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1

Nuclear Structure - "ab initio"  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

2

Ab initio Ehrenfest dynamics.  

Science.gov (United States)

We present an ab initio direct Ehrenfest dynamics scheme using a three time-step integrator. The three different time steps are implemented with nuclear velocity Verlet, nuclear-position-coupled midpoint Fock integrator, and time-dependent Hartree-Fock with a modified midpoint and unitary transformation algorithm. The computational cost of the ab initio direct Ehrenfest dynamics presented here is found to be only a factor of 2-4 larger than that of Born-Oppenheimer (BO) dynamics. As an example, we compute the vibration of the NaCl molecule and the intramolecular torsional motion of H2C=NH2+ by Ehrenfest dynamics compared with BO dynamics. For the vibration of NaCl with an initial kinetic energy of 1.16 eV, Ehrenfest dynamics converges to BO dynamics with the same vibrational frequency. The intramolecular rotation of H2C=NH2+ produces significant electronic excitation in the Ehrenfest trajectory. The amount of nonadiabaticity, suggested by the amplitude of the coherent progression of the excited and ground electronic states, is observed to be directly related to the strength of the electron-nuclear coupling. Such nonadiabaticity is seen to have a significant effect on the dynamics compared with the adiabatic approximation. PMID:16164281

Li, Xiaosong; Tully, John C; Schlegel, H Bernhard; Frisch, Michael J

2005-08-22

3

Ab Initio.  

Science.gov (United States)

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 _{?}^{7}Li, _{?}^{9}Be, and _{?}^{13}C. We show that the chiral hyperon-nucleon interactions provide ground-state and excitation energies that generally agree with experiment within the cutoff dependence. At the same time we demonstrate that hypernuclear spectroscopy provides tight constraints on the hyperon-nucleon interactions. PMID:25415901

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

2014-11-01

4

Ab-initio calculations and phase diagram assessments of An-Al systems (An = U, Np, Pu)  

Science.gov (United States)

The enthalpies of formation of binary intermetallic compounds AnAl n(n=2,3,4, An=U,Np,Pu) were assessed from first principle calculations of total energies performed using full potential APW + lo technique within density functional theory ( WIEN2k). The substantial contribution to entropies, S298°, arising from lattice vibrations was calculated by direct method within harmonic crystal approximation ( Phonon software + VASP for obtaining Hellmann-Feynman forces). The electronic heat capacity and the corresponding contribution to entropy were estimated from the density of states at Fermi level obtained from electronic structure calculations. The phase diagrams of the relevant systems An-Al were calculated based on the thermodynamic data assessed from ab-initio calculations, known equilibrium and calorimetry data by employing the FactSage program.

Sedmidubský, D.; Konings, R. J. M.; Sou?ek, P.

2010-02-01

5

AB INITIO AND CALPHAD THERMODYNAMICS OF MATERIALS  

Energy Technology Data Exchange (ETDEWEB)

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

Turchi, P A

2004-04-14

6

Ab initio random structure searching.  

Science.gov (United States)

It is essential to know the arrangement of the atoms in a material in order to compute and understand its properties. Searching for stable structures of materials using first-principles electronic structure methods, such as density-functional-theory (DFT), is a rapidly growing field. Here we describe our simple, elegant and powerful approach to searching for structures with DFT, which we call ab initio random structure searching (AIRSS). Applications to discovering the structures of solids, point defects, surfaces, and clusters are reviewed. New results for iron clusters on graphene, silicon clusters, polymeric nitrogen, hydrogen-rich lithium hydrides, and boron are presented. PMID:21406903

Pickard, Chris J; Needs, R J

2011-02-01

7

Novel Algebraic Approach to Ab Initio Calculation  

CERN Document Server

This article addresses a fundamental problem faced by the ab initio community: the lack of an effective formalism for the rapid exploration and exchange of new methods. To rectify this, we introduce a novel, basis-set independent, matrix-based formulation of generalized density-functional theories which reduces the development, implementation, and dissemination of new ab initio techniques to the derivation and transcription of a few lines of algebra. This new framework enables us to herein provide complete instructions for the construction of fully functional, highly efficient production codes for ab initio calculations employing arbitrary basis sets. Within this framework, we also discuss in full detail a variety of leading-edge ab initio techniques, minimization algorithms, and highly efficient computational kernels for use with scalar as well as shared and distributed-memory supercomputer architectures.

Ismail-Beigi, S; Ismail-Beigi, Sohrab

1999-01-01

8

Ab initio nuclear structure theory  

Science.gov (United States)

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

Negoita, Gianina Alina

9

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.

Stokbro, Kurt; Jacobsen, Karsten Wedel

1992-01-01

10

Ab Initio Study of Polonium  

Science.gov (United States)

Polonium is the only element with a simple cubic (sc) crystal structure. Atoms in solid polonium sit at the corners of a simple cubic unit cell and no where else. Polonium has a valence electron configuration 6s26p4 (Z = 84). The low temperature ?-phase transforms into the rhombohedral (trigonal) ? structure at ˜348 K. The sc ?-Po unit cell constant is a = 3.345 Å. The beta form of polonium (?-Po) has the lattice parameters, aR = 3.359 Å and a rhombohedral angle 98°13'. We have performed an ab initio electronic structure calculation by using the density functional theory. We have performed the calculation with and without spin-orbit (SO) coupling by using both the LDA and the GGA for the exchange-correlations. The k-points in a simple cubic BZ are determined by R (0.5, 0.5, 0.5), ? (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and ? (0, 0, 0). Other directions of k-points are ? (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and ? (0, 0, 0). The SO splittings of p states at the ? point in the GGA+SO scheme for ?-Po are 0.04 eV and 0.02 eV while for the ?-Po these are 0.03 eV and 0.97 eV. We have also calculated the vibrational spectra for the unit cells in both the structures. We find that exchanging of a Po atom by Pb atom produces several more bands and destabilizes the ? phase.

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

2008-05-01

11

Ab initio model of porous periclase  

International Nuclear Information System (INIS)

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

12

Ab initio valence calculations in chemistry  

CERN Document Server

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

13

Ab initio approach of the zircaloy-4 oxidation process  

International Nuclear Information System (INIS)

This thesis is linked to the study of fuel cladding corrosion in Pressurized Water Reactors. Despite all the alloys which could be used as fuel cells, we focused on Zircaloy-4 where alloying elements like iron and chromium, insolubles in the zirconium matrice, precipitate in the intermetallic form. The aim of our work is to justified, on a theoretical point of view, the role of iron concentration redistributed in the metal as in the oxide on the oxidation process of the fuel claddings under irradiation. Our approach relies on electronic structure calculations based on the density functional theory and more specifically on the pseudopotentials technique. We use the code VASP (Vienna Ab initio Simulation Package) developed by G. Kresse and J. Hafner at the Institut for Materials Physics of Vienna University. After a quick stage designed to validate our computational approach, we study the early stages of zirconium ? (0001) surface. Performing both static and dynamic calculations, we are able to show that there is one reaction channel which can explained the dissociation of an oxygen molecule on this surface and the incorporation of one of the two oxygen atoms under the metal surface. At least, we used VASP to tackle the technological problem which has motivated this thesis. We first conclude that substoichiometry can explain the stabilisation of the high temperature phases of zirconia (tetragonal and cubic structures), this stabilisation is more evident in the case wheilisation is more evident in the case where oxygen vacancies are doubly charged (this corresponds to extract an O2- ion to the ZrO2 crystal). The second conclusion is that doping zirconia with iron could not lead to the stabilisation of the tetragonal or cubic structures directly. But as iron enhances the formation of oxygen vacancies (which have been shown to have a stabilizing effect) it can indirectly contribute to stabilize these two high temperature polymorphs. (author)

14

Modeling Brown Dwarfs using ab initio equation of state data  

Science.gov (United States)

We present wide-range equations of state (EOS) for hydrogen and helium including accurate data derived from finite-temperature density functional theory molecular dynamics (FT-DFT-MD) simulations for the warm dense matter regime using the VASP package [1]. This hydrogen/helium Rostock EOS (H/He-REOS) cover a wide range of temperatures and densities with a maximum error of 5%. Based on this ab initio data set we calculate interior models and mass-radius (MR) relations for Giant Planets and particularly for Brown Dwarfs. The latter need EOS data for the 1 bar level (? - 10-5g/cm3, T - 1000 K) as well as for central conditions with - 150 Gbar (? - 250g/cm3, T - 3 MK). We compare our interior models and the MR relations with those based on the Saumon-Chabrier-van Horn (SCvH) EOS [2]. [1] G. Kresse and J. Furthmüller, Phys. Rev. B 54, 11169 (1996) [2] D. Saumon, G. Chabrier, and H. M. van Horn, Astrophys. J. Suppl. Ser. 99, 713 (1995)

Becker, Andreas; Lorenzen, Winfried; Nettelmann, Nadine; Redmer, Ronald

2013-07-01

15

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

16

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

17

Towards hydrogen metallization: an Ab initio approach  

International Nuclear Information System (INIS)

The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H2)2 which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author)

18

Materials Design from ab initio Calculations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This thesis presents a theoretical study of bulk materials using ab initio methods based on the density functional theory (DFT). Crystallographic structural phase transformations and phase stability for 5f-dioxides, ABO3 perovskites, and ABO4 compounds have been extensively studied. Different approaches such as static total energy calculations, elastic stability and dynamical stability (phonon calculations) criteria have been used to determine the phase stability. As a special case, the latti...

Li, Sa

2004-01-01

19

Calculation of integrals over ab initio pseudopotentials  

International Nuclear Information System (INIS)

An approach is presented for the evaluation of the two distinct types of one-electron integrals arising from the ab initio pseudopotentials introduced by Kahn and Goddard. The integrals are shown to reduce to a sum over products of angular and radial integrals, the latter being approximated by power and asymptotic series combined with appropriate recursion relations. The method is valid for arbitrary angular momenta of both the pseudopotential and the Cartesian Gaussian basis functions

20

Ab initio no core full configuration approach for light nuclei  

Science.gov (United States)

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

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

2014-07-01

 
 
 
 
21

Ab initio simulation of magnetic tunnel junctions  

Energy Technology Data Exchange (ETDEWEB)

In this paper, we present the mathematical and implementation details of an ab initio method for calculating spin-polarized quantum transport properties of atomic scale spintronic devices under external bias potential. The method is based on carrying out density functional theory (DFT) within the Keldysh non-equilibrium Green's function (NEGF) formalism to calculate the self-consistent spin densities. We apply this method to investigate nonlinear and non-equilibrium spin-polarized transport in a Fe/MgO/Fe trilayer structure as a function of external bias voltage.

Waldron, Derek; Liu Lei; Guo Hong [Centre for the Physics of Materials and Department of Physics, McGill University, Montreal, PQ, H3A 2T8 (Canada)

2007-10-24

22

Ab initio simulation of magnetic tunnel junctions.  

Science.gov (United States)

In this paper, we present the mathematical and implementation details of an ab initio method for calculating spin-polarized quantum transport properties of atomic scale spintronic devices under external bias potential. The method is based on carrying out density functional theory (DFT) within the Keldysh non-equilibrium Green's function (NEGF) formalism to calculate the self-consistent spin densities. We apply this method to investigate nonlinear and non-equilibrium spin-polarized transport in a Fe/MgO/Fe trilayer structure as a function of external bias voltage. PMID:21730459

Waldron, Derek; Liu, Lei; Guo, Hong

2007-10-24

23

Ab initio simulation of magnetic tunnel junctions  

International Nuclear Information System (INIS)

In this paper, we present the mathematical and implementation details of an ab initio method for calculating spin-polarized quantum transport properties of atomic scale spintronic devices under external bias potential. The method is based on carrying out density functional theory (DFT) within the Keldysh non-equilibrium Green's function (NEGF) formalism to calculate the self-consistent spin densities. We apply this method to investigate nonlinear and non-equilibrium spin-polarized transport in a Fe/MgO/Fe trilayer structure as a function of external bias voltage

24

Ab initio calculations of the hydrogen bond  

CERN Document Server

Recent x-ray Compton scattering experiments in ice have provided useful information about the quantum nature of the interaction between H$_2$O monomers. The hydrogen bond is characterized by a certain amount of charge transfer which could be determined in a Compton experiment. We use ab-initio simulations to investigate the hydrogen bond in H$_2$O structures by calculating the Compton profile and related quantities in three different systems, namely the water dimer, a cluster containing 12 water molecules and the ice crystal. We show how to extract estimates of the charge transfer from the Compton profiles.

Barbiellini, B

2002-01-01

25

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

26

Ab initio energetics of nonsubstituted monocyclic pyrones  

Energy Technology Data Exchange (ETDEWEB)

The monocyclic nonsubstituted pyrones were studied computationally using state-of-the-art ab initio composite computational techniques. Combination of the accurate energies so obtained with conveniently chosen isodesmic or homodesmotic chemical reactions lead to very confident predictions of their corresponding standard enthalpy of formation. The internal consistency of the results obtained from a vast number of independent chemical schemes serves as a further support of the quality of our results, which are thus proposed to establish the energetics of {alpha}-pyrone and {gamma}-pyrone.

Morais, Victor M.F., E-mail: vmmorais@icbas.up.p [Instituto de Ciencias Biomedicas Abel Salazar, ICBAS, Universidade do Porto, P-4099-003 Porto (Portugal); Centro de Investigacao em Quimica, Departamento de Quimica, Faculdade de Ciencias da Universidade do Porto, Rua do Campo Alegre, 687, P-4169-007 Porto (Portugal)

2011-01-15

27

Ab initio structure solution by charge flipping  

CERN Document Server

In this paper we present an extremely simple structure solution method termed charge flipping. It works ab initio on high resolution x-ray diffraction data in the manner of Fourier recycling. The real space modification simply changes the sign of charge density below a threshold, while in reciprocal space the modification is the Fobs map without any weighting. We test the algorithm using synthetic data for a wide range of structures, analyse the solution statistics and check the quality of reconstruction. Finally, we reconsider mathematical aspects of the algorithm in detail, showing that in this chaotic iteration process the solution is a limit cycle and not a fixed point.

Oszlanyi, G; Oszlanyi, Gabor; Suto, Andras

2003-01-01

28

AIDA: ab initio domain assembly server.  

Science.gov (United States)

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

29

AIDA: ab initio domain assembly server  

Science.gov (United States)

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

2014-01-01

30

Ab initio based polarizable force field parametrization.  

Science.gov (United States)

Experimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics simulations. Structural and dynamical features are deeply influenced by molecular and ionic polarizability, which parametrization in classical force field has been an object of long-standing efforts. Although when classical models are compared to ab initio calculations at condensed phase, it is found that the water dipole moments are underestimated by approximately 30%, while the anion shows an overpolarization at short distances. A model for chloride-water polarizable interaction is parametrized here, making use of Car-Parrinello simulations at condensed phase. The results hint to an innovative approach in polarizable force fields development, based on ab initio simulations, which do not suffer for the mentioned drawbacks. The method is general and can be applied to the modeling of different systems ranging from biomolecular to solid state simulations. PMID:18532799

Masia, Marco

2008-05-14

31

Ab initio Quantum and ab initio Molecular Dynamics of the Dissociative Adsorption of Hydrogen on Pd(100)  

CERN Document Server

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 determine an analytical representation. Then, in an independent second step dynamical calculations are performed on the analytical representation of the PES. Thus the dissociation dynamics is investigated without any crucial assumption except for the Born-Oppenheimer approximation which is anyhow employed when density-functional theory calculations are performed. The ab initio molecular dynamics is compared to detailed quantum dynamical calculations on exactly the same ab initio PES. The occurence of quantum oscillations in the sticking probab...

Gross, A; Gross, Axel; Scheffler, Matthias

1997-01-01

32

Integrated design of Nb-based superalloys: Ab initio calculations, computational thermodynamics and kinetics, and experimental results  

International Nuclear Information System (INIS)

An optimal integration of modern computational tools and efficient experimentation is presented for the accelerated design of Nb-based superalloys. Integrated within a systems engineering framework, we have used ab initio methods along with alloy theory tools to predict phase stability of solid solutions and intermetallics to accelerate assessment of thermodynamic and kinetic databases enabling comprehensive predictive design of multicomponent multiphase microstructures as dynamic systems. Such an approach is also applicable for the accelerated design and development of other high performance materials. Based on established principles underlying Ni-based superalloys, the central microstructural concept is a precipitation strengthened system in which coherent cubic aluminide phase(s) provide both creep strengthening and a source of Al for Al2O3 passivation enabled by a Nb-based alloy matrix with required ductile-to-brittle transition temperature, atomic transport kinetics and oxygen solubility behaviors. Ultrasoft and PAW pseudopotentials, as implemented in VASP, are used to calculate total energy, density of states and bonding charge densities of aluminides with B2 and L21 structures relevant to this research. Characterization of prototype alloys by transmission and analytical electron microscopy demonstrates the precipitation of B2 or L21 aluminide in a (Nb) matrix. Employing Thermo-Calc and DICTRA software systems, thermod-Calc and DICTRA software systems, thermodynamic and kinetic databases are developed for substitutional alloying elements and interstitial oxygen to enhance the diffusivity ratio of Al to O for promotion of Al2O3 passivation. However, the oxidation study of a Nb-Hf-Al alloy, with enhanced solubility of Al in (Nb) than in binary Nb-Al alloys, at 1300 deg. C shows the presence of a mixed oxide layer of NbAlO4 and HfO2 exhibiting parabolic growth

33

Investigation of molybdenum and caesium behaviour in urania by ab initio calculations  

International Nuclear Information System (INIS)

A theoretical study of molybdenum and caesium solution in uranium dioxide is carried out. Calculations are performed using the density functional theory with the projector-augmented-wave method as implemented in the Vienna ab initio simulation package (VASP). Correlation effects are taken into account within the DFT+U approach. Molybdenum is preferentially inserted in uranium-oxygen divacancies for understoichiometric urania and uranium vacancies for overstoichiometric urania. The favourable sites for caesium solution are the Schottky defect for understoichiometric urania and U vacancies and U-O divacancies for overstoichiometric urania. Using the stability of many binary and ternary compounds in comparison to soluted atoms, we show that caesium and molybdenum are insoluble in uranium dioxide whatever the stoichiometric regime.

34

Ab initio study of high-pressure phase transitions in silicon and germanium  

CERN Document Server

We have investigated the structural sequence of the high-pressure phases of silicon and germanium. We have focussed on the cd -> beta-tin -> Imma -> sh phase transitions. We have used the plane-wave pseudopotential approach to the density-functional theory implemented within the Vienna ab-initio simulation package (VASP). We have determined the equilibrium properties of each structure and the values of the critical parameters including a hysteresis effect at the phase transitions. The order of the phase transitions has been obtained from the pressure dependence of the enthalpy. Our calculations identify a first-order phase transition from the cd to the beta-tin and from the Imma to the sh phase, and they indicate the possibility of a second-order phase-transition from the beta-tin to the Imma phase. Finally, we have derived the enthalpy barriers between the phases.

Gaál-Nagy, K; Strauch, D; Gaal-Nagy, Katalin; Pavone, Pasquale; Strauch, Dieter

2003-01-01

35

Giant magnetoresistance An ab-initio description  

CERN Document Server

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

36

Ab-initio nanoplasmonics: atoms matter  

CERN Document Server

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

37

Ab initio determination of light hadron masses.  

Science.gov (United States)

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

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

2008-11-21

38

Discovering chemistry with an ab initio nanoreactor.  

Science.gov (United States)

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

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

2014-12-01

39

{ital Ab initio} thermoelasticity of magnesium  

Energy Technology Data Exchange (ETDEWEB)

The elastic moduli of magnesium (Mg) have been evaluated as functions of pressure and temperature through the use of fluctuation formulas and Monte Carlo simulation. The simulations employ {ital ab initio} interatomic potentials for Mg derived from generalized pseudopotential theory and used previously to predict the temperature-pressure phase diagram of this metal to 60 GPa [Phys. Rev. B {bold 51}, 5609 (1995)]. Comparison with experimental data at ambient pressure and low temperature shows that the calculated elastic constants agree with the measured values to within about 10{percent}. The temperature and pressure derivatives of the moduli are likewise closely reproduced. Theoretical results are also given for high pressures (to 40 GPa) and high temperatures (to 1500 K) in the relevant hcp and bcc crystal structures. No elastic anomalies are seen on approaching the predicted hcp-bcc phase transition. Implications for the detection of this transition in shock experiments are discussed. {copyright} {ital 1999} {ital The American Physical Society}

Greeff, C.W. [Los Alamos National Laboratory, Applied Theoretical and Computational Physics, Los Alamos, New Mexico 87545 (United States); Moriarty, J.A. [Lawrence Livermore National Laboratory, University of California, Livermore, California 94551 (United States)

1999-02-01

40

Operator evolution for ab initio nuclear theory  

CERN Document Server

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

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

2014-01-01

 
 
 
 
41

Ab Initio Modeling of Molecular Radiation  

Science.gov (United States)

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

Jaffe, Richard; Schwenke, David

2014-01-01

42

Ab Initio Description of p -Shell Hypernuclei  

Science.gov (United States)

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

43

Ab Initio Path to Heavy Nuclei  

CERN Document Server

We present the first ab initio calculations of nuclear ground states up into the domain of heavy nuclei, spanning the range from 16-O to 132-Sn based on two- plus three-nucleon interactions derived within chiral effective field theory. We employ the similarity renormalization group for preparing the Hamiltonian and use coupled-cluster theory to solve the many-body problem for nuclei with closed sub-shells. Through an analysis of theoretical uncertainties resulting from various truncations in this framework, we identify and eliminate the technical hurdles that previously inhibited the step beyond medium-mass nuclei, allowing for reliable validations of nuclear Hamiltonians in the heavy regime. Following this path we show that chiral Hamiltonians qualitatively reproduce the systematics of nuclear ground-state energies up to the neutron-rich Sn isotopes.

Binder, Sven; Calci, Angelo; Roth, Robert

2013-01-01

44

Ab initio path to heavy nuclei  

Science.gov (United States)

We present the first ab initio calculations of nuclear ground states up into the domain of heavy nuclei, spanning the range from 16O to 132Sn, based on two- plus three-nucleon interactions derived within chiral effective field theory. We employ the similarity renormalization group for preparing the Hamiltonian and use coupled-cluster theory to solve the many-body problem for nuclei with closed sub-shells. Through an analysis of theoretical uncertainties resulting from various truncations in this framework, we identify and eliminate the technical hurdles that previously inhibited the step beyond medium-mass nuclei, allowing for reliable validations of nuclear Hamiltonians in the heavy regime. Following this path we show that chiral Hamiltonians qualitatively reproduce the systematics of nuclear ground-state energies up to the neutron-rich Sn isotopes.

Binder, Sven; Langhammer, Joachim; Calci, Angelo; Roth, Robert

2014-09-01

45

Why ferroelectricity? synchrotron radiation and ab initio answers  

Scientific Electronic Library Online (English)

Full Text Available SciELO Mexico | Language: English Abstract in spanish 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

46

Cálculos ab initio con correlación electrónica  

Science.gov (United States)

Estamos entrando en una era donde la ortogonalidad entre las investigaciones de carácter experimental y de naturaleza teórica se irá difuminando progresivamente y la problemática a resolver quedará en escena como el único actor principal de la obra. Como premisa para una cooperación teórico-experimental de igual a igual, la metodología químico-cuántica utilizada debe ser capaz de ofrecer resultados de carácter predictivo. Sin duda, esta madurez en la metodología químico-cuántica ya la hemos alcanzado hace algunos años, tal y como muestra entre otras muchas, la labor que nuestro grupo ha realizado en el transcurso de la última década, dentro del campo de la Espectroscopía Teórica. Los estudios realizados comprenden una amplia gama de sistemas, variando tanto en tamaño como en complejidad, abordando problemáticas espectroscópicas consideradas tradicionalmente como especialmente controvertidas. Nuestra contribución científica más relevante reside en el carácter cuantitativo de las asignaciones espectroscópicas que hemos propuesto en base a resultados ab initio. Recordemos que en los años noventa los resultados ab initio solían presentar para las energías de excitación de sistemas de tamaño molecular moderado, como el benceno, errores de más de 1 eV. En comparación con el éxito relativo de los métodos semiempíricos, la frustración de la metodología ab initio quedaba todavía más patente. Los estudios que hemos presentado representan una comprensión profunda de los espectros electrónicos en sistemas orgánicos claves, mostrando el camino a seguir para obtener asignaciones espectroscópicas precisas (entre 0.1-0.2 eV). La naturaleza del método CASPT2 junto al diseño de estrategias computacionales nos ha permitido alcanzar el carácter cuantitativo con el que se caracterizan nuestras contribuciones[1,2]. Por todo ello, algunos de los trabajos publicados se consideran clásicos dentro del campo, pues en cierto modo definen el campo, y se reflejan en libros publicados recientemente. En la conferencia se analizarán ciertos pormenores de las investigaciones realizadas. El tipo de aplicaciones llevadas a cabo hasta la fecha se ilustrará mediante el estudio teórico del espectro electrónico de ciclooctatetraeno. Dando un paso más en la evolución de nuestra investigación, pretendemos en la actualidad describir, desde un formalismo teórico y al mismo nivel de exigencia, los mecanismos subyacentes que tienen lugar en las reacciones biológicas fototoinducidas, es decir, reacciones que se inician mediante la absorción de luz[3]. Como muestra de la caracterización de los procesos fotofísicos y fotoquímicos en fotobiología teórica, hemos elegido la descripción de la conversión interna ultrarrápida que tiene lugar en los cromóforos del ADN. Los estados excitados de las moléculas de los ácidos nucleicos presentan tiempos de vida media que se encuentran en el rango de sub-picosegundos, sugiriendo la presencia de un canal ultrarrápido de conversión interna, lo que normalmente se asocia en la fotoquímica contemporánea a una intersección cónica entre el estado excitado y el fundamental[4]. De esta forma nuestro ADN previene de forma eficaz posibles reacciones en el estado excitado y se revela como un excelente protector solar.

Merchán Bonete, M.

47

Ab initio atomistic simulation of metals and multicomponent alloys  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

48

Ab Initio Protein Structure Prediction Using Chunk-TASSER  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We have developed an ab initio protein structure prediction method called chunk-TASSER that uses ab initio folded supersecondary structure chunks of a given target as well as threading templates for obtaining contact potentials and distance restraints. The predicted chunks, selected on the basis of a new fragment comparison method, are folded by a fragment insertion method. Full-length models are built and refined by the TASSER methodology, which searches conformational space via parallel hyp...

Zhou, Hongyi; Skolnick, Jeffrey

2007-01-01

49

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

Science.gov (United States)

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

50

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

51

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

52

Ab-initio Study on the Adsorption of H, H2 and CO on the Reduced Ceria CeO_2-x (111) Surface  

Science.gov (United States)

Ceria plays an important role in catalysis. Ceria supported metal catalysts find a broad range of applications (e.g. Three-Way Catalysts used in automobiles). Ceria readily releases and takes up Oxygen at its surface for oxidation and reduction reactions. The presence of Oxygen defect sites at the surface is important for catalytic activity. Therefore the (111) surface of Ceria, which is the most stable surface, is investigated with two ab-initio approaches: the full potential linearized augmented plane wave method (FLAPW) [1] and the pseudopotential-based Vienna ab-initio simulation package (VASP) [2], at several defect concentrations. Furthermore,adsorption of H, H2 and CO is studied. The results for the most stable adsorption geometries are analyzed in terms of the electronic structure. [1] Wimmer et al., Phys. Rev. B 24, 864 (1981) [2] Kresse and Furthmüller, Comput. Mat. Sci 6, 15 (1996); Phys. Rev. B 54, 11169 (1996)

Grohmann, Rainer; Vogtenhuber, Doris; Podloucky, Raimund; Redinger, Joseph; Kresse, Georg

2001-03-01

53

Ab Initio Studies of Stratospheric Ozone Depletion Chemistry  

Science.gov (United States)

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

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

1995-01-01

54

Reactions at surfaces studied by ab initio dynamics calculations  

CERN Document Server

Due to the development of efficient algorithms and the improvement of computer power it is now possible to map out potential energy surfaces (PES) of reactions at surfaces in great detail. This achievement has been accompanied by an increased effort in the dynamical simulation of processes on surfaces. The paradigm for simple reactions at surfaces -- the dissociation of hydrogen on metal surfaces -- can now be treated fully quantum dynamically in the molecular degrees of freedom from first principles, i.e., without invoking any adjustable parameters. This relatively new field of ab initio dynamics simulations of reactions at surfaces will be reviewed. Mainly the dissociation of hydrogen on clean and adsorbate covered metal surfaces and on semiconductor surfaces will be discussed. In addition, the ab initio molecular dynamics treatment of reactions of hydrogen atoms with hydrogen-passivated semiconductor surfaces and recent achievements in the ab initio description of laser-induced desorption and further devel...

Gross, A

1998-01-01

55

Recent achievements in ab initio modelling of liquid water  

CERN Document Server

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

56

Structure prediction based on ab initio simulated annealing  

International Nuclear Information System (INIS)

The prediction of possible crystal structures, with the type of atoms as the only input, has become a fast growing field of research. The general approach consists of the global exploration of the energy landscape of the chemical system, with typical methods being simulated annealing or genetic algorithms. In the case of simulated annealing, combinations of model potentials and ab initio calculations for the energy evaluation are state of the art. Only very recently, the possibility of simulated annealing based on ab initio calculations at all stages of the calculations has become feasible. This article summarizes the recent developments in this area

57

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

58

Use of ab initio quantum chemical methods in battery technology  

Energy Technology Data Exchange (ETDEWEB)

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

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

1997-06-01

59

Structural, electronic and optical properties of cubic SrTiO{sub 3} and KTaO{sub 3}: Ab initio and GW calculations  

Energy Technology Data Exchange (ETDEWEB)

We present first-principles VASP calculations of the structural, electronic, vibrational, and optical properties of paraelectric SrTiO{sub 3} and KTaO{sub 3}. The ab initio calculations are performed in the framework of density functional theory with different exchange-correlation potentials. Our calculated lattice parameters, elastic constants, and vibrational frequencies are found to be in good agreement with the available experimental values. Then, the bandstructures are calculated with the GW approximation, and the corresponding band gap is used to obtain the optical properties of SrTiO{sub 3} and KTaO{sub 3}.

