SIMPLE: Software for ab initio reconstruction of heterogeneous single-particles.
Elmlund, Dominika; Elmlund, Hans
2012-12-01
The open source software suite SIMPLE: Single-particle IMage Processing Linux Engine provides data analysis methods for single-particle cryo-electron microscopy (cryo-EM). SIMPLE addresses the problem of obtaining 3D reconstructions from 2D projections only, without using an input reference volume for approximating orientations. The SIMPLE reconstruction algorithm is tailored to asymmetrical and structurally heterogeneous single-particles. Its basis is global optimization with the use of Fourier common lines. The advance that enables ab initio reconstruction and heterogeneity analysis is the separation of the tasks of in-plane alignment and projection direction determination via bijective orientation search - a new concept in common lines-based strategies. Bijective orientation search divides the configuration space into two groups of paired parameters that are optimized separately. The first group consists of the rotations and shifts in the plane of the projection; the second group consists of the projection directions and state assignments. In SIMPLE, ab initio reconstruction is feasible because the 3D in-plane alignment is approximated using reference-free 2D rotational alignment. The subsequent common lines-based search hence searches projection directions and states only. Thousands of class averages are analyzed simultaneously in a matter of hours. Novice SIMPLE users get a head start via the well documented front-end. The structured, object-oriented back-end invites advanced users to develop new alignment and reconstruction algorithms. An overview of the package is presented together with benchmarks on simulated data. Executable binaries, source code, and documentation are available at http://simple.stanford.edu. PMID:22902564
Ab-initio calculations and phase diagram assessments of An-Al systems (An = U, Np, Pu)
Energy Technology Data Exchange (ETDEWEB)
Sedmidubsky, D., E-mail: sedmidub@vscht.c [European Commission, Joint Research Centre, Institute for Transuranium Elements, Post Box 2340, D-76125 Karlsruhe (Germany); Institute of Chemical Technology, Technicka 5, 166 28 Prague (Czech Republic); Konings, R.J.M.; Soucek, P. [European Commission, Joint Research Centre, Institute for Transuranium Elements, Post Box 2340, D-76125 Karlsruhe (Germany)
2010-02-15
The enthalpies of formation of binary intermetallic compounds AnAl{sub 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, S{sub 298}{sup o}, 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.
Ab-initio calculations and phase diagram assessments of An-Al systems (An = U, Np, Pu)
International Nuclear Information System (INIS)
The enthalpies of formation of binary intermetallic compounds AnAln(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, S298o, 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.
AB INITIO AND CALPHAD THERMODYNAMICS OF MATERIALS
Energy Technology Data Exchange (ETDEWEB)
Turchi, P A
2004-04-14
Ab initio electronic structure methods can supplement CALPHAD in two major ways for subsequent applications to stability in complex alloys. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics {acute a} la CALPHAD. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys.
Ab initio valence calculations in chemistry
Cook, D B
1974-01-01
Ab Initio Valence Calculations in Chemistry describes the theory and practice of ab initio valence calculations in chemistry and applies the ideas to a specific example, linear BeH2. Topics covered include the Schrödinger equation and the orbital approximation to atomic orbitals; molecular orbital and valence bond methods; practical molecular wave functions; and molecular integrals. Open shell systems, molecular symmetry, and localized descriptions of electronic structure are also discussed. This book is comprised of 13 chapters and begins by introducing the reader to the use of the Schrödinge
Ab initio theoretical predictions of fullerenes
International Nuclear Information System (INIS)
Recent methodological improvements combined with advances in computer speed have dramatically extended the range of applicability of ab initio quantum chemistry techniques. The authors have recently developed a hybrid of Hartree-Fock and density functional theories that is specifically suited for accurate predictions on fullerene systems. The ab initio theoretical predictions produced by this research group will be discussed in light of the most recent experimental results. Among the topics to be addressed in this talk are: (1) annealing mechanisms for fullerenes including all possible 4 center-2 bond reactions, (2) some novel C2 loss mechanisms from the fullerene surface, and (3) coalescence reactions of fullerenes, specifically C60+C60
Accelerating Ab Initio Nuclear Physics Calculations with GPUs
Potter, Hugh; Maris, Pieter; Sosonkina, Masha; Vary, James; Binder, Sven; Calci, Angelo; Langhammer, Joachim; Roth, Robert; Çatalyürek, Ümit; Saule, Erik
2014-01-01
This paper describes some applications of GPU acceleration in ab initio nuclear structure calculations. Specifically, we discuss GPU acceleration of the software package MFDn, a parallel nuclear structure eigensolver. We modify the matrix construction stage to run partly on the GPU. On the Titan supercomputer at the Oak Ridge Leadership Computing Facility, this produces a speedup of approximately 2.2x - 2.7x for the matrix construction stage and 1.2x - 1.4x for the entire run.
Modeling Brown Dwarfs using ab initio equation of state data
Becker, Andreas; Lorenzen, Winfried; Nettelmann, Nadine; Redmer, Ronald
2013-07-01
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)
Macromolecular ab initio phasing enforcing secondary and tertiary structure.
Millán, Claudia; Sammito, Massimo; Usón, Isabel
2015-01-01
Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors' approach relies on the combination of locating model fragments such as polyalanine ?-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a 'still-life', but some are correct enough for density modification and main-chain tracing to reveal the protein's true portrait. Beyond ?-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, ?-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2?Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases. PMID:25610631
Ab initio modeling of small proteins by iterative TASSER simulations
Directory of Open Access Journals (Sweden)
Zhang Yang
2007-05-01
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.
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)
Grain boundary magnetism - an ab initio study.
Czech Academy of Sciences Publication Activity Database
?ák, Miroslav; Šob, Mojmír; Hafner, J.
Brno : Masarykova univerzita, 2007 - (Trnková, L.; Janderka, P.; Kizek, R.), s. 23-24 ISBN 978-80-210-4235-3. [Pracovní setkání fyzikálních chemik? a elektrochemik? /7./. Brno (CZ), 29.01.2007-30.01.2007] R&D Projects: GA AV ?R IAA1041302; GA MŠk OC 147; GA ?R GD106/05/H008 Institutional research plan: CEZ:AV0Z20410507 Keywords : grain boundaries * magnetism * ab initio calculations Subject RIV: BM - Solid Matter Physics ; Magnetism
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
Ab Initio Neutron Drops with Chiral Hamiltonians
Potter, Hugh; Maris, Pieter; Vary, James
2015-04-01
Ab initio calculations for neutron drops are of interest for insights into neutron-rich nuclei and neutron star matter, and for examining the neutron-only sector of nucleon-nucleon and 3-nucleon interactions. I present ab initio results calculated using the no-core shell model with 2- and 3-body chiral Hamiltonians for neutron drops up to 20 neutrons confined in a 10 MeV harmonic trap. I discuss ground state energies, internal energies, radii, and evidence for pairing. In addition, excitation energies can be used to investigate the spin-orbit splittings in the p-shell and sd -shell. Prior Green's Function Monte Carlo calculations using the Argonne v8' potential with added 3-nucleon forces serve as a comparison. Ab initio calculations for neutron drops are of interest for insights into neutron-rich nuclei and neutron star matter, and for examining the neutron-only sector of nucleon-nucleon and 3-nucleon interactions. I present ab initio results calculated using the no-core shell model with 2- and 3-body chiral Hamiltonians for neutron drops up to 20 neutrons confined in a 10 MeV harmonic trap. I discuss ground state energies, internal energies, radii, and evidence for pairing. In addition, excitation energies can be used to investigate the spin-orbit splittings in the p-shell and sd -shell. Prior Green's Function Monte Carlo calculations using the Argonne v8' potential with added 3-nucleon forces serve as a comparison. Supported by DOE Grants DESC0008485 (SciDAC/NUCLEI), DE-FG02-87ER40371, and NSF Grant 0904782; computational resources provided by the Oak Ridge Leadership Computing Facility (DOE Office of Science Contract DE-AC05-00OR22725) under an INCITE award.
Thiessen, P. A.; Treder, H.-J.
Jedes initium wird durch experimenta crucis zum eventus. Jedes theoretisch interpretierbare ex-eventu-Resultat führt auf ein neues Initium. Gerade dies ist die gemeinsame Aussage von Atomistik, Quantenmechanik und Relativitätstheorie.Translated AbstractAb initio vel ex eventu. IIEvery initium becomes an eventus by experimenta crucis. Every theoretically interpretable ex-eventu result leads to a new initium. Right this is the joint assertion of atomism, quantum mechanics, and relativity.
International Nuclear Information System (INIS)
Extensively correlated ab initio potential energy and dipole moment curves are calculated for the X 1?+, a 3PI, A 1?+, and 3?+ states of CaO over the range 3.0 au approx. 1?+ is the ground state of CaO. Vertical spectra, adiabatic spectra, spectroscopic constants, curve crossings, and dipole moments are determined. The 3?+ results are apparently the first accurate values available. The dipole moment function is a linear function of bondlength for the PI states and 3?+. Two extrema occur in the dipole moment function of X 1?+. Combined with experimental results, this suggests that ?(X 1?+) exhibits a maximum near Rsub(e) in the heavy alkaline earth monoxides. The ?(A 1?+) increases sharply near Rsub(e). The X 1?+ calculations require special attention near Rsub(e): Localized ionic entities are involved which have different MO configurations and different correlation requirements. A second-order theory which correctly describes atomic correlation is necessary. The ab initio bondlengths are systematically larger than the experimental bondlengths by amounts that are greater than the expected accuracy limits of the calculations. This overestimation is tions. This overestimation is also observed in KF, KCl and KOH, but ab initio bondlengths of the lighter metal alkali halides and alkaline earth monoxides agree closely with experiment. It appears that the core electrons must be responsible, possibly because of explicit core correlation requirements and/or relativistic corrections. (orig.)
Ab initio study of alkali metal hydrides
International Nuclear Information System (INIS)
Using ab-initio calculations the ground state properties and electronic structure of AlMH (AlM = Li, Na, K, Rb, Cs) have been studied. It is shown that AlMH are wide band gap materials with well dispersive conduction band minimum and valence band maximum. The band extremes are found to be located at high symmetry points, other than G point. Electrical parameters have been estimated. Chemical bonding is found to be mixed, ionic and covalence, with predominant ionic type of bonding. (authors)
Ab initio calculations of material strength.
Czech Academy of Sciences Publication Activity Database
Šob, Mojmír; Friák, Martin; Vitek, V.
Tokyo : The Japan Society of Mechanical Engineers, 2003, s. 467-475. [International Symposium on Micro-Mechanical Engineering - Heat Transfer, Fluid Dynamics, Reliability and Mechanotronics.. Tsuchiura and Tsukuba (JP), 01.12.2003-03.12.2003] R&D Projects: GA AV ?R IAA1041302; GA ?R GA202/03/1351; GA MŠk OC 523.90 Institutional research plan: CEZ:AV0Z2041904 Keywords : ab initio calculations * electronic structure * theoretical tensile strength Subject RIV: BM - Solid Matter Physics ; Magnetism
Germacrene D Cyclization: An Ab Initio Investigation
Directory of Open Access Journals (Sweden)
William N. Setzer
2008-01-01
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.
Ab initio non-relativistic spin dynamics.
Ding, Feizhi; Goings, Joshua J; Frisch, Michael J; Li, Xiaosong
2014-12-01
Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li3 molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain. PMID:25481133
Why ferroelectricity? synchrotron radiation and ab initio answers
Scientific Electronic Library Online (English)
R, Olivera; M.E, Fuentes; F, Espinosa; M, García; E, Macías; A, Durán; J, Siqueiros; L, Fuentes.
2007-02-01
Full Text Available Una pregunta histórica de la física del estado sólido está encontrando respuesta en nuestros tiempos: la explicación a nivel atómico del origen de la ferroelectricidad. Las ideas tradicionales sobre fenómenos ferroeléctricos se relacionan con el "ablandamiento" de los fonones en el origen de la zona [...] de Brillouin y con funciones en forma de "W" para la energía libre de Landau. Las contribuciones experimentales (radiación sincrotrónica, neutrones) y teóricas (Cohen, Resta, Spaldin) de la última década han esclarecido aspectos del comportamiento atómico que conducen a la polarización espontánea en estructuras perovskitas y asociadas. Se presenta el trabajo desarrollado por nuestro grupo interdisciplinario. Se obtienen fases ferroeléctricas perovskitas y Aurivillius por diferentes métodos. Se investigan detalles finos de las estructuras cristalinas mediante radiación sincrotrónica en el Laboratorio de Radiación Sincrotrónica de Stanford. Las estructuras electronicas de las fases consideradas se caracterizan por métodos ab initio. Los experimentos de difraccion en alta resolución demuestran ruptura de simetría en un número de sistemas perovskita y Aurivillius. Se discute la relación estructura-simetría- polarización. Se presenta una explicación ab initio de la polarizacion ferroeléctrica en perovskitas. La energía del sistema se calcula mediante el codigo CASTEP bajo un funcional GGA. La optimización de la energía conduce a la ruptura de simetría cubica, con desplazamiento del catión Ti fuera del centro, vía una transformación Jahn-Teller de segundo orden. La estructura electrónica se investiga mediante el software BandLab, bajo un funcional LDA, con el método LMTO. La causa de la deformación de la perovskita es la degeneración de los orbitales Ti 3d z² y Ti 3d (x²+y²). Abstract in english An old question of solid state physics is being answered nowadays: the atomic-level understanding of ferroelectricity. Traditional ideas about ferroelectric phenomena relate with softening of optical phonons at the Brillouin zone origin and with "W-shaped" Landau free energy functions. Last decade e [...] xperimental (synchrotron radiation, neutrons) and quantum-theoretical (Cohen, Resta, Spaldin) contributions have clarified detailed descriptions and explanations for atomic behavior leading to spontaneous polarization in perovskite and perovskite-related crystal structures. Work being performed by our interdisciplinary group on ferroelectricity is presented. Perovskite and Aurivillius ferroelectric phases are obtained by different methods. Fine details on crystal structures are investigated by means of synchrotron radiation at Stanford Synchrotron Radiation Laboratory. Electronic structures of considered phases are theoretically characterized by ab initio methods. High-resolution diffraction experiments demonstrate several symmetry break-downs in perovskite and Aurivillius phases. The structure-symmetry-polarization relationship is discussed for a number of representative cases. Ab initio explanation of ferroelectric polarization in perovskite structures is given. Energy calculation is performed by means of CASTEP code under GGA functional. Energy optimization leads to cubic-tetragonal symmetry break-down with off-centering cation displacements via second-order Jahn-Teller effect. Electronic structure is investigated with BandLab code, under LDA functional with LMTO method. Degeneracy of Ti 3d z² and Ti 3d (x²+y²) orbitals is the cause of cubic-perovskite deformation.
Discovering chemistry with an ab initio nanoreactor.
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S; Martínez, Todd J
2014-12-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor--a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings. PMID:25411881
Ab-initio nanoplasmonics: atoms matter
Zhang, Pu; Rubio, Angel; Garcia-Gonzalez, Pablo; Garcia-Vidal, F J
2014-01-01
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.
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-12-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor—a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey–Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.
Ab initio alpha-alpha scattering
Elhatisari, Serdar; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G
2015-01-01
Processes involving alpha particles and alpha-like nuclei comprise a major part of stellar nucleosynthesis and hypothesized mechanisms for thermonuclear supernovae. In an effort towards understanding alpha processes from first principles, we describe in this letter the first ab initio calculation of alpha-alpha scattering. We use lattice effective field theory to describe the low-energy interactions of nucleons and apply a technique called the adiabatic projection method to reduce the eight-body system to an effective two-cluster system. We find good agreement between lattice results and experimental phase shifts for S-wave and D-wave scattering. The computational scaling with particle number suggests that alpha processes involving heavier nuclei are also within reach in the near future.
Ab Initio Derivation of Model Energy Density Functionals
Dobaczewski, J
2015-01-01
I propose a simple and manageable method that allows for deriving coupling constants of model energy density functionals (EDFs) directly from ab initio calculations performed for finite fermion systems. A proof-of-principle application allows for linking properties of finite nuclei, determined by using the nuclear nonlocal Gogny functional, to the coupling constants of the quasilocal Skyrme functional. The method does not rely on properties of infinite fermion systems but on the ab initio calculations in finite systems. It also allows for quantifying merits of different model EDFs in describing the ab initio results.
Ab initio thermodynamic study of defective strontium titanate
Blokhin, Evgeny
2013-01-01
In the presented thesis the perfect and defective SrTiO3 bulk crystals and their (001) surfaces are considered on ab initio level. Since the experimental study of the complex defective systems is comparatively expensive and difficult, and the computer performance has been greatly increased in the last years, the ab initio modeling became very efficient tool to be applied in this field. Additionally, there is a significant industrial demand for the investigation and improvements of the perform...
Ab initio atomistic simulation of metals and multicomponent alloys
Tian, Fuyang
2013-01-01
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...
Multiple solutions in the refinement of ab initio force constants
Lacy, M.
The existence of a double minimum in the refinement of the force constants of the water molecule to ab initio energies is reported. The indeterminacy arises because of an unsatisfactory distribution of points, as defined by their molecular geometries, and may be removed by further calculation of energies at selected geometries. The claim that Diab and Simons' ? coordinate [3] is superior as an expansion variable for the representation of ab initio energy surfaces has been reassessed.
A Probabilistic Graphical Model for Ab Initio Folding
Zhao, Feng; Peng, Jian; DeBartolo, Joe; Freed, Karl F; Sosnick, Tobin R.; Xu, Jinbo
2009-01-01
Despite significant progress in recent years, ab initio folding is still one of the most challenging problems in structural biology. This paper presents a probabilistic graphical model for ab initio folding, which employs Conditional Random Fields (CRFs) and directional statistics to model the relationship between the primary sequence of a protein and its three-dimensional structure. Different from the widely-used fragment assembly method and the lattice model for protein folding, our graphic...
Ab initio study of rare gas halides
International Nuclear Information System (INIS)
The electronic structures of the Ne2F, Ar2F, Kr2F, Xe2F, Ar2Cl, Kr2Cl, Xe2Cl, Kr2Br, Xe2Br, and Xe2I molecules have been studied on the CASSCF/CASPT2 level, with inclusion of the spin–orbit interaction. For the lowest strongly bound Rg2X(42?) state we report RRg–Rg and RRg–X equilibrium bond lengths, dissociation energy, radiative lifetime and frequencies of three vibrational modes. Except for the antisymmetric stretch mode, a similar set of results was obtained for another five bound states above Rg2X(42?). To compare equilibrium bond lengths and some other molecular properties, calculations were also performed for Rg2+ and RgX diatomics on the same level of theory and using the same basis sets. The ab initio results obtained in this work are of interest for experimental and theoretical studies of Rg2X(42?) formation mechanisms. (paper)
Ab initio molecular crystal structures, spectra, and phase diagrams.
Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni
2014-09-16
Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling 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
Why ferroelectricity? synchrotron radiation and ab initio answers
Directory of Open Access Journals (Sweden)
R. Olivera
2007-01-01
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.
Skutterudites under pressure: An ab initio study
International Nuclear Information System (INIS)
Ab initio results on the band structure, density of states, and Fermi surface (FS) properties of LaRu4X12 (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-pz orbital for LaRu4P12 and Ru-dz2 orbital in the case of As and Sb containing compounds. More interestingly, Fermi surface nesting feature is observed only in the case of the LaRu4P12. Under compression, we observe the topology of the complicated FS sheet of LaRu4As12 to change around V/V0?=?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/V0?=?0.8 for the same compound. Apart from this, we find the hole pocket to vanish at V/V0?=?0.8 in the case of LaRu4Sb12 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
THERMODYNAMICS OF MATERIALS: FROM AB INITIO TO PHENOMENOLOGY
Energy Technology Data Exchange (ETDEWEB)
Turchi, P A
2004-09-24
Quantum mechanical-based (or ab initio) methods are used to predict the stability properties of materials although their application is limited to relatively simple systems in terms of structures and number of alloy components. However thermodynamics of complex multi-component alloys requires a more versatile approach afforded within the CALPHAD formalism. Despite its success, the lack of experimental data very often prevents the design of robust thermodynamic databases. After a brief survey of ab initio methodologies and CALPHAD, it will be shown how ab initio electronic structure methods can supplement in two ways CALPHAD for subsequent applications. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics '{acute a} la CALPHAD'. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys. Finally, comments will be made on challenges and future prospects.
Benrekia, A. R.; Benkhettou, N.; Nassour, A.; Driz, M.; Sahnoun, M.; Lebègue, S.
2012-07-01
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.
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.
Energy Technology Data Exchange (ETDEWEB)
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
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}.
Energy Technology Data Exchange (ETDEWEB)
Barrett, B R; Navratil, P; Vary, J P
2011-04-11
A long-standing goal of nuclear theory is to determine the properties of atomic nuclei based on the fundamental interactions among the protons and neutrons (i.e., nucleons). By adopting nucleon-nucleon (NN), three-nucleon (NNN) and higher-nucleon interactions determined from either meson-exchange theory or QCD, with couplings fixed by few-body systems, we preserve the predictive power of nuclear theory. This foundation enables tests of nature's fundamental symmetries and offers new vistas for the full range of complex nuclear phenomena. Basic questions that drive our quest for a microscopic predictive theory of nuclear phenomena include: (1) What controls nuclear saturation; (2) How the nuclear shell model emerges from the underlying theory; (3) What are the properties of nuclei with extreme neutron/proton ratios; (4) Can we predict useful cross sections that cannot be measured; (5) Can nuclei provide precision tests of the fundamental laws of nature; and (6) Under what conditions do we need QCD to describe nuclear structure, among others. Along with other ab initio nuclear theory groups, we have pursued these questions with meson-theoretical NN interactions, such as CD-Bonn and Argonne V18, that were tuned to provide high-quality descriptions of the NN scattering phase shifts and deuteron properties. We then add meson-theoretic NNN interactions such as the Tucson-Melbourne or Urbana IX interactions. More recently, we have adopted realistic NN and NNN interactions with ties to QCD. Chiral perturbation theory within effective field theory ({chi}EFT) provides us with a promising bridge between QCD and hadronic systems. In this approach one works consistently with systems of increasing nucleon number and makes use of the explicit and spontaneous breaking of chiral symmetry to expand the strong interaction in terms of a dimensionless constant, the ratio of a generic small momentum divided by the chiral symmetry breaking scale taken to be about 1 GeV/c. The resulting NN and NNN interactions, characterized by the order of the expansion retained (e.g. 'next-to-next-to leading order' is NNLO), provide a high-quality fit to the NN data and the A = 3 ground-state (g.s.) properties. The derivations of NN, NNN, etc. interactions within meson-exchange and {chi}EFT are well-established but are not subjects of this review. Our focus is solution of the non-relativistic quantum many-body Hamiltonian that includes these interactions using our no core shell model (NCSM) formalism. In the next section we will briefly outline the NCSM formalism and then present applications, results and extensions in later sections.
Use of ab initio quantum chemical methods in battery technology
Energy Technology Data Exchange (ETDEWEB)
Deiss, E. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)
1997-06-01
Ab initio quantum chemistry can nowadays predict physical and chemical properties of molecules and solids. An attempt should be made to use this tool more widely for predicting technologically favourable materials. To demonstrate the use of ab initio quantum chemistry in battery technology, the theoretical energy density (energy per volume of active electrode material) and specific energy (energy per mass of active electrode material) of a rechargeable lithium-ion battery consisting of a graphite electrode and a nickel oxide electrode has been calculated with this method. (author) 1 fig., 1 tab., 7 refs.
Cyanogen Azide. Ionization Potentials and Ab Initio SCF MO Calculation
DEFF Research Database (Denmark)
Bak, Börge; Jansen, Peter
1975-01-01
The Ne(I) and He(I) photoelectron(PE) spectra of cyanogen azide, NCN3, have been recorded at high resolution. Their interpretation is achieved by comparison with the PE spectrum of HN3 and an ab initio LCGO SCF MO calculation. Deviations from Koopmans' theorem of quite different magnitudes are found dependent on the type of ionisation process.
Ab-Initio SCF investigation of glycolic acid
International Nuclear Information System (INIS)
The potential energy surface of glycolic acid was investigated using ab initio 4-31G SCF calculations. Geometries, energies, and wavenumbers for all seven symmetry-unique local minima are reported together with all reaction paths and their energetical barriers
Ab initio determination of thermal conductivity of dense hydrogen plasmas.
Recoules, Vanina; Lambert, Flavien; Decoster, Alain; Canaud, Benoit; Clérouin, Jean
2009-02-20
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
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
Ab initio study of C14 laves phases in Fe-based systems
Directory of Open Access Journals (Sweden)
Pavlu J.
2012-01-01
Full Text Available Structural properties and energetics of Fe-based C14 Laves phases at various compositions (i.e. Fe2Fe, Fe2X, X2Fe, X2X, where X stands for Si, Cr, Mo, W, Ta were investigated using the pseudopotential VASP (Vienna Ab initio Simulation Package code employing the PAW-PBE (Projector Augmented Wave - Perdew Burke-Ernzerhof pseudopotentials. Full relaxation was performed for all structures studied including the reference states of elemental constituents and the equilibrium structure parameters as well as bulk moduli were found. The structure parameters of experimentally found structures were very well reproduced by our calculations. It was also found that the lattice parameters and volumes of the unit cell decrease with increasing molar fraction of iron. Thermodynamic analysis shows that the Fe2X configurations of Laves phases are more stable than the X2Fe ones. Some of the X2Fe configurations are even unstable with respect to the weighted average of the Laves phases of elemental constituents. Our calculations predict the stability of Fe2Ta. On the other hand, Fe2Mo and Fe2W are slightly unstable (3.19 and 0.68 kJ.mol-1, respectively and hypothetical structures Fe2Cr and Fe2Si are found unstable as well.
Kletsov, Aleksey; Dahnovsky, Yuri
2007-10-14
In this work we study current-voltage characteristics in transport molecular junctions with a 1,4-benzene dithiol molecule as a bridge by using different ab initio electron propagator methods such as OVGF and P3 which are both programs in a Gaussian software package. The current-voltage characteristics are calculated for different values of Fermi energy in various basis sets such as 6-311++G(p,d) and cc-pVDZ and are compared with the experimental data. A good agreement is found in almost the entire voltage range. In addition, the results of our calculations indicate that the accuracy of ab initio electron propagator methods is in the range of 0.2-0.3 eV. Since the computational methods are truly ab initio, implying no adjustable parameters, functions, or functionals, the theoretical predictions can be improved only by changing the model of a transport device. The current-voltage characteristics predict peaks, i.e., negative differential resistances, for the various values of Fermi energy. As shown, the origin of the negative differential resistances is related to the voltage dependences of overlap integrals for the active terminal orbitals, expansion coefficients of partial atomic wavefunctions in Dyson orbitals, and the voltage dependences of Dyson poles (ionization potentials). We find that two peak behavior in the current-voltage characteristics can be explained by the anharmonicity of potential energy surfaces. As a result of our studies, we predict that negative differential resistances can be experimentally found by changing a position of Fermi level, i.e., by using different metal electrodes coated by a gold atomic monolayer. PMID:17935432
Augmented wave ab initio EFG calculations: some methodological warnings
International Nuclear Information System (INIS)
We discuss some accuracy aspects inherent to ab initio electronic structure calculations in the understanding of nuclear quadrupole interactions. We use the projector augmented wave method to study the electric-field gradient (EFG) at both Sn and O sites in the prototype cases SnO and SnO2. The term ab initio is used in the standard context of the also called first principles methods in the framework of the Density Functional Theory. As the main contributions of EFG calculations to problems in condensed matter physics are related to structural characterizations on the atomic scale, we discuss the 'state of the art' on theoretical EFG calculations and make a brief critical review on the subject, calling attention to some fundamental theoretical aspects
The density matrix renormalization group for ab initio quantum chemistry
Wouters, Sebastian
2014-01-01
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 co...
Ab Initio Nuclear Structure Theory: From Few to Many
International Nuclear Information System (INIS)
We summarize recent advances in ab initio nuclear structure theory, aiming to connect few- and many-body systems in a coherent theoretical framework. Starting from chiral effective field theory to construct the nuclear Hamiltonian and the similarity renormalization group to soften it, we address several many-body approaches that have seen major developments over the past few years. We show that the domain of ab initio nuclear structure theory has been pushed well beyond the p-shell and that quantitative predictions connected to QCD via chiral effective field theory are becoming possible all the way from the proton to the neutron drip line up into the medium-mass regime. (author)
Spin-orbit decomposition of ab initio nuclear wave functions
Johnson, Calvin W.
2015-03-01
Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum j , leading to j -j coupling, decades ago phenomenological models suggested that a simpler picture for 0 p -shell nuclides can be realized via coupling of the total spin S and total orbital angular momentum L . I revisit this idea with large-basis, no-core shell-model calculations using modern ab initio two-body interactions and dissect the resulting wave functions into their component L - and S -components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly 50 years and six orders of magnitude in basis dimensions. I suggest that L -S decomposition may be a useful tool for analyzing ab initio wave functions of light nuclei, for example, in the case of rotational bands.
Spin-orbit decomposition of ab initio wavefunctions
Johnson, Calvin W
2014-01-01
Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum $j$, leading to $j$-$j$ coupling, phenomenological models suggested decades ago that for $0p$-shell nuclides a simpler picture can be realized via coupling of total spin $S$ and total orbital angular momentum $L$. I revisit this idea with large-basis, no-core shell model (NCSM) calculations using modern \\textit{ab initio} two-body interactions, and dissect the resulting wavefunctions into their component $L$- and $S$-components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly fifty years and six orders of magnitude in basis dimensions. I suggest $L$-$S$ may be a useful tool for analyzing \\textit{ab initio} wavefunctions of light nuclei, for example in the case of rotational bands.
DNA base trimers: empirical and quantum chemical ab initio calculations.
Czech Academy of Sciences Publication Activity Database
Kabelá?, Martin; Sherer, E. C.; Cramer, Ch. J.; Hobza, Pavel
2007-01-01
Ro?. 13, ?. 7 (2007), s. 2067-2077. ISSN 0947-6539 R&D Projects: GA MŠk LC512; GA ?R GA203/05/0009 Institutional research plan: CEZ:AV0Z40550506 Keywords : ab initio calculations * nucleic acid bases trimer * empirical force field * Amber * potential energy surface Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.330, year: 2007
Pursuit Evasion: An ab initio Two Dimensional Model .
Directory of Open Access Journals (Sweden)
T. Chitra
1991-04-01
Full Text Available A two dimensional pursuit-evasion game is studied using a kinematic model described by algebraic equations of motion. This is the first part of a study aimed at obtaining complete three-dimensional solutions for a full dynamic system including detailed aerodynamic characteristics of the aircraft involved. Comparison with an existing method shows that substantial savings in computer time may be possible using the ab initio approach.
AB INITIO study of Curie temperature of diluted magnetic semiconductors.
Czech Academy of Sciences Publication Activity Database
Kudrnovský, Josef; Turek, Ilja; Drchal, Václav; Máca, František; Mašek, Jan; Weinberger, P.; Bruno, P.
2003-01-01
Ro?. 16, ?. 1 (2003), s. 119-122. ISSN 0896-1107 R&D Projects: GA ?R GA202/00/0122; GA AV ?R IAA1010203; GA MŠk OC P5.30 Institutional research plan: CEZ:AV0Z2041904; CEZ:AV0Z1010914 Keywords : Curie temperature * heisenberg model * diluted magnetic semiconductors * ab initio approach * As antisites Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.794, year: 2003
Ab initio studies of electromechanical effects in carbon nanotubes
Scientific Electronic Library Online (English)
M. Verissimo, Alves; R.B., Capaz; Belita, Koiller; Emilio, Artacho; H., Chacham.
2002-06-01
Full Text Available Carbon nanotubes have recently attracted interest for their possible applications as nanoactuators and nanoswitches, as well as possible building blocks for nanoelectronics. We present ab initio calculations for uniformly charged graphene and (11,0),(9,0) and (5,5) carbon nanotubes. We also consider [...] the effects of polaron formation in these systems. The strain-charge coeÆcient is calculated and compared for both graphene and the nanotubes under study.
Ab initio approach for atomic relaxations in supported magnetic clusters
Stepanyuk, V. S.; Klavsyuk, A. L.; Niebergall, L.; Saletsky, A. M.; Hergert, W.; Bruno, P.
2004-01-01
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 ...
Ab initio investigation of intermolecular interactions in solid benzene
Bludsky, O.; Rubes, M.; Soldan, P.
2008-01-01
A computational strategy for the evaluation of the crystal lattice constants and cohesive energy of the weakly bound molecular solids is proposed. The strategy is based on the high level ab initio coupled-cluster determination of the pairwise additive contribution to the interaction energy. The zero-point-energy correction and non-additive contributions to the interaction energy are treated using density functional methods. The experimental crystal lattice constants of the s...
GAUSSIAN 76: an ab initio molecular orbital program
International Nuclear Information System (INIS)
Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans
Correlated ground state ab initio studies of polymers
Abdurahman, Ayjamal
2000-01-01
In this thesis we have investigated the correlated ground state properties of polymers by applying wave-function-based ab-initio quantum-chemical methods such as the Hartree-Fock approach, the full configuration interaction method (FCI), coupled-cluster (CC) and Moller-Plesset second-order perturbation (MP2) theory. The polymers we have studied are the boron-nitrogen polymers, i.e., polyiminoborane (PIB) and polyaminoborane (PAB), the lithium hydride chain and the beryllium hydride polymer as...
Ab initio Interlayer Potentials For Metals and Alloys
Tian, Fuyang
2012-01-01
Many modern materials and material systems are layered. The properties related to layers are connected to interactions between atomic layers. In the present thesis, we introduce the interlayer potential (ILP), a novel model potential which fully describes the interaction between layers. The ILPs are different from the usual interatomic potentials which present interaction between atoms. We use the Chen-Möbius inversion method to extract the ILPs from ab initio total energy calculations. The ...
Ab initio molecular dynamics calculations of ion hydration free energies
Leung, Kevin; Rempe, Susan B.; Von Lilienfeld, O. Anatole
2009-01-01
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...
Ab initio Green's function formalism for band structures
Buth, Christian; Birkenheuer, Uwe; Albrecht, Martin; Fulde, Peter
2004-01-01
Using the Green's function formalism, an ab initio theory for band structures of crystals is derived starting from the Hartree-Fock approximation. It is based on the algebraic diagrammatic construction scheme for the self-energy which is formulated for crystal orbitals (CO-ADC). In this approach, the poles of the Green's function are determined by solving a suitable Hermitian eigenvalue problem. The method is not only applicable to the outer valence and conduction bands, it ...
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics
Makhov, Dmitry V.; Glover, William J.; Martinez, Todd J.; Shalashilin, Dmitrii V.
2014-08-01
We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.
Use of symmetry in molecular ab-initio SCF calculations
International Nuclear Information System (INIS)
Today's molecular ab-initio SCF calculations approximate Hartree-Fock solutions of the electronic Schroedinger equation by a linear combination ansatz and the iterative process. The use of Gauss-type functions as basis functions by standard computer programs for ab-initio molecular orbital calculations demands rather large basis sets and, consequently, a very large number of two electron integrals whose time-consuming computations limit routinely performed ab-initio calculations to a maximum of 80 to 130 basis functions. The most important use of molecular symmetry in these calculations thus becomes the reduction of the number of two electron integrals. A second use of molecular symmetry is the symmetry adaptation of the basis set. To demonstrate these techniques and their ability to reduce computer time the authors carried out single-point calculations with the Univac version of GAUSSIAN 80 for H3BOH2BH3, H3BNH2CH3, and FN3 in their 4-31G optimized geometries under these three stipulations: no use of symmetry al all; use of symmetry only in the integral calculation; and full use of symmetry. Results for computer time and number of two electron integrals are tabulated. 33 references, 2 figures, 6 tables
Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes
Energy Technology Data Exchange (ETDEWEB)
Draayer, Jerry P [Louisiana State University
2014-09-28
We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).
Energy Technology Data Exchange (ETDEWEB)
Bernard, St
1998-12-31
The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H{sub 2}){sub 2} which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author) 109 refs.
Ab initio characterization of C5
Massó, Helena; Veryazov, V.; Malmqvist, P. A.; Roos, B. O.; Senent Díez, María Luisa
2007-01-01
In this paper, the structure and spectroscopic parameters of the C5 cluster are determined using multiconfigurational quantum chemical methods as implemented in the MOLCAS software. A number of spectroscopic properties (band center positions, l-doubling parameters, and rotational constants) have been characterized. From the new results, the assignments of previous astrophysical observations [ J. Goicoechea et al., Astrophys. J. 609, 225 (2004) ] are discussed. A detailed exploration of the gl...
Equations of state of heavy metals: ab initio approaches
International Nuclear Information System (INIS)
The determination of equations of states of heavy metals through ab initio calculation, i.e. without any adjustable parameter, allows to access to pressure and temperature thermodynamic conditions sometimes inaccessible to experiment. To perform such calculations, density functional theory (DFT) is a good starting point: when electronic densities are homogeneous enough, the local density approximation (LDA) remarkably accounts for thermodynamic properties of heavy metals, such as tantalum, or the light actinides, as well for static properties - equilibrium volume, elastic constants - as for dynamical quantities like phonon spectra. For heavier elements, like neptunium or plutonium, relativistic effects and strong electronic interactions must be taken into account, which requires more sophisticated theoretical approaches. (authors)
Ozone adsorption on graphene: ab initio study and experimental validation
Lee, Geunsik; Lee, Bongki; Kim, Jiyoung; Cho, Kyeongjae
2009-01-01
We have investigated ozone adsorption on graphene using the ab initio density functional theory method. Ozone molecules adsorb on graphene basal plane with binding energy of 0.25 eV, and the physisorbed molecule can chemically react with graphene to form an epoxide group and an oxygen molecule. The activation energy barrier from physisorption to chemisorption is 0.72 eV, and the chemisorbed state has the binding energy of 0.33 eV. These binding energies and energy barrier in...
Hydrogen diffusion in liquid aluminum from ab initio molecular dynamics
Jakse, N.; Pasturel, A.
2014-05-01
Ab initio molecular dynamics simulations are used to describe the diffusion of hydrogen in liquid aluminum at different temperatures. Quasi-instantaneous jumps separating periods of localized vibrations around a mean position are found to characterize the hydrogen motion at the microscopic scale. The hydrogen motion is furthermore analyzed using the van Hove function. We highlight a non-Fickian behavior for the hydrogen diffusion due to a large spatial distribution of hydrogen jumps. We show that a generalized continuous time random walk (CTRW) model describes the experimental diffusion coefficients in a satisfactory manner. Finally, the impact of impurities and alloying elements on hydrogen diffusion in aluminum is discussed.
Ab initio study of phase equilibria in TiCx
DEFF Research Database (Denmark)
Korzhavyi, P.A.; Pourovskii, L.V.
2002-01-01
The phase diagram for the vacancy-ordered structures in the substoichiometric TiCx (x = 0.5-1.0) has been established from Monte Carlo simulations with the long-range pair and multisite effective interactions obtained from ab initio calculations. Three ordered superstructures of vacancies (Ti2C, Ti3C2, and Ti6C5) are found to be ground state configurations. Their stability has been verified by full-potential total energy calculations of the fully relaxed structures.
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
Current rectification by asymmetric molecules: An ab initio study
Zhou, Y; Xu, Y; Zeng, Z Y; Zhou, Yan-hong; Zheng, Xiao-hong; Xu, Ying; Zeng, Zhao Yang
2006-01-01
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 $n=5$.
Ab initio calculations and modelling of atomic cluster structure
DEFF Research Database (Denmark)
Solov'yov, Ilia; Lyalin, Andrey G.
2004-01-01
The optimized structure and electronic properties of small sodium and magnesium clusters have been investigated using it ab initio theoretical methods based on density-functional theory and post-Hartree-Fock many-body perturbation theory accounting for all electrons in the system. A new theoretical 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.
Ab initio electronic structure of rare earth orthoferrites
International Nuclear Information System (INIS)
Ab initio FP-APW+lo calculations were performed for the rare earth orthoferrites RFeO3 with R=La, Nd, Sm, Gd, Dy, Lu using the well-known WIEN2k package. Ferromagnetic and antiferromagnetic alignments between the iron moments were studied using the GGA (PBE) functional for the exchange-correlation energy. Antiferromagnetic structures are energetically favoured in all cases. Except for SmFeO3, all antiferromagnetic configurations are insulators, while the ferromagnetic ones give metals except for LaFeO3 and LuFeO3. Hyperfine fields at the iron sites agree with experiment to within 25%
Ab initio calculation of the static structural properties of Be
International Nuclear Information System (INIS)
An ab initio calculation of the static structural properties of Be is presented. The total structural energy is calculated using pseudopotentials and the local density-functional formalism with the atomic number as the only input. The lattice constant, Poisson's ratio, and the bulk modulus are predicted by calculating the total energy of the system. The deviations of the calculated results for lattice constants c, a and c/a are approximately 1% when compared with experimental results. Poisson's ratio and the bulk modulus are also in reasonably good agreement with the measured values. (author)
Ab initio theory of perpendicular transport in metallic magnetic multilayers.
Czech Academy of Sciences Publication Activity Database
Kudrnovský, Josef; Drchal, Václav; Blass, C.; Weinberger, P.; Turek, Ilja; Bruno, P.
New York : Kluwer Academic/Plenum Publishers, 2000 - (Meike, A.; Gonis, A.; Turchi, E.; Rajan, K.), s. 343-364 ISBN 0-306-46498-5. [Proceedings of the Second International Alloy Conference. Davos (CH), 08.08.1999-13.08.1999] R&D Projects: GA MŠk OC P3.70; GA ?R GA202/97/0598; GA AV ?R IAA1010829 Grant ostatní: TMR network(XX) EMRX-CT96-0089; Aktion(XX) WTZ I.23 Institutional research plan: CEZ:AV0Z1010921 Keywords : magnetic multilayers * CPP transport * ab-initio theory Subject RIV: BM - Solid Matter Physics ; Magnetism
Ab initio and Gordon-Kim intermolecular potentials for two nitrogen molecules
Ree, Francis H.; Winter, Nicholas W.
1980-07-01
Both ab initio MO-LCAO-SCF and the electron-gas (or Gordon-Kim) methods have been used to compute the intermolecular potential (?) of N2 molecules for seven different N2-N2 orientations. The ab initio calculations were carried out using a [4s3p] contracted Gaussian basis set with and without 3d polarization functions. The larger basis set provides adequate results for ??0.002 hartree or intermolecular separations less than 6.5-7 bohr. We use a convenient analytic expression to represent the ab initio data in terms of the intermolecular distance and three angles defining the orientations of the two N2 molecules. The Gordon-Kim method with Rae's self-exchange correction yields ?, which agrees reasonably well over a large repulsive range. However, a detailed comparison of the electron kinetic energy contributions shows a large difference between the ab initio and the Gordon-Kim calculations. Using the ab initio data we derive an atom-atom potential of the two N2 molecules. Although this expression does not accurately fit the data at some orientations, its spherical average agrees with the corresponding average of the ab initio ? remarkably well. The spherically averaged ab initio ? is also compared with the corresponding quantities derived from experimental considerations. The approach of the ab initio ? to the classical quadrupole-quadrupole interaction at large intermolecular separation is also discussed.
