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1

Ab initio pseudopotential theory

International Nuclear Information System (INIS)

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

2

Nuclear Structure - "ab initio"

An ab-initio description of atomic nuclei that solves the nuclear many-body problem for realistic nuclear forces is expected to possess a high degree of predictive power. In this contribution we treat the main obstacle, namely the short-ranged repulsive and tensor correlations induced by the realistic nucleon-nucleon interaction, by means of a unitary correlation operator. This correlator applied to uncorrelated many-body states imprints short-ranged correlations that cannot...

Feldmeier, Hans; Neff, Thomas; Roth, Robert

2003-01-01

3

Ab initio potential for solids

A total-energy theory for a solid is presented. It is based on density-functional theory and consists of a succession of approximations. At the most accurate level, the theory consists of a systematic derivation of an ansatz for the electron density which is best suited for the Harris functional. 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 i...

Chetty, N.; Stokbro, Kurt; Jacobsen, Karsten Wedel; Nørskov, Jens Kehlet

1992-01-01

4

Computer simulations and molecular dynamics in particular, is a very powerful method to provide detailed and essentially exact informations of classical many-body problems. With the advent of \\textit{ab-initio} molecular dynamics, where the forces are computed on-the-fly by accurate electronic structure calculations, the scope of either method has been greatly extended. This new approach, which unifies Newton's and Schr\\"odinger's equations, allows for complex simulations without relying on any adjustable parameter. This review is intended to outline the basic principles as well as a survey of the field. Beginning with the derivation of Born-Oppenheimer molecular dynamics, the Car-Parrinello method as well as novel hybrid scheme that unifies best of either approach are discussed. The predictive power is demonstrated by a series of applications ranging from insulators to semiconductors and even metals in condensed phases.

Kühne, Thomas D

2012-01-01

5

Ab initio potential for solids

DEFF Research Database (Denmark)

A total-energy theory for a solid is presented. It is based on density-functional theory and consists of a succession of approximations. At the most accurate level, the theory consists of a systematic derivation of an ansatz for the electron density which is best suited for the Harris functional. 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 thus be tested independently. The theory is applied to calculations of the surface energies and vacancy formation energy of Al. At the most accurate level, the theory gives results that are in almost complete agreement with self-consistent calculations. At the more approximate, but also computationally much less demanding, level, the theory gives results that are still in excellent agreement with the self-consistent results.

Chetty, N.; Stokbro, Kurt

1992-01-01

6

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

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

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

2013-01-01

7

Ab initio calculation of valley splitting in monolayer ?-doped phosphorus in silicon

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

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

2013-02-01

8

Ab initio valence calculations in chemistry

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

Cook, D B

1974-01-01

9

Ab initio calculations of free-energy reaction barriers.

The theoretical description of chemical reactions was until recently limited to a 'static' approach in which important parameters such as the rate constant are deduced from the local topology of the potential energy surface close to minima and saddle points. Such an approach has, however, serious limitations. The growing computational power allows us now to use advanced simulation techniques to determine entropic effects accurately for medium-sized systems at ab initio level. Recently, we have implemented free-energy simulation techniques based on molecular dynamics, in particular on the blue-moon ensemble technique and on metadynamics, in the popular DFT code VASP. In the thermodynamic integration (blue-moon ensemble) technique, the free-energy profile is calculated as the path integral over the restoring forces along a parametrized reaction coordinate. In metadynamics, an image of the free-energy surface is constructed on the fly during the simulation by adding small repulsive Gaussian-shaped hills to the Lagrangian driving the dynamics. The two methods are tested on a simple chemical reaction-the nucleophilic substitution of methyl chloride by a chlorine anion. PMID:21693873

Bucko, T

2008-02-13

10

Ab initio calculations of free-energy reaction barriers

Energy Technology Data Exchange (ETDEWEB)

The theoretical description of chemical reactions was until recently limited to a 'static' approach in which important parameters such as the rate constant are deduced from the local topology of the potential energy surface close to minima and saddle points. Such an approach has, however, serious limitations. The growing computational power allows us now to use advanced simulation techniques to determine entropic effects accurately for medium-sized systems at ab initio level. Recently, we have implemented free-energy simulation techniques based on molecular dynamics, in particular on the blue-moon ensemble technique and on metadynamics, in the popular DFT code VASP. In the thermodynamic integration (blue-moon ensemble) technique, the free-energy profile is calculated as the path integral over the restoring forces along a parametrized reaction coordinate. In metadynamics, an image of the free-energy surface is constructed on the fly during the simulation by adding small repulsive Gaussian-shaped hills to the Lagrangian driving the dynamics. The two methods are tested on a simple chemical reaction-the nucleophilic substitution of methyl chloride by a chlorine anion.

Bucko, T [Fakultaet fuer Physik and Center for Computational Materials Science, Universitaet Wien, Sensengasse, Vienna 1090 (Austria)

2008-02-13

11

Ab initio calculations of free-energy reaction barriers

International Nuclear Information System (INIS)

The theoretical description of chemical reactions was until recently limited to a 'static' approach in which important parameters such as the rate constant are deduced from the local topology of the potential energy surface close to minima and saddle points. Such an approach has, however, serious limitations. The growing computational power allows us now to use advanced simulation techniques to determine entropic effects accurately for medium-sized systems at ab initio level. Recently, we have implemented free-energy simulation techniques based on molecular dynamics, in particular on the blue-moon ensemble technique and on metadynamics, in the popular DFT code VASP. In the thermodynamic integration (blue-moon ensemble) technique, the free-energy profile is calculated as the path integral over the restoring forces along a parametrized reaction coordinate. In metadynamics, an image of the free-energy surface is constructed on the fly during the simulation by adding small repulsive Gaussian-shaped hills to the Lagrangian driving the dynamics. The two methods are tested on a simple chemical reaction-the nucleophilic substitution of methyl chloride by a chlorine anion

12

Ab initio modeling of small proteins by iterative TASSER simulations

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Predicting 3-dimensional protein structures from amino-acid sequences is an important unsolved problem in computational structural biology. The problem becomes relatively easier if close homologous proteins have been solved, as high-resolution models can be built by aligning target sequences to the solved homologous structures. However, for sequences without similar folds in the Protein Data Bank (PDB library, the models have to be predicted from scratch. Progress in the ab initio structure modeling is slow. The aim of this study was to extend the TASSER (threading/assembly/refinement method for the ab initio modeling and examine systemically its ability to fold small single-domain proteins. Results We developed I-TASSER by iteratively implementing the TASSER method, which is used in the folding test of three benchmarks of small proteins. First, data on 16 small proteins (?-root mean square deviation (RMSD of 3.8Å, with 6 of them having a C?-RMSD ?-RMSD ?-RMSD of the I-TASSER models was 3.9Å, whereas it was 5.9Å using TOUCHSTONE-II software. Finally, 20 non-homologous small proteins (?-RMSD of 3.9Å was obtained for the third benchmark, with seven cases having a C?-RMSD Conclusion Our simulation results show that I-TASSER can consistently predict the correct folds and sometimes high-resolution models for small single-domain proteins. Compared with other ab initio modeling methods such as ROSETTA and TOUCHSTONE II, the average performance of I-TASSER is either much better or is similar within a lower computational time. These data, together with the significant performance of automated I-TASSER server (the Zhang-Server in the 'free modeling' section of the recent Critical Assessment of Structure Prediction (CASP7 experiment, demonstrate new progresses in automated ab initio model generation. The I-TASSER server is freely available for academic users http://zhang.bioinformatics.ku.edu/I-TASSER.

Zhang Yang

2007-05-01

13

Operator evolution for ab initio nuclear theory

The past two decades have seen a revolution in ab initio calculations of nuclear properties. One key element has been the development of a rigorous effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence as a function of the model space size. For consistency, however, one ought to apply the same transformation to other operators when calculating transitions and mean values from the eigenstates of t...

Schuster, Micah D.; Quaglioni, Sofia; Johnson, Calvin W.; Jurgenson, Eric D.; Navratil, Petr

2014-01-01

14

Ab initio conformational study of caffeic acid

A complete conformational analysis of caffeic acid, a phenolic derivative with well known antioxidant properties, was carried out by ab initio calculations, at the density funtional theory (DFT) level. Fourteen different conformers were obtained, the most stable ones being planar, as the conformational preferences of this molecule were found to be mainly determined by the stabilising effect of [pi]-electron delocalisation. Harmonic vibrational frequencies, as well as potential energy profiles...

Vanbesien, E.; Marques, M. P. M.

2003-01-01

15

The dissociative adsorption of hydrogen on Pd(100) has been studied by ab initio quantum dynamics and ab initio molecular dynamics calculations. Treating all hydrogen degrees of freedom as dynamical coordinates implies a high dimensionality and requires statistical averages over thousands of trajectories. An efficient and accurate treatment of such extensive statistics is achieved in two steps: In a first step we evaluate the ab initio potential energy surface (PES) and dete...

Gross, Axel; Scheffler, Matthias

1997-01-01

16

Ab initio calculations of material strength.

Czech Academy of Sciences Publication Activity Database

Tokyo : The Japan Society of Mechanical Engineers, 2003, s. 467-475. [International Symposium on Micro-Mechanical Engineering - Heat Transfer, Fluid Dynamics, Reliability and Mechanotronics.. Tsuchiura and Tsukuba (JP), 01.12.2003-03.12.2003] R&D Projects: GA AV ?R IAA1041302; GA ?R 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

Šob, Mojmír; Friák, Martin; Vitek, V.

17

Germacrene D Cyclization: An Ab Initio Investigation

Directory of Open Access Journals (Sweden)

Full Text Available Essential oils that contain large concentrations of germacrene D are typically accompanied by cadinane sesquiterpenoids. The acid-catalyzed cyclization of germacrene D to give cadinane and selinane sesquiterpenes has been computationally investigated using both density functional (B3LYP/6-31G* and post Hartree-Fock (MP2/6-31G** ab initio methods. The calculated energies are in general agreement with experimentally observed product distributions, both from acid-catalyzed cyclizations as well as distribution of the compounds in essential oils.

William N. Setzer

2008-01-01

18

Ab initio non-relativistic spin dynamics

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

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

2014-12-01

19

AIDA: ab initio domain assembly server.

AIDA: ab initio domain assembly server, available at http://ffas.burnham.org/AIDA/ is a tool that can identify domains in multi-domain proteins and then predict their 3D structures and relative spatial arrangements. The server is free and open to all users, and there is an option for a user to provide an e-mail to get the link to result page. Domains are evolutionary conserved and often functionally independent units in proteins. Most proteins, especially eukaryotic ones, consist of multiple domains while at the same time, most experimentally determined protein structures contain only one or two domains. As a result, often structures of individual domains in multi-domain proteins can be accurately predicted, but the mutual arrangement of different domains remains unknown. To address this issue we have developed AIDA program, which combines steps of identifying individual domains, predicting (separately) their structures and assembling them into multiple domain complexes using an ab initio folding potential to describe domain-domain interactions. AIDA server not only supports the assembly of a large number of continuous domains, but also allows the assembly of domains inserted into other domains. Users can also provide distance restraints to guide the AIDA energy minimization. PMID:24831546

Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam

2014-07-01

20

Ab initio study of solution energy and diffusion of caesium in uranium dioxide

Energy Technology Data Exchange (ETDEWEB)

The behaviour of caesium in nuclear fuels is investigated using density functional theory (DFT). In a first step, the incorporation and solution energies of Cs in pre-existing trap sites of UO{sub 2} (vacancies, interstitials, U-O di-vacancy and Schottky trio defects) are calculated using the projector-augmented-wave (PAW) derived pseudopotentials as implemented in the Vienna ab initio simulation package (VASP). Correlation effects are taken into account within the DFT + U approach. The solubility of caesium is found to be very low, in agreement with experimental data. The migration of Cs is found to be highly anisotropic, it is controlled by uranium diffusion with an Arrhenius activation energy of 4.8 eV in hyperstoichiometric UO{sub 2+x}, in good agreement with experimental values.

Gupta, F. [IRSN, DPAM, SEMIC, LETR, 13115 Saint Paul Lez Durance (France); Pasturel, A. [CNRS, Laboratoire de Physique et Modelisation des Milieux Condenses, Maison des Magisteres, 25 Avenue des Martyrs BP166, 38042 Grenoble (France); Brillant, G. [IRSN, DPAM, SEMIC, LETR, 13115 Saint Paul Lez Durance (France)], E-mail: guillaume.brillant@irsn.fr

2009-03-31

21

Ab Initio Simulations of Hydrogen in Crystalline and Amorphous Metal Membranes

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

Huhn, William; Widom, Mike

2011-03-01

22

Why ferroelectricity? synchrotron radiation and ab initio answers

Scientific Electronic Library Online (English)

Full Text Available Una pregunta histórica de la física del estado sólido está encontrando respuesta en nuestros tiempos: la explicación a nivel atómico del origen de la ferroelectricidad. Las ideas tradicionales sobre fenómenos ferroeléctricos se relacionan con el "ablandamiento" de los fonones en el origen de la zona [...] de Brillouin y con funciones en forma de "W" para la energía libre de Landau. Las contribuciones experimentales (radiación sincrotrónica, neutrones) y teóricas (Cohen, Resta, Spaldin) de la última década han esclarecido aspectos del comportamiento atómico que conducen a la polarización espontánea en estructuras perovskitas y asociadas. Se presenta el trabajo desarrollado por nuestro grupo interdisciplinario. Se obtienen fases ferroeléctricas perovskitas y Aurivillius por diferentes métodos. Se investigan detalles finos de las estructuras cristalinas mediante radiación sincrotrónica en el Laboratorio de Radiación Sincrotrónica de Stanford. Las estructuras electronicas de las fases consideradas se caracterizan por métodos ab initio. Los experimentos de difraccion en alta resolución demuestran ruptura de simetría en un número de sistemas perovskita y Aurivillius. Se discute la relación estructura-simetría- polarización. Se presenta una explicación ab initio de la polarizacion ferroeléctrica en perovskitas. La energía del sistema se calcula mediante el codigo CASTEP bajo un funcional GGA. La optimización de la energía conduce a la ruptura de simetría cubica, con desplazamiento del catión Ti fuera del centro, vía una transformación Jahn-Teller de segundo orden. La estructura electrónica se investiga mediante el software BandLab, bajo un funcional LDA, con el método LMTO. La causa de la deformación de la perovskita es la degeneración de los orbitales Ti 3d z² y Ti 3d (x²+y²). Abstract in english An old question of solid state physics is being answered nowadays: the atomic-level understanding of ferroelectricity. Traditional ideas about ferroelectric phenomena relate with softening of optical phonons at the Brillouin zone origin and with "W-shaped" Landau free energy functions. Last decade e [...] xperimental (synchrotron radiation, neutrons) and quantum-theoretical (Cohen, Resta, Spaldin) contributions have clarified detailed descriptions and explanations for atomic behavior leading to spontaneous polarization in perovskite and perovskite-related crystal structures. Work being performed by our interdisciplinary group on ferroelectricity is presented. Perovskite and Aurivillius ferroelectric phases are obtained by different methods. Fine details on crystal structures are investigated by means of synchrotron radiation at Stanford Synchrotron Radiation Laboratory. Electronic structures of considered phases are theoretically characterized by ab initio methods. High-resolution diffraction experiments demonstrate several symmetry break-downs in perovskite and Aurivillius phases. The structure-symmetry-polarization relationship is discussed for a number of representative cases. Ab initio explanation of ferroelectric polarization in perovskite structures is given. Energy calculation is performed by means of CASTEP code under GGA functional. Energy optimization leads to cubic-tetragonal symmetry break-down with off-centering cation displacements via second-order Jahn-Teller effect. Electronic structure is investigated with BandLab code, under LDA functional with LMTO method. Degeneracy of Ti 3d z² and Ti 3d (x²+y²) orbitals is the cause of cubic-perovskite deformation.

R, Olivera; M.E, Fuentes; F, Espinosa; M, García; E, Macías; A, Durán; J, Siqueiros; L, Fuentes.

2007-02-01

23

Ab Initio Characterization of C6

Structural and spectroscopy parameters of C6 are determined with ab initio calculations confirming the existence of nine isomers. Those geometries with high stability (the linear, where the electronic ground state is a triplet (X3?g-), and the slightly distorted cyclic singlet (X1A1')) are determined with CASPT2/CASSCF. The effect of the correlation energy on the isomer stability is discussed. The local potential energy surfaces of the first electronic states of linear-C6 are determined with CASPT2/CASSCF calculations and the ANO-L C[4s3p2d1f] basis set. We provide minimum energy geometries and excitation energies for 19 electronic states. A new assignment of the electronic spectrum transitions involving high-energy symmetry states is proposed. Electron affinity and ionization potential have been computed to be EA = 3.97 eV and IP = 9.73 eV.

Massó, H.; Senent, M. L.

2009-05-01

24

Ab-initio nanoplasmonics: atoms matter

We present an ab-initio study of the hybridization of localized surface plasmons in a metal nanoparticle dimer. The atomic structure, which is often neglected in theoretical studies of quantum nanoplasmonics, has a strong impact on the optical absorption properties when sub-nanometric gaps between the nanoparticles are considered. We demonstrate that this influences the hybridization of optical resonances of the dimer, and leads to significantly smaller electric field enhancements as compared to the standard jellium model. In addition we show that the corrugation of the metal surface at a microscopic scale becomes as important as other well-known quantum corrections to the plasmonic response, implying that the atomic structure has to be taken into account to obtain quantitative predictions for realistic nanoplasmonic devices.

Zhang, Pu; Rubio, Angel; Garcia-Gonzalez, Pablo; Garcia-Vidal, F J

2014-01-01

25

Giant magnetoresistance An ab-initio description

A new theoretical concept to study the microscopic origin of Giant Magnetoresistance (GMR) from first principles is presented. The method is based on ab-initio electronic structure calculations within the spin density functional theory using a Screened KORRINGA-KOHNROSTOKER method. Scattering at impurity atoms in the multilayers is described by means of a GREEN's-function method. The scattering potentials are calculated self-consistently. The transport properties are treated quasi-classically solving the BOLTZMANN equation including the electronic structure of the layered system and the anisotropic scattering. The solution of the BOLTZMANN equation is performed iteratively taking into account both scattering out and scattering in terms (vertex corrections). The method is applied to Co/Cu and Fe/Cr multilayers. Trends of scattering cross sections, residual resistivities and GMR ratios are discussed for various transition metal impurities at different positions in the Co/Cu or Fe/Cr multilayers. Furthermore the...

Binder, J

2000-01-01

26

Ab Initio Description of p -Shell Hypernuclei

We present the first ab initio calculations for p -shell single-? hypernuclei. For the solution of the many-baryon problem, we develop two variants of the no-core shell model with explicit ? and ?+,?0,?- hyperons including ? -? conversion, optionally supplemented by a similarity renormalization group transformation to accelerate model-space convergence. In addition to state-of-the-art chiral two- and three-nucleon interactions, we use leading-order chiral hyperon-nucleon interactions and a recent meson-exchange hyperon-nucleon interaction. We validate the approach for s -shell hypernuclei and apply it to p -shell hypernuclei, in particular to Li7? , Be9? , and C13? . We show that the chiral hyperon-nucleon interactions provide ground-state and excitation energies that generally agree with experiment within the cutoff dependence. At the same time we demonstrate that hypernuclear spectroscopy provides tight constraints on the hyperon-nucleon interactions.

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

2014-11-01

27

Ab Initio Treatment of Lower Mantle Mineral Solvi.

The lower mantle of the Earth extends from about 670 to 2980 km depth and consists mainly of MgSiO3- perovskite (~ 70 vol%), (Mg,Fe)O magnesiowüstite (~ 20 vol%) and CaSiO3-perovskite (~ 10 vol%). To obtain a realistic picture of the lower mantle, it is necessary to consider the perovskite minerals as coexisting solid solutions with a large miscibility gap, as this is the case in nature. In this work we investigate the solvi of the three binaries in the Ca-perovskite - Mg-perovskite - corundum ternary, i.e. the solid solutions relevant for the Earth's lower mantle minerals in a simplified CMAS system. It is possible to calculate thermodynamic properties, structures and energetics of the individual minerals at extreme conditions of the mantle using ab initio methods, such as the density functional theory (DFT). We use the DFT together with the generalized gradient approximation (GGA) and the projector augmented wave (PAW) method, as implemented in the VASP code. The binary solvi are modelled through a subregular solid solution model together with point defect calculations at different pressures in the lower mantle regime. Point defects in the (Ca,Mg)-perovskite system are simple substitutions, but in MgSiO3-Al2O3 there is a coupled charge substitution of 2Al3+ with Mg2+Si^{4+}. Additionally, different symmetries of the perovskite (and akimotoite/ilmenite for MgSiO3) structures have been taken into account, thus allowing for phase transitions in solid solutions. At pressures and temperatures of the lower mantle, the solvus in the (Ca,Mg)SiO3 system remains wide open and solubilities of Ca in Mg-perovskite and Mg in Ca-perovskite decrease with pressure (at constant temperature and along any adiabatic geotherm). Calculations on the MgSiO3-Al2O3 (akimotoite-corundum) solvus show higher solubilities. Still, we find it unlikely that Ca-perovskite would disappear (i.e. fully dissolve in Mg-perovskite) at conditions of the lower mantle, at last not in the simplified CMAS system. Information on the solubility of Ca in MgSiO3 in Al- and Fe-bearing systems will elucidate the mineralogical composition of the lower mantle of the Earth.

Jung, D. Y.; Oganov, A. R.; Schmidt, M. W.

2006-12-01

28

Toward ab initio density functional theory for nuclei

We survey approaches to nonrelativistic density functional theory (DFT) for nuclei using progress toward ab initio DFT for Coulomb systems as a guide. Ab initio DFT starts with a microscopic Hamiltonian and is naturally formulated using orbital-based functionals, which generalize the conventional local-density-plus-gradients form. The orbitals satisfy single-particle equations with multiplicative (local) potentials. The DFT functionals can be developed starting from internuc...

Drut, J. E.; Furnstahl, R. J.; Platter, L.

2009-01-01

29

Ab Initio Theory of Gate Induced Gaps in Graphene Bilayers

We study the gate voltage induced gap that occurs in graphene bilayers using \\textit{ab initio} density functional theory. Our calculations confirm the qualitative picture suggested by phenomenological tight-binding and continuum models. We discuss enhanced screening of the external interlayer potential at small gate voltages, which is more pronounced in the \\textit{ab initio} calculations, and quantify the role of crystalline inhomogeneity using a tight-binding model self-c...

Min, Hongki; Sahu, B. R.; Banerjee, Sanjay K.; Macdonald, A. H.

2006-01-01

30

Ab initio thermodynamic study of defective strontium titanate

In the presented thesis the perfect and defective SrTiO3 bulk crystals and their (001) surfaces are considered on ab initio level. Since the experimental study of the complex defective systems is comparatively expensive and difficult, and the computer performance has been greatly increased in the last years, the ab initio modeling became very efficient tool to be applied in this field. Additionally, there is a significant industrial demand for the investigation and improvements of the perform...

Blokhin, Evgeny

2013-01-01

31

Ab initio energy landscape of LiF clusters

A global search for possible LiF cluster structures is performed, up to (LiF)8. The method is based on simulated annealing, where all the energies are evaluated on the ab initio level. In addition, the threshold algorithm is employed to determine the energy barriers for the transitions among these structures, for the cluster (LiF)4, again on the ab initio level; and the corresponding tree graph is obtained.

Doll, K; Jansen, M; 10.1063/1.3455708

2010-01-01

32

Ab initio atomistic simulation of metals and multicomponent alloys

Ab initio theory provides a powerful tool to understand and predict the behavior of materials. This thesis contains both of these aspects. First we use ab initio alloy theory to investigate a new kind of complex alloy (high-entropy alloy). Second we introduce a novel potential (interlayer potential), which can be extracted from ab inito total energy calculations using the Chen-Möbius inversion method. High-entropy alloys (HEAs) are composed of four or more metallic elements with nearly equim...

Tian, Fuyang

2013-01-01

33

Molecular Spectroscopy by Ab Initio Methods

Due to recent advances in methods and computers, the accuracy of ab calculations has reached a point where these methods can be used to provide accurate spectroscopic constants for small molecules; this will be illustrated with several examples. We will show how ab initio calculations where used to identify the Hermann infrared system in N2 and two band systems in CO. The identification of all three of these band systems relied on very accurate calculations of quintet states. The analysis of the infrared spectra of cool stars requires knowledge of the intensity of vibrational transitions in SiO for high nu and J levels. While experiment can supply very accurate dipole moments for nu = 0 to 3, this is insufficient to construct a global dipole moment function. We show how theory, combined by the experiment, can be used to generate the line intensities up to nu = 40 and J = 250. The spectroscopy of transition metal containing systems is very difficult for both theory and experiment. We will discuss the identification of the ground state of Ti2 and the spectroscopy of AlCu as examples of how theory can contribute to the understanding of these complex systems.

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

1994-01-01

34

Ab initio study of rare gas halides

International Nuclear Information System (INIS)

The electronic structures of the Ne2F, Ar2F, Kr2F, Xe2F, Ar2Cl, Kr2Cl, Xe2Cl, Kr2Br, Xe2Br, and Xe2I molecules have been studied on the CASSCF/CASPT2 level, with inclusion of the spin–orbit interaction. For the lowest strongly bound Rg2X(42?) state we report RRg–Rg and RRg–X equilibrium bond lengths, dissociation energy, radiative lifetime and frequencies of three vibrational modes. Except for the antisymmetric stretch mode, a similar set of results was obtained for another five bound states above Rg2X(42?). To compare equilibrium bond lengths and some other molecular properties, calculations were also performed for Rg2+ and RgX diatomics on the same level of theory and using the same basis sets. The ab initio results obtained in this work are of interest for experimental and theoretical studies of Rg2X(42?) formation mechanisms. (paper)

35

Ab Initio Equation of State for ?-HMX

An ab initio equation of state for the molecular crystal ?-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (?-HMX) has been calculated for temperatures between 0 and 400 K, and for specific volumes from 0.42 to 0.55 cm^3/gm, corresponding to relative volumes from 0.8 to 1.03. The calculated 300 K isotherm agrees well with the experimentally measured pressure-volume relation reported by Gump and Peiris (J. Appl. Phys. 97, 053513 (2005)), and by Yoo and Cynn (J. Chem. Phys. 111, 10229 (1999)). The calculated specific heat agrees well with experimental data reported over the range from 300 to 400 K (Hanson-Parr and Parr, J. Energetic Mater. 17, 1-47 (1999)). The main source of error in the calculations is due to the absence of an adequate ab inito treatment of non local van der Waals interactions which are important in molecular crystals. Work is underway to include these interactions.

Zerilli, Frank; Kuklja, Maija

2007-06-01

36

Why ferroelectricity? synchrotron radiation and ab initio answers

Directory of Open Access Journals (Sweden)

Full Text Available Una pregunta hist´orica de la f´?sica del estado s´olido est´a encontrando respuesta en nuestros tiempos: la explicaci´on a nivel at´omico del origen de la ferroelectricidad. Las ideas tradicionales sobre fen´omenos ferroel´ectricos se relacionan con el ?ablandamiento? de los fonones en el origen de la zona de Brillouin y con funciones en forma de ?W? para la energ´?a libre de Landau. Las contribuciones experimentales (radiaci´on sincrotr´onica, neutrones y te´oricas (Cohen, Resta, Spaldin de la ´ultima d´ecada han esclarecido aspectos del comportamiento at´omico que conducen a la polarizaci´on espont´anea en estructuras perovskitas y asociadas. Se presenta el trabajo desarrollado por nuestro grupo interdisciplinario. Se obtienen fases ferroel´ectricas perovskitas y Aurivillius por diferentes m´etodos. Se investigan detalles finos de las estructuras cristalinas mediante radiaci´on sincrotr´onica en el Laboratorio de Radiaci´on Sincrotr´onica de Stanford. Las estructuras electr´onicas de las fases consideradas se caracterizan por m´etodos ab initio. Los experimentos de difracci´on en alta resoluci´on demuestran ruptura de simetr´?a en un n´umero de sistemas perovskita y Aurivillius. Se discute la relaci ´on estructura-simetr´?a- polarizaci´on. Se presenta una explicaci´on ab initio de la polarizaci´on ferroel´ectrica en perovskitas. La energ´?a del sistema se calcula mediante el c´odigo CASTEP bajo un funcional GGA. La optimizaci´on de la energ´?a conduce a la ruptura de simetr´?a c´ubica, con desplazamiento del cati´on Ti fuera del centro, v´?a una transformaci´on Jahn-Teller de segundo orden. La estructura electr´onica se investiga mediante el software BandLab, bajo un funcional LDA, con el m´etodo LMTO. La causa de la deformaci´on de la perovskita es la degeneraci´on de los orbitales Ti 3d z2 y Ti 3d (x2+y2.

R. Olivera

2007-01-01

37

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

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 illustrations of their unprecedented power in addressing some of the outstanding problems of solid-state chemistry, high-pressure chemistry, or geochemistry. They are the structure and spectra of ice Ih, in particular, the origin of two peaks in the hydrogen-bond-stretching region of its inelastic neutron scattering spectra, a solid-solid phase transition from CO2-I to elusive, metastable CO2-III, pressure tuning of Fermi resonance in solid CO2, and the structure and spectra of solid formic acid, all at the level of second-order Møller-Plesset perturbation theory or higher. PMID:24754304

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

2014-09-16

38

Skutterudites under pressure: An ab initio study

Energy Technology Data Exchange (ETDEWEB)

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

Ram, Swetarekha; Kanchana, V., E-mail: kanchana@iith.ac.in [Department of Physics, Indian Institute of Technology Hyderabad, Ordnance Factory Estate, Yeddumailaram 502 205, Andhra Pradesh (India); Valsakumar, M. C. [School of Engineering Sciences and Technology (SEST), University of Hyderabad, Prof. C. R. Rao Road, Gachibowli, Hyderabad 500 046, Andhra Pradesh (India)

2014-03-07

39

Ab initio simulation of transport phenomena in rarefied gases

Ab initio potentials are implemented into the direct simulation Monte Carlo (DSMC) method. Such an implementation allows us to model transport phenomena in rarefied gases without any fitting parameter of intermolecular collisions usually extracted from experimental data. Applying the method proposed by Sharipov and Strapasson [Phys. FluidsPHFLE61070-663110.1063/1.3676060 24, 011703 (2012)], the use of ab initio potentials in the DSMC requires the same computational efforts as the widely used potentials such as hard spheres, variable hard sphere, variable soft spheres, etc. At the same time, the ab initio potentials provide more reliable results than any other one. As an example, the transport coefficients of a binary mixture He-Ar, viz., viscosity, thermal conductivity, and thermal diffusion factor, have been calculated for several values of the mole fraction.

Sharipov, Felix; Strapasson, José L.

2012-09-01

40

P-V Relation for Mercuric Calcogenides: Ab Initio Method

Directory of Open Access Journals (Sweden)

Full Text Available Mercuric Calcogenides found many applications in electronic and optical devices as semiconducting materials. An equation of state provides useful information about the relationship between pressure (P, volume (V and temperature (T that helps to understand the behaviour of materials under the effect of high pressure and high temperature. The present paper sheds light on the electronic structure of Mercuric Calcogenides by simulating its electronic properties through ab initio method. This ab initio method is extended to derive the equation of state for Mercuric Calcogenides. The present equation of state has also been tested for the prediction of End Point. The computed results compare well with Quantum statistical data.

G. Misra

2011-01-01

41

Recent achievements in ab initio modelling of liquid water

The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.

Khaliullin, Rustam Z

2013-01-01

42

Ab initio lattice dynamics of MnO.

Czech Academy of Sciences Publication Activity Database

Ro?. 21, ?. 27 (2009), Art. N. 275402. ISSN 0953-8984 Institutional research plan: CEZ:AV0Z20410507 Keywords : lattice dynamics * MnO * ab initio Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.964, year: 2009

Legut, Dominik; Wdowik, U.

2009-01-01

43

Multiple time step integrators in ab initio molecular dynamics

International Nuclear Information System (INIS)

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

44

Motif based Hessian matrixfor ab initio geometry optimization ofnanostructures

Energy Technology Data Exchange (ETDEWEB)

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

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

2006-04-05

45

AB INITIO calculations of magneto-optical effects.

Czech Academy of Sciences Publication Activity Database

Ro?. 2, - (2002), s. 141-146. ISSN 1346-7948 R&D Projects: GA AV ?R 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

Kuneš, Jan; Oppeneer, P. M.

2002-01-01

46

Energy Technology Data Exchange (ETDEWEB)

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.)

Ventelon, L. [CEA Saclay, Dept. des Materiaux pour le Nucleaire (DEN/DANS/DMN/SRMP), 91 - Gif-sur-Yvette (France)

2008-07-01

47

Ab Initio Calculations Of Light-Ion Reactions

Energy Technology Data Exchange (ETDEWEB)

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.

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

2012-03-12

48

Ab Initio Calculations Of Light-Ion Reactions

International Nuclear Information System (INIS)

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.

49

Multiple Time Step Integrators in Ab Initio Molecular Dynamics

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 show that such a timescale separation is possible using two different schemes: 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 dynami...

Luehr, Nathan; Martinez, Todd J

2013-01-01

50

Ab Initio Calculations of Light-Ion Reactions

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.

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

51

Spin-orbit decomposition of ab initio wavefunctions

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

Johnson, Calvin W

2014-01-01

52

Spin-orbit decomposition of ab initio nuclear wave functions

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

Johnson, Calvin W.

2015-03-01

53

Serine Proteases an Ab Initio Molecular Dynamics Study

In serine proteases (SP's), the H-bond between His-57 and Asp-102, and that between Gly-193 and the transition state intermediate play a crucial role for enzymatic function. To shed light on the nature of these interactions, we have carried out ab initio molecular dynamics simulations on complexes representing adducts between the reaction intermediate and elastase (one protein belonging to the SP family). Our calculations indicate the presence of a low--barrier H-bond between His-57 and Asp-102, in complete agreement with NMR experiments on enzyme--transition state analog complexes. Comparison with an ab initio molecular dynamics simulation on a model of the substrate--enzyme adduct indicates that the Gly-193--induced strong stabilization of the intermediate is accomplished by charge/dipole interactions and not by H-bonding as previously suggested. Inclusion of the protein electric field in the calculations does not affect significantly the charge distribution.

De Santis, L

1999-01-01

54

Ab Initio Nuclear Structure Theory: From Few to Many

International Nuclear Information System (INIS)

We summarize recent advances in ab initio nuclear structure theory, aiming to connect few- and many-body systems in a coherent theoretical framework. Starting from chiral effective field theory to construct the nuclear Hamiltonian and the similarity renormalization group to soften it, we address several many-body approaches that have seen major developments over the past few years. We show that the domain of ab initio nuclear structure theory has been pushed well beyond the p-shell and that quantitative predictions connected to QCD via chiral effective field theory are becoming possible all the way from the proton to the neutron drip line up into the medium-mass regime. (author)

55

Ab initio vibrational-rotational spectrum of potassium cyanide: KCN

Dynamical calculations are performed on an ab initio potential energy surface for KCN. Approximate variational solutions of the vibrational Eckart hamiltonian are presented for several states. Fundamental vibrations are found to lie at 302·7 cm-1 and 119·7 cm-1. An effective rotational hamiltonian is solved for several vibrational states allowing vibrational assignments to be made to the observed rotational spectrum.

Tennyson, Jonathan; Sutcliffe, Brian T.

56

Ab initio modeling of TiO2 nanotubes

TiO2 nanotubes constructed from a lepidocrocite-like TiO2 layer were investigated with ab initio methods employing the periodic CRYSTAL code. The dependence of strain energies, structural and electronic properties on the tube diameter was investigated in the 18–57 A range. Nanotubes constructed by a (0,n) rollup proved to be the most stable at all diameters. All three types of rollup undergo significant reconstruction at diameters

Szieberth, Denes; Ferrabone, Matteo; Ferrari, Anna Maria

2010-01-01

57

DNA base trimers: empirical and quantum chemical ab initio calculations.

Czech Academy of Sciences Publication Activity Database

Ro?. 13, ?. 7 (2007), s. 2067-2077. ISSN 0947-6539 R&D Projects: GA MŠk LC512; GA ?R GA203/05/0009 Institutional research plan: CEZ:AV0Z40550506 Keywords : ab initio calculations * nucleic acid bases trimer * empirical force field * Amber * potential energy surface Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.330, year: 2007

Kabelá?, Martin; Sherer, E. C.; Cramer, Ch. J.; Hobza, Pavel

2007-01-01

58

Ab initio Green's function formalism for band structures

Using the Green's function formalism, an ab initio theory for band structures of crystals is derived starting from the Hartree-Fock approximation. It is based on the algebraic diagrammatic construction scheme for the self-energy which is formulated for crystal orbitals (CO-ADC). In this approach, the poles of the Green's function are determined by solving a suitable Hermitian eigenvalue problem. The method is not only applicable to the outer valence and conduction bands, it ...

Buth, Christian; Birkenheuer, Uwe; Albrecht, Martin; Fulde, Peter

2004-01-01

59

Quantitative Verification of Ab Initio Self-consistent Laser Theory

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 tha...

Ge, Li; Tandy, Robert J.; Stone, A. Douglas; Tu?reci, Hakan E.

2008-01-01

60

Complementary approaches to the ab initio calculation of melting properties

Several research groups have recently reported {\\em ab initio} calculations of the melting properties of metals based on density functional theory, but there have been unexpectedly large disagreements between results obtained by different approaches. We analyze the relations between the two main approaches, based on calculation of the free energies of solid and liquid and on direct simulation of the two coexisting phases. Although both approaches rely on the use of classical...