Benrekia, A.R., E-mail: benrekia.ahmed@yahoo.com [Faculty of Science and Technology, University of Medea (Algeria); Benkhettou, N. [Laboratoire des Materiaux Magnetiques, Faculte des Sciences, Universite Djillali Liabes de Sidi Bel Abbes (Algeria); Nassour, A. [Laboratoire de Cristallographie, Resonance Magnetique et Modelisations (CRM2, UMR CNRS 7036) Institut Jean Barriol, Nancy Universite BP 239, Boulevard des Aiguillettes, 54506 Vandoeuvre-les-Nancy (France); Driz, M. [Applied Material Laboratory (AML), Electronics Department, University of Sidi bel Abbes (DZ 22000) (Algeria); Sahnoun, M. [Laboratoire de Physique Quantique de la Matiere et Modelisations Mathematique (LPQ3M), Faculty of Science and Technology,University of Mascara (Algeria); Lebegue, S. [Laboratoire de Cristallographie, Resonance Magnetique et Modelisations (CRM2, UMR CNRS 7036) Institut Jean Barriol, Nancy Universite BP 239, Boulevard des Aiguillettes, 54506 Vandoeuvre-les-Nancy (France)

2012-07-01

60

Structural, electronic and optical properties of cubic SrTiO3 and KTaO3: Ab initio and GW calculations  

International Nuclear Information System (INIS)

We present first-principles VASP calculations of the structural, electronic, vibrational, and optical properties of paraelectric SrTiO3 and KTaO3. The ab initio calculations are performed in the framework of density functional theory with different exchange-correlation potentials. Our calculated lattice parameters, elastic constants, and vibrational frequencies are found to be in good agreement with the available experimental values. Then, the bandstructures are calculated with the GW approximation, and the corresponding band gap is used to obtain the optical properties of SrTiO3 and KTaO3.

 
 
 
 
61

Experimental, semi-experimental and ab initio equilibrium structures  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract The determination of equilibrium structures of molecules by spectroscopic methods or by quantum mechanical calculations is reviewed. The following structures are described in detail: experimental equilibrium structures, empirical structures, semi-experimental structures and ab initio structures. The approximations made by the different methods are discussed and their accuracies are compared.

2007-01-01

62

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

63

Ab initio determination of thermal conductivity of dense hydrogen plasmas.  

Science.gov (United States)

Ab initio molecular dynamics is used to compute the thermal conductivity of hydrogen at 80 g cm(-3) and temperature up to 800 eV. Pressures and ionic structure are compared with orbital-free calculations. Thermal conductivity is evaluated using the Kubo-Greenwood formula and is compared with models currently used in hydrodynamical simulations of inertial confinement fusion. PMID:19257679

Recoules, Vanina; Lambert, Flavien; Decoster, Alain; Canaud, Benoit; Clérouin, Jean

2009-02-20

64

Ab Initio Determination of Thermal Conductivity of Dense Hydrogen Plasmas  

International Nuclear Information System (INIS)

Ab initio molecular dynamics is used to compute the thermal conductivity of hydrogen at 80 g cm-3 and temperature up to 800 eV. Pressures and ionic structure are compared with orbital-free calculations. Thermal conductivity is evaluated using the Kubo-Greenwood formula and is compared with models currently used in hydrodynamical simulations of inertial confinement fusion

65

Ab initio simulation of dislocation cores in metals  

International Nuclear Information System (INIS)

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.)

66

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

67

Ab initio simulation of dislocation cores in metals; Simulation ab initio des coeurs de dislocation dans les metaux  

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

68

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

Directory of Open Access Journals (Sweden)

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

Pavlu J.

2012-01-01

69

Carrier Scattering Rates in Zincblende Structure Semiconductors derived from 14 × 14 k · p and ab initio Pseudopotential Methods  

Digital Repository Infrastructure Vision for European Research (DRIVER)

A set of programs for calculating carrier-phonon and carrier-alloy scat-tering rates have been constructed. Energy bands, gradients of the energy, second derivatives of the energy and eigenvectors of the carrier states were first calculated using a 14 × 14 kp-method. Scattering rates were then derived, based upon the calculations of the developed kp software. Furthermore, scattering rates have also been derived using band structures from the ab initio pseudopotential code ABINIT. A progr...

Karlsen, Bjørnar

2013-01-01

70

Computational methods for ab initio detection of microRNAs.  

Science.gov (United States)

MicroRNAs are small RNA sequences of 18-24 nucleotides in length, which serve as templates to drive post-transcriptional gene silencing. The canonical microRNA pathway starts with transcription from DNA and is followed by processing via the microprocessor complex, yielding a hairpin structure. Which is then exported into the cytosol where it is processed by Dicer and then incorporated into the RNA-induced silencing complex. All of these biogenesis steps add to the overall specificity of miRNA production and effect. Unfortunately, their modes of action are just beginning to be elucidated and therefore computational prediction algorithms cannot model the process but are usually forced to employ machine learning approaches. This work focuses on ab initio prediction methods throughout; and therefore homology-based miRNA detection methods are not discussed. Current ab initio prediction algorithms, their ties to data mining, and their prediction accuracy are detailed. PMID:23087705

Allmer, Jens; Yousef, Malik

2012-01-01

71

Multiple Time Step Integrators in Ab Initio Molecular Dynamics  

CERN Document Server

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

72

Toward the Ab-initio Description of Medium Mass Nuclei  

CERN Document Server

As ab-initio calculations of atomic nuclei enter the A=40-100 mass range, a great challenge is how to approach the vast majority of open-shell (degenerate) isotopes. We add realistic three-nucleon interactions to the state of the art many-body Green's function theory of closed-shells, and find that physics of neutron driplines is reproduced with very good quality. Further, we introduce the Gorkov formalism to extend ab-initio theory to semi-magic, fully open-shell, isotopes. Proof-of-principle calculations for Ca-44 and Ni-74 confirm that this approach is indeed feasible. Combining these two advances (open-shells and three-nucleon interactions) requires longer, technical, work but it is otherwise within reach.

Barbieri, C; Soma, V; Duguet, T; Navratil, P

2012-01-01

73

Ab initio effective rotational Hamiltonians - A comparative study  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Two independent methods to obtain ab initio effective rotational Hamiltonians have been implemented recently. The first one is based on a generalization of perturbation theory to non-commutative rings, the other one on contact transformation techniques. In principle, both methods are able to give rotational Hamiltonians including centrugal distortion effects of arbitrary high orders. These methods are compared for the first time in this article with regard to calculations of the rotational le...

Cassam-chenai?, Patrick; Bouret, Yann; Rey, Michae?l; Tashkun, S. A.; Nikitin, Andrei; Tyuterev, Vladimir G.

2012-01-01

74

Ab Initio Molecular Dynamics of Metallic Hydrogen at High Densities  

International Nuclear Information System (INIS)

The fully ionized (metallic) hydrogen plasma is studied by ab initio molecular dynamics simulations, for classical protons and fully degenerate electrons, in the strong coupling regime of the protons. The calculated ion-electron pair distribution function signals the breakdown of linear screening with decreasing density while the melting temperature of the proton crystal drops rapidly. The simulations reveal the remarkable persistence of a weakly damped high-frequency ion acoustic mode, even under conditions of strong electron screening

75

Vibrational Spectra from Quasiclassical Direct Ab Initio Dynamics  

Energy Technology Data Exchange (ETDEWEB)

The theory of vibrational spectral analysis from classical trajectories has been available for some time.1-3. It is only recently that, with the availability of powerful computers, it has become practical to apply the method to the ab initio calculation of molecular spectra. These spectra account for anharmonicities and couplings of all the modes. The modern application of the approach combines the methodology of direct ab initio dynamics to generate classical trajectories of the molecular system and of Fourier decomposition of the fluctuations of the velocity autocorrelation function to obtain the density of vibrational states. Infrared and Raman intensities are obtained from Fourier decompositions of the fluctuations of the autocorrelation function of the dipole moment time derivative4 and polarizability time second-derivatives respectively5. In this chapter we review the essential equations of the method and illustrate its application to two simple molecular systems, water H2O and its deuterated analog D2O, and water dimer (H2O)2. The spectra were generated by applying the protocol of quasiclassical direct dynamics with forces obtained on the fly from accurate electron-correlated ab initio levels of theory. In the quasiclassical protocol the initial conditions of atomic velocities (directions and magnitudes) are chosen to be consistent with the level v=0 for all the harmonic normal modes of the molecule. The calculated spectra are found in excellent quantitative agreement with the experimentally observed spectra. A detailed analysis for D2O shows that this choice of initial conditions (quasiclassical with ?=0 for all the modes) offers an accurate account of anharmonicities and mode couplings. The method holds promise for the calculation of very accurate ab initio spectra, including IR and Raman intensities, directly comparable to experimental spectra for increasingly larger molecules.

Dupuis, Michel; Aida, Misako

2004-11-01

76

Ab initio investigation of lasing thresholds in photonic molecules  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We investigate lasing thresholds in a representative photonic molecule composed of two coupled active cylinders of slightly different radii. Specifically, we use the recently formulated steady-state ab initio laser theory (SALT) to assess the effect of the underlying gain transition on lasing frequencies and thresholds. We find that the order in which modes lase can be modified by choosing suitable combinations of the gain center frequency and linewidth, a result that cannot...

Gagnon, Denis; Dumont, Joey; De?ziel, Jean-luc; Dube?, Louis J.

2014-01-01

77

Ab initio calculation of anisotropic interfacial excess free energies  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We describe a simple method to determine, from ab initio calculations, the complete orientation-dependence of interfacial free energies in solid-state crystalline systems. We illustrate the method with an application to precipitates in the Al-Ti alloy system. The method combines the cluster expansion formalism in its most general form (to model the system's energetics) with the inversion of the well-known Wulff construction (to recover interfacial energies from equilibrium p...

Walle, Axel; Gopal, Chirranjeevi Balaji; Demers, Steve; Hong, Qijun; Kowalski, Adam; Miljacic, Ljubomir; Pomrehn, Gregory; Tiwary, Pratyush

2013-01-01

78

Nuclear forces and ab initio calculations of atomic nuclei  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

79

Ab initio approach for atomic relaxations in supported magnetic clusters  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We present a newly developed scheme for atomic relaxations of magnetic supported clusters. Our approach is based on the full potential Korringa-Kohn-Rostoker Green's function method and the second moment tight-binding approximation for many-body potentials. We demonstrate that only a few iterations in ab initio calculations are necessary to find an equilibrium structure of supported clusters. As an example, we present our results for small Co clusters on Cu(001). Changes in ...

Stepanyuk, V. S.; Klavsyuk, A. L.; Niebergall, L.; Saletsky, A. M.; Hergert, W.; Bruno, P.

2004-01-01

80

Ab initio molecular dynamics simulations of Aluminum solvation  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The solvation of Al and its hydrolyzed species in water clusters has been studied by means of ab initio molecular dynamics simulations. The hexa-hydrate aluminum ion formed a stable complex in the finite temperature cluster simulation of one aluminum ion and 16 waters. The average dipole moment of strongly polarized hydrated water molecules in the first solvation shell of the hexa-hydrate aluminum ion was found to be 5.02 Debye. The deprotonated hexa-hydrate complex evolves ...

Lubin, M. I.; Bylaska, J. H.; Weare, J. H.

1999-01-01

 
 
 
 
81

Ab initio calculation of tight-binding parameters  

Energy Technology Data Exchange (ETDEWEB)

We calculate ab initio values of tight-binding parameters for the f- electron metal Ce and various phases of Si, from local-density functional one-electron Hamiltonian and overlap matrix elements. Our approach allows us to unambiguously test the validity of the common minimal basis and two-center approximations as well as to determine the degree of transferability of both nonorthogonal and orthogonal hopping parameters in the cases considered.

McMahan, A.K.; Klepeis, J.E.

1997-12-01

82

Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes  

Energy Technology Data Exchange (ETDEWEB)

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

Draayer, Jerry P [Louisiana State University

2014-09-28

83

Acceleration of the Convergence in ab initio Atomic Relaxations  

Science.gov (United States)

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

84

Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.  

Science.gov (United States)

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

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

2014-08-01

85

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

Energy Technology Data Exchange (ETDEWEB)

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

Bernard, St

1998-12-31

86

A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy.  

Science.gov (United States)

Structure determination of a novel macromolecular complex via single-particle electron microscopy depends upon overcoming the challenge of establishing a reliable 3-D reconstruction using only 2-D images. There are a variety of strategies that deal with this issue, but not all of them are readily accessible and straightforward to use. We have developed a "toolbox" of ab initio reconstruction techniques that provide several options for calculating 3-D volumes in an easily managed and tightly controlled work-flow that adheres to standard conventions and formats. This toolbox is designed to streamline the reconstruction process by removing the necessity for bookkeeping, while facilitating transparent data transfer between different software packages. It currently includes procedures for calculating ab initio reconstructions via random or orthogonal tilt geometry, tomograms, and common lines, all of which have been tested using the 50S ribosomal subunit. Our goal is that the accessibility of multiple independent reconstruction algorithms via this toolbox will improve the ease with which models can be generated, and provide a means of evaluating the confidence and reliability of the final reconstructed map. PMID:20018246

Voss, Neil R; Lyumkis, Dmitry; Cheng, Anchi; Lau, Pick-Wei; Mulder, Anke; Lander, Gabriel C; Brignole, Edward J; Fellmann, Denis; Irving, Christopher; Jacovetty, Erica L; Leung, Albert; Pulokas, James; Quispe, Joel D; Winkler, Hanspeter; Yoshioka, Craig; Carragher, Bridget; Potter, Clinton S

2010-03-01

87

Never born proteins as a test case for ab initio protein structures prediction.  

Science.gov (United States)

The number of natural proteins although large is significantly smaller than the theoretical number of proteins that can be obtained combining the 20 natural amino acids, the so-called "never born proteins" (NBPs). The study of the structure and properties of these proteins allows to investigate the sources of the natural proteins being of unique characteristics or special properties. However the structural study of NPBs can also been intended as an ideal test for evaluating the efficiency of software packages for the ab initio protein structure prediction. In this research, 10.000 three-dimensional structures of proteins of completely random sequence generated according to ROSETTA and FOD model were compared. The results show the limits of these software packages, but at the same time indicate that in many cases there is a significant agreement between the prediction obtained. PMID:19238243

Minervini, Giovanni; Evangelista, Giuseppe; Polticelli, Fabio; Piwowar, Monika; Kochanczyk, Marek; Flis, Lukasz; Malawski, Maciej; Szepieniec, Tomasz; Wi?niowski, Zdzis?aw; Matczy?ska, Ewa; Prymula, Katarzyna; Roterman, Irena

2008-01-01

88

Accelerating VASP electronic structure calculations using graphic processing units.  

Science.gov (United States)

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

89

Ab initio simulations for material properties inside Jupiter  

Science.gov (United States)

The behavior of warm dense matter is of paramount importance for interior and dynamo models for solar and extrasolar giant planets. For instance, nonmetal-to-metal transitions (e.g. metallization in hydrogen), demixing phenomena (in H-He or C-N-O-H mixtures), and new exotic phases (e.g. with proton conduction in water and ammonia) may occur at high pressures and elevated temperatures. These effects have to be taken into account consistently in corresponding planetary models. Therefore, we apply ab initio molecular dynamics simulations based on finite-temperature density functional theory to calculate thermophysical properties of warm dense matter. In particular we determine the equation of state (thermal and caloric), material (sound velocity, specific heat) and transport properties (electrical and thermal conductivity, viscosity, diffusion coefficient) along the adiabat of Jupiter, i.e. from ambient conditions up to the multi-megabar range [1,2]. This ab initio data set can be used as input in future interior (structure) and dynamo models (magnetic fields, flow dynamics) for this planet. Similar data sets can also be compiled for interior conditions of other solar giant planets so that important problems such as the size of planetary cores necessary for the accretion of gaseous (H/He) or icy (C-N-O hydrides) envelopes, the origin, location and stability of layer boundaries, or the source of an excess (e.g. Saturn) or deficit luminosity (e.g. Uranus) can be studied. The increasing sample of extrasolar planets poses new questions that can be addressed based on such ab initio data sets, e.g. to explain the wide range of radii for planets with similar mass. [1] N. Nettelmann, A. Becker, B. Holst, R. Redmer, Astrophys. J. 750, 52 (2012). [2] M. French, A. Becker, W. Lorenzen, N. Nettelmann, M. Bethkenhagen, J. Wicht, R. Redmer, Astrophys. J. Suppl. Ser. 202, 5 (2012).

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

2013-07-01

90

Ab initio electronic properties of dual phosphorus monolayers in silicon  

Science.gov (United States)

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.; Budi, Akin; Hollenberg, Lloyd CL; Russo, Salvy P.

2014-08-01

91

Current rectification by asymmetric molecules: An ab initio study  

CERN Document Server

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 when $n\\ge 2$. The rectification effect arises from the asymmetric structure of the molecule and the molecule-electrode couplings. A significant rectification ratio of $\\sim$38 can be achieved when $n=5$.

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

2006-01-01

92

Ab initio study of water interaction with a Cu surface.  

Science.gov (United States)

We have performed a first principles investigation of water interaction with a Cu surface. The calculated surface energy of a Cu(100) slab is in reasonable agreement with experimental data. The energy of water dissociation is in agreement with experiment. The results of the ab initio calculations are compared to experimental data on hydrogen partial pressure. It is concluded that Cu(OH)(ads) is formed due to a reaction between Cu and anoxic water. The energy of the Cu(100) slab with OH and H adsorbed is lower than the energy of the same slab with an adsorbed water molecule. PMID:20804187

Belonoshko, A B; Rosengren, A

2010-11-01

93

Ab initio studies of electromechanical effects in carbon nanotubes  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english 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

94

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

95

Ab initio electronic properties of dual phosphorus monolayers in silicon  

Science.gov (United States)

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.

2014-01-01

96

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

2004-01-01

97

TiAl doping by vanadium: ab initio study  

International Nuclear Information System (INIS)

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

98

Ab Initio study of neutron drops with chiral Hamiltonians  

CERN Document Server

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

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

2014-01-01

99

Hydrogen Desorption from Mg Hydride: An Ab Initio Study  

Directory of Open Access Journals (Sweden)

Full Text Available Hydrogen desorption from hydride matrix is still an open field of research. By means of accurate first-principle molecular dynamics (MD simulations an Mg–MgH2 interface is selected, studied and characterized. Electronic structure calculations are used to determine the equilibrium properties and the behavior of the surfaces in terms of structural deformations and total energy considerations. Furthermore, extensive ab-initio molecular dynamics simulations are performed at several temperatures to characterize the desorption process at the interface. The numerical model successfully reproduces the experimental desorption temperature for the hydride.

Simone Giusepponi

2012-07-01

100

Ab initio studies of electromechanical effects in carbon nanotubes  

Scientific Electronic Library Online (English)

Full Text Available SciELO Brazil | Language: English Abstract in english 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.

 
 
 
 
101

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

102

Ab initio photoionization dynamics of beta-alanine.  

Science.gov (United States)

Photoionization dynamics of beta-alanine is studied by the trajectory simulations using the ab initio potential energy surface. Vertical photoionization in the spirit of the Franck-Condon principle is assumed both for the adiabatic and thermostatic simulations. Both intramolecular proton transfer and fragmentation while only the proton transfer are found in the thermostatic and adiabatic simulations, respectively, for the conformer having the intramolecular hydrogen bond N...H-O. The theoretical predictions are in line with the experimental observations available in the literatures. It is reported for the first time that the thermostatic temperatures strongly affect the fragmentation processes induced by photoionization. PMID:17444694

Tian, Shan Xi; Yang, Jinlong

2007-04-14

103

Ab-initio study of napthelene based conducting polymer  

International Nuclear Information System (INIS)

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

104

Communication: Ab initio Joule-Thomson inversion data for argon  

Science.gov (United States)

The Joule-Thomson coefficient ?H(P, T) is computed from the virial equation of state up to seventh-order for argon obtained from accurate ab initio data. Higher-order corrections become increasingly more important to fit the low-temperature and low-pressure regime and to avoid the early onset of divergence in the Joule-Thomson inversion curve. Good agreement with experiment is obtained for temperatures T > 250 K. The results also illustrate the limitations of the virial equation in regions close to the critical temperature.

Wiebke, Jonas; Senn, Florian; Pahl, Elke; Schwerdtfeger, Peter

2013-02-01

105

Toward an Ab-initio Description of Quasiparticle Properties  

CERN Document Server

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

2010-01-01

106

Ab initio design on new push pull sila- and germastilbene  

Science.gov (United States)

Ab initio complete active space self-consistent field and second order Möller-Plesset perturbation calculations have been performed to examine the capabilities of the second order non-linear optics (NLO) of 4-dimethylamino,4 '-cyano,i-sila(or germa)stilbenes (i-DCSS, or i-DCSG) where the carbon at the position i of the parent 4-dimethylamino,4 '-cyanostilbene (DCS) is replaced by more electro-positive silicon or germanium atom. 1-DCSS and 1-DCSG, which have not been synthesized yet, were found to have better NLO properties than DCS.

Amatatsu, Yoshiaki; Ohara, Yuhki

2003-05-01

107

Ab initio calculations on the thermodynamic properties of azaborospiropentanes.  

Science.gov (United States)

Following our recent studies of the thermodynamic properties of azaspiropentane and borospiropentane, in consideration of their usefulness as new potential high energy materials, we follow up with ab initio calculations on the thermodynamic properties of azaborospiropentanes. Properties reported in this study include optimized structural parameters, vibrational frequencies, enthalpies of formation, specific enthalpies of combustion, proton affinities, and hydride affinities. Our results indicate that azatriborospiropentane gives off most energy when combusted, as evidenced by its specific enthalpy of combustion of about -52 kJ per gram. PMID:18594880

Richard, Ryan M; Ball, David W

2008-09-01

108

Ab initio investigation of lasing thresholds in photonic molecules  

CERN Document Server

We investigate lasing thresholds in a representative photonic molecule composed of two coupled active cylinders of slightly different radii. Specifically, we use the recently formulated steady-state ab initio laser theory (SALT) to assess the effect of the underlying gain transition on lasing frequencies and thresholds. We find that the order in which modes lase can be modified by choosing suitable combinations of the gain center frequency and linewidth, a result that cannot be obtained using the conventional approach of quasi-bound modes. The impact of the gain transition center on the lasing frequencies, the frequency pulling effect, is also quantified.

Gagnon, Denis; Déziel, Jean-Luc; Dubé, Louis J

2014-01-01

109

Stretching siloxanes: An ab initio molecular dynamics study  

Science.gov (United States)

We present an ab initio molecular dynamics study of siloxane elastomers placed under tensile stress for comparison with single molecule AFM experiments. Of particular interest is stress-induced chemical bond breaking in the high force regime, where a description of the molecular electronic structure is essential to determine the rupture mechanism. We predict an ionic mechanism for the bond breaking process with a rupture force of 4.4 nN for an isolated siloxane decamer pulled at a rate of 27.3 m/s and indicate lower values at experimental polymer lengths and pulling rates.

Lupton, E. M.; Nonnenberg, C.; Frank, I.; Achenbach, F.; Weis, J.; Bräuchle, C.

2005-10-01

110

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

111

Ab-Initio Shell Model with a Core  

Energy Technology Data Exchange (ETDEWEB)

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

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

2008-06-04

112

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)

113

Stabilization of planar hexacoordinate boron: ab initio study  

International Nuclear Information System (INIS)

Using ab initio (MP2 (full)/6-31 G**) and DFT (B3LYP/6-311 + + G**) potentiality of existence of a stable anion BB6 (NH2)2- with a plane hexacoordinated boron atom was predicted and influence of Li+ counter ion on its stability and structural characteristics was studied. Transfer from isolated anion to lithium salt involves inessential upsetting of planarity of the central hypercoordinated node. The B-Li bond length amounts to 2.17-2.33 A, according to different levels of the calculation, being within standard values of ordinary bonds

114

Ab initio study of the structural, elastic, thermodynamic, electronic and vibration properties of TbMg intermetallic compound  

Science.gov (United States)

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

115

Ab initio MO and quasi-classical direct ab initio MD studies on the nitrogen inversion of trimethylamine  

Science.gov (United States)

A coupled motion of the skeletal inversion and methyl torsion in trimethylamine is investigated theoretically at various levels up to MP4(SDQ)/aug-cc-pVTZ. Among possible structures, the pyramidal C 3v is the only minimum energy structure, and the planar C s is the transition state structure of the nitrogen inversion. Our best estimate of the barrier height (without zero-point energy) is 3290 cm -1. The quasi-classical direct ab initio MD using HF/6-31G* starting from the pyramidal C 3v structure indicates that the coupled methyl torsional motion is the primary factor for the nitrogen inversion of trimethylamine.

Tanaka, Masato; Aida, Misako

2006-01-01

116

GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders.  

Science.gov (United States)

We present three programs for ab initio gene prediction in eukaryotes: Exonomy, Unveil and GlimmerM. Exonomy is a 23-state Generalized Hidden Markov Model (GHMM), Unveil is a 283-state standard Hidden Markov Model (HMM) and GlimmerM is a previously-described genefinder which utilizes decision trees and Interpolated Markov Models (IMMs). All three are readily re-trainable for new organisms and have been found to perform well compared to other genefinders. Results are presented for Arabidopsis thaliana. Cases have been found where each of the genefinders outperforms each of the others, demonstrating the collective value of this ensemble of genefinders. These programs are all accessible through webservers at http://www.tigr.org/software. PMID:12824375

Majoros, William H; Pertea, Mihaela; Antonescu, Corina; Salzberg, Steven L

2003-07-01

117

Electron propagator theory approach to ab initio calculations of electron transfer rate and molecular conductance  

Science.gov (United States)

The ab initio theoretical approach to calculations of molecular electron transfer rate and molecular junction conductance is presented. The implemented approach is founded on Landauer formalism coupled to electron propagator theory (Green-Keldysh functions formalism) of solving the Dyson equation for molecular junction. The electron transfer rate calculation algorithm implementing quantum chemistry computational software output is proposed. The conductance through a single molecular orbital is found to be equal to a quantum of conductance, 2e2/h. The existence of the maximal value of electron transfer rate through a single molecular orbital is proposed, (?2/4h)?L?RF, whose order-of-magnitude estimate is 1011-1013 s-1.

Kletsov, Aleksey A.

2014-09-01

118

Computer simulation of trifluoromethane properties with ab initio force field.  

Science.gov (United States)

Intermolecular interaction potentials of the trifluoromethane dimer in 15 orientations have been calculated using the Hartree-Fock (HF) self-consistent theory and the second-order Møller-Plesset (MP2) perturbation theory. Single point energies at important geometries were also calibrated by the coupled cluster with single and double and perturbative triple excitation [CCSD(T)] calculations. We have employed Pople's medium size basis sets [up to 6-311++G(3df,3pd)] and Dunning's correlation consistent basis sets (up to aug-cc-pVQZ). Basis set limit potential values were obtained through well-studied extrapolation methods. The calculated MP2 potential data were employed to parameterize a 5-site force field for molecular simulations. We performed molecular dynamics simulations using the constructed ab initio force field and compared the simulation results with experiments. Quantitative agreements for the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions can be obtained, thus validating the ab initio force field without using experimental data a priori. PMID:21598276

Chung, Yi-Hsing; Li, Arvin Huang-Te; Chao, Sheng D

2011-08-01

119

The density matrix renormalization group for ab initio quantum chemistry  

Science.gov (United States)

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 systematically increased until numerical convergence is reached. The MPS ansatz naturally captures exponentially decaying correlation functions. Therefore DMRG works extremely well for noncritical one-dimensional systems. The active orbital spaces in quantum chemistry are however often far from one-dimensional, and relatively large virtual dimensions are required to use DMRG for ab initio quantum chemistry (QC-DMRG). The QC-DMRG algorithm, its computational cost, and its properties are discussed. Two important aspects to reduce the computational cost are given special attention: the orbital choice and ordering, and the exploitation of the symmetry group of the Hamiltonian. With these considerations, the QC-DMRG algorithm allows to find numerically exact solutions in active spaces of up to 40 electrons in 40 orbitals.

Wouters, Sebastian; Van Neck, Dimitri

2014-09-01

120

Semiconductor alloys for optoelectronic applications: ab initio modeling  

Science.gov (United States)

Semiconductor alloys, for example group III metal nitrides and phosphides, such as AxB1-xN or ANxP1-x (where A,B metal atoms: Al, In, Ga) have been materials of interest for optoelectronic applications (light emitting diodes, lasers, detectors) for more then two decades. The potential possibility of tuning (via variation of the composition) of the band-gap and the lattice constant make them particularly attractive. The idea of tuning the band-gap (from infrared to ultraviolet), although simple in principle, requires solving a variety of practical problems, like lattice constants misfit of parent compounds, associated with atom sizes, thermodynamically determined phase segregation, system stability, band-gap bowing, efficiency of radiative transitions etc. The ab initio modeling is of particular importance in the field, since it allows to predict in a purely theoretical way the physical limits for various properties. It also provides a hint in which direction, technologically and experimentally, to proceed. We present the basic ideas behind the ab initio modeling and, as an example, the calculation results of structural, elastic and the electronic properties of chosen alloys are presented.

Scharoch, Pawel; Winiarski, Maciej; Polak, Maciej

2013-10-01

 
 
 
 
121

Ab initio thermodynamic model for magnesium carbonates and hydrates.  

Science.gov (United States)

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

Chaka, Anne M; Felmy, Andrew R

2014-09-01

122

Accessing the limits of ab initio docking methods  

Science.gov (United States)

Ab initio protein docking is the prediction of the three dimensional structure of a protein-protein complex from the structures of two interacting proteins, receptor and ligand. Here we report our instigation of the performance of several popular ab initio docking algorithms (ZDOCK, GRAMM and 3D-Garden) in a bound test (lock-and-key) on very large set of 2903 cases taken from ProCom database. The bound test was preferred over the unbound because of two reasons (1) to test the performance of docking algorithms without obscuring the results with the effects originating from possible conformational changes and (2) to expand the benchmarking set since we do not need the 3D structures of isolated monomers. The assessment of the predictions was made by computing the ligand RMSD (L/RMSD). The first ten ranked predictions were taken. It was found that, on average, only 28% of the predictions resulted in L/RMSD < 10 A, which is the standard criterion of acceptable models in CAPRI. The performance of the methods was investigated with respect to physical characteristics of the receptor and ligand as well.

