Thiessen, P. A.; Treder, H.-J.
Der gegenwärtige Stand der physikalischen Erkenntnis, in Sonderheit die Atomistik und die Quantentheorie, ermöglicht (in wohldefinierten Energie-Bereichen) eine ab initio-Berechnung aller physikalischen und chemischen Prozesse und Strukturen. Die Schrödinger-Gleichung erlaubt zusammen mit den Prinzipien der Quantenstatistik (Pauli-Prinzip) aus dem Planckschen Wirkungsquantum h und den atomischen Konstanten die Berechnung aller Energieumsätze, Zeitabläufe etc., die insbesondere die chemische Physik bestimmen. Die Rechenresultate gelten auch quantitativ bis auf die unvermeidliche Stochastik.Die ab initio-Berechnungen korrespondieren einerseits und sind andererseits komplementär zu den auf den Methoden der theoretischen Chemie und der klassischen Thermodynamik beruhenden Ergebnissen ex eventu. Die theoretische Behandlung ab initio führt zu mathematischen Experimenten, die die Laboratoriums-Experimente ergänzen oder auch substituieren.Translated AbstractAb initio vel ex eventuThe present state of physical knowledge, in peculiar atomistic and quantum theory, makes an ab initio calculation of all physical and chemical processes and structures possible (in well defined reaches of energy). The Schrödinger equation together with the principles of quantum statistics (Pauli principle) permits from the Planck and atomistic constants to calculate all exchanges of energy, courses of time, etc. which govern chemical physics. The calculated results are valid even quantitatively apart from the unavoidable stochastics.These ab initio calculations on the one hand correspond and are on the other complimentary to results ex eventu based on the methods of theoretical chemistry and classical thermodynamics. Theoretical treatment ab initio leads to mathematical experiments which add to or even substitute experiments in the laboratory.
Energy Technology Data Exchange (ETDEWEB)
Feller, D.F.
1993-07-01
This collection of benchmark timings represents a snapshot of the hardware and software capabilities available for ab initio quantum chemical calculations at Pacific Northwest Laboratory`s Molecular Science Research Center in late 1992 and early 1993. The ``snapshot`` nature of these results should not be underestimated, because of the speed with which both hardware and software are changing. Even during the brief period of this study, we were presented with newer, faster versions of several of the codes. However, the deadline for completing this edition of the benchmarks precluded updating all the relevant entries in the tables. As will be discussed below, a similar situation occurred with the hardware. The timing data included in this report are subject to all the normal failures, omissions, and errors that accompany any human activity. In an attempt to mimic the manner in which calculations are typically performed, we have run the calculations with the maximum number of defaults provided by each program and a near minimum amount of memory. This approach may not produce the fastest performance that a particular code can deliver. It is not known to what extent improved timings could be obtained for each code by varying the run parameters. If sufficient interest exists, it might be possible to compile a second list of timing data corresponding to the fastest observed performance from each application, using an unrestricted set of input parameters. Improvements in I/O might have been possible by fine tuning the Unix kernel, but we resisted the temptation to make changes to the operating system. Due to the large number of possible variations in levels of operating system, compilers, speed of disks and memory, versions of applications, etc., readers of this report may not be able to exactly reproduce the times indicated. Copies of the output files from individual runs are available if questions arise about a particular set of timings.
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.
Kühne, Thomas D.
2012-01-01
Computer simulation methods, such as Monte Carlo or Molecular Dynamics, are very powerful computational techniques that provide detailed and essentially exact information on classical many-body problems. With the advent of ab-initio molecular dynamics, where the forces are computed on-the-fly by accurate electronic structure calculations, the scope of either method has been greatly extended. This new approach, which unifies Newton's and Schr\\"odinger's equations, allows for ...
Ab initio study of the beta$-tin->Imma->sh phase transitions in silicon and germanium
Gaal-Nagy, Katalin; Pavone, Pasquale; Strauch, Dieter
2003-01-01
We have investigated the structural sequence of the high-pressure phases of silicon and germanium. We have focussed on the cd->beta-tin->Imma->sh phase transitions. We have used the plane-wave pseudopotential approach to the density-functional theory implemented within the Vienna ab-initio simulation package (VASP). We have determined the equilibrium properties of each structure and the values of the critical parameters including a hysteresis effect at the phase transitions....
International Nuclear Information System (INIS)
Formation energies of defects were estimated from an ab initio calculation for uranium dioxide with different valences of the fission products. The VASP (Vienna Ab initio Simulation Package) was used in this study, which is based on a density function theory (DFT) to express the total energy with the density of electrons. One uranium element was replaced with an element of the fission products to calculate the oxygen and uranium defection energy. Additionally, the formation energy of the Schottky defects (two oxygen vacancies and one uranium vacancy) was obtained. This data will be very useful to estimate a diffusion mechanism of fission gases in a nuclear fuel
Kühne, Thomas D
2012-01-01
Computer simulations and molecular dynamics in particular, is a very powerful method to provide detailed and essentially exact informations of classical many-body problems. With the advent of \\textit{ab-initio} molecular dynamics, where the forces are computed on-the-fly by accurate electronic structure calculations, the scope of either method has been greatly extended. This new approach, which unifies Newton's and Schr\\"odinger's equations, allows for complex simulations without relying on any adjustable parameter. This review is intended to outline the basic principles as well as a survey of the field. Beginning with the derivation of Born-Oppenheimer molecular dynamics, the Car-Parrinello method as well as novel hybrid scheme that unifies best of either approach are discussed. The predictive power is demonstrated by a series of applications ranging from insulators to semiconductors and even metals in condensed phases.
Collective rotation from ab initio theory
Caprio, M A; Vary, J P; Smith, R
2015-01-01
Through ab initio approaches in nuclear theory, we may now seek to quantitatively understand the wealth of nuclear collective phenomena starting from the underlying internucleon interactions. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments, and electromagnetic transitions. In this review, NCCI calculations of 7-9Be are used to illustrate and explore ab initio rotational structure, and the resulting predictions for rotational band properties are compared with experiment. We highlight the robustness of ab initio rotational predictions across different choices for the internucleon interaction.