Alfe, D.; Gillan, M. J.; Price, G. D.

2001-01-01

61

Ab initio theory of the interlayer exchange coupling

Ab initio formulations of the interlayer exchange coupling (IEC) between two, in general non-collinearly aligned magnetic slabs embedded in a non-magnetic spacer are reviewed whereby both the spacer and the magnetic slabs as well as their interfaces may be either ideal or random. These formulations are based on the spin-polarized surface Green function technique within the tight-binding linear muffin-tin orbital method, the Lloyd formulation of the IEC, and the coherent pote...

Kudrnovsky, Josef; Drchal, Vaclav; Turek, Ilja; Bruno, Patrick; Dederichs, Peter; Weinberger, Peter

1998-01-01

62

The study of molecular spectroscopy by ab initio methods

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

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

1991-01-01

63

Ab initio theory of temperature dependent magneto-resistivities

Abstract We present the first ab initio type descriptions of the temperature dependence of the magnetic part of the electrical conductivity. We implemented the disordered local moment (DLM) scheme into Kubo's linear response formalism using the screened Korringa-Kohn-Rostoker (KKR) approach. In order to test the proposed scheme, we calculated the magnetic resistivity of bulk Fe and Co. The results seem to give a qualitatively correct temperature dependence of the ...

Buruzs, Adam; Szunyogh, La?szlo?; Weinberger, Peter

2008-01-01

64

Energetics of complex metallic phases from ab initio calculations.

Czech Academy of Sciences Publication Activity Database

Schwäbisch Gmünd , 2005. s. 495-495. [PSI-K 2005. 17.09.2005-21.09.2005, Schwäbisch Gmünd ] R&D Projects: GA ?R(CZ) GP106/03/P002; GA ?R(CZ) GA106/02/0877 Institutional research plan: CEZ:AV0Z20410507 Keywords : sigma phase * Laves phase * ab initio Subject RIV: BM - Solid Matter Physics ; Magnetism

Houserová, Jana; Šob, Mojmír

65

Ab initio quantum dynamics using coupled-cluster

The curse of dimensionality (COD) limits the current state-of-the-art {\\it ab initio} propagation methods for non-relativistic quantum mechanics to relatively few particles. For stationary structure calculations, the coupled-cluster (CC) method overcomes the COD in the sense that the method scales polynomially with the number of particles while still being size-consistent and extensive. We generalize the CC method to the time domain while allowing the single-particle functio...

Kvaal, Simen

2012-01-01

66

The equilibrium structure of methyl pseudohalides: an ab initio study

Ab initio calculations have been carried out on the molecules CH 3NCX and CH 3XCN (X?O, S and Se). It was found that these molecules all have a bent equilibrium structure. The relatively more rigid CH 3XCN molecules can be sufficiently well ever, requires that at least partial allowance is made for the correlation energy. According to these calculations, CH 3NCO, CH 3NCS and CH 3SeCN are the more stable isomers.

Pasinszki, Tibor; Veszprémi, Tamás; Fehér, Miklós

1992-02-01

67

Periodic ab initio study of silico-faujasite

Silico-faujasite (144 atoms in the unit cell) has been investigated using an ab initio periodic Hartree-Fock scheme and an all-electron basis set. The structure has been fully optimized; it turns out that this system is less stable than ?-quartz by about 4 kcal mol -1 per SiO 2 unit. The electron density and electrostatic potential maps are used for discussing the differences between pores limited by 6- and 12-membered rings in faujasite.

Zicovich-Wilson, C. M.; Dovesi, R.

1997-10-01

68

Uniaxial Phase Transition in Si : Ab initio Calculations

Based on a previously proposed thermodynamic analysis, we study the relative stabilities of five Si phases under uniaxial compression using ab initio methods. The five phases are diamond, beta-tin, sh, sc, and hcp structures. The possible phase-transition patterns were investigated by considering the phase transitions between any two chosen phases of the five phases. By analyzing the different conributions to the relative pahse stability, we identified the most important fac...

Cheng, C.

2002-01-01

69

Nuclear forces and ab initio calculations of atomic nuclei

Nuclear forces and the nuclear many-body problem have been some of Gerry Brown's main topics in his so productive life as a theoretical physicist. In this talk, I outline how Gerry's work laid the foundations of the modern theory of nuclear forces and ab initio calculations of atomic nuclei. I also present some recent developments obtained in the framework of nuclear lattice simulations.

Meißner, Ulf-G

2014-01-01

70

Screw dislocation in zirconium: An ab initio study

Plasticity in zirconium is controlled by 1/3 screw dislocations gliding in the prism planes of the hexagonal close-packed structure. This prismatic and not basal glide is observed for a given set of transition metals like zirconium and is known to be related to the number of valence electrons in the d band. We use ab initio calculations based on the density functional theory to study the core structure of screw dislocations in zirconium. Dislocations are found to dissociate ...

Clouet, Emmanuel

2012-01-01

71

Ab-initio nanoplasmonics: The impact of atomic structure

We present an ab-initio study of the hybridization of localized surface plasmons in a metal nanoparticle dimer. The atomic structure, which is often neglected in theoretical studies of quantum nanoplasmonics, has a strong impact on the optical absorption properties when sub-nanometric gaps between the nanoparticles are considered. We demonstrate that this influences the hybridization of optical resonances of the dimer, and leads to significantly smaller electric field enhanc...

Zhang, Pu; Feist, Johannes; Rubio, Angel; Garcia-gonzalez, Pablo; Garcia-vidal, F. J.

2014-01-01

72

Ab-initio calculations for dilute magnetic semiconductors

Der Schwerpunkt dieser Arbeit sind ab-initio Rechnungen zu der elektronischen Struktur und den magnetischen Eigenschaften von verdünnten magnetischen Halbleitern (DMS). Ein besonderes Ziel ist es, die komplexen Austausch-Wechselwirkungen, die in diesen Systemen auftreten, zu verstehen. Unsere Rechnungen basieren auf der Dichte-Funktional-Theorie, die sehr gut für die Beschreibung der material-spezifischen Eigenschaften von DMS geeignet ist. Wir verwenden die Koringa-Kohn-Rostoker (KKR) Gre...

Belhadji, Brahim

2009-01-01

73

The density matrix renormalization group for ab initio quantum chemistry

During the past 15 years, the density matrix renormalization group (DMRG) has become increasingly important for ab initio quantum chemistry. Its underlying wavefunction ansatz, the matrix product state (MPS), is a low-rank decomposition of the full configuration interaction tensor. The virtual dimension of the MPS, the rank of the decomposition, controls the size of the corner of the many-body Hilbert space that can be reached with the ansatz. This parameter can be systemati...

Wouters, Sebastian; Neck, Dimitri

2014-01-01

74

Ab initio studies of electromechanical effects in carbon nanotubes

Scientific Electronic Library Online (English)

Full Text Available Carbon nanotubes have recently attracted interest for their possible applications as nanoactuators and nanoswitches, as well as possible building blocks for nanoelectronics. We present ab initio calculations for uniformly charged graphene and (11,0),(9,0) and (5,5) carbon nanotubes. We also consider [...] the effects of polaron formation in these systems. The strain-charge coeÆcient is calculated and compared for both graphene and the nanotubes under study.

M. Verissimo, Alves; R.B., Capaz; Belita, Koiller; Emilio, Artacho; H., Chacham.

2002-06-01

75

Current rectification by asymmetric molecules: An ab initio study

We study current rectification effect in an asymmetric molecule HOOC-C$_6$H$_4$-(CH$_2$)$_n$ sandwiched between two Aluminum electrodes using an {\\sl ab initio} nonequilibrium Green function method. The conductance of the system decreases exponentially with the increasing number $n$ of CH$_2$. The phenomenon of current rectification is observed such that a very small current appears at negative bias and a sharp negative differential resistance at a critical positive bias whe...

Zhou, Yan-hong; Zheng, Xiao-hong; Xu, Ying; Zeng, Zhao Yang

2006-01-01

76

An Ab Initio Approach to the Solar Coronal Heating Problem

We present an ab initio approach to the solar coronal heating problem by modelling a small part of the solar corona in a computational box using a 3D MHD code including realistic physics. The observed solar granular velocity pattern and its amplitude and vorticity power spectra, as reproduced by a weighted Voronoi tessellation method, are used as a boundary condition that generates a Poynting flux in the presence of a magnetic field. The initial magnetic field is a potential...

Gudiksen, B. V.; Nordlund, A?

2004-01-01

77

GAUSSIAN 76: an ab initio molecular orbital program

Energy Technology Data Exchange (ETDEWEB)

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.

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

78

Ab Initio Theory of Light-ion Reactions

International Nuclear Information System (INIS)

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. Above all nuclear scattering and reactions, which require the solution of the many-body quantum-mechanical problem in the continuum, represent a theoretical and computational challenge for ab initio approaches. After a brief overview of the field, we present 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 (RGM) with the ab initio no-core shell model (NCSM), we complement a microscopic cluster technique with the use of realistic interactions and a microscopic and consistent description of the clusters. We show results for neutron and proton scattering on light nuclei, including p-7Be and n-8He. We also highlight the first results of the d-3He and d-3H fusion calculations obtained within this approach.

79

Principles, challenges and advances in ab initio protein structure prediction.

The gap between known protein sequences and structures is increasing rapidly and experimental methods alone will not be able to fill in this gap. Therefore it is necessary to use computational methods to predict protein structures. Template based modeling methods could be used for sequences, which have detectable relationship with sequences of one or more experimentally determined protein structures. For predicting the structure of proteins, which does not share a detectable sequence relationship with experimental structures, ab initio protein structure prediction techniques must be used. The methods under ab initio protein structure prediction category aim to predict the structure of a protein from the sequence information alone, without any explicit use of previously known structures. These methods use thermodynamic principles and try to identify the native structure of a protein as the global minimum of a potential energy landscape. However, such methods are computationally complex and are extraordinarily challenging. There has been significant progress in the development of ab inito protein structure prediction methods over the past few years. This review describes the basic principles, the complexity, challenges and recent progresses of ab initio protein structure prediction. PMID:22587787

Jothi, Arunachalam

2012-11-01

80

Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

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.

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

2014-08-01

81

Ab initio theories of nuclear structure and reactions

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 with two-nucleon, three-nucleon and possibly even four-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD employing Hamiltonians constructed within chiral effective field theory. I will discuss recent breakthroughs that allow for ab initio calculations for ground states and spectroscopy of nuclei throughout the p- and sd-shell and beyond with two- and three-nucleon interactions. I will highlight results obtained within the NCSM, CCM, QMC, and nuclear lattice EFT. I will also present new ab initio many-body approaches capable of describing both bound and scattering states in light nuclei simultaneously and discuss results for reactions important for astrophysics, such as ^7Be(p,?)^8B radiative capture, and for ^3H(d,n)^4He fusion.

Navratil, Petr

2012-10-01

82

Acceleration of the Convergence in ab initio Atomic Relaxations

Atomic relaxations is often required to accurately describe the properties of nanosystems. In ab initio calculations, a common practice is to use a standard search algorithm, such as BFGS (Broyden-Fletcher-Goldfarb-Shanno) or CG (conjugate gradient) method, which starts the atomic relaxations without any knowledge of the Hessian matrix of the system. For example, the initial Hessian in BFGS method is often set to identity, and there is no preconditioning to CG method. One way to accelerate the convergence of the atomic relaxations is to estimate an approximate Hessian matrix of the system and then use it as the initial Hessian in BFGS method or a preconditioner in CG method. Previous attempts to obtain the approximated Hessian were focused on the use of classical force field models which rely on the existence of good parameters. Here, we present an alternative method to estimate the Hessian matrix of a nanosystem. First, we decompose the system into motifs which consist of a few atoms, then calculate the Hessian matrix elements on different motif types from ab initio calculations for small prototype systems. Then we generate the Hessian Matrix of the whole system by putting together these motif Hessians. We have applied our motif-based Hessian matrix in ab initio atomic relaxations in several bulk (with/without impurity) and quantum dot systems, and have found a speed up factor of 2 to 4 depending on the system size.

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

2006-03-01

83

Ab initio calculations for industrial materials engineering: successes and challenges

Computational materials science based on ab initio calculations has become an important partner to experiment. This is demonstrated here for the effect of impurities and alloying elements on the strength of a Zr twist grain boundary, the dissociative adsorption and diffusion of iodine on a zirconium surface, the diffusion of oxygen atoms in a Ni twist grain boundary and in bulk Ni, and the dependence of the work function of a TiN-HfO2 junction on the replacement of N by O atoms. In all of these cases, computations provide atomic-scale understanding as well as quantitative materials property data of value to industrial research and development. There are two key challenges in applying ab initio calculations, namely a higher accuracy in the electronic energy and the efficient exploration of large parts of the configurational space. While progress in these areas is fueled by advances in computer hardware, innovative theoretical concepts combined with systematic large-scale computations will be needed to realize the full potential of ab initio calculations for industrial applications.

Wimmer, Erich; Najafabadi, Reza; Young, George A., Jr.; Ballard, Jake D.; Angeliu, Thomas M.; Vollmer, James; Chambers, James J.; Niimi, Hiroaki; Shaw, Judy B.; Freeman, Clive; Christensen, Mikael; Wolf, Walter; Saxe, Paul

2010-09-01

84

Ab initio nuclear structure - the large sparse matrix eigenvalue problem

International Nuclear Information System (INIS)

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 1010 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.

85

Use of symmetry in molecular ab-initio SCF calculations

International Nuclear Information System (INIS)

Today's molecular ab-initio SCF calculations approximate Hartree-Fock solutions of the electronic Schroedinger equation by a linear combination ansatz and the iterative process. The use of Gauss-type functions as basis functions by standard computer programs for ab-initio molecular orbital calculations demands rather large basis sets and, consequently, a very large number of two electron integrals whose time-consuming computations limit routinely performed ab-initio calculations to a maximum of 80 to 130 basis functions. The most important use of molecular symmetry in these calculations thus becomes the reduction of the number of two electron integrals. A second use of molecular symmetry is the symmetry adaptation of the basis set. To demonstrate these techniques and their ability to reduce computer time the authors carried out single-point calculations with the Univac version of GAUSSIAN 80 for H3BOH2BH3, H3BNH2CH3, and FN3 in their 4-31G optimized geometries under these three stipulations: no use of symmetry al all; use of symmetry only in the integral calculation; and full use of symmetry. Results for computer time and number of two electron integrals are tabulated. 33 references, 2 figures, 6 tables

86

The structural, elastic, thermodynamic, electronic and vibrational properties of CsCl-type TbMg have been studied by performing ab initio calculations based on density functional theory using the Vienna Ab initio Simulation Package (VASP). The exchange correlation potential within the generalized-gradient approximation (GGA) of projector augmented wave (PAW) method is used. The calculated structural parameters, such as the lattice constant, bulk modulus, its pressure derivative, formation energy and second-order elastic constants are presented in this paper. The obtained results are compared with related experimental and theoretical studies. The electronic band calculations, total density of states (DOS), partial DOS and charge density are also presented. Formation enthalpy and Cauchy pressure are determined. In order to obtain more information the elastic properties such as Zener anisotropy factor, Poisson’s ratio, Young modulus, isotropic shear modulus, Debye temperature and melting point have been carried out. The elastic constants are calculated in zero and different pressure ranges (0-50 GPa) with bulk modulus. We have performed the thermodynamic properties of TbMg by using quasi-harmonic Debye model. The temperature and pressure variation of the volume, bulk modulus, and thermal expansion coefficient have been predicted over a pressure range of 0-25 GPa for of TbMg. Pressure dependence of the anisotropy factors, Young’s modulus, Poisson’s ratios, bulk modulus and axis compressibility of TbMg are presented along different directions and planes. Finally, the phonon dispersion curves are presented for TbMg.

Mogulkoc, Y.; Ciftci, Y. O.; Kabak, M.; Colakoglu, K.

2014-07-01

87

Accelerating VASP electronic structure calculations using graphic processing units.

We present a way to improve the performance of the electronic structure Vienna Ab initio Simulation Package (VASP) program. We show that high-performance computers equipped with graphics processing units (GPUs) as accelerators may reduce drastically the computation time when offloading these sections to the graphic chips. The procedure consists of (i) profiling the performance of the code to isolate the time-consuming parts, (ii) rewriting these so that the algorithms become better-suited for the chosen graphic accelerator, and (iii) optimizing memory traffic between the host computer and the GPU accelerator. We chose to accelerate VASP with NVIDIA GPU using CUDA. We compare the GPU and original versions of VASP by evaluating the Davidson and RMM-DIIS algorithms on chemical systems of up to 1100 atoms. In these tests, the total time is reduced by a factor between 3 and 8 when running on n (CPU core + GPU) compared to n CPU cores only, without any accuracy loss. PMID:22903247

Hacene, Mohamed; Anciaux-Sedrakian, Ani; Rozanska, Xavier; Klahr, Diego; Guignon, Thomas; Fleurat-Lessard, Paul

2012-12-15

88

Ab initio investigation of intermolecular interactions in solid benzene

A computational strategy for the evaluation of the crystal lattice constants and cohesive energy of the weakly bound molecular solids is proposed. The strategy is based on the high level ab initio coupled-cluster determination of the pairwise additive contribution to the interaction energy. The zero-point-energy correction and non-additive contributions to the interaction energy are treated using density functional methods. The experimental crystal lattice constants of the solid benzene are reproduced, and the value of 480 meV/molecule is calculated for its cohesive energy.

Bludsky, O; Soldan, P; 10.1103/PhysRevB.77.092103

2009-01-01

89

Ab initio molecular dynamics via density based energy functionals

The use of energy functionals based on density as the basic variable is advocated for ab initio molecular dynamics. It is demonstrated that the constraint of positivity of density can be incorporated easily by using square root density for minimization of the energy functional. An ad hoc prescription for including nonlocal pseudopotentials for plane wave based calculations is proposed and is shown to yield improved results. Applications are reported for equilibrium geometries of small finite systems, viz. dimers and trimers of simple metal atoms like Na and Mg, which represent a rather stringent test for approximate kinetic energy functionals involved in such calculations.

Shah, V; Kanhere, D G; Vaishali Shah; Dinesh Nehete

1994-01-01

90

Recent advances of ab initio calculations in condensed matter physics

International Nuclear Information System (INIS)

Recent advances of ab initio calculations in condensed matter physics are presented, with regard to the following eight issues. 1.Two ways of thought in static density functional theory; 2.Functional forms in solid state theory; 3.Time dependent density functional theory and density matrix functional theory; 4.Calculations of band structure in semiconductors:band gap and band order; 5.f electrons and strong correlated metals; 6.Mott insulators; 7.Noncovalent (weak)interactions; 8.Wave function based research. Some background knowledge is presented also. (authors)

91

Symmetry-Adapted Ab Initio Open Core Shell Model Theory

International Nuclear Information System (INIS)

By using only a fraction of the model space, we gain further insight – within a symmetry-guided no-core shell model framework – into the many-body nuclear dynamics that gives rise to important single-particle configurations together with correlated highly-deformed and alpha-cluster structures. We show results of the novel ab initio symmetry-adapted no-core shell model for large-scale nuclear structure computations. In addition, we use the symmetry patterns unveiled in these results to explore ultra-large model spaces.

92

Ozone adsorption on graphene: ab initio study and experimental validation

We have investigated ozone adsorption on graphene using the ab initio density functional theory method. Ozone molecules adsorb on graphene basal plane with binding energy of 0.25 eV, and the physisorbed molecule can chemically react with graphene to form an epoxide group and an oxygen molecule. The activation energy barrier from physisorption to chemisorption is 0.72 eV, and the chemisorbed state has the binding energy of 0.33 eV. These binding energies and energy barrier in...

Lee, Geunsik; Lee, Bongki; Kim, Jiyoung; Cho, Kyeongjae

2009-01-01

93

Toward an Ab-initio Description of Quasiparticle Properties

Preliminary ab-initio applications of many-body Green's functions theory to the ground state of He-4 suggest that high accuracy can be achieved in the so-called Faddeev-random-phase-approximation method. We stress the potentialities of this approach for microscopic studies of medium-large nuclei and report applications to 1s0d and 1p0f-shell nuclei. In particular, we discuss the role of long-range correlations on spectroscopic factors and their dependence on asymmetry.

Barbieri, C.

2009-01-01

94

Ab initio studies of transition-metal dihydrogen chemistry

International Nuclear Information System (INIS)

Examples of transition metal complexes containing dihydrogen ligands are investigated using ab initio electronic structure calculations employing effective core potentials. Calculated geometrical structures and relative energies of various forms of WL5(H2) complexes (L = CO, PR3) are reported, and the influence of the ligand on the relative stabilities of the dihydrogen and dihydride forms is studied. The possible intramolecular mechanisms for H/D scrambling are investigated in another d6 complex, Cr(CO)4(H2)2, where various polyhydride intermediates are possible. 8 refs., 6 figs., 1 tab

95

Equations of state of heavy metals: ab initio approaches

International Nuclear Information System (INIS)

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)

96

Ab Initio and Ab Exitu No-Core Shell Model

Energy Technology Data Exchange (ETDEWEB)

We outline two complementary approaches based on the no core shell model (NCSM) and present recent results. In the ab initio approach, nuclear properties are evaluated with two-nucleon (NN) and three-nucleon interactions (TNI) derived within effective field theory (EFT) based on chiral perturbation theory (ChPT). Fitting two available parameters of the TNI generates good descriptions of light nuclei. In a second effort, an ab exitu approach, results are obtained with a realistic NN interaction derived by inverse scattering theory with off-shell properties tuned to fit light nuclei. Both approaches produce good results for observables sensitive to spin-orbit properties.

Vary, J P; Navratil, P; Gueorguiev, V G; Ormand, W E; Nogga, A; Maris, P; Shirokov, A

2007-10-02

97

Robust mixing for ab initio quantum mechanical calculations

We study the general problem of mixing for ab initio quantum mechanical problems. Guided by general mathematical principles and the underlying physics, we propose a multisecant form of Broyden’s second method for solving the self-consistent field equations of Kohn-Sham density-functional theory. The algorithm is robust, requires relatively little fine tuning, and appears to outperform the current state of the art, converging for cases that defeat many other methods. We compare our technique to the conventional methods for problems ranging from simple to nearly pathological.

Marks, L. D.; Luke, D. R.

2008-08-01

98

Ab-initio study of transition metal hydrides

International Nuclear Information System (INIS)

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

99

Ab Initio Calculations Applied to Problems in Metal Ion Chemistry

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

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

1994-01-01

100

Quantum confinement effects in gallium nitride nanostructures: ab initio investigations

International Nuclear Information System (INIS)

We present ab initio density functional investigations of the atomic and electronic structure of gallium nitride nanodots and nanowires. With increasing diameter, the average Ga-N bond length in the nanostructures increases, as does the relative stability (heat of formation), approaching the values for bulk GaN. As the diameter decreases, the band gap increases, with the variation for the nanodots greater than that for the nanowires, in qualitative accordance with expectations based on simple geometrical quantum confinement considerations. Interestingly, in contrast to nanowires, the lowest unoccupied states of the nanodots exhibit an extended delocalized (Ga-derived) character, weighted in the centre of the nanodot.

101

Ab initio study of phase equilibria in TiCx

DEFF Research Database (Denmark)

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, Ti3C2, and Ti6C5) are found to be ground state configurations. Their stability has been verified by full-potential total energy calculations of the fully relaxed structures.

Korzhavyi, P.A.; Pourovskii, L.V.

2002-01-01

102

Ab-initio study of napthelene based conducting polymer

Energy Technology Data Exchange (ETDEWEB)

In this paper, we have identified structural and electronic properties of conducting polymers by using DFT based ATK-VNL ab-initio tool. Naphthalene derivative structures were stabilized by varying the bond length between two atoms of the molecule C-N and C-C. We have also studied the molecular energy spectrum of naphthalene derivatives and found the HOMOLUMO for the same. A comparison of structural and electronic properties of naphthalene derivatives by attaching the functional group of amine, have been performed and found that they show good semi conducting properties.

Ruhela, Ankur [Advanced Materials Research Group, Computational Nanoscience and Technology Lab (CNTL), ABV-Indian Institute of Information Technology and Management, Gwalior -474010, India and Amity Institute of Nanotechnology, Amity University, Noida-201303 (India); Kanchan, Reena, E-mail: reena.kanchan1977@gmail.com [Department of Chemistry, Jiwaji University, Gwalior-474001 (India); Srivastava, Anurag [Advanced Materials Research Group, Computational Nanoscience and Technology Lab (CNTL), ABV-Indian Institute of Information Technology and Management, Gwalior -474010 (India); Sinha, O. P. [Amity Institute of Nanotechnology, Amity University, Noida-201303 (India)

2014-04-24

103

Ab initio calculations and modelling of atomic cluster structure

DEFF Research Database (Denmark)

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 framework for modelling the fusion process of noble gas clusters is presented. We report the striking correspondence of the peaks in the experimentally measured abundance mass spectra with the peaks in the size-dependence of the second derivative of the binding energy per atom calculated for the chain of the noble gas clusters up to 150 atoms.

Solov'yov, Ilia; Lyalin, Andrey G.

2004-01-01

104

Benchmarks of the ab initio FCI, MCSM and NCFC methods

We report ab initio no-core solutions for properties of light nuclei with three different approaches in order to assess the accuracy and convergence rates of each method. Full Configuration Interaction (FCI), Monte Carlo Shell Model (MCSM) and No Core Full Configuration (NCFC) approaches are solved separately for the ground state energy and other properties of seven light nuclei using the realistic JISP16 nucleon-nucleon interaction. The results are consistent among the different approaches. The methods differ significantly in how the required computational resources scale with increasing particle number for a given accuracy.

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

2012-01-01

105

Ab-initio study of transition metal hydrides

Energy Technology Data Exchange (ETDEWEB)

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

Sharma, Ramesh [Dept. of Physics, Feroze Gandhi Insititute of Engineering and Technology, Raebareli-229001 (India); Shukla, Seema, E-mail: sharma.yamini62@gmail.com; Dwivedi, Shalini, E-mail: sharma.yamini62@gmail.com; Sharma, Yamini, E-mail: sharma.yamini62@gmail.com [Theoretical Condensed Matter Physics Laboratory, Dept. of Physics Feroze Gandhi College, Raebareli-229001 (India)

2014-04-24

106

Ab initio calculations of inelastic losses and optical constants

Ab initio approaches are introduced for calculations of inelastic losses and vibrational damping in core level x-ray and electron spectroscopies. From the dielectric response function we obtain system-dependent self-energies, inelastic mean free paths, and losses due to multiple-electron excitations, while from the dynamical matrix we obtain phonon spectra and Debye-Waller factors. These developments yield various spectra and optical constants from the UV to x-ray energies in aperiodic materials, and significantly improve both the near edge and extended fine structure.

Rehr, J J; Prange, M P; Vila, F D; Ankudinov, A L; Campbell, L W; Sorini, A P

2006-01-01

107

AB INITIO SIMULATIONS FOR MATERIAL PROPERTIES ALONG THE JUPITER ADIABAT

International Nuclear Information System (INIS)

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

108

Ab Initio Simulations for Material Properties along the Jupiter Adiabat

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

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

2012-09-01

109

Why ferro electricity? synchrotron radiation and ab initio answers

International Nuclear Information System (INIS)

An old question of solid state physics is being answered nowadays: the atomic-level understanding of ferro electricity. Traditional ideas about ferroelectric phenomena relate with softening of optical phonons at the Brillouin zone origin and with 'W-shaped' Landau free energy functions. Last decade experimental (synchrotron radiation, neutrons) and quantum-theoretical (Cohen, Resta, Spaldin) contributions have clarified detailed descriptions and explanations for atomic behavior leading to spontaneous polarization in perovskite and perovskite-related crystal structures. Work being performed by our interdisciplinary group on ferro electricity is presented. Perovskite and Aurivillius ferroelectric phases are obtained by different methods. Fine details on crystal structures are investigated by means of synchrotron radiation at Stanford Synchrotron Radiation Laboratory. Electronic structures of considered phases are theoretically characterized by ab initio methods. High-resolution diffraction experiments demonstrate several symmetry break-downs in perovskite and Aurivillius phases. The structure- symmetry-polarization relationship is discussed for a number of representative cases. Ab initio explanation of ferroelectric polarization in perovskite structures is given. Energy calculation is performed by means of CASTEP code under GGA functional. Energy optimization leads to cubic-tetragonal symmetry break-down with off-centering cation displacements via second-order Jahn-Telln displacements via second-order Jahn-Teller effect. Electronic structure is investigated with Band Lab code, under LDA functional with LMTO method. Degeneracy of Ti 3d z2 and Ti 3d (x2 + y2) orbitals is the cause of cubic-perovskite deformation. (Author)

110

Ab initio dynamics of the cytochrome P450 hydroxylation reaction

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

Elenewski, Justin E.; Hackett, John C.

2015-02-01

111

Ab initio prediction of the critical thickness of a precipitate

International Nuclear Information System (INIS)

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

112

New Horizons in Ab Initio Nuclear Structure Theory

International Nuclear Information System (INIS)

Nuclear interactions derived within chiral effective field theory enable nuclear structure and reaction calculations solidly rooted in QCD. Using chiral two- and three-body interactions in ab initio studies of a variety of nuclear observables is, both, promising and challenging. Particularly the inclusion of chiral 3N interactions into exact and approximate many-body calculations is demanding and computationally expensive. We present recent key developments that facilitate ab initio calculations of ground and low-lying excited states of p- and sd-shell nuclei with full 3N interactions in the Importance-Truncated No-Core Shell Model using consistent Similarity Renormalization Group transformations of the NN+3N Hamiltonian. The treatment of 3N interactions without approximations allows for first studies of the dependence of nuclear-structure observables on the details of chiral interactions. Moreover, we present results for heavy nuclei obtained in Coupled Cluster calculations using a normal-ordered two-body approximation of the 3N interaction.

113

Ab Initio Protein Structure Prediction Using Pathway Models

Directory of Open Access Journals (Sweden)

Full Text Available Ab initio prediction is the challenging attempt to predict protein structures based only on sequence information and without using templates. It is often divided into two distinct sub-problems: (a the scoring function that can distinguish native, or native-like structures, from non-native ones; and (b the method of searching the conformational space. Currently, there is no reliable scoring function that can always drive a search to the native fold, and there is no general search method that can guarantee a significant sampling of near-natives. Pathway models combine the scoring function and the search. In this short review, we explore some of the ways pathway models are used in folding, in published works since 2001, and present a new pathway model, HMMSTR-CM, that uses a fragment library and a set of nucleation/propagation-based rules. The new method was used for ab initio predictions as part of CASP5. This work was presented at the Winter School in Bioinformatics, Bologna, Italy, 10Ã¢Â€Â“14 February 2003.

Christopher Bystroff

2006-04-01

114

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

International Nuclear Information System (INIS)

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.

115

International Nuclear Information System (INIS)

Self-associates of nucleic acid components (stacking trimers and tetramers of the base pairs of nucleic acids) and short fragments of nucleic acids are nanoparticles (linear sizes of these particles are more than 10 A). Modern quantum-mechanical methods and softwares allow one to perform ab initio calculations of the systems consisting of 150-200 atoms with enough large basis sets (for example, 6-31G*). The aim of this work is to reveal the peculiarities of molecular and electronic structures, as well as the energy features of nanoparticles of nucleic acid components. We had carried out ab initio calculations of the molecular structure and interactions in the stacking dimer, trimer, and tetramer of nucleic base pairs and in the stacking (TpG)(ApC) dimer and (TpGpC) (ApCpG) trimer of nucleotides, which are small DNA fragments. The performed calculations of molecular structures of dimers and trimers of nucleotide pairs showed that the interplanar distance in the structures studied is equal to 3.2 A on average, and the helical angle in a trimer is approximately equal to 30o: The distance between phosphor atoms in neighboring chains is 13.1 A. For dimers and trimers under study, we calculated the horizontal interaction energies. The analysis of interplanar distances and angles between nucleic bases and their pairs in the calculated short oligomers of nucleic acid base pairs (stacking dimer, trimer, and tetramer) has been carried out. Studies of interactions in the calculated short oligomers showed a considerable role of the cross interaction in the stabilization of the structures. The contribution of cross interactions to the horizontal interactions grows with the length of an oligomer. Nanoparticle components get electric charges in nanoparticles. Longwave low-intensity bands can appear in the electron spectra of nanoparticles.

116

Ab initio calculation of thermodynamic functions for crystals

International Nuclear Information System (INIS)

The knowledge of thermodynamic functions is essential to investigate crystal stability and chemical reactivity. These functions are not always experimentally known, as for some crystalline host phases for radioactive waste. Fortunately, it is possible to calculate them. Although possible, the full ab initio calculation is not realistic because the calculation time rapidly becomes too long. These functions are obtained using an analytical model containing physical quantities determined by ab initio calculations. This enabled us to estimate the main thermodynamic functions of zircon ZrSiO4, fluor-apatite Ca10(PO4)6F2 and stoichiometric iodo-apatite Pb10(VO4)6I2 from the variation of cohesive energy with volume and the harmonic vibration frequencies at the center of the first Brillouin zone for the unit cell corresponding to maximum cohesive energy. These ab initio quantities are calculated with the DMOL3 code that solves the electronic Schroedinger equation using the electronic density functional theory (DFT) in local density approximation, corrected (NLDA) or not (LDA) with its gradient. To limit calculation time, we made additional approximations: - acoustic and optical vibrations beyond the first Brillouin zone center are described by the Debye and Einstein models respectively; - to allow thermal expansion of the crystal we used the quasi-harmonic approximation which assumes that frequency variations are proportional to volume variations. The proportionality coefficients known as Gruneisen coefficients are derived in this study, with specific approximations; - we used the spherical cellular approximation and considered the crystal as isotropic. The thermodynamic functions calculated with this model are the following measurable quantities : enthalpy and free enthalpy, heat capacity at constant pressure, bulk modulus and thermal expansion coefficient. For zircon and fluor-apatite, for which the main thermodynamic functions are experimentally known, the enthalpy of formation are determined with less than 2% uncertainty, and heat capacities at constant pressure are well reproduced: For iodo-apatite, there are as yet no published experimental data to compare with the present theoretical results. This model can be applied to a wide range of crystals. (author)

117

SURPRISES: when ab initio meets statistics in extended systems

International Nuclear Information System (INIS)

The surface photoelectron and inner shell electron spectroscopy (SURPRISES) program suite performs ab initio calculations of photoionization and non-radiative decay spectra in nanoclusters and solid state systems by using a space-energy similarity procedure to reproduce the band-like part of the spectra. This approach provides an extension of Fano resonant multichannel scattering theory dealing with the complexity arising from condensed matter calculations at a computational cost comparable to that of molecules. The bottleneck of electron spectroscopy ab initio calculations in condensed matter is the size of the Hilbert space where the wavefunctions are expanded and the increase in number of final decay states in comparison to that of atoms and molecules. In particular, the diagonalization of the interchannel interaction to take into account the correlation between the double ion and the escaping electron is impracticable when hole delocalization on valence bands and electronic excitations are included in the model. To overcome this problem SURPRISES uses a 'space-energy similarity' approach, which allows the spreading of the Auger probability over the bands without tuning semi-empirical parameters. Furthermore, a completely new feature in the landscape of ab initio resonant decay processes calculations is represented by including energy loss through a statistical approach. Using the calculated lineshape as electron source, a Monte Carlo routine simulates the effect oMonte Carlo routine simulates the effect of inelastic losses on the original lineshape. In this process, the computed spectrum can be directly compared with acquired experimental spectra, thus avoiding background subtraction, a procedure not free from uncertainty. The program can exploit the symmetry of the system under investigation to reduce the calculation scaling and may compute photoemission and Auger decay angular distribution patterns including energy loss for the electrons emitted in resonance-affected photoionization processes. In this paper, we present general methods, computational techniques and a number of numerical tests applied to the calculation of Si K-LL and O K-LL Auger spectra from different SiO2 nanoclusters.

118

The atomic string potential: An ab initio calculation

International Nuclear Information System (INIS)

The interaction energy between a helium atom and a string of beryllium atoms is evaluated by means of a non-empirical ab inito pseudopotential method normally used for molecular calculations. It is shown that four beryllium atoms in the string adequately define the interaction with the helium atom. The effect of adding further atoms to the string is for all practical purposes negligible. A superposition of binary potentials in the evaluation of the total interaction is shown to be satisfactory provided that the binary potential employed is itself realistic. Lindhard's continuum approximation is in excellent agreement with the ab initio average potential. A brief discussion of quantities of interest in axial channeling, and of their sensitivity to the accuracy of the interatomic potential, is also presented. (orig.)

119

Ab initio H2O in realistic hydrophilic confinement.

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

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

2014-12-15

120

Ab initio based multiscale modeling of alloy surface segregation.