Why ferro electricity? synchrotron radiation and ab initio answers
Energy Technology Data Exchange (ETDEWEB)
Olivera, R.; Espinosa, F.; Garcia, M.; Macias, E. [Centro de Investigacion en Materiales Avanzados (CIMAV), Chihuahua (Mexico); Fuentes, M.E. [Universidad Autonoma de Chihuahua (UACh), Chihuahua (Mexico); Duran, A.; Siqueiros, J. [Centro de Ciencias de la Materia Condensada (CCMC), Ensenada (Mexico)]. e-mail: luis.fuentes@cimav.edu.mx
2007-07-01
An old question of solid state physics is being answered nowadays: the atomic-level understanding of ferro electricity. Traditional ideas about ferroelectric phenomena relate with softening of optical phonons at the Brillouin zone origin and with 'W-shaped' Landau free energy functions. Last decade experimental (synchrotron radiation, neutrons) and quantum-theoretical (Cohen, Resta, Spaldin) contributions have clarified detailed descriptions and explanations for atomic behavior leading to spontaneous polarization in perovskite and perovskite-related crystal structures. Work being performed by our interdisciplinary group on ferro electricity is presented. Perovskite and Aurivillius ferroelectric phases are obtained by different methods. Fine details on crystal structures are investigated by means of synchrotron radiation at Stanford Synchrotron Radiation Laboratory. Electronic structures of considered phases are theoretically characterized by ab initio methods. High-resolution diffraction experiments demonstrate several symmetry break-downs in perovskite and Aurivillius phases. The structure- symmetry-polarization relationship is discussed for a number of representative cases. Ab initio explanation of ferroelectric polarization in perovskite structures is given. Energy calculation is performed by means of CASTEP code under GGA functional. Energy optimization leads to cubic-tetragonal symmetry break-down with off-centering cation displacements via second-order Jahn-Teller effect. Electronic structure is investigated with Band Lab code, under LDA functional with LMTO method. Degeneracy of Ti 3d z{sup 2} and Ti 3d (x{sup 2} + y{sup 2}) orbitals is the cause of cubic-perovskite deformation. (Author)
Ab initio calculation of lattice dynamics in BeO
International Nuclear Information System (INIS)
Ground state lattice vibrational properties of wurtzite-BeO are reported using an ab initio plane-wave pseudopotential method. The ab initio results for the phonon dispersion relations are in good agreement with the available experimental data. The only discrepancy observed between experiment and present data for the longitudinal optic frequency at the centre of the Brillouin zone for a displacement along the symmetry axis is expected to be due to the indirect measurement of that mode in the experiment. The dielectric constant, the Born effective charges and the elastic constants for the compound are computed from the lattice dynamics. All of them agree well with the experimental results. The elastic constants calculated using the phonon spectra agree reasonably well with the results from other first-principles calculations. The good agreement of the quantities calculated, with the experimental results pave the way for future studies on the contribution of lattice vibrations to the pressure-induced phase transition in this compound. We try to understand the features of the phonon spectra from the component-projected phonon densities of states and by analysing the contributions of each atom type towards each normal mode. We find that the phonon spectra of BeO contains features common to some of the members with the same crystal structure as well as to some of the members in the same alkaline earth oxide group
Ab initio determination of solid-state nanostructure
Juhás, P.; Cherba, D. M.; Duxbury, P. M.; Punch, W. F.; Billinge, S. J. L.
2006-03-01
Advances in materials science and molecular biology followed rapidly from the ability to characterize atomic structure using single crystals. Structure determination is more difficult if single crystals are not available. Many complex inorganic materials that are of interest in nanotechnology have no periodic long-range order and so their structures cannot be solved using crystallographic methods. Here we demonstrate that ab initio structure solution of these nanostructured materials is feasible using diffraction data in combination with distance geometry methods. Precise, sub-ångström resolution distance data are experimentally available from the atomic pair distribution function (PDF). Current PDF analysis consists of structure refinement from reasonable initial structure guesses and it is not clear, a priori, that sufficient information exists in the PDF to obtain a unique structural solution. Here we present and validate two algorithms for structure reconstruction from precise unassigned interatomic distances for a range of clusters. We then apply the algorithms to find a unique, ab initio, structural solution for C60 from PDF data alone. This opens the door to sub-ångström resolution structure solution of nanomaterials, even when crystallographic methods fail.
Ab initio constrained crystal-chemical Rietveld refinement of Ca10(VxP1-xO4)6F2 apatites
International Nuclear Information System (INIS)
Extraction of reliable bond distances and angles for Ca10(VxP1-xO4)6F2 apatites using standard Rietveld refinement with Cu K? X-ray powder data was significantly impaired by large imprecision for the O-atom coordinates. An initial attempt to apply crystal-chemical Rietveld refinements to the same compounds was partly successful, and exposed the problematic determination of two oxygen-metal- oxygen angles. Ab initio modeling with VASP in space groups P63/m, P21/m and Pm showed that both these angular parameters exhibited a linear dependence with the vanadium content. Stable crystal-chemical Rietveld refinements in agreement with quantum results were obtained by fixing these angles at the values from ab initio simulations. Residuals were comparable with the less precise standard refinements. The larger vanadium ion is accommodated primarily by uniform expansion and rotation of BO4 tetrahedra combined with a rotation of the Ca-Ca-Ca triangular units. It is proposed that the reduction of symmetry for the vanadium end-member is necessary to avoid considerable departures from formal valences at the AII and B sites in P63/m. The complementarity of quantum methods and structural analysis by powder diffraction in cases with problematic least-squares extraction of the crystal chemistry is discussed. (orig.)
Ab initio calculation of thermodynamic functions for crystals
International Nuclear Information System (INIS)
The knowledge of thermodynamic functions is essential to investigate crystal stability and chemical reactivity. These functions are not always experimentally known, as for some crystalline host phases for radioactive waste. Fortunately, it is possible to calculate them. Although possible, the full ab initio calculation is not realistic because the calculation time rapidly becomes too long. These functions are obtained using an analytical model containing physical quantities determined by ab initio calculations. This enabled us to estimate the main thermodynamic functions of zircon ZrSiO4, fluor-apatite Ca10(PO4)6F2 and stoichiometric iodo-apatite Pb10(VO4)6I2 from the variation of cohesive energy with volume and the harmonic vibration frequencies at the center of the first Brillouin zone for the unit cell corresponding to maximum cohesive energy. These ab initio quantities are calculated with the DMOL3 code that solves the electronic Schroedinger equation using the electronic density functional theory (DFT) in local density approximation, corrected (NLDA) or not (LDA) with its gradient. To limit calculation time, we made additional approximations: - acoustic and optical vibrations beyond the first Brillouin zone center are described by the Debye and Einstein models respectively; - to allow thermal expansion of the crystal we used the quasi-harmonic approximation which assumes that frequency variations are proportional to volume variations. The proportionality coefficients known as Gruneisen coefficients are derived in this study, with specific approximations; - we used the spherical cellular approximation and considered the crystal as isotropic. The thermodynamic functions calculated with this model are the following measurable quantities : enthalpy and free enthalpy, heat capacity at constant pressure, bulk modulus and thermal expansion coefficient. For zircon and fluor-apatite, for which the main thermodynamic functions are experimentally known, the enthalpy of formation are determined with less than 2% uncertainty, and heat capacities at constant pressure are well reproduced: For iodo-apatite, there are as yet no published experimental data to compare with the present theoretical results. This model can be applied to a wide range of crystals. (author)
Improved Embedding Ab Initio Model Potentials for Embedded Cluster Calculations
Pascual, José Luis; Barros, Noémi; Barandiarán, Zoila; Seijo, Luis
2009-06-01
An improvement in the method of production of embedding ab initio model potentials (AIMP) for embedded cluster calculations in ionic solids is proposed and applied to the oxides CeAlO3, CeO2, and UO2. The improvement affects the calculation of one of the AIMP components, the Pauli repulsion operator, which prevents the cluster electrons from collapsing onto the occupied orbitals of the host in embedded cluster calculations and, so, their over occupancy. The linear constants involved in such operator are proposed to be obtained in embedded cluster calculations in the perfect host, with the requirement that local structures calculated with working embedded clusters of relatively small size agree with those calculated with reference embedded clusters of much larger size.
Fabrication and ab initio study of downscaled graphene nanoelectronic devices
Mizuta, Hiroshi; Moktadir, Zakaria; Boden, Stuart A.; Kalhor, Nima; Hang, Shuojin; Schmidt, Marek E.; Cuong, Nguyen Tien; Chi, Dam Hieu; Otsuka, Nobuo; Muruganathan, Manoharan; Tsuchiya, Yoshishige; Chong, Harold; Rutt, Harvey N.; Bagnall, Darren M.
2012-09-01
In this paper we first present a new fabrication process of downscaled graphene nanodevices based on direct milling of graphene using an atomic-size helium ion beam. We address the issue of contamination caused by the electron-beam lithography process to pattern the contact metals prior to the ultrafine milling process in the helium ion microscope (HIM). We then present our recent experimental study of the effects of the helium ion exposure on the carrier transport properties. By varying the time of helium ion bombardment onto a bilayer graphene nanoribbon transistor, the change in the transfer characteristics is investigated along with underlying carrier scattering mechanisms. Finally we study the effects of various single defects introduced into extremely-scaled armchair graphene nanoribbons on the carrier transport properties using ab initio simulation.
Ab-initio study of diluted magnetic semiconductors.
Czech Academy of Sciences Publication Activity Database
Kudrnovský, Josef; Drchal, Václav; Máca, František; Turek, Ilja; Bouzerar, G.; Bruno, P.
New York : Springer Science+ Business Media, Inc, 2005 - (Turchi, P.; Gonis, A.; Rajan, K.; Meike, A.), s. 277-293 ISBN 0-387-24811-0. [Third International Alloy Conference. Estoril Sol (PT), 30.06.2002-05.07.2002] R&D Projects: GA ?R(CZ) GA202/00/0122; GA AV ?R(CZ) IAA1010203; GA AV ?R IAA1010214; GA MŠk(CZ) OC P5.30 Grant ostatní: RTN(XE) HPRN-CT-2000-00143 Institutional research plan: CEZ:AV0Z10100520 Keywords : ab-initio * diluted magnetic semiconductors * Curie temperatures * III-V semiconductors Subject RIV: BM - Solid Matter Physics ; Magnetism
An Efficient Approach to Ab Initio Monte Carlo Simulation
Leiding, Jeff
2013-01-01
We present a Nested Markov Chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, is used to substantially decorrelate configurations at which the potential of interest is evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure is maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature \\beta^0), which is otherwise unconstrained. Local density approximation (LDA) results are presented for shocked states in argon at pressures from 4 to 60 GPa. Depending on the quality of the reference potential, the acceptance probability is enhanced by factors of 1.2-28 relative to unoptimized NMC sampling, and the procedure's efficiency is found to be competitive with that of standard ab initio...
Symplectic ab initio no-core shell model
International Nuclear Information System (INIS)
The present study confirms the significance of the symplectic Sp(3,R) symmetry in nuclear dynamics as unveiled, for the first time, by examinations of realistic nucleon-nucleon interactions as well as of eigenstates calculated in the framework of the ab initio No-Core Shell Model (NCSM). The results 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 JISP 16 and CD-Bonn realistic nucleon-nucleon interactions, which points to a more fundamental origin of the symplectic symmetry. (Author)
Quantitative Verification of Ab Initio Self-consistent Laser Theory
Ge, Li; Stone, A Douglas; Türeci, Hakan E
2008-01-01
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.
Self-vacancies in Gallium Arsenide: an ab initio calculation
El-Mellouhi, F; El-Mellouhi, Fedwa; Mousseau, Normand
2004-01-01
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.
Atmospheric oxidation of trichloroethylene: an ab initio study.
Christiansen, Carrie J; Francisco, Joseph S
2010-09-01
The atmospheric oxidation of trichloroethylene has previously been studied experimentally. Phosgene is thought to be the dominant product, although the mechanism of production is not well understood. Additionally, studies omitting a chlorine scavenger show the production of dichloroacetyl chloride. This influence of the chlorine atom on the trichloroethylene oxidation is not well understood. Using ab initio methods, this study presents a comprehensive computational study of both the hydroxyl radical and chlorine atom initiated atmospheric oxidation mechanisms of trichloroethylene (C(2)HCl(3)). Potential energy surfaces, including activation energies and enthalpies, are determined. The results from this study, in connection with experimental work, confirm the influence of the Cl-initiated oxidation in determining the product profile of the trichloroethylene oxidation. These products include dichloroacetyl chloride [Cl(2)CHC(O)Cl], formyl chloride [CH(O)Cl], phosgene [C(O)Cl(2)], and regeneration of the chlorine atom. PMID:20687539
Local Structure Analysis in $Ab$ $Initio$ Liquid Water
Santra, Biswajit; Martelli, Fausto; Car, Roberto
2015-01-01
Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion (vdW) interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively agrees with experiment. In this work, we have used the local structure index (LSI) order parameter to analyze the local structure in such highly accurate $ab$ $initio$ liquid water. At ambient conditions, the LSI probability distribution, P($I$), was unimodal with most water molecules characterized by more disordered high-density-like local environments. With thermal excitations removed, the resultant bimodal P($I$) in the inherent potential energy surface (IPES) exhibited a 3:1 ratio between high- and low-density-like molecules, with the latter forming small connected clusters amid the predominant population. By considering the spatial correlations and hydrogen bond network topologies $among$ water molecules with the same LSI identities, we demonstrate that the signatures of th...
A Review on Ab Initio Approaches for Multielectron Dynamics
Ishikawa, Kenichi L
2015-01-01
In parallel with the evolution of femtosecond and attosecond laser as well as free-electron laser technology, a variety of theoretical methods have been developed to describe the behavior of atoms, molecules, clusters, and solids under the action of those laser pulses. Here we review major ab initio wave-function-based numerical approaches to simulate multielectron dynamics in atoms and molecules driven by intense long-wavelength and/or ultrashort short-wavelength laser pulses. Direct solution of the time-dependent Schr\\"odinger equation (TDSE), though its applicability is limited to He, ${\\rm H}_2$, and Li, can provide an exact description and has been greatly contributing to the understanding of dynamical electron-electron correlation. Multiconfiguration self-consistent-field (MCSCF) approach offers a flexible framework from which a variety of methods can be derived to treat both atoms and molecules, with possibility to systematically control the accuracy. The equations of motion of configuration interactio...
Ab initio MCDHF calculations of electron–nucleus interactions
Biero?, Jacek; Froese Fischer, Charlotte; Fritzsche, Stephan; Gaigalas, Gediminas; Grant, Ian P.; Indelicato, Paul; Jönsson, Per; Pyykkö, Pekka
2015-05-01
We present recent advances in the development of atomic ab initio multiconfiguration Dirac–Hartree–Fock theory, implemented in the GRASP relativistic atomic structure code. For neutral atoms, the deviations of properties calculated within the Dirac–Hartree–Fock (DHF) method (based on independent particle model of an atomic cloud) are usually dominated by electron correlation effects, i.e. the non-central interactions of individual electrons. We present the recent advances in accurate calculations of electron correlation effects in small, medium, and heavy neutral atoms. We describe methods of systematic development of multiconfiguration expansions leading to systematic, controlled improvement of the accuracy of the ab initio calculations. These methods originate from the concept of the complete active space (CAS) model within the DHF theory, which, at least in principle, permits fully relativistic calculations with full account of electron correlation effects. The calculations within the CAS model on currently available computer systems are feasible only for very light systems. For heavier atoms or ions with more than a few electrons, restrictions have to be imposed on the multiconfiguration expansions. We present methods and tools, which are designed to extend the numerical calculations in a controlled manner, where multiconfiguration expansions account for all leading electron correlation effects. We show examples of applications of the GRASP code to calculations of hyperfine structure constants, but the code may be used for calculations of arbitrary bound-state atomic properties. In recent years it has been applied to calculations of atomic and ionic spectra (transition energies and rates), to determinations of nuclear electromagnetic moments, as well as to calculations related to interactions of bound electrons with nuclear electromagnetic moments leading to violations of discrete symmetries.
Constructing ab initio and empirical potential energy surfaces for water
International Nuclear Information System (INIS)
The infrared spectrum of water is possibly one of the most well studied and yet portions of it are still poorly understood. Recently, significant advances have been made in assigning water spectra using variational nuclear calculations. The major factor determining the accuracy of ro-vibrational spectra of water is the accuracy of the underlying Potential Energy Surface. Even the most accurate ab initio Potential Energy Surface does not reproduce the Born-Oppenheimer surface to sufficient accuracy for spectroscopic studies. Furthermore, effects beyond this model such as the adiabatic correction, the relativistic correction and the non-adiabatic correction have to be considered. This thesis includes a discussion on how the relativistic correction was calculated, for the water molecule, from first-order perturbation theory. The relativistic correction improved vibrational stretching motion while making the prediction of the bending modes far worse. For rotational motion the relativistic effect had an increasing effect with increasing Ka. A further alteration to the ab initio calculations is introduced by adjusting the barrier to linearity in the water potential. This alteration to the barrier was considered in order to compensate for the lack of convergence of quantum chemical calculations of the Born-Oppenheimer surface. This barrier attempts to represent the change in the potential from linear to equilibrium. We show the improvements this has on the calculated energy vements this has on the calculated energy levels by comparison with the HITRAN database. This then led the way to the improved spectroscopic potential presented here in this thesis. This new spectroscopic potential reduces the overall standard deviation significantly for vibrational and rotational energy levels. (author)
Emergence of rotational bands in ab initio no-core configuration interaction calculations
Caprio, M A; Vary, J P; Smith, R
2015-01-01
Rotational bands have been observed to emerge in ab initio no-core configuration interaction (NCCI) calculations for p-shell nuclei, as evidenced by rotational patterns for excitation energies, electromagnetic moments, and electromagnetic transitions. We investigate the ab initio emergence of nuclear rotation in the Be isotopes, focusing on 9Be for illustration, and make use of basis extrapolation methods to obtain ab initio predictions of rotational band parameters for comparison with experiment. We find robust signatures for rotational motion, which reproduce both qualitative and quantitative features of the experimentally observed bands.
Czech Academy of Sciences Publication Activity Database
Meliá, C.; Ferrer, S.; ?ezá?, Jan; Parisel, O.; Reinaud, O.; Moliner, V.; de la Lande, A.
2013-01-01
Ro?. 19, ?. 51 (2013), s. 17328-17337. ISSN 0947-6539 Institutional support: RVO:61388963 Keywords : ab initio calculations * copper * electron transfer * enzymes * molecular dynamics * reaction mechanisms Subject RIV: CC - Organic Chemistry Impact factor: 5.696, year: 2013
DEFF Research Database (Denmark)
Wolf, T. J. A.; Kuhlman, Thomas Scheby
Time-resolved photoelectron spectroscopy and ab initio multiple spawning were applied to the ultrafast non-adiabatic dynamics of hexamethylcyclopentadiene. The high level of agreement between experiment and theory associates wavepacket motion with a distinct degree of freedom.
On triplet tetraoxygen: ab initio study along minimum energy path and global modelling
Varandas, A. J. C.; Llanio-Trujillo, J. L.
2002-04-01
MRCI calculations are reported for O4( 3A) using two distinct CASSCF reference wave functions, and the results compared with previous ab initio calculations. By combining the force field of the best ab initio CASSCF surface at the saddle point with the recommended estimate for the barrier height, a four-body analytic term is obtained which added to the popular double many-body expansion potential energy surface for the title system makes it fit well such properties.
Pierce, Levi C. T.; Markwick, Phineus R. L.; Mccammon, J. Andrew; Doltsinis, Nikos L.
2011-01-01
A biased potential molecular dynamics simulation approach, accelerated molecular dynamics (AMD), has been implemented in the framework of ab initio molecular dynamics for the study of chemical reactions. Using two examples, the double proton transfer reaction in formic acid dimer and the hypothetical adiabatic ring opening and subsequent rearrangement reactions in methylenecyclopropane, it is demonstrated that ab initio AMD can be readily employed to efficiently explore the reactive potential...
Ab initio quality study of the graphite-diamond phase coexistence
Khaliullin, Rustam Z.; Eshet, Hagai; Kühne, Thomas D.; Behler, Jörg; Parrinello, Michele
2010-01-01
An interatomic potential for the diamond and graphite phases of carbon has been created using a neural-network (NN) representation of the ab initio potential energy surface. The NN potential combines the accuracy of a first-principle description of both phases with the efficiency of empirical force fields and allows one to perform, for the first time, a molecular dynamics study, of ab initio quality, of the thermodynamics of graphite-diamond coexistence. Good agreement betwe...
Ab initio no-core shell model calculations for light nuclei
Navratil, Petr
2007-01-01
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.
Ab Initio Calculations and Raman and SERS Spectral Analyses of Amphetamine Species
Berg, Rolf W.; Nørbygaard, Thomas; White, Peter C.; Abdali, Salim
2011-01-01
For the first time, the differences between the spectra of amphetamine and amphetamine-H+ and between different conformers are thoroughly studied by ab initio model calculations, and Raman and surface-enhanced Raman spectroscopy (SERS) spectra are measured for different species of amphetamine. The spectra of amphetamine and amphetamine-H+ sampleswere obtained and assigned according to a comparison of the experimental spectra and the ab initio MO calculations, performed using the Gaussia...
Predicting lattice thermal conductivity with help from ab initio methods
Broido, David
2015-03-01
The lattice thermal conductivity is a fundamental transport parameter that determines the utility a material for specific thermal management applications. Materials with low thermal conductivity find applicability in thermoelectric cooling and energy harvesting. High thermal conductivity materials are urgently needed to help address the ever-growing heat dissipation problem in microelectronic devices. Predictive computational approaches can provide critical guidance in the search and development of new materials for such applications. Ab initio methods for calculating lattice thermal conductivity have demonstrated predictive capability, but while they are becoming increasingly efficient, they are still computationally expensive particularly for complex crystals with large unit cells . In this talk, I will review our work on first principles phonon transport for which the intrinsic lattice thermal conductivity is limited only by phonon-phonon scattering arising from anharmonicity. I will examine use of the phase space for anharmonic phonon scattering and the Grüneisen parameters as measures of the thermal conductivities for a range of materials and compare these to the widely used guidelines stemming from the theory of Liebfried and Schölmann. The lattice thermal conductivity is a fundamental transport parameter that determines the utility a material for specific thermal management applications. Materials with low thermal conductivity find applicability in thermoelectric cooling and energy harvesting. High thermal conductivity materials are urgently needed to help address the ever-growing heat dissipation problem in microelectronic devices. Predictive computational approaches can provide critical guidance in the search and development of new materials for such applications. Ab initio methods for calculating lattice thermal conductivity have demonstrated predictive capability, but while they are becoming increasingly efficient, they are still computationally expensive particularly for complex crystals with large unit cells . In this talk, I will review our work on first principles phonon transport for which the intrinsic lattice thermal conductivity is limited only by phonon-phonon scattering arising from anharmonicity. I will examine use of the phase space for anharmonic phonon scattering and the Grüneisen parameters as measures of the thermal conductivities for a range of materials and compare these to the widely used guidelines stemming from the theory of Liebfried and Schölmann. This research was supported primarily by the NSF under Grant CBET-1402949, and by the S3TEC, an Energy Frontier Research Center funded by the US DOE, office of Basic Energy Sciences under Award No. DE-SC0001299.
Ab-initio calculations of the Optical band-gap of TiO2 thin films
Wunderlich, W; Tanemura, M; Tanemura, S; Jin, P; Kaneko, K; Terai, A; Nabatova-Gabin, N; Belkada, R; Wunderlich, Wilfried; Miao, Lei; Tanemura, Masaki; Tanemura, Sakae; Jin, Ping; Kaneko, Kenji; Terai, Asuka; Nabatova-Gabin, Nataliya; Belkada, Rachid
2004-01-01
Titanium dioxide has been extensively studied in recent decades for its important photocatalytic application in environmental purification. The search for a method to narrow the optical band-gap of TiO2 plays a key role for enhancing its photocatalytic application. The optical band gap of epitaxial rutile and anatase TiO2 thin films deposited by helicon magnetron sputtering on sapphire and on SrTiO3 substrates was correlated to the lattice constants estimated from HRTEM images and SAED. The optical band-gap of 3.03 eV for bulk-rutile increased for the thin films to 3.37 on sapphire. The band gap of 3.20 eV for bulk-anatase increases to 3.51 on SrTiO3. In order to interpret the optical band gap expansion for both phases, ab-initio calculations were performed using the Vienna ab-initio software. The calculations for rutile as well anatase show an almost linear increase of the band gap width with decreasing volume or increasing lattice constant a. The calculated band gap fits well with the experimental values. T...
Challenges for large scale ab initio Quantum Monte Carlo
Kent, Paul
2015-03-01
Ab initio Quantum Monte Carlo is an electronic structure method that is highly accurate, well suited to large scale computation, and potentially systematically improvable in accuracy. Due to increases in computer power, the method has been applied to systems where established electronic structure methods have difficulty reaching the accuracies desired to inform experiment without empiricism, a necessary step in the design of materials and a helpful step in the improvement of cheaper and less accurate methods. Recent applications include accurate phase diagrams of simple materials through to phenomena in transition metal oxides. Nevertheless there remain significant challenges to achieving a methodology that is robust and systematically improvable in practice, as well as capable of exploiting the latest generation of high-performance computers. In this talk I will describe the current state of the art, recent applications, and several significant challenges for continued improvement. Supported through the Predictive Theory and Modeling for Materials and Chemical Science program by the Office of Basic Energy Sciences (BES), Department of Energy (DOE).
Ab initio transport across bismuth selenide surface barriers
Narayan, Awadhesh; Rungger, Ivan; Droghetti, Andrea; Sanvito, Stefano
2014-11-01
We investigate the effect of potential barriers in the form of step edges on the scattering properties of Bi2Se3 (111) topological surface states by means of large-scale ab initio transport simulations. Our results demonstrate the suppression of perfect backscattering, while all other scattering processes, which do not entail a complete spin and momentum reversal, are allowed. Furthermore, we find that the spin of the surface state develops an out-of-plane component as it traverses the barrier. Our calculations reveal the existence of quasibound states in the vicinity of the surface barriers, which appear in the form of an enhanced density of states in the energy window corresponding to the topological state. For double barriers we demonstrate the formation of quantum well states. To complement our first-principles results we construct a two-dimensional low-energy effective model and illustrate its shortcomings. Our findings are discussed in the context of a number of recent experimental works.
Hydrogen adsorption on the ?-graphyne using ab initio calculations
Drogar, J.; Roknabadi, M. R.; Behdani, M.; Modarresi, M.; Kari, A.
2014-11-01
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.
Ab-initio strength functions in light nuclei
Kruse, Michael; Ormand, W. Erich; Johnson, Calvin
2014-09-01
Strength functions are an excellent tool to determine the collective excitation mechanism of a nucleus in the presence of electromagnetic fields. Since the discovery of the giant-dipole resonance in heavy nuclei much theoretical and experimental work has been devoted to studying strength functions. We present strength function calculations for the light nuclei A = 6, A = 10 and C-12 within an ab initio framework. We show results for the isoscalar and isovector monopole modes as well as the electric- and magnetic dipole response. The calculations are performed with the No-Core Shell Model. As input we use an isoscalar Hamiltonian derived from a similarity renormalized two-body chiral N3LO interaction and perform the calculation for basis-space sizes up to Nmax = 14 for A = 6 and Nmax = 8 for A = 10. Further, we present evidence supporting the Brink hypothesis that if a giant dipole resonance is found for the ground-state then the excited states will also exhibit such a resonance.
Ab initio study of alanine polypeptide chain twisting
DEFF Research Database (Denmark)
Solov'yov, Ilia; Yakubovich, Alexander V.
2006-01-01
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.
Ab initio simulations of peptide-mineral interactions
Hug, Susanna; Hunter, Graeme K.; Goldberg, Harvey; Karttunen, Mikko
We performed Car-Parrinello Molecular Dynamics (CPMD) simulations of two amino acids, aspartic acid (Asp) and phophoserine (pSer), on a calcium oxalate monohydrate (COM) surface as a model of the interactions of phosphoproteins with biominerals. In our earlier work using in vitro experiments and classical Molecular Dynamics (MD) simulations we have demonstrated the importance of phosphorylation of serine on the interactions of osteopontin (OPN) with COM. We used configurations from our previous classical MD simulations as a starting point for the ab initio simulations. In the case of Asp we found that the ?-carboxyl and amine groups form temporary close contacts with the surface. For the dipeptide Asp-pSer the carboxyl groups form permanent close contacts with the surface and the distances of its other functional groups do not vary much. We show how the interaction of carboxyl groups with COM crystal is established and confirm the importance of phosphorylation in mediating the interactions between COM surfaces and OPN.
Ab initio and kinetic modeling studies of formic acid oxidation
DEFF Research Database (Denmark)
Marshall, Paul; Glarborg, Peter
2015-01-01
A detailed chemical kinetic model for oxidation of formic acid (HOCHO) in flames has been developed, based on theoretical work and data from literature. Ab initio calculations were used to obtain rate coefficients for reactions of HOCHO with H, O, and HO2. Modeling predictions with the mechanism have been compared to the experimental results of de Wilde and van Tiggelen (1968) who measured the laminar burning velocities for HOCHO flames over a range of stoichiometries and dilution ratios. The modeling predictions are generally satisfactory. The governing reaction mechanisms are outlined based on calculations with the kinetic model. Formic acid is consumed mainly by reaction with OH, yielding OCHO, which dissociates rapidly to CO2 + H, and HOCO, which may dissociate to CO + OH or CO2 + H, or react with H, OH, or O2 to form more stable products. The branching fraction of the HOCHO + OH reaction, as well as the fate of HOCO, determines the oxidation rate of formic acid. At lower temperatures HO2, formed from HOCO + O2, is an important chain carrier and modeling predictions become sensitive to the HOCHO + HO2 reaction. © 2014 The Combustion Institute.
FTIR, Raman spectra and ab initio calculations of 2-mercaptobenzothiazole.
Rai, Amareshwar K; Singh, Rachana; Singh, K N; Singh, V B
2006-02-01
FTIR and Raman spectra of a rubber vulcanization accelerator, 2-mercaptobenzothiazole (MBT), were recorded in the solid phase. The harmonic vibrational wavenumbers, for both the toutomeric forms of MBT, as well as for its dimeric complex, have been calculated, using ab initio RHF and density functional B3LYP methods invoking different basis sets upto RHF/6-31G** and B3LYP/6-31G** and the results were compared with the experimental values. Conformational studies have been also carried out regarding its toutomeric monomer forms and its dimer form. With all the basis sets the thione form of MBT (II) is predicted to be more stable than thiol form (I) and dimeric conformation (III) is predicted to be more stable with monomeric conformations (I) and (II). Vibrational assignments have been made, and it has been found that the calculated normal mode frequencies of dimeric conformation (III) are required for the analysis of IR and Raman bands of the MBT. The predicted shift in NH- stretching vibration towards the lower wave number side with the B3LYP/6-31G** calculations for the most stable dimer form (III), is in better agreement with experimental results. The intermolecular sulfur-nitrogen distance in N-H...S hydrogen bond was found to be 3.35 angstroms from these calculations, is also in agreement to the experimental value. PMID:16098806
Ab initio effective interactions for sd-shell valence nucleons
Dikmen, E; Barrett, B R; Maris, P; Shirokov, A M; Vary, J P
2015-01-01
We perform \\textit{ab initio} no core shell model calculations for $A=18$ and $19$ nuclei in a $4\\hbar\\Omega$, or $N_{\\rm max}=4$, model space using the effective JISP16 and chiral N3LO nucleon-nucleon potentials and transform the many-body effective Hamiltonians into the $0\\hbar\\Omega$ model space to construct the $A$-body effective Hamiltonians in the $sd$-shell. We separate the $A$-body effective Hamiltonians with $A=18$ and $A=19$ into inert core, one- and two-body components. Then, we use these core, one- and two-body components to perform standard shell model calculations for the $A=18$ and $A=19$ systems with valence nucleons restricted to the $sd$-shell. Finally, we compare the standard shell model results in the $0\\hbar\\Omega$ model space with the exact no core shell model results in the $4\\hbar\\Omega$ model space for the $A=18$ and $A=19$ systems and find good agreement.
Ab initio molecular dynamics calculations of ion hydration free energies
International Nuclear Information System (INIS)
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or '?-path' technique to compute the intrinsic hydration free energies of Li+, Cl-, and Ag+ ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (?) contributions, we obtain absolute AIMD hydration free energies (?Ghyd) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model ? predictions. The sums of Li+/Cl- and Ag+/Cl- AIMD ?Ghyd, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag++Ni+?Ag+Ni2+ in water. The predictions for this reaction suggest that existing estimates of ?Ghyd for unstable radiolysis intermediates such as Ni+ may need to be extensively revised.
Ab initio simulations on rutile-based titania nanowires
International Nuclear Information System (INIS)
The rod symmetry groups for monoperiodic (1D) nanostructures have been applied for construction of models for bulk-like TiO2 nanowires (NWs) cut from a rutile-based 3D crystal along the chosen [001] and [110] directions of crystallographic axes. In this study, we have considered nanowires described by both the Ti-atom centered rotation axes as well as the hollow site centered axes passing through the interstitial positions between the Ti and O atoms closest to the axes. The most stable [001]-oriented TiO2 NWs with rhombic cross sections are found to display the energetically preferable {110} facets only while the nanowires with quasi-square sections across the [110] axis are formed by the alternating { 11-bar 0 } and {001} facets. For simulations on rutile-based nanowires possessing different diameters for each NW type, we have performed large-scale ab initio Density Functional Theory (DFT) and hybrid DFT-Hartree Fock (DFT-HF) calculations with total geometry optimization within the Generalized Gradient Approximation (GGA) in the form of the Perdew-Becke-Ernzenhof (PBE) exchange-correlation functionals (PBE and PBE0, respectively), using the formalism of linear combination of localized atomic functions (LCAO). We have simulated both structural and electronic properties of TiO2 NWs depending both on orientation and position of symmetry axes as well as on diameter and morphology of nanowires.
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
The AB Initio Mia Method: Theoretical Development and Practical Applications
Peeters, Anik
The bottleneck in conventional ab initio Hartree -Fock calculations is the storage of the electron repulsion integrals because their number increases with the fourth power of the number of basis functions. This problem can be solved by a combination of the multiplicative integral approximation (MIA) and the direct SCF method. The MIA approach was successfully applied in the geometry optimisation of some biologically interesting compounds like the neurolepticum Haloperidol and two TIBO derivatives, inactivators of HIV1. In this thesis the potency of the MIA-method is shown by the application of this method in the calculation of the forces on the nuclei. In addition, the MIA method enabled the development of a new model for performing crystal field studies: the supermolecule model. The results for this model are in better agreement with experimental data than the results for the point charge model. This is illustrated by the study of some small molecules in the solid state: 2,3-diketopiperazine, formamide oxime and two polymorphic forms of glycine, alpha-glycine and beta-glycine.
Ab initio molecular simulations for proposing potent inhibitors to butyrylcholinesterases.
Murakawa, Takeru; Matsushita, Yuki; Suzuki, Tomoya; Khan, Mahmud Tareq Hassan; Kurita, Noriyuki
2014-11-01
Butyrylcholinesterase (BChE) exists mainly at neuromuscular junctions and plays an important role in the hydrolyzing mechanism of neurotransmitter acetylcholine. A variety of compounds have been produced in order to inhibit the function of BChE. We here investigate the specific interactions between BChE and some ligands (Kx) with large binding affinity to BChE, using ligand-docking, classical molecular mechanics and ab initio fragment molecular orbital (FMO) methods. The binding energies between BChE and Kx evaluated by the FMO method have a correlation with the 50% inhibition concentration obtained by the previous experiments. In addition, the FMO calculations highlight that Asp70, Trp82 and Tyr128 residues of BChE contribute significantly to the binding between BChE and Kx. Based on the results, we propose some novel ligands and elucidate that one of the proposed ligands can bind strongly to BChE. The present results are useful for developing potent inhibitors to BChE. PMID:25259414
Ab-initio calculations for dilute magnetic semiconductors
Energy Technology Data Exchange (ETDEWEB)
Belhadji, Brahim
2008-03-03
This thesis focusses on ab-initio calculations for the electronic structure and the magnetic properties of dilute magnetic semiconductors (DMS). In particular we aim at the understanding of the complex exchange interactions in these systems. Our calculations are based on density functional theory, being ideally suited for a description of the material specific properties of the considered DMS. Moreover we use the KKR Green function method in connection with the coherent potential approximation (CPA), which allows to include the random substitutional disorder in a mean field-like approximation for the electronic structure. Finally we calculate the exchange coupling constants J{sub ij} between two impurities in a CPA medium by using the Lichtenstein formula and from this calculate the Curie temperature by a numerically exact Monte Carlo method. Based on this analysis we found and investigated four different exchange mechanisms being of importance in DMS systems: Double exchange, p-d exchange, antiferromagnetic superexchanges, and ferromagnetic superexchange. A second topic we have investigated in this thesis is the pressure dependence of the exchange interactions and the Curie temperatures in (Ga,Mn)As and (In,Mn)As, using the LDA and the LDA+U approximations. Exact calculations of T{sub C} by Monte Carlo simulations show a somehow different behavior. (orig.)
Thermal, spectroscopic, and ab initio structural characterization of carprofen polymorphs.
Bruni, Giovanna; Gozzo, Fabia; Capsoni, Doretta; Bini, Marcella; Macchi, Piero; Simoncic, Petra; Berbenni, Vittorio; Milanese, Chiara; Girella, Alessandro; Ferrari, Stefania; Marini, Amedeo
2011-06-01
Commercial and recrystallized polycrystalline samples of carprofen, a nonsteroidal anti-inflammatory drug, were studied by thermal, spectroscopic, and structural techniques. Our investigations demonstrated that recrystallized sample, stable at room temperature (RT), is a single polymorphic form of carprofen (polymorph I) that undergoes an isostructural polymorphic transformation by heating (polymorph II). Polymorph II remains then metastable at ambient conditions. Commercial sample is instead a mixture of polymorphs I and II. The thermodynamic relationships between the two polymorphs were determined through the construction of an energy/temperature diagram. The ab initio structural determination performed on synchrotron X-Ray powder diffraction patterns recorded at RT on both polymorphs allowed us to elucidate, for the first time, their crystal structure. Both crystallize in the monoclinic space group type P2(1) /c, and the unit cell similarity index and the volumetric isostructurality index indicate that the temperature-induced polymorphic transformation I ? II is isostructural. Polymorphs I and II are conformational polymorphs, sharing a very similar hydrogen bond network, but with different conformation of the propanoic skeleton, which produces two different packing. The small conformational change agrees with the low value of transition enthalpy obtained by differential scanning calorimetry measurements and the small internal energy computed with density functional methods. PMID:21246561
Ab initio studies of the conformations of hydrogen peroxide
International Nuclear Information System (INIS)
The Hamiltonian for hindered C2-rotation in molecules H2O2, H DO2, D2O2, H18O16OH, D18O16OH, D18O18OH and D218O2, consisting of the 6-dimensional potential energy surface and tunneling coordinate dependent operator of kinetic energy is reconstructed using iso-dynamic symmetry group consideration and ab initio quantum-chemical data on the equilibrium geometry, eigenfrequencies and eigenvectors of normal vibrations in the ground and two nonequivalent (cis and trans) transition states. Fourier expansion of torsional 1D potential contains five harmonics, two harmonics are held in the kinetic matrix, while the potential gated and squeezed couplings are characterized by four and two harmonic terms, respectively. This multi-parameter Hamiltonian reproduces the internal motion in the wide energy region up to the cis-barrier height. The perturbative instanton approach is generalized for the excited states, whose energy exceeds the trans-barrier height. Tunneling splitting in the ground and lowest excited states of all vibrations are evaluated from solution of semiclassical dynamical problem in the satisfactory agreement with available experimental data. The strong kinematic coupling between torsion and bending is shown to results in the vibrationally assisted tunneling and manifests itself in the transverse quantum number dependence of tunneling splittings. The mode specific isotope effect are predicted. Coupling between internal and overall rotations of molecule of symmetric top type is treated perturbatively (author)
Ab initio molecular dynamics calculations of ion hydration free energies
Leung, Kevin; von Lilienfeld, Anatole O; 10.1063/1.3137054
2010-01-01
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...
Ab initio molecular orbital calculations on alpha-quartz
International Nuclear Information System (INIS)
The calculation of properties of solids using SCF MO theory has been generally recognized as being difficult, because of the large numbers of atoms which are required to produce a credible representation of the system. Using the extremely powerful lCAP1 and lCAP2 parallel systems at IBM Kingston, it was possible to perform a large number of ab initio calculations, using a 3-21G basis, on an Si5016 12- model 'molecule' surrounded by 956 point ions to simulate the alpha-quartz lattice. Calculations were carried out to investigate the effect of altering the charge on the point ions - which were positioned at the lattice sites determined using X-ray diffraction, and accurately reproduced the electrostatic fields of alpha-quartz in the SCF MO treated region. The effect of truncating the Si5016 'molecule' with hydrogen atoms was also investigated. Once an optimum cluster had been determined, a series of calculations to investigate the geometry and defect binding energies of radiation induced defects in quartz were carried out. The results of these calculations show general agreement with experimental results and previous theoretical investigation of radiation damage in alpha-quartz
PSI3: an open-source Ab Initio electronic structure package.
Crawford, T Daniel; Sherrill, C David; Valeev, Edward F; Fermann, Justin T; King, Rollin A; Leininger, Matthew L; Brown, Shawn T; Janssen, Curtis L; Seidl, Edward T; Kenny, Joseph P; Allen, Wesley D
2007-07-15
PSI3 is a program system and development platform for ab initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input, accessing commonly used data such as basis-set information or molecular orbital coefficients, and retrieving and storing binary data (with no software limitations on file sizes or file-system-sizes), especially multi-index quantities such as electron repulsion integrals. This platform is useful for the rapid implementation of both standard quantum chemical methods, as well as the development of new models. Features that have already been implemented include Hartree-Fock, multiconfigurational self-consistent-field, second-order Møller-Plesset perturbation theory, coupled cluster, and configuration interaction wave functions. Distinctive capabilities include the ability to employ Gaussian basis functions with arbitrary angular momentum levels; linear R12 second-order perturbation theory; coupled cluster frequency-dependent response properties, including dipole polarizabilities and optical rotation; and diagonal Born-Oppenheimer corrections with correlated wave functions. This article describes the programming infrastructure and main features of the package. PSI3 is available free of charge through the open-source, GNU General Public License. PMID:17420978
Symplectic ab initio no-core shell model
Scientific Electronic Library Online (English)
J.P., Draayer; T., Dytrych; K.D., Sviratcheva; C, Bahri; J.P., Vary.
2008-12-01
Full Text Available 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.
Ab initio investigations of zinc chalcogenides semiconductor alloys
International Nuclear Information System (INIS)
The present work performs self-consistent ab initio full potential-linearized augmented plane wave method to study the structural, electronic and thermodynamic properties of ZnSxSe1-x, ZnSxTe1-x and ZnSexTe1-x semiconductor alloys. The ground-state properties were determined for the bulk materials (ZnS, ZnSe, and ZnTe) and for their alloys in cubic phase at various concentrations (x=0.25, 0.5 and 0.75). A marginal deviation of the lattice parameter from Vegard's law was observed for ZnSxSe1-x and ZnSexTe1-x alloys, while the lattice bowing of ZnSxTe1-x alloy was found to be significant. This is mainly because of the large mismatch of the lattice parameters of the binary compounds ZnS and ZnTe. A large deviation of the bulk modulus from linear concentration dependence was observed for all the three alloys. We have also investigated the effect of composition on bonding properties and correlated it to the charge-exchange effect in the optical bowing. Using the approach of Zunger et al. [21], the microscopic origins of the gap bowing were explained. The disorder parameter (gap bowing) for the alloys of interest was found to be mainly caused by the structural relaxation contributions. The charge-exchange contributions for all the three alloys were also found to be significant. The calculated phase diagram showed a broad miscibility gap for allram showed a broad miscibility gap for all the alloys of interest with a high critical temperature
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)
An ab initio study of plutonium oxides surfaces; Etude ab initio des surfaces d'oxydes de Pu
Energy Technology Data Exchange (ETDEWEB)
Jomard, G.; Bottin, F.; Amadon, B
2007-07-01
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)
Ab initio and DFT studies of the vibrational spectra of benzofuran and some of its derivatives
Singh, V. B.
