nanolaminar Ti3SiC2 challenges ab initio calculations

    International Nuclear Information System (INIS)

    Kisi, E H; Zhang, J F; Kirstein, O; Riley, D P; Styles, M J; Paradowska, A M

    2010-01-01

    Nanolaminates such as the M n+1 AX n (MAX) phases are a material class with ab initio derived elasticity tensors published for over 250 compounds. We have for the first time experimentally determined the full elasticity tensor of the archetype MAX phase, Ti 3 SiC 2 , using polycrystalline samples and in situ neutron diffraction. The experimental elastic constants show extreme shear stiffness, with c 44 more than five times greater than expected for an isotropic material. Such shear stiffness is quite rare in hexagonal materials and strongly contradicts the predictions of all published MAX phase elastic constants derived from ab initio calculations. It is concluded that second order properties such as elastic moduli derived from ab initio calculations require careful experimental verification. The diffraction technique used currently provides the only method of verification for the elasticity tensor for the majority of new materials where single crystals are not available. (fast track communication)

  2. Proper construction of ab initio global potential surfaces with accurate long-range interactions

    International Nuclear Information System (INIS)

    Ho, Tak-San; Rabitz, Herschel

    2000-01-01

    An efficient procedure based on the reproducing kernel Hilbert space interpolation method is presented for constructing intermolecular potential energy surfaces (PES) using not only calculated ab initio data but also a priori information on long-range interactions. Explicitly, use of the reciprocal power reproducing kernel on the semiinfinite interval [0,∞) yields a set of exact linear relations between dispersion (multipolar) coefficients and PES data points at finite internuclear separations. Consequently, given a combined set of ab initio data and the values of dispersion (multipolar) coefficients, the potential interpolation problem subject to long-range interaction constraints can be solved to render globally smooth, asymptotically accurate ab initio potential energy surfaces. Very good results have been obtained for the one-dimensional He-He potential curve and the two-dimensional Ne-CO PES. The construction of the Ne-CO PES was facilitated by invoking a new reproducing kernel for the angular coordinate based on the optimally stable and shape-preserving Bernstein basis functions. (c) 2000 American Institute of Physics

  3. Ab initio calculations and modelling of atomic cluster structure

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Lyalin, Andrey G.; Solov'yov, Andrey V.

    2004-01-01

    The optimized structure and electronic properties of small sodium and magnesium clusters have been investigated using it ab initio theoretical methods based on density-functional theory and post-Hartree-Fock many-body perturbation theory accounting for all electrons in the system. A new theoretical...

  4. Large-scale ab initio configuration interaction calculations for light nuclei

    International Nuclear Information System (INIS)

    Maris, Pieter; Potter, Hugh; Vary, James P; Aktulga, H Metin; Ng, Esmond G; Yang Chao; Caprio, Mark A; Çatalyürek, Ümit V; Saule, Erik; Oryspayev, Dossay; Sosonkina, Masha; Zhou Zheng

    2012-01-01

    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 12 C including emerging collective phenomena such as rotational band structures using SRG evolved chiral N3LO interactions.

  5. Analysis of the x-ray spectrum emitted by laser-produced plasma of dysprosium

    International Nuclear Information System (INIS)

    Marcus, Gilad; Louzon, Einat; Henis, Zohar; Maman, Shlomo; Mandelbaum, Pinchas

    2007-01-01

    A detailed analysis of the x-ray spectrum (5-10.2 A ring ) emitted by laser-produced plasma of dysprosium (Dy) is given using ab initio calculations with the HULLAC relativistic code and isoelectronic trends. Resonance 3d-4p, 3d-nf (n=4 to 7), 3p-4s, and 3p-4d transitions of Ni I-like Dy XXXIX and neighboring ion satellite transitions (from Dy XXXIV to Dy XL) are identified

  6. Virtual synthesis of crystals using ab initio MD: Case study on LiFePO4

    Science.gov (United States)

    Mishra, S. B.; Nanda, B. R. K.

    2017-05-01

    Molecular dynamics simulation technique is fairly successful in studying the structural aspects and dynamics of fluids. Here we study the ability of ab initio molecular dynamics (ab initio MD) to carry out virtual experiments to synthesize new crystalline materials and to predict their structures. For this purpose the olivine phosphate LiFePO4 (LFPO) is used as an example. As transition metal oxides in general are stabilized with layered geometry, we carried out ab initio MD simulations over a hypothetical layered configuration consisting of alternate LiPO2 and FeO2 layers. With intermittent steps of electron minimization, the resulted equilibrium lattice consist of PO4 tetrahedra and distorted Fe-O complexes similar to the one observed in the experimental lattice.

  7. Thermal, spectroscopic, and ab initio structural characterization of carprofen polymorphs.

    Science.gov (United States)

    Bruni, Giovanna; Gozzo, Fabia; Capsoni, Doretta; Bini, Marcella; Macchi, Piero; Simoncic, Petra; Berbenni, Vittorio; Milanese, Chiara; Girella, Alessandro; Ferrari, Stefania; Marini, Amedeo

    2011-06-01

    Commercial and recrystallized polycrystalline samples of carprofen, a nonsteroidal anti-inflammatory drug, were studied by thermal, spectroscopic, and structural techniques. Our investigations demonstrated that recrystallized sample, stable at room temperature (RT), is a single polymorphic form of carprofen (polymorph I) that undergoes an isostructural polymorphic transformation by heating (polymorph II). Polymorph II remains then metastable at ambient conditions. Commercial sample is instead a mixture of polymorphs I and II. The thermodynamic relationships between the two polymorphs were determined through the construction of an energy/temperature diagram. The ab initio structural determination performed on synchrotron X-Ray powder diffraction patterns recorded at RT on both polymorphs allowed us to elucidate, for the first time, their crystal structure. Both crystallize in the monoclinic space group type P2(1) /c, and the unit cell similarity index and the volumetric isostructurality index indicate that the temperature-induced polymorphic transformation I → II is isostructural. Polymorphs I and II are conformational polymorphs, sharing a very similar hydrogen bond network, but with different conformation of the propanoic skeleton, which produces two different packing. The small conformational change agrees with the low value of transition enthalpy obtained by differential scanning calorimetry measurements and the small internal energy computed with density functional methods. Copyright © 2011 Wiley-Liss, Inc.

  8. Modeling of nuclear glasses by classical and ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Ganster, P.

    2004-01-01

    A calcium aluminosilicate glass of molar composition 67 % SiO 2 - 12 % Al 2 O 3 - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri-coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminum atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author) [fr

  9. Modelling of nuclear glasses by classical and ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Ganster, P.

    2004-10-01

    A calcium aluminosilicate glass of molar composition 67 % SiO 2 - 12 % Al 2 O 3 - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminium atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)

  10. Biological effect of ultrasoft x-ray, 1

    International Nuclear Information System (INIS)

    Narita, Noboru

    1985-01-01

    Biological effect on Escherichia coli by ultrasoft X-ray have been studied by comparing with that by uv light (2537 A) and by soft X-ray (40 kVp, 5 mA). Ultrasoft X-ray is aluminium characteristic X-ray (about 1.5 keV) produced by low energy electron collision on aluminium foil target and is obtained from Lea-type transmission target discharge tube. Escherichia coli used here are AB1157, AB1886 (uvrA6), JC1569 (recA), AB2470 (recB) and AB2480 (uvr rec) for inactivation experiment and WP2, WP2uvrA, WP2pKM101 and WP2uvrApKM101 for mutation induction experiment. These strains are all irradiated in buffer. Results obtained are summerized as follows : (i) inactivation by ultrasoft X-ray is located between ones by uv light and by soft X-ray, or ultrasoft X-ray gives a lethal damage that uvrA6 gene seems to contribute, and (ii) ultrasoft X-ray does not show the remarkable mutation induction like that induced by low dose irradiation of uv light or soft X-ray. (author)

  11. Ab initio results for intermediate-mass, open-shell nuclei

    Science.gov (United States)

    Baker, Robert B.; Dytrych, Tomas; Launey, Kristina D.; Draayer, Jerry P.

    2017-01-01

    A theoretical understanding of nuclei in the intermediate-mass region is vital to astrophysical models, especially for nucleosynthesis. Here, we employ the ab initio symmetry-adapted no-core shell model (SA-NCSM) in an effort to push first-principle calculations across the sd-shell region. The ab initio SA-NCSM's advantages come from its ability to control the growth of model spaces by including only physically relevant subspaces, which allows us to explore ultra-large model spaces beyond the reach of other methods. We report on calculations for 19Ne and 20Ne up through 13 harmonic oscillator shells using realistic interactions and discuss the underlying structure as well as implications for various astrophysical reactions. This work was supported by the U.S. NSF (OCI-0904874 and ACI -1516338) and the U.S. DOE (DE-SC0005248), and also benefitted from the Blue Waters sustained-petascale computing project and high performance computing resources provided by LSU.

  12. Ab Initio Many-Body Calculations Of Nucleon-Nucleus Scattering

    Energy Technology Data Exchange (ETDEWEB)

    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.

  13. Resonant inelastic x-ray scattering on iso-C₂H₂Cl₂ around the chlorine K-edge: structural and dynamical aspects.

    Science.gov (United States)

    Kawerk, Elie; Carniato, Stéphane; Journel, Loïc; Marchenko, Tatiana; Piancastelli, Maria Novella; Žitnik, Matjaž; Bučar, Klemen; Bohnic, Rok; Kavčič, Matjaž; Céolin, Denis; Khoury, Antonio; Simon, Marc

    2014-10-14

    We report a theoretical and experimental study of the high resolution resonant K(α) X-ray emission lines around the chlorine K-edge in gas phase 1,1-dichloroethylene. With the help of ab initio electronic structure calculations and cross section evaluation, we interpret the lowest lying peak in the X-ray absorption and emission spectra. The behavior of the K(α) emission lines with respect to frequency detuning highlights the existence of femtosecond nuclear dynamics on the dissociative Potential Energy Surface of the first K-shell core-excited state.

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

    Energy Technology Data Exchange (ETDEWEB)

    Makhov, Dmitry V.; Shalashilin, Dmitrii V. [Department of Chemistry, University of Leeds, Leeds LS2 9JT (United Kingdom); Glover, William J.; Martinez, Todd J. [Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Keegan, Ronan M. [STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); Bibby, Jaclyn; Thomas, Jens [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Xu, Dong [Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037 (United States); Zhang, Yang [University of Michigan, Ann Arbor, MI 48109 (United States); Mayans, Olga [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Winn, Martyn D. [Science and Technology Facilities Council Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Rigden, Daniel J., E-mail: drigden@liv.ac.uk [University of Liverpool, Liverpool L69 7ZB (United Kingdom); STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom)

    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.

  16. Ab initio assisted process modeling for Si-based nanoelectronic devices

    International Nuclear Information System (INIS)

    Windl, Wolfgang

    2005-01-01

    In this paper, we discuss concepts and examples of ab initio calculations assisting physics-based process simulation. We focus on how to determine diffusion and reaction constants, where modern methods such as the nudged elastic band method allow a systematic and reliable search for the minimum energy migration path and barrier. We show that once the saddle point is determined, the underlying harmonic transition state theory also allows to calculate the prefactors. The discussed examples include nitrogen diffusion, boron deactivation and boron interface segregation. Finally, some concepts are discussed for future device technologies such as molecular devices, where the currently prevalent multiscale approach (kinetic parameters used in higher level models like diffusion-reaction or kinetic Monte Carlo modeling) would not be sensible anymore. As an example, we described the ab initio temperature-accelerated dynamics modeling of contact formation in carbon nanotube devices

  17. Ab initio calculation of Ti NMR shieldings for titanium oxides and halides

    Science.gov (United States)

    Tossell, J. A.

    Titanium NMR shielding constants have been calculated using ab initio coupled Hartree-Fock perturbation theory and polarized double-zeta basis sets for TiF 4, TiF 62-, TiCI 4, Ti(OH) 4, Ti(OH 2) 64+, Ti(OH) 4O, and Ti(OH) 3O -. In all cases the calculations were performed at Hartree-Fuck energy-optimized geometries. For Ti(OH) 4 a S4-symmetry geometry with nonlinear ∠ TiOH was employed. Relative shieldings are in reasonable agreement with experiment for TiF 62-, TiCI 4, and Ti(OR) 4, where R = H or alkyl. Ti(OH 2) 64+ is predicted to be more highly shielded than Ti(OH) 4 by about 340 ppm. The five-coordinate complex Ti(OH) 4O, whose calculated structure matches well that measured by extended X-ray absorption fine structure in K 2O · TiO 2 · SiO 2 glass, is actually deshielded compared to Ti(OH) 4 by about 40 ppm. X-ray absorption-near-edge spectral energies have also been calculated for TiF 4, TiCI 4, Ti(OH) 4, and Ti(OH) 4O using an equivalent ionic core virtual-orbital method and the observed reduction in term energy for the five-coordinate species compared to Ti(OH) 4 has been reproduced. Replacement of the H atoms in Ti(OH) 4 by point charges has only a slight effect upon σTi, suggesting a possible means of incorporating second-neighbor effects in NMR calculations for condensed phases.

  18. Water structure as a function of temperature from X-ray scatteringexperiments and ab initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Hura, Greg; Russo, Daniela; Glaeser, Robert M.; Head-Gordon,Teresa; Krack, Matthias; Parrinello, Michele

    2003-03-01

    We present high-quality X-ray scattering experiments on pure water taken over a temperature range of 2 to 77 C using a synchrotron beam line at the advanced light source (ALS) at Lawrence Berkeley National Laboratory. The ALS X-ray scattering intensities are qualitatively different in trend of maximum intensity over this temperature range compared to older X-ray experiments. While the common procedure is to report both the intensity curve and radial distribution function(s), the proper extraction of the real-space pair correlation functions from the experimental scattering is very difficult due to uncertainty introduced in the experimental corrections, the proper weighting of OO, OH, and HH contributions, and numerical problems of Fourier transforming truncated data in Q-space. Instead, we consider the direct calculation of X-ray scattering spectra using electron densities derived from density functional theory based on real-space configurations generated with classical water models. The simulation of the experimental intensity is therefore definitive for determining radial distribution functions over a smaller Q-range. We find that the TIP4P, TIP5P and polarizable TIP4P-Pol2 water models, with DFT-LDA densities, show very good agreement with the experimental intensities, and TIP4P-Pol2 in particular shows quantitative agreement over the full temperature range. The resulting radial distribution functions from TIP4P-Pol2 provide the current best benchmarks for real-space water structure over the biologically relevant temperature range studied here.

  19. Ab initio interaction potentials for X and B excited states of He-I2 for studying dynamics

    International Nuclear Information System (INIS)

    Prosmiti, Rita; Garcia-Gutierrez, Leonor; Delgado-Tellez, Laura; Valdes, Alvaro; Villarreal, Pablo; Delgado-Barrio, Gerardo

    2009-01-01

    Ab initio CCSD(T) and MRCI approaches were employed to construct potential energy surfaces of the ground and the B electronic excited states of He-I 2 complex, while full quantum mechanical methods were applied to study its spectroscopy and dynamics. A description of the approach adopted, together with the results obtained and their comparison with recent experimental data, as well as further improvements are presented.

  20. Structural and vibrational study of 2-MethoxyEthylAmmonium Nitrate (2-OMeEAN): Interpretation of experimental results with ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Campetella, M.; Caminiti, R.; Bencivenni, L.; Gontrani, L.; Bovi, D.; Guidoni, L.

    2016-01-01

    In this work we report an analysis of the bulk phase of 2-methoxyethylammonium nitrate based on ab initio molecular dynamics. The structural and dynamical features of the ionic liquid have been characterized and the computational findings have been compared with the experimental X-ray diffraction patterns, with infrared spectroscopy data, and with the results obtained from molecular dynamics simulations. The experimental infrared spectrum was interpreted with the support of calculated vibrational density of states as well as harmonic frequency calculations of selected gas phase clusters. Particular attention was addressed to the high frequency region of the cation (ω > 2000 cm −1 ), where the vibrational motions involve the NH 3 + group responsible for hydrogen bond formation, and to the frequency range 1200-1400 cm −1 where the antisymmetric stretching mode (ν 3 ) of nitrate is found. Its multiple absorption lines in the liquid arise from the removal of the degeneracy present in the D 3h symmetry of the isolated ion. Our ab initio molecular dynamics leads to a rationalization of the frequency shifts and splittings, which are inextricably related to the structural modifications induced by a hydrogen bonding environment. The DFT calculations lead to an inhomogeneous environment.

  1. Structural and vibrational study of 2-MethoxyEthylAmmonium Nitrate (2-OMeEAN): Interpretation of experimental results with ab initio molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Campetella, M.; Caminiti, R.; Bencivenni, L.; Gontrani, L., E-mail: lorenzo.gontrani@uniroma1.it [Dipartimento di Chimica, Università di Roma, “La Sapienza,” P. le Aldo Moro 5, I-00185 Roma (Italy); Bovi, D. [Dipartimento di Fisica, Università di Roma, “La Sapienza,” P. le Aldo Moro 5, I-00185 Roma (Italy); Guidoni, L. [Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’Aquila, Via Vetoio, Coppito, I-67100 L’Aquila (Italy)

    2016-07-14

    In this work we report an analysis of the bulk phase of 2-methoxyethylammonium nitrate based on ab initio molecular dynamics. The structural and dynamical features of the ionic liquid have been characterized and the computational findings have been compared with the experimental X-ray diffraction patterns, with infrared spectroscopy data, and with the results obtained from molecular dynamics simulations. The experimental infrared spectrum was interpreted with the support of calculated vibrational density of states as well as harmonic frequency calculations of selected gas phase clusters. Particular attention was addressed to the high frequency region of the cation (ω > 2000 cm{sup −1}), where the vibrational motions involve the NH{sub 3}+ group responsible for hydrogen bond formation, and to the frequency range 1200-1400 cm{sup −1} where the antisymmetric stretching mode (ν{sub 3}) of nitrate is found. Its multiple absorption lines in the liquid arise from the removal of the degeneracy present in the D{sub 3h} symmetry of the isolated ion. Our ab initio molecular dynamics leads to a rationalization of the frequency shifts and splittings, which are inextricably related to the structural modifications induced by a hydrogen bonding environment. The DFT calculations lead to an inhomogeneous environment.

  2. Ab initio and empirical studies on the asymmetry of molecular current-voltage characteristics

    International Nuclear Information System (INIS)

    Hoft, R C; Armstrong, N; Ford, M J; Cortie, M B

    2007-01-01

    We perform theoretical calculations of the tunnelling current through various small organic molecules sandwiched between gold electrodes by using both a tunnel barrier model and an ab initio transport code. The height of the tunnelling barrier is taken to be the work function of gold as modified by the adsorbed molecule and calculated from an ab initio electronic structure code. The current-voltage characteristics of these molecules are compared. Asymmetry is introduced into the system in two ways: an asymmetric molecule and a gap between the molecule and the right electrode. The latter is a realistic situation in scanning probe experiments. The asymmetry is also realized in the tunnel barrier model by two distinct work functions on the left and right electrodes. Significant asymmetry is observed in the ab initio i(V) curves. The tunnel barrier i(V) curves show much less pronounced asymmetry. The relative sizes of the currents through the molecules are compared. In addition, the performance of the WKB approximation is compared to the results obtained from the exact Schroedinger solution to the tunnelling barrier problem

  3. An Ab Initio Description of the Excitonic Properties of LH2 and Their Temperature Dependence.

    Science.gov (United States)

    Cupellini, Lorenzo; Jurinovich, Sandro; Campetella, Marco; Caprasecca, Stefano; Guido, Ciro A; Kelly, Sharon M; Gardiner, Alastair T; Cogdell, Richard; Mennucci, Benedetta

    2016-11-10

    The spectroscopic properties of light-harvesting (LH) antennae in photosyntehtic organisms represent a fingerprint that is unique for each specific pigment-protein complex. Because of that, spectroscopic observations are generally combined with structural data from X-ray crystallography to obtain an indirect representation of the excitonic properties of the system. Here, an alternative strategy is presented which goes beyond this empirical approach and introduces an ab initio computational description of both structural and electronic properties and their dependence on the temperature. The strategy is applied to the peripheral light-harvesting antenna complex (LH2) present in purple bacteria. By comparing this model with the one based on the crystal structure, a detailed, molecular level explanation of the absorption and circular dichroism (CD) spectra and their temperature dependence is achieved. The agreement obtained with the experiments at both low and room temperature lays the groundwork for an atomistic understanding of the excitation dynamics in the LH2 system.

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

    Science.gov (United States)

    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.

  5. Modelling of nuclear glasses by classical and ab initio molecular dynamics; Modelisation de verres intervenant dans le conditionnement des dechets radioactifs par dynamiques moleculaires classique et ab initio

    Energy Technology Data Exchange (ETDEWEB)

    Ganster, P

    2004-10-15

    A calcium aluminosilicate glass of molar composition 67 % SiO{sub 2} - 12 % Al{sub 2}O{sub 3} - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminium atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)

  6. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

    Science.gov (United States)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-28

    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.

  7. Ab initio chemical kinetics for SiH3 reactions with Si(x)H2x+2 (x = 1-4).

    Science.gov (United States)

    Raghunath, P; Lin, M C

    2010-12-30

    Gas-phase kinetics and mechanisms of SiH(3) reactions with SiH(4), Si(2)H(6), Si(3)H(8), and Si(4)H(10), processes of relevance to a-Si thin-film deposition, have been investigated by ab initio molecular orbital and transition-state theory (TST) calculations. Geometric parameters of all the species involved in the title reactions were optimized by density functional theory at the B3LYP and BH&HLYP levels with the 6-311++G(3df,2p) basis set. The potential energy surface of each reaction was refined at the CCSD(T)/6-311++G(3df,2p) level of theory. The results show that the most favorable low energy pathways in the SiH(3) reactions with these silanes occur by H abstraction, leading to the formation of SiH(4) + Si(x)H(2x+1) (silanyl) radicals. For both Si(3)H(8) and n-Si(4)H(10) reactions, the lowest energy barrier channels take place by secondary Si-H abstraction, yielding SiH(4) + s-Si(3)H(7) and SiH(4) + s-Si(4)H(9), respectively. In the i-Si(4)H(10) reaction, tertiary Si-H abstraction has the lowest barrier producing SiH(4) + t-Si(4)H(9). In addition, direct SiH(3)-for-X substitution reactions forming Si(2)H(6) + X (X = H or silanyls) can also occur, but with significantly higher reaction barriers. A comparison of the SiH(3) reactions with the analogous CH(3) reactions with alkanes has been made. The rate constants for low-energy product channels have been calculated for the temperature range 300-2500 K by TST with Eckart tunneling corrections. These results, together with predicted heats of formation of various silanyl radicals and Si(4)H(10) isomers, have been tabulated for modeling of a-Si:H film growth by chemical vapor deposition.

  8. Ab-Initio Investigations of Magnetic Properties and Induced Half-Metallicity in Ga1-xMnxP (x = 0.03, 0.25, 0.5, and 0.75) Alloys.

    Science.gov (United States)

    Laref, Amel; AlMudlej, Abeer; Laref, Slimane; Yang, Jun Tao; Xiong, Yong-Chen; Luo, Shi Jun

    2017-07-07

    Ab-initio calculations are performed to examine the electronic structures and magnetic properties of spin-polarized Ga 1- x Mn x P ( x = 0.03, 0.25, 0.5, and 0.75) ternary alloys. In order to perceive viable half-metallic (HM) states and unprecedented diluted magnetic semiconductors (DMSs) such as spintronic materials, the full potential linearized augmented plane wave method is utilized within the generalized gradient approximation (GGA). In order to tackle the correlation effects on 3d states of Mn atoms, we also employ the Hubbard U (GGA + U) technique to compute the magnetic properties of an Mn-doped GaP compound. We discuss the emerged global magnetic moments and the robustness of half-metallicity by varying the Mn composition in the GaP compound. Using GGA + U, the results of the density of states demonstrate that the incorporation of Mn develops a half-metallic state in the GaP compound with an engendered band gap at the Fermi level ( E F ) in the spin-down state. Accordingly, the half-metallic feature is produced through the hybridization of Mn-d and P-p orbitals. However, the half-metallic character is present at a low x composition with the GGA procedure. The produced magnetic state occurs in these materials, which is a consequence of the exchange interactions between the Mn-element and the host GaP system. For the considered alloys, we estimated the X-ray absorption spectra at the K edge of Mn. A thorough clarification of the pre-edge peaks is provided via the results of the theoretical absorption spectra. It is inferred that the valence state of Mn in Ga 1- x Mn x P alloys is +3. The predicted theoretical determinations surmise that the Mn-incorporated GaP semiconductor could inevitably be employed in spintronic devices.

  9. Quantifying transition voltage spectroscopy of molecular junctions: Ab initio calculations

    DEFF Research Database (Denmark)

    Chen, Jingzhe; Markussen, Troels; Thygesen, Kristian Sommer

    2010-01-01

    Transition voltage spectroscopy (TVS) has recently been introduced as a spectroscopic tool for molecular junctions where it offers the possibility to probe molecular level energies at relatively low bias voltages. In this work we perform extensive ab initio calculations of the nonlinear current...

  10. Speciation of magnesium in monohydrocalcite: XANES, ab initio and geochemical modeling

    Science.gov (United States)

    Fukushi, Keisuke; Suzuki, Yuma; Kawano, Jun; Ohno, Takeshi; Ogawa, Masahiro; Yaji, Toyonari; Takahashi, Yoshio

    2017-09-01

    Monohydrocalcite (MHC: CaCO3·H2O), a rare carbonate mineral formed under surface conditions, is usually observed in nature as containing a variable amount of Mg, with a 0.007-0.45 Mg/Ca mole ratio. The variable Mg composition in MHC is anticipated as a promising proxy to assess paleo-hydrochemistry especially in saline lakes. Although the roles of Mg on the formation and stability of MHC have been studied intensively, the Mg speciation in MHC has remained unclear and controversial. This study examined Mg speciation in MHC using X-ray absorption near edge structure (XANES), ab initio molecular simulation, and geochemical modeling. Mg-XANES spectra of MHC with different Mg/Ca ratios prepared from mixing solutions of Na2CO3, CaCl2 and MgCl2 revealed that the Mg in MHC is a mixture of amorphous Mg carbonate (AMC) and other Mg containing phase. The contribution of AMC to total Mg is negatively correlated to the crystallinity of MHC. Results show that AMC might play a protective role in the crystallization and the transformation to stable calcium carbonates. Ab initio calculation of Mg2+ substitution into MHC showed that a limited amount of Mg2+ can be incorporated into the MHC structure. Six-fold coordination of Mg2+ is substituted for eight-fold coordination of Ca2+ in the MHC structure. The other type of Mg in MHC revealed from the XANES analyses most likely corresponds to the structural Mg in MHC. The contribution of the structural Mg is almost constant at 0.06 in Mg/Ca, representing the limit of solid solubility of Mg in MHC. The solubility products of the MHC with the limit of solid solubility of Mg and the AMC associated with MHC were estimated from the reacted solution compositions. Prediction of the Mg/Ca ratio as a function of the initial solution conditions using solubility reasonably reproduces the observed apparent Mg/Ca ratios in MHC from the present study and earlier studies. The apparent Mg/Ca ratio of MHC is useful to elucidate water chemistry

  11. Chandra X-ray Time-Domain Study of Alpha Centauri AB, Procyon, and their Environs

    Science.gov (United States)

    Ayres, Thomas R.

    2018-06-01

    For more than a decade, Chandra X-ray Observatory has been monitoring the central AB binary (G2V+K1V) of the α Centauri triple system with semi-annual pointings, using the High-Resolution Camera. This study has been extended in recent years to the mid-F subgiant, Procyon. The main objective is to follow the coronal (T~1MK) activity variations of the three stars, analogous to the Sun's 11-year sunspot cycle. Tentative periods of 20 yr and 8 yr have been deduced for α Cen A and B, respectively; but so far Procyon has shown only a slow, very modest decline in count rate, which could well reflect a slight instrumental degradation rather than intrinsic behavior. The negligible high-energy variability of Procyon sits in stark contrast to the dramatic factor of several to ten changes in the X-ray luminosities of α Cen AB and the Sun over their respective cycles. Further, although sunlike α Cen A has been observed by successive generations of X-ray observatories for nearly four decades, albeit sporadically, there are key gaps in the coverage that affect the determination of the cycle period. In fact, the most recent pointings suggest a downturn in A's count rate that might be signaling a shorter, more solar-like cycle following a delayed minimum in the 2005--2010 time frame (perhaps an exaggerated version of the extended solar minimum between recent Cycles 23 and 24). Beyond the coronal cycles of the three stars, the sequence of periodic X-ray images represents a unique time-domain history concerning steady as well as variable sources in the two 30'x30' fields. The most conspicuous of the variable objects -- in the α Cen field -- will be described here.

  12. Ab Initio Calculations for the BaTiO3 (001) Surface Structure

    Institute of Scientific and Technical Information of China (English)

    XUE Xu-Yan; WANG Chun-Lei; ZHONG Wei-Lie

    2004-01-01

    @@ The ab initio method within the local density approximation is applied to calculate cubic BaTiO3 (001) surface relaxation and rumpling for two different terminations (BaO and TiO2). Our calculations demonstrate that cubic perovskite BaTiO3 crystals possess surface polarization, accompanied by the presence of the relevant electric field.We analyse their electronic structures (band structure, density of states and the electronic density redistribution with emphasis on the covalency effects). The results are also compared with that of the previous ab initio calculations. Considerable increases of Ti-O chemical bond covalency nearby the surface have been observed.The band gap reduces especially for the TiO2 termination.

  13. Ab initio calculations of mechanical properties: Methods and applications

    Czech Academy of Sciences Publication Activity Database

    Pokluda, J.; Černý, Miroslav; Šob, Mojmír; Umeno, Y.

    2015-01-01

    Roč. 73, AUG (2015), s. 127-158 ISSN 0079-6425 R&D Projects: GA ČR(CZ) GAP108/12/0311 Institutional support: RVO:68081723 Keywords : Ab initio methods * Elastic moduli * Intrinsic hardness * Stability analysis * Theoretical strength * Intrinsic brittleness/ductility Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 31.083, year: 2015

  14. Early stage precipitation in aluminum alloys : An ab initio study

    NARCIS (Netherlands)

    Zhang, X.

    2017-01-01

    Multiscale computational materials science has reached a stage where many complicated phenomena or properties that are of great importance to manufacturing can be predicted or explained. The word “ab initio study” becomes commonplace as the development of density functional theory has enabled the

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

    DEFF Research Database (Denmark)

    Drumm, Daniel W.; Per, Manolo C.; Budi, Akin

    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...

  16. Common lines modeling for reference free Ab-initio reconstruction in cryo-EM.

    Science.gov (United States)

    Greenberg, Ido; Shkolnisky, Yoel

    2017-11-01

    We consider the problem of estimating an unbiased and reference-free ab initio model for non-symmetric molecules from images generated by single-particle cryo-electron microscopy. The proposed algorithm finds the globally optimal assignment of orientations that simultaneously respects all common lines between all images. The contribution of each common line to the estimated orientations is weighted according to a statistical model for common lines' detection errors. The key property of the proposed algorithm is that it finds the global optimum for the orientations given the common lines. In particular, any local optima in the common lines energy landscape do not affect the proposed algorithm. As a result, it is applicable to thousands of images at once, very robust to noise, completely reference free, and not biased towards any initial model. A byproduct of the algorithm is a set of measures that allow to asses the reliability of the obtained ab initio model. We demonstrate the algorithm using class averages from two experimental data sets, resulting in ab initio models with resolutions of 20Å or better, even from class averages consisting of as few as three raw images per class. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Structural insights and ab initio sequencing within the DING proteins family

    International Nuclear Information System (INIS)

    Elias, Mikael; Liebschner, Dorothee; Gotthard, Guillaume; Chabriere, Eric

    2011-01-01

    DING proteins constitute a recently discovered protein family that is ubiquitous in eukaryotes. The structural insights and the physiological involvements of these intriguing proteins are hereby deciphered. DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated

  18. Structural insights and ab initio sequencing within the DING proteins family

    Energy Technology Data Exchange (ETDEWEB)

    Elias, Mikael, E-mail: mikael.elias@weizmann.ac.il [Weizmann Institute of Science, Rehovot (Israel); Liebschner, Dorothee [CRM2, Nancy Université (France); Gotthard, Guillaume; Chabriere, Eric [AFMB, Université Aix-Marseille II (France)

    2011-01-01

    DING proteins constitute a recently discovered protein family that is ubiquitous in eukaryotes. The structural insights and the physiological involvements of these intriguing proteins are hereby deciphered. DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated.

  19. Permanent and induced dipole requirements in ab initio calculations of electron affinities of polar molecules

    International Nuclear Information System (INIS)

    Garrett, W.R.

    1979-01-01

    Through the use of a molecular pseudopotential method, we determine the a approximate magnitudes of errors that result when electron affinity determinations of polar negative ions are made through ab initio calculations in which the use of a given basis set yields inappropriate values for permanent and induced dipole moments of the neutral molecule. These results should prove useful in assessing the adequacy of basis sets in ab initio calculations of molecular electron affinities for simple linear polar molecules

  20. Ab initio/interpolated quantum dynamics on coupled electronic states with full configuration interaction wave functions

    International Nuclear Information System (INIS)

    Thompson, K.; Martinez, T.J.

    1999-01-01

    We present a new approach to first-principles molecular dynamics that combines a general and flexible interpolation method with ab initio evaluation of the potential energy surface. This hybrid approach extends significantly the domain of applicability of ab initio molecular dynamics. Use of interpolation significantly reduces the computational effort associated with the dynamics over most of the time scale of interest, while regions where potential energy surfaces are difficult to interpolate, for example near conical intersections, are treated by direct solution of the electronic Schroedinger equation during the dynamics. We demonstrate the concept through application to the nonadiabatic dynamics of collisional electronic quenching of Li(2p). Full configuration interaction is used to describe the wave functions of the ground and excited electronic states. The hybrid approach agrees well with full ab initio multiple spawning dynamics, while being more than an order of magnitude faster. copyright 1999 American Institute of Physics

  1. Hydrogen Bond Dynamics in Aqueous Solutions: Ab initio Molecular ...

    Indian Academy of Sciences (India)

    Rate equation for the decay of CHB(t) · Definition of Hydrogen Bonds · Results of Molecular Dynamics · Dynamics of anion-water and water-water hydrogen bonds · Structural relaxation of anion-water & water-water H-bonds · Ab initio Molecular Dynamics : · Slide 14 · Dynamics of hydrogen bonds : CPMD results · Slide 16.

  2. Elucidating the breathing of the metal-organic framework MIL-53(Sc) with ab initio molecular dynamics simulations and in situ X-ray powder diffraction experiments.

    Science.gov (United States)

    Chen, Linjiang; Mowat, John P S; Fairen-Jimenez, David; Morrison, Carole A; Thompson, Stephen P; Wright, Paul A; Düren, Tina

    2013-10-23

    Ab initio molecular dynamics (AIMD) simulations have been used to predict structural transitions of the breathing metal-organic framework (MOF) MIL-53(Sc) in response to changes in temperature over the range 100-623 K and adsorption of CO2 at 0-0.9 bar at 196 K. The method has for the first time been shown to predict successfully both temperature-dependent structural changes and the structural response to variable sorbate uptake of a flexible MOF. AIMD employing dispersion-corrected density functional theory accurately simulated the experimentally observed closure of MIL-53(Sc) upon solvent removal and the transition of the empty MOF from the closed-pore phase to the very-narrow-pore phase (symmetry change from P2(1)/c to C2/c) with increasing temperature, indicating that it can directly take into account entropic as well as enthalpic effects. We also used AIMD simulations to mimic the CO2 adsorption of MIL-53(Sc) in silico by allowing the MIL-53(Sc) framework to evolve freely in response to CO2 loadings corresponding to the two steps in the experimental adsorption isotherm. The resulting structures enabled the structure determination of the two CO2-containing intermediate and large-pore phases observed by experimental synchrotron X-ray diffraction studies with increasing CO2 pressure; this would not have been possible for the intermediate structure via conventional methods because of diffraction peak broadening. Furthermore, the strong and anisotropic peak broadening observed for the intermediate structure could be explained in terms of fluctuations of the framework predicted by the AIMD simulations. Fundamental insights from the molecular-level interactions further revealed the origin of the breathing of MIL-53(Sc) upon temperature variation and CO2 adsorption. These simulations illustrate the power of the AIMD method for the prediction and understanding of the behavior of flexible microporous solids.

  3. Ab initio molecular dynamics simulation of laser melting of silicon

    NARCIS (Netherlands)

    Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.

    1996-01-01

    The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting

  4. Ab initio I-V characteristics of short C-20 chains

    DEFF Research Database (Denmark)

    Roland, C.; Larade, B.; Taylor, Jeremy Philip

    2002-01-01

    We have calculated the I-V characteristics of short chains of C-20 molecular cages between Al and Au leads with an ab initio formalism. The results indicate that a linear chain of such molecules acts primarily as metallic nanowires. The transmission, however, depends sensitively both...

  5. Iron -chromium alloys and free surfaces: from ab initio calculations to thermodynamic modeling

    International Nuclear Information System (INIS)

    Levesque, M.

    2010-11-01

    Ferritic steels possibly strengthened by oxide dispersion are candidates as structural materials for generation IV and fusion nuclear reactors. Their use is limited by incomplete knowledge of the iron-chromium phase diagram at low temperatures and of the phenomena inducing preferential segregation of one element at grain boundaries or at surfaces. In this context, this work contributes to the multi-scale study of the model iron-chromium alloy and their free surfaces by numerical simulations. This study begins with ab initio calculations of properties related to the mixture of atoms of iron and chromium. We highlight complex dependency of the magnetic moments of the chromium atoms on their local chemical environment. Surface properties are also proving sensitive to magnetism. This is the case of impurity segregation of chromium in iron and of their interactions near the surface. In a second step, we construct a simple energy model for high numerical efficiency. It is based on pair interactions on a rigid lattice to which are given local chemical environment and temperature dependencies. With this model, we reproduce the ab initio results at zero temperature and experimental results at high temperature. We also deduce the solubility limits at all intermediate temperatures with mean field approximations that we compare to Monte Carlo simulations. The last step of our work is to introduce free surfaces in our model. We then study the effect of ab initio calculated bulk and surface properties on surface segregation.Finally, we calculate segregation isotherms. We therefore propose an evolution model of surface composition of iron-chromium alloys as a function of bulk composition. which are given local chemical environment and temperature dependencies. With this model, we reproduce the ab initio results at zero temperature and experimental results at high temperature. We also deduce the solubility limits at all intermediate temperatures with mean field approximations that

  6. Ab initio investigation of barium-scandium-oxygen coatings on tungsten for electron emitting cathodes

    Science.gov (United States)

    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

  7. Ab initio quantum chemistry in parallel-portable tools and applications

    International Nuclear Information System (INIS)

    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 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

  8. Structure of the glass-forming metallic liquids by ab-initio and classical molecular dynamics, a case study: Quenching the Cu{sub 60}Ti{sub 20}Zr{sub 20} alloy

    Energy Technology Data Exchange (ETDEWEB)

    Amokrane, S.; Ayadim, A.; Levrel, L. [Groupe “Physique des Liquides et Milieux Complexes,” Faculté des Sciences et Technologie, Université Paris-Est (Créteil), 61 av. du Général de Gaulle, 94010 Créteil Cedex (France)

    2015-11-21

    We consider the question of the amorphization of metallic alloys by melt quenching, as predicted by molecular dynamics simulations with semi-empirical potentials. The parametrization of the potentials is discussed on the example of the ternary Cu-Ti-Zr transition metals alloy, using the ab-initio simulation as a reference. The pair structure in the amorphous state is computed from a potential of the Stillinger-Weber form. The transferability of the parameters during the quench is investigated using two parametrizations: from solid state data, as usual and from a new parametrization on the liquid structure. When the adjustment is made on the pair structure of the liquid, a satisfactory transferability is found between the pure components and their alloys. The liquid structure predicted in this way agrees well with experiment, in contrast with the one obtained using the adjustment on the solid. The final structure, after quenches down to the amorphous state, determined with the new set of parameters is shown to be very close to the ab-initio one, the latter being in excellent agreement with recent X-rays diffraction experiments. The corresponding critical temperature of the glass transition is estimated from the behavior of the heat capacity. Discussion on the consistency between the structures predicted using semi-empirical potentials and ab-initio simulation, and comparison of different experimental data underlines the question of the dependence of the final structure on the thermodynamic path followed to reach the amorphous state.