A fully integrated ab initio based multiscale model for analysis of segregation at alloy surfaces is presented. Major components of the model include a structure-energy analysis from the first-principles density functional theory (DFT), a Monte Carlo/molecular dynamics (MC/MD) hybrid simulation scheme for atomic transport, and a reactive force field formalism that binds the two. The multiscale model accurately describes the atomic transport processes in a multi-component alloy system at finite temperature, and is capable of providing quantitative predictions for surface compositions. The validity of the model was demonstrated by investigating the temperature-dependent segregation behavior of B2 FeAl binary alloy surfaces with a detailed description of the segregation mechanism. Based on the model's prediction capabilities, potential extension of the model to the analysis of systems undergoing rapid chemical reactions is discussed. PMID:23114706

Kwak, Hyunwook; Shin, Yun Kyung; van Duin, Adri C T; Vasenkov, Alex V

2012-12-01

121

Towards kinetic Monte-Carlo simulations with ab initio accuracy

International Nuclear Information System (INIS)

Full text: For the Ni-Pt and Fe-Cu alloy system we present the rst steps towards kinetic Monte-Carlo (KMC) simulations with ab initio accuracy. Many body interactions which describe the energetics of both the local minima and migration states are included by cluster expansions (CE) in the framework of the UNCLE code. In this model approach single atoms jump to vacant nearest-neighbor sites and have to overcome configuration dependent migration barriers. According to transition state theory (TST) jump rates are then derived by the energy difference between initial and saddle point state. The KMC simulations require a) vacant lattice sites, which enforce a ternary CE for a binary compound, and b) the configuration dependent height of the saddle points, which have to be calculated and included in the CE. We discuss different aspects of jump profiles in the respective systems computed by density functional theory (DFT) calculations. (author)

122

Relativistic ab initio calculations for ion-atom collisions

International Nuclear Information System (INIS)

Within the independent particle model we solve the time---dependent single-particle equation using ab initio SCF-DIRAC-FOCK-SLATER wavefunctions as a basis. To reinstate the many-particle aspect of the collision system we use the inclusive probability formalism to answer experimental questions. As an example we show an application to the case of S15+ on Ar where experimental data on the K-K charge transfer are available for a wide range of impact energies from 4.7 to 90 MeV. Our molecular adiabatic calculations and the evaluation using the inclusive probability formalism show good results in the low energy range from 4.7 to 16 MeV impact energy

123

The ab initio no-core shell model

International Nuclear Information System (INIS)

This contribution reviews a number of applications of the ab initio no-core shell model (NCSM) within nuclear physics and beyond. We will highlight a nuclear-structure study of the A = 12 isobar using a chiral NN + 3NF interaction. In the spirit of this workshop we will also mention the new development of the NCSM formalism to describe open channels and to approach the problem of nuclear reactions. Finally, we will illustrate the universality of the many-body problem by presenting the recent adaptation of the NCSM effective-interaction approach to study the many-boson problem in an external trapping potential with short-range interactions. This article is based on the presentation by C. Forssen at the Fifth Workshop on Critical Stability, Erice, Sicily. (author)

124

Ab initio shallow acceptor levels in gallium nitride

Impurity levels and formation energies of acceptors in wurtzite GaN are predicted ab initio. Be_Ga is found to be the shallow (thermal ionization energy $\\sim$ 0.06 eV); $Mg_{Ga}$ and $Zn_{Ga}$ are mid-deep acceptors (0.23 eV and 0.33 eV respectively); $Ca_{Ga}$ and $Cd_{Ga}$ are deep acceptors ($\\sim$0.65 eV); $Si_N$ is a midgap trap with high formation energy; finally, contrary to recent claims, $C_N$ is a deep acceptor (0.65 eV). Interstitials and heteroantisites are energetically not competitive with substitutional incorporation.

Fiorentini, V; Bosin, A; Vanderbilt, D

1996-01-01

125

Isofulminic acid, HONC: Ab initio theory and microwave spectroscopy

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

Mladenovi?, Mirjana; Lewerenz, Marius; McCarthy, Michael C.; Thaddeus, Patrick

2009-11-01

126

The ab-initio density matrix renormalization group in practice

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: ?-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.

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

2015-01-01

127

Ab initio quantum dynamics using coupled-cluster

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

Kvaal, Simen

2012-05-01

128

Ab initio nanoplasmonics: The impact of atomic structure

We present an ab initio study of the hybridization of localized surface plasmons in a metal nanoparticle dimer. The atomic structure, which is often neglected in theoretical studies of quantum nanoplasmonics, has a strong impact on the optical absorption properties when subnanometric gaps between the nanoparticles are considered. We demonstrate that this influences the hybridization of optical resonances of the dimer, and leads to significantly smaller electric field enhancements as compared to the standard jellium model. In addition, we show that the corrugation of the metal surface at a microscopic scale becomes as important as other well-known quantum corrections to the plasmonic response, implying that the atomic structure has to be taken into account to obtain quantitative predictions for realistic nanoplasmonic devices.

Zhang, Pu; Feist, Johannes; Rubio, Angel; García-González, Pablo; García-Vidal, F. J.

2014-10-01

129

Ab initio based multiscale modeling of alloy surface segregation

A fully integrated ab initio based multiscale model for analysis of segregation at alloy surfaces is presented. Major components of the model include a structure-energy analysis from the first-principles density functional theory (DFT), a Monte Carlo/molecular dynamics (MC/MD) hybrid simulation scheme for atomic transport, and a reactive force field formalism that binds the two. The multiscale model accurately describes the atomic transport processes in a multi-component alloy system at finite temperature, and is capable of providing quantitative predictions for surface compositions. The validity of the model was demonstrated by investigating the temperature-dependent segregation behavior of B2 FeAl binary alloy surfaces with a detailed description of the segregation mechanism. Based on the model’s prediction capabilities, potential extension of the model to the analysis of systems undergoing rapid chemical reactions is discussed.

Kwak, Hyunwook; Shin, Yun Kyung; van Duin, Adri C. T.; Vasenkov, Alex V.

2012-12-01

130

A hydronitrogen solid: high pressure ab initio evolutionary structure searches

Energy Technology Data Exchange (ETDEWEB)

High pressure ab initio evolutionary structure searches resulted in a hydronitrogen solid with a composition of (NH){sub 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)

Hu Anguang; Zhang Fan, E-mail: Anguang.Hu@drdc-rddc.gc.ca [Defence Research and Development Canada-Suffield, PO Box 4000 Stn Main, Medicine Hat, AB, T1A 8K6 (Canada)

2011-01-19

131

Ab initio methods for electron-molecule collisions

Energy Technology Data Exchange (ETDEWEB)

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 (approx. = 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.

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

1987-01-01

132

Quantifying transition voltage spectroscopy of molecular junctions: Ab initio calculations

DEFF Research Database (Denmark)

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-voltage relations for a broad class of single-molecule transport junctions in order to assess the applicability and limitations of TVS. We find, that in order to fully utilize TVS as a quantitative spectroscopic tool, it is important to consider asymmetries in the coupling of the molecule to the two electrodes. When this is taken properly into account, the relation between the transition voltage and the energy of the molecular orbital closest to the Fermi level closely follows the trend expected from a simple, analytical model.

Chen, Jingzhe; Markussen, Troels

2010-01-01

133

A Review on Ab Initio Approaches for Multielectron Dynamics

In parallel with the evolution of femtosecond and attosecond laser as well as free-electron laser technology, a variety of theoretical methods have been developed to describe the behavior of atoms, molecules, clusters, and solids under the action of those laser pulses. Here we review major ab initio wave-function-based numerical approaches to simulate multielectron dynamics in atoms and molecules driven by intense long-wavelength and/or ultrashort short-wavelength laser pulses. Direct solution of the time-dependent Schr\\"odinger equation (TDSE), though its applicability is limited to He, ${\\rm H}_2$, and Li, can provide an exact description and has been greatly contributing to the understanding of dynamical electron-electron correlation. Multiconfiguration self-consistent-field (MCSCF) approach offers a flexible framework from which a variety of methods can be derived to treat both atoms and molecules, with possibility to systematically control the accuracy. The equations of motion of configuration interactio...

Ishikawa, Kenichi L

2015-01-01

134

Elements of the ab initio No Core Shell Model

International Nuclear Information System (INIS)

We outline the ab initio no core shell model and present recent results. Nuclear properties are evaluated with two-nucleon (NN) and three-nucleon interactions (TNI) derived within effective field theory (EFT) based on chiral perturbation theory (ChPT). Fitting two available parameters of the TNI generates good descriptions of light nuclei. In another effort, referred to as the ab exitu approach, results are obtained with a realistic NN interaction derived by inverse scattering theory with off-shell properties tuned to fit light nuclei. Both approaches produce good results for observables sensitive to spin-orbit properties. In a third approach, we supplement the derived realistic effective interaction with phenomenological NN interaction terms with the goal to describe spectra of fp-shell nuclei in the limited basis spaces currently available

135

Ab initio study of intramolecular proton transfer reactions in cytosine

The activation energies of intramolecular proton transfer reactions of cytosine in the gas phase were computed through ab initio calculations. MP2/6-31G ** and MP2/D95 ** energy calculations were performed over geometries obtained at the HF/3-21G, HF/6-31G(N8 *) and HF/D95(N8 *) level (d-type polarisation functions were added on the N8 atom). Corrections for the zero-point vibrational energy were included. It is suggested that not only thermodynamic but also kinetic factors may be responsible for the distribution of the tautomeric species in the gas phase. Results are discussed with reference to spectroscopic data in the literature.

Morpurgo, Simone; Bossa, Mario; Morpurgo, Giorgio O.

1997-12-01

136

Electronic correlation effects in superconducting picene from ab initio calculations

We show, by means of ab initio calculations, that electron-electron correlations play an important role in potassium-doped picene (Kx-picene), recently characterized as a superconductor with Tc=18K. The inclusion of exchange interactions by means of hybrid functionals reproduces the correct gap for the undoped compound and predicts an antiferromagnetic state for x=3, where superconductivity has been observed. These calculations, which do not require us to assume a value for the interaction strength, indirectly suggest that these materials should have a sizable ratio between the effective Coulomb repulsion U and the bandwidth. This is fully compatible with simple estimates of this ratio. Using these values of U in a simple effective Hubbard model, an antiferromagnetic state is indeed stabilized. Our results highlight the similarity between potassium-doped picene and alkali-doped fulleride superconductors.

Giovannetti, Gianluca; Capone, Massimo

2011-04-01

137

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

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

Mladenovi?, Mirjana; Lewerenz, Marius; McCarthy, Michael C; Thaddeus, Patrick

2009-11-01

138

Improved Embedding Ab Initio Model Potentials for Embedded Cluster Calculations

An improvement in the method of production of embedding ab initio model potentials (AIMP) for embedded cluster calculations in ionic solids is proposed and applied to the oxides CeAlO3, CeO2, and UO2. The improvement affects the calculation of one of the AIMP components, the Pauli repulsion operator, which prevents the cluster electrons from collapsing onto the occupied orbitals of the host in embedded cluster calculations and, so, their over occupancy. The linear constants involved in such operator are proposed to be obtained in embedded cluster calculations in the perfect host, with the requirement that local structures calculated with working embedded clusters of relatively small size agree with those calculated with reference embedded clusters of much larger size.

Pascual, José Luis; Barros, Noémi; Barandiarán, Zoila; Seijo, Luis

2009-06-01

139

Ab initio water pair potential with flexible monomers.

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

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

2015-03-26

140

Ab initio quantum dynamics using coupled-cluster

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

Kvaal, Simen

2012-01-01

141

An Efficient Approach to Ab Initio Monte Carlo Simulation

We present a Nested Markov Chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, is used to substantially decorrelate configurations at which the potential of interest is evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure is maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature \\beta^0), which is otherwise unconstrained. Local density approximation (LDA) results are presented for shocked states in argon at pressures from 4 to 60 GPa. Depending on the quality of the reference potential, the acceptance probability is enhanced by factors of 1.2-28 relative to unoptimized NMC sampling, and the procedure's efficiency is found to be competitive with that of standard ab initio...

Leiding, Jeff

2013-01-01

142

Self-vacancies in Gallium Arsenide: an ab initio calculation

We report here a reexamination of the static properties of vacancies in GaAs by means of first-principles density-functional calculations using localized basis sets. Our calculated formation energies yields results that are in good agreement with recent experimental and {\\it ab-initio} calculation and provide a complete description of the relaxation geometry and energetic for various charge state of vacancies from both sublattices. Gallium vacancies are stable in the 0, -, -2, -3 charge state, but V_Ga^-3 remains the dominant charge state for intrinsic and n-type GaAs, confirming results from positron annihilation. Interestingly, Arsenic vacancies show two successive negative-U transitions making only +1, -1 and -3 charge states stable, while the intermediate defects are metastable. The second transition (-/-3) brings a resonant bond relaxation for V_As^-3 similar to the one identified for silicon and GaAs divacancies.

El-Mellouhi, F; El-Mellouhi, Fedwa; Mousseau, Normand

2004-01-01

143

Electron transport through heterocyclic molecule: ab initio molecular orbital theory

International Nuclear Information System (INIS)

We have calculated the electron transport properties of molecule wires by an ab initio molecule orbital theory on the basis of the first-principles density functional theory (DFT) and the non-equilibrium Green function (NEGF) technique. The wires are made of heterocyclic molecule (furan, thiophene, and pyrrole, shown in first figure), in contact with the atomic scale Au electrodes. The results of our calculation reveal: (1) the furan has a much high conductance in contrast to the others and (2) the heteroatom can significantly affect the transport property by changing electronic structure of the heterocyclic molecule. We find the step-like I-V feature qualitative agreement with the experimental findings

144

H3 +: Ab initio calculation of the vibration spectrum

International Nuclear Information System (INIS)

The vibration spectrum of H3 + 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 R1=R2=0.91396 A, theta=60.0012degree, where theta is the angle between the two equivalent bonds. The transition frequencies for the E and A1 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 A1 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 cmber 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 A1 and E vibrational bands is suggested

145

Primary kinetic hydrogen isotope effects in hydride transfer: ab initio MO and experimental studies

International Nuclear Information System (INIS)

Measurement of the primary kinetic hydrogen isotope effects for the intramolecular migration of hydride from alcohol methine to ketonic carbonyl in hydroxy-ketones and their interpretation using ab initio MO calculations show good agreement between theory and experiment. (author)

146

Czech Academy of Sciences Publication Activity Database

Ro?. 19, ?. 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

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

2013-01-01

147

Hydrogen adsorption on boron doped graphene: an {\\it ab initio} study

The electronic and structural properties of (i) boron doped graphene sheets, and (ii) the chemisorption processes of hydrogen adatoms on the boron doped graphene sheets have been examined by {\\it ab initio} total energy calculations.

Miwa, R. H.; Martins, T. B.; Fazzio, A.

2007-01-01

148

DEFF Research Database (Denmark)

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.

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

149

International Nuclear Information System (INIS)

Recent progress in the ab initio quantum chemistry study of cathode oxygen reduction on fuel cell catalysts is reviewed with emphasis on density functional theory and ab initio molecular dynamics methods. The capabilities of these methods are illustrated using examples of oxygen adsorption on transition metals and alloys, and the reduction mechanism. Ab initio studies can calculate adsorption geometry, energy, the dissociation energy barrier, reversible potential, activation energy, and potential dependant properties for elementary electron transfer steps. Even though ab initio study in this field is still at an early stage, it has already demonstrated its predictive ability in the trend of adsorption energy on transition metals and alloys, and illustrated its potential in identifying better electrocatalysts

150

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—...

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

2009-01-01

151

On-the-fly ab initio molecular dynamics with multiconfigurational Ehrenfest method

In this article we report the formalism and first implementation of the ab initio multiconfigurational Ehrenfest (AI-MCE) method for simulation of ultrafast nonadiabatic dynamics, which uses the MOLPRO electronic structure program to calculate the potential energy surfaces on the fly. The approach is tested on the benchmark of the excited ??* state dynamics of ethylene producing the dynamics which agree with previous simulations by ab initio multiple spawning technique. The AI-MCE seems to be robust, stable and efficient.

Saita, Kenichiro; Shalashilin, Dmitrii V.

2012-12-01

152

ARCIMBOLDO, un método de supercomputación para la determinación cristalográfica ab initio de estructuras de proteínas con resolución inferior a la atómica. RESUMEN: Los actuales métodos Ab initio para la resolución de estructuras macromoleculares están generalmente limitados a casos de proteínas pequeñas que difractan a resolución atómica (1.2Å máximo) a menos que contengan átomos pesados. ARCIMBOLDO1 es un método general para la resolución de es...

Rodri?guez Marti?nez, Dayte? Dayana

2013-01-01

153

International Nuclear Information System (INIS)

Two complex perovskite-related structures were solved by ab initio from precession electron diffraction intensities. Structure models were firstly derived from HREM images and than have been confirmed independently using two and three-dimensional sets of precession intensities. Patterson techniques prove to be effective for ab initio structure resolution, specially in case of projections with no overlapping atoms. Quality of precession intensity data may be suitable enough to resolve unknown heavy oxide structures

154

Ab initio and finite-temperature molecular dynamics studies of lattice resistance in tantalum

This manuscript explores the apparent discrepancy between experimental data and theoretical calculations of the lattice resistance of bcc tantalum. We present the first results for the temperature dependence of the Peierls stress in this system and the first ab initio calculation of the zero-temperature Peierls stress to employ periodic boundary conditions, which are those best suited to the study of metallic systems at the electron-structure level. Our ab initio value for t...

Segall, D. E.; Strachan, Alejandro; Ismail-beigi, Sohrab; Goddard Iii, William A.; Arias, T. A.

2002-01-01

155

Ab-initio simulation of atomic adsorption on Vanadium surfaces

International Nuclear Information System (INIS)

My thesis shows two important results: first, state-of-the-art ab-initio methods are able to derive even complex surface structures. Second, a close cooperation with experimentalists is necessary to solve such complex structures. Then, experiment and theory are of equal importance. This work has been done within a 'Joint Research Project' about 'Gas Surface Interactions', in which a close cooperation between experimental and theoretical groups occurs. The aim is the determination of structures that cannot be resolved only experimentally. Because theory can predict energetics and structures, it plays an equally important role as experiment. After a short methodic introduction, several applications on the clean V(100) surface as well as on adsorption and reconstruction of the V(100) and V(110) surface follow. All calculations were done with the 'Vienna Ab-initio Simulation Package'. It can be shown that a careful choice of the pseudopotential is necessary to exclude magnetic artefacts. Then, the (1x5) reconstruction of V(100) upon O adsorption is investigated. O then adsorbs not only in hollow sites, but also in bridged sites. Because of the strong O-V bond of about 1.9 Angstroem, a (1x5) reconstruction occurs at a coverage of about 80 %. C adsorption on V(100) is studied as well, and the observed superstructures are extensively discussed. According to our calculations, C adsorbs in rows, whereas experiments show c(2x2) patterns. In case of a coadsorption of C and O, th. In case of a coadsorption of C and O, theory claims that an O concentration of only 0.13 monolayers drives the p(1x2) C pattern into a c(2x2) pattern. This could be proved by later experiments. Further, H adsorption, absorption and diffusion into V bulk is studied. A theoretical interpretation of experimentally not clearly assigned desorption peaks is given. A strong dependence of adsorption energy on the H concentration, as well as on contaminations like O or C and adsorption sites is observed. Finally, the O induced c(6x2) reconstruction of V(110) is discussed. Many models had to be considered to solve this complex structure. Again, the strong O-V bond is the driving force for this reconstruction. A row shift in the surface leads to fourfold and threefold hollow sites that are favourable for adsorption. (author)

156

Ab-initio calculations of the Optical band-gap of TiO2 thin films

Titanium dioxide has been extensively studied in recent decades for its important photocatalytic application in environmental purification. The search for a method to narrow the optical band-gap of TiO2 plays a key role for enhancing its photocatalytic application. The optical band gap of epitaxial rutile and anatase TiO2 thin films deposited by helicon magnetron sputtering on sapphire and on SrTiO3 substrates was correlated to the lattice constants estimated from HRTEM images and SAED. The optical band-gap of 3.03 eV for bulk-rutile increased for the thin films to 3.37 on sapphire. The band gap of 3.20 eV for bulk-anatase increases to 3.51 on SrTiO3. In order to interpret the optical band gap expansion for both phases, ab-initio calculations were performed using the Vienna ab-initio software. The calculations for rutile as well anatase show an almost linear increase of the band gap width with decreasing volume or increasing lattice constant a. The calculated band gap fits well with the experimental values. T...

Wunderlich, W; Tanemura, M; Tanemura, S; Jin, P; Kaneko, K; Terai, A; Nabatova-Gabin, N; Belkada, R; Wunderlich, Wilfried; Miao, Lei; Tanemura, Masaki; Tanemura, Sakae; Jin, Ping; Kaneko, Kenji; Terai, Asuka; Nabatova-Gabin, Nataliya; Belkada, Rachid

2004-01-01

157

Ab initio determination of diffusion mechanisms in FeAl

Energy Technology Data Exchange (ETDEWEB)

Iron aluminides are a promising material class for industrial high temperature applications. FeAl shows a very high vacancy concentration (several percent at T>1000 K) which severely affects its mechanical properties. It is therefore crucial to understand the generation and diffusion behavior of those vacancies. The simplest diffusion mechanism which preserves long-range order in B2-FeAl is the next-nearest neighbor (NNN) jump of a vacancy. As a first step we performed ab initio calculations to determine the formation energies of the defects in FeAl. Four defects were investigated, namely vacancies and antisite atoms on the Fe and Al sublattices. We found that the Al vacancy has a large formation energy compared to the other defects. Therefore the NNN jump was only investigated for Fe vacancies. In a second step we calculated the migration barrier of this process using the climbing image nudged elastic band method. Several more sophisticated mechanisms are proposed in the literature. A very promising candidate is the triple defect mechanism. We also performed nudged elastic band calculations for this mechanism and found a migration barrier which is significantly lower than for the NNN jump and several other diffusion mechanisms. We therefore conclude that the triple defect mechanism is the energetically most favorable diffusion mechanism.

Sandschneider, Niko; Hickel, Tilmann; Neugebauer, Joerg [Max-Planck-Institut fuer Eisenforschung GmbH, Max-Planck-Str. 1, 40237 Duesseldorf (Germany)

2011-07-01

158

Ab initio simulations of MgO under extreme conditions

We determined the phase diagram of magnesium oxide with finite-temperature density functional theory molecular dynamics simulations up to temperatures and pressures as relevant for the deep interior of super-Earths and in rocky cores of giant planets such as Jupiter. The equation of state data, the Hugoniot, and a ramp compression curve are computed and compared to earlier results from diamond anvil cell and (decaying) shock wave experiments. In addition, the dynamical electrical conductivity and the reflectivity along the experimental Hugoniot curve are calculated in order to characterize electronic structure changes under compression. The structural properties of MgO are identified using pair correlation functions and self-diffusion coefficients. The solid-solid coexistence line is calculated by comparing the free enthalpies of the B1 and the B2 phase. The free energy of the solid phases is determined via thermodynamic relations using the ab initio simulation results and phonon calculations in the harmonic approximation. Our results indicate that the solid B2 phase of MgO does not occur in the interior of the Earth but may play an important role in super-Earths and in rocky planetary cores.

Cebulla, Daniel; Redmer, Ronald

2014-04-01

159

Ab initio and kinetic modeling studies of formic acid oxidation

DEFF Research Database (Denmark)

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 have been compared to the experimental results of de Wilde and van Tiggelen (1968) who measured the laminar burning velocities for HOCHO flames over a range of stoichiometries and dilution ratios. The modeling predictions are generally satisfactory. The governing reaction mechanisms are outlined based on calculations with the kinetic model. Formic acid is consumed mainly by reaction with OH, yielding OCHO, which dissociates rapidly to CO2 + H, and HOCO, which may dissociate to CO + OH or CO2 + H, or react with H, OH, or O2 to form more stable products. The branching fraction of the HOCHO + OH reaction, as well as the fate of HOCO, determines the oxidation rate of formic acid. At lower temperatures HO2, formed from HOCO + O2, is an important chain carrier and modeling predictions become sensitive to the HOCHO + HO2 reaction. © 2014 The Combustion Institute.

Marshall, Paul; Glarborg, Peter

2015-01-01

160

An Ab Initio Based Potential Energy Surface for Water

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

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

1996-01-01

161

Ab initio molecular dynamics calculations of ion hydration free energies

We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li+, Cl-, and Ag+ ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (Delta G(hyd)) within a few kcal/mol, or better than 4%, of Tissandier 's [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li+/Cl- and Ag+/Cl- AIMD Delta G(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag++Ni+-> Ag+Ni2+ in water. The predictions for this reaction suggest that existing estimates of Delta G(hyd) for unstable radiolysis interme...

Leung, Kevin; von Lilienfeld, Anatole O; 10.1063/1.3137054

2010-01-01

162

Ab initio transport across bismuth selenide surface barriers

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.

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

2014-11-01

163

Valence quantum Monte Carlo with ab initio effective core potentials

International Nuclear Information System (INIS)

Effective-core potentials (ECP's) obtained from ab initio methods are implemented in molecular quantum Monte Carlo (QMC). The theory is presented, and applied to the calculation of electron affinities (EA) of Li and Na, the ionization potential (IP) of Mg, the binding energies (D/sub e/) of NaH and Na2, and the potential energy curve of Na2. In all cases ECP--QMC results are found to be as accurate as previous all-electron results. In particular, the calculated quantities (vs experimental values) are (in eV): EA(Li) = 0.611 +- 0.020 (0.620), EA(Na) = 0.555 +- 0.021 (0.546), IP(Mg) = 7.637 +- 0.026 (7.646), D/sub e/ (NaH) = 1.954 +- 0.073 (1.971), and D/sub e/ (Na2) = 0.746 +- 0.020 (0.747). In addition, the statistical precision obtained surpasses that which can be readily achieved in all-electron QMC calculations on these systems

164

Ab initio molecular dynamics calculations of ion hydration free energies

International Nuclear Information System (INIS)

We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or '?-path' technique to compute the intrinsic hydration free energies of Li+, Cl-, and Ag+ ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (?) contributions, we obtain absolute AIMD hydration free energies (?Ghyd) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model ? predictions. The sums of Li+/Cl- and Ag+/Cl- AIMD ?Ghyd, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag++Ni+?Ag+Ni2+ in water. The predictions for this reaction suggest that existing estimates of ?Ghyd for unstable radiolysis intermediates such as Ni+ may need to be extensively revised.

165

Ab initio studies of niobium defects in uranium

Energy Technology Data Exchange (ETDEWEB)

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

Xiang, S; Huang, H; Hsiung, L

2007-06-01

166

Ab-initio vibrational properties of SiGe alloys

International Nuclear Information System (INIS)

We report on the vibrational properties of Si1-xGex alloys by means of a pseudopotential density-functional study. We employ randomly generated supercells, and a wide range of Ge concentration (x = 19, 50, 81%) to investigate the alloys. Accordingly, Si atoms were occasionally replaced by Ge atoms in an otherwise perfect 32 Si atom supercell, with the atomic and volumetric degrees of freedom being allowed to relax. The dynamical matrix of 32 atom supercell was determined directly from the ab-initio code. Calculated Raman spectra were obtained averaging over 15 SiGe supercell configurations for each Ge concentration. The experimental three main wide bands were reproduced. The calculated Si-Si and Ge-Ge frequencies shift linearly with Ge concentration. The Si-Si frequency downward shift agrees well with experimental data, while the agreement is not so good for Ge-Ge mode. The highest Si-Ge frequency occurs when Ge composition reaches 50%, which agrees with experimental data. However the asymmetry of the downward frequency shift is not reproduced, which may be due to the limited size of the supercell

167

Ab-initio calculations for dilute magnetic semiconductors

Energy Technology Data Exchange (ETDEWEB)

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.)

Belhadji, Brahim

2008-03-03

168

Ab initio and RRKM study of photodissociation of azulene cation.

The ab initio/Rice-Ramsperger-Kassel-Marcus (RRKM) approach has been applied to investigate the photodissociation mechanism of the azulene cation at different values of the photon energy. Reaction pathways leading to various decomposition products have been mapped out at the G3(MP2,CC)//B3LYP level and then the RRKM and microcanonical variational transition state theories have been applied to compute rate constants for individual reaction steps. Relative product yields (branching ratios) for the dissociation products have been calculated using the steady-state approach. The results show that a photoexcited azulene cation can readily isomerize to a naphthalene cation. The major dissociation channels are elimination of atomic hydrogen, an H2 molecule, and acetylene. The branching ratio of the H elimination channel decreases with an increase of the photon energy. The branching ratio of the acetylene elimination as well as that of the H2 elimination rise as the photon energy increases. The main C8H6+ fragment at all photon energies considered is a pentalene cation, and its yield decreases slightly with increasing excitation energy, whereas the branching ratios of the other C8H6+ fragments, phenylacetylene and benzocyclobutadiene cations, grow. PMID:16633622

Dyakov, Yu A; Ni, C-K; Lin, S H; Lee, Y T; Mebel, A M

2006-03-28

169

Ab initio evaluations of the He solubility in liquid Li

International Nuclear Information System (INIS)

Modified embedding atom methods (MEAM) are developed to have predictions of the partial molar heat of solution (-Hs) by direct simulation of metal cohesion, He-metal and He-He interaction. Transitions from crystalline Li to configurations, having the liquid Li structure's factors (h-bar (q)), are simulated ab initio. Once h-bar (q) reproduced, He atoms are added, one by one, to the Li system. Parallel lines for each case, with slopes clearly independent on the number of He atoms in the system, are obtained for energy versus pressure at given temperatures. Average differences between two adjacent parallels at zero pressure, once kinetic energy of the system discounted, represents the energy gained by an He atom when added to the Li system, related to the solution energy -Hs. The molar excess entropy of gas in solution (S-bar lex) is previously evaluated following diverse fundamental approaches: a 'thermodynamic liquid-hole' (TL-H) model for alkali liquids and a statistical-mechanics (Neff and McQuarrie's) model (SMM). Between 600 and 900 deg. C, a typical range of interest for the use of Li in fusion technology, the computed values for the (He) Henry's constant in Li range from 8x10-14 to 10-13 at. fr. Pa-1

170

Ab initio thermodynamic modeling of distal multisite transcription regulation.

Transcription regulation typically involves the binding of proteins over long distances on multiple DNA sites that are brought close to each other by the formation of DNA loops. The inherent complexity of assembling regulatory complexes on looped DNA challenges the understanding of even the simplest genetic systems, including the prototypical lac operon. Here we implement a scalable approach based on thermodynamic molecular properties to model ab initio systems regulated through multiple DNA sites with looping. We show that this approach applied to the lac operon accurately predicts the system behavior for a wide range of cellular conditions, which include the transcription rate over five orders of magnitude as a function of the repressor concentration for wild type and all seven combinations of deletions of three operators, as well as the observed induction curves for cells with and without active catabolite activator protein. Our results provide new insights into the detailed functioning of the lac operon and reveal an efficient avenue to incorporate the required underlying molecular complexity into fully predictive models of gene regulation. PMID:18056082

Saiz, Leonor; Vilar, Jose M G

2008-02-01

171

An efficient approach to ab initio Monte Carlo simulation

Energy Technology Data Exchange (ETDEWEB)

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

Leiding, Jeff; Coe, Joshua D., E-mail: jcoe@lanl.gov [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

2014-01-21

172

An efficient approach to ab initio Monte Carlo simulation

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

Leiding, Jeff; Coe, Joshua D.

2014-01-01

173

Ab Initio Description of p-Shell Hypernuclei

We present the first ab initio calculations for p-shell single-Lambda hypernuclei. For the solution of the many-baryon problem, we develop two variants of the no-core shell model with explicit Lambda and Sigma+, Sigma0, Sigma- hyperons including Lambda-Sigma conversion, optionally supplemented by a similarity renormalization group transformation to accelerate model-space convergence. In addition to state-of-the-art chiral two- and three-nucleon interactions, we use leading-order chiral hyperon-nucleon interactions and a recent meson-exchange hyperon-nucleon interaction. We validate the approach for s-shell hypernuclei and apply it to p-shell hypernuclei, in particular to Lambda-Li-7, Lambda-Be-9 and Lambda-C-13. We show that the chiral hyperon-nucleon interactions provide ground-state and excitation energies that agree with experiment within the cutoff dependence. At the same time we demonstrate that hypernuclear spectroscopy provides tight constraints on the hyperon-nucleon interactions and we discuss the im...

Wirth, Roland; Navratil, Petr; Calci, Angelo; Langhammer, Joachim; Roth, Robert

2014-01-01

174

An Ab Initio Approach to the Solar Coronal Heating Problem

We present an ab initio approach to the solar coronal heating problem by modeling a small part of the solar corona in a computational box using a three-dimensional MHD code including realistic physics. The observed solar granular velocity pattern and its amplitude and vorticity power spectra, as reproduced by a weighted Voronoi tessellation method, are used as a boundary condition that generates a Poynting flux in the presence of a magnetic field. The initial magnetic field is a potential extrapolation of a SOHO/MDI high-resolution magnetogram, and a standard stratified atmosphere is used as a thermal initial condition. Except for the chromospheric temperature structure, which is kept nearly fixed, the initial conditions are quickly forgotten because the included Spitzer conductivity and radiative cooling function have typical timescales much shorter than the time span of the simulation. After a short initial start-up period, the magnetic field is able to dissipate (3-4)×106ergscm-2s-1 in a highly intermittent corona, maintaining an average temperature of ~106 K, at coronal density values for which simulated images of the TRACE 171 and 195 Å passbands reproduce observed photon count rates.

Gudiksen, Boris Vilhelm; Nordlund, Åke

2005-01-01

175

An Ab Initio Approach to the Solar Coronal Heating Problem

We present an ab initio approach to the solar coronal heating problem by modelling a small part of the solar corona in a computational box using a 3D MHD code including realistic physics. The observed solar granular velocity pattern and its amplitude and vorticity power spectra, as reproduced by a weighted Voronoi tessellation method, are used as a boundary condition that generates a Poynting flux in the presence of a magnetic field. The initial magnetic field is a potential extrapolation of a SOHO/MDI high resolution magnetogram, and a standard stratified atmosphere is used as a thermal initial condition. Except for the chromospheric temperature structure, which is kept fixed, the initial conditions are quickly forgotten because the included Spitzer conductivity and radiative cooling function have typical timescales much shorter than the time span of the simulation. After a short initial start up period, the magnetic field is able to dissipate 3-4 10^6 ergs cm^{-2} s^{-1} in a highly intermittent corona, mai...

Gudiksen, B V

2004-01-01

176

Nature of magnetism in iron pnictides: an ab initio study

Energy Technology Data Exchange (ETDEWEB)

While it is commonly believed that magnetic-mediate pairing is the source of superconductivity in the iron-based superconductors, the nature of magnetism is still under debate. We apply ab initio molecular dynamics to investigate physical properties of LaOFePn, BaFe{sub 2}Pn{sub 2} and LiFePn (Pn=As,Sb), so-called 1111, 122 and 111 compounds, respectively. We find that, with substitution of As by Sb, the stripe-type antiferromagnetic orderings are always enhanced. By calculating Pauli susceptibility, we attribute the enhancement of magnetization to the increase of instability at ({pi},{pi}) when As is substituted by Sb. Furthermore, we study the magnetic and lattice properties of LaOFePn (Pn=P,As,Sb,Bi) as well as ScOFeP, ScOFeAs and YOFeP and argue that LaOFeSb would be a candidate for a superconductor with highest transition temperature among the investigated compounds. We further suggest that the absence of antiferromagnetic phase in LaOFeP and the presence in LaOFeAs are due to the competition of instability in Pauli susceptibility between ({pi},{pi}) and (0,0) and therefore argue that superconductivity can only occur through doping in LaOFeSb.

Zhang, Yu-Zhong; Opahle, Ingo; Jeschke, Harald; Valenti, Roser [Goethe-Universitaet Frankfurt, Max-von-Laue-Strasse 1, 60438 Frankfurt am Main (Germany)

2010-07-01

177

Ab-initio description of p-shell hypernuclei

Energy Technology Data Exchange (ETDEWEB)

Tremendous progress is being made on the experimental study of hypernuclei, especially on the spectroscopy of p-shell hypernuclei. Their theoretical description, however, is limited to phenomenological models or very light (i.e. s-shell) systems. We present the first ab-initio calculations of p-shell hypernuclei using chiral Hamiltonians including hyperon-nucleon and two- plus three-nucleon interactions, which to date constitute the most consistent starting-point to solving the hypernuclear many-body problem. The many-body calculations are performed in the framework of the importance-truncated no-core shell model using leading-order (LO) chiral hyperon-nucleon and chiral two- plus three-body nucleon-nucleon interactions at N{sup 3}LO and N{sup 2}LO, respectively. To improve convergence with respect to model space size, the interactions are evolved consistently using a similarity renormalization group transformation. We show absolute energies and spectra for selected single-lambda-hypernuclei up to the {sub ?}Li isotope chain.

Wirth, Roland; Calci, Angelo; Langhammer, Joachim; Roth, Robert [Technische Univ. Darmstadt (Germany). Inst. fuer Kernphysik

2013-07-01

178

Ab initio prediction of nano-structured materials using supercomputer

International Nuclear Information System (INIS)

Full text: Nano-structured materials are currently attracting great attention due to their promise in future nano-technologies. In the scale of a nanometer, properties of matter are sensitive to the atomic details that are often difficult to obtain from experiments. Impurities could change the properties very significantly. Predictive computer simulations based on ab initio methods are playing a very important role in not only supporting and explaining the experimental findings but also suggesting new possibilities. We shall present a brief overview of the current research done in our group using the supercomputing facilities of the IMR in designing and predicting nano-structured materials. These include the areas of molecular electronics, carbon fullerenes and nanotubes, super-structures on surfaces, multilayers, clusters and nanowires using calculational approaches such as all electron mixed basis, augmented plane wave, localized basis and pseudopotential plane wave methods. More accurate descriptions based on GW and QMC methods are also used. The possibilities of doing large scale calculations are also allowing the study of biological systems such as DNA. We shall discuss in more detail our recent predictions of novel metal encapsulated silicon fullerenes and nanotubes that offer new possibilities in developing silicon based technologies at the nano-scale

179

Ab initio modelling of boron related defects in amorphous silicon

Energy Technology Data Exchange (ETDEWEB)

We have modeled boron related point defects in amorphous silicon, using an ab initio method, the Density functional theory-pseudopotential code Aimpro. The boron atoms were embedded in 64 atom amorphous silicon cubic supercells. The calculations were performed using boron defects in 15 different supercells. These supercells were developed using a modified Wooten-Winer-Weaire bond switching mechanism. In average, the properties of the 15 supercells agree with the observed radial and bond angle distributions, as well the electronic and vibrational density of states and Raman spectra. In amorphous silicon it has been very hard to find real self-interstitials, since for almost all the tested configurations, the amorphous lattice relaxes overall. We found that substitutional boron prefers to be 4-fold coordinated. We find also an intrinsic hole-trap in the non-doped amorphous lattice, which may explain the low efficiency of boron doping. The local vibrational modes are, in average, higher than the correspondent crystalline values (copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Oliveira, Tiago A.; Torres, Vitor J.B. [Department of Physics, University of Aveiro, Campus Santiago, 3810-193 Aveiro (Portugal)

2012-10-15

180

Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods a...