Shyam, Radhey; Alexov, Emil

2009-11-01

123

Ab Initio Molecular Dynamics Simulation of Liquid and Amorphous Te  

Science.gov (United States)

Contrary to almost all other elements, liquid and amorphous phases of pure tellurium have proven difficult to simulate using ab initio molecular dynamics. Standard DFT calculations yield structures in relatively poor agreement with available diffraction experiments, especially regarding first neighbor distance and coordination number. In this work, we use ab initio molecular dynamics to simulate liquid Tellurium and test different exchange correlation functionals and approximations to show their influence on liquid and amorphous structures. In particular, we show that the treatment of dispersion forces is yielding a clear improvement over recent hybrid functional calculations, with significant local order modifications in both phases. Especially, the structure evolution along the density anomaly is shown to be related to the creation of many interconnections between Te chains, these chains having increasing lengths upon temperature reduction. In the amorphous phase, Te chains are almost perfectly isolated with specific dihedral angle distributions. These structural changes are reflected on dynamical properties, such as atomic diffusion coefficient and vibrational density of states. We then apply the same method to revisit the structure of some Te based alloys.

Raty, Jean-Yves; Baris Malcioglu, Osman; Bichara, Christophe

2013-03-01

124

Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates  

Energy Technology Data Exchange (ETDEWEB)

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

Chaka, Anne M.; Felmy, Andrew R.

2014-03-28

125

Ab Initio Studies of Liquid and Amorphous Ge  

CERN Document Server

We review our previous work on the dynamic structure factor S(k,omega) of liquid Ge (l-Ge) at temperature T = 1250 K, and of amorphous Ge (a-Ge) at T = 300 K, using ab initio molecular dynamics [Phys. Rev. B67, 104205 (2003)]. The electronic energy is computed using density-functional theory, primarily in the generalized gradient approximation, together with a plane wave representation of the wave functions and ultra-soft pseudopotentials. We use a 64-atom cell with periodic boundary conditions, and calculate averages over runs of up to 16 ps. The calculated liquid S(k,omega) agrees qualitatively with that obtained by Hosokawa et al, using inelastic X-ray scattering. In a-Ge, we find that the calculated S(k,omega) is in qualitative agreement with that obtained experimentally by Maley et al. Our results suggest that the ab initio approach is sufficient to allow approximate calculations of S(k,omega) in both liquid and amorphous materials.

Chai, J D

2004-01-01

126

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)

127

Ab initio theory and calculations of X-ray spectra; Theorie et calculs ab initio des spectres de rayons X  

Energy Technology Data Exchange (ETDEWEB)

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

Rehr, J.J.; Kas, J.J.; Prange, M.P.; Sorini, A.P.; Takimoto, Y.; Vila, F. [Washington Univ., Dept. of Physics, Seattle, WA (United States)

2009-07-15

128

NestedMICA as an ab initio protein motif discovery tool  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background Discovering overrepresented patterns in amino acid sequences is an important step in protein functional element identification. We adapted and extended NestedMICA, an ab initio motif finder originally developed for finding transcription binding site motifs, to find short protein signals, and compared its performance with another popular protein motif finder, MEME. NestedMICA, an open source protein motif discovery tool written in Java, is driven by a Monte Carlo technique called Nested Sampling. It uses multi-class sequence background models to represent different "uninteresting" parts of sequences that do not contain motifs of interest. In order to assess NestedMICA as a protein motif finder, we have tested it on synthetic datasets produced by spiking instances of known motifs into a randomly selected set of protein sequences. NestedMICA was also tested using a biologically-authentic test set, where we evaluated its performance with respect to varying sequence length. Results Generally NestedMICA recovered most of the short (3–9 amino acid long test protein motifs spiked into a test set of sequences at different frequencies. We showed that it can be used to find multiple motifs at the same time, too. In all the assessment experiments we carried out, its overall motif discovery performance was better than that of MEME. Conclusion NestedMICA proved itself to be a robust and sensitive ab initio protein motif finder, even for relatively short motifs that exist in only a small fraction of sequences. Availability NestedMICA is available under the Lesser GPL open-source license from: http://www.sanger.ac.uk/Software/analysis/nmica/

Down Thomas A

2008-01-01

129

Quasi-Ab initio molecular dynamic study of Fe melting  

Science.gov (United States)

We have investigated the melting of hcp Fe at high pressure by employing molecular dynamics simulations in conjunction with the full potential linear muffin tin orbital method. Apart from being of fundamental value, the melting of iron at high pressure is also important for our understanding of the Earth. The subject of iron melting at high pressures is controversial. The experimental data for the iron melting temperature can be separated into two regions, "low" and "high." Here we present an ab initio simulated iron melting curve which is in agreement with the low temperatures at lower pressures, but is in excellent agreement with the high-mostly shockwave-temperatures at high pressures. A comparison with available data lends support to the presented iron melting curve. PMID:11019165

Belonoshko; Ahuja; Johansson

2000-04-17

130

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)

131

Ab initio study of alanine polypeptide chains twisting  

CERN Document Server

We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable corres...

Solovyov, I A; Solovyov, A V; Yakubovitch, A V; Greiner, Walter; Solov'yov, Andrey V.; Solov'yov, Ilia A.; Yakubovitch, Alexander V.

2005-01-01

132

Ab-initio melting curve and principal Hugoniot of tantalum  

International Nuclear Information System (INIS)

We report first principles calculations of the melting curve and principal Hugoniot (P - V curve) of body centered cubic (bcc) tantalum in the pressure range 0-300 GPa. A description of lattice dynamics and thermal properties of bcc Ta using finite temperature density functional theory (DFT) is presented. The approach works within the projector augmented wave (PAW) implementation of DFT and explicitly treats in valence the 5p, 6s and 5d electrons. The principal Hugoniot (P - V curve), obtained using the Rankine-Hugoniot equation, is investigated using the generalized gradient approximations (GGA). Very good agreement with the shock experiments is obtained with GGA in all the range of pressure. We also report the temperature-pressure relation on the shock Hugoniot and the full ab-initio melting curve of Ta

133

Ab-initio melting curve and principal Hugoniot of tantalum  

Energy Technology Data Exchange (ETDEWEB)

We report first principles calculations of the melting curve and principal Hugoniot (P - V curve) of body centered cubic (bcc) tantalum in the pressure range 0-300 GPa. A description of lattice dynamics and thermal properties of bcc Ta using finite temperature density functional theory (DFT) is presented. The approach works within the projector augmented wave (PAW) implementation of DFT and explicitly treats in valence the 5p, 6s and 5d electrons. The principal Hugoniot (P - V curve), obtained using the Rankine-Hugoniot equation, is investigated using the generalized gradient approximations (GGA). Very good agreement with the shock experiments is obtained with GGA in all the range of pressure. We also report the temperature-pressure relation on the shock Hugoniot and the full ab-initio melting curve of Ta.

Taioli, S; Alfe, D [Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT (United Kingdom); Cazorla, C; Gillan, M J [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT (United Kingdom)

2008-07-15

134

Ab initio based multiscale modeling of alloy surface segregation  

International Nuclear Information System (INIS)

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.

135

Ab initio based multiscale modelling for materials science  

International Nuclear Information System (INIS)

Materials modelling of extended defects in semiconductors (and many other systems) requires both detailed electronic models of matter to account for bond breaking and formation at the atomic scale and the representation of material systems at large scales, in the micrometre–microsecond range. These twin demands, if implemented directly by ab initio calculations, are unachievable with potentially available computational resources for the foreseeable future. An alternative approach is to develop multiscale simulations, where the level of simulation detail can vary in time and space, thus saving on computational cost without sacrificing the necessary detailed modelling. This paper introduces the basic concepts and reviews some progress in this field, and the related challenges along two main strands: (i) sequential multiscale modelling to construct larger-scale material models from first principles and (ii) hybrid multiscale modelling for the description of unitary systems which are too large for monoscale modelling at the desired accuracy

136

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

Science.gov (United States)

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

Olsson, P; Vidal, J; Lincot, D

2011-10-12

137

Ab initio description of the exotic unbound 7He nucleus  

CERN Document Server

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

Baroni, Simone; Quaglioni, Sofia

2012-01-01

138

Ab initio based multiscale modeling of alloy surface segregation  

Science.gov (United States)

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

139

Ab initio based multiscale modeling of alloy surface segregation.  

Science.gov (United States)

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

140

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

 
 
 
 
141

Ab initio theory of spin-transfer torques  

Energy Technology Data Exchange (ETDEWEB)

We develop an ab initio material-specific theory of current induced magnetization switching. The formulation is based on non-equilibrium Green's functions (NEGF) formalism applied to the so-called spin-mixing conductance, i.e., the linear response of the spin torque exerted on a magnetic layer to a spin accumulation in an adjacent non-magnetic layer. The numerical implementation employs the local spin density approximation (LSDA) and the linear muffin-tin orbital (LMTO) method. Possible substitutional disorder is treated using the coherent potential approximation (CPA) that allows for evaluation of the coherent (ballistic) and incoherent (diffusive) parts of the spin-mixing conductance. The developed scheme is applied to a few selected magnetic layers including systems containing diluted magnetic semiconductors and Heusler alloys. Their halfmetallic character leads to enhanced spin-mixing conductances with respect to charge conductances.

Carva, Karel [Charles University, Faculty of Mathematics and Physics, Department of Condensed Matter Physics, Ke Karlovu 5, CZ-12116 Prague 2 (Czech Republic)]. E-mail: carva@karlov.mff.cuni.cz; Turek, Ilja [Institute of Physics of Materials, Academy of Sciences of the Czech Republic, Zizkova 22, CZ-61662 Brno (Czech Republic)

2007-09-15

142

Ab initio theory of spin-transfer torques  

International Nuclear Information System (INIS)

We develop an ab initio material-specific theory of current induced magnetization switching. The formulation is based on non-equilibrium Green's functions (NEGF) formalism applied to the so-called spin-mixing conductance, i.e., the linear response of the spin torque exerted on a magnetic layer to a spin accumulation in an adjacent non-magnetic layer. The numerical implementation employs the local spin density approximation (LSDA) and the linear muffin-tin orbital (LMTO) method. Possible substitutional disorder is treated using the coherent potential approximation (CPA) that allows for evaluation of the coherent (ballistic) and incoherent (diffusive) parts of the spin-mixing conductance. The developed scheme is applied to a few selected magnetic layers including systems containing diluted magnetic semiconductors and Heusler alloys. Their halfmetallic character leads to enhanced spin-mixing conductances with respect to charge conductances

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

Ab initio molecular dynamics study on photodissociation of polydimethylsiloxane  

International Nuclear Information System (INIS)

The periodic boundary conditions structure of polydimethylsiloxane (PDMS) with two repeat units is full optimized using B3LYP/6-31G(d) method and the photodissociation of PDMS is studied using ab initio molecular dynamics (AIMD) method. The result shows that the hydrogen atom attached to methyl is the easiest cracking type in the bond dissociation process. Through the whole trajectory of PDMS, the C-H bond is the first one to disassociate, which produce H radical and silicone-methyl radical. And then the C-Si bonds break up into methyl radical and main chain radical. The calculated result agrees with the gamma radiolysis gases of PDMS in our early experiment data. (authors)

145

Ab initio study of II-(VI){sub 2} dichalcogenides  

Energy Technology Data Exchange (ETDEWEB)

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

Olsson, P; Vidal, J; Lincot, D, E-mail: polsson@kth.se [Institut de R and D sur l' energie photovoltaique (IRDEP), UMR 7174-EDF-CNRS-ENSCP, 6 quai Watier, 78401 Chatou Cedex (France)

2011-10-12

146

Tailoring exchange interactions in engineered nanostructures: an ab initio study.  

Science.gov (United States)

We present a novel approach to spin manipulation in atomic-scale nanostructures. Our ab initio calculations clearly demonstrate that it is possible to tune magnetic properties of subnanometer structures by adjusting the geometry of the system. By the example of two surface-based systems we demonstrate the following. (i) The magnetic moment of a single adatom coupled to a buried magnetic Co layer can be stabilized in either a ferromagnetic or an antiferromagnetic configuration depending on the spacer thickness. It is found that a buried Co layer has a profound effect on the exchange interaction between two magnetic impurities on the surface. (ii) The exchange interaction between magnetic adatoms can be manipulated by introducing artificial nonmagnetic Cu chains to link them. PMID:18764280

Brovko, O O; Ignatiev, P A; Stepanyuk, V S; Bruno, P

2008-07-18

147

Ab initio calculation of molecular energies including parity violating interactions  

International Nuclear Information System (INIS)

udies of Epv. To this end, we have completely reproduced the previous work, which has been done in the RHF-SDE frame-work, and developed it further, studying how the RHF-SDE results vary when changing size and quality of basis sets. This last resource does not save the RHF-SDE formalism for evaluations of Epv from the general failure. Packages of FORTRAN routines called ENWEAK/RHFSDE-93 and ENWEAK/RHFCIS-94 have been developed which run on top of an ab initio MO package. We used 6-31G and 6-31G**, DZ and DZ**, TZ and TZ**, and (10s, 6p,**) basis sets. We will discuss the importance of the present results for possible measurement of the parity violating energy difference between enantiomers of chiral molecules. (author). Abstract only

148

Ab initio calculations on the thermodynamic properties of azaspiropentanes.  

Science.gov (United States)

Following our recent study on the usefulness of borospiropentanes as new potential high-energy materials, we propose a new series of substituted spiropentane molecules, the azaspiropentanes. Presented here are the results of our ab initio calculations at the MP2 and B3LYP levels of theory using the 6-311++G(d,p) basis set. Results include optimized structural parameters, enthalpies of formation, specific enthalpies of combustion, and proton affinities. Our results indicate that azaspiropentane gives off the most energy of any of the nitrogen-containing spiropentanes, as indicated by its specific enthalpy of combustion of -41 kJ g(-1); however, it does not give off as much energy as spiropentane itself, which gives off about 48 kJ g(-1). PMID:18311947

Richard, Ryan M; Ball, David W

2008-03-27

149

Quantitative Verification of Ab Initio Self-consistent Laser Theory  

CERN Document Server

We generalize and test the recent "ab initio" self-consistent (AISC) time-independent semiclassical laser theory. This self-consistent formalism generates all the stationary lasing properties in the multimode regime (frequencies, thresholds, internal and external fields, output power and emission pattern) from simple inputs: the dielectric function of the passive cavity, the atomic transition frequency, and the transverse relaxation time of the lasing transition. We find that the theory gives excellent quantitative agreement with full time-dependent simulations of the Maxwell-Bloch equations after it has been generalized to drop the slowly-varying envelope approximation. The theory is infinite order in the non-linear hole-burning interaction; the widely used third order approximation is shown to fail badly.

Ge, Li; Stone, A Douglas; Türeci, Hakan E

2008-01-01

150

Ab initio studies on complexes formed by melamine and cyclotrione  

Directory of Open Access Journals (Sweden)

Full Text Available Ab initio methods were used to study the binding energies of non-bonded complexes formed by melamine and cyclotrione, with the STO-3G, 3-21G and 6-31G (d basis sets. The electronic spectra were computed using the INDO/CIS method, and the IR spectra, Raman and NMR spectra with the RHF/6-31G (dmethod. It was demonstrated that the complexes could be formed because of the negative binding energies, which were changed with the change in the electronic properties of the monomers. A red-shift of the first absorptions in the electronic spectra and the vibrational frequencies of the N–H bonds in the IR and Raman spectra of the complexes, compared with those of the monomers, occurred; simultaneously, the 1Hand 13C chemical shifts were altered, due to the non-bonded interaction.

LIANGIANG ZHU

2007-04-01

151

Self-vacancies in Gallium Arsenide: an ab initio calculation  

CERN Document Server

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

152

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

Science.gov (United States)

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

153

Ab initio study of the electronic spectrum of peroxyacetyl nitrate.  

Science.gov (United States)

A theoretical study of the ground and excited states of peroxyacetyl nitrate (PAN), CH3C(O)OONO2, has been carried out using high level ab initio molecular orbital methods. The ground state geometry and vibrational frequencies are calculated using the coupled-cluster method. The vertical excitation energies for the lowest three excited states are calculated using the complete active space self-consistent field method along with the multireference internally contracted configuration interaction method. These results are compared with vertical excitation energies calculated with the coupled cluster equation of motion method. The calculation provides relevant insight into the origin of PAN absorption in the UV wavelength region from 200 to 300 nm. The nature of the electron transitions for these excited states is discussed. PMID:15446924

Francisco, Joseph S; Li, Yumin

2004-10-01

154

Ab initio electronic structure calculations for high-k dielectrics  

Science.gov (United States)

In current semiconductor industry, continuing improvement in the performance of MOSFET requires aggressive scaling down of the dimensions of CMOS devices. A better capacitance/unit area can be gained as gate oxide thickness decreases. An equivalent oxide thickness (EOT) less than 1.0nm is required according to the 2002 International Technology Roadmap for Semiconductor (ITRS). However, as gate oxide thickness scaling down, tunneling current will increase, which will lower the device performance. SiO2, as the widely used gate oxide material, has reached its scaling limit due to the high current leakage at this thickness. Non-crystalline alloys of (i) group IIIB, IVB and VB TM oxides and (ii) first row RE oxides with SiO2 and Al 2O3 have been proposed as alternative high-k gate dielectrics for advanced Si devices. This dissertation addresses differences between the electronic structure of alternative high-k transition metal dielectrics and SiO2. Ab initio calculations, based on small clusters identify unique aspects of electronic structure that are associated with the TM atoms. The lowest conduction band states are derived from atomic d-states of the TM atoms, and are localized on these atoms. Excitations into these states (i) from TM core states, (ii) from oxygen K1, (iii) from oxygen atom derived valence band states, are simulated by using ab initio calculations at self-consistent-field (SCF) Hartree-Fock and Configuration Interaction (CI) level. And these electronic structure calculations are used to interpret optical, ultra-violet (UV), X-ray and electron spectroscopies, including UV and X-ray photoemission (UPS and XPS, respectively), and Auger electron spectroscopy (AES), and also provide a basis for interpretation of electrical results and narrowing the field of possible replacement dielectrics for advanced semiconductor devices.

Zhang, Yu

155

Raman spectra of BN-nanotubes: Ab-initio and bond-polarizability model calculations  

CERN Document Server

We present it ab-initio calculations of the non-resonant Raman spectra of zigzag and armchair BN nanotubes. In comparison, we implement a generalized bond-polarizability model where the parameters are extracted from first-principles calculations of the polarizability tensor of a BN sheet. For light-polarization along the tube-axis, the agreement between model and it ab-initio spectra is almost perfect. For perpendicular polarization, depolarization effects have to be included in the model in order to reproduce the it ab-initio Raman intensities.

Wirtz, L; Mauri, F; Rubio, A; Wirtz, Ludger; Lazzeri, Michele; Mauri, Francesco; Rubio, Angel

2005-01-01

156

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

Science.gov (United States)

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

Good, Brian S.

2004-01-01

157

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

International Nuclear Information System (INIS)

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

158

Ab-initio study of fluorine-doped tin dioxide: A prospective catalyst support for water electrolysis  

International Nuclear Information System (INIS)

In an attempt to identify new electrochemically stable catalyst supports for electrolysis of water, the electronic structure of SnO2 doped with different fluorine concentrations has been calculated using the Vienna ab-initio simulation package (VASP) in the projector-augmented wave (PAW) method with the general gradient approximation (GGA) for conducting the exchange-correlation corrections. The role of fluorine in improving the electronic conductivity is discussed. An increase in the density of electronic states at the Fermi level with increase in the concentration of fluorine incorporated into the main SnO2 matrix agrees well with published experimental observations. Despite a gradual decrease in the cohesive energies for the fluorine-doped tin oxide with increase in fluorine concentration, the doped material still remains an appropriate candidate for use as catalyst supports in water electrolysis warranting further experimental validation. -- Research Highlights: ? Fluorine-doped tin oxide is a potentially stable catalyst support for water electrolysis. ? Electronic conductivity dependence on fluorine concentration is determined by the electronic structure. ? Chemical and structural stability-marginal decrease compared to undoped oxide. ? Catalyst support-fluorine-doped tin oxide is a promising catalyst support for water electrolysis.

159

Current status of ab initio quantum chemistry study for oxygen electroreduction on fuel cell catalysts  

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

160

Ab initio methods to oxides, and atomic orbitals in te PAW framework  

International Nuclear Information System (INIS)

The accuracy of ab initio density functional theory calculations depends crucially on the applied exchange-correlation functional. In recent years, a true zoo of functionals has emerged in particular in the quantum chemistry community. All these developments were aimed on an improved description of different properties of molecules, solids and surfaces. In the first part of this thesis we apply four different exchange-correlation functionals (LDA, PBE, PBEsol and HSE03) to two model perovskites, namely SrTiO3 and BaTiO3. We evaluate structural, electronic and phonon properties in the high temperature cubic as well as the tetragonal distorted phase with special attention on the zone-centred phonon mode. Our results show that the ferroelectric instability strongly depends on the volume and to a lesser extent on the applied functional. The second part of the thesis concentrates on the description of the polar oxygen terminated surface of ZnO. In the simple ionic picture the surface is electrostatically unstable due to a diverging electrostatic energy and has to adopt a modified surface structure to compensate for the polarity. In a close collaboration with experiment, a novel reconstruction is suggested. The remarkable observation is that the previously investigated oxygen terminated surface behaves very different than the zinc terminated surface. The difference is explained by the different bond preferences of Zn and O atoms: as a d-element Zn atom of Zn and O atoms: as a d-element Zn atoms are more flexible than O atoms. The final part of the thesis concentrates on the implementation of a local basis set code in VASP. We derive all required formulas for an atomic orbital basis set expanded in spherical Bessel functions within the projector augmented wave framework. Particular emphasis was placed on an implementation that maintains to a very high accuracy the translational invariance of the Hamiltonian. The basis set was optimized to achieve this aim. This is demonstrated for few simple test cases. (author)

 
 
 
 
161

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

162

Ab initio no-core shell model calculations for light nuclei  

Digital Repository Infrastructure Vision for European Research (DRIVER)

An overview of the ab initio no-core shell model is presented. Recent results for light nuclei obtained with the chiral two-nucleon and three-nucleon interactions are highlighted. Cross section calculations of capture reactions important for astrophysics are discussed. The extension of the ab initio no-core shell model to the description of nuclear reactions by the resonating group method technique is outlined.

Navratil, Petr

2007-01-01

163

Ab initio determination of heavy oxide perovskite related structures from precession electron diffraction data  

Energy Technology Data Exchange (ETDEWEB)

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.

Boulahya, Khalid; Ruiz-Gonzalez, Luisa; Parras, Marina [Dpto. Quimica Inorganica, Facultad de Ciencias Quimicas, Universidad Complutense de Madrid, E28040 Madrid (Spain); Gonzalez-Calbet, Jose M. [Dpto. Quimica Inorganica, Facultad de Ciencias Quimicas, Universidad Complutense de Madrid, E28040 Madrid (Spain)], E-mail: jgcalbet@quim.ucm.es; Nickolsky, M.S. [NanoMEGAS, Boulevard Edmond Machtens 79, Brussels B-1080 (Belgium); Nicolopoulos, Stavros [Universidad Politecnica de Valencia/ITQ Avda de los Naranjos, Valencia 46022 (Spain); NanoMEGAS, Boulevard Edmond Machtens 79, Brussels B-1080 (Belgium)], E-mail: info@nanomegas.com

2007-06-15

164

Ab initio determination of heavy oxide perovskite related structures from precession electron diffraction data  

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

165

Ab initio calculations of As-vacancy interactions in silicon  

Energy Technology Data Exchange (ETDEWEB)

Atomistic simulation of a vacancy-assisted dopant diffusion in silicon needs details of the dopant-vacancy interaction, i.e., the potential as a functional of dopant-vacancy separations. In this paper, the authors present a detailed study on the energetics of As-vacancy reaction in silicon and the lattice distortions surrounding the As-vacancy defect by using an ab initio plane wave pseudopotential method and the density functional theory (DFT). A potential-energy diagram as a function of As-vacancy separation is provided, which can be used in the atomistic diffusion simulations. The authors also calculate the binding energy and the formation energy of different complexes such as AsV, As{sub 2}V and AsV{sub 2} (V represents vacancy). They find that the stable configuration of As{sub 2}V is As-V-As, while the stable configuration of AsV{sub 2} is As-V-V. The nature of the binding between As and vacancy is explained from the lattice distortions and the change of chemical bond configuration introduced by the As-vacancy complex.

Xie, J.; Chen, S.P.

1999-04-01

166

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

167

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

168

Ab Initio Study of Anisotropic Magnetism in US  

Science.gov (United States)

Among the uranium monochalcogenides US lies closest to the itinerant regime of f-electron behavior and exhibits strong magnetic anisotropy along the direction with magnetic moment of 1.55 ?B and a Curie temperature of 180 K. We have applied two different ab initio methods to investigate the origin in the electronic structure of the magnetic behavior. First, we have carried out full-potential Linearized Muffin-Tin Orbital (FPLMTO) polarized electronic structure calculations, with only spin-polarization (orbital polarization only via spin-orbit coupling) and also with explicit orbital polarization. While both calculations give the correct ground-state (ferromagnetic state), only the spin-and-orbitally polarized calculation gives an ordered moment of 1.61 ?B in agreement with experiment. Second, we have carried out first-principles calculations synthesizing 1) a phenomenological theory of orbitally driven magentism which incorporates the hybridization-induced and RKKY exchange interactions on an equal footing, and 2) FPLMTO electronic structure calculations allowing a first-principles evaluation of the parameters entering the model Hamiltonian. Results for the ordered moment and ordering temperature will be presented, and the validity and limitations of the two methods will be discussed.

Collins, Eric; Kioussis, Nicholas; Lim, Say-Peng; Cooper, Bernard R.

1998-03-01

169

An ab initio study of xenon retention in ?-quartz.  

Science.gov (United States)

It has recently been suggested that a significant amount of Xe can be absorbed in ?-quartz and that this might be a significant process in the recycling of Xe from the atmosphere to the interior of the Earth. This suggestion is tested by ab initio calculations of Xe in ?-quartz using DFT. Three distinct candidate sites for Xe absorption are identified-substitutional at the silicon vacancy (Xe@V(Si)), at the oxygen vacancy (Xe@V(O)) and at an interstitial site (Xe@I)-and each is shown to be mechanically stable at both P=0 and 2 GPa. The energetics and electronic properties of these defect structures are analysed and it is shown that there is an energy barrier to the absorption at all sites at T=0. If the Xe absorption is a single-stage process in a perfect crystal then the lowest formation energy barrier (at both P=0 and 2 GPa) is for Xe@I at the interstitial site. If absorption is a two-stage process due to vacancies being already present at finite temperatures, then the subsequent barrier to Xe absorption is much lower and Xe@V(Si) has the lowest formation energy. However, it should be expected that there will be a much higher density of oxygen vacancies available for Xe absorption under realistic Earth core conditions and so in this scenario it is to be expected that all three candidate sites should be occupied. PMID:21386255

Probert, M I J

2010-01-20

170

Ab initio and DFT studies on hydrolyses of phosphorus halides.  

Science.gov (United States)

Hydrolyses of phosphorus halides, (RO)(2)POX where R = H or Me and X = F or Cl, in the gas phase and in the reaction field have been investigated theoretically with ab initio and the density functional theory (DFT). The free energy of activation in the reaction field was also estimated using the Onsager method with a correction of entropy change and basis set superposition error (BSSE). The reaction of (MeO)(2)POF proceeds through a path with bifunctional catalysis regardless of the medium, but the reaction of (MeO)(2)POCl proceeds through bifunctional and general base catalysis in the gas phase and in water, respectively. The estimated free energy barrier of 23 kcal/mol for the hydrolysis of (MeO)(2)POF is in good agreement with the experimental values of 24 kcal/mol, and relative barrier of 3 kcal/mol to the (MeO)(2)POCl is also in good agreement with the experimental values of 5 kcal/mol of diisopropyl phosphorus halides ((Pr(i)O)(2)POX, X = F and Cl). PMID:15362131

Lee, Oh-Seuk; Yang, Kiyull; Kang, Keum Duck; Koo, In Sun; Kim, Chan-Kyung; Lee, Ikchoon

2004-11-15

171

Hydrogen adsorption on the ?-graphyne using ab initio calculations  

Science.gov (United States)

In this study, we use the Siesta ab initio code based on Density Functional Theory (DFT) to determine the feasibility of hydrogen storage on the ?-graphyne. We examined the effect of hydrogen adsorption on the structural properties, the density of states of this nano structure. Calculations were performed in the GGA and LDA approximations. We find that in the case of chemical adsorption of hydrogen, functional exchange-correlation PBE (GGA) in explaining chemical bonds have more accuracy and leads to more stable structures. Adsorption is chemical and the binding energy of single and double hydrogen adsorption is -2.28 eV and -3.48 eV, respectively. Our calculations show that the adsorption of one hydrogen atom induces a magnetic moment as 1 ?B, because of breaking of ?-bonds and generate unpaired electron and system find ferromagnetic configuration. Further analysis indicates that adsorption of second hydrogen eliminates magnetization and the semi metalic ?-graphyne structure attains a band gap of 2 eV upon hydrogenation.

Drogar, J.; Roknabadi, M. R.; Behdani, M.; Modarresi, M.; Kari, A.

2014-11-01

172

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

173

Ab initio study of phase transformations in boron nitride  

Science.gov (United States)

The structural properties and phase stability of the four common polytypes of boron nitride, cubic zinc blende (c-BN), hexagonal (h-BN), wurtzite (w-BN) and rhombohedral (r-BN), are studied by ab initio calculations. Electronic energies are calculated using an ultra soft pseudopotential method under the density-functional theory, and phonon dispersions are calculated using the first-principles force-constant method. The p-T phase diagrams of these four boron nitride phases are constructed with the quasiharmonic approximation. Direct compression simulations are then performed to find probable phase transformation paths among these polytypes, with additional energy calculations of plausible transition structures. The c-BN phase is the most thermodynamically stable in ambient conditions among these four polytypes, and the transformation between r-BN and c-BN has the smallest energy barrier. Direct transformation between h-BN and c-BN is far less favorable than indirect transformation, with w-BN or r-BN as an intermediate. The presence of structural defects is a key attribute in reducing the energy barrier of phase transformation. The results in this work offer theoretical clues to experimental data on c-BN film growth, particularly the absence of w-BN.