International Nuclear Information System (INIS)
Polonium is the only element with a simple cubic (sc) crystal structure. Atoms in solid polonium sit at the corners of a simple cubic unit cell and no where else. Polonium has a valence electron configuration 6s26p4 (Z = 84). The low temperature ?-phase transforms into the rhombohedral (trigonal) ? structure at ?348 K. The sc ?-Po unit cell constant is a = 3.345 A. The beta form of polonium (?-Po) has the lattice parameters, aR = 3.359 A and a rhombohedral angle 98 deg. 13'. We have performed an ab initio electronic structure calculation by using the density functional theory. We have performed the calculation with and without spin-orbit (SO) coupling by using both the LDA and the GGA for the exchange-correlations. The k-points in a simple cubic BZ are determined by R (0.5, 0.5, 0.5), ? (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and ? (0, 0, 0). Other directions of k-points are ? (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and ? (0, 0, 0). The SO splittings of p states at the ? point in the GGA+SO scheme for ?-Po are 0.04 eV and 0.02 eV while for the ?-Po these are 0.03 eV and 0.97 eV. We have also calculated the vibrational spectra for the unit cells in both the structures. We find that exchanging of a Po atom by Pb atom produces several more bands and destabilizes the ? phase
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
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.
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)
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.
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
Highly scalable Ab initio genomic motif identification
Marchand, Benoît
2011-01-01
We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.
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.)
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 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
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)
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.
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 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.
Ab Initio Modeling of Molecular Radiation
Jaffe, Richard; Schwenke, David
2014-01-01
Radiative emission from excited states of atoms and molecules can comprise a significant fraction of the total heat flux experienced by spacecraft during atmospheric entry at hypersonic speeds. For spacecraft with ablating heat shields, some of this radiative flux can be absorbed by molecular constituents in the boundary layer that are formed by the ablation process. Ab initio quantum mechanical calculations are carried out to predict the strengths of these emission and absorption processes. This talk will describe the methods used in these calculations using, as examples, the 4th positive emission bands of CO and the 1g+ 1u+ absorption in C3. The results of these calculations are being used as input to NASA radiation modeling codes like NeqAir, HARA and HyperRad.
Ab initio studies on liquids and neutron experiments
International Nuclear Information System (INIS)
The recent development of ab initio simulation techniques enables us to carry out reliable simulations for liquid-state materials. As an example, we describe the results of ab initio molecular-dynamics simulations for liquid alkali-chalcogen mixtures and molten noble-metal halides. It is shown that the calculated structure factors are in good agreement with those obtained by neutron scattering experiments. We discuss the relationship between ab initio studies on liquids and neutron experiments from the viewpoint of theoretical research. (author)
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.
Cálculos ab initio con correlación electrónica
Merchán Bonete, M.
Estamos entrando en una era donde la ortogonalidad entre las investigaciones de carácter experimental y de naturaleza teórica se irá difuminando progresivamente y la problemática a resolver quedará en escena como el único actor principal de la obra. Como premisa para una cooperación teórico-experimental de igual a igual, la metodología químico-cuántica utilizada debe ser capaz de ofrecer resultados de carácter predictivo. Sin duda, esta madurez en la metodología químico-cuántica ya la hemos alcanzado hace algunos años, tal y como muestra entre otras muchas, la labor que nuestro grupo ha realizado en el transcurso de la última década, dentro del campo de la Espectroscopía Teórica. Los estudios realizados comprenden una amplia gama de sistemas, variando tanto en tamaño como en complejidad, abordando problemáticas espectroscópicas consideradas tradicionalmente como especialmente controvertidas. Nuestra contribución científica más relevante reside en el carácter cuantitativo de las asignaciones espectroscópicas que hemos propuesto en base a resultados ab initio. Recordemos que en los años noventa los resultados ab initio solían presentar para las energías de excitación de sistemas de tamaño molecular moderado, como el benceno, errores de más de 1 eV. En comparación con el éxito relativo de los métodos semiempíricos, la frustración de la metodología ab initio quedaba todavía más patente. Los estudios que hemos presentado representan una comprensión profunda de los espectros electrónicos en sistemas orgánicos claves, mostrando el camino a seguir para obtener asignaciones espectroscópicas precisas (entre 0.1-0.2 eV). La naturaleza del método CASPT2 junto al diseño de estrategias computacionales nos ha permitido alcanzar el carácter cuantitativo con el que se caracterizan nuestras contribuciones[1,2]. Por todo ello, algunos de los trabajos publicados se consideran clásicos dentro del campo, pues en cierto modo definen el campo, y se reflejan en libros publicados recientemente. En la conferencia se analizarán ciertos pormenores de las investigaciones realizadas. El tipo de aplicaciones llevadas a cabo hasta la fecha se ilustrará mediante el estudio teórico del espectro electrónico de ciclooctatetraeno. Dando un paso más en la evolución de nuestra investigación, pretendemos en la actualidad describir, desde un formalismo teórico y al mismo nivel de exigencia, los mecanismos subyacentes que tienen lugar en las reacciones biológicas fototoinducidas, es decir, reacciones que se inician mediante la absorción de luz[3]. Como muestra de la caracterización de los procesos fotofísicos y fotoquímicos en fotobiología teórica, hemos elegido la descripción de la conversión interna ultrarrápida que tiene lugar en los cromóforos del ADN. Los estados excitados de las moléculas de los ácidos nucleicos presentan tiempos de vida media que se encuentran en el rango de sub-picosegundos, sugiriendo la presencia de un canal ultrarrápido de conversión interna, lo que normalmente se asocia en la fotoquímica contemporánea a una intersección cónica entre el estado excitado y el fundamental[4]. De esta forma nuestro ADN previene de forma eficaz posibles reacciones en el estado excitado y se revela como un excelente protector solar.
Recent achievements in ab initio modelling of liquid water
Khaliullin, Rustam Z.; Kühne, Thomas D.
2013-01-01
The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulat...
Ab-initio numerical studies in semiconductor alloys
Gironcoli, Stefano de
1992-01-01
This thesis is devoted to the theoretical study, by ab initio numerical methods, of the physical properties of substitutional semiconductor alloys. Nowadays, ab initio numerical methods allow to study quite accurately the physical properties of moderately complex periodic systems. These methods exploit the periodicity of the system, and can be applied to disordered systems (such as the substitutional semiconductor alloys), where the periodicity is lost, by replacing the original non-periodic ...
Ab initio calculation of the Hoyle state
Epelbaum, Evgeny; Lee, Dean; Meißner, Ulf-G
2011-01-01
The Hoyle state plays a crucial role in the hydrogen burning of stars heavier than our sun and in the production of carbon and other elements necessary for life. This excited state of the carbon-12 nucleus was postulated by Hoyle^{1} as a necessary ingredient for the fusion of three alpha particles to produce carbon at stellar temperatures. Although the Hoyle state was seen experimentally more than a half century ago^{2,3}, nuclear theorists have not yet uncovered the nature of this state from first principles. In this letter we report the first ab initio calculation of the low-lying states of carbon-12 using supercomputer lattice simulations and a theoretical framework known as effective field theory. In addition to the ground state and excited spin-2 state, we find a resonance at -85(3) MeV with all of properties of the Hoyle state and in agreement with the experimentally observed energy. These lattice simulations provide insight into the structure of this unique state and new clues as to the amount of fine...