2006-12-01
The vibrational spectra of benzofuran and some of its derivatives have been systematically investigated by ab initio and density functional B3LYP methods. The harmonic vibrational wavenumbers and intensity of vibrational bands were calculated at ab initio and DFT levels invoking different basis sets up to 6-311++g**. Vibrational assignments have been made and it has been found that the calculated DFT frequencies agree well in most cases with the observed frequencies for each molecule. Conformational studies have also been carried out and it is evident from ab initio calculations that 2(3H) benzofuranone is more stable than 3(2H) benzofuranone in support to our earlier semiempirical results.
Energy Technology Data Exchange (ETDEWEB)
Keegan, Ronan M. [STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); Bibby, Jaclyn; Thomas, Jens [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Xu, Dong [Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037 (United States); Zhang, Yang [University of Michigan, Ann Arbor, MI 48109 (United States); Mayans, Olga [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Winn, Martyn D. [Science and Technology Facilities Council Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Rigden, Daniel J., E-mail: drigden@liv.ac.uk [University of Liverpool, Liverpool L69 7ZB (United Kingdom); STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom)
2015-02-01
Two ab initio modelling programs solve complementary sets of targets, enhancing the success of AMPLE with small proteins. AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.
Ab initio calculation of molecular energies including parity violating interactions
International Nuclear Information System (INIS)
A new approach, RHF-CIS, based on the perturbation of the ground state RHF wave function by the CIS excitations, has been implemented for evaluation of energy of parity violating interaction in molecules, Epv. The earlier approach, RHF-SDE, was based on the perturbation of the RHF ground states by the single-determinant ''excitations'' (SDE). The results obtained show the dramatic difference between Epv values in the RHF-CIS framework and those in the RHF-SDE framework: the Epv values of the RHF-CIS formalism are more than one order of magnitude greater compared to the RHF-SDE formalism as well as the corresponding tensor components. The maximal total value obtained for hydrogen peroxide in the RHF-CIS framework is 3.661 X 10-19 EH (DZ** basis set) while the maximal Epv value for the RHF-SDE formalism is just 3.635 X 10-20 EH (TZ basis set). It is remarkable that both in the RFH-CIS and in the RHF-SDE approaches the diagonal tensor components of Epv strictly follow the geometry of a molecule and are always different from zero at chiral conformations. The zeros of the total Epv at chiral geometries are now found to be the results of the interplay between the diagonal tensor components values. We have carried out exhaustive analysis of the RHF-SDE formalism and found that it is not sufficiently accurate for studies of Epv. To this end, we hudies 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
International Nuclear Information System (INIS)
The ab initio/classical free energy perturbation (ABC-FEP) method proposed previously by Wood et al. [J. Chem. Phys. 110, 1329 (1999)] uses classical simulations to calculate solvation free energies within an empirical potential model, then applies free energy perturbation theory to determine the effect of changing the empirical solute-solvent interactions to corresponding interactions calculated from ab initio methods. This approach allows accurate calculation of solvation free energies using an atomistic description of the solvent and solute, with interactions calculated from first principles. Results can be obtained at a feasible computational cost without making use of approximations such as a continuum solvent or an empirical cavity formation energy. As such, the method can be used far from ambient conditions, where the empirical parameters needed for approximate theories of solvation may not be available. The sources of error in the ABC-FEP method are the approximations in the ab initio method, the finite sample of configurations, and the classical solvent model. This article explores the accuracy of various approximations used in the ABC-FEP method by comparing to the experimentally well-known free energy of hydration of water at two state points (ambient conditions, and 973.15 K and 600 kg/m3). The TIP4P-FQ model [J. Chem. Phys. 101, 6141 (1994)] is found to be a reliable solvent model for use with this method, even at supercritical conditions. Results depend supercritical conditions. Results depend strongly on the ab initio method used: a gradient-corrected density functional theory is not adequate, but a localized MP2 method yields excellent agreement with experiment. Computational costs are reduced by using a cluster approximation, in which ab initio pair interaction energies are calculated between the solute and up to 60 solvent molecules, while multi-body interactions are calculated with only a small cluster (5 to 12 solvent molecules). Sampling errors for the ab initio contribution to solvation free energies are ±2 kJ/mol or less when 50-200 configurations are used. Using the largest clusters and most accurate ab initio methods, ABC-FEP predicts hydration free energies of water at both state points that agree with equations of state, within the sampling error. These results are the first calculation of a free energy of solvation at extreme conditions from a fully atomistic model with ab initio methods. (c) 2000 American Institute of Physics
Estudo da geometria da uréia por métodos ab initio e simulação computacional de líquidos
Directory of Open Access Journals (Sweden)
Cirino José Jair Vianna
2002-01-01
Full Text Available A study was carried out on the urea geometries using ab initio calculation and Monte Carlo computational simulation of liquids. The ab initio calculated results showed that urea has a non-planar conformation in the gas phase in which the hydrogen atoms are out of the plane formed by the heavy atoms. Free energies associated to the rotation of the amino groups of urea in water were obtained using the Monte Carlo method in which the thermodynamic perturbation theory is implemented. The magnitude of the free energy obtained from this simulation did not permit us to conclude that urea is non-planar in water.
Accurate ab initio quartic force fields for borane and BeH 2
Martin, J. M. L.; Lee, Timothy J.
1992-12-01
The quartic force fields of BH 3 and BeH 2 have been computed ab initio using an augmented coupled cluster (CCSD/T)) method and basis sets of spdf and spdfg quality. For BH 3, the computed spectroscopic constants are in very good agreement with recent experimental data, and definitely confirm misassignments in some older work, in agreement with recent ab initio studies. Using the computed spectroscopic constants, the rovibrational partition function for both molecules has been constructed using a modified direct numerical summation algorithm, and JANAF-style thermochemical tables are presented.
Ab initio potential energy surfaces for NH-NH with analytical long range
Janssen, Liesbeth M. C.; Groenenboom, Gerrit C.; van der Avoird, Ad; ?uchowski, Piotr. S.; Podeszwa, Rafal
2009-01-01
We present four-dimensional ab initio potential energy surfaces for the three spin states of the NH-NH complex. The potentials are partially based on the work of Dhont et al. [J. Chem. Phys. 123, 184302 (2005)]. The surface for the quintet state is obtained at the RCCSD(T)/aug-cc-pVTZ level of theory and the energy diferences with the singlet and triplet states are calculated at the CASPTn/aug-cc-pVTZ (n = 2; 3) level of theory. The ab initio potentials are fitted to coupled...
Ab initio Defect Energetics in LaBO3 Perovskite Solid Oxide Fuel Cell Materials
DEFF Research Database (Denmark)
Lee, Yueh-Lin; Morgan, Dane
2009-01-01
Perovskite materials of the form ABO3 are a promising family of compounds for use in solid oxide fuel cell (SOFC) cathodes. Study of the physics of these compounds under SOFC conditions with ab initio methods is particularly challenging due to high temperatures, exchange of oxygen with O2 gas, and correlated electron effects. This paper discusses an approach to performing ab initio studies on these materials for SOFC applications and applies the approach to calculate vacancy formation energies in LaBO3 (B = Mn, Fe, Co, Ni) compounds.
Keegan, Ronan M; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D; Rigden, Daniel J
2015-02-01
AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5?min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected. PMID:25664744
Ab initio calculations of 14N and 15N hyperfine structures
Jönsson, Per; Carette, T.; Nemouchi, Messaoud; Godefroid, Michel
2010-01-01
Abstract Hyperfine structure parameters are calculated for the 2p 2 (3 P)3s 4 P J, 2p 2 (3 P)3p 4 P o J and 2p 2 (3 P)3p 4 D o 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. [ 1 ] deduced from the analysis of the near-infrared Doppler-free saturated absorption spectra. Ab initio calculations of 14 N and 15 N hyperfine structures...
Oxidation pathways in Phosphorene: an ab-initio investigation
Paes Lima, Matheus Paes; Fazzio, Adalberto; da Silva, Antonio Jose Roque
2015-03-01
Phosphorene is a recently isolated single layer of Black Phosphorus. In this 2D material, the combination of a direct band gap with a high charge carrier mobility opens up the possibility of its use in nano devices. However, the exposure of Black Phosphorus to air leads to its fast degradation, which indicates the relevance to understand its oxidation processes. In the present work we investigate the initial steps of the oxidation process, focusing on the interaction of a single O2 molecule with the phosphorene layer. We show the existence of oxidation pathways having only a single barrier of 0.13eV occurring between the free O2 (triplet) and the triplet-singlet potential energy surface (PES) crossing point. We estimate a room temperature triplet-singlet transition probability of Pt --> s = 0 . 015 , using the Landau-Zener model. Once the O2 switches to the singlet PES, there is an oxygen incorporation with an energy gain of 4.2eV with respect to the PES crossing point, with the O2 molecule spontaneously dissociating without any barrier. In this process, the final geometry has one O bonded to a P lone pair, and the other located between two P atoms. Our investigations were performed with DFT calculations at the GGA level as implemented in the VASP code.
Energy Technology Data Exchange (ETDEWEB)
Ganster, P
2004-10-15
A calcium aluminosilicate glass of molar composition 67 % SiO{sub 2} - 12 % Al{sub 2}O{sub 3} - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminium atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)
Pototschnig, Johann V.; Krois, Günter; Lackner, Florian; Ernst, Wolfgang E.
2014-06-01
Recently interest in polar diatomic molecules with a magnetic dipole moment has been growing. An example for such molecules is the combination of an alkali metal atom and an alkaline earth metal atom. These systems are quite small, containing only three valence electrons. Nevertheless calculations of excited states are challenging. Ab initio calculations for two sample systems, LiCa and RbSr, will be presented. The potential energy curves and transition dipole moments for the ground state and several excited states were determined, up to 25000 wn for LiCa and up to 22000 wn for RbSr. Multireference configuration interaction calculations (MRCI) based on complete active space self-consistent field wave functions (CASSCF) were used to determine the properties of the system as implemented in the MOLPRO software package. Effective core potentials (ECPs) and core polarization potentials (CCPs) were applied to reduce the computational effort, while retaining accuracy. The similarities and differences of the two systems will be discussed. In both systems the accurate description of the asymptotic values of the PECs corresponding to atomic D-states proved to be difficult. The results will be compared to recent experiments, showing that a combination of theory and experiment gives a reliable description of the systems. G. Krois, J.V. Pototschnig, F. Lackner and W.E. Ernst, J. Phys. Chem. A, 117, 13719-13731 (2013) H.-J. Werner and P. J. Knowles and G. Knizia and F. R. Manby and M. {Schütz} et al., MOLPRO, version 2010.1, see http://www.molpro.net/
Ab Initio Inverstagation of the Excited States of Nucleobases and Nucleosides
Szalay, Péter G.; Fogarasi, Géza; Watson, Thomas; Perera, Ajith; Lotrich, Victor; Bartlett, Rod J.
2011-06-01
Most living bodies are exposed to sunlight, essential life sustaining processes are using this natural radiation. Sunlight has, however, several components (has a broad "spectrum") and in particular the invisible component (UV, ultraviolet) is harmful for living organisms. Scientists around the word are busy to understand what happens in the cell when it is exposed to light: it seems that the building blocks of cells and in particular those carrying the genetic information (DNA and RNA) are highly protected against this exposition. Our research focuses on the spectral properties of the building blocks of DNA and RNA, the so called nucleobases and nucleosides, in order to understand this mechanism. Due to improvement in computer technology both at hardware and software side we are now able to use the most accurate methods of ab initio quantum chemistry to investigate the spectroscopic properties of these building blocks. These calculations provide direct information on the properties of these molecules but also provide important benchmarks for cheaper methods which can be used for even larger systems. We have calculated the excited state properties for the nucleobases (cytosine, guanine and adenine), their complexes with water and with each other (Watson-Crick base pairs and stacks) as well as corresponding nucleosides at the EOM-CCSD(T)/aug-cc-pVDZ level of theory and try to answer the following questions: (1) how the order of excited states varies in different nucleobases; (2) how hydration influences the excitation energy and order of excited states; (3) is there any effect of the sugar substituent; (4) how do close lying other bases change the spectrum. The calculations involve over hundred correlated electrons and up to thousand basis functions. Such calculations are now routinely available with the recently developed ACESIII code and can make use of hundreds or even several thousand of processors. V. Lotrich, N. Flocke, M. Ponton, A. Yau, A. Perera, E. Deumens, R. J. Bartlett, J. Chem. Phys, 2008, 128, 194104.
Czech Academy of Sciences Publication Activity Database
Dra?ínský, Martin; Möller, H. M.; Exner, T. E.
2013-01-01
Ro?. 9, ?. 8 (2013), s. 3806-3815. ISSN 1549-9618 R&D Projects: GA ?R GA13-24880S Institutional support: RVO:61388963 Keywords : ab initio molecular dynamics * NMR spectroscopy * DFT calculations * hydration Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.310, year: 2013
Ab-initio modeling of ultrafast demagnetization after laser irradiation in nickel, iron and cobalt
Illg, Christian Michael
2013-01-01
Diese Arbeit beschäftigt sich mit der ultraschnellen Entmagnetisierung innerhalb weniger hundert Femtosekunden nach Laserpulsbestrahlung in Nickel, Eisen und kubisch-flächenzentriertem (fcc) Kobalt. Es wird mit Hilfe der ab-initio Dichtefunktionaltheorie und physikalischer Modellierung untersucht, ob die Elektron-Phonon-Spin-Flip-Streuung als zu Grunde liegender Mechanismus für die ultraschnelle Entmagnetisierung in Frage kommt.
Mechanical properties of carbynes investigated by ab initio total-energy calculations
DEFF Research Database (Denmark)
Castelli, Ivano E.; Salvestrini, Paolo
2012-01-01
As sp carbon chains (carbynes) are relatively rigid molecular objects, can we exploit them as construction elements in nanomechanics? To answer this question, we investigate their remarkable mechanical properties by ab initio total-energy simulations. In particular, we evaluate their linear response to small longitudinal and bending deformations and their failure limits for longitudinal compression and elongation.
Czech Academy of Sciences Publication Activity Database
Sandlöbes, S.; Pei, Z.; Friák, Martin; Zhu, L.-F.; Wang, F.; Zaefferer, S.; Raabe, D.; Neugebauer, J.
2014-01-01
Ro?. 70, MAY (2014), s. 92-104. ISSN 1359-6454 Grant ostatní: GA MŠk(CZ) LM2010005 Institutional support: RVO:68081723 Keywords : Magnesium * Rare-earth elements * Ductility * Modeling * Ab initio Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.940, year: 2013
Dispersion Interactions between Rare Gas Atoms: Testing the London Equation Using ab Initio Methods
Halpern, Arthur M.
2011-01-01
A computational chemistry experiment is described in which students can use advanced ab initio quantum mechanical methods to test the ability of the London equation to account quantitatively for the attractive (dispersion) interactions between rare gas atoms. Using readily available electronic structure applications, students can calculate the…
An accurate, global, ab initio potential energy surface for the H+3 molecule
Polyansky, Oleg L.; Prosmiti, Rita; Klopper, Wim; Tennyson, Jonathan
A new global, ground-state, Born-Oppenheimer surface is presented for the H+3 system. The energy switching approach has been used to combine different functional forms for three different regimes: a spectroscopic expansion at low energy, a Sorbie-Murrell function at high energy and known long-range terms combined with accurate diatomic potentials at large separations. At low energies we have used the ultra high accuracy ab initio data of Cencek et al. (1998, J. chem. Phys., 108, 2831). At intermediate energy we have calculated 134 new ab initio energies using a high accuracy, explicitly correlated procedure. The ab initio data of Schinke et al. (1980, J. chem. Phys., 72, 3909) has been used to constrain the high energy region. Two fits are presented which differ somewhat in their behaviour at energies over 45000cm-1 above the H+3 minimum. Below this energy, the fits reproduce each set of ab initio data close to their intrinsic accuracy. The ground state surface should provide a suitable starting point for renewed studies of the near-threshold photodissociation spectrum originally reported by Carrington et al. (1982, Molec. Phys., 45, 753).
Stabilization of Ab Initio Molecular Dynamics Simulations at Large Time Steps
Tsuchida, Eiji
2014-01-01
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.
Ab initio prediction of vacancy properties in concentrated alloys: The case of fcc Cu-Ni
Zhang, Xi; Sluiter, Marcel H. F.
2015-05-01
Vacancy properties in concentrated alloys continue to be of great interest because nowadays ab initio supercell simulations reach a scale where even defect properties in disordered alloys appear to be within reach. We show that vacancy properties cannot generally be extracted from supercell total energies in a consistent manner without a statistical model. Essential features of such a model are knowledge of the chemical potential and imposition of invariants. In the present work, we derive the simplest model that satisfies these requirements and we compare it with models in the literature. As illustration we compute ab initio vacancy properties of fcc Cu-Ni alloys as a function of composition and temperature. Ab initio density functional calculations were performed for SQS supercells at various compositions with and without vacancies. Various methods of extracting alloy vacancy properties were examined. A ternary cluster expansion yielded effective cluster interactions (ECIs) for the Cu-Ni-Vac system. Composition and temperature dependent alloy vacancy concentrations were obtained using statistical thermodynamic models with the ab initio ECIs. An Arrhenius analysis showed that the heat of vacancy formation was well represented by a linear function of temperature. The positive slope of the temperature dependence implies a negative configurational entropy contribution to the vacancy formation free energy in the alloy. These findings can be understood by considering local coordination effects.
Ab initio study of C14 Laves phases in Fe-based systems.
Czech Academy of Sciences Publication Activity Database
Pavl?, Jana; Šob, Mojmír
2012-01-01
Ro?. 48, ?. 3 (2012), s. 395-401. ISSN 1450-5339 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081723 Keywords : ab initio calculations * C14 Laves phases * Lattice Stability Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.435, year: 2012
The onset of ion solvation by ab initio calculations: Comparison of water and methanol.
Czech Academy of Sciences Publication Activity Database
Pluha?ová, Eva; Jungwirth, Pavel
2008-01-01
Ro?. 73, 6/7 (2008), s. 733-744. ISSN 0010-0765 R&D Projects: GA MŠk LC512; GA ?R GA203/07/1006 Institutional research plan: CEZ:AV0Z40550506 Keywords : ions * water cluster * methanol * ab initio calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.784, year: 2008
Application of AB INITIO and CALPHAD thermodynamics to Mo-Ta-W alloys.
Czech Academy of Sciences Publication Activity Database
Turchi, P.E.A.; Drchal, Václav; Kudrnovský, Josef; Colinet, C.; Kaufman, L.; Liu, Z.-K.
2005-01-01
Ro?. 71, ?. 9 (2005), 094206/1-094206/14. ISSN 1098-0121 R&D Projects: GA AV ?R(CZ) IAA1010203 Institutional research plan: CEZ:AV0Z1010914 Keywords : AB INITIO * CALPHAD thermodynamics * Mo-Ta-W alloys Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.185, year: 2005
Modelling The Sigma Phase in the Mo-based Systems Using Ab Initio Electronic Structure Calculations.
Czech Academy of Sciences Publication Activity Database
Houserová, Jana; V?eš?ál, J.; Šob, Mojmír
Krakow, 2004. s. 75. [CALPHAD /33./. 30.05.2004-04.06.2004, Krakov] R&D Projects: GA ?R GP106/03/P002; GA ?R GA106/02/0877 Keywords : ab initio calculations * sigma phase * phase diagram Subject RIV: BM - Solid Matter Physics ; Magnetism
Unraveling the structure of the h-BN/Rh(111) nanomesh with ab initio calculations
International Nuclear Information System (INIS)
The properties of a single layer of h-BN on top of a Rh(111) surface are discussed in terms of an ab initio generated force field approach as well as by direct ab initio density-functional theory (DFT) calculations. A single-layer model for the h-BN/Rh(111) nanomesh, in contrast to a previously considered (incomplete) double-layer model of h-BN, can explain the experimental data. The main focus of this work is to compare a force field approach described earlier in (Laskowski et al 2007 Phys. Rev. Lett. 98 106802) with direct ab initio calculations. The calculated geometry of the h-BN layer is very similar to the structure predicted by the force field approach. The ab initio calculated density of states projected on N-px,y of BN corresponding to 'low' and 'high' regions with respect to the Rh surface shows a 1 eV splitting and thus explains the observed ?-band splitting. Moreover, we find good agreement between calculated and experimental scanning tunneling microscope (STM) images of this system
Ab initio molecular dynamics approach to a quantitative description of ion pairing in water.
Czech Academy of Sciences Publication Activity Database
Pluha?ová, Eva; Maršálek, Ond?ej; Schmidt, B.; Jungwirth, Pavel
2013-01-01
Ro?. 4, ?. 23 (2013), s. 4177-4181. ISSN 1948-7185 R&D Projects: GA ?R GBP208/12/G016 Institutional support: RVO:61388963 Keywords : ion pairing * charge transfer * water * ab initio molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.687, year: 2013
Vanduyfhuys, Louis; Vandenbrande, Steven; Verstraelen, Toon; Schmid, Rochus; Waroquier, Michel; Van Speybroeck, Veronique
2015-05-15
QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three-step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal-organic frameworks (MOFs), QuickFF is used to determine force fields for MIL-53(Al) and MOF-5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc. PMID:25740170
Energy Technology Data Exchange (ETDEWEB)
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
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)
Martin, G. B.; Kirtman, B.; Spera, F. J.
2010-12-01
Computational studies implementing Density Functional Theory (DFT) methods have become very popular in the Materials Sciences in recent years. DFT codes are now used routinely to simulate properties of geomaterials—mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only 100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it would be useful to be able to compute larger systems especially for extracting transport properties and coordination statistics. Previous studies have used codes such as VASP where CPU time increases as N2, making calculations on systems of more than 100 atoms computationally very taxing. SIESTA (Soler, et al. 2002) is a an order-N (linear-scaling) DFT code that enables electronic structure and MD computations on larger systems (N 1000) by making approximations such as localized numerical orbitals. Here we test the applicability of SIESTA to simulate geosilicates in the liquid and glass state. We have used SIESTA for MD simulations of liquid Mg2SiO4 at various state points pertinent to the Earth’s mantle and congruous with those calculated in a previous DFT study using the VASP code (DeKoker, et al. 2008). The core electronic wave functions of Mg, Si, and O were approximated using pseudopotentials with a core cutoff radius of 1.38, 1.0, and 0.61 Angstroms respectively. The Ceperly-Alder parameterization of the Local Density Approximation (LDA) was used as the exchange-correlation functional. Known systematic overbinding of LDA was corrected with the addition of a pressure term, P 1.6 GPa, which is the pressure calculated by SIESTA at the experimental zero-pressure volume of forsterite under static conditions (Stixrude and Lithgow-Bertollini 2005). Results are reported here that show SIESTA calculations of T and P on densities in the range of 2.7 - 5.0 g/cc of liquid Mg2SiO4 are similar to the VASP calculations of DeKoker et al. (2008), which used the same functional. This opens the possibility of conducting fast /emph{ab initio} MD simulations of geomaterials with a hundreds of atoms.
FREE ENERGIES OF CHEMICAL REACTIONS IN SOLUTION AND IN ENZYMES WITH AB INITIO QM/MM METHODS
Hu, Hao; Yang, Weitao
2008-01-01
Combined QM/MM methods provide an accurate and efficient energetic description of complex chemical and biological systems, leading to significant advances in the understanding of chemical reactions in solution and in enzymes. Progress in QM/MM methodology and application will be reviewed, with a focus on ab initio QM based approaches. Ab initio QM/MM methods capitalize on the accuracy and reliability of the associated quantum mechanical approaches, however at a much higher computational cost ...
Ab-initio statistical mechanics for ordering and segregation at the (110) surface of Ni90%-Al
Drautz, Ralf
2003-01-01
Synchrotron-Streuexperimente finden eine geordnete NiAl-Monolage als erste Oberflächenlage der (110) Oberfläche eines ungeordneten Ni90%-Al Kristalls. Das parameterfreie theoretische Verständnis der Oberflächensegregation und Oberflächenordnung an der (110) Oberfläche von Ni90%-Al ist das zentrale Thema dieser Arbeit. In der ersten Hälfte der Dissertation wird die zur ab-initio Modellierung einer Metalloberfläche benötigte "Ab-initio Statistische Mechanik" vorgestellt und entwicke...
Kamarulzaman Abdul Ghani; Mohammad Shiham Mahfuz; Abdul Jamir Md. Saad; Nik Mohd. Rahimi Nik Yusoff
2014-01-01
This study was aimed to investigate the relationship between Language Learning Strategies (LLS) and the level of proficiency of students in Arabic Ab Initio language. There were also several studies done to investigate the achievement of students and their frequent usage of these Language Learning Strategies. Meanwhile, the level of student proficiency was measured by their results based on college-level exam results before they were registered in the Arabic Ab Initio classes. 162 year 1 stud...
Ab-initio chemical potentials of solid and liquid solutions and the chemistry of the Earth's core
Alfe, D.; Gillan, M. J.; Price, G. D.
2001-01-01
A general set of methods is presented for calculating chemical potentials in solid and liquid mixtures using {\\em ab initio} techniques based on density functional theory (DFT). The methods are designed to give an {\\em ab initio} approach to treating chemical equilibrium between coexisting solid and liquid solutions, and particularly the partitioning ratio of solutes between such solutions. For the liquid phase, the methods are based on the general technique of thermodynamic...
Ab-initio molecular dynamics simulation of liquid water by Quantum Monte Carlo
Zen, Andrea; Mazzola, Guglielmo; Guidoni, Leonardo; Sorella, Sandro
2014-01-01
Despite liquid water is ubiquitous in chemical reactions at roots of life and climate on earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in excellent agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous Density Functional Theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab-initio simulations of complex chemical systems.
Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo
Zen, Andrea; Luo, Ye; Mazzola, Guglielmo; Guidoni, Leonardo; Sorella, Sandro
2015-04-01
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.
Ab-initio prediction and reliability of protein structural genomics by PROPAINOR algorithm.
Joshi, Rajani R; Jyothi, S
2003-07-01
We have formulated the ab-initio prediction of the 3D-structure of proteins as a probabilistic programming problem where the inter-residue 3D-distances are treated as random variables. Lower and upper bounds for these random variables and the corresponding probabilities are estimated by nonparametric statistical methods and knowledge-based heuristics. In this paper we focus on the probabilistic computation of the 3D-structure using these distance interval estimates. Validation of the predicted structures shows our method to be more accurate than other computational methods reported so far. Our method is also found to be computationally more efficient than other existing ab-initio structure prediction methods. Moreover, we provide a reliability index for the predicted structures too. Because of its computational simplicity and its applicability to any random sequence, our algorithm called PROPAINOR (PROtein structure Prediction by AI an Nonparametric Regression) has significant scope in computational protein structural genomics. PMID:12927100
Bridging a gap between continuum-QCD and ab initio predictions of hadron observables
Binosi, Daniele; Papavassiliou, Joannis; Roberts, Craig D
2014-01-01
Within contemporary hadron physics there are two common methods for determining the momentum-dependence of the interaction between quarks: the top-down approach, which works toward an ab initio computation of the interaction via direct analysis of the gauge-sector gap equations; and the bottom-up scheme, which aims to infer the interaction by fitting data within a well-defined truncation of those equations in the matter sector that are relevant to bound-state properties. We unite these two approaches by demonstrating that the renormalisation-group-invariant running-interaction predicted by contemporary analyses of QCD's gauge sector coincides with that required in order to describe ground-state hadron observables using a nonperturbative truncation of QCD's Dyson-Schwinger equations in the matter sector. This bridges a gap that had lain between nonperturbative continuum-QCD and the ab initio prediction of bound-state properties.
Bridging a gap between continuum-QCD and ab initio predictions of hadron observables
Binosi, Daniele; Chang, Lei; Papavassiliou, Joannis; Roberts, Craig D.
2015-03-01
Within contemporary hadron physics there are two common methods for determining the momentum-dependence of the interaction between quarks: the top-down approach, which works toward an ab initio computation of the interaction via direct analysis of the gauge-sector gap equations; and the bottom-up scheme, which aims to infer the interaction by fitting data within a well-defined truncation of those equations in the matter sector that are relevant to bound-state properties. We unite these two approaches by demonstrating that the renormalisation-group-invariant running-interaction predicted by contemporary analyses of QCD's gauge sector coincides with that required in order to describe ground-state hadron observables using a nonperturbative truncation of QCD's Dyson-Schwinger equations in the matter sector. This bridges a gap that had lain between nonperturbative continuum-QCD and the ab initio prediction of bound-state properties.
Bridging a gap between continuum-QCD and ab initio predictions of hadron observables
Directory of Open Access Journals (Sweden)
Daniele Binosi
2015-03-01
Full Text Available Within contemporary hadron physics there are two common methods for determining the momentum-dependence of the interaction between quarks: the top-down approach, which works toward an ab initio computation of the interaction via direct analysis of the gauge-sector gap equations; and the bottom-up scheme, which aims to infer the interaction by fitting data within a well-defined truncation of those equations in the matter sector that are relevant to bound-state properties. We unite these two approaches by demonstrating that the renormalisation-group-invariant running-interaction predicted by contemporary analyses of QCD's gauge sector coincides with that required in order to describe ground-state hadron observables using a nonperturbative truncation of QCD's Dyson–Schwinger equations in the matter sector. This bridges a gap that had lain between nonperturbative continuum-QCD and the ab initio prediction of bound-state properties.
Spin-orbit ab initio investigation of the photolysis of o-, m-, and p-bromotoluene
International Nuclear Information System (INIS)
The photodissociations of o-, m-, and p-bromotoluene were investigated by ab initio and spin-orbit ab initio calculations. The possible photodissociation mechanisms at 266 and 193 nm were clarified by multistate second order multiconfigurational perturbation theory (MS-CASPT2) calculated potential energy curves, vertical excitation energies, and oscillator strengths of low-lying states. The dissociation products with spin-orbit-coupled states of Br*(2P1/2) and Br(2P3/2) were identified by the MS-CASPT2 method in conjunction with spin-orbit interaction through complete active space state interaction (MS-CASPT2/CASSI-SO) calculations. The effects of methyl rotation and substituent on the photodissociation mechanism were discussed
Ab initio NMR Confirmed Evolutionary Structure Prediction for Organic Molecular Crystals
Pham, Cong-Huy; Kucukbenli, Emine; de Gironcoli, Stefano
2015-03-01
Ab initio crystal structure prediction of even small organic compounds is extremely challenging due to polymorphism, molecular flexibility and difficulties in addressing the dispersion interaction from first principles. We recently implemented vdW-aware density functionals and demonstrated their success in energy ordering of aminoacid crystals. In this work we combine this development with the evolutionary structure prediction method to study cholesterol polymorphs. Cholesterol crystals have paramount importance in various diseases, from cancer to atherosclerosis. The structure of some polymorphs (e.g. ChM, ChAl, ChAh) have already been resolved while some others, which display distinct NMR spectra and are involved in disease formation, are yet to be determined. Here we thoroughly assess the applicability of evolutionary structure prediction to address such real world problems. We validate the newly predicted structures with ab initio NMR chemical shift data using secondary referencing for an improved comparison with experiments.
Ab Initio Calculations of Even Oxygen Isotopes with Chiral Two- Plus Three-Nucleon Interactions
Hergert, H; Calci, A; Langhammer, J; Roth, R
2013-01-01
We formulate the In-Medium Similarity Renormalization Group (IM-SRG) for open-shell nuclei using a multi-reference formalism based on a generalized Wick theorem introduced in quantum chemistry. The resulting multi-reference IM-SRG (MR-IM-SRG) is used to perform the first ab initio study of even oxygen isotopes with chiral NN and 3N Hamiltonians, from the proton to the neutron drip lines. We obtain an excellent reproduction of experimental ground-state energies with quantified uncertainties, which is validated by results from the Importance-Truncated No-Core Shell Model and the Coupled Cluster method. The agreement between conceptually different many-body approaches and experiment highlights the predictive power of current chiral two- and three-nucleon interactions, and establishes the MR-IM-SRG as a promising new tool for ab initio calculations of medium-mass nuclei far from shell closures.
Ab Initio Calculations of Even Oxygen Isotopes with Chiral Two-Plus-Three-Nucleon Interactions
Hergert, H.; Binder, S.; Calci, A.; Langhammer, J.; Roth, R.
2013-06-01
We formulate the in-medium similarity renormalization group (IM-SRG) for open-shell nuclei using a multireference formalism based on a generalized Wick theorem introduced in quantum chemistry. The resulting multireference IM-SRG (MR-IM-SRG) is used to perform the first ab initio study of all even oxygen isotopes with chiral nucleon-nucleon and three-nucleon interactions, from the proton to the neutron drip lines. We obtain an excellent reproduction of experimental ground-state energies with quantified uncertainties, which is validated by results from the importance-truncated no-core shell model and the coupled cluster method. The agreement between conceptually different many-body approaches and experiment highlights the predictive power of current chiral two- and three-nucleon interactions, and establishes the MR-IM-SRG as a promising new tool for ab initio calculations of medium-mass nuclei far from shell closures.
Microscopic dynamics in liquid binary alloys: orbital-free ab-initio molecular dynamics studies
Directory of Open Access Journals (Sweden)
D.J.González
2008-03-01
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.
Ab Initio No-Core Shell Model Calculations Using Realistic Two- and Three-Body Interactions
Energy Technology Data Exchange (ETDEWEB)
Navratil, P; Ormand, W E; Forssen, C; Caurier, E
2004-11-30
There has been significant progress in the ab initio approaches to the structure of light nuclei. One such method is the ab initio no-core shell model (NCSM). Starting from realistic two- and three-nucleon interactions this method can predict low-lying levels in p-shell nuclei. In this contribution, we present a brief overview of the NCSM with examples of recent applications. We highlight our study of the parity inversion in {sup 11}Be, for which calculations were performed in basis spaces up to 9{Dirac_h}{Omega} (dimensions reaching 7 x 10{sup 8}). We also present our latest results for the p-shell nuclei using the Tucson-Melbourne TM three-nucleon interaction with several proposed parameter sets.
Ab initio studies of equations of state and chemical reactions of reactive structural materials
Zaharieva, Roussislava
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
Optimized Unrestricted Kohn-Sham Potentials from Ab Initio Spin Densities
Boguslawski, Katharina; Reiher, Markus
2012-01-01
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...
Comparison between classical potentials and ab initio methods for silicon under large shear
International Nuclear Information System (INIS)
The homogeneous shear of the {111} planes along the [110] direction of bulk silicon has been investigated using ab initio techniques, to better understand the strain properties of both shuffle and glide set planes. Similar calculations have been done with three empirical potentials, Stillinger-Weber, Tersoff and EDIP, in order to find the one giving the best results under large shear strains. The generalized stacking fault energies have also been calculated with these potentials to complement this study. It turns out that the Stillinger-Weber potential better reproduces the ab initio results, for the smoothness and the amplitude of the energy variation as well as the localization of shear in the shuffle set
Ab initio simulations and neutron scattering studies of structure and dynamics in PdH
Totolici, I E
2001-01-01
The work presented in this PhD thesis is concerned with the interpretation of the neutron scattering measurements from the palladium hydrogen system by means of ab initio electronic structure calculations. The motivation of performing such calculations was due to recent neutron scattering studies on this system that showed a strong directional dependence to the dynamical structure factor together with a complex dependence on energy. Here we attempt to describe the origin of these features by ab initio simulations of the dynamical structure factor. The method assumes an adiabatic separation of the motion of the proton and palladium atoms. The proton wave functions are calculated by a direct solution of the associated single-particle Schroedinger equation using a plane wave basis set method and a mapping of the adiabatic surface. The Fourier components of the adiabatic potential are obtained from LDA pseudopotential calculations. Using Fermi's golden rule within the Born approximation we were then able to calcu...
Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo.
Zen, Andrea; Luo, Ye; Mazzola, Guglielmo; Guidoni, Leonardo; Sorella, Sandro
2015-04-14
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems. PMID:25877566
Driving nuclei with resonant electrons: Ab initio study of (e+H2) 2?u+
International Nuclear Information System (INIS)
We have calculated the cross sections for vibrational excitation and dissociative attachment in H2 below 5 eV scattering energy. This completely ab initio calculation uses the frame-transformation method of Greene and Jungen [Adv. At. Mol. Phys. 21, 51 (1985)] for electron-vibronic coupling in resonant scattering from a neutral molecule. We found it necessary to modify their method to obtain good agreement with previous theory and experiment for v=0?vf with vf=1--3; for larger vf and for dissociative attachment we obtained good agreement with previous theory and qualitative agreement with experiment. The fixed-nuclei phase shifts were derived from a fully ab initio calculation in prolate spheroidal coordinates and then transformed to spherical l=1 phase shifts. The vibrational structure of H2- becomes evident for excitation from higher vibrational states of H2 as well as for larger ?v's, confirming previous theory and experiment
Ab initio parameterisation of the 14 band k·p Hamiltonian: Zincblende study
Lundie, Mark; Tomi?, Stanko
2014-06-01
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.
Implementation of ab initio multiple spawning in the MOLPRO quantum chemistry package
International Nuclear Information System (INIS)
The ab initio multiple spawning (AIMS) method has been developed to solve the electronic and nuclear Schrodinger equations simultaneously for application to photochemical reaction dynamics. We discuss some details of the implementation of AIMS in the MOLPRO program package. A few aspects of the implementation are highlighted, including a new multiple timescale integrator and a scheme for solving the coupled-perturbed multiconfiguration self-consistent field (CP-MCSCF) equations in the context of ab initio molecular dynamics. The implementation is very efficient and we demonstrate calculations on the photoisomerization of ethylene using more than 5000 trajectory basis functions. We have included the capability for hybrid quantum mechanics/molecular mechanics (QM/MM) simulations within AIMS, and we investigate the role of an argon solvent in the photoisomerization of ethylene. Somewhat surprisingly, the surrounding argon has little effect on the timescale of non-adiabatic quenching in ethylene
Ab initio potential energy surfaces for NH-NH with analytical long range
Janssen, Liesbeth M C; van der Avoird, Ad; Zuchowski, Piotr S \\; Podeszwa, Rafal
2009-01-01
We present four-dimensional ab initio potential energy surfaces for the three spin states of the NH-NH complex. The potentials are partially based on the work of Dhont et al. [J. Chem. Phys. 123, 184302 (2005)]. The surface for the quintet state is obtained at the RCCSD(T)/aug-cc-pVTZ level of theory and the energy diferences with the singlet and triplet states are calculated at the CASPTn/aug-cc-pVTZ (n = 2; 3) level of theory. The ab initio potentials are fitted to coupled spherical harmonics in the angular coordinates, and the long range is further expanded as a power series in 1/R. The RCCSD(T) potential is corrected for a size-consistency error prior to fitting. The long-range coeficients obtained from the fit are found to be in good agreement with perturbation theory calculations.
Shibuta, Yasushi; Shimamura, Kohei; Oguri, Tomoya; Arifin, Rizal; Shimojo, Fuyuki; Yamaguchi, Shu
2015-03-01
The growth mechanism of carbon nanotubes (CNT) has been widely discussed both from experimental and computational studies. Regarding the computational studies, most of the studies focuses on the aggregation of isolate carbon atoms on the catalytic metal nanoparticle, whereas the initial dissociation of carbon source molecules should affect the yield and quality of the products. On the other hand, we have studied the dissociation process of carbon source molecules on the metal surface by the ab initio molecular dynamics simulation. In the study, we investigate the ethanol dissociation on Pt and Ni clusters by ab initio MD simulations to discuss the initial stage of CNT growth by alcohol CVD technique. Part of this research is supported by the Grant-in-Aid for Young Scientists (a) (No. 24686026) from MEXT, Japan.
Complex coupled-cluster approach to an ab-initio description of open quantum systems
International Nuclear Information System (INIS)
We develop ab-initio coupled-cluster theory to describe resonant and weakly bound states along the neutron drip line. We compute the ground states of the helium chain 3-10He within coupled-cluster theory in singles and doubles (CCSD) approximation. We employ a spherical Gamow-Hartree-Fock basis generated from the low-momentum N3LO nucleon-nucleon interaction. This basis treats bound, resonant, and continuum states on an equal footing, and is therefore optimal for the description of properties of drip line nuclei where continuum features play an essential role. Within this formalism, we present an ab-initio calculation of energies and decay widths of unstable nuclei starting from realistic interactions
Ab initio Stellar Astrophysics: Reliable Modeling of Cool White Dwarf Atmospheres
Kowalski, Piotr M.; Kilic, Mukremin
2010-01-01
Over the last decade {\\it ab initio} modeling of material properties has become widespread in diverse fields of research. It has proved to be a powerful tool for predicting various properties of matter under extreme conditions. We apply modern computational chemistry and materials science methods, including density functional theory (DFT), to solve lingering problems in the modeling of the dense atmospheres of cool white dwarfs ($T_{\\rm eff}\\rm
Ab initio calculations of phosphate mediated degradation of glucose in biological cell
Rama K Barman
2012-01-01
Ab initio quantum mechanical calculations in Harte Fock (HF) 6-31G(d) levels for different intermediate species- glucose -6 phosphate (2), fructose- 6 phosphate(3), fructose 1,6-bis- hosphate(4) have been carried out along with the starting glucose(1) molecule to phosphate mediated degraded products of it - dihydroxy acetone phosphate and glyceraldehyde-3 phosphate intermediates. Chemical potential, hardness and softness, which are described as the global reactivity parameters, follow the pos...
The role of ab initio electronic structure calculations in multiscale modelling of materials.
Czech Academy of Sciences Publication Activity Database
Šob, Mojmír
Cambridge, England : Woodhead Publishing and Maney Publishing, 2007 - (Guo, Z.), s. 1-24 ISBN 978-1-84569-071-7 R&D Projects: GA ?R GA202/03/1351; GA AV ?R IAA1041302; GA MŠk OC 147 Institutional research plan: CEZ:AV0Z20410507 Keywords : multiscale modelling * electronic structure * ab initio calculations Subject RIV: BM - Solid Matter Physics ; Magnetism
Interplay of force constants in the lattice dynamics of disordered alloys : An ab-initio study
Chouhan, Rajiv K.; Alam, Aftab; Ghosh, Subhradip; Mookerjee, Abhijit
2013-01-01
A reliable prediction of interatomic force constants in disordered alloys is an outstanding problem. This is due to the need for a proper treatment of multisite (atleast pair) correlation within a random environment. The situation becomes even more challenging for systems with large difference in atomic size and mass. We propose a systematic density functional theory (DFT) based study to predict the ab-initio force constants in random alloys. The method is based on a marriag...
Anharmonic Raman spectra in high-pressure ice from ab initio simulations.
Putrino, Anna; Parrinello, Michele
2002-04-29
We calculate from ab initio molecular dynamics the Raman scattering of high-pressure ice. To this effect we apply a new method based on the Berry phase theory of polarization. Our results are in agreement with recent and difficult experiments and are compatible with a picture in which ice VII is a proton-disordered system and in ice X the hydrogen bond is symmetric. PMID:12005769
NestedMICA as an ab initio protein motif discovery tool
Down Thomas A; Do?ruel Mutlu; Hubbard Tim JP
2008-01-01
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 ...
Like-Charge Guanidinium Pairing from Molecular Dynamics and Ab Initio Calculations.