Yu, W. J.; Lau, W. M.; Chan, S. P.; Liu, Z. F.; Zheng, Q. Q.

2003-01-01

174

Ab initio simulations of MgO under extreme conditions  

Science.gov (United States)

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

175

Ab initio simulation of p-type silicon crystals  

Science.gov (United States)

Porous silicon (p-Si) morphology depends on several parameters of the crystalline silicon substrate such as doping type and carriers concentration. Experimental results on (p-Si) show that although in the porous samples carriers are greatly reduced, boron atoms remain in the bulk. The study of p-type silicon crystals substrates by means of ab initio computational simulations will help to understand how boron atoms behave during the electrochemical reaction of porous silicon (p-Si) fabrication. Here we studied the properties of p-types crystalline silicon models analyzed using the ABINIT code. We constructed 4 silicon crystal models with a maximum of 216 atoms by simulation cell. The optimized geometries and some electronic properties were obtained. We observed that around the boron impurity the crystal lattice is deformed because of the bonding length Si-B. The total energy increases with the number of boron atoms by simulation cell. The relative electronic densities indicated that the charge contributions to the dangling bond, produced by the presence of the boron impurity, are mainly distributed around its first silicon neighbors.

Loustau, E. R. L.; del Río, J. A.; Tagüeña-Martínez, J.; Sansores, L. E.; Nava, R.; de la Mora, M. B.

2012-09-01

176

Ab initio lattice dynamics: Methods, results, and applications  

Science.gov (United States)

The density-functional perturbation theory (DFPT) introduced by Baroni and co-workers, allows for the ab initio (parameter-free) calculation of lattice-dynamical properties. The method is sketched and set into relation to other approaches. Biased by personal view, we present current applications of the DFPT to the calculation of the harmonic lattice dynamics, i.e., phonon dispersion curves and eigenvectors for various systems ranging from insulators to metals. Since the phonon frequencies and eigenvectors are in extremely good agreement with the available experimental data the calculations have a very reliable predictive power for a number of crystals which have not yet been experimentally investigated. Within and beyond the harmonic approximation several thermal quantities can be calculated such as heat capacity, Debye-Waller factors, cumulants (for EXAFS experiments), and others, often with a precision exceeding the experimental one. Last but not least, the combination of the results of the DFPT with frozen-phonon techniques allows a straightforward calculation of nonlinear coefficients of the lattice potential such as anharmonic coupling coefficients, nonlinear dipole-moment coefficients, and Raman coupling constants. Within this context, numerical results are presented for Grüneisen constants, thermal expansion coefficients, various pressure and temperature effects, and Raman and infrared two-phonon spectra.

Strauch, D.; Pavone, P.; Mayer, A. P.; Karch, K.; Sterner, H.; Schmid, A.; Pletl, Th.; Bauer, R.; Schmitt, M.

177

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

Science.gov (United States)

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

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

2006-02-01

178

An efficient approach to ab initio Monte Carlo simulation  

International Nuclear Information System (INIS)

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

179

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

180

Computing vibrational spectra from ab initio molecular dynamics.  

Science.gov (United States)

We review several methods for the calculation of vibrational spectra from ab initio molecular dynamics (AIMD) simulations and we present a new implementation in the trajectory analyzer TRAVIS. In particular, we show mass-weighted power spectra, infrared spectra, and Raman spectra with corresponding depolarization ratios, which are based on time-correlation functions of velocities, dipole moments, and polarizabilities, respectively. Using the four organic molecules methanol, acetone, nitromethane, and pinacol as test systems, we compare the spectra from AIMD simulations of the isolated molecules in gas phase to static calculations relying on the harmonic approximation and to experimental spectra recorded in a nonpolar solvent. The AIMD approach turns out to give superior results when anharmonicity effects are of particular importance. Using the example of methanol, we demonstrate the application to bulk phase systems, which are not directly accessible by static calculations, but for which the AIMD spectra also provide a very good approximation to experimental data. Finally, we investigate the influence of simulation time and temperature in the AIMD on the resulting spectra. PMID:23416970

Thomas, Martin; Brehm, Martin; Fligg, Reinhold; Vöhringer, Peter; Kirchner, Barbara

2013-05-14

 
 
 
 
181

Ab initio molecular dynamics calculations of ion hydration free energies  

CERN Document Server

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

182

Ab Initio Description of p-Shell Hypernuclei  

CERN Document Server

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

183

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

184

Ab initio study of alanine polypeptide chain twisting  

DEFF Research Database (Denmark)

We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles ph$ and psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of the proteins folding process. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable correspondence of the most prominent minima on the calculated potential energy surfaces to the experimentally measured angles phi and psi for alanine chains appearing in native proteins. We have also investigated the influence of the secondary structure of polypeptide chains on the formation of the potential energy landscape. This analysis has been performed for the sheet and the helix conformations of chains of six amino acids.

Solov'yov, Ilia; Yakubovich, Alexander V.

2006-01-01

185

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

186

An ab initio study of plutonium oxides surfaces  

International Nuclear Information System (INIS)

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 PuO2 and ?-Pu2O3 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 PuO2 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 (pO2). We conclude that at room temperature and for pO2?10 atm., the polar O2-(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)

187

AN AB INITIO MODEL FOR COSMIC-RAY MODULATION  

Energy Technology Data Exchange (ETDEWEB)

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

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

2013-07-20

188

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

189

Cosmic-Ray Modulation: an Ab Initio Approach  

Science.gov (United States)

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

190

Ab Initio Study on the Densest Phase of Silica  

Science.gov (United States)

Recent improvements in detection methods have allowed for the observation of terrestrial exoplanets with 1~10 times Earth's mass, so-called "super-Earths". However, their interior is currently highly unclear, because understanding of the ultrahigh-pressure phase relations of major Earth and planetary materials still remains quite limited. Those should be clarified before developing models of the internal structures of such objects. So we tried to establish the ultrahigh-pressure and temperature phase relations of SiO2 silica by means of ab initio techniques and successfully discovered a new phase change from the pyrite to an unexpected Fe2P form above 600 GPa with an intermediate cotunnite form only at high temperatures (Tsuchiya and Tsuchiya, PNAS, 2011). Since this transition pressure in SiO2 is quite high and almost unreachable experimentally, we searched for substitutable low-P analogs and succeeded in confirming the Fe2P phase in TiO2 both theoretically and experimentally (Dekura, Tsuchiya, Kuwayama, and Tsuchiya, PRL, 2011), which proves that this phase is the densest one currently identified in major dioxides. Further calculations elucidated that this phase is yielded by the dissociation of some important silicate compounds of MgSiO3 and CaSiO3 in the conditions relevant to the mantle of super-Earths and the core of giant planets. Although the Fe2P structure has not been inferred for the high-pressure phase of silica, we found a surprisingly simple structural relationship between this phase and lower-pressure phase connected via an intermediate form unreported in dioxides so far. Research supported by KAKENHI (20001005, 21740379, 23540560) and the Ehime Univ G-COE program "Deep Earth Mineralogy".

Tsuchiya, T.

2011-12-01

191

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

Science.gov (United States)

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

192

Nonlinear elasticity in III-N compounds: Ab initio calculations  

Science.gov (United States)

We have studied the nonlinear elasticity effects in zinc-blende and wurtzite crystallographic phases of III-N compounds. Particularly, we have determined the pressure dependences of elastic constants in InN, GaN, and AlN by performing ab initio calculations in the framework of plane-wave pseudopotential implementation of the density-functional theory. The calculations have been performed employing two exchange-correlation functionals, one within the local density approximation and the other within the generalized gradient approximation. We have found that C11 , C12 in zinc-blende nitrides and C11 , C12 , C13 , C33 in wurtzite nitrides depend significantly on hydrostatic pressure. Much weaker dependence on pressure has been observed for C44 elastic constant in both zinc-blende and wurtzite phases. Further, we have examined the influence of pressure dependence of elastic constants on the pressure coefficient of light emission, dEE/dP , in wurtzite InGaN/GaN and GaN/AlGaN quantum wells. We have shown that the pressure dependence of elastic constants leads to a significant reduction of dEE/dP in nitride quantum wells. Finally, we have considered the influence of nonlinear elasticity of III-N compounds on the properties of hexagonal nitride quantum dots (QDs). For typical wurtzite GaN/AlN QDs, we have shown that taking into account pressure dependence of elastic constants results in the decrease of volumetric strain in the QD region by about 7%. Simultaneously, the average z component of the piezoelectric polarization in the QDs increases by 0.1MV/cm compared to the case when linear elastic theory is used. Both effects, i.e., decrease of volumetric strain as well as increase of piezoelectric field, decrease the band-to-band transition energies in the QDs.

?epkowski, S. P.; Majewski, J. A.; Jurczak, G.

2005-12-01

193

Ab initio molecular dynamics of liquid hydrogen chloride.  

Science.gov (United States)

We carried out an ab initio molecular dynamics simulation of liquid hydrogen chloride (l-HCl) at a temperature of 313 K. Comparison with inelastic neutron scattering data shows that the simulation achieves an overall good description of the structural correlations, improving significantly upon a description based on classical interaction potentials. Despite some minor differences between theory and experiment in the H-H partial structure factor, the simulation gives a description of the hydrogen bonding in impressive agreement with experiment, for both the amount and the bond-length distribution of the bonds. In the simulation, 40% of the molecules are nonbonded, while the hydrogen-bonded chains are short, principally consisting of dimers (25%) and trimers (15%). Neighboring molecules in the simulation are found to form L-shaped arrangements, like in the isolated (HCl)(2) dimer and in crystalline phases of HCl. The time correlation of the molecular-axis orientation is found to be characterized by a very short decay time (0.13 ps), consistent with the short length of the hydrogen-bonded chains. Other dynamical properties investigated in this work include the diffusion coefficient and the vibrational density of states. We evaluated the molecular dipole of the HCl molecule in the liquid using a definition based on the coupling of rotational modes to an external electric field. The average dipole moment (1.53 D) derived in this way is found to be considerably larger than for the isolated molecule (1.11 D). Our results show that the dipole moment in [script-l]-HCl undergoes large fluctuations, both in orientation and in modulus. Upon the onset of an external field, such dipole fluctuations concur to reduce the fluctuations of the dielectric response. PMID:15836234

Dubois, Vincent; Pasquarello, Alfredo

2005-03-15

194

Ab initio structure determination of interlayer expanded zeolites by single crystal rotation electron diffraction.  

Science.gov (United States)

Layered solids often form thin plate-like crystals that are too small to be studied by single-crystal X-ray diffraction. Although powder X-ray diffraction (PXRD) is the conventional method for studying such solids, it has limitations because of peak broadening and peak overlapping. We have recently developed a software-based rotation electron diffraction (RED) method for automated collection and processing of 3D electron diffraction data. Here we demonstrate the ab initio structure determination of two interlayer expanded zeolites, the microporous silicates COE-3 and COE-4 (COE-n stands for International Network of Centers of Excellence-n), from submicron-sized crystals by the RED method. COE-3 and COE-4 are built of ferrierite-type layers pillared by (-O-Si(CH3)2-O-) and (-O-Si(OH)2-O-) linker groups, respectively. The structures contain 2D intersecting 10-ring channels running parallel to the ferrierite layers. Because both COE-3 and COE-4 are electron-beam sensitive, a combination of RED datasets from 2 to 3 different crystals was needed for the structure solution and subsequent structure refinement. The structures were further refined by Rietveld refinement against the PXRD data. The structure models obtained from RED and PXRD were compared. PMID:24809825

Guo, Peng; Liu, Leifeng; Yun, Yifeng; Su, Jie; Wan, Wei; Gies, Hermann; Zhang, Haiyan; Xiao, Feng-Shou; Zou, Xiaodong

2014-07-21

195

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

196

Hydrogen adsorption on boron doped graphene: an ab initio study.  

Science.gov (United States)

(i) The electronic and structural properties of boron doped graphene sheets, and (ii) the chemisorption processes of hydrogen adatoms on the boron doped graphene sheets have been examined by ab initio total energy calculations. In (i) we find that the structural deformations are very localized around the boron substitutional sites, and in accordance with previous studies (Endo et al 2001 J. Appl. Phys. 90 5670) there is an increase of the electronic density of states near the Fermi level. Our simulated scanning tunneling microscope (STM) images, for occupied states, indicate the formation of bright (triangular) spots lying on the substitutional boron (center) and nearest-neighbor carbon (edge) sites. Those STM images are attributed to the increase of the density of states within an energy interval of 0.5 eV below the Fermi level. For a boron concentration of ?2.4%, we find that two boron atoms lying on the opposite sites of the same hexagonal ring (B1-B2 configuration) represents the energetically most stable configuration, which is in contrast with previous theoretical findings. Having determined the energetically most stable configuration for substitutional boron atoms on graphene sheets, we next considered the hydrogen adsorption process as a function of the boron concentration, (ii). Our calculated binding energies indicate that the C-H bonds are strengthened near boron substitutional sites. Indeed, the binding energy of hydrogen adatoms forming a dimer-like structure on the boron doped B1-B2 graphene sheet is higher than the binding energy of an isolated H(2) molecule. Since the formation of the H dimer-like structure may represent the initial stage of the hydrogen clustering process on graphene sheets, we can infer that the formation of H clusters is quite likely not only on clean graphene sheets, which is in consonance with previous studies (Hornekær et al 2006 Phys. Rev. Lett. 97 186102), but also on B1-B2 boron doped graphene sheets. However, for a low concentration of boron atoms, the formation of H dimer structures is not expected to occur near a single substitutional boron site. That is, the formation (or not) of H clusters on graphene sheets can be tuned by the concentration of substitutional boron atoms. PMID:21825632

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

2008-04-16

197

Imidazolium-based ionic liquids. 1-methyl imidazolium nitrate: thermochemical measurements and ab initio calculations.  

Science.gov (United States)

In this work data of the molar enthalpies of formation of the ionic liquid 1-methylimidazolium nitrate [H-MIM][NO3] was measured by means of combustion calorimetry. The molar enthalpy of fusion of [H-MIM][NO3] was measured using DSC. Experiments to vaporize the ionic liquid into vacuum or nitrogen stream in order to obtain vaporization enthalpy have been performed. Ab initio calculations of the enthalpy of formation in the gaseous phase have been performed for the ionic species using the G3MP2 theory. The combination of traditional combustion calorimertry with modern high-level ab initio calculations allow the determination of the molar enthalpy of vaporization of the ionic liquid under study. The ab initio calculations indicate that [H-MIM][NO3] is most probably separated into the neutral species methyl-imidazole and HNO3 in the gaseous phase at conditions of the vaporization experiments. PMID:19555083

Emel'yanenko, Vladimir N; Verevkin, Sergey P; Heintz, Andreas; Voss, Karsten; Schulz, Axel

2009-07-23

198

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

Science.gov (United States)

We have developed an empirical erbium-helium (Er-He) potential by fitting to the results calculated from the 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, L.; Ye, Y. T.; Fan, K. M.; Shen, H. H.; Peng, S. M.; Long, X. G.; Zhou, X. S.; Zu, X. T.; Gao, F.

2014-09-01

199

Un modelo multi-objetivo ab-initio para la predicción de plegamiento de proteínas a un nivel de conformaciones atómicas / A multi-objective Ab-initio model for protein folding prediction at an atomic conformation level  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Becerra Romero, David Camilo (2010) Un modelo multi-objetivo ab-initio para la predicción de plegamiento de proteínas a un nivel de conformaciones atómicas / A multi-objective Ab-initio model for protein folding prediction at an atomic conformation level. Maestría thesis, Universidad Nacional de Colombia.

Becerra Romero, David Camilo

2010-01-01

200

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

Science.gov (United States)

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

 
 
 
 
201

Ab initio Monte Carlo simulations for finite-temperature properties Application to lithium clusters and bulk liquid lithium  

CERN Document Server

Ab initio Monte Carlo simulations have been performed to determine the equilibrium properties of liquid lithium and lithium clusters at different temperatures. First-principles density-functional methods were employed to calculate the potential-energy change for each proposed change of configuration, which was then accepted or rejected according to the Metropolis Monte Carlo scheme. The resulting structural properties are compared to data from experimental measurements and ab initio molecular dynamics simulations. It is shown that accurate structural information can be obtained with ab initio Monte Carlo simulations at computational costs comparable to ab initio molecular dynamics methods. We demonstrate that ab initio Monte Carlo simulations for the properties of fairly large condensed-matter systems at nonzero temperatures are feasible.

Wang, S; Rikvold, P A; Wang, Sanwu; Mitchell, Steven J.; Rikvold, Per Arne

2004-01-01

202

Stabilization of Ab Initio Molecular Dynamics Simulations at Large Time Steps  

CERN Document Server

The Verlet method is still widely used to integrate the equations of motion in ab initio molecular dynamics simulations. We show that the stability limit of the Verlet method may be significantly increased by setting an upper limit on the kinetic energy of each atom with only a small loss in accuracy. The validity of this approach is demonstrated for molten lithium fluoride.

Tsuchida, Eiji

2014-01-01

203

Review on DFT and ab initio Calculations of Scalar Coupling Constants  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract: The present review summarizes the information available on the ab initio calculations of spin-spin nuclear coupling constants through hydrogen bonds or in van der Waals complexes. It also reports the sources of experimental data on nhJXY scalar couplings.

José Elguero

2003-02-01

204

Vibrational Properties of Hexagonal Boron Nitride: Inelastic X-Ray Scattering and AbInitio Calculations  

Science.gov (United States)

The phonon dispersion relations of bulk hexagonal boron nitride have been determined from inelastic x-ray scattering measurements and analyzed by ab initio calculations. Experimental data and calculations show an outstanding agreement and reconcile the controversies raised by recent experimental data obtained by electron-energy loss spectroscopy and second-order Raman scattering.

Serrano, J.; Bosak, A.; Arenal, R.; Krisch, M.; Watanabe, K.; Taniguchi, T.; Kanda, H.; Rubio, A.; Wirtz, L.

2007-03-01

205

Vibrational Properties of Hexagonal Boron Nitride: Inelastic X-Ray Scattering and Ab Initio Calculations  

International Nuclear Information System (INIS)

The phonon dispersion relations of bulk hexagonal boron nitride have been determined from inelastic x-ray scattering measurements and analyzed by ab initio calculations. Experimental data and calculations show an outstanding agreement and reconcile the controversies raised by recent experimental data obtained by electron-energy loss spectroscopy and second-order Raman scattering

206

Vibrational properties of hexagonal boron nitride: inelastic X-ray scattering and ab initio calculations.  

Science.gov (United States)

The phonon dispersion relations of bulk hexagonal boron nitride have been determined from inelastic x-ray scattering measurements and analyzed by ab initio calculations. Experimental data and calculations show an outstanding agreement and reconcile the controversies raised by recent experimental data obtained by electron-energy loss spectroscopy and second-order Raman scattering. PMID:17359168

Serrano, J; Bosak, A; Arenal, R; Krisch, M; Watanabe, K; Taniguchi, T; Kanda, H; Rubio, A; Wirtz, L

2007-03-01

207

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

International Nuclear Information System (INIS)

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

208

Magnetoelastic coupling in epitaxial magnetic films An ab-initio study  

CERN Document Server

A method is developed which allows to determine the first-order and the second-order magnetoelastic coefficients of a magnetic bulk material from the ab-initio calculation of the magnetocrystalline anisotropy energy as function of a prestrain. Excplicit results are given for bcc Fe, and they agree well with experimental data obtained from the magnetostrictive stress measurements for epitaxial Fe films.

Komelj, M; Komelj, Matej; Faehnle, Manfred

2000-01-01

209

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

210

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

211

An efficient and accurate molecular alignment and docking technique using ab initio quality scoring.  

Science.gov (United States)

An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561

Füsti-Molnár, László; Merz, Kenneth M

2008-07-14

212

Ab initio density functional approach for noncollinear molecular magnetism of multicenter metal clusters  

International Nuclear Information System (INIS)

We investigated the spin structure of a bi-pyramidal Cr5 cluster using ab initio linear combination of Gaussian type orbitals generalized spin density functional theory. We found that a three-dimensional spin state is most stable among several candidates for stable spin structures

213

Ab initio density functional approach for noncollinear molecular magnetism of multicenter metal clusters  

Science.gov (United States)

We investigated the spin structure of a bi-pyramidal Cr5 cluster using ab initio linear combination of Gaussian type orbitals generalized spin density functional theory. We found that a three-dimensional spin state is most stable among several candidates for stable spin structures.

Yamanaka, Shusuke; Takeda, Ryo; Kawakami, Takashi; Nakata, Kazuto; Sakuma, Toshihiro; Takada, Toshikazu; Yamaguchi, Kizashi

2004-05-01

214

Combining instanton theory and ab initio data to model tunneling dynamics  

Energy Technology Data Exchange (ETDEWEB)

To describe tunneling dynamics in polyatomic systems the Instanton formalism is combined with the complete potential-energy surface generated from ab-initio calculations. The applications range from the rate constant of molecular inversion in aziridine molecule, oxyranyl and dioxolanyl radical, to tunneling splittings in malonaldehyde and hydrogenoxalate anion, indoline, and tropolone, including mode-specific effects.

Smedarchina, Z. [Inst. of Organic Chemistry, Sofia (Bulgaria); Siebrand, W.; Zgierski, M.Z. [NRCC Ottawa (Canada); Zerbetto, F. [Univ. of Bologna (Italy)

1996-12-31

215

Combining instanton theory and ab initio data to model tunneling dynamics  

International Nuclear Information System (INIS)

To describe tunneling dynamics in polyatomic systems the Instanton formalism is combined with the complete potential-energy surface generated from ab-initio calculations. The applications range from the rate constant of molecular inversion in aziridine molecule, oxyranyl and dioxolanyl radical, to tunneling splittings in malonaldehyde and hydrogenoxalate anion, indoline, and tropolone, including mode-specific effects

216

The Raman Spectrum of Triclinic Albite: A Comparison Between Ab Initio Calculated and Measured Frequencies  

Science.gov (United States)

The Raman spectrum of triclinic low-albite is presented, where all 39 Ag modes are identified. A good agreement is found with ab initio calculations using the CRYSTAL14 program at the hybrid HF/DFT level, using WC1LYP Hamiltonian.

Aliatis, I.; Lambruschi, E.; Mantovani, L.; Bersani, D.; Ando, S.; Gatta, G. D.; Gentile, P.; Salvioli-Mariani, E.; Prencipe, M.; Tribaudino, M.; Lottici, P. P.

2014-06-01

217

Vibrational properties of hexagonal boron nitride: Inelastic X-ray scattering and ab initio calculations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The phonon dispersion relations of bulk hexagonal boron nitride have been determined from inelastic x-ray scattering measurements and analyzed by ab initio calculations. Experimental data and calculations show an outstanding agreement and reconcile the controversies raised by recent experimental data obtained by electron-energy loss spectroscopy and second-order Raman scattering.

Serrano, J.; Bosak, A.; Arenal, R.; Krisch, M.; Watanabe, K.; Taniguchi, M.; Kanda, H.; Rubio Secades, A?ngel; Wirtz, Ludger

2007-01-01

218

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

Science.gov (United States)

Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K+ ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K+ ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K+ ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K+ ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

Timko, Jeff; Kuyucak, Serdar

2012-11-01

219

Cálculo ab initio de intensidades Raman dinâmicas utilizando a teoria da resposta linear Ab initio calculation of dynamic Raman intensities using the linear response theory  

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.

Luciano N. Vidal

2003-08-01

220

Iron-chromium alloys and surfaces: from ab initio calculations to segregation isotherms; L'alliage fer-chrome et ses surfaces: des calculs ab initio aux isothermes de segregation  

Energy Technology Data Exchange (ETDEWEB)

As a first step, we calculated ab initio the solubility and mixing energies of iron and chromium that confirm previous calculations. The same methodology is used to calculate free surface energies of iron and chromium (100), (110), (111) and (211). Refuting extrapolations from high temperatures measurements, ab initio calculations show that chromium surface energies are always higher that iron ones. We also calculated the segregation energy of a chromium impurity in iron (100) which is endothermic. Finally, we propose an interaction model parameterized on the ab initio calculations that we use to calculate segregation isotherms. We show that the large difference in surface energies between chromium and iron we highlighted from ab initio calculations causes the surfaces to be always depleted in chromium. (authors)

Levesque, M.; Soisson, F.; Fu, C.C.; Nastar, M. [CEA, DEN, DMN, Service de Recherches de Metallurgie Physique, 91191 Gif-sur-Yvette, (France); Martinez, E. [Los Alamos National Laboratory, 87545 Los Alamos, New Mexico, (United States)

2011-07-01

 
 
 
 
221

Ab initio simulations of iron-nickel alloys at Earth's core conditions  

Science.gov (United States)

We report ab initio density functional theory calculations on iron-nickel (Fe?Ni) alloys at conditions representative of the Earth's inner core. We test different concentrations of Ni, up to ?39 wt% using ab initio lattice dynamics, and investigate the thermodynamic and vibrational stability of the three candidate crystal structures (bcc, hcp and fcc). First of all, at inner core pressures, we find that pure Fe transforms from the hcp to the fcc phase at around 6000 K. Secondly, in agreement with low pressure experiments on Fe-Ni alloys, we find the fcc structure is stabilised by the incorporation of Ni under core pressures and temperatures. Our results show that the fcc structure may, therefore, be stable under core conditions depending on the temperature in the inner core and the Ni content. Lastly, we find that within the quasi-harmonic approximation, there is no stability field for Fe?Ni alloys in the bcc structure under core conditions.

Côté, Alexander S.; Voc?adlo, Lidunka; Brodholt, John P.

2012-09-01

222

Ultracold mixtures of metastable He and Rb: Scattering lengths from ab initio calculations and thermalization measurements  

Science.gov (United States)

We have investigated the ultracold interspecies scattering properties of metastable triplet He and Rb. We performed state-of-the-art ab initio calculations of the relevant interaction potential, and measured the interspecies elastic cross section for an ultracold mixture of metastable triplet He4 and Rb87 in a quadrupole magnetic trap at a temperature of 0.5 mK. Our combined theoretical and experimental study gives an interspecies scattering length a4+87=+17-4+1a0, which prior to this work was unknown. More general, our work shows the possibility of obtaining accurate scattering lengths using ab initio calculations for a system containing a heavy, many-electron atom, such as Rb.

Knoop, S.; ?uchowski, P. S.; KÈ©dziera, D.; Mentel, ?.; Puchalski, M.; Mishra, H. P.; Flores, A. S.; Vassen, W.

2014-08-01

223

Molecular dynamics simulation of liquid carbon tetrachloride using ab initio force field.  

Science.gov (United States)

Intermolecular interaction potentials of the carbon tetrachloride dimer in 12 orientations have been calculated using the Hartree-Fock self-consistent theory and the second-order Moller-Plesset (MP2) perturbation theory. We have employed basis sets from Pople's medium size basis sets [up to 6-311++G(3df,3pd)] to Dunning's correlation consistent basis sets (up to aug-cc-pVQZ). The calculated MP2 potential data were employed to parametrize a four-site force field for molecular simulations. We performed molecular dynamics simulations using the ab initio force field and compared the simulation results to experiments. Quantitative agreements for the atomwise radial distribution functions, the self-diffusion coefficients, and the neutron and x-ray diffraction scattering functions over a wide range of experimental conditions can be obtained, thus validating the ab initio force field without using experimental data a priori. PMID:20095686

Li, Arvin Huang-Te; Huang, Shou-Cheng; Chao, Sheng D

2010-01-14

224

Ultracold mixtures of metastable He and Rb: scattering lengths from ab initio calculations and thermalization measurements  

CERN Document Server

We have investigated the ultracold interspecies scattering properties of metastable triplet He and Rb. We performed state-of-the-art ab initio calculations of the relevant interaction potential, and measured the interspecies elastic cross section for an ultracold mixture of metastable triplet $^4$He and $^{87}$Rb at a temperature of 0.5 mK. Our combined theoretical and experimental study gives an interspecies scattering length $a_{4+87}=+17^{+1}_{-4}$ $a_0$, which prior to this work was unknown. More general, our work shows the possibility of obtaining accurate scattering lengths using ab initio calculations for a system containing a heavy, many-electron atom, such as Rb.

Knoop, S; K?dziera, D; Mentel, ?; Puchalski, M; Mishra, H P; Flores, A S; Vassen, W

2014-01-01

225

Microscopic dynamics in liquid binary alloys: orbital-free ab-initio molecular dynamics studies  

Directory of Open Access Journals (Sweden)

Full Text Available We report an ab-initio molecular dynamics study on the collective excitations in several s-p bonded liquid binary alloys. Results are reported for the Li-Na, Li-Mg, K-Cs and Li-Ba liquid alloys at different concentrations, which display mass ratios ranging from ?3 for Li-Na to ?20 for Li-Ba, and varying ordering tendencies, ranging from strong homocoordinating in Li-Na to mildly heterocoordinating for one concentration of Li-Ba. The study has been carried out using the orbital free ab-initio molecular dynamics method, combined with local ionic pseudopotentials constructed within the same framework. We analyze the dependence of the collective modes on the concentration and the mass ratio of the alloy, finding a common behaviour for all systems notwithstanding the different ordering tendencies.

D.J.González

2008-03-01

226

Direct calculation of equilibrium constants for isotopic exchange reactions by ab initio molecular orbital theory  

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

227

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

Energy Technology Data Exchange (ETDEWEB)

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

Grinyer, G. F.; Bazin, D.; Gade, A.; Tostevin, J. A.; Adrich, P.; Bowen, M. D.; Brown, B. A.; Campbell, C. M.; Cook, J. M.; Glasmacher, T.; McDaniel, S.; Navratil, P.; Obertelli, A.; Quaglioni, S.; Siwek, K.; Terry, J. R.; Weisshaar, D.; Wiringa, R. B. (Physics); (Michigan State Univ.); (Univ. of Surrey); (LLNL)

2011-04-22

228

Ab initio force constant approach to phonon dispersion relations of diamond and graphite  

International Nuclear Information System (INIS)

The phonon dispersion relations of diamond and graphite are calculated using an ab initio force constant method. The force constants are calculated via a self-consistent supercell approach in the local-density approximation in terms of the Hellmann-Feynman forces induced by the displacement of a single atom in the supercell. For diamond our ab initio results are in very good agreement with the neutron inelastic scattering and Raman data. For graphite we find good agreement with the neutron data for the low-energy modes as well as with the reflections electron energy loss spectroscopy (REELS) and optical data at higher energies. Significant differences to the predictions of semi-empirical models appear. (orig.)