Hu, Hao; Yang, Weitao

2009-01-01

181

Ab Initio Study of Thermodynamic Properties of Lithium, Sodium, and Potassium Sulfates

The thermodynamic parameters of lithium, sodium, and potassium single and double sulfate crystals are determined by the method of ab initio calculation of a linear combination of atomic orbitals in the gradient approximation of density functional theory using the software package CRYSTAL09 within the framework of the quasi-harmonic approximation of the Debye theory. It is demonstrated that the standard entropies and heat capacities as well as the temperature dependences are in satisfactory agreement with the available experimental data. The average frequency, Debye temperature, and thermal conductivity coefficient increase with external pressure, whereas the Gruneisen parameter decreases. The dependences of the potentials of free and internal energies on the temperature and volume are expressed through the Birch-Murnaghan equation of state and a square-law dependence on these parameters of their vibrational components. The thermodynamic parameters of lithium-potassium sulfate appear closer to potassium sulfate, whereas for sodium-potassium, they lie between the corresponding parameters for single compounds.

Zhuravlev, Yu. N.; Bugaeva, I. A.; Zhuravleva, L. V.

2013-11-01

182

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80% and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test data set of 198 proteins, achieving a Q3 accuracy of 80.7% and a Sov accuracy of 74.2%. PMID:25750595

Spencer, Matt; Eickholt, Jesse; Cheng, Jianlin

2014-01-01

183

Ab initio investigations of zinc chalcogenides semiconductor alloys

International Nuclear Information System (INIS)

The present work performs self-consistent ab initio full potential-linearized augmented plane wave method to study the structural, electronic and thermodynamic properties of ZnSxSe1-x, ZnSxTe1-x and ZnSexTe1-x semiconductor alloys. The ground-state properties were determined for the bulk materials (ZnS, ZnSe, and ZnTe) and for their alloys in cubic phase at various concentrations (x=0.25, 0.5 and 0.75). A marginal deviation of the lattice parameter from Vegard's law was observed for ZnSxSe1-x and ZnSexTe1-x alloys, while the lattice bowing of ZnSxTe1-x alloy was found to be significant. This is mainly because of the large mismatch of the lattice parameters of the binary compounds ZnS and ZnTe. A large deviation of the bulk modulus from linear concentration dependence was observed for all the three alloys. We have also investigated the effect of composition on bonding properties and correlated it to the charge-exchange effect in the optical bowing. Using the approach of Zunger et al. [21], the microscopic origins of the gap bowing were explained. The disorder parameter (gap bowing) for the alloys of interest was found to be mainly caused by the structural relaxation contributions. The charge-exchange contributions for all the three alloys were also found to be significant. The calculated phase diagram showed a broad miscibility gap for allram showed a broad miscibility gap for all the alloys of interest with a high critical temperature

184

Cosmic-Ray Modulation: an Ab Initio Approach

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.

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

2014-10-01

185

AN AB INITIO MODEL FOR COSMIC-RAY MODULATION

International Nuclear Information System (INIS)

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 anied 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

186

Ab initio kinetics of gas phase decomposition reactions.

The thermal and kinetic aspects of gas phase decomposition reactions can be extremely complex due to a large number of parameters, a variety of possible intermediates, and an overlap in thermal decomposition traces. The experimental determination of the activation energies is particularly difficult when several possible reaction pathways coexist in the thermal decomposition. Ab initio calculations intended to provide an interpretation of the experiment are often of little help if they produce only the activation barriers and ignore the kinetics of the decomposition process. To overcome this ambiguity, a theoretical study of a complete picture of gas phase thermo-decomposition, including reaction energies, activation barriers, and reaction rates, is illustrated with the example of the ?-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) molecule by means of quantum-chemical calculations. We study three types of major decomposition reactions characteristic of nitramines: the HONO elimination, the NONO rearrangement, and the N-NO(2) homolysis. The reaction rates were determined using the conventional transition state theory for the HONO and NONO decompositions and the variational transition state theory for the N-NO(2) homolysis. Our calculations show that the HMX decomposition process is more complex than it was previously believed to be and is defined by a combination of reactions at any given temperature. At all temperatures, the direct N-NO(2) homolysis prevails with the activation barrier at 38.1 kcal/mol. The nitro-nitrite isomerization and the HONO elimination, with the activation barriers at 46.3 and 39.4 kcal/mol, respectively, are slow reactions at all temperatures. The obtained conclusions provide a consistent interpretation for the reported experimental data. PMID:21077597

Sharia, Onise; Kuklja, Maija M

2010-12-01

187

Ab initio study of hydrogen migration in 1-alkylperoxy radicals.

Alkylperoxy and hydroperoxyalkyl radicals are key reactive intermediates in hydrocarbon oxidation mechanisms. An understanding of the interconversion of these two species via a hydrogen migration reaction is of fundamental importance to the prediction of chain branching reactions and end product composition. An extensive ab initio investigation of the hydrogen migration reaction in 1-ethyl, 1-propyl, 1-butyl, 1-pentyl, and 1-hexylperoxy radicals is conducted to assess the validity of using cycloalkanes to model the ring strain of their transition states as well as the effect of both location of the migrating hydrogen and directionality of the remaining alkyl chain in the transition state of the reaction involving a secondary hydrogen. The G2 and CBS-Q composite methods are used to determine the activation energy and enthalpy of reaction relative to the alkylperoxy radical. Both methods show good agreement with five experimentally determined reaction enthalpies, having root mean squared deviations of 0.7 and 1.3 kcal mol(-1) for the CBS-Q and G2 methods, respectively. The effect of hydrogen abstraction site and transition state geometry, particularly axial and equatorial geometries of the remaining alkyl chain, on the activation energy, Arrhenius A-factor, tunneling, and rate coefficient are discussed. Differences between terminal adjacent and nonterminal adjacent secondary sites result in small but consistent differences in barrier height. Failure of key assumptions within the cycloalkane based estimation method leads to the break down in the accuracy for both small and large transition states. For large transition states, the breakdown of these assumptions also results in the failure of the current cycloalkane method as a conceptual model. Of great interest is the observed alteration in the preferred H-migration from the 1,5 to the 1,6 H-migration within the temperature region where these reactions are particularly important to the combustion mechanism. PMID:20883006

Davis, Alexander C; Francisco, Joseph S

2010-11-01

188

Ab initio calculations of ^12C and neutron drops

Ab initio calculations of nuclei, which treat a nucleus as a system of A nucleons interacting by realistic two- and three-nucleon forces, have made tremendous progress in the last 15 years. This is a result of better Hamiltonians, rapidly increasing computer power, and new or improved many-body methods. Three methods are principally being used: Green's function Monte Carlo (GFMC), no-core shell model, and coupled cluster. In the limit of large computer resources, all three methods produce exact eigenvalues of a given nuclear Hamiltonian. With DOE SciDAC and INCITE support, all three methods are using the largest computers available today. Under the UNEDF SciDAC grant, the Argonne GFMC program was modified to efficiently use more than 2000 processors. E. Lusk (Argonne), R.M. Butler (Middle Tennessee State U.) and I have developed an Asynchronous Dynamic Load-Balancing (ADLB) library. In addition all the cores in a node are used via OpenMP as one ADLB/MPI client. In this way we obtain very good scalability up to 30,000 processors on Argonne's IBM Blue Gene/P. Two systems of particular interest that require this computer power are ^12C and neutron drops. V.R. Pandharipande (UIUC, deceased), J. Carlson (LANL), R.B. Wiringa (Argonne), and I have developed new trial wave functions that explicitly contain the three-alpha particle structure of ^12C. These are being used with the Argonne V18 and Illinois-7 potentials which reproduce the energies of 51 states in 3interacting with realistic NN and NNN potentials. Their properties can be used as ``experimental data'' for developing energy-density functionals.

Pieper, Steven C.

2009-10-01

189

Symplectic ab initio no-core shell model

Scientific Electronic Library Online (English)

Full Text Available SciELO Mexico | Language: English Abstract in spanish En el presente trabajo se confirma la importancia de la simetría simpléctica Sp(3,R) en la dinámica nuclear a través de estudios de interacciones nucleón-nucleón realistas así como de eigenestados calculados en el marco del modelo de capas sin carozo (NCSM, por sus siglas en inglés). Los resultados [...] demuestran para núcleos ligeros un gran traslapo entre la funciones de onda NCSM usando nada más los estados base con simetría Sp(3,R) con mayor deformación, lo cual abre la posibilidad para obtener convergencia de modos colectivos con energías altas y poder describir nucleos más pesados con una extensión del espacio de los estados base NCSM usando estados con simetría Sp(3,R). Además, las interacciones nucleón-nucleón realistas JISP16 y CD-Bonn favorecen la simetría simpléctica lo cual apunta a una explicación a nivel mas fundamental de la simetría simpléctica. Abstract in english The present study confirm the significanc of the symplectic Sp(3,R) symmetry in nuclear dynamics as unveiled, for the firs time, by examinations of realistic nucleon-nucleon (N N) interactions as well as of eigenstates calculated in the framework of the ab initio No-Core Shell Model (NCSM). The resu [...] lts reveal that the NCSM wave functions for light nuclei highly overlap (at the 90% level) with only a few of the most deformed Sp(3,R)-symmetric basis states. This points to the possibility of achieving convergence of higher-lying collective modes and reaching heavier nuclei by expanding the NCSM basis space beyond its current limits through Sp(3,R) basis states. Furthermore, the symplectic symmetry is found to be favored by the JISP16 and CD-Bonn realistic nucleon-nucleon interactions, which points to a more fundamental origin of the symplectic symmetry.

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

2008-12-01

190

Ab initio study of thiolate-protected Au102 nanocluster.

A total structural determination of the Au(102)(p-MBA)(44) nanocluster has been recently achieved via successful crystallization of the thiolated-protected gold nanocluster (Jadzinsky et al. Science 2007, 318, 430). The embedded Au(102) cluster may be viewed as a multilayered structure described as Au(54)(penta-star)@Au(38)(ten wings)@Au(10)(two pentagon caps), where the inner Au(54) "penta-star" consists of five twinned Au(20) tetrahedral subunits. To gain more insight into high stability of the Au(102)(p-MBA)(44) nanocluster, we have performed ab initio calculations to study electronic properties of a homologue Au(102)(SCH(3))(44) nanocluster, an Au(102)(SCH(3))(42) nanocluster (with two SCH(3) groups less), and an "effectively isoelectronic" Au(104)(SCH(3))(46) nanocluster with a more symmetric embedded Au(104) structure. Electronic structure calculations suggest that the Au(102)(SCH(3))(44) nanocluster possesses a reasonably large gap (approximately 0.54 eV) between the highest occupied molecular orbital and the lowest unoccupied molecular orbital (HOMO-LUMO gap), which is comparable to the measured HOMO-LUMO gap (approximately 0.65 eV) of the bare Au(58) cluster. Likewise, the Au(104)(SCH(3))(46) nanocluster has a HOMO-LUMO gap of approximately 0.51 eV, comparable to that of Au(102)(SCH(3))(44) nanocluster. In contrast, the Au(102)(SCH(3))(42) nanocluster has a zero HOMO-LUMO gap. These results confirm that high stability of the Au(102)(p-MBA)(44) nanocluster may be attributed in part to the electronic shell closing of effective 58 (= 102 - 44) valence electrons, as in the case of Au(25)(SCH(2)CH(2)Ph)(18)(-) cluster whose high stability may be attributed to the electronic shell closing of effective 8 (= 26 -18) valence electrons. PMID:19206321

Gao, Yi; Shao, Nan; Zeng, Xiao Cheng

2008-07-01

191

An ab initio study of plutonium oxides surfaces; Etude ab initio des surfaces d'oxydes de Pu

Energy Technology Data Exchange (ETDEWEB)

By means of first-principles calculations, we have studied the atomic structure as well as the thermodynamic stability of various plutonium dioxide surfaces in function of their environment (in terms of oxygen partial pressure and temperature). All these simulations have been performed with the ABINIT code. It is well known that DFT fails to describe correctly plutonium-based materials since 5f electrons in such systems are strongly correlated. In order to go beyond DFT, we have treated PuO{sub 2} and {beta}-Pu{sub 2}O{sub 3} in a DFT+U framework. We show that the couple of parameters (U,J) that works well for pure Pu is also well designed for describing ground state (GS) properties of these two oxides. The major improvement with respect with DFT is that we are able to predict an insulating GS in agreement with experiments. The presence of a gap in the DOS (Density of States) of plutonium oxides should play a significant role in the predicted surface reactivity. However, performing DFT+U calculations on surfaces of plutonium oxide from scratch was too ambitious. That is why we decided, as a first step, to study the stability of the (100), (110) and (111) surfaces of PuO{sub 2} in a DFT-GGA framework. For each of these orientations, we considered various terminations. These ab initio results have been introduced in a thermodynamic model which allows us to predict the relative stability of the different terminations as a function of temperature and oxygen partial pressure (p{sub O{sub 2}}). We conclude that at room temperature and for p{sub O{sub 2}}{approx}10 atm., the polar O{sub 2}-(100) termination is favoured. The stabilization of such a polar stoichiometric surface is surprising and should be confirmed by DFT+U calculations before any final conclusion. (authors)

Jomard, G.; Bottin, F.; Amadon, B

2007-07-01

192

Shear stiffness in nanolaminar Ti3SiC2 challenges ab initio calculations

International Nuclear Information System (INIS)

Nanolaminates such as the Mn+1AXn (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, Ti3SiC2, using polycrystalline samples and in situ neutron diffraction. The experimental elastic constants show extreme shear stiffness, with c44 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)

193

Energy Technology Data Exchange (ETDEWEB)

We present the results of extensive ab initio simulations for phosphorus clusters, arsenic clusters and mixed phosphorus/arsenic clusters in silicon. The specific defects and the parameters that are investigated are selected according to the needs of state-of-the-art diffusion and activation models, taking into account the availability of experimental data, the capabilities of current ab initio methods and the requirements for advanced technology development. The calculated binding energies are used to determine a good starting point for the calibration of a new clustering model implemented in an atomistic process simulator. The defect species V, I, P, PV, PI, As, AsV, AsI and clusters containing up to four dopant atoms and up to one V or I are considered in all relevant charge states. The ab initio results are discussed as well as the challenges arising in the transfer of this information into the process simulation model.

Sahli, Beat [Integrated Systems Laboratory, ETH Zurich, Gloriastrasse 35, 8092 Zurich (Switzerland)], E-mail: sahli@iis.ee.ethz.ch; Vollenweider, Kilian [Integrated Systems Laboratory, ETH Zurich, Gloriastrasse 35, 8092 Zurich (Switzerland); Zographos, Nikolas; Zechner, Christoph [Synopsys Switzerland LLC, Affolternstrasse 52, 8050 Zurich (Switzerland)

2008-12-05

194

International Nuclear Information System (INIS)

We present the results of extensive ab initio simulations for phosphorus clusters, arsenic clusters and mixed phosphorus/arsenic clusters in silicon. The specific defects and the parameters that are investigated are selected according to the needs of state-of-the-art diffusion and activation models, taking into account the availability of experimental data, the capabilities of current ab initio methods and the requirements for advanced technology development. The calculated binding energies are used to determine a good starting point for the calibration of a new clustering model implemented in an atomistic process simulator. The defect species V, I, P, PV, PI, As, AsV, AsI and clusters containing up to four dopant atoms and up to one V or I are considered in all relevant charge states. The ab initio results are discussed as well as the challenges arising in the transfer of this information into the process simulation model

195

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

International Nuclear Information System (INIS)

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-3H and d-3He fusion calculation obtained within our ab initio approach. We will also discuss our d-4He, 3H-4He and 3H-3H scattering calculations and the outline of the extension of the formalism to include three-cluster final states with the goal to calculate the 3H(3H,2n)4He cross section

196

He diffusion in irradiated ?-Fe: An ab-initio-based rate theory model

International Nuclear Information System (INIS)

The diffusion of He in irradiated ?-Fe is studied using a rate theory model addressing the effect of impurities. Ab initio values for the migration and binding energies of He, He-vacancy complexes, vacancy, and self-interstitial clusters are used to model desorption experiments of He-implanted ?-Fe. Using the brute ab initio data yields a significant discrepancy with experimental measurements. On the other hand, good agreement is obtained when the vacancy migration energy is increased from the original ab initio value while the binding energies of vacancies with substitutional and interstitial helium are lowered. The presence of impurities, with carbon being the most likely candidate, is proposed as a justification for these effective energies. Our simulations also provide a detailed description of the diffusion mechanisms of He active under these particular experimental conditions

197

Shear stiffness in nanolaminar Ti3SiC2 challenges ab initio calculations.

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. PMID:21386405

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

2010-04-28

198

Computer modeling of natural silicate melts: what can we learn from ab initio simulations

The structural and dynamical properties of four silicate liquids (silica, rhyolite, a model basalt and enstatite) are evaluated by ab initio molecular dynamics simulation using the density functional theory and are compared with classical simulations using a simple empirical force field. For a given composition, the structural parameters of the simulated melt vary little between the two calculations (ab initio versus empirical) and are in satisfactory agreement with structure data available in the literature. In contrast, ionic diffusivities and atomic vibration motions are found to be more sensitive to the details of the interactions. Furthermore, it is pointed out that the electronic polarization, as evaluated by the ab initio calculation, contributes significantly to the intensity of the infrared absorption spectra of molten silicates, a spectral feature which cannot be reproduced using nonpolarizable force field. However the vibration modes of TO4 species and some structural details are not accurately rep...

Vuilleumier, R; Guillot, B

2009-01-01

199

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2014-09-01

200

Vibrational properties of ultralong Rydberg Cs$_2$ molecules are investigated on corresponding potential curves obtained by perturbation theory. The Rydberg Cs$_2$ molecules are associated by a Rydberg Cs($nS/nP$) atom $(n=30-70)$ and a ground state Cs($6s$) atom. The starting point for the perturbation treatment of corresponding Rydberg molecular potential curves is to generate accurate atomic Rydberg states from realistic {\\it ab initio} effective core potential. The calculated results have similar characteristics with available experimental and theoretical investigations on Rydberg Rb$_2$ molecules. And this is the first time that Rydberg molecules are studied at the {\\it ab initio} level.

Liu, Xiaomeng; Zhao, Jianming; Xiao, Liantuan; Jia, Suotang

2013-01-01

201

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

DEFF Research Database (Denmark)

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, and correlated electron effects. This paper discusses an approach to performing ab initio studies on these materials for SOFC applications and applies the approach to calculate vacancy formation energies in LaBO3 (B = Mn, Fe, Co, Ni) compounds.

Lee, Yueh-Lin; Morgan, Dane

2009-01-01

202

Convergent recursive O(N) calculations for ab initio tight-binding

A theory is presented for a novel recursion method for O(N) ab initio tight-binding calculations. A long-standing problem of generalizing the recursion method to a non-orthogonal basis, which is a crucial step to make the recursion method applicable to ab initio calculations, is solved by the introduction of the hybrid representation and the two-sided block Lanczos algorithm. As a test of efficiency of the new method, convergence properties in energy and force of insulators,...

Ozaki, T.; Terakura, K.

2001-01-01

203

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. PMID:25664744

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

2015-02-01

204

Ab initio study of collective excitations in a disparate mass molten salt.

Ab initio molecular dynamics simulations and the approach of generalized collective modes are applied for calculations of spectra of longitudinal and transverse collective excitations in molten LiBr. Dispersion and damping of low- and high-frequency branches of collective excitations as well as wave-number dependent relaxing modes were calculated. The main mode contributions to partial, total, and concentration dynamic structure factors were estimated in a wide region of wave numbers. A role of polarization effects is discussed from comparison of mode contributions to concentration dynamic structure factors calculated for molten LiBr from ab initio and classical rigid ion simulations. PMID:23249018

Bryk, Taras; Klevets, Ivan

2012-12-14

205

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

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

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

2014-07-01

206

Estudo da geometria da uréia por métodos ab initio e simulação computacional de líquidos

Directory of Open Access Journals (Sweden)

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.

Cirino José Jair Vianna

2002-01-01

207

Reduced dimensionality quantum dynamics of Cl + CH4 --> HCl + CH3 on an ab initio potential.

We study the reaction Cl + CH(4)--> HCl + CH(3) using a 2-D potential energy surface obtained by fitting a double Morse analytical function to high level (CCSD(T)/cc-pVTZ//MP2/cc-pVTZ)ab initio data. Dynamics simulations are performed in hyperspherical coordinates with the close-coupled equations being solved using R-matrix propagation. Quantum contributions from spectator modes are included via a harmonic zero-point correction to the ab initio data prior to fitting the potential. This is the...

Banks, St; Clary, Dc

2007-01-01

208

In this paper a methodology for the computation of Raman scattering cross-sections and depolarization ratios within the Placzek Polarizability Theory is described. The polarizability gradients are derived from the values of the dynamic polarizabilities computed at the excitation frequencies using ab initio Linear Response Theory. A sample application of the computational program, at the HF, MP2 and CCSD levels of theory, is presented for H2O and NH3. The results show that high correlated leve...

Vidal, Luciano N.; Vazquez, Pedro A. M.

2003-01-01

209

Ab initio techniques based on density functional theory in the projector-augmented-wave implementation are used to calculate the free energy and a range of other thermodynamic properties of liquid iron at high pressures and temperatures relevant to the Earth’s core. The ab initio free energy is obtained by using thermodynamic integration to calculate the change of free energy on going from a simple reference system to the ab initio system, with thermal averages computed by ab initio molecul...

Alfe, D.; Price, G. D.; Gillan, M. J.

2002-01-01

210

Energy Technology Data Exchange (ETDEWEB)

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)

Ganster, P

2004-10-15

211

Recently interest in polar diatomic molecules with a magnetic dipole moment has been growing. An example for such molecules is the combination of an alkali metal atom and an alkaline earth metal atom. These systems are quite small, containing only three valence electrons. Nevertheless calculations of excited states are challenging. Ab initio calculations for two sample systems, LiCa and RbSr, will be presented. The potential energy curves and transition dipole moments for the ground state and several excited states were determined, up to 25000 wn for LiCa and up to 22000 wn for RbSr. Multireference configuration interaction calculations (MRCI) based on complete active space self-consistent field wave functions (CASSCF) were used to determine the properties of the system as implemented in the MOLPRO software package. Effective core potentials (ECPs) and core polarization potentials (CCPs) were applied to reduce the computational effort, while retaining accuracy. The similarities and differences of the two systems will be discussed. In both systems the accurate description of the asymptotic values of the PECs corresponding to atomic D-states proved to be difficult. The results will be compared to recent experiments, showing that a combination of theory and experiment gives a reliable description of the systems. G. Krois, J.V. Pototschnig, F. Lackner and W.E. Ernst, J. Phys. Chem. A, 117, 13719-13731 (2013) H.-J. Werner and P. J. Knowles and G. Knizia and F. R. Manby and M. {Schütz} et al., MOLPRO, version 2010.1, see http://www.molpro.net/

Pototschnig, Johann V.; Krois, Günter; Lackner, Florian; Ernst, Wolfgang E.

2014-06-01

212

Corynebacterium pseudotuberculosis is a bacterium which causes diseases such as caseous lymphadenitis in small ruminants, resulting in large-scale economic losses for agribusiness worldwide. Consequently, this bacterium including its transcriptional profile analysis has been the focus of various studies. Identification of the transcripts that appear under conditions that simulate the environment encountered by this bacterial species in the host is of great importance in discovering new targets for the production of more efficient vaccines. We sequenced the cDNA of Corynebacterium pseudotuberculosis strain 1002, using the SOLiD V3 system, under the following conditions: osmotic stress (2 M), acidity (pH), heat shock (50 °C) and control condition (N). To identify the transcripts shared among the stimulons and integrate this information with the results from BLAST and BLAST2GO, we developed the software CoreStImulon (CSI) which allows the user to individually distinguish the genes in terms of their participation in biological processes, their function and cellular location. In the biosynthetic processes, eleven genes represented in the core stimulon and twenty genes in the control were observed. This validates the hypothesis that the organisms strategy for surviving in a hostile environment is through growth reduction. The oxidation reduction process, response to stress process, and cell adhesion are controlled by genes that contribute to bacterial cell maintenance under stress conditions; these could be involved in their pathogenicity. The methodology for identification of transcripts obtained by ab initio assembly and shared among the stimulons permitted candidates selection for vaccine studies. CSI is available at https://sourceforge.net/projects/corestimulon/. PMID:22641428

Pinto, Anne Cybelle; Ramos, Rommel T J; Silva, Wanderson Marques; Rocha, Flávia Souza; Barbosa, Silvanira; Miyoshi, Anderson; Schneider, Maria P C; Silva, Artur; Azevedo, Vasco

2012-07-01

213

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

Czech Academy of Sciences Publication Activity Database

Ro?. 4, ?. 23 (2013), s. 4177-4181. ISSN 1948-7185 R&D Projects: GA ?R 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

Pluha?ová, Eva; Maršálek, Ond?ej; Schmidt, B.; Jungwirth, Pavel

2013-01-01

214

An ab initio calculation of three-particle correlation in Np3+

International Nuclear Information System (INIS)

A non-relativistic ab initio calculation of the six Judd (three-electron correlation) parameters Tsup(i) has been carried out using second- and third-order perturbation theory with a localised basis set. It is shown that the third-order perturbation contributions are significant and their inclusion considerably improves agreement between theoretical and experimental results. (author)

215

Ab initio studies of the properties of intracellular thiols ergothioneine and ovothiol.

Intracellular naturally occurring aromatic thiols such as ergothioneine and the ovothiols have been shown to play a variety of roles in cellular function. A detailed ab initio electronic structure analysis of these thiols is reported evaluating the thermodynamics of the reactions of these intracellular thiols with alkyl thiols, HO*, H2O2, ascorbate and their disulfides. PMID:15713386

Hand, Christine E; Taylor, Nicholas J; Honek, John F

2005-03-01

216

Structure, Dynamics, and Reactivity of Hydrated Electrons by Ab Initio Molecular Dynamics.

Czech Academy of Sciences Publication Activity Database

Ro?. 45, ?. 1 (2012), s. 23-32. ISSN 0001-4842 R&D Projects: GA ?R GA203/08/0114; GA MŠk LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : solvated electron * water clusters * ab initio molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 20.833, year: 2012

Maršálek, Ond?ej; Uhlig, Frank; Vandevondele, J.; Jungwirth, Pavel

2012-01-01

217

Optical Spectroscopy of the Bulk and Interfacial Hydrated Electron from Ab Initio Calculations.

Czech Academy of Sciences Publication Activity Database

Ro?. 118, ?. 35 (2014), s. 7507-7515. ISSN 1089-5639 R&D Projects: GA ?R GBP208/12/G016 Institutional support: RVO:61388963 Keywords : hydrated electron * optical spectrum * ab initio molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.775, year: 2013

Uhlig, Frank; Herbert, J. M.; Coons, M. P.; Jungwirth, Pavel

2014-01-01

218

Czech Academy of Sciences Publication Activity Database

Ro?. 13, ?. 26 (2011), s. 12123-12137. ISSN 1463-9076 R&D Projects: GA ?R GA203/09/0422; GA ?R GAP208/11/0161 Institutional research plan: CEZ:AV0Z40400503 Keywords : photochemistry * hydrogen bonded heterocycles * ab initio methods Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.573, year: 2011

Slaví?ek, Petr; Fárník, Michal

2011-01-01

219

Czech Academy of Sciences Publication Activity Database

Ro?. 9, ?. 8 (2013), s. 3806-3815. ISSN 1549-9618 R&D Projects: GA ?R 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

Dra?ínský, Martin; Möller, H. M.; Exner, T. E.

2013-01-01

220

Ab initio calculations on the inclusion complexation of cyclobis(paraquat- p-phenylene)

Semiempirical PM3, ab initio HF/3-21g ?, and DFT B3LYP/6-31g ? calculations in vacuum and in solution were performed on the inclusion complexation of cyclobis(paraquat- p-phenylene) with nine symmetric aromatic substrates. A good correlation was found between the theoretical stabilization energies and experimental free energy changes upon complexation.

Zhang, Ke-Chun; Liu, Lei; Mu, Ting-Wei; Guo, Qing-Xiang

2001-01-01

221

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

Energy Technology Data Exchange (ETDEWEB)

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)

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

1996-10-01

222

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

DEFF Research Database (Denmark)

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 response to small longitudinal and bending deformations and their failure limits for longitudinal compression and elongation.

Castelli, Ivano E.; Salvestrini, Paolo

2012-01-01

223

Czech Academy of Sciences Publication Activity Database

Ro?. 70, MAY (2014), s. 92-104. ISSN 1359-6454 Grant ostatní: 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: 3.940, year: 2013

Sandlöbes, S.; Pei, Z.; Friák, Martin; Zhu, L.-F.; Wang, F.; Zaefferer, S.; Raabe, D.; Neugebauer, J.

2014-01-01

224

Ab initio treatment of ion-water molecule collisions with a three-center pseudo potential

International Nuclear Information System (INIS)

We calculate electron capture cross sections in collisions of protons with water molecules, using two simple ab initio approaches. The formalism involves the calculation of one-electron scattering wave functions and the use of three-center pseudo potential to represent the electron H2O+ interaction. Several methods to obtain many-electron cross sections are considered.

225

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three-step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal-organic frameworks (MOFs), QuickFF is used to determine force fields for MIL-53(Al) and MOF-5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc. PMID:25740170

Vanduyfhuys, Louis; Vandenbrande, Steven; Verstraelen, Toon; Schmid, Rochus; Waroquier, Michel; Van Speybroeck, Veronique

2015-05-15

226

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: Portuguese Abstract in portuguese [...] Abstract in english In this paper a methodology for the computation of Raman scattering cross-sections and depolarization ratios within the Placzek Polarizability Theory is described. The polarizability gradients are derived from the values of the dynamic polarizabilities computed at the excitation frequencies using ab [...] initio Linear Response Theory. A sample application of the computational program, at the HF, MP2 and CCSD levels of theory, is presented for H2O and NH3. The results show that high correlated levels of theory are needed to achieve good agreement with experimental data.

Luciano N., Vidal; Pedro A. M., Vazquez.

2003-08-01

227

This study was aimed to investigate the relationship between Language Learning Strategies (LLS) and the level of proficiency of students in Arabic Ab Initio language. There were also several studies done to investigate the achievement of students and their frequent usage of these Language Learning Strategies. Meanwhile, the level of student proficiency was measured by their results based on college-level exam results before they were registered in the Arabic Ab Initio classes. 162 year 1 stud...

Kamarulzaman Abdul Ghani; Mohammad Shiham Mahfuz; Abdul Jamir Md. Saad; Nik Mohd. Rahimi Nik Yusoff

2014-01-01

228

FREE ENERGIES OF CHEMICAL REACTIONS IN SOLUTION AND IN ENZYMES WITH AB INITIO QM/MM METHODS

Combined QM/MM methods provide an accurate and efficient energetic description of complex chemical and biological systems, leading to significant advances in the understanding of chemical reactions in solution and in enzymes. Progress in QM/MM methodology and application will be reviewed, with a focus on ab initio QM based approaches. Ab initio QM/MM methods capitalize on the accuracy and reliability of the associated quantum mechanical approaches, however at a much higher computational cost ...

Hu, Hao; Yang, Weitao

2008-01-01

229

Next generation sequencing technology is advancing genome sequencing at an unprecedented level. By unravelling the code within a pathogen’s genome, every possible protein (prior to post-translational modifications) can theoretically be discovered, irrespective of life cycle stages and environmental stimuli. Now more than ever there is a great need for high-throughput ab initio gene finding. Ab initio gene finders use statistical models to predict genes and their exon-intron structures from ...

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

2012-01-01

230

Using indium as a test case, we investigate the accuracy of the electron-phonon coupling calculated with state-of-the-art ab initio and many-body theory methods. The ab initio calculations -- where electrons are treated in the local-density approximation, and phonons and the electron-phonon interaction are treated within linear response -- predict an electron-phonon spectral function alpha^2 F(omega) which translates into a relative tunneling conductance that agrees with exp...

Rudin, Sven P.; Bauer, R.; Liu, Amy Y.; Freericks, J. K.

1998-01-01

231

Ab initio parameterisation of the 14 band k·p Hamiltonian: Zincblende study

Despite continued and rapid progress in high performance computing, atomistic level device modelling is still largely out of reach, necessitating the use of quantum mechanical continuum methods, including k·p perturbation theory. The effective use of such methods requires reliable parameterisation, often obtained from experiment and ab initio calculations. A major limitation of this, the systematic tendency of ab initio density functional theory to underestimate semiconducting material energy band gaps and related properties, can be greatly improved upon by the inclusion of exact exchange, calculated within the Hartree-Fock formalism. We demonstrate that the 14 band k·p Hamiltonian can be effectively parameterised using this method, at greatly reduced cost in comparison to GW methods.

Lundie, Mark; Tomi?, Stanko

2014-06-01

232

Implementation of ab initio multiple spawning in the MOLPRO quantum chemistry package

International Nuclear Information System (INIS)

The ab initio multiple spawning (AIMS) method has been developed to solve the electronic and nuclear Schrodinger equations simultaneously for application to photochemical reaction dynamics. We discuss some details of the implementation of AIMS in the MOLPRO program package. A few aspects of the implementation are highlighted, including a new multiple timescale integrator and a scheme for solving the coupled-perturbed multiconfiguration self-consistent field (CP-MCSCF) equations in the context of ab initio molecular dynamics. The implementation is very efficient and we demonstrate calculations on the photoisomerization of ethylene using more than 5000 trajectory basis functions. We have included the capability for hybrid quantum mechanics/molecular mechanics (QM/MM) simulations within AIMS, and we investigate the role of an argon solvent in the photoisomerization of ethylene. Somewhat surprisingly, the surrounding argon has little effect on the timescale of non-adiabatic quenching in ethylene

233

Ab-initio Gorkov-Green's function calculations of open-shell nuclei

We present results from a new ab-initio method that uses the self-consistent Gorkov Green's function theory to address truly open-shell systems. The formalism has been recently worked out up to second order and is implemented here in nuclei for the first time on the basis of realistic nuclear forces. We find good convergence of the results with respect to the basis size in Ca44 and Ni74 and discuss quantities of experimental interest including ground-state energies, pairing gaps and particle addition/removal spectroscopy. These results demonstrate that the Gorkov method is a valid alternative to multireference approaches for tackling degenerate or near degenerate quantum systems. In particular, it increases the number of mid-mass nuclei accessible in an ab-initio fashion from a few tens to a few hundreds.

Soma, V; Duguet, T

2012-01-01

234

We present theoretical studies for the third-order elastic constants $C_{ijk}$ in zinc-blende nitrides AlN, GaN, and InN. Our predictions for these compounds are based on detailed ab initio calculations of strain-energy and strain-stress relations in the framework of the density functional theory. To judge the computational accuracy, we compare the ab initio calculated results for $C_{ijk}$ with experimental data available for Si and GaAs. We also underline the relation of the third-order elastic constants to other quantities characterizing anharmonic behaviour of materials, such as pressure derivatives of the second-order elastic constants and the mode Gr\\"uneisen constants for long-wavelength acoustic modes.

Lopuszynski, M; Lopuszynski, Michal; Majewski, Jacek A.

2007-01-01

235

Ab initio study of AlxMoNbTiV high-entropy alloys

The AlxMoNbTiV (x = 0–1.5) high-entropy alloys (HEAs) adopt a single solid-solution phase, having the body centered cubic (bcc) crystal structure. Here we employ the ab initio exact muffin-tin orbitals method in combination with the coherent potential approximation to investigate the equilibrium volume, elastic constants, and polycrystalline elastic moduli of AlxMoNbTiV HEAs. A comparison between the ab initio and experimental equilibrium volumes demonstrates the validity and accuracy of the present approach. Our results indicate that Al addition decreases the thermodynamic stability of the bcc structure with respect to face-centered cubic and hexagonal close packed lattices. For the elastically isotropic Al0.4MoNbTiV HEAs, the valence electron concentration (VEC) is about 4.82, which is slightly different from VEC ˜ 4.72 obtained for the isotropic Gum metals and refractory—HEAs.

Cao, Peiyu; Ni, Xiaodong; Tian, Fuyang; Varga, Lajos K.; Vitos, Levente

2015-02-01

236

Ab-initio approach to study hydrogen diffusion in 9Cr steels

International Nuclear Information System (INIS)

We calculate the equilibrium energies and migration barriers of Fe, Cr and H interstitial defects in ?-FeX(X=Cr). We use the ab-initio electronic structure code, SIESTA, coupled to the monomer method to find activated states (or migration barriers), in order to study atomic defects diffusion. Ab-initio calculations reveal that in the presence of Cr the H migration barriers are higher than in pure ?-Fe. On the other hand, our permeation tests on 9%Cr-91%Fe alloys reveal a permeation coefficient 10 times lower and a diffusion coefficient 200 times lower than in pure, annealed iron. Focusing on our experimental results, we explore very simple model of new H trapping sites and possible migration paths that can explain the experimental observations.