  9. Towards an ab initio theory for metal L-edge soft X-ray spectroscopy of molecular aggregates.

    Science.gov (United States)

    Preuße, Marie; Bokarev, Sergey I; Aziz, Saadullah G; Kühn, Oliver

    2016-11-01

    The Frenkel exciton model was adapted to describe X-ray absorption and resonant inelastic scattering spectra of polynuclear transition metal complexes by means of the restricted active space self-consistent field method. The proposed approach allows to substantially decrease the requirements on computational resources if compared to a full supermolecular quantum chemical treatment. This holds true, in particular, in cases where the dipole approximation to the electronic transition charge density can be applied. The computational protocol was applied to the calculation of X-ray spectra of the hemin complex, which forms dimers in aqueous solution. The aggregation effects were found to be comparable to the spectral alterations due to the replacement of the axial ligand by solvent molecules.

  10. Resonant inelastic x-ray scattering on iso-C2H2Cl2 around the chlorine K-edge: Structural and dynamical aspects

    International Nuclear Information System (INIS)

    Kawerk, Elie; Carniato, Stéphane; Journel, Loïc; Marchenko, Tatiana; Simon, Marc; Piancastelli, Maria Novella; Žitnik, Matjaž; Bučar, Klemen; Bohnic, Rok

    2014-01-01

    We report a theoretical and experimental study of the high resolution resonant K α X-ray emission lines around the chlorine K-edge in gas phase 1,1-dichloroethylene. With the help of ab initio electronic structure calculations and cross section evaluation, we interpret the lowest lying peak in the X-ray absorption and emission spectra. The behavior of the K α emission lines with respect to frequency detuning highlights the existence of femtosecond nuclear dynamics on the dissociative Potential Energy Surface of the first K-shell core-excited state

  11. Resonant inelastic x-ray scattering on iso-C2H2Cl2 around the chlorine K-edge: Structural and dynamical aspects

    Science.gov (United States)

    Kawerk, Elie; Carniato, Stéphane; Journel, Loïc; Marchenko, Tatiana; Piancastelli, Maria Novella; Žitnik, Matjaž; Bučar, Klemen; Bohnic, Rok; Kavčič, Matjaž; Céolin, Denis; Khoury, Antonio; Simon, Marc

    2014-10-01

    We report a theoretical and experimental study of the high resolution resonant Kα X-ray emission lines around the chlorine K-edge in gas phase 1,1-dichloroethylene. With the help of ab initio electronic structure calculations and cross section evaluation, we interpret the lowest lying peak in the X-ray absorption and emission spectra. The behavior of the Kα emission lines with respect to frequency detuning highlights the existence of femtosecond nuclear dynamics on the dissociative Potential Energy Surface of the first K-shell core-excited state.

  12. Studies of urea geometry by means of ab initio methods and computer simulations of liquids

    OpenAIRE

    Cirino, José Jair Vianna; Bertran, Celso Aparecido

    2002-01-01

    A study was carried out on the urea geometries using ab initio calculation and Monte Carlo computational simulation of liquids. The ab initio calculated results showed that urea has a non-planar conformation in the gas phase in which the hydrogen atoms are out of the plane formed by the heavy atoms. Free energies associated to the rotation of the amino groups of urea in water were obtained using the Monte Carlo method in which the thermodynamic perturbation theory is implemented. The magnitud...

  13. Cyanogen Azide. Ionization Potentials and Ab Initio SCF MO Calculation

    DEFF Research Database (Denmark)

    Bak, Börge; Jansen, Peter; Stafast, Herbert

    1975-01-01

    The Ne(I) and He(I) photoelectron(PE) spectra of cyanogen azide, NCN3, have been recorded at high resolution. Their interpretation is achieved by comparison with the PE spectrum of HN3 and an ab initio LCGO SCF MO calculation. Deviations from Koopmans' theorem of quite different magnitudes...

  14. Young Modulus of Crystalline Polyethylene from ab Initio Molecular Dynamics

    NARCIS (Netherlands)

    Hageman, J.C.L.; Meier, Robert J.; Heinemann, M.; Groot, R.A. de

    1997-01-01

    The Young modulus for crystalline polyethylene is calculated using ab initio molecular dynamics based on density functional theory in the local density approximation (DFT-LDA). This modulus, which can be seen as the ultimate value for the Young modulus of polyethylene fibers, is found to be 334 GPa.

  15. Ab initio and kinetic modeling studies of formic acid oxidation

    DEFF Research Database (Denmark)

    Marshall, Paul; Glarborg, Peter

    2015-01-01

    A detailed chemical kinetic model for oxidation of formic acid (HOCHO) in flames has been developed, based on theoretical work and data from literature. Ab initio calculations were used to obtain rate coefficients for reactions of HOCHO with H, O, and HO2. Modeling predictions with the mechanism...

  16. The Properties of Some Simple Covalent Hydrides: An Ab Initio ...

    African Journals Online (AJOL)

    Some properties of the monomeric binary hydrides of the elements of the first two rows of the periodic table have been determined using ab initio molecular orbital theory. The properties in question are the energetic, structural, electronic, topological and vibrational characteristics. In general, a gradual convergence towards ...

  17. Materials Screening for the Discovery of New Half-Heuslers: Machine Learning versus ab Initio Methods.

    Science.gov (United States)

    Legrain, Fleur; Carrete, Jesús; van Roekeghem, Ambroise; Madsen, Georg K H; Mingo, Natalio

    2018-01-18

    Machine learning (ML) is increasingly becoming a helpful tool in the search for novel functional compounds. Here we use classification via random forests to predict the stability of half-Heusler (HH) compounds, using only experimentally reported compounds as a training set. Cross-validation yields an excellent agreement between the fraction of compounds classified as stable and the actual fraction of truly stable compounds in the ICSD. The ML model is then employed to screen 71 178 different 1:1:1 compositions, yielding 481 likely stable candidates. The predicted stability of HH compounds from three previous high-throughput ab initio studies is critically analyzed from the perspective of the alternative ML approach. The incomplete consistency among the three separate ab initio studies and between them and the ML predictions suggests that additional factors beyond those considered by ab initio phase stability calculations might be determinant to the stability of the compounds. Such factors can include configurational entropies and quasiharmonic contributions.

  18. Ab initio calculation of tensile strength in iron

    Czech Academy of Sciences Publication Activity Database

    Friák, Martin; Šob, Mojmír; Vitek, V.

    2003-01-01

    Roč. 83, 31-34 (2003), s. 3529-3537 ISSN 1478-6435. [Multiscale Materials Modelling: Working Theory for Industry /1./. London, 17.06.2002-20.06.2002] R&D Projects: GA AV ČR IAA1041302; GA ČR GA202/03/1351; GA MŠk OC 523.90 Institutional research plan: CEZ:AV0Z2041904 Keywords : ab initio calculations * electronic structure * theoretical tensile strength Subject RIV: BM - Solid Matter Physics ; Magnetism

  19. Mechanical properties of carbynes investigated by ab initio total-energy calculations

    DEFF Research Database (Denmark)

    Castelli, Ivano E.; Salvestrini, Paolo; Manini, Nicola

    2012-01-01

    As sp carbon chains (carbynes) are relatively rigid molecular objects, can we exploit them as construction elements in nanomechanics? To answer this question, we investigate their remarkable mechanical properties by ab initio total-energy simulations. In particular, we evaluate their linear...

  20. Water structure as a function of temperature from X-ray scattering experiments and ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Hura, Greg; Russo, Daniela; Glaeser, Robert M.; Head-Gordon, Teresa; Krack, Matthias; Parrinello, Michele

    2003-01-01

    We present high-quality X-ray scattering experiments on pure water taken over a temperature range of 2 to 77 C using a synchrotron beam line at the advanced light source (ALS) at Lawrence Berkeley National Laboratory. The ALS X-ray scattering intensities are qualitatively different in trend of maximum intensity over this temperature range compared to older X-ray experiments. While the common procedure is to report both the intensity curve and radial distribution function(s), the proper extraction of the real-space pair correlation functions from the experimental scattering is very difficult due to uncertainty introduced in the experimental corrections, the proper weighting of OO, OH, and HH contributions, and numerical problems of Fourier transforming truncated data in Q-space. Instead, we consider the direct calculation of X-ray scattering spectra using electron densities derived from density functional theory based on real-space configurations generated with classical water models. The simulation of the experimental intensity is therefore definitive for determining radial distribution functions over a smaller Q-range. We find that the TIP4P, TIP5P and polarizable TIP4P-Pol2 water models, with DFT-LDA densities, show very good agreement with the experimental intensities, and TIP4P-Pol2 in particular shows quantitative agreement over the full temperature range. The resulting radial distribution functions from TIP4P-Pol2 provide the current best benchmarks for real-space water structure over the biologically relevant temperature range studied here

  1. Towards an ab initio theory for metal L-edge soft X-ray spectroscopy of molecular aggregates

    Directory of Open Access Journals (Sweden)

    Marie Preuße

    2016-11-01

    Full Text Available The Frenkel exciton model was adapted to describe X-ray absorption and resonant inelastic scattering spectra of polynuclear transition metal complexes by means of the restricted active space self-consistent field method. The proposed approach allows to substantially decrease the requirements on computational resources if compared to a full supermolecular quantum chemical treatment. This holds true, in particular, in cases where the dipole approximation to the electronic transition charge density can be applied. The computational protocol was applied to the calculation of X-ray spectra of the hemin complex, which forms dimers in aqueous solution. The aggregation effects were found to be comparable to the spectral alterations due to the replacement of the axial ligand by solvent molecules.

  2. X-Ray Absorption Spectra of Water from First Principles Calculations

    International Nuclear Information System (INIS)

    Prendergast, David; Galli, Giulia

    2006-01-01

    We present a series of ab initio calculations of the x-ray absorption cross section (XAS) of ice and liquid water at ambient conditions. Our results show that all available experimental data and theoretical results are consistent with the standard model of the liquid as comprising molecules with approximately four hydrogen bonds. Our simulations of ice XAS including the lowest lying excitonic state are in excellent agreement with experiment and those of a quasitetrahedral model of water are in reasonable agreement with recent measurements. Hence we propose that the standard, quasitetrahedral model of water, although approximate, represents a reasonably accurate description of the local structure of the liquid

  3. Ab initio calculation of intermolecular potentials for dimer Cl_2-Cl_2 and prediction of second virial coefficients

    International Nuclear Information System (INIS)

    Nguyen Thanh Duoc; Nguyen Thi Ai Nhung; Tran Duong; Pham Van Tat

    2015-01-01

    The results presented in this paper are the ab initio intermolecular potentials and the second virial coefficient, B_2 (T) of the dimer Cl_2-Cl_2. These ab initio potentials were proposed by the quantum chemical calculations at high level of theory CCSD(T) with basis sets of Dunning valence correlation-consistent aug-cc-pVmZ (m = 2, 3); these results were extrapolated to complete basis set limit aug-cc-pV23Z. The ab initio energies of complete basis set limit aug-cc-pV23Z resulted from the exponential extrapolation were used to construct the 5-site pair potential functions. The second virial coefficients for this dimer were predicted from those with four-dimensional integration. The second virial coefficients were also corrected to first-order quantum effects. The results turn out to be in good agreement with experimental data, if available, or with those from empirical correlation. The quality of ab initio 5-site potentials proved the reliability for prediction of molecular thermodynamic properties. (author)

  4. Ultrafast absorption of intense x rays by nitrogen molecules

    Energy Technology Data Exchange (ETDEWEB)

    Buth, Christian [Max-Planck-Institut fuer Kernphysik, Saupfercheckweg 1, 69117 Heidelberg (Germany); PULSE Institute for Ultrafast Energy Science, SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States); Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803 (United States); Argonne National Laboratory, Argonne, Illinois 60439 (United States); Liu Jicai [Max-Planck-Institut fuer Kernphysik, Saupfercheckweg 1, 69117 Heidelberg (Germany); Department of Mathematics and Physics, North China Electric Power University, 102206 Beijing (China); Chen, Mau Hsiung [Physics Division, Lawrence Livermore National Laboratory, Livermore, California 94550 (United States); Cryan, James P. [PULSE Institute for Ultrafast Energy Science, SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States); Department of Physics, Stanford University, Stanford, California 94305 (United States); Fang Li; Hoener, Matthias; Berrah, Nora [Department of Physics, Western Michigan University, Kalamazoo, Michigan 49008 (United States); Glownia, James M. [PULSE Institute for Ultrafast Energy Science, SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States); Department of Applied Physics, Stanford University, Stanford, California 94305 (United States); Coffee, Ryan N. [PULSE Institute for Ultrafast Energy Science, SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States); Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States)

    2012-06-07

    We devise a theoretical description for the response of nitrogen molecules (N{sub 2}) to ultrashort and intense x rays from the free electron laser Linac Coherent Light Source (LCLS). We set out from a rate-equation description for the x-ray absorption by a nitrogen atom. The equations are formulated using all one-x-ray-photon absorption cross sections and the Auger and radiative decay widths of multiply-ionized nitrogen atoms. Cross sections are obtained with a one-electron theory and decay widths are determined from ab initio computations using the Dirac-Hartree-Slater (DHS) method. We also calculate all binding and transition energies of nitrogen atoms in all charge states with the DHS method as the difference of two self-consistent field (SCF) calculations ({Delta}SCF method). To describe the interaction with N{sub 2}, a detailed investigation of intense x-ray-induced ionization and molecular fragmentation are carried out. As a figure of merit, we calculate ion yields and the average charge state measured in recent experiments at the LCLS. We use a series of phenomenological models of increasing sophistication to unravel the mechanisms of the interaction of x rays with N{sub 2}: a single atom, a symmetric-sharing model, and a fragmentation-matrix model are developed. The role of the formation and decay of single and double core holes, the metastable states of N{sub 2}{sup 2+}, and molecular fragmentation are explained.

  5. Hexamethylcyclopentadiene: time-resolved photoelectron spectroscopy and ab initio multiple spawning simulations

    DEFF Research Database (Denmark)

    Wolf, T. J. A.; Kuhlman, Thomas Scheby; Schalk, O.

    2014-01-01

    comparing time-resolved photoelectron spectroscopy (TRPES) with ab initio multiple spawning (AIMS) simulations on the MS-MR-CASPT2 level of theory. We disentangle the relationship between two phenomena that dominate the immediate molecular response upon light absorption: a spectrally dependent delay...

  6. Precise Ab-initio prediction of terahertz vibrational modes in crystalline systems

    DEFF Research Database (Denmark)

    Jepsen, Peter Uhd; Clark, Stewart J.

    2007-01-01

    We use a combination of experimental THz time-domain spectroscopy and ab-initio density functional perturbative theory to accurately predict the terahertz vibrational spectrum of molecules in the crystalline phase. Our calculations show that distinct vibrational modes found in solid-state materials...

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

    Science.gov (United States)

    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

  8. Studies Of Urea Geometry By Means Of Ab Initio Methods And Computer Simulations Of Liquids [estudo Da Geometria Da Uréia Por Métodos Ab Initio E Simulaição Computacional De Líquidos

    OpenAIRE

    Cirino J.J.V.; Bertran C.A.

    2002-01-01

    A study was carried out on the urea geometries using ab initio calculation and Monte Carlo computational simulation of liquids. The ab initio calculated results showed that urea has a non-planar conformation in the gas phase in which the hydrogen atoms are out of the plane formed by the heavy atoms. Free energies associated to the rotation of the amino groups of urea in water were obtained using the Monte Carlo method in which the thermodynamic perturbation theory is implemented. The magnitud...

  9. GAUSSIAN 76: an ab initio molecular orbital program

    International Nuclear Information System (INIS)

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

    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

  10. Elastic and thermo-physical properties of TiC, TiN, and their intermediate composition alloys using ab initio calculations

    International Nuclear Information System (INIS)

    Kim, Jiwoong; Kang, Shinhoo

    2012-01-01

    Highlights: ► Elastic properties of TiC, TiN and their alloys were calculated by ab initio calculations. ► Debye temperature and Gruneisen constant of TiC, TiN and their alloys were calculated as a function of nitrogen content. ► Thermo-physical properties were calculated as a function of nitrogen content. ► Thermal expansion of the alloys was fitted in different temperature range. - Abstract: The equilibrium lattice parameters, elastic properties, material brittleness, heat capacities, and thermal expansion coefficients of TiC, TiN, and their intermediate composition alloys (Ti(C 1−x N x ), x = 0.25, 0.5, and 0.75) were calculated using ab initio density functional theory (DFT) methods. We employed the Debye–Gruneisen model to calculate a finite temperature heat capacity and thermal expansion coefficient. The calculated elastic moduli and thermal expansion coefficients agreed well with the experimental data and with other DFT calculations. Accurate heat capacities of TiC, TiN, and their intermediate composition alloys were obtained by calculating not only the phonon contributions but also the electron contributions to the heat capacity. Our calculations indicated that the heat capacity differences between each composition originated mainly from the electronic contributions.

  11. X-ray Crystal Structure, Raman Spectroscopy and Ab Initio Density Functional Theory Calculations on 1,1,3,3-Tetramethylguanidinium Bromide

    DEFF Research Database (Denmark)

    Berg, Rolf W.; Riisager, Anders; Nguyen van Buu, Olivier

    2010-01-01

    The salt 1,1,3,3-tetramethylguanidinium bromide, [((CH3)2N)2C=NH2]+Br- or [tmgH]Br, was found to melt at 135(5) °C, forming what may be referred to as a moderate temperature ionic liquid. The chemistry was studied and compared with the corresponding chloride compound. We present X-ray diffraction...... and Raman evidence to show that also the bromide salt contains dimeric ion pair “molecules” in the crystalline state and probably also in the liquid state. The structure of [tmgH]Br determined at 120(2) K was found to be monoclinic, space group P21/n, with a = 7.2072(14), b = 13.335(3), c = 9.378(2) Å, beta......, for example, a characteristic strong band at 2229 cm-1. This band was interpreted by some of us to show that the [tmgH]Cl gas phase should consist of monomeric ion pair “molecules” held together by a single N-H+ · · · Cl- hydrogen bond, the stretching vibration of which should be causing the band, based on ab...

  12. Semiconductor-metal transitions in liquid In100-xSex alloys: A concentration-induced transition

    International Nuclear Information System (INIS)

    Ferlat, G.; San Miguel, A.; Xu, H.; Aouizerat, A.; Blase, X.; Zuniga, J.; Munoz-Sanjose, V.

    2004-01-01

    The electronic and structural properties of In 100-x Se x liquid alloys close to their melting points have been investigated by combining x-ray-absorption experiments with ab initio molecular-dynamics simulations. Extended x-ray-absorption fine-structure data have been acquired at both the In and Se K edges in a large concentration range (x=20% to x=50% of Se content). Ab initio molecular-dynamics simulations have been carried out at the two most extreme concentrations explored experimentally. Liquid InSe is found to retain a semiconducting behavior which results from a low-dimensional structure, reminiscent of that of the ambient solid phase, characterized by strong In-Se interactions within tetrahedral units. On the other side, the In 80 Se 20 liquid alloy shows a metalliclike behavior which is correlated to a more dense-packed structure

  13. Communication: A hydrogen-bonded difluorocarbene complex: Ab initio and matrix isolation study

    Science.gov (United States)

    Sosulin, Ilya S.; Shiryaeva, Ekaterina S.; Tyurin, Daniil A.; Feldman, Vladimir I.

    2017-10-01

    Structure and spectroscopic features of the CF2⋯HF complexes were studied by ab initio calculations at the CCSD(T) level and matrix isolation FTIR spectroscopy. The calculations predict three stable structures. The most energetically favorable structure corresponds to hydrogen bonding of HF to the lone pair of the C atom (the interaction energy of 3.58 kcal/mol), whereas two less stable structures are the H⋯F bonded complexes (the interaction energies of 0.30 and 0.24 kcal/mol). The former species was unambiguously characterized by the absorptions in the FTIR spectra observed after X-ray irradiation of fluoroform in a xenon matrix at 5 K. The corresponding features appear at 3471 (H-F stretching), 1270 (C-F symmetric stretching, shoulder), 1175 (antisymmetric C-F stretching), and 630 (libration) cm-1, in agreement with the computational predictions. To our knowledge, it is the first hydrogen-bonded complex of dihalocarbene. Possible weaker manifestations of the H⋯F bonded complexes were also found in the C-F stretching region; however, their assignment is tentative. The H⋯C bonded complex is protected from reaction yielding a fluoroform molecule by a remarkably high energy barrier (23.85 kcal/mol), so it may be involved in various chemical reactions.

  14. A fragment-based approach towards ab-initio treatment of polymeric ...

    Indian Academy of Sciences (India)

    Reshma S Pingale

    2017-06-20

    Jun 20, 2017 ... Keywords. π-Conjugated polymer; divide and conquer; ab-initio; fragmentation. PACS Nos 31.15.A−; 36.20. ... cut the parent system into a set of overlapping small fragments and .... some oligomers, we approached the problem by increas- ..... Financial support of DST, Govt. of India, New Delhi, in the form of ...

  15. Ab initio study of the bcc-hcp transformation in iron

    Czech Academy of Sciences Publication Activity Database

    Friák, Martin; Šob, Mojmír

    2008-01-01

    Roč. 77, č. 17 (2008), 174117/1-174117/7 ISSN 1098-0121 R&D Projects: GA MŠk OC 147; GA AV ČR IAA1041302 Institutional research plan: CEZ:AV0Z20410507 Keywords : ab initio calculations * phase transformations * iron Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.322, year: 2008

  16. Ab initio study of isomerism in molecular ions Li2AB+ with 10 valence electrons

    International Nuclear Information System (INIS)

    Charkin, O.P.; Mak-Ki, M.L.; Shlojer, P.R.

    1997-01-01

    Ab initio calculations of surfaces of Li 2 AB + molecular ion potential energy with biatomic anions AB - with 10 valence electrons have been made in the framework of approximations MP2/6-31G 1 /HF/6-31G*+ZPE(HF/6-31G*) and MP4SDTQ/631G*//MP2/6-31G*+ZPE(MP2/6-31G*). Influence of electron correlation on the accuracy of calculations of their structural and vibrational characteristics is studied. The following most favourable structures have been found: linear for Li 2 BO + , Li 2 CN + , and bent one for Li 2 BS + , with cations coordinated at different anion atoms; onium one for AlOLi 2 + , AlSLi 2 + , SiNLi 2 + and SiPLi 2 + with both cations at electronegative atom of anion

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

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Hanchao; Wang, Yimin; Bowman, Joel M. [Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322 (United States)

    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.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

    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 H 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 −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

  19. Ab-Initio Investigations of Magnetic Properties and Induced Half-Metallicity in Ga1−xMnxP (x = 0.03, 0.25, 0.5, and 0.75 Alloys

    Directory of Open Access Journals (Sweden)

    Amel Laref

    2017-07-01

    Full Text Available Ab-initio calculations are performed to examine the electronic structures and magnetic properties of spin-polarized Ga1−xMnxP (x = 0.03, 0.25, 0.5, and 0.75 ternary alloys. In order to perceive viable half-metallic (HM states and unprecedented diluted magnetic semiconductors (DMSs such as spintronic materials, the full potential linearized augmented plane wave method is utilized within the generalized gradient approximation (GGA. In order to tackle the correlation effects on 3d states of Mn atoms, we also employ the Hubbard U (GGA + U technique to compute the magnetic properties of an Mn-doped GaP compound. We discuss the emerged global magnetic moments and the robustness of half-metallicity by varying the Mn composition in the GaP compound. Using GGA + U, the results of the density of states demonstrate that the incorporation of Mn develops a half-metallic state in the GaP compound with an engendered band gap at the Fermi level (EF in the spin–down state. Accordingly, the half-metallic feature is produced through the hybridization of Mn-d and P-p orbitals. However, the half-metallic character is present at a low x composition with the GGA procedure. The produced magnetic state occurs in these materials, which is a consequence of the exchange interactions between the Mn-element and the host GaP system. For the considered alloys, we estimated the X-ray absorption spectra at the K edge of Mn. A thorough clarification of the pre-edge peaks is provided via the results of the theoretical absorption spectra. It is inferred that the valence state of Mn in Ga1−xMnxP alloys is +3. The predicted theoretical determinations surmise that the Mn-incorporated GaP semiconductor could inevitably be employed in spintronic devices.

  20. Ab initio study of H + + H 2 collisions: Elastic/inelastic and charge transfer processes

    Science.gov (United States)

    Saieswari, A.; Kumar, Sanjay

    2007-12-01

    An ab initio full configuration interaction study has been undertaken to obtain the global potential energy surfaces for the ground and the first excited electronic state of the H + + H 2 system employing Dunning's cc-pVQZ basis set. Using the ab initio approach the corresponding quasi-diabatic potential energy surfaces and coupling potentials have been obtained. A time-independent quantum mechanical study has been also undertaken for both the inelastic and charge transfer processes at the experimental collision energy Ec.m. = 20.0 eV and the preliminary results show better agreement with the experimental data as compared to the earlier available theoretical studies.

  1. The computation of ionization potentials for second-row elements by ab initio and density functional theory methods

    International Nuclear Information System (INIS)

    Jursic, B.S.

    1996-01-01

    Up to four ionization potentials of elements from the second-row of the periodic table were computed using the ab initio (HF, MP2, MP3, MP4, QCISD, GI, G2, and G2MP2) and DFT (B3LY, B3P86, B3PW91, XALPHA, HFS, HFB, BLYP, BP86, BPW91, BVWN, XAPLY, XAP86, XAPW91, XAVWN, SLYR SP86, SPW91 and SVWN) methods. In all of the calculations, the large 6-311++G(3df,3pd) gaussian type of basis set was used. The computed values were compared with the experimental results and suitability of the ab initio and DFF methods were discussed, in regard to reproducing the experimental data. From the computed ionization potentials of the second-row elements, it can be concluded that the HF ab initio computation is not capable of reproducing the experimental results. The computed ionization potentials are too low. However, by using the ab initio methods that include electron correlation, the computed IPs are becoming much closer to the experimental values. In all cases, with the exception of the first ionization potential for oxygen, the G2 computation result produces ionization potentials that are indistinguishable from the experimental results

  2. Ab initio theory of charge-carrier conduction in ultrapure organic crystals

    NARCIS (Netherlands)

    Hannewald, K.; Bobbert, P.A.

    2004-01-01

    We present an ab initio description of charge-carrier mobilities in organic molecular crystals of high purity. Our approach is based on Holstein's original concept of small-polaron bands but generalized with respect to the inclusion of nonlocal electron-phonon coupling. By means of an explicit

  3. Force fields for silicas and aluminophosphates based on ab initio calculations

    NARCIS (Netherlands)

    Beest, van B.W.H.; Kramer, G.J.; Santen, van R.A.

    1990-01-01

    Authors address the problem of finding interat. force fields for silicas from ab initio calcns. on small clusters. The force field cannot be detd. from cluster data alone; incorporation of bulk-system information into the force field remains essential. Bearing this in mind, authors derive a force

  4. Ab initio study on stacking sequences, free energy, dynamical stability and potential energy surfaces of graphite structures

    International Nuclear Information System (INIS)

    Anees, P; Valsakumar, M C; Chandra, Sharat; Panigrahi, B K

    2014-01-01

    Ab initio simulations have been performed to study the structure, energetics and stability of several plausible stacking sequences in graphite. These calculations suggest that in addition to the standard structures, graphite can also exist in AA-simple hexagonal, AB-orthorhombic and ABC-hexagonal type stacking. The free energy difference between these structures is very small (∼1 meV/atom), and hence all the structures can coexist from purely energetic considerations. Calculated x-ray diffraction patterns are similar to those of the standard structures for 2θ ⩽ 70°. Shear elastic constant C 44 is negative in AA-simple hexagonal, AB-orthorhombic and ABC-hexagonal structures, suggesting that these structures are mechanically unstable. Phonon dispersions show that the frequencies of some modes along the Γ–A direction in the Brillouin zone are imaginary in all of the new structures, implying that these structures are dynamically unstable. Incorporation of zero point vibrational energy via the quasi-harmonic approximation does not result in the restoration of dynamical stability. Potential energy surfaces for the unstable normal modes are seen to have the topography of a potential hill for all the new structures, confirming that all of the new structures are inherently unstable. The fact that the potential energy surface is not in the form of a double well implies that the structures are linearly as well as globally unstable. (paper)

  5. Using Ab-Initio Calculations to Appraise Stm-Based - and Kink-Formation Energies

    Science.gov (United States)

    Feibelman, Peter J.

    2001-03-01

    Ab-initio total energies can and should be used to test the typically model-dependent results of interpreting STM morphologies. The benefits of such tests are illustrated here by ab-initio energies of step- and kink-formation on Pb and Pt(111) which show that the STM-based values of the kink energies must be revised. On Pt(111), the computed kink-energies for (100)- and (111)-microfacet steps are about 0.25 and 0.18 eV. These results imply a specific ratio of formation energies for the two step types, namely 1.14, in excellent agreement with experiment. If kink-formation actually cost the same energy on the two step types, an inference drawn from scanning probe observations of step wandering,(M. Giesen et al., Surf. Sci. 366, 229(1996).) this ratio ought to be 1. In the case of Pb(111), though computed energies to form (100)- and (111)-microfacet steps agree with measurement, the ab-initio kink-formation energies for the two step types, 41 and 60 meV, are 40-50% below experimental values drawn from STM images.(K. Arenhold et al., Surf. Sci. 424, 271(1999).) The discrepancy results from interpreting the images with a step-stiffness vs. kink-energy relation appropriate to (100) but not (111) surfaces. Good agreement is found when proper account of the trigonal symmetry of Pb(111) is taken in reinterpreting the step-stiffness data.

  6. Nuclear quantum effects in ab initio dynamics: Theory and experiments for lithium imide

    Science.gov (United States)

    Ceriotti, Michele; Miceli, Giacomo; Pietropaolo, Antonino; Colognesi, Daniele; Nale, Angeloclaudio; Catti, Michele; Bernasconi, Marco; Parrinello, Michele

    2010-11-01

    Owing to their small mass, hydrogen atoms exhibit strong quantum behavior even at room temperature. Including these effects in first-principles calculations is challenging because of the huge computational effort required by conventional techniques. Here we present the first ab initio application of a recently developed stochastic scheme, which allows to approximate nuclear quantum effects inexpensively. The proton momentum distribution of lithium imide, a material of interest for hydrogen storage, was experimentally measured by inelastic neutron-scattering experiments and compared with the outcome of quantum thermostatted ab initio dynamics. We obtain favorable agreement between theory and experiments for this purely quantum-mechanical property, thereby demonstrating that it is possible to improve the modeling of complex hydrogen-containing materials without additional computational effort.

  7. Ab initio study of hot electrons in GaAs

    OpenAIRE

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

    2015-01-01

    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...

  8. Room temperature single-crystal diffuse scattering and ab initio lattice dynamics in CaTiSiO5.

    Science.gov (United States)

    Gutmann, M J; Refson, K; Zimmermann, M V; Swainson, I P; Dabkowski, A; Dabkowska, H

    2013-08-07

    Single-crystal diffuse scattering data have been collected at room temperature on synthetic titanite using both neutrons and high-energy x-rays. A simple ball-and-springs model reproduces the observed diffuse scattering well, confirming its origin to be primarily due to thermal motion of the atoms. Ab initio phonons are calculated using density-functional perturbation theory and are shown to reproduce the experimental diffuse scattering. The observed diffuse x-ray and neutron scattering patterns are consistent with a summation of mode frequencies and displacement eigenvectors associated with the entire phonon spectrum, rather than with a simple, short-range static displacement. A band gap is observed between 600 and 700 cm(-1) with only two modes crossing this region, both associated with antiferroelectric Ti-O motion along a. One of these modes (of Bu symmetry), displays a large LO-TO mode-splitting (562-701.4 cm(-1)) and has a dominant component coming from Ti-O bond-stretching and, thus, the mode-splitting is related to the polarizability of the Ti-O bonds along the chain direction. Similar mode-splitting is observed in piezo- and ferroelectric materials. The calculated phonon dispersion model may be of use to others in future to understand the phase transition at higher temperatures, as well as in the interpretation of measured phonon dispersion curves.

  9. Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study

    International Nuclear Information System (INIS)

    Sharma, Nalini; Ahluwalia, P. K.; Thakur, Anil

    2016-01-01

    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 (Hg_1_0In_9_0, Hg_3_0In_7_0_,_. Hg_5_0In_5_0, Hg_7_0In_3_0, and Hg_9_0Pb_1_0) 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.

  10. Resonant inelastic x-ray scattering on iso-C{sub 2}H{sub 2}Cl{sub 2} around the chlorine K-edge: Structural and dynamical aspects

    Energy Technology Data Exchange (ETDEWEB)

    Kawerk, Elie, E-mail: eliekawerk@hotmail.com, E-mail: ekawerk@units.it [CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris (France); Sorbonne Universités, UPMC Université Paris 06, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris (France); Laboratoire de Physique Appliquée, Faculté des Sciences II, Université Libanaise, 90656 Jdeidet el Metn, Liban (Libya); Dipartimento di Scienze Chimiche, Università di Trieste, Via L. Giorgieri 1, I-34127 Trieste (Italy); Carniato, Stéphane; Journel, Loïc; Marchenko, Tatiana; Simon, Marc [CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris (France); Sorbonne Universités, UPMC Université Paris 06, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris (France); Piancastelli, Maria Novella [CNRS, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris (France); Sorbonne Universités, UPMC Université Paris 06, UMR 7614, Laboratoire de Chimie Physique-Matière et Rayonnement, F-75005 Paris (France); Department of Physics and Astronomy, Uppsala University, P.O. Box 516, SE-751 20 Uppsala (Sweden); Žitnik, Matjaž; Bučar, Klemen; Bohnic, Rok [Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana (Slovenia); and others

    2014-10-14

    We report a theoretical and experimental study of the high resolution resonant K{sub α} X-ray emission lines around the chlorine K-edge in gas phase 1,1-dichloroethylene. With the help of ab initio electronic structure calculations and cross section evaluation, we interpret the lowest lying peak in the X-ray absorption and emission spectra. The behavior of the K{sub α} emission lines with respect to frequency detuning highlights the existence of femtosecond nuclear dynamics on the dissociative Potential Energy Surface of the first K-shell core-excited state.

  11. Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks

    Directory of Open Access Journals (Sweden)

    Martin Alberto JM

    2009-01-01

    Full Text Available Abstract Background Prediction of protein structures from their sequences is still one of the open grand challenges of computational biology. Some approaches to protein structure prediction, especially ab initio ones, rely to some extent on the prediction of residue contact maps. Residue contact map predictions have been assessed at the CASP competition for several years now. Although it has been shown that exact contact maps generally yield correct three-dimensional structures, this is true only at a relatively low resolution (3–4 Å from the native structure. Another known weakness of contact maps is that they are generally predicted ab initio, that is not exploiting information about potential homologues of known structure. Results We introduce a new class of distance restraints for protein structures: multi-class distance maps. We show that Cα trace reconstructions based on 4-class native maps are significantly better than those from residue contact maps. We then build two predictors of 4-class maps based on recursive neural networks: one ab initio, or relying on the sequence and on evolutionary information; one template-based, or in which homology information to known structures is provided as a further input. We show that virtually any level of sequence similarity to structural templates (down to less than 10% yields more accurate 4-class maps than the ab initio predictor. We show that template-based predictions by recursive neural networks are consistently better than the best template and than a number of combinations of the best available templates. We also extract binary residue contact maps at an 8 Å threshold (as per CASP assessment from the 4-class predictors and show that the template-based version is also more accurate than the best template and consistently better than the ab initio one, down to very low levels of sequence identity to structural templates. Furthermore, we test both ab-initio and template-based 8

  12. Local coordination structure and electronic structure of the large electron mobility amorphous oxide semiconductor In-Ga-Zn-O: Experiment and ab initio calculations

    International Nuclear Information System (INIS)

    Nomura, Kenji; Ohta, Hiromichi; Hirano, Masahiro; Kamiya, Toshio; Uruga, Tomoya; Hosono, Hideo

    2007-01-01

    Ionic amorphous oxide semiconductors (IAOSs) are new materials for flexible thin film transistors that exhibit field-effect mobilities of ∼10 cm 2 V -1 s -1 [K. Nomura et al., Nature 488, 432 (2004)]. The local coordination structure in an IAOS, In-Ga-Zn-O (a-IGZO), was examined using extended x-ray absorption fine structure analysis combined with ab initio calculations. The short-range ordering and coordination structures in a-IGZO are similar to those in the corresponding crystalline phase, InGaZnO 4 , and edge-sharing structures consisting of In-O polyhedra remain in the amorphous structure. The In 3+ 5s orbitals form an extended state with a band effective mass of ∼0.2m e at the conduction band bottom

  13. Combined experimental powder X-ray diffraction and DFT data to obtain the lowest energy molecular conformation of friedelin

    International Nuclear Information System (INIS)

    Oliveira, Djalma Menezes de; Mussel, Wagner da Nova; Duarte, Lucienir Pains; Silva, Gracia Divina de Fatima; Duarte, Helio Anderson; Gomes, Elionai Cassiana de Lima; Guimaraes, Luciana; Vieira Filho, Sidney A.

    2012-01-01

    Friedelin molecular conformers were obtained by Density Functional Theory (DFT) and by ab initio structure determination from powder X-ray diffraction. Their conformers with the five rings in chair-chair-chair-boat-boat, and with all rings in chair, are energy degenerated in gas-phase according to DFT results. The powder diffraction data reveals that rings A, B and C of friedelin are in chair, and rings D and E in boat-boat, conformation. The high correlation values among powder diffraction data, DFT and reported single crystal data indicate that the use of conventional X-ray diffractometer can be applied in routine laboratory analysis in the absence of a single-crystal diffractometer. (author)

  14. Combined experimental powder X-ray diffraction and DFT data to obtain the lowest energy molecular conformation of friedelin

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, Djalma Menezes de; Mussel, Wagner da Nova; Duarte, Lucienir Pains; Silva, Gracia Divina de Fatima; Duarte, Helio Anderson; Gomes, Elionai Cassiana de Lima [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Quimica; Guimaraes, Luciana [Universidade Federal de Sao Joao Del-Rei (UFSJ), MG (Brazil). Dept. de Ciencias Naturais; Vieira Filho, Sidney A., E-mail: bibo@ef.ufop.br [Universidade Federal de Ouro Preto (UFOP), MG (Brazil). Dept. de Farmacia

    2012-07-01

    Friedelin molecular conformers were obtained by Density Functional Theory (DFT) and by ab initio structure determination from powder X-ray diffraction. Their conformers with the five rings in chair-chair-chair-boat-boat, and with all rings in chair, are energy degenerated in gas-phase according to DFT results. The powder diffraction data reveals that rings A, B and C of friedelin are in chair, and rings D and E in boat-boat, conformation. The high correlation values among powder diffraction data, DFT and reported single crystal data indicate that the use of conventional X-ray diffractometer can be applied in routine laboratory analysis in the absence of a single-crystal diffractometer. (author)

  15. Ab initio quantum chemical calculation as a tool of evaluating diamagnetic susceptibility of magnetically levitating substances

    International Nuclear Information System (INIS)

    Fujiwara, Y; Tanimoto, Y

    2009-01-01

    On magnetic force evaluation necessary for magnetically levitated diamagnetic substances, isotropic diamagnetic susceptibility estimation by the ab initio quantum chemical calculation using Gaussian03W was verified for more than 300 molecules in a viewpoint of the accuracy in the absolute value and the calculation level affording good cost performance. From comparison, the method of B3PW91 / 6-311+G(d,p) was found to give the adequate absolute value by the relation of (observed) = (1.03 ± 0.005) x (calculated) - (1.22 ± 0.60) x 10 -6 in a unit of cm 3 mol -1 and good cost performance.

  16. Ab initio quantum chemical calculation as a tool of evaluating diamagnetic susceptibility of magnetically levitating substances

    Energy Technology Data Exchange (ETDEWEB)

    Fujiwara, Y [Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526 (Japan); Tanimoto, Y [Faculty of Pharmacy, Osaka Ohtani University, Nishikiorikita, Tondabayashi 584-8540 (Japan)], E-mail: fuji0710@sci.hiroshima-u.ac.jp

    2009-03-01

    On magnetic force evaluation necessary for magnetically levitated diamagnetic substances, isotropic diamagnetic susceptibility estimation by the ab initio quantum chemical calculation using Gaussian03W was verified for more than 300 molecules in a viewpoint of the accuracy in the absolute value and the calculation level affording good cost performance. From comparison, the method of B3PW91 / 6-311+G(d,p) was found to give the adequate absolute value by the relation of (observed) = (1.03 {+-} 0.005) x (calculated) - (1.22 {+-} 0.60) x 10{sup -6} in a unit of cm{sup 3} mol{sup -1} and good cost performance.

  17. Ab initio calculations and experimental measurement of the deuterium quadrupole coupling constant in Na2PDO3

    International Nuclear Information System (INIS)

    Trudeau, J.D.; Schwartz, J.L.; Farrar, T.C.