229

Ab-initio molecular dynamics simulations of liquid Hg-Pb alloys  

Science.gov (United States)

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-Pb alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-Pb mixtures (Hg30Pb70, Hg50Pb50 and Hg90Pb10) at 600K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and lead (l-Pb). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered three alloys. Among the all considered alloys, Hg50Pb50 alloy shows presence of more chemical ordering and presence of hetero-coordination.

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

2014-04-01

230

Ab initio parametrized model of strain-dependent solubility of H in ?-iron  

International Nuclear Information System (INIS)

The calculated effects of interstitial hydrogen on the elastic properties of ?-iron from our earlier work are used to describe the H interactions with homogeneous strain fields using ab initio methods. In particular, we calculate the H solublility in Fe subject to hydrostatic, uniaxial and shear strain. For comparison, these interactions are parametrized successfully using a simple model with parameters entirely derived from ab initio methods. The results are used to predict the solubility of H in spatially varying elastic strain fields, representative of realistic dislocations outside their core. We find a strong directional dependence of the H-dislocation interaction, leading to strong attraction of H by the axial strain components of edge dislocations and by screw dislocations oriented along the critical ?1?1?1? slip direction. We further find a H-concentration enhancement around dislocation cores, consistent with experimental observations. (paper)

231

Ab initio studies of equations of state and chemical reactions of reactive structural materials  

Science.gov (United States)

The motivations for the research issues addressed in this thesis are based on the needs of the aerospace structural analysis and the design community. The specific focus is related to the characterization and shock induced chemical reactions of multi-functional structural-energetic materials that are also known as the reactive structural materials and their reaction capabilities. Usually motivation for selection of aerospace structural materials is to realize required strength characteristics and favorable strength to weight ratios. The term strength implies resistance to loads experienced during the service life of the structure, including resistance to fatigue loads, corrosion and other extreme conditions. Thus, basically the structural materials are single function materials that resist loads experienced during the service life of the structure. However, it is desirable to select materials that are capable of offering more than one basic function of strength. Very often, the second function is the capability to provide functions of sensing and actuation. In this thesis, the second function is different. The second function is the energetic characteristics. Thus, the choice of dual functions of the material are the structural characteristics and energetic characteristics. These materials are also known by other names such as the reactive material structures or dual functional structural energetic materials. Specifically the selected reactive materials include mixtures of selected metals and metal oxides that are also known as thermite mixtures, reacting intermetallic combinations and oxidizing materials. There are several techniques that are available to synthesize these structural energetic materials or reactive material structures and new synthesis techniques constitute an open research area. The focus of this thesis, however, is the characterization of chemical reactions of reactive material structures that involve two or more solids (or condensed matter). The subject of studies of the shock or thermally induced chemical reactions of the two solids comprising these reactive materials, from first principles, is a relatively new field of study. The published literature on ab initio techniques or quantum mechanics based approaches consists of the ab initio or ab initio-molecular dynamics studies in related fields that contain a solid and a gas. One such study in the literature involves a gas and a solid. This is an investigation of the adsorption of gasses such as carbon monoxide (CO) on Tungsten. The motivation for these studies is to synthesize alternate or synthetic fuel technology by Fischer-Tropsch process. In this thesis these studies are first to establish the procedure for solid-solid reaction and then to extend that to consider the effects of mechanical strain and temperature on the binding energy and chemisorptions of CO on tungsten. Then in this thesis, similar studies are also conducted on the effect of mechanical strain and temperature on the binding energies of Titanium and hydrogen. The motivations are again to understand the method and extend the method to such solid-solid reactions. A second motivation is to seek strained conditions that favor hydrogen storage and strain conditions that release hydrogen easily when needed. Following the establishment of ab initio and ab initio studies of chemical reactions between a solid and a gas, the next step of research is to study thermally induced chemical reaction between two solids (Ni+Al). Thus, specific new studies of the thesis are as follows: (1) Ab initio Studies of Binding energies associated with chemisorption of (a) CO on W surfaces (111, and 100) at elevated temperatures and strains and (b) adsorption of hydrogen in titanium base. (2) Equations of state of mixtures of reactive material structures from ab initio methods. (3) Ab initio studies of the reaction initiation, transition states and reaction products of intermetallic mixtures of (Ni+Al) at elevated temperatures and strains. (4) Press-cure synthesis of Nano-nickel and nano-aluminum based reacti

Zaharieva, Roussislava

232

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2004-11-30

233

Effects of Mg II and Ca II ionization on ab-initio solar chromosphere models  

Science.gov (United States)

Acoustically heated solar chromosphere models are computed considering radiation damping by (non-LTE) emission from H(-) and by Mg II and Ca II emission lines. The radiative transfer equations for the Mg II k and Ca II K emission lines are solved using the core-saturation method with complete redistribution. The Mg II k and Ca II K cooling rates are compared with the VAL model C. Several substantial improvements over the work of Ulmschneider et al. (1987) are included. It is found that the rapid temperature rises caused by the ionization of Mg II are not formed in the middle chromosphere, but occur at larger atmospheric heights. These models represent the temperature structure of the 'real' solar chromosphere much better. This result is a major precondition for the study of ab-initio models for solar flux tubes based on MHD wave propagation and also for ab-initio models for the solar transition layer.

Rammacher, W.; Cuntz, M.

1991-01-01

234

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

International Nuclear Information System (INIS)

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

235

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.)

236

Nuclear quantum effects in liquid water from an ab initio force matching approach  

CERN Document Server

We have applied path integral simulations, in combination with new ab initio based water potentials, to investigate nuclear quantum effects in liquid water. Because direct ab initio path integral simulations are computationally expensive, a flexible water model is parameterized by force-matching to density functional theory-based molecular dynamics simulations. The resulting effective potentials provide an inexpensive replacement for direct \\textit{ab inito} molecular dynamics simulations and furthermore allow an efficient simulation of nuclear quantum effects. Static and dynamic properties of liquid water at ambient conditions are presented and the role of nuclear quantum effects, exchange-correlation functionals and dispersion corrections are discussed in regards to reproducing the experimental properties of liquid water.

Spura, Thomas; Habershon, Scott; Kühne, Thomas D

2014-01-01

237

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

Science.gov (United States)

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

238

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

239

Ab initio Hartree--Fock calculation of the elastic electron scattering cross section of sulphur hexafluoride  

International Nuclear Information System (INIS)

The ab initio Hartree--Fock calculation of the elastic electron scattering cross section of sulphur hexafluoride is reported. The integrals for the Born scattering amplitudes have been evaluated by a new simple technique, based on Gaussian quadrature. Spherical averaging was performed numerically; different techniques for spherical averaging are discussed. An estimated r/sub e/ structure was used and vibrational effects have been neglected. In order to assess the effect of the basis set on the intensities, calculations have been performed for the nitrogen molecule with six different basis sets. Using these results as a guide, a triple-zeta basis set, augmented with polarization functions and diffuse functions, was selected for SF6. The results confirm Bartell's hypothesis that the observed residuals from the independent atom model intensities are due to electronic bonding effects. It is suggested that, for very accurate electron diffraction work, the effect of electron redistribution has to be taken into account by ab initio calculations

240

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

CERN Document Server

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

 
 
 
 
241

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

Science.gov (United States)

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

242

Optimized Unrestricted Kohn-Sham Potentials from Ab Initio Spin Densities  

CERN Document Server

The reconstruction of the exchange-correlation potential from accurate ab initio electron densities can provide insights into the limitations of the currently available approximate functionals and provide guidance for devising improved approximations for density-functional theory (DFT). For open-shell systems, the spin density is introduced as an additional fundamental variable in Spin-DFT. Here, we consider the reconstruction of the corresponding unrestricted Kohn-Sham potentials from accurate ab initio spin densities. In particular, we investigate whether it is possible to reconstruct the spin exchange-correlation potential, which determines the spin density in spin-unrestricted Kohn-Sham-DFT, despite the numerical difficulties inherent to the optimization of potentials with finite orbital basis sets. We find that the recently developed scheme for unambiguously singling out an optimal optimized potential [J. Chem. Phys. 135, 244102 (2011)] can provide such spin potentials accurately. This is demonstrated fo...

Boguslawski, Katharina; Reiher, Markus

2012-01-01

243

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

Science.gov (United States)

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

Reevaluating electron-phonon coupling strengths: Indium as a test case for ab initio and many-body-theory methods  

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

245

Implementing the Keldysh formalism into the ab initio Gaussian Embedded Cluster Method for the calculation of quantum transport  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We discuss the key steps that have to be followed to calculate quantum transport out of equilibrium by means of the {\\it ab initio} Gaussian Embedded Cluster Method recently developed by the authors. Our main aim is to emphasize through several examples that, if a sufficiently large portion of the electrodes is included in the {\\it ab initio} calculation, which does also incorporate an electrochemical potential difference $\\mu_L-\\mu_R=eV$, there is no need to impose an elect...

Louis, E.; Verges, J. A.; Palacios, J. J.; Perez-jimenez, A. J.; Sanfabian, E.

2002-01-01

246

Ab initio potential energy surface for the highly nonlinear dynamics of the KCN molecule  

Energy Technology Data Exchange (ETDEWEB)

An accurate ab initio quantum chemistry study at level of quadratic configuration interaction method of the electronic ground state of the KCN molecule is presented. A fitting of the results to an analytical series expansion was performed to obtain a global potential energy surface suitable for the study of the associated vibrational dynamics. Additionally, classical Poincaré surfaces of section for different energies and quantum eigenstates were calculated, showing the highly nonlinear behavior of this system.

Párraga, H.; Arranz, F. J., E-mail: fj.arranz@upm.es; Benito, R. M., E-mail: rosamaria.benito@upm.es [Grupo de Sistemas Complejos, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid (Spain); Borondo, F., E-mail: f.borondo@uam.es [Departamento de Química and Instituto de Ciencias Matemáticas (ICMAT), Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid (Spain)

2013-11-21

247

Insights into Materials Properties from Ab Initio Theory : Diffusion, Adsorption, Catalysis & Structure  

Digital Repository Infrastructure Vision for European Research (DRIVER)

In this thesis, density functional theory (DFT) calculations and DFT based ab initio molecular dynamics simulations have been employed in order to gain insights into materials properties like diffusion, adsorption, catalysis, and structure. In transition metals, absorbed hydrogen atoms self-trap due to localization of metal d-electrons. The self-trapping state is shown to highly influence hydrogen diffusion in the classical over-barrier jump temperature region. Li diffusion in Li-N-H systems ...

Blomqvist, Andreas

2010-01-01

248

GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We present three programs for ab initio gene prediction in eukaryotes: Exonomy, Unveil and GlimmerM. Exonomy is a 23-state Generalized Hidden Markov Model (GHMM), Unveil is a 283-state standard Hidden Markov Model (HMM) and GlimmerM is a previously-described genefinder which utilizes decision trees and Interpolated Markov Models (IMMs). All three are readily re-trainable for new organisms and have been found to perform well compared to other genefinders. Results are presented for Arabidopsis ...

Majoros, William H.; Pertea, Mihaela; Antonescu, Corina; Salzberg, Steven L.

2003-01-01

249

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

DEFF Research Database (Denmark)

We have calculated the I-V characteristics of short chains of C-20 molecular cages between Al and Au leads with an ab initio formalism. The results indicate that a linear chain of such molecules acts primarily as metallic nanowires. The transmission, however, depends sensitively both on the orientation and distance between the individual C-20 molecules. Transport through the molecular chains is accompanied by a significant amount of charge transfer, which remains localized at the electrode/molecular interface.

Taylor, Jeremy Philip

2002-01-01

250

Ab initio investigation of elastic constants of superconducting MgB 2  

Science.gov (United States)

The five different elastic constants of the new superconducting MgB 2 are calculated by ab initio method using a density functional theory Hamiltonian with both correlation and exchange potentials. The results are compared with those from a recent FPLMTO calculation. The fully relaxed and isotropic bulk moduli were also estimated and the implication of their comparison is made, e.g., MgB 2 is less anisotropic than one would otherwise suppose on the basis of its `planar' crystal structure.

Islam, A. K. M. A.; Islam, F. N.

2001-11-01

251

I-PI: A Python interface for ab initio path integral molecular dynamics simulations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques...

Ceriotti, M.; More, J.; Manolopoulos, DE

2014-01-01

252

Scaling factors for ab initio vibrational frequencies: comparison of uncertainty models for quantified prediction  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Bayesian Model Calibration is used to revisit the problem of scaling factor calibration for semi-empirical correction of ab initio calculations. A particular attention is devoted to uncertainty evaluation for scaling factors, and to their effect on prediction of observables involving scaled properties. We argue that linear models used for calibration of scaling factors are generally not statistically valid, in the sense that they are not able to fit calibration data within their uncertainty l...

Pernot, Pascal

2008-01-01

253

Study of carvedilol by combined Raman spectroscopy and ab initio MO calculations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The novel cardioprotective drug carvedilol was studied by both Raman spectroscopy and ab initio molecular orbital methods (using the density functional theory approach). The spectra, acquired both for the solid samples and DMSO solutions as a function of pH, were assigned in view of the calculated wavenumbers and intensities, and also based on the experimental data obtained for individual compounds which comprise the molecule, namely carbazole and 1,2-dimethoxybenzene. The pH dependence of th...

Marques, M. P. M.; Oliveira, P. J.; Moreno, A. J. M.; Carvalho, L. A. E. Batista

2002-01-01

254

Electron ejection cross sections in electron and ion impact ionization: ab initio and semiempirical calculations  

International Nuclear Information System (INIS)

Ab initio calculations of single and double differential cross sections for ionization by fast, charged particles within the framework of Born approximation are presented. In addition, a semiempirical method based on the asymptotic Bethe-Born expansion is also discussed. Both are applied to ionization of helium by electrons and protons in an effort to assess their accuracy and validity. Agreement with experiment is quite good. The implications for other targets is discussed

255

High-pressure ion-thermal properties of metals from ab initio interatomic potentials  

International Nuclear Information System (INIS)

It has recently become possible for the first time to calculate ab initio two-ion and three-ion interatomic potentials in d-electron transition metals. The nature of these potentials for the 3d series metals is discussed. In the case of copper, where three-ion contributions may be neglected, application is made to the ion-thermal component of the equation of state and to the calculation of melting on the shock Hugoniot. 13 refs., 3 figs

256

High-pressure ion-thermal properties of metals from ab initio interatomic potentials  

Energy Technology Data Exchange (ETDEWEB)

It has recently become possible for the first time to calculate ab initio two-ion and three-ion interatomic potentials in d-electron transition metals. The nature of these potentials for the 3d series metals is discussed. In the case of copper, where three-ion contributions may be neglected, application is made to the ion-thermal component of the equation of state and to the calculation of melting on the shock Hugoniot. 13 refs., 3 figs.

Moriarty, J.A.

1985-06-01

257

Electronic transport coefficients from ab initio simulations and application to dense liquid hydrogen  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Using Kubo's linear response theory, we derive expressions for the frequency-dependent electrical conductivity (Kubo-Greenwood formula), thermopower, and thermal conductivity in a strongly correlated electron system. These are evaluated within ab initio molecular dynamics simulations in order to study the thermoelectric transport coefficients in dense liquid hydrogen, especially near the nonmetal-to-metal transition region. We also observe significant deviations from the wid...

Holst, Bastian; French, Martin; Redmer, Ronald

2012-01-01

258

Hydrogen and deuterium in shock wave experiments, ab initio simulations and chemical picture modeling  

CERN Document Server

We present equation of state data of shock compressed hydrogen and deuterium. These have been calculated in the physical picture by using {\\it ab initio} molecular dynamics simulations based on finite temperature density functional theory as well as in the chemical picture via the Saha-D model. The results are compared in detail with data of shock wave experiments obtained for condensed and gaseous precompressed hydrogen and deuterium targets in a wide range of shock compressions from low pressures up to megabars.

Holst, Bastian; Gryaznov, Victor K; Fortov, Vladimir E; Iosilevskiy, Igor L; 10.1140/epjd/e2012-20650-3

2012-01-01

259

Recent developments in ab-initio few-body scattering calculations including the Coulomb interaction  

International Nuclear Information System (INIS)

Recent progress on the solution of ab-initio three- and four-nucleon scattering equations in momentum space that include the correct treatment of the Coulomb interaction is reviewed; results for specific observables in reactions initiated by p + d, p + 3He and n + 3He are shown. In addition three-body calculations of d + 12C reactions are compared with equivalent CDCC calculations. Presented at the 20th Few-Body Conference, Pisa, Italy, 10-14 September 2007 (author)

260

Exchange interaction between magnetic nanowires on stepped and flat Cu surfaces: ab initio study  

Energy Technology Data Exchange (ETDEWEB)

We report on the ab initio study of the indirect exchange interaction between magnetic nanowires on flat and stepped Cu(111) surfaces. Several geometrical arrangements of Fe nanostructures on stepped and flat surfaces are considered. The exchange interaction is found to exhibit an oscillatory behavior and depends on the chain-chain separation. We compare the exchange interaction between magnetic nanowires on stepped and flat Cu surfaces.

Hashemi, Hossein; Hergert, Wolfram [Institute of Physics, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Germany); Ignatiev, Pavel A.; Stepanyuk, Valeri S. [Max-Planck-Institute of Microstructure Physics, Weinberg 2, 06120 Halle (Germany)

2008-07-01

 
 
 
 
261

A transferable ab-initio based force field for aqueous ions  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We present a new polarizable force field for aqueous ions (Li+, Na+, K+, Rb+, Cs+, Mg2+, Ca2+, Sr2+ and Cl-) derived from condensed phase ab-initio calculations. We use Maximally Localized Wannier Functions together with a generalized force and dipole-matching procedure to determine the whole set of parameters. Experimental data is then used only for validation purposes and a good agreement is obtained for structural, dynamic and thermodynamic properties. The same procedure ...

Tazi, Sami; Molina, John J.; Rotenberg, Benjamin; Turq, Pierre; Vuilleumier, Rodolphe; Salanne, Mathieu

2012-01-01

262

A fully ab initio quartic force field of spectroscopic quality for SO_3  

Digital Repository Infrastructure Vision for European Research (DRIVER)

The quartic force field of SO$_3$ was computed fully ab initio using coupled cluster (CCSD(T)) methods and basis sets of up to $spdfgh$ quality. The effect of inner-shell correlation was taken into account. The addition of tight $d$ functions is found to be essential for accurate geometries and harmonic frequencies. The equilibrium geometry and vibrational fundamentals are reproduced to within 0.0003 \\AA and (on average) 1.15 cm^{-1}, respectively. We recommend the following...

Martin, Jan M. L.

1998-01-01

263

NestedMICA as an ab initio protein motif discovery tool  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Abstract Background Discovering overrepresented patterns in amino acid sequences is an important step in protein functional element identification. We adapted and extended NestedMICA, an ab initio motif finder originally developed for finding transcription binding site motifs, to find short protein signals, and compared its performance with another popular protein motif finder, MEME. NestedMICA, an open source protein motif discovery tool written in Java, is driven by a Monte...

Down Thomas A; Do?ruel Mutlu; Jp, Hubbard Tim

2008-01-01

264

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

Digital Repository Infrastructure Vision for European Research (DRIVER)

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

265

Generation of Electrical Conductivity Data of Al using Ab-initio Molecular Dynamics simulations  

Science.gov (United States)

Electrical conductivity data of Al for the densities from normal to a fraction of normal density and temperatures up to a few thousand Kelvin are important inputs for the hydrodynamic simulations of exploding aluminium foils. We have generated conductivity data of aluminium, by using ab-initio molecular dynamics simulations and the Kubo Greenwood formula. ABINIT code has been used for performing AIMD simulations. Our results are in good agreement with published results.

Mishra, Vinayak; Chaturvedi, S.

2011-07-01

266

Ab initio calculation of the 6Li binding energy with the hybrid multideterminant scheme  

Science.gov (United States)

We perform an ab initio calculation for the binding energy of 6Li using the CD-Bonn 2000 NN potential renormalized with the Lee-Suzuki method. The many-body approach to the problem is the hybrid multideterminant method. The results indicate a binding energy of about 31MeV, within a few hundreds keV uncertainty. The center-of-mass diagnostics are also discussed.

Puddu, G.

2010-08-01

267

Structure, electronic, and optical properties of TiO2 atomic clusters: An ab initio study  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Atomic clusters of TiO 2 are modeled by means of state-of-the-art techniques to characterize their structural, electronic and optical properties. We combine ab initio molecular dynamics, static density functional theory, time-dependent density functional theory, and many body techniques, to provide a deep and comprehensive characterization of these systems. TiO 2 clusters can be considered as the starting seeds for the synthesis of larger nanostructures, which are of technological interest in...

Chiodo, Letizia; Romero, A. H.; Rubio Secades, A?ngel

2011-01-01

268

Steady state Ab-initio Theory of Lasers with Injected Signals  

CERN Document Server

We present an ab-initio treatment of steady-state lasing with injected signals that treats both multimode lasing and spatial hole burning, and describes the transition to injection locking or partial locking in the multimode case. The theory shows that spatial hole burning causes a shift in the frequency of free-running laser modes away from the injection frequency, in contrast to standard approaches.

Cerjan, Alexander

2013-01-01

269

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

Science.gov (United States)

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

270

Ab-initio Berechnung des elektronischen Spektrums von Halbleiterlegierungen mit großer Bandlücke  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Ziel dieser Arbeit war es, die elektronische Struktur der wide-gap Legierungen Ga (x) Al (1-x) N und Ga (x) In (1-x) N sowie der narrow-gap Legierung Cd (x) Hg (1-x) Te mit ab-initio Methoden zu bestimmen und auszuwerten. Im Rahmen der beschriebenen Untersuchungen wurde die Konzentrationsabhängigkeit wichtiger physikalischer Eigenschaften, wie des Bandgaps oder der Spin-Bahn Aufspaltung, ermittelt. Die Bandstrukturen wurden auf der Grundlage der Dichtefunktional Theorie (DFT) unter Verwendun...

So?keland, F.

2002-01-01

271

On Possible Pitfalls in ab initio QM/MM Minimization Approaches For Studies of Enzymatic Reactions  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Reliable studies of enzymatic reactions by combined quantum mechanics /molecular mechanics (QM/MM) approaches, with an ab initio description of the quantum region, presents a major challenge to computational chemists. The main problem is the need for a very large computer time for the evaluation of the QM energy, which in turn makes it extremely challenging to perform proper configurational sampling. A seemingly reasonable alternative is to perform energy minimization studies of the type used...

Kla?hn, Marco; Braun-sand, Sonja; Rosta, Edina; Warshel, Arieh

2005-01-01

272

Melting curve and Hugoniot of molybdenum up to 400 GPa by ab initio simulations  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We report ab initio calculations of the melting curve and Hugoniot of molybdenum for the pressure range 0-400 GPa, using density functional theory (DFT) in the projector augmented wave (PAW) implementation. We use the ``reference coexistence'' technique to overcome uncertainties inherent in earlier DFT calculations of the melting curve of Mo. Our calculated melting curve agrees well with experiment at ambient pressure and is consistent with shock data at high pressure, but d...

Cazorla, C.; Gillan, M. J.; Taioli, S.; Alfe?, D.

2007-01-01

273

On limits of ab initio calculations of pairing gap in nuclei  

CERN Document Server

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

274

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

CERN Document Server

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

275

The structural and electronic properties of tin oxide nanowires: an {\\it ab initio} investigation  

Digital Repository Infrastructure Vision for European Research (DRIVER)

We performed an {\\it ab initio} investigation on the properties of rutile tin oxide (SnO$_{x}$) nanowires. We computed the wire properties determining the equilibrium geometries, binding energies and electronic band structures for several wire dimensions and surface facet configurations. The results allowed to establish scaling laws for the structural properties, in terms of the nanowire perimeters. The results also showed that the surface states control most of the electron...

Garcia, Joelson Cott; Assali, Lucy Vitoria Credidio; Filho, Joao Francisco Justo

2012-01-01

276

Ab initio determination of structural and dynamical properties of the InP(110)-S interface  

Energy Technology Data Exchange (ETDEWEB)

We have presented an ab initio pseudopotential study within the local density approximation of the structural properties of the S-treated InP(110) surface for an exchange model. The calculated structural parameters for this model are in good agreement with previous ab initio calculations. With these structural papameters, we have used an ab initio linear-response approach based on the density functional theory to investigate the dynamical properties of this surface. We discuss the similarities and contrast the differences in the phonon dispersion curves of the S-treated InP(110) and the clean InP(110) surfaces. We have found that the rotational phonon mode predicted for the clean surface can be also identified for the S-treated InP(110) surface. In addition to this, two new surface-localized phonon states appear in the acoustic-optical gap range due to the adsorption of S atoms. (copyright 2004 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Tuetuencue, H.M.; Bagci, S. [Sakarya Ueniversitesi, Fen-Edebiyat Fakueltesi, Fizik Boeluemue, 54100, Adapazari (Turkey); Srivastava, G.P. [School of Physics, University of Exeter, Stocker Road, Exeter EX4 4QL (United Kingdom)

2004-11-01

277

Ab initio determination of structural and dynamical properties of the InP(110)-S interface  

International Nuclear Information System (INIS)

We have presented an ab initio pseudopotential study within the local density approximation of the structural properties of the S-treated InP(110) surface for an exchange model. The calculated structural parameters for this model are in good agreement with previous ab initio calculations. With these structural papameters, we have used an ab initio linear-response approach based on the density functional theory to investigate the dynamical properties of this surface. We discuss the similarities and contrast the differences in the phonon dispersion curves of the S-treated InP(110) and the clean InP(110) surfaces. We have found that the rotational phonon mode predicted for the clean surface can be also identified for the S-treated InP(110) surface. In addition to this, two new surface-localized phonon states appear in the acoustic-optical gap range due to the adsorption of S atoms. (copyright 2004 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

278

The Gamow Shell Model as a tool for ab-initio nuclear structure calculations  

Science.gov (United States)

No core Gamow shell model (NCGSM) is applied for the first time to study selected well-bound and unbound states of helium isotopes. This model, formulated in the rigged Hilbert space and using a complete Berggren ensemble, is appropriate for a description of bound states, resonances, and the many-body scattering states. The ``dimensional catastrophe'' in NCGSM when increasing the number of active particles is much more serious than in the No Core Shell Model (NCSM). This problem has been alleviated by the application of the Density Matrix Renormalization Group (DMRG) method, opening a possibility for the ab initio calculation of exotic states in hydrogen, helium and lithium chains of isotopes. The ab initio NCGSM calculations start from either bare interaction or various renormalized two-body interactions such as Vlow-k. The single-particle Berggren ensemble consisting of bound, resonance and non-resonant continuum states is generated by the corresponding Gamow-Hartree-Fock potential. To test the validity of our approach, we benchmarked the NCGSM results against Fadeev and Fadeev-Yakubovsky exact calculations for ^3H and ^4He nuclei. We also performed ab-initio NCGSM calculations for the unstable nucleus ^5He and determined the ground state energy and decay width, starting from a realistic N^3LO interaction.

Papadimitriou, George; Barrett, Bruce; Rotureau, Jimmy; Ploszajczak, Marek

2012-10-01

279

Ab initio calculation of the anomalous Hall conductivity by Wannier interpolation  

CERN Document Server

The intrinsic anomalous Hall effect in ferromagnets depends on subtle spin-orbit-induced effects in the electronic structure, and recent ab-initio studies found that it was necessary to sample the Brillouin zone at millions of k-points to converge the calculation. We present an efficient first-principles approach for computing the anomalous Hall conductivity. We start out by performing a conventional electronic-structure calculation including spin-orbit coupling on a uniform and relatively coarse k-point mesh. From the resulting Bloch states, maximally-localized Wannier functions are constructed which reproduce the ab-initio states up to the Fermi level. The Hamiltonian and position-operator matrix elements, needed to represent the energy bands and Berry curvatures, are then set up between the Wannier orbitals. This completes the first stage of the calculation, whereby the low-energy ab-initio problem is transformed into an effective tight-binding form. The second stage only involves Fourier transforms and un...

Wang, X; Souza, I; Vanderbilt, D; Wang, Xinjie; Yates, Jonathan R.; Souza, Ivo; Vanderbilt, David

2006-01-01

280

An accurate ab initio HOCl potential energy surface, vibrational and rotational calculations, and comparison with experiment  

International Nuclear Information System (INIS)

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

 
 
 
 
281

Ab initio study of ionic liquids by KS-DFT/3D-RISM-KH theory.  

Science.gov (United States)

Properties of molecules solvated in ionic liquids (ILs) are strongly affected by solvent environment. For this reason, to give reliable results, ab initio calculations on solutes in ILs, including ions constituting ionic liquid itself, have to self-consistently account for the change of both electronic and classical solvation structure in ILs. Here, we study the electronic structure of the methyl-methylimidazolium ion in the bulk liquid of [mmim][Cl] by using the self-consistent field coupling of Kohn-Sham density functional theory and three-dimensional molecular theory of solvation (aka 3D-RISM) with the closure approximation of Kovalenko and Hirata. The KS-DFT/3D-RISM-KH method yields the 3D distribution of the IL solvent species around the [mmim] solute, underlying the most important peculiarities of this kind of systems such as the stacking interaction between neighboring cations, and reproduces the enhancement of the dipole moment resulting from the polarization of the cation by the solvent in a very good agreement with the results of an ab initio MD calculation. The KS-DFT/3D-RISM-KH method offers an accurate and computationally efficient procedure to perform ab initio calculations on species solvated in ionic liquids. PMID:19278268

Malvaldi, Marco; Bruzzone, Samantha; Chiappe, Cinzia; Gusarov, Sergey; Kovalenko, Andriy

2009-03-19

282

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

Science.gov (United States)

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

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

2014-01-01

283

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)

284

A web-deployed interface for performing ab initio molecular dynamics, optimization, and electronic structure in FIREBALL  

Science.gov (United States)

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

285

Molecular dynamics simulations of fluid methane properties using ab initio intermolecular interaction potentials.  