237

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

International Nuclear Information System (INIS)

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.)

238

International Nuclear Information System (INIS)

The ability of simple levels of ab initio molecular orbital theory to describe with reasonable accuracy the energetics of isotopic exchange processes is demonstrated. Three levels of ab initio molecular orbital theory have been surveyed. The first two levels are single-determinant Hartree-Foch methods utilizing the 3-21G split-valence and 6-31G* polarization basis sets. The third level, which is computationally the most complex, uses the 6-31G* basis set but allows for partial account of electron correlation by way of Moller-Plesset perturbation theory terminated at second order. Theoretical and spectroscopic equilibrium constants for reactions XH + XD reversible XD + H2 where XD is a hydride of the first row of the periodic table are tabulated

239

Symmetry-Guided Ab Initio Approach to Light and Medium-Mass Nuclei

International Nuclear Information System (INIS)

We use algorithms of computational group theory to perform ab initio configuration-interaction calculations in a SU(3)-based coupling scheme for p-shell nuclei. Details given for 6Li are reflective of similar results found for 8B, 8Be, 12C and 16O, all of which exhibit a strong preference for large quadrupole deformations and a narrow set of intrinsic spin quantum numbers. Our results suggest that a small subspace of symmetry-adapted configurations can very closely approximate the exact solutions while allowing for exact factorization of the center-of-mass degrees of freedom. This, in turns, promises to allows us to extend the reach of the ab initio framework for structure and reaction studies towards sd-shell nuclei and beyond.

240

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.

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

2015-02-01

241

Vibrational properties of a sodium tetrasilicate glass: Ab initio versus Classical Force Fields

We compare some vibrational properties of a sodium tetrasilicate (Na$_{2}$Si$_{4}$O$_{9}$) glass model generated by molecular dynamics simulations. The vibrational study has been carried out using a classical valence force fields approach as well as an {\\it ab initio} approach in the framework of the density functional theory. The total and partial vibrational densities of states (VDOS) are presented, and some characteristics of the vibrational modes (participation ratios, correlation lengths) are determined using both approaches. We find that the shapes of the two calculated VDOS as well as those of their corresponding partial VDOS are quite similar, especially for a low-frequency band below 550 cm${}^{-1}$. For the intermediate- and high-frequency ranges, we observe larger discrepencies between the two calculations. Polarized Raman spectra are also calculated from the {\\it ab initio} and the valence-force-field eigenvectors in the bond-polarizability approximation. We find an overall agreement between the c...

Ispas, S; De Wispelaere, S; Kob, W

2003-01-01

242

Ab initio nuclear structure calculations of p-shell nuclei with JISP16

International Nuclear Information System (INIS)

We review energies and magnetic moments of p-shell nuclei obtained with the ab initio No-Core Full Configuration (NCFC) approach using the JISP16 realistic nucleon–nucleon interaction. We present calculated ground state energies for all stable p-shell nuclei and selected unstable isotopes, as well as their magnetic moments. We also review excitation energies for narrow resonances of A = 6 to 9 nuclei. We compare our results with experimental data and with other ab initio calculations, where available. We illustrate how the decomposition of total angular momentum into intrinsic spin and orbital components provides insights into the structure of states and relationships among states. We illustrate the challenges of obtaining converged results for radii, quadrupole moments and B(E2) values. (author)

243

Ab initio model of optical properties of two-temperature warm dense matter

We present a model to describe thermophysical and optical properties of two-temperature systems consisted of heated electrons and cold ions in a solid lattice that occur during ultrafast heating experiments. Our model is based on ab initio simulations within the framework of density functional theory. The optical properties are obtained by evaluating the Kubo-Greenwood formula. By applying the material parameters of our ab initio model to a two-temperature model we are able to describe the temperature relaxation process of femtosecond-laser-heated gold and its optical properties within the same theoretical framework. Recent time-resolved measurements of optical properties of ultrafast heated gold revealed the dynamics of the interaction between femtosecond laser pulses and solid state matter. Different scenarios obtained from simulations of our study are compared with experimental data [Chen, Holst, Kirkwood, Sametoglu, Reid, Tsui, Recoules, and Ng, Phys. Rev. Lett. 110, 135001 (2013), 10.1103/PhysRevLett.110.135001].

Holst, B.; Recoules, V.; Mazevet, S.; Torrent, M.; Ng, A.; Chen, Z.; Kirkwood, S. E.; Sametoglu, V.; Reid, M.; Tsui, Y. Y.

2014-07-01

244

Constant pressure ab initio molecular dynamics with discrete variable representation basis sets

The use of discrete variable representation (DVR) basis sets within ab initio molecular dynamics calculations allows the latter to be performed with converged energies and, more importantly, converged forces. In this paper, we show how to carry out ab initio molecular dynamics calculations in the isothermal-isobaric ensemble with fully flexible simulation boxes within the DVR basis set framework. In particular, we derive the appropriate DVR based expression for the pressure tensor when the electronic structure is represented using Kohn-Sham density functional theory, and we examine the convergence of this expression as a function of the basis set size. An illustrative example using 64 silicon atoms in a fully flexible box using a combination of the Martyna-Tobias-Klein [Martyna et al., J. Chem. Phys. 101, 4177 (1994)] and Car-Parrinello [Car and Parinello, Phys. Rev. Lett. 55, 2471 (1985)] algorithms is presented to demonstrate the efficacy of the approach.

Ma, Zhonghua; Tuckerman, Mark

2010-11-01

245

Ab initio modelling of vacancy–solute dragging in dilute irradiated iron-based alloys

Energy Technology Data Exchange (ETDEWEB)

The formation of solute–defect nanoclusters in RPV steels is the main cause of radiation induced embrittlement. Solute atoms may diffuse in the alloy by a vacancy drag mechanism, depending on the strength of interaction with point defects. A multifrequency model based on ab initio computed migration barriers was applied in order to investigate the possibility of solute drag in iron-based bcc binary alloys containing Ni, Cr, Cu or Mn, and the obtained solute diffusion coefficients were compared with previous experiments. The results show that Ni is expected to be dragged at temperatures below approximately 900 K, while Cr and Mn are not involved in the dragging mechanism. As for Cu, the results are controversial because the computed migration barriers are strongly affected by the particular choice of the ab initio method.

Messina, Luca, E-mail: messina@kth.se [Reactor Physics, KTH, Albanova University Centre, 106 91 Stockholm (Sweden); Chang, Zhongwen, E-mail: zhongwen@kth.se [Reactor Physics, KTH, Albanova University Centre, 106 91 Stockholm (Sweden); Olsson, Pär, E-mail: polsson@kth.se [Reactor Physics, KTH, Albanova University Centre, 106 91 Stockholm (Sweden)

2013-05-15

246

A periodic ab initio study of the structure and relative stability of silica polymorphs

The equilibrium geometry and total energy of four all-silica zeolite frameworks, sodalite, chabazite, faujasite and edingtonite, have been obtained at a periodic ab initio all-electron level (CRYSTAL code) and compared with the corresponding quantities for ?- and ?-quartz. The dependence of the results on the adopted basis set and hamiltonian (Hartree-Fock, or with an a posteriori correlation correction; various local and gradient-corrected density functional methods and Becke's hybrid scheme) is discussed. The various methods provide a similar order in the relative stabilities; large quantitative differences are however observed, Hartree-Fock and LDA results being at the extremes. The combined use of force-field and ab initio schemes in the geometry optimization is discussed.

Civalleri, B.; Zicovich-Wilson, C. M.; Ugliengo, P.; Saunders, V. R.; Dovesi, R.

1998-08-01

247

Ab initio generalized valence force field for zeolite modelling 2. Aluminosilicates

A generalized valence force field for modelling the vibrational spectra of aluminosilicates is developed on the basis of ab initio calculations (3-21G ? and DZP/MP2) performed on small clusters: Si(OH) 4, (OH) 3SiOSi(OH) 3, Al(OH) -4, H 3SiOHAlH 3, (OH) 3SiOAl(OH) -3 and (OH) 3SiOHAl(OH) 3. The Cartesian force constants from the ab initio calculations are transformed into internal coordinates and used in molecular dynamics simulations of protonated and non-protonated faujasite structures. Calculated positions of the bands in the infrared and Raman spectra of the zeolite are in good agreement with those observed. The force field explains the main features in the vibrational spectra OH(OD) groups of protonated structures.

Ermoshin, Vladimir A.; Smirnov, Konstantin S.; Bougeard, Daniel

1996-09-01

248

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

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.

Binosi, Daniele; Chang, Lei; Papavassiliou, Joannis; Roberts, Craig D.

2015-03-01

249

{\\it Ab initio} nuclear structure - the large sparse matrix eigenvalue problem

The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several {\\it ab initio} methods have now emerged that provide nearly exact solutions for some nuclear properties. The {\\it 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 t...

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

2009-01-01

250

Ab Initio Many-Body Calculations Of Nucleon-Nucleus Scattering

Energy Technology Data Exchange (ETDEWEB)

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.

Quaglioni, S; Navratil, P

2008-12-17

251

Ab initio calculation of valley splitting in monolayer \\delta-doped phosphorus in silicon

The differences in energy between electronic bands due to valley splitting are of paramount importance in interpreting transport spectroscopy experiments on state-of-the-art quantum devices defined by scanning tunneling microscope lithography. We develop a plane-wave density functional theory description of these systems which is size-limited due to computational tractability. We then develop a less resource-intensive alternative via localized basis functions, retaining the physics of the plane-wave description, and extend this model beyond the capability of plane-wave methods to determine the ab initio valley splitting of well-isolated \\delta-layers. In obtaining agreement between plane-wave and delocalized methods, we show that the valley splitting has been overestimated in previous ab initio calculations by more than 50%.

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

2012-01-01

252

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

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. PMID:25877566

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

2015-04-14

253

Ab-initio molecular dynamics simulation of liquid water by Quantum Monte Carlo

Despite liquid water is ubiquitous in chemical reactions at roots of life and climate on 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 excellent 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.

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

2014-01-01

254

Driving nuclei with resonant electrons: Ab initio study of (e+H2) 2?u+

International Nuclear Information System (INIS)

We have calculated the cross sections for vibrational excitation and dissociative attachment in H2 below 5 eV scattering energy. This completely ab initio calculation uses the frame-transformation method of Greene and Jungen [Adv. At. Mol. Phys. 21, 51 (1985)] for electron-vibronic coupling in resonant scattering from a neutral molecule. We found it necessary to modify their method to obtain good agreement with previous theory and experiment for v=0?vf with vf=1--3; for larger vf and for dissociative attachment we obtained good agreement with previous theory and qualitative agreement with experiment. The fixed-nuclei phase shifts were derived from a fully ab initio calculation in prolate spheroidal coordinates and then transformed to spherical l=1 phase shifts. The vibrational structure of H2- becomes evident for excitation from higher vibrational states of H2 as well as for larger ?v's, confirming previous theory and experiment

255

Ab initio SCF calculations on the potential energy surface of potassium cyanide (KCN)

The potential energy surface of KCN has been generated by ab initio SCF calculations in the region of equilibrium bond distances. An analytic representation of the surface is presented. The calculations show that the bonding between K and CN is ionic, and that the structure of KCN is triangular, which confirms recent experimental findings. The computed geometry is &KCN = 62.4°, rCK = 5.492a0, and rCN = 2.186a0.

Wormer, Paul E. S.; Tennyson, Jonathan

1981-08-01

256

Ab initio verification of the analytical R-matrix theory for strong field ionization

International Nuclear Information System (INIS)

We summarize the key aspects of the recently developed analytical R-matrix (ARM) theory for strong field ionization (Torlina and Smirnova 2012 Phys. Rev. A 86 043408; Kaushal and Smirnova 2013 Phys. Rev. A 88 013421), and present tests of this theory using ab initio numerical simulations for hydrogen and helium atoms in long circularly polarized laser pulses. We find excellent agreement between the predictions of ARM and the numerical calculations. (paper)

257

Nuclear quantum effects in ab initio dynamics theory and experiments for lithium imide

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 inter...

Ceriotti, M.; Miceli, G.; Pietropaolo, A.; Colognesi, D.; Nale, A.; Catti, M.; Bernasconi, M.; Parrinello, M.

2010-01-01

258

Minimal parameter implicit solvent model for ab initio electronic structure calculations

We present an implicit solvent model for ab initio electronic structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comp. Chem. 23, 6 (2002)). While this model depends on only two parameters, we demonstrate that by using appropriate boundary conditions and dispersi...

Dziedzic, Jacek; Helal, Hatem H.; Skylaris, Chris-kriton; Mostofi, Arash A.; Payne, Mike C.

2011-01-01

259

Ab initio study of ideal tensile strength and mechanical stability of transition-metal disilicides.

Czech Academy of Sciences Publication Activity Database

Ro?. 68, ?. 18 (2003), s. 184101-1 - 181101-10. ISSN 0163-1829 R&D Projects: GA AV ?R IAA1041302; GA ?R 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 Impact factor: 2.962, year: 2003

Friák, Martin; Šob, Mojmír; Vitek, V.

2003-01-01

260

Carbon Nanotube with Square Cross-section: An Ab Initio Investigation

Recently, Lagos et al. (Nature Nanotechnology 4, 149 (2009)) reported the discovery of the smallest possible silver square cross-section nanotube. A natural question is whether similar carbon nanotubes can exist. In this work we report ab initio results for the structural, stability and electronic properties for such hypothetical structures. Our results show that stable (or at least metastable) structures are possible with metallic properties. They also show that these struc...

Autreto, P. A. S.; Legoas, S. B.; Flores, M. Z. S.; Galvao, D. S.

2010-01-01

261

On the ab initio calculation of CVV Auger spectra in closed-shell systems

We propose an ab initio method to evaluate the core-valence-valence (CVV) Auger spectrum of systems with filled valence bands. The method is based on the Cini-Sawatzky theory, and aims at estimating the parameters by first-principles calculations in the framework of density-functional theory (DFT). Photoemission energies and the interaction energy for the two holes in the final state are evaluated by performing DFT simulations for the system with varied population of electro...

Fratesi, G.; Trioni, M. I.; Brivio, G. P.; Ugenti, S.; Perfetto, E.; Cini, M.

2008-01-01

262

Expanded phase of ZrO{sub 2}: An ab initio constant-pressure study

Energy Technology Data Exchange (ETDEWEB)

The stability of ZrO{sub 2} in the tensile regime is studied using an ab initio constant-pressure technique. A first-order phase transformation from the baddeleyite structure to an anatase-like structure (I4{sub 1}/amd) is predicted through the constant-pressure simulation. A transformation mechanism at the atomistic level is discussed. Furthermore this phase transformation is studied from the energy-volume calculations. (author)

Durandurdu, M. [Texas at El Paso - El Paso Univ., Dept. of Physics, TX (United States); Ahi Evran Univ., Fizik Bolumu, Kirsehir (Turkey)

2009-12-15

263

Expanded phase of ZrO2: An ab initio constant-pressure study

International Nuclear Information System (INIS)

The stability of ZrO2 in the tensile regime is studied using an ab initio constant-pressure technique. A first-order phase transformation from the baddeleyite structure to an anatase-like structure (I41/amd) is predicted through the constant-pressure simulation. A transformation mechanism at the atomistic level is discussed. Furthermore this phase transformation is studied from the energy-volume calculations. (author)

264

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

DEFF Research Database (Denmark)

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 as its static and dynamic properties. The results obtained show good agreement with well established data, and, moreover, we were able to show significant changes within the structure depending on the system's temperature and density.

Kreitmeir, M.; Bertagnolli, H.

2003-01-01

265

Ab Initio Design of Potent Anti-MRSA Peptides based on Database Filtering Technology

To meet the challenge of antibiotic resistance worldwide, a new generation of antimicrobials must be developed.1 This communication demonstrates ab initio design of potent peptides against methicillin-resistant Staphylococcus aureus (MRSA). Our idea is that the peptide is very likely to be active when most probable parameters are utilized in each step of the design. We derived the most probable parameters (e.g. amino acid composition, peptide hydrophobic content, and net charge) from the anti...

Mishra, Biswajit; Wang, Guangshun

2012-01-01

266

Steady state Ab-initio Theory of Lasers with Injected Signals

We present an ab-initio treatment of the steady-state of lasers with injected signals that describes a regime, valid for micro lasers, in which the locking transition is dominated by cross-saturation and spatial hole-burning. The theory goes beyond standard approaches and treats multimode lasing with injected signals and finds the possibility of partially locked states and as well as repulsion of the free-running frequencies from the injected signal. The theory agrees well w...

Cerjan, Alexander; Stone, A. Douglas

2013-01-01

267

Ab initio quasiparticle bandstructure of ABA and ABC-stacked graphene trilayers

We obtain the quasiparticle band structure of ABA and ABC-stacked graphene trilayers through ab initio density functional theory (DFT) and many-body quasiparticle calculations within the GW approximation. To interpret our results, we fit the DFT and GW $\\pi$ bands to a low energy tight-binding model, which is found to reproduce very well the observed features near the K point. The values of the extracted hopping parameters are reported and compared with available theoretical...

Menezes, Marcos G.; Capaz, Rodrigo B.; Louie, Steven G.

2014-01-01

268

Ab initio methods for finite temperature two-dimensional Bose gases

The stochastic Gross-Pitaevskii equation and modified Popov theory are shown to provide an ab initio description of finite temperature, weakly-interacting two-dimensional Bose gas experiments. Using modified Popov theory, a systematic approach is developed in which the momentum cut-off inherent to classical field methods is removed as a free parameter. This is shown to yield excellent agreement with the recent experiment of Hung et al. [Nature, 470, 236 (2011)], verifying th...

Cockburn, S. P.; Proukakis, N. P.

2012-01-01

269

Boron and nitrogen impurities in SiC nanoribbons: an ab initio investigation

Using ab initio calculations based on density-functional theory we have performed a theoretical investigation of substitutional boron and nitrogen impurities in silicon carbide (SiC) nanoribbons. We have considered hydrogen terminated SiC ribbons with zigzag and armchair edges. In both systems we verify that the boron and nitrogen atoms energetically prefer to be localized at the edges of the nanoribbons. However, while boron preferentially substitutes a silicon atom, nitrog...

Costa, C. D.; Morbec, J. M.

2011-01-01

270

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

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 s...

Bergli, Elise; Hjorth-jensen, M.

2010-01-01

271

Towards a full ab initio theory of strong electronic correlations in nanoscale devices

In this paper I give a detailed account of an ab initio methodology for describing strong electronic correlations in nanoscale devices hosting transition metal atoms with open $d$- or $f$-shells. The method combines Kohn-Sham Density Functional Theory for treating the weakly interacting electrons on a static mean-field level with non-perturbative many-body methods for the strongly interacting electrons in the open $d$- and $f$-shells. An effective description of the strongly...

Jacob, D.

2015-01-01

272

An ab initio variationally computed room-temperature line list for SO3

{\\it Ab initio} potential energy and dipole moment surfaces are computed for sulfur trioxide (SO$_3$) at the CCSD(T)-F12b level of theory and appropriate triple-zeta basis sets. These surfaces are fitted and used, with a slight correction for the equilibrium S--O distance, to compute pure rotational and rotation-vibraton spectra of \\sothree\\ using the variational nuclear motion program TROVE. The calculations considered transitions in the region 0--4000 \\cm\\ with rotational ...

Underwood, Daniel S.; Tennyson, Jonathan; Yurchenko, Sergei N.

2013-01-01

273

Ab initio Bogoliubov coupled cluster theory for open-shell nuclei

Ab initio many-body methods address closed-shell nuclei up to mass A ~ 130 on the basis of realistic two- and three-nucleon interactions. Several routes to address open-shell nuclei are currently under investigation, including ideas which exploit spontaneous symmetry breaking. Singly open-shell nuclei can be efficiently described via the sole breaking of $U(1)$ gauge symmetry associated with particle number conservation, to account for their superfluid character. The present...

Signoracci, Angelo; Duguet, Thomas; Hagen, Gaute; Jansen, Gustav

2014-01-01

274

Ab initio theory of galvanomagnetic phenomena in ferromagnetic metals and disordered alloys

We present an ab initio theory of transport quantities of metallic ferromagnets developed in the framework of the fully relativistic tight-binding linear muffin-tin orbital method. The approach is based on the Kubo-Streda formula for the conductivity tensor, on the coherent potential approximation for random alloys, and on the concept of interatomic electron transport. The developed formalism is applied to pure 3d transition metals (Fe, Co, Ni) and to random Ni-based ferroma...

Turek, Ilja; Kudrnovsky, Josef; Drchal, Vaclav

2011-01-01

275

Ab Initio Study of Phase Stability in Doped TiO2

Ab-initio density functional theory (DFT) calculations of the relative stability of anatase and rutile polymorphs of TiO2 were carried using all-electron atomic orbitals methods with local density approximation (LDA). The rutile phase exhibited a moderate margin of stability of ~ 3 meV relative to the anatase phase in pristine material. From computational analysis of the formation energies of Si, Al, Fe and F dopants of various charge states across different Fermi level ener...

Hanaor, Dorian A. H.; Assadi, Mohammed H. N.; Li, Sean; Yu, Aibing; Sorrell, Charles C.

2012-01-01

276

Converging sequences in the ab initio no-core shell model

We demonstrate the existence of multiple converging sequences in the ab initio no-core shell model. By examining the underlying theory of effective operators, we expose the physical foundations for the alternative pathways to convergence. This leads us to propose a revised strategy for evaluating effective interactions for $A$-body calculations in restricted model spaces. We suggest that this strategy is particularly useful for applications to nuclear processes in which stat...

Forsse?n, C.; Vary, J. P.; Caurier, E.; Navra?til, P.

2008-01-01

277

Steady-State Ab Initio Laser Theory for N-level Lasers

We show that Steady-state Ab initio Laser Theory (SALT) can be applied to find the stationary multimode lasing properties of an N-level laser. This is achieved by mapping the N-level rate equations to an effective two-level model of the type solved by the SALT algorithm. This mapping yields excellent agreement with more computationally demanding N-level time domain solutions for the steady state.

Cerjan, Alexander; Chong, Yidong; Ge, Li; Stone, A. Douglas

2011-01-01

278

Ab initio theory of Fano resonances in plasmonic nanostructures and metamaterials

An ab initio theory for Fano resonances in plasmonic nanostructures and metamaterials is de- veloped using Feshbach formalism. It reveals the role played by the electromagnetic modes and material losses in the system, and enables the engineering of Fano resonances in arbitrary geome- tries. A general formula for the asymmetric resonance in a non-conservative system is derived. The influence of the electromagnetic interactions on the resonance line shape is discussed and it is shown that intri...

Martin, O. J. F.; Gallinet, Benjamin

2011-01-01

279

Ab initio strategy for muon site assignment in wide band gap fluorides

We report on an ab initio strategy based on Density Functional Theory to identify the muon sites. Two issues must be carefully addressed, muon delocalization about candidate interstitial sites and local structural relaxation of the atomic positions due to $\\mu^+$-sample interaction. Here, we report on the validation of our strategy on two wide band gap materials, LiF and YF3, where localization issues are important because of the interplay between muon localization and latti...

Bernardini, F.; Bonfa, P.; Massidda, S.; Renzi, R.

2013-01-01

280

Ab initio study of the TiO$_2$ Rutile(110)/Fe interface

Adsorption of Fe on the rutile (110)-surface is investigated by means of {\\it ab initio} density functional theory calculations. We discuss the deposition of single Fe atoms, an increasing Fe coverage, as well as the adsorption of small Fe clusters. It is shown that the different interface structures found in experiment can be understood in terms of the adsorption of the Fe atoms landing first on the rutile surface. On the one hand, strong interface bonds form if single Fe a...

Gruenebohm, Anna; Herper, Heike C.; Entel, Peter

2013-01-01

281

Steady-state ab initio laser theory for complex gain media

We derive and test a generalization of Steady-State Ab Initio Laser Theory (SALT) to treat complex gain media. The generalized theory (C-SALT) is able to treat atomic and molecular gain media with diffusion and multiple lasing transitions, and semiconductor gain media in the free carrier approximation including fully the effect of Pauli blocking. The key assumption of the theory is stationarity of the level populations, which leads to coupled self-consistent equations for th...

Cerjan, Alexander; Chong, Y. D.; Stone, A. Douglas

2014-01-01

282

Ab initio theory of Cr$_2$O$_3$ surface chemistry in solution

Using a new form of density functional theory for the {\\em ab initio} description of electronic systems in contact with a dielectric environment, we present the first detailed study of the impact of a solvent on the surface chemistry of Cr$_2$O$_3$, the passivating layer of stainless steel alloys. Compared to vacuum, we predict that the presence of water has little impact on the adsorption of chloride ions to the oxygen-terminated surface but a dramatic effect on the binding...

Petrosyan, S.; Rigos, A. A.; Arias, T. A.

2004-01-01

283

Ab initio molecular dynamics study of manganese porphine hydration and interaction with nitric oxide

The authors use ab initio molecular dynamics and the density functional theory+U (DFT+U) method to compute the hydration environment of the manganese ion in manganese (II) and manganese (III) porphines (MnP) dispersed in liquid water. These are intended as simple models for more complex water soluble porphyrins, which have important physiological and electrochemical applications. The manganese ion in Mn(II)P exhibits significant out-of-porphine plane displacement and binds s...

Leung, Kevin; Medforth, Craig J.

2007-01-01

284

The multiferroic phase of DyFeO$_{3}$:an ab--initio study

By performing accurate ab-initio density functional theory calculations, we study the role of $4f$ electrons in stabilizing the magnetic-field-induced ferroelectric state of DyFeO$_{3}$. We confirm that the ferroelectric polarization is driven by an exchange-strictive mechanism, working between adjacent spin-polarized Fe and Dy layers, as suggested by Y. Tokunaga [Phys. Rev. Lett, \\textbf{101}, 097205 (2008)]. A careful electronic structure analysis suggests that coupling be...

Stroppa, Alessandro; Marsman, Martijn; Kresse, Georg; Picozzi, Silvia

2009-01-01

285

Calculation of a Deuterium Double Shock Hugoniot from Ab initio Simulations

We calculate the equation of state of dense deuterium with two ab initio simulations techniques, path integral Monte Carlo and density functional theory molecular dynamics, in the density range of 0.67 < rho < 1.60 g/cc. We derive the double shock Hugoniot and compare with the recent laser-driven double shock wave experiments by Mostovych et al. [1]. We find excellent agreement between the two types of microscopic simulations but a significant discrepancy with the laser-driv...

Militzer, B.; Ceperley, D. M.; Kress, J. D.; Johnson, J. D.; Collins, L. A.; Mazevet, S.

2001-01-01

286

Mechanics properties of Mono-layer Hexagonal Boron Nitride: Ab initio study

We introduced a method to obtain the continuum description of the elastic properties of mono- layer h-BN through ab initio density functional theory. This thermodynamically rigorous contin- uum description of the elastic response is formulated by expanding the elastic strain energy density in a Taylor series in strain truncated after the fifth-order term. we obtained a total of fourteen nonzero independent elastic constants for the up to tenth-order tensor. We predicted the ...

Peng, Qing; Zamiri, Amir R.; De, Suvranu

2011-01-01

287

Scalable numerical approach for the steady-state ab initio laser theory

We present an efficient and flexible method for solving the non-linear lasing equations of the steady-state ab initio laser theory. Our strategy is to solve the underlying system of partial differential equations directly, without the need of setting up a parametrized basis of constant flux states. We validate this approach in one-dimensional as well as in cylindrical systems, and demonstrate its scalability to full-vector three-dimensional calculations in photonic-crystal s...

Esterhazy, S.; Liu, D.; Liertzer, M.; Cerjan, A.; Ge, L.; Makris, K. G.; Stone, A. D.; Melenk, J. M.; Johnson, S. G.; Rotter, S.

2013-01-01

288

Anharmonic Self-Energy of Phonons: Ab Initio Calculations and Neutron Spin Echo Measurements

We have calculated (ab initio) and measured (by spin-echo techniques) the anharmonic self-energy of phonons at the X-point of the Brillouin zone for isotopically pure germanium. The real part agrees with former, less accurate, high temperature data obtained by inelastic neutron scattering on natural germanium. For the imaginary part our results provide evidence that transverse acoustic phonons at the X-point are very long lived at low temperatures, i.e. their probability of ...

Debernardi, A.; Geuser, F.; Kulda, J.; Cardona, M.; Haller, E. E.

2002-01-01

289

Anharmonic Raman Spectra in High-Pressure Ice from Ab Initio Simulations

We calculate from ab initio molecular dynamics the Raman scattering of high-pressure ice. To this effect we apply a new method based on the Berry phase theory of polarization. Our results are in agreement with recent and difficult experiments and are compatible with a picture in which ice VII is a proton-disordered system and in ice X the hydrogen bond is symmetric.

Putrino, Anna; Parrinello, Michele

2002-04-01

290

Ab initio molecular dynamics study of dissociation of water under an electric field

The behavior of liquid water under an electric field is a crucial phenomenon in science and engineering. However, its detailed description at a microscopic level is difficult to achieve experimentally. Here we report on the first ab initio molecular-dynamics study on water under an electric field. We observe that the hydrogen-bond length and the molecular orientation are significantly modified at low-to-moderate field intensities. Fields beyond a threshold of about 0.35 V/\\A...

Saitta, A. Marco; Saija, Franz; Giaquinta, Paolo V.

2012-01-01

291

Ab initio study of electronic structure and crystalline phases of tellurium.

Czech Academy of Sciences Publication Activity Database

Brno : Masarykova univerzita, 2007 - (Trnková, L.; Janderka, P.; Kizek, R.), s. 57-58 ISBN 978-80-210-4235-3. [Pracovní setkání fyzikálních chemik? a elektrochemik? /7./. Brno (CZ), 29.01.2007-30.01.2007] R&D Projects: GA AV ?R IAA1041302; GA MŠk OC 147 Institutional research plan: CEZ:AV0Z20410507 Keywords : electronic structure * tellurium * ab initio calculations Subject RIV: BM - Solid Matter Physics ; Magnetism

Hemzalová, P.; Legut, Dominik; Šob, Mojmír

292

Ab-initio calculations of diffusion barriers of small vacancy clusters in silicon

Esta tese apresenta os resultados de um programa de investigação sobre a difusão da lacuna, bi-lacuna e tri-lacuna em silício utilizando simulações numéricas pelo método da teoria do funcional da densidade. Este método está implementado na forma de um programa informático referido como AIMPRO (Ab Initio Modelling PROgram). Para o cálculo dos pontos cela dos mecanismos de difusão foi usado o método “Nudged Elastic Band”. As condições fronteira dos problemas foram i...

Markevich, Alexander

2009-01-01

293

Modelação Ab initio de defeitos pontuais de boro em silício amorfo

O presente trabalho tem como principal objectivo modelar os defeitos pontuais de boro em silício amorfo, usando um método ab initio, o código de teoria da densidade funcional – pseudopotencial (AIMPRO). Os complexos de boro foram introduzidos em supercélulas de 64 átomos de silício. Os defeitos de boro foram estudados em 15 supercélulas diferentes. Estas supercélulas foram obtidas por um mecanismo de troca de ligação Wooten-Winer-Weaire por Ribeiro et al. (2010)....

Oliveira, Tiago Jose? A?gueda

2011-01-01

294

Ab initio study of the migration of intrinsic defects in 3C-SiC

The diffusion of intrinsic defects in 3C-SiC is studied using an ab initio method based on density functional theory. The vacancies are shown to migrate on their own sublattice. The carbon split-interstitials and the two relevant silicon interstitials, namely the tetrahedrally carbon-coordinated interstitial and the -oriented split-interstitial, are found to be by far more mobile than the vacancies. The metastability of the silicon vacancy, which transforms into a vacancy-an...

Bockstedte, Michel; Mattausch, Alexander; Pankratov, Oleg

2003-01-01

295

Based on a numerical ab initio study, we discuss a structure model for a broad boron sheet, which is the analog of a single graphite sheet, and the precursor of boron nanotubes. The sheet has linear chains of sp hybridized sigma bonds lying only along its armchair direction, a high stiffness, and anisotropic bonds properties. The puckering of the sheet is explained as a mechanism to stabilize the sp sigma bonds. The anisotropic bond properties of the boron sheet lead to a tw...

Kunstmann, Jens; Quandt, Alexander

2005-01-01

296

Strain energy calculations of hexagonal boron nanotubes: An ab-initio approach

An ab initio calculations have been carried out for examining the curvature effect of small diameter hexagonal boron nanotubes. The considered conformations of boron nanotubes are namely armchair (3,3), zigzag (5,0) and chiral (4,2), and consist of 12, 20, and 56 atoms, respectively. The strain energy is evaluated in order to examine the curvature effect. It is found that the strain energy of hexagonal BNT strongly depends upon the radius, whereas the strain energy of triang...

Jain, S. K.; Srivastava, P.

2013-01-01

297

We review our recent work on ab initio nonadiabatic molecular dynamics, based on linear-response timedependent density functional theory for the calculation of the nuclear forces, potential energy surfaces, and nonadiabatic couplings. Furthermore, we describe how nuclear quantum dynamics beyond the Born-Oppenheimer approximation can be performed using quantum trajectories. Finally, the coupling and control of an external electromagnetic field with mixed quantum/classical trajectory surface hopping is discussed.

Curchod, Basile; Penfold, Thomas; Rothlisberger, Ursula; Tavernelli, Ivano

2013-09-01

298

Comparative classical and ab initio Molecular Dynamics study of molten and glassy germanium dioxide

A Molecular Dynamics (MD) study of static and dynamic properties of molten and glassy germanium dioxide is presented. The interactions between the atoms are modelled by the classical pair potential proposed by Oeffner and Elliott (OE) [Oeffner R D and Elliott S R 1998, Phys. Rev. B, 58, 14791]. We compare our results to experiments and previous simulations. In addition, an ab initio method, the so-called Car-Parrinello Molecular Dynamics (CPMD), is applied to check the accur...

Hawlitzky, Michael; Horbach, Juergen; Ispas, Simona; Krack, Matthias; Binder, Kurt

2008-01-01

299

Electronic structure of superconducting gallium-doped germanium from ab-initio calculations

Using ab-initio calculations, we study the electronic structure of gallium-doped germanium, which was found recently to be a superconductor, with a critical temperature of 0.5 Kelvins, and a particularly low density of Cooper pairs. The calculations of the electronic properties reveal that no sign of an impurity band is observed, and that the Fermi level lies in the valence band of Germanium. Moreover, the calculation of the phonon frequencies shows that a new mode associate...

Lebegue, S.

2009-01-01

300

Structural evolution in high-pressure amorphous CO$_2$ from \\textit{ab initio} molecular dynamics

By employing $ab$ $initio$ molecular dynamics simulations at constant pressure, we investigated behavior of amorphous carbon dioxide between 0-100 GPa and 200-500 K and found several new amorphous forms. We focused on evolution of the high-pressure polymeric amorphous form known as a-carbonia on its way down to zero pressure, where it eventually converts into a molecular amorphous solid. During decompression, two nonmolecular amorphous forms with different proportion of thre...

Plas?ienka, Dus?an; Marton?a?k, Roman

2013-01-01

301

Ab initio study of the double row model of the Si(553)-Au reconstruction

Using x-ray diffraction Ghose et al. [Surf. Sci. {\\bf 581} (2005) 199] have recently produced a structural model for the quantum-wire surface Si(553)-Au. This model presents two parallel gold wires located at the step edge. Thus, the structure and the gold coverage are quite different from previous proposals. We present here an ab initio study using density functional theory of the stability, electronic band structure and scanning tunneling microscopy images of this model.

Riikonen, Sampsa; Sanchez-portal, Daniel

2005-01-01

302

A theory of liquid water is developed by means of the combined ab initio electronic structure theory and the integral equation method of liquids. Effective atomic charges in the liquid water are determined such that the electronic structure and the liquid properties become self-consistent. The temperature dependence of those quantities is calculated to demonstrate the importance of proper account of the mutual dependency between the electronic structure and the liquid state properties.

Maw, Sarah; Sato, Hirofumi; Ten-no, Seiichiro; Hirata, Fumio

1997-09-01

303

Direct ab initio MD simulation of silver ion diffusion in chalcogenide glasses

In this paper, we present new models of germanium selenide chalcogenide glasses heavily doped with silver. The models were readily obtained with ab initio molecular dynamics and their structure agrees closely with diffraction measurements. Thermal molecular dynamics simulation reveals the dynamics of Ag+ ions and the existence of trapping centers as conjectured in other theory work. We show that first principles simulation is a powerful tool to reveal the motion of ions in glass.

Tafen, D N; Mitkova, M; Tafen, De Nyago

2005-01-01

304

Direct ab initio MD simulation of silver ion diffusion in chalcogenide glasses

In this paper, we present new models of germanium selenide chalcogenide glasses heavily doped with silver. The models were readily obtained with ab initio molecular dynamics and their structure agrees closely with diffraction measurements. Thermal molecular dynamics simulation reveals the dynamics of Ag+ ions and the existence of trapping centers as conjectured in other theory work. We show that first principles simulation is a powerful tool to reveal the motion of ions in g...

Tafen, Nyago; Drabold, D. A.; Mitkova, M.