    1991-01-01

    The deuterium quadrupole coupling constant, χ D , in the PDO 3 2- anion has been measured in solution by NMR spin-lattice (T 1 ) relaxation time measurements and it has been calculated via ab initio methods. The experimental value of 94.7 ± 0.5 kHz is in excellent agreement with the ab initio value of 95.0 kHz. The activation energy for the ion reorientation is 2.23 ± 0.01 kJ mol -1

  18. Feasible and realiable ab initio atomistic modeling for nuclear waste management

    Energy Technology Data Exchange (ETDEWEB)

    Beridze, George

    2016-07-01

    The studies in this PhD dissertation focus on finding a computationally feasible ab initio methodology which would make the reliable first principle atomistic modeling of nuclear materials possible. Here we tested the performance of the different DFT functionals and the DFT-based methods that explicitly account for the electronic correlations, such as the DFT+U approach, for prediction of structural and thermochemical properties of lanthanide- and actinide-bearing materials. In the previous studies, the value of the Hubbard U parameter, required by the DFT+U method, was often guessed or empirically derived. We applied and extensively tested the recently developed ab initio methods such as the constrained local density approximation (cLDA) and the constrained random phase approximation (cRPA), to compute the Hubbard U parameter values from first principles, thus making the DFT+U method a real it ab initio parameter free approach. Our successful benchmarking studies of the parameter-free DFT+U method, for prediction of the structures and the reaction enthalpies of actinide- and lanthanide-bearing molecular compounds and solids indicate, that the linear response method (cLDA) provides a very good, and consistent with the cRPA prediction, estimate of the Hubbard U parameter. In particular, we found that the Hubbard U parameter value, which describes the strength of the on-site Coulomb repulsion between f-electrons, depends strongly on the oxidation state of the f-element, its local bonding environment and crystalline structure of the materials, which has never been considered in such detail before. We have shown, that the applied computational approach substantially, if not dramatically, reduces the error of the predicted reaction enthalpies making the accuracy of the prediction comparable with the uncertainty of the computational unfeasible, higher order methods of quantum chemistry, and experiments. The derived methodology resulted in various, already published

  19. Feasible and realiable ab initio atomistic modeling for nuclear waste management

    International Nuclear Information System (INIS)

    Beridze, George

    2016-01-01

    The studies in this PhD dissertation focus on finding a computationally feasible ab initio methodology which would make the reliable first principle atomistic modeling of nuclear materials possible. Here we tested the performance of the different DFT functionals and the DFT-based methods that explicitly account for the electronic correlations, such as the DFT+U approach, for prediction of structural and thermochemical properties of lanthanide- and actinide-bearing materials. In the previous studies, the value of the Hubbard U parameter, required by the DFT+U method, was often guessed or empirically derived. We applied and extensively tested the recently developed ab initio methods such as the constrained local density approximation (cLDA) and the constrained random phase approximation (cRPA), to compute the Hubbard U parameter values from first principles, thus making the DFT+U method a real it ab initio parameter free approach. Our successful benchmarking studies of the parameter-free DFT+U method, for prediction of the structures and the reaction enthalpies of actinide- and lanthanide-bearing molecular compounds and solids indicate, that the linear response method (cLDA) provides a very good, and consistent with the cRPA prediction, estimate of the Hubbard U parameter. In particular, we found that the Hubbard U parameter value, which describes the strength of the on-site Coulomb repulsion between f-electrons, depends strongly on the oxidation state of the f-element, its local bonding environment and crystalline structure of the materials, which has never been considered in such detail before. We have shown, that the applied computational approach substantially, if not dramatically, reduces the error of the predicted reaction enthalpies making the accuracy of the prediction comparable with the uncertainty of the computational unfeasible, higher order methods of quantum chemistry, and experiments. The derived methodology resulted in various, already published

  20. Ab initio study of gas phase and water-assisted tautomerization of ...

    Indian Academy of Sciences (India)

    WINTEC

    Water-assisted tautomerization in maleimide and formamide showed that difference in energy barrier reduces to 2⋅83 kcal/mol from 10⋅41 kcal/mol (in gas phase) at B3LYP level, which resulted that maleimide readily undergoes tautomerization in water molecule. Keywords. Ab Initio calculations; maleimide; formamide; ...

  1. X-ray spectrum in the range (6-12) A emitted by laser-produced plasma of samarium

    International Nuclear Information System (INIS)

    Louzon, Einat; Henis, Zohar; Levi, Izhak; Hurvitz, Gilad; Ehrlich, Yosi; Fraenkel, Moshe; Maman, Shlomo; Mandelbaum, Pinchas

    2009-01-01

    A detailed analysis of the x-ray spectrum emitted by laser-produced plasma of samarium (6-12 A) is presented, using ab initio calculations with the HULLAC relativistic code and isoelectronic considerations. Resonance 3d-nf (n=4 to 7), 3p-4d, 3d-4p, and 3p-4s transitions in Ni samarium ions and in neighboring ionization states (from Mn to Zn ions) were identified. The experiment results show changes in the fine details of the plasma spectrum for different laser intensities.

  2. Ab initio and density functional force field studies on the IR spectra and structure of diazonium dicyanomethylide (diazodicyanomethane)

    Science.gov (United States)

    Georgieva, Miglena K.

    2004-03-01

    The structure of diazonium dicyanomethylide (diazodicyanomethane) +N 2-C(CN) 2-↔N 2C(CN) 2 has been studied on the basis of ab initio HF, MP2 and DFT BLYP force field calculations, as well as of literature IR spectra and X-ray diffraction structural data. The results have been compared with those obtained for a series of chemical relatives of the title compound, i.e. molecules, push-pull molecules, anions and zwitterions, containing α-dicyano or diazo fragments, and especially substituted ammonium dicyanomethylides and diazomethane +N 2-CH 2-↔N 2CH 2. It has been found on the basis of spectral, bond length, bond order and electric charge analyses that the diazonium (or carbanionic, left) canonical form is much more important for the title zwitterion, than the corresponding one for diazomethane. So, the title compound can be named (and considered as) both diazonium dicyanomethylide and dicyanodiazomethane.

  3. Ab Initio Calculations on Halogen Bond Between N-Br and Electron-donating Groups

    Institute of Scientific and Technical Information of China (English)

    WANG Yan-hua; CHEN Xue-song; ZOU Jian-wei; YU Qing-sen

    2007-01-01

    Ab initio calculations of complexes formed between N-bromosuccinimide and a series of electron-donating groups were performed at the level of MP2/Lanl2DZ* to gain a deeper insight into the nature of the N-Br halogen stronger halogen-bonding complex than the C-Br. A comparison of neutral hydrogen bond complex series reveals that the electron-donating capacities of the atoms decrease in the order, N>O>S; O(sp3)>O(sp2), which is adequate for the C-Br halogen bonding. Interaction energies, in conjunction with the geometrical parameters show that the affinitive capacity of trihalide anions X-3 with N-bromosuccinimide are markedly lower than that of the corresponding X- with N-bromosuccinimide, even lower than those of neutral molecules with N-bromosuccinimide. AIM analyses further confirmed the above results.

  4. An Efficient Method for Electron-Atom Scattering Using Ab-initio Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Yuan; Yang, Yonggang; Xiao, Liantuan; Jia, Suotang [Shanxi University, Taiyuan (China)

    2017-02-15

    We present an efficient method based on ab-initio calculations to investigate electron-atom scatterings. Those calculations profit from methods implemented in standard quantum chemistry programs. The new approach is applied to electron-helium scattering. The results are compared with experimental and other theoretical references to demonstrate the efficiency of our method.

  5. Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10.

    Science.gov (United States)

    Zhang, Yang

    2014-02-01

    We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. Copyright © 2013 Wiley Periodicals, Inc.

  6. Ab initio theories of electric transport in solid systems with reduced dimensions

    International Nuclear Information System (INIS)

    Weinberger, Peter

    2003-01-01

    Ab initio theories of electric transport in solid systems with reduced dimensions, i.e., systems that at best are characterized by two-dimensional translational invariance, are reviewed in terms of a fully relativistic description of the Kubo-Greenwood equation. As the use of this equation requires concepts such as collinearity and non-collinearity in order to properly define resistivities or resistances corresponding to particular magnetic configurations, respective consequences of the (local) density functional theory are recalled in quite a detailed manner. Furthermore, since theoretical descriptions of solid systems with reduced dimensions require quantum mechanical methods different from bulk systems (three-dimensional periodicity), the so-called Screened Korringa-Kohn-Rostoker (SKKR-) method for layered systems is introduced together with a matching coherent potential approximation (inhomogeneous CPA). The applications shown are mainly meant to illustrate various aspects of electric transport in solid systems with reduced dimensions and comprise not only current-in-plane (CIP) experiments, but also current perpendicular to the planes of atoms geometries, consequences of tunneling, and finite nanostructures at or on metallic substrates. In order to give a more complete view of available ab initio methods also a non-relativistic approach based on the Tight Binding Linear Combination of muffin tin orbitals (TB-LMTO-) method and the so-called Kubo-Landauer equation in terms of transmission and reflection matrices is presented. A compilation of references with respect to ab-initio type approaches not explicitly discussed in here finally concludes the discussion of electric properties in solid systems with reduced dimensions

  7. Ab-initio atomic level stress and role of d-orbitals in CuZr, CuZn and CuY

    Science.gov (United States)

    Ojha, Madhusudan; Nicholson, Don M.; Egami, Takeshi

    2015-03-01

    Atomic level stress offers a new tool to characterize materials within the local approximation to density functional theory (DFT). Ab-initio atomic level stresses in B2 structures of CuZr, CuZn and CuY are calculated and results are explained on the basis of d-orbital contributions to Density of States (DOS). The overlap of d-orbital DOS plays an important role in the relative magnitude of atomic level stresses in these structures. The trends in atomic level stresses that we observed in these simple B2 structures are also seen in complex structures such as liquids, glasses and solid solutions. The stresses are however modified by the different coordination and relaxed separation distances in these complex structures. We used the Locally Self-Consistent Multiple Scattering (LSMS) code and Vienna Ab-initio Simulation Package (VASP) for ab-initio calculations.

  8. TiAl doping by vanadium: ab initio study

    International Nuclear Information System (INIS)

    Smirnova, E.A.; Isaev, Eh.I.; Vekilov, Yu.Kh.

    2004-01-01

    Tetragonality degree in TiAl and vanadium doping effect on it were studied using the methods of calculation based on approximation of coherent potential and ab initio pseudopotentials. It is shown that vanadium substitution for Ti sublattice atoms entails increase in tetragonality degree but with substitution of the atoms in aluminium sublattice the tetragonality of the TiAl:V alloy decreases and at the content of vanadium about 8 at. % the lattice becomes actually cubical. In its turn, it may result in increase in TiAl ductility, the alloy being brittle at low temperatures [ru

  9. Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation.

    Science.gov (United States)

    Yang, Lina; Minnich, Austin J

    2017-03-14

    Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials.

  10. Lithium ion diffusion in Li4+xTi5O12: From ab initio studies

    International Nuclear Information System (INIS)

    Chen, Y.C.; Ouyang, C.Y.; Song, L.J.; Sun, Z.L.

    2011-01-01

    Highlights: → Li diffusion pathways in Li 4 Ti 5 O 12 and Li 7 Ti 5 O 12 are obtained from ab initio calculations. → Cooperative Li migration in Li 7+δ Ti 5 O 12 with very low energy barrier is proposed. → Li diffusion is faster in lithiated state than in delithiated state is confirmed theoretically. - Abstract: Lithium ion dynamics in Li 4+x Ti 5 O 12 spinel are investigated from first principles calculations. The diffusion pathways are optimized and the energy barriers of lithium migration under four types of dilute defect extremes: Li 4+δ Ti 5 O 12 , Li 4-δ Ti 5 O 12 , Li 7+δ Ti 5 O 12 and Li 7-δ Ti 5 O 12 (δ << 1) are calculated with the nudged elastic band method. Results show that lithium diffusion in the charged state (energy barriers are 1.0 and 0.7 eV for interstitial Li and Li vacancy diffusion, respectively) is much slower than in the discharged state (energy barriers are 0.13 and 0.35 eV for interstitial Li and Li vacancy diffusion, respectively). The diffusion coefficients are evaluated based on lattice gas model and hopping mechanism. The obtained results are compared with available experimental data within a two-phase co-existence framework.

  11. Ab initio molecular dynamics simulation of hydrogen fluoride at several thermodynamic states

    DEFF Research Database (Denmark)

    Kreitmeir, M.; Bertagnolli, H.; Mortensen, Jens Jørgen

    2003-01-01

    Liquid hydrogen fluoride is a simple but interesting system for studies of the influence of hydrogen bonds on physical properties. We have performed ab initio molecular dynamics simulations of HF at several thermodynamic states, where we examine the microscopic structure of the liquid as well...

  12. Ab initio Calculations of Charge Symmetry Breaking in the A=4 Hypernuclei

    Czech Academy of Sciences Publication Activity Database

    Gazda, Daniel; Gal, A.

    2016-01-01

    Roč. 116, č. 12 (2016), s. 122501 ISSN 0031-9007 R&D Projects: GA ČR(CZ) GA15-04301S Institutional support: RVO:61389005 Keywords : ab initio * shell model * four-body calculations Subject RIV: BE - Theoretical Physics Impact factor: 8.462, year: 2016

  13. Ab initio calculation atomics ground state wave function for interactions Ion- Atom

    International Nuclear Information System (INIS)

    Shojaee, F.; Bolori zadeh, M. A.

    2007-01-01

    Ab initio calculation atomics ground state wave function for interactions Ion- Atom Atomic wave function expressed in a Slater - type basis obtained within Roothaan- Hartree - Fock for the ground state of the atoms He through B. The total energy is given for each atom.

  14. Single-Molecule Imaging with X-Ray Free-Electron Lasers: Dream or Reality?

    KAUST Repository

    Fratalocchi, Andrea

    2011-03-09

    X-ray free-electron lasers (XFEL) are revolutionary photon sources, whose ultrashort, brilliant pulses are expected to allow single-molecule diffraction experiments providing structural information on the atomic length scale of nonperiodic objects. This ultimate goal, however, is currently hampered by several challenging questions basically concerning sample damage, Coulomb explosion, and the role of nonlinearity. By employing an original ab initio approach, we address these issues showing that XFEL-based single-molecule imaging will be only possible with a few-hundred long attosecond pulses, due to significant radiation damage and the formation of preferred multisoliton clusters which reshape the overall electronic density of the molecular system at the femtosecond scale.

  15. Single-Molecule Imaging with X-Ray Free-Electron Lasers: Dream or Reality?

    KAUST Repository

    Fratalocchi, Andrea; Ruocco, G.

    2011-01-01

    X-ray free-electron lasers (XFEL) are revolutionary photon sources, whose ultrashort, brilliant pulses are expected to allow single-molecule diffraction experiments providing structural information on the atomic length scale of nonperiodic objects. This ultimate goal, however, is currently hampered by several challenging questions basically concerning sample damage, Coulomb explosion, and the role of nonlinearity. By employing an original ab initio approach, we address these issues showing that XFEL-based single-molecule imaging will be only possible with a few-hundred long attosecond pulses, due to significant radiation damage and the formation of preferred multisoliton clusters which reshape the overall electronic density of the molecular system at the femtosecond scale.

  16. Coupling of ab initio density functional theory and molecular dynamics for the multiscale modeling of carbon nanotubes

    International Nuclear Information System (INIS)

    Ng, T Y; Yeak, S H; Liew, K M

    2008-01-01

    A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods

  17. Ab initio electronic stopping power in materials

    International Nuclear Information System (INIS)

    Shukri, Abdullah-Atef

    2015-01-01

    The average energy loss of an ion per unit path length when it is moving through the matter is named the stopping power. The knowledge of the stopping power is essential for a variety of contemporary applications which depend on the transport of ions in matter, especially ion beam analysis techniques and ion implantation. Most noticeably, the use of proton or heavier ion beams in radiotherapy requires the knowledge of the stopping power. Whereas experimental data are readily available for elemental solids, the data are much more scarce for compounds. The linear response dielectric formalism has been widely used in the past to study the electronic stopping power. In particular, the famous pioneering calculations due to Lindhard evaluate the electronic stopping power of a free electron gas. In this thesis, we develop a fully ab initio scheme based on linear response time-dependent density functional theory to predict the impact parameter averaged quantity named the random electronic stopping power (RESP) of materials without any empirical fitting. The purpose is to be capable of predicting the outcome of experiments without any knowledge of target material besides its crystallographic structure. Our developments have been done within the open source ab initio code named ABINIT, where two approximations are now available: the Random-Phase Approximation (RPA) and the Adiabatic Local Density Approximation (ALDA). Furthermore, a new method named 'extrapolation scheme' have been introduced to overcome the stringent convergence issues we have encountered. These convergence issues have prevented the previous studies in literature from offering a direct comparison to experiment. First of all, we demonstrate the importance of describing the realistic ab initio electronic structure by comparing with the historical Lindhard stopping power evaluation. Whereas the Lindhard stopping power provides a first order description that captures the general features of the

  18. Ab-initio calculations of electric field gradient in Ru compounds and ...

    Indian Academy of Sciences (India)

    S N Mishra

    2017-07-11

    Jul 11, 2017 ... with calculated electric field gradient (EFG) for a large number of Ru-based compounds. The ab-initio ... zz assumed to stem from geometric arrangement of ... tant nuclear probes for the measurements of quadrupole ... with the unit cell including the nucleus and no restriction is put on ..... The effect of on-site ...

  19. Ab initio molecular dynamics model for density, elastic properties and short range order of Co-Fe-Ta-B metallic glass thin films

    International Nuclear Information System (INIS)

    Hostert, C; Music, D; Schneider, J M; Bednarcik, J; Keckes, J; Kapaklis, V; Hjörvarsson, B

    2011-01-01

    Density, elastic modulus and the pair distribution function of Co-Fe-Ta-B metallic glasses were obtained by ab initio molecular dynamics simulations and measured for sputtered thin films using x-ray reflectivity, nanoindentation and x-ray diffraction using high energy photons. The computationally obtained density of 8.19 g cm -3 for Co 43 Fe 20 Ta 5.5 B 31.5 and 8.42 g cm -3 for Co 45.5 Fe 24 Ta 6 B 24.5 , as well as the Young’s moduli of 273 and 251 GPa, respectively, are consistent with our experiments and literature data. These data, together with the good agreement between the theoretical and the experimental pair distribution functions, indicate that the model established here is useful to describe the density, elasticity and short range order of Co-Fe-Ta-B metallic glass thin films. Irrespective of the investigated variation in chemical composition, (Co, Fe)-B cluster formation and Co-Fe interactions are identified by density-of-states analysis. Strong bonds within the structural units and between the metallic species may give rise to the comparatively large stiffness. (paper)

  20. Ab initio study of electron-ion structure factors in binary liquids with different types of chemical bonding

    International Nuclear Information System (INIS)

    Klevets, Ivan; Bryk, Taras

    2014-01-01

    Electron-ion structure factors, calculated in ab initio molecular dynamics simulations, are reported for several binary liquids with different kinds of chemical bonding: metallic liquid alloy Bi–Pb, molten salt RbF, and liquid water. We derive analytical expressions for the long-wavelength asymptotes of the partial electron-ion structure factors of binary systems and show that the analytical results are in good agreement with the ab initio simulation data. The long-wavelength behaviour of the total charge structure factors for the three binary liquids is discussed

  1. An ab-initio study of mechanical, dynamical and electronic properties of MgEu intermetallic

    Science.gov (United States)

    Kumar, S. Ramesh; Jaiganesh, G.; Jayalakshmi, V.

    2018-04-01

    The theoretical investigation on the mechanical, dynamical and electronic properties of MgEu in CsCl-type structure has been carried out through the ab-initio calculations within the framework of the density functional theory and the density functional perturbation theory. For the purpose, Vienna Ab initio Simulation Package and Phonopy packages were used. Our calculated ground-state properties of MgEu are in good agreement with other available results. Our computed elastic constants and phonon spectrum results suggest that MgEu is mechanically and dynamically stable up to 5 GPa. The thermodynamic quantities as a function of temperatures are also reported and discussed. The band structure, density of states and charge density also calculated to understand the electronic properties of MgEu.

  2. Ab Initio theory of the Gilbert damping in random ferromagnetic alloys

    Czech Academy of Sciences Publication Activity Database

    Drchal, Václav; Turek, I.; Kudrnovský, Josef

    2017-01-01

    Roč. 30, č. 6 (2017), s. 1669-1672 ISSN 1557-1939 R&D Projects: GA ČR GA15-13436S Institutional support: RVO:68378271 Keywords : Gilbert damping * ferromagnetic alloys * ab initio * nonlocal torques Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 1.180, year: 2016

  3. Energetic, electronic and optical properties of lanthanide doped TiO2: An ab initio LDA+U study

    CSIR Research Space (South Africa)

    Mulwa, WM

    2016-05-01

    Full Text Available potential, J. Chem. Phys. 118 (2003) 8207. doi:10.1063/1.1564060. [23] X. Ren, Beyond LDA and GGA - Tackling exact exchange , hybrid functional , MP2 , and RPA with numeric atom-centered orbitals The Fritz-Haber-Institute ab initio molecular simulations.... Calzolari, A. Ruini, A. Catellani, Anchor Group versus Conjugation: Toward the Gap-State Engineering of Functionalized ZnO (101̅0) Surface for Optoelectronic Applications, J. Am. Chem. Soc. 133 (2011) 5893–5899. [36] R. Gillen, S.J. Clark, J. Robertson...

  4. Ab initio calculations on hydrogen storage in porous carbons

    International Nuclear Information System (INIS)

    Maresca, O.; Marinelli, F.; Pellenq, R.J.M.; Duclaux, L.; Azais, Ph.; Conard, J.

    2005-01-01

    We have investigated through ab initio computations the possible ways to achieve efficient hydrogen storage on carbons. Firstly, we have considered how the curvature of a carbon surface could affect the chemisorption of atomic H 0 Secondly, we show that electron donor elements such as Li and K, used as dopants for the carbon substrate, strongly enhance the physi-sorption energy of H 2 , allowing in principle its storage in this type of material at room temperature under mild conditions of pressure. (authors)

  5. Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects.

    Science.gov (United States)

    Sumner, Isaiah; Iyengar, Srinivasan S

    2007-10-18

    We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.

  6. Ab initio, mean field theory and series expansions calculations study of electronic and magnetic properties of antiferromagnetic MnSe alloys

    Energy Technology Data Exchange (ETDEWEB)

    Masrour, R., E-mail: rachidmasrour@hotmail.com [Laboratory of Materials, Processes, Environment and Quality, Cady Ayyed University, National School of Applied Sciences, BP. 63, 46000 Safi (Morocco); LMPHE (URAC 12), Faculty of Science, Mohammed V-Agdal University, Rabat (Morocco); Hlil, E.K. [Institut Néel, CNRS et Université Joseph Fourier, BP 166, F-38042 Grenoble Cedex 9 (France); Hamedoun, M. [Institute of Nanomaterials and Nanotechnologies, MAScIR, Rabat (Morocco); Benyoussef, A. [LMPHE (URAC 12), Faculty of Science, Mohammed V-Agdal University, Rabat (Morocco); Institute of Nanomaterials and Nanotechnologies, MAScIR, Rabat (Morocco); Hassan II Academy of Science and Technology, Rabat (Morocco); Mounkachi, O.; El Moussaoui, H. [Institute of Nanomaterials and Nanotechnologies, MAScIR, Rabat (Morocco)

    2014-06-01

    Self-consistent ab initio calculations, based on DFT (Density Functional Theory) approach and using FLAPW (Full potential Linear Augmented Plane Wave) method, are performed to investigate both electronic and magnetic properties of the MnSe lattice. Polarized spin and spin–orbit coupling are included in calculations within the framework of the antiferromagnetic state between two adjacent Mn lattices. Magnetic moments considered to lie along (001) axes are computed. Obtained data from ab initio calculations are used as input for the high temperature series expansions (HTSEs) calculations to compute other magnetic parameters. The zero-field high temperature static susceptibility series of the spin −4.28 nearest-neighbor Ising model on face centered cubic (fcc) and lattices is thoroughly analyzed by means of a power series coherent anomaly method (CAM). The exchange interaction between the magnetic atoms and the Néel temperature are deduced using the mean filed and HTSEs theories. - Highlights: • Ab initio calculations are used to investigate both electronic and magnetic properties of the MnSe alloys. • Obtained data from ab initio calculations are used as input for the HTSEs. • The Néel temperature is obtained for MnSe alloys.

  7. Short-range order in ab initio computer generated amorphous and liquid Cu–Zr alloys: A new approach

    International Nuclear Information System (INIS)

    Galván-Colín, Jonathan; Valladares, Ariel A.; Valladares, Renela M.; Valladares, Alexander

    2015-01-01

    Using ab initio molecular dynamics and a new approach based on the undermelt-quench method we generated amorphous and liquid samples of Cu x Zr 100−x (x=64, 50, 36) alloys. We characterized the topology of our resulting structures by means of the pair distribution function and the bond-angle distribution; a coordination number distribution was also calculated. Our results for both amorphous and liquids agree well with experiment. Dependence of short-range order with the concentration is reported. We found that icosahedron-like geometry plays a major role whenever the alloys are Cu-rich or Zr-rich disregarding if the samples are amorphous or liquid. The validation of these results, in turn would let us calculate other properties so far disregarded in the literature

  8. 4He Thermophysical Properties: New Ab Initio Calculations

    Science.gov (United States)

    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

  9. Equations of state of heavy metals: ab initio approaches; Equations d'etat des metaux lourds: approches ab initio

    Energy Technology Data Exchange (ETDEWEB)

    Bernard, S.; Jollet, F.; Jomard, G.; Siberchicot, B.; Torrent, M.; Zerah, G.; Amadon, B.; Bouchet, J.; Richard, N.; Robert, G. [CEA Bruyeres-le-Chatel, 91 (France)

    2005-07-01

    The determination of equations of states of heavy metals through ab initio calculation, i.e. without any adjustable parameter, allows to access to pressure and temperature thermodynamic conditions sometimes inaccessible to experiment. To perform such calculations, density functional theory (DFT) is a good starting point: when electronic densities are homogeneous enough, the local density approximation (LDA) remarkably accounts for thermodynamic properties of heavy metals, such as tantalum, or the light actinides, as well for static properties - equilibrium volume, elastic constants - as for dynamical quantities like phonon spectra. For heavier elements, like neptunium or plutonium, relativistic effects and strong electronic interactions must be taken into account, which requires more sophisticated theoretical approaches. (authors)

  10. Computational prediction of muon stopping sites using ab initio random structure searching (AIRSS)

    Science.gov (United States)

    Liborio, Leandro; Sturniolo, Simone; Jochym, Dominik

    2018-04-01

    The stopping site of the muon in a muon-spin relaxation experiment is in general unknown. There are some techniques that can be used to guess the muon stopping site, but they often rely on approximations and are not generally applicable to all cases. In this work, we propose a purely theoretical method to predict muon stopping sites in crystalline materials from first principles. The method is based on a combination of ab initio calculations, random structure searching, and machine learning, and it has successfully predicted the MuT and MuBC stopping sites of muonium in Si, diamond, and Ge, as well as the muonium stopping site in LiF, without any recourse to experimental results. The method makes use of Soprano, a Python library developed to aid ab initio computational crystallography, that was publicly released and contains all the software tools necessary to reproduce our analysis.

  11. Ab initio theoretical calculations of the electronic excitation energies of small water clusters.

    Science.gov (United States)

    Tachikawa, Hiroto; Yabushita, Akihiro; Kawasaki, Masahiro

    2011-12-14

    A direct ab initio molecular dynamics method has been applied to a water monomer and water clusters (H(2)O)(n) (n = 1-3) to elucidate the effects of zero-point energy (ZPE) vibration on the absorption spectra of water clusters. Static ab initio calculations without ZPE showed that the first electronic transitions of (H(2)O)(n), (1)B(1)←(1)A(1), are blue-shifted as a function of cluster size (n): 7.38 eV (n = 1), 7.58 eV (n = 2) and 8.01 eV (n = 3). The inclusion of the ZPE vibration strongly affects the excitation energies of a water dimer, and a long red-tail appears in the range of 6.42-6.90 eV due to the structural flexibility of a water dimer. The ultraviolet photodissociation of water clusters and water ice surfaces is relevant to these results.

  12. Bridging a gap between continuum-QCD and ab initio predictions of hadron observables

    Energy Technology Data Exchange (ETDEWEB)

    Binosi, Daniele [European Centre for Theoretical Studies in Nuclear Physics and Related Areas - ECT* and Fondazione Bruno Kessler, Villa Tambosi, Strada delle Tabarelle 286, I-38123 Villazzano (Italy); Chang, Lei [CSSM, School of Chemistry and Physics, University of Adelaide, Adelaide, SA 5005 (Australia); Papavassiliou, Joannis [Department of Theoretical Physics and IFIC, University of Valencia and CSIC, E-46100, Valencia (Spain); Roberts, Craig D., E-mail: cdroberts@anl.gov [Physics Division, Argonne National Laboratory, Argonne, IL 60439 (United States)

    2015-03-06

    Within contemporary hadron physics there are two common methods for determining the momentum-dependence of the interaction between quarks: the top-down approach, which works toward an ab initio computation of the interaction via direct analysis of the gauge-sector gap equations; and the bottom-up scheme, which aims to infer the interaction by fitting data within a well-defined truncation of those equations in the matter sector that are relevant to bound-state properties. We unite these two approaches by demonstrating that the renormalisation-group-invariant running-interaction predicted by contemporary analyses of QCD's gauge sector coincides with that required in order to describe ground-state hadron observables using a nonperturbative truncation of QCD's Dyson–Schwinger equations in the matter sector. This bridges a gap that had lain between nonperturbative continuum-QCD and the ab initio prediction of bound-state properties.

  13. Ab initio study of C14 laves phases in Fe-based systems

    Directory of Open Access Journals (Sweden)

    Pavlu J.

    2012-01-01

    Full Text Available Structural properties and energetics of Fe-based C14 Laves phases at various compositions (i.e. Fe2Fe, Fe2X, X2Fe, X2X, where X stands for Si, Cr, Mo, W, Ta were investigated using the pseudopotential VASP (Vienna Ab initio Simulation Package code employing the PAW-PBE (Projector Augmented Wave - Perdew Burke-Ernzerhof pseudopotentials. Full relaxation was performed for all structures studied including the reference states of elemental constituents and the equilibrium structure parameters as well as bulk moduli were found. The structure parameters of experimentally found structures were very well reproduced by our calculations. It was also found that the lattice parameters and volumes of the unit cell decrease with increasing molar fraction of iron. Thermodynamic analysis shows that the Fe2X configurations of Laves phases are more stable than the X2Fe ones. Some of the X2Fe configurations are even unstable with respect to the weighted average of the Laves phases of elemental constituents. Our calculations predict the stability of Fe2Ta. On the other hand, Fe2Mo and Fe2W are slightly unstable (3.19 and 0.68 kJ.mol-1, respectively and hypothetical structures Fe2Cr and Fe2Si are found unstable as well.

  14. Ab initio identification of the Li-rich phase in LiFePO4.

    Science.gov (United States)

    Zeng, Hua; Gu, Yue; Teng, Gaofeng; Liu, Yimeng; Zheng, Jiaxin; Pan, Feng

    2018-06-27

    A recent discovery of anionic redox activity in Li-rich layered compounds opens a new direction for the design of high-capacity cathode materials for lithium-ion batteries. Here using extensive ab initio calculations, the thermodynamic existence of the Li-rich phase in LiFePO4 to form Li1+xFe1-xPO4 with x not exceeding 12.5% has been proved. Anionic redox activity and structural stability during delithiation are further investigated. Interestingly, it is found that Li1+xFe1-xPO4 cannot be delithiated completely and thus cannot achieve extra capacity by anionic redox activity, because the local oxygen-ion redox will cause the fracture of the rigid framework formed by phosphate tetrahedral polyanions. Although an extra capacity cannot be realized, the excess Li-ions at Fe sites can enhance the Li-ion diffusivity along the adjacent [010] channel and contribute to the shift from 1D to 2D/3D diffusion. This study provides a fresh perspective on olivine-type LiFePO4 and offers some important clues on designing Li-rich cathode materials with high energy density.

  15. Finite temperature effects on the X-ray absorption spectra of energy related materials

    Science.gov (United States)

    Pascal, Tod; Prendergast, David

    2014-03-01

    We elucidate the role of room-temperature-induced instantaneous structural distortions in the Li K-edge X-ray absorption spectra (XAS) of crystalline LiF, Li2SO4, Li2O, Li3N and Li2CO3 using high resolution X-ray Raman spectroscopy (XRS) measurements and first-principles density functional theory calculations within the eXcited electron and Core Hole (XCH) approach. Based on thermodynamic sampling via ab-initio molecular dynamics (MD) simulations, we find calculated XAS in much better agreement with experiment than those computed using the rigid crystal structure alone. We show that local instantaneous distortion of the atomic lattice perturbs the symmetry of the Li 1 s core-excited-state electronic structure, broadening spectral line-shapes and, in some cases, producing additional spectral features. This work was conducted within the Batteries for Advanced Transportation Technologies (BATT) Program, supported by the U.S. Department of Energy Vehicle Technologies Program under Contract No. DE-AC02-05CH11231.

  16. X-ray Emission Cross Sections following Charge Exchange by Multiply-Charged Ions of Astrophysical Interest.

    Science.gov (United States)

    Otranto, Sebastian; Olson, Ronald; Beiersdorfer, Peter

    2006-05-01

    State selective nl-electron capture cross sections calculated using the classical trajectory Monte Carlo (CTMC) model are presented for highly charged ions with Z = 6-10 colliding with atoms and molecules. The energy dependence of the l-level populations is investigated. The calculated cross sections are compared with measurements made by Greenwood et al [1], using O^8+ and Ne^10+ on various targets at 3 keV/amu, and with recent x-ray emission cross sections measured with the EBIT machine at LLNL using O^8+ and Ne^9+,10+ on different targets at 10 eV/amu. We use the calculated cross sections to present an ab initio determination of the soft x-ray spectrum of comet C/Linear 1999 S4 that was observed on the Chandra X-ray Observatory [2]. [1] J. B. Greenwood, I. D. Williams, S. J. Smith and A. Chutjian, Phys. Rev. A 63, 062707 (2001). [2] C. M. Lisse, D. J. Christian, K. Dennerl, K. J. Meech, R. Petre, H. A. Weaver and S. J. Wolk, Science 292, 1343 (2001).

  17. Surface chemical analysis and ab initio investigations of CsI coated C fiber cathodes for high power microwave sources

    Science.gov (United States)

    Vlahos, Vasilios; Morgan, Dane; LaCour, Matthew; Golby, Ken; Shiffler, Don; Booske, John H.

    2010-02-01

    CsI coated C fiber cathodes are promising electron emitters utilized in field emission applications. Ab initio calculations, in conjunction with experimental investigations on CsI-spray coated C fiber cathodes, were performed in order to better understand the origin of the low turn-on E-field obtained, as compared to uncoated C fibers. One possible mechanism for lowering the turn-on E-field is surface dipole layers reducing the work function. Ab initio modeling revealed that surface monolayers of Cs, CsI, Cs2O, and CsO are all capable of producing low work function C fiber cathodes (1 eV<Φ<1.5 eV), yielding a reduction in the turn-on E-field by as much as ten times, when compared to the bare fiber. Although a CsI-containing aqueous solution is spray deposited on the C fiber surface, energy dispersive x-ray spectroscopy and scanning auger microscopy measurements show coabsorption of Cs and I into the fiber interior and Cs and O on the fiber surface, with no surface I. It is therefore proposed that a cesium oxide (CsxOy) surface coating is responsible, at least in part, for the low turn E-field and superior emission characteristics of this type of fiber cathode. This CsxOy layer could be formed during preconditioning heating. CsxOy surface layers cannot only lower the fiber work function by the formation of surface dipoles (if they are thin enough) but may also enhance surface emission through their ability to emit secondary electrons due to a process of grazing electron impact. These multiple electron emission processes may explain the reported 10-100 fold reduction in the turn-on E-field of coated C fibers.

  18. Ab Initio Values of the Thermophysical Properties of Helium as Standards

    Science.gov (United States)

    Hurly, John J.; Moldover, Michael R.

    2000-01-01

    Recent quantum mechanical calculations of the interaction energy of pairs of helium atoms are accurate and some include reliable estimates of their uncertainty. We combined these ab initio results with earlier published results to obtain a helium-helium interatomic potential that includes relativistic retardation effects over all ranges of interaction. From this potential, we calculated the thermophysical properties of helium, i.e., the second virial coefficients, the dilute-gas viscosities, and the dilute-gas thermal conductivities of 3He, 4He, and their equimolar mixture from 1 K to 104 K. We also calculated the diffusion and thermal diffusion coefficients of mixtures of 3He and 4He. For the pure fluids, the uncertainties of the calculated values are dominated by the uncertainties of the potential; for the mixtures, the uncertainties of the transport properties also include contributions from approximations in the transport theory. In all cases, the uncertainties are smaller than the corresponding experimental uncertainties; therefore, we recommend the ab initio results be used as standards for calibrating instruments relying on these thermophysical properties. We present the calculated thermophysical properties in easy-to-use tabular form. PMID:27551630

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

    Science.gov (United States)

    Chaka, Anne M; Felmy, Andrew R

    2014-09-04

    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.

  20. Using ab initio 'data' to accurately determine the fourth density virial coefficient of helium

    International Nuclear Information System (INIS)

    Moldover, Michael R.; McLinden, Mark O.

    2010-01-01

    We combine accurate ab initio calculations of the second and third density virial coefficients, B(T) and C(T), of 4 He with measurements of its (p-ρ-T) behavior to determine the fourth density virial coefficient D(T). The measurements were made with a two-sinker, magnetic-suspension densimeter at pressures up to 38 MPa. The measurements on isotherms from T = 223 K to T = 323 K were previously published; new measurements from T = 323 K to T = 500 K are presented here. On each isotherm, a regression of the virial expansion was constrained to the ab initio values of B(T) and C(T); the regression determined D(T) as well as two apparatus-dependent parameters that compensated for systematic errors in the measurements. The percentage uncertainties of D(T) ranged from 2.6% at T = 223 K to 9.5% at T = 400 K to 24.7% at T = 500 K, where these uncertainties are expanded uncertainties with coverage factor of k = 2 corresponding to a 95% confidence interval. These uncertainties are 1/6th of the uncertainty obtained without the ab initio values of B(T) and C(T). The apparatus-dependent parameters can be used to calibrate the densimeter, and this will reduce the uncertainty of other measurements made with this two-sinker densimeter. The new values of D(T) will find applications in accurate gas metrology, such as a primary pressure standard based on the refractive index of helium.

  1. Ab Initio Predictions of Hexagonal Zr(B,C,N) Polymorphs for Coherent Interface Design

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Chongze [Univ. of Minnesota-Twin Cities, Minneapolis, MN (United States); Huang, Jingsong [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sumpter, Bobby G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Meletis, Efstathios [Univ. of Texas at Arlington, Arlington, TX (United States); Dumitrica, Traian [Univ. of Minnesota-Twin Cities, Minneapolis, MN (United States)

    2017-10-27

    Density functional theory calculations are used to explore hexagonal (HX) NiAs-like polymorphs of Zr(B,C,N) and compare with corresponding Zr(B,C,N) Hagg-like face-centered cubic rocksalt (B1) phases. While all predicted compounds are mechanically stable according to the Born-Huang criteria, only HX Zr(C,N) are found dynamically stable from ab initio molecular dynamics simulations and lattice dynamics calculations. HX ZrN emerges as a candidate structure with ground state energy, elastic constants, and extrinsic mechanical parameters comparable with those of B1 ZrN. Ab initio band structure and semi-classical Boltzmann transport calculations predict a metallic character and a monotonic increase in electrical conductivity with the number of valence electrons. Electronic structure calculations indicate that the HX phases gain their stability and mechanical attributes by Zr d- non-metal p hybridization and by broadening of Zr d bands. Furthermore, it is shown that the HX ZrN phase provides a low-energy coherent interface model for connecting B1 ZrN domains, with significant energetic advantage over an atomistic interface model derived from high resolution transmission electron microscopy images. The ab initio characterizations provided herein should aid the experimental identification of non-Hagg-like hard phases. Furthermore, the results can also enrich the variety of crystalline phases potentially available for designing coherent interfaces in superhard nanostructured materials and in materials with multilayer characteristics.

  2. Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules

    DEFF Research Database (Denmark)

    Zhang, Hao; Lund, Ole; Nielsen, Morten

    2010-01-01

    potentials derived from the analysis of known protein structures; energetic evaluation of different peptide snapshots in a molecular dynamics simulation; and direct analysis of contacts made in known 3D structures of peptide:MHC complexes. These methods are ab initio in that they require structural data...

  3. Ab initio and work function and surface energy anisotropy of LaB6

    NARCIS (Netherlands)

    Uijttewaal, M. A.; de Wijs, G. A.; de Groot, R. A.