Science.gov (United States)

Intermolecular interaction energy data for the methane dimer have been calculated at a spectroscopic accuracy and employed to construct an ab initio potential energy surface (PES) for molecular dynamics (MD) simulations of fluid methane properties. The full potential curves of the methane dimer at 12 symmetric conformations were calculated by the supermolecule counterpoise-corrected second-order Møller-Plesset (MP2) perturbation theory. Single-point coupled cluster with single and double and perturbative triple excitations [CCSD(T)] calculations were also carried out to calibrate the MP2 potentials. We employed Pople's medium size basis sets [up to 6-311++G(3df, 3pd)] and Dunning's correlation consistent basis sets (cc-pVXZ and aug-cc-pVXZ, X = D, T, Q). For each conformer, the intermolecular carbon-carbon separation was sampled in a step 0.1 A for a range of 3-9 A, resulting in a total of 732 configuration points calculated. The MP2 binding curves display significant anisotropy with respect to the relative orientations of the dimer. The potential curves at the complete basis set (CBS) limit were estimated using well-established analytical extrapolation schemes. A 4-site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen-hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show quantitative agreements on both the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions. PMID:19090563

Chao, Shih-Wei; Li, Arvin Huang-Te; Chao, Sheng D

2009-09-01

286

Ab initio studies of anisotropic magnetism in uranium and cerium monopnictides and monochalcogenides  

Science.gov (United States)

We have applied two ab initio based methods to investigate the origin in the electronic structure of the unusual magnetic behavior of the cerium and uranium monopnictides and monochalcogenides. First, we have carried out spin-polarized electronic structure calculations, based on the full potential linear muffin tin (FPLMTO) method, with spin polarization (orbital polarization only via spin-orbit coupling) and also with orbital polarization correction. Second, we have carried out ab initio based calculations synthesizing (1) a phenomenological theory of orbitally driven magnetism based on the Anderson and Kondo, lattice model which incorporates explicitly the hybridization induced and the Coulomb exchange interactions on an equal footing, and (2) FPLMTO electronic structure calculations allowing a first principles evaluation of all the parameters entering the model Hamiltonian. For the cerium compounds, we also include the crystal field interactions on an equal footing with the hybridization and Coulomb exchange interactions with a scaling determined by experiment. The results for the uranium compound calculations show that both methods are limited to the extremes to which they are best suited. The pure band structure calculations provide the best agreement for the lighter uranium compounds, while the model hamiltonian approach provides better agreement for the heavier uranium compounds. In the case of the cerium compounds, while the pure FPLMTO calculations yield values for the magnetic moment in agreement with experiment for the lighter cerium chalcogenides, they fail to give, even qualitatively, the magnetic properties for all other systems. On the other hand, the ab initio based model Hamiltonian calculations reveal for the first time the interplay of hybridization, Coulomb exchange, and crystal field interactions across the cerium series, and give results for the low-temperature moment and ordering temperature in excellent agreement with experiment, for the full range of both types of cerium compounds.

Collins, Eric Mason

287

Ab initio simulations and neutron scattering studies of structure and dynamics in PdH  

International Nuclear Information System (INIS)

The work presented in this PhD thesis is concerned with the interpretation of the neutron scattering measurements from the palladium hydrogen system by means of ab initio electronic structure calculations. The motivation of performing such calculations was due to recent neutron scattering studies on this system that showed a strong directional dependence to the dynamical structure factor together with a complex dependence on energy. Here we attempt to describe the origin of these features by ab initio simulations of the dynamical structure factor. The method assumes an adiabatic separation of the motion of the proton and palladium atoms. The proton wave functions are calculated by a direct solution of the associated single-particle Schroedinger equation using a plane wave basis set method and a mapping of the adiabatic surface. The Fourier components of the adiabatic potential are obtained from LDA pseudopotential calculations. Using Fermi's golden rule within the Born approximation we were then able to calculate the dynamical structure factor, S(Q,?), for exciting the proton from its ground state to various excited states as a function of the magnitude and direction of the scattering wave vector. The results are in agreement with the inelastic neutron scattering spectra and allow us to identify the origin of previous inexplicable features, in particular the strong directional dependence to the experimental data. The method was extended to investigate the expansion os extended to investigate the expansion of the equilibrium lattice constant as a function of the H isotope when the zero-point energy of the proton/deuterium is explicitly taken into account in the relaxation process. The results we obtained predicted a bigger lattice constant for the hydride, as expected. Furthermore, other complex ab initio calculations were carried out in order to describe the origin of the large optic dispersion, seen previously in the coherent neutron scattering data. Our calculated dispersion proved to be in good agreement with the experimental results. (author)

288

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

Science.gov (United States)

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

289

Improved parametric fits for the HeH2 ab initio energy surface  

International Nuclear Information System (INIS)

A brief history of the development of ab initio calculations for the HeH2 quasi-molecule energy surface, and the parametric fits to these ab initio calculations, is presented. The concept of 'physical reasonableness' of the parametric fit is discussed. Several new improved parametric fits for the energy surface, meeting these requirements, are then proposed. One fit extends the Russek-Garcia parametric fit for the deep repulsion region to include r-dependent parameters, resulting in a more physically reasonable fit with smaller average error. This improved surface fit is applied to quasi-elastic collisions of He on H2 in the impulse approximation. Previous classical calculations of the scaled inelastic vibrorotational excitation energy distributions are improved with this more accurate parametric fit of the energy surface and with the incorporation of quantum effects in vibrational excitation. It is shown that Sigmund's approach in developing his scaling law is incomplete in the contribution of the three-body interactions to vibrational excitation of the H2 molecule is concerned. The Sigmund theory is extended to take into account for r-dependency of three-body interactions. A parametric fit for the entire energy surface from essentially 0 ?R?? and 1.2?r?1.6 a.u., where R is the intermolecular spacing and r is the hydrogen bonding length, is also presented. This fit is physically reasonable in all asymptotic limits. This first, full surface parametric fit is based primarily upon a composite of ab initio studies by Russek and Garcia and Meyer, Hariharan and Kutzelnigg. Parametric fits for the H2(1s?g)2, H2+(1s?g), H2+(2p?u) and (LiH2)+ energy surfaces are also presented. The new parametric fits for H2, H2+(1s?g) are shown to be improvements over the well-known Morse potentials for these surfaces

290

Hydrogen fluoride phase behavior and molecular structure: Ab initio derived potential models  

Science.gov (United States)

Several variations of ab initio based molecular models for hydrogen fluoride (HF) are examined by Monte Carlo molecular simulation to determine their bulk-phase properties. The models are taken from the literature, and represent fits of functional forms to the potential energy surface of the HF dimer as given by ab initio computational chemistry calculations. For one of these models, we examine three variations for bulk-phase modeling. In particular, we consider first the effect of including versus neglecting an Ewald sum for the long-range dipole-dipole interactions; second, we examine a modification of the form for the short range repulsive region of the potential; and third, we add three-body contributions to the energy via an available 12-dimensional potential for the trimer, again representing a fit to ab initio energy calculations. The simulations examine the density (via isothermal-isobaric simulation) and radial distribution function (via canonical-ensemble simulations) each at two state points where corresponding experimental data are available. We also examine vapor-liquid coexistence properties, considering the saturation densities, heat of vaporization, and vapor pressure from 225 K to states approaching (but not closely) each model's critical point. Inclusion of the three-body energy is the only variation that has any beneficial effect on the radial distribution function as compared to experiment, and this variation also gives good results for the vapor pressure, and significantly raises the critical point toward the experimental value. However this model also grossly overestimates the liquid-phase coexistence density. In almost all regards none of the models or variations can be considered to give a satisfactory representation of the bulk-phase behavior. Improvements to the models require more careful attention to the balance between repulsive and attractive pair interactions at short range.

Wierzchowski, Scott J.; Kofke, David A.

2003-09-01

291

smyRNA: A Novel Ab Initio ncRNA Gene Finder  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Non-coding RNAs (ncRNAs) have important functional roles in the cell: for example, they regulate gene expression by means of establishing stable joint structures with target mRNAs via complementary sequence motifs. Sequence motifs are also important determinants of the structure of ncRNAs. Although ncRNAs are abundant, discovering novel ncRNAs on genome sequences has proven to be a hard task; in particular past attempts for ab initio ncRNA search mostly failed with the exception of tools that...

Sahinalp, S. Cenk; Salari, Raheleh; Aksay, Cagri; Hajirasouliha, Iman; Karakoc, Emre; Unrau, Peter J.

2009-01-01

292

The hydrogen diffusion in liquid aluminum alloys from ab initio molecular dynamics  

Science.gov (United States)

We study the hydrogen diffusion in liquid aluminum alloys through extensive ab initio molecular dynamics simulations. At the microscopic scale, we show that the hydrogen motion is characterized by a broad distribution of spatial jumps that does not correspond to a Brownian motion. To determine the self-diffusion coefficient of hydrogen in liquid aluminum alloys, we use a generalized continuous time random walk model recently developed to describe the hydrogen diffusion in pure aluminum. In particular, we show that the model successfully accounts the effects of alloying elements on the hydrogen diffusion in agreement with experimental features.

Jakse, N.; Pasturel, A.

2014-09-01

293

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

Energy Technology Data Exchange (ETDEWEB)

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

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

2009-03-01

294

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

295

Ab-initio simulations on growth and interface properties of epitaxial oxides on silicon  

CERN Document Server

The replacement of SiO2 by so-called high-k oxides is one of the major challenges for the semiconductor industry to date. Based on electronic structure calculations and ab-initio molecular dynamics simulations, we are able to provide a consistent picture of the growth process of a class of epitaxial oxides around SrO and SrTiO3. The detailed understanding of the interfacial binding principles has also allowed us to propose a way to engineer the band-offsets between the oxide and the silicon substrate.

Först, C J; Schwarz, K; Blöchl, P E; Foerst, Clemens J.; Ashman, Christopher R.; Schwarz, Karlheinz; Bloechl, Peter E.

2005-01-01

296

Electronic and magnetic properties at the edges of nanostructures in an electric field: ab initio study.  

Science.gov (United States)

State of the art ab initio calculations of the electronic and magnetic properties at the edges of magnetic nanostructures in an external electric field are presented in this paper. Our results for the Fe stripes on Fe(0?0?1) reveal the existence of spin-polarized edge states. A spatially inhomogeneous electronic structure is found at the edge. We demonstrate that the spin-dependent screening density varies greatly at the atomic scale. Tuning of the spin-polarization by the external electric field is demonstrated. PMID:25273916

Polyakov, Oleg P; Stepanyuk, Oleg V; Saletsky, Alexander M; Stepanyuk, Valeri S

2014-11-01

297

Nonlinear magnetoelastic coupling coefficients in Fe from an ab initio calculation  

International Nuclear Information System (INIS)

Based on the nonlinear theory of magnetoelasticity, a general method is developed which allows the determination of first-order and second-order magnetoelastic coefficients of a magnetic material from the ab initio calculation of magnetocrystalline anisotropy energies as functions of various modes of imposed strain. Explicit results are given for BCC Fe. The data confirm the hints from the magnetostrictive stress experiments that nonlinear magnetoelastic coupling effects are essential for the magnetic properties of thin epitaxial magnetic films with large epitaxial strains

298

Ab initio molecular simulations on specific interactions between amyloid beta and monosaccharides  

Science.gov (United States)

Aggregation of amyloid ? (A?) peptides, which is a key pathogenetic event in Alzheimer's disease, can be caused by cell-surface saccharides. We here investigated stable structures of the solvated complexes of A? with some types of monosaccharides using molecular simulations based on protein-ligand docking and classical molecular mechanics methods. Moreover, the specific interactions between A? and the monosaccharides were elucidated at an electronic level by ab initio fragment molecular orbital calculations. Based on the results, we proposed which type of monosaccharide prefers to have large binding affinity to A? and inhibit the A? aggregation.

Nomura, Kazuya; Okamoto, Akisumi; Yano, Atsushi; Higai, Shin'ichi; Kondo, Takashi; Kamba, Seiji; Kurita, Noriyuki

2012-09-01

299

Molecular PO2Cl: matrix IR investigations and ab initio SCF calculations  

International Nuclear Information System (INIS)

PO2Cl produced by a photochemical reaction between O3 and POCl in solid Ar has been studied by IR spectroscopy. The same species is formed in a high-temperature reaction between POCl3, O2, and Ag. IR spectra including 16O/18O and 35Cl/37Cl shifts show that the OPO angle is about 1350 and that the PCl bond is unexpectedly strong (f(PCl) = 3.7 mdyn A-1). These results are confirmed by ab initio SCF calculations. Bonding in PO2Cl is compared with that of similar molecules

300

Ab initio molecular dynamics simulations using a Chebyshev-filtered subspace iteration technique  

Science.gov (United States)

A method for performing ab initio molecular dynamics simulations using a real-space pseudopotential density-functional approach is presented in this work. The Kohn-Sham equation is represented on a real-space grid and solved using higher-order finite differencing. A crucial ingredient of our method is the replacement of “standard” diagonalizations at each self-consistent-field iteration by a Chebyshev subspace filtering step, resulting in a speed up of an order of magnitude or more. This increase in computational efficiency allows molecular dynamics simulations to be carried out for large systems. As an illustration, we apply this method to the study of liquid Al.

Khoo, K. H.; Kim, M.; Schofield, G.; Chelikowsky, James R.

2010-08-01

 
 
 
 
301

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

302

Ab initio quantum mechanical simulations confirm the formation of all postulated species in ionic dissociation.  

Science.gov (United States)

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

303

Ab initio calculations of 14N and 15N hyperfine structures  

CERN Document Server

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

304

Testing the density matrix expansion against ab initio calculations of trapped neutron drops  

CERN Document Server

Microscopic input to a universal nuclear energy density functional can be provided through the density matrix expansion (DME), which has recently been revived and improved. Several DME implementation strategies are tested for neutron drop systems in harmonic traps by comparing to Hartree-Fock (HF) and ab initio no-core full configuration (NCFC) calculations with a model interaction (Minnesota potential). The new DME with exact treatment of Hartree contributions is found to best reproduce HF results and supplementing the functional with fit Skyrme-like contact terms shows systematic improvement toward the full NCFC results.

Bogner, S K; Hergert, H; Kortelainen, M; Maris, P; Stoitsov, M; Vary, J P

2011-01-01

305

Ab initio deconstruction of the vibrational relaxation pathways of dilute HOD in ice Ih.  

Science.gov (United States)

Coupled intramolecular and intermolecular vibrational quantum dynamics, using an ab initio potential energy surface, successfully describes the subpicosecond relaxation of the OD and OH stretch fundamental and first overtone of dilute HOD in ice Ih. The calculations indicate that more than one intermolecular mode along with the three intramolecular modes is needed to describe the relaxation, in contrast to a recent study using a phenomenological potential in just two degrees of freedom. Detailed time-dependent relaxation pathways from 6-mode calculations are also given. PMID:24717075

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

2014-04-23

306

Cobalt-doped ZnO nanocrystals: quantum confinement and surface effects from ab initio methods.  

Science.gov (United States)

Cobalt-doped ZnO nanocrystals were studied through ab initio methods based on the Density Functional Theory. Both quantum confinement and surface effects were explicitly taken into account. When only quantum confinement effects are considered, Co atoms interact through a superexchange mechanism, stabilizing an antiferromagnetic ground state. Usually, this is the case for high quality nanoparticles with perfect surface saturation. When the surfaces were considered, a strong hybridization between the Co atoms and surfaces was observed, strongly changing their electronic and magnetic properties. Our results indicated that the surfaces might qualitatively change the properties of impurities in semiconductor nanocrystals. PMID:23942732

Schoenhalz, Aline L; Dalpian, Gustavo M

2013-10-14

307

Ab initio study of low-energy electron collisions with tetrafluoroethene C2 F4  

Science.gov (United States)

We report the results of variational calculations of elastic electron scattering by tetrafluoroethene (C2F4) with incident electron energies ranging from 0.5to20eV , using the complex Kohn method and effective core potentials. These are the first fully ab initio calculations to reproduce experimental angular differential cross sections at energies below 10eV . Low-energy electron scattering by C2F4 is sensitive to the inclusion of electronic correlation and target-distortion effects. We therefore present results that describe the dynamic polarization of the target by the incident electron. The calculated cross sections are compared with recent experimental measurements.

Trevisan, C. S.; Orel, A. E.; Rescigno, T. N.

2004-07-01

308

Ab initio calculation of the ground-state properties of CoSi2  

International Nuclear Information System (INIS)

We have investigated the structural and electronic properties of CoSi2 by using a generalized gradient approximation of the density functional theory and ab initio pseudopotentials. The calculated lattice constant and electronic band structure have been used in the application of a linear response approach based on density functional perturbation theory for phonon studies. The structural results are in good agreement with previous works. The calculated phonon spectra are in good agreement with available experimental data. A detailed discussion of atomic displacement pattern is provided corresponding to the two sets of LO and TO phonon modes

309

Ab initio calculation of the ground-state properties of CoSi{sub 2}  

Energy Technology Data Exchange (ETDEWEB)

We have investigated the structural and electronic properties of CoSi{sub 2} by using a generalized gradient approximation of the density functional theory and ab initio pseudopotentials. The calculated lattice constant and electronic band structure have been used in the application of a linear response approach based on density functional perturbation theory for phonon studies. The structural results are in good agreement with previous works. The calculated phonon spectra are in good agreement with available experimental data. A detailed discussion of atomic displacement pattern is provided corresponding to the two sets of LO and TO phonon modes.

Ugur, G [Gazi Ueniversitesi Fen-Edebiyat Fakueltesi Fizik Boeluemue, 06500, Ankara (Turkey); Soyalp, F [Gazi Ueniversitesi Fen-Edebiyat Fakueltesi Fizik Boeluemue, 06500, Ankara (Turkey); Tuetuencue, H M [Sakarya Ueniversitesi Fen-Edebiyat Fakueltesi Fizik Boeluemue, 54100, Adapazari (Turkey); Duman, S [Sakarya Ueniversitesi Fen-Edebiyat Fakueltesi Fizik Boeluemue, 54100, Adapazari (Turkey); Srivastava, G P [University of Exeter, School of Physics, Stocker Road, Exeter EX4 4QL (United Kingdom)

2005-11-09

310

Atomic structure evolution during solidification of liquid niobium from ab initio molecular dynamics simulations  

Energy Technology Data Exchange (ETDEWEB)

Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt–Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K.

Debela, T. T. [Zhejiang University; Wang, X. D. [Zhejiang University; Cao, Q. P. [Zhejiang University; Zhang, D. X. [Zhejiang University; Wang, S. Y. [Fudan University; Wang, Cai-Zhuang [Ames Laboratory; Jiang, J. Z. [Zhejiang University

2013-12-12

311

Atomic structure evolution during solidification of liquid niobium from ab initio molecular dynamics simulations.  

Science.gov (United States)

Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt-Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K. PMID:24334654

Debela, T T; Wang, X D; Cao, Q P; Zhang, D X; Wang, S Y; Wang, C Z; Jiang, J Z

2014-02-01

312

Ab Initio Simulation of Optical Limiting: The Case of Metal-Free Phthalocyanine  

Science.gov (United States)

We present a fully ab initio, nonperturbative description of the optical limiting properties of a metal-free phthalocyanine by simulating the effects of a broadband electric field of increasing intensity. The results confirm reverse saturable absorption as the leading mechanism for optical limiting phenomena in this system and reveal that a number of dipole-forbidden excitations are populated by excited-state absorption at more intense external fields. The excellent agreement with the experimental data supports our approach as a powerful tool to predict optical limiting in view of applications.

Cocchi, Caterina; Prezzi, Deborah; Ruini, Alice; Molinari, Elisa; Rozzi, Carlo A.

2014-05-01

313

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

CERN Document Server

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 structures can be obtained by a direct interconversion from SWNT(2,2). Large finite cubane-like oligomers, topologically related to these new tubes were also investigated.

Autreto, P A S; Flores, M Z S; Galvao, D S; 10.1063/1.348323

2010-01-01

314

Carbon nanotube with square cross-section: An ab initio investigation  

Science.gov (United States)

Recently, Lagos et al. [Nat. Nanotechnol. 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 structures can be obtained by a direct interconversion from SWNT(2,2). Large finite cubanelike oligomers, topologically related to these new tubes, were also investigated.

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

2010-09-01

315

Conformer-selected photodissociation: Ab Initio Multiple Spawning Dynamics of Excited Propanal Cation  

Science.gov (United States)

Recent experiments have shown that pure cis and gauche propanal cations can be prepared using REMPI (Resonance Enhanced Multiphoton Ionization Spectroscopy). The H elimination pathway which results when these conformer-selected cations are photoexcited was found to depend on the conformer (cis vs. gauche). This dependence is very surprising since the interconversion barrier of the two conformers is small compared to the excited energy. We use the ab initio multiple spawning (AIMS) method developed in our group to model the conformer-specific photodissociation and to elucidate its origins.

Tao, Hongli; Martinez, Todd

2007-03-01

316

Fundamental absorption frequency from quasi-classical direct ab initio molecular dynamics: diatomic molecule  

Energy Technology Data Exchange (ETDEWEB)

A new approach is proposed to extract the fundamental absorption frequency from classical molecular dynamics simulation in which the oscillator amplitude is specified by setting the total energy equal to the harmonic zero-point energy. This approach is applied to D2 molecule. The fundamental absorption frequency and the anharmonic constant of D2, obtained from the quasiclassical direct ab initio molecular dynamics simulation method with the full Configuration Interaction level of theory with the aug-cc-pVTZ basis set, compare well with the experimentally observed values.

Aida, Misako; Dupuis, Michel

2005-01-31

317

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

Science.gov (United States)

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

318

Temperature-Dependent Diffusion Coefficients from ab initio Computations: Hydrogen in Nickel  

Energy Technology Data Exchange (ETDEWEB)

The temperature-dependent mass diffusion coefficient is computed using transition state theory. Ab initio supercell phonon calculations of the entire system provide the attempt frequency, the activation enthalpy, and the activation entropy as a function of temperature. Effects due to thermal lattice expansion are included and found to be significant. Numerical results for the case of hydrogen in nickel demonstrate a strong temperature dependence of the migration enthalpy and entropy. Trapping in local minima along the diffusion path has a pronounced effect especially at low temperatures. The computed diffusion coefficients with and without trapping bracket the available experimental values over the entire temperature range between 0 and 1400 K.

E Wimmer; W Wolf; J Sticht; P Saxe; C Geller; R Najafabadi; G Young

2006-03-16

319

Ab initio investigation of the vibrational structure of absorption and emission spectra of FCO  

Science.gov (United States)

Results of an ab initio study of the vibrational structure of several electronic spectral systems of FCO are presented. An interpretation of hitherto recorded spectra, as well as a prediction of features of yet unobserved electronic transitions is given. The absorption spectra observed in the uv spectral region are ascribed to the transitions involving the first excited states of 2A' and 2A` character. The emission spectrum obtained by Toby and Toby [J. Phys. Chem. 85, 4071 (1981)] is assigned to the transition X 2A'?2 2A`. Reassignment of some observed vibrational bands is proposed.

Krossner, Th.; Peri?, M.; Vetter, R.; Zülicke, L.

1994-09-01

320

Electronic transport properties of fullerene functionalized carbon nanotubes: Ab initio and tight-binding calculations  

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; Markussen, Troels

2009-01-01

 
 
 
 
321

ab-initio electronic and magnetic properties of Fe-al alloys  

Digital Repository Infrastructure Vision for European Research (DRIVER)

This work presents ab-initio self-consistent calculations performed with the TB-LMTO code to study the different phases of the Fe-Al phase diagram, corresponding to the ordered structures B2, DO3 and B32 and for Fe50Al50 and Fe3Al compositions. Both, unpolarized and spin-polarized calculations have been performed to deduce the energetic difference between the paramagnetic and ferromagnetic state of the corresponding structure. Calculations for the disordered structures have also been performe...

Apin?aniz, E.; Plazaola, F.

2000-01-01

322

Mechanical, electronic, and transport properties of functionalized graphene monolayers from ab initio studies  

Energy Technology Data Exchange (ETDEWEB)

We present exemplary results of extensive studies of mechanical, electronic and transport properties of covalent functionalization of graphene monolayers (GML). We report new results of ab initio studies for covalent functionalization of GML with ?NH{sub 2} groups up to 12.5 % concentration. Our studies are performed in the framework of the density functional theory (DFT) and non-equilibrium Green’s function (NEGF). We discuss the stability (adsorption energy), elastic moduli, electronic structure, band gaps, and effective electron masses as a function of the density of the adsorbed molecules. We also show the conductance and current – voltage I(V) characteristics for these systems.

Milowska, Karolina Z.; Birowska, Magdalena; Majewski, Jacek A. [Faculty of Physics, University of Warsaw, ul. Ho?a 69, 00-681 Warszawa (Poland)

2013-12-04

323

Mechanical, electronic, and transport properties of functionalized graphene monolayers from ab initio studies  

International Nuclear Information System (INIS)

We present exemplary results of extensive studies of mechanical, electronic and transport properties of covalent functionalization of graphene monolayers (GML). We report new results of ab initio studies for covalent functionalization of GML with ?NH2 groups up to 12.5 % concentration. Our studies are performed in the framework of the density functional theory (DFT) and non-equilibrium Green’s function (NEGF). We discuss the stability (adsorption energy), elastic moduli, electronic structure, band gaps, and effective electron masses as a function of the density of the adsorbed molecules. We also show the conductance and current – voltage I(V) characteristics for these systems

324

Graphene nanoribbon intercalated with hexagonal boron nitride: Electronic transport properties from ab initio calculations  

Science.gov (United States)

A magnetic tunnel junction consisting of a boron nitride nanoribbon contacted by two semi-infinite electrodes composed of (3,0) ferromagnetic zig-zag graphene nanoribbons was investigated. Performing spin-polarized ab initio transport calculations based on a scheme that combines non-equilibrium Green's function with density functional theory (NEGF+DFT) we predict that such system could act as spin-filter (the efficiency reaches 50%) and present a magnetoristance of 105%, depending on the length of the boron nitride region.

Padilha, José Eduardo; Pontes, Renato Borges; da Silva, Antônio José Roque; Fazzio, Adalberto

2013-11-01

325

Mechanical, electronic, and transport properties of functionalized graphene monolayers from ab initio studies  

Science.gov (United States)

We present exemplary results of extensive studies of mechanical, electronic and transport properties of covalent functionalization of graphene monolayers (GML). We report new results of ab initio studies for covalent functionalization of GML with -NH2 groups up to 12.5 % concentration. Our studies are performed in the framework of the density functional theory (DFT) and non-equilibrium Green's function (NEGF). We discuss the stability (adsorption energy), elastic moduli, electronic structure, band gaps, and effective electron masses as a function of the density of the adsorbed molecules. We also show the conductance and current - voltage I(V) characteristics for these systems.

Milowska, Karolina Z.; Birowska, Magdalena; Majewski, Jacek A.

2013-12-01

326

g-Hartree Ab-Initio Calculation of Atomic Ionization Energy of Small Atoms  

Science.gov (United States)

The g-Hartree method is adapted to the direct ab-initio calculation of atomic transition energy. For the improvement of numerical accuracy the new g-Hartree code is developed and used for the calculations of atomic ionization energies of selected levels of small atoms He(Z=2), Be(Z=4), Ne(Z=10), Mg(Z=12) and Ar(Z=18). The results are very similar to those obtained in a previous work. The agreement between theory and experiment is excellent.

Ohno, M.

1987-03-01

327

Optimised mean fields for atoms. 5. g-Hartree ab initio calculation of ionisation energies  

Energy Technology Data Exchange (ETDEWEB)

The g-Hartree method is adapted to the direct ab initio calculation of transition energies in atoms. For the elements He (Z=2), Li (Z=3), Be (Z=4), Ne (Z=10), Mg (Z=12) and Ar (Z=18) all ionisation energies have been computed and found to agree with available experimental data within the computational errors. The systematic aspect is emphasised and is shown to match experimental data significantly better than second-order Brueckner-Hartree-Fock calculations. A detailed comparison of the present method with other published approximation schemes shows a systematic improvement over the results obtained in conventional many-body theories.

Dietz, K.; Ohno, M.; Weymans, G.

1986-10-14

328

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

Science.gov (United States)

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.

Yu, Hua-Gen

2011-08-01

329

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.

330

The ab initio potential energy surface and spectroscopic constants of HOCl  

Science.gov (United States)

The potential energy surface of hypochlorous acid, HOCl, has been determined from large-scale ab initio calculations using the coupled-cluster method CCSD(T), with basis sets of quadruple- and quintuple-zeta quality. The effect of core-electron correlation on the calculated structural parameters has been investigated. The vibrational-rotational energy levels of the three isotopic species of HOCl have then been calculated using the variational method and have been further characterized by the spectroscopic constants determined using the perturbational approach. The spectroscopic constants determined, are found to be in excellent agreement with experimental data.

Koput, Jacek; Peterson, Kirk A.

1998-02-01

331

Calculation of a Deuterium Double Shock Hugoniot from Ab initio Simulations  

CERN Document Server

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-driven shock measurements.

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

2001-01-01

332

An ab initio molecular orbital study of the electron affinity of boron clusters  

Science.gov (United States)

The electron affinities of boron clusters were studied using ab initio molecular orbital methods to discuss the phenomenon of clustered boron anions emitted during sputtering. Calculations were performed at the MP4(SDQ)/CBSB5 level. The calculated electron affinities of B, B 2, and B 3 were found to be 0.214, 3.66, and 3.20 eV, respectively. These values are qualitatively consistent with the experimental data of sputtering yield of B -, B 2-, and B 3-.

Takeuchi, T.; Yamamoto, M.; Kiuchi, M.

1999-06-01

333

An ab initio molecular orbital study of the electron affinity of boron clusters  

Energy Technology Data Exchange (ETDEWEB)

The electron affinities of boron clusters were studied using ab initio molecular orbital methods to discuss the phenomenon of clustered boron anions emitted during sputtering. Calculations were performed at the MP4(SDQ)/CBSB5 level. The calculated electron affinities of B, B{sub 2}, and B{sub 3} were found to be 0.214, 3.66, and 3.20 eV, respectively. These values are qualitatively consistent with the experimental data of sputtering yield of B{sup -}, B{sub 2}{sup -}, and B{sub 3}{sup -}.