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.
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.
P-V Relation for Mercuric Calcogenides: Ab Initio Method
Directory of Open Access Journals (Sweden)
G. Misra
2011-01-01
Full Text Available Mercuric Calcogenides found many applications in electronic and optical devices as semiconducting materials. An equation of state provides useful information about the relationship between pressure (P, volume (V and temperature (T that helps to understand the behaviour of materials under the effect of high pressure and high temperature. The present paper sheds light on the electronic structure of Mercuric Calcogenides by simulating its electronic properties through ab initio method. This ab initio method is extended to derive the equation of state for Mercuric Calcogenides. The present equation of state has also been tested for the prediction of End Point. The computed results compare well with Quantum statistical data.
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.
Recent achievements in ab initio modelling of liquid water
Khaliullin, Rustam Z
2013-01-01
The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.
Ab initio lattice dynamics of MnO.
Czech Academy of Sciences Publication Activity Database
Legut, Dominik; Wdowik, U.
2009-01-01
Ro?. 21, ?. 27 (2009), Art. N. 275402. ISSN 0953-8984 Institutional research plan: CEZ:AV0Z20410507 Keywords : lattice dynamics * MnO * ab initio Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.964, year: 2009
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.
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.
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.
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...
High Level Ab Initio Kinetics as a Tool for Astrochemistry
Klippenstein, Stephen
2015-05-01
We will survey the application of ab initio theoretical kinetics to reactions of importance to astrochemistry. Illustrative examples will be taken from our calculations for (i) interstellar chemistry, (ii) Titan's atmospheric chemistry, and (iii) the chemistry of extrasolar giant planets. The accuracy of various aspects of the calculations will be summarized including (i) the underlying ab initio electronic structure calculations, (ii) the treatment of the high pressure recombination process, and (iii) the treatment of the pressure dependence of the kinetics. The applications will consider the chemistry of phosphorous on giant planets, the kinetics of water dimerization, the chemistry of nitrogen on Titan's atmosphere, as well as various reactions of interstellar chemistry interest such as the recombination of OH with H, and O(3P) reacting with C2H5, CH2, and CCS. Chemical Sciences and Engineering Division.
Multiple Time Step Integrators in Ab Initio Molecular Dynamics
Luehr, Nathan; Martinez, Todd J
2013-01-01
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we show that such a timescale separation is possible using two different schemes: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynami...
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
Clustering in nuclei from ab initio nuclear lattice simulations
Meißner, Ulf-G
2015-01-01
Nuclear Lattice Effective Field Theory is a new many-body approach that is firmly rooted in the symmetries of QCD. In particular, it allows for truly ab initio calculations of nuclear structure and reactions. In this talk, I focus on the emergence of alpha-clustering in nuclei based on this approach. I also discuss various recent achievements, the deficiencies of the chiral forces used at present and the prospects to improve upon these and the calculations of nuclear properties and dynamics.
Matrix isolation and ab initio studies of oxalic acid
International Nuclear Information System (INIS)
Rotamerization and UV photochemical decomposition of oxalic acid were studied in various matrices and ab initio calculations in this paper. Two conformers, cTc (2 intramolecular hydrogen bonds) and cTt (one intramolecular hydrogen bond) and their conversion energy from one form to the other were observed and studied. Full Xe arc irradiation decomposes matrix oxalic acid. For 6 oxalic acid conformers other spectra are calculated and assigned along with their potential energy distributions. 25 refs., 8 figs., 11 tabs
Ab Initio Method for Obtaining Exactly Solvable Quantum Mechanical Potentials
Gangopadhyaya, Asim; Mallow, Jeffry V.
2007-01-01
The shape invariance condition is the integrability condition in supersymmetric quantum mechanics (SUSYQM). It is a difference-differential equation connecting the superpotential W and its derivative at two different values of parameters. We show that this difference equation is equivalent to a non-linear partial differential equation whose solutions are translational shape invariant superpotentials. In lieu of trial and error, this method provides the first ab initio techni...
Uniaxial Phase Transition in Si : Ab initio Calculations
Cheng, C.
2002-01-01
Based on a previously proposed thermodynamic analysis, we study the relative stabilities of five Si phases under uniaxial compression using ab initio methods. The five phases are diamond, beta-tin, sh, sc, and hcp structures. The possible phase-transition patterns were investigated by considering the phase transitions between any two chosen phases of the five phases. By analyzing the different conributions to the relative pahse stability, we identified the most important fac...
Ab initio simulation of helium inside carbon nanotubes
International Nuclear Information System (INIS)
In present work we consider the complex behaviour of quantum liquids like liquid He-4 inside carbon nanotubes. Interactions between helium atoms and carbon atoms of the short-length atomistic model and model with periodical boundary conditions of carbon nanotube were studied via ab initio quantum simulations. Effects of geometrical confinement of the tube on the He behaviour inside CNT (13,0) have been explored. Nanotubes with typical average diameter of 10 angstroms are under consideration.
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
Ab initio DFT - the seamless connection between WFT and DFT
Grabowski, Ireneusz; Hirata, So; Lotrich, Victor F.
2010-01-01
Abstract Orbital-dependent exchange-correlation functionals and potentials play an increasingly important role in Density Functional Theory (DFT). Methods which use explicit orbital-dependent functionals can be viewed as a natural extension to the standard Kohn-Sham (KS) procedure in DFT, that traditionally have used functionals with explicit density-dependence but only implicit orbital-dependence. Ab initio DFT, invented at the Quantum Theory Project, is the m...
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...
Local Structure Analysis in $Ab$ $Initio$ Liquid Water
Santra, Biswajit; DiStasio Jr, Robert A.; 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($I$...
Screw dislocation in zirconium: An ab initio study
Clouet, Emmanuel
2012-01-01
Plasticity in zirconium is controlled by 1/3 screw dislocations gliding in the prism planes of the hexagonal close-packed structure. This prismatic and not basal glide is observed for a given set of transition metals like zirconium and is known to be related to the number of valence electrons in the d band. We use ab initio calculations based on the density functional theory to study the core structure of screw dislocations in zirconium. Dislocations are found to dissociate ...