2005-01-01

305

Association and dissociation mechanisms for BnOm. Ab-initio molecular orbital method

International Nuclear Information System (INIS)

We have discussed the collision induced dissociation (CID) and association (CIA) of low-Z clusters. The cross sections of CID and CIA had been measured for cationic boron clusters, Bn+ (n=1-13), on colliding with O2 beam at very low energy below 10 eV. We perform theoretical calculations using ab initio Molecular Orbital method and investigate the reaction path, whether CIA or CID is preferred. (author)

306

On limits of ab initio calculations of pairing gap in nuclei

Energy Technology Data Exchange (ETDEWEB)

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

Saperstein, E. E., E-mail: saper@mbslab.kiae.ru [Kurchatov Institute (Russian Federation); Baldo, M. [Sezione di Catania, INFN (Italy); Lombardo, U. [INFN-LNS and University of Catania (Italy); Pankratov, S. S.; Zverev, M. V. [Kurchatov Institute (Russian Federation)

2011-11-15

307

On limits of ab initio calculations of pairing gap in nuclei

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

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

2010-01-01

308

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

Czech Academy of Sciences Publication Activity Database

-, 23 June (2009), s. 25. ISSN 1432-2234 R&D Projects: GA AV ?R 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

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

309

Ab initio study of phase transformations in transition-metal disilicides.

Czech Academy of Sciences Publication Activity Database

Ro?. 19, ?. 7 (2011), s. 919-926. ISSN 0966-9795 R&D Projects: GA AV ?R IAA100100920; GA MŠk(CZ) OC10008 Institutional research plan: CEZ:AV0Z20410507 Keywords : silicides various * phase transformation * plastic deformation mechanisms * defects * dislocation geometry and arrangement * ab-initio calculations * aero- engine components Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.649, year: 2011

Ká?a, Tomáš; Šob, Mojmír; Vitek, V.

2011-01-01

310

Contact dependence of carrier injection in carbon nanotubes: An ab initio study

We combine ab initio density functional theory with transport calculations to provide a microscopic basis for distinguishing between `good' and `poor' metal contacts to nanotubes. Comparing Ti and Pd as examples of different contact metals, we trace back the observed superiority of Pd to the nature of the metal-nanotube hybridization. Based on large scale Landauer transport calculations, we suggest that the `optimum' metal-nanotube contact combines a weak hybridization with a large contact length between the metal and the nanotube.

Nemec, N; Cuniberti, G

2006-01-01

311

Static ion structure factor for dense plasmas: Semi-classical and ab initio calculations

We calculate the static structure factor of dense multi-component plasmas. Large scale ab initio finite-temperature DFT molecular dynamics simulations are performed in order to cover the region where a consistent quantum treatment for the electrons is inevitable. Especially, the behavior at small wave numbers k can be inferred from the relation to the isothermal compressibility. Alternatively, the static structure factor is obtained by solving the integral equations for the pair correlation f...

Schwarz, V.; Holst, B.; Bornath, T.; Fortmann, C.; Kraeft, W-d; Thiele, R.; Redmer, R.; Gregori, G.; Lee, Hj; Doeppner, T.; Glenzer, Sh

2010-01-01

312

Ab initio study of the electronic spectrum of BeO

Directory of Open Access Journals (Sweden)

Full Text Available Low-lying singlet and triplet electronic states of the BeO molecule are calculated by means of the quantum chemical ab initio method. It was found that all states in the energy range from 0 to 50000 cm-1 are of valence character. Particular attention was paid to the investigation of the dissociative behavior of the states considered. The vibrational structure of the AIP<-XIS and BIS+<-XIS+ spectral systems was calculated.

MILJENKO PERIC

1999-12-01

313

How fragility makes phase-change data storage robust: insights from ab initio simulations

Phase-change materials are technologically important due to their manifold applications in data storage. Here we report on ab initio molecular dynamics simulations of crystallization of the phase change material Ag4In3Sb67Te26 (AIST). We show that, at high temperature, the observed crystal growth mechanisms and crystallization speed are in good agreement with experimental data. We provide an in-depth understanding of the crystallization mechanisms at the atomic level. At temperatures below 55...

Zhang, Wei; Ronneberger, Ider; Zalden, Peter; Xu, Ming; Salinga, Martin; Wuttig, Matthias; Mazzarello, Riccardo

2014-01-01

314

Spectroscopic and ab initio study of an intramolecular charge transfer (ICT) rhodanine derivative

The steady state absorption and emission studies of the rhodanine derivative 5-( p-dimethylaminobenzylidene) rhodanine (PDR) have been investigated. A dual fluorescence associated with an intramolecular charge transfer (ICT) phenomenon is reported. The characteristic emission band at low temperature (77 K) has also been reported. In support of the experimental results ab initio SCF and DFT calculations have been performed. The theoretical calculations also indicate that the chosen compound has significant non-linear optical (NLO) properties.

Ray, Jayanta; Panja, Nabamita; Nandi, Prasanta K.; Martin, Justin J.; Jones, Wayne E., Jr.

2008-02-01

315

Ab initio calculations of phosphate mediated degradation of glucose in biological cell

Ab initio quantum mechanical calculations in Harte Fock (HF) 6-31G(d) levels for different intermediate species- glucose -6 phosphate (2), fructose- 6 phosphate(3), fructose 1,6-bis- hosphate(4) have been carried out along with the starting glucose(1) molecule to phosphate mediated degraded products of it - dihydroxy acetone phosphate and glyceraldehyde-3 phosphate intermediates. Chemical potential, hardness and softness, which are described as the global reactivity parameters, follow the pos...

Barman, Rama K.

2012-01-01

316

Ab initio study of vibronic transitions between x2? and 12?+ electronic states of HCP+ ion

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 X2? state of ?, ?, ?, and ? 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 lev...

Stojanovi? Ljiljana

2013-01-01

317

Study of pressure-induced amorphization in sulfur using \\textit{ab initio} molecular dynamics

We report results of ab initio constant-pressure molecular dynamics simulations of sulfur compression leading to structural transition and pressure-induced amorphization. Starting from the orthorhombic S-I phase composed of S$_8$ ring molecules we find at room temperature and pressure of 20 GPa a transformation to monoclinic phase where half of the molecules develop a different conformation. Upon further compression, the monoclinic phase undergoes pressure-induced amorphizat...

Plas?ienka, Dus?an; Marton?a?k, Roman

2014-01-01

318

Fluorination-induced magnetism in boron nitride nanotubes from ab initio calculations

Ab initio calculations were conducted to investigate the electronic structures and magnetic properties of fluorinated boron nitride nanotube (F-BNNT). It was found that the chemisorption of F atoms on the B atoms of BNNT can induce spontaneous magnetization, whereas no magnetism can be produced when the B and N atoms are equally fluorinated. This provides a different approach to tune the magnetic properties of BNNTs as well as a synthetic route toward metal-free magnetic materials.

Li, Feng; Zhu, Zhonghua; Yao, Xiangdong; Lu, Gaoqing; Zhao, Mingwen; Xia, Yueyuan; Chen, Ying

2008-03-01

319

Two-gap superconductivity in heavily n-doped graphene: ab initio Migdal-Eliashberg theory

Graphene is the only member of the carbon family from zero- to three-dimensional materials for which superconductivity has not been observed yet. At this time, it is not clear whether the quest for superconducting graphene is hindered by technical challenges, or else by the fluctuation of the order parameter in two dimensions. In this area, ab initio calculations are useful to guide experimental efforts by narrowing down the search space. In this spirit, we investigate from first principles t...

Margine, Er; Giustino, F.

2014-01-01

320

An ab initio study of the structure and properties of aluminum hydroxide: Gibbsite and bayerite

The two most important polymorphs of aluminum hydroxide, namely gibbsite and bayerite, have been studied for the first time using solid state ab initio quantum mechanical methods, both using plane wave and localized basis set methodologies, within the framework of nonlocal density functional theory. The fully optimized structures have been determined for both phases, yielding improved hydrogen positions in the case of gibbsite for which the only previous information is from X-ray data. Mechan...

Gale, Jd; Rohl, Al; Milman, V.; Warren, Mc

2001-01-01

321

International Nuclear Information System (INIS)

We have devised a technique for spectral imaging using accurate ab initio electron energy loss near edge structure (ELNES) data and function field visualization. The technique is initially applied to a planar defect model in Si with different ring structures and no broken bonds where experimental probes are severely limited. The same model with B doping is also considered. It is shown that specific deviations in different energy ranges of the ELNES spectra are correlated with different structural components of the models.

322

The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without resorting to experiment. The global minimum of eclipsed C_s symmetry is characterized by a significantly bent hydrogen bond which deviates from linearity by about 20 degrees. In addition, the so-called cyclic C_{2h} structure is extremely close ...

Boese, A. Daniel; Chandra, Amalendu; Martin, Jan M. L.; Marx, Dominik

2003-01-01

323

Advances and applications in the FIREBALL ab initio tight-binding molecular-dynamics formalism.

Czech Academy of Sciences Publication Activity Database

Ro?. 248, ?. 9 (2011), 1989-2007. ISSN 0370-1972 R&D Projects: GA ?R GA202/09/0545; GA ?R GAP204/10/0952 Grant ostatní: AV?R(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

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

324

Ab-initio simulation and experimental validation of beta-titanium alloys

In this progress report we present a new approach to the ab-initio guided bottom up design of beta-Ti alloys for biomedical applications using a quantum mechanical simulation method in conjunction with experiments. Parameter-free density functional theory calculations are used to provide theoretical guidance in selecting and optimizing Ti-based alloys with respect to three constraints: (i) the use of non-toxic alloy elements; (ii) the stabilization of the body centered cubic...

Raabe, D.; Sander, B.; Friak, M.; Ma, D.; Neugebauer, J.

2008-01-01

325

Ab initio calculations for the elastic properties of magnesium under pressure

Results of ab initio calculations of the elastic constants for the hcp, bcc, double hcp (dhcp), and fcc magnesium in a wide range of pressures are presented. The calculated elastic constants are compared with available experimental and theoretical data. We discuss the effect of the electron topological transition that occurs when the hcp structure is compressed on results of calculations and consider possibility of observing the hcp?dhcp transition on the magnesium Hugoniot.

Sin'Ko, G. V.; Smirnov, N. A.

2009-09-01

326

Pair potentials for alumina from ab initio results on the Al2O3 molecule

International Nuclear Information System (INIS)

We use results from an ab initio investigation by Chang et al. on energetically low-lying stationary points of the Al2O3 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)

327

Ab initio electronic and optical spectra of free-base porphyrins: The role of electronic correlation

We present a theoretical investigation of electronic and optical properties of free-base porphyrins based on density functional theory and many-body perturbation theory. The electronic levels of free-base porphine (H2P) and its phenyl derivative, free-base tetraphenylporphyrin (H2TPP) are calculated using the ab initio GW approximation for the self-energy. The approach is found to yield results that compare favorably with the available photoemission spectra. The excitonic nature of the optica...

Palummo, Maurizia; Hogan, Conor; Sottile, Francesco; Bagala?, Paolo; Rubio Secades, A?ngel

2009-01-01

328

Base pairing motifs involving 1,8-naphthyridine: an ab initio study.

Czech Academy of Sciences Publication Activity Database

Ro?. 7, - (2006), s. 124-127. ISBN 90-6764-443-9. ISSN 1573-4196. [International Conference on Computational Methods in Sciences and Engineering. Chania, Crete, 27.10.2006-01.11.2006] R&D Projects: GA AV ?R KJB400500602; GA AV ?R 1ET400500402 Institutional research plan: CEZ:AV0Z40500505 Keywords : ab initio * electron correlation * MP2 Subject RIV: CD - Macromolecular Chemistry

Czernek, Ji?í

2006-01-01

329

Influence of the ab-initio nd cross sections in the critical heavy-water benchmarks

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). The results obtained using thes ab initio n-d cross sections are compared with those provided by the most renown international libraries.

Morillon, B; Carbonell, J

2013-01-01

330

Ab initio investigation of the Renner-Teller effect in the ground electronic state of HCCD+

Results of an ab initio treatment of the Renner-Teller effect in the ground electronic state of HCCD+ are presented. The model Hamiltonian employed involves four nuclear degrees of freedom correlating at linear geometry with two degenerate bending vibrations. Computations of vibronic energy levels and wave functions are carried out by means of a variational approach. The results of calculations are compared with those for symmetric isotopic species HCCH+ and DCCD+.

Peri?, M.; Ostoji?, B.; Radi?-Peri?, J.

1999-03-01

331

Ab initio modeling of layered materials with the CRYSTAL code: an overview

Ab initio simulations play an increasingly relevant role in the study of layered materials. Here we give an overview of the capabilities of modeling tools as applied to the characterization of simple layered hydroxides (e.g. alkali metal and aluminum hydroxides) and clays (e.g. kaolinite and lizardite). In particular, applications of the CRYSTAL code, in the study of such systems, are discussed.

Dovesi, Roberto; Ugliengo, Piero; Civalleri, Bartolomeo

2009-01-01

332

Ab initio study of energy band structures of GaAs nanoclusters

Electronic states and optical transitions of hydrogen terminated GaAs nanoclusters up to 16.9 nm in diameter were studied using a large-scale quantum chemistry approach called central insertion scheme by which the quantum confinement effect is shown to quantitatively agree with experimental results. The ab initio study further reveals that the effective mass of the conduction-band electron (valence-band hole) in the GaAs nanocluster is larger (smaller) than the bulk material value.

Jiang, J.; Gao, B.; Han, T.-T.; Fu, Y.

2009-03-01

333

International Nuclear Information System (INIS)

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)

334

Electronic ab initio quantum-defect theory. Low-resolution H2 photoionization spectrum

International Nuclear Information System (INIS)

This paper presents a global ab initio approach, called the electronic ab initio quantum-defect theory (EAQDT), to molecular photoionization spectrum calculations. This method first obtains the ab initio electronic parameters by the hereafter developed electronic iterative-variational eigenchannel approach (EIVEA). Then these electronic parameters are used in the calculation of the final state and the corresponding photoionization cross section by the multichannel quantum-defect theory (MQDT) [Jungen and Atabek, J. Chem. Phys. 66, 5584 (1977)]. In EIVEA, an elaborate N-electron correlated final-state wave function is introduced. This wave function allows us to take into account the ionic-core relaxation, many ionic cores and electronic autoionizing interactions. In calculating the transition probability we also use an electron-correlated initial state. Compared with the standard MQDT, the EAQDT is free from the use of semiempirical parameters and therefore has a wider applicability. This method is applied, as a test, to the low-resolution photoionization spectrum of H2. In the energy range between threshold and 23 eV studied here, where electronic autoionization does not take place, we obtain a theoretical cross section which bears comparison with the experimental one above 17.5 eV

335

Ab initio and empirical energy landscapes of (MgF2)n clusters (n = 3, 4).

We explore the energy landscape of (MgF(2))(3) on both the empirical and ab initio level using the threshold algorithm. In order to determine the energy landscape and the dynamics of the trimer we investigate not only the stable isomers but also the barriers separating these isomers. Furthermore, we study the probability flows in order to estimate the stability of all the isomers found. We find that there is reasonable qualitative agreement between the ab initio and empirical potential, and important features such as sub-basins and energetic barriers follow similar trends. However, we observe that the energies are systematically different for the less compact clusters, when comparing empirical and ab initio energies. Since the underlying motivation of this work is to identify the possible clusters present in the gas phase during a low-temperature atom beam deposition synthesis of MgF(2), we employ the same procedure to additionally investigate the energy landscape of the tetramer. For this case, however, we use only the empirical potential. PMID:22139092

Neelamraju, S; Schön, J C; Doll, K; Jansen, M

2012-01-21

336

Modeling of nuclear glasses by classical and ab initio molecular dynamics

International Nuclear Information System (INIS)

A calcium aluminosilicate glass of molar composition 67 % SiO2 - 12 % Al2O3 - 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)

337

Modelling of nuclear glasses by classical and ab initio molecular dynamics

International Nuclear Information System (INIS)

A calcium aluminosilicate glass of molar composition 67 % SiO2 - 12 % Al2O3 - 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)

338

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

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.

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

2015-01-01

339

Structures of 13-atom clusters of fcc transition metals by ab initio and semiempirical calculations

We report the results of ab initio calculations of the structures and magnetic moments of Ni13 , Pd13 , Pt13 , Cu13 , Ag13 , and Au13 that were performed using a density-functional method that employs linear combinations of pseudoatomic orbitals as basis sets (SIESTA). Our structural results for Pt13 , Cu13 , Ag13 , and Au13 show that a buckled biplanar structure (BBP) is more stable than the icosahedral configuration, in keeping with results obtained recently by Chang and Chou [Phys. Rev. Lett. 93, 133401 (2004)] using the Vienna ab initio simulation package with a plane-wave basis. However, for Ni13 and Pd13 we found that the icosahedral structure is more stable than BBP. For all these clusters, two semiempirical methods based on spherically symmetric potentials both found the icosahedral structure to be the more stable, while the modified embedded atom model method, which uses a direction-dependent potential, found BBP to be the more stable structure. When low-energy structures found in recent ab initio studies of Pt13 , Cu13 , and Au13 other than Chang and Chou were optimized with SIESTA, those reported for Pt13 and Cu13 were found to be less stable than BBP, but the two-dimensional planar configuration reported for Au13 proved to be more stable than BBP.

Longo, R. C.; Gallego, L. J.

2006-11-01

340

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

International Nuclear Information System (INIS)

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 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. (author)

341

FIREBALL is an ab initio technique for fast local orbital simulations of nanotechnological, solid state, and biological systems. We have implemented a convenient interface for new users and software architects in the platform-independent Java language to access FIREBALL's unique and powerful capabilities. The graphical user interface can be run directly from a web server or from within a larger framework such as the Computational Science and Engineering Online (CSE-Online) environment or the Distributed Analysis of Neutron Scattering Experiments (DANSE) framework. We demonstrate its use for high-throughput electronic structure calculations and a multi-100 atom quantum molecular dynamics (MD) simulation. Program summaryProgram title: FireballUI Catalogue identifier: AECF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 279 784 No. of bytes in distributed program, including test data, etc.: 12 836 145 Distribution format: tar.gz Programming language: Java Computer: PC and workstation Operating system: The GUI will run under Windows, Mac and Linux. Executables for Mac and Linux are included in the package. RAM: 512 MB Word size: 32 or 64 bits Classification: 4.14 Nature of problem: The set up and running of many simulations (all of the same type), from the command line, is a slow process. But most research quality codes, including the ab initio tight-binding code FIREBALL, are designed to run from the command line. The desire is to have a method for quickly and efficiently setting up and running a host of simulations. Solution method: We have created a graphical user interface for use with the FIREBALL code. Once the user has created the files containing the atomic coordinates for each system that they are going to run a simulation on, the user can set up and start the computations of up to hundreds of simulations. Running time: 3 to 5 minutes on a 2 GHz Pentium IV processor.

Keith, J. Brandon; Fennick, Jacob R.; Junkermeier, Chad E.; Nelson, Daniel R.; Lewis, James P.

2009-03-01

342

International Nuclear Information System (INIS)

The total energies and lattice constants of binary hcp- and fcc-TiN, AlN and ternary Ti0.5Al0.5N phases are calculated by ab initio method using the Vienna ab initio simulation package (VASP). The values of total energies are then used to calculate the lattice stabilities of binary hcp- and fcc-TiN, AlN and the interaction parameter of ternary Ti1-xAl xN phases on the basis of the semiempirical, thermodynamic sub-lattice model. Based on these data, the Gibbs free energy diagram of the immiscible quasi-binary TiN-AlN system are constructed in order to discuss the relative phase stability of the metastable ternary hcp- and fcc-Ti1-xAl xN phases over the entire range of compositions. The prediction is compared with the published results from PVD and CVD experiments. The calculated lattice energy and the constructed Gibbs free energy diagram show, in agreement with the experiments, that metastable fcc-Ti1-xAl xN coatings can easily undergo spinodal decomposition into coherent fcc-TiN and fcc-AlN, but there is a relatively large barrier for the formation of the stable hcp-AlN. A comparison with the TiN-Si3N4 system shows that, due to the much higher de-mixing energy of this system as compared to the TiN-AlN one, spinodal decomposition may occur in that system also for semicoherent TiN and Si3N4 phases

343

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

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

2014-06-01

344

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

Velaga, Srinath C; Anderson, Brian J

2014-01-16

345

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

International Nuclear Information System (INIS)

We combine accurate ab initio calculations of the second and third density virial coefficients, B(T) and C(T), of 4He with measurements of its (p-?-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.

346

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

Energy Technology Data Exchange (ETDEWEB)

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.

Vukmirovic, Nenad; Wang, Lin-Wang

2009-11-10

347

Ab initio molecular dynamics calculations of H2O on BaO(001)

Density functional theory calculations are used to explore water adsorption on BaO(001). The stable configuration is found to be a novel hydroxide pair. A detailed analysis demonstrates that the electrostatic repulsion between the OH- species is screened by Ba2+ cations and that the net interaction is provided by hydrogen bonding. Ab initio molecular dynamics at low coverage reveals that the pair is stable at elevated temperatures. The large structural flexibility of the hydoxylated surface may, however, lead to pair dissociation at high coverage. Simulations of a mixed (H2O+OH) overlayer uncover proton transfer between H2O and OH groups.

Grönbeck, Henrik; Panas, Itai

2008-06-01

348

Ab initio calculations of theoretical tensile strength in metals and intermetalics.

Czech Academy of Sciences Publication Activity Database

Warrendale, PA : The Minerals, Metals & Materials Society, 2001 - (Cross, M.; Evans, J.; Bailey, C.), s. 715-724 ISBN 0-87339-513-1. [TMS ANNUAL MEETING. Seattle (US), 17.02.2002-20.02.2002] R&D Projects: GA AV ?R IAA1010817; GA ?R GA106/99/1178; GA MŠk ME 264; GA MŠk OC P3.10 Grant ostatní: -(US) INT9605232; -(US) DEFG0298ER45702 Institutional research plan: CEZ:AV0Z2041904 Keywords : theoretical tensile strength * ab initio Subject RIV: BM - Solid Matter Physics ; Magnetism

Šob, Mojmír; Friák, Martin; Wang, L. G.; Vitek, V.

349

Atomic ionization of germanium by neutrinos from an ab initio approach

Energy Technology Data Exchange (ETDEWEB)

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.

Chen, Jiunn-Wei [Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China); National Center for Theoretical Sciences and Leung Center for Cosmology and Particle Astrophysics, National Taiwan University, Taipei 10617, Taiwan (China); Chi, Hsin-Chang [Department of Physics, National Dong Hwa University, Shoufeng, Hualien 97401, Taiwan (China); Huang, Keh-Ning [Department of Physics, Sichuan University, Chengdu, Sichuan (China); Department of Physics, Fuzhou University, Fuzhou, Fujian (China); Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China); Liu, C.-P. [Department of Physics, National Dong Hwa University, Shoufeng, Hualien 97401, Taiwan (China); Shiao, Hao-Tse [Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China); Singh, Lakhwinder [Institute of Physics, Academia Sinica, Taipei 11529, Taiwan (China); Department of Physics, Banaras Hindu University, Varanasi 221005 (India); Wong, Henry T. [Institute of Physics, Academia Sinica, Taipei 11529, Taiwan (China); Wu, Chih-Liang; Wu, Chih-Pan [Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China)

2014-04-04

350

Abstract A series of ab initio quantum chemistry calculations on a trinuclear mixed-valence system [(NH3)6Cu3O2]+3 have been performed in order to simultaneously evaluate its magnetic and electronic parameters, namely the magnetic coupling constants J1 and J2, the electron transfer integrals t1 and t2, and the exchange-transfer terms h1 and h2. The procedure is based on the use of the effective Hamiltonian theory. The results evidence the presence of two ferromagnetic interactions ...

Calzado, Carmen J.

2009-01-01

351

Ab initio calculations on low-energy structures of perindopril erbumine.

Czech Academy of Sciences Publication Activity Database

Cavtat : World Scientific and Engineering Academy and Society (WSEAS), 2006, s. 26-29. ISBN 960-8457-46-7. ISSN 1790-5109. [International Conference on Mathematics and Computers in Biology and Chemistry /7./. Cavtat (HR), 12.06.2006-15.06.2006] R&D Projects: GA AV ?R 1ET400500402; GA AV ?R IAA400500602 Institutional research plan: CEZ:AV0Z40500505 Keywords : perindopril erbumine * perindoprilat * ab initio Subject RIV: CD - Macromolecular Chemistry http://www.wseas.org

Czernek, Ji?í

352

We have performed an approximate ab initio calculation of vibrational properties of hydrogenated amorphous silicon (a-Si:H) using a molecular dynamics method. A 216 atom model for pure amorphous silicon (a-Si) has been employed as a starting point for our a-Si:H models with voids that were made by removing a cluster of silicon atoms out of the bulk and terminating the resulting dangling bonds with hydrogens. Our calculation shows that the presence of voids leads to localized low energy (30-50 cm^{-1}) states in the vibrational spectrum of the system. The nature and localization properties of these states are analyzed by various visualization techniques.

Nakhmanson, S M; Nakhmanson, Serge M.

1998-01-01

353

AB INITIO STUDY OF COBALT MAGNETISM ALONG THE TETRAGONAL DEFORMATION PATHS.

Czech Academy of Sciences Publication Activity Database

Brno : Ústav fyziky materiál? AV ?R v Brn?, 2005 - (Dlouhý, I.; Švejcar, J.; Šob, M.; Strnadel, B.), s. 21-26 ISBN 80-239-6145-4. [Víceúrov?ový design pokrokových materiál? 05. Brno (CZ), 01.12.2005] R&D Projects: GA ?R(CZ) GA202/03/1351; GA ?R(CZ) GD106/05/H008; GA AV ?R(CZ) IAA1041302; GA AV ?R(CZ) IBS2041105 Institutional research plan: CEZ:AV0Z20410507 Keywords : electronic structure * magnetism in metals * ab initio calculations Subject RIV: BM - Solid Matter Physics ; Magnetism

Zelený, Martin; Legut, Dominik; Šob, Mojmír

354

Converging sequences in the ab initio no-core shell model

International Nuclear Information System (INIS)

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

355

Steady-state Ab Initio Laser Theory: Generalizations and Analytic Results

We improve the steady-state ab initio laser theory (SALT) of Tureci et al. by expressing its fundamental self-consistent equation in a basis set of threshold constant flux states that contains the exact threshold lasing mode. For cavities with non-uniform index and/or non-uniform gain, the new basis set allows the steady-state lasing properties to be computed with much greater efficiency. This formulation of the SALT can be solved in the single-pole approximation, which give...

Ge, Li; Chong, Y. D.; Stone, A. Douglas

2010-01-01

356

DEFF Research Database (Denmark)

Fullerene functionalized carbon nanotubes-NanoBuds-form a novel class of hybrid carbon materials, which possesses many advantageous properties as compared to the pristine components. Here, we report a theoretical study of the electronic transport properties of these compounds. We use both ab initio techniques and tight-binding calculations to illustrate these materials' transmission properties and give physical arguments to interpret the numerical results. Specifically, above the Fermi energy we find a strong reduction in electron transmission due to localized states in certain regions of the structure while below the Fermi energy all considered structures exhibit a high-transmission energy band with a geometry-dependent width.

Fürst, Joachim Alexander; Hashemi, J.

2009-01-01

357

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

DEFF Research Database (Denmark)

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 are best described as phonon modes with strong coupling to the intramolecular degrees of freedom. Hence a computational method taking the periodicity of the crystal lattice as well as intramolecular motion into account is a prerequisite for the correct prediction of vibrational modes in such materials.

Jepsen, Peter Uhd; Clark, Stewart J.

2007-01-01

358

Ab-initio density functional theory study of a WO3 NH3-sensing mechanism

International Nuclear Information System (INIS)

WO3 bulk and various surfaces are studied by an ab-initio density functional theory technique. The band structures and electronic density states of WO3 bulk are investigated. The surface energies of different WO3 surfaces are compared and then the (002) surface with minimum energy is computed for its NH3 sensing mechanism which explains the results in the experiments. Three adsorption sites are considered. According to the comparisons of the energy and the charge change between before and after adsorption in the optimal adsorption site O1c, the NH3 sensing mechanism is obtained. (nuclear physics)

359

Ab-initio Gorkov-Green's function calculations of open-shell nuclei

We present results from a new ab-initio method that uses the self-consistent Gorkov Green's function theory to address truly open-shell systems. The formalism has been recently worked out up to second order and is implemented here in nuclei for the first time on the basis of realistic nuclear forces. We find good convergence of the results with respect to the basis size in Ca44 and Ni74 and discuss quantities of experimental interest including ground-state energies, pairing ...

Soma, V.; Barbieri, C.; Duguet, T.

2012-01-01

360

Ab initio results for the electronic structure of C_50Cl_10

In this paper we use ab initio density functional theory (DFT) to calculate the electronic properties of C_50Cl_10. In comparison with the unstable C_50 which has a small t_lu(LUMO) - h_u(HOMO) energy gap and a high total free energy compared with C_60, the belt of chlorines atoms stabilize the C_50Cl_10 fullerene by increasing the energy gap to approximately that of C_60 and lowering the total free energy. We also examine the effects of inter-cage separation on the band str...

Bailey, Steven W. D.; Lambert, Colin J.

2004-01-01

361

Closed-shell properties of $^{24}$O with {\\em ab initio} coupled-cluster theory

We present an \\emph{ab initio} calculation of spectroscopic factors for neutron and proton removal from $^{24}$O using the coupled-cluster method and a state-of-the-art chiral nucleon-nucleon interaction at next-to-next-to-next-to-leading order. In order to account for the coupling to the scattering continuum we use a Berggren single-particle basis that treats bound, resonant, and continuum states on an equal footing. We report neutron removal spectroscopic factors for the $...

Jensen, Ø.; Hagen, G.; Hjorth-jensen, M.; Vaagen, Jan S.

2010-01-01

362

Ab-initio theory of NMR chemical shifts in solids and liquids

We present a theory for the ab-initio computation of NMR chemical shifts (sigma) in condensed matter systems, using periodic boundary conditions. Our approach can be applied to periodic systems such as crystals, surfaces, or polymers and, with a super-cell technique, to non-periodic systems such as amorphous materials, liquids, or solids with defects. We have computed the hydrogen sigma for a set of free molecules, for an ionic crystal, LiH, and for a H-bonded crystal, HF, u...

Mauri, Francesco; Pfrommer, Bernd G.; Louie, Steven G.

1996-01-01

363

Cálculo ab initio de intensidades Raman dinâmicas utilizando a teoria da resposta linear

Directory of Open Access Journals (Sweden)

Full Text Available In this paper a methodology for the computation of Raman scattering cross-sections and depolarization ratios within the Placzek Polarizability Theory is described. The polarizability gradients are derived from the values of the dynamic polarizabilities computed at the excitation frequencies using ab initio Linear Response Theory. A sample application of the computational program, at the HF, MP2 and CCSD levels of theory, is presented for H2O and NH3. The results show that high correlated levels of theory are needed to achieve good agreement with experimental data.

Vidal Luciano N.

2003-01-01

364

Electronic structure of two-dimensional crystals from ab-initio theory

We report on ab-initio calculations of the two-dimensional systems MoS2 and NbSe2, which recently were synthesized. We find that two-dimensional MoS$_2$ is a semiconductor with a gap which is rather close to that of the three dimensional analogue, and that NbSe$_2$ is a metal, which is similar to the three dimensional analogue of this compound. We further computed the electronic structure of the two-dimensional hexagonal (graphene like) lattices of Si and Ge, and compare t...

Eriksson, S. Lebegue O.

2009-01-01

365

Complex coupled-cluster approach to an ab-initio description of open quantum systems

We develop ab-initio coupled-cluster theory to describe resonant and weakly bound states along the neutron drip line. We compute the ground states of the helium chain 3-10He within coupled-cluster theory in singles and doubles (CCSD) approximation. We employ a spherical Gamow-Hartree-Fock basis generated from the low-momentum N3LO nucleon-nucleon interaction. This basis treats bound, resonant, and continuum states on equal footing, and is therefore optimal for the descriptio...

Hagen, G.; Dean, D. J.; Hjorth-jensen, M.; Papenbrock, T.

2006-01-01

366

Fully ab initio atomization energy of benzene via W2 theory

The total atomization energy at absolute zero, (TAE$_0$) of benzene, C$_6$H$_6$, was computed fully {\\em ab initio} by means of W2h theory as 1306.6 kcal/mol, to be compared with the experimentally derived value 1305.7+/-0.7 kcal/mol. The computed result includes contributions from inner-shell correlation (7.1 kcal/mol), scalar relativistic effects (-1.0 kcal/mol), atomic spin-orbit splitting (-0.5 kcal/mol), and the anharmonic zero-point vibrational energy (62.1 kcal/mol). ...

Parthiban, S.; Martin, J. M. L.

2001-01-01

367

Anharmonic Self-Energy of Phonons Ab Initio Calculations and Neutron Spin Echo Measurements

We have calculated (ab initio) and measured (by spin-echo techniques) the anharmonic self-energy of phonons at the X-point of the Brillouin zone for isotopically pure germanium. The real part agrees with former, less accurate, high temperature data obtained by inelastic neutron scattering on natural germanium. For the imaginary part our results provide evidence that transverse acoustic phonons at the X-point are very long lived at low temperatures, i.e. their probability of decay approaches zero, as a consequence of an unusual decay mechanism allowed by energy conservation.

Debernardi, A; Kulda, Yu; Cardona, M; Haller, E E

2002-01-01

368

A single sodium chloride molecule in aqueous solution was simulated by the ab initio quantum mechanical charge field-molecular dynamics (QMCF-MD) approach. During a series of simulations the solvated molecule (CIP), dissociated solvated ions and - most noticeably - a solvent separated ion pair (SSIP) were observed and the structural and dynamical characteristics of these systems were investigated. In addition to a detailed structural analysis of the observed species, vibrational spectra and charge distributions were calculated to elucidate the mechanism of the NaCl dissociation. PMID:24623175

Wiedemair, Martin J; Weiss, Alexander K H; Rode, Bernd M

2014-04-28

369

Low-lying electronic states of nitrosyl cyanide (NCNO): An ab initio MCHF study

International Nuclear Information System (INIS)

Ab initio multiconfiguration Hartree--Fock calculations of the electronic structure of several low-lying electronic states of nitrosyl cyanide (NCNO) are reported. The essential features of the electronic structure of these states were analyzed to provide a qualitative correlation diagram for the dissociation process NCNO ? NC+NO. It is found that the four lowest-lying states 1/sup ,/3A' and 1/sup ,/3A'' are connected directly to ground state products. Excitation energies and geometrical parameters for these states and for the 2- 1A'' and 2- 1A' states are presented. Implications of these findings for NCNO photodissociation processes are discussed

370

Ab initio study of the EFG at the N sites in imidazole

International Nuclear Information System (INIS)

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.

371

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.

Pietrucci, Fabio; Andreoni, Wanda

2011-08-01

372

We have studied the Metal-Insulator like Transition (MIT) in lithium and beryllium ring-shaped clusters through ab initio Density Matrix Renormalization Group (DMRG) method. Performing accurate calculations for different interatomic distances and using Quantum Information Theory (QIT) we investigated the changes occurring in the wavefunction between a metallic-like state and an insulating state built from free atoms. We also discuss entanglement and relevant excitations among the molecular orbitals in the Li and Be rings and show that the transition bond length can be detected using orbital entropy functions. Also, the effect of different orbital basis on the effectiveness of the DMRG procedure is analyzed comparing the convergence behavior.

Fertitta, E; Barcza, G; Legeza, Ö

2014-01-01

373

The pressure induced phase transition of confined water from ab initio molecular dynamics simulation

International Nuclear Information System (INIS)

We present an ab initio molecular dynamics study of pressure induced melting of an ice thin film confined between two parallel metal surfaces. The ice-to-water phase transition was observed at a pressure of roughly 0.5 GPa, when the film was compressed by 6.6%. The latter is in agreement with the volume change in the melting of bulk ice. The effects of nonadiabatic compression on the layer-dependent momentum distribution and the electronic redistribution at the interfaces are presented and discussed

374

International Nuclear Information System (INIS)

We examine how the misorientation of a few stacked graphene layers affects the electronic structure of carbon nanosystems. We present ab initio calculations on bilayer and trilayer systems to demonstrate that the massless fermion behavior typical of single-layered graphene is also found in incommensurate multilayered graphitic systems. We also investigate the consequences of this property on experimental fingerprints, such as Raman spectroscopy and scanning tunneling microscopy (STM). Our simulations reveal that STM images of turbostratic few-layer graphite are sensitive to the layer arrangement. We also predict that the resonant Raman signals of graphitic samples are more sensitive to the orientation of the layers than to their number

375

Experimental and ab initio study of the photofragmentation of DNA and RNA sugars

International Nuclear Information System (INIS)

The photoelectron-photoion-photoion coincidence method is used to measure the photodissociation of doubly charged D-ribose (C5H10O5), the RNA sugar molecules, and 2-deoxy-D-ribose (C5H10O4), the DNA sugar molecules, following normal Auger decay after initial C 1s and O 1s core ionizations. The fragment identification is facilitated by measuring isotopically labeled D-ribose, such as D-ribose deuterated at C(1), and with 13C at the C(5) position. Ab initio quantum chemistry calculations are used to gain further insight into the abundant appearance of the CHO+ fragment.

376

Ab initio coupled cluster calculations for nuclei using methods of quantum chemistry

International Nuclear Information System (INIS)

We report preliminary large scale ab initio calculations of ground and excited states of 16O using quantum chemistry inspired coupled cluster methods and realistic two-body interactions. By using the renormalized Hamiltonians obtained with a no-core G-matrix approach, we obtain the virtually converged results at the level of two-body interactions. Due to the polynomial scaling with the system size that characterizes coupled cluster methods, we can probe large model spaces with up to seven major oscillator shells, for which standard non-truncated shell-model calculations are not possible. (orig.)