Czech Academy of Sciences Publication Activity Database
Vazdar, Mario; Vym?tal, Ji?í; Heyda, Jan; Vondrášek, Ji?í; Jungwirth, Pavel
2011-01-01
Ro?. 115, ?. 41 (2011), s. 11193-11201. ISSN 1089-5639 R&D Projects: GA MŠk LC512; GA ?R GA203/08/0114; GA MŠk(CZ) LH11020 Institutional research plan: CEZ:AV0Z40550506 Keywords : guanidinium * arginine * molecular dynamics * ab initio calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.946, year: 2011
Association and dissociation mechanisms for BnOm. Ab-initio molecular orbital method
International Nuclear Information System (INIS)
We have discussed the collision induced dissociation (CID) and association (CIA) of low-Z clusters. The cross sections of CID and CIA had been measured for cationic boron clusters, Bn+ (n=1-13), on colliding with O2 beam at very low energy below 10 eV. We perform theoretical calculations using ab initio Molecular Orbital method and investigate the reaction path, whether CIA or CID is preferred. (author)
Ab initio study of phase transformations in transition-metal disilicides.
Czech Academy of Sciences Publication Activity Database
Ká?a, Tomáš; Šob, Mojmír; Vitek, V.
2011-01-01
Ro?. 19, ?. 7 (2011), s. 919-926. ISSN 0966-9795 R&D Projects: GA AV ?R IAA100100920; GA MŠk(CZ) OC10008 Institutional research plan: CEZ:AV0Z20410507 Keywords : silicides various * phase transformation * plastic deformation mechanisms * defects * dislocation geometry and arrangement * ab-initio calculations * aero-engine components Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.649, year: 2011
XU, DONG; Zhang, Yang
2012-01-01
Ab initio protein folding is one of the major unsolved problems in computational biology due to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1–20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-ex...
Ab initio simulation of three-axial deformation of perfect iron crystal.
Czech Academy of Sciences Publication Activity Database
?erný, M.; Šandera, P.; Pokluda, J.; Friák, Martin; Šob, Mojmír
Brno : Vutium, 2001, s. 146-150. ISBN 80-214-1892-3. [Materials Structure and Micromechanics of Fracture /3./. VUT Brno (CZ), 27.06.2001-29.06.2001] R&D Projects: GA AV ?R IAA1010817; GA ?R GA106/99/1178 Institutional research plan: CEZ:AV0Z2041904 Keywords : ab initio calculations * ideal strength * lmto-asa Subject RIV: BK - Fluid Dynamics
Structural evolution in high-pressure amorphous CO$_2$ from \\textit{ab initio} molecular dynamics
Plašienka, Dušan; Marto?ák, Roman
2013-01-01
By employing $ab$ $initio$ molecular dynamics simulations at constant pressure, we investigated behavior of amorphous carbon dioxide between 0-100 GPa and 200-500 K and found several new amorphous forms. We focused on evolution of the high-pressure polymeric amorphous form known as a-carbonia on its way down to zero pressure, where it eventually converts into a molecular amorphous solid. During decompression, two nonmolecular amorphous forms with different proportion of thre...
Structural, electronic, and optical properties of ZrO2 from ab initio calculations
Garcia, Joelson Cott; Scolfaro, L. M. R.; Lino, A. T.; Freire, V. N.; Farias, G. A.; Silva, C. C.; Alves, H. W. Leite; Rodrigues, S. C. P.; Silva Jr, E. F. Da
2012-01-01
Structural, electronic, and optical properties for the cubic, tetragonal, and monoclinic crystalline phases of ZrO2, as derived from it ab initio full-relativistic calculations, are presented. The electronic structure calculations were carried out by means of the all-electron full potential linear augmented plane wave method, within the framework of the density functional theory and the local density approximation. The calculated carrier effective masses are shown to be high...
Ab initio calculations in a uniform magnetic field using periodic supercells
Energy Technology Data Exchange (ETDEWEB)
Cai, W; Galli, G
2003-10-21
We present a formulation of ab initio electronic structure calculations in a finite magnetic field, which retains the simplicity and efficiency of techniques widely used in first principles molecular dynamics simulations, based on plane-wave basis sets and Fourier transforms. In addition we discuss results obtained with this method for the energy spectrum of interacting electrons in quantum wells, and for the electronic properties of dense fluid deuterium in a uniform magnetic field.
Ab initio studies of defect concentrations and diffusion in metal oxides
Frensch, Kilian
2011-01-01
This work presents a methodology for determining the concentrations and diffusion coefficients of point defects in metal oxides using ab initio calculations of defect formation energies and diffusion barriers, and the binding energies of defect-impurity clusters. The methodology is applied to analyse the long-standing mysteries surrounding the mechanism of self-diffusion in ?-Al2O3. Al2O3 is a prototypical large band gap ceramic with extensive applications, many of which dep...
Ab-initio GMR and current-induced torques in Au/Cr multilayers
Haney, P. M.; Waldron, D.; Duine, R. A.; Nunez, A. S.; Guo, H.; Macdonald, A. H.
2006-01-01
We report on an {\\em ab-initio} study of giant magnetoresistance (GMR) and current-induced-torques (CITs) in Cr/Au multilayers that is based on non-equilibrium Green's functions and spin density functional theory. We find substantial GMR due primarily to a spin-dependent resonance centered at the Cr/Au interface and predict that the CITs are strong enough to switch the antiferromagnetic order parameter at current-densities $\\sim 100$ times smaller than typical ferromagnetic ...
Ab Initio Study of Different Acid Molecules Interacting with H2O
Zakharenko, Aleksey A.; Karthikyan, S.; Kim, K.S.
2008-01-01
Using the Gaussian-03 for ab initio calculations, we have studied interaction of different acid molecules with a single water molecule. The molecular and supermolecular optimized structures were found with the Becke-3-Lee-Yang-Parr (B3LYP-hybrid potential) calculations of density-functional theory (DFT) methods as well as the Moeller-Plesset second-order perturbation theory, using the basis set of Aug-cc-pVDZ quality and the CRENBL ECP effective core potential for molecules ...
Yan, Qing-Bo; Sheng, Xian-Lei; Zheng, Qing-Rong; Zhang, Li-Zhi; Su, Gang
2008-01-01
A set of general constructing schemes is unveiled to predict a large family of stable boron monoelemental, hollow fullerenes with magic numbers 32+8k (k>=0). The remarkable stabilities of these new boron fullerenes are then studied by intense ab initio calculations. An electron counting rule as well as an isolated hollow rule are proposed to readily show the high stability and the electronic bonding property, which are also revealed applicable to a number of newly predicted ...
Testing the density matrix expansion against ab initio calculations of trapped neutron drops
Bogner, S. K.; Furnstahl, R. J.; Hergert, H.; Kortelainen, M.; Maris, P.; Stoitsov, M.; Vary, J. P.
2011-01-01
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 b...
Molecular physisorption on graphene and carbon nanotubes: A comparative ab initio study
Henwood, Daniel; Carey, David
2008-01-01
Abstract The results of ab initio density functional theory calculations of molecular physisorption on a number of different adsorption sites on a graphene sheet and on a (10, 0) single walled carbon nanotube are discussed. Both the Vosko-Wilk-Nusair (VWN) local density approximation (LDA) functional and the Perdew-Wang (PW91) generalized gradient approximation (GGA) functional were employed in calculating the binding energy of a hydrogen molecule to the appropriate carbon nanostr...
Electric-field control of magnetism in graphene quantum dots: Ab initio calculations
Agapito, Luis A.; Kioussis, Nicholas; Kaxiras, Efthimios
2010-01-01
Employing ab initio calculations we predict that the magnetic states of hydrogenated diamond-shaped zigzag graphene quantum dots (GQDs), each exhibiting unique electronic structure, can be selectively tuned with gate voltage, through Stark or hybridization electric-field modulation of the spatial distribution and energy of the spin-polarized molecular orbitals, leading to transitions between these states. Electrical read-out of the GQD magnetic state can be accomplished by exploiting the dist...
Ab initio determination of the ionization potentials of DNA and RNA nucleobases.
Roca-Sanjuán, Daniel; Rubio, Mercedes; Merchán, Manuela; Serrano-Andrés, Luis
2006-08-28
Quantum chemical high level ab initio coupled-cluster and multiconfigurational perturbation methods have been used to compute vertical and adiabatic ionization potentials of the five canonical DNA and RNA nucleobases: uracil, thymine, cytosine, adenine, and guanine. Several states of their cations have been also calculated. The present results represent a systematic compendium of these magnitudes, establishing theoretical reference values at a level not reported before, calibrating computational strategies, and guiding the assignment of the features in the experimental photoelectron spectra. PMID:16965007
Direct ab initio MD simulation of silver ion diffusion in chalcogenide glasses
Tafen, D N; Mitkova, M; Tafen, De Nyago
2005-01-01
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.
Generation of Electrical Conductivity Data of Al using Ab-initio Molecular Dynamics simulations
Mishra, Vinayak; Chaturvedi, S.
2011-07-01
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.
Ab initio verification of the analytical R-matrix theory for strong field ionization
International Nuclear Information System (INIS)
We summarize the key aspects of the recently developed analytical R-matrix (ARM) theory for strong field ionization (Torlina and Smirnova 2012 Phys. Rev. A 86 043408; Kaushal and Smirnova 2013 Phys. Rev. A 88 013421), and present tests of this theory using ab initio numerical simulations for hydrogen and helium atoms in long circularly polarized laser pulses. We find excellent agreement between the predictions of ARM and the numerical calculations. (paper)
Knyazev, D. V.; Levashov, P. R.
2013-01-01
This work is devoted to the \\textit{ab initio} calculation of transport and optical properties of aluminum. The calculation is based on the quantum molecular dynamics simulation, density functional theory and the Kubo-Greenwood formula. Mainly the calculations are performed for liquid aluminum at near-normal densities for the temperatures from melting up to 20000 K. The results on dynamic electrical conductivity, static electrical conductivity and thermal conductivity are ob...
Holst, Bastian; French, Martin; Redmer, Ronald
2012-01-01
Using Kubo's linear response theory, we derive expressions for the frequency-dependent electrical conductivity (Kubo-Greenwood formula), thermopower, and thermal conductivity in a strongly correlated electron system. These are evaluated within ab initio molecular dynamics simulations in order to study the thermoelectric transport coefficients in dense liquid hydrogen, especially near the nonmetal-to-metal transition region. We also observe significant deviations from the wid...
Ab initio calculation of the anomalous Hall conductivity by Wannier interpolation
Wang, X.; Yates, Jr; Souza, I.; Vanderbilt, D.
2006-01-01
The intrinsic anomalous Hall conductivity 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 this quantity. We start out by performing a conventional electronic-structure calculation including spin-orbit coupling on a uniform and relatively coarse k -poi...
Czech Academy of Sciences Publication Activity Database
Ehala, Sille; Dybal, Ji?í; Makrlík, E.; Kaši?ka, Václav
2009-01-01
Ro?. 32, ?. 4 (2009), s. 597-604. ISSN 1615-9306 R&D Projects: GA ?R(CZ) GA203/06/1044; GA ?R(CZ) GA203/08/1428; GA AV ?R 1ET400500402 Institutional research plan: CEZ:AV0Z40550506; CEZ:AV0Z40500505 Keywords : capillary affinity electrophoresis * valinomycin * ab initio calculation Subject RIV: CB - Analytical Chemistry, Separation Impact factor: 2.551, year: 2009
Ab-initio approach to effective single-particle energies in doubly closed shell nuclei
Duguet, T.; Hagen, G.
2011-01-01
The present work discusses, from an ab-initio standpoint, the definition, the meaning, and the usefulness of effective single-particle energies (ESPEs) in doubly closed shell nuclei. We perform coupled-cluster calculations to quantify to what extent selected closed-shell nuclei in the oxygen and calcium isotopic chains can effectively be mapped onto an effective independent-particle picture. To do so, we revisit in detail the notion of ESPEs in the context of strongly correl...
Forced coalescence phasing: a method for ab initio determination of crystallographic phases.
Drendel, W. B.; Dave?, R. D.; Jain, S.
1995-01-01
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. ...
On the ab initio calculation of CVV Auger spectra in closed-shell systems
Fratesi, G.; Trioni, M. I.; Brivio, G. P.; Ugenti, S.; Perfetto, E.; Cini, M.
2008-01-01
We propose an ab initio method to evaluate the core-valence-valence (CVV) Auger spectrum of systems with filled valence bands. The method is based on the Cini-Sawatzky theory, and aims at estimating the parameters by first-principles calculations in the framework of density-functional theory (DFT). Photoemission energies and the interaction energy for the two holes in the final state are evaluated by performing DFT simulations for the system with varied population of electro...
Fertitta, E.; Paulus, B.; Barcza, G.; Legeza, O?
2014-01-01
We have studied the Metal-Insulator like Transition (MIT) in lithium and beryllium ring-shaped clusters through ab initio Density Matrix Renormalization Group (DMRG) method. Performing accurate calculations for different interatomic distances and using Quantum Information Theory (QIT) we investigated the changes occurring in the wavefunction between a metallic-like state and an insulating state built from free atoms. We also discuss entanglement and relevant excitations amon...
Rurali, Riccardo
2007-01-01
We propose an approach to the fabrication of one-dimensional nanostructures, based on the design of a pattern of channels onto a semiconductor surface. The feasibility of this approach is demonstrated by means of ab initio and empirical electronic structure calculations. When the channel diameter is sufficiently larger than the interstitial space, the resulting pillars constitute an ordered array of electronically independent, though mechanically connected nanowires. In the opposite regime a ...
Water pair and three-body potential of spectroscopic quality from Ab initio calculations
Groenenboom; Mas; Bukowski; Szalewicz; Wormer; van Der Avoird A
2000-05-01
We present the first pair plus three-body potential of water from ab initio calculations that quantitatively reproduces the experimental far-infrared spectra of the water dimer and trimer. The dimer spectrum was obtained from the pair potential through rigorous six-dimensional quantum calculations of the vibration-rotation-tunneling levels. The three-body interactions, together with the pair potential, produce an accurate representation of the hydrogen bond torsional levels of the water trimer. PMID:10990613
Belousov, Roman; Prencipe, Mauro
2014-01-01
The isothermal compression of magnesium perovskite and postperovskite is examined through the F-f plot and the diagnostic plot of Vinet universal model theoretically from the ab initio quantum-mechanical calculations at the hybrid Hartree-Fock / Density Functional Theory level. A purely numerical approach, first time applied in this paper, shows that the discrepancies largely observed between studies on the perovskite and criticized in geophysical applications are due to the...
Melting curve and Hugoniot of molybdenum up to 400 GPa by ab initio simulations
Cazorla, C.; Gillan, M. J.; Taioli, S.; Alfe`, D.
2007-01-01
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...
Ab initio melting curve of molybdenum by the phase coexistence method
Cazorla, C.; Gillan, M. J.; Taioli, S.; Alfe?, D.
2007-01-01
We report ab initio calculations of the melting curve of molybdenum for the pressure range 0-400 GPa. The calculations employ density functional theory (DFT) with the Perdew-Burke-Ernzerhof exchange-correlation functional in the projector augmented wave (PAW) implementation. We present tests showing that these techniques accurately reproduce experimental data on low-temperature b.c.c. Mo, and that PAW agrees closely with results from the full-potential linearized augmented p...
Ab initio study of the double row model of the Si(553)-Au reconstruction
Riikonen, S; Riikonen, Sampsa; Sanchez-Portal, Daniel
2005-01-01
Using x-ray diffraction Ghose et al. [Surf. Sci. {\\bf 581} (2005) 199] have recently produced a structural model for the quantum-wire surface Si(553)-Au. This model presents two parallel gold wires located at the step edge. Thus, the structure and the gold coverage are quite different from previous proposals. We present here an ab initio study using density functional theory of the stability, electronic band structure and scanning tunneling microscopy images of this model.
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
Modeling of nuclear glasses by classical and ab initio molecular dynamics
International Nuclear Information System (INIS)
A calcium aluminosilicate glass of molar composition 67 % SiO2 - 12 % Al2O3 - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri-coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminum atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)
3H(d,n)4He S-factor from Ab Initio Overlap Functions
International Nuclear Information System (INIS)
We present coupled channel calculations of the S-factor of 3H(d,n)4He transfer reaction. Potentials between different subclusters relevant for description of the transfer reaction are obtained by fits to cluster overlap functions calculated within the ab initio no-core shell model. This type of combined ab initio/potential model approach was successfully applied in the past to describe low-energy capture reactions important for nuclear astrophysics. For those reactions, typically a single or just a few channels were needed for an accurate description of the S-factor. For the 3H(d,n)4He transfer reaction, many channels are relevant, which makes the application of the combined approach quite challenging. In this report, we briefly outline the formalism, give overview of the capture reaction results obtained in the past, present in detail the calculations performed for the 3H(d,n)4He transfer reaction and give outlook for a full ab initio approach with predictive power capable to describe 3H(d,n)4He transfer reaction without ambiguities due to adjustable parameters
Geng, Hua Y.
2015-02-01
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model-the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of rs = 0.912.
International Nuclear Information System (INIS)
The behaviour of silicon carbide under irradiation has been studied using classical and ab initio simulations, focusing on the nano scale elementary processes. First, we have been interested in the calculation of threshold displacement energies, which are difficult to determine both experimentally and theoretically, and also the associated Frenkel pairs. In the framework of this thesis, we have carried out simulations in classical and ab initio molecular dynamics. For the classical approach, two types of potentials have been used: the Tersoff potential, which led to non satisfactory results, and a new one which has been developed during this thesis. This potential allows a better modelling of SiC under irradiation than most of the empirical potentials available for SiC. It is based on the EDIP potential, initially developed to describe defects in silicon, that we have generalized to SiC. For the ab initio approach, the feasibility of the calculations has been validated and average energies of 19 eV for the C and 38 eV for the Si sublattices have been determined, close to the values empirically used in the fusion community. The results obtained with the new potential EDIP are globally in agreement with those values. Finally, the elementary processes involved in the crystal recovery have been studied by calculating the stability of the created Frenkel pairs and determining possible recombination mechanisms with the nudged elastic band method. (author)
Ab initio study of the reaction of ozone with bromide ion.
Gladich, Ivan; Francisco, Joseph S; Buszek, Robert J; Vazdar, Mario; Carignano, Marcelo A; Shepson, Paul B
2015-05-14
Surface level ozone destruction in polar environments may be initiated by oxidation of bromide ions by ozone, ultimately leading to Br2 production. Ab initio calculations are used to support the development of atmospheric chemistry models, but errors can occur in study of the bromide-ozone reaction due to inappropriate treatment of the many-electron species and the ionic nature of the reaction. In this work, a high level ab initio study is used to take into account the electronic correlation and the polarization effects. Our results show three possible pathways for the reaction. In particular, we find that this process, though endothermic on the singlet spin state surface, can be energetically feasible on the triplet surface. The triplet surface can be reached through photoexcitation of ozone or by the spin crossing of the potential energy surface. Because this process is known to occur in the dark, it may be that it occurs after intersystem crossing to a triplet surface. This paper also provides a starting point calibration for any future ab initio calculation studies of the bromide-ozone reaction, from the gas to the condensed phase. PMID:25642913
Modelling of nuclear glasses by classical and ab initio molecular dynamics
International Nuclear Information System (INIS)
A calcium aluminosilicate glass of molar composition 67 % SiO2 - 12 % Al2O3 - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminium atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)
Ab initio calculation of the anomalous Hall conductivity by Wannier interpolation
Wang, X; Souza, I; Vanderbilt, D; Wang, Xinjie; Yates, Jonathan R.; Souza, Ivo; Vanderbilt, David
2006-01-01
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...
Geng, Hua Y
2014-01-01
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model, the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4 fold for a two-level implementation, and can be increased to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibration...
Dominant Modes in Light Nuclei - Ab Initio View of Emergent Symmetries
Draayer, J. P.; Dytrych, T.; Launey, K. D.; Dreyfuss, A. C.; Langr, D.
2015-01-01
An innovative symmetry-guided concept is discussed with a focus on emergent symmetry patterns in complex nuclei. In particular, the ab initio symmetry-adapted no-core shell model (SA-NCSM), which capitalizes on exact as well as partial symmetries that underpin the structure of nuclei, provides remarkable insight into how simple symmetry patterns emerge in the many-body nuclear dynamics from first principles. This ab initio view is complemented by a fully microscopic no-core symplectic shell-model framework (NCSpM), which, in turn, informs key features of the primary physics responsible for the emergent phenomena of large deformation and alpha-cluster substructures in studies of the challenging Hoyle state in Carbon-12 and enhanced collectivity in intermediate-mass nuclei. Furthermore, by recognizing that deformed configurations often dominate the low-energy regime, the SA-NCSM provides a strategy for determining the nature of bound states of nuclei in terms of a relatively small subspace of the symmetry-reorganized complete model space, which opens new domains of nuclei for ab initio investigations, namely, the intermediate-mass region, including isotopes of Ne, Mg, and Si.
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)
Vogel, Eckhard; Hellmann, Robert; Bich, Eckard
2008-01-01
Abstract A neon-neon interatomic potential energy curve was derived from quantum-mechanical ab initio calculations using basis sets of up to t-aug-cc-pV6Z quality supplemented with bond functions and ab initio methods up to CCSDT(Q). In addition, corrections for relativistc effects were determined. An analytical potential function was fitted to the ab initio values and utilized to calculate the rovibrational spectra. The quality of the interatomic potential function was tested by c...
Faghaninia, Alireza; Ager, Joel W.; Lo, Cynthia S.
2015-06-01
Accurate models of carrier transport are essential for describing the electronic properties of semiconductor materials. To the best of our knowledge, the current models following the framework of the Boltzmann transport equation (BTE) either rely heavily on experimental data (i.e., semiempirical), or utilize simplifying assumptions, such as the constant relaxation time approximation (BTE-cRTA). While these models offer valuable physical insights and accurate calculations of transport properties in some cases, they often lack sufficient accuracy—particularly in capturing the correct trends with temperature and carrier concentration. We present here a transport model for calculating low-field electrical drift mobility and Seebeck coefficient of n -type semiconductors, by explicitly considering relevant physical phenomena (i.e., elastic and inelastic scattering mechanisms). We first rewrite expressions for the rates of elastic scattering mechanisms, in terms of ab initio properties, such as the band structure, density of states, and polar optical phonon frequency. We then solve the linear BTE to obtain the perturbation to the electron distribution—resulting from the dominant scattering mechanisms—and use this to calculate the overall mobility and Seebeck coefficient. Therefore, we have developed an ab initio model for calculating mobility and Seebeck coefficient using the Boltzmann transport (aMoBT) equation. Using aMoBT, we accurately calculate electrical transport properties of the compound n -type semiconductors, GaAs and InN, over various ranges of temperature and carrier concentration. aMoBT is fully predictive and provides high accuracy when compared to experimental measurements on both GaAs and InN, and vastly outperforms both semiempirical models and the BTE-cRTA. Therefore, we assert that this approach represents a first step towards a fully ab initio carrier transport model that is valid in all compound semiconductors.
Velaga, Srinath C; Anderson, Brian J
2014-01-16
Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest–host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the “VAS” model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site–site ab initio intermolecular potentials) as ??(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
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 firsall 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
Majumder, Moumita; Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker; Li, Jun; Guo, Hua; Manzhos, Sergei
2014-06-01
New potential energy surfaces for methane were constructed, represented as analytic fits to about 100,000 individual high-level ab initio data. Explicitly-correlated multireference data (MRCI-F12(AE)/CVQZ-F12) were computed using Molpro [1] and fit using multiple strategies. Fits with small to negligible errors were obtained using adaptations of the permutation-invariant-polynomials (PIP) approach [2,3] based on neural-networks (PIP-NN) [4,5] and the interpolative moving least squares (IMLS) fitting method [6] (PIP-IMLS). The PESs were used in full-dimensional vibrational calculations with an exact kinetic energy operator by representing the Hamiltonian in a basis of products of contracted bend and stretch functions and using a symmetry adapted Lanczos method to obtain eigenvalues and eigenvectors. Very close agreement with experiment was produced from the purely ab initio PESs. References 1- H.-J. Werner, P. J. Knowles, G. Knizia, 2012.1 ed. 2012, MOLPRO, a package of ab initio programs. see http://www.molpro.net. 2- Z. Xie and J. M. Bowman, J. Chem. Theory Comput 6, 26, 2010. 3- B. J. Braams and J. M. Bowman, Int. Rev. Phys. Chem. 28, 577, 2009. 4- J. Li, B. Jiang and Hua Guo, J. Chem. Phys. 139, 204103 (2013). 5- S Manzhos, X Wang, R Dawes and T Carrington, JPC A 110, 5295 (2006). 6- R. Dawes, X-G Wang, A.W. Jasper and T. Carrington Jr., J. Chem. Phys. 133, 134304 (2010).
An Ab Initio Approach Towards Engineering Fischer-Tropsch Surface Chemistry
Energy Technology Data Exchange (ETDEWEB)
Matthew Neurock; David A. Walthall
2006-05-07
One of the greatest societal challenges over the next decade is the production of cheap, renewable energy for the 10 billion people that inhabit the earth. This will require the development of various different energy sources potentially including fuels derived from methane, coal, and biomass and alternatives sources such as solar, wind and nuclear energy. One approach will be to synthesize gasoline and other fuels from simpler hydrocarbons such as CO derived from methane or other U.S. based sources such as coal. Syngas (CO and H{sub 2}) can be readily converted into higher molecular weight hydrocarbons through Fischer-Tropsch synthesis. Fischer-Tropsch synthesis involves the initiation or activation of CO and H{sub 2} bonds, the subsequent propagation steps including hydrogenation and carbon-carbon coupling, followed by chain termination reactions. Commercially viable catalysts include supported Co and Co-alloys. Over the first two years of this project we have used ab initio methods to determine the adsorption energies for all reactants, intermediates, and products along with the overall reaction energies and their corresponding activation barriers over the Co(0001) surface. Over the third year of the project we developed and advanced an ab initio-based kinetic Monte Carlo simulation code to simulate Fischer Tropsch synthesis. This report details our work over the last year which has focused on the derivation of kinetic parameters for the elementary steps involved in FT synthesis from ab initio density functional theoretical calculations and the application of the kinetic Monte Carlo algorithm to simulate the initial rates of reaction for FT over the ideal Co(0001) surface. The results from our simulations over Co(0001) indicate the importance of stepped surfaces for the activation of adsorbed CO. In addition, they demonstrate that the dominant CH{sub x}* surface intermediate under steady state conditions is CH*. This strongly suggests that hydrocarbon coupling occurs through reaction with the adsorbed CH*.
Ab initio calculations of theoretical tensile strength in metals and intermetalics.
Czech Academy of Sciences Publication Activity Database
Šob, Mojmír; Friák, Martin; Wang, L. G.; Vitek, V.
Warrendale, PA : The Minerals, Metals & Materials Society, 2001 - (Cross, M.; Evans, J.; Bailey, C.), s. 715-724 ISBN 0-87339-513-1. [ TMS ANNUAL MEETING. Seattle (US), 17.02.2002-20.02.2002] R&D Projects: GA AV ?R IAA1010817; GA ?R GA106/99/1178; GA MŠk ME 264; GA MŠk OC P3.10 Grant ostatní: -(US) INT9605232; -(US) DEFG0298ER45702 Institutional research plan: CEZ:AV0Z2041904 Keywords : theoretical tensile strength * ab initio Subject RIV: BM - Solid Matter Physics ; Magnetism
Ab initio calculations of the electronic structure of cuprates using large scale cluster techniques
Renold, S.; Bersier, C.; Stoll, E. P.; Meier, P. F.
2007-01-01
The local electronic structures of La2CuO4, three members of the Yttrium-family (YBa2Cu3O6, YBa2Cu3O7, and YBa2Cu4O8), and to some extent of Nd2CuO4 have been determined using all-electron ab-initio cluster calculations for clusters comprising up to thirteen planar copper atoms associated with their nearest planar and apical oxygen atoms. Spin-polarized calculations in the framework of density functional theory have enabled an estimation of the superexchange couplings J. Ele...
Comparison between ab initio energy band structures of various chlorinated polyethylene derivatives
Assad Abdel-Raouf, Mohamed
1989-09-01
The band structures of various chlorinated polyethylene derivatives are calculated using an ab initio self-consisten field (SCF) linear combination of atomic orbitals (LCAO) technique. The results illustrate that the conduction band is shifted steadily towards lower energies as the number of chlorine atoms in the unit cell increases, and the gap between valence and conduction bands is decreased monotonically. The possibility of n-doping is explored. The comparison between the band structures of the chlorinated polymers and that of polytrifluorochloroethylene shows that the latter possesses a lower-lying conduction band and is, therefore, more adequate for doping.
Ab initio relativistic effective potentials with spin-orbit operators. VII. Am through element 118
International Nuclear Information System (INIS)
Ab initio averaged relativistic effective core potentials (AREP) and spin-orbit (SO) operators are reported for the elements Am through element 118. Two sets have been calculated for certain elements to provide AREPs with varying core/valence space definition, thereby permitting the treatment of core/valence correlation interactions. The AREPs and SO operators are tabulated as expansions in Gaussian-type functions (GTF). GTF valence basis sets are derived for the lowest energy state of each atom. The reliability of the AREPs and SO operators is gauged by comparing calculated atomic orbital eigenvalues and SO splitting energies with all-electron relativistic values. copyright 1997 American Institute of Physics
Ab initio relativistic effective potentials with spin-orbit operators. VII. Am through element 118
Nash, Clinton S.; Bursten, Bruce E.; Ermler, Walter C.
1997-03-01
Ab initio averaged relativistic effective core potentials (AREP) and spin-orbit (SO) operators are reported for the elements Am through element 118. Two sets have been calculated for certain elements to provide AREPs with varying core/valence space definition, thereby permitting the treatment of core/valence correlation interactions. The AREPs and SO operators are tabulated as expansions in Gaussian-type functions (GTF). GTF valence basis sets are derived for the lowest energy state of each atom. The reliability of the AREPs and SO operators is gauged by comparing calculated atomic orbital eigenvalues and SO splitting energies with all-electron relativistic values.
An ab initio study of the electronic structure of boron arsenide, BAs
Magoulas, Ilias; Kalemos, Apostolos
2013-10-01
The completely unexplored BAs diatomic has been thoroughly studied by high level multireference variational ab initio methods. Potential energy curves for 42 molecular states dissociating to the first four asymptotic channels and covering an energy range of 5.8 eV have been constructed revealing an interesting morphology and a rich spectroscopy. The ground state is of 3? symmetry while its first excited 1?+ state lies ˜8 kcal/mol higher. A general feature of the potential curves is the presence of avoided crossings that challenge the validity of the Born Oppenheimer approximation.
Thorium in tungsten: construction of interatomic EAM potentials from ab initio data
Eberhard, Bernd; Haider, Ferdinand
2013-07-01
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.
Lithium incorporation at the MoS2/graphene interface: an ab initio investigation
Miwa, Roberto H.; Scopel, Wanderla L.
2013-01-01
Based on ab initio calculations, we examine the incorporation of Li atoms in the MoS2/graphene interface. We find that the intercalated Li atoms are energetically more stable than Li atoms adsorbed on the MoS2 surface. The intercalated atoms interact with both graphene sheet and MoS2 layer, increasing the Li binding energies. However, the equilibrium geometries are ruled by the MoS2 layer, where the intercalated Li atoms lie on the top (Li_T) and hollow (Li_H) sites of the M...
Ab initio calculations of 14N and 15N hyperfine structures
Jönsson, P; Nemouchi, M; Godefroid, M
2010-01-01
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.
Ozaki, T
2005-01-01
An efficient and robust linear scaling method is presented for large scale {\\it ab initio} electronic structure calculations of a wide variety of materials including metals. The detailed short range and the effective long range contributions to the electronic structure are taken into account by solving an embedded cluster defined in a Krylov subspace, which provides rapid convergence for not only insulators but also metals. As an illustration of the method, we present a large scale calculation based on density functional theory for a palladium cluster with a single iron impurity.
International Nuclear Information System (INIS)
We present the results of ab-initio molecular dynamics studies of selected microclusters of sodium, silicon and magnesium at finite temperatures, and especially discuss those obtained around room temperature. In particular, from the analysis of the atomic trajectories we can identify in some cases the existence of different isomers and the isomerization pathways. We have also calculated vibrational spectra at low temperatures and find that they can be used a very sensitive structural probe also in sodium clusters, where the electronic properties are quite insensitive to the geometry. (orig.)
Ab-Initio Optical Properties of BN(110) and GAN(110) Surfaces
Cappellini, G.; Satta, G.; Palummo, M.; Onida, G.
2004-02-01
First-principle calculations of the linear optical properties of the nonpolar (110) surface of cubic Boron and Gallium Nitride are presented. We analyze the reflectance anisotropy (RA) spectra in relation to the better known spectrum of the GaAs(110) surface and to the existing tight-binding results for GaN(110). Previous results for the RA spectrum of GaN(110) obtained in tight-binding scheme are confirmed. The present first ab-initio results for BN(110) show the important role played by surface states transitions at the onset of the RA spectrum.
Ab initio piezoelectricity and energy landscape of Y0.375Al0.625N
Tholander, Christopher
2011-01-01
There is high industrial demand for materials with a high piezoelectrical response which are stable at high temperatures. A recent study on ScAlN has explained the microscopic origin of the increased piezoelectric response in the alloy and its effect on the energy landscape. Y is a promising candidate to observe the same phenomena. The ab initio DFT-GGA calculations for Y0.375Al0.625N, using a 128 atom SQS model, show a less pronounced increase of the piezoelectric response. The Y0.375Al0.625...
Pietrucci, Fabio; Andreoni, Wanda
2011-08-01
Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.
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
Spin polarized surface states on stepped magnetic surfaces: ab-initio approach
Stepanyuk, Oleg; Polyakov, Oleg; Saletsky, Alexander; Hergert, Wolfram
2012-02-01
It was shown that surface states electrons become spin polarized above magnetic layers and nanoislands [1]. In the present work we perform the state of the art ab-initio studies of surface state electrons at steps of magnetic metals. We focus on steps of 3d metals on Cu(111) surface. We have revealed a spin-dependent charge transfer at step ages which is explained by Smoluchowski effect. Strongly inhomogeneous spin polarization of surface statates [1] at steps is revealed. Our results indicate that tunneling magnetoresistance at steps can exhibit very strong changes at the atomic scale. [4pt] [1] L. Diekhoner et. al. Phys. Rev. Lett. 90, 236801
Testing the density matrix expansion against ab initio calculations of trapped neutron drops
Bogner, S. K.; Furnstahl, R. J.; Hergert, H.; Kortelainen, M.; Maris, P.; Stoitsov, M.; Vary, J. P.
2011-10-01
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.
Ab Initio Calculations of Even Oxygen Isotopes with Chiral Two- Plus Three-Nucleon Interactions
Hergert, H.; Binder, S.; Calci, A.; Langhammer, J.; Roth, R.
2013-01-01
We formulate the In-Medium Similarity Renormalization Group (IM-SRG) for open-shell nuclei using a multi-reference formalism based on a generalized Wick theorem introduced in quantum chemistry. The resulting multi-reference IM-SRG (MR-IM-SRG) is used to perform the first ab initio study of even oxygen isotopes with chiral NN and 3N Hamiltonians, from the proton to the neutron drip lines. We obtain an excellent reproduction of experimental ground-state energies with quantifie...
Ab initio study of mirages and magnetic interactions in quantum corrals
Stepanyuk, V. S.; Niebergall, L.; Hergert, W.; Bruno, P.
2005-01-01
The state of the art ab initio calculations of quantum mirages,the spin-polarization of surface-state electrons and the exchange interaction between magnetic adatoms in Cu and Co corrals on Cu(111) are presented. We find that the spin-polarization of the surface-state electrons caused by magnetic adatoms can be projected to a remote location and can be strongly enhanced in corrals compared to an open surface.Our studies give a clear evidence that quantum corrals could permit...
Ab initio study of mirages and magnetic interactions in quantum corrals.
Stepanyuk, V S; Niebergall, L; Hergert, W; Bruno, P
2005-05-13
The state of the art ab initio calculations of quantum mirages, the spin polarization of surface-state electrons, and the exchange interaction between magnetic adatoms in Cu and Co corrals on Cu(111) are presented. We find that the spin polarization of the surface-state electrons caused by magnetic adatoms can be projected to a remote location and can be strongly enhanced in corrals, compared to an open surface. Our studies give clear evidence that quantum corrals could permit one to tailor the exchange interaction between magnetic adatoms at large separations. PMID:15904405
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.
Interplay between magnetism and structure in atomic-size Pd contacts: Ab initio studies
Smelova, K. M.; Bazhanov, D. I.; Stepanyuk, V. S.; Hergert, W.; Saletsky, A. M.; Bruno, P.
2008-01-01
We present ab initio study of the interplay between atomic structure and magnetic properties in palladium atomic-size contacts suspended between palladium electrodes. This study was motivated by recent controversy between Delin [Phys. Rev. Lett. 96, 079702 (2006)] and Alexandre [Phys. Rev. Lett. 96, 079701 (2006)] about possible onset of magnetism in palladium (Pd) contacts. Here, we elucidate the effect of atomic arrangement and structure relaxations revealed in contracted and elongated Pd contacts on their magnetic properties. Planelike and pyramidlike geometries for electrodes are studied. We demonstrate that palladium contacts exhibit magnetic properties distributed inhomogeneously within the contact for a wide range of distances between separated electrodes.
Testing the density matrix expansion against ab initio calculations of trapped neutron drops
Bogner, S K; Hergert, H; Kortelainen, M; Maris, P; Stoitsov, M; Vary, J P
2011-01-01
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.
Switching a Single Spin on Metal Surfaces by a STM Tip: AbInitio Studies
Tao, Kun; Stepanyuk, V. S.; Hergert, W.; Rungger, I.; Sanvito, S.; Bruno, P.
2009-07-01
The exchange coupling between single 3d magnetic adatoms (Cr, Mn, Fe, and Co) adsorbed on a Cu(001) surface and a Cr STM tip is studied with ab initio calculations. We demonstrate that the spin direction of single adatoms can be controlled by varying the tip-substrate distance, and the sign of the exchange energy is determined by the competition of the direct and the indirect interactions between the tip and the adatom. Based on the spin-dependent transport calculations, we find a magnetoresistance of about 70% at short tip-substrate distances.
Physisorption of an organometallic platinum complex on silica. An ab initio study
Shen, Juan; Muthukumar, Kaliappan; Jeschke, Harald O.; Valenti, Roser
2012-01-01
The interaction of trimethyl methylcyclopentadienyl platinum (MeCpPtMe3) with a fully hydroxylated SiO2 surface has been explored by means of ab initio calculations. A large slab model cut out from the hydroxylated beta-cristobalite SiO2 (111) surface was chosen to simulate a silica surface. Density functional theory calculations were performed to evaluate the energies of MeCpPtMe3 adsorption to the SiO2 surface. Our results show that the physisorption of the molecule is dep...
Ab initio calculations on low-energy structures of perindopril erbumine.
Czech Academy of Sciences Publication Activity Database
Czernek, Ji?í
Cavtat : World Scientific and Engineering Academy and Society (WSEAS), 2006, s. 26-29. ISBN 960-8457-46-7. ISSN 1790-5109. [International Conference on Mathematics and Computers in Biology and Chemistry /7./. Cavtat (HR), 12.06.2006-15.06.2006] R&D Projects: GA AV ?R 1ET400500402; GA AV ?R IAA400500602 Institutional research plan: CEZ:AV0Z40500505 Keywords : perindopril erbumine * perindoprilat * ab initio Subject RIV: CD - Macromolecular Chemistry http://www.wseas.org
The hydrogen diffusion in liquid aluminum alloys from ab initio molecular dynamics.
Jakse, N; Pasturel, A
2014-09-01
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. PMID:25194378
Energy Technology Data Exchange (ETDEWEB)
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
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.
Solvent effects on 2-methoxyethanol conformers: an ab initio DFT study using the SCI-PCModel
Gil, Francisco P. S. C.; Teixeira-Dias, J. J. C.
1999-01-01
The four stable conformers of 2-methoxyethanol, CH3O-CH2-CH2-OH (tgg', ggg', ttg and ttt) are studied by ab initio calculations using the SCRF theory and the SCI-PCModel to assess solvent effects on the structure and vibrational spectra of this compound. Full geometry optimizations were carried out at the B3LYP/6-311+G(3df,2df,2p)//B3LYP/6-31G(d) level, and normal mode calculations were performed within the harmonic approximation using the B3LYP/6-31G(d) derived force fields. The solvent, her...
AB INITIO STUDY OF COBALT MAGNETISM ALONG THE TETRAGONAL DEFORMATION PATHS.
Czech Academy of Sciences Publication Activity Database
Zelený, Martin; Legut, Dominik; Šob, Mojmír
Brno : Ústav fyziky materiál? AV ?R v Brn?, 2005 - (Dlouhý, I.; Švejcar, J.; Šob, M.; Strnadel, B.), s. 21-26 ISBN 80-239-6145-4. [Víceúrov?ový design pokrokových materiál? 05. Brno (CZ), 01.12.2005] R&D Projects: GA ?R(CZ) GA202/03/1351; GA ?R(CZ) GD106/05/H008; GA AV ?R(CZ) IAA1041302; GA AV ?R(CZ) IBS2041105 Institutional research plan: CEZ:AV0Z20410507 Keywords : electronic structure * magnetism in metals * ab initio calculations Subject RIV: BM - Solid Matter Physics ; Magnetism
Large-scale ab initio nanostructure electronic structure calculations for energy applications
International Nuclear Information System (INIS)
Nanostructures have often been used to construct third-generation solar cells and for solid state lighting. To fully explore the potential for such energy applications, we need to understand the electronic and optical properties of the corresponding nanosystems. These include the quantum confinement effects, the electron hole separations, the exciton binding energy, and optical absorption spectrums. In the past ten years, we have developed a systematic approach to study such properties of thousand atom nanostructures based on ab initio calculations and large -cale comutations. In this paper, we present a few examples using such an approach to study the nanostructure properties related to energy applications
Hoshino, K.; Shimojo, F.; Zempo, Y.
2000-02-01
The structural and electronic properties of liquid Rbx Te1-x mixtures (x = 0.0, 0.2, and 0.5) are studied by ab initio molecular-dynamics simulations. It is shown that the transition from the metallic to the semiconducting state induced by adding Rb atoms is reproduced, and that this transition is related to the structural change in the Te chain. It is also shown from the calculated electronic density of states that almost complete charge transfer from Rb to Te occurs in the mixtures. The correlation between the spatial distribution of the transferred charge in the Te chains and the positions of Rb+ ions is investigated.
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.
Holst, Bastian; Redmer, Ronald; 10.1103/PhysRevB.83.235120
2012-01-01
Using Kubo's linear response theory, we derive expressions for the frequency-dependent electrical conductivity (Kubo-Greenwood formula), thermopower, and thermal conductivity in a strongly correlated electron system. These are evaluated within ab initio molecular dynamics simulations in order to study the thermoelectric transport coefficients in dense liquid hydrogen, especially near the nonmetal-to-metal transition region. We also observe significant deviations from the widely used Wiedemann-Franz law which is strictly valid only for degenerate systems and give an estimate for its valid scope of application towards lower densities.
Ab initio coupled cluster calculations for nuclei using methods of quantum chemistry
W?och, M.; Dean, D. J.; Gour, J. R.; Piecuch, P.; Hjorth-Jensen, M.; Papenbrock, T.; Kowalski, K.