Microscopic theory and ab initio simulation of atomic heat transport
Marcolongo, Aris; Umari, Paolo; Baroni, Stefano
2015-01-01
Quantum simulation methods based on density-functional theory are currently deemed to be unfit to cope with atomic thermal transport in materials within the Green-Kubo formalism. In contrast with this belief, we derive an expression for the adiabatic energy flux from density-functional theory, that permits the ab initio simulation of atomic thermal transport using equilibrium molecular dy- namics. The resulting thermal conductivity is shown to be unaffected by the inherent i...
Nuclear forces and ab initio calculations of atomic nuclei
Meißner}, Ulf-G.
2014-01-01
Nuclear forces and the nuclear many-body problem have been some of Gerry Brown's main topics in his so productive life as a theoretical physicist. In this talk, I outline how Gerry's work laid the foundations of the modern theory of nuclear forces and ab initio calculations of atomic nuclei. I also present some recent developments obtained in the framework of nuclear lattice simulations.
Electronic excitations, spectroscopy and quantum transport from ab initio theory
Olevano, Valerio
2009-01-01
Spectroscopy and quantum transport constitute powerful ways to study the physics of matter and to access the electronic and atomic structure. Excitations, in turn determined by the electronic and atomic structure, lie at the origin of spectroscopy and quantum transport. Ab initio calculation of excited states requires to go beyond ground-state density-functional theory (DFT). In this work we review three theoretical frameworks beyond DFT: the first is time-dependent density-functional theory ...
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 structure determination using nano electron diffraction :
XU, Q
2008-01-01
This thesis is the summary of the development of electron diffraction into a mature method for ab initio structure determination. The progress is illustrated with the structure determination of some complicated unknown inorganic materials. The main step forwards is that it is now possible to apply electron crystallography method on solving the structure with a relatively large unit cell dimension along all directions and with both very heavy atoms and very light atoms. One main issue abo...
Ab initio nuclear structure - the large sparse matrix eigenvalue problem
International Nuclear Information System (INIS)
The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several ab initio methods have now emerged that provide nearly exact solutions for some nuclear properties. The ab initio no core shell model (NCSM) and the no core full configuration (NCFC) method, frame this quantum many-particle problem as a large sparse matrix eigenvalue problem where one evaluates the Hamiltonian matrix in a basis space consisting of many-fermion Slater determinants and then solves for a set of the lowest eigenvalues and their associated eigenvectors. The resulting eigenvectors are employed to evaluate a set of experimental quantities to test the underlying potential. For fundamental problems of interest, the matrix dimension often exceeds 1010 and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. We survey recent results and advances in solving this large sparse matrix eigenvalue problem. We also outline the challenges that lie ahead for achieving further breakthroughs in fundamental nuclear theory using these ab initio approaches.
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.
Ab initio calculations of reactions with light nuclei
Quaglioni, S; Calci, A; Navratil, P; Roth, R
2015-01-01
An {\\em ab initio} (i.e., from first principles) theoretical framework capable of providing a unified description of the structure and low-energy reaction properties of light nuclei is desirable to further our understanding of the fundamental interactions among nucleons, and provide accurate predictions of crucial reaction rates for nuclear astrophysics, fusion-energy research, and other applications. In this contribution we review {\\em ab initio} calculations for nucleon and deuterium scattering on light nuclei starting from chiral two- and three-body Hamiltonians, obtained within the framework of the {\\em ab initio} no-core shell model with continuum. This is a unified approach to nuclear bound and scattering states, in which square-integrable energy eigenstates of the $A$-nucleon system are coupled to $(A-a)+a$ target-plus-projectile wave functions in the spirit of the resonating group method to obtain an efficient description of the many-body nuclear dynamics both at short and medium distances and at long...
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...
Ab-initio modelling of transport in atomic scale devices
Taylor, Jeremy P.
In this thesis, we develop a novel ab-initio technique to study transport in atomic scale devices based on a self-consistent solution of the Kohn-Sham equations for open systems in and out of equilibrium. Starting from the central motivating theorems of density functional theory, we introduce the basis of the ab-initio technique as currently practiced in condensed matter physics. The Kohn-Sham Hamiltonian is solved numerically by employing a Fireball atomic orbital basis set to transform the problem into matrix form. In order to study open systems, a natural screening approximation is introduced and it is demonstrated that, for the systems studied in this work, the Kohn-Sham potential is effectively screened and the screening approximation is appropriate for the study of atomic scale devices. The method developed in this thesis is contrasted with previous studies of transport in atomic scale devices and it is argued that it presents a significant advance and makes it possible to solve problems which could not previously be studied. A few representative studies were undertaken in order to illustrate the advantage of using a self-consistent ab-initio method to study quantum transport in open systems. Several short carbon chains were coupled to Al electrodes and it was found that charge transfer plays a role in aligning the Fermi level with standing wave resonance peaks inside the atomic chain. Our study of a C60 molecular junction predicts a substantial equilibrium conductance due to charge transfer doping of three extra electrons inside the C60. Furthermore, these extra electrons may be depleted by an external gate voltage, reducing the conductance and thus producing a field-effect molecular switch. Transport and charge transfer were studied in a number of nanotube devices. Preliminary results are in agreement with recent experimental and theoretical results.
Ab initio molecular simulations with numeric atom-centered orbitals
Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias
2009-11-01
We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.
Ab-initio study of transition metal hydrides
Energy Technology Data Exchange (ETDEWEB)
Sharma, Ramesh [Dept. of Physics, Feroze Gandhi Insititute of Engineering and Technology, Raebareli-229001 (India); Shukla, Seema, E-mail: sharma.yamini62@gmail.com; Dwivedi, Shalini, E-mail: sharma.yamini62@gmail.com; Sharma, Yamini, E-mail: sharma.yamini62@gmail.com [Theoretical Condensed Matter Physics Laboratory, Dept. of Physics Feroze Gandhi College, Raebareli-229001 (India)
2014-04-24
We have performed ab initio self consistent calculations based on Full potential linearized augmented plane wave (FP-LAPW) method to investigate the optical and thermal properties of yttrium hydrides. From the band structure and density of states, the optical absorption spectra and specific heats have been calculated. The band structure of Yttrium metal changes dramatically due to hybridization of Y sp orbitals with H s orbitals and there is a net charge transfer from metal to hydrogen site. The electrical resistivity and specific heats of yttrium hydrides are lowered but the thermal conductivity is slightly enhanced due to increase in scattering from hydrogen sites.