    2006-01-01

    Lanthanum hexaboride is one of the cathode materials most used in high-power electronics technology, but the many experimental results do not provide a consistent picture of the surface properties. Therefore, we report the first ab initio calculations of the work functions and surface energies of

  4. Extended x-ray absorption fine structure in Ga1-xMnxN/SiC films with high Mn content

    Science.gov (United States)

    Sancho-Juan, O.; Martínez-Criado, O.; Cantarero, A.; Garro, N.; Salomé, M.; Susini, J.; Olguín, D.; Dhar, S.; Ploog, K.

    2011-05-01

    In this study, the local atomic structure of highly homogeneous Ga1-xMnxN alloy films (0.03<x<0.09) is analyzed by means of Mn and Ga K-edge extended x-ray absorption fine structure measurements. From the curve fitting, the structural parameters corresponding to the first two atomic shells surrounding both Ga and Mn atoms are reported. In the Ga1-xMnxN films, grown by molecular beam epitaxy, the Mn atoms are in tetrahedral configuration, independent of the Mn concentration; that is, they are in a substitutional site, MnGa, in the wurtzite structure. A small increase in the interatomic distances has been found with increasing Mn content. The Debye-Waller factor does not show a significant trend as Mn content increases, which suggests the presence of short-range disorder in the GaN lattice. Ab initio calculations of the structural parameter for two different Mn concentrations are consistent with the experimental results.

  5. Ground state analytical ab initio intermolecular potential for the Cl2-water system

    International Nuclear Information System (INIS)

    Hormain, Laureline; Monnerville, Maurice; Toubin, Céline; Duflot, Denis; Pouilly, Brigitte; Briquez, Stéphane; Bernal-Uruchurtu, Margarita I.; Hernández-Lamoneda, Ramón

    2015-01-01

    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 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 2 − H 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 2 interacting with an increasing number of water molecules. Finally, the model potential is used to study the physisorption of Cl 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

  6. A General Approach to Access Morphologies of Polyoxometalates in Solution by Using SAXS: An Ab Initio Modeling Protocol.

    Science.gov (United States)

    Li, Mu; Wang, Weiyu; Yin, Panchao

    2018-05-02

    Herein, we reported a general protocol for an ab initio modeling approach to deduce structure information of polyoxometalates (POMs) in solutions from scattering data collected by the small-angle X-ray scattering (SAXS) technique. To validate the protocol, the morphologies of a serious of known POMs in either aqueous or organic solvents were analyzed. The obtained particle morphologies were compared and confirmed with previous reported crystal structures. To extend the feasibility of the protocol to an unknown system of aqueous solutions of Na 2 MoO 4 with the pH ranging from -1 to 8.35, the formation of {Mo 36 } clusters was probed, identified, and confirmed by SAXS. The approach was further optimized with a multi-processing capability to achieve fast analysis of experimental data, thereby, facilitating in situ studies of formations of POMs in solutions. The advantage of this approach is to generate intuitive 3D models of POMs in solutions without confining information such as symmetries and possible sizes. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. 1-(2-furoyl)-3,3-(diphenyl)thiourea: spectroscopic characterization and structural study from X-ray powder diffraction using simulated annealing

    Energy Technology Data Exchange (ETDEWEB)

    Estevez H, O.; Duque, J. [Universidad de La Habana, Instituto de Ciencia y Tecnologia de Materiales, 10400 La Habana (Cuba); Rodriguez H, J. [UNAM, Instituto de Investigaciones en Materiales, 04510 Mexico D. F. (Mexico); Yee M, H., E-mail: oestevezh@yahoo.com [Instituto Politecnico Nacional, Escuela Superior de Fisica y Matematicas, 07738 Mexico D. F. (Mexico)

    2015-07-01

    1-Furoyl-3,3-diphenylthiourea (FDFT) was synthesized, and characterized by Ftir, {sup 1}H and {sup 13}C NMR and ab initio X-ray powder structure analysis. FDFT crystallizes in the monoclinic space group P2{sub 1} with a = 12.691(1), b = 6.026(2), c = 11.861(1) A, β = 117.95(2) and V = 801.5(3) A{sup 3}. The crystal structure has been determined from laboratory X-ray powder diffraction data using direct space global optimization strategy (simulated annealing) followed by the Rietveld refinement. The thiourea group makes a dihedral angle of 73.8(6) with the furoyl group. In the crystal structure, molecules are linked by van der Waals interactions, forming one-dimensional chains along the a axis. (Author)

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

    Science.gov (United States)

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-07-19

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. Calibration of Sn-119 isomer shift using ab initio wave function methods

    NARCIS (Netherlands)

    Kurian, Reshmi; Filatov, Michael

    2009-01-01

    The isomer shift for the 23.87 keV M1 resonant transition in the Sn-119 nucleus is calibrated with the help of ab initio calculations. The calibration constant alpha(Sn-119) obtained from Hartree-Fock (HF) calculations (alpha(HF)(Sn-119)=(0.081 +/- 0.002)a(0)(-3) mm/s) and from second-order

  11. DNA oligonucleotide-cis-platin Binding: Ab initio interpretation of the vibrational spectra

    Czech Academy of Sciences Publication Activity Database

    Andrushchenko, Valery; Wieser, H.; Bouř, Petr

    2007-01-01

    Roč. 111, č. 39 (2007), s. 9714-9723 ISSN 1089-5639 R&D Projects: GA AV ČR IAA400550702; GA ČR GA202/07/0732 Institutional research plan: CEZ:AV0Z40550506 Keywords : cis - platin * DNA * vibrational spektra * ab initio Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.918, year: 2007

  12. Short-range order in ab initio computer generated amorphous and liquid Cu–Zr alloys: A new approach

    Energy Technology Data Exchange (ETDEWEB)

    Galván-Colín, Jonathan, E-mail: jgcolin@ciencias.unam.mx [Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Apartado Postal 70-360, México, D.F. 04510, México (Mexico); Valladares, Ariel A., E-mail: valladar@unam.mx [Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Apartado Postal 70-360, México, D.F. 04510, México (Mexico); Valladares, Renela M.; Valladares, Alexander [Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-542, México, D.F. 04510, México (Mexico)

    2015-10-15

    Using ab initio molecular dynamics and a new approach based on the undermelt-quench method we generated amorphous and liquid samples of Cu{sub x}Zr{sub 100−x} (x=64, 50, 36) alloys. We characterized the topology of our resulting structures by means of the pair distribution function and the bond-angle distribution; a coordination number distribution was also calculated. Our results for both amorphous and liquids agree well with experiment. Dependence of short-range order with the concentration is reported. We found that icosahedron-like geometry plays a major role whenever the alloys are Cu-rich or Zr-rich disregarding if the samples are amorphous or liquid. The validation of these results, in turn would let us calculate other properties so far disregarded in the literature.

  13. AB INITIO molecular orbital studies of some high temperature metal halide complexes

    International Nuclear Information System (INIS)

    Curtiss, L.A.

    1978-01-01

    The use of ab initio molecular orbital calculations to aid in the characterization, i.e., structures and energies, of metal halide complexes present in high temperature salt vapors has been investigated. Standard LCAO-SCF methods were used and calculations were carried out using the minimal STO-3G basis set. The complexes included in this study were Al 2 F 6 , Al 2 Cl 6 , AlF 3 NH 3 , AlCl 3 NH 3 , and AlF 3 N 2 . The Al 2 X 6 complexes are found to have D/sub 2h/ symmetry in agreement with most experimental results. A planar form was found to be considerably higher in energy. The AlX 3 NH 3 complexes are found to have C/sub 3v/ symmetry with a small barrier to rotation about the Al-N axis. The AlF 3 N 2 complex is found to be weakly bound together with a binding energy of -8.2 kcal/mole at the STO-3G level

  14. All-electron ab initio investigations of the electronic states of the NiC molecule

    DEFF Research Database (Denmark)

    Shim, Irene; Gingerich, Karl. A.

    1999-01-01

    The low-lying electronic states of NiC are investigated by all-electron ab initio multi-configuration self-consistent-field (CASSCF) calculations including relativistic corrections. The electronic structure of NiC is interpreted as perturbed antiferromagnetic couplings of the localized angular...

  15. Understanding hydration of Zn(2+) in hydrothermal fluids with ab initio molecular dynamics

    NARCIS (Netherlands)

    Liu, X.; Lu, X.; Wang, R.; Meijer, E.J.

    2011-01-01

    With ab initio molecular dynamics simulations, the free-energy profiles of hydrated Zn2+ are calculated for both gaseous and aqueous systems from ambient to supercritical conditions, and from the derived free-energy information, the speciation of hydrated Zn2+ has been revealed. It is shown that the

  16. Conformational Sampling by Ab Initio Molecular Dynamics Simulations Improves NMR Chemical Shift Predictions

    Czech Academy of Sciences Publication Activity Database

    Dračínský, Martin; Möller, H. M.; Exner, T. E.

    2013-01-01

    Roč. 9, č. 8 (2013), s. 3806-3815 ISSN 1549-9618 R&D Projects: GA ČR GA13-24880S Institutional support: RVO:61388963 Keywords : ab initio molecular dynamics * NMR spectroscopy * DFT calculations * hydration Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.310, year: 2013

  17. Ab initio investigation of superconductivity in orthorhombic MgPtSi

    Energy Technology Data Exchange (ETDEWEB)

    Tütüncü, H.M., E-mail: tutuncu@sakarya.edu.tr [Sakarya Üniversitesi, Fen-Edebiyat Fakültesi, Fizik Bölümü, 54187, Adapazarı (Turkey); Sakarya Üniversitesi, BIMAYAM Biyomedikal, Manyetik ve Yarıiletken Malzemeler Araştırma Merkezi, 54187, Adapazarı (Turkey); Ertuǧrul Karaca [Sakarya Üniversitesi, Fen-Edebiyat Fakültesi, Fizik Bölümü, 54187, Adapazarı (Turkey); Srivastava, G.P. [School of Physics, University of Exeter, Stocker Road, Exeter EX4 4QL (United Kingdom)

    2016-07-15

    We have performed an ab initio study of electronic, vibrational and superconducting properties of the orthorhombic MgPtSi by employing the density functional theory, a linear-response formalism, and the plane-wave pseudopotential method. Our electronic results suggest that the density of states at the Fermi level is primarily contributed by Pt 5d and Si 3p states with much smaller contribution from Mg electronic states. Phonon anomalies have been found for all three acoustic branches. Due to these phonon anomalies, the acoustic branches make large contributions to the average electron-phonon coupling parameter. From the Eliashberg spectral function, the value of average electron-phonon coupling parameter is found to 0.707. Using this value, the superconducting critical temperature is obtained to be 2.4 K, in excellent accordance with its experimental value of 2.5 K. - Highlights: • The electronic structure of MgPtSi is studied using ab initio pseudopotential method. • Phonons and electron–phonon interaction in MgPtSi are studied using a linear response theory. • The acoustic phonon modes couple more strongly with electrons. • The value of λ is found to be 0.707 which shows that MgPtSi is a conventional honon-mediated superconductor. • The calculated T{sub c} of 2.4 K is in excellent accordance with its experimental value of 2.5 K.

  18. Ab initio studies of structural, electronic, optical, elastic and thermal properties of silver gallium dichalcogenides (AgGaX2: X = S, Se, Te)

    International Nuclear Information System (INIS)

    Sharma, Sheetal; Verma, A.S.; Jindal, V.K.

    2014-01-01

    Graphical abstract: - Highlights: • FP-LAPW method has been used to compute the solid state properties of AgGaX 2 (X = S, Se, Te). • Electronic and optical properties reported with recently developed mBJ potential. • Thermal expansion, heat capacity, Debye temperature, entropy and Grüneisen parameter were evaluated. • Hardness was calculated for the first time at different temperature and pressure. - Abstract: We have performed ab initio calculations for the structural, electronic, optical, elastic and thermal properties of the silver gallium dichalcogenides (AgGaX 2 : X = S, Se, Te). In this study, we have used the accurate full potential linearized augmented plane wave (FP-LAPW) method to find the equilibrium structural parameters and to compute the six elastic constants (C 11 , C 12 , C 13 , C 33 , C 44 and C 66 ). We have reported electronic and optical properties with the recently developed density functional theory of Tran and Blaha, and this theory is used along with the Wu-Cohen generalized gradient approximation (WC-GGA) for the exchange-correlation potential. Furthermore, optical features such as dielectric functions, refractive indices, extinction coefficient, optical reflectivity, absorption coefficients and optical conductivities were calculated for photon energies up to 40 eV. The thermodynamical properties such as thermal expansion, heat capacity, debye temperature, entropy, Grüneisen parameter and bulk modulus were calculated employing the quasi-harmonic Debye model at different temperatures (0–900 K) and pressures (0–8 GPa) and the silent results were interpreted. Hardness of the materials was calculated for the first time at different temperatures and pressures

  19. Ab initio study of isomerism in molecular Li2AB+ ions with 12 and 14 valence electrons

    International Nuclear Information System (INIS)

    Charkin, O.P.; Klimenko, N.M.; Mak-Ki, M.L.; Shlojer, P.R.

    1997-01-01

    Ab initio calculations of potential energy surfaces (PES) of molecular ions Li 2 AB + with 12 and 14 valence electrons have been made in the framework of approximations MP2/6-31G*//HF/6-31G*+ZPE(HF/6-31G*) and MP4SDTQ/6-31*//MP2/6-31G*+ZPE(MP2/6-31G*). The following most favourable structures have been found: a double-terminal linear for LiNO + (a triplet); a plane bicyclic one for Li 2 OF + , Li 2 SCl + , Li 2 NO + (a singlet) and Li 2 PS + (a singlet), where both cations are coordinated to A-B bond; rectangular (T-shaped) for Li 2 OCl + and SFLi + , as well as for LiNS + and POLi 2 + ions in singlet and triplet states; in the form of a half-opened butterfly for Li 2 PS + (a triplet) and Li 2 SCl +

  20. Study on the surface hydroxyl group on solid breeding materials by ab-initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, Satoru; Taniguchi, Masaki [Tokyo Univ. (Japan). Faculty of Engineering

    1996-10-01

    The nature of -OH on the surface of Li{sub 2}O was analyzed with the ab-initio quantum chemical calculation technique. Calculation results showed that the stretching vibration of O-H is affected by the chemical species around the -OH. (author)

  1. All electron ab initio investigations of the electronic states of the FeC molecule

    DEFF Research Database (Denmark)

    Shim, Irene; Gingerich, Karl A.

    1999-01-01

    The low lying electronic states of the molecule FeC have been investigated by performing all electron ab initio multi-configuration self-consistent-field (CASSCF) and multi reference configuration interaction (MRCI) calculations. The relativistic corrections for the one electron Darwin contact term...

  2. All Electron ab initio Investigations of the Electronic States of the MoN Molecule

    DEFF Research Database (Denmark)

    Shim, Irene; Gingerich, Karl A.

    1999-01-01

    The low lying electronic states of the molecule MoN have been investigated by performing all electron ab initio multi-configuration self-consistent-field (CASSCF) calculations. The relativistic corrections for the one electron Darwin contact term and the relativistic mass-velocity correction have...

  3. Atomic defects in monolayer WSe2 tunneling FETs studied by systematic ab initio calculations

    Science.gov (United States)

    Wu, Jixuan; Fan, Zhiqiang; Chen, Jiezhi; Jiang, Xiangwei

    2018-05-01

    Atomic defects in monolayer WSe2 tunneling FETs (TFETs) are studied through systematic ab initio calculations aiming at performance predictions and enhancements. The effects of various defect positions and different passivation atoms are characterized in WSe2 TFETs by rigorous ab initio quantum transport simulations. It is suggested that the Se vacancy (VSe) defect located in the gate-controlled channel region tends to increase the OFF current (I off), whereas it can be well suppressed by oxygen passivation. It is demonstrated that chlorine (Cl) passivation at the source-side tunneling region can largely suppress I off, leading to an impressively improved on–off ratio (I on/I off) compared with that without any defect. However, it is also observed that randomly positioned atomic defects tend to induce significant fluctuation of the TFET output. Further discussions are made with focus on the performance-variability trade-off for robust circuit design.

  4. Theoretical study of silicon carbide under irradiation at the nano scale: classical and ab initio modelling; Etude theorique a l'echelle nanometrique du carbure de silicium sous irradiation: modelisation classique et ab initio

    Energy Technology Data Exchange (ETDEWEB)

    Lucas, G

    2006-10-15

    The behaviour of silicon carbide under irradiation has been studied using classical and ab initio simulations, focusing on the nano scale elementary processes. First, we have been interested in the calculation of threshold displacement energies, which are difficult to determine both experimentally and theoretically, and also the associated Frenkel pairs. In the framework of this thesis, we have carried out simulations in classical and ab initio molecular dynamics. For the classical approach, two types of potentials have been used: the Tersoff potential, which led to non satisfactory results, and a new one which has been developed during this thesis. This potential allows a better modelling of SiC under irradiation than most of the empirical potentials available for SiC. It is based on the EDIP potential, initially developed to describe defects in silicon, that we have generalized to SiC. For the ab initio approach, the feasibility of the calculations has been validated and average energies of 19 eV for the C and 38 eV for the Si sublattices have been determined, close to the values empirically used in the fusion community. The results obtained with the new potential EDIP are globally in agreement with those values. Finally, the elementary processes involved in the crystal recovery have been studied by calculating the stability of the created Frenkel pairs and determining possible recombination mechanisms with the nudged elastic band method. (author)

  5. Ab initio excited states calculations of Kr3+, probing semi-empirical modelling

    Czech Academy of Sciences Publication Activity Database

    Milko, Petr; Kalus, R.; Paidarová, Ivana; Hrušák, Jan; Gadéa, F. X.

    -, 23 June (2009), s. 25 ISSN 1432-2234 R&D Projects: GA AV ČR IAA100400501 Institutional research plan: CEZ:AV0Z40400503 Keywords : cluster modelling * rare gas ions * ab initio potential energie * evaporation energies Subject RIV: CF - Physical ; Theoretical Chemistry http://www.springerlink.com/content/100493/?Content+Status=Accepted&sort=p_OnlineDate&sortorder=desc&v=condensed&o=20

  6. Ab initio quantum-enhanced optical phase estimation using real-time feedback control

    DEFF Research Database (Denmark)

    Berni, Adriano; Gehring, Tobias; Nielsen, Bo Melholt

    2015-01-01

    of a quantum-enhanced and fully deterministic ab initio phase estimation protocol based on real-time feedback control. Using robust squeezed states of light combined with a real-time Bayesian adaptive estimation algorithm, we demonstrate deterministic phase estimation with a precision beyond the quantum shot...... noise limit. The demonstrated protocol opens up new opportunities for quantum microscopy, quantum metrology and quantum information processing....

  7. Calcium ions in aqueous solutions: Accurate force field description aided by ab initio molecular dynamics and neutron scattering

    Science.gov (United States)

    Martinek, Tomas; Duboué-Dijon, Elise; Timr, Štěpán; Mason, Philip E.; Baxová, Katarina; Fischer, Henry E.; Schmidt, Burkhard; Pluhařová, Eva; Jungwirth, Pavel

    2018-06-01

    We present a combination of force field and ab initio molecular dynamics simulations together with neutron scattering experiments with isotopic substitution that aim at characterizing ion hydration and pairing in aqueous calcium chloride and formate/acetate solutions. Benchmarking against neutron scattering data on concentrated solutions together with ion pairing free energy profiles from ab initio molecular dynamics allows us to develop an accurate calcium force field which accounts in a mean-field way for electronic polarization effects via charge rescaling. This refined calcium parameterization is directly usable for standard molecular dynamics simulations of processes involving this key biological signaling ion.

  8. Ab initio methods for electron-molecule collisions

    International Nuclear Information System (INIS)

    Collins, L.A.; Schneider, B.I.

    1987-01-01

    This review concentrates on the recent advances in treating the electronic aspect of the electron-molecule interaction and leaves to other articles the description of the rotational and vibrational motions. Those methods which give the most complete treatment of the direct, exchange, and correlation effects are focused on. Such full treatments are generally necessary at energies below a few Rydbergs (≅ 60 eV). This choice unfortunately necessitates omission of those active and vital areas devoted to the development of model potentials and approximate scattering formulations. The ab initio and model approaches complement each other and are both extremely important to the full explication of the electron-scattering process. Due to the rapid developments of recent years, the approaches that provide the fullest treatment are concentrated on. 81 refs

  9. A GENERALIZED TWO-COMPONENT MODEL OF SOLAR WIND TURBULENCE AND AB INITIO DIFFUSION MEAN-FREE PATHS AND DRIFT LENGTHSCALES OF COSMIC RAYS

    Energy Technology Data Exchange (ETDEWEB)

    Wiengarten, T.; Fichtner, H.; Kleimann, J.; Scherer, K. [Institut für Theoretische Physik IV, Ruhr-Universität Bochum (Germany); Oughton, S. [Department of Mathematics, University of Waikato, Hamilton 3240 (New Zealand); Engelbrecht, N. E. [Center for Space Research, North-West University, Potchefstroom 2520 (South Africa)

    2016-12-10

    We extend a two-component model for the evolution of fluctuations in the solar wind plasma so that it is fully three-dimensional (3D) and also coupled self-consistently to the large-scale magnetohydrodynamic equations describing the background solar wind. The two classes of fluctuations considered are a high-frequency parallel-propagating wave-like piece and a low-frequency quasi-two-dimensional component. For both components, the nonlinear dynamics is dominanted by quasi-perpendicular spectral cascades of energy. Driving of the fluctuations by, for example, velocity shear and pickup ions is included. Numerical solutions to the new model are obtained using the Cronos framework, and validated against previous simpler models. Comparing results from the new model with spacecraft measurements, we find improved agreement relative to earlier models that employ prescribed background solar wind fields. Finally, the new results for the wave-like and quasi-two-dimensional fluctuations are used to calculate ab initio diffusion mean-free paths and drift lengthscales for the transport of cosmic rays in the turbulent solar wind.

  10. A GENERALIZED TWO-COMPONENT MODEL OF SOLAR WIND TURBULENCE AND AB INITIO DIFFUSION MEAN-FREE PATHS AND DRIFT LENGTHSCALES OF COSMIC RAYS

    International Nuclear Information System (INIS)

    Wiengarten, T.; Fichtner, H.; Kleimann, J.; Scherer, K.; Oughton, S.; Engelbrecht, N. E.

    2016-01-01

    We extend a two-component model for the evolution of fluctuations in the solar wind plasma so that it is fully three-dimensional (3D) and also coupled self-consistently to the large-scale magnetohydrodynamic equations describing the background solar wind. The two classes of fluctuations considered are a high-frequency parallel-propagating wave-like piece and a low-frequency quasi-two-dimensional component. For both components, the nonlinear dynamics is dominanted by quasi-perpendicular spectral cascades of energy. Driving of the fluctuations by, for example, velocity shear and pickup ions is included. Numerical solutions to the new model are obtained using the Cronos framework, and validated against previous simpler models. Comparing results from the new model with spacecraft measurements, we find improved agreement relative to earlier models that employ prescribed background solar wind fields. Finally, the new results for the wave-like and quasi-two-dimensional fluctuations are used to calculate ab initio diffusion mean-free paths and drift lengthscales for the transport of cosmic rays in the turbulent solar wind.

  11. Phase diagrams from ab-initio calculations: Re-W and Fe-B

    Energy Technology Data Exchange (ETDEWEB)

    Hammerschmidt, Thomas; Bialon, Arthur; Palumbo, Mauro; Fries, Suzana G.; Drautz, Ralf [ICAMS, Ruhr-Universitaet Bochum (Germany)

    2011-07-01

    The CALPHAD (CaLculation of Phase Diagrams) method relies on Gibbs energy databases and is of limited predictive power in cases where only limited experimental data is available for constructing the Gibbs energy databases. This is problematic for, e.g., the calculation of the phase transformation kinetics within phase field simulations that not only require the thermodynamic equilibrium data but also information on metastable phases. Such information is difficult to obtain directly from experiment but ab-initio calculations may supplement experimental databases as they comprise metastable phases and arbitrary chemical compositions. We present simulations for two prototypical systems: Re-W and Fe-B. For both systems we calculate the heat of formation for an extensive set of structures using ab-initio calculations and employ the total energies in CALPHAD in order to determine the corresponding phase diagrams. We account for the configurational entropy within the Bragg-Williams approximation and neglect the phenomenological excess-term that is commonly used in CALPHAD as well as the contribution of phonons and electronic excitations to the free energy. According to our calculations the complex intermetallic phases in Re-W are stabilized by the configurational entropy. For Fe-B, we calculate metastable and stable phase diagrams including recently predicted new stable phases.

  12. Ab initio studies on [bmim][PF6]–CO2 mixture and CO2 clusters

    Indian Academy of Sciences (India)

    Wintec

    Ionic liquids; supercritical carbon dioxide; ab initio; molecular dynamics. 1. Introduction .... Several experi- mental and simulation studies have been carried out to .... from an analysis of its electronic polarizability (α), which is a measure of the ...

  13. Study of wide band-gap crystal LiCaAlF6 by IR-reflection spectroscopy and ab initio calculations

    International Nuclear Information System (INIS)

    Novikova, N.N.; Klimin, S.A.; Mavrin, B.N.

    2017-01-01

    Polarized IR-reflection spectra and results of ab initio calculations of vibrational and electronic properties of LiCaAlF6 single crystal are presented. It is shown that the crystal band gap is direct. Experimental and theoretical parameters are obtained for dipole-active and all phonons, respectively, including silent modes. Experimental IR-reflection and Raman spectra are well described in the frame of results obtained by ab initio calculations. The peculiarities are discussed concerning the structure of electronic bands, the interatomic interactions, the character of lattice vibrations, and the phonon dispersion.

  14. Phonocatalysis. An ab initio simulation experiment

    Directory of Open Access Journals (Sweden)

    Kwangnam Kim

    2016-06-01

    Full Text Available 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.

  15. Routine calculation of ab initio melting curves: application to aluminum

    OpenAIRE

    Robert, Grégory; Legrand, Philippe; Arnault, Philippe; Desbiens, Nicolas; Clérouin, Jean

    2014-01-01

    We present a simple, fast, and reliable method to compute the melting curves of materials with ab initio molecular dynamics. It is based on the two-phase thermodynamic model of [Lin et al., J. Chem. Phys. 119, 11792 (2003)] and its improved version given by [Desjarlais, Phys. Rev. E, 88, 062145 (2013)]. In this model, the velocity autocorrelation function is utilized to calculate the contribution of the nuclei motion to the entropy of the solid and liquid phases. It is then possible to find t...

  16. Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Thomas, Jordan W.; Iftimie, Radu; Tuckerman, Mark E.

    2004-01-01

    Techniques from gauge-field theory are employed to derive an alternative formulation of the Car-Parrinello ab initio molecular-dynamics method that allows maximally localized Wannier orbitals to be generated dynamically as the calculation proceeds. In particular, the Car-Parrinello Lagrangian is mapped onto an SU(n) non-Abelian gauge-field theory and the fictitious kinetic energy in the Car-Parrinello Lagrangian is modified to yield a fully gauge-invariant form. The Dirac gauge-fixing method is then employed to derive a set of equations of motion that automatically maintain orbital locality by restricting the orbitals to remain in the 'Wannier gauge'. An approximate algorithm for integrating the equations of motion that is stable and maintains orbital locality is then developed based on the exact equations of motion. It is shown in a realistic application (64 water molecules plus one hydrogen-chloride molecule in a periodic box) that orbital locality can be maintained with only a modest increase in CPU time. The ability to keep orbitals localized in an ab initio molecular-dynamics calculation is a crucial ingredient in the development of emerging linear scaling approaches

  17. Ab-initio electronic structure calculations and properties of [Si{sub x}Sn{sub 1−x}]{sub 3}N{sub 4} ternary nitrides

    Energy Technology Data Exchange (ETDEWEB)

    Pavloudis, Th. [Department of Physics, Aristotle University of Thessaloniki, GR-54124 Thessaloniki (Greece); Zervos, M. [Nanostructured Materials and Devices Laboratory, Department of Mechanical and Manufacturing Engineering, PO Box 20537, Nicosia 1678 (Cyprus); Komninou, Ph. [Department of Physics, Aristotle University of Thessaloniki, GR-54124 Thessaloniki (Greece); Kioseoglou, J., E-mail: sifisl@auth.gr [Department of Physics, Aristotle University of Thessaloniki, GR-54124 Thessaloniki (Greece)

    2016-08-31

    We carry out ab initio electronic structure calculations of (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} using density functional theory with projector augmented-wave potentials under the generalized gradient approximation. We find that the energetically favorable structure of Sn{sub 3}N{sub 4} is the face-centered cubic spinel structure, followed by the hexagonal structure which has energy band gaps of 1.85 eV and 1.44 eV respectively. The (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} ternary compound can exhibit both cubic and hexagonal crystal structures over the full range of x. However, the cubic structure is found to be energetically favorable for x < 0.3 above which the hexagonal structure of (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} dominates. The energy band gap can be tuned continuously from 1.44 eV up to 5.8 eV in the case of the hexagonal crystal structure of (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} and from 1.85 eV to 4.82 eV in the case of cubic (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4}. Nevertheless the energy gap of (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} is direct only for x < 0.3 when it is cubic and for x < 0.5 when hexagonal. - Highlights: • (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} exhibits both cubic and hexagonal crystal structures. • The cubic structure is favorable for x < 0.3 and the hexagonal structure for x > 0.3. • The bandgap of hexagonal (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4} may be tuned from 1.44 eV up to 5.8 eV. • The bandgap may be tuned from 1.85 eV to 4.82 eV for the cubic (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4}. • Bandgaps are direct for x < 0.3 (cubic) and for x < 0.5 3 (hexagonal (Si{sub x}Sn{sub 1−x}){sub 3}N{sub 4}).

  18. Investigation of the Hydroxylation Mechanism of Noncoupled Copper Oxygenases by Ab Initio Molecular Dynamics Simulations

    Czech Academy of Sciences Publication Activity Database

    Meliá, C.; Ferrer, S.; Řezáč, Jan; Parisel, O.; Reinaud, O.; Moliner, V.; de la Lande, A.

    2013-01-01

    Roč. 19, č. 51 (2013), s. 17328-17337 ISSN 0947-6539 Institutional support: RVO:61388963 Keywords : ab initio calculations * copper * electron transfer * enzymes * molecular dynamics * reaction mechanisms Subject RIV: CC - Organic Chemistry Impact factor: 5.696, year: 2013

  19. Ab-initio modeling of an iron laser-induced plasma: Comparison between theoretical and experimental atomic emission spectra

    International Nuclear Information System (INIS)

    Colgan, J.; Judge, E.J.; Kilcrease, D.P.; Barefield, J.E.

    2014-01-01

    We report on efforts to model the Fe emission spectrum generated from laser-induced breakdown spectroscopy (LIBS) measurements on samples of pure iron oxide (Fe 2 O 3 ). Our modeling efforts consist of several components. We begin with ab-initio atomic structure calculations performed by solving the Hartree–Fock equations for the neutral and singly ionized stages of Fe. Our energy levels are then adjusted to their experimentally known values. The atomic transition probabilities and atomic collision quantities are also computed in an ab-initio manner. We perform LTE or non-LTE calculations that generate level populations and, subsequently, an emission spectrum for the iron plasma for a range of electron temperatures and electron densities. Such calculations are then compared to the experimental spectrum. We regard our work as a preliminary modeling effort that ultimately strives towards the modeling of emission spectra from even more complex samples where less atomic data are available. - Highlights: • LIBS plasma of iron oxide • Ab-initio theoretical Modeling • Discussion of LTE versus non-LTE criteria and assessment • Boltzmann plots for Fe—determination of when LTE is a valid assumption • Emission spectra for Fe—comparison of theoretical modeling and measurement: good agreement obtained

  20. Improved parametric fits for the HeH2 ab initio energy surface

    International Nuclear Information System (INIS)

    Muchnick, P.

    1992-01-01

    A brief history of the development of ab initio calculations for the HeH 2 quasi-molecule energy surface, and the parametric fits to these ab initio calculations, is presented. The concept of 'physical reasonableness' of the parametric fit is discussed. Several new improved parametric fits for the energy surface, meeting these requirements, are then proposed. One fit extends the Russek-Garcia parametric fit for the deep repulsion region to include r-dependent parameters, resulting in a more physically reasonable fit with smaller average error. This improved surface fit is applied to quasi-elastic collisions of He on H 2 in the impulse approximation. Previous classical calculations of the scaled inelastic vibrorotational excitation energy distributions are improved with this more accurate parametric fit of the energy surface and with the incorporation of quantum effects in vibrational excitation. It is shown that Sigmund's approach in developing his scaling law is incomplete in the contribution of the three-body interactions to vibrational excitation of the H 2 molecule is concerned. The Sigmund theory is extended to take into account for r-dependency of three-body interactions. A parametric fit for the entire energy surface from essentially 0 ≤R≤∞ and 1.2≤r≤1.6 a.u., where R is the intermolecular spacing and r is the hydrogen bonding length, is also presented. This fit is physically reasonable in all asymptotic limits. This first, full surface parametric fit is based primarily upon a composite of ab initio studies by Russek and Garcia and Meyer, Hariharan and Kutzelnigg. Parametric fits for the H 2 (1sσ g ) 2 , H 2 + (1sσ g ), H 2 + (2pσ u ) and (LiH 2 ) + energy surfaces are also presented. The new parametric fits for H 2 , H 2 + (1sσ g ) are shown to be improvements over the well-known Morse potentials for these surfaces

  1. Computationally efficient and quantitatively accurate multiscale simulation of solid-solution strengthening by ab initio calculation

    Czech Academy of Sciences Publication Activity Database

    Ma, D.; Friák, Martin; von Pezold, J.; Raabe, D.; Neugebauer, J.

    2015-01-01

    Roč. 85, FEB (2015), s. 53-66 ISSN 1359-6454 Institutional support: RVO:68081723 Keywords : Solid-solution strengthening * DFT * Peierls–Nabarro model * Ab initio * Al alloys Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 5.058, year: 2015

  2. Efficacy of the semiempirical sparkle model as compared to ECP ab-initio calculations for the prediction of ligand field parameters of europium (III) complexes

    International Nuclear Information System (INIS)

    Freire, Ricardo O.; Rocha, Gerd B.; Albuquerque, Rodrigo Q.; Simas, Alfredo M.

    2005-01-01

    The second version of the sparkle model for the calculation of lanthanide complexes (SMLC II) as well as ab-initio calculations (HF/STO-3G and HF/3-21G) have been used to calculate the geometries of a series of europium (III) complexes with different coordination numbers (CN=7, 8 and 9), ligating atoms (O and N) and ligands (mono, bi and polydentate). The so-called ligand field parameters, Bqk's, have been calculated from both SMLC II and ab-initio optimized structures and compared to the ones calculated from crystallographic data. The results show that the SMLC II model represents a significant improvement over the previous version (SMLC) and has given good results when compared to ab-initio methods, which demand a much higher computational effort. Indeed, ab-initio methods take around a hundred times more computing time than SMLC. As such, our results indicate that our sparkle model can be a very useful and a fast tool when applied to the prediction of both ground state geometries and ligand field parameters of europium (III) complexes

  3. Ab initio molecular dynamics approach to a quantitative description of ion pairing in water

    Czech Academy of Sciences Publication Activity Database

    Pluhařová, Eva; Maršálek, Ondřej; Schmidt, B.; Jungwirth, Pavel

    2013-01-01

    Roč. 4, č. 23 (2013), s. 4177-4181 ISSN 1948-7185 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : ion pairing * charge transfer * water * ab initio molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.687, year: 2013

  4. Tailoring magnetoresistance at the atomic level: An ab initio study

    KAUST Repository

    Tao, Kun; Stepanyuk, V. S.; Rungger, I.; Sanvito, S.

    2012-01-01

    The possibility of manipulating the tunneling magnetoresistance (TMR) of antiferromagnetic nanostructures is predicted in the framework of ab initio calculations. By the example of a junction composed of an antiferromagnetic dimer and a spin-polarized scanning tunneling microscopy tip we show that the TMR can be tuned and even reversed in sign by lateral and vertical movements of the tip. Moreover, our finite-bias calculations demonstrate that the magnitude and the sign of the TMR can also be tuned by an external voltage. © 2012 American Physical Society.

  5. Tailoring magnetoresistance at the atomic level: An ab initio study

    KAUST Repository

    Tao, Kun

    2012-01-05

    The possibility of manipulating the tunneling magnetoresistance (TMR) of antiferromagnetic nanostructures is predicted in the framework of ab initio calculations. By the example of a junction composed of an antiferromagnetic dimer and a spin-polarized scanning tunneling microscopy tip we show that the TMR can be tuned and even reversed in sign by lateral and vertical movements of the tip. Moreover, our finite-bias calculations demonstrate that the magnitude and the sign of the TMR can also be tuned by an external voltage. © 2012 American Physical Society.

  6. Ammonia-hydrogen bromide and ammonia-hydrogen iodide complexes: anion photoelectron and ab initio studies.

    Science.gov (United States)

    Eustis, S N; Whiteside, A; Wang, D; Gutowski, M; Bowen, K H

    2010-01-28

    The ammonia-hydrogen bromide and ammonia-hydrogen iodide, anionic heterodimers were studied by anion photoelectron spectroscopy. In complementary studies, these anions and their neutral counterparts were also investigated via ab initio theory at the coupled cluster level. In both systems, neutral NH(3)...HX dimers were predicted to be linear, hydrogen-bonded complexes, whereas their anionic dimers were found to be proton-transferred species of the form, (NH(4)(+)X(-))(-). Both experimentally measured and theoretically predicted vertical detachment energies (VDE) are in excellent agreement for both systems, with values for (NH(4)(+)Br(-))(-) being 0.65 and 0.67 eV, respectively, and values for (NH(4)(+)I(-))(-) being 0.77 and 0.81 eV, respectively. These systems are discussed in terms of our previous study of (NH(4)(+)Cl(-))(-).

  7. Structural properties of iron nitride on Cu(100): An ab-initio molecular dynamics study

    KAUST Repository

    Heryadi, Dodi

    2011-01-01

    Due to their potential applications in magnetic storage devices, iron nitrides have been a subject of numerous experimental and theoretical investigations. Thin films of iron nitride have been successfully grown on different substrates. To study the structural properties of a single monolayer film of FeN we have performed an ab-initio molecular dynamics simulation of its formation on a Cu(100) substrate. The iron nitride layer formed in our simulation shows a p4gm(2x2) reconstructed surface, in agreement with experimental results. In addition to its structural properties, we are also able to determine the magnetization of this thin film. Our results show that one monolayer of iron nitride on Cu(100) is ferromagnetic with a magnetic moment of 1.67 μ B. © 2011 Materials Research Society.

  8. Efficient approach to compute melting properties fully from ab initio with application to Cu

    Science.gov (United States)

    Zhu, Li-Fang; Grabowski, Blazej; Neugebauer, Jörg

    2017-12-01

    Applying thermodynamic integration within an ab initio-based free-energy approach is a state-of-the-art method to calculate melting points of materials. However, the high computational cost and the reliance on a good reference system for calculating the liquid free energy have so far hindered a general application. To overcome these challenges, we propose the two-optimized references thermodynamic integration using Langevin dynamics (TOR-TILD) method in this work by extending the two-stage upsampled thermodynamic integration using Langevin dynamics (TU-TILD) method, which has been originally developed to obtain anharmonic free energies of solids, to the calculation of liquid free energies. The core idea of TOR-TILD is to fit two empirical potentials to the energies from density functional theory based molecular dynamics runs for the solid and the liquid phase and to use these potentials as reference systems for thermodynamic integration. Because the empirical potentials closely reproduce the ab initio system in the relevant part of the phase space the convergence of the thermodynamic integration is very rapid. Therefore, the proposed approach improves significantly the computational efficiency while preserving the required accuracy. As a test case, we apply TOR-TILD to fcc Cu computing not only the melting point but various other melting properties, such as the entropy and enthalpy of fusion and the volume change upon melting. The generalized gradient approximation (GGA) with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional and the local-density approximation (LDA) are used. Using both functionals gives a reliable ab initio confidence interval for the melting point, the enthalpy of fusion, and entropy of fusion.

  9. H3+: Ab initio calculation of the vibration spectrum

    International Nuclear Information System (INIS)

    Carney, G.D.; Porter, R.N.