2005-09-01
We report preliminary large scale ab initio calculations of ground and excited states of 16O using quantum chemistry inspired coupled cluster methods and realistic two-body interactions. By using the renormalized Hamiltonians obtained with a no-core G-matrix approach, we obtain the virtually converged results at the level of two-body interactions. Due to the polynomial scaling with the system size that characterizes coupled cluster methods, we can probe large model spaces with up to seven major oscillator shells, for which standard non-truncated shell-model calculations are not possible.
Ab initio coupled cluster calculations for nuclei using methods of quantum chemistry
Energy Technology Data Exchange (ETDEWEB)
Wloch, M.; Gour, J.R.; Kowalski, K. [Michigan State University, Department of Chemistry, East Lansing, MI (United States); Dean, D.J. [Oak Ridge National Laboratory, Physics Division, P.O. Box 2008, Oak Ridge, TN (United States); University of Tennessee, Department of Physics and Astronomy, Knoxville, TN (United States); University of Oslo, Center of Mathematics for Applications, Oslo (Norway); Piecuch, P. [Michigan State University, Department of Chemistry, East Lansing, MI (United States); Michigan State University, Department of Physics and Astronomy, East Lansing, MI (United States); Hjorth-Jensen, M. [University of Oslo, Center of Mathematics for Applications, Oslo (Norway); Michigan State University, Department of Physics and Astronomy, East Lansing, MI (United States); University of Oslo, Department of Physics, Oslo (Norway); Papenbrock, T. [Oak Ridge National Laboratory, Physics Division, P.O. Box 2008, Oak Ridge, TN (United States); University of Tennessee, Department of Physics and Astronomy, Knoxville, TN (United States)
2005-09-01
We report preliminary large scale ab initio calculations of ground and excited states of {sup 16}O using quantum chemistry inspired coupled cluster methods and realistic two-body interactions. By using the renormalized Hamiltonians obtained with a no-core G-matrix approach, we obtain the virtually converged results at the level of two-body interactions. Due to the polynomial scaling with the system size that characterizes coupled cluster methods, we can probe large model spaces with up to seven major oscillator shells, for which standard non-truncated shell-model calculations are not possible. (orig.)
Ab Initio Coupled-Cluster Calculations for Nuclei Using Methods of Quantum Chemistry
Energy Technology Data Exchange (ETDEWEB)
Wloch, M. [Michigan State University, East Lansing; Dean, David Jarvis [ORNL; Gour, J. R. [Michigan State University, East Lansing; Piecuch, P. [Michigan State University, East Lansing; Hjorth-Jensen, M. [University of Oslo, Norway; Papenbrock, Thomas F [ORNL; Kowalski, K. [Michigan State University, East Lansing
2005-09-01
We report preliminary large scale ab initio calculations of ground and excited states of {sup 16}O using quantum chemistry inspired coupled cluster methods and realistic two-body interactions. By using the renormalized Hamiltonians obtained with a no-core G-matrix approach, we obtain the virtually converged results at the level of two-body interactions. Due to the polynomial scaling with the system size that characterizes coupled cluster methods, we can probe large model spaces with up to seven major oscillator shells, for which standard non-truncated shell-model calculations are not possible.
Ab initio coupled cluster calculations for nuclei using methods of quantum chemistry
International Nuclear Information System (INIS)
We report preliminary large scale ab initio calculations of ground and excited states of 16O using quantum chemistry inspired coupled cluster methods and realistic two-body interactions. By using the renormalized Hamiltonians obtained with a no-core G-matrix approach, we obtain the virtually converged results at the level of two-body interactions. Due to the polynomial scaling with the system size that characterizes coupled cluster methods, we can probe large model spaces with up to seven major oscillator shells, for which standard non-truncated shell-model calculations are not possible. (orig.)
Monte Carlo methods in AB initio quantum chemistry quantum Monte Carlo for molecules
Lester, William A; Reynolds, PJ
1994-01-01
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
Tuning ab initio data to scattering length: the a (3)Sigma(+) state of KRb.
Soldán, Pavel; Spirko, Vladimír
2007-09-28
Interaction energies for the lowest triplet state a (3)Sigma(+) of KRb are calculated using high level ab initio methods. The interaction energies are then morphed so that the resulting potential energy curve yields 32 bound states and the correct scattering length for (40)K(87)Rb. Calculated vibrational spacings are shown to be in very good agreement with the available experimental Fourier transform and photoassociation vibrational data, but a different numbering scheme has to be used for the experimental vibrational assignment. PMID:17902885
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
Polarization effects in semiconductors from ab initio theory to device applications
Wood, Colin
2007-01-01
This book presents the latest understanding of the solid physics, electronic implications and practical applications of the unique spontaneous or pyro-electric polarization charge of hexagonal semiconductors, and the piezo-electric effects in thin film hetero-structures, which are used in wide forbidden band gap sensor, electronic and opto-electronic semiconductor devices. The book covers ab initio theory of polarization in cubic and hexagonal semiconductors, growth of thin film GaN, and GaN/AlGaN GaAlN/ AlGaInN and other nitride, and SiC hetero-structures; graded structures for distributed pi
The role of ab initio electronic structure calculations in studies of the strength of materials.
Czech Academy of Sciences Publication Activity Database
Šob, Mojmír; Friák, Martin; Legut, Dominik; Fiala, J.; Vitek, V.
387-389, - (2004), s. 148-157. ISSN 0032-3888. [International Conference on the Strength of Materials /13./. Budapest, 25.08.2003-30.08.2003] R&D Projects: GA AV ?R(CZ) IAA1041302; GA ?R(CZ) GA202/03/1351; GA MŠk(CZ) OC 523.90 Institutional research plan: CEZ:AV0Z2041904 Keywords : theoretical strength * ab initio calculations * metallic materials Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.224, year: 2004
DEFF Research Database (Denmark)
Fürst, Joachim Alexander; Hashemi, J.
2009-01-01
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.
International Nuclear Information System (INIS)
The results of ab initio calculations of the electronic structure of Si nanocrystals doped with shallow donors (Li, P) are reported. It is shown that phosphorus introduces much more significant distortions into the electronic structure of the nanocrystal than lithium, which is due to the stronger central cell potential of the phosphorus ion. It is found that the Li-induced splitting of the ground state in the conduction band of the nanocrystal into the singlet, doublet, and triplet retains its inverse structure typical for bulk silicon
The ground state of (He-H-He)(+) from correlated ab initio calculations
Komasa, Jacek; Rychlewski, Jacek
1998-01-01
He2H+ ion in its ground state is studied by means of ab initio methods taking into account the electron correlation. Geometry optimization at the CCSD(T)/cc-pV5Z level of theory has been performed and the potential energy hypersurface scan is presented. The optimum conformation is linear and symmetric with the proton at the He-He midpoint and the He-H distance equal to 1.75 bohr. Stabilization energy with respect to the He2H+ --> HeH+ + He dissociation channel has been computed. Additionally,...
Second generation wave-function thermostat for ab-initio molecular dynamics
Blöchl, P E
2001-01-01
A rigorous two-thermostat formulation for ab-initio molecular dynamics using the fictitious Lagrangian approach is presented. It integrates the concepts of mass renormalization and temperature control for the wave functions. The new thermostat adapts to the instantaneous kinetic energy of the nuclei and thus minimizes its influence on the dynamics. Deviations from the canonical ensemble, which are possible in the previous two-thermostat formulation, are avoided. The method uses a model for the effective mass of the wave functions, which is open to systematic improvement.
Atomic ionization of germanium by neutrinos from an ab initio approach
International Nuclear Information System (INIS)
An ab initio calculation of atomic ionization of germanium by neutrinos was carried out in the framework of multiconfiguration relativistic random phase approximation and benchmarked by related atomic structure and photoabsorption data. This improves over the conventional approach based on scattering off free electrons whose validity at sub-keV energy transfer is questionable. Limits on neutrino magnetic moments are derived using reactor neutrino data taken with low threshold germanium detectors. Future applications of these atomic techniques will greatly reduce the atomic uncertainties in low-energy neutrino and dark matter detections.
Vibrational energy levels for CH4 from an ab initio potential
Schwenke, D. W.; Partridge, H.
2001-01-01
Many areas of astronomy and astrophysics require an accurate high temperature spectrum of methane (CH4). The goal of the present research is to determine an accurate ab initio potential energy surface (PES) for CH4. As a first step towards this goal, we have determined a PES including up to octic terms. We compare our results with experiment and to a PES based on a quartic expansion. Our octic PES gives good agreement with experiment for all levels, while the quartic PES only for the lower levels.
Fertitta, E; Barcza, G; Legeza, Ö
2014-01-01
We have studied the Metal-Insulator like Transition (MIT) in lithium and beryllium ring-shaped clusters through ab initio Density Matrix Renormalization Group (DMRG) method. Performing accurate calculations for different interatomic distances and using Quantum Information Theory (QIT) we investigated the changes occurring in the wavefunction between a metallic-like state and an insulating state built from free atoms. We also discuss entanglement and relevant excitations among the molecular orbitals in the Li and Be rings and show that the transition bond length can be detected using orbital entropy functions. Also, the effect of different orbital basis on the effectiveness of the DMRG procedure is analyzed comparing the convergence behavior.
Pride, Prejudice, and Penury of {\\it ab initio} transport calculations for single molecules
Evers, F
2006-01-01
Recent progress in measuring the transport properties of individual molecules has triggered a substantial demand for {\\it ab initio} transport calculations. Even though program packages are commercially available and placed on custom tailored to address this task, reliable information often is difficult and very time consuming to attain in the vast majority of cases, namely when the molecular conductance is much smaller than $e^2/h$. The article recapitulates procedures for molecular transport calculations from the point of view of time-dependent density functional theory. Emphasis is describing the foundations of the ``standard method''. Pitfalls will be uncovered and the domain of applicability discussed.
Atomic ionization of germanium by neutrinos from an ab initio approach
Energy Technology Data Exchange (ETDEWEB)
Chen, Jiunn-Wei [Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China); National Center for Theoretical Sciences and Leung Center for Cosmology and Particle Astrophysics, National Taiwan University, Taipei 10617, Taiwan (China); Chi, Hsin-Chang [Department of Physics, National Dong Hwa University, Shoufeng, Hualien 97401, Taiwan (China); Huang, Keh-Ning [Department of Physics, Sichuan University, Chengdu, Sichuan (China); Department of Physics, Fuzhou University, Fuzhou, Fujian (China); Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China); Liu, C.-P. [Department of Physics, National Dong Hwa University, Shoufeng, Hualien 97401, Taiwan (China); Shiao, Hao-Tse [Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China); Singh, Lakhwinder [Institute of Physics, Academia Sinica, Taipei 11529, Taiwan (China); Department of Physics, Banaras Hindu University, Varanasi 221005 (India); Wong, Henry T. [Institute of Physics, Academia Sinica, Taipei 11529, Taiwan (China); Wu, Chih-Liang; Wu, Chih-Pan [Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China)
2014-04-04
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.
Phosphine adsorption and dissociation on the Si(001) surface: An ab initio survey of structures
Warschkow, O.; Wilson, H. F.; Marks, N. A.; Schofield, S. R.; Curson, N. J.; Smith, P. V.; Radny, M. W.; McKenzie, D. R.; Simmons, M. Y.
2005-09-01
We report a comprehensive ab initio survey of possible dissociation intermediates of phosphine (PH3) on the Si(001) surface. We assign three scanning tunneling microscopy (STM) features, commonly observed in room-temperature dosing experiments, to PH2+H , PH+2H , and P+3H species, respectively, on the basis of calculated energetics and STM simulation. These assignments and a time series of STM images which shows these three STM features converting into another, allow us to outline a mechanism for the complete dissociation of phosphine on the Si(001) surface. This mechanism closes an important gap in the understanding of the doping process of semiconductor devices.
Rurali, R.; Suñé, J.; Cartoixà, X.
2007-02-01
We propose an approach to the fabrication of one-dimensional nanostructures, based on the design of a pattern of channels onto a semiconductor surface. The feasibility of this approach is demonstrated by means of ab initio and empirical electronic structure calculations. When the channel diameter is sufficiently larger than the interstitial space, the resulting pillars constitute an ordered array of electronically independent, though mechanically connected nanowires. In the opposite regime a tunable metamaterial results. The proposed method provides a path to the realization of uniform quantum wires—both in size and doping characteristics—while easing electrical contacting.
Ab initio potential-energy surface for the reaction Ca+HCl --> CaCl+H
Verbockhaven, Gilles; Sanz, Cristina; Groenenboom, Gerrit C.; Roncero, Octavio; van der Avoird, Ad
2005-01-01
The potential-energy surface of the ground electronic state of CaHCl has been obtained from 6400 ab initio points calculated at the multireference configuration-interaction level and represented by a global analytical fit. The Ca+HCl --> CaCl+H reaction is endothermic by 5100 cm–1 with a barrier of 4470 cm–1 at bent geometry, taking the zero energy in the Ca+HCl asymptote. On both sides of this barrier are potential wells at linear geometries, a shallow one due to van der Waals interactions i...
A transferable ab-initio based force field for aqueous ions
Tazi, Sami; Rotenberg, Benjamin; Turq, Pierre; Vuilleumier, Rodolphe; Salanne, Mathieu; 10.1063/1.3692965
2012-01-01
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.
Ab Initio Investigations of the C2F4S Isomers and of Their Interconversions
DEFF Research Database (Denmark)
Shim, Irene; Vallano-Lorenzo, Sandra
2003-01-01
The transition states and the activation energies for the unobserved isomerization reactions between the three possible C2F4S isomers with divalent sulfur, trifluorothioacetyl fluoride 1, tetrafluorothiirane 2, and trifluoroethenesulfenyl fluoride 3, have been determined by ab initio Hartree-Fock, Møller-Plesset second order perturbation calculations and by Gaussian-3 theory. The results show that the unobserved isomerization reactions are feasible. Furthermore, all three isomers should exist as stable species, but the unknown isomer, 3, is considerably less stable than the known isomers, 1 and 2.
Ab initio calculations of Curie temperatures in GdX compounds
International Nuclear Information System (INIS)
We present calculations of Curie temperatures of selected GdX (X = Zn, Rh, Mg, Cd) compounds with a cubic CsCl structure. Exchange interactions are obtained from ab initio electronic structure calculations in the framework of density functional theory. Critical temperatures are evaluated using two approaches, namely the mean-field approximation (MFA) and a more involved, random phase approximation (RPA). Calculated critical temperatures serve as theoretical upper estimate (MFA) and lower estimate (RPA) of an exact critical temperature given by the Heisenberg model. Obtained results are in fair agreement with experimental values
Ab initio studies of structure and magnetic structure in YCo3H2
International Nuclear Information System (INIS)
We present an ab initio density functional study of magnetic phase transitions in the YCo3H2 system. The augmented plane wave and local orbital method as employed in the WIEN2K code is used to predict the structure and electronic structure of this compound. Comparison is made with recent X-ray diffraction and magnetization studies. The calculations suggest that the YCo3H2 system is ferrimagnetic in character. Further, fixed spin moment calculations are used to predict and interpret magnetic phase transitions observed in externally applied magnetic fields
Santi, G; Dugdale, S B; Jarlborg, T
2001-12-10
The recent discovery of superconductivity coexisting with weak itinerant ferromagnetism in the d-electron intermetallic compound ZrZn2 strongly suggests spin-fluctuation mediated superconductivity. Ab initio electronic structure calculations of the Fermi surface and generalized susceptibilities are performed to investigate the viability of longitudinal spin-fluctuation-induced spin-triplet superconductivity in the ferromagnetic state. The critical temperature is estimated to be of the order of 1 K. Additionally, it is shown that in spite of a strong electron-phonon coupling ( lambda(ph) = 0.7), conventional s-wave superconductivity is inhibited by the presence of strong spin fluctuations. PMID:11736533
Ab-initio study of disorder broadening of core photoemission spectra in random metallic alloys
Marten, Tobias
2004-01-01
Ab-initio results of the core-level shift and the distribution about the average for the 3d5/2 electrons of Ag, Pd and 2p3/2 of Cu are presented for the face-centered-cubic AgPd and CuPd random alloys. The complete screening model, which includes both initial and final states effects in the same scheme, has been used in the investigations. The alloys have been modeled with a supercell containing 256 atoms. Density-functional theory calculations are carried out using the locally self consiste...
Quantum chemistry the development of ab initio methods in molecular electronic structure theory
Schaefer III, Henry F
2012-01-01
This guide is guaranteed to prove of keen interest to the broad spectrum of experimental chemists who use electronic structure theory to assist in the interpretation of their laboratory findings. A list of 150 landmark papers in ab initio molecular electronic structure methods, it features the first page of each paper (which usually encompasses the abstract and introduction). Its primary focus is methodology, rather than the examination of particular chemical problems, and the selected papers either present new and important methods or illustrate the effectiveness of existing methods in predi
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)
Ab initio electronic properties of dual phosphorus monolayers in silicon
DEFF Research Database (Denmark)
Drumm, Daniel W.; Per, Manolo C.
2014-01-01
In the midst of the epitaxial circuitry revolution in silicon technology, we look ahead to the next paradigm shift: effective use of the third dimension - in particular, its combination with epitaxial technology. We perform ab initio calculations of atomically thin epitaxial bilayers in silicon, investigating the fundamental electronic properties of monolayer pairs. Quantitative band splittings and the electronic density are presented, along with effects of the layers’ relative alignment and comments on disordered systems, and for the first time, the effective electronic widths of such device components are calculated.
International Nuclear Information System (INIS)
Pentacoordination of boron, carbon, aluminium, and silicon atoms in bicyclic organic compounds of the pentalene type was studied using the ab initio RHF/6-31G** and MP2(full)/6-31G** methods. It was shown that the ability of the atom, i.e. as the number of the element of Group 3A or 4A of the Periodic system increases. At the same time, the reverse tendencies are observed in the 2nd and 3rd periods of the Periodic system, viz., the ability of the atom to form pentacoordinate structures increases on going from C to B and from Al to Si atom
Temperature dependent mechanical properties of Mo–Si–B compounds via ab initio molecular dynamics
Dharmawardhana, C. C.; R. Sakidja; S. Aryal; Ching, W. Y.
2013-01-01
A new method was proposed to obtain high temperature mechanical properties with a combination of ab initio molecular dynamics and stress-strain analyses. It was applied to compounds in the Mo–Si–B ternary system, namely, T1 (Mo5Si3) and T2 (Mo5SiB2) phases. The calculated coefficient of thermal expansion, thermal expansion anisotropy, and elastic constants agree well with those from the available experiments. The method enables us to theoretically access these properties up to 2000 K.
Enhancing mechanical toughness of aluminum surfaces by nano-boron implantation: An ab initio study
Zhu, Zhen; Kwon, Dae-Gyeon; Kwon, Young-Kyun; Tománek, David
2015-01-01
Searching for ways to enhance surface hardness of aluminum, we study the equilibrium structure, stability, elastic properties and formation dynamics of a boron-enriched surface using ab initio density functional calculations. We used molecular dynamics simulations to model the implantation of energetic boron nanoparticles in Al and identify structural arrangements that optimize the formation of strong covalent Bsbnd Al bonds. Nano-indentation simulations based on constrained optimization suggest that presence of boron nanostructures in the subsurface region enhances significantly the mechanical hardness of aluminum surfaces.
Relativistic ab initio spectroscopy study of forbidden lines of singly ionized zinc
International Nuclear Information System (INIS)
The ab initio calculation has been carried out to study the astrophysically important forbidden electromagnetic transition rates of singly ionized zinc (Zn II). Electron correlations are considered to all orders using coupled-cluster theory in the relativistic framework. Calculated excitation energies are in excellent agreement with the experimental values, wherever available. Forbidden transition rates due to the magnetic dipole and electric quadrupole transitions are estimated for the first time in the literature, to our knowledge. These transitions span the range of ultraviolet, visible and near infrared regions, and are crucial for astrophysical observations.
Complex coupled-cluster approach to an ab-initio description of open quantum systems
Hagen, G.; Dean, D. J.; Hjorth-jensen, M.; Papenbrock, T.
2006-01-01
We develop ab-initio coupled-cluster theory to describe resonant and weakly bound states along the neutron drip line. We compute the ground states of the helium chain 3-10He within coupled-cluster theory in singles and doubles (CCSD) approximation. We employ a spherical Gamow-Hartree-Fock basis generated from the low-momentum N3LO nucleon-nucleon interaction. This basis treats bound, resonant, and continuum states on equal footing, and is therefore optimal for the descriptio...
Ramírez-Solís, A.; Jolibois, F.; Maron, L.
2010-01-01
We study the finite temperature dynamical process followed by the D 2d singlet ground state of tetraoxygen, O 4. Born-Oppenheimer ab initio molecular dynamics (AIMD) simulations are done at near-room temperature and at 700 K using a calibrated DFT-based electronic structure description. The vibrational spectra are reported and the lowest vibrational modes are identified, which correlate well with ab initio static predictions. The largest non-harmonic contributions on the spectra are found for the modes involving ?5(B 1) and ?6(A 1) quanta. The relative vibrational peak intensities provide valuable information for the identification of this as yet undetected stable polyoxygen species.
Lee, Jeehye
2010-01-01
We present the first systematic {\\em ab initio} study of anti-ferrodistortive (AFD) order in Ruddlesden-Popper (RP) phases of strontium titanate, Sr$_{1+n}$Ti$_n$O$_{3n+1}$, as a function of both compressive epitaxial strain and phase number $n$. We find all RP phases to exhibit AFD order under a significant range of strains, recovering the bulk AFD order as $\\sim 1/n^2$. A Ginzburg-Landau Hamiltonian generalized to include inter-octahedral interactions reproduces our {\\em ab initio} results well, opening a pathway to understanding other nanostructured perovskite systems.
Palacios Clemente, Pablo; Aguilera Bonet, Irene; Wahno?n Benarroch, Perla
2008-01-01
In this work, we present frozen phonon and linear response ab-initio research into the vibrational properties of the CuGaS2 chalcopyrite and transition metal substituted (CuGaS2)M alloys. These systems are potential candidates for developing a novel solar-cell material with enhanced optoelectronic properties based in the implementation of the intermediate-band concept. We have previously carried out ab-initio calculations of the electronic properties of these kinds of chalcopyrite metal alloy...
K?dziera, Dariusz; ?uchowski, Piotr S; Knoop, Steven
2015-01-01
We have obtained accurate ab initio quartet potentials for the diatomic metastable triplet helium + alkali-metal (Li, Na, K, Rb) systems, using all-electron restricted open-shell coupled cluster singles and doubles with noniterative triples corrections [CCSD(T)] calculations and accurate calculations of the long-range $C_6$ coefficients. These potentials provide accurate ab initio quartet scattering lengths, which for these many-electron systems is possible, because of the small reduced masses and shallow potentials that results in a small amount of bound states. Our results are relevant for ultracold metastable triplet helium + alkali-metal mixture experiments.
Janisch, Rebecca; Hartmaier, Alexander
2010-01-01
We have performed ab-initio tensile tests of bulk Al along different tensile axes, as well as perpendicular to different grain boundaries to determine mechanical properties such as interface energy, work of separation and theoretical strength. We show that all the different investigated geometries exhibit energy-displacement curves that can be brought into coincindence in the spirit of the well known UBER curve. This simplyfies significantly the calculation of ab-initio tensile strengths for the whole parameter space of grain boundaries.
Han, Huixian; Li, Anyang; Guo, Hua
2014-12-01
A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S0) electronic state has been constructed by fitting ˜37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm-1. The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies up to 12 700 cm-1 above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction.
Deviational simulation of phonon transport in graphene ribbons with ab initio scattering
International Nuclear Information System (INIS)
We present a deviational Monte Carlo method for solving the Boltzmann-Peierls equation with ab initio 3-phonon scattering, for temporally and spatially dependent thermal transport problems in arbitrary geometries. Phonon dispersion relations and transition rates for graphene are obtained from density functional theory calculations. The ab initio scattering operator is simulated by an energy-conserving stochastic algorithm embedded within a deviational, low-variance Monte Carlo formulation. The deviational formulation ensures that simulations are computationally feasible for arbitrarily small temperature differences, while the stochastic treatment of the scattering operator is both efficient and exhibits no timestep error. The proposed method, in which geometry and phonon-boundary scattering are explicitly treated, is extensively validated by comparison to analytical results, previous numerical solutions and experiments. It is subsequently used to generate solutions for heat transport in graphene ribbons of various geometries and evaluate the validity of some common approximations found in the literature. Our results show that modeling transport in long ribbons of finite width using the homogeneous Boltzmann equation and approximating phonon-boundary scattering using an additional homogeneous scattering rate introduces an error on the order of 10% at room temperature, with the maximum deviation reaching 30% in the middle of the transition regime.
Goubet, Manuel; Motiyenko, Roman A; Margulès, Laurent; Guillemin, Jean-Claude
2012-06-01
The millimeter-wave rotational spectrum of an organomercury compound, ethylmercury hydride, has been recorded and assigned for the first time. The spectroscopic study is complemented by quantum chemical calculations taking into account relativistic effects on the mercury atom. The very good agreement between theoretical and experimental molecular parameters validates the chosen ab initio method, in particular its capability to predict accurate quartic centrifugal distortion constants related to this type of compound. Estimations of the nuclear quadrupole coupling constants have less predictive power than those of the structural parameters, but are good enough to satisfy the spectroscopic needs. In addition, the orientation of the axis of the H-Hg-C bonds deduced from the experimental nuclear quadrupole coupling constants compares well with the corresponding ab initio value. From the good agreement between experimental and theoretical results, together with the observation of the six most abundant isotopes of mercury, ethylmercury hydride is unambiguously identified as the product of the chemical reaction described here, and its calculated equilibrium geometry is confirmed. PMID:22587478
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
Renison, C Alicia; Fernandes, Kyle D; Naidoo, Kevin J
2015-07-01
This article describes an extension of the quantum supercharger library (QSL) to perform quantum mechanical (QM) gradient and optimization calculations as well as hybrid QM and molecular mechanical (QM/MM) molecular dynamics simulations. The integral derivatives are, after the two-electron integrals, the most computationally expensive part of the aforementioned calculations/simulations. Algorithms are presented for accelerating the one- and two-electron integral derivatives on a graphical processing unit (GPU). It is shown that a Hartree-Fock ab initio gradient calculation is up to 9.3X faster on a single GPU compared with a single central processing unit running an optimized serial version of GAMESS-UK, which uses the efficient Schlegel method for s- and l-orbitals. Benchmark QM and QM/MM molecular dynamics simulations are performed on cellobiose in vacuo and in a 39 Å water sphere (45 QM atoms and 24843 point charges, respectively) using the 6-31G basis set. The QSL can perform 9.7 ps/day of ab initio QM dynamics and 6.4 ps/day of QM/MM dynamics on a single GPU in full double precision. © 2015 Wiley Periodicals, Inc. PMID:25975864
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.
Xu, Dong; Zhang, Yang
2012-07-01
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
Magnetism of small Co clusters as a probe of ab initio theory
Troparevsky, Claudia
2007-03-01
We report ab initio calculations of the electronic and magnetic properties of small Co clusters. We performed pseudopotential-based and all-electron calculations. In view of the ``unwritten theorem'' that electron localization enhances the electronic correlations, we have also considered the LDA+U functional, which is tailored for the strong-correlation problem associated with, e.g., partially-filled d shells. As a result of the weak dependence of the total energy on the calculated magnetic moment, the latter is very sensitive to the method employed. Thus, the magnetic moments obtained in the all-electron and pseudopotential calculations are quite different. Furthermore, the on-site Hubbard U enhances the magnetic moment significantly. The available experimental data for the magnetic moment of small clusters [Billas et al., Science 265, 1682 (1994)] are consistent with this enhancement. Additional Stern-Gerlach measurements for smaller clusters would, in combination with our ab initio results, constitute a direct determination of the U for these prototypes of correlated-electron behavior. (*) Supported by NSF Grant ITR DMR-0219332 (+) Managed by UT-Battelle for the U.S. DOE under contract DE- AC05-00OR22725
Ab Initio Calculations and Raman and SERS Spectral Analyses of Amphetamine Species
DEFF Research Database (Denmark)
Berg, Rolf W.; NØrbygaard, Thomas
2011-01-01
For the first time, the differences between the spectra of amphetamine and amphetamine-H+ and between different conformers are thoroughly studied by ab initio model calculations, and Raman and surface-enhanced Raman spectroscopy (SERS) spectra are measured for different species of amphetamine. The spectra of amphetamine and amphetamine-H+ sampleswere obtained and assigned according to a comparison of the experimental spectra and the ab initio MO calculations, performed using the Gaussian 03W program (Gaussian, Inc., Pittsburgh, PA). The analyses were based on complete geometry minimization 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.
Ab initio quantum chemistry in parallel-portable tools and applications
International Nuclear Information System (INIS)
In common with many of the computational sciences, ab initio chemistry faces computational constraints to which a partial solution is offered by the prospect of highly parallel computers. Ab initio codes are large and complex (O(105) lines of FORTRAN), representing a significant investment of communal effort. The often conflicting requirements of portability and efficiency have been successfully resolved on vector computers by reliance on matrix oriented kernels. This proves inadequate even upon closely-coupled shared-memory parallel machines. We examine the algorithms employed during a typical sequence of calculations. Then we investigate how efficient portable parallel implementations may be derived, including the complex multi-reference singles and doubles configuration interaction algorithm. A portable toolkit, modeled after the Intel iPSC and the ANL-ACRF PARMACS, is developed, using shared memory and TCP/IP sockets. The toolkit is used as an initial platform for programs portable between LANS, Crays and true distributed-memory MIMD machines. Timings are presented. 53 refs., 4 tabs
Symmetry-Adapted Ab Initio Shell Model for Nuclear Structure Calculations
International Nuclear Information System (INIS)
An innovative concept, the symmetry-adapted ab initio shell model, that capitalizes on partial as well as exact symmetries that underpin the structure of nuclei, is discussed. This framework is expected to inform the leading features of nuclear structure and reaction data for light and medium mass nuclei, which are currently inaccessible by theory and experiment and for which predictions of modern phenomenological models often diverge. We use powerful computational and group-theoretical algorithms to perform ab initio CI (configuration-interaction) calculations in a model space spanned by SU(3) symmetry-adapted many-body configurations with the JISP16 nucleon-nucleon interaction. We demonstrate that the results for the ground states of light nuclei up through A = 16 exhibit a strong dominance of low-spin and high-deformation configurations together with an evident symplectic structure. This, in turn, points to the importance of using a symmetry-adapted framework, one based on an LS coupling scheme with the associated spatial configurations organized according to deformation.
Ab initio study on electron excitation and electron transfer in tryptophan-tyrosine system
International Nuclear Information System (INIS)
In this article, ab initio calculation has been performed to evaluate the transition energy of electronic excitation in tryptophan and tyrosine by using semiempirical molecular orbital method AM1 and complete active space self-consistent field method. The solvent effect has been considered by means of the conductor-like screening model. After geometric optimizations of isolated tryptophan and tyrosine, and their corresponding radicals and cations, reaction heat of these electron transfer reactions have been obtained by the means of complete active space self-consistent field method. The transition energies from the ground state, respectively, to the lowest excited state and to the lowest triplet state of these two amino acids are also calculated and compared with the experimentally observed values. The ionization potential and electron affinity are also calculated for tryptophan and tyrosine employing Koopmans' theorem and ab initio calculation. Compared with the experimental measurements, the theoretical results are found satisfactory. Theoretical results give good explanations on the experimental phenomena that N3· can preferably oxide the side chain of tryptophan residue and then the electron transfer from tyrosine residue to tryptophan residue follows in peptides involving tryptophan and tyrosine
Ab initio study on electron excitation and electron transfer in tryptophan tyrosine system
Tong, Jing; Li, Xiang-Yuan
2002-11-01
In this article, ab initio calculation has been performed to evaluate the transition energy of electronic excitation in tryptophan and tyrosine by using semiempirical molecular orbital method AM1 and complete active space self-consistent field method. The solvent effect has been considered by means of the conductor-like screening model. After geometric optimizations of isolated tryptophan and tyrosine, and their corresponding radicals and cations, reaction heat of these electron transfer reactions have been obtained by the means of complete active space self-consistent field method. The transition energies from the ground state, respectively, to the lowest excited state and to the lowest triplet state of these two amino acids are also calculated and compared with the experimentally observed values. The ionization potential and electron affinity are also calculated for tryptophan and tyrosine employing Koopmans' theorem and ab initio calculation. Compared with the experimental measurements, the theoretical results are found satisfactory. Theoretical results give good explanations on the experimental phenomena that N 3rad can preferably oxide the side chain of tryptophan residue and then the electron transfer from tyrosine residue to tryptophan residue follows in peptides involving tryptophan and tyrosine.
Operator evolution for ab initio electric dipole transitions of 4 He
Schuster, Micah; Quaglioni, Sofia; Johnson, Calvin; Jurgenson, Eric; Navratil, Petr
2015-04-01
A goal of nuclear theory is to make quantitative predictions of low-energy nuclear observables starting from accurate microscopicinternucleon forces. Modern effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence of ab initio calculations as a function of the model space size, is a major element of such an effort. The consistent simultaneous transformation of external operators, however, has been overlooked in applications of the theory, particularly for non-scalar transitions. We study the evolution of the electric dipole operator in the framework of the similarity-renormalization group method and apply the renormalized matrix elements to the calculation of the 4 He total photo absorption cross section and electric dipole polarizability. All observables are calculated within the ab initio no-core shell model. We find that, although seemingly small, the effects of induced operators on the photo absorption cross section are comparable in magnitude to the correction produced by including the three-nucleon force and cannot be neglected. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
Deviational simulation of phonon transport in graphene ribbons with ab initio scattering
Energy Technology Data Exchange (ETDEWEB)
Landon, Colin D.; Hadjiconstantinou, Nicolas G. [Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)
2014-10-28
We present a deviational Monte Carlo method for solving the Boltzmann-Peierls equation with ab initio 3-phonon scattering, for temporally and spatially dependent thermal transport problems in arbitrary geometries. Phonon dispersion relations and transition rates for graphene are obtained from density functional theory calculations. The ab initio scattering operator is simulated by an energy-conserving stochastic algorithm embedded within a deviational, low-variance Monte Carlo formulation. The deviational formulation ensures that simulations are computationally feasible for arbitrarily small temperature differences, while the stochastic treatment of the scattering operator is both efficient and exhibits no timestep error. The proposed method, in which geometry and phonon-boundary scattering are explicitly treated, is extensively validated by comparison to analytical results, previous numerical solutions and experiments. It is subsequently used to generate solutions for heat transport in graphene ribbons of various geometries and evaluate the validity of some common approximations found in the literature. Our results show that modeling transport in long ribbons of finite width using the homogeneous Boltzmann equation and approximating phonon-boundary scattering using an additional homogeneous scattering rate introduces an error on the order of 10% at room temperature, with the maximum deviation reaching 30% in the middle of the transition regime.
He, Yuping
2015-03-01
We present calculations of the thermal transport coefficients of Si-based clathrates and solar perovskites, as obtained from ab initio calculations and models, where all input parameters derived from first principles. We elucidated the physical mechanisms responsible for the measured low thermal conductivity in Si-based clatherates and predicted their electronic properties and mobilities, which were later confirmed experimentally. We also predicted that by appropriately tuning the carrier concentration, the thermoelectric figure of merit of Sn and Pb based perovskites may reach values ranging between 1 and 2, which could possibly be further increased by optimizing the lattice thermal conductivity through engineering perovskite superlattices. We present calculations of the thermal transport coefficients of Si-based clathrates and solar perovskites, as obtained from ab initio calculations and models, where all input parameters derived from first principles. We elucidated the physical mechanisms responsible for the measured low thermal conductivity in Si-based clatherates and predicted their electronic properties and mobilities, which were later confirmed experimentally. We also predicted that by appropriately tuning the carrier concentration, the thermoelectric figure of merit of Sn and Pb based perovskites may reach values ranging between 1 and 2, which could possibly be further increased by optimizing the lattice thermal conductivity through engineering perovskite superlattices. Work done in collaboration with Prof. G. Galli, and supported by DOE/BES Grant No. DE-FG0206ER46262.
Tanha, Matteus; Cappiello, Alex; Gordon, Geoffrey J; Yaron, David J
2013-01-01
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...
Time-domain ab initio modeling of photoinduced dynamics at nanoscale interfaces.
Wang, Linjun; Long, Run; Prezhdo, Oleg V
2015-04-01
Nonequilibrium processes involving electronic and vibrational degrees of freedom in nanoscale materials are under active experimental investigation. Corresponding theoretical studies are much scarcer. The review starts with the basics of time-dependent density functional theory, recent developments in nonadiabatic molecular dynamics, and the fusion of the two techniques. Ab initio simulations of this kind allow us to directly mimic a great variety of time-resolved experiments performed with pump-probe laser spectroscopies. The focus is on the ultrafast photoinduced charge and exciton dynamics at interfaces formed by two complementary materials. We consider purely inorganic materials, inorganic-organic hybrids, and all organic interfaces, involving bulk semiconductors, metallic and semiconducting nanoclusters, graphene, carbon nanotubes, fullerenes, polymers, molecular crystals, molecules, and solvent. The detailed atomistic insights available from time-domain ab initio studies provide a unique description and a comprehensive understanding of the competition between electron transfer, thermal relaxation, energy transfer, and charge recombination processes. These advances now make it possible to directly guide the development of organic and hybrid solar cells, as well as photocatalytic, electronic, spintronic, and other devices relying on complex interfacial dynamics. PMID:25622188
Ground state analytical ab initio intermolecular potential for the Cl2-water system.
Hormain, Laureline; Monnerville, Maurice; Toubin, Céline; Duflot, Denis; Pouilly, Brigitte; Briquez, Stéphane; Bernal-Uruchurtu, Margarita I; Hernández-Lamoneda, Ramón
2015-04-14
The chlorine/water interface is of crucial importance in the context of atmospheric chemistry. Modeling the structure and dynamics at this interface requires an accurate description of the interaction potential energy surfaces. We propose here an analytical intermolecular potential that reproduces the interaction between the Cl2 molecule and a water molecule. Our functional form is fitted to a set of high level ab initio data using the coupled-cluster single double (triple)/aug-cc-p-VTZ level of electronic structure theory for the Cl2 - H2O complex. The potential fitted to reproduce the three minima structures of 1:1 complex is validated by the comparison of ab initio results of Cl2 interacting with an increasing number of water molecules. Finally, the model potential is used to study the physisorption of Cl2 on a perfectly ordered hexagonal ice slab. The calculated adsorption energy, in the range 0.27 eV, shows a good agreement with previous experimental results. PMID:25877581
Ab-initio electronic and magnetic properties of Fe-Al alloys
Directory of Open Access Journals (Sweden)
Apiñaniz, E.
2000-06-01
Full Text Available This work presents ab-initio self-consistent calculations performed with the TB-LMTO code to study the different phases of the Fe-Al phase diagram, corresponding to the ordered structures B2, DO3 and B32 and for Fe50Al50 and Fe3Al compositions. Both, unpolarized and spin-polarized calculations have been performed to deduce the energetic difference between the paramagnetic and ferromagnetic state of the corresponding structure. Calculations for the disordered structures have also been performed for the previously mentioned compositions. These results show that by disordering the alloy magnetism is enhanced and that the equilibrium lattice parameter increases.
En este trabajo se presentan cálculos autoconsistentes ab-initio realizados con el método TB-LMTO (Tight Binding Linear Muffin Tin Orbital con el fin de estudiar las diferentes estructuras que se presentan en el diagrama de fases de las aleaciones Fe-Al. Se han estudiado las estructuras ordenadas B2, DO3 y B32 para las siguientes concentraciones: Fe50Al50 y Fe3Al. Asimismo, se han realizado cálculos teniendo y sin tener en cuenta la polarización de spin con el fin de poder deducir la diferencia energética entre los estados ferromágneticos y paramágneticos de la misma estructura. Por otra parte se han realizado estos mismos cálculos para estructuras desordenadas y las mismas concentraciones. Los resultados muestran que mediante el desorden aumenta el magnetismo de estas aleaciones y crece el parámetro de red.
Energy Technology Data Exchange (ETDEWEB)
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
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.
Ab initio investigation of the spin Hall effect for non-magnetic alloys
Energy Technology Data Exchange (ETDEWEB)
Lowitzer, Stephan; Koedderitzsch, Diemo; Ebert, Hubert [Department Chemie, Physikalische Chemie, Universitaet Muenchen, Butenandstr. 5-13, 81377 Muenchen (Germany)
2010-07-01
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.
Electron transport in extended carbon-nanotube/metal contacts: Ab initio based Green function method
Fediai, Artem; Ryndyk, Dmitry A.; Cuniberti, Gianaurelio
2015-04-01
We have developed a new method that is able to predict the electrical properties of the source and drain contacts in realistic carbon nanotube field effect transistors (CNTFETs). It is based on large-scale ab initio calculations combined with a Green function approach. For the first time, both internal and external parts of a realistic CNT-metal contact are taken into account at the ab initio level. We have developed the procedure allowing direct calculation of the self-energy for an extended contact. Within the method, it is possible to calculate the transmission coefficient through a contact of both finite and infinite length; the local density of states can be determined in both free and embedded CNT segments. We found perfect agreement with the experimental data for Pd and Al contacts. We have explained why CNTFETs with Pd electrodes are p -type FETs with ohmic contacts, which can carry current close to the ballistic limit (provided contact length is large enough), whereas in CNT-Al contacts transmission is suppressed to a significant extent, especially for holes.
Forced coalescence phasing: a method for ab initio determination of crystallographic phases.
Drendel, W B; Davé, R D; Jain, S
1995-01-17
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
Embedding parameters in ab initio theory to develop approximations based on molecular similarity
Tanha, Matteus; Kaul, Shiva; Cappiello, Alexander; Gordon, Geoffrey J; Yaron, David J
2015-01-01
A means to take advantage of molecular similarity to lower the computational cost of electronic structure theory is explored, in which parameters are embedded into a low-cost, low-level (LL) ab initio model and adjusted to obtain agreement with results from a higher-level (HL) ab initio model. A parametrized LL (pLL) model is created by multiplying selected matrix elements of the Hamiltonian operators by scaling factors that depend on element types. Various schemes for applying the scaling factors are compared, along with the impact of making the scaling factors linear functions of variables related to bond lengths, atomic charges, and bond orders. The models are trained on ethane and ethylene, substituted with -NH2, -OH and -F, and tested on substituted propane, propylene and t-butane. Training and test datasets are created by distorting the molecular geometries and applying uniform electric fields. The fitted properties include changes in total energy arising from geometric distortions or applied fields, an...
Time-Domain Ab Initio Modeling of Photoinduced Dynamics at Nanoscale Interfaces
Wang, Linjun; Long, Run; Prezhdo, Oleg V.
2015-04-01
Nonequilibrium processes involving electronic and vibrational degrees of freedom in nanoscale materials are under active experimental investigation. Corresponding theoretical studies are much scarcer. The review starts with the basics of time-dependent density functional theory, recent developments in nonadiabatic molecular dynamics, and the fusion of the two techniques. Ab initio simulations of this kind allow us to directly mimic a great variety of time-resolved experiments performed with pump-probe laser spectroscopies. The focus is on the ultrafast photoinduced charge and exciton dynamics at interfaces formed by two complementary materials. We consider purely inorganic materials, inorganic-organic hybrids, and all organic interfaces, involving bulk semiconductors, metallic and semiconducting nanoclusters, graphene, carbon nanotubes, fullerenes, polymers, molecular crystals, molecules, and solvent. The detailed atomistic insights available from time-domain ab initio studies provide a unique description and a comprehensive understanding of the competition between electron transfer, thermal relaxation, energy transfer, and charge recombination processes. These advances now make it possible to directly guide the development of organic and hybrid solar cells, as well as photocatalytic, electronic, spintronic, and other devices relying on complex interfacial dynamics.