Takeuchi, T.; Yamamoto, M.; Kiuchi, M. E-mail: dd160@onri.go.jp

1999-06-01

334

Ab Initio Electronic Structure Calculations of Cytochrome P450 -- Ligand Interactions  

Science.gov (United States)

The Cytochrome P450 superfamily of enzymes are of great interest in pharmacology as they participate in an enormous range of physiological processes including drug deactivation and xenobiotic detoxification. We apply ab initio electronic structure calculations to model the interactions of the haem molecule at the P450 active site with substrate and inhibitor ligands. These calculations, based on density function theory, were performed with the CETEP code which uses a plane wave basis set and pseudopotentials to perform efficient LDA, GGA and spin dependent calculations. A change in the spin state of the haem iron atom is observed on binding of a substrate molecule, consistent with the accepted reaction mechanism.

Segall, M. D.; Payne, M. C.; Ellis, S. W.; Tucker, G. T.

1997-03-01

335

Massless Fermions in multilayer graphitic systems with misoriented layers: Ab initio calculations and experimental fingerprints  

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

336

Ab initio infrared spectrum of lower frequency vibrations in cyclohexene: Paper I  

Science.gov (United States)

Cyclohexene molecule possesses two low frequency modes assigned to the ring-twisting and ring-bending vibrations. In this paper, the ab initio potential energy associated with these vibrations is calculated at the MP2 level by varying a single internal variable (namely a dihedral angle of the molecule), by steps of two degrees. Calculation of the molecular dipole moment variation during the vibration and numerical integration of the equation of motion lead to infrared spectra in fairly good agreement with experimental ones. Potentials fitting the experimental spectra are presented and the comparison between calculated and fitted potentials is discussed.

Lespade, L.

2008-11-01

337

Ab initio molecular dynamics of Al irradiation-induced processes during Al2O3 growth  

International Nuclear Information System (INIS)

Al bombardment induced structural changes in ?-Al2O3 (R-3c) and ?-Al2O3 (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 ?-Al2O3(001) subplantation of impinging Al causes significantly larger irradiation damage and hence larger mobility as compared to ?-Al2O3. Consequently, fast diffusion along ?-Al2O3(001) gives rise to preferential ?-Al2O3(0001) growth, which is consistent with published structure evolution experiments.

338

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)

339

Electronic transport coefficients from ab initio simulations and application to dense liquid hydrogen  

CERN Document Server

Using Kubo's linear response theory, we derive expressions for the frequency-dependent electrical conductivity (Kubo-Greenwood formula), thermopower, and thermal conductivity in a strongly correlated electron system. These are evaluated within ab initio molecular dynamics simulations in order to study the thermoelectric transport coefficients in dense liquid hydrogen, especially near the nonmetal-to-metal transition region. We also observe significant deviations from the widely used Wiedemann-Franz law which is strictly valid only for degenerate systems and give an estimate for its valid scope of application towards lower densities.

Holst, Bastian; Redmer, Ronald; 10.1103/PhysRevB.83.235120

2012-01-01

340

Ab initio many-body calculations of the 4He photo-absorption cross section  

CERN Document Server

A major goal of nuclear theory is to make quantitative calculations of low-energy nuclear observables starting from microscopic internucleon forces. Computationally, this is complicated by the large model spaces needed to reach convergence in many-body approaches, such as the no-core shell model (NCSM). In recent years, the similarity renormalization group (SRG) has provided a powerful and versatile means to soften interactions for ab initio structure calculations, thus leading to convergence within smaller model spaces. Here we compute the 4He total photo absorption cross section and study, for the first time, the consistency of the SRG approach in a continuum observable.

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

2013-01-01

 
 
 
 
341

An ab initio investigation of the structure, vibrational frequencies, and intensities of HO2 and HOCl  

Science.gov (United States)

The infrared spectral intensities for HOCl and HO2 have been calculated using a new ab initio technique. Theoretical results for the geometries, vibrational frequencies, and the dipole moments of these species are also reported. All of the calculations were performed at the SCF level using near Hartree-Fock quality basis sets. The results for the molecular geometries and the vibrational frequencies are in good agreement with available experimental data. It is believed that the computed intensities are accurate to at least 50%. The results should be helpful in attempts to determine the stratospheric abundance of HOCl and HO2 by in situ infrared spectroscopic measurements.

Komornicki, A.; Jaffe, R. L.

1979-01-01

342

Complementary ab initio and X-ray nano-diffraction study of Ta2O5  

Digital Repository Infrastructure Vision for European Research (DRIVER)

Numerous different crystal structures of Ta2O5 are reported in literature. Although experimentally and computationally obtained lattice parameters and mechanical properties are in excellent agreement there is a pronounced deviation when it comes to electronic structures of Ta2O5. Based on ab initio studies and nano-beam X-ray diffraction of sputtered Ta2O5 thin films, we introduce an orthorhombic basic structure with a = 0.6425, b = 0.3769, and c = 0.7706 nm, which is stabil...

Hollerweger, R.; Holec, D.; Paulitsch, J.; Bartosik, M.; Daniel, R.; Rachbauer, R.; Polcik, P.; Keckes, J.; Krywka, C.; Mayrhofer, P. H.

2014-01-01

343

Monte Carlo methods in AB initio quantum chemistry quantum Monte Carlo for molecules  

CERN Document Server

This book presents the basic theory and application of the Monte Carlo method to the electronic structure of atoms and molecules. It assumes no previous knowledge of the subject, only a knowledge of molecular quantum mechanics at the first-year graduate level. A working knowledge of traditional ab initio quantum chemistry is helpful, but not essential.Some distinguishing features of this book are: Clear exposition of the basic theory at a level to facilitate independent study. Discussion of the various versions of the theory: diffusion Monte Carlo, Green's function Monte Carlo, and release n

Lester, William A; Reynolds, PJ

1994-01-01

344

A high-precision ab initio determination of the equilibrium geometry and force field of HOC(+)  

Science.gov (United States)

The results of an ab initio molecular orbital investigation of the isoformyl cation, HOC(+), shape are reported. The effects of expanding the basis set to near the Hartree-Fock limit and of electron correlation were examined, and the results indicate that near the Hartree-Fock limit the HOC(+) is linear. An analytic potential function is presented, from which the calculated rotational energies are only 0.03 percent different from the experimental values. This represents a nearly two orders of magnitude reduction in error from earlier work.

Defrees, D. J.; Bunker, P. R.; Binkley, J. S.; Mclean, A. D.

1987-01-01

345

Ab Initio Calculations of Singlet and Triplet Excited States of Chlorine Nitrate and Nitric Acid  

Science.gov (United States)

Ab initio calculations of vertical excitations to singlet and triplet excited states of chlorine nitrate and nitric acid are reported. The nature of the electronic transitions are examined by decomposing the difference density into the sum of detachment and attachment densities. Counterparts for the three lowest singlet excited states of nitric acid survive relatively unperturbed in chlorine nitrate, while other low-lying singlet states of chlorine nitrate appear to be directly dissociative in the ClO chromophore. These results suggest an assignment of the two main peaks in the experimental chlorine nitrate absorption spectrum. In addition, triplet vertical excitations and the lowest optimized triplet geometries of both molecules are studied.

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

1994-01-01

346

Nanotubules of bare boron clusters: Ab initio and density functional study  

Science.gov (United States)

Using ab initio quantum-chemical and density functional methods we have determined novel structures of bare boron clusters. In addition to previously reported quasi-planar, convex and spherical cluster forms, boron nanotubules seem to be highly stable as well. These novel nanotubular structures are composed of hexagonal pyramids only and can be considered as segments of extended pipes. Applying a previously reported "Aufbau Principle", one can easily construct stable boron structures besides the new nanotubular clusters described below. Thus the Aufbau principle should help in illuminating the chemical and physical nature of new boron materials based on boron nanotubules.

Boustani, I.; Quandt, A.

1997-09-01

347

An ab initio molecular orbital study of the electron affinity of boron clusters  

International Nuclear Information System (INIS)

The electron affinities of boron clusters were studied using ab initio molecular orbital methods to discuss the phenomenon of clustered boron anions emitted during sputtering. Calculations were performed at the MP4(SDQ)/CBSB5 level. The calculated electron affinities of B, B2, and B3 were found to be 0.214, 3.66, and 3.20 eV, respectively. These values are qualitatively consistent with the experimental data of sputtering yield of B-, B2-, and B3-

348

Atomic defects in D03-Ni3Sb: An ab initio study  

Science.gov (United States)

The effective formation energies and the effective formation volumes of atomic defects in the ordered compound NixSb1-x in the D03 structure are calculated by the statistical mechanics in combination with the ab initio electron theory. For the Sb-rich compounds the structural defect is the Ni vacancy on the ? sublattice. The stoichiometric compound is a pentadefect system where on the average four Ni vacancies on the ? sublattice and one Ni antistructure atom are generated. The calculations strongly support the interpretation of results from neutron-scattering experiments.

Bester, G.; Meyer, B.; Fähnle, M.

1998-05-01

349

Composition of tautomeric mixtures studied by nitrogen chemical shifts and ab initio molecular orbital calculations  

International Nuclear Information System (INIS)

Some nitrogen and carbon chemical shifts and ab initio Gauge Invariant Atomic Orbitals - Coupled-Perturbed Hartree-Fock (GIAO-CPHF) calculations are reported for benzotriazole 1, 5-nitrobenzimidazole 2, 5-nitrobenzotriazole 3, 4-nitrobenzotriazole 4, and N-methyl derivatives of compounds 1-3. A good correlation is found between the calculated and observed 13C and 15N chemical shifts. Two methods were employed for calculation of equilibrium constants. The prototropic equilibria exhibited by the system studied are found to be controlled by enthalpy rather than entropy. (author)

350

A transferable ab-initio based force field for aqueous ions  

CERN Document Server

We present a new polarizable force field for aqueous ions (Li+, Na+, K+, Rb+, Cs+, Mg2+, Ca2+, Sr2+ and Cl-) derived from condensed phase ab-initio calculations. We use Maximally Localized Wannier Functions together with a generalized force and dipole-matching procedure to determine the whole set of parameters. Experimental data is then used only for validation purposes and a good agreement is obtained for structural, dynamic and thermodynamic properties. The same procedure applied to crystalline phases allows to parametrize the interaction between cations and the chloride anion. Finally, we illustrate the good transferability of the force field to other thermodynamic conditions by investigating concentrated solutions.

Tazi, Sami; Rotenberg, Benjamin; Turq, Pierre; Vuilleumier, Rodolphe; Salanne, Mathieu; 10.1063/1.3692965

2012-01-01

351

Implications of ab initio energetics on the thermodynamics of Fe-Cr alloys  

International Nuclear Information System (INIS)

The authors analyze the implications of the recently reported results of ab initio calculations of formation energies of the Fe-Cr alloy. The formation energies show a change in sign from negative to positive as Cr composition increases above ?10%. By developing a classic potential to evaluate the thermodynamic properties, they determine the location of the solubility limit and compare it with earlier results. A significant difference appears in a region of temperature and composition that is relevant for the nuclear applications of this alloy. Experimental results seem to confirm the validity of the location of the new solvus line

352

Ab-initio prediction of materials properties with CRYSTAL: MOF-5 as a case study  

Digital Repository Infrastructure Vision for European Research (DRIVER)

MOF-5 is by far the most relevant member of the new class of metal - organic framework materials and has been adopted as a case study to show that reliable ab initio prediction of materials properties of complex systems can be obtained by means of a solid state computational tool like the CRYSTAL code. Structure, electronic properties and vibrational frequencies of MOF-5 computed at the B3LYP level of theory are reported and discussed. Animations representing MOF-5 vibrations are available at...

Dovesi, Roberto; Roetti, Carla; Civalleri, Bartolomeo; Napoli, Francesco

2006-01-01

353

Ab initio determination of the electron affinities of DNA and RNA nucleobases  

Science.gov (United States)

High-level quantum-chemical ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute the vertical and adiabatic electron affinities of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. The present results aim for the accurate determination of the intrinsic electron acceptor properties of the isolated nucleic acid bases as described by their electron affinities, establishing an overall set of theoretical reference values at a level not reported before and helping to rule out less reliable theoretical and experimental data and to calibrate theoretical strategies.

Roca-Sanjuán, Daniel; Merchán, Manuela; Serrano-Andrés, Luis; Rubio, Mercedes

2008-09-01

354

Ab Initio calculation of band gap renormalization in highly excited GaAs  

CERN Document Server

We present ab initio quasiparticle self-energy calculations in crystalline GaAs for cases of intense electronic excitation (~ 10% of valence electrons excited into conduction band), relevant for high-intensity ultra-short pulsed laser experiments. Calculations are performed using an out-of-equilibrium generalization of the GW approximation based on the Keldysh Green's function approach. Our results indicate that while the band gap is a sensitive function of the amount of excitation, it is not possible to induce complete band gap closure in this system by purely electronic means.

Spataru, C D; Louie, S G; Spataru, Catalin D.; Benedict, Lorin X.; Louie, Steven G.

2004-01-01

355

Ab initio simulation of effects of structural singularities in aerogel absorption potential  

International Nuclear Information System (INIS)

In the present work simulation of Van der Waals potential between helium atom and part of silica aerogel strand by means of ab initio methods was performed. Cell with alpha quartz structure was used as building block of aerogel strand, because it is the most stable structure at low temperature, and only the surface layer of aerogel has been considered. For modeling absorption potential field in plane, summation of potential from individual building blocks has been provided. Two dimensional Van der Waals energy field was calculated for different geometries of aerogel strands. A rather deep potential well has been found in the corner formed due to aerogel strand crossing.

356

Raman spectra of barium halides in orthorhombic and hexagonal symmetry: An ab initio study  

Science.gov (United States)

Vibrational properties of bulk crystalline barium halides BaCl2, BaBr2, and BaI2 are theoretically investigated for orthorhombic and hexagonal symmetry with ab initio methods in density functional theory. It is demonstrated that the used method is capable of predicting frequencies of vibrational modes, their symmetry types, and corresponding Raman intensities in reasonable agreement with experimental data for orthorhombic and hexagonal BaCl2 and BaBr2 nanocrystals embedded in fluorozirconate glasses. For orthorhombic BaCl2, a Raman-active phonon mode could be predicted theoretically that was not observed in measurements before.

Bohley, Christian; Wagner, Jan-Martin; Pfau, Charlotte; Miclea, Paul-Tiberiu; Schweizer, Stefan

2011-01-01

357

Ab initio studies of ionization potentials of hydrated hydroxide and hydronium  

CERN Document Server

The ionization potential distributions of hydrated hydroxide and hydronium are computed with many-body approach for electron excitations with configurations generated by {\\it ab initio} molecular dynamics. The experimental features are well reproduced and found to be closely related to the molecular excitations. In the stable configurations, the ionization potential is mainly perturbed by water molecules within the first solvation shell. On the other hand, electron excitation is delocalized on both proton receiving and donating complex during proton transfer, which shifts the excitation energies and broadens the spectra for both hydrated ions.

Swartz, Charles W

2013-01-01

358

Ab initio studies on the mechanic and magnetic properties of PdHx  

Science.gov (United States)

Based on ab initio total energy calculations, the structural, electronic, mechanic, and magnetic properties of PdHx are investigated. It is found that bulk modulus of PdHx is larger than the metal Pd with the hydrogen storage except Pd4H2. The calculated results for the magnetic moments show that the hydrogen addition weakens the magnetic properties of the PdHx systems. A strong magneto-volume effect is found in PdHx structures as well as Pd. The transition from paramagnetism to ferromagnetism is discussed. The corresponding densities of states for both structures are also shown to understand the magnetic behaviour.

Cui, Xin; Liang, Xi-Xia; Wang, Jian-Tao; Zhao, Guo-Zhong

2011-02-01

359

Ground state vibrations of citric acid and the citrate trianion—an ab initio study  

Science.gov (United States)

Ab initio force fields for the vibrations of citric acid and citrate trianion in their ground electronic states have been determined at the Hartree—Fock level using the 4-21G basis set. The calculated geometries have been compared to the corresponding X-ray structures of citric acid and magnesium citrate, respectively. The calculated vibrational frequencies have been used to assign the experimental IR and Raman spectra of citric acid and sodium citrate. The calculated potential energy distribution, Raman activities and IR intensities have been used as aids in the assignment of the vibrational spectra of citric acid and sodium citrate.

Tarakeshwar, P.; Manogaran, S.

1994-12-01

360

Ab-initio study of high temperature lattice dynamics of BCC zirconium (?-Zr) and uranium (?-U)  

Energy Technology Data Exchange (ETDEWEB)

Using self consistent ab-initio lattice dynamics calculations, we show that bcc structures of Zr and U phases become stable at high temperature by phonon-phonon interactions. The calculated temperature dependent phonon dispersion curve (PDC) of ?-Zr match excellently with experimental PDC. But the calculated PDC for ?-U shows negative phonon frequencies even at solid to liquid transition temperature. We show that this discrepancy is due to an overestimation of instability depth of bcc U phase which is removed by incorporation of spin-orbit coupling in the electronic structure calculations.

Ghosh, Partha S., E-mail: parthasarathi13@gmail.com; Arya, A., E-mail: parthasarathi13@gmail.com; Dey, G. K., E-mail: parthasarathi13@gmail.com [Materials Science Division, Bhabha Atomic Research Centre, Mumbai-400085 (India)

2014-04-24

 
 
 
 
361

Ab-initio study of high temperature lattice dynamics of BCC zirconium (?-Zr) and uranium (?-U)  

International Nuclear Information System (INIS)

Using self consistent ab-initio lattice dynamics calculations, we show that bcc structures of Zr and U phases become stable at high temperature by phonon-phonon interactions. The calculated temperature dependent phonon dispersion curve (PDC) of ?-Zr match excellently with experimental PDC. But the calculated PDC for ?-U shows negative phonon frequencies even at solid to liquid transition temperature. We show that this discrepancy is due to an overestimation of instability depth of bcc U phase which is removed by incorporation of spin-orbit coupling in the electronic structure calculations

362

Testing the density matrix expansion against ab initio calculations of trapped neutron drops  

International Nuclear Information System (INIS)

Microscopic input to a universal nuclear energy density functional can be provided through the density matrix expansion (DME), which has recently been revived and improved. Several DME implementation strategies are tested for neutron drop systems in harmonic traps by comparing to Hartree-Fock (HF) and ab initio no-core full configuration (NCFC) calculations with a model interaction (Minnesota potential). The new DME with exact treatment of Hartree contributions is found to best reproduce HF results and supplementing the functional with fit Skyrme-like contact terms shows systematic improvement toward the full NCFC results.

363

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

2007-01-01

364

Synthesis and Ab Initio/DFT Studies on 2-(4-methoxyphenylbenzo[d]thiazole  

Directory of Open Access Journals (Sweden)

Full Text Available 2-aminothiophenol and 4-methoxybenzaldehyde were cyclized under microwaveirridation and solvent free conditions to synthesize 2-(4-methoxyphenylbenzo[d]thiazole.The molecular structure and vibrational frequencies of the title compound in the groundstate have been investigated with ab initio (HF and density functional theory methods(BLYP, B3LYP, B3PW91 and mPW1PW91 implementing the standard 6-311G(d,p basisset. Comparison of the observed fundamental vibrational frequencies of title compound andcalculated results by HF and DFT methods indicate that B3LYP is superior to the scaledHF approach for molecular problems.

Öztekin Algül

2007-08-01

365

Ab initio investigation of VOSeO3, a spin gap system with coupled spin dimers  

CERN Document Server

Motivated by an early experimental study of VOSeO3, which suggested that it is a quasi-2D system of weakly coupled spin dimers with a small spin gap, we have investigated the electronic structure of this material via density-functional calculations. These ab initio results indicate that the system is better thought of as an alternating spin-1/2 chain with moderate interchain interactions, an analog of (VO)2P2O7. The potential interest of this system for studies in high magnetic field given the presumably small value of the spin gap is emphasized.

Valenti, R; Mila, F; Valenti, Roser

2003-01-01

366

Electronic transport in monolayer graphene with extreme physical deformation: ab initio density functional calculation  

International Nuclear Information System (INIS)

The electronic transport properties of monolayer graphene with extreme physical deformation are studied using ab initio calculations. The aim is to explore the influence of physical bending on transport properties and identify the most important geometrical parameter. The transmission spectra are relatively insensitive to the geometrical parameters in low-energy regions-even in the extreme case of uniaxial bending. The results suggest that graphene, with its superb electromechanical robustness, could serve as a viable nanoscale material platform in a wide spectrum of applications such as photovoltaics, flexible electronics, and 3D carbon chips.

367

Ab initio phase stability at high temperatures and pressures in the V-Cr system  

Science.gov (United States)

The phase stability of vanadium metal and vanadium-chromium alloys at high temperatures and pressures is explored by means of first-principles electronic-structure calculations. Utilizing the self-consistent ab initio lattice dynamics approach in conjunction with density-functional theory, we show that pressure-induced mechanical instability of body-centered cubic vanadium metal, which results in formation of a rhombohedral phase at around 60-70 GPa at room temperature, will survive significant heating and compression. Furthermore, alloying with chromium decreases the temperature at which stabilization of the body-centered cubic phase occurs at elevated pressure.

Landa, A.; Söderlind, P.; Yang, L. H.

2014-01-01

368

Electronic transport coefficients from ab initio simulations and application to dense liquid hydrogen  

International Nuclear Information System (INIS)

Using Kubo's linear response theory, we derive expressions for the frequency-dependent electrical conductivity (Kubo-Greenwood formula), thermopower, and thermal conductivity in a strongly correlated electron system. These are evaluated within ab initio molecular dynamics simulations in order to study the thermoelectric transport coefficients in dense liquid hydrogen, especially near the nonmetal-to-metal transition region. We also observe significant deviations from the widely used Wiedemann-Franz law, which is strictly valid only for degenerate systems, and give an estimate for its valid scope of application toward lower densities.

369

Dissolution of cellulose in ionic liquids: an ab initio molecular dynamics simulation study.  

Science.gov (United States)

Interactions determining the dissolution of a monomer of ?-cellulose, i.e., cellobiose in a room temperature ionic liquid, [Emim][OAc], have been studied using ab initio molecular dynamics simulations. Although anions are the predominant species in the first coordination shell of cellobiose, cations too are present to a minor extent around it. The presence of low concentration of water in the solution does not significantly alter the nature of the coordination environment of cellobiose. All intra-molecular hydrogen bonds of anti-syn cellobiose are replaced by inter-molecular hydrogen bonds formed with the anions, whereas the anti-anti conformer retains an intramolecular hydrogen bond. PMID:25012815

Payal, Rajdeep Singh; Balasubramanian, Sundaram

2014-09-01

370

Ab Initio Calculations of Optical Properties of TlBr and TlCl Radiation Detectors  

Directory of Open Access Journals (Sweden)

Full Text Available We report on ab initio calculations of the optical properties of TlBr and TlCl binary semiconductor compounds using the self-consistent scalar relativistic full potential linear augmented plane wave band method (FP-LAPW within the local density approximation (LDA including the generalized gradient approximation (GGA. The accurate calculations of linear optical function (refractive index, reflectance, coefficient of absorption, and both imaginary and real dielectric function is performed in the photon energy range up to 20 eV. The predicted optical constants agree well with the available experimental data.

Noureddine Amrane

2011-08-01

371

Atomic ionization of germanium by neutrinos from an ab initio approach  

Science.gov (United States)

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; Chi, Hsin-Chang; Huang, Keh-Ning; Liu, C.-P.; Shiao, Hao-Tse; Singh, Lakhwinder; Wong, Henry T.; Wu, Chih-Liang; Wu, Chih-Pan

2014-04-01

372

Metastable phases and spinodal decomposition in Ti1-xAl xN system studied by ab initio and thermodynamic modeling, a comparison with the TiN-Si3N4 system  

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

373

Estudo da geometria da uréia por métodos ab initio e simulação computacional de líquidos Studies of urea geometry by means of ab initio methods and computer simulations of liquids  

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.

José Jair Vianna Cirino

2002-05-01

374

Unified ab initio description of the intrinsic and extrinsic anomalous Hall effect in disordered alloys  

Energy Technology Data Exchange (ETDEWEB)

We present a coherent ab initio, i.e. parameter free, description of the anomalous Hall effect (AHE) that is applicable to pure as well as disordered alloy systems by treating all sources of the AHE on equal footing. We employ an implementation of the Kubo-Streda equation using the fully relativistic Korringa-Kohn-Rostoker (KKR) Green's function method in conjunction with the Coherent Potential Approximation (CPA) alloy theory. Applications to the pure elemental ferromagnets bcc-Fe, hcp-Co and fcc-Ni lead to results in full accordance to previous ab initio studies determining the intrinsic contribution only. However, the power of the approach presented is the ability to explicitly treat also extrinsic contributions to the AHE which is demonstrated by an application to the fcc alloy systems Fe{sub x}Pd{sub 1-x}, Co{sub x}Pd{sub 1-x} and Ni{sub x}Pd{sub 1-x}. We obtain a very satisfying qualitative agreement with experiment over the whole concentration range including the sign reversal of the AH-conductivity. A detailed discussion of skew and side-jump scattering processes exemplifies the capability of the proposed method.

Koedderitzsch, Diemo; Chadova, Kristina; Lowitzer, Stephan; Ebert, Hubert [Ludwig-Maximilians-Universitaet Muenchen, Department Chemie und Biochemie, Physikalische Chemie, Butenandtstrasse 11, D-81377 Muenchen (Germany)

2011-07-01

375

Liquid properties of dimethyl ether from molecular dynamics simulations using ab initio force fields.  

Science.gov (United States)

We have used molecular dynamic simulations to study the structural and dynamical properties of liquid dimethyl ether (DME) with a newly constructed ab initio force field in this article. The ab initio potential energy data were calculated at the second order Møller-Plesset (MP2) perturbation theory with Dunning's correlation consistent basis sets (up to aug-cc-pVQZ). We considered 17 configurations of the DME dime for the orientation sampling. The calculated MP2 potential data were used to construct a 3-site united atom force field model. The simulation results are compared with those using the empirical force field of Jorgensen and Ibrahim (Jorgensen and Ibrahim, J Am Chem Soc 1981, 103, 3976) and with available experimental measurements. We obtain quantitative agreements for the atom-wise radial distribution functions, the self-diffusion coefficients, and the shear viscosities over a wide range of experimental conditions. This force field thus provides a suitable starting point to predict liquid properties of DME from first principles intermolecular interactions with no empirical data input a priori. PMID:22278976

Wang, Shi-Bao; Li, Arvin Huang-Te; Chao, Sheng D

2012-04-01

376

Liquid chloroform structure from computer simulation with a full ab initio intermolecular interaction potential  

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

377

Ab-initio study of competing magnetic configurations in cubic BiFeO3 alloys  

International Nuclear Information System (INIS)

Using ab-initio calculations, we study the properties of the multiferroic BiFeO3 compounds in the perfect cubic perovskite lattice structure. We show that the appearance of magnetism is energetically favorable. Except the ferromagnetic structure, there are three possible antiferromagnetic arrangements, which are close in energy, and for large values of the lattice constant a G-type antiferromagnetism is the most stable magnetic order. Fe atoms are responsible for the spin magnetic moments while the values of the induced spin moments at the other sites depend strongly on the local environment of the atoms. There is a significant charge transfer from the Fe and Bi atoms towards the p-states of O atoms. - Highlights: ? Ab-initio calculations are employed to study BiFeO3 in its cubic phase. ? Fe atoms carry mainly the spin magnetic moments. ? Fe spin moments depend only on the lattice constant and not their relative orientation. ? For small lattice constants the ferromagnetic ordering of Fe moments is favoured. ? For larger lattice constants a G-type antiferromagnetism is the ground-state.

378

Ab initio calculations and interatomic potentials for iron and iron alloys: Achievements within the Perfect Project  

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

379

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

International Nuclear Information System (INIS)

direction of research is a new empirical potential based on the Environment Dependent Interaction Potential (EDIP) recently developed for silicon. The EDIP approach represents a promising direction for empirical potentials through its use of ab initio data to motivate the functional form as well as the more conventional parametrisation. By inverting ab initio cohesive energy curves the authors of EDIP arrived at a pair potential expression which reduces to the well-known Stillinger-Weber form at integer coordination, while providing interpolation and extrapolation to situations where the coordination was either fractional or beyond the fitting data set. The application of EDIP to carbon has thus far been quite encouraging, in particular the two-body pair potential which exhibits a remarkably good degree of transferability to coordinations two and six, despite being fitted to only the graphene and diamond structures. Current development work is concentrating on the c-axis ?-repulsion and dihedral rotation penalties which are absent from the original EDIP. Preliminary molecular dynamics simulations using this modified EDIP provide a visual and intuitive demonstration of why these effects are so important when modelling amorphous carbons

380

Simulations of vibrational spectra from classical trajectories: Calibration with ab initio force fields  

Science.gov (United States)

An algorithm allowing simulating vibrational spectra from classical time-dependent trajectories was applied for infrared absorption, vibrational circular dichroism, Raman, and Raman optical activity of model harmonic systems. The implementation of the theory within the TINKER molecular dynamics (MD) program package was tested with ab initio harmonic force fields in order to determine the feasibility for more extended MD simulations. The results suggest that sufficiently accurate frequencies can be simulated with integration time steps shorter than about 0.5fs. For a given integration time step, lower vibrational frequencies (˜0-2000cm-1) could be reproduced with a higher accuracy than higher-frequency vibrational modes (e.g., O-H and C-H stretching). In principle, the algorithm also provides correct intensities for ideal systems. In applied simulations, however, the intensity profiles are affected by an unrealistic energy distribution between normal modes and a slow energy relaxation. Additionally, the energy fluctuations may cause weakening of the intensities on average. For ab initio force fields, these obstacles could be overcome by an arbitrary normal mode energy correction. For general MD simulations, averaging of many shorter MD trajectories started with randomly distributed atomic velocities provided the best spectral shapes. ?-pinene, D-gluconic acid, formaldehyde dimer, and the acetylprolineamide molecule were used in the tests.

Horní?ek, Jan; Kaprálová, Petra; Bou?, Petr

2007-08-01

 
 
 
 
381

Forced coalescence phasing: a method for ab initio determination of crystallographic phases.  