    1976-01-01

    The vibration spectrum of H 3 + is calculated from the representation of a previously reported [J. Chem Phys. 60, 4251 (1974)] ab initio potential-energy surface in a fifth degree Simons--Parr--Finlan (SPF) expansion. Morse- and harmonic-oscillator basis functions are used to describe the motions of the three oscillators and the Harris--Engerholm--Gwinn quadrature technique is used to obtain matrix elements of the Hamiltonian in the basis of vibrational configurations. Our variational method is thus analogous to configuration--interaction calculations for electronic states. The ground state is found to have a zero-point energy of 4345 cm -1 and a vibrationally averaged geometry of R 1 =R 2 =0.91396 A, theta=60.0012degree, where theta is the angle between the two equivalent bonds. The transition frequencies for the E and A 1 fundamentals are nu-bar/sub E/=2516 cm -1 and nu-bar/sub A/=3185 cm -1 and those for the corresponding first overtones of the bending mode are 2nu-bar/sub E/=5004 +- 4 cm -1 and 2nu-bar/sub A/=4799 cm -1 . The first overtone of the breathing mode is 6264 cm -1 . The first-excited A 1 vibration state is metastable with a dipole--radiation lifetime of 3 sec. Transition frequencies, Einstein coefficients, and lifetimes are reported for a total of 21 transitions. Analysis of results for Dunham number and normal-coordinate expansions in comparison with those for SPF expansion show the latter to be superior for ab initio vibrational calculations. A scheme for possible direct measurement of the fundamental A 1 and E vibrational bands is suggested

  10. On the room-temperature phase diagram of high pressure hydrogen: An ab initio molecular dynamics perspective and a diffusion Monte Carlo study

    International Nuclear Information System (INIS)

    Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge

    2014-01-01

    The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results

  11. From empirical to ab initio: transferable potentials in the atomistic simulation of amorphous carbons

    International Nuclear Information System (INIS)

    Marks, N.A.; Goringe, C.M.; McKenzie, D.R.; McCulloch, D.G.; Royal Melbourne Institute of Technology University, Melbourne, VIC

    2000-01-01

    Full text: Silicon is often described as the prototype covalent material, and when it comes to developing atomistic models this situation is well described by the sentiment that 'everything works for silicon'. The same cannot be said for carbon though, where the interaction potential has always proved problematical, be it with empirical, tight-binding or ab initio methods. Thus far the most decisive contributions to understanding amorphous carbon networks have come from ab initio simulations using the Car-Parrinello method, where the fully quantum treatment of the valence electrons has provided unexpected insight into the local structure. However such first principles calculations are restricted spatially and temporally to systems with approximately 100 atoms and times of order one picosecond. There is therefore demand for less expensive techniques capable of resolving important questions whose solution can only to found with larger simulations running for longer times. In the case of tetrahedral amorphous carbon, such issues include the release of compressive stress through annealing, the origin of graphitic surface layers and the nature of the film growth process and thermal spike. Against this background tight-binding molecular dynamics has emerged as a popular alternative to first principles methods, and our group has an ongoing program to understand film growth using one of the efficient variants of tight-binding. Another direction of research is a new empirical potential based on the Environment Dependent Interaction Potential (EDIP) recently developed for silicon. The EDIP approach represents a promising direction for empirical potentials through its use of ab initio data to motivate the functional form as well as the more conventional parametrisation. By inverting ab initio cohesive energy curves the authors of EDIP arrived at a pair potential expression which reduces to the well-known Stillinger-Weber form at integer coordination, while providing

  12. Crystallization and preliminary X-ray analysis of AbsC, a novel regulator of antibiotic production in Streptomyces coelicolor

    International Nuclear Information System (INIS)

    Stevenson, Clare E. M.; Kock, Holger; Mootien, Saraspadee; Davies, Sîan C.; Bibb, Mervyn J.; Lawson, David M.

    2007-01-01

    A novel regulator of antibiotic production in S. coelicolor, AbsC, has been crystallized in space group P2 1 2 1 2 1 . X-ray data to 2.25 Å resolution were collected on station PX 14.1 at Daresbury. Crystals of recombinant AbsC (subunit MW = 18 313 Da; 158 amino acids), a novel regulator of antibiotic production from Streptomyces coelicolor, were grown by vapour diffusion. The protein crystallizes in space group P2 1 2 1 2 1 , with unit-cell parameters a = 43.53, b = 121.30, c = 143.75 Å. Native data to a resolution of 2.25 Å were recorded at station PX 14.1 (Daresbury) from a single crystal. Preliminary analysis of these data suggests that the asymmetric unit contains four copies of the AbsC monomer, giving an estimated solvent content of 47.0%. AbsC belongs to the MarR family of proteins that mediate ligand-responsive transcriptional control

  13. Efficient Ab-Initio Electron Transport Calculations for Heterostructures by the Nonequilibrium Green’s Function Method

    Directory of Open Access Journals (Sweden)

    Hirokazu Takaki

    2014-01-01

    Full Text Available We present an efficient computation technique for ab-initio electron transport calculations based on density functional theory and the nonequilibrium Green’s function formalism for application to heterostructures with two-dimensional (2D interfaces. The computational load for constructing the Green’s functions, which depends not only on the energy but also on the 2D Bloch wave vector along the interfaces and is thus catastrophically heavy, is circumvented by parallel computational techniques with the message passing interface, which divides the calculations of the Green’s functions with respect to energy and wave vectors. To demonstrate the computational efficiency of the present code, we perform ab-initio electron transport calculations of Al(100-Si(100-Al(100 heterostructures, one of the most typical metal-semiconductor-metal systems, and show their transmission spectra, density of states (DOSs, and dependence on the thickness of the Si layers.

  14. Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Matsushita, Y., E-mail: kurita@cs.tut.ac.jp; Murakawa, T., E-mail: kurita@cs.tut.ac.jp; Shimamura, K., E-mail: kurita@cs.tut.ac.jp; Oishi, M., E-mail: kurita@cs.tut.ac.jp; Ohyama, T., E-mail: kurita@cs.tut.ac.jp; Kurita, N., E-mail: kurita@cs.tut.ac.jp [Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580 (Japan)

    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.

  15. Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

    International Nuclear Information System (INIS)

    Matsushita, Y.; Murakawa, T.; Shimamura, K.; Oishi, M.; Ohyama, T.; Kurita, N.

    2015-01-01

    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

  16. Cooperative effects in spherical spasers: Ab initio analytical model

    Science.gov (United States)

    Bordo, V. G.

    2017-06-01

    A fully analytical semiclassical theory of cooperative optical processes which occur in an ensemble of molecules embedded in a spherical core-shell nanoparticle is developed from first principles. Both the plasmonic Dicke effect and spaser generation are investigated for the designs in which a shell/core contains an arbitrarily large number of active molecules in the vicinity of a metallic core/shell. An essential aspect of the theory is an ab initio account of the feedback from the core/shell boundaries which significantly modifies the molecular dynamics. The theory provides rigorous, albeit simple and physically transparent, criteria for both plasmonic superradiance and surface plasmon generation.

  17. Ab initio Defect Energetics in LaBO3 Perovskite Solid Oxide Fuel Cell Materials

    DEFF Research Database (Denmark)

    Lee, Yueh-Lin; Morgan, Dane; Kleis, Jesper

    2009-01-01

    Perovskite materials of the form ABO3 are a promising family of compounds for use in solid oxide fuel cell (SOFC) cathodes. Study of the physics of these compounds under SOFC conditions with ab initio methods is particularly challenging due to high temperatures, exchange of oxygen with O2 gas...

  18. Ab initio calculation of positron distribution, ACAR and lifetime in TTF-TCNQ

    International Nuclear Information System (INIS)

    Ishibashi, Shoji; Kohyama, Masanori

    2000-01-01

    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.

  19. X-ray Outburst in Mira A

    OpenAIRE

    Karovska, M.; Schlegel, E.; Hack, W.; Wood, B.

    2005-01-01

    We report here the Chandra ACIS-S detection of a bright soft X-ray transient in the Mira AB interacting symbiotic-like binary. We resolved the system for the first time in the X-rays. Using Chandra and HST images we determined that the unprecedented outburst is likely associated with the cool AGB star (Mira A), the prototype of Mira-type variables. X-rays have never before been detected from an AGB star, and the recent activity signals that the system is undergoing dramatic changes. The total...

  20. Ductility improvement of Mg alloys by solid solution: Ab initio modeling, synthesis and mechanical properties

    Czech Academy of Sciences Publication Activity Database

    Sandlöbes, S.; Pei, Z.; Friák, Martin; Zhu, L.-F.; Wang, F.; Zaefferer, S.; Raabe, D.; Neugebauer, J.

    2014-01-01

    Roč. 70, MAY (2014), s. 92-104 ISSN 1359-6454 Grant - others:GA MŠk(CZ) LM2010005 Institutional support: RVO:68081723 Keywords : Magnesium * Rare-earth elements * Ductility * Modeling * Ab initio Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 4.465, year: 2014

  1. Advances and applications in the FIREBALL ab initio tight-binding molecular-dynamics formalism

    Czech Academy of Sciences Publication Activity Database

    Lewis, J.P.; Jelínek, Pavel; Ortega, J.; Demkov, A.A.; Trabada, D.G.; Haycock, B.; Wang, H.; Adams, G.; Tomfohr, J.K.; Abad, E.; Wang, Ho.; Drabold, D.A.

    2011-01-01

    Roč. 248, č. 9 (2011), 1989-2007 ISSN 0370-1972 R&D Projects: GA ČR GA202/09/0545; GA ČR GAP204/10/0952 Grant - others:AVČR(CZ) M100100904 Institutional research plan: CEZ:AV0Z10100521 Keywords : DFT * ab initio molecular-dynamics Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.316, year: 2011

  2. Mirnacle: machine learning with SMOTE and random forest for improving selectivity in pre-miRNA ab initio prediction.

    Science.gov (United States)

    Marques, Yuri Bento; de Paiva Oliveira, Alcione; Ribeiro Vasconcelos, Ana Tereza; Cerqueira, Fabio Ribeiro

    2016-12-15

    MicroRNAs (miRNAs) are key gene expression regulators in plants and animals. Therefore, miRNAs are involved in several biological processes, making the study of these molecules one of the most relevant topics of molecular biology nowadays. However, characterizing miRNAs in vivo is still a complex task. As a consequence, in silico methods have been developed to predict miRNA loci. A common ab initio strategy to find miRNAs in genomic data is to search for sequences that can fold into the typical hairpin structure of miRNA precursors (pre-miRNAs). The current ab initio approaches, however, have selectivity issues, i.e., a high number of false positives is reported, which can lead to laborious and costly attempts to provide biological validation. This study presents an extension of the ab initio method miRNAFold, with the aim of improving selectivity through machine learning techniques, namely, random forest combined with the SMOTE procedure that copes with imbalance datasets. By comparing our method, termed Mirnacle, with other important approaches in the literature, we demonstrate that Mirnacle substantially improves selectivity without compromising sensitivity. For the three datasets used in our experiments, our method achieved at least 97% of sensitivity and could deliver a two-fold, 20-fold, and 6-fold increase in selectivity, respectively, compared with the best results of current computational tools. The extension of miRNAFold by the introduction of machine learning techniques, significantly increases selectivity in pre-miRNA ab initio prediction, which optimally contributes to advanced studies on miRNAs, as the need of biological validations is diminished. Hopefully, new research, such as studies of severe diseases caused by miRNA malfunction, will benefit from the proposed computational tool.

  3. Local versus global electronic properties of chalcopyrite alloys: X-ray absorption spectroscopy and ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Sarmiento-Pérez, Rafael; Botti, Silvana, E-mail: silvana.botti@univ-lyon1.fr [Institut Lumière Matière and ETSF, UMR5306 Université Lyon 1-CNRS, Université de Lyon, F-69622 Villeurbanne Cedex (France); Schnohr, Claudia S., E-mail: c.schnohr@uni-jena.de [Institut für Festkörperphysik, Friedrich-Schiller-Universität Jena, Max-Wien-Platz 1, 07743 Jena (Germany); Lauermann, Iver [Helmholtz-Zentrum Berlin für Materialien und Energie, Hahn-Meitner Platz 1, 14109 Berlin (Germany); Rubio, Angel [Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Departamento de Física de Materiales, Centro de Física de Materiales CSIC-MPC and DIPC, Universidad del País Vasco UPV/EHU, Avenida de Tolosa 72, E-20018 San Sebastián (Spain); Fritz Haber Institute, Max Planck Society, Faradayweg 4-6, 14195 Berlin (Germany); Johnson, Benjamin, E-mail: benjamin.johnson@alumni.tu-berlin.de [Fritz Haber Institute, Max Planck Society, Faradayweg 4-6, 14195 Berlin (Germany)

    2014-09-07

    Element-specific unoccupied electronic states of Cu(In, Ga)S{sub 2} were studied as a function of the In/Ga ratio by combining X-ray absorption spectroscopy with density functional theory calculations. The S absorption edge shifts with changing In/Ga ratio as expected from the variation of the band gap. In contrast, the cation edge positions are largely independent of composition despite the changing band gap. This unexpected behavior is well reproduced by our calculations and originates from the dependence of the electronic states on the local atomic environment. The changing band gap arises from a changing spatial average of these localized states with changing alloy composition.

  4. Theoretical study of silicon carbide under irradiation at the nano scale: classical and ab initio modelling

    International Nuclear Information System (INIS)

    Lucas, G.

    2006-10-01

    The behaviour of silicon carbide under irradiation has been studied using classical and ab initio simulations, focusing on the nano scale elementary processes. First, we have been interested in the calculation of threshold displacement energies, which are difficult to determine both experimentally and theoretically, and also the associated Frenkel pairs. In the framework of this thesis, we have carried out simulations in classical and ab initio molecular dynamics. For the classical approach, two types of potentials have been used: the Tersoff potential, which led to non satisfactory results, and a new one which has been developed during this thesis. This potential allows a better modelling of SiC under irradiation than most of the empirical potentials available for SiC. It is based on the EDIP potential, initially developed to describe defects in silicon, that we have generalized to SiC. For the ab initio approach, the feasibility of the calculations has been validated and average energies of 19 eV for the C and 38 eV for the Si sublattices have been determined, close to the values empirically used in the fusion community. The results obtained with the new potential EDIP are globally in agreement with those values. Finally, the elementary processes involved in the crystal recovery have been studied by calculating the stability of the created Frenkel pairs and determining possible recombination mechanisms with the nudged elastic band method. (author)

  5. Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Dytrych, T. [Academy of Sciences of the Czech Republic (ASCR), Prague (Czech Republic); Louisiana State Univ., Baton Rouge, LA (United States); Maris, Pieter [Iowa State Univ., Ames, IA (United States); Launey, K. D. [Louisiana State Univ., Baton Rouge, LA (United States); Draayer, J. P. [Louisiana State Univ., Baton Rouge, LA (United States); Vary, James [Iowa State Univ., Ames, IA (United States); Langr, D. [Czech Technical Univ., Prague (Czech Republic); Aerospace Research and Test Establishment, Prague (Czech Republic); Saule, E. [Univ. of North Carolina, Charlotte, NC (United States); Caprio, M. A. [Univ. of Notre Dame, IN (United States); Catalyurek, U. [The Ohio State Univ., Columbus, OH (United States). Dept. of Electrical and Computer Engineering; Sosonkina, M. [Old Dominion Univ., Norfolk, VA (United States)

    2016-06-09

    We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for 6Li and 12C in large harmonic oscillator model spaces and SU(3)-selected subspaces. We demonstrate LSU3shell's strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and signi cant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis a ords memory savings in calculations of states with a fixed total angular momentum in large model spaces while exactly preserving translational invariance.

  6. Ab-initio electronic and magnetic properties of Fe-Al alloys

    Directory of Open Access Journals (Sweden)

    Apiñaniz, E.

    2000-06-01

    Full Text Available This work presents ab-initio self-consistent calculations performed with the TB-LMTO code to study the different phases of the Fe-Al phase diagram, corresponding to the ordered structures B2, DO3 and B32 and for Fe50Al50 and Fe3Al compositions. Both, unpolarized and spin-polarized calculations have been performed to deduce the energetic difference between the paramagnetic and ferromagnetic state of the corresponding structure. Calculations for the disordered structures have also been performed for the previously mentioned compositions. These results show that by disordering the alloy magnetism is enhanced and that the equilibrium lattice parameter increases.

    En este trabajo se presentan cálculos autoconsistentes ab-initio realizados con el método TB-LMTO (Tight Binding Linear Muffin Tin Orbital con el fin de estudiar las diferentes estructuras que se presentan en el diagrama de fases de las aleaciones Fe-Al. Se han estudiado las estructuras ordenadas B2, DO3 y B32 para las siguientes concentraciones: Fe50Al50 y Fe3Al. Asimismo, se han realizado cálculos teniendo y sin tener en cuenta la polarización de spin con el fin de poder deducir la diferencia energética entre los estados ferromágneticos y paramágneticos de la misma estructura. Por otra parte se han realizado estos mismos cálculos para estructuras desordenadas y las mismas concentraciones. Los resultados muestran que mediante el desorden aumenta el magnetismo de estas aleaciones y crece el parámetro de red.

  7. Ab initio study of structural, electronic, optical, and vibrational properties of Zn x S y ( x + y = 2 to 5) nanoclusters

    Science.gov (United States)

    Yadav, P. S.; Pandey, D. K.; Agrawal, S.; Agrawal, B. K.

    2010-03-01

    An ab initio study of the stability, structural, electronic. and optical properties has been performed for 46 zinc sulfide nanoclusters Zn x S y ( x + y = n = 2 to 5). Five out of them are seen to be unstable as their vibrational frequencies are found to be imaginary. A B3LYP-DFT/6-311G(3df) method is employed to optimize the geometries and a TDDFT method is used for the study of the optical properties. The binding energies (BE), HOMO-LUMO gaps and the bond lengths have been obtained for all the clusters. For the ZnS2, ZnS3, and ZnS4 nanoclusters, our stable structures are seen to be different from those obtained earlier by using the effective core potentials. We have also considered the zero point energy (ZPE) corrections ignored by the earlier workers. For a fixed value of n, we designate the most stable structure the one, which has maximum final binding energy per atom. The adiabatic and vertical ionization potentials (IP) and electron affinities (EA), charges on the atoms, dipole moments, optical properties, vibrational frequencies, infrared intensities, relative infrared intensities, and Raman scattering activities have been investigated for the most stable structures. The nanoclusters containing large number of S atoms for each n is found to be most stable. The HOMO-LUMO gap decreases from n = 2-3 and then increases above n = 3. The IP and EA both fluctuate with the cluster size n. The optical absorption is quite weak in visible region but strong in the ultraviolet region in most of the nanoclusters except a few. The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every nanocluster and may be used to characterize a specific nanocluster. The growth of most stable nanoclusters may be possible in the experiments.

  8. Ab initio study on electron excitation and electron transfer in tryptophan-tyrosine system

    International Nuclear Information System (INIS)

    Tong Jing; Li Xiangyuan

    2002-01-01

    In this article, ab initio calculation has been performed to evaluate the transition energy of electronic excitation in tryptophan and tyrosine by using semiempirical molecular orbital method AM1 and complete active space self-consistent field method. The solvent effect has been considered by means of the conductor-like screening model. After geometric optimizations of isolated tryptophan and tyrosine, and their corresponding radicals and cations, reaction heat of these electron transfer reactions have been obtained by the means of complete active space self-consistent field method. The transition energies from the ground state, respectively, to the lowest excited state and to the lowest triplet state of these two amino acids are also calculated and compared with the experimentally observed values. The ionization potential and electron affinity are also calculated for tryptophan and tyrosine employing Koopmans' theorem and ab initio calculation. Compared with the experimental measurements, the theoretical results are found satisfactory. Theoretical results give good explanations on the experimental phenomena that N 3 · can preferably oxide the side chain of tryptophan residue and then the electron transfer from tyrosine residue to tryptophan residue follows in peptides involving tryptophan and tyrosine

  9. Raman Spectroscopy and Ab-Initio Model Calculations on Ionic Liquids:Invited Review

    OpenAIRE

    Berg, Rolf W.

    2007-01-01

    A review of the recent developments in the study and understanding of room temperature ionic liquids are given. An intimate picture of how and why these liquids are not crystals at ambient conditions is attempted, based on evidence from crystallographical results combined with vibrational spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT-Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methylimidazolium ([...

  10. The onset of ion solvation by ab initio calculations: Comparison of water and methanol

    Czech Academy of Sciences Publication Activity Database

    Pluhařová, Eva; Jungwirth, Pavel

    2008-01-01

    Roč. 73, 6/7 (2008), s. 733-744 ISSN 0010-0765 R&D Projects: GA MŠk LC512; GA ČR GA203/07/1006 Institutional research plan: CEZ:AV0Z40550506 Keywords : ions * water cluster * methanol * ab initio calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.784, year: 2008

  11. Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions

    International Nuclear Information System (INIS)

    Wang, Yimin; Bowman, Joel M.; Kamarchik, Eugene

    2016-01-01

    We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na + H 2 O, F − H 2 O, and Cl − H 2 O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H 2 O potentials are permutationally invariant fits to roughly 20 000 coupled cluster CCSD(T) energies (awCVTZ basis for Na + and aVTZ basis for Cl − and F − ), over a large range of distances and H 2 O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.

  12. Vibrational inelastic and charge transfer processes in H++H2 system: An ab initio study

    Science.gov (United States)

    Amaran, Saieswari; Kumar, Sanjay

    2007-12-01

    State-resolved differential cross sections, total and integral cross sections, average vibrational energy transfer, and the relative probabilities are computed for the H++H2 system using the newly obtained ab initio potential energy surfaces at the full CI/cc-pVQZ level of accuracy which allow for both the direct vibrational inelastic and the charge transfer processes. The quantum dynamics is treated within the vibrational close-coupling infinite-order-sudden approximation approach using the two ab initio quasidiabatic potential energy surfaces. The computed collision attributes for both the processes are compared with the available state-to-state scattering experiments at Ec.m.=20eV. The results are in overall good agreement with most of the observed scattering features such as rainbow positions, integral cross sections, and relative vibrational energy transfers. A comparison with the earlier theoretical study carried out on the semiempirical surfaces (diatomics in molecules) is also made to illustrate the reliability of the potential energy surfaces used in the present work.

  13. Ab initio study of hydrogen adsorption on benzenoid linkers in metal-organic framework materials

    International Nuclear Information System (INIS)

    Gao Yi; Zeng, X C

    2007-01-01

    We have computed the energies of adsorption of molecular hydrogen on a number of molecular linkers in metal-organic framework solid materials using density functional theory (DFT) and ab initio molecular orbital methods. We find that the hybrid B3LYP (Becke three-parameter Lee-Yang-Parr) DFT method gives a qualitatively incorrect prediction of the hydrogen binding with benzenoid molecular linkers. Both local-density approximation (LDA) and generalized gradient approximation (GGA) DFT methods are inaccurate in predicting the values of hydrogen binding energies, but can give a qualitatively correct prediction of the hydrogen binding. When compared to the more accurate binding-energy results based on the ab initio Moeller-Plesset second-order perturbation (MP2) method, the LDA results may be viewed as an upper limit while the GGA results may be viewed as a lower limit. Since the MP2 calculation is impractical for realistic metal-organic framework systems, the combined LDA and GGA calculations provide a cost-effective way to assess the hydrogen binding capability of these systems

  14. Ab initio molecular dynamics in a finite homogeneous electric field.

    Science.gov (United States)

    Umari, P; Pasquarello, Alfredo

    2002-10-07

    We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

  15. Hydrogen atom injection into carbon surfaces by comparison between Monte-Carlo, molecular dynamics and ab-initio calculations

    International Nuclear Information System (INIS)

    Ito, A.; Kenmotsu, T.; Kikuhara, Y.; Inai, K.; Ohya, K.; Wang, Y.; Irle, S.; Morokuma, K.; Nakamura, H.

    2009-01-01

    Full text: To understand the plasma-wall interaction on divertor plates, we investigate the interaction of hydrogen atoms and carbon materials used in the high heat flux components by the use of the following simulations. Monte-Carlo (MC) method based on binary collision approximation can calculate the sputtering process of hydrogen atoms on the carbon material quickly. Classical molecular dynamics (MD) method employs multi-body potential models and can treat realistic structures of crystal and molecule. The ab-initio method can calculate electron energy in quantum mechanics, which is regarded as realistic potential for atoms. In the present paper, the interaction of the hydrogen and the carbon material is investigated using the multi-scale (MC, MD and ab-initio) methods. The bombardment of hydrogen atoms onto the carbon material is simulated by the ACAT-code of the MC method, which cannot represent the structure of crystal, and the MD method using modified reactive empirical bond order (REBO) potential, which treats single crystal graphite and amorphous carbon. Consequently, we clarify that the sputtering yield and the reflection rate calculated by the ACAT-code agree with those on the amorphous carbon calculated by the MD. Moreover, there are many kinds of REBO potential for the MD. Adsorption, reflection and penetration rates between a hydrogen atom and a graphene surface are calculated by the MD simulations using the two kinds of potential model. For the incident energy of less than 1 eV, the MD simulation using the modified REBO potential, which is based on Brenner's REBO potential in 2002, shows that reflection is dominant, while the most popular Brenner's REBO potential in 1990 shows that adsorption is dominant. This reflection of the low energy injection is caused by a small potential barrier for the hydrogen atom in the modified REBO potential. The small potential barrier is confirmed by the ab-initio calculations, which are hybrid DFT (B3LYP/cc-pVDZ), ab-initio

  16. Magnetism and metal insulator transition in FeSi and FeGe. Ab Initio investigations of the electronic structure; Magnetismus und Metall-Isolator-Uebergang in FeSi und FeGe. Ab-initio-Untersuchungen der elektronischen Struktur

    Energy Technology Data Exchange (ETDEWEB)

    Neef, Matthias

    2007-03-19

    Aim of this thesis was to reach by a systematic study of different ab initio procedures an improved description of the electronic properties of FeSi and FeGe. Central result is the itinerant description of FeSi as a semiconductor in the neighbourhood of a ferromagnetic instability. The regardment of the nonlocal exchange in the effective one-particle approximation leads to a metastable magnetic state scarcely above the magnetic ground state. The application of the hybrid functional leads to a 1st order metal-isolator transition for large lattice parameters: FeSi transforms at increasement of the lattice parameter from an unmagnetic isolator to a magnetic metal. A similar behavior is found in the isostructural compound FeGe. The two systems FeSi and FeGe were systematically and detailedly analyzed by means of ab initio procedures. Thereby the structural, electronic, and magnetic properties were studied with DFT and HF calculations. Both calculations with spin polarization and without spin polarization were performed.

  17. Ab Initio Analysis of Auger-Assisted Electron Transfer.

    Science.gov (United States)

    Hyeon-Deuk, Kim; Kim, Joonghan; Prezhdo, Oleg V

    2015-01-15

    Quantum confinement in nanoscale materials allows Auger-type electron-hole energy exchange. We show by direct time-domain atomistic simulation and analytic theory that Auger processes give rise to a new mechanism of charge transfer (CT) on the nanoscale. Auger-assisted CT eliminates the renown Marcus inverted regime, rationalizing recent experiments on CT from quantum dots to molecular adsorbates. The ab initio simulation reveals a complex interplay of the electron-hole and charge-phonon channels of energy exchange, demonstrating a variety of CT scenarios. The developed Marcus rate theory for Auger-assisted CT describes, without adjustable parameters, the experimental plateau of the CT rate in the region of large donor-acceptor energy gap. The analytic theory and atomistic insights apply broadly to charge and energy transfer in nanoscale systems.

  18. Spin-Orbit Effect on the Molecular Properties of TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4): A Density Functional Theory and Ab Initio Study.

    Science.gov (United States)

    Moon, Jiwon; Kim, Joonghan

    2016-09-29

    Density functional theory (DFT) and ab initio calculations, including spin-orbit coupling (SOC), were performed to investigate the spin-orbit (SO) effect on the molecular properties of tellurium halides, TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4). SOC elongates the Te-X bond and slightly reduces the vibrational frequencies. Consideration of SOC leads to better agreement with experimental values. Møller-Plesset second-order perturbation theory (MP2) seriously underestimates the Te-X bond lengths. In contrast, B3LYP significantly overestimates them. SO-PBE0 and multireference configuration interactions with the Davidson correction (MRCI+Q), which include SOC via a state-interaction approach, give the Te-I bond length of TeI2 that matches the experimental value. On the basis of the calculated thermochemical energy and optimized molecular structure, TeI4 is unlikely to be stable. The use of PBE0 including SOC is strongly recommended for predicting the molecular properties of Te-containing compounds.

  19. Probing warm dense lithium by inelastic X-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Garcia Saiz, E; Riley, D [School of Mathematics and Physics, Queen' s University of Belfast, Belfast (United Kingdom); Gregori, G [Clarendon Laboratory, University of Oxford, Parks Road, Oxford (United Kingdom); Gregori, G; Clarke, R J; Neely, D; Notley, M M; Spindloe, C [Central Laser Facility, Rutherford Appleton Laboratory, Chilton, Didcot, OX (United Kingdom); Gericke, D O; Vorberger, J; Wunsch, K [Centre for Fusion, Space and Astrophysics, Department of Physics, University of Warwick, Coventry (United Kingdom); Barbrel, B; Koenig, M [Laboratoire pour l' Utilisation des Laser Intenses, Ecole Polytechnique - Universite Paris-6, 91 - Palaiseau (France); Freeman, R R; Weber, R L; Van Woerkom, L [Department of Physics, The Ohio State University, Columbus, Ohio (United States); Glenzer, S H; Landen, O L; Neumayer, P; Price, D [Lawrence Livermore National Laboratory, Livermore, California (United States); Khattak, F Y [Department of Physics, Kohat University of Science and Technology, Kohat-26000, NWFP (Pakistan); Pelka, A; Roth, M; Schollmeier, M [Institut fur Kernphysik, Technische Universitat Darmstadt (Germany)

    2008-10-15

    One of the grand challenges of contemporary physics is understanding strongly interacting quantum systems comprising such diverse examples as ultracold atoms in traps, electrons in high-temperature superconductors and nuclear matter. Warm dense matter, defined by temperatures of a few electron volts and densities comparable with solids, is a complex state of such interacting matter. Moreover, the study of warm dense matter states has practical applications for controlled thermonuclear fusion, where it is encountered during the implosion phase, and it also represents laboratory analogues of astrophysical environments found in the core of planets and the crusts of old stars. Here we demonstrate how warm dense matter states can be diagnosed and structural properties can be obtained by inelastic X-ray scattering measurements on a compressed lithium sample. Combining experiments and ab initio simulations enables us to determine its microscopic state and to evaluate more approximate theoretical models for the ionic structure. (authors)

  20. Ab initio calculation of the electronic spectrum of azobenzene dyes and its impact on the design of optical data storage materials

    DEFF Research Database (Denmark)

    Åstrand, Per-Olof; Ramanujam, P.S.; Hvilsted, Søren

    2000-01-01

    Electronic excitation energies of 16 azobenzene dyes have been calculated by ab initio methods within the second-order polarization propagator approximation (SOPPA). Good agreement with expriment is found for the lowest singlet and triplet states for both the trans- and cis-azobenzene molecules......, the experimental singlet π → π* transitions are reproduced for a set of azobenzene dyes with different electron donor and acceptor groups and the correct shifts in excitation energy are obtained for the different substituents. It has also been demonstrated that ab initio methods can be used to determine suitable...

  1. Quantitative verification of ab initio self-consistent laser theory.

    Science.gov (United States)

    Ge, Li; Tandy, Robert J; Stone, A D; Türeci, Hakan E

    2008-10-13

    We generalize and test the recent "ab initio" self-consistent (AISC) time-independent semiclassical laser theory. This self-consistent formalism generates all the stationary lasing properties in the multimode regime (frequencies, thresholds, internal and external fields, output power and emission pattern) from simple inputs: the dielectric function of the passive cavity, the atomic transition frequency, and the transverse relaxation time of the lasing transition.We find that the theory gives excellent quantitative agreement with full time-dependent simulations of the Maxwell-Bloch equations after it has been generalized to drop the slowly-varying envelope approximation. The theory is infinite order in the non-linear hole-burning interaction; the widely used third order approximation is shown to fail badly.

  2. One Size Fits All? Learning Conditions and Working Memory Capacity in "Ab Initio" Language Development

    Science.gov (United States)

    Sanz, Cristina; Lin, Hui-Ju; Lado, Beatriz; Stafford, Catherine A.; Bowden, Harriet W.

    2016-01-01

    The article summarizes results from two experimental studies (N = 23, N = 21) investigating the extent to which working memory capacity (WMC) intervenes in "ab initio" language development under two pedagogical conditions [± grammar lesson + input-based practice + explicit feedback]. The linguistic target is the use of morphosyntax to…

  3. Ab Initio Assessment of the Bonding in Disulfonates Containing Divalent Nitrogen and Phosphorus Atoms

    DEFF Research Database (Denmark)

    Andersen, Vinca Bonde; Berg, Rolf W.; Shim, Irene

    2017-01-01

    The iminodisulfonate, [N(SO3)2]3–, and phosphinodisulfonate, [P(SO3)2]3–, ions have been investigated by performing ab initio MP2/6-311+G**calculations. The nitrogen and phosphorus atoms as part of the ions are shown to be divalent with a negative charge and two lone pairs on the nitrogen...

  4. Introducing ab initio based neural networks for transition-rate prediction in kinetic Monte Carlo simulations

    Science.gov (United States)

    Messina, Luca; Castin, Nicolas; Domain, Christophe; Olsson, Pär

    2017-02-01

    The quality of kinetic Monte Carlo (KMC) simulations of microstructure evolution in alloys relies on the parametrization of point-defect migration rates, which are complex functions of the local chemical composition and can be calculated accurately with ab initio methods. However, constructing reliable models that ensure the best possible transfer of physical information from ab initio to KMC is a challenging task. This work presents an innovative approach, where the transition rates are predicted by artificial neural networks trained on a database of 2000 migration barriers, obtained with density functional theory (DFT) in place of interatomic potentials. The method is tested on copper precipitation in thermally aged iron alloys, by means of a hybrid atomistic-object KMC model. For the object part of the model, the stability and mobility properties of copper-vacancy clusters are analyzed by means of independent atomistic KMC simulations, driven by the same neural networks. The cluster diffusion coefficients and mean free paths are found to increase with size, confirming the dominant role of coarsening of medium- and large-sized clusters in the precipitation kinetics. The evolution under thermal aging is in better agreement with experiments with respect to a previous interatomic-potential model, especially concerning the experiment time scales. However, the model underestimates the solubility of copper in iron due to the excessively high solution energy predicted by the chosen DFT method. Nevertheless, this work proves the capability of neural networks to transfer complex ab initio physical properties to higher-scale models, and facilitates the extension to systems with increasing chemical complexity, setting the ground for reliable microstructure evolution simulations in a wide range of alloys and applications.

  5. Cost-Effective Method for Free-Energy Minimization in Complex Systems with Elaborated Ab Initio Potentials.

    Science.gov (United States)

    Bistafa, Carlos; Kitamura, Yukichi; Martins-Costa, Marilia T C; Nagaoka, Masataka; Ruiz-López, Manuel F

    2018-05-22

    We describe a method to locate stationary points in the free-energy hypersurface of complex molecular systems using high-level correlated ab initio potentials. In this work, we assume a combined QM/MM description of the system although generalization to full ab initio potentials or other theoretical schemes is straightforward. The free-energy gradient (FEG) is obtained as the mean force acting on relevant nuclei using a dual level strategy. First, a statistical simulation is carried out using an appropriate, low-level quantum mechanical force-field. Free-energy perturbation (FEP) theory is then used to obtain the free-energy derivatives for the target, high-level quantum mechanical force-field. We show that this composite FEG-FEP approach is able to reproduce the results of a standard free-energy minimization procedure with high accuracy, while simultaneously allowing for a drastic reduction of both computational and wall-clock time. The method has been applied to study the structure of the water molecule in liquid water at the QCISD/aug-cc-pVTZ level of theory, using the sampling from QM/MM molecular dynamics simulations at the B3LYP/6-311+G(d,p) level. The obtained values for the geometrical parameters and for the dipole moment of the water molecule are within the experimental error, and they also display an excellent agreement when compared to other theoretical estimations. The developed methodology represents therefore an important step toward the accurate determination of the mechanism, kinetics, and thermodynamic properties of processes in solution, in enzymes, and in other disordered chemical systems using state-of-the-art ab initio potentials.

  6. An experimental and ab initio study of the electronic spectrum of the jet-cooled F{sub 2}BO free radical

    Energy Technology Data Exchange (ETDEWEB)

    Grimminger, Robert; Clouthier, Dennis J., E-mail: dclaser@uky.edu [Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506-0055 (United States); Sheridan, Phillip M. [Department of Chemistry and Biochemistry, Canisius College, Buffalo, New York 14208 (United States)

    2014-04-28

    We have studied the B{sup ~} {sup 2}A{sub 1}–X{sup ~} {sup 2}B{sub 2} laser-induced fluorescence (LIF) spectrum of the jet-cooled F{sub 2}BO radical for the first time. The transition consists of a strong 0{sub 0}{sup 0} band at 446.5 nm and eight weak sequence bands to shorter wavelengths. Single vibronic level emission spectra obtained by laser excitation of individual levels of the B{sup ~} state exhibit two electronic transitions: a very weak, sparse B{sup ~}–X{sup ~} band system in the 450–500 nm region and a stronger, more extensive set of B{sup ~} {sup 2}A{sub 1}–A{sup ~} {sup 2}B{sub 1} bands in the 580–650 nm region. We have also performed a series of high level ab initio calculations to predict the electronic energies, molecular structures, vibrational frequencies, and rotational and spin-rotation constants in the X{sup ~} {sup 2}B{sub 2}, A{sup ~2}B{sub 1} and B{sup ~} {sup 2}A{sub 1} electronic states as an aid to the analysis of the experimental data. The theoretical results have been used as input for simulations of the rotationally resolved B{sup ~} {sup 2}A{sub 1}–X{sup ~} {sup 2}B{sub 2} 0{sub 0}{sup 0} LIF band and Franck-Condon profiles of the LIF and single vibronic level emission spectra. The agreement between the simulations obtained with purely ab initio parameters and the experimental spectra validates the geometries calculated for the ground and excited states and the conclusion that the radical has C{sub 2v} symmetry in the X{sup ~}, A{sup ~}, and B{sup ~} states. The spectra provide considerable new information about the vibrational energy levels of the X{sup ~} and A{sup ~} states, but very little for the B{sup ~} state, due to the very restrictive Franck-Condon factors in the LIF spectra.

  7. Ab initio study of isomerism of Li2AB2 molecules and Li2AB2+ ions with 16 valent electrons

    International Nuclear Information System (INIS)

    Charkin, O.P.; Klimenko, N.M.; MakKi, M.L.

    2000-01-01

    In the framework of MP2(6-31*//HF/6-31G + ZPE(HF/6-31G*) and MP4SDTQ/6-31G*//MP2/6-31G* + ZPE(MP2/6-31G*) approximations ab initio calculations of surfaces of potential energy of molecules of lithium salts of Li 2 AB 2 (Li 2 BeO 2 , L 2 MgO 2 , Li 2 BeS 2 , Li 2 MgS 2 , Li 2 CN 2 , Li 2 SiN 2 , Li 2 CP 2 ) type and ions of Li 2 AB 2 + (Li 2 BO 2 + , Li 2 AlO 2 + , Li 2 BS 2 + , Li 2 AlS 2 + , Li 2 N 3 + , Li 2 PN 2 + , Li 2 P 3 + ) type with 16 valent electrons are done. For oxide and nitride systems global minimum corresponds to symmetric linear structure D ∞h and for their sulfide and phosphorus analogues curved plane or unplane (C 2 ) structure with bond angle φ(LBA)=90-110 Deg are preferable. Equilibrium geometric parameters, relative energies and energies of isomer decomposition, frequencies and IR-intensities of normal vibrations are determined [ru

  8. Raman spectroscopy, ab-initio model calculations, and conformational, equilibria in ionic liquids

    OpenAIRE

    Berg, Rolf W.

    2009-01-01

    A review of the recent developments in the study and understanding of room temperature ionic liquids are given. An intimate picture of how and why these liquids are not crystals at ambient conditions is attempted, based on evidence from crystallographical results combined with vibrational spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT- Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methyl-imidazolium ...

  9. Study of carvedilol by combined Raman spectroscopy and ab initio MO calculations

    OpenAIRE

    Marques, M. P. M.; Oliveira, P. J.; Moreno, A. J. M.; Carvalho, L. A. E. Batista de

    2002-01-01

    The novel cardioprotective drug carvedilol was studied by both Raman spectroscopy and ab initio molecular orbital methods (using the density functional theory approach). The spectra, acquired both for the solid samples and DMSO solutions as a function of pH, were assigned in view of the calculated wavenumbers and intensities, and also based on the experimental data obtained for individual compounds which comprise the molecule, namely carbazole and 1,2-dimethoxybenzene. The pH dependence of th...