Ab Initio Based Understanding of the Segregation and Diffusion Mechanisms of Hydrogen in Steels
Hickel, T.; Nazarov, R.; McEniry, E. J.; Leyson, G.; Grabowski, B.; Neugebauer, J.
2014-08-01
A microscopic understanding of the processes that lead to hydrogen embrittlement is of critical importance for developing new generations of high-strength steels. With this article, we provide an overview of insights that can be gained from ab initio based methods when investigating the segregation and diffusion mechanisms of hydrogen in steels. We first discuss the solubility and diffusion behavior of hydrogen in the ferrite, austenite, and martensite phases. We consider not only defect-free bulk phases but also the influence of alloying elements and geometric defects such as vacancies and grain boundaries. In the second part, the behavior of hydrogen in the presence of precipitates, the solubility, the surface absorption, and the influence of hydrogen on the interface cohesion are studied. Finally, we provide simulation results for the interaction of hydrogen with dislocations. For all these applications, we will comment on advantages and shortcomings of ab initio methods and will demonstrate how the obtained data and insights can complement experimental approaches to extract general trends and to identify causes of hydrogen embrittlement.
Ab initio studying of topological insulator Bi2Se3 under the stress
International Nuclear Information System (INIS)
A topological insulator is an unusual state of quantum matter which, while being an insulator in the bulk, has topologically protected electronic states at the surface. These states could be used in different applications, such as spintronics and quantum computing. However, it is difficult to distinguish the surface and bulk contributions into transport properties, such as conductivity. In order to distinguish surface and bulk contributions an external pressure could be applied. In the present work we have performed ab initio calculations of topological insulator Bi2Se3 under the stress for bulk and surface models. Calculations have been made by means of density functional theory within generalized gradient approximation, the spin-orbit interaction was taken into account as well. It was found that topologically protected surface states remains robust under the stress. Moreover, pressure tends to increase the Fermi velocity of surface electrons, as well as increase electronic density of states at the bottom of the conduction band of the bulk of Bi2Se3. Thus, the results of ab initio calculations could complement the experimental investigations of high pressure transport properties of topological insulators. The experimentally detected increase of carrier density could be related to the effects of the bulk.
Rotational spectrum, internal rotation barrier and ab initio calculations on 1-chloro-1-fluoroethane
Hinze, R.; Lesarri, A.; López, J. C.; Alonso, J. L.; Guarnieri, A.
1996-06-01
The microwave spectrum of 1-chloro-1-fluoroethane (CFC 151-a) has been studied in the frequency region 8-250 GHz using waveguide Fourier transform, Stark, and source modulation spectrometers. Accurate rotational, quartic, and sextic centrifugal distortion and quadrupole coupling constants have been obtained from a global fit for the ground, v17=1 (Cl-F skeletal bending mode), and v18=1 (CH3 torsional) vibrational states of the 35Cl isotopomer and for the ground state of the 37Cl isotopomer. The larger off-diagonal element of the ? tensor was also determined for the 35Cl isotopomer. Assignment of the v17=1 and v18=1 states was confirmed by the presence of small A-E internal rotation splittings in the v18=1 state, in agreement with ab initio calculations, but in contradiction with previous assignment of the microwave spectrum by Thomas et al. [J. Chem. Phys. 61, 5072 (1974)]. The barrier height for the internal rotation of the methyl group was determined to be 3814(11) cal/mol, and compared with the result of ab initio calculations made for 1-chloro-1-fluoroethane and other related chlorine or fluorine substituted ethanes.
Ground state analytical ab initio intermolecular potential for the Cl2-water system
Hormain, Laureline; Monnerville, Maurice; Toubin, Céline; Duflot, Denis; Pouilly, Brigitte; Briquez, Stéphane; Bernal-Uruchurtu, Margarita I.; Hernández-Lamoneda, Ramón
2015-04-01
The chlorine/water interface is of crucial importance in the context of atmospheric chemistry. Modeling the structure and dynamics at this interface requires an accurate description of the interaction potential energy surfaces. We propose here an analytical intermolecular potential that reproduces the interaction between the Cl2 molecule and a water molecule. Our functional form is fitted to a set of high level ab initio data using the coupled-cluster single double (triple)/aug-cc-p-VTZ level of electronic structure theory for the Cl2 - H2O complex. The potential fitted to reproduce the three minima structures of 1:1 complex is validated by the comparison of ab initio results of Cl2 interacting with an increasing number of water molecules. Finally, the model potential is used to study the physisorption of Cl2 on a perfectly ordered hexagonal ice slab. The calculated adsorption energy, in the range 0.27 eV, shows a good agreement with previous experimental results.
Importance-truncated no-core shell model for ab-initio nuclear structure calculations
International Nuclear Information System (INIS)
Ab-initio methods for the solution of the nuclear many-body problem play a crucial role for the development of a consistent QCD-based theory of nuclear structure and reactions. Many of the established ab-initio methods, like the no-core shell model (NCSM), are limited to light nuclei or very small N max??, simply because the model spaces become prohibitively large. In this talk an adaptive importance-truncation scheme is presented, which employs an a priori selection of the important basis states via perturbation theory and thus reduces the model-space dimension to a tractable size. The major elements and properties of this importance-truncated no-core shell model (IT-NCSM) are discussed. Results for ground and excited states of closed and open-shell nuclei up to mass A?40 are presented and compared to full NCSM calculations. The properties of the IT-NCSM are contrasted with those of coupled-cluster approaches. An outlook to reaction calculations using IT-NCSM wave functions is given.
Ab initio potential energy surfaces for NH(3?-)-NH(3?-) with analytical long range
Janssen, Liesbeth M. C.; Groenenboom, Gerrit C.; van der Avoird, Ad; ?uchowski, Piotr S.; Podeszwa, Rafa?
2009-12-01
We present four-dimensional ab initio potential energy surfaces for the three different spin states of the NH(?3-)-NH(?3-) complex. The potentials are partially based on the work of Dhont et al. [J. Chem. Phys. 123, 184302 (2005)]. The surface for the quintet state is obtained at the RCCSD(T)/augmented correlation-consistent polarized valence triple-zeta (aug-cc-pVTZ) level of theory and the energy differences with the singlet and triplet states are calculated at the complete active space with nth-order perturbation theory/aug-cc-pVTZ (n =2,3) level of theory. The ab initio potentials are fitted to coupled spherical harmonics in the angular coordinates, and the long range is further expanded as a power series in 1/R. The RCCSD(T) potential is corrected for a size-consistency error of about 0.5×10-6 Eh prior to fitting. The long-range coefficients obtained from the fit are found to be in good agreement with first and second-order perturbation theory calculations.
Darkhalil, Ikhlas D; Paquet, Charles; Waqas, Mohammad; Gounev, Todor K; Durig, James R
2015-02-01
Variable temperature (-60 to -100 °C) studies of ethyldichlorophosphine, CH3CH2PCl2, of the infrared spectra (4000-400 cm(-1)) dissolved in liquid xenon have been carried out. From these data, the two conformers have been identified and the enthalpy difference has been determined between the more stable trans conformer and the less stable gauche form to be 88±9 cm(-1) (1.04±0.11 kJ/mol). The percentage of abundance of the gauche conformer is estimated to be 57% at ambient temperature. The conformational stabilities have been predicted from ab initio calculations by utilizing many different basis sets up to aug-cc-pVTZ for both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been provided for both conformers which have been predicted by MP2(full)/6-31G(d) ab initio calculations to predict harmonic force fields, wavenumbers of the fundamentals, infrared intensities, Raman activities and depolarization ratios for both conformers. Estimated r0 structural parameters have been obtained from adjusted MP2(full)/6-311+G(d,p) calculations. The results are discussed and compared to the corresponding properties of some related molecules. PMID:24618201
Ab-initio description of spin-dependent transport in disordered alloys
Energy Technology Data Exchange (ETDEWEB)
Koedderitzsch, Diemo; Lowitzer, Stephan; Ebert, Hubert [Ludwig-Maximilians-Universitaet Muenchen, Department Chemie und Biochemie, Physikalische Chemie, Muenchen (Germany)
2011-07-01
Spin-orbit induced couplings are the source of many interesting physical phenomena like the anomalous- and spin-Hall-effects (AHE, SHE), which recently received a lot of attention due to their potential application in the field of spintronics. During the last years several theoretical works have dealt with the intrinsic AHE and SHE, based on the band structure of pure materials and only few of them use a parameter free ab initio approach. We present a coherent ab initio description of both, the AHE and SHE, that is applicable to pure and disordered alloys by treating all sources, i.e. intrinsic as well as extrinsic contributions, on equal footing. We use an implementation of the Kubo-Streda equation employing the fully relativistic Korringa-Kohn-Rostoker (KKR) Green's function method in conjunction with the Coherent Potential Approximation (CPA) alloy theory. For discussing spin currents we employ our recently devised relativistic spin projection scheme and a corresponding generalization of the Kubo-Streda equation. We illustrate the power and versatility of the approach by giving several examples.
Schwenk, Christian F.; Rode, Bernd M.
2003-11-01
Copper(II) was used as a model system to investigate the relevance of including the full second hydration shell in ab initio treatment while describing hydrated ions in hybrid quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulations. Three different simulation techniques were applied (Hartree-Fock, B3LYP, and resolution of the identity density functional theory) to find a good compromise between accuracy and simulation speed. To discuss details of the hydration structure radial distribution functions, coordination number distributions and various angular distributions have been used. Dynamical properties such as vibrational motions of water molecules and ion-oxygen stretching motions were investigated using approximative normal coordinate analyses. QM/MM MD simulations offer a detailed time picture of the dynamic Jahn-Teller effect of Cu2+ showing short-term as well as long-term distortions to occur within <200 fs and 2-3 ps. The results prove that for transition metal ions such as Cu2+ the inclusion of the second shell into the ab initio treated region can be of decisive importance for obtaining accurate results and that such simulations can offer new insights into chemical dynamics on the picosecond scale.
Darkhalil, Ikhlas D.; Paquet, Charles; Waqas, Mohammad; Gounev, Todor K.; Durig, James R.
2015-02-01
Variable temperature (-60 to -100 °C) studies of ethyldichlorophosphine, CH3CH2PCl2, of the infrared spectra (4000-400 cm-1) dissolved in liquid xenon have been carried out. From these data, the two conformers have been identified and the enthalpy difference has been determined between the more stable trans conformer and the less stable gauche form to be 88 ± 9 cm-1 (1.04 ± 0.11 kJ/mol). The percentage of abundance of the gauche conformer is estimated to be 57% at ambient temperature. The conformational stabilities have been predicted from ab initio calculations by utilizing many different basis sets up to aug-cc-pVTZ for both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been provided for both conformers which have been predicted by MP2(full)/6-31G(d) ab initio calculations to predict harmonic force fields, wavenumbers of the fundamentals, infrared intensities, Raman activities and depolarization ratios for both conformers. Estimated r0 structural parameters have been obtained from adjusted MP2(full)/6-311 + G(d,p) calculations. The results are discussed and compared to the corresponding properties of some related molecules.
International Nuclear Information System (INIS)
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.
PreDisorder: ab initio sequence-based prediction of protein disordered regions
Directory of Open Access Journals (Sweden)
Eickholt Jesse
2009-12-01
Full Text Available Abstract Background Disordered regions are segments of the protein chain which do not adopt stable structures. Such segments are often of interest because they have a close relationship with protein expression and functionality. As such, protein disorder prediction is important for protein structure prediction, structure determination and function annotation. Results This paper presents our protein disorder prediction server, PreDisorder. It is based on our ab initio prediction method (MULTICOM-CMFR which, along with our meta (or consensus prediction method (MULTICOM, was recently ranked among the top disorder predictors in the eighth edition of the Critical Assessment of Techniques for Protein Structure Prediction (CASP8. We systematically benchmarked PreDisorder along with 26 other protein disorder predictors on the CASP8 data set and assessed its accuracy using a number of measures. The results show that it compared favourably with other ab initio methods and its performance is comparable to that of the best meta and clustering methods. Conclusion PreDisorder is a fast and reliable server which can be used to predict protein disordered regions on genomic scale. It is available at http://casp.rnet.missouri.edu/predisorder.html.
Energy Technology Data Exchange (ETDEWEB)
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
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.
Chiral three-nucleon interactions in ab-initio nuclear structure and reactions
International Nuclear Information System (INIS)
The prediction of nuclear structure and reaction observables based on nuclear Hamiltonians including two- and three-nucleon (NN+3N) interactions derived from chiral effective field theory constitutes a challenging task for ab-initio nuclear theory. In particular, the consistent inclusion of 3N interactions requires formal extensions of the many-body methods and, at the same time, causes a significant increase of the computational cost. This work presents the necessary steps for the inclusion and the subsequent application of 3N interactions in different ab-initio nuclear structure and reaction approaches. The first part is dedicated to the preparation of the chiral nuclear forces before they enter the many-body methods. It addresses the similarity renormalization group (SRG) as a tool to soften the initial chiral interactions and its generalization to consistently include 3N interactions. Moreover, the technically important 3N matrix-element management in a convenient basis for the subsequent many-body methods including an efficient storage scheme is discussed. In addition, a possibility to derive approximative schemes for 3N interactions using normal ordering is presented. In the second part the SRG-evolved chiral NN+3N Hamiltonians are applied in nuclear structure calculations using the importance truncated no-core shell model (IT-NCSM) as well as coupled-cluster theory. The impact of SRG-induced and chiral 3N interactions on ground-state energies and low-energy spectra of different p-shell nuclei is studied, including a sensitivity analysis concerning uncertainties of the chiral interactions in the 12C and 10B spectra. Furthermore, the first ab-initio study of even oxygen isotopes with explicit 3N interactions is presented, and by means of the normal-ordered two-body approximation the ground-state energy systematics of selected closed-shell nuclei throughout the calcium, nickel, and tin isotopic chains are obtained in qualitative agreement with experiment. The third part of this work focuses on 3N interactions in ab-initio nuclear scattering approaches. This includes a detailed discussion of the inclusion of 3N interactions in the no-core shell model combined with the resonating-group method (NCSM/RGM) with emphasis on the ability to treat targets beyond the lightest nuclei. The extended formalism is then applied to nucleon-4He scattering, where the 3N interaction overall improves scattering phase shifts, differential cross sections and analyzing powers. Finally, the no-core shell model with continuum approach, which constitutes a unified ab-initio approach to bound and scattering states resulting from the combination of the NCSM and the NCSM/RGM, is generalized to 3N interactions and applied to the neutron-8Be system to study the impact of the continuum on the 9Be energy levels. The results demonstrate the importance of the consistent treatment of continuum states.
Chiral three-nucleon interactions in ab-initio nuclear structure and reactions
Energy Technology Data Exchange (ETDEWEB)
Langhammer, Joachim
2014-04-23
The prediction of nuclear structure and reaction observables based on nuclear Hamiltonians including two- and three-nucleon (NN+3N) interactions derived from chiral effective field theory constitutes a challenging task for ab-initio nuclear theory. In particular, the consistent inclusion of 3N interactions requires formal extensions of the many-body methods and, at the same time, causes a significant increase of the computational cost. This work presents the necessary steps for the inclusion and the subsequent application of 3N interactions in different ab-initio nuclear structure and reaction approaches. The first part is dedicated to the preparation of the chiral nuclear forces before they enter the many-body methods. It addresses the similarity renormalization group (SRG) as a tool to soften the initial chiral interactions and its generalization to consistently include 3N interactions. Moreover, the technically important 3N matrix-element management in a convenient basis for the subsequent many-body methods including an efficient storage scheme is discussed. In addition, a possibility to derive approximative schemes for 3N interactions using normal ordering is presented. In the second part the SRG-evolved chiral NN+3N Hamiltonians are applied in nuclear structure calculations using the importance truncated no-core shell model (IT-NCSM) as well as coupled-cluster theory. The impact of SRG-induced and chiral 3N interactions on ground-state energies and low-energy spectra of different p-shell nuclei is studied, including a sensitivity analysis concerning uncertainties of the chiral interactions in the {sup 12}C and {sup 10}B spectra. Furthermore, the first ab-initio study of even oxygen isotopes with explicit 3N interactions is presented, and by means of the normal-ordered two-body approximation the ground-state energy systematics of selected closed-shell nuclei throughout the calcium, nickel, and tin isotopic chains are obtained in qualitative agreement with experiment. The third part of this work focuses on 3N interactions in ab-initio nuclear scattering approaches. This includes a detailed discussion of the inclusion of 3N interactions in the no-core shell model combined with the resonating-group method (NCSM/RGM) with emphasis on the ability to treat targets beyond the lightest nuclei. The extended formalism is then applied to nucleon-{sup 4}He scattering, where the 3N interaction overall improves scattering phase shifts, differential cross sections and analyzing powers. Finally, the no-core shell model with continuum approach, which constitutes a unified ab-initio approach to bound and scattering states resulting from the combination of the NCSM and the NCSM/RGM, is generalized to 3N interactions and applied to the neutron-{sup 8}Be system to study the impact of the continuum on the {sup 9}Be energy levels. The results demonstrate the importance of the consistent treatment of continuum states.
i-PI: A Python interface for ab initio path integral molecular dynamics simulations
Ceriotti, Michele; More, Joshua; Manolopoulos, David E.
2014-03-01
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic 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.
Ab initio identification of human microRNAs based on structure motifs
Directory of Open Access Journals (Sweden)
Wiuf Carsten
2007-12-01
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.
Ab initio study of the low-lying electronic states of the CaO molecule
Energy Technology Data Exchange (ETDEWEB)
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
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.
Czech Academy of Sciences Publication Activity Database
?ársky, Petr
2010-01-01
Ro?. 43, ?. 17 (2010), s. 175203. ISSN 0953-4075 R&D Projects: GA MŠk OC09079; GA MŠk(CZ) OC10046; GA ?R GA202/08/0631 Institutional research plan: CEZ:AV0Z40400503 Keywords : ab initio calculations * electron scattering * polyatomic molecules Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.902, year: 2010
Czech Academy of Sciences Publication Activity Database
?ársky, Petr
2010-01-01
Ro?. 43, ?. 17 (2010), s. 175204. ISSN 0953-4075 R&D Projects: GA MŠk OC09079; GA MŠk(CZ) OC10046; GA ?R GA202/08/0631 Institutional research plan: CEZ:AV0Z40400503 Keywords : ab initio calculations * electron scattering * polyatomic molecules Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.902, year: 2010
International Nuclear Information System (INIS)
Principal values of magnetic shielding tensors of acetylenic carbon nuclei for butadiynyltrimethylsilane and its reorientation rate in solution have been obtained from the interpretation of the 13C longitudinal relaxation data. The ab initio GIAO-CHF calculations of shielding parameters have been performed and the experimental and theoretical results have been compared. (author)
International Nuclear Information System (INIS)
The atomic valence indices VA (doubled charge dispersions) and hybrid AOs have been calculated for molecules Li2, B2, C2, N2, and F2 using the Cade and Wahl ab initio SCF MOs and Clementi and Roetti SCF AO bases. A comparison of alternative definitions of VA has been performed
Czech Academy of Sciences Publication Activity Database
Zeizinger, M.; Burda, J. V.; Šponer, Ji?í; Kapsa, V.; Leszczynski, J.
2001-01-01
Ro?. 105, ?. 34 (2001), s. 8086-8092. ISSN 0305-4470 R&D Projects: GA AV ?R IAA4050702; GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : palladium square-planar complexes * platinum analogues * ab initio Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.542, year: 2001
International Nuclear Information System (INIS)
This paper presents fundamental researches based on the electronic structure calculations and X absorption spectroscopy, allowing the knowledge on nuclear fuels at an atomic scale. They bring a better understanding of these material behavior to accurate the macroscopic simulation. The calculation methods, the experimental techniques of validation and the ab initio calculations results are detailed. (A.L.B.)
International Nuclear Information System (INIS)
This paper discuss basics of high performance computing on the example of the Latvian SuperCluster (LASC), installed at the Institute of Solid State Physics of the University of Latvia. The application of LASC to ab-initio simulations of x-ray absorption spectra from nanoparticles is considered as a particular case. (author)
Czech Academy of Sciences Publication Activity Database
Pavl?, Jana; V?eš?ál, Jan; Šob, Mojmír
Ljubljana, 2009. s. 14-14. [Workshop of the Associated Phase Diagram and Thermodynamic Committee /11./. 18.09.2009-20.09.2009, Ljubljana] Institutional research plan: CEZ:AV0Z20410507 Keywords : ab initio calculations * Laves phases * thermodynamic modelling Subject RIV: BJ - Thermodynamics
Czech Academy of Sciences Publication Activity Database
Štrof, J.; Pavl?, Jana; Wdowik, U.; Buršík, Ji?í; Šob, Mojmír; V?eš?ál, Jan
2014-01-01
Ro?. 44, MAR (2014), s. 62-69. ISSN 0364-5916 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081723 Keywords : laves phases * V-Zr system * ab initio calculations Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.394, year: 2013
Czech Academy of Sciences Publication Activity Database
Chocholoušová, Jana; Vacek, Jaroslav; Hobza, Pavel
2002-01-01
Ro?. 4, - (2002), s. 2119-2122. ISSN 1463-9076 R&D Projects: GA MŠk LN00A032 Institutional research plan: CEZ:AV0Z4040901 Keywords : formic acid dimer * ab initio calculations * molecular dynamics simulations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.838, year: 2002
Ab initio study of thermodynamics and structure of Fe-Mo and Fe-Ta C14 Laves phases.
Czech Academy of Sciences Publication Activity Database
Houserová, Jana; Šob, Mojmír
Vienna, 2004. s. -. [ TOFA 2004. 12.09.2004-17.09.2004, Vienna] R&D Projects: GA ?R GP106/03/P002; GA ?R GA106/02/0877 Keywords : ab initio calculations * Laves phase * thermodynamics Subject RIV: BM - Solid Matter Physics ; Magnetism
International Nuclear Information System (INIS)
Ab initio X? discrete variation method was used for calculation of quadrupole splitting for the rough heme models in ?- and ?-subunits of tetrameric deoxyhemoglobin accounting small stereochemical variations. The differences of theoretical values of quadrupole splitting for these heme models were obtained.
Ab-initio calculations, FT-IR and FT-Raman spectra of 2-chloro-6-methyl benzonitrile.
Czech Academy of Sciences Publication Activity Database
Kumar, V.; Panikar, Y.; Palafox, M. A.; Vats, J.K.; Kostova, I.; Lang, Kamil; Rastori, V. K.
2010-01-01
Ro?. 48, ?. 2 (2010), s. 85-94. ISSN 0019-5596 Institutional research plan: CEZ:AV0Z40320502 Keywords : Ab-initio calculations * FT-IR * FT- Raman spectra Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.511, year: 2010
Ab initio modeling of the behavior of helium and xenon in actinide dioxide nuclear fuels
International Nuclear Information System (INIS)
By means of an ab initio plane wave pseudopotential method, the behavior of helium in UO2, PuO2, AmO2 and (Am0.5Pu0.5)O2 and of xenon in UO2 is studied. We first show that a pseudopotential approach in the generalized gradient approximation (GGA) can satisfactorily describe the cohesive properties of these actinide dioxides. We then calculate the formation energies of point defects (vacancies and interstitials), as well as the incorporation and solution energies of helium in UO2, PuO2, AmO2 and (Am0.5Pu0.5)O2, and of xenon in UO2. The results are discussed according to the incorporation site of the gas atom in the fluorite lattice and according to the dioxide stoichiometry
Organic peracids: a structural puzzle for 17O NMR and ab initio chemical shift calculations.
Castiglione, Franca; Baggioli, Alberto; Citterio, Attilio; Mele, Andrea; Raos, Guido
2012-02-23
We have applied (17)O NMR spectroscopy to investigate the structure of the organic peracids formed by reaction of acetic acid (AA) or lactic acid (LA) with aqueous hydrogen peroxide (HP), which are used in several "green chemistry" applications. The interpretation of the experimental spectra has been supported by ab initio calculations of the (17)O chemical shifts for several possible species, using a continuum representation of the solvent. The combined use of these tools has also allowed us to discuss the decomposition mechanism of LA/HP solutions. The calculated electric field gradients for water, HP, and CO(2) (a decomposition product of LA) correlate well with the experimental (17)O line widths. PMID:22236273
Systematic ab initio calculations on the energetics and stability of covalent O4
Hernández-Lamoneda, Ramón; Ramírez-Solís, Alejandro
2004-06-01
Ab initio calculations with highly correlated methods together with extensive basis sets have been used to obtain the most accurate heat of formation and stability with respect to dissociation (into molecular oxygen) for the chemically bound tetraoxygen molecule. Our calculations show that the heat of formation is significantly smaller and that the barrier to dissociation is larger than previously assumed. In particular, we have shown that the previous theoretical estimate for the heat of formation of tetraoxygen was in error by a significant amount (18%-24%) owing to lack of accuracy in the theoretical method then used. Our best estimates places that value in the range 93-95 kcal/mol and this should be taken into consideration when discussing the possible relevance of tetraoxygen in a variety of experiments, as well as in the fundamental atmospheric chemical processes where oxygen species participate.
Ab-initio No-Core Gamow Shell Model calculations with realistic interactions
Papadimitriou, G; Michel, N; P?oszajczak, M; Barrett, B R
2013-01-01
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 is formulated in the rigged Hilbert space and, by using a complete Berggren ensemble, treats bound, resonant, and scattering states on equal footing. We use the Density Matrix Renormalization Group method to solve the many-body Schr\\'{o}dinger equation. To test the validity of our approach, we benchmarked the NCGSM results against Faddeev and Faddeev-Yakubovsky exact calculations for $^3$H and $^4$He nuclei. We also performed {\\textit ab initio} NCGSM calculations for the unstable nucleus $^5$He and determined the ground state energy and decay width, starting from a realistic N$^3$LO chiral interaction.
Ab initio study of topological surface states of strained HgTe
Wu, Shu-Chun; Yan, Binghai; Felser, Claudia
2014-09-01
The topological surface states of mercury telluride (HgTe) are studied by ab initio calculations assuming different strains and surface terminations. For the Te-terminated surface, a single Dirac cone exists at the ?-point. The Dirac point shifts up from the bulk valence bands into the energy gap when the substrate-induced strain increases. At the experimental strain value (0.3%), the Dirac point lies slightly below the bulk valence band maximum. A left-handed spin texture was observed in the upper Dirac cone, similar to that of the Bi2Se3-type topological insulator. For the Hg-terminated surface, three Dirac cones appear at three time-reversal-invariant momenta, excluding the ?-point, with non-trivial spin textures.
Ab initio study on the reaction between uranium and O2
International Nuclear Information System (INIS)
Optimized geometries, total energies and electronic structures of some gaseous atoms and molecules of uranium-oxygen system are calculated with harmonic vibration analysis using ab initio method. The potential energy surfaces (PESs) of the uranium oxidation process are also constructed. The calculated optimized geometries, infrared vibrational frequencies and the first ionized potential energies are in well accordance with available experimental data. Although U6p, U7s and U6d valence orbital electrons take part in the formation of U-O bond, the U5f electrons play an dominant role in this process and because the energies of U5f, U6d, U7s and Uds atomic orbitals are close to each other, these orbitals may hybrid and interact with O2p orbital, simultaneously, to form molecular orbitals of uranium oxides. The PESs show that different reaction modes result in different product geometries
International Nuclear Information System (INIS)
Using ab initio method and bearing in mind the electronic correlations, the wave functions and enthalpies of formation of basic states of CH4-xIx iodomethanes and iodomethyl radicals CH3-xIx (x=1-3) were calculated. For the molecules mentioned their geometry, frequencies of normal vibrations and other parameters were found, which permitted calculation of thermodynamic functions in the range 0-1500 K. From the latter equilibrium constants CH4-xIx?CH4-xIx-1+I and CH4-xIx+I?CH4-xIx-1 were calculated, which in their turn permitted calculating the relevant rate constants within high concentration limit
Fertitta, E.; Paulus, B.; Barcza, G.; Legeza, Ö.
2014-12-01
We have studied the metal-insulator-like transition in pseudo-one-dimensional systems, i.e., lithium and beryllium rings, through the ab initio density matrix renormalization group (DMRG) method. Performing accurate calculations for different interatomic distances and using quantum information theory, we investigated the changes occurring in the wave function between a metallic-like state and an insulating state built from free atoms. We also discuss entanglement and relevant excitations among the molecular orbitals in the Li and Be rings and show that the transition bond length can be detected using orbital entropy functions. Also, the effect of different orbital bases on the effectiveness of the DMRG procedure is analyzed comparing the convergence behavior.
Electronic states of lithium passivated germanium nanowires: An ab-initio study
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A study of the electronic and structural properties of germanium nanowires (GeNWs) was performed using the ab-initio Density Functional Theory within the generalized gradient approximation where electron-ion interactions are described by ultrasoft pseudopotentials. To study the effects of the lithium in the surface of the GeNWs we compare the electronic band structures of Hydrogen passivated GeNWs with those of partial and totally Li passivated GeNWs. The nanowires were constructed in the [001], [111] and [110] directions, using the supercell model to create different wire diameters. The results show that in the case of partial Li passivation there are localized orbitals near the valence band maximum, which would create a p-doped-kind of state. The total Li passivation created metallic states for all the wires
Electronic states of lithium passivated germanium nanowires: An ab-initio study
Trejo, A.; Carvajal, E.; Vázquez-Medina, R.; Cruz-Irisson, M.
2014-05-01
A study of the electronic and structural properties of germanium nanowires (GeNWs) was performed using the ab-initio Density Functional Theory within the generalized gradient approximation where electron-ion interactions are described by ultrasoft pseudopotentials. To study the effects of the lithium in the surface of the GeNWs we compare the electronic band structures of Hydrogen passivated GeNWs with those of partial and totally Li passivated GeNWs. The nanowires were constructed in the [001], [111] and [110] directions, using the supercell model to create different wire diameters. The results show that in the case of partial Li passivation there are localized orbitals near the valence band maximum, which would create a p-doped-kind of state. The total Li passivation created metallic states for all the wires.
Feng, Wen-Ling; Tian, Shan Xi
2015-03-12
Dissociative electron attachment (DEA) processes of six low-lying conformers (1-6) of dialanine in the gas phase are investigated by using ab initio molecular dynamics simulations. The incoming electron is captured and primarily occupies the virtual molecular orbital ?*, which is followed by the different dissociation processes. The electron attachments to conformers 1 and 2 having the stronger N-H···N and O-H···O intramolecular hydrogen bonds do not lead to fragmentations, but two different backbone bonds are broken in the DEAs to conformers 3 (or 4) and 6, respectively. It is interesting that the hydrogen abstraction of -NH from the terminal methyl group -CH3 is found in the roaming dissociation of the temporary anion of conformer 3. The present simulations enable us to have more insights into the peptide backbone bond breaks in the DEA process and demonstrate a promising way toward understanding of the radiation damages of complicated biological system. PMID:25679256
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Chemical nature of superficial hydrogen on the lithium silicate and lithium silicate doped with B, Al and Ga has been investigated by ab initio molecular orbital calculations. The charge distributions and the deprotonation energy have been obtained for the model clusters: LixH4-xSiO4 and LixH7-xSiAO7 (x=0,1; A=B, Al, Ga). It has been shown that the ionicity of surface hydrogen is strengthened by the interaction of dopant units, that operate as an electron acceptor, with surface oxygen, while it is weakened by Li atom bonded to non-bridging oxygen. Also, the deprotonation energy decreases with increasing ionicity of the superficial hydrogen. The H7SiAlO7 cluster models have the largest ionicity of surface hydrogen and the smallest deprotonation energy among the cluster models investigated
First high resolution spectroscopic studies and ab initio calculations of ethanetellurol.
Motiyenko, Roman A; Margulès, Laurent; Goubet, Manuel; Møllendal, Harald; Konovalov, Alexey; Guillemin, Jean-Claude
2010-03-01
The millimeter-wave rotational spectrum of ethanetellurol has been recorded and assigned for the first time. The spectroscopic study has been complemented by high level ab initio calculations. Geometries, total electronic energies, and harmonic vibrational frequencies have been determined at the MP2 level. A small-core relativistic pseudopotential basis set (cc-pVTZ-PP) was employed to describe the tellurium atom. Two stable conformers, synclinal and antiperiplanar, have been identified. Both theory and experiment have shown the synclinal form to be more stable by 2 kJ/mol. The doublet structure observed in the rotational spectrum of synclinal conformer is attributed to tunneling motion of tellurol functional group. The energy difference between 0(+) and 0(-) substates split by tunneling has been determined from the observed spectra. PMID:20136116
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C and N atoms are the most frequent foreign interstitial atoms (FIAs), and often incorporated into the surface layers of steels to enhance their properties by thermochemical treatments. Al, Si, Ti, V, Cr, Mn, Co, Ni, Cu, Nb and Mo are the most common alloying elements in steels, also can be called foreign substitutional atoms (FSAs). The FIA and FSA interactions play an important role in the diffusion of C and N atoms, and the microstructures and mechanical properties of surface modified layers. Ab initio calculations based on the density functional theory are carried out to investigate FIA interactions with FSA in ferromagnetic bcc iron. The FIA–FSA interactions are analyzed systematically from five aspects, including interaction energies, density of states (DOS), bond populations, electron density difference maps and local magnetic moments
AB INITIO Modeling of Thermomechanical Properties of Mo-Based Alloys for Fossil Energy Conversion
Energy Technology Data Exchange (ETDEWEB)
Ching, Wai-Yim
2013-12-31
In this final scientific/technical report covering the period of 3.5 years started on July 1, 2011, we report the accomplishments on the study of thermo-mechanical properties of Mo-based intermetallic compounds under NETL support. These include computational method development, physical properties investigation of Mo-based compounds and alloys. The main focus is on the mechanical and thermo mechanical properties at high temperature since these are the most crucial properties for their potential applications. In particular, recent development of applying ab initio molecular dynamic (AIMD) simulations to the T1 (Mo{sub 5}Si{sub 3}) and T2 (Mo{sub 5}SiB{sub 2}) phases are highlighted for alloy design in further improving their properties.
Theoretical ab initio study the hydrogen bonding nature of the A:T base pair
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The effect of applied external electric field on DNA occurs mostly at high field intensity. The results of the theoretical ab initio study on the applied electric field on A:T base pair components are reported. The geometries of the local minima were optimized at DFT level. The 6-31 G(d,p) basis set was used. The geometrical parameters, relative stability, interaction energies and nature of hydrogen bonding energy are reported. Also, focus on the range of hydrogen bonding energy and the flexibility of the rotation angle between the A:T base pair. So that the electric field mutation may be able to be classified as multi-point mutation
Dislocation constriction and cross-slip in Al and Ag an ab initio study
Lu, G; Kioussis, N; Lu, Gang; Bulatov, Vasily V.; Kioussis, Nicholas
2002-01-01
A novel model based on the Peierls framework of dislocations is developed. The new theory can deal with a dislocation spreading at more than one slip planes. As an example, we study dislocation cross-slip and constriction process of two fcc metals, Al and Ag. The energetic parameters entering the model are determined from ab initio calculations. We find that the screw dislocation in Al can cross-slip spontaneously in contrast with that in Ag, which splits into partials and cannot cross-slip without first being constricted. The dislocation response to an external stress is examined in detail. We determine dislocation constriction energy and critical stress for cross-slip, and from the latter, we estimate the cross-slip energy barrier for the straight screw dislocations.
Experimental and ab initio molecular dynamics simulation studies of liquid Al60Cu40 alloy
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X-ray diffraction and ab initio molecular dynamics simulation studies of molten Al60Cu40 have been carried out between 973 and 1323 K. The structures obtained from our simulated atomic models are fully consistent with the experimental results. The local structures of the models analyzed using Honeycutt-Andersen and Voronoi tessellation methods clearly demonstrate that as the temperatures of the liquid is lowered it becomes more ordered. While no one cluster-type dominates the local structure of this liquid, the most prevalent polyhedra in the liquid structure can be described as distorted icosahedra. No obvious correlations between the clusters observed in the liquid and known stable crystalline phases in this system were observed.
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Aggregation of amyloid-? (A?) peptides is believed to play a key role in the mechanism of molecular pathogenesis of Alzheimer's disease (AD). To inhibit the aggregation and prevent AD, numerous compounds have been synthesized. A previous experimental study elucidated that a triazine derivative AA3E2 has anti-amyloidogenic ability, while a triazine derivative AA3D2 having a different substituent has no inhibitory effect. However, the reason for this remarkable difference in the ability cannot be explained by the chemical structures of these derivatives. In the present study, we present stable structures of the solvated complexes with A? and AA3E2/AA3D2 obtained by classical molecular mechanics method. The specific interactions between A? and AA3E2/AA3D2 in the complexes are investigated by ab initio fragment molecular orbital calculations. Based on the results obtained, we attempt to propose new potent inhibitors for the A? aggregation.
Ab initio study of structural and mechanical property of solid molecular hydrogens
Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng
2015-06-01
Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.
Ab Initio Calculations of the Electronic Structures and Biological Functions of Protein Molecules
Zheng, Haoping
2003-04-01
The self-consistent cluster-embedding (SCCE) calculation method reduces the computational effort from M3 to about M1 (M is the number of atoms in the system) with unchanged calculation precision. So the ab initio, all-electron calculation of the electronic structure and biological function of protein molecule becomes a reality, which will promote new proteomics considerably. The calculated results of two real protein molecules, the trypsin inhibitor from the seeds of squash Cucurbita maxima (CMTI-I, 436 atoms) and the Ascaris trypsin inhibitor (912 atoms, two three-dimensional structures), are presented. The reactive sites of the inhibitors are determined and explained. The precision of structure determination of inhibitors are tested theoretically.
Stress reduction of Cu-doped diamond-like carbon films from ab initio calculations
Directory of Open Access Journals (Sweden)
Xiaowei Li
2015-01-01
Full Text Available Structure and properties of Cu-doped diamond-like carbon films (DLC were investigated using ab initio calculations. The effect of Cu concentrations (1.56?7.81 at.% on atomic bond structure was mainly analyzed to clarify the residual stress reduction mechanism. Results showed that with introducing Cu into DLC films, the residual compressive stress decreased firstly and then increased for each case with the obvious deterioration of mechanical properties, which was in agreement with the experimental results. Structural analysis revealed that the weak Cu-C bond and the relaxation of both the distorted bond angles and bond lengths accounted for the significant reduction of residual compressive stress, while at the higher Cu concentration the increase of residual stress attributed to the existence of distorted Cu-C structures and the increased fraction of distorted C-C bond lengths.
Ab initio calculation of linear and nonlinear optical properties of semiconductor structures
Scientific Electronic Library Online (English)
F., Bechstedt; B., Adolph; W. G., Schmidt.
1999-12-01
Full Text Available The theoretical and numerical approaches are discussed for ab initio calculations of optical properties. The density functional theory (DFT) combined with the local-density approximation (LDA) allows the calculation of the geometry of crystalline solids and their surfaces with a precision of about o [...] ne percent. The DFT-LDA band structure and single-electron states therefore provide a reasonable starting point for the calculation of linear and nonlinear susceptibilities within the independent-particle approximation. However, this approach has to be improved by taking into account many-body interactions: self-energy effects, local-field corrections, and electron-hole attraction. Three types of optical spectra are studied: the frequency-dependent dielectric function, the second-harmonic generation, and surface reflectance anisotropy spectra. The systems considered are two-atomic semiconductors, their polytypes and their surfaces.
Ab initio determination of the (100) surfaces phonon dispersions of the SiC
Scientific Electronic Library Online (English)
J. S., Soares; H. W. Leite, Alves.
2006-06-01
Full Text Available In this work, we presented our preliminary ab initio results for the vibrational modes and the phonon frequencies of the SiC (100) surfaces. Our results are in good agreement with the available experimental data whenever this comparison is possible. For the accepted models of the C-terminated surfac [...] es in the c(2×2) reconstruction, while in the bridge-dimer model there is an acetylene-like vibrational A1 mode at 2031 cm-1, which is infrared active, in the staggered-dimer model, there is a Füchs-Kliewer (FK) mode at 1328 cm-1, which is experimentally detected. For Si-terminated surfaces in the p(2×1) reconstruction, instead, no FK was obtained, in contradiction with the HREELS experimental results for the Si-terminated surfaces, but they are in consonance with the fact that this surface should be described by a (3×2) or more complex models.
Faghaninia, Alireza; Lo, Cynthia S
2015-01-01
Accurate models of carrier transport are essential for describing the electronic properties of semiconductor materials. To the best of our knowledge, the current models following the framework of the Boltzmann transport equation (BTE) either rely heavily on experimental data (i.e., semi-empirical), or utilize simplifying assumptions, such as the constant relaxation time approximation (BTE-cRTA). While these models offer valuable physical insights and accurate calculations of transport properties in some cases, they often lack sufficient accuracy -- particularly in capturing the correct trends with temperature and carrier concentration. We present here a general transport model for calculating low-field electrical drift mobility and Seebeck coefficient of n-type semiconductors, by explicitly considering all relevant physical phenomena (i.e. elastic and inelastic scattering mechanisms). We first rewrite expressions for the rates of elastic scattering mechanisms, in terms of ab initio properties, such as the ban...
Ab initio relativistic effective potentials with spin-orbit operators. IV. Cs through Rn
Ross, R. B.; Powers, J. M.; Atashroo, T.; Ermler, W. C.; LaJohn, L. A.; Christiansen, P. A.
1990-11-01
Ab initio averaged relativistic effective core potentials (AREP) and spin-orbit (SO) operators are reported for the elements Cs through Rn. Two sets have been calculated for certain elements to provide AREPs with varying core/valence space definitions thereby permitting the treatment of core-valence correlation interactions. The AREPs and SO operators are tabulated as expansions in Gaussian-type functions (GTF). GTF valence basis sets for the lowest energy state of each atom are tabulated. The reliability of the AREPs and SO operators is gauged by comparing calculated atomic excitation energies and SO splitting energies with all-electron relativistic values. Calculated atomic excitation energies are found to agree to 0.12 eV and SO energies to 3.4%.
Ab initio relativistic effective potentials with spin--orbit operators. IV. Cs through Rn
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Ab initio averaged relativistic effective core potentials (AREP) and spin--orbit (SO) operators are reported for the elements Cs through Rn. Two sets have been calculated for certain elements to provide AREPs with varying core/valence space definitions thereby permitting the treatment of core--valence correlation interactions. The AREPs and SO operators are tabulated as expansions in Gaussian-type functions (GTF). GTF valence basis sets for the lowest energy state of each atom are tabulated. The reliability of the AREPs and SO operators is gauged by comparing calculated atomic excitation energies and SO splitting energies with all-electron relativistic values. Calculated atomic excitation energies are found to agree to 0.12 eV and SO energies to 3.4%
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We performed high-pressure ADXRD studies on Fe5Si3 and Ni2Si up to 75 GPa. No evidence of the occurrence of a phase transition was observed in them. Fe5Si3 was found to compress isotropically, but an anisotropic compression was observed in Ni2Si. These results are supported by ab initio total-energy calculations, which for Fe5Si3 also predicted a transition at 283 GPa from the hexagonal P63/mcm phase to a cubic phase. High-pressure melting studies were conducted on FeSi up to 70 GPa. We found a change in the melting slope at 12 GPa, which is attributed to the intersection of the melting curve with the phase boundary between ?-FeSi and CsCl-type FeSi. Finally, an equation of state for Fe5Si3 and Ni2Si is reported
Ab initio study of the electronic structure and elastic properties of Al5C3N
Xu, Xue-Wen; Hu, Long; Yu, Xiao; Lu, Zun-Ming; Fan, Ying; Li, Yang-Xian; Tang, Cheng-Chun
2011-12-01
We investigate the electronic structure, chemical bonding and elastic properties of the hexagonal aluminum carbonitride, Al5C3N, by ab initio calculations. Al5C3N is a semiconductor with a narrow indirect gap of 0.81 eV. The valence bands below the Fermi level (EF) originate from the hybridized Al p—C p and Al p—N p states. The calculated bulk and Young's moduli are 201 GPa and 292 GPa, which are slightly lower than those of Ti3SiC2. The values of the bulk-to-shear-modulus and bulk-modulus-to-c44 are 1.73 and 1.97, respectively, which are higher than those of Ti2AlC and Ti2AlN, indicating that Al5C3N is a ductile ceramic.