Science.gov (United States)

A method has been developed for ab initio determination of crystallographic phases. This technique, called forced coalescence phasing (FCP), is implemented on a computer and uses an automated iterative procedure that combines real space filtering with numerically seeded Fourier transforms to solve the crystallographic phase problem. This approach is fundamentally different from that of traditional direct methods of phasing, which rely on structure invariant probabilistic phase relationships. In FCP, the process begins with an appropriate set of atoms randomly distributed throughout the unit cell. In subsequent cycles of the program, these atoms undergo continual rearrangements ultimately forming the correct molecular structure(s) consistent with the observed x-ray data. In each cycle, the molecular rearrangement is directed by an electron density (Fourier) map calculated using specially formulated numerical seed coefficients that, along with the phase angles for the map, are derived from the arrangement of atoms in the preceding cycle. The method has been tested using actual x-ray data from three organic compounds. For each data set, 100 separate phase determination trials were conducted, each trial beginning with a different set of randomly generated starting phases. Correct phase sets were successfully determined in all of the trials with most trials requiring fewer than 50 cycles of the FCP program. In addition to its effectiveness in small molecule phase determination, FCP offers unexplored potential in the application of real-space methods to ab initio phasing of proteins and other macromolecule structures. PMID:11607507

Drendel, W B; Davé, R D; Jain, S

1995-01-17

382

Evolved Chiral NN+3N Hamiltonians for Ab Initio Nuclear Structure Calculations  

CERN Document Server

We discuss the building blocks for a consistent inclusion of chiral three-nucleon (3N) interactions into ab initio nuclear structure calculations beyond the lower p-shell. We highlight important technical developments, such as the similarity renormalization group (SRG) evolution in the 3N sector, a JT-coupled storage scheme for 3N matrix elements with efficient on-the-fly decoupling, and the importance truncated no-core shell model with 3N interactions. Together, these developments make converged ab initio calculations with explicit 3N interactions possible also beyond the lower p-shell. We analyze in detail the impact of various truncations of the SRG-evolved Hamiltonian, in particular the truncation of the harmonic-oscillator model space used for solving the SRG flow equations and the omission of the induced beyond-3N contributions of the evolved Hamiltonian. Both truncations lead to sizable effects in the upper p-shell and beyond and we present options to remedy these truncation effects. The analysis of th...

Roth, Robert; Langhammer, Joachim; Binder, Sven

2013-01-01

383

Ab initio modelling of defect properties with substitutional and interstitials elements in steels and Zr alloys  

International Nuclear Information System (INIS)

In alloys, the different elements interact with each other as well as with the various defects present: point defects or extended defects (stacking faults, dislocations, grain boundaries). These interactions are responsible for the elementary mechanisms governing the kinetics of the system, and they are among the key parameters to model the time evolution of the microstructure, under ageing or irradiation. Indeed the microstructure properties are directly linked to the chemical interactions between the different constituting elements, and these defects. Ab initio methods allow to determine properties such as defect formation, binding or migration energies. These crucial quantities can shed light on the various mechanisms involved in the evolution of the microstructure as well as be used as input for various models. In this article, data obtained by ab initio calculation of point defects (vacancies and self-interstitial atoms, foreign interstitial defects (C, N, H and He) in different matrix element (Fe and Zr) as well as of some substitutional elements (Cu, Ni, Mn, Si, Cr and P ...)) in bcc Fe will be presented and discussed. When available, comparison with experimental data will be made in order to assess the validity of the results. The link between the obtained atomic quantities and the related consequences on the macroscopic properties will be discussed

384

Ab initio modelling of defect properties with substitutional and interstitials elements in steels and Zr alloys  

Science.gov (United States)

In alloys, the different elements interact with each other as well as with the various defects present: point defects or extended defects (stacking faults, dislocations, grain boundaries). These interactions are responsible for the elementary mechanisms governing the kinetics of the system, and they are among the key parameters to model the time evolution of the microstructure, under ageing or irradiation. Indeed the microstructure properties are directly linked to the chemical interactions between the different constituting elements, and these defects. Ab initio methods allow to determine properties such as defect formation, binding or migration energies. These crucial quantities can shed light on the various mechanisms involved in the evolution of the microstructure as well as be used as input for various models. In this article, data obtained by ab initio calculation of point defects (vacancies and self-interstitial atoms, foreign interstitial defects (C, N, H and He) in different matrix element (Fe and Zr) as well as of some substitutional elements (Cu, Ni, Mn, Si, Cr and P …)) in bcc Fe will be presented and discussed. When available, comparison with experimental data will be made in order to assess the validity of the results. The link between the obtained atomic quantities and the related consequences on the macroscopic properties will be discussed.

Domain, Christophe

2006-06-01

385

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

CERN Document Server

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

386

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

DEFF Research Database (Denmark)

For the first time, the differences between the spectra of amphetamine and amphetamine-H+ and between different conformers are thoroughly studied by ab initio model calculations, and Raman and surface-enhanced Raman spectroscopy (SERS) spectra are measured for different species of amphetamine. The spectra of amphetamine and amphetamine-H+ sampleswere obtained and assigned according to a comparison of the experimental spectra and the ab initio MO calculations, performed using the Gaussian 03W program (Gaussian, Inc., Pittsburgh, PA). The analyses were based on complete geometry minimization of the conformational energy of the S-plus-amphetamine molecule and the S-plus-amphetamine-H+ ion. The harmonic frequency calculations provide information about the characteristic features of the Raman spectra and the nature of the bonding in the molecule. It is concluded that vibrational bands from salt anions with internal bonds (sulfates, hydrogen phosphates, etc.) need to be taken into account when employing these spectra for identification purposes. These results also show how Raman spectroscopy can assist the forensic community in drug profiling studies. Furthermore, because their spectra are different, discrimination between the free and protonated forms of amphetamine salts can be observed. Here, we provide evidence for this difference and show experimentally how it has been overseen.

Berg, Rolf W.; NØrbygaard, Thomas

2011-01-01

387

Liquid chloroform structure from computer simulation with a full ab initio intermolecular interaction potential  

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

388

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field.  

Science.gov (United States)

Ab initio protein folding is one of the major unsolved problems in computational biology owing to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1-20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 nonhomologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in one-third cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction experiment, QUARK server outperformed the second and third best servers by 18 and 47% based on the cumulative Z-score of global distance test-total scores in the FM category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress toward the solution of the most important problem in the field. PMID:22411565

Xu, Dong; Zhang, Yang

2012-07-01

389

Large basis ab initio shell model investigation of 9-Be and 11-Be  

CERN Document Server

We are presenting the first ab initio structure investigation of the loosely bound 11-Be nucleus, together with a study of the lighter isotope 9-Be. The nuclear structure of these isotopes is particularly interesting due to the appearance of a parity-inverted ground state in 11-Be. Our study is performed in the framework of the ab initio no-core shell model. Results obtained using four different, high-precision two-nucleon interactions, in model spaces up to 9\\hbar\\Omega, are shown. For both nuclei, and all potentials, we reach convergence in the level ordering of positive- and negative-parity spectra separately. Concerning their relative position, the positive-parity states are always too high in excitation energy, but a fast drop with respect to the negative-parity spectrum is observed when the model space is increased. This behavior is most dramatic for 11-Be. In the largest model space we were able to reach, the 1/2+ level has dropped down to become either the first or the second excited state, depending ...

Forssén, C; Ormand, W E; Caurier, E

2004-01-01

390

Ab initio investigation of the spin Hall effect for non-magnetic alloys  

Energy Technology Data Exchange (ETDEWEB)

Spin-orbit coupling is responsible for several interesting phenomena like e.g. the anomalous Hall effect (AHE) in magnetic materials. The AHE results from the interaction between spin-orbit coupling and the spin polarization. In comparison to the AHE the spin Hall effect (SHE) needs no spin polarization and is therefore even present in non-magnetic systems. This was shown by several experimental works e.g. During the last years several publications have appeared which studied the spin Hall effect for pure systems via ab initio e.g. or model calculations. However, up to now no publication is available in which the SHE is calculated for alloy systems on an ab initio level. To calculate the SHE we have implemented the Kubo-Streda equation in our fully relativistic SPR-KKR package. The Kubo-Streda equation gives access to the full anti-symmetric conductivity tensor what is necessary for the calculation of the SHE. The disorder is treated via the coherent potential approximation (CPA). We show first results for several non-magnetic 3d and 4d transition metal alloys.

Lowitzer, Stephan; Koedderitzsch, Diemo; Ebert, Hubert [Department Chemie, Physikalische Chemie, Universitaet Muenchen, Butenandstr. 5-13, 81377 Muenchen (Germany)

2010-07-01

391

Evolved chiral NN +3N Hamiltonians for ab initio nuclear structure calculations  

Science.gov (United States)

We discuss the building blocks for a consistent inclusion of chiral three-nucleon (3N) interactions into ab initio nuclear structure calculations beyond the lower p shell. We highlight important technical developments, such as the similarity renormalization group (SRG) evolution in the 3N sector, a JT-coupled storage scheme for 3N matrix elements with efficient on-the-fly decoupling, and the importance-truncated no-core shell model with 3N interactions. Together, these developments make converged ab initio calculations with explicit 3N interactions possible also beyond the lower p shell. We analyze in detail the impact of various truncations of the SRG-evolved Hamiltonian, in particular the truncation of the harmonic-oscillator model space used for solving the SRG flow equations and the omission of the induced beyond-3N contributions of the evolved Hamiltonian. Both truncations lead to sizable effects in the upper p shell and beyond and we present options to remedy these truncation effects. The analysis of the different truncations is a first step towards a systematic uncertainty quantification of all stages of the calculation.

Roth, Robert; Calci, Angelo; Langhammer, Joachim; Binder, Sven

2014-08-01

392

Ab-initio electronic and magnetic properties of Fe-Al alloys  

Directory of Open Access Journals (Sweden)

Full Text Available This work presents ab-initio self-consistent calculations performed with the TB-LMTO code to study the different phases of the Fe-Al phase diagram, corresponding to the ordered structures B2, DO3 and B32 and for Fe50Al50 and Fe3Al compositions. Both, unpolarized and spin-polarized calculations have been performed to deduce the energetic difference between the paramagnetic and ferromagnetic state of the corresponding structure. Calculations for the disordered structures have also been performed for the previously mentioned compositions. These results show that by disordering the alloy magnetism is enhanced and that the equilibrium lattice parameter increases.

En este trabajo se presentan cálculos autoconsistentes ab-initio realizados con el método TB-LMTO (Tight Binding Linear Muffin Tin Orbital con el fin de estudiar las diferentes estructuras que se presentan en el diagrama de fases de las aleaciones Fe-Al. Se han estudiado las estructuras ordenadas B2, DO3 y B32 para las siguientes concentraciones: Fe50Al50 y Fe3Al. Asimismo, se han realizado cálculos teniendo y sin tener en cuenta la polarización de spin con el fin de poder deducir la diferencia energética entre los estados ferromágneticos y paramágneticos de la misma estructura. Por otra parte se han realizado estos mismos cálculos para estructuras desordenadas y las mismas concentraciones. Los resultados muestran que mediante el desorden aumenta el magnetismo de estas aleaciones y crece el parámetro de red.

Apiñaniz, E.

2000-06-01

393

Ab initio prediction of the critical thickness of a precipitate.  

Science.gov (United States)

Segregation and precipitation of second phases in metals and metallic alloys is an important phenomenon that has a strong influence on the mechanical properties of the material. Models exist that describe the growth of coherent, semi-coherent and incoherent precipitates. One important parameter of these models is the energy of the interface between matrix and precipitate. In this work we apply ab initio density functional theory calculations to obtain this parameter and to understand how it depends on chemical composition and mechanical strain at the interface.Our example is a metastable Mo-C phase, the body-centred tetragonal structure, which exists as a semi-coherent precipitate in body-centred cubic molybdenum. The interface of this precipitate is supposed to change from coherent to semi-coherent during the growth of the precipitate. We predict the critical thickness of the precipitate by calculating the different contributions to a semi-coherent interface energy by means of ab initio density functional theory calculations. The parameters in our model include the elastic strain energy stored in the precipitate, as well as a misfit dislocation energy that depends on the dislocation core width and the dislocation spacing. Our predicted critical thickness agrees well with experimental observations. PMID:23896820

Sampath, S; Janisch, R

2013-09-01

394

Thermodynamic assessment of the Ho–Te system supported by ab initio calculations  

Energy Technology Data Exchange (ETDEWEB)

Highlights: ? We calculated enthalpies of formation of the HoTe and Ho{sub 2}Te{sub 5} compounds by using ab initio method. ? We modeled the Gibbs energy of the HoTe intermediate phase for the first time. ? The thermodynamic parameters of the all phases existing in the system were determined. ? The complete phase diagram of the system (Ho–Te) is calculated. -- Abstract: The phase diagram of the Ho–Te binary system has been assessed by using the CALPHAD (Calculation of Phase Diagrams) method on the basis of the experimental data of the phase equilibria and enthalpies of formation from ab initio electronic-structure calculations within the framework of density-functional theory. Reasonable models were constructed for all the phases of the system. The liquid phase was described as the substitutional solution model with excess energy expressed by Redlich–Kister polynomial. The compounds Ho{sub 2}Te{sub 5} and HoTe{sub 3} were expressed as stoichiometric phases. The (HoTe) phase was modeled by two-sublattices; (Ho,Va){sub 1}(Te){sub 1}. A consistent set of thermodynamic parameters has been derived, and calculated phase diagram was compared with the experimental data. A good agreement between the calculated results and experimental data was obtained.

Ghamri, H.; Belgacem-Bouzida, A. [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria); Djaballah, Y., E-mail: ydjaballah@yahoo.fr [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria); Hidoussi, A. [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria)

2013-03-05

395

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

International Nuclear Information System (INIS)

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

396

Ab initio study of electronic confinement on stepped Cu(111) surfaces  

Energy Technology Data Exchange (ETDEWEB)

We report on study of surface states on clean and decorated Cu(111) stepped surfaces by means of ab initio Korringa-Kohn-Rostoker (KKR) Green's function method. Surfaces with the terrace width ranging from 12 to 21 A are considered. Confined electronic states are revealed close to the Fermi energy. This finding is in agreement with experiments of M. Hansmann et al. Our calculations confirmed that the position of such states strongly depends on the terrace width. The strength of the potential barrier at the step edges calculated using the Kronig-Penney model and our ab initio results is found to be in a good agreement with experimentally determined values. It is shown that the strength of the confining barriers on Cu(111) vicinals can be significantly affected by decoration of step edges with monoatomic Fe wires, similar to recent experimental finding of S. Shiraki et al. Due to spin-dependent scattering of surface-states electrons at Fe wires surface states become spin-polarized. The majority states remain unaffected, but the confinement picture of the minority states is suppressed by a strong scattering of surface-states electrons at the minority states on Fe wires.

Ignatiev, Pavel; Stepanyuk, Valeriy; Klavsyuk, Andriy; Bruno, Patrick [Max- Planck-Institut fuer Mikrostrukturphysik, Weinberg 2, D-06120 Halle (Germany); Hergert, Wolfram [Fachbereich Physik, Martin-Luther-Universitaet, Halle- Wittenberg, Friedemann-Bach-Platz 6, D-06099 Halle (Germany)

2007-07-01

397

Estudio ab initio del mecanismo de la reacción HSO + O3  

Science.gov (United States)

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.

398

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

399

Ab initio density matrix renormalization group study of magnetic coupling in dinuclear iron and chromium complexes  

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

400

Ab initio study of the SeS local oscillator in zinc sulfide  

Science.gov (United States)

A method is presented to calculate the energy and symmetry of local vibrational modes (LVM's) at point defects in semiconductors from first principles. The force constants for the disturbed and undisturbed systems are calculated using a variant of the direct approach. The ab initio results are used as input parameters for a cluster simulation with up to 489 vibrating atoms, which accounts for hybridization effects between the LVM and the host lattice modes. The method is applied to the LVM of ZnS:SeS, which shows a pronounced fine structure due to both host and ligand induced isotope effects. The energy of the main peak, which represents the most abundant Selen isotope 80Se, is calculated as 229.6 cm-1. This agrees very well with the result of 229.2 cm-1 from Fourier transform infrared experiments found in the literature. It is shown that the ab initio result improves the understanding of the LVM, when compared to the previously used ad hoc model, especially in the low-energy region.

Petzke, K.

1999-11-01

 
 
 
 
401

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

CERN Document Server

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

402

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

Science.gov (United States)

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

403

Thermodynamic assessment of the Ho–Te system supported by ab initio calculations  

International Nuclear Information System (INIS)

Highlights: ? We calculated enthalpies of formation of the HoTe and Ho2Te5 compounds by using ab initio method. ? We modeled the Gibbs energy of the HoTe intermediate phase for the first time. ? The thermodynamic parameters of the all phases existing in the system were determined. ? The complete phase diagram of the system (Ho–Te) is calculated. -- Abstract: The phase diagram of the Ho–Te binary system has been assessed by using the CALPHAD (Calculation of Phase Diagrams) method on the basis of the experimental data of the phase equilibria and enthalpies of formation from ab initio electronic-structure calculations within the framework of density-functional theory. Reasonable models were constructed for all the phases of the system. The liquid phase was described as the substitutional solution model with excess energy expressed by Redlich–Kister polynomial. The compounds Ho2Te5 and HoTe3 were expressed as stoichiometric phases. The (HoTe) phase was modeled by two-sublattices; (Ho,Va)1(Te)1. A consistent set of thermodynamic parameters has been derived, and calculated phase diagram was compared with the experimental data. A good agreement between the calculated results and experimental data was obtained

404

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

405

Evaluation of stabilization energies in ?-? and cation-? interactions involved in biological macromolecules by ab initio calculations  

International Nuclear Information System (INIS)

Non-covalent interactions involving aromatic rings contribute significantly to the stability of three-dimensional structures of biological macromolecules. Therefore, accurate descriptions of such interactions are crucial in understanding the functional mechanisms of biological molecules. However, it is also well known that, for some cases where van der Waals interactions make a dominant contribution, conventional ab initio electronic structure calculations, such as density functional theory, do not produce accurate interaction energies. In this study, we evaluated molecular mechanics (MM) calculations for two types of interactions involving aromatic rings, ?-? interactions and cation-? interactions, by comparing our results with those obtained by advanced ab initio calculations at the coupled-cluster with singles, doubles and perturbative triples level. In structures with stacked aromatic rings, interaction energies obtained by MM calculations are overestimated. On the other hand, for cation-? interactions, the energies in MM calculations are significantly underestimated. In both cases, addition of an induction energy based on polarization effects also fails to improve the estimate given by MM calculations. The results indicate that current effective pairwise potentials are inappropriate to represent ?-? and cation-? interactions.

406

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)

407

Vibrational predissociation dynamics of the aniline-neon Van der Waals complex: an ab initio study  

International Nuclear Information System (INIS)

The aniline-neon van der Waals complex has been investigated from a theoretical point of view. The intermolecular distance, structure and rotational constants in the ground electronic state have been obtained by ab initio calculations using second-order Moeller-Plesset (MP2) theory. The potential energy surface has also been determined. It has been found that two conformers exist: the anti, where the neon atom and the NH bonds are located on opposite sides of the ring, is slightly more stable than the syn conformer. All the ab initio results agree with those obtained by the analysis of the rotational and laser induced fluorescence spectra of this complex. We have also modeled the interaction of the van der Waals bending mode with others internal motions of the aniline molecule such as the inversion mode of the amino group and the breathing mode of the ring. The theoretical results predict that there is a significant coupling between the van der Waals bending and the inversion mode in agreement with the experimental behavior found in both the ground and the first excited electronic states of this complex

408

Ab initio density matrix renormalization group study of magnetic coupling in dinuclear iron and chromium complexes.  

Science.gov (United States)

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. PMID:24511936

Harris, Travis V; Kurashige, Yuki; Yanai, Takeshi; Morokuma, Keiji

2014-02-01

409

Ab initio study of perovskite type oxide materials for solid oxide fuel cells  

Science.gov (United States)

Perovskite type oxides form a family of materials of significant interest for cathodes and electrolytes of solid oxide fuel cells (SOFCs). These perovskites not only are active catalysts for surface oxygen reduction (OR) reactions but also allow incorporating the spilt oxygen monomers into their bulk, an unusual and poorly understood catalytic mechanism that couples surface and bulk properties. The OR mechanisms can be influenced strongly by defects in perovskite oxides, composition, and surface defect structures. This thesis work initiates a first step in developing a general strategy based on first-principles calculations for detailed control of oxygen vacancy content, transport rates of surface and bulk oxygen species, and surface/interfacial reaction kinetics. Ab initio density functional theory methods are used to model properties relevant for the OR reactions on SOFC cathodes. Three main research thrusts, which focus on bulk defect chemistry, surface defect structures and surface energetics, and surface catalytic properties, are carried to investigate different level of material chemistry for improved understanding of key physics/factors that govern SOFC cathode OR activity. In the study of bulk defect chemistry, an ab initio based defect model is developed for modeling defect chemistry of LaMnO 3 under SOFC conditions. The model suggests an important role for defect interactions, which are typically excluded in previous defect models. In the study of surface defect structures and surface energetics, it is shown that defect energies change dramatically (1˜2 eV lower) from bulk values near surfaces. Based on the existing bulk defect model with the calculated ab initio surface defect energetics, we predict the (001) MnO 2 surface oxygen vacancy concentration of (La0.9Sr0.1 )MnO3 is about 5˜6 order magnitude higher than that of the bulk under typical SOFC conditions. Finally, for surface catalytic properties, we show that area specific resistance, oxygen exchange rates, and key OR energetics of the SOFC cathode perovskites, can be described by a single descriptor, either the bulk O p-band or the bulk oxygen vacancy formation energy. These simple descriptors will further enable first-principles optimization/design of new SOFC cathodes.

Lee, Yueh-Lin

410

Ab initio identification of human microRNAs based on structure motifs  

Directory of Open Access Journals (Sweden)

Full Text Available Abstract Background MicroRNAs (miRNAs are short, non-coding RNA molecules that are directly involved in post-transcriptional regulation of gene expression. The mature miRNA sequence binds to more or less specific target sites on the mRNA. Both their small size and sequence specificity make the detection of completely new miRNAs a challenging task. This cannot be based on sequence information alone, but requires structure information about the miRNA precursor. Unlike comparative genomics approaches, ab initio approaches are able to discover species-specific miRNAs without known sequence homology. Results MiRPred is a novel method for ab initio prediction of miRNAs by genome scanning that only relies on (predicted secondary structure to distinguish miRNA precursors from other similar-sized segments of the human genome. We apply a machine learning technique, called linear genetic programming, to develop special classifier programs which include multiple regular expressions (motifs matched against the secondary structure sequence. Special attention is paid to scanning issues. The classifiers are trained on fixed-length sequences as these occur when shifting a window in regular steps over a genome region. Various statistical and empirical evidence is collected to validate the correctness of and increase confidence in the predicted structures. Among other things, we propose a new criterion to select miRNA candidates with a higher stability of folding that is based on the number of matching windows around their genome location. An ensemble of 16 motif-based classifiers achieves 99.9 percent specificity with sensitivity remaining on an acceptable high level when requiring all classifiers to agree on a positive decision. A low false positive rate is considered more important than a low false negative rate, when searching larger genome regions for unknown miRNAs. 117 new miRNAs have been predicted close to known miRNAs on human chromosome 19. All candidate structures match the free energy distribution of miRNA precursors which is significantly shifted towards lower free energies. We employed a human EST library and found that around 75 percent of the candidate sequences are likely to be transcribed, with around 35 percent located in introns. Conclusion Our motif finding method is at least competitive to state-of-the-art feature-based methods for ab initio miRNA discovery. In doing so, it requires less previous knowledge about miRNA precursor structures while programs and motifs allow a more straightforward interpretation and extraction of the acquired knowledge.

Wiuf Carsten

2007-12-01

411

i-PI: A Python interface for ab initio path integral molecular dynamics simulations  

Science.gov (United States)

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic coordinates from the Python interface, and to return the forces and energy that are used to integrate the equations of motion. Restrictions: This code only deals with distinguishable particles. It does not include fermonic or bosonic exchanges between equivalent nuclei, which can become important at very low temperatures. Running time: Depends dramatically on the nature of the simulation being performed. A few minutes for short tests with empirical force fields, up to several weeks for production calculations with ab initio forces. The examples provided with the code run in less than an hour.

Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

2014-03-01

412

Ab initio study of the low-lying electronic states of the CaO molecule  

International Nuclear Information System (INIS)

Graphical abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X1?+, a3?, A'1?, b3?+ and A1?+, and the corresponding dipole moment functions have been determined using internally contracted multi-reference configuration interaction approaches. The spectroscopic constants associated with these electronic states are compared to experimental values. The corresponding electronic wavefunctions have also been analyzed using the dipole moment functions. Display Omitted Highlights: ? The five lowest electronic states of Cao have been determined ab initio at a high level of accuracy. ? Large active space, core-valence correlation and configuration interaction are required. ? The multi-configurational nature of the electronic ground state is confirmed as well as its monovalent and divalent ionic nature using dipole moment analysis. ? These interacting potentials will serve for future obtention of spin-rovibronic levels. - Abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X1?+, a3?, A'1?, b3?+ and A1?+, and the corresponding dipole moment functions have been determined using internally contracted multi-reference configuration interaction approaches. The spectroscopic constants associated with these electronic states are compared to experimental values. The corresponding electronic wavefunctions have also been analyzed using the dipole moment functions.

413

Ab initio study of the low-lying electronic states of the CaO molecule  

Energy Technology Data Exchange (ETDEWEB)

Graphical abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X{sup 1}{Sigma}{sup +}, a{sup 3}{Pi}, A'{sup 1{Pi}}, b{sup 3}{Sigma}{sup +} and A{sup 1}{Sigma}{sup +}, and the corresponding dipole moment functions have been determined using internally contracted multi-reference configuration interaction approaches. The spectroscopic constants associated with these electronic states are compared to experimental values. The corresponding electronic wavefunctions have also been analyzed using the dipole moment functions. Display Omitted Highlights: {yields} The five lowest electronic states of Cao have been determined ab initio at a high level of accuracy. {yields} Large active space, core-valence correlation and configuration interaction are required. {yields} The multi-configurational nature of the electronic ground state is confirmed as well as its monovalent and divalent ionic nature using dipole moment analysis. {yields} These interacting potentials will serve for future obtention of spin-rovibronic levels. - Abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X{sup 1}{Sigma}{sup +}, a{sup 3}{Pi}, A'{sup 1}{Pi}, b{sup 3}{Sigma}{sup +} and A{sup 1}{Sigma}{sup +}, and the corresponding dipole moment functions have been determined using internally contracted multi-reference configuration interaction approaches. The spectroscopic constants associated with these electronic states are compared to experimental values. The corresponding electronic wavefunctions have also been analyzed using the dipole moment functions.

Khalil, Hossain; Brites, Vincent; Quere, Frederic Le [Universite Paris-Est, Laboratoire de Modelisation et Simulation Multi Echelle, UMR 8208 CNRS, Batiment Lavoisier, 5 boulevard Descartes, Champs sur Marne, 77454 Marne-la-Vallee, Cedex 2 (France); Leonard, Celine, E-mail: celine.leonard@univ-paris-est.fr [Universite Paris-Est, Laboratoire de Modelisation et Simulation Multi Echelle, UMR 8208 CNRS, Batiment Lavoisier, 5 boulevard Descartes, Champs sur Marne, 77454 Marne-la-Vallee, Cedex 2 (France)

2011-07-28

414

Combinatorial screening of polymer precursors for preparation of benzo[?] pyrene imprinted polymer: an ab initio computational approach.  

Science.gov (United States)

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

415

Ab initio calculation of Electron Energy Loss spectra of clean and 1ML Fe-covered Ni(111)  

Science.gov (United States)

The dielectric and the loss functions of Ni(111) are calculated by the Full Potential Linear Muffin Tin Orbitals (FPLMTO) ab initio method whithin the three-layers model (vacuum/surface/bulk). Particular attention is devoted to determine surface and bulk state contributions to the spectra. Good agreement is found with recent experimental EELS data on the Fe-covered Ni(111) surface.

Capelli, R.; Monachesi, P.; Del Sole, R.; Gazzadi, G. C.

2002-11-01

416

Ab initio nuclear shielding parameters and spin-rotation coupling constants of FBO, ClBO and FBS  

Science.gov (United States)

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

417

Gas-phase electrophilic aromatic substitution mechanism with strong electrophiles explained by ab initio non-adiabatic dynamics.  

Science.gov (United States)

Ab initio non-adiabatic dynamics is used to monitor the attack of CH3(+) to benzene. The results show that in the gas phase the reaction is ultrafast and is governed by a single electron transfer producing a radical pair. PMID:25080210

Kinzel, Daniel; Zilberg, Shmuel; González, Leticia

2014-09-21

418

The electronic structure of LaMO3 (M=Ti-Ni) compounds from an ab-initio approach  

International Nuclear Information System (INIS)

The results obtained from the ab-initio band structure calculations based on the linearized muffin tin orbital atomic sphere approximation for LaMO3 (M=Ti-Ni) in terms of a parametrized nearest-neighbour tight binding (TB) model are analysed and also extracted various interaction strengths

419

Accurate ab initio near-equilibrium potential energy and dipole moment functions of the ground electronic state of ozone  

International Nuclear Information System (INIS)

We report a highly correlated multireference configuration interaction calculation of the near-equilibrium potential energy surface of ozone using a large correlation consistent basis set. Three-dimensional analytical expressions are obtained for the potential energy and dipole moment functions using least-squares fits to ab initio points near the C2v equilibrium geometry. Low-lying vibrational band origins of 16O3 and some of its isotopic variants are calculated using the ab initio potential energy function. The calculated fundamental frequencies for the symmetric stretching and bending vibrations are within about 3 cm-1 of the observed values, while that for the antisymmetric stretch deviates from experiment by about 13 cm-1. The agreement with experiment can be significantly improved if the ab initio potential energy function is scaled in the antisymmetric stretching coordinate. Absolute infrared absorption intensities are also calculated using ab initio electric dipole moment functions and in good agreement with the available experimental data. (c) 2000 American Institute of Physics

420

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

Science.gov (United States)

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

2014-01-01

 
 
 
 
421

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

Science.gov (United States)

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