  10. Static, dynamic and electronic properties of expanded fluid mercury in the metal-nonmetal transition range. An ab initio study

    International Nuclear Information System (INIS)

    CalderIn, L; Gonzalez, L E; Gonzalez, D J

    2011-01-01

    Fluid Hg undergoes a metal-nonmetal (M-NM) transition when expanded toward a density of around 9 g cm -3 . We have performed ab initio molecular dynamics simulations for several thermodynamic states around the M-NM transition range and the associated static, dynamic and electronic properties have been analyzed. The calculated static structure shows a good agreement with the available experimental data. It is found that the volume expansion decreases the number of nearest neighbors from 10 (near the triple point) to around 8 at the M-NM transition region. Moreover, these neighbors are arranged into two subshells and the decrease in the number of neighbors occurs in the inner subshell. The calculated dynamic structure factors agree fairly well with their experimental counterparts obtained by inelastic x-ray scattering experiments, which display inelastic side peaks. The derived dispersion relation exhibits some positive dispersion for all the states, although its value around the M-NM transition region is not as marked as suggested by the experiment. We have also calculated the electronic density of states, which shows the appearance of a gap at a density of around 8.3 g cm -3 . (paper)

  11. TH-AB-209-07: High Resolution X-Ray-Induced Acoustic Computed Tomography

    Energy Technology Data Exchange (ETDEWEB)

    Xiang, L; Tang, S [University of Oklahoma, Norman, OK (United States); Ahmad, M [Stanford University, Palo Alto, CA (United States); Xing, L [Stanford University School of Medicine, Stanford, CA (United States)

    2016-06-15

    Purpose: X-ray radiographic absorption imaging is an invaluable tool in medical diagnostics, biology and materials science. However, the use of conventional CT is limited by two factors: the detection sensitivity to weak absorption material and the radiation dose from CT scanning. The purpose of this study is to explore X-ray induced acoustic computed tomography (XACT), a new imaging modality, which combines X-ray absorption contrast and high ultrasonic resolution to address these challenges. Methods: First, theoretical models was built to analyze the XACT sensitivity to X-ray absorption and calculate the minimal radiation dose in XACT imaging. Then, an XACT system comprised of an ultrashort X-ray pulse, a low noise ultrasound detector and a signal acquisition system was built to evaluate the X-ray induced acoustic signal generation. A piece of chicken bone and a phantom with two golden fiducial markers were exposed to 270 kVp X-ray source with 60 ns exposure time, and the X-ray induced acoustic signal was received by a 2.25MHz ultrasound transducer in 200 positions. XACT images were reconstructed by a filtered back-projection algorithm. Results: The theoretical analysis shows that X-ray induced acoustic signals have 100% relative sensitivity to X-ray absorption, but not to X-ray scattering. Applying this innovative technology to breast imaging, we can reduce radiation dose by a factor of 50 compared with newly FDA approved breast CT. The reconstructed images of chicken bone and golden fiducial marker phantom reveal that the spatial resolution of the built XACT system is 350µm. Conclusion: In XACT, the imaging sensitivity to X-ray absorption is improved and the imaging dose is dramatically reduced by using ultrashort pulsed X-ray. Taking advantage of the high ultrasonic resolution, we can also perform 3D imaging with a single X-ray pulse. This new modality has the potential to revolutionize x-ray imaging applications in medicine and biology.

  12. Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

    Energy Technology Data Exchange (ETDEWEB)

    Genderen, E. van; Clabbers, M. T. B. [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands); Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel (Switzerland); Das, P. P. [Nanomegas SPRL, Boulevard Edmond Machtens 79, B 1080, Brussels (Belgium); Stewart, A. [Department of Physics and Energy, Materials and Surface Science Institute (MSSI), University of Limerick, Limerick (Ireland); Nederlof, I. [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands); Amsterdam Scientific Instruments, Postbus 41882, 1009 DB Amsterdam (Netherlands); Barentsen, K. C. [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands); Portillo, Q. [Nanomegas SPRL, Boulevard Edmond Machtens 79, B 1080, Brussels (Belgium); Centres Científics i Tecnològics de la Universitat de Barcelona, University of Barcelona, Carrer de Lluís Solé i Sabaris, 1-3, Barcelona (Spain); Pannu, N. S. [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands); Nicolopoulos, S. [Nanomegas SPRL, Boulevard Edmond Machtens 79, B 1080, Brussels (Belgium); Gruene, T., E-mail: tim.gruene@psi.ch [Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen (Switzerland); Abrahams, J. P., E-mail: tim.gruene@psi.ch [Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Netherlands); Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, CH-4058 Basel (Switzerland); Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen (Switzerland)

    2016-02-05

    A specialized quantum area detector for electron diffraction studies makes it possible to solve the structure of small organic compound nanocrystals in non-cryo conditions by direct methods. Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e{sup −} Å{sup −2} s{sup −1}) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014)

  13. Atomic ionization of germanium by neutrinos from an ab initio approach

    International Nuclear Information System (INIS)

    Chen, Jiunn-Wei; Chi, Hsin-Chang; Huang, Keh-Ning; Liu, C.-P.; Shiao, Hao-Tse; Singh, Lakhwinder; Wong, Henry T.; Wu, Chih-Liang; Wu, Chih-Pan

    2014-01-01

    An ab initio calculation of atomic ionization of germanium by neutrinos was carried out in the framework of multiconfiguration relativistic random phase approximation and benchmarked by related atomic structure and photoabsorption data. This improves over the conventional approach based on scattering off free electrons whose validity at sub-keV energy transfer is questionable. Limits on neutrino magnetic moments are derived using reactor neutrino data taken with low threshold germanium detectors. Future applications of these atomic techniques will greatly reduce the atomic uncertainties in low-energy neutrino and dark matter detections.

  14. Spin-orbit interaction effects in zincblende semiconductors: Ab initio pseudopotential calculations

    International Nuclear Information System (INIS)

    Li, Ming-Fu; Surh, M.P.; Louie, S.G.

    1988-06-01

    Ab initio band structure calculations have been performed for the spin-orbit interaction effects at the top of the valence bands for GaAs and InSb. Relativistic, norm-conserving pseudopotentials are used with no correction made for the gaps from the local density approximation. The spin-orbit splitting at Γ and linear terms in the /rvec char/k dependence of the splitting are found to be in excellent agreement with existing experiments and previous theoretical results. The effective mass and the cubic splitting terms are also examined. 6 refs., 1 fig., 2 tabs

  15. Ab initio electronic structure and correlations in pristine and potassium-doped molecular crystals of copper phthalocyanine

    NARCIS (Netherlands)

    Giovannetti, G.; Brocks, G.; van den Brink, J.

    2008-01-01

    We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic

  16. Structural, dynamical, electronic, and bonding properties of laser-heated silicon: An ab initio molecular-dynamics study

    NARCIS (Netherlands)

    Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.

    1997-01-01

    The method of ab initio molecular dynamics, based on finite-temperature density-functional theory, is used to simulate laser heating of crystalline silicon. We found that a high concentration of excited electrons dramatically weakens the covalent bonding. As a result the system undergoes a melting

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

    Science.gov (United States)

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

    1993-01-01

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

  18. Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yimin, E-mail: yimin.wang@emory.edu; Bowman, Joel M., E-mail: jmbowma@emory.edu [Department of Chemistry, Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322 (United States); Kamarchik, Eugene, E-mail: eugene.kamarchik@gmail.com [Quantum Pomegranate, LLC, 2604 Kings Lake Court NE, Atlanta, Georgia 30345 (United States)

    2016-03-21

    We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na{sup +}H{sub 2}O, F{sup −}H{sub 2}O, and Cl{sup −}H{sub 2}O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H{sub 2}O potentials are permutationally invariant fits to roughly 20 000 coupled cluster CCSD(T) energies (awCVTZ basis for Na{sup +} and aVTZ basis for Cl{sup −} and F{sup −}), over a large range of distances and H{sub 2}O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.

  19. Analysis of the X-ray spectra emitted by laser-produced plasma of highly ionized lanthanum and praseodymium in the 8. 4 to 12. 0 A wavelength range

    Energy Technology Data Exchange (ETDEWEB)

    Zigler, A [Racah Inst. of Physics, Hebrew Univ., Jerusalem (Israel); Mandelbaum, P [Racah Inst. of Physics, Hebrew Univ., Jerusalem (Israel); Schwob, J L [Racah Inst. of Physics, Hebrew Univ., Jerusalem (Israel); Mitnik, D [Racah Inst. of Physics, Hebrew Univ., Jerusalem (Israel)

    1994-06-01

    A detailed analysis of the X-ray spectra emitted by laser produced plasma of lanthanum (8.5-12.5 A) and praseodymium (8.4-11.3 A) is given, using ab-initio calculations with the HULLAC relativistic code. Resonance 3d-nf (n 4, 5, 6) and 3p-4s, 4d transitions of the La XXX and Pr XXXII Ni I-like ions and neighbouring ionization states (La XXVIII to La XXXVI, Pr XXX to Pr XXXVI) have been identified. (orig.).

  20. Ab initio molecular dynamics of the reaction of quercetin with superoxide radical

    International Nuclear Information System (INIS)

    Lespade, Laure

    2016-01-01

    Highlights: • Ab initio molecular dynamics is performed to describe the reaction of quercetin and superoxide. • The reaction occurs near the sites 4′ and 7 when the system contains sufficiently water molecules. • The difference of reactivity of superoxide compared to commonly used radicals as DPPH · or ABTS ·+ is explained. - Abstract: Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car–Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.

  1. The complex ion structure of warm dense carbon measured by spectrally resolved x-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Kraus, D.; Barbrel, B.; Falcone, R. W. [Department of Physics, University of California, Berkeley, California 94720 (United States); Vorberger, J. [Max-Planck-Institut für Physik komplexer Systeme, Nöthnitzer Straße 38, 01187 Dresden (Germany); Helfrich, J.; Frydrych, S.; Ortner, A.; Otten, A.; Roth, F.; Schaumann, G.; Schumacher, D.; Siegenthaler, K.; Wagner, F.; Roth, M. [Institut für Kernphysik, Technische Universität Darmstadt, Schlossgartenstraße 9, 64289 Darmstadt (Germany); Gericke, D. O.; Wünsch, K. [Centre for Fusion, Space and Astrophysics, Department of Physics, University of Warwick, Coventry CV4 7AL (United Kingdom); Bachmann, B.; Döppner, T. [Lawrence Livermore National Laboratory, Livermore, California 94550 (United States); Bagnoud, V.; Blažević, A. [GSI Helmholtzzentrum für Schwerionenforschung GmbH, Planckstraße 1, 64291 Darmstadt (Germany); and others

    2015-05-15

    We present measurements of the complex ion structure of warm dense carbon close to the melting line at pressures around 100 GPa. High-pressure samples were created by laser-driven shock compression of graphite and probed by intense laser-generated x-ray sources with photon energies of 4.75 keV and 4.95 keV. High-efficiency crystal spectrometers allow for spectrally resolving the scattered radiation. Comparing the ratio of elastically and inelastically scattered radiation, we find evidence for a complex bonded liquid that is predicted by ab-initio quantum simulations showing the influence of chemical bonds under these conditions. Using graphite samples of different initial densities we demonstrate the capability of spectrally resolved x-ray scattering to monitor the carbon solid-liquid transition at relatively constant pressure of 150 GPa. Showing first single-pulse scattering spectra from cold graphite of unprecedented quality recorded at the Linac Coherent Light Source, we demonstrate the outstanding possibilities for future high-precision measurements at 4th Generation Light Sources.

  2. Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds

    Directory of Open Access Journals (Sweden)

    Felix Simkovic

    2016-07-01

    Full Text Available For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based structure prediction. Such models can be used in structure solution by molecular replacement (MR where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions (`decoys', is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue–residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing.

  3. Ab Initio Symmetry-Adapted No-Core Shell Model

    International Nuclear Information System (INIS)

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

    2011-01-01

    A multi-shell extension of the Elliott SU(3) model, the SU(3) symmetry-adapted version of the no-core shell model (SA-NCSM), is described. The significance of this SA-NCSM emerges from the physical relevance of its SU(3)-coupled basis, which – while it naturally manages center-of-mass spuriosity – provides a microscopic description of nuclei in terms of mixed shape configurations. Since typically configurations of maximum spatial deformation dominate, only a small part of the model space suffices to reproduce the low-energy nuclear dynamics and hence, offers an effective symmetry-guided framework for winnowing of model space. This is based on our recent findings of low-spin and high-deformation dominance in realistic NCSM results and, in turn, holds promise to significantly enhance the reach of ab initio shell models.

  4. Double ionization in Helium. Ab initio calculations beyond the one dimensional approximation

    International Nuclear Information System (INIS)

    Camilo Ruiz; Luis Plaja; Luis Roso; Andreas Becker

    2006-01-01

    Complete test of publication follows. We present ab-initio computations of the ionization of two-electron atoms by short pulses of coherent radiation beyond the one-dimensional approximation. In the model the electron correlation is included in its full dimensionality, while the center-of-mass motion is restricted along the polarization axis. We show some result for Non Sequential Double Ionization (NSDI) as well as for SDI for high intensity low IR frequency. Some recent applications for this correlated system is also presented.

  5. Estudo da geometria da uréia por métodos ab initio e simulação computacional de líquidos

    OpenAIRE

    Cirino,José Jair Vianna; Bertran,Celso Aparecido

    2002-01-01

    A study was carried out on the urea geometries using ab initio calculation and Monte Carlo computational simulation of liquids. The ab initio calculated results showed that urea has a non-planar conformation in the gas phase in which the hydrogen atoms are out of the plane formed by the heavy atoms. Free energies associated to the rotation of the amino groups of urea in water were obtained using the Monte Carlo method in which the thermodynamic perturbation theory is implemented. The magnitud...

  6. Ab initio study of antiphase boundaries and stacking faults in L12 and DO22 compounds

    DEFF Research Database (Denmark)

    Rosengaard, N. M.; Skriver, Hans Lomholt

    1994-01-01

    We have performed ab initio calculations of the energies of antiphase boundaries as well as complex and superlattice intrinsic stacking faults in nine intermetallic compounds observed in the face-centered-cubic L1(2) and DO22 structures. The calculations were performed by means of a Green...

  7. Ab initio study of II-(VI){sub 2} dichalcogenides

    Energy Technology Data Exchange (ETDEWEB)

    Olsson, P; Vidal, J; Lincot, D, E-mail: polsson@kth.se [Institut de R and D sur l' energie photovoltaique (IRDEP), UMR 7174-EDF-CNRS-ENSCP, 6 quai Watier, 78401 Chatou Cedex (France)

    2011-10-12

    The structural stabilities of the (Zn,Cd)(S,Se,Te){sub 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{sub 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. (paper)

  8. Ab initio investigation of isomerism, structure and stability of complex molecules of salts of oxo- and thiohalide and dihydride borates and aluminates Li[X2MY] (M=B, Al; X=F, Cl, H; Y=O, S)

    International Nuclear Information System (INIS)

    Charkin, D.O.; MakKi, M.L.; Charkin, O.P.

    2000-01-01

    To obtain full summary molecular constants of mixed salts Li[X 2 MY] and to analyze tendencies of their changes during substitution of B for Al, F - for C and H, and O - for S and to trace the character of polarization and deformation of X 2 MY - anions in the field of Li + cation in the cases of their different coordination in the framework of correlated approximation method MP4/6-31(+)G**//MP2/6-31G* + ZPE(MP2/6-31G*) ab initio calculation of surfaces of potential energy of plane trigonal anions X 2 MY - (M=B, Al; X=F, Cl, H; Y=O, S) and their lithium salts are done. Equilibrium geometrical parameters of isomers, frequencies and relative IR intensities of normal vibrations, their relative energies and decomposition energies are determined. Structure where Li + cation is coordinated bidentately to chalcogen and one of the X atom is the most profitable one. Polarization and deformation of X 2 MY - anion in the field of Li + cation in the cases of different ways of their coordination, tendencies in changes of the calculated parameters during B substitution are analyzed [ru

  9. Multiscale modeling of current-induced switching in magnetic tunnel junctions using ab initio spin-transfer torques

    Science.gov (United States)

    Ellis, Matthew O. A.; Stamenova, Maria; Sanvito, Stefano

    2017-12-01

    There exists a significant challenge in developing efficient magnetic tunnel junctions with low write currents for nonvolatile memory devices. With the aim of analyzing potential materials for efficient current-operated magnetic junctions, we have developed a multi-scale methodology combining ab initio calculations of spin-transfer torque with large-scale time-dependent simulations using atomistic spin dynamics. In this work we introduce our multiscale approach, including a discussion on a number of possible schemes for mapping the ab initio spin torques into the spin dynamics. We demonstrate this methodology on a prototype Co/MgO/Co/Cu tunnel junction showing that the spin torques are primarily acting at the interface between the Co free layer and MgO. Using spin dynamics we then calculate the reversal switching times for the free layer and the critical voltages and currents required for such switching. Our work provides an efficient, accurate, and versatile framework for designing novel current-operated magnetic devices, where all the materials details are taken into account.

  10. CONFOLD2: improved contact-driven ab initio protein structure modeling.

    Science.gov (United States)

    Adhikari, Badri; Cheng, Jianlin

    2018-01-25

    Contact-guided protein structure prediction methods are becoming more and more successful because of the latest advances in residue-residue contact prediction. To support contact-driven structure prediction, effective tools that can quickly build tertiary structural models of good quality from predicted contacts need to be developed. We develop an improved contact-driven protein modelling method, CONFOLD2, and study how it may be effectively used for ab initio protein structure prediction with predicted contacts as input. It builds models using various subsets of input contacts to explore the fold space under the guidance of a soft square energy function, and then clusters the models to obtain the top five models. CONFOLD2 obtains an average reconstruction accuracy of 0.57 TM-score for the 150 proteins in the PSICOV contact prediction dataset. When benchmarked on the CASP11 contacts predicted using CONSIP2 and CASP12 contacts predicted using Raptor-X, CONFOLD2 achieves a mean TM-score of 0.41 on both datasets. CONFOLD2 allows to quickly generate top five structural models for a protein sequence when its secondary structures and contacts predictions at hand. The source code of CONFOLD2 is publicly available at https://github.com/multicom-toolbox/CONFOLD2/ .

  11. Ab initio thermodynamics for the growth of ultra-thin Cu film on a perfect Mg O(001) surface

    Energy Technology Data Exchange (ETDEWEB)

    Zhukovskii, Yuri F. [Institute for Solid State Physics, University of Latvia, Kengaraga str. 8, Riga LV-1063 (Latvia)]. E-mail: quantzh@latnet.lv; Fuks, David [Materials Engineering Department, Ben-Gurion University of the Negev, POB 653, Beer-Sheva IL-84105 (Israel); Kotomin, Eugene A. [Institute for Solid State Physics, University of Latvia, Kengaraga str. 8, Riga LV-1063 (Latvia); Dorfman, Simon [Department of Physics, Israel Institute of Technology-Technion, Haifa IL-32000 (Israel)

    2005-12-15

    Controlled growth of thin metallic films on oxide substrates is important for numerous micro-and nano electronic applications. Our ab initio study is devoted to the periodic slab simulations for a series of ordered 2a Cu superlattices on the regular Mg O(001) substrate. Submonolayer and monolayer substrate Cu coverages were calculated using the Daft-Gaga method, as implemented into the Crystal-98 code. The results of ab initio calculations have been combined with thermodynamic theory which allows US to predict the growth mode of ultra-thin metal films (spinodal decomposition vs. nucleation-and-growth regime) as a function of the metal coverage and the temperature, and to estimate the metal density in clusters. We show that 3a cluster formation becomes predominant already at low Cu coverages, in agreement with the experiment.

  12. Ab initio thermodynamics for the growth of ultra-thin Cu film on a perfect Mg O(001) surface

    International Nuclear Information System (INIS)

    Zhukovskii, Yuri F.; Fuks, David; Kotomin, Eugene A.; Dorfman, Simon

    2005-01-01

    Controlled growth of thin metallic films on oxide substrates is important for numerous micro-and nano electronic applications. Our ab initio study is devoted to the periodic slab simulations for a series of ordered 2a Cu superlattices on the regular Mg O(001) substrate. Submonolayer and monolayer substrate Cu coverages were calculated using the Daft-Gaga method, as implemented into the Crystal-98 code. The results of ab initio calculations have been combined with thermodynamic theory which allows US to predict the growth mode of ultra-thin metal films (spinodal decomposition vs. nucleation-and-growth regime) as a function of the metal coverage and the temperature, and to estimate the metal density in clusters. We show that 3a cluster formation becomes predominant already at low Cu coverages, in agreement with the experiment

  13. Toward spectroscopically accurate global ab initio potential energy surface for the acetylene-vinylidene isomerization

    International Nuclear Information System (INIS)

    Han, Huixian; Li, Anyang; Guo, Hua

    2014-01-01

    A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S 0 ) electronic state has been constructed by fitting ∼37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm −1 . The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies up to 12 700 cm −1 above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction

  14. Ab Initio periodic Hartree-Fock study of group IA cations in ANA-type zeolites

    International Nuclear Information System (INIS)

    Anchell, J.L.; White, J.C.; Thompson, M.R.; Hess, A.C.

    1994-01-01

    This study investigates the electronic structure of Group IA cations intercalated into zeolites with the analcime (ANA) framework using ab initio periodic Hartree-Fock theory. The purpose of the study is to gain a better understanding of the role played by electron-donating species in zeolites in general, with specific applications to materials that have been suggested as storage matrices for radioactive materials. The effect of the intercalated species (Na, K, Rb, and Cs) on the electronic structure of the zeolite is presented on the basis of an analysis of the total and projected density of states, Mulliken charges, and charge density differences. The results of those analyses indicate that, relative to a charge neutral atomic state, the Group IA species donate an electron to the zeolite lattice and interact most strongly with the s and p atomic states of oxygen as the species are moved through the lattice. In addition, estimates of the self-diffusion constants of Na, K, Rb, and Cs based upon a one-dimensional diffusion model parameterized from the ab initio total energy data will be presented. 24 refs., 8 figs., 4 tabs

  15. Communication: A benchmark-quality, full-dimensional ab initio potential energy surface for Ar-HOCO

    International Nuclear Information System (INIS)

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

    2014-01-01

    A full-dimensional, global ab initio potential energy surface (PES) for the Ar-HOCO system is presented. The PES consists of a previous intramolecular ab initio PES for HOCO [J. Li, C. Xie, J. Ma, Y. Wang, R. Dawes, D. Xie, J. M. Bowman, and H. Guo, J. Phys. Chem. A 116, 5057 (2012)], plus a new permutationally invariant interaction potential based on fitting 12 432 UCCSD(T)-F12a/aVDZ counterpoise-corrected energies. The latter has a total rms fitting error of about 25 cm −1 for fitted interaction energies up to roughly 12 000 cm −1 . Two additional fits are presented. One is a novel very compact permutational invariant representation, which contains terms only involving the Ar-atom distances. The rms fitting error for this fit is 193 cm −1 . The other fit is the widely used pairwise one. The pairwise fit to the entire data set has an rms fitting error of 427 cm −1 . All of these potentials are used in preliminary classical trajectory calculations of energy transfer with a focus on comparisons with the results using the benchmark potential

  16. Communication: A benchmark-quality, full-dimensional ab initio potential energy surface for Ar-HOCO

    Energy Technology Data Exchange (ETDEWEB)

    Conte, Riccardo, E-mail: riccardo.conte@emory.edu, E-mail: jmbowma@emory.edu; Bowman, Joel M., E-mail: riccardo.conte@emory.edu, E-mail: jmbowma@emory.edu [Department of Chemistry and Cherry L. Emerson Center for Scientific Calculation, Emory University, Atlanta, Georgia 30322 (United States); Houston, Paul L., E-mail: paul.houston@cos.gatech.edu [School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States)

    2014-04-21

    A full-dimensional, global ab initio potential energy surface (PES) for the Ar-HOCO system is presented. The PES consists of a previous intramolecular ab initio PES for HOCO [J. Li, C. Xie, J. Ma, Y. Wang, R. Dawes, D. Xie, J. M. Bowman, and H. Guo, J. Phys. Chem. A 116, 5057 (2012)], plus a new permutationally invariant interaction potential based on fitting 12 432 UCCSD(T)-F12a/aVDZ counterpoise-corrected energies. The latter has a total rms fitting error of about 25 cm{sup −1} for fitted interaction energies up to roughly 12 000 cm{sup −1}. Two additional fits are presented. One is a novel very compact permutational invariant representation, which contains terms only involving the Ar-atom distances. The rms fitting error for this fit is 193 cm{sup −1}. The other fit is the widely used pairwise one. The pairwise fit to the entire data set has an rms fitting error of 427 cm{sup −1}. All of these potentials are used in preliminary classical trajectory calculations of energy transfer with a focus on comparisons with the results using the benchmark potential.

  17. Toward spectroscopically accurate global ab initio potential energy surface for the acetylene-vinylidene isomerization

    Science.gov (United States)

    Han, Huixian; Li, Anyang; Guo, Hua

    2014-12-01

    A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S0) electronic state has been constructed by fitting ˜37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm-1. The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies up to 12 700 cm-1 above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction.

  18. Influence of the ab initio n–d cross sections in the critical heavy-water benchmarks

    International Nuclear Information System (INIS)

    Morillon, B.; Lazauskas, R.; Carbonell, J.

    2013-01-01

    Highlights: ► We solve the three nucleon problem using different NN potential (MT, AV18 and INOY) to calculate the Neutron–deuteron cross sections. ► These cross sections are compared to the existing experimental data and to international libraries. ► We describe the different sets of heavy water benchmarks for which the Monte Carlo simulations have been performed including our new Neutron–deuteron cross sections. ► The results obtained by the ab initio INOY potential have been compared with the calculations based on the international library cross sections and are found to be of the same quality. - Abstract: The n–d elastic and breakup cross sections are computed by solving the three-body Faddeev equations for realistic and semi-realistic nucleon–nucleon potentials. These cross sections are inserted in the Monte Carlo simulation of the nuclear processes considered in the International Handbook of Evaluated Criticality Safety Benchmark Experiments (ICSBEP Handbook). The results obtained using thes ab initio n–d cross sections are compared with those provided by the most renown international libraries

  19. Controlling Magnetic and Ferroelectric Order Through Geometry: Synthesis, Ab Initio Theory, Characterization of New Multi-Ferric Fluoride Materials

    Energy Technology Data Exchange (ETDEWEB)

    Halasyamani, Shiv [Univ. of Houston, TX (United States); Fennie, Craig [Cornell Univ., Ithaca, NY (United States)

    2016-11-03

    We have focused on the synthesis, characterization, and ab initio theory on multi-functional mixed-metal fluorides. With funding from the DOE, we have successfully synthesized and characterized a variety of mixed metal fluoride materials.

  20. Static structure, microscopic dynamics and electronic properties of the liquid Bi–Li alloy. An ab initio molecular dynamics study

    International Nuclear Information System (INIS)

    Souto, J; Alemany, M M G; Gallego, L J; González, L E; González, D J

    2013-01-01

    We report an ab initio molecular dynamics study of the static, dynamic and electronic properties of the liquid Bi x Li 1−x alloy, which is a complex binary system with a marked tendency to heterocoordination. The calculated total static structure factors are in good agreement with the available experimental data. The partial dynamic structure factors exhibit side peaks indicative of propagating density fluctuations, and for some concentrations we have found a density fluctuation mode with phase velocity greater than the hydrodynamic sound velocity. We have also evaluated other dynamical properties such as the diffusion coefficients, the shear viscosity and the adiabatic sound velocity. The electronic density of states show that the liquid Bi x Li 1−x alloy has a metallic character, although with strong deviations from the free-electron parabolic curve. The results reported improve the understanding of binary liquid alloys with both fast and slow propagating collective modes. (paper)

  1. Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei

    Czech Academy of Sciences Publication Activity Database

    Dytrych, Tomáš; Maris, P.; Launey, K. D.; Draayer, J. P.; Vary, J. P.; Langr, D.; Saule, E.; Caprio, M. A.; Catalyurek, U.; Sosonkina, M.

    2016-01-01

    Roč. 207, OCT (2016), s. 202-210 ISSN 0010-4655 R&D Projects: GA ČR GA16-16772S Institutional support: RVO:61389005 Keywords : nuclear structure * Ab initio methods * Shell model * models based on group theory Subject RIV: BE - Theoretical Physics Impact factor: 3.936, year: 2016

  2. Ab-initio crystal structure analysis and refinement approaches of oligo p-benzamides based on electron diffraction data

    DEFF Research Database (Denmark)

    Gorelik, Tatiana E; van de Streek, Jacco; Kilbinger, Andreas F M

    2012-01-01

    Ab-initio crystal structure analysis of organic materials from electron diffraction data is presented. The data were collected using the automated electron diffraction tomography (ADT) technique. The structure solution and refinement route is first validated on the basis of the known crystal stru...

  3. Classification of x-ray spectra of 2-3 transitions in the Ne-like and Na-like isoelectronic sequences of the elements from krypton to molybdenum

    International Nuclear Information System (INIS)

    Gordon, H.; Hobby, M.G.; Peacock, N.J.; Cowan, R.D.

    1979-01-01

    Plasmas produced by the laser irradiation of solid targets and in a plasma focus device have been employed as sources of x-ray spectra of the elements Kr(Z = 36)-Mo(Z = 42). The Ne-like isoelectronic sequence has been investigated by comparing observed wavelengths with ab initio atomic structure calculations and isoelectronic interpolation. Previous identifications in Ne-like ions have been extended to krypton, rubidium and strontium. The Na-like satellite structure of these elements has also been studied and a detailed classification of these satellites is presented. (author)

  4. Ab-initio calculation of quasi-particle bandstructure, exciton binding energies and dielectric properties of polythiophene

    NARCIS (Netherlands)

    van der Horst, J.W.; Bobbert, P.A.; Bobbert, Peter A.; Michels, M.A.J.; Brocks, G.; Kelly, Paul J.

    1999-01-01

    We use the ab-initio many-body GW method to calculate the quasi-particle spectrum of polythiophene. For the isolated chain, we find a large increase of the gap compared to DFT-LDA calculations (1.2 eV). The result (4.1 eV) exceeds experimental values, due to the absence of long-range screening in

  5. X-ray magnetic circular dichroism in (Ge,Mn) compounds: Experiments and modeling

    International Nuclear Information System (INIS)

    Tardif, Samuel; Titov, Andrey; Arras, Emmanuel; Slipukhina, Ivetta; Hlil, El-Kébir; Cherifi, Salia; Joly, Yves; Jamet, Matthieu; Barski, André; Cibert, Joël; Kulatov, Erkin; Uspenskii, Yurii A.; Pochet, Pascal

    2014-01-01

    X-ray absorption (XAS) and x-ray magnetic circular dichroism (XMCD) spectra at the L 2,3 edges of Mn in (Ge,Mn) compounds have been measured and are compared to the results of first principles calculation. Early ab initio studies show that the Density Functional Theory (DFT) can very well describe the valence band electronic properties but fails to reproduce a characteristic change of sign in the L 3 XMCD spectrum of Mn in Ge 3 Mn 5 , which is observed in experiments. In this work we demonstrate that this disagreement is partially related to an underestimation of the exchange splitting of Mn 2p core states within the local density approximation. It is shown that the change in sign experimentally observed is reproduced if the exchange splitting is accurately calculated within the Hartree–Fock approximation, while the final states can be still described by the DFT. This approach is further used to calculate the XMCD in different (Ge,Mn) compounds. It demonstrates that the agreement between experimental and theoretical spectra can be improved by combining state of the art calculations for the core and valence states respectively. - Highlights: • X-ray absorption and magnetic circular dichroism spectra are measured and compared to first principles calculations in (Ge,Mn) compounds. • Standard density functional theory fails in properly describing peculiar features observed in the experiment. • A new approach to calculate theoretical X-ray absorption and magnetic circular dichroism spectra is proposed. • Improved modeling of the core levels splitting using the Hartree–Fock approximation allows for a better matching with the experiment. • This new method could be generalized to any 3d metallic-like system

  6. A study of the atmospherically important reactions between dimethyl selenide (DMSe) and molecular halogens (X2 = Cl2, Br2, and I2) with ab initio calculations.

    Science.gov (United States)

    Rhyman, Lydia; Armata, Nerina; Ramasami, Ponnadurai; Dyke, John M

    2012-06-14

    The atmospherically relevant reactions between dimethyl selenide (DMSe) and the molecular halogens (X(2) = Cl(2), Br(2), and I(2)) have been studied with ab initio calculations at the MP2/aug-cc-pVDZ level of theory. Geometry optimization calculations showed that the reactions proceed from the reagents to the products (CH(3)SeCH(2)X + HX) via three minima, a van der Waals adduct (DMSe:X(2)), a covalently bound intermediate (DMSeX(2)), and a product-like complex (CH(3)SeCH(2)X:HX). The computed potential energy surfaces are used to predict what molecular species are likely to be observed in spectroscopic experiments such as gas-phase photoelectron spectroscopy and infrared matrix isolation spectroscopy. It is concluded that, for the reactions of DMSe with Cl(2) and Br(2), the covalent intermediate should be seen in spectroscopic experiments, whereas, in the DMSe + I(2) reaction, the van der Waals adduct DMSe:I(2) should be observed. Comparison is made with previous related calculations and experiments on dimethyl sulfide (DMS) with molecular halogens. The relevance of the results to atmospheric chemistry is discussed. The DMSeX(2) and DMSe:X(2) intermediates are likely to be reservoirs of molecular halogens in the atmosphere which will lead on photolysis to ozone depletion.

  7. Ab initio simulations and neutron scattering studies of structure and dynamics in PdH

    International Nuclear Information System (INIS)

    Totolici, I.E.

    2001-07-01

    The work presented in this PhD thesis is concerned with the interpretation of the neutron scattering measurements from the palladium hydrogen system by means of ab initio electronic structure calculations. The motivation of performing such calculations was due to recent neutron scattering studies on this system that showed a strong directional dependence to the dynamical structure factor together with a complex dependence on energy. Here we attempt to describe the origin of these features by ab initio simulations of the dynamical structure factor. The method assumes an adiabatic separation of the motion of the proton and palladium atoms. The proton wave functions are calculated by a direct solution of the associated single-particle Schroedinger equation using a plane wave basis set method and a mapping of the adiabatic surface. The Fourier components of the adiabatic potential are obtained from LDA pseudopotential calculations. Using Fermi's golden rule within the Born approximation we were then able to calculate the dynamical structure factor, S(Q,ω), for exciting the proton from its ground state to various excited states as a function of the magnitude and direction of the scattering wave vector. The results are in agreement with the inelastic neutron scattering spectra and allow us to identify the origin of previous inexplicable features, in particular the strong directional dependence to the experimental data. The method was extended to investigate the expansion of the equilibrium lattice constant as a function of the H isotope when the zero-point energy of the proton/deuterium is explicitly taken into account in the relaxation process. The results we obtained predicted a bigger lattice constant for the hydride, as expected. Furthermore, other complex ab initio calculations were carried out in order to describe the origin of the large optic dispersion, seen previously in the coherent neutron scattering data. Our calculated dispersion proved to be in good

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  9. Benefits of Parallel I/O in Ab Initio Nuclear Physics Calculations

    International Nuclear Information System (INIS)

    Laghave, Nikhil; Sosonkina, Masha; Maris, Pieter; Vary, James P.

    2009-01-01

    Many modern scientific applications rely on highly parallel calculations, which scale to 10's of thousands processors. However, most applications do not concentrate on parallelizing input/output operations. In particular, sequential I/O has been identified as a bottleneck for the highly scalable MFDn (Many Fermion Dynamics for nuclear structure) code performing ab initio nuclear structure calculations. In this paper, we develop interfaces and parallel I/O procedures to use a well-known parallel I/O library in MFDn. As a result, we gain efficient input/output of large datasets along with their portability and ease of use in the downstream processing.

  10. X-ray diffraction analysis and MO calculations of 1H-tetrazole; 1H-tetorazoru no Xsen kessho kozo kaiseki to bunshi kido keisan

    Energy Technology Data Exchange (ETDEWEB)

    Ono, Yoshio.; Akutsu, Yoshiaki.; Arai, Mitsuru.; Tamura, Masamitsu. [The University of Tokyo, Tokyo (Japan). School of Engineering; Matsunaga, Takehiro. [National Institute of Materials and Chemical Research, Tsukuba (Japan)

    1999-02-28

    The X-ray diffraction analysis and the MO calculations of 1H-tetrazole were carried out, in order to explain its high stability. From the X-ray diffraction analysis, five bonds in the ring have intermediate lengths between single and double bond lengths. Therefore, 1H-tetrazole is quite stable because of its aromaticity. The N1-C5 distance of 1.315A is significantly short. The molecular structure which was calculated by the ab initio MO calculation of one 1H-tetrazole molecule at MP2/6-31G* level, showed a good agreement with our experimental one, except for the abnormal short N1-C5 distance. From the calculations of dimers and trimers, 1H-tetrazole is shown to be stabilized by a strong intermolecular electrostatic interaction between the protons and the delocalized electrons over the ring. (author)

  11. Comparison between s - and d -electron mediated transport in a photoswitching dithienylethene molecule using ab initio transport methods

    KAUST Repository

    Odell, Anders; Delin, Anna; Johansson, Bö rje; Ulman, Kanchan; Narasimhan, Shobhana; Rungger, Ivan; Sanvito, Stefano

    2011-01-01

    The influence of the electrode's Fermi surface on the transport properties of a photoswitching molecule is investigated with state-of-the-art ab initio transport methods. We report results for the conducting properties of the two forms

  12. Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent

    Science.gov (United States)

    Bryce, Richard A.; Vincent, Mark A.; Malcolm, Nathaniel O. J.; Hillier, Ian H.; Burton, Neil A.

    1998-08-01

    A new hybrid quantum mechanical/molecular mechanical model of solvation is developed and used to describe the structure and dynamics of small fluoride/water clusters, using an ab initio wave function to model the ion and a fluctuating charge potential to model the waters. Appropriate parameters for the water-water and fluoride-water interactions are derived, with the fluoride anion being described by density functional theory and a large Gaussian basis. The role of solvent polarization in determining the structure and energetics of F(H2O)4- clusters is investigated, predicting a slightly greater stability of the interior compared to the surface structure, in agreement with ab initio studies. An extended Lagrangian treatment of the polarizable water, in which the water atomic charges fluctuate dynamically, is used to study the dynamics of F(H2O)4- cluster. A simulation using a fixed solvent charge distribution indicates principally interior, solvated states for the cluster. However, a preponderance of trisolvated configurations is observed using the polarizable model at 300 K, which involves only three direct fluoride-water hydrogen bonds. Ab initio calculations confirm this trisolvated species as a thermally accessible state at room temperature, in addition to the tetrasolvated interior and surface structures. Extension of this polarizable water model to fluoride clusters with five and six waters gave less satisfactory agreement with experimental energies and with ab initio geometries. However, our results do suggest that a quantitative model of solvent polarization is fundamental for an accurate understanding of the properties of anionic water clusters.

  13. Electronic structure of human hemoglobin: ultrasoft X-ray emission study

    International Nuclear Information System (INIS)

    Soldatov, A.V.; Kravtsova, A.N.; Fedorovich, E.N.; Kurmaev, E.Z.; Moewes, A.

    2004-01-01

    Full text: The iron L 2,3 and carbon, nitrogen and oxygen Kα X-ray emission spectra (XES) of human hemoglobin have been recorded at the soft X-ray spectroscopy endstation on Undulator Beam line 8.0 at Advanced Light Source (ALS) located at the Lawrence Berkeley National Laboratory. The theoretical calculations of Fe L 3 -XES have been performed using ab initio code FEFF8.2. The calculations have been carried out for the structure of hemoglobin presented in PDB (entry 3HHB) as well as for the molecule with symmetrical heme plane. It was found that the Fe L 3 emission spectrum calculated for the ideal molecule agrees slightly better with the experiment as compared with those calculated for the real molecule. Thus, one can use the structure of the ideal molecule for theoretical Fe L 3 -XES simulations. The theoretical analysis has shown that the fist peak of experimental Fe L 3 - emission spectrum is enhanced by the nearest nitrogen atoms lying in heme plane around the central iron atom. The theoretical C K- and N K-XES spectra of hemoglobin have been calculated. A good agreement between theoretical and experimental spectra has been obtained. The distribution of the partial electronic densities of states in the valence and conduction bands of hemoglobin has been determined

  14. Ab initio study of perovskite type oxide materials for solid oxide fuel cells

    Science.gov (United States)

    Lee, Yueh-Lin

    2011-12-01

    Perovskite type oxides form a family of materials of significant interest for cathodes and electrolytes of solid oxide fuel cells (SOFCs). These perovskites not only are active catalysts for surface oxygen reduction (OR) reactions but also allow incorporating the spilt oxygen monomers into their bulk, an unusual and poorly understood catalytic mechanism that couples surface and bulk properties. The OR mechanisms can be influenced strongly by defects in perovskite oxides, composition, and surface defect structures. This thesis work initiates a first step in developing a general strategy based on first-principles calculations for detailed control of oxygen vacancy content, transport rates of surface and bulk oxygen species, and surface/interfacial reaction kinetics. Ab initio density functional theory methods are used to model properties relevant for the OR reactions on SOFC cathodes. Three main research thrusts, which focus on bulk defect chemistry, surface defect structures and surface energetics, and surface catalytic properties, are carried to investigate different level of material chemistry for improved understanding of key physics/factors that govern SOFC cathode OR activity. In the study of bulk defect chemistry, an ab initio based defect model is developed for modeling defect chemistry of LaMnO 3 under SOFC conditions. The model suggests an important role for defect interactions, which are typically excluded in previous defect models. In the study of surface defect structures and surface energetics, it is shown that defect energies change dramatically (1˜2 eV lower) from bulk values near surfaces. Based on the existing bulk defect model with the calculated ab initio surface defect energetics, we predict the (001) MnO 2 surface oxygen vacancy concentration of (La0.9Sr0.1 )MnO3 is about 5˜6 order magnitude higher than that of the bulk under typical SOFC conditions. Finally, for surface catalytic properties, we show that area specific resistance, oxygen

  15. Study of CeOx, PrOx, and CexPr1-xO2-δ films on Si(111) by means of high-energetic X-ray photoelectron spectroscopy

    International Nuclear Information System (INIS)

    Allahgholi, Aschkan

    2013-03-01

    The intention of this work is to shed light on two much discussed topics in the study of rare earth oxides (REO) by hard x-ray photoelectron spectroscopy (HAXPES): (i) Due to the complex spectral shape of the Ce3d region, there have been many discussions on proper approaches to determine the concentration of Ce 3+ and Ce 4+ species in CeO x over the last decades. (ii) Recently, the true electron structure of rare earth oxides gained new attention, since ab initio calculations showed the necessity of considering additional inter atomic charge transfer to Ce5d levels. Using HAXPES and resonant HAXPES, the question of the true electronic structure of rare earth oxides is approached from the experimental side. As a third topic, the obtained results for cerium oxide and praseodymium oxide are applied in order to investigate the plasma oxidized mixed oxide Ce x Pr 1-x O 2-δ grown on Si(111) during thermal reduction. (orig.)