Ab initio contribution to the study of complexes formed during dilute FeCu alloys radiation
Becquart, C S
2003-01-01
Cu plays an important role in the embrittlement of pressure vessel steels under radiation and entities containing both Cu atoms and vacancies seem to appear as a consequence of displacement cascades. The characterisation of the stability as well as the migration of small Cu-vacancy complexes is thus necessary to understand and simulate the formation of these entities. For instance, cascade ageing studied by kinetic Monte Carlo or by rate theory models requires a good characterisation of such complexes which are parameters for these methods. We have investigated, by ab initio calculations based on the density functional theory, point defects and small defects in dilute FeCu alloys. The structure of small Cu clusters and Cu-vacancy complexes has been determined, as well as their formation and binding energies. Their relative stability is discussed. Vacancy migration energies in the presence of Cu atoms have been calculated and analysed. All the results are compared to the figures obtained with empirical interat...
Ab initio modeling of Al adsorption on CaF2 surfaces
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Ab initio simulations of the adsorption of Al atoms on CaF2 (0 0 1) and (1 1 1) surfaces have been performed for supercells with 7 different atomic configurations, using density functional theory. For (1 1 1) surfaces, a repulsive interaction was observed for most configurations, while a weak attraction was obtained when the Al atom was placed above F atoms. For the Ca-terminated (0 0 1) surface, the adsorption energy was about 5 times larger, whereas for the F-terminated (0 0 1) surface it was about 20 times greater. The comparative analysis indicates that the (0 0 1) surfaces are reactive and have a strong Al adatom bonding (chemisorption), especially for the F-terminated substrate. On the contrary, the (1 1 1) plane may be considered as non-reactive (physisorption), having a weak bonding of the Al adatom above the F site
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The field of computational materials physics has grown very quickly in the past decade, and it is now possible to simulate properties of complex materials completely from first principles. The presentation has mostly focused on first-principles dynamic simulations. Such simulations have been pioneered by Car and Parrinello, who introduced a method for performing realistic simulations within the context of density functional theory. The Car-Parrinello method and related plane wave approaches are reviewed in depth. The Car-Parrinello method was reviewed and illustrated with several applications: the dynamics of the C60 solid, diffusion across Si steps, and computing free energy differences. Alternative ab initio simulation schemes, which use preconditioned conjugate gradient techniques for energy minimization and dynamics were also discussed
Ab initio potential energy surface and rovibrational bound states for the Kr-HCCCN complex
Sun, Xueli; Hu, Yun; Zhu, Hua
2013-04-01
The first ab initio potential energy surface for Kr-HCCCN was calculated using the coupled-cluster singles and doubles with noniterative inclusion of connected triples [CCSD(T)] with a large basis set containing bond functions. The potential has a T-shaped global minimum and a local linear minimum with the Kr atom facing the H atom. The radial discrete variables representation (DVR)/angular finite basis representation (FBR) method and the Lanczos algorithm were employed to calculate the rovibrational energy levels for three isotopomers 84Kr-HCCCN, 82Kr-HCCCN, and 86Kr-HCCCN. The spectroscopic constants for the ground and the first excited states of Kr-HCCCN were predicted.
Ab initio potential energy surfaces, bound states and electronic spectrum of the Ar-SH complex
Doyle, R J; Hutson, J M; Doyle, Richard J.; Hirst, David M.; Hutson, Jeremy M.
2006-01-01
New ab initio potential energy surfaces for the doublet pi ground electronic state of the Ar-SH complex are presented, calculated at the RCCSD(T)/aug-cc-pV5Z level. Weakly bound rotation-vibration levels are calculated using coupled-channel methods that properly account for the coupling between the two electronic states. The resulting wavefunctions are analysed and a new adiabatic approximation including spin-orbit coupling is proposed. The ground-state wavefunctions are combined with those obtained for the excited doublet sigma + state [Phys. Chem. Chem. Phys. 6, 5463 (2004)] to produce transition dipole moments. Modelling the transition intensities as a combination of these dipole moments and calculated lifetime values [J. Chem. Phys. 109, 170 (1998)] leads to a good representation of the experimental fluorescence excitation spectrum [J. Chem. Phys. 98, 4301 (1993)].
Ab initio investigation of the switching behavior of the dithiole-benzene nano-molecular wire
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We report a first-principle study of electrical transport and switching behavior in a single molecular conductor consisting of a dithiole-benzene sandwiched between two Au( 100) electrodes. Ab initio total energy calculations reveal dithiole-benzene molecules on a gold surface, contacted by a monoatomic gold scanning tunneling microscope tip to have two classes of low energy conformations with differing symmetries. Lateral motion of the tip or excitation of the molecule cause it 10 change from one conformation class to the other and to switch between a strongly and a weakly conducting state. Thus, surprisingly. despite their apparent simplicity, these Au-dithiole-benzene -Au nano wires are shown to be electrically bi-stable switches, the smallest two-terminal molecular switches to date. The projected density of states and transmission coefficients are analyzed, and it suggests that the variation of the coupling between the molecule and the electrodes with external bias leads to switching behavior
Ab initio approach to model x-ray diffraction in warm dense matter
Vorberger, J.; Gericke, D. O.
2015-03-01
It is demonstrated how the static electron-electron structure factor in warm dense matter can be obtained from density functional theory in combination with quantum Monte Carlo data. In contrast to theories assuming well-separated bound and free states, this ab initio approach yields also valid results for systems close to the Mott transition (pressure ionization), where bound states are strongly modified and merge with the continuum. The approach is applied to x-ray Thomson scattering and compared to predictions of the Chihara formula whereby we use the ion-ion and electron-ion structure from the same simulations. The results show significant deviations of the screening cloud from the often applied Debye-like form.
Ab-initio and atomistic study of the ferroelectric properties of Cu doped potassium niobate
International Nuclear Information System (INIS)
KNbO3 is one end member of the solid solution (K,Na)NbO3 (KNN), which has promising ferroelectric properties to become a future lead-free substitute for lead zirconate titanate Pb(Zr,Ti)O3 (PZT) in piezoelectric actors and sensors. Both KNN and PZT exhibit a phase transition with composition and a morphotropic phase boundary, at which enhanced piezoelectric coefficients are obtained. The material properties of PZT and KNN are commonly optimized by doping. E.g., CuO can be added when fabricating KNN as a sintering aid. Ab initio density functional theory and atomistic simulation using a classical shell model potential have been combined to investigate low Cu concentrations in the KNbO3-CuNbO3 system. The atomistic model predicts a morphotropic phase boundary at a few percent Cu, analogous to the one found in the LiNbO3-KNbO3 system.
Ab Initio No Core Shell Model - Recent Results and Further Prospects
Vary, James P; Potter, Hugh; Caprio, Mark A; Smith, Robin; Binder, Sven; Calci, Angelo; Fischer, Sebastian; Langhammer, Joachim; Roth, Robert; Aktulga, Hasan Metin; Ng, Esmond; Yang, Chao; Oryspayev, Dossay; Sosonkina, Masha; Saule, Erik; Çatalyürek, Ümit
2015-01-01
There has been significant recent progress in solving the long-standing problems of how nuclear shell structure and collective motion emerge from underlying microscopic inter-nucleon interactions. We review a selection of recent significant results within the ab initio No Core Shell Model (NCSM) closely tied to three major factors enabling this progress: (1) improved nuclear interactions that accurately describe the experimental two-nucleon and three-nucleon interaction data; (2) advances in algorithms to simulate the quantum many-body problem with strong interactions; and (3) continued rapid development of high-performance computers now capable of performing $20 \\times 10^{15}$ floating point operations per second. We also comment on prospects for further developments.
Accurate ab initio potential energy curve of F2. III. The vibration rotation spectrum
Bytautas, L.; Matsunaga, N.; Nagata, T.; Gordon, M. S.; Ruedenberg, K.
2007-11-01
An analytical expression is found for the accurate ab initio potential energy curve of the fluorine molecule that has been determined in the preceding two papers. With it, the vibrational and rotational energy levels of F2 are calculated using the discrete variable representation. The comparison of this theoretical spectrum with the experimental spectrum, which had been measured earlier using high-resolution electronic spectroscopy, yields a mean absolute deviation of about 5cm-1 over the 22 levels. The dissociation energy with respect to the lowest vibrational energy is calculated within 30cm-1 of the experimental value of 12953±8cm-1. The reported agreement of the theoretical spectrum and dissociation energy with experiment is contingent upon the inclusion of the effects of core-generated electron correlation, spin-orbit coupling, and scalar relativity. The Dunham analysis [Phys. Rev. 41, 721 (1932)] of the spectrum is found to be very accurate. New values are given for the spectroscopic constants.
A theoretical study of ozone isotopic effects using a modified ab initio potential energy surface
Gao, Yi Qin; Chen, Wei-Chen; Marcus, R. A.
2002-07-01
A modified ab initio potential energy surface (PES) is used for calculations of ozone recombination and isotopic exchange rate constants. The calculated low-pressure isotopic effects on the ozone formation reaction are consistent with the experimental results and with the theoretical results obtained earlier [J. Chem. Phys. 116, 137 (2002)]. They are thereby relatively insensitive to the properties of these PES. The topics discussed include the dependence of the calculated low-pressure recombination rate constant on the hindered-rotor PES, the role of the asymmetry of the potential for a general X+YZ reaction (Y?Z), and the partitioning to form each of the two recombination products: XYZ and XZY.
Ab initio study of mirages and magnetic interactions in quantum corrals
Stepanyuk, V S; Hergert, W; Bruno, P
2005-01-01
The state of the art ab initio calculations of quantum mirages,the spin-polarization of surface-state electrons and the exchange interaction between magnetic adatoms in Cu and Co corrals on Cu(111) are presented. We find that the spin-polarization of the surface-state electrons caused by magnetic adatoms can be projected to a remote location and can be strongly enhanced in corrals compared to an open surface.Our studies give a clear evidence that quantum corrals could permit to tailor the exchange interaction between magnetic adatoms at large separations. The spin-polarization of surface-state electrons at the empty focus in the Co corral used in the experimental setup of Manoharan et al., (Nature 403, 512 (2000)) is revealed.
Tight-binding model for carbon nanotubes from ab initio calculations
International Nuclear Information System (INIS)
Here we present a parametrized tight-binding (TB) model to calculate the band structure of single-wall carbon nanotubes (SWNTs). On the basis of ab initio calculations we fit the band structure of nanotubes of different radii with results obtained with an orthogonal TB model to third neighbors, which includes the effects of orbital hybridization by means of a reduced set of parameters. The functional form for the dependence of these parameters on the radius of the tubes can be used to interpolate appropriate TB parameters for different SWNTs and to study the effects of curvature on their electronic properties. Additionally, we have shown that the model gives an appropriate description of the optical spectra of SWNTs, which can be useful for a proper assignation of SWNTs' specific chirality from optical absorption experiments.
Ab initio study of ladder-type polymers polythiophene and polypyrrole
Pesant, S; Côté, M; Ernzerhof, M; Pesant, Simon; Boulanger, Paul; C\\^ot\\'e, Michel; Ernzerhof, Matthias
2006-01-01
This article presents an \\textit{ab initio} study of four polymers, polythiophene, polypyrrole, ladder-type polythiophene, and ladder-type polypyrrole. Upon an analysis of the variation of the band gap when comparing the unconstrained and the ladder-type polymers, a discrepancy was found between the thiophene and the pyrrole polymer families. For polythiophene, the ladder-type polymer has a larger gap than the unconstrained polymer whereas the opposite is found for the pyrrole polymers. The structural properties and the charge densities using the Bader charge analysis of these four compounds are investigated. The different band gap behaviors in thiophene and pyrrole polymers can be explained in terms of the competition between the bond length alternation and the effect of the charge density in the carbon backbone.
Electron-scattering form factors for 6Li in the ab initio symmetry-guided framework
Dytrych, T; Launey, K D; Draayer, J P; Maris, P; Vary, J P; Langr, D; Oberhuber, T
2015-01-01
We present an ab initio symmetry-adapted no-core shell-model description for $^{6}$Li. We study the structure of the ground state of $^{6}$Li and the impact of the symmetry-guided space selection on the charge density components for this state in momentum space, including the effect of higher shells. We accomplish this by investigating the electron scattering charge form factor for momentum transfers up to $q \\sim 4$ fm$^{-1}$. We demonstrate that this symmetry-adapted framework can achieve significantly reduced dimensions for equivalent large shell-model spaces while retaining the accuracy of the form factor for any momentum transfer. These new results confirm the previous outcomes for selected spectroscopy observables in light nuclei, such as binding energies, excitation energies, electromagnetic moments, E2 and M1 reduced transition probabilities, as well as point-nucleon matter rms radii.
A set of molecular models based on quantum mechanical ab initio calculations and thermodynamic data
Eckl, Bernhard; Hasse, Hans
2009-01-01
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic data. The geometry of the molecular models is specified according to the atom positions determined by QM energy minimization. The electrostatic interactions are modeled by reducing the electron density distribution to point dipoles and point quadrupoles located in the center of mass of the molecules. Dispersive and repulsive interactions are described by Lennard-Jones sites, for which the parameters are iteratively optimized to experimental vapor-liquid equilibrium (VLE) data, i.e. vapor pressure, saturated liquid density, and enthalpy of vaporization of the considered substance. The proposed modeling strategy was applied to a sample set of ten molecules from different substance classes. New molecular models are presented for iso-butane, cyclohexane, formaldehyde, dimethyl...
Quantum fluctuations and isotope effects in ab initio descriptions of water
International Nuclear Information System (INIS)
Isotope substitution is extensively used to investigate the microscopic behavior of hydrogen bonded systems such as liquid water. The changes in structure and stability of these systems upon isotope substitution arise entirely from the quantum mechanical nature of the nuclei. Here, we provide a fully ab initio determination of the isotope exchange free energy and fractionation ratio of hydrogen and deuterium in water treating exactly nuclear quantum effects and explicitly modeling the quantum nature of the electrons. This allows us to assess how quantum effects in water manifest as isotope effects, and unravel how the interplay between electronic exchange and correlation and nuclear quantum fluctuations determine the structure of the hydrogen bond in water
International Nuclear Information System (INIS)
Experimental measurements and theoretical calculations of the electrical conductivity of aluminum are presented in the strongly coupled partially degenerate regime (?=0.3 g/cm3, 5000< T<15 000 K). The experiments were performed in an isochoric plasma closed vessel designed to confine electrical plasma discharges up to 1.5 GPa. Aluminum properties were determined theoretically by ab initio molecular dynamics simulations in the local density approximation, from which the conductivity was computed using the Kubo-Greenwood formula. The theoretical results were validated in the dense coupled regime against previously published experimental results and then applied to our experimental low density regime, showing that the theoretical results overestimate the experimental conductivities
Knyazev, D V
2013-01-01
This work is devoted to the \\textit{ab initio} calculation of transport and optical properties of aluminum. The calculation is based on the quantum molecular dynamics simulation, density functional theory and the Kubo-Greenwood formula. Mainly the calculations are performed for liquid aluminum at near-normal densities for the temperatures from melting up to 20000 K. The results on dynamic electrical conductivity, static electrical conductivity and thermal conductivity are obtained and compared with available reference and experimental data and the calculations of other authors. The influence of the technical parameters on the results is investigated in detail. The error of static electrical conductivity calculation is estimated to be about 20%; more accurate results require bigger number of atoms.
Dynamical screening and ionic conductivity in water from ab initio simulations.
French, Martin; Hamel, Sebastien; Redmer, Ronald
2011-10-28
We present a method to calculate ionic conductivities of complex fluids from ab initio simulations. This is achieved by combining density functional theory molecular dynamics simulations with polarization theory. Conductivities are then obtained via a Green-Kubo formula using time-dependent effective charges of electronically screened ions. The method is applied to two different phases of warm dense water. We observe large fluctuations in the effective charges; protons can transport effective charges greater than +e for ultrashort time scales. Furthermore, we compare our results with a simpler model of ionic conductivity in water that is based on diffusion coefficients. Our approach can be directly applied to study ionic conductivities of electronically insulating materials of arbitrary composition, e.g., complex molecular mixtures under such extreme conditions that occur deep inside giant planets. PMID:22107646
Ab initio theory of galvanomagnetic phenomena in ferromagnetic metals and disordered alloys
Turek, I.; Kudrnovský, J.; Drchal, V.
2012-07-01
We present an ab initio theory of transport quantities of metallic ferromagnets developed in the framework of the fully relativistic tight-binding linear muffin-tin orbital method. The approach is based on the Kubo-St?eda formula for the conductivity tensor, on the coherent potential approximation for random alloys, and on the concept of interatomic electron transport. The developed formalism is applied to pure 3d transition metals (Fe, Co, Ni) and to random Ni-based ferromagnetic alloys (Ni-Fe, Ni-Co, Ni-Mn). High values of the anisotropic magnetoresistance (AMR), found for Ni-rich alloys, are explained by a negligible disorder in the majority spin channel, while a change of the sign of the anomalous Hall effect (AHE) on alloying is interpreted as a band-filling effect without a direct relation to the high AMR. The influence of disorder on the AHE in concentrated alloys is investigated as well.
Study of pressure-induced amorphization in sulfur using \\textit{ab initio} molecular dynamics
Plašienka, Dušan
2014-01-01
We report results of ab initio constant-pressure molecular dynamics simulations of sulfur compression leading to structural transition and pressure-induced amorphization. Starting from the orthorhombic S-I phase composed of S$_8$ ring molecules we find at room temperature and pressure of 20 GPa a transformation to monoclinic phase where half of the molecules develop a different conformation. Upon further compression, the monoclinic phase undergoes pressure-induced amorphization into an amorphous phase, in agreement with experiments. We study the dynamics of the amorphization transition and investigate the evolution of intra and intermolecular distances in the monoclinic phase in order to provide a microscopic insight into the rings disintegration process leading to amorphization. In the amorphous form we examine the structural properties and discuss its relation to the experimentally found amorphous form and to underlying crystal phases as well. The amorphous form we find appears to correspond to the experime...
New amorphous forms of solid CO2 from ab initio molecular dynamics
Plašienka, Dušan
2013-01-01
By employing ab initio molecular dynamics simulations at constant pressure, we investigated behavior of amorphous carbon dioxide between 0-100 GPa and 200-500 K and found several new amorphous forms. We focused on evolution of the high-pressure tetrahedral amorphous form known as a-carbonia on its way down to zero pressure, where it eventually converts into a molecular amorphous solid. During decompression, two nonmolecular amorphous forms with different proportion of three and four-coordinated carbons and two mixed molecular-nonmolecular forms were observed. Transformation from a-carbonia to the molecular state appears to proceed discontinuously via several intermediate stages. This suggests that solid CO2 might belong to the group of materials exhibiting polyamorphism. We also studied relations of the amorphous forms to their crystalline counterparts. The predominantly four-coordinated a-carbonia is related to phase V according to their structural properties, while existence of the mixed forms may reflect h...
Raman and ab initio studies of simple and binary 1-alkyl-3-methylimidazolium ionic liquids
DEFF Research Database (Denmark)
Berg, R.W.; Deetlefs, M.
2005-01-01
Raman spectra of the ionic liquids, 1-butyl-3-methylimidazolium hexafluorophosphate ([C(4)mim][PF6]), 1-hexyl-3-methylimidazolium chloride ([C(6)mim]Cl), and 1-hexyl-3-methylimidazolium hexafluorophosphate ([C(6)mim][PF6]), and binary mixtures thereof, have been assigned using ab initio MP2 calculations. The previously reported anti and gauche forms of the [C(4)mim](+) cation have been observed, and this study reveals this to be a general feature of the long-chain I-alkyl derivatives. Analysis of mixtures Of [C(6)mim]Cl and [C(6)mim][PF6] has provided information on the nature of the hydrogen bonding between the imidazolium headgroup and the anions, and the invariance of the essentially 50:50 mixture of the predominant conformers informs on the nature of glass formation in these systems.
DEFF Research Database (Denmark)
Abild-Pedersen, Frank; NØrskov, Jens Kehlet
2006-01-01
Mechanisms and energetics of graphene growth catalyzed by nickel nanoclusters were studied using ab initio density functional theory calculations. It is demonstrated that nickel step-edge sites act as the preferential growth centers for graphene layers on the nickel surface. Carbon is transported from the deposition site at the free nickel surface to the perimeter of the growing graphene layer via surface or subsurface diffusion. Three different processes are identified to govern the growth of graphene layers, depending on the termination of the graphene perimeter at the nickel surface, and it is argued how these processes may lead to different nanofiber structures. The proposed growth model is found to be in good agreement with previous findings.
Ab initio modeling of radiation damage in MgF{sub 2} crystals
Energy Technology Data Exchange (ETDEWEB)
Abuova, F.U. [L. N. Gumilyov Eurasian National University, 3 Munaitpasova Str., Astana (Kazakhstan); Kotomin, E.A., E-mail: kotomin@latnet.lv [Institute of Solid State Physics, University of Latvia, 8 Kengaraga Str., LV-1063, Riga (Latvia); Lisitsyn, V.M. [Tomsk Polytechnical University, Tomsk 634003 (Russian Federation); Akilbekov, A.T. [L. N. Gumilyov Eurasian National University, 3 Munaitpasova Str., Astana (Kazakhstan); Piskunov, S. [Institute of Solid State Physics, University of Latvia, 8 Kengaraga Str., LV-1063, Riga (Latvia)
2014-05-01
MgF{sub 2} with a rutile structure is important radiation-resistant material with numerous applications due to its transparency from vacuum ultraviolet to infrared range of photon energies. We present and discuss the results of calculations for basic radiation defects in this crystal. The study is based on the large scale ab initio DFT calculations using hybrid B3PW exchange–correlation functional and atomic basis set. We analyzed the electronic structure, atomic displacements, charge density distribution as well as defect formation energies using large supercells. We compared properties of close and well separated F?H (Frenkel) defect pairs as well as individual defects. We simulated also formation and energetic preference of inert F{sub 2} interstitial molecules as sinks of mobile interstitial fluorine atoms which is relevant for material radiation stability. We discussed also diffusion of the primary electronic defects—F centers.
Ab initio study of structural and electronic properties of partially reduced graphene oxide
International Nuclear Information System (INIS)
Controlled reduction of graphene oxide (GO) is a promising method to tune the electronic band gap of this two-dimensional material in the energy range of the visible light spectrum. By means of ab initio calculations, based on density functional theory at the generalized gradient approximation level, we investigated electronic properties of partially reduced graphene oxide, modelled as periodic array of small islands of pristine graphene embedded in an infinite sheet of GO. The calculations demonstrated that, by varying the size of the graphene islands from two to eight carbon atoms, it was possible to tune the electronic band gap in a range from 4.38 to 1.31 eV, which is of great importance to the utilization of graphene-based materials in photonic devices. (paper)
Ab initio study of nitrogen-multisubstituted neutral and positively charged C{sub 20} fullerene
Energy Technology Data Exchange (ETDEWEB)
Rani, Anita, E-mail: ranianita64@gmail.com [Guru Nanak College for Girls, Sri Muktsar Sahib, Punjab-141002 (India); Kumar, Ranjan [Department of Physics, Panjab University, Chandigarh-160014 (India)
2014-04-24
Ab initio investigation of structural and electronic properties of Nitrogen doped fullerenes, obtained from C{sub 20} by replacing up to 10 C atoms with N atoms, are studied by means of first principals density functional theory calculations using numerical orbitals as basis sets. We have obtained the ground state structures for C{sub 20?n}N{sub n} for n=1-10. While substituting nitrogen atoms, we cannot substitute more than 9 nitrogen atoms. Nitrogen doping in C20 shows a significant change in density of states. For a better comparison with experimental measurements, we have also considered some positively charged ions and report the differences between properties of these ions and the corresponding neutral molecules.
Femtosecond laser processing of germanium: an ab initio molecular dynamics study
International Nuclear Information System (INIS)
An ab initio molecular dynamics study of femtosecond laser processing of germanium is presented in this paper. The method based on the finite temperature density functional theory is adopted to probe the structural change, thermal motion of the atoms, dynamic property of the velocity autocorrelation, and the vibrational density of states. Starting from a cubic system at room temperature (300 K) containing 64 germanium atoms with an ordered arrangement of 1.132 nm in each dimension, the femtosecond laser processing is simulated by applying a Nosé–Hoover thermostat to the electronic subsystem for ?100 fs and continuing with a microcanonical ensemble simulation of ?200 fs. The simulation results show solid, liquid and gas phases of germanium under adjusted intensities of the femtosecond laser irradiation. We find that the irradiated germanium is distinguishable from the usual germanium crystal by analysing their melting and dynamic properties. (paper)
Hadži, D.; Hodoš?ek, M.; Grdadolnik, J.; Avbelj, F.
1992-03-01
A major difficulty in the study of nonbonded effects, particularly hydration, upon the phosphate group frequencies in phospholipids and other biologically important systems lays in the lack of reference for the nonbonded species, i.e. inaccessiblity to measurement of isolated, ionic phosphodiesters. We have therefore ab-initio calculated (3-21 G* basis set) the frequencies of the isolated dimethylphosphate (DMP), its mono- and dihydrates and its sodium, ammonium and tetramethylammonium salts. The computed results (unscaled frequencies, PED) will be compared with experimental ones obtained with stepwise hydrated lecithins and dialkylphosphate salts. The antisymmetric N(CH 3) 3 frequencies turned out to be useful in interpreting the observed phosphate frequency trends upon hydration. The discussion of the results will be centered on the behaviour and vibrational character of the PO 2- frequencies. A molecular representation of phophatidylcholine hydration is proposed.
Prediction of toxicity of nitrobenzenes using ab initio and least squares support vector machines.
Niazi, Ali; Jameh-Bozorghi, Saeed; Nori-Shargh, Davood
2008-03-01
A quantitative structure-property relationship (QSPR) study is suggested for the prediction of toxicity (IGC50) of nitrobenzenes. Ab initio theory was used to calculate some quantum chemical descriptors including electrostatic potentials and local charges at each atom, HOMO and LUMO energies, etc. Modeling of the IGC50 of nitrobenzenes as a function of molecular structures was established by means of the least squares support vector machines (LS-SVM). This model was applied for the prediction of the toxicity (IGC50) of nitrobenzenes, which were not in the modeling procedure. The resulted model showed high prediction ability with root mean square error of prediction of 0.0049 for LS-SVM. Results have shown that the introduction of LS-SVM for quantum chemical descriptors drastically enhances the ability of prediction in QSAR studies superior to multiple linear regression and partial least squares. PMID:17630186
Minimal parameter implicit solvent model for ab initio electronic structure calculations
Dziedzic, Jacek; Skylaris, Chris-Kriton; Mostofi, Arash A; Payne, Mike C
2011-01-01
We present an implicit solvent model for ab initio electronic structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comp. Chem. 23, 6 (2002)). While this model depends on only two parameters, we demonstrate that by using appropriate boundary conditions and dispersion-repulsion contributions, solvation energies obtained for an extensive test set including neutral and charged molecules show dramatic improvement compared to existing models. Our approach is implemented in, but not restricted to, a linear-scaling density functional theory (DFT) framework, opening the path for self-consistent implicit solvent DFT calculations on systems of unprecedented size, which we demonstrate with calculations on a 2615-atom protein-ligand complex.
Lattice thermal conductivity of UO2 using ab-initio and classical molecular dynamics
International Nuclear Information System (INIS)
We applied the non-equilibrium ab-initio molecular dynamics and predict the lattice thermal conductivity of the pristine uranium dioxide for up to 2000?K. We also use the equilibrium classical molecular dynamics and heat-current autocorrelation decay theory to decompose the lattice thermal conductivity into acoustic and optical components. The predicted optical phonon transport is temperature independent and small, while the acoustic component follows the Slack relation and is in good agreement with the limited single-crystal experimental results. Considering the phonon grain-boundary and pore scatterings, the effective lattice thermal conductivity is reduced, and we show it is in general agreement with the sintered-powder experimental results. The charge and photon thermal conductivities are also addressed, and we find small roles for electron, surface polaron, and photon in the defect-free structures and for temperatures below 1500?K
Physical properties of a GeS2 glass using approximate ab initio molecular dynamics
Blaineau, S; Drabold, D A; Blaineau, Sebastien; Jund, Philippe; Drabold, David A.
2003-01-01
With the use of {\\em ab initio} based molecular dynamics simulations we study the structural, dynamical and electronic properties of glassy g-GeS$_2$ at room temperature. From the radial distribution function we find nearest neighbor distances almost identical to the experimental values and the static structure factor is close to its experimental counterpart. From the Ge-S-Ge bond angle distribution we obtain the correct distribution of corner and edge-sharing GeS$_4$ tetrahedra. Concerning the dynamical characteristics we find in the mean square displacement of the atoms discontinuous variations corresponding either to the removal of coordination defects around a single particle or to structural rearrangements involving a larger number of atoms. Finally we calculate the vibrational density of states, which exhibits two well separated bands as well as some features characteristic of the amorphous state, and the electronic density of states showing an optical gap of 3.27 eV.
Ab initio study of pressure induced structural and electronic properties in TmPo
Makode, Chandrabhan; Panwar, Y. S.; Aynyas, Mahendra; Pataiya, Jagdish; Sanyal, Sankar P.
2015-06-01
We report an ab initio calculation of pressure induced structural phase transition and electronic properties of Thulium Polonide (TmPo).The total energy as a function of volume is obtained by means of self-consistent tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). It is found that TmPo is stable in NaCl-type (B1-phase) structure to CsCl-type (B2-phase) structure of this compound in the pressure range of 7.0 GPa. We also calculate the lattice parameter (a0), bulk modulus (B0), band structure and density of states. From energy diagram it is observed that TmPo exhibit metallic behavior. The calculated values of equilibrium lattice parameter and bulk modulus are in general good agreement.
Thermoelectric properties of amorphous ZnO-based materials using ab initio methods
Roy, Anindya; Cheng, Yu-Ting; Falk, Michael L.
2015-03-01
We use a combination of computational methods - molecular dynamics and density functional theory, to predict thermoelectric properties of amorphous ZnO-based materials. We use BoltzTraP to calculate properties such as Seebeck coefficient and electrical conductivity within semiclassical Boltzman transport theory, and compare with available experimental results. Additionally, we investigate the change in the thermoelectric parameters caused by alloying amorphous ZnO with tin and other elements. Our preliminary calculations suggest that the thermoelectric performance of amorphous ZnO is on par with the crystalline counterpart. This is encouraging - since amorphous materials are yet to be studied in depth for their potential as thermoelectric materials, and they could see much improvement with sustained effort. Also, while ab initio methods are routinely used to predict properties of crystalline systems, their application in amorphous systems is a less-explored area.
Liu, Li-Min; Car, Roberto; Selloni, Annabella; Dabbs, Daniel M; Aksay, Ilhan A; Yetter, Richard A
2012-11-21
The burning rate of the monopropellant nitromethane (NM) has been observed to increase by adding and dispersing small amounts of functionalized graphene sheets (FGSs) in liquid NM. Until now, no plausible mechanisms for FGSs acting as combustion catalysts have been presented. Here, we report ab initio molecular dynamics simulations showing that carbon vacancy defects within the plane of the FGSs, functionalized with oxygen-containing groups, greatly accelerate the thermal decomposition of NM and its derivatives. This occurs through reaction pathways involving the exchange of protons or oxygens between the oxygen-containing functional groups and NM and its derivatives. FGS initiates and promotes the decomposition of the monopropellant and its derivatives, ultimately forming H(2)O, CO(2), and N(2). Concomitantly, oxygen-containing functional groups on the FGSs are consumed and regenerated without significantly changing the FGSs in accordance with experiments indicating that the FGSs are not consumed during combustion. PMID:23101732
An ab initio variationally computed room-temperature line list for SO3
Underwood, Daniel S; Yurchenko, Sergei N
2013-01-01
{\\it Ab initio} potential energy and dipole moment surfaces are computed for sulfur trioxide (SO$_3$) at the CCSD(T)-F12b level of theory and appropriate triple-zeta basis sets. These surfaces are fitted and used, with a slight correction for the equilibrium S--O distance, to compute pure rotational and rotation-vibraton spectra of \\sothree\\ using the variational nuclear motion program TROVE. The calculations considered transitions in the region 0--4000 \\cm\\ with rotational states up to J=85. The resulting line list of 349~348~513 transitions is appropriate for modelling room temperature SO3 spectra. Good agreement is found with the observed infrared absorption spectra and the calculations are used to place the measured relative intensities on an absolute scale. A list of 10~878 experimental transitions is provided in a form suitable for inclusion in standard atmospheric and planetary spectroscopic databases.
International Nuclear Information System (INIS)
Charge transfer ?Q = 0.35e at the Si-N bond in silicon nitride is determined experimentally using photoelectron spectroscopy, and the ionic formula of silicon nitride Si3+1.4N4-1.05 is derived. The electronic structure of ?-Si3N4 is studied ab initio using the density functional method. The results of calculations (partial density of states) are compared with experimental data on X-ray emission spectroscopy of amorphous Si3N4. The electronic structure of the valence band of amorphous Si3N4 is studied using synchrotron radiation at different excitation energies. The electron and hole effective masses me* ? mh* ? 0.5me are estimated theoretically. The calculated values correspond to experimental results on injection of electrons and holes into silicon nitride.
Barbosa, Marcelo
A review about the nuclear properties, namely the nuclear moments (magnetic dipole moment and electric quadrupole moment) and their interaction with electromagnetic fields external to the nucleus (hyperfine interactions), as well as the angular distribution of radiation produced by $\\gamma$-decay, is presented. A detailed description about the theory of Perturbed Angular Correlations was done, including the comparison between $\\gamma - \\gamma$ correlations and $e^{-}- \\gamma$ correlations. For dynamic nuclear interactions, an introduction to the theory of stochastic states in PAC was performed. We focused on ab-initio implementation of observables for analyzing fluctuating quadrupole hyperfine interactions on time dependent perturbed angular correlations experiments. The development of computacional codes solving the full problem, adapted to fit data obtained on single crystals or polycrystals for two-state transient fields with any axial symmetry and orientation was the main purpose of this work. The final p...
Ab initio computed diabatic potential energy surfaces of OH-HCl
Wormer, Paul E. S.; K?os, Jacek A.; Groenenboom, Gerrit C.; van der Avoird, Ad
2005-06-01
The two four-dimensional diabatic potential energy surfaces (DPESs) for OH-HCl are computed that correlate with the twofold degenerate ?2 ground state of the free OH radical. About 20 000 points on the surface are obtained by the ab initio coupled-cluster and multi-reference configuration interaction methods. Analytic forms for the diabatic potential energy surfaces are derived as expansions in complete sets of orthogonal functions depending on the three intermolecular angles. The numeric computation of the angular expansion coefficients is discussed. The distance-dependence of the angular coefficients is represented by the reproducing kernel Hilbert space method. It is checked that both diabatic potentials converge for large intermolecular separations to the values computed directly from the electrostatic multipole expansion. The final DPESs are discussed and illustrated by some physically meaningful one- and two-dimensional cuts through them.
Raman spectra from ab initio molecular dynamics and its application to liquid S-methyloxirane.
Luber, Sandra; Iannuzzi, Marcella; Hutter, Jürg
2014-09-01
We describe the calculation of Raman spectra for periodic systems via ab initio molecular dynamics (AIMD) utilizing the Gaussian and plane wave method in the program package CP2K. The electric-dipole-electric-dipole polarizability tensor has been implemented for an arbitrary shape of the simulation cell. In addition, a computationally efficient approach for its decomposition into local contributions is presented. As an example for the application of computational Raman spectroscopy to liquids, the Raman spectra of S-methyloxirane in the liquid phase have been calculated together with Raman spectra obtained from static calculations employing the double-harmonic approximation. The comparison to experimental data illustrates that a very good agreement between experiment and simulated spectra can be obtained employing AIMD, which takes into account anharmonicities and dynamical effects at ambient conditions. PMID:25194377
Ab initio MO studies of interaction mechanisms of Protein Kinase C with cell membranes
Tsuda, Ken-ichiro; Kaneko, Hiroki; Shimada, Jiro; Takada, Toshikazu
2001-12-01
Protein Kinase C (PKC) is a family of regulatory enzymes. It is considered that binding with phorbol ester which are PKC activators, increases affinity of PKC for the membranes and consequently induces its conformation change. Electrostatic interactions between PKC and the membrane is assumed to be important, and performed ab initio MO calculations of one domain of PKC consisting of 50 amino acids and its complex with the ester is performed to investigate how the electrostatic potential of PKC changes through docking with the substrate. From the calculation, it is shown that the electrostatic potential of PKC near the binding site is dramatically affected through the binding, suggesting attractive interactions with the cell membrane.
Acidity of HOCH, HSCN, HNCO, HNCS: a treatment from the viewpoint of ab initio approach
ALEXEI N. PANKRATOV; SERGEI S. KHMELEV
2005-01-01
The electronic structures of the molecules HOCN, HSCN, HNCO, HNCS and the anions [OCN]-, [SCN]- have been investigated ab initio at the RHF/6-31G(d), RHF/6-31G(d,p), MP2/6-31G(d)//RHF/6-31G(d) and MP2/6-31G(d,p)//RHF/6-31G(d,p) theory levels. The thermodynamic stability of the HNCO and HNCS molecules was shown to be higher than that of the HOCH and HSCN molecules, respectively.The following series of the alteration of the protolytes strength HSCN > HOCH, HNCS > HNCO, HOCN > HNCO, HSCN > HNCS ...
Ab initio analysis of the topological phase diagram of the Haldane model
Ibañez-Azpiroz, Julen; Bergara, Aitor; Pettini, Giulio; Modugno, Michele
2015-01-01
We present an ab initio analysis of a continuous Hamiltonian that maps into the celebrated Haldane model. The tunnelling coefficients of the tight-binding model are computed by means of two independent methods - one based on the maximally localised Wannier functions, the other through analytic expressions in terms of gauge-invariant properties of the spectrum - that provide a remarkable agreement and allow to accurately reproduce the exact spectrum of the continuous Hamiltonian. By combining these results with the numerical calculation of the Chern number, we are able to draw the phase diagram in terms of the physical parameters of the microscopic model. Remarkably, we find that only a small fraction of the original phase diagram of the Haldane model can be accessed, and that the topological insulator phase is suppressed in the deep tight-binding regime. Moreover, we find that in the case of parity breaking, the topological phase transition for the continuous Hamiltonian takes place without gap closing.
Ab-initio calculations on two-electron ions in strongly coupled plasma environment
Bhattacharyya, S; Mukherjee, T K
2015-01-01
In this work, the controversy between the interpretations of recent measurements on dense aluminum plasma created with Linac coherent light sources (LCLS) X-ray free electron laser (FEL) and Orion laser has been addressed. In both kind of experiments, helium-like and hydrogen-like spectral lines are used for plasma diagnostics . However, there exist no precise theoretical calculations for He-like ions within dense plasma environment. The strong need for an accurate theoretical estimates for spectral properties of He-like ions in strongly coupled plasma environment leads us to perform ab initio calculations in the framework of Rayleigh-Ritz variation principle in Hylleraas coordinates where ion-sphere potential is used. An approach to resolve the long-drawn problem of numerical instability for evaluating two-electron integrals with extended basis inside a finite domain is presented here. The present values of electron densities corresponding to disappearance of different spectral lines obtained within the fram...
Ab initio pseudopotential studies of equilibrium lattice structures and phonon modes of bulk BC3
International Nuclear Information System (INIS)
Different stacking arrangements of BC3 layered crystals are studied with the use of the ab initio pseudopotential density-functional method. The total energies, lattice constants, electron energy band structures and density of states, as well as phonon frequencies are calculated for the possible bulk BC3 structures obtained by full relaxations starting from different initial atomic configurations of ABAB (or ABCABC)... layer stacking. Two stable BC3 structures, one semiconductor and the other metal, are obtained, which have lower total energies compared with those of the structures proposed previously. Our calculations show that except for these two BC3 structures, all the structures we studied, including the BC3 structures proposed previously, have imaginary phonon frequencies corresponding to the relative, parallel motion of the adjacent BC3 layers, indicating the instability of the layer stacking in these structures
Magnetoelastic coupling in ?-iron investigated within an ab initio spin spiral approach
Okatov, S. V.; Gornostyrev, Yu. N.; Lichtenstein, A. I.; Katsnelson, M. I.
2011-12-01
Exchange interactions in ?- and ?-Fe are investigated within an ab initio spin spiral approach. We have performed total-energy calculations for different magnetic structures as a function of lattice distortions, related to various cell volumes and the Bain tetragonal deformations. The effective exchange parameters in ?-Fe are very sensitive to the lattice distortions, leading to the ferromagnetic ground state for the tetragonal deformation or increase of the volume cell. At the same time, the magnetic-structure-independent part of the total energy changes very slowly with the tetragonal deformations. The computational results demonstrate a strong mutual dependence of crystal and magnetic structures in Fe and explain the observable “anti-Invar” behavior of thermal-expansion coefficient in ?-Fe.
DEFF Research Database (Denmark)
Svendsen, Casper Steinmann; Fedorov, Dmitri G.
2013-01-01
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be [Formula: see text] kcal mol(-1) for MP2/cc-pVDZ and [Formula: see text] for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively.
Trends in magnetism of free Rh clusters via relativistic ab-initio calculations.
Šipr, O; Ebert, H; Minár, J
2015-02-11
A fully relativistic ab-initio study on free Rh clusters of 13-135 atoms is performed to identify general trends concerning their magnetism and to check whether concepts which proved to be useful in interpreting magnetism of 3d metals are applicable to magnetism of 4d systems. We found that there is no systematic relation between local magnetic moments and coordination numbers. On the other hand, the Stoner model appears well-suited both as a criterion for the onset of magnetism and as a guide for the dependence of local magnetic moments on the site-resolved density of states at the Fermi level. Large orbital magnetic moments antiparallel to spin magnetic moments were found for some sites. The intra-atomic magnetic dipole Tz term can be quite large at certain sites but as a whole it is unlikely to affect the interpretation of x-ray magnetic circular dichroism experiments based on the sum rules. PMID:25604525
Erba, A.
2014-09-01
A general-purpose, fully automated, computationally efficient implementation is presented of a series of techniques for the simultaneous description of pressure and temperature effects on structural properties of materials, by means of standard ab initio simulations. Equilibrium volume, bulk modulus, thermal expansion coefficient, equation-of-state, Grüneisen parameter, constant-pressure and constant-volume specific heats are computed as a function of temperature and pressure for the simple crystal of diamond and compared with accurate experimental data. Convergence of computed properties with respect to super-cell size is critically discussed. The effect on such properties of the adopted exchange-correlation functional of the density-functional-theory is discussed by considering three different levels of approximation (including hybrids): it is found to be rather small for the temperature dependence of equilibrium volume and bulk modulus, whereas it is quite large as regards their absolute values.