Ab initio prediction of the mechanical properties of alloys
Wang, Guisheng
2015-01-01
At the time of the 50th anniversary of the Kohn-Sham method, ab initio calculations based on density functional theory have formed an accurate, efficient, and reliable method to work on the properties of engineering materials. In this thesis, we use the exact muffin-tin orbitals method combined with the coherent-potential approximation to study the mechanical properties of high-technology materials. The thesis includes two parts: a study of long-range chemical order effects and a study of all...
Ab initio shallow acceptor levels in gallium nitride
Fiorentini, V; Bernardini, F.; Bosin, A.; Vanderbilt, D
1996-01-01
Impurity levels and formation energies of acceptors in wurtzite GaN are predicted ab initio. Be_Ga is found to be the shallow (thermal ionization energy $\\sim$ 0.06 eV); $Mg_{Ga}$ and $Zn_{Ga}$ are mid-deep acceptors (0.23 eV and 0.33 eV respectively); $Ca_{Ga}$ and $Cd_{Ga}$ are deep acceptors ($\\sim$0.65 eV); $Si_N$ is a midgap trap with high formation energy; finally, contrary to recent claims, $C_N$ is a deep acceptor (0.65 eV). Interstitials and heteroantisites are ener...
Ab initio calculations of the Cr-based Laves phases.
Czech Academy of Sciences Publication Activity Database
Houserová, Jana; Šob, Mojmír
Vienna : Editio Amici -Physicae et chimicae solidorum amici, 2006, s. 160-160. ISBN 3-902548-00-2. [DFTEM 2006 Conference. Vienna (AT), 21.04.2006-23.04.2006] R&D Projects: GA ?R(CZ) GA202/06/1509; GA ?R(CZ) GP106/03/P002; GA AV ?R(CZ) IAA1041302 Institutional research plan: CEZ:AV0Z20410507 Keywords : ab initio * Laves phase * cromium-based Subject RIV: CF - Physical ; Theoretical Chemistry
Ab-initio Study of Small Silver Nanoclusters
International Nuclear Information System (INIS)
We explore the lowest energy structures and investigate the structural and electronic properties of small AgN (N = 1-10) clusters by employing an ab-initio self-consistent density functional method in the local density approximation. The calculation of binding energy, bond length and the energy difference of HOMO-LUMO states have been carried out in a large energy interval for different isomeric forms of Ag clusters. The cluster binding energies increases rapidly with cluster size, which is consistent with the size dependence properties of clusters but our values are slightly higher than the other calculations
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 Calculations Applied to Problems in Metal Ion Chemistry
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Partridge, Harry; Arnold, James O. (Technical Monitor)
1994-01-01
Electronic structure calculations can provide accurate spectroscopic data (such as molecular structures) vibrational frequencies, binding energies, etc.) that have been very useful in explaining trends in experimental data and in identifying incorrect experimental measurements. In addition, ab initio calculations. have given considerable insight into the many interactions that make the chemistry of transition metal systems so diverse. In this review we focus on cases where calculations and experiment have been used to solve interesting chemical problems involving metal ions. The examples include cases where theory was used to differentiate between disparate experimental values and cases where theory was used to explain unexpected experimental results.
Ab-initio study of napthelene based conducting polymer
Energy Technology Data Exchange (ETDEWEB)
Ruhela, Ankur [Advanced Materials Research Group, Computational Nanoscience and Technology Lab (CNTL), ABV-Indian Institute of Information Technology and Management, Gwalior -474010, India and Amity Institute of Nanotechnology, Amity University, Noida-201303 (India); Kanchan, Reena, E-mail: reena.kanchan1977@gmail.com [Department of Chemistry, Jiwaji University, Gwalior-474001 (India); Srivastava, Anurag [Advanced Materials Research Group, Computational Nanoscience and Technology Lab (CNTL), ABV-Indian Institute of Information Technology and Management, Gwalior -474010 (India); Sinha, O. P. [Amity Institute of Nanotechnology, Amity University, Noida-201303 (India)
2014-04-24
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 $n=5$.
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...
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 simulation of radiation damage in nuclear reactor pressure vessel materials
Watts, Daniel; Finkenstadt, Daniel
2012-02-01
Using Kinetic Monte Carlo we developed a code to study point defect hopping in BCC metallic alloys using energetics and attempt frequencies calculated using VASP, an electronic structure software package. Our code provides a way of simulating the effects of neutron radiation on potential reactor materials. Specifically we will compare the Molybdenum-Chromium alloy system to steel alloys for use in nuclear reactor pressure vessels.
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.
Ab initio study of Cu diffusion in ?-cristobalite
International Nuclear Information System (INIS)
We have studied the geometries, formation energies, migration barriers and diffusion of a copper interstitial with different charge states with and without an external electric field in the ?-cristobalite crystalline form of SiO2 using ab initio computer simulation. The most stable state almost throughout the band gap is charge q = + 1. The height of the migration barrier depends slightly on the charge state and varies between 0.11 and 0.18 eV. However, the charge has a strong influence on the shape of the barrier, as metastable states exist in the middle of the diffusion path for Cu with q = + 1. The heights and shapes of barriers also depend on the density of SiO2, because volume expansion has a similar effect to increase the positive charge on Cu. Furthermore, diffusion coefficients have been deduced from our calculations according to transition-state theory and these calculations confirm the experimental result that oxidation of Cu is a necessary condition for diffusion. Our molecular dynamics simulations show a similar ion diffusion, and dependence on charge state. These simulations also confirm the fact that diffusion of ions can be directly simulated using ab initio molecular dynamics. (paper)
Scattering and reactions in ab initio nuclear theory
Nollett, Kenneth
2006-10-01
Over the past decade, much progress has been made toward understanding nuclei as collections of neutrons and protons, taking into account all of the complications of their interactions. Precise characterizations of the those interactions together with vast increases in computer power now allow ab initio calculations of many nuclear energy levels. Several ab initio computational methods are being pursued by different groups, and each has a distinct set of advantages and disadvantages. I will discuss the Argonne v18 interaction, the Illinois three-body interactions, and the quantum Monte Carlo computational methods. I will describe their past successes and the efforts currently under way to apply them to nuclear scattering and reactions. These methods have significant advantages in describing unbound states, because they involve no spatial basis functions and therefore do not require recourse to specialized bases or generator coordinate methods. Our results so far include radiative capture calculations in A=6 and A=7 systems, and a set of scattering calculations for A=5. Our initial calculation of low-energy ^4He-neutron scattering has been particularly successful. General single-channel scattering and electroweak capture reactions for Ainformation about processes not observable in the laboratory. It will also greatly expand the range of laboratory tests for the nuclear potentials.