  16. Ab initio study of intrinsic profiles of liquid metals and their reflectivity

    Science.gov (United States)

    del Rio, B. G.; Souto, J.; Alemany, M. M. G.; González, L. E.

    2017-08-01

    The free surfaces of liquid metals are known to exhibit a stratified profile that, in favourable cases, shows up in experiments as a peak in the ratio between the reflectivity function and that of an ideal step-like profile. This peak is located at a wave-vector related to the distance between the layers of the profile. In fact the surface roughness produced by thermally induced capillary waves causes a depletion of the previous so called intrinsic reflectivity by a damping factor that may hinder the observation of the peak. The behaviour of the intrinsic reflectivity below the layering peak is however far from being universal, with systems as Ga or In where the reflectiviy falls uniformly towards the q → 0 value, others like Sn or Bi where a shoulder appears at intermediate wavevectors, and others like Hg which show a minimum. We have performed extensive ab initio simulations of the free liquid surfaces of Bi, Pb and Hg, that yield direct information on the structure of the profiles and found that the macroscopic capillary wave theory usually employed in order to remove the capillary wave components fails badly in some cases for the typical sample sizes affordable in ab initio simulations. However, a microscopic method for the determination of the intrinsic profile is shown to be succesful in obtaining meaningful intrinsic profiles and corresponding reflectivities which reproduce correctly the qualitative behaviour observed experimentally.

  17. Ab initio molecular dynamics of the reaction of quercetin with superoxide radical

    Energy Technology Data Exchange (ETDEWEB)

    Lespade, Laure, E-mail: l.lespade@ism.u-bordeaux1.fr

    2016-08-22

    Highlights: • Ab initio molecular dynamics is performed to describe the reaction of quercetin and superoxide. • The reaction occurs near the sites 4′ and 7 when the system contains sufficiently water molecules. • The difference of reactivity of superoxide compared to commonly used radicals as DPPH{sup ·} or ABTS{sup ·+} is explained. - Abstract: Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car–Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.

  18. Ab initio calculation of the shear viscosity of neon in the liquid and hypercritical state over a wide pressure and temperature range

    Science.gov (United States)

    Eggenberger, Rolf; Gerber, Stefan; Huber, Hanspeter; Searles, Debra; Welker, Marc

    1992-08-01

    The shear viscosity is calculated ab initio for the liquid and hypercritical state, i.e. a previously published potential for Ne 2, obtained from ab initio calculations including electron correlation, is used in classical equilibrium molecular dynamics simulations to obtain the shear viscosity from a Green-Kubo integral. The quality of the results is quite uniform over a large pressure range up to 1000 MPa and a wide temperature range from 26 to 600 K. In most cases the calculated shear viscosity deviates by less than 10% from the experimental value, in general the error being only a few percent.

  19. Ab initio Eliashberg Theory: Making Genuine Predictions of Superconducting Features

    Science.gov (United States)

    Sanna, Antonio; Flores-Livas, José A.; Davydov, Arkadiy; Profeta, Gianni; Dewhurst, Kay; Sharma, Sangeeta; Gross, E. K. U.

    2018-04-01

    We present an application of Eliashberg theory of superconductivity to study a set of novel superconducting systems with a wide range of structural and chemical properties. The set includes three intercalated group-IV honeycomb layered structures, SH3 at 200 GPa (the superconductor with the highest measured critical temperature), the similar system SeH3 at 150 GPa, and a lithium doped mono-layer of black phosphorus. The theoretical approach we adopt is a recently developed, fully ab initio Eliashberg approach that takes into account the Coulomb interaction in a full energy-resolved fashion avoiding any free parameters like μ*. This method provides reasonable estimations of superconducting properties, including TC and the excitation spectra of superconductors.

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

    Energy Technology Data Exchange (ETDEWEB)

    Olivares-Amaya, Roberto; Hu, Weifeng; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic [Department of Chemistry, Princeton University, Princeton, New Jersey 08544 (United States); Nakatani, Naoki [Department of Chemistry, Princeton University, Princeton, New Jersey 08544 (United States); Catalysis Research Center, Hokkaido University, Kita 21 Nishi 10, Sapporo, Hokkaido 001-0021 (Japan)

    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.

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

    Science.gov (United States)

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

    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.

  2. X-ray spectral and quantum-chemical investigation of electronic structure of 6,9-bis-(ammonia)-nido-decarborane(12)

    International Nuclear Information System (INIS)

    Yumatov, V.D.; Il'inchik, E.A.; Murakhtanov, V.V.; Dunaev, S.T.; Volkov, V.V.

    1993-01-01

    Electron structure of 6.9-bis-(ammonia)-nide-decarborane(12), that is, B 10 H 12 (NH 3 ) 2 , is studied by means of ultrasoft X-ray spectroscopy using nitrogen and boron atoms. Calculations of MNDO and ab initio are conducted. Electron structure of ammonia and of /B 10 H 12 / cluster is studied and its variation at complex formation is investigated, as well. On the basis of calculations one shows, that some vacant orbitals belonging to borane cluster participate into chemical bond of donor-acceptor type among the fragments. Presence of π-component of bond between NH 3 and /B 10 H 12 / and occurrence of four-central bound in borane cluster are detected

  3. Microscopic nucleon spectral function for finite nuclei featuring two- and three-nucleon short-range correlations: The model versus ab initio calculations for three-nucleon systems

    Science.gov (United States)

    Ciofi degli Atti, Claudio; Mezzetti, Chiara Benedetta; Morita, Hiko

    2017-04-01

    Background: Two-nucleon (2 N ) short-range correlations (SRC) in nuclei have been recently thoroughly investigated, both theoretically and experimentally and the study of three-nucleon (3 N ) SRC, which could provide important information on short-range hadronic structure, is underway. Novel theoretical ideas concerning 2 N and 3 N SRC are put forward in the present paper. Purpose: The general features of a microscopic one-nucleon spectral function which includes the effects of both 2 N and 3 N SRC and its comparison with ab initio spectral functions of the three-nucleon systems are illustrated. Methods: A microscopic and parameter-free one-nucleon spectral function expressed in terms of a convolution integral involving ab initio relative and center-of-mass (c.m.) momentum distributions of a 2 N pair and aimed at describing two- and three-nucleon short-range correlations, is obtained by using: (i) the two-nucleon momentum distributions obtained within ab initio approaches based upon nucleon-nucleon interactions of the Argonne family; (ii) the exact relation between one- and two-nucleon momentum distributions; (iii) the fundamental property of factorization of the nuclear wave function at short internucleon ranges. Results: The comparison between the ab initio spectral function of 3He and the one based upon the convolution integral shows that when the latter contains only two-nucleon short-range correlations the removal energy location of the peaks and the region around them exhibited by the ab initio spectral function are correctly predicted, unlike the case of the high and low removal energy tails; the inclusion of the effects of three-nucleon correlations brings the convolution model spectral function in much better agreement with the ab initio one; it is also found that whereas the three-nucleon short-range correlations dominate the high energy removal energy tail of the spectral function, their effects on the one-nucleon momentum distribution are almost one

  4. The Influence of Square Planar Platinum Complexes on DNA Bases Pairing. An ab initio DFT Study

    Czech Academy of Sciences Publication Activity Database

    Burda, J. V.; Šponer, Jiří; Leszczynski, J.

    2001-01-01

    Roč. 3, č. 19 (2001), s. 4404-4411 ISSN 1463-9076 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : DNA base pairing * platinated base pairs * ab initio DFT study Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.787, year: 2001

  5. Mechanisms for catalytic carbon nanofiber growth studied by ab initio density functional theory calculations

    DEFF Research Database (Denmark)

    Abild-Pedersen, Frank; Nørskov, Jens Kehlet; Rostrup-Nielsen, Jens

    2006-01-01

    Mechanisms and energetics of graphene growth catalyzed by nickel nanoclusters were studied using ab initio density functional theory calculations. It is demonstrated that nickel step-edge sites act as the preferential growth centers for graphene layers on the nickel surface. Carbon is transported......, and it is argued how these processes may lead to different nanofiber structures. The proposed growth model is found to be in good agreement with previous findings....

  6. Ab initio study of the EFG at the N sites in imidazole

    Energy Technology Data Exchange (ETDEWEB)

    Brown Goncalves, Marcos, E-mail: browngon@if.usp.br [Universidade de Sao Paulo, Instituto de Fisica (Brazil); Di Felice, R. [National Center on Nanostructures and Biosystems at Surfaces (S3) of INFM-CNR (Italy); Poleshchuk, O. Kh. [Tomsk State Pedagogical University (Russian Federation); Petrilli, H. M. [Universidade de Sao Paulo, Instituto de Fisica (Brazil)

    2008-01-15

    We study the nuclear quadrupole interaction at the nitrogen sites in the molecular and crystalline phases of the imidazole compound. We use PAW which is a state-of-the-art method to calculate the electronic structure and electric field gradient at the nucleus in the framework of the density functional theory. The quadrupole frequencies at both imino and amino N sites are in excellent agreement with measurements. This is the first time that the electric field gradient at crystalline imidazole is correctly treated by an ab initio theoretical approach.

  7. Weak interactions in Graphane/BN systems under static electric fields—A periodic ab-initio study.

    Science.gov (United States)

    Steinkasserer, Lukas Eugen Marsoner; Gaston, Nicola; Paulus, Beate

    2015-04-21

    Ab-initio calculations via periodic Hartree-Fock (HF) and local second-order Møller-Plesset perturbation theory (LMP2) are used to investigate the adsorption properties of combined Graphane/boron nitride systems and their response to static electric fields. It is shown how the latter can be used to alter both structural as well as electronic properties of these systems.

  8. Ab initio study of structural, electronic, optical, and vibrational properties of Zn{sub x}S{sub y} (x + y = 2 to 5) nanoclusters

    Energy Technology Data Exchange (ETDEWEB)

    Yadav, P. S.; Pandey, D. K., E-mail: pdhiraj2000@gmail.com; Agrawal, S.; Agrawal, B. K. [Allahabad University, Department of Physics (India)

    2010-03-15

    An ab initio study of the stability, structural, electronic. and optical properties has been performed for 46 zinc sulfide nanoclusters Zn{sub x}S{sub y} (x + y = n = 2 to 5). Five out of them are seen to be unstable as their vibrational frequencies are found to be imaginary. A B3LYP-DFT/6-311G(3df) method is employed to optimize the geometries and a TDDFT method is used for the study of the optical properties. The binding energies (BE), HOMO-LUMO gaps and the bond lengths have been obtained for all the clusters. For the ZnS{sub 2}, ZnS{sub 3}, and ZnS{sub 4} nanoclusters, our stable structures are seen to be different from those obtained earlier by using the effective core potentials. We have also considered the zero point energy (ZPE) corrections ignored by the earlier workers. For a fixed value of n, we designate the most stable structure the one, which has maximum final binding energy per atom. The adiabatic and vertical ionization potentials (IP) and electron affinities (EA), charges on the atoms, dipole moments, optical properties, vibrational frequencies, infrared intensities, relative infrared intensities, and Raman scattering activities have been investigated for the most stable structures. The nanoclusters containing large number of S atoms for each n is found to be most stable. The HOMO-LUMO gap decreases from n = 2-3 and then increases above n = 3. The IP and EA both fluctuate with the cluster size n. The optical absorption is quite weak in visible region but strong in the ultraviolet region in most of the nanoclusters except a few. The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every nanocluster and may be used to characterize a specific nanocluster. The growth of most stable nanoclusters may be possible in the experiments.

  9. Phonon spectra in the parent superconducting iron-tuned telluride F e1 +xTe from inelastic neutron scattering and ab initio calculations

    Science.gov (United States)

    Zbiri, Mohamed; Viennois, Romain

    2017-10-01

    We report inelastic neutron scattering measurements of phonon spectra in the parent superconductor iron-tuned chalcogenide F e1 +xTe for two different x contents (x ≤0.11 ) using neutron time-of-flight technique. Thermal neutron spectroscopy allowed the collection of the low-temperature Stokes spectra over an extended Q range at 2, 40, and 120 K, hence covering both the magnetic monoclinic and the paramagnetic tetragonal phases, whereas cold neutrons allowed the measurement of high-resolution anti-Stokes spectra at 140, 220, and 300 K, thus covering the tetragonal phase. Our results evidence a spin-phonon coupling behavior towards the observed noticeable temperature-dependent change of the Stokes spectra across the transition temperatures. On the other hand, the anti-Stokes spectra reveal a pronounced hardening of the low-energy, acoustic region of the phonon spectrum upon heating, indicating a strong anharmonicity and a subtle dependence of phonons on structural evolution within the tetragonal phase. Experimental results are accompanied by ab initio calculations of phonon spectra of the tetragonal stoichiometric phase for a comparison with the high-resolution anti-Stokes spectra. Calculations included different density functional methods. Spin polarization and van der Waals interaction were either considered or neglected, individually or concomitantly, in order to study their respective effect on lattice dynamics description. Our results suggest that including van der Waals interaction has only a slight effect on phonon dynamics; however, phonon spectra are better described when spin polarization is included in a cooperative way with van der Waals interactions.

  10. Ab-initio vibrational properties of transition metal chalcopyrite alloys determined as high-efficiency intermediate-band photovoltaic materials

    International Nuclear Information System (INIS)

    Palacios, P.; Aguilera, I.; Wahnon, P.

    2008-01-01

    In this work, we present frozen phonon and linear response ab-initio research into the vibrational properties of the CuGaS 2 chalcopyrite and transition metal substituted (CuGaS 2 )M alloys. These systems are potential candidates for developing a novel solar-cell material with enhanced optoelectronic properties based in the implementation of the intermediate-band concept. We have previously carried out ab-initio calculations of the electronic properties of these kinds of chalcopyrite metal alloys showing a narrow transition metal band isolated in the semiconductor band gap. The substitutes used in the present work are the 3d metal elements, Titanium and Chromium. For the theoretical calculations we use standard density functional theory at local density and generalized gradient approximation levels. We found that the optical phonon branches of the transition metal chalcopyrite, are very sensitive to the specific bonding geometry and small changes in the transition metal environment

  11. Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure.

    Science.gov (United States)

    Hoy, Erik P; Mazziotti, David A

    2015-08-14

    Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.

  12. Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure

    Energy Technology Data Exchange (ETDEWEB)

    Hoy, Erik P.; Mazziotti, David A., E-mail: damazz@uchicago.edu [Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637 (United States)

    2015-08-14

    Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.

  13. A theoretical-spectroscopy, ab initio-based study of the electronic ground state of 121SbH3

    International Nuclear Information System (INIS)

    Yurchenko, Sergei N.; Carvajal, Miguel; Yachmenev, Andrey; Thiel, Walter; Jensen, Per

    2010-01-01

    For the stibine isotopologue 121 SbH 3 , we report improved theoretical calculations of the vibrational energies below 8000 cm -1 and simulations of the rovibrational spectrum in the 0-8000 cm -1 region. The calculations are based on a refined ab initio potential energy surface and on a new dipole moment surface obtained at the coupled cluster CCSD(T) level. The theoretical results are compared with the available experimental data in order to validate the ab initio surfaces and the TROVE computational method [Yurchenko SN, Thiel W, Jensen P. J Mol Spectrosc 2007;245:126-40] for calculating rovibrational energies and simulating rovibrational spectra of arbitrary molecules in isolated electronic states. A number of predicted vibrational energies of 121 SbH 3 are provided in order to stimulate new experimental investigations of stibine. The local-mode character of the vibrations in stibine is demonstrated through an analysis of the results in terms of local-mode theory.

  14. Ab-Initio-Based Kinetic Modeling to Understand RAFT Exchange: The Case of 2-Cyano-2-Propyl Dodecyl Trithiocarbonate and Styrene.

    Science.gov (United States)

    Desmet, Gilles B; De Rybel, Nils; Van Steenberge, Paul H M; D'hooge, Dagmar R; Reyniers, Marie-Françoise; Marin, Guy B

    2018-01-01

    Ab-initio-calculated rate coefficients for addition and fragmentation in reversible-addition fragmentation chain transfer (RAFT) polymerization of styrene with 2-cyano-2-propyl dodecyl trithiocarbonate initiated by azobisisobutyronitrile allow the reliable simulation of the experimentally observed conversion, number average chain length, and dispersity. The rate coefficient for addition of a macroradical R i to the macroRAFT agent R i X at 333 K (6.8 10 4 L mol -1 s -1 ) is significantly lower than to the initial RAFT agent R 0 X (3.2 10 6 L mol -1 s -1 ), mainly due to a difference in activation energy (15.4 vs 3.0 kJ mol -1 ), which causes the dispersity to spike in the beginning of the polymerization. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Ab initio electronic structure of quasi-two-dimensional materials: A “native” Gaussian–plane wave approach

    Energy Technology Data Exchange (ETDEWEB)

    Trevisanutto, Paolo E. [Graphene Research Centre and CA2DM, National University of Singapore, Singapore 117542, Singapore and Singapore Synchrotron Light Source, National University of Singapore, Singapore 117603 (Singapore); Vignale, Giovanni, E-mail: vignaleg@missouri.edu [Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211 (United States)

    2016-05-28

    Ab initio electronic structure calculations of two-dimensional layered structures are typically performed using codes that were developed for three-dimensional structures, which are periodic in all three directions. The introduction of a periodicity in the third direction (perpendicular to the layer) is completely artificial and may lead in some cases to spurious results and to difficulties in treating the action of external fields. In this paper we develop a new approach, which is “native” to quasi-2D materials, making use of basis function that are periodic in the plane, but atomic-like in the perpendicular direction. We show how some of the basic tools of ab initio electronic structure theory — density functional theory, GW approximation and Bethe-Salpeter equation — are implemented in the new basis. We argue that the new approach will be preferable to the conventional one in treating the peculiarities of layered materials, including the long range of the unscreened Coulomb interaction in insulators, and the effects of strain, corrugations, and external fields.

  16. Repulsive energy and the Grueneisen parameter of alkali halides calculated on the basis of a quantum-statistical ab initio theory

    International Nuclear Information System (INIS)

    Kucharczyk, M.; Olszewski, S.

    1982-01-01

    The Grueneisen parameter of alkali halides is calculated by an ab initio quantum-statistical method and then compared with the experimental data. The crystal model applied assumes the crystal ions to be compressible but impenetrable spheres. The ions are described with the aid of a modified Thomas-Fermi theory with exchange. At the next step it is possible to calculate the energy needed to transform the system of the non-interacting ions into the ionic system represented by the crystal lattice. This calculation allows for an ab initio estimate of the parameters entering the Born, or the Born-Mayer, repulsive part of the crystal energy. The parameters are then used in the calculation of the Grueneisen parameter and its dependence on the crystal compression. (author)

  17. Ab initio transport across bismuth selenide surface barriers

    KAUST Repository

    Narayan, Awadhesh

    2014-11-24

    © 2014 American Physical Society. We investigate the effect of potential barriers in the form of step edges on the scattering properties of Bi2Se3(111) topological surface states by means of large-scale ab initio transport simulations. Our results demonstrate the suppression of perfect backscattering, while all other scattering processes, which do not entail a complete spin and momentum reversal, are allowed. Furthermore, we find that the spin of the surface state develops an out-of-plane component as it traverses the barrier. Our calculations reveal the existence of quasibound states in the vicinity of the surface barriers, which appear in the form of an enhanced density of states in the energy window corresponding to the topological state. For double barriers we demonstrate the formation of quantum well states. To complement our first-principles results we construct a two-dimensional low-energy effective model and illustrate its shortcomings. Our findings are discussed in the context of a number of recent experimental works.

  18. Ab-Initio Description and Prediction of Properties of Carbon-Based and Other Non-Metallic Materials

    Science.gov (United States)

    Bagayoko, D.; Zhao, G. L.; Hasan, S.

    2001-01-01

    We have resolved the long-standing problem consisting of 30%-50% theoretical underestimates of the band gaps of non-metallic materials. We describe the Bagayoko, Zhao, and Williams (BZW) method that rigorously circumvents the basis-set and variational effect presumed to be a cause of these underestimates. We present ab-initio, computational results that are in agreement with experiment for diamond (C), silicon (Si), silicon carbides (3C-SiC and 4H-SiC), and other semiconductors (GaN, BaTiO3, AlN, ZnSe, ZnO). We illustrate the predictive capability of the BZW method in the case of the newly discovered cubic phase of silicon nitride (c-Si3N4) and of selected carbon nanotabes [(10,0), and (8,4)]. Our conclusion underscores the inescapable need for the BZW method in ab-initio calculations that employ a basis set in a variational approach. Current nanoscale trends amplify this need. We estimate that the potential impact of applications of the BZW method in advancing our understanding of nonmetallic materials, in informing experiment, and particularly in guiding device design and fabrication is simply priceless.

  19. Measurement of the elastic tensor of SmScO3 and NdScO3 using resonant ultrasound spectroscopy with ab initio calculations

    Directory of Open Access Journals (Sweden)

    K. A. Pestka II

    2011-09-01

    Full Text Available The complete elastic tensors of SmScO3 and NdScO3 were measured using resonant ultrasound spectroscopy (RUS in combination with ab-initio calculations. Measurement of the elastic tensor of these recently synthesized single crystal RE scandates is essential for understanding dynamic lattice applications including phonon confinement, strain induced thin film growth and superlattice construction. On average, the experimental elastic constants differed by less than 5% of the theoretical values, further validating the accuracy of modern ab-initio calculations as a means of estimating the initial elastic constants used in RUS measurements.

  20. Pair potentials for alumina from ab initio results on the Al2O3 molecule

    International Nuclear Information System (INIS)

    Akdeniz, Z.; Cicek, Z.; Tosi, M.P.

    2000-08-01

    We use results from an ab initio investigation by Chang et al. on energetically low-lying stationary points of the Al 2 O 3 molecule to determine interionic potentials for the Al-O, O-O and Al-Al pairs. Our results are discussed in the perspective of previous studies of the condensed phases of alumina, with special regard to the structure of its molten state. (author)

  1. Ab initio study of structural, electronic, optical, and vibrational properties of ZnxSy (x + y = 2 to 5) nanoclusters

    International Nuclear Information System (INIS)

    Yadav, P. S.; Pandey, D. K.; Agrawal, S.; Agrawal, B. K.

    2010-01-01

    An ab initio study of the stability, structural, electronic. and optical properties has been performed for 46 zinc sulfide nanoclusters Zn x S y (x + y = n = 2 to 5). Five out of them are seen to be unstable as their vibrational frequencies are found to be imaginary. A B3LYP-DFT/6-311G(3df) method is employed to optimize the geometries and a TDDFT method is used for the study of the optical properties. The binding energies (BE), HOMO-LUMO gaps and the bond lengths have been obtained for all the clusters. For the ZnS 2 , ZnS 3 , and ZnS 4 nanoclusters, our stable structures are seen to be different from those obtained earlier by using the effective core potentials. We have also considered the zero point energy (ZPE) corrections ignored by the earlier workers. For a fixed value of n, we designate the most stable structure the one, which has maximum final binding energy per atom. The adiabatic and vertical ionization potentials (IP) and electron affinities (EA), charges on the atoms, dipole moments, optical properties, vibrational frequencies, infrared intensities, relative infrared intensities, and Raman scattering activities have been investigated for the most stable structures. The nanoclusters containing large number of S atoms for each n is found to be most stable. The HOMO-LUMO gap decreases from n = 2-3 and then increases above n = 3. The IP and EA both fluctuate with the cluster size n. The optical absorption is quite weak in visible region but strong in the ultraviolet region in most of the nanoclusters except a few. The optical absorption spectrum or electron energy loss spectrum (EELS) is unique for every nanocluster and may be used to characterize a specific nanocluster. The growth of most stable nanoclusters may be possible in the experiments.

  2. Magnetic properties of vanadium doped CdTe: Ab initio calculations

    Energy Technology Data Exchange (ETDEWEB)

    Goumrhar, F. [Laboratory of Physics of High Energy, Modeling & Simulations (LPHE-MS), Faculty of Sciences, Mohammed V University of Rabat, Av. Ibn Batouta, B.P. 1014 Rabat (Morocco); Bahmad, L., E-mail: bahmad@fsr.ac.ma [Laboratory of Magnetism and High Energy Physics (LMPHE-URAC12), Faculty of Sciences, Mohammed V University of Rabat, Av. Ibn Batouta, B.P. 1014 Rabat (Morocco); Mounkachi, O. [Material and Nanomaterial Center, MAScIR Fondation, Rabat (Morocco); Benyoussef, A. [Laboratory of Magnetism and High Energy Physics (LMPHE-URAC12), Faculty of Sciences, Mohammed V University of Rabat, Av. Ibn Batouta, B.P. 1014 Rabat (Morocco); Material and Nanomaterial Center, MAScIR Fondation, Rabat (Morocco); Hassan II Academy of Sciences and Technology, Rabat (Morocco)

    2017-04-15

    In this paper, we are applying the ab initio calculations to study the magnetic properties of vanadium doped CdTe. This study is based on the Korringa–Kohn–Rostoker method (KKR) combined with the coherent potential approximation (CPA), within the local density approximation (LDA). This method is called KKR-CPA-LDA. We have calculated and plotted the density of states (DOS) in the energy diagram for different concentrations of dopants. We have also investigated the magnetic and half-metallic properties of this compound and shown the mechanism of exchange interaction. Moreover, we have estimated the Curie temperature T{sub c} for different concentrations. Finally, we have shown how the crystal field and the exchange splittings vary as a function of the concentrations.

  3. Manipulating magnetism and conductance of an adatom-molecule junction on a metal surface: An ab initio study

    DEFF Research Database (Denmark)

    Tao, Kun; Stepanyuk, V.S.; Bruno, P.

    2008-01-01

    The state of the art ab initio calculations reveal the effect of a scanning tunneling microscopy tip on magnetic properties and conductance of a benzene-adatom sandwich on Cu(001). We concentrate on a benzene-Co system interacting with a Cr tip. Our studies give a clear evidence that magnetism...

  4. An Ab Initio MP2 Study of HCN-HX Hydrogen Bonded Complexes

    Directory of Open Access Journals (Sweden)

    Araújo Regiane C.M.U.

    1998-01-01

    Full Text Available An ab initio MP2/6-311++G** study has been performed to obtain geometries, binding energies and vibrational properties of HCN-HX H-bonded complexes with X = F, Cl, NC, CN and CCH. These MP2/6-311++G** results have revealed that: (i the calculated H-bond lengths are in very good agreement with the experimental ones; (ii the H-bond strength is associated with the intermolecular charge transfer and follows the order: HCN-HNC ~ HCN-HF > HCN-HCl ~ HCN-HCN > HCN-HCCH; (iii BSSE correction introduces an average reduction of 2.4 kJ/mol on the MP2/6-311++G** binding energies, i.e. 11% of the uncorrected binding energy; (iv the calculated zero-point energies reduce the stability of these complexes and show a good agreement with the available experimental values; (v the H-X stretching frequency is shifted downward upon H-bond formation. This displacement is associated with the H-bond length; (vi The more pronounced effect on the infrared intensities occurs with the H-X stretching intensity. It is much enhanced after complexation due to the charge-flux term; (vii the calculated intermolecular stretching frequencies are in very good agreement with the experimental ones; and, finally, (viii the results obtained for the HCN-HX complexes follow the same profile as those found for the acetylene-HX series but, in the latter case, the effects on the properties of the free molecules due to complexation are less pronounced than those in HCN-HX.

  5. New type of in-gap states at a spinel/perovskite interface: combined resonant soft x-ray photoemission spectroscopy and first-principles study.

    Science.gov (United States)

    Borisov, Vladislav; Schuetz, Philipp; Pfaff, Florian; Scheiderer, Philipp; Dudy, Lenart; Zapf, Michael; Gabel, Judith; Christensen, Dennis Valbjorn; Chen, Yunzhong; Pryds, Nini; Strocov, Vladimir; Rogalev, Victor; Schlueter, Christoph; Lee, Tien-Lin; Jeschke, Harald O.; Valenti, Roser; Sing, Michael; Claessen, Ralph

    Oxygen vacancies in oxide heterostructures create a plethora of electronic phenomena not observed in the stoichiometric systems. In this talk we will discuss the presence of a new type of in-gap states at the spinel/perovskite γ-Al2O3/SrTiO3 interface, as observed in soft x-ray resonant photoemission spectroscopy. Based on ab initio calculations and crystal-field analysis of different atomic environments, we identify the origin of this behavior and we argue on the possible origin of the extraordinarily high electron mobility measured in this heterostructure. This work was financially supported by the Deutsche Forschungsgemeinschaft SFB/TR 49 and SFB 1170.

  6. Ab initio predictions on the rotational spectra of carbon-chain carbene molecules

    Science.gov (United States)

    Maluendes, S. A.; McLean, A. D.; Loew, G. H. (Principal Investigator)

    1992-01-01

    We predict rotational constants for the carbon-chain molecules H2C=(C=)nC, n=3-8, using ab initio computations, observed values for the earlier members in the series, H2CCC and H2CCCC with n=1 and 2, and empirical geometry corrections derived from comparison of computation and experiment on related molecules. H2CCC and H2CCCC have already been observed by radioastronomy; higher members in the series, because of their large dipole moments, which we have calculated, are candidates for astronomical searches. Our predictions can guide searches and assist in both astronomical and laboratory detection.

  7. Ab-initio theoretical study of electronic excitations and optical properties in nanostructures

    OpenAIRE

    Marchesín, Federico

    2017-01-01

    218 p. La miniaturización de los dispositivos electrónicos para la transferencia de información y procesado de señales ha impulsado el estudio de las propiedades electrónicas y la dinámica de excitaciones electrónicas en nanoestructuras. En particular, los cálculos ab-initio de las repuestas ópticas y los modos plasmónicos colectivos de nanoestructuras metálicas y de grafeno, han permitido profundizar en el conocimiento de la física y así poder avanzar hacia aplicaciones industriales en mu...

  8. Mechanistic Aspects of the Reversible Binding of SO2 on Arylplatinum Complexes: Experimental and ab Initio Studies

    NARCIS (Netherlands)

    Koten, G. van; Albrecht, M.A.; Gossage, R.A.; Frey, H.; Ehlers, A.W.; Baerends, E.J.; Merbach, A.E.

    2001-01-01

    The detailed mechanism of the reversible binding and fast exchange of SO2 on the organoplatinum(II) complex [PtI(NCN)], 1, has been studied experimentally in solution (C2F4Br2) using low-temperature NMR spectroscopy and theoretically by ab initio calculations. Direct bonding of SO2 and formation of

  9. Theoretical studies of H2--H2 collisions. IV. Ab initio calculations of anisotropic transport phenomena in para-hydrogen gas

    International Nuclear Information System (INIS)

    Koehler, W.E.; Schaefer, J.

    1983-01-01

    The temperature dependence of the effective Waldmann--Snider cross sections determining the Senftleben--Beenakker effects of viscosity and heat conductivity has been studied for pH 2 gas between 10 and 200 K. From ab initio nonspherical potentials of H 2 --H 2 , scattering matrices have been determined in close-coupling calculations. From these, the elements of the scattering amplitude matrix have been obtained and used as input quantities for the evaluation of the various Waldmann--Snider collision integrals. The results of these first ab initio numerical calculations of anisotropic transport coefficients show excellent agreement of calculated and measured effective cross sections, especially for the most recent improved version of the interaction potential. In addition, it has been shown that the polarization production cross sections are quite sensitive to the potential anisotropy

  10. Study of CeO{sub x}, PrO{sub x}, and Ce{sub x}Pr{sub 1-x}O{sub 2-{delta}} films on Si(111) by means of high-energetic X-ray photoelectron spectroscopy; Untersuchung von CeO{sub x}-, PrO{sub x}- und Ce{sub x}Pr{sub 1-x}O{sub 2-{delta}}- Filmen auf Si (111) mittels hochenergetischer Roentgen-Photoelektronenspektroskopie

    Energy Technology Data Exchange (ETDEWEB)

    Allahgholi, Aschkan

    2013-03-15

    The intention of this work is to shed light on two much discussed topics in the study of rare earth oxides (REO) by hard x-ray photoelectron spectroscopy (HAXPES): (i) Due to the complex spectral shape of the Ce3d region, there have been many discussions on proper approaches to determine the concentration of Ce{sup 3+} and Ce{sup 4+} species in CeO{sub x} over the last decades. (ii) Recently, the true electron structure of rare earth oxides gained new attention, since ab initio calculations showed the necessity of considering additional inter atomic charge transfer to Ce5d levels. Using HAXPES and resonant HAXPES, the question of the true electronic structure of rare earth oxides is approached from the experimental side. As a third topic, the obtained results for cerium oxide and praseodymium oxide are applied in order to investigate the plasma oxidized mixed oxide Ce{sub x}Pr{sub 1-x}O{sub 2-{delta}} grown on Si(111) during thermal reduction. (orig.)

  11. Ab initio analytical potential energy surface and quasiclassical trajectory study of the O+(4S)+H2(X 1Σg+)→OH+(X 3Σ-)+H(2S) reaction and isotopic variants

    International Nuclear Information System (INIS)

    Martinez, Rodrigo; Millan, Judith; Gonzalez, Miguel

    2004-01-01

    An analytical potential energy surface (PES) representation of the O + ( 4 S)+H 2 (X 1 Σ g + ) system was developed by fitting around 600 CCSD(T)/cc-pVQZ ab initio points. Rate constant calculations for this reaction and its isotopic variants (D 2 and HD) were performed using the quasiclassical trajectory (QCT) method, obtaining a good agreement with experimental data. Calculations conducted to determine the cross section of the title reaction, considering collision energies (E T ) below 0.3 eV, also led to good accord with experiments. This PES appears to be suitable for kinetics and dynamics studies. Moreover, the QCT results show that, although the hypotheses of a widely used capture model are not satisfied, the resulting expression for the cross section can be applied within a suitable E T interval, due to errors cancellation. This could be a general situation regarding the application of this simple model to ion-molecule processes

  12. Ab initio study of thermodynamic, electronic, magnetic, structural, and elastic properties of Ni4N allotropes

    Czech Academy of Sciences Publication Activity Database

    Hemzalová, P.; Friák, Martin; Šob, Mojmír; Ma, D.; Udyansky, A.; Raabe, D.; Neugebauer, J.

    2013-01-01

    Roč. 88, č. 17 (2013), Art. no. 174103 ISSN 1098-0121 R&D Projects: GA ČR(CZ) GAP108/12/0311; GA ČR GD106/09/H035; GA AV ČR IAA100100920 Institutional support: RVO:68081723 Keywords : nitrides * ab initio * thermodynamics * elasticity Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.664, year: 2013

  13. Electronic and thermoelectric properties of InN studied using ab initio density functional theory and Boltzmann transport calculations

    Energy Technology Data Exchange (ETDEWEB)

    Borges, P. D., E-mail: pdborges@gmail.com, E-mail: lscolfaro@txstate.edu; Scolfaro, L., E-mail: pdborges@gmail.com, E-mail: lscolfaro@txstate.edu [Department of Physics, Texas State University, San Marcos, Texas 78666 (United States)

    2014-12-14

    The thermoelectric properties of indium nitride in the most stable wurtzite phase (w-InN) as a function of electron and hole concentrations and temperature were studied by solving the semiclassical Boltzmann transport equations in conjunction with ab initio electronic structure calculations, within Density Functional Theory. Based on maximally localized Wannier function basis set and the ab initio band energies, results for the Seebeck coefficient are presented and compared with available experimental data for n-type as well as p-type systems. Also, theoretical results for electric conductivity and power factor are presented. Most cases showed good agreement between the calculated properties and experimental data for w-InN unintentionally and p-type doped with magnesium. Our predictions for temperature and concentration dependences of electrical conductivity and power factor revealed a promising use of InN for intermediate and high temperature thermoelectric applications. The rigid band approach and constant scattering time approximation were utilized in the calculations.

  14. Ionization energies of aqueous nucleic acids: Photoelectron spectroscopy of pyridine nucleosides and ab initio calculations

    Czech Academy of Sciences Publication Activity Database

    Slavíček, Petr; Winter, B.; Faubel, M.; Bradforth, S. E.; Jungwirth, Pavel

    2009-01-01

    Roč. 131, č. 18 (2009), s. 6460-6467 ISSN 0002-7863 R&D Projects: GA MŠk LC512; GA ČR GA203/08/0114 Grant - others:GA ČR(CZ) GP203/07/P449 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z40400503 Keywords : DNA bases * photoelectron spectroscopy * ab initio calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 8.580, year: 2009

  15. Combined experimental and ab-initio investigation of the physical properties of Ni{sub 3}Ge and Ni{sub 3}Al

    Energy Technology Data Exchange (ETDEWEB)

    Dinkel, Markus; Janisch, Rebecca; Pyczak, Florian; Goeken, Mathias [Institute General Materials Properties, University Erlangen-Nuernberg, Erlangen (Germany)

    2008-07-01

    Germanium is a promising element for brazing alloys to repair single crystalline ni-base superalloys. Germanium has the advantage that it forms an ordered Ni{sub 3}Ge phase with the same crystal structure as Ni{sub 3}Al ({gamma}' phase). The {gamma}' phase is responsible for the excellent mechanical properties of Ni-base superalloys at high temperature. Interdiffusion between the braze and the base material causes a decreasing concentration of germanium from the brazing zone to the base material and vice versa for aluminum. In the {gamma}' precipitates germanium is more and more substituted by aluminum, which should lead to changing properties of the {gamma}' phase between brazing zone center and base material. In our investigations we determined the chemical composition of binary Ni-Ge by energy dispersive spectroscopy in the electron microscope, the lattice constants using X-ray diffraction investigated the mechanical properties by nanoindentation in an atomic force microscope. Additionally, equilibrium lattice constants, energies of formation, bulk moduli and defect energies of pure Ni{sub 3}Ge and Ni{sub 3}Al phases were calculated by means of a spin-polarized ab initio density-functional method in the general-gradient approximation. The results are discussed in the light of the experimental data.

  16. Spectroscopic study of uracil, 1-methyluracil and 1-methyl-4-thiouracil: Hydrogen bond interactions in crystals and ab-initio molecular dynamics

    Science.gov (United States)

    Brela, Mateusz Z.; Boczar, Marek; Malec, Leszek M.; Wójcik, Marek J.; Nakajima, Takahito

    2018-05-01

    Hydrogen bond networks in uracil, 1-methyluracil and 1-methyl-4-thiouracil were studied by ab initio molecular dynamics as well as analysis of the orbital interactions. The power spectra calculated by ab initio molecular dynamics for atoms involved in hydrogen bonds were analyzed. We calculated spectra by using anharmonic approximation based on the autocorrelation function of the atom positions obtained from the Born-Oppenheimer simulations. Our results show the differences between hydrogen bond networks in uracil and its methylated derivatives. The studied methylated derivatives, 1-methyluracil as well as 1-methyl-4-thiouracil, form dimeric structures in the crystal phase, while uracil does not form that kind of structures. The presence of sulfur atom instead oxygen atom reflects weakness of the hydrogen bonds that build dimers.