Ab initio calculations on magnetism induced by composite defects in magnesium oxide
International Nuclear Information System (INIS)
The local magnetic state induced by the composite defects, composed of an oxygen vacancy and a nitrogen substituting oxygen, in magnesium oxide has been studied by using ab initio calculation based on density functional theory. The calculated results show that local magnetic moment can be induced by the composite defects around the oxygen vacancy, when the exchange split of the oxygen vacancy is enhanced either by the hybridization between the N-p and nearest neighbor O-p orbitals or by applying on-site Coulomb repulsion (U) and exchange interaction (J). We show that the magnetic state induced by the composite defect is energetically more stable than the non-magnetic state. In addition, we show that the U and J applied on the p-orbitals of N and O atoms may significantly impact the calculated magnetic state of the composite defect, resulting in magnetic state for a configuration that is non-magnetic by generalized gradient approximation
Ab initio Kinetic Monte Carlo simulations of dissolution at the NaCl-water interface.
Chen, Jian-Cheng; Reischl, Bernhard; Spijker, Peter; Holmberg, Nico; Laasonen, Kari; Foster, Adam S
2014-11-01
We have used ab initio molecular dynamics (AIMD) simulations to study the interaction of water with the NaCl surface. As expected, we find that water forms several ordered hydration layers, with the first hydration layer having water molecules aligned so that oxygen atoms are on average situated above Na sites. In an attempt to understand the dissolution of NaCl in water, we have then combined AIMD with constrained barrier searches, to calculate the dissolution energetics of Na(+) and Cl(-) ions from terraces, steps, corners and kinks of the (100) surface. We find that the barrier heights show a systematic reduction from the most stable flat terrace sites, through steps to the smallest barriers for corner and kink sites. Generally, the barriers for removal of Na(+) ions are slightly lower than for Cl(-) ions. Finally, we use our calculated barriers in a Kinetic Monte Carlo as a first order model of the dissolution process. PMID:25227553
Ab initio investigation of the electronic spectrum of the chloroformyl radical ClCO
Krossner, Th.; Zülicke, L.; Staikova, M.; Peyerimhoff, S. D.
1995-08-01
An ab initio MRD-CI study is carried out to obtain a theoretical prediction of the vertical electronic spectrum of the chloroformyl radical ClCO up to energies of approximately 9 eV, including Rydberg s and p states. Furthermore, an estimation of the oscillator strengths for doublet transitions is given. The spectrum is characterized by three low-lying doublet states at 3.2, 3.4 and 3.7 eV, whereas the first quartet states as well as the first members of the Rydberg series are located in the energy region between 6.3 and 7.5 eV. Parallels are drawn with corresponding theoretical data obtained for the formyl and fluoroformyl radicals.
Ab initio study on the mechanism of the HCO+O 2?HO 2+CO reaction
Martínez-Ávila, Mónica; Peiró-García, Julio; Ramírez-Ramírez, Víctor M.; Nebot-Gil, Ignacio
2003-03-01
The gas-phase reaction HCO+O 2?CO+HO 2 has been investigated by means of ab initio calculations. The mechanism can proceed through either a direct hydrogen abstraction or addition of O 2 to the formyl radical. The energy barriers calculated at the QCISD(T)/6-311G(2df,2p) level of theory upon QCISD/6-311G(d,p) optimized structures are, respectively, of 2.98 kcal mol -1 for the direct abstraction and of 2.26 kcal mol -1 for the addition. Thus, the results obtained show that there is not a dominant pathway in the HCO+O 2 reaction under atmospheric conditions of temperature and pressure.
The interaction of OH(X²?) with H?: ab initio potential energy surfaces and bound states.
Ma, Qianli; K?os, Jacek; Alexander, Millard H; van der Avoird, Ad; Dagdigian, Paul J
2014-11-01
For the interaction of OH(X(2)?) with H2, under the assumption of fixed OH and H2 bond distances, we have determined two new sets of four-dimensional ab initio potential energy surfaces (PES's). The first set of PES's was computed with the multi-reference configuration interaction method [MRCISD+Q(Davidson)], and the second set with an explicitly correlated coupled cluster method [RCCSD(T)-F12a] sampling the subset of geometries possessing a plane of symmetry. Both sets of PES's are fit to an analytical form suitable for bound state and scattering calculations. The CCSD(T) dissociation energies (D0) of the OH-para-H2 and the OH-ortho-H2 complexes are computed to be 36.1 and 53.7 cm(-1). The latter value is in excellent agreement with the experimental value of 54 cm(-1). PMID:25381516
Ab initio prediction of environmental embrittlement at a crack tip in aluminum
Warner, Derek
2013-03-01
This talk reports on our ab initio predictions of environmental embrittlement in aluminum. We have used an atomistic-continuum multiscale framework to simulate the behavior of a loaded crack tip in the presence of oxygen and hydrogen. The multiscale simulations and subsequent analysis suggest that electronegative surface impurities can inhibit dislocation nucleation from a loaded crack tip, thus raising the likelihood for incremental brittle crack growth to occur during near-threshold fatigue. The metal-impurity bonding characteristics have been analyzed using a Bader charge transfer approximation, and the effect of this bond on the theoretical slip distribution has been investigated using a continuum Peierls model. The Peierls model, which is a function of the position dependent stacking fault energy along the slip plane, was used to estimate the effects of several common environmental impurities.
An ab initio model for the modulation of galactic cosmic-ray electrons
International Nuclear Information System (INIS)
The modulation of galactic cosmic-ray electrons is studied using an ab initio three-dimensional steady state cosmic-ray modulation code in which the effects of turbulence on both the diffusion and drift of these cosmic-rays are treated as self-consistently as possible. A significant refinement is that a recent two-component turbulence transport model is used. This model yields results in reasonable agreement with observations of turbulence quantities throughout the heliosphere. The sensitivity of computed galactic electron intensities to choices of various turbulence parameters pertaining to the dissipation range of the slab turbulence spectrum, and to the choice of model of dynamical turbulence, is demonstrated using diffusion coefficients derived from the quasi-linear and extended nonlinear guiding center theories. Computed electron intensities and latitude gradients are also compared with spacecraft observations.
Quantum fluctuations and isotope effects in ab initio descriptions of water
Wang, Lu; Markland, Thomas E
2014-01-01
Nuclear quantum effects, such as zero-point energy and tunneling, cause significant changes to the structure and dynamics of hydrogen bonded systems such as liquid water. However, due to the current inability to simulate liquid water using an exact description of its electronic structure, the interplay between nuclear and electronic quantum effects remains unclear. Here we use simulations that incorporate the quantum mechanical nature of both the nuclei and electrons to provide a fully ab initio determination of the particle quantum kinetic energies, free energy change upon exchanging hydrogen for deuterium and the isotope fractionation ratio in water. These properties, which selectively probe the quantum nature of the nuclear degrees of freedom, allow us to make direct comparison to recent experiments and elucidate how electronic exchange and correlation and nuclear quantum fluctuations determine the structure of the hydrogen bond in water.
Estudo ab-initio da a-alanina em meio aquoso
Directory of Open Access Journals (Sweden)
Sambrano Júlio Ricardo
1999-01-01
Full Text Available Ab initio Hartree-Fock (HF, Density Functional (B3LYP and electron correlation (MP2 methods have been used to caracterize the aqueous medium intramolecular hydrogen bond in a-alanine. The 6-31G* and 6-31++G** were taken from Gaussian94 library. We were concerned on the structure of three conformers of a-alanine, in their neutral form plus on the structure of the zwitterionic form (Z. The Z structure is a stationary point at the HF/6-31G* level but it is not when diffuse functions and electron correlation are included. This results shows that the Z form does not exist in the gas phase. The inclusion of solvent effects changed significantly the results obtained in gas phase, therefore this inclusion make the Z form a stationary point within all level of theory, and the relative energy depends dramatically on the level of calculation.
International Nuclear Information System (INIS)
The absolute photoabsorption spectrum of ethylene oxide (C2H4O) has been measured between onset and 30 eV, using monochromated synchrotron radiation. Below the ionization threshold (10.56 eV) the spectrum is dominated by sharp peaks related to excitation of Rydberg series converging on the first ionization energy. Above the ionization threshold, valence-excited states, which give rise to broad bands, predominate. Underlying Rydberg states are signalled in weak vibrational structure on the valence bands. Ab initio multireference configuration interaction (MRDCI) calculations have been carried out to assist in assignment of the excited states, both valence and Rydberg. The lowest-lying valence state is electric-dipole forbidden; the first optically allowed valence state lies close to the ionization onset. The spectrum of the oxide is compared with those of cyclopropane (C3H6) and ethylene sulphide (C2H4S)
Structure and reactivity of PMMA ion radicals - an ab-initio approach
International Nuclear Information System (INIS)
Ab initio molecular orbital (MO) calculations were carried out on the anion radical of methyl isobutyrate, a model of the poly(methylmethacrylate) (PMMA) anion. Calculations were also made on the cation radical for comparison. It was found, from the geometry optimisation, that the carbonyl group of the anion was bent and the carbonyl oxygen had deviated from the sp2 plane of the carbonyl carbon. Molecular orbital contour maps of singly occupied MO suggested that the excess electrons were mainly distributed on the carbonyl group of the polymer. The stability of the PMMA anion and cation is discussed in terms of the potential energy curves calculated as a function of the O-CH3 distance. (author)
Evolution of local atomic structure during solidification of Al2Au liquid: An ab initio study
International Nuclear Information System (INIS)
The local atomic structure evolution in Al2Au alloy during solidification from 2000 K to 400 K was studied by ab initio molecular dynamics simulations and analyzed using the structure factor, pair correlation functions, bond angle distributions, the Honeycutt–Anderson (HA) index and Voronoi tessellation methods. It was found that the icosahedral-like clusters are negligible in the Al2Au stable liquid and supercooled liquid states, and the most abundant clusters are those having HA indices of 131 and 120 or Voronoi indices of ?0, 4, 4, 0?, ?0, 3, 6, 0? and ?0, 4, 4, 2? with coordination numbers of 8, 9 and 10, respectively. These clusters are similar to the local atomic structures in the CaF2-type Al2Au crystal, revealing the existence of structure heredity between liquid and crystalline phase in Al2Au alloy
Ab initio modelling of the behaviour of helium in americium and plutonium oxides
International Nuclear Information System (INIS)
By means of an ab initio plane wave pseudo potential method, plutonium dioxide and americium dioxide are modelled, and the behaviour of helium in both these materials is studied. We first show that a pseudo potential approach in the Generalized Gradient Approximation (GGA) can satisfactorily describe the cohesive properties of PuO2 and AmO2. We then calculate the formation energies of point defects (vacancies and interstitials), as well as the incorporation and solution energies of helium in PuO2 and AmO2. The results are discussed according to the incorporation site of the gas atom in the lattice and to the stoichiometry of PuO2±x and AmO2±x. (authors)
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Karl-Heinz Böhm
2014-04-01
Full Text Available We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2Hethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.
Ab Initio Study of Different Acid Molecules Interacting with H2O
Zakharenko, Aleksey A; Kim, K S
2008-01-01
Using the Gaussian-03 for ab initio calculations, we have studied interaction of different acid molecules with a single water molecule. The molecular and supermolecular optimized structures were found with the Becke-3-Lee-Yang-Parr (B3LYP-hybrid potential) calculations of density-functional theory (DFT) methods as well as the Moeller-Plesset second-order perturbation theory, using the basis set of Aug-cc-pVDZ quality and the CRENBL ECP effective core potential for molecules containing heavy iodine atom. Possible isomers of studied acids and supermolecules, consisting of acid molecules coupled with a single water molecule, are shown. Energies, zero-point energies (ZPEs), thermal enthalpies and free energies, as well as the corresponding binding energies for the theoretical methods were calculated. It was found that optimized structures of supermolecular isomers with lowest energies corresponding to the global minimum on the potential energy surfaces can be different for both theories. The simplest structure ac...
Ab initio molecular-replacement phasing for symmetric helical membrane proteins
International Nuclear Information System (INIS)
An ab initio molecular-replacement method for phasing X-ray diffraction data for symmetric helical membrane proteins has been developed. The described method is based on generating all possible orientations of idealized transmembrane helices and using each model in a molecular-replacement search. Obtaining phases for X-ray diffraction data can be a rate-limiting step in structure determination. Taking advantage of constraints specific to membrane proteins, an ab initio molecular-replacement method has been developed for phasing X-ray diffraction data for symmetric helical membrane proteins without prior knowledge of their structure or heavy-atom derivatives. The described method is based on generating all possible orientations of idealized transmembrane helices and using each model in a molecular-replacement search. The number of models is significantly reduced by taking advantage of geometrical and structural restraints specific to membrane proteins. The top molecular-replacement results are evaluated based on noncrystallographic symmetry (NCS) map correlation, OMIT map correlation and Rfree value after refinement of a polyalanine model. The feasibility of this approach is illustrated by phasing the mechanosensitive channel of large conductance (MscL) with only 4 Å diffraction data. No prior structural knowledge was used other than the number of transmembrane helices. The search produced the correct spatial organization and the position in the asymmetric unit of all transmembrane helices of MscL. The resulting electron-density maps were of sufficient quality to automatically build all helical segments of MscL including the cytoplasmic domain. The method does not require high-resolution diffraction data and can be used to obtain phases for symmetrical helical membrane proteins with one or two helices per monomer
Towards a full ab initio theory of strong electronic correlations in nanoscale devices.
Jacob, David
2015-06-24
In this paper I give a detailed account of an ab initio methodology for describing strong electronic correlations in nanoscale devices hosting transition metal atoms with open d- or f-shells. The method combines Kohn-Sham density functional theory for treating the weakly interacting electrons on a static mean-field level with non-perturbative many-body methods for the strongly interacting electrons in the open d- and f-shells. An effective description of the strongly interacting electrons in terms of a multi-orbital Anderson impurity model is obtained by projection onto the strongly correlated subspace properly taking into account the non-orthogonality of the atomic basis set. A special focus lies on the ab initio calculation of the effective screened interaction matrix U for the Anderson model. Solution of the effective Anderson model with the one-crossing approximation or other impurity solver techniques yields the dynamic correlations within the strongly correlated subspace giving rise e.g. to the Kondo effect. As an example the method is applied to the case of a Co adatom on the Cu(0?0?1) surface. The calculated low-bias tunnel spectra show Fano-Kondo lineshapes similar to those measured in experiments. The exact shape of the Fano-Kondo feature as well as its width depend quite strongly on the filling of the Co 3d-shell. Although this somewhat hampers accurate quantitative predictions regarding lineshapes and Kondo temperatures, the overall physical situation can be predicted quite reliably. PMID:26037313
Liu, Hanchao; Wang, Yimin; Bowman, Joel M.
2015-05-01
The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm-1 is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.
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Wagner B. De Almeida
2000-10-01
Full Text Available The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase and ab initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions.
International Nuclear Information System (INIS)
Ab initio and MNDO calculations predict the hydroxide anion-catalysed intramolecular hydride transfer reaction of glyoxal to exhibit a larger kinetic hydrogen isotope effect than the intermolecular Cannizzaro reaction of formaldehyde. (author)
Molecular tailoring approach: a route for ab initio treatment of large clusters.
Sahu, Nityananda; Gadre, Shridhar R
2014-09-16
Conspectus Chemistry on the scale of molecular clusters may be dramatically different from that in the macroscopic bulk. Greater understanding of chemistry in this size regime could greatly influence fields such as materials science and atmospheric and environmental chemistry. Recent advances in experimental techniques and computational resources have led to accurate investigations of the energies and spectral properties of weakly bonded molecular clusters. These have enabled researchers to learn how the physicochemical properties evolve from individual molecules to bulk materials and to understand the growth patterns of clusters. Experimental techniques such as infrared, microwave, and photoelectron spectroscopy are the most popular and powerful tools for probing molecular clusters. In general, these experimental techniques do not directly reveal the atomistic details of the clusters but provide data from which the structural details need to be unearthed. Furthermore, the resolution of the spectral properties of energetically close cluster conformers can be prohibitively difficult. Thus, these investigations of molecular aggregates require a combination of experiments and theory. On the theoretical front, researchers have been actively engaged in quantum chemical ab initio calculations as well as simulation-based studies for the last few decades. To obtain reliable results, there is a need to use correlated methods such as Møller-Plesset second order method, coupled cluster theory, or dispersion corrected density functional theory. However, due to nonlinear scaling of these methods, optimizing the geometry of large clusters still remains a formidable quantum chemistry challenge. Fragment-based methods, such as divide-and-conquer, molecular tailoring approach (MTA), fragment molecular orbitals, and generalized energy-based fragmentation approach, provide alternatives for overcoming the scaling problem for spatially extended molecular systems. Within MTA, a large system is broken down into two or more subsystems that can be readily treated computationally. Finally, the properties of the large system are obtained by patching the corresponding properties of all the subsystems. Due to these approximations, the resulting MTA-based energies carry some error in comparison with calculations based on the full system. An approach for correcting these errors has been attempted by grafting the error at a lower basis set onto a higher basis set. Furthermore, investigating the growth patterns and nucleation processes in clusters is necessary for understanding the structural transitions and the phenomena of magic numbers in cluster chemistry. Therefore, systematic building-up or the introduction of stochastics for generating molecular assemblies is the most crucial step for studying large clusters. In this Account, we discuss the working principle of MTA for probing molecular clusters at ab initio level followed by a brief summary of an automated and electrostatics-guided algorithm for building molecular assemblies. The molecular aggregates presented here as test cases are generated based on either an electrostatic criterion or the basin hopping method. At MP2 level computation, the errors in MTA-based grafted energies are typically reduced to a submillihartree level, reflecting the potential of finding accurate energies of molecular clusters much more quickly. In summary, MTA provides a platform for effectively studying large molecular clusters at ab initio level of theory using minimal computer hardware. PMID:24798296
Energy Technology Data Exchange (ETDEWEB)
Lucas, G
2006-10-15
The behaviour of silicon carbide under irradiation has been studied using classical and ab initio simulations, focusing on the nano scale elementary processes. First, we have been interested in the calculation of threshold displacement energies, which are difficult to determine both experimentally and theoretically, and also the associated Frenkel pairs. In the framework of this thesis, we have carried out simulations in classical and ab initio molecular dynamics. For the classical approach, two types of potentials have been used: the Tersoff potential, which led to non satisfactory results, and a new one which has been developed during this thesis. This potential allows a better modelling of SiC under irradiation than most of the empirical potentials available for SiC. It is based on the EDIP potential, initially developed to describe defects in silicon, that we have generalized to SiC. For the ab initio approach, the feasibility of the calculations has been validated and average energies of 19 eV for the C and 38 eV for the Si sublattices have been determined, close to the values empirically used in the fusion community. The results obtained with the new potential EDIP are globally in agreement with those values. Finally, the elementary processes involved in the crystal recovery have been studied by calculating the stability of the created Frenkel pairs and determining possible recombination mechanisms with the nudged elastic band method. (author)
Qureshi, N.; Zbiri, M.; Rodri?guez-carvajal, J.; Stunault, A.; Ressouche, E.; Hansen, T. C.; Ferna?ndez-di?az, M. T.; Johnson, M. R.; Fuess, H.; Ehrenberg, H.; Sakurai, Y.; Itou, M.; Gillon, B.; Wolf, Th; Rodri?guez-velamazan, J. A.
2008-01-01
We present a combination of ab initio calculations, magnetic Compton scattering and polarized neutron experiments, which elucidate the density distribution of unpaired electrons in the kagome staircase system Co3V2O8. Ab initio wave functions were used to calculate the spin densities in real and momentum space, which show good agreement with the respective experiments. It has been found that the spin polarized orbitals are equally distributed between the t2g and the eg level...
International Nuclear Information System (INIS)
In this work, we present frozen phonon and linear response ab-initio research into the vibrational properties of the CuGaS2 chalcopyrite and transition metal substituted (CuGaS2)M alloys. These systems are potential candidates for developing a novel solar-cell material with enhanced optoelectronic properties based in the implementation of the intermediate-band concept. We have previously carried out ab-initio calculations of the electronic properties of these kinds of chalcopyrite metal alloys showing a narrow transition metal band isolated in the semiconductor band gap. The substitutes used in the present work are the 3d metal elements, Titanium and Chromium. For the theoretical calculations we use standard density functional theory at local density and generalized gradient approximation levels. We found that the optical phonon branches of the transition metal chalcopyrite, are very sensitive to the specific bonding geometry and small changes in the transition metal environment
Philipp, Dean Michael
Methodology is discussed for mixed ab initio quantum mechanics/molecular mechanics modeling of systems where the quantum mechanics (QM) and molecular mechanics (MM) regions are within the same molecule. The ab initio QM calculations are at the restricted Hartree-Fock level using the pseudospectral method of the Jaguar program while the MM part is treated with the OPLS force fields implemented in the IMPACT program. The interface between the QM and MM regions, in particular, is elaborated upon, as it is dealt with by ``breaking'' bonds at the boundaries and using Boys-localized orbitals found from model molecules in place of the bonds. These orbitals are kept frozen during QM calculations. The mixed modeling presented here can be used for single point energy calculations and geometry optimizations. Results from tests of the method to find relative conformational energies and geometries of alanine tetrapeptides are presented along with comparisons to pure QM and pure MM calculations.
Borges, P. D.; Scolfaro, L.
2014-12-01
The thermoelectric properties of indium nitride in the most stable wurtzite phase (w-InN) as a function of electron and hole concentrations and temperature were studied by solving the semiclassical Boltzmann transport equations in conjunction with ab initio electronic structure calculations, within Density Functional Theory. Based on maximally localized Wannier function basis set and the ab initio band energies, results for the Seebeck coefficient are presented and compared with available experimental data for n-type as well as p-type systems. Also, theoretical results for electric conductivity and power factor are presented. Most cases showed good agreement between the calculated properties and experimental data for w-InN unintentionally and p-type doped with magnesium. Our predictions for temperature and concentration dependences of electrical conductivity and power factor revealed a promising use of InN for intermediate and high temperature thermoelectric applications. The rigid band approach and constant scattering time approximation were utilized in the calculations.
Ab initio phase diagram of ultracold 87Rb in a one-dimensional two-colour superlattice
International Nuclear Information System (INIS)
We investigate the ab initio phase diagram of ultracold 87Rb atoms in a one-dimensional two-colour superlattice. Using single-particle band structure calculations we map the experimental setup onto the parameters of the Bose-Hubbard model. This ab initio ansatz allows us to express the phase diagrams in terms of the experimental control parameters, i.e. the intensities of the lasers that form the optical superlattice. In order to solve the many-body problem for experimental system sizes we adopt the density-matrix renormalization-group algorithm. A detailed study of convergence and finite-size effects for all observables is presented. Our results show that all relevant quantum phases, i.e. superfluid, Mott insulator and quasi Bose glass, can be accessed through intensity variation of the lasers alone. However, it turns out that the phase diagram is strongly affected by the longitudinal trapping potential.
Abdurahman, A; Seifert, G; Abdurahman, Ayjamal; Shukla, Alok; Seifert, Gotthard
2002-01-01
In this paper we report a theoretical study of the static dipole polarizability of two one-dimensional structures: (a) linear carbon chains C$_{n} (n=2-10)$ and (b) ladder-like planar boron chains B$_{n} (n=4-14)$. The polarizabilities of these chains are calculated both at the Hartree-Fock and the correlated level by applying accurate ab initio quantum chemical methods. Methods such as restricted Hartree-Fock, multi-configuration self-consistent field, multi-reference configuration-interaction method, M{\\o}ller-Plesset second-order perturbation theory, and coupled-cluster singles, doubles and triples level of theory were employed. Results obtained from ab initio wave-function-based methods are compared with the ones obtained from the density-functional theory. For the clusters studied, directionally averaged polarizability per atom for both the systems is seen to increase with the chain size.
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Martin Alberto JM
2009-01-01
Full Text Available Abstract Background Prediction of protein structures from their sequences is still one of the open grand challenges of computational biology. Some approaches to protein structure prediction, especially ab initio ones, rely to some extent on the prediction of residue contact maps. Residue contact map predictions have been assessed at the CASP competition for several years now. Although it has been shown that exact contact maps generally yield correct three-dimensional structures, this is true only at a relatively low resolution (3–4 Å from the native structure. Another known weakness of contact maps is that they are generally predicted ab initio, that is not exploiting information about potential homologues of known structure. Results We introduce a new class of distance restraints for protein structures: multi-class distance maps. We show that C? trace reconstructions based on 4-class native maps are significantly better than those from residue contact maps. We then build two predictors of 4-class maps based on recursive neural networks: one ab initio, or relying on the sequence and on evolutionary information; one template-based, or in which homology information to known structures is provided as a further input. We show that virtually any level of sequence similarity to structural templates (down to less than 10% yields more accurate 4-class maps than the ab initio predictor. We show that template-based predictions by recursive neural networks are consistently better than the best template and than a number of combinations of the best available templates. We also extract binary residue contact maps at an 8 Å threshold (as per CASP assessment from the 4-class predictors and show that the template-based version is also more accurate than the best template and consistently better than the ab initio one, down to very low levels of sequence identity to structural templates. Furthermore, we test both ab-initio and template-based 8 Å predictions on the CASP7 targets using a pre-CASP7 PDB, and find that both predictors are state-of-the-art, with the template-based one far outperforming the best CASP7 systems if templates with sequence identity to the query of 10% or better are available. Although this is not the main focus of this paper we also report on reconstructions of C? traces based on both ab initio and template-based 4-class map predictions, showing that the latter are generally more accurate even when homology is dubious. Conclusion Accurate predictions of multi-class maps may provide valuable constraints for improved ab initio and template-based prediction of protein structures, naturally incorporate multiple templates, and yield state-of-the-art binary maps. Predictions of protein structures and 8 Å contact maps based on the multi-class distance map predictors described in this paper are freely available to academic users at the url http://distill.ucd.ie/.
Colgan, J.; Judge, E. J.; Kilcrease, D. P.; Barefield, J. E.
2014-07-01
We report on efforts to model the Fe emission spectrum generated from laser-induced breakdown spectroscopy (LIBS) measurements on samples of pure iron oxide (Fe2O3). Our modeling efforts consist of several components. We begin with ab-initio atomic structure calculations performed by solving the Hartree-Fock equations for the neutral and singly ionized stages of Fe. Our energy levels are then adjusted to their experimentally known values. The atomic transition probabilities and atomic collision quantities are also computed in an ab-initio manner. We perform LTE or non-LTE calculations that generate level populations and, subsequently, an emission spectrum for the iron plasma for a range of electron temperatures and electron densities. Such calculations are then compared to the experimental spectrum. We regard our work as a preliminary modeling effort that ultimately strives towards the modeling of emission spectra from even more complex samples where less atomic data are available.
AB Initio Study of the Structure and Spectroscopic Properties of Halogenated Thioperoxy Radicals
Munoz, Luis A.; Binning, R. C., Jr.; Weiner, Brad R.; Ishikawa, Yasuyuki
1997-01-01
Thioperoxy (XSO or XOS) radicals exist in a variety of chemical environments, and they have as a consequence drawn some interest. HSO, an important species in the chemistry of the troposphere, has been examined both experimentally. The halogenated (X = F, Cl or Br) peroxy species and isovalent thioperoxy species have been studied less, but they too are potentially interesting because oxidized sulfur species and halogen sources are present in the atmosphere. Learning the fate of XSO and XOS radicals is important to understanding the atmospheric oxidation chemistry of sulfur compounds. Of these, FSO and ClSO are particularly interesting because they have been directly detected spectroscopically. Recent studies in our laboratory on the photochemistry of thionyl halides (X2SO; where X = F or Cl) have suggested new ways to generate XSO species. The laser-induced photodissociation of thionyl fluoride, F2SO, at 193 nm and thionyl chloride, ClSO, at 248 nm is characterized by a radical mechanism, X2SO -> XSO + X. The structure of FSO has been characterized experimentally by Endo et cd. employing microwave spectroscopy. Using the unrestricted Hartree-Fock (UHF) self-consistent field (SCF) method, Sakai and Morokuma computed the electronic structure of the ground (sup 2)A" and the first excited (sup 2)A' states of FSO. Electron correlation was not taken into account in their study. In a laser photodissociation experiment, Huber et al. identified ClSO mass spectromctrically. ClSO has also been detected in low temperature matrices by EPR and in the gas phase by far IR laser magnetic resonance. Although the structure of FSO is known in detail, the only study, experimental or theoretical, of CISO has been an ab initio HFSCF study by Hinchliffe. Electron correlation corrections were also excluded from this study. In order to better understand the isomerization and dissociation dynamics of the radical species, we have performed ab initio correlated studies of the potential energy surfaces (PES) of ClSO and its isomer ClOS at the QCISD(T)/6-31 G* level of theory. For FSO and FOS, more extensive QCISD/6-31 1G(2df) calculations have been possible, and the results are summarized here.
Spectra of water dimer from a new ab initio potential with flexible monomers
Leforestier, Claude; Szalewicz, Krzysztof; van der Avoird, Ad
2012-07-01
We report the definition and testing of a new ab initio 12-dimensional potential for the water dimer with flexible monomers. Using our recent accurate CCpol-8s rigid water pair potential [W. Cencek, K. Szalewicz, C. Leforestier, R. van Harrevelt, and A. van der Avoird, Phys. Chem. Chem. Phys. 10, 4716 (2008), 10.1039/b809435g] as a reference for the undistorted monomers' geometries, a distortion correction has been added, which was taken from a former flexible-monomer ab initio potential. This correction allows us to retrieve the correct binding energy D_e = 21.0{kJ mol}^{-1}, and leads to an equilibrium geometry in close agreement with the one obtained from benchmark calculations. The kinetic energy operator describing the flexible-monomer water dimer has been expressed in terms of Radau coordinates for each monomer and a recent general cluster polyspherical formulation describing their relative motions. Within this formulation, an adiabatic scheme has been invoked in order to decouple fast (intramolecular) modes and slow (intermolecular) ones. Different levels of approximation were tested, which differ in the way in which the residual potential coupling between the intramolecular modes located on different monomers and the dependence of the monomer rotational constants on the dimer geometry are handled. Accurate calculations of the vibration-rotation-tunneling levels of (H2O)2 and (D2O)2 were performed, which show the best agreement with experiments achieved so far for any water potential. Intramolecular excitations of the two monomers were calculated within two limiting cases, to account for the lack of non-adiabatic coupling between intramolecular modes due to the intermolecular motion. In the first model, the excitation was assumed to stay either on the donor or the acceptor molecule, and to hop between the two moieties upon donor-acceptor interchange. In the second model, the excitation remains on the same molecule whatever is the dimer geometry. Marginal frequency differences, less than 2 {cm}^{-1}, were obtained for all modes, and the resulting infrared shifts are in good agreement with experiments.
Dézerald, Lucile; Ventelon, Lisa; Willaime, François; Clouet, Emmanuel; Rodney, David
2014-06-01
Ab initio methods, based on the Density Functional Theory (DFT), have been extensively used to study point defects and defect clusters in materials. Present HPC resources and DFT codes now allow similar investigations to be performed on dislocations. The study of these extended defects requires not only larger simulation cells but also a higher accuracy because the energy differences, which are involved, are rather small, typically 50-to-100 meV for supercells containing 50-to-500 atoms. The topology of the Peierls potential of screw dislocations with 1/2 Burgers vector, i.e. the 2D energy landscape seen by these dislocations, is being completely revisited by DFT calculations. From results obtained in all body-centered cubic (bcc) transition metals, except Cr (V, Nb, Ta, Mo, W and Fe), using the PWSCF code, which is part of the Quantum-Espresso package, we concluded that the 2D Peierls potentials have two common features: the single-hump shape of the barrier between two minima of the potential, and the presence of a maximum - and not a minimum as predicted by most empirical potentials - around the split core. In iron, the topology of the Peierls potential is reversed compared to the classical sinusoidal picture: the location of the saddle point and the maximum are indeed inverted with unexpected flat regions. The first results obtained within the framework of the PRACE project, DIMAIM (DIslocations in Metals using Ab Initio Methods), started at the beginning of 2013, will also be presented. In particular, in order to address the twinning-antitwinning asymmetry often observed in bcc metals and regarded as the major contribution to the breakdown of Schmid's law, we have determined the crystal orientation dependence of the Peierls stress, i.e. the critical stress required for dislocation motion. These computationally most expensive simulations were performed on the PRACE Tier-0 system at Barcelona Supercomputing Center (Marenostrum III). The scalability results using the various parallelization levels of the PWSCF code up to 10 000 cores will be presented.
Ab initio STM and STS simulations on magnetic and nonmagnetic metallic surfaces
Energy Technology Data Exchange (ETDEWEB)
Dick, Alexey
2008-04-14
The aim of this work was to provide an in-depth understanding of a new generation of scan- ning tunneling microscopy experiments, performed employing different regimes of the STM: the spectroscopy-mode (the so-called Fourier Transformed STM, FT-STM), and the spin-sensitive mode (the so-called spin-polarized STM, SP-STM). In the present thesis ab initio tools are proposed that are based on DFT calculations to theoretically predict and analyze such types of the STM. The first part of this thesis focusses on the simulation of FT-STM, the mode that allows to probe local dispersion properties of the electrons at the surface. In order to provide the theoretical counterpart of the experimental FT-STM spectra we have introduced a new implicit approach that is derived from Tersoff-Hamann theory of the STM. The importance of an accurate description of surface wavefunctions at 5-15 A above the surface as well as the spurious quantum- size effects have been discussed in detail together with approaches to obtain converged FT-STM images. We applied our method to FT-STM experiments performed on Ag(110) surfaces. In the second part of the thesis we discuss the modeling of the spin-resolved STM, the mode that allows to characterize the magnetic structure of a surface. As a case system we studied here the magnetically-ordered transition-metal nitride surface Mn{sub 3}N{sub 2}(010). Because SP-STM experiments did not allow a conclusive understanding of the surface structure, we have first employed ab initio thermodynamics to figure out the most stable magnetic and atomic configuration of the surface that are consistent with experiments. To simulate SP-STM images on the most stable Mn{sub 3}N{sub 2}(010) surface we have employed the spin-generalized transfer-Hamiltonian formalism, assuming that the tip wavefunctions have dominant radial symmetry (s-like tip). (orig.)
Raman spectroscopy, ab-initio model calculations, and conformational, equilibria in ionic liquids
DEFF Research Database (Denmark)
Berg, Rolf W.
2009-01-01
A review of the recent developments in the study and understanding of room temperature ionic liquids are given. An intimate picture of how and why these liquids are not crystals at ambient conditions is attempted, based on evidence from crystallographical results combined with vibrational spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT- Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methyl-imidazolium ([C4C1Im]+X-) salts. The rotational isomerism of the [C4C1Im]+ cation is described: the presence of anti and gauche conformational forms that has been elucidated in remarkable papers by Hamaguchi et al. Such presence of a conformational equilibrium seems to be a general feature of the room temperature liquids. The “localised structure features” that apparently exist in ionic liquids are described. It is hoped that the structural resolving power of Raman spectroscopy will be appreciated by the reader, when used on crystals of known conformation and on the corresponding liquids, especially in combination with modern quantum mechanics calculations. It is hoped that these inetrdisciplinary methods will be applied to many more systems in the future. A few examples will be discussed. Contents 12.1 Introduction...........307 12.2 Brief introduction to Raman spectroscopy ..............309 12.2.1 Basics .....................309 12.2.2 Experimental, fluorescence and fouriertransform- Raman spectroscopy instrumentation ...... 311 12.3 Brief introduction to ab-initio model calculations .... 312 12.4 Case study on Raman spectroscopy and structure of imidazolium-based ionic liquids ..... 312 12.5 Raman spectra and structure of [C4C1Im]+ liquids ..... 315 12.6 Normal mode analysis and rotational isomerism of the [C4C1Im]+ cation .........318 12.7 Other studies on [CnC1Im]+ liquids ... 329 12.8 Conformations equilibria in liquids versus temperature .... 332 12.9 Local structures in ionic liquids .....335 12.10 Other systems .................338 12.11 Other applications of Raman spectroscopy .................346 12.12 Conclusions .............346 Acknowledgments .............347 References ..................347 12.1 Introduction
International Nuclear Information System (INIS)
The full text of publication follows. Ab initio methods, based on the Density Functional Theory (DFT), have been extensively used to study point defects and defect clusters in materials. Present HPC resources and DFT codes now allow similar investigations to be performed on dislocations. The study of these extended defects requires not only larger simulation cells but also a higher accuracy because the energy differences, which are involved, are rather small, typically 50-to-100 meV for super cells containing 50-to-500 atoms. The topology of the Peierls potential of screw dislocations with 1/2 Burgers vector, i.e. the 2D energy landscape seen by these dislocations, is being completely revisited by DFT calculations. From results obtained in all body-centered cubic (bcc) transition metals, except Cr (V, Nb, Ta, Mo, W and Fe), using the PWSCF code, which is part of the Quantum-Espresso package, we concluded that the 2D Peierls potentials have two common features: the single-hump shape of the barrier between two minima of the potential, and the presence of a maximum - and not a minimum as predicted by most empirical potentials - around the split core. In iron, the topology of the Peierls potential is reversed compared to the classical sinusoidal picture: the location of the saddle point and the maximum are indeed inverted with unexpected flat regions. The first results obtained within the framework of the PRACE project, DIMAIM (Dislocations in Metals using Ab Initio Methods), started at the beginning of 2013, will also be presented. In particular, in order to address the twinning anti-twinning asymmetry often observed in bcc metals and regarded as the major contribution to the breakdown of Schmid's law, we have determined the crystal orientation dependence of the Peierls stress, i.e. the critical stress required for dislocation motion. These computationally most expensive simulations were performed on the PRACE Tier-0 system at Barcelona Supercomputing Center (Marenostrum III). The scalability results using the various parallelization levels of the PWSCF code up to 10.000 cores will be presented. (authors)
Durig, James R; Klaassen, Joshua J; Sawant, Dattatray K; Deodhar, Bhushan S; Panikar, Savitha S; Gurusinghe, Ranil M; Darkhalil, Ikhlas D; Tubergen, Michael J
2015-02-01
The infrared and Raman spectra (3200-50 cm(-1)) of the gas, liquid or solution, and solid have been recorded of isocyanocyclopentane, c-C5H9NC. FT-microwave studies have also been carried out and 23 transitions were recorded for the envelope-axial (Ax) conformer. Variable temperature (-65 to -100 °C) studies of the infrared spectra (3200-400 cm(-1)) dissolved in liquid xenon have been carried out. From these data, both the Ax and envelope-equatorial (Eq) conformers have been identified and their relative stabilities obtained. The enthalpy difference has been determined to be 102±10 cm(-1) (1.21±0.11 kJ mol(-1)) with the Ax conformer the more stable form. The percentage of the Eq conformer is estimated to be 38±1% at ambient temperature. The conformational stabilities have been predicted from ab initio calculations by utilizing several different basis sets up to aug-cc-pVTZ from both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been made for the observed bands for both conformers with initial predictions by MP2(full)/6-31G(d) ab initio calculations to obtain harmonic force constants, wavenumbers, infrared intensities, Raman activities and depolarization ratios for both conformers. The structural parameter values for the Ax form are; for the heavy atom distances (Å): C?N = 1.176 (3); C?-N=1.432 (3); C?-C?,C?'=1.534 (3); C?-C?,C?'=1.542 (3); C?-C?'=1.554 (3) and angles (°):?C?-N?C=177.8 (5); ?C?C?-N=110.4 (5);
Lu, Zhenyu; Zhang, Yingkai
2008-01-01
In order to further improve the accuracy and applicability of combined quantum mechanical/molecular mechanical (QM/MM) methods, we have interfaced the ab initio QM method with the classical Drude oscillator polarizable MM force field (ai-QM/MM-Drude). Different coupling approaches have been employed and compared: 1. the conventional dual self-consistent-field (SCF) procedure; 2. the direct SCF scheme, in which QM densities and MM Drude positions are converged simultaneously; 3. the micro-iter...
Smeyers, Y. G.; Senent Díez, María Luisa; Villa, M.
1998-01-01
The ab initio determination of the band structures of infrared spectra is described giving as examples the methyl torsion and amine wagging in methylamine and the double torsion in dimethylamine. In addition, the influence of the amine hydrogen symmetric bending and the CNC skeleton symmetric bending is considered in methylamine and dimethylamine, respectively. For this purpose, the potential energy sufaces and kinetic parameters are determined at the RHF/MP2 levels with large basis sets. The...
Czech Academy of Sciences Publication Activity Database
V?eš?ál, J.; Houserová, Jana; Šob, Mojmír; Friák, Martin
Rio de Janeiro, 2003, s. 760-770. [CONGRESSO ANUAL DA ABM /58./. Rio de Janeiro (BR), 21.07.2003-24.07.2003] R&D Projects: GA ?R GP106/03/P002; GA ?R GA106/02/0877 Institutional research plan: CEZ:AV0Z2041904 Keywords : sigma phase * phase diagram ? ab initio methods Subject RIV: BM - Solid Matter Physics ; Magnetism
Taming the resistive switching in Fe/MgO/V/Fe magnetic tunnel junctions: An ab initio study
Aguiar-hualde, J. M.; Alouani, M.
2014-01-01
A possible mechanism for the resistive switching observed experimentally in Fe/MgO/V/Fe junctions is presented. Ab initio total energy calculations within the local density approximation and pseudopotential theory shows that by moving the oxygen ions across the MgO/V interface one obtains a metastable state. It is argued that this state can be reached by applying an electric field across the interface. In addition, the ground state and the metastable state show different ele...
Paschedag, N.; Suter, H. U.; Meier, P. F.
1997-04-01
The electronic structure of hydrogen and muonium at the bond-centered site (anomalous muonium) in silicon is investigated using ab initio cluster calculations. Correlation effects are accounted for by the configuration interaction method and by density functional calculations. A detailed investigation of the different functionals is presented. The calculations using configuration interaction and the different gradient corrected density functionals are in good agreement with each other. The effect of the zero point motion was included in the investigation.
International Nuclear Information System (INIS)
The electronic structure of hydrogen and muonium at the bond-centered site (anomalous muonium) in silicon is investigated using ab initio cluster calculations. Correlation effects are accounted for by the configuration interaction method and by density functional calculations. A detailed investigation of the different functionals is presented. The calculations using configuration interaction and the different gradient corrected density functionals are in good agreement with each other. The effect of the zero point motion was included in the investigation
Hooydonk, G.
2005-01-01
Ab initio quantum chemistry reveals how the charge-antisymmetric antihydrogenic antiHH+ state, deriving from conventional positional antisymmetry of a 3-unit charge system, is hidden in the PEC (potential energy curve) of the molecular hydrogen cation. Only with internal charge inversion and Coulomb's law, the anti-symmetry generated by positional coordinates can be understood but this solution was persistently overlooked. Stabilizing matter-antimatter interactions not only ...
Gorelik, Tatiana E.; Van de Streek, Jacco; Kilbinger, Andreas F. M.; Brunklaus, Gunther; Kolb, Ute
2012-01-01
Ab-initio crystal structure analysis of organic materials from electron diffraction data is presented. The data were collected using the automated electron diffraction tomography (ADT) technique. The structure solution and refinement route is first validated on the basis of the known crystal structure of tri-p-benzamide. The same procedure is then applied to solve the previously unknown crystal structure of tetra-p-benzamide. In the crystal structure of tetra-p-benzamide, an unusual hydrogen-...
An ab initio study of 3s core-level x-ray photoemission spectra in transition metals
Takahashi, Manabu; Igarashi, Jun-ichi
2010-01-01
We calculate the $3s$- and $4s$-core-level x-ray photoemission spectroscopy (XPS) spectra in the ferromagnetic and nonmagnetic transition metals by developing an \\emph{ab initio} method. We obtain the spectra exhibiting the characteristic shapes as a function of binding energy in good agreement with experimental observations. The spectral shapes are strikingly different between the majority spin channel and the minority spin channel for ferromagnetic metals Ni, Co, and Fe, t...