Emission Spectroscopy and Ab Initio Calculations for TaN
Ram, R. S.; Liévin, J.; Bernath, P. F.
2002-10-01
The emission spectra of TaN have been investigated in the region 3000-35 000 cm -1 using a Fourier transform spectrometer. The spectra were observed in a tantalum hollow-cathode lamp by discharging a mixture of 1.5 Torr of Ne and about 6 mTorr of N 2. In addition to previously known bands, numerous additional bands were observed and assigned to a number of new transitions. The spectroscopic properties of the low-lying electronic states of TaN were also predicted by ab initio calculations. A 1? + state, with equilibrium constants of Be=0.457 852 1(48) cm -1, ? e=0.002 235 9(67) cm -1, and Re=1.683 099 9(88) Å, has been identified as the ground state of TaN based on our experimental observations supported by the ab initio results. The first excited state has been identified as the a3? 1 spin component at 2827 cm -1 above the ground state. To higher energies, the states become difficult to assign because of their Hund's case (c) behavior and extensive interactions between the spin components of the electronic terms.
New Horizons in Ab Initio Nuclear Structure Theory
International Nuclear Information System (INIS)
Nuclear interactions derived within chiral effective field theory enable nuclear structure and reaction calculations solidly rooted in QCD. Using chiral two- and three-body interactions in ab initio studies of a variety of nuclear observables is, both, promising and challenging. Particularly the inclusion of chiral 3N interactions into exact and approximate many-body calculations is demanding and computationally expensive. We present recent key developments that facilitate ab initio calculations of ground and low-lying excited states of p- and sd-shell nuclei with full 3N interactions in the Importance-Truncated No-Core Shell Model using consistent Similarity Renormalization Group transformations of the NN+3N Hamiltonian. The treatment of 3N interactions without approximations allows for first studies of the dependence of nuclear-structure observables on the details of chiral interactions. Moreover, we present results for heavy nuclei obtained in Coupled Cluster calculations using a normal-ordered two-body approximation of the 3N interaction.
AB INITIO SIMULATIONS FOR MATERIAL PROPERTIES ALONG THE JUPITER ADIABAT
International Nuclear Information System (INIS)
We determine basic thermodynamic and transport properties of hydrogen-helium-water mixtures for the extreme conditions along Jupiter's adiabat via ab initio simulations, which are compiled in an accurate and consistent data set. In particular, we calculate the electrical and thermal conductivity, the shear and longitudinal viscosity, and diffusion coefficients of the nuclei. We present results for associated quantities like the magnetic and thermal diffusivity and the kinematic shear viscosity along an adiabat that is taken from a state-of-the-art interior structure model. Furthermore, the heat capacities, the thermal expansion coefficient, the isothermal compressibility, the Grüneisen parameter, and the speed of sound are calculated. We find that the onset of dissociation and ionization of hydrogen at about 0.9 Jupiter radii marks a region where the material properties change drastically. In the deep interior, where the electrons are degenerate, many of the material properties remain relatively constant. Our ab initio data will serve as a robust foundation for applications that require accurate knowledge of the material properties in Jupiter's interior, e.g., models for the dynamo generation.
International Nuclear Information System (INIS)
Self-associates of nucleic acid components (stacking trimers and tetramers of the base pairs of nucleic acids) and short fragments of nucleic acids are nanoparticles (linear sizes of these particles are more than 10 A). Modern quantum-mechanical methods and softwares allow one to perform ab initio calculations of the systems consisting of 150-200 atoms with enough large basis sets (for example, 6-31G*). The aim of this work is to reveal the peculiarities of molecular and electronic structures, as well as the energy features of nanoparticles of nucleic acid components. We had carried out ab initio calculations of the molecular structure and interactions in the stacking dimer, trimer, and tetramer of nucleic base pairs and in the stacking (TpG)(ApC) dimer and (TpGpC) (ApCpG) trimer of nucleotides, which are small DNA fragments. The performed calculations of molecular structures of dimers and trimers of nucleotide pairs showed that the interplanar distance in the structures studied is equal to 3.2 A on average, and the helical angle in a trimer is approximately equal to 30o: The distance between phosphor atoms in neighboring chains is 13.1 A. For dimers and trimers under study, we calculated the horizontal interaction energies. The analysis of interplanar distances and angles between nucleic bases and their pairs in the calculated short oligomers of nucleic acid base pairs (stacking dimer, trimer, and tetramer) has been carried out. Studies of interactions in the calculated short oligomers showed a considerable role of the cross interaction in the stabilization of the structures. The contribution of cross interactions to the horizontal interactions grows with the length of an oligomer. Nanoparticle components get electric charges in nanoparticles. Longwave low-intensity bands can appear in the electron spectra of nanoparticles.
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)
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.
Ab Initio Calculations of Co Shielding in Model Complexes
Directory of Open Access Journals (Sweden)
Elaine A. Moore
2002-08-01
Full Text Available Abstract: Recent ab initio calculations of cobalt NMR shielding show that DFT-GIAO calculations using hybrid functionals are found to reproduce experimental values well. This method is used to calculate the variation of the cobalt NMR shielding tensor of sqaure pyramidal nitrosyl complexes with respect to the CoNO geometry and to differing basal ligands. The isotropic shielding is shown to have a large negative derivative with respect to CoX distance where X is a ligating atom.; the derivative with respect to NO distance is smaller but still significant. The zz component where z is along the CoN(NO bond is more sensitive to the basal ligands but the other two principal components are sensitive to the CoNO geometry.
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)
Ab initio calculation of excitons in ZnO
Laskowski, Robert; Christensen, Niels Egede
2006-01-01
The optical absorption and excitonic properties of wurtzite ZnO are investigated by means of an ab initio approach taking into account electron-hole correlations. This is done by solving the Bethe-Salpeter equation, using the results of density functional theory calculations as a starting point. Our main focus is the calculation of the band edge optical spectra. We have identified ground states for three excitons ( A , B , and C ), with binding energies around 68meV . Excitons A and B are excited mainly by light polarized perpendicular to the c crystallographic axis. The C exciton absorbs mainly light polarized parallel to the c axis. Due to spin-orbit interactions, excitons A and C show a tiny absorption for the parallel polarization and perpendicular polarizations, respectively.
Hydrocarbon enthalpies of formation and ab initio calculations
Herndon, William C.