  17. Many-body perturbation theory for ab initio nuclear structure

    International Nuclear Information System (INIS)

    Tichai, Alexander

    2017-01-01

    The solution of the quantum many-body problem for medium-mass nuclei using realistic nuclear interactions poses a superbe challenge for nuclear structure research. Because an exact solution can only be provided for the lightest nuclei, one has to rely on approximate solutions when proceeding to heavier systems. Over the past years, tremendous progress has been made in the development and application of systematically improvable expansion methods and an accurate description of nuclear observables has become viable up to mass number A ∼ 100. While closed-shell systems are consistently described via a plethora of different many-body methods, the extension to genuine open-shell systems still remains a major challenge and up to now there is no ab initio many-body method which applies equally well to systems with even and odd mass numbers. The goal of this thesis is the development and implementation of innovative perturbative approaches with genuine open-shell capabilities. This requires the extension of well-known single-reference approaches to more general vacua. In this work we choose two complementary routes for the usage of generalized reference states. First, we derive a new ab initio approach based on multi-configurational reference states that are conveniently derived from a prior no-core shell model calculation. Perturbative corrections are derived via second-order many-body perturbation theory, thus, merging configuration interaction and many-body perturbation theory. The generality of this ansatz enables for a treatment of medium-mass systems with arbitrary mass number, as well as the extension to low-lying excited states such that ground and excited states are treated on an equal footing. In a complementary approach, we use reference states that break a symmetry of the underlying Hamiltonian. In the simplest case this corresponds to the expansion around a particle-number-broken Hartree-Fock-Bogolyubov vacuum which is obtained from a mean-field calculation

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

    Science.gov (United States)

    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

  19. Development and characterization of a tunable ultrafast X-ray source via inverse-Compton-scattering

    International Nuclear Information System (INIS)

    Jochmann, Axel

    2014-01-01

    Ultrashort, nearly monochromatic hard X-ray pulses enrich the understanding of the dynamics and function of matter, e.g., the motion of atomic structures associated with ultrafast phase transitions, structural dynamics and (bio)chemical reactions. Inverse Compton backscattering of intense laser pulses from relativistic electrons not only allows for the generation of bright X-ray pulses which can be used in a pump-probe experiment, but also for the investigation of the electron beam dynamics at the interaction point. The focus of this PhD work lies on the detailed understanding of the kinematics during the interaction of the relativistic electron bunch and the laser pulse in order to quantify the influence of various experiment parameters on the emitted X-ray radiation. The experiment was conducted at the ELBE center for high power radiation sources using the ELBE superconducting linear accelerator and the DRACO Ti:sapphire laser system. The combination of both these state-of-the-art apparatuses guaranteed the control and stability of the interacting beam parameters throughout the measurement. The emitted X-ray spectra were detected with a pixelated detector of 1024 by 256 elements (each 26μm by 26μm) to achieve an unprecedented spatial and energy resolution for a full characterization of the emitted spectrum to reveal parameter influences and correlations of both interacting beams. In this work the influence of the electron beam energy, electron beam emittance, the laser bandwidth and the energy-anglecorrelation on the spectra of the backscattered X-rays is quantified. A rigorous statistical analysis comparing experimental data to ab-initio 3D simulations enabled, e.g., the extraction of the angular distribution of electrons with 1.5% accuracy and, in total, provides predictive capability for the future high brightness hard X-ray source PHOENIX (Photon electron collider for Narrow bandwidth Intense X-rays) and potential all optical gamma-ray sources. The results

  20. Quantum chemistry the development of ab initio methods in molecular electronic structure theory

    CERN Document Server

    Schaefer III, Henry F

    2004-01-01

    This guide is guaranteed to prove of keen interest to the broad spectrum of experimental chemists who use electronic structure theory to assist in the interpretation of their laboratory findings. A list of 150 landmark papers in ab initio molecular electronic structure methods, it features the first page of each paper (which usually encompasses the abstract and introduction). Its primary focus is methodology, rather than the examination of particular chemical problems, and the selected papers either present new and important methods or illustrate the effectiveness of existing methods in predi

  1. Electronic transport coefficients from ab initio simulations and application to dense liquid hydrogen

    International Nuclear Information System (INIS)

    Holst, Bastian; French, Martin; Redmer, Ronald

    2011-01-01

    Using Kubo's linear response theory, we derive expressions for the frequency-dependent electrical conductivity (Kubo-Greenwood formula), thermopower, and thermal conductivity in a strongly correlated electron system. These are evaluated within ab initio molecular dynamics simulations in order to study the thermoelectric transport coefficients in dense liquid hydrogen, especially near the nonmetal-to-metal transition region. We also observe significant deviations from the widely used Wiedemann-Franz law, which is strictly valid only for degenerate systems, and give an estimate for its valid scope of application toward lower densities.

  2. Solid-State Polymerization of Acetylene under Pressure: {ital Ab Initio} Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Bernasconi, M.; Parrinello, M. [Max-Planck-Institut fuer Festkoerperforschung, Heisenbergstr.1, D-70569 Stuttgart (Germany); Bernasconi, M. [Istituto Nazionale Fisica della Materia and Dipartimento di Fisica, Universita di Milano, Via Celoria 16, 20133 Milano (Italy); Chiarotti, G.; Focher, P.; Tosatti, E. [Istituto Nazionale Fisica della Materia and International School for Advanced Studies, Via Beirut 4, I-34014 Trieste (Italy); Tosatti, E. [International Centre for Theoretical Physics (ICTP), P.O.Box 586, I-34014 Trieste (Italy)

    1997-03-01

    We have simulated by {ital ab initio} constant pressure molecular dynamics the solid-state polymerization of acetylene recently observed experimentally in the pressure range 3.5{endash}14 GPa. We have found a massive polymerization only at much higher pressure (25 GPa). However, we have also found that a triplet exciton self-trapped on a single, {ital cis}-bent molecule in crystalline acetylene is a very effective polymerization seed at lower pressure ({lt}9GPa), much closer to the experimental threshold. Therefore, we propose that the polymerization observed experimentally is possibly catalyzed by a similar seed. We predict that injection of triplet excitons would greatly enhance the polymerization rate. {copyright} {ital 1997} {ital The American Physical Society}

  3. Ab initio research of stopping power for energetic ions in solids

    Energy Technology Data Exchange (ETDEWEB)

    He, Bin, E-mail: hebin-rc@163.com; Meng, Xu-Jun; Wang, Jian-Guo

    2017-03-01

    A new physical scenario is suggested to estimate the stopping power of energetic α particles in solid-density Be, Na, and Al at room temperature in an ab initio way based on the average atom model. In the scenario the stopping power is caused by the transition of free electrons to higher energy states and the ionization of bound electrons of the atom. Our results are found generally in good agreement with the recommended data in Al, Be and Na as well as the experimental data in Al. A comparison of energy loss with the recent experiment of protons in Be indicates that the scenario is more reasonable than the local density approximation in this case.

  4. Experimental and ab initio study of Ta-doped ZnO semiconductor

    Energy Technology Data Exchange (ETDEWEB)

    Munoz, E. L., E-mail: munoz@fisica.unlp.edu.ar; Richard, D., E-mail: richard@fisica.unlp.edu.ar [UNLP, Departamento de Fisica and Instituto de Fisica La Plata (IFLP, CCT La Plata, CONICET), Fac. de Ciencias Exactas (Argentina); Eversheim, P. D. [Universitaet Bonn, Helmholtz-Institut fuer Strahlen-und Kernphysik (H-ISKP) (Germany); Renteria, M., E-mail: renteria@fisica.unlp.edu.ar [UNLP, Departamento de Fisica and Instituto de Fisica La Plata (IFLP, CCT La Plata, CONICET), Fac. de Ciencias Exactas (Argentina)

    2010-04-15

    In this work, we present {gamma}-{gamma} Perturbed-Angular-Correlation results in polycrystalline ZnO semiconductor implanted with {sup 181}Hf({yields}{sup 181}Ta) probes. Calculations in Ta-doped ZnO were carried out using the Full-Potential Augmented Plane Wave plus local orbital method in a supercell and varying self-consistently the charge state of the impurity. Ta is a triple donor impurity with respect to Zn{sup 2 + } in ZnO and thus it can loose 1, 2 or 3 donor electrons under certain circumstances. As expected, the comparison between the experimental Electric-Field-Gradient tensor results and our ab initio predictions shows that the Ta impurity is in an ionized charge state at room temperature.

  5. Experimental and ab initio study of Ta-doped ZnO semiconductor

    International Nuclear Information System (INIS)

    Muñoz, E. L.; Richard, D.; Eversheim, P. D.; Rentería, M.

    2010-01-01

    In this work, we present γ–γ Perturbed-Angular-Correlation results in polycrystalline ZnO semiconductor implanted with 181 Hf(→ 181 Ta) probes. Calculations in Ta-doped ZnO were carried out using the Full-Potential Augmented Plane Wave plus local orbital method in a supercell and varying self-consistently the charge state of the impurity. Ta is a triple donor impurity with respect to Zn 2 +  in ZnO and thus it can loose 1, 2 or 3 donor electrons under certain circumstances. As expected, the comparison between the experimental Electric-Field-Gradient tensor results and our ab initio predictions shows that the Ta impurity is in an ionized charge state at room temperature.

  6. Ab initio determination of effective electron-phonon coupling factor in copper

    Science.gov (United States)

    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.

  7. Estudo da geometria da uréia por métodos ab initio e simulação computacional de líquidos

    Directory of Open Access Journals (Sweden)

    Cirino José Jair Vianna

    2002-01-01

    Full Text Available A study was carried out on the urea geometries using ab initio calculation and Monte Carlo computational simulation of liquids. The ab initio calculated results showed that urea has a non-planar conformation in the gas phase in which the hydrogen atoms are out of the plane formed by the heavy atoms. Free energies associated to the rotation of the amino groups of urea in water were obtained using the Monte Carlo method in which the thermodynamic perturbation theory is implemented. The magnitude of the free energy obtained from this simulation did not permit us to conclude that urea is non-planar in water.

  8. Estudo ab-initio da a-alanina em meio aquoso

    Directory of Open Access Journals (Sweden)

    Sambrano Júlio Ricardo

    1999-01-01

    Full Text Available Ab initio Hartree-Fock (HF, Density Functional (B3LYP and electron correlation (MP2 methods have been used to caracterize the aqueous medium intramolecular hydrogen bond in a-alanine. The 6-31G* and 6-31++G** were taken from Gaussian94 library. We were concerned on the structure of three conformers of a-alanine, in their neutral form plus on the structure of the zwitterionic form (Z. The Z structure is a stationary point at the HF/6-31G* level but it is not when diffuse functions and electron correlation are included. This results shows that the Z form does not exist in the gas phase. The inclusion of solvent effects changed significantly the results obtained in gas phase, therefore this inclusion make the Z form a stationary point within all level of theory, and the relative energy depends dramatically on the level of calculation.

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

    International Nuclear Information System (INIS)

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

    1985-01-01

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

  10. Theoretical study (ab initio and DFT methods on acidic dissociation constant of xylenol orange in aqueous solution

    Directory of Open Access Journals (Sweden)

    F. Kiani

    2017-07-01

    Full Text Available Analytical measurement of materials requires exact knowledge of their acid dissociation constant (pKa values. In recent years, quantum mechanical calculations have been extensively used to study of acidities in the aqueous solutions and the results were compared with the experimental values. In this study, a theoretical study was carried out on xylenol orange (in water solution by ab initio method. We calculated the pKa values of xylenol orange in water, using high-level ab initio (PM3, DFT (HF, B3LYP/6-31+G(d and SCRF methods. The experimental determination of these values (pKa,s is a challenge because xylenol orange has a low solubility in water. We considered several ionization reactions and equilibriums in water that constitute the indispensable theoretical basis to calculate the pKa values of xylenol orange. The results show that the calculated pKa values have a comparable agreement with the experimentally determined pKa values. Therefore, this method can be used to predict such properties for indicators, drugs and other important molecules.

  11. Thermodynamic properties by equation of state and from Ab initio molecular dynamics of liquid potassium under pressure

    Science.gov (United States)

    Li, Huaming; Tian, Yanting; Sun, Yongli; Li, Mo; Nonequilibrium materials; physics Team; Computational materials science Team

    In this work, we apply a general equation of state of liquid and Ab initio molecular-dynamics method to study thermodynamic properties in liquid potassium under high pressure. Isothermal bulk modulus and molar volume of molten sodium are calculated within good precision as compared with the experimental data. The calculated internal energy data and the calculated values of isobaric heat capacity of molten potassium show the minimum along the isothermal lines as the previous result obtained in liquid sodium. The expressions for acoustical parameter and nonlinearity parameter are obtained based on thermodynamic relations from the equation of state. Both parameters for liquid potassium are calculated under high pressure along the isothermal lines by using the available thermodynamic data and numeric derivations. Furthermore, Ab initio molecular-dynamics simulations are used to calculate some thermodynamic properties of liquid potassium along the isothermal lines. Scientific Research Starting Foundation from Taiyuan university of Technology, Shanxi Provincial government (``100-talents program''), China Scholarship Council and National Natural Science Foundation of China (NSFC) under Grant No. 51602213.

  12. Ab initio investigation of isomerism, structure and stability of dimer molecules of (LiMgH3)2 and (LiMgF3)2salts and their fragments

    International Nuclear Information System (INIS)

    Charkin, O.P.; Klimenko, N.M.; MakKi, M.L.

    2000-01-01

    Ab initio calculations of potential energy surfaces in neighborhood of key structures of non rigid dimer molecules of lithium salts of (LiMgX 3 ) 2 and binuclear anions Mg 2 X 5 - , dianions MgX 6 2- and molecules Mg 2 X 4 (X=H, F) are done in the framework of QCI-SD(T)/6-31(+)G**//MP2/6-31G* + ZPE(MP2/6-31G*) and MP2/6-31G*//HF/6-31G* + ZPE(HF/6-31G*) approximations. Equilibrium geometric parameters, relative energy and energy of decomposition of isomers, frequencies and IR-intensities of normal vibrations are determined. Data obtained are compared with results of analogous calculations for beryllium related compounds [ru

  13. A hydronitrogen solid: high pressure ab initio evolutionary structure searches

    International Nuclear Information System (INIS)

    Hu Anguang; Zhang Fan

    2011-01-01

    High pressure ab initio evolutionary structure searches resulted in a hydronitrogen solid with a composition of (NH) 4 . The structure searches also provided two molecular isomers, ammonium azide (AA) and trans-tetrazene (TTZ) which were previously discovered experimentally and can be taken as molecular precursors for high pressure synthesis of the hydronitrogen solid. The computed pressure versus enthalpy diagram showed that the transformation pressure to the hydronitrogen solid is 36 GPa from AA and 75 GPa from TTZ. Its metastability was analyzed by the phonon dispersion spectrum and room-temperature vibrational density of state together with the transformation energy barrier back to molecular phases at 298 K. The predicted energy barrier of 0.21 eV/atom means that the proposed hydronitrogen solid should be very stable at ambient conditions. (fast track communication)

  14. Ab initio, density functional theory, and continuum solvation model prediction of the product ratio in the S(N)2 reaction of NO2(-) with CH3CH2Cl and CH3CH2Br in DMSO solution.

    Science.gov (United States)

    Westphal, Eduard; Pliego, Josefredo R

    2007-10-11

    The reaction pathways for the interaction of the nitrite ion with ethyl chloride and ethyl bromide in DMSO solution were investigated at the ab initio level of theory, and the solvent effect was included through the polarizable continuum model. The performance of BLYP, GLYP, XLYP, OLYP, PBE0, B3PW91, B3LYP, and X3LYP density functionals has been tested. For the ethyl bromide case, our best ab initio calculations at the CCSD(T)/aug-cc-pVTZ level predicts product ratio of 73% and 27% for nitroethane and ethyl nitrite, respectively, which can be compared with the experimental values of 67% and 33%. This translates to an error in the relative DeltaG* of only 0.17 kcal mol(-1). No functional is accurate (deviation X3LYP functional presents the best performance with deviation 0.82 kcal mol(-1). The present problem should be included in the test set used for the evaluation of new functionals.

  15. Interaction of single-walled carbon nanotubes and saxitoxin: Ab initio simulations and biological responses in hippocampal cell line HT-22.

    Science.gov (United States)

    Ramos, Patrícia; Schmitz, Marcos; Filgueira, Daza; Votto, Ana Paula; Durruthy, Michael; Gelesky, Marcos; Ruas, Caroline; Yunes, João; Tonel, Mariana; Fagan, Solange; Monserrat, José

    2017-07-01

    Saxitoxins (STXs) are potent neurotoxins that also induce cytotoxicity through the generation of reactive oxygen species. Carbon nanotubes (CNTs) are nanomaterials that can promote a Trojan horse effect, facilitating the entry of toxic molecules to cells when adsorbed to nanomaterials. The interaction of pristine single-walled (SW)CNTs and carboxylated (SWCNT-COOH) nanotubes with STX was evaluated by ab initio simulation and bioassays using the cell line HT-22. Cells (5 × 10 4  cells/mL) were exposed to SWCNT and SWCNT-COOH (5 μg mL -1 ), STX (200 μg L -1 ), SWCNT+STX, and SWCNT-COOH+STX for 30 min or 24 h. Results of ab initio simulation showed that the interaction between SWCNT and SWCNT-COOH with STX occurs in a physisorption. The interaction of SWCNT+STX induced a decrease in cell viability. Cell proliferation was not affected in any treatment after 30 min or 24 h of exposure (p > 0.05). Treatment with SWCNT-COOH induced high reactive oxygen species levels, an effect attenuated in SWCNT-COOH+STX treatment. In terms of cellular oxygen consumption, both CNTs when coexposed with STX antagonize the toxin effect. Based on these results, it can be concluded that the results obtained in vitro corroborate the semiempirical evidence found using density functional theory ab initio simulation. Environ Toxicol Chem 2017;36:1728-1737. © 2016 SETAC. © 2016 SETAC.

  16. Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations

    Science.gov (United States)

    Martins, Luan Carvalho; Torres, Pedro Henrique Monteiro; de Oliveira, Renata Barbosa; Pascutti, Pedro Geraldo; Cino, Elio A.; Ferreira, Rafaela Salgado

    2018-05-01

    Chagas disease remains a major health problem in South America, and throughout the world. The two drugs clinically available for its treatment have limited efficacy and cause serious adverse effects. Cruzain is an established therapeutic target of Trypanosoma cruzi, the protozoan that causes Chagas disease. Our group recently identified a competitive cruzain inhibitor (compound 1) with an IC50 = 15 µM that is also more synthetically accessible than the previously reported lead, compound 2. Prior studies, however, did not propose a binding mode for compound 1, hindering understanding of the structure-activity relationship and optimization. Here, the cruzain binding mode of compound 1 was investigated using docking, molecular dynamics (MD) simulations with ab initio derived parameters, ab initio calculations, and MM/PBSA. Two ligand protonation states and four binding poses were evaluated. A careful ligand parameterization method was employed to derive more physically meaningful parameters than those obtained by automated tools. The poses of unprotonated 1 were unstable in MD, showing large conformational changes and diffusing away from the binding site, whereas the protonated form showed higher stability and interaction with negatively charged residues Asp161 and Cys25. MM/PBSA also suggested that these two residues contribute favorably to binding of compound 1. By combining results from MD, ab initio calculations, and MM/PBSA, a binding mode of 1 is proposed. The results also provide insights for further optimization of 1, an interesting lead compound for the development of new cruzain inhibitors.

  17. Ab initio study of energetics and magnetism of sigma phase in Co–Mo and Fe–Mo systems

    Czech Academy of Sciences Publication Activity Database

    Pavlů, Jana; Vřešťál, Jan; Šob, Mojmír

    2016-01-01

    Roč. 24, č. 2 (2016), č. článku Art. Number 025009. ISSN 0965-0393 R&D Projects: GA ČR GA14-15576S Institutional support: RVO:68081723 Keywords : intermetallics * magnetic properties * phase stability * thermodynamic properties * site occupancy * ab-initio calculations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.891, year: 2016

  18. Ab initio study of thermoelectric properties of doped SnO_2 superlattices

    International Nuclear Information System (INIS)

    Borges, P.D.; Silva, D.E.S.; Castro, N.S.; Ferreira, C.R.; Pinto, F.G.; Tronto, J.; Scolfaro, L.

    2015-01-01

    Transparent conductive oxides, such as tin dioxide (SnO_2), have recently shown to be promising materials for thermoelectric applications. In this work we studied the thermoelectric properties of Fe-, Sb- and Zn-uniformly doping and co-doping SnO_2, as well as of Sb and Zn planar (or delta)-doped layers in SnO_2 forming oxide superlattices (SLs). Based on the semiclassical Boltzmann transport equations (BTE) in conjunction with ab initio electronic structure calculations, the Seebeck coefficient (S) and figure of merit (ZT) are obtained for these systems, and are compared with available experimental data. The delta doping approach introduces a remarkable modification in the electronic structure of tin dioxide, when compared with the uniform doping, and colossal values for ZT are predicted for the delta-doped oxide SLs. This result is a consequence of the two-dimensional electronic confinement and the strong anisotropy introduced by the doped planes. In comparison with the uniformly doped systems, our predictions reveal a promising use of delta-doped SnO_2 SLs for enhanced S and ZT, which emerge as potential candidates for thermoelectric applications. - Graphical abstract: Band structure and Figure of merit for SnO2:Sb superlattice along Z direction, P. D. Borges, D. E. S. Silva, N. S. Castro, C. R. Ferreira, F. G. Pinto, J. Tronto and L. Scolfaro, Ab initio study of thermoelectric properties of doped SnO2 superlattices. - Highlights: • Thermoelectric properties of SnO_2-based alloys and superlattices. • High figure of merit is predicted for planar-doped SnO_2 superlattices. • Nanotechnology has an important role for the development of thermoelectric devices.

  19. Ab initio study of MgH2 formation

    International Nuclear Information System (INIS)

    Novakovic, Nikola; Matovic, Ljiljana; Novakovic, Jasmina Grbovic; Manasijevic, Miodrag; Ivanovic, Nenad

    2009-01-01

    Even if there is considerable literature dealing with structure and properties of MgH 2 compound there are still some uncertain details about nature of bonding governing its formation and decomposition. In order to better understand the processes essential for absorption and desorption of MgH 2 , ab initio DFT based calculations of rutile MgH 2 compound, elemental hcp-Mg, and three different hypothetical hcp-Mg-derived hydrides are performed. Our findings show that all structures are unstable, and that MgH (Wurtzite) is a closest possible candidate for intermediate phase between the hcp-Mg and MgH 2 at 1:1 stoichiometry. An alternative hydration pathway is suggested, including promotion of hcp-Mg to bcc-Mg and consecutive transformation to rutile MgH 2 by means of hydrogen incorporation into Mg matrix. Rutile MgH 2 calculations with various hydrogen vacancies concentration are performed. Calculation shows that at high hydrogen concentration close to 1:2, stable substoichiometric hydride is possible. Calculation also shows that high vacancy (low hydrogen) concentration favors bcc-Mg 2 H over rutile Mg 2 H structure.

  20. Double-walled silicon nanotubes: an ab initio investigation

    Science.gov (United States)

    Lima, Matheus P.

    2018-02-01

    The synthesis of silicon nanotubes realized in the last decade demonstrates multi-walled tubular structures consisting of Si atoms in {{sp}}2 and the {{sp}}3 hybridizations. However, most of the theoretical models were elaborated taking as the starting point {{sp}}2 structures analogous to carbon nanotubes. These structures are unfavorable due to the natural tendency of the Si atoms to undergo {{sp}}3. In this work, through ab initio simulations based on density functional theory, we investigated double-walled silicon nanotubes proposing layered tubes possessing most of the Si atoms in an {{sp}}3 hybridization, and with few {{sp}}2 atoms localized at the outer wall. The lowest-energy structures have metallic behavior. Furthermore, the possibility to tune the band structure with the application of a strain was demonstrated, inducing a metal-semiconductor transition. Thus, the behavior of silicon nanotubes differs significantly from carbon nanotubes, and the main source of the differences is the distortions in the lattice associated with the tendency of Si to make four chemical bonds.

  1. Ab initio modelling of methane hydrate thermophysical properties.

    Science.gov (United States)

    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.

  2. Ab initio theory of the N2V defect in diamond for quantum memory implementation

    Science.gov (United States)

    Udvarhelyi, Péter; Thiering, Gergő; Londero, Elisa; Gali, Adam

    2017-10-01

    The N2V defect in diamond is characterized by means of ab initio methods relying on density functional theory calculated parameters of a Hubbard model Hamiltonian. It is shown that this approach appropriately describes the energy levels of correlated excited states induced by this defect. By determining its critical magneto-optical parameters, we propose to realize a long-living quantum memory by N2V defect, i.e., H 3 color center in diamond.

  3. Ab initio study of Co and Ni under uniaxial and biaxial loading and in epitaxial overlayers

    Czech Academy of Sciences Publication Activity Database

    Zelený, Martin; Legut, Dominik; Šob, Mojmír

    2008-01-01

    Roč. 78, č. 22 (2008), 224105/1-224105/11 ISSN 1098-0121 R&D Projects: GA ČR GD106/05/H008; GA AV ČR IAA1041302; GA MŠk OC 147 Institutional research plan: CEZ:AV0Z20410507 Keywords : ab initio calculations * epitaxial overlayers * uniaxial and biaxial loading Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.322, year: 2008

  4. Towards efficient ab initio calculations of electron scattering by polyatomic molecules: III. Modelling correlation-polarization interactions

    Czech Academy of Sciences Publication Activity Database

    Čurík, Roman; Šulc, M.

    2010-01-01

    Roč. 43, č. 17 (2010), s. 175205 ISSN 0953-4075 R&D Projects: GA MŠk(CZ) OC10046; GA MŠk OC09079; GA AV ČR KJB400400803; GA ČR GA202/08/0631 Institutional research plan: CEZ:AV0Z40400503 Keywords : Ab initio calculations * Commonly used * DFT potential Subject RIV: CF - Physical ; The oretical Chemistry Impact factor: 1.902, year: 2010

  5. Ab-initio simulations of pressure effects on structural and electronic properties of iron based superconductors

    International Nuclear Information System (INIS)

    Tomic, Milan

    2013-01-01

    The ab-initio molecular dynamics framework has been the cornerstone of computational solid state physics in the last few decades. Although it is already a mature field it is still rapidly developing to accommodate the growth in solid state research as well as to efficiently utilize the increase in computing power. Starting from the first principles, the ab-initio molecular dynamics provides essential information about structural and electronic properties of matter under various external conditions. In this thesis we use the ab-initio molecular dynamics to study the behavior of BaFe 2 As 2 and CaFe 2 As 2 under the application of external pressure. BaFe 2 As 2 and CaFe 2 As 2 belong to the family of iron based superconductors which are a novel and promising superconducting materials. The application of pressure is one of two key methods by which electronic and structural properties of iron based superconductors can be modified, the other one being doping (or chemical pressure). In particular, it has been noted that pressure conditions have an important effect, but their exact role is not fully understood. To better understand the effect of different pressure conditions we have performed a series of ab-initio simulations of pressure application. In order to apply the pressure with arbitrary stress tensor we have developed a method based on the Fast Inertial Relaxation Engine, whereby the unit cell and the atomic positions are evolved according to the metadynamical equations of motion. We have found that the application of hydrostatic and c axis uniaxial pressure induces a phase transition from the magnetically ordered orthorhombic phase to the non-magnetic collapsed tetragonal phase in both BaFe 2 As 2 and CaFe 2 As 2 . In the case of BaFe 2 As 2 , an intermediate tetragonal non-magnetic tetragonal phase is observed in addition. Application of the uniaxial pressure parallel to the c axis reduces the critical pressure of the phase transition by an order of magnitude

  6. Ab initio Hartree-Fock study on surface desorption process in tritium release

    International Nuclear Information System (INIS)

    Taniguchi, M.; Tanaka, S.

    1998-01-01

    Dissociative adsorption of hydrogen on Li 2 O (110) surface has been investigated with ab initio Hartree-Fock quantum chemical calculation technique. Heat of adsorption and surface potential energy for H 2 dissociative adsorption were evaluated by calculating the total energy of the system. The calculated results on adsorption heat indicated that H 2 adsorption is endothermic. However, when an oxygen vacancy exists adjacent to the adsorption site, the heat of adsorption became less endothermic and the activation energy required to dissociate the H-H bonding was smaller than that for the terrace site. This is considered to be caused by the excess charge localized near the defect. (orig.)

  7. Core structure of screw dislocations in Fe from first-principles; Simulation ab initio des coeurs de dislocation vis dans le fer

    Energy Technology Data Exchange (ETDEWEB)

    Ventelon, L

    2008-11-15

    The various methods appropriate for the simulation of dislocations within first-principles calculations have been set up, improved and compared between them. They have been applied to study screw dislocations in body-centered cubic iron using the SIESTA code. A non-degenerate core structure is obtained; its detailed analysis reveals a dilatation effect. Taking it into account in an anisotropic elasticity model, allows explaining the cell-size dependence of the energetics, obtained within the dipole approach. The Peierls potential obtained in ab initio suggests that the metastable core configuration at halfway position in the Peierls barrier, predicted by empirical potential, does not exist. We show how to construct tri-periodic cells optimized to study kinked dislocations. Using empirical potential, we demonstrate the feasibility of ab initio calculations of Peierls stress and kink formation. (author)

  8. Graph Theory Meets Ab Initio Molecular Dynamics: Atomic Structures and Transformations at the Nanoscale

    Science.gov (United States)

    Pietrucci, Fabio; Andreoni, Wanda

    2011-08-01

    Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.

  9. Experimental and theoretical study of electronic structure of aluminum in extreme conditions with X-ray absorption spectroscopy

    International Nuclear Information System (INIS)

    Festa, Floriane

    2013-01-01

    Matter in extreme conditions belongs to Warm Dense Matter regime which lays between dense plasma regime and condensed matter. This regime is still not well known, indeed it is very complex to generate such plasma in the laboratory to get experimental data and validate models. The goal of this thesis is to study electronic structure of aluminum in extreme conditions with X-ray absorption spectroscopy. Experimentally aluminum has reached high densities and high temperatures, up to now unexplored. An X-ray source has also been generated to probe highly compressed aluminum. Two spectrometers have recorded aluminum absorption spectra and aluminum density and temperature conditions have been deduced thanks to optical diagnostics. Experimental spectra have been compared to ab initio spectra, calculated in the same conditions. The theoretical goal was to validate the calculation method in high densities and high temperatures regime with the study of K-edge absorption modifications. We also used absorption spectra to study the metal-non metal transition which takes place at low density (density ≤ solid density). This transition could be study with electronic structure modifications of the system. (author) [fr

  10. Isomerism of OBe3F3+ cation: an ab initio study

    International Nuclear Information System (INIS)

    Klimenko, N.M.; Rykova, E.A.; MakKi, M.L.; Senchenya, I.N.

    1999-01-01

    Ab initio MP2/6-31G*/HF/6-31G*+ZPE(HF/6-31G*) calculations of the potential energy surface in the vicinity of stationary points and the pathways of intramolecular rearrangements between low-lying structures of the OBe 3 F 3 + cation detected in the mass spectra of μ 4 -Be 4 O(CF 3 COO) 6 were carried out. Ten stable isomers with di- and tricoordinate oxygen atoms were localized. The relative energies of six structures lie in the range 0-8 kcal mol -1 and those of the rest four structures lie in the range 20-40 kcal mol -1 . two most favorable isomers are a planar C 2 , isomer and a pyramidal C 3 isomer [ru

  11. Towards efficient ab initio calculations of electron scattering by polyatomic molecules: II. Efficient evaluation of exchange integrals

    Czech Academy of Sciences Publication Activity Database

    Čársky, Petr

    2010-01-01

    Roč. 43, č. 17 (2010), s. 175204 ISSN 0953-4075 R&D Projects: GA MŠk OC09079; GA MŠk(CZ) OC10046; GA ČR GA202/08/0631 Institutional research plan: CEZ:AV0Z40400503 Keywords : ab initio calculations * electron scattering * polyatomic molecules Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.902, year: 2010

  12. Simple calculation of ab initio melting curves: Application to aluminum.

    Science.gov (United States)

    Robert, Grégory; Legrand, Philippe; Arnault, Philippe; Desbiens, Nicolas; Clérouin, Jean

    2015-03-01

    We present a simple, fast, and promising method to compute the melting curves of materials with ab initio molecular dynamics. It is based on the two-phase thermodynamic model of Lin et al [J. Chem. Phys. 119, 11792 (2003)] and its improved version given by Desjarlais [Phys. Rev. E 88, 062145 (2013)]. In this model, the velocity autocorrelation function is utilized to calculate the contribution of the nuclei motion to the entropy of the solid and liquid phases. It is then possible to find the thermodynamic conditions of equal Gibbs free energy between these phases, defining the melting curve. The first benchmark on the face-centered cubic melting curve of aluminum from 0 to 300 GPa demonstrates how to obtain an accuracy of 5%-10%, comparable to the most sophisticated methods, for a much lower computational cost.

  13. Phénomènes de transport : contribution de l'approche ab initio et applications

    OpenAIRE

    Vérot, Martin

    2013-01-01

    In a first part, we studied the magnetic properties of organic radicals (coupled with rare earth or between each other). We calculated the magnetic exchange and the g-tensor of these compounds to understand their magnetic susceptibility and thei magnetization curves via ab initio calculations based on the wave-function. We studied how the chemistry and the crystal stacking affect meaningful parameters linked to magnetism and conduction. Those parameters were extracted with the thory of effect...

  14. Ab-initio calculations for dilute magnetic semiconductors

    Energy Technology Data Exchange (ETDEWEB)

    Belhadji, Brahim

    2008-03-03

    This thesis focusses on ab-initio calculations for the electronic structure and the magnetic properties of dilute magnetic semiconductors (DMS). In particular we aim at the understanding of the complex exchange interactions in these systems. Our calculations are based on density functional theory, being ideally suited for a description of the material specific properties of the considered DMS. Moreover we use the KKR Green function method in connection with the coherent potential approximation (CPA), which allows to include the random substitutional disorder in a mean field-like approximation for the electronic structure. Finally we calculate the exchange coupling constants J{sub ij} between two impurities in a CPA medium by using the Lichtenstein formula and from this calculate the Curie temperature by a numerically exact Monte Carlo method. Based on this analysis we found and investigated four different exchange mechanisms being of importance in DMS systems: Double exchange, p-d exchange, antiferromagnetic superexchanges, and ferromagnetic superexchange. A second topic we have investigated in this thesis is the pressure dependence of the exchange interactions and the Curie temperatures in (Ga,Mn)As and (In,Mn)As, using the LDA and the LDA+U approximations. Exact calculations of T{sub C} by Monte Carlo simulations show a somehow different behavior. (orig.)

  15. The effect of 3-aminobenzamide on X-ray induction of chromosome aberrations in Down syndrome lymphocytes

    International Nuclear Information System (INIS)

    McLaren, R.A.; Au, W.W.; Legator, M.S.

    1989-01-01

    Human lymphocytes from normal and Down syndrome (DS) subjects were examined to determine the effect of 3-aminobenzamide (3AB) on X-ray-induced chromosome aberrations. Lymphocytes were treated with 150 or 300 rad of X-rays in the presence of 3 mM 3AB for various times after irradiation, and then the cells were analyzed for the presence of chromosome aberrations in mitotic cells. 3-Aminobenzamide had no effect on the frequency of chromosome aberrations as a result of treatment with X-rays in the presence of 3AB. These observations indicate that DS lymphocytes are more sensitive to the inhibition of poly(ADP)ribose synthetase than normal lymphocytes. (author). 44 refs.; 3 tabs

  16. Ab initio investigation of isomerism, structure and stability of dimer molecules of Beryllate salts (LiBeH3)2, (LiBeF3)2 and their fragments

    International Nuclear Information System (INIS)

    Charkin, O.P.; Klimenko, N.M.; MakKi, M.L.

    2000-01-01

    In the framework of correlated approximation method QCI-SD(T)/6-31(+)G** + ZPE(MP2/6-31G*) and MP2/6-31(+)G* + ZPE(HF/6-31G*) ab initio calculations of surfaces and potential energy in the surroundings of key structures of not rigid dimer molecules of beryllate and fluoroberyllate complex salts (LiBeX 3 ) 2 , binuclear anions Be 2 X 5 - , dianions Be 2 X 6 2- and molecules Be 2 X 4 (X=H, F) are done. Equilibrium geometrical parameters of isomers, frequencies and relative IR intensities of normal vibrations, their relative energies and decomposition energies are determined. Similarity and differences of hydrides and fluorides, deformation and polarization of anions under cation effect in the case of their different mutual orientation are analyzed [ru

  17. State-of-the-art ab initio potential energy curve for the xenon atom pair and related spectroscopic and thermophysical properties

    Science.gov (United States)

    Hellmann, Robert; Jäger, Benjamin; Bich, Eckard

    2017-07-01

    A new ab initio interatomic potential energy curve for two ground-state xenon atoms is presented. It is based on supermolecular calculations at the coupled-cluster level with single, double, and perturbative triple excitations [CCSD(T)] employing basis sets up to sextuple-zeta quality, which were developed as part of this work. In addition, corrections were determined for higher coupled-cluster levels up to CCSDTQ as well as for scalar and spin-orbit relativistic effects at the CCSD(T) level. A physically motivated analytical function was fitted to the calculated interaction energies and used to compute the vibrational spectrum of the dimer, the second virial coefficient, and the dilute gas transport properties. The agreement with the best available experimental data for the investigated properties is excellent; the new potential function is superior not only to previous ab initio potentials but also to the most popular empirical ones.

  18. State-of-the-art ab initio potential energy curve for the xenon atom pair and related spectroscopic and thermophysical properties.

    Science.gov (United States)

    Hellmann, Robert; Jäger, Benjamin; Bich, Eckard

    2017-07-21

    A new ab initio interatomic potential energy curve for two ground-state xenon atoms is presented. It is based on supermolecular calculations at the coupled-cluster level with single, double, and perturbative triple excitations [CCSD(T)] employing basis sets up to sextuple-zeta quality, which were developed as part of this work. In addition, corrections were determined for higher coupled-cluster levels up to CCSDTQ as well as for scalar and spin-orbit relativistic effects at the CCSD(T) level. A physically motivated analytical function was fitted to the calculated interaction energies and used to compute the vibrational spectrum of the dimer, the second virial coefficient, and the dilute gas transport properties. The agreement with the best available experimental data for the investigated properties is excellent; the new potential function is superior not only to previous ab initio potentials but also to the most popular empirical ones.

  19. Substituent Inductive Effects on the Electrochemical Oxidation of Flavonoids Studied by Square Wave Voltammetry and Ab Initio Calculations.

    Science.gov (United States)

    Arroyo-Currás, Netzahualcóyotl; Rosas-García, Víctor M; Videa, Marcelo

    2016-10-27

    Flavonoids are natural products commonly found in the human diet that show antioxidant, anti-inflammatory and anti-hepatotoxic activities. These nutraceutical properties may relate to the electrochemical activity of flavonoids. To increase the understanding of structure-electrochemical activity relations and the inductive effects that OH substituents have on the redox potential of flavonoids, we carried out square-wave voltammetry experiments and ab initio calculations of eight flavonoids selected following a systematic variation in the number of hydroxyl substituents and their location on the flavan backbone: three flavonols, three anthocyanidins, one anthocyanin and the flavonoid backbone flavone. We compared the effect that the number of -OH groups in the ring B of flavan has on the oxidation potential of the flavonoids considered, finding linear correlations for both flavonols and anthocyanidins ( R 2 = 0.98 ). We analyzed the effects that position and number of -OH substituents have on electron density distributions via ab initio quantum chemical calculations. We present direct correlations between structural features and oxidation potentials that provide a deeper insight into the redox chemistry of these molecules.

  20. X-ray diffraction study of directionally grown perylene crystallites

    DEFF Research Database (Denmark)

    Breiby, Dag W.; Lemke, H. T.; Hammershøj, P.

    2008-01-01

    Using grazing incidence X-ray diffraction, perylene crystallites grown on thin highly oriented poly(tetrafluoroethylene) (PTFE) films on silicon substrates have been investigated. All the perylene crystallites are found to orient with the ab plane of the monoclinic unit cell parallel to the subst......Using grazing incidence X-ray diffraction, perylene crystallites grown on thin highly oriented poly(tetrafluoroethylene) (PTFE) films on silicon substrates have been investigated. All the perylene crystallites are found to orient with the ab plane of the monoclinic unit cell parallel...... to the substrate. The scattering data is interpreted as a trimodal texture of oriented perylene crystallites, induced by interactions between the perylene molecules and the oriented PTFE substrate. Three families of biaxial orientations are seen, with the axes (h = 1, 2, or 3) parallel to the PTFE alignment......, all having the ab-plane parallel to the substrate. About 92% of the scattered intensity corresponds to a population with highly parallel to (PTFE)....