377

Ab initio calculations of 14N and 15N hyperfine structures

Hyperfine structure parameters are calculated for the 2p2(3P)3s 4P_J, 2p2(3P)3p 4Po_J and 2p2(3P)3p 4Do_J levels, using the ab initio multiconfiguration Hartree-Fock method. The theoretical hyperfine coupling constants are in complete disagreement with the experimental values of Jennerich et al. (EPJD 40(2006), 81) deduced from the analysis of the near-infrared Doppler-free saturated absorption spectra.

Jönsson, P; Nemouchi, M; Godefroid, M

2010-01-01

378

Step-induced unusual magnetic properties of ultrathin Co\\/Cu films ab initio study

We have performed ab initio studies to elucidate the unusual magnetic behavior recently observed in epitaxial Co films upon absorption of submonolayers of Cu and other materials. We find that a submonolayer amount of Cu on a stepped Co/Cu (100) film changes dramatically the electronic and magnetic structure of the system. The effect is mainly due to hybridization of Co and Cu $d$-electrons when copper forms a ``wire'' next to a Co step at the surface. As a result, a non-collinear arrangement of magnetic moments (switching of the easy axis) is promoted. [PACS 75.70.Ak,75.70.-i

Smirnov, A V

1996-01-01

379

Atomic ionization of germanium by neutrinos from an ab initio approach

International Nuclear Information System (INIS)

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.

380

Thorium in tungsten: construction of interatomic EAM potentials from ab initio data

International Nuclear Information System (INIS)

The interatomic interaction potential of tungsten and thorium crystals and those of hypothetical tungsten and thorium alloys within the embedded atom approach are considered. The corresponding Ansatz functions are fitted against full potential linear augmented plane wave data of real tungsten- and thorium- and hypothetical tungsten-thorium-crystals. The result is interatomic potentials, ready for use within classical molecular dynamics schemes. A cross check of the resulting force scheme derived by comparison of ab initio and classical molecular dynamics data is provided. Furthermore, we used the potentials to calculate the phonon dispersion relations, which then serve as an additional check. (paper)

381

AbInitio Simulation of the Spin Transition during Chemisorption: H/Al(111)

Electronically nonadiabatic effects during the chemisorption of hydrogen atoms on an Al(111) surface are simulated ab initio using time-dependent density-functional theory for the electrons in combination with Ehrenfest dynamics for the nuclei. Strongly nonadiabatic effects close to the spin transition of the H atom are identified, and the dissipated energy as well as the electron-hole pair excitation spectra are calculated. The recent Newns-Anderson model approach by Mizielinski et al. is confirmed. The simulations illustrate the physical processes that contribute to internal exoelectron emission.

Lindenblatt, M.; Pehlke, E.

2006-11-01

382

Ab initio no-core shell model for light nuclei and other applications

Energy Technology Data Exchange (ETDEWEB)

The ab initio No-Core Shell Model (NCSM) begins with an intrinsic Hamiltonian for all nucleons in the nucleus. Realistic two-nucleon and tri-nucleon interactions are incorporated such as those recently developed from effective-field theory and chiral perturbation theory. We then derive a finite basis-space dependent Hermitian effective Hamiltonian that conserves all the symmetries of the initial Hamiltonian. The resulting finite Hamiltonian matrix problem is solved by diagonalization on parallel computers. Applications range from light nuclei to multiquark systems and, recently, to quantum-field theory including systems with bosons. We present this approach with a sample of recent results.

Vary, J P [Department of Physics and Astronomy, Iowa State University, Ames, IA 50011 (United States); Atramentov, O V [Department of Physics and Astronomy, Iowa State University, Ames, IA 50011 (United States); Barrett, B R [Department of Physics, University of Arizona, Tucson, AZ 85721 (United States); Hasan, M [Department of Physics, University of Jordan, Amman, Jordan (Jordan); Hayes, A C [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Lloyd, R [Department of Physics and Chemistry, Arkansas State University, State University, AR 72467 (United States); Mazur, A I [Physics Department, Khabarovsk State Technical University, Khabarovsk 680035, Russia (Russian Federation); Navrati, P [Lawrence Livermore National Laboratory, Livermore, CA 94551 (United States); Negoita, A G [Horia Hulubei National Institute of Physics and Nuclear Engineering, Bucharest-Magurele (Romania); Nogga, A [Institut fuer Kernphysik, Forschungszentrum Juelich, 52425 Juelich (Germany); Ormand, W E [Lawrence Livermore National Laboratory, Livermore, CA 94551 (United States); Popescu, S [Horia Hulubei National Institute of Physics and Nuclear Engineering, Bucharest-Magurele (Romania); Shehadeh, B [Department of Physics and Astronomy, Iowa State University, Ames, IA 50011 (United States); Shirokov, A M [Skobeltsyn Institute of Nuclear Physics, Moscow State University, Moscow 119992, Russia (Russian Federation); Spence, J R [Department of Physics and Astronomy, Iowa State University, Ames, IA 50011 (United States); Stetcu, I [Department of Physics, University of Arizona, Tucson, AZ 85721 (United States); Stoica, S [Horia Hulubei National Institute of Physics and Nuclear Engineering, Bucharest-Magurele (Romania); Weber, T A [Department of Physics and Astronomy, Iowa State University, Ames, IA 50011 (United States); Zaytsev, S A [Physics Department, Khabarovsk State Technical University, Khabarovsk 680035 (Russian Federation)

2005-01-01

383

Ab initio R-matrix calculations of e+-molecule scattering

The adaptation of the molecular R-matrix method, originally developed for electron-molecule collision studies, to positron scattering is discussed. Ab initio R-matrix calculations are presented for collisions of low energy positrons with a number of diatomic systems including H2, HF and N2. Differential elastic cross sections for positron-H2 show a minimum at about 45 deg for collision energies between 0.3 and 0.5 Ryd. The calculations predict a bound state of positronHF. Calculations on inelastic processes in N2 and O2 are also discussed.

Danby, Grahame; Tennyson, Jonathan

1990-01-01

384

An interaction pair potential function for 1,4,7,10-tetraaza-cyclododecane (cyclen) and water has been derived from ab-initio molecular orbital computations. The 250 computed points of the energy surface for the water-cyclen interaction have been fitted with an analytical potential of the form where A, B. C, and D are constants, and qi, and qj are the atomic charges of the i-th atom of water and the j-th atom of cyclen at infinite separation.

Hannongbua, Supot V.; Rode, Bernd M.

1985-06-01

385

Comprehensive ab initio study of doping in bulk ZnO with group-V elements

Despite the lack of reproducible experimental confirmation, group-V elements have been considered as possible sources of p-type doping in ZnO in the form of simple and complex defects. Using ab initio calculations, based on state-of-the-art hybrid exchange-correlation functional, we study a wide range of defects and defect complexes related with N, P, As, and Sb impurities. We show that none of the candidates for p-type doping can be considered a good source of holes in the ...

Petretto, Guido; Bruneval, Fabien

2014-01-01

386

Oxygen vacancy formation energies in Sr-doped complex perovskites: ab initio thermodynamic study

La1-xSrxCo0.25Fe0.75O3-delta is known as one of the best cathode materials for permeation membranes and solid oxide fuel cells. Optimization of its chemical composition is a challenging problem. One of the key properties is concentration of oxygen vacancies, controlled by their formation energies. Ab initio calculations were employed in order to study the formation of oxygen vacancies in La1-xSrxCo0.25Fe0.75O3-delta perovskites by varying the Sr content from x = 12.5% to 50%...

Gryaznov, Denis; Finnis, Mike W.; Evarestov, Robert; Maier, Joachim

2012-01-01

387

Scalable numerical approach for the steady-state ab initio laser theory

We present an efficient and flexible method for solving the non-linear lasing equations of the steady-state ab initio laser theory. Our strategy is to solve the underlying system of partial differential equations directly, without the need of setting up a parametrized basis of constant flux states. We validate this approach in one-dimensional as well as in cylindrical systems, and demonstrate its scalability to full-vector three-dimensional calculations in photonic-crystal slabs. Our method paves the way for efficient and accurate simulations of microlasers which were previously inaccessible.

Esterhazy, S.; Liu, D.; Liertzer, M.; Cerjan, A.; Ge, L.; Makris, K. G.; Stone, A. D.; Melenk, J. M.; Johnson, S. G.; Rotter, S.

2014-08-01

388

A scalable numerical approach for the Steady-State Ab-Initio Laser Theory

We present an efficient and flexible method for solving the non-linear lasing equations of the steady-state ab-initio laser theory. Unlike previous techniques, we solve the underlying system of partial differential equations directly, without the need of setting up a parametrized basis of constant flux states. We validate our approach in one-dimensional as well as in cylindrical systems, and demonstrate its scalability to full-vector three-dimensional calculations in photonic-crystal slabs. Our approach paves the way for efficient and accurate simulations of lasing structures which were previously inaccessible.

Esterhazy, S; Liertzer, M; Cerjan, A; Ge, L; Makris, K G; Stone, A D; Melenk, J M; Johnson, S G; Rotter, S

2013-01-01

389

Communication: Multiple-timestep ab initio molecular dynamics with electron correlation

A time-reversible, multiple-timestep protocol is presented for ab initio molecular dynamics simulations using correlated, wavefunction-based underlying potentials. The method is motivated by the observation that electron correlation contributions to forces vary on a slower timescale than their Hartree-Fock counterparts. An efficient dynamics algorithm, involving short-timestep Hartree-Fock and long-timestep Møller-Plesset perturbation theory, is presented and tested. Results indicate stable trajectories and relative speedups comparable to those seen in force field-based multiple-timestep schemes, with the highest efficiency improvement occurring for large systems.

Steele, Ryan P.

2013-07-01

390

An efficient and robust linear scaling method is presented for large scale {\\it ab initio} electronic structure calculations of a wide variety of materials including metals. The detailed short range and the effective long range contributions to the electronic structure are taken into account by solving an embedded cluster defined in a Krylov subspace, which provides rapid convergence for not only insulators but also metals. As an illustration of the method, we present a large scale calculation based on density functional theory for a palladium cluster with a single iron impurity.

Ozaki, T

2005-01-01

391

Polarization effects in semiconductors from ab initio theory to device applications

This book presents the latest understanding of the solid physics, electronic implications and practical applications of the unique spontaneous or pyro-electric polarization charge of hexagonal semiconductors, and the piezo-electric effects in thin film hetero-structures, which are used in wide forbidden band gap sensor, electronic and opto-electronic semiconductor devices. The book covers ab initio theory of polarization in cubic and hexagonal semiconductors, growth of thin film GaN, and GaN/AlGaN GaAlN/ AlGaInN and other nitride, and SiC hetero-structures; graded structures for distributed pi

Wood, Colin

2007-01-01

392

The response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser, electron and ion irradiations. PMID:25660219

Xiao, H Y; Weber, W J; Zhang, Y; Zu, X T; Li, S

2015-01-01

393

Electronic and transport properties edge functionalized graphene nanoribbons-An ab initio approach

Energy Technology Data Exchange (ETDEWEB)

With the help of ab initio approach we have investigated the electronic and transport properties of edge functionalized zigzag graphene nanoribbons using density functional theory. We have studied the energetic stability and Fermi energy of ZGNRs. We have reported that the edge functionalization of zigzag graphene nanoribbons can break the degeneracy that can be used to promote the onset of a semiconducting to metal transition or a half metal to semiconducting state. The edge functionalization also promotes a metal-semimetal transition. It has also been observed that the transmission spectrum of the edge functionalized ZGNRs are different from those of pristine.

Chauhan, Satyendra Singh, E-mail: sschauhan-71@rediffmail.com [Institute of Information Technology and Management, ITM University, Gwalior - 474001 (India); Srivastava, Pankaj [ABV Indian Institute of Information Technology and Management, Gwalior - 474010 (India); Shrivastva, A. K. [School of Studies in Physics, Jiwaji University, Gwalior- 474011 (India)

2014-04-24

394

Electronic and transport properties edge functionalized graphene nanoribbons-An ab initio approach

International Nuclear Information System (INIS)

With the help of ab initio approach we have investigated the electronic and transport properties of edge functionalized zigzag graphene nanoribbons using density functional theory. We have studied the energetic stability and Fermi energy of ZGNRs. We have reported that the edge functionalization of zigzag graphene nanoribbons can break the degeneracy that can be used to promote the onset of a semiconducting to metal transition or a half metal to semiconducting state. The edge functionalization also promotes a metal-semimetal transition. It has also been observed that the transmission spectrum of the edge functionalized ZGNRs are different from those of pristine

395

Ab initio molecular dynamics simulations of overlapping recoil events in ThO2

International Nuclear Information System (INIS)

Ab initio molecular dynamics is used to study defect production and interactions from overlapping atomic recoil events in thoria. The pre-existing defects, charge redistribution, and structural distortion from an initial recoil event significantly affect the dynamics of defect production processes that occur from a subsequent overlapping recoil event. The final defect configurations and increase in system energy are dependent on the incident directions and sequence of the recoils. A linear relationship between system potential energy and charge transfer at the distance of closest approach between the recoil and atomic nuclei demonstrates the important role of charge transfer in the response of thoria to single and overlapping recoils. (paper)

396

Ab initio calculation of the Cu-Pd one-dimensional long period superstructure phase diagram

International Nuclear Information System (INIS)

The FCC superstructure phase diagram for Cu-Pd is calculated by means of isotropic effective interactions derived from an ab initio KKR-CPA electronic structure calculation. The authors of this paper prove the existence of a region in which one-dimensional long period superstructures are stable. This region is composed of several single phase fields in which the modulation period is constant. The value of the modulation period is in close agreement with results from High Resolution Electron Microscopy. Adding oxygen to Cu-Pd is found to sharpen the antiphase boundaries. This experiment enables us to clarify the role of the Fermi surface in these alloys

397

Temperature dependent mechanical properties of Mo–Si–B compounds via ab initio molecular dynamics

Directory of Open Access Journals (Sweden)

Full Text Available A new method was proposed to obtain high temperature mechanical properties with a combination of ab initio molecular dynamics and stress-strain analyses. It was applied to compounds in the Mo–Si–B ternary system, namely, T1 (Mo5Si3 and T2 (Mo5SiB2 phases. The calculated coefficient of thermal expansion, thermal expansion anisotropy, and elastic constants agree well with those from the available experiments. The method enables us to theoretically access these properties up to 2000 K.

C. C. Dharmawardhana

2013-07-01

398

Solvent effects on 2-methoxyethanol conformers: an ab initio DFT study using the SCI-PCModel

The four stable conformers of 2-methoxyethanol, CH3O-CH2-CH2-OH (tgg', ggg', ttg and ttt) are studied by ab initio calculations using the SCRF theory and the SCI-PCModel to assess solvent effects on the structure and vibrational spectra of this compound. Full geometry optimizations were carried out at the B3LYP/6-311+G(3df,2df,2p)//B3LYP/6-31G(d) level, and normal mode calculations were performed within the harmonic approximation using the B3LYP/6-31G(d) derived force fields. The solvent, her...

Gil, Francisco P. S. C.; Teixeira-dias, J. J. C.

1999-01-01

399

An ab initio molecular dynamics study of the roaming mechanism of the H2+HOC+ reaction

International Nuclear Information System (INIS)

We report here a direct ab initio molecular dynamics study of the p-/o-H2+HOC+ reaction on the basis of the accurate SAC-MP2 potential energy surface. The quasi-classical trajectory method was employed. This work largely focuses on the study of reaction mechanisms. A roaming mechanism was identified for this molecular ion-molecule reaction. The driving forces behind the roaming mechanism were thoroughly investigated by using a trajectory dynamics approach. In addition, the thermal rate coefficients of the H2+HOC+ reaction were calculated in the temperature range [25, 300] K and are in good agreement with experiments.

400

Quantum chemistry the development of ab initio methods in molecular electronic structure theory

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

Schaefer III, Henry F

2012-01-01

401

Ab initio no-core shell model for light nuclei and other applications

International Nuclear Information System (INIS)

The ab initio No-Core Shell Model (NCSM) begins with an intrinsic Hamiltonian for all nucleons in the nucleus. Realistic two-nucleon and tri-nucleon interactions are incorporated such as those recently developed from effective-field theory and chiral perturbation theory. We then derive a finite basis-space dependent Hermitian effective Hamiltonian that conserves all the symmetries of the initial Hamiltonian. The resulting finite Hamiltonian matrix problem is solved by diagonalization on parallel computers. Applications range from light nuclei to multiquark systems and, recently, to quantum-field theory including systems with bosons. We present this approach with a sample of recent results

402

Ab initio Study of Hyperconjugative Effect on Electronic Wavefunctions of 2-chloroethanol

The electronic structure of five conformers of 2-chloroethanol was studied by ab initio calculations at B3LYP and MP2 levels of theory with aug-cc-pVTZ basis set. The existing hydrogen bond and hyperconjugation effects on the stability of 2-chloroethanol conformers were discussed on the base of natural bond orbital analyses. The result exhibits that hyper-conjugation is the main factor to determine the stability of conformers. Such effects on the electron wavefunctions of the highest-occupied molecular orbital (HOMO) of different conformers are demonstrated with electron momentum spectroscopy, exhibiting the obviously different symmetries of the HOMO wavefunctions in momentum space.

Wang, Ke-dong; Zhang, Hai-xia; Liu, Yu-fang

2011-08-01

403

*Ab initio* electronic properties of dual phosphorus monolayers in silicon

DEFF Research Database (Denmark)

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

Drumm, Daniel W.; Per, Manolo C.

2014-01-01

404

Under ambient conditions, pure antimony pentafluoride (SbF5) is a strongly associated liquid. Early NMR works established that the molecules oligomerize via cis-fluorine chains. We have employed ab initio molecular dynamics to investigate the structure of liquid SbF5. The simulation confirms the strong tendency of molecules to oligomerize via a barrierless, diffusion-limited process. The nature of the SbF5 chemical bond and the experimentally observed propensity to form cis-fluorine chains has been analyzed in terms of Wannier localized orbital functions. The calculation indicated a very strong ionic character for the Sb-F bond.

Raugei, Simone; Klein, Michael L.

2002-04-01

405

Ab initio molecular dynamics of Al irradiation-induced processes during Al(2)O(3) growth

Al bombardment induced structural changes in alpha-Al(2)O(3) (R-3c) and gamma-Al(2)O(3) (Fd-3m) were studied using ab initio molecular dynamics. Diffusion and irradiation damage occur for both polymorphs in the kinetic energy range from 3.5 to 40 eV. However, for gamma-Al(2)O(3)(001) subplantation of impinging Al causes significantly larger irradiation damage and hence larger mobility as compared to alpha-Al(2)O(3). Consequently, fast diffusion along gamma-Al(2)O(3)(001) gives rise to prefere...

Music, Denis; Nahif, Farwah; Sarakinos, Kostas; Friederichsen, Niklas; M Schneider, Jochen

2011-01-01

406

"Ab initio" studies of hydrogen-enhanced oxygen diffusion in silicon

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english A novel microscopic mechanism for hydrogen-enhanced oxygen diffusion in p-doped silicon is proposed. A path for joint diffusion of O and H is obtained from an ab-initio molecular dynamics "kick" simulation. The migration pathway consists of a two-step mechanism, with a maximum energy of 1.46 eV. Thi [...] s path represents a 0.54 eV reduction in the static barrier when compared with the diffusion of isolated O in Si, in excellent agreement with experiments.

R. B., Capaz; L. V. C., Assali; L. C., Kimerling; K., Cho; J. D., Joannopoulos.

1999-12-01

407

Directory of Open Access Journals (Sweden)

Full Text Available Possible reasons of low reactivities of some N-(2-X-benzoyl imidazoles utilising ab initio Hartree-Fock calculations have been studied in imidazole-catalyzed hydrolysis. The elucidation of its molecular structures display that the inhibition of resonance, between the carbonyl group and the aromatic moiety, due to steric effects are very much important than that a possible stabilization of the reactant state by a donor-acceptor effects interaction between the orto nitro group of benzene ring and the imidazole ring.

Paulo Meneghelli

2001-01-01

408

Ab initio molecular dynamics simulations of overlapping recoil events in ThO2

Ab initio molecular dynamics is used to study defect production and interactions from overlapping atomic recoil events in thoria. The pre-existing defects, charge redistribution, and structural distortion from an initial recoil event significantly affect the dynamics of defect production processes that occur from a subsequent overlapping recoil event. The final defect configurations and increase in system energy are dependent on the incident directions and sequence of the recoils. A linear relationship between system potential energy and charge transfer at the distance of closest approach between the recoil and atomic nuclei demonstrates the important role of charge transfer in the response of thoria to single and overlapping recoils.

Liu, B.; Xiao, H. Y.; Zhang, Y.; Weber, W. J.

2013-10-01

409

We have determined ab initio potential energy surfaces of the S0 and S1 states of dimethylnitrosamine, with particular care for the N-N bond dissociation pathway. The electronic correlation has been taken into account by a multireference perturbation method, CIPSI. Classical trajectories in the S1 surface have been run with statistically determined initial conditions. Computed lifetimes and orientation parameters for the recoil velocity and the NO fragment angular momentum are in agreement with experimental data. Large amplitude internal motions are of primary importance in determining such quantities.

Persico, Maurizio; Cacelli, Ivo; Ferretti, Alessandro

1991-04-01

410

Energy Technology Data Exchange (ETDEWEB)

The results of ab initio calculations of the electronic structure of Si nanocrystals doped with shallow donors (Li, P) are reported. It is shown that phosphorus introduces much more significant distortions into the electronic structure of the nanocrystal than lithium, which is due to the stronger central cell potential of the phosphorus ion. It is found that the Li-induced splitting of the ground state in the conduction band of the nanocrystal into the singlet, doublet, and triplet retains its inverse structure typical for bulk silicon.

Kurova, N. V., E-mail: kurova_natasha@mail.ru; Burdov, V. A. [Lobachevskii Nizhni Novgorod State University (Russian Federation)

2013-12-15

411

Ab initio MO calculations of the repulsion energies in HClsup(n+) ions

International Nuclear Information System (INIS)

The calculations of the electronic structures of the highly charged HCl ions were performed with ab initio MO method. The repulsion energies of two fragments (H+ and Cl(n-1)+) and the kinetic energies of H+ were evaluated by the following two methods: (i) Coulomb repulsion of two positive sites and (ii) total energy difference between HCln+ (R(H-Cl) - 1,274 A) and H++Cl(n-1)+(R(H-Cl)). Coulomb explosion model proposed by CARLSON and WHITE was found to be well applied to these highly charged ions. (orig.)

412

Ab initio model potential study of pressure effects on K2NaGaF6:Cr3 +

In this paper we present the results of an ab initio study of the pressure effects on the 4A2g ground state and the 4T2g and 2Eg excited states of Cr3+-doped K2NaGaF6. Complete active space SCF (CASSCF) and averaged coupled-pair functional (ACPF) calculations are performed on a CrF63- cluster embedded in an ab initio model potential (AIMP) representation of the K2NaGaF6 lattice at ambient and high pressure. The results are in close agreement with the experimentally measured pressure shifts of vibrational frequencies and emission spectra, which demonstrates the ability of the ab initio embedding model potential method to accurately model hydrostatic pressure experiments in this type of defect crystals. It is also shown that if only the standard Madelung embedding potential is used, none of the observed effects of pressure are reproduced.

Seijo, Luis; Barandiarán, Zoila; Pettersson, Lars G. M.

1993-03-01

413

VASP-4096: a very high performance programmable device for digital media processing applications

Over the past few years, technology drivers for microprocessors have changed significantly. Media data delivery and processing--such as telecommunications, networking, video processing, speech recognition and 3D graphics--is increasing in importance and will soon dominate the processing cycles consumed in computer-based systems. This paper presents the architecture of the VASP-4096 processor. VASP-4096 provides high media performance with low energy consumption by integrating associative SIMD parallel processing with embedded microprocessor technology. The major innovations in the VASP-4096 is the integration of thousands of processing units in a single chip that are capable of support software programmable high-performance mathematical functions as well as abstract data processing. In addition to 4096 processing units, VASP-4096 integrates on a single chip a RISC controller that is an implementation of the SPARC architecture, 128 Kbytes of Data Memory, and I/O interfaces. The SIMD processing in VASP-4096 implements the ASProCore architecture, which is a proprietary implementation of SIMD processing, operates at 266 MHz with program instructions issued by the RISC controller. The device also integrates a 64-bit synchronous main memory interface operating at 133 MHz (double-data rate), and a 64- bit 66 MHz PCI interface. VASP-4096, compared with other processors architectures that support media processing, offers true performance scalability, support for deterministic and non-deterministic data processing on a single device, and software programmability that can be re- used in future chip generations.

Krikelis, Argy

2001-03-01

414

A mechanism for the enhanced splitting detected in the millimeter-wave rotational spectra of the first excited S-S stretching state of HSSH (disulfane) has been studied. The mechanism, which involves a potential coupling between the first excited S-S stretching state and excited torsional states, has been investigated in part by the use of ab initio theory. Based on an ab initio potential surface, coupling matrix elements have been calculated, and the amount of splitting has then been estimated by second-order perturbation theory. The result, while not in quantitative agreement with the measured splitting, lends plausibility to the assumed mechanism.

Herbst, Eric; Winnewisser, G.; Yamada, K. M. T.; Defrees, D. J.; Mclean, A. D.

1989-01-01

415

International Nuclear Information System (INIS)

Ab initio molecular orbital calculations on the structure and stability of the nitrate and sulfate complexes of uranyl (UO22+) and plutonyl (PuO22+) using effective core potentials are reported. It is found that the binding energy of sulfate is greater than that of nitrate to both uranyl and plutonyl, with a slight preference for plutonyl. A method of decomposing the binding energy into electrostatic, Pauli repulsion, polarization, and charge-transfer components is described which predicts that electrostatic forces are dominant. A simple molecular mechanics potential is developed by using this finding, which is successful in reproducing the ab initio results. 38 refs., 2 figs., 6 tabs

416

Variable temperature (-60 to -100 °C) studies of ethyldichlorophosphine, CH3CH2PCl2, of the infrared spectra (4000-400 cm-1) dissolved in liquid xenon have been carried out. From these data, the two conformers have been identified and the enthalpy difference has been determined between the more stable trans conformer and the less stable gauche form to be 88 ± 9 cm-1 (1.04 ± 0.11 kJ/mol). The percentage of abundance of the gauche conformer is estimated to be 57% at ambient temperature. The conformational stabilities have been predicted from ab initio calculations by utilizing many different basis sets up to aug-cc-pVTZ for both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been provided for both conformers which have been predicted by MP2(full)/6-31G(d) ab initio calculations to predict harmonic force fields, wavenumbers of the fundamentals, infrared intensities, Raman activities and depolarization ratios for both conformers. Estimated r0 structural parameters have been obtained from adjusted MP2(full)/6-311 + G(d,p) calculations. The results are discussed and compared to the corresponding properties of some related molecules.

Darkhalil, Ikhlas D.; Paquet, Charles; Waqas, Mohammad; Gounev, Todor K.; Durig, James R.

2015-02-01

417

Density functional tight binding: values of semi-empirical methods in an ab initio era.

Semi-empirical (SE) methods are derived from Hartree-Fock (HF) or Density Functional Theory (DFT) by neglect and approximation of electronic integrals. Thereby, parameters are introduced which have to be determined from reference calculations and/or by fitting to available experimental data. This leads to computational methods that are about 2-3 orders of magnitude faster than the standard HF/DFT methods using medium sized basis sets while being about 3 orders of magnitude slower than empirical force field methods (Molecular Mechanics: MM). Therefore, SE methods are most appropriate for a specific range of applications. These include the study of systems that contain a large number of atoms and therefore being too large for ab initio or DFT methods and also problems where dynamic or entropic effects are particularly important. In the latter case, the errors made by considering a very limited number of molecular structures or neglecting entropic contributions can be much larger than the accuracy lost due to the use of SE methods. Another area where SE methods are attractive concerns the analysis of systems for which reliable MM models are not readily available. Therefore, even in an era when rapid progress is being made in ab initio methods, there is considerable interest in further developing SE methods. We illustrate this point by focusing on the discussion of recent development and application of the Density Functional Tight Binding method. PMID:24850383

Cui, Qiang; Elstner, Marcus

2014-07-28

418

Ab initio quantum chemistry in parallel-portable tools and applications

Energy Technology Data Exchange (ETDEWEB)

In common with many of the computational sciences, ab initio chemistry faces computational constraints to which a partial solution is offered by the prospect of highly parallel computers. Ab initio codes are large and complex (O(10{sup 5}) lines of FORTRAN), representing a significant investment of communal effort. The often conflicting requirements of portability and efficiency have been successfully resolved on vector computers by reliance on matrix oriented kernels. This proves inadequate even upon closely-coupled shared-memory parallel machines. We examine the algorithms employed during a typical sequence of calculations. Then we investigate how efficient portable parallel implementations may be derived, including the complex multi-reference singles and doubles configuration interaction algorithm. A portable toolkit, modeled after the Intel iPSC and the ANL-ACRF PARMACS, is developed, using shared memory and TCP/IP sockets. The toolkit is used as an initial platform for programs portable between LANS, Crays and true distributed-memory MIMD machines. Timings are presented. 53 refs., 4 tabs.

Harrison, R.J.; Shepard, R. (Argonne National Lab., IL (United States)); Kendall, R.A. (Battelle Pacific Northwest Lab., Richland, WA (United States))

1991-01-01

419

Nonadiabatic ab initio molecular dynamics including spin-orbit coupling and laser fields.

Nonadiabatic ab initio molecular dynamics (MD) including spin-orbit coupling (SOC) and laser fields is investigated as a general tool for studies of excited-state processes. Up to now, SOCs are not included in standard ab initio MD packages. Therefore, transitions to triplet states cannot be treated in a straightforward way. Nevertheless, triplet states play an important role in a large variety of systems and can now be treated within the given framework. The laser interaction is treated on a non-perturbative level that allows nonlinear effects like strong Stark shifts to be considered. As MD allows for the handling of many atoms, the interplay between triplet and singlet states of large molecular systems will be accessible. In order to test the method, IBr is taken as a model system, where SOC plays a crucial role for the shape of the potential curves and thus the dynamics. Moreover, the influence of the nonresonant dynamic Stark effect is considered. The latter is capable of controlling reaction barriers by electric fields in time-reversible conditions, and thus a control laser using this effect acts like a photonic catalyst. In the IBr molecule, the branching ratio at an avoided crossing, which arises from SOC, can be influenced. PMID:22452086

Marquetand, Philipp; Richter, Martin; González-Vázquez, Jesús; Sola, Ignacio; González, Leticia

2011-01-01

420

A means to take advantage of molecular similarity to lower the computational cost of electronic structure theory is proposed, in which parameters are embedded into a low-cost, low-level (LL) ab initio theory and adjusted to obtain agreement with a higher level (HL) ab initio theory. This approach is explored by training such a model on data for ethane and testing the resulting model on methane, propane and butane. The electronic distribution of the molecules is varied by placing them in strong electrostatic environments consisting of random charges placed on the corners of a cube. The results find that parameters embedded in HF/STO-3G theory can be adjusted to obtain agreement, to within about 2 kcal/mol, with results of HF/6-31G theory. Obtaining this level of agreement requires the use of parameters that are functions of the bond lengths, atomic charges, and bond orders within the molecules. The argument is made that this approach provides a well-controlled means to take advantage of molecular similarity in...

Tanha, Matteus; Cappiello, Alex; Gordon, Geoffrey J; Yaron, David J

2013-01-01

421

International Nuclear Information System (INIS)

We have calculated the intermolecular interaction energies of the chloroform dimer in 12 orientations using the second-order Møller-Plesset perturbation theory. Single point energies of important geometries were calibrated by the coupled cluster with single and double and perturbative triple excitation method. Dunning's correlation consistent basis sets up to aug-cc-pVQZ have been employed in extrapolating the interaction energies to the complete basis set limit values. With the ab initio potential data we constructed a 5-site force field model for molecular dynamics simulations. We compared the simulation results with recent experiments and obtained quantitative agreements for the detailed atomwise radial distribution functions. Our results were also consistent with previous results using empirical force fields with polarization effects. Moreover, the calculated diffusion coefficients reproduced the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with existing empirical force fields for liquid chloroform

422

Ab-initio calculations of spin tunneling through an indirect barrier

Directory of Open Access Journals (Sweden)

Full Text Available Abstract We use a fully relativistic layer Green's functions approach to investigate spin-dependent tunneling through a symmetric indirect band gap barrier like GaAs/AlAs/GaAs heterostructure along [100] direction. The method is based on Linear Muffin Tin Orbitals and it is within the Density Functional Theory (DFT in the Local Density Approximation (LDA. We find that the results of our ab-initio calculations are in good agreement with the predictions of our previous empirical tight binding model [Phys. Rev. B, 075313 (2006]. In addition we show the k||-dependence of the spin polarization which we did not previously include in the model. The ab-initio calculations indicate a strong k||-dependence of the transmission and the spin polarization due to band non-parabolicity. A large window of 25–50% spin polarization was found for a barrier of 8 AlAs monolayers at k|| = 0.03 2?/a. Our calculations show clearly that the appearance of energy windows with significant spin polarization depends mostly on the location of transmission resonances and their corresponding zeros and not on the magnitude of the spin splitting in the barrier. PACS Codes: 71.70.Ej, 71.15.Mb, 71.55.Eq

Sandu Titus

2008-06-01

423

Variable temperature (-60 to -100 °C) studies of ethyldichlorophosphine, CH3CH2PCl2, of the infrared spectra (4000-400 cm(-1)) dissolved in liquid xenon have been carried out. From these data, the two conformers have been identified and the enthalpy difference has been determined between the more stable trans conformer and the less stable gauche form to be 88±9 cm(-1) (1.04±0.11 kJ/mol). The percentage of abundance of the gauche conformer is estimated to be 57% at ambient temperature. The conformational stabilities have been predicted from ab initio calculations by utilizing many different basis sets up to aug-cc-pVTZ for both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been provided for both conformers which have been predicted by MP2(full)/6-31G(d) ab initio calculations to predict harmonic force fields, wavenumbers of the fundamentals, infrared intensities, Raman activities and depolarization ratios for both conformers. Estimated r0 structural parameters have been obtained from adjusted MP2(full)/6-311+G(d,p) calculations. The results are discussed and compared to the corresponding properties of some related molecules. PMID:24618201

Darkhalil, Ikhlas D; Paquet, Charles; Waqas, Mohammad; Gounev, Todor K; Durig, James R

2015-02-01

424

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.

Han, Huixian; Li, Anyang; Guo, Hua

2014-12-01

425

The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without resorting to experiment. The global minimum of eclipsed C_s symmetry is characterized by a significantly bent hydrogen bond which deviates from linearity by about 20 degrees. In addition, the so-called cyclic C_{2h} structure is extremely close in energy on an overall flat potential energy surface. It is demonstrated that none of the currently available (GGA, meta--GGA, and hybrid) density functionals satisfactorily describe the structure and relative energies of this nonlinear hydrogen bond. We present a novel density functional, HCTH/407+, designed to describe this sort of hydrogen bond quantitatively on the level of the dimer, contrary to e.g. the widely used BLYP functional. This improved functional is employed in Car-Parrinello ab initio molecular dynamics simulations of liq...

Boese, A D; Martin, J M L; Marx, D; Chandra, Amalendu; Martin, Jan M.L.; Marx, Dominik

2003-01-01

426

Ab initio molecular dynamics study of dissociation of water under an electric field.

The behavior of liquid water under an electric field is a crucial phenomenon in science and engineering. However, its detailed description at a microscopic level is difficult to achieve experimentally. Here we report on the first ab initio molecular-dynamics study on water under an electric field. We observe that the hydrogen-bond length and the molecular orientation are significantly modified at low-to-moderate field intensities. Fields beyond a threshold of about 0.35??V/Å are able to dissociate molecules and sustain an ionic current via a series of correlated proton jumps. Upon applying even more intense fields (?1.0??V/Å), a 15%-20% fraction of molecules are instantaneously dissociated and the resulting ionic flow yields a conductance of about 7.8???-1?cm-1, in good agreement with experimental values. This result paves the way to quantum-accurate microscopic studies of the effect of electric fields on aqueous solutions and, thus, to massive applications of ab initio molecular dynamics in neurobiology, electrochemistry, and hydrogen economy. PMID:23003187

Saitta, A Marco; Saija, Franz; Giaquinta, Paolo V

2012-05-18

427

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

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

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

2015-04-01

428

Ab initio predictions of the structures and spectra of some simple thiosulfeno (XS2) free radicals

International Nuclear Information System (INIS)

Ab initio theory with split-valence plus polarization function and larger basis sets at the self-consistent field (SCF) and second order Moller--Plesset (UMP2) levels was used to predict the geometries and spectroscopic parameters for the ground and first excited electronic states of the HS2, FS2, and ClS2 free radicals. The ground-state species are predicted to be bent and may be described as having a sulfur--sulfur double bond, a sulfur-substituent single bond, and an unpaired electron which is delocalized principally over the sulfur centers. The first electronic transition involves an (n,?*) electron promotion which leads to a longer S--S bond, smaller bond angle, and greater localization of the unpaired electron on the terminal sulfur atom. The adiabatic transition energies are predicted to be at ?6700, 13 700, and 10 600 cm-1 for HS2, FS2, and ClS2, respectively. The theoretical results are in good agreement with the rather limited amount of experimental data available. These ab initio predictions provide critical information to aid in future experimental studies of the matrix isolation or gas-phase spectra of the thiosulfeno radicals

429

Ab Initio periodic Hartree-Fock study of group IA cations in ANA-type zeolites

International Nuclear Information System (INIS)

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

430

Comment on 'Shear stiffness in nanolaminar Ti3SiC2 challenges ab initio calculations'

International Nuclear Information System (INIS)

In a recent publication by Kisi et al (2010 J. Phys.: Condens. Matter 22 162202) the authors present experimentally measured elastic constants for the Mn+1AXn (MAX) phase, Ti3SiC2, that differ from density functional theory calculations. They then conclude that 'prediction [by ab initio calculation] of the full elasticity tensor for Ti3SiC2 has not been successful'. However the authors do not compare with previous experimental work in which Finkel et al measure the elastic moduli (Finkel et al 2000 J. Appl. Phys. 87 1701). The predictions of ab initio calculations (Yu et al 2005 J. Mater. Res. 20 1180) agree with the measurements of Finkel et al as well as with most other experimentally measured elastic moduli for MAX phases (Cover et al 2008 10 935; Cover et al 2009 J. Phys.: Condens. Matter 21 305403). The unrealistically high value of the C44 constant obtained by Kisi et al, which would mean that Ti3SiC2 is almost as resistant to shear as diamond, undermines confidence in their results. (comment)

431

Comment on 'Shear stiffness in nanolaminar Ti3SiC2 challenges ab initio calculations'

In a recent publication by Kisi et al (2010 J. Phys.: Condens. Matter 22 162202) the authors present experimentally measured elastic constants for the Mn + 1AXn (MAX) phase, Ti3SiC2, that differ from density functional theory calculations. They then conclude that 'prediction [by ab initio calculation] of the full elasticity tensor for Ti3SiC2 has not been successful'. However the authors do not compare with previous experimental work in which Finkel et al measure the elastic moduli (Finkel et al 2000 J. Appl. Phys. 87 1701). The predictions of ab initio calculations (Yu et al 2005 J. Mater. Res. 20 1180) agree with the measurements of Finkel et al as well as with most other experimentally measured elastic moduli for MAX phases (Cover et al 2008 10 935; Cover et al 2009 J. Phys.: Condens. Matter 21 305403). The unrealistically high value of the C44 constant obtained by Kisi et al, which would mean that Ti3SiC2 is almost as resistant to shear as diamond, undermines confidence in their results.