1995-03-01
Simple protocols to convert calculated HF ab initio energies for hydrocarbons to accurate heats of formation are described. The optimum procedures use the numbers of carbon and hydrogen atoms, and 6-31G ? energies as independent variables. The 6-31G ? energies are calculated at either 6-31G ? or STO-3G optimized geometries. The data set of 65 compounds includes planar and nonplanar polycyclic aromatics, alkyl-substituted benzenes, highly strained alkenes and alkanes, and alkynes. The experimental ?Hf0(g) cover a range of -50 to +150 kcal/mol. The mean deviation between experimental and calculated ?Hf0(g) is 1.1 kcal, and the correlation coefficient is 0.9998 for the 6-31G ? // STO-3G calculation.
Quantifying transition voltage spectroscopy of molecular junctions: Ab initio calculations
DEFF Research Database (Denmark)
Chen, Jingzhe; Markussen, Troels
2010-01-01
Transition voltage spectroscopy (TVS) has recently been introduced as a spectroscopic tool for molecular junctions where it offers the possibility to probe molecular level energies at relatively low bias voltages. In this work we perform extensive ab initio calculations of the nonlinear current-voltage relations for a broad class of single-molecule transport junctions in order to assess the applicability and limitations of TVS. We find, that in order to fully utilize TVS as a quantitative spectroscopic tool, it is important to consider asymmetries in the coupling of the molecule to the two electrodes. When this is taken properly into account, the relation between the transition voltage and the energy of the molecular orbital closest to the Fermi level closely follows the trend expected from a simple, analytical model.
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 investigation of the mechanical properties of copper
International Nuclear Information System (INIS)
Employing the ab initio total energy method based on the density functional theory with the generalized gradient approximation, we have systematically investigated the theoretical mechanical properties of copper (Cu). The theoretical tensile strengths are calculated to be 25.3 GPa, 5.9 GPa, and 37.6 GPa for the fcc Cu single crystal in the [001], [110], and [111] directions, respectively. Among the three directions, the [110] direction is the weakest one due to the occurrence of structure transition at the lower strain and the weakest interaction of atoms between the (110) planes, while the [111] direction is the strongest direction because of the strongest interaction of atoms between the (111) planes. In terms of the elastic constants of Cu single crystal, we also estimate some mechanical quantities of polycrystalline Cu, including bulk modulus B, shear modulus G, Young's modulus Ep, and Poisson's ratio ?
Ab initio structural, elastic, and vibrational properties of carbon nanotubes
Sánchez-Portál, D; Soler, J M; Rubio, A; Ordejón, P
1999-01-01
A study based on ab initio calculations is presented on the estructural, elastic, and vibrational properties of single-wall carbon nanotubes with different radii and chiralities. We use SIESTA, an implementation of pseudopotential-density-functional theory which allows calculations on systems with a large number of atoms per cell. Different quantities like bond distances, Young moduli, Poisson ratio and the frequencies of different phonon branches are monitored versus tube radius. The validity of expectations based on graphite is explored down to small radii, where some deviations appear related to the curvature effects. For the phonon spectra, the results are compared with the predictions of the simple zone-folding approximation. Except for the known defficiencies of this approximation in the low-frequency vibrational regions, it offers quite accurate results, even for relatively small radii.
Solvation of the chloride anion in water: ab initio simulations
Zhang, Cui; Donadio, Davide; Gygi, Francois; Galli, Giulia
2012-02-01
We studied the structural, vibrational and electronic properties of the chloride anion in water using ab initio molecular dynamics. Our investigation has three main objectives: understand the range of perturbation exerted by the anion on the water hydrogen bonded network; identify signatures of the anion perturbation in infrared spectra of the solution and study the extent of charge localization on the anion, as predicted by semi-local (PBE) and hybrid functionals (PBE0). In agreement with recent experiments, we find that the presence of the anion substantially affects only the hydrogen bonding in the first solvation shell, due to a decrease of the dipole moment of the first shell water molecules and thus a weakening of the hydrogen bonds. Such a weakening leads to a slightly blue shifted band in the computed IR spectra. While structural and vibrational properties of the solution are similar within PBE and PBE0, the electronic properties exhibit marked differences.
Simple calculation of ab initio melting curves: Application to aluminum.
Robert, Grégory; Legrand, Philippe; Arnault, Philippe; Desbiens, Nicolas; Clérouin, Jean
2015-03-01
We present a simple, fast, and promising method to compute the melting curves of materials with ab initio molecular dynamics. It is based on the two-phase thermodynamic model of Lin et al [J. Chem. Phys. 119, 11792 (2003)] and its improved version given by Desjarlais [Phys. Rev. E 88, 062145 (2013)]. In this model, the velocity autocorrelation function is utilized to calculate the contribution of the nuclei motion to the entropy of the solid and liquid phases. It is then possible to find the thermodynamic conditions of equal Gibbs free energy between these phases, defining the melting curve. The first benchmark on the face-centered cubic melting curve of aluminum from 0 to 300 GPa demonstrates how to obtain an accuracy of 5%-10%, comparable to the most sophisticated methods, for a much lower computational cost. PMID:25871249
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...
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.
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
2014-01-01
Time-resolved photoelectron spectroscopy and ab initio multiple spawning were applied to the ultrafast non-adiabatic dynamics of hexamethylcyclopentadiene. The high level of agreement between experiment and theory associates wavepacket motion with a distinct degree of freedom.
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...
Ab-Initio Molecular Dynamics Acceleration Scheme with an Adaptive Machine Learning Framework
Botu, Venkatesh; Ramprasad, Rampi
2014-01-01
Quantum mechanics based ab-initio molecular dynamics (MD) simulation schemes offer an accurate and direct means to monitor the time-evolution of materials. Nevertheless, the expensive and repetitive energy and force computations required in such simulations lead to significant bottlenecks. Here, we lay the foundations for such an accelerated ab-initio MD approach integrated with a machine learning framework. The proposed algorithm learns from previously visited configuration...
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...
Ab initio study of electronic transport for DNA sequencing
Mehrez, H.; Maragkakis, P.; Barnett, R. L.; Kaxiras, E.