Cover, M. F.; Bilek, M. M. M.; McKenzie, D. R.

2011-07-01

432

Ionization dynamics of the water trimer: A direct ab initio MD study

International Nuclear Information System (INIS)

Highlights: ? We calculated ionization dynamics of water trimer. ? Direct ab initio molecular dynamics (MD) method is applied. ? Proton transfer dynamics were discussed. ? The proton transfer process calculated are well reproduced in recent experiments. - Abstract: Ionization dynamics of the cyclic water trimer (H2O)3 have been investigated by means of direct ab initio molecular dynamics (AIMD) method. Two reaction channels, complex formation and OH dissociation, were found following the ionization of (H2O)3. In both channels, first, a proton was rapidly transferred from H2O+ to H2O (time scale is ?15 fs after the ionization). In complex channel, an ion–radical contact pair (H3O+–OH) solvated by the third water molecule was formed as a long-lived H3O+(OH)H2O complex. In OH dissociation channel, the second proton transfer further takes place from H3O+(OH) to H2O (time scale is 50–100 fs) and the OH radical is separated from the H3O+. At the same time, the OH dissociation takes place when the excess energy is efficiently transferred into the kinetic energy of OH radical. The OH dissociation channel is significantly minor, and almost all product channels were the complex formation. The reaction mechanism was discussed on the basis of theoretical results

433

Ab Initio Study of Hot Carriers in the First Picosecond after Sunlight Absorption in Silicon

Hot carrier thermalization is a major source of efficiency loss in solar cells. Because of the subpicosecond time scale and complex physics involved, a microscopic characterization of hot carriers is challenging even for the simplest materials. We develop and apply an ab initio approach based on density functional theory and many-body perturbation theory to investigate hot carriers in semiconductors. Our calculations include electron-electron and electron-phonon interactions, and require no experimental input other than the structure of the material. We apply our approach to study the relaxation time and mean free path of hot carriers in Si, and map the band and k dependence of these quantities. We demonstrate that a hot carrier distribution characteristic of Si under solar illumination thermalizes within 350 fs, in excellent agreement with pump-probe experiments. Our work sheds light on the subpicosecond time scale after sunlight absorption in Si, and constitutes a first step towards ab initio quantification of hot carrier dynamics in materials.

Bernardi, Marco; Vigil-Fowler, Derek; Lischner, Johannes; Neaton, Jeffrey B.; Louie, Steven G.

2014-06-01

434

FTIR and FTRaman spectra, assignments, ab initio HF and DFT analysis of 4-nitrotoluene

In this work, the experimental and theoretical study on molecular structure and vibrational spectra of 4-nitrotoluene are studied. The FTIR and FTRaman experimental spectra of the molecule have been recorded in the range of 4000-100 cm -1. Making use of the recorded data, the complete vibrational assignments are made and analysis of the observed fundamental bands of molecule is carried out. The experimental determinations of vibrational frequencies are compared with those obtained theoretically from ab initio HF and DFT quantum mechanical calculations using HF/6-31G (d, p), B3LYP/6-31++G* (d, p) and B3LYP/6-311++G* (d, p) methods. The differences between the observed and scaled wave number values of most of the fundamentals are very small in B3LYP than HF. The geometries and normal modes of vibrations obtained from ab initio HF and B3LYP calculations are in good agreement with the experimentally observed data. Comparison of the simulated spectra provides important information about the ability of the computational method (B3LYP) to describe the vibrational modes. The vibrations of NO 2 and CH 3 groups coupled with skeletal vibrations are also investigated.

Ramalingam, S.; Periandy, S.; Govindarajan, M.; Mohan, S.

2010-04-01

435

Ab initio molecular dynamics study of dissociation of water under an electric field

The behavior of liquid water under an electric field is a crucial phenomenon in science and engineering. However, its detailed description at a microscopic level is difficult to achieve experimentally. Here we report on the first ab initio molecular-dynamics study on water under an electric field. We observe that the hydrogen-bond length and the molecular orientation are significantly modified at low-to-moderate field intensities. Fields beyond a threshold of about 0.35 V/\\AA are able to dissociate molecules and sustain an ionic current via a series of correlated proton jumps. Upon applying even more intense fields (1.0 V/\\AA), a 15-20% fraction of molecules are instantaneously dissociated and the resulting ionic flow yields a conductance of about 7.8 $\\Omega^{-1}cm^{-1}$, in good agreement with experimental values. This result paves the way to quantum-accurate microscopic studies of the effect of electric fields on aqueous solutions and, thus, to massive applications of ab initio molecular dynamics in neurob...

Saitta, A Marco; Giaquinta, Paolo V

2012-01-01

436

Energy Technology Data Exchange (ETDEWEB)

The objective of the FP6 Perfect Project was to develop a first example of integrated multiscale computational models, capable of describing the effects of irradiation in nuclear reactor components, namely vessel and internals. The use of ab initio techniques to study, in the most reliable way currently possible, atomic-level interactions between species and defects, and the transfer of this knowledge to interatomic potentials, of use for large scale dynamic simulations, lie at the core of this effort. The target materials of the Project were bainitic steels (vessel) and austenitic steels (internals), i.e. iron alloys. In this article, the advances made within the Project in the understanding of defect properties in Fe alloys, by means of ab initio calculations, and in the development of interatomic potentials for Fe and Fe alloys are overviewed, thereby providing a reference basis for further progress in the field. Emphasis is put in showing how the produced data have enhanced our level of understanding of microstructural processes occurring under irradiation in model alloys and steels used in existing nuclear power plants.

Malerba, L., E-mail: lmalerba@sckcen.b [Structural Materials Group, Institute of Nuclear Materials Science, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Ackland, G.J. [School of Physics, CSEC and SUPA, Univ. of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ (United Kingdom); Becquart, C.S. [Unite de Materiaux et Techniques, UMR 8207, Universite Lille-1, F-59655 Villeneuve d' Ascq Cedex (France); Bonny, G. [Structural Materials Group, Institute of Nuclear Materials Science, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Domain, C. [Dept. MMC, EDF-R and D, Site des Renardieres, F-77218 Moret-sur-Loing (France); Dudarev, S.L. [EURATOM/UKAEA Fusion Association, Culham Science Centre, Oxfordshire OX14 3DB (United Kingdom); Fu, C.-C. [CEA, DEN, Service de Recherches de Metallurgie Physique, F- 91191 Gif-sur-Yvette (France); Hepburn, D. [School of Physics, CSEC and SUPA, Univ. of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ (United Kingdom); Marinica, M.C. [CEA, DEN, Service de Recherches de Metallurgie Physique, F- 91191 Gif-sur-Yvette (France); Olsson, P. [Dept. MMC, EDF-R and D, Site des Renardieres, F-77218 Moret-sur-Loing (France); Pasianot, R.C. [CAC-CNEA, Depto. de Materiales, Avda. Gral. Paz 1499, 1650 San Martin, Pcia. Buenos Aires (Argentina); CONICET, Avda. Rivadavia 1917, 1033 Buenos Aires (Argentina); Raulot, J.M. [Institut Superieur de Genie Mecanique et Productique, UMR CNRS 7078, Bat. B, Ile du Saulcy, F57045 Metz, Cedex 1 (France); Terentyev, D. [Structural Materials Group, Institute of Nuclear Materials Science, SCK-CEN, Boeretang 200, B-2400 Mol (Belgium); Vincent, E. [Unite de Materiaux et Techniques, UMR 8207, Universite Lille-1, F-59655 Villeneuve d' Ascq Cedex (France); Dept. MMC, EDF-R and D, Site des Renardieres, F-77218 Moret-sur-Loing (France); Soisson, F.; Willaime, F. [CEA, DEN, Service de Recherches de Metallurgie Physique, F- 91191 Gif-sur-Yvette (France)

2010-11-01

437

Ab initio quantum chemistry in parallel-portable tools and applications

International Nuclear Information System (INIS)

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(105) 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

438

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. PMID:25554156

Han, Huixian; Li, Anyang; Guo, Hua

2014-12-28

439

Energy Technology Data Exchange (ETDEWEB)

We have calculated the intermolecular interaction energies of the chloroform dimer in 12 orientations using the second-order Møller-Plesset perturbation theory. Single point energies of important geometries were calibrated by the coupled cluster with single and double and perturbative triple excitation method. Dunning's correlation consistent basis sets up to aug-cc-pVQZ have been employed in extrapolating the interaction energies to the complete basis set limit values. With the ab initio potential data we constructed a 5-site force field model for molecular dynamics simulations. We compared the simulation results with recent experiments and obtained quantitative agreements for the detailed atomwise radial distribution functions. Our results were also consistent with previous results using empirical force fields with polarization effects. Moreover, the calculated diffusion coefficients reproduced the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with existing empirical force fields for liquid chloroform.

Yin, Chih-Chien; Li, Arvin Huang-Te; Chao, Sheng D., E-mail: sdchao@spring.iam.ntu.edu.tw [Institute of Applied Mechanics, National Taiwan University, Taipei 106, Taiwan (China)

2013-11-21

440

Estudio ab initio del mecanismo de la reacción HSO + O3

La reacción entre el radical HSO y el ozono ha sido ampliamente estudiada desde el punto de vista experimental debido a la importancia que tiene el radical HSO en la oxidación de los compuestos de azufre reductores y a que puede contribuir a la producción de H2SO4 [1-4]. Se realizaron diversos estudios teóricos sobre la cinética de la reacción entre el radical HSO y el ozono. La reacción del HSO con el ozono presenta tres canales diferentes : HSO + O3 &rightarrow &HSO2 + O2 &rightarrow &HS + 2 O2 &rightarrow &SO + OH + O2 La controversia existente entre los grupos experimentales sobre cuál de las tres vías es la predominante, se ha resuelto mediante un estudio teórico de todas ellas utilizando métodos ab initio. La estructura de todos los reactivos, productos, intermedios y estados de transición ha sido optimizada a nivel ab initio utilizando los métodos UMP2 /6-31G** y QCISD/6-31G**.

Nebot Gil, I.

441

International Nuclear Information System (INIS)

The applicability of ab initio multireference wavefunction-based methods to the study of magnetic complexes has been restricted by the quickly rising active-space requirements of oligonuclear systems and dinuclear complexes with S > 1 spin centers. Ab initio density matrix renormalization group (DMRG) methods built upon an efficient parameterization of the correlation network enable the use of much larger active spaces, and therefore may offer a way forward. Here, we apply DMRG-CASSCF to the dinuclear complexes [Fe2OCl6]2? and [Cr2O(NH3)10]4+. After developing the methodology through systematic basis set and DMRG M testing, we explore the effects of extended active spaces that are beyond the limit of conventional methods. We find that DMRG-CASSCF with active spaces including the metal d orbitals, occupied bridging-ligand orbitals, and their virtual double shells already capture a major portion of the dynamic correlation effects, accurately reproducing the experimental magnetic coupling constant (J) of [Fe2OCl6]2? with (16e,26o), and considerably improving the smaller active space results for [Cr2O(NH3)10]4+ with (12e,32o). For comparison, we perform conventional MRCI+Q calculations and find the J values to be consistent with those from DMRG-CASSCF. In contrast to previous studies, the higher spin states of the two systems show similar deviations from the Heisenberg spectrum, regardless of the computational method

442

Embedding parameters in ab initio theory to develop approximations based on molecular similarity

A means to take advantage of molecular similarity to lower the computational cost of electronic structure theory is explored, in which parameters are embedded into a low-cost, low-level (LL) ab initio model and adjusted to obtain agreement with results from a higher-level (HL) ab initio model. A parametrized LL (pLL) model is created by multiplying selected matrix elements of the Hamiltonian operators by scaling factors that depend on element types. Various schemes for applying the scaling factors are compared, along with the impact of making the scaling factors linear functions of variables related to bond lengths, atomic charges, and bond orders. The models are trained on ethane and ethylene, substituted with -NH2, -OH and -F, and tested on substituted propane, propylene and t-butane. Training and test datasets are created by distorting the molecular geometries and applying uniform electric fields. The fitted properties include changes in total energy arising from geometric distortions or applied fields, an...

Tanha, Matteus; Kaul, Shiva; Cappiello, Alexander; Gordon, Geoffrey J; Yaron, David J

2015-01-01

443

Ab Initio Based Understanding of the Segregation and Diffusion Mechanisms of Hydrogen in Steels

A microscopic understanding of the processes that lead to hydrogen embrittlement is of critical importance for developing new generations of high-strength steels. With this article, we provide an overview of insights that can be gained from ab initio based methods when investigating the segregation and diffusion mechanisms of hydrogen in steels. We first discuss the solubility and diffusion behavior of hydrogen in the ferrite, austenite, and martensite phases. We consider not only defect-free bulk phases but also the influence of alloying elements and geometric defects such as vacancies and grain boundaries. In the second part, the behavior of hydrogen in the presence of precipitates, the solubility, the surface absorption, and the influence of hydrogen on the interface cohesion are studied. Finally, we provide simulation results for the interaction of hydrogen with dislocations. For all these applications, we will comment on advantages and shortcomings of ab initio methods and will demonstrate how the obtained data and insights can complement experimental approaches to extract general trends and to identify causes of hydrogen embrittlement.

Hickel, T.; Nazarov, R.; McEniry, E. J.; Leyson, G.; Grabowski, B.; Neugebauer, J.

2014-08-01

444

We have calculated the intermolecular interaction energies of the chloroform dimer in 12 orientations using the second-order Møller-Plesset perturbation theory. Single point energies of important geometries were calibrated by the coupled cluster with single and double and perturbative triple excitation method. Dunning's correlation consistent basis sets up to aug-cc-pVQZ have been employed in extrapolating the interaction energies to the complete basis set limit values. With the ab initio potential data we constructed a 5-site force field model for molecular dynamics simulations. We compared the simulation results with recent experiments and obtained quantitative agreements for the detailed atomwise radial distribution functions. Our results were also consistent with previous results using empirical force fields with polarization effects. Moreover, the calculated diffusion coefficients reproduced the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with existing empirical force fields for liquid chloroform. PMID:24320333

Yin, Chih-Chien; Li, Arvin Huang-Te; Chao, Sheng D

2013-11-21

445

Deviational simulation of phonon transport in graphene ribbons with ab initio scattering

Energy Technology Data Exchange (ETDEWEB)

We present a deviational Monte Carlo method for solving the Boltzmann-Peierls equation with ab initio 3-phonon scattering, for temporally and spatially dependent thermal transport problems in arbitrary geometries. Phonon dispersion relations and transition rates for graphene are obtained from density functional theory calculations. The ab initio scattering operator is simulated by an energy-conserving stochastic algorithm embedded within a deviational, low-variance Monte Carlo formulation. The deviational formulation ensures that simulations are computationally feasible for arbitrarily small temperature differences, while the stochastic treatment of the scattering operator is both efficient and exhibits no timestep error. The proposed method, in which geometry and phonon-boundary scattering are explicitly treated, is extensively validated by comparison to analytical results, previous numerical solutions and experiments. It is subsequently used to generate solutions for heat transport in graphene ribbons of various geometries and evaluate the validity of some common approximations found in the literature. Our results show that modeling transport in long ribbons of finite width using the homogeneous Boltzmann equation and approximating phonon-boundary scattering using an additional homogeneous scattering rate introduces an error on the order of 10% at room temperature, with the maximum deviation reaching 30% in the middle of the transition regime.

Landon, Colin D.; Hadjiconstantinou, Nicolas G. [Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)

2014-10-28

446

Ab initio Reconstructions of the Shape of Cellobiose Dehydrogenase and its Domains in Solution

Three-dimensional low-resolution models of the biochemically and biotechno- logically significant enzyme cellobiose dehydrogenase (CDH) were predicted by advanced modeling approaches based on experimental one-dimensional low-resolution small-angle x-ray scattering (SAXS) data. In particular, the ab initio modeling program DAMMIN by Svergun was used to predict the shape of both the whole protein and the two major constituent units (heme and FAD domains). The validity of the approach applied was tested in a systematic way by a critical assessment of scattering profiles (scattering intensities, pair-distance distribution functions) and structural and hydrodynamic parameters (hydrated particle volume, radius of gyration, maximum particle diameter, sedimentation and diffusion coefficients) and a comparison to available experimental data. Obviously, the applied approach enables the prediction of the solution structure of both CDH and its domains with a high degree of probability, though the problem of shape uniqueness remains crucial, similar to the use of other solution methods. The obtained results demonstrate the possibility to unravel particle shapes by ab initio calculations, without knowledge of high-resolution data, and confirm earlier trial-and-error models.

Zipper, P.; Durchschlag, H.

2005-01-01

447

Ab Initio Nuclear Structure from Helium to Oxygen Final Report: 00-ERD-028

Energy Technology Data Exchange (ETDEWEB)

Final report for a research program in theoretical nuclear physics to develop methods and computer programs to perform ab initio calculations for light nuclei ranging from Helium to Oxygen. The method employed is based effective interaction theory within the framework of the shell model. The principal accomplishments were: (1) participation in the validation of ab initio for {sup 4}He; the first study of A = 6 nuclei with the realistic, non-local CD-Bonn potential; (2) a study of ''intruder'' states in {sup 8}Be, (3) the first shell-model calculations implementing three-body clusters in the effective interaction for nuclei with A > 4; (4) the discovery that two-nucleon interactions by themselves are inadequate to describe the structure of the nucleus {sup 10}B, which provides proof that three-nucleon forces affect nuclear structure; (5) first calculations including the Tucson-Melbourne three-nucleon force, which gives better agreement with the experimental spectrum for {sup 10}B and (6) the development of a new shell-model code designed for public release.

Ormand, W E; Navratil, P

2003-02-04

448

Ab initio SCF MO study of the chemisorption of methane on Al and La oxide surfaces

Energy Technology Data Exchange (ETDEWEB)

A theoretical approach to the rate-determining step for methane activation on Al and La oxides has been performed by means of ab initio quantum mechanical calculations. In a first approach, transition states and products for the heterolytic chemisorption of CH{sub 4} on Al(OH){sub 3} and La(OH){sub 3} molecules have been determined at the RHF-SCF level of theory. Transition-state structures correspond to a four-center interaction with an energy barrier of about 40 kcal/mol. This high activation barrier supports the heterolytic mechanism proposed for this reaction. The products are methyl-metal compounds, CH{sub 3}-Me(Me= Al, La), with the carbon atom negatively charged. Catalytic surfaces have been modeled by introducing the effects due to the lattice through both point charges and ab initio model potentials. The selectivity of these catalysts towards C2 is discussed on the grounds of the differences found for the relative stability of the methy-metal intermediates. 42 refs., 4 figs., 2 tabs.

Capitan, M.J.; Odriozola, J.A.; Marquez, A. [Univ. of Sevilla (Spain)] [and others

1995-10-01

449

Can an ab initio three-body virial equation describe the mercury gas phase?

We report a sixth-order ab initio virial equation of state (EOS) for mercury. The virial coefficients were determined in the temperature range from 500 to 7750 K using a three-body approximation to the N-body interaction potential. The underlying two-body and three-body potentials were fitted to highly accurate Coupled-Cluster interaction energies of Hg2 (Pahl, E.; Figgen, D.; Thierfelder, C.; Peterson, K. A.; Calvo, F.; Schwerdtfeger, P. J. Chem. Phys. 2010, 132, 114301-1) and equilateral-triangular configurations of Hg3. We find the virial coefficients of order four and higher to be negative and to have large absolute values over the entire temperature range considered. The validity of our three-body, sixth-order EOS seems to be limited to small densities of about 1.5 g cm(-3) and somewhat higher densities at higher temperatures. Termwise analysis and comparison to experimental gas-phase data suggest a small convergence radius of the virial EOS itself as well as a failure of the three-body interaction model (i.e., poor convergence of the many-body expansion for mercury). We conjecture that the nth-order term of the virial EOS is to be evaluated from the full n-body interaction potential for a quantitative picture. Consequently, an ab initio three-body virial equation cannot describe the mercury gas phase. PMID:24547987

Wiebke, J; Wormit, M; Hellmann, R; Pahl, E; Schwerdtfeger, P

2014-03-27

450

VASP-E: specificity annotation with a volumetric analysis of electrostatic isopotentials.

Algorithms for comparing protein structure are frequently used for function annotation. By searching for subtle similarities among very different proteins, these algorithms can identify remote homologs with similar biological functions. In contrast, few comparison algorithms focus on specificity annotation, where the identification of subtle differences among very similar proteins can assist in finding small structural variations that create differences in binding specificity. Few specificity annotation methods consider electrostatic fields, which play a critical role in molecular recognition. To fill this gap, this paper describes VASP-E (Volumetric Analysis of Surface Properties with Electrostatics), a novel volumetric comparison tool based on the electrostatic comparison of protein-ligand and protein-protein binding sites. VASP-E exploits the central observation that three dimensional solids can be used to fully represent and compare both electrostatic isopotentials and molecular surfaces. With this integrated representation, VASP-E is able to dissect the electrostatic environments of protein-ligand and protein-protein binding interfaces, identifying individual amino acids that have an electrostatic influence on binding specificity. VASP-E was used to examine a nonredundant subset of the serine and cysteine proteases as well as the barnase-barstar and Rap1a-raf complexes. Based on amino acids established by various experimental studies to have an electrostatic influence on binding specificity, VASP-E identified electrostatically influential amino acids with 100% precision and 83.3% recall. We also show that VASP-E can accurately classify closely related ligand binding cavities into groups with different binding preferences. These results suggest that VASP-E should prove a useful tool for the characterization of specific binding and the engineering of binding preferences in proteins. PMID:25166865

Chen, Brian Y

2014-08-01

451

A combinatorial screening procedure was used for the selection of polymer precursors in the preparation of molecularly imprinted polymer (MIP), which is useful in the detection of the air pollution marker molecule benzo[a]pyrene (BAP). Molecular imprinting is a technique for the preparation of polymer materials with specific molecular recognition receptors. The preparation of imprinted polymers requires polymer precursors such as functional monomer, cross-linking monomer, solvent, an initiator of polymerization and thermal or UV radiation. A virtual library of functional monomers was prepared based on interaction binding scores computed using HyperChem Release 8.0 software. Initially, the possible minimum energy conformation of the monomers and BAP were optimized using the semi-empirical (PM3) quantum method. The binding energy between the functional monomer and the template (BAP) was computed using the Hartree-Fock (HF) method with 6-31 G basis set, which is an ab initio approach based on Moller-Plesset second order perturbation theory (MP2). From the computations, methacrylic acid (MAA) and ethylene glycol dimethacrylate (EGDMA) were selected for preparation of BAP imprinted polymer. The larger interaction energy (?E) represents possibility of more affinity binding sites formation in the polymer, which provides high binding capacity. The theoretical predictions were complimented through adsorption experiments. There is a good agreement between experimental binding results and theoretical computations, which provides further evidence of the validity of the usefulness of computational screening procedures in the selection of appropriate MIP precursors in an experiment-free way. PMID:21877152

Khan, Muntazir S; Wate, Prateek S; Krupadam, Reddithota J

2012-05-01

452

International Nuclear Information System (INIS)

This paper discuss basics of high performance computing on the example of the Latvian SuperCluster (LASC), installed at the Institute of Solid State Physics of the University of Latvia. The application of LASC to ab-initio simulations of x-ray absorption spectra from nanoparticles is considered as a particular case. (author)

453

Czech Academy of Sciences Publication Activity Database

Ro?. 43, ?. 17 (2010), s. 175203. ISSN 0953-4075 R&D Projects: GA MŠk OC09079; GA MŠk(CZ) OC10046; GA ?R 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

?ársky, Petr

2010-01-01

454

Czech Academy of Sciences Publication Activity Database

Ro?. 43, ?. 17 (2010), s. 175204. ISSN 0953-4075 R&D Projects: GA MŠk OC09079; GA MŠk(CZ) OC10046; GA ?R 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

?ársky, Petr

2010-01-01

455

International Nuclear Information System (INIS)

Iterative ab initio structure solution algorithms were tested on their performance power in phasing diffraction data. Statistical investigations on the reproducibility of the recovered phases allow an estimate about the reliability of the results. The working principle is demonstrated on synthetic structures and on experimental diffraction data of decagonal AlCuCo, AlFeNi and AlCoNi quasicrystals.

456

Czech Academy of Sciences Publication Activity Database

Ro?. 105, ?. 34 (2001), s. 8086-8092. ISSN 0305-4470 R&D Projects: GA AV ?R IAA4050702; GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : palladium square-planar complexes * platinum analogues * ab initio Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.542, year: 2001

Zeizinger, M.; Burda, J. V.; Šponer, Ji?í; Kapsa, V.; Leszczynski, J.

2001-01-01

457

Energy Technology Data Exchange (ETDEWEB)

Iterative ab initio structure solution algorithms were tested on their performance power in phasing diffraction data. Statistical investigations on the reproducibility of the recovered phases allow an estimate about the reliability of the results. The working principle is demonstrated on synthetic structures and on experimental diffraction data of decagonal AlCuCo, AlFeNi and AlCoNi quasicrystals.

Fleischer, F; Weber, T; Steurer, W, E-mail: frank.fleischer@mat.ethz.c [Laboratory of Crystallography, Department of Materials, ETH Zurich, 8093 Zurich (Switzerland)

2010-04-01

458

Czech Academy of Sciences Publication Activity Database

Ro?. 3, ?. 15 (2012), s. 2021-2024. ISSN 1948-7185 R&D Projects: GA ?R GA203/08/0114 Institutional research plan: CEZ:AV0Z40550506 Keywords : guanidinium * ion pairing * ab initio molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.585, year: 2012

Vazdar, Mario; Uhlig, Frank; Jungwirth, Pavel

2012-01-01

459

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. PMID:23760925

Zhang, Yang

2014-02-01

460

Energy Technology Data Exchange (ETDEWEB)

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.

Jursic, B.S. [Univ. of New Orleans, LA (United States)

1996-12-31

461

Czech Academy of Sciences Publication Activity Database

Ro?. 44, MAR (2014), s. 62-69. ISSN 0364-5916 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081723 Keywords : laves phases * V-Zr system * ab initio calculations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.394, year: 2013

Štrof, J.; Pavl?, Jana; Wdowik, U.; Buršík, Ji?í; Šob, Mojmír; V?eš?ál, Jan

2014-01-01

462

Ab initio nuclear shielding parameters and spin-rotation coupling constants of FBO, ClBO and FBS

Ab initio nuclear shielding parameters and nuclear spin-rotation coupling constants of FBO, ClBO and FBS have been calculated using the multi-configuration self consistent field (MCSCF) method. The dependence of these parameters upon the basis set and active space employed in the calculation was investigated. The results are compared with the experimental values obtained from microwave spectra.

Gatehouse, Bethany

1998-05-01

463

Czech Academy of Sciences Publication Activity Database

Ljubljana, 2009. s. 14-14. [Workshop of the Associated Phase Diagram and Thermodynamic Committee /11./. 18.09.2009-20.09.2009, Ljubljana] Institutional research plan: CEZ:AV0Z20410507 Keywords : ab initio calculations * Laves phases * thermodynamic modelling Subject RIV: BJ - Thermodynamics

Pavl?, Jana; V?eš?ál, Jan; Šob, Mojmír

464

By means of ab initio calculations and kinetic Monte Carlo simulations we demonstrate that the indirect interaction mediated by conduction electrons of nonmagnetic metallic substrate could stabilize magnetic order of ensemble of magnetic nanoclusters at high temperatures. We especially focus on the conditions necessary for such magnetic ordering.

Ignatiev, P. A.; Negulyaev, N. N.; Smirnov, A. S.; Niebergall, L.; Saletsky, A. M.; Stepanyuk, V. S.

2009-10-01

465

Acidity of HOCH, HSCN, HNCO, HNCS: a treatment from the viewpoint of ab initio approach

The electronic structures of the molecules HOCN, HSCN, HNCO, HNCS and the anions [OCN]-, [SCN]- have been investigated ab initio at the RHF/6-31G(d), RHF/6-31G(d,p), MP2/6-31G(d)//RHF/6-31G(d) and MP2/6-31G(d,p)//RHF/6-31G(d,p) theory levels. The thermodynamic stability of the HNCO and HNCS molecules was shown to be higher than that of the HOCH and HSCN molecules, respectively.The following series of the alteration of the protolytes strength HSCN > HOCH, HNCS > HNCO, HOCN > HNCO, HSCN > HNCS ...

Pankratov, Alexei N.; Khmelev, Sergei S.

2005-01-01

466

Ab initio study of nitrogen-multisubstituted neutral and positively charged C{sub 20} fullerene

Energy Technology Data Exchange (ETDEWEB)

Ab initio investigation of structural and electronic properties of Nitrogen doped fullerenes, obtained from C{sub 20} by replacing up to 10 C atoms with N atoms, are studied by means of first principals density functional theory calculations using numerical orbitals as basis sets. We have obtained the ground state structures for C{sub 20?n}N{sub n} for n=1-10. While substituting nitrogen atoms, we cannot substitute more than 9 nitrogen atoms. Nitrogen doping in C20 shows a significant change in density of states. For a better comparison with experimental measurements, we have also considered some positively charged ions and report the differences between properties of these ions and the corresponding neutral molecules.

Rani, Anita, E-mail: ranianita64@gmail.com [Guru Nanak College for Girls, Sri Muktsar Sahib, Punjab-141002 (India); Kumar, Ranjan [Department of Physics, Panjab University, Chandigarh-160014 (India)

2014-04-24

467

Lattice thermal conductivity of UO2 using ab-initio and classical molecular dynamics

International Nuclear Information System (INIS)

We applied the non-equilibrium ab-initio molecular dynamics and predict the lattice thermal conductivity of the pristine uranium dioxide for up to 2000?K. We also use the equilibrium classical molecular dynamics and heat-current autocorrelation decay theory to decompose the lattice thermal conductivity into acoustic and optical components. The predicted optical phonon transport is temperature independent and small, while the acoustic component follows the Slack relation and is in good agreement with the limited single-crystal experimental results. Considering the phonon grain-boundary and pore scatterings, the effective lattice thermal conductivity is reduced, and we show it is in general agreement with the sintered-powder experimental results. The charge and photon thermal conductivities are also addressed, and we find small roles for electron, surface polaron, and photon in the defect-free structures and for temperatures below 1500?K

468

Ab initio correlated potential energy surfaces for monomeric sodium and potassium cyanides

Ab initio molecular orbital calculations using large Gaussian basis sets have been performed for NaCN and KCN with full geometry optimization. Potential energy surface obtained are sensitive to the quality of polarization functions used on C and N. A bent structure, as found experimentally for KCN, is the lowest energy geometry for both NaCN and KCN, with the isocyanide form only 5-6 kJ mol-1 higher at the SCF level. Inclusion of electron correlation using third-order perturbation theory leads to a substantial relative destabilization of the isocyanide form for the both NaCN and KCN, and improves agreement between observed and theoretical geometries for KCN.

Marsden, C. J.

1982-06-01

469

We calculate the electronic and optical excitations of polythiophene using the GW approximation for the electronic self-energy, and include excitonic effects by solving the electron-hole Bethe-Salpeter equation. Two different situations are studied: excitations on isolated chains and excitations on chains in crystalline polythiophene. The dielectric tensor for the crystalline situation is obtained by modeling the polymer chains as polarizable line objects, with a long-wavelength polarizability tensor obtained from the ab-initio polarizability function of the isolated chain. With this model dielectric tensor we construct a screened interaction for the crystalline case, including both intra- and interchain screening. In the crystalline situation both the quasi-particle band gap and the exciton binding energies are drastically reduced in comparison with the isolated chain. However, the optical gap is hardly affected. We expect this result to be relevant for conjugated polymers in general.

Van der Horst, J W; De Jong, P H L; Michels, M A J; Brocks, G; Kelly, P J

2000-01-01

470

Ab initio study of the uranyl oxide hydrates: a proton transfer mediated by water

We present a first-principles study of the UO3·n(H2O) uranyl oxide hydrates, namely, schoepite (n = 2.25), metaschoepite (n = 2) and dehydrated metaschoepite (n = 1.75), which appear as the alteration U(VI) products of aqueous corrosion of nuclear fuel. For these compounds, the calculated enthalpy of formation is in good agreement with calorimetry and solubility measurements. We discuss the key electronic state factors behind the phase stability of uranyl oxide hydrates. An unexplored proton-transfer mechanism, which produces the H3O hydronium ions in UO3·nH2O, has been studied using ab initio molecular dynamics simulations at room temperature. For the hydronium ion, a very short lifetime of around 20 fs has been suggested.

Ostanin, S.; Zeller, P.

2007-06-01

471

Ab initio calculations on magnetism induced by composite defects in magnesium oxide

The local magnetic state induced by the composite defects, composed of an oxygen vacancy and a nitrogen substituting oxygen, in magnesium oxide has been studied by using ab initio calculation based on density functional theory. The calculated results show that local magnetic moment can be induced by the composite defects around the oxygen vacancy, when the exchange split of the oxygen vacancy is enhanced either by the hybridization between the N-p and nearest neighbor O-p orbitals or by applying on-site Coulomb repulsion (U) and exchange interaction (J). We show that the magnetic state induced by the composite defect is energetically more stable than the non-magnetic state. In addition, we show that the U and J applied on the p-orbitals of N and O atoms may significantly impact the calculated magnetic state of the composite defect, resulting in magnetic state for a configuration that is non-magnetic by generalized gradient approximation.

Zhang, Yao-Fang; Feng, Min; Shao, Bin; Lu, Yuan; Liu, Hong; Zuo, Xu

2014-05-01

472

International Nuclear Information System (INIS)

The pressure dependence of the structural and electronic properties of liquid Te is investigated by means of ab initio molecular-dynamics simulations. The anomalous pressure-induced structural change is successfully reproduced by our simulations being in agreement with the observations by the recent synchrotron X-ray-diffraction experiments. Our analyses including the overlap populations reveal that there are two stages in the compression process of the liquid Te. In the first stage under pressure up to about 6 GPa, the elongation of the nearest-neighbor distance is induced by forming a weak covalent bonding state between two Te atoms. In the second stage for further compression, the anisotropy of atomic configuration around each Te atom is reduced with increasing pressure, and the electronic states have a weak pressure dependence. (author)

473

1\\/2,1\\/2 Representation space An ab initio construct

A careful ab initio construction of the finite-mass (1/2,1/2) representation space of the Lorentz group reveals it to be a spin-parity multiplet. In general, it does not lend itself to a single-spin interpretation. We find that (1/2,1/2) representation space for massive particles naturally bifurcates into a triplet and a singlet of opposite relative intrinsic parties. The text-book separation into spin one and spin zero states occurs only for certain limited kinematical settings. We construct a wave equation for the (1/2,1/2) multiplet, and show that the particles and antiparticles in this representation space do not carry a definite spin but only a definite relative intrinsic parity. In general, both spin one and spin zero are covariantly inseparable inhabitants of massive vector fields. This last observation suggests that scalar particles, such as the Higgs, may be intrinsic part of massive vector gauge fields.

Ahluwalia, D V

2001-01-01

474

Ab initio prediction of high-pressure structural phase transition in BaH{sub 2}

Energy Technology Data Exchange (ETDEWEB)

We have performed ab initio electronic structure calculations to calculate the structural properties and high-pressure phase transition in Barium dihydride (BaH{sub 2}). Our results show that BaH{sub 2} crystallizes the orthorhombic phase (CoSi{sub 2}-type structure) with Pnma space group at ambient conditions. A phase transition to the hexagonal (Ni{sub 2}In-type structure) with P6{sub 3}/mmc space group is found at pressure around 4 GPa. At the phase transition, the coordination number of hydrogen increases from 9 to 11 and the average bond length of Ba-H increases. The results show a band gap of 2