2002-03-01
Electronic sequencing of DNA bases is challenging for both experimental and theoretical investigations. Experimentally, fabricating well controlled nano-device system, to which DNA is attached and I-V characteristics are measured through each individual base, is difficult if not impossible. Recently, a new experimental approach is developed. Nanopores (R 0.1 nm) on Si_3N4 membrane have been fabricated and single strand DNA's have been directed to pass through them. The ultimate goal, is to attach contact leads on the Nanopore and measure transport properties across the contacts as the DNA is flowing through the hole. This would serve as DNA bases analyzer. However, to understand these experimental results, extensive,first principle investigation is required. This would determine the effects of the contacts, DNA bases orientation with respect to the leads and DNA bases neighbor interactions. In this talk we show our ab initio analysis, within Density Fuctional Theory appraoch, of zero bias conductance of different DNA basis between Au(111) contacts. We mainly investigate the effect of contacts and their interactions with DNA bases at different orientations.
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.)
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 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.
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 theory of perpendicular magnetotransport in metallic multilayers
Kudrnovský, J.; Drchal, V.; Blaas, C.; Weinberger, P.; Turek, I.; Bruno, P.
2000-12-01
The current-perpendicular-to-plane (CPP) magnetotransport of a metallic sample sandwiched by two ideal leads is described at an ab initio level. The so-called ``active'' part of the system is either a trilayer consisting of two magnetic slabs of finite thickness separated by a nonmagnetic spacer or a multilayer formed by alternating magnetic and nonmagnetic layers. We use a transmission matrix formulation of the conductance based on surface Green's functions as formulated by means of the tight-binding linear muffin-tin orbital method. The formalism is extended to the case of lateral supercells with random arrangements of atoms of two types, which in turn allows to deal with specular and diffusive scattering on equal footing, and which is applicable also to the case of noncollinear alignments of the magnetization in the layers. Applications refer to fcc-based Co/Cu/Co(001) trilayers and multilayers, considering in detail the effect of substitutional alloying in the spacer and in the magnetic layers, as well as interdiffusion at the interfaces.
Ab initio Calculations of Elastic Constants of Superalloys
Isaev, Eyvaz I.; Ponomareva, Alena V.; Bleskov, Ivan D.; Vekilov, Yuri Kh.
2011-05-01
Using the-state-of-the-art ab initio method we have studied elastic constants of alloys potentially interesting for high temperature applications. We have shown that Cr substitutes the Al sublattice in B2 NiAl at concentration up to 40 at. %, but at higher Cr content it prefers the Ni-sublattice. Alloying of NiAl with Cr yields reduced strength but improves the ductility of the alloys. Alloying of NiAl with W which substitutes the Al sublattice, leads to a strong decrease of the shear modulus, and near 50 at. % of W the alloy becomes mechanically unstable as elastic constant C' is negative. This is in agreement with our phonon calculations where we found soft modes along the [110] direction for B2 NiW. According to our calculations in (Ru,Ni)Al alloys the shear modulus is almost constant up to 40 at. % of Ni, at higher Ni concentrations it is drastically reduced. We have shown that the changes in elastic properties of (Ru-X)Al alloys are due to electronic topological transitions.
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. 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 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.
Ab-Initio Study of Incongruent Melting in Silicates
Pinilla, C.; Stixrude, L. P.
2014-12-01
Knowledge of the multi-component thermodynamics and phase equilibria of silicate melts at Earth's interior conditions are key to understand the chemical and thermal evolution of the planet. Yet they remain poorly constrained with a wide uncertainty on the eutectic composition and temperature. In this work we present results from ab-initio molecular dynamics in combination with the two-phase coexistance method to study properties of a system of MgSiO3 liquid coexisting with crystalline MgO at conditions of the deep lower mantle. During incongruent melting the crystal may either grow via partial freezing of the liquid or shrink via partial melting at a given temperature and pressure. The melting process can be studied using the two-phases method where liquid and solid are in contact at a given temperature and pressure and so under thermodynamic equilibrium. We characterise the composition and densities of the resultant solid and liquid phases, provide chemical potentials of the liquid phase and study the structural and dynamical properties of the melt. In addition, we discuss the performance of alternative computational methods applied to the study of incongruent melting in silicate systems where long simulation times and a large number of atoms are usually needed. Finally, we discuss the implication of our findings for the evolution of the Earth's interior.
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
Ab initio study of edge sites reactivity on pyrophyllite
International Nuclear Information System (INIS)
The crystal chemistry and surface site reactivity of the phyllosilicate minerals is a key issue for modelling the ion mobility and retardation in clay sediments. Various cation substitutions in the TOT layer of the 2:1 phyllosilicates result in a permanent structural charge near basal plane which is responsible for swelling and the sorption of ions by a cation exchange mechanism. In contrast, the pH-dependent uptake of cations is controlled by protonation/de-protonation reactions on the edge sites of the TOT layer. Various models have been proposed to explain the reactivity of the edge sites based on macroscopic experiments. A detailed understanding of this process on an atomistic level is still missing. We are using electronic structure calculations and ab initio MD simulations in order to understand the mechanism of pH dependent sorption of cations on edge sites of pyrophyllite and the transport properties of aqueous solutions in compacted pyrophyllite. The calculations provide important constrains for the macroscopic surface complexation models of clay minerals. (authors)
Ab initio study of edge sites reactivity on pyrophyllite
Energy Technology Data Exchange (ETDEWEB)
Churakov, S.V. [Paul Scherrer Institute, Nuclear Energy and Safety Department, Lab. for Waste Management, Villigen PSI (Switzerland)
2005-07-01
The crystal chemistry and surface site reactivity of the phyllosilicate minerals is a key issue for modelling the ion mobility and retardation in clay sediments. Various cation substitutions in the TOT layer of the 2:1 phyllosilicates result in a permanent structural charge near basal plane which is responsible for swelling and the sorption of ions by a cation exchange mechanism. In contrast, the pH-dependent uptake of cations is controlled by protonation/de-protonation reactions on the edge sites of the TOT layer. Various models have been proposed to explain the reactivity of the edge sites based on macroscopic experiments. A detailed understanding of this process on an atomistic level is still missing. We are using electronic structure calculations and ab initio MD simulations in order to understand the mechanism of pH dependent sorption of cations on edge sites of pyrophyllite and the transport properties of aqueous solutions in compacted pyrophyllite. The calculations provide important constrains for the macroscopic surface complexation models of clay minerals. (authors)
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.
Microsolvation of methyl hydrogen peroxide: Ab initio quantum chemical approach
Kulkarni, Anant D.; Rai, Dhurba; Bartolotti, Libero J.; Pathak, Rajeev K.
2009-08-01
Methyl hydrogen peroxide (MHP), one of the simplest organic hydroperoxides, is a strong oxidant, with enhanced activity in aqueous ambience. The present study investigates, at the molecular level, the role of hydrogen bonding that is conducive to cluster formation of MHP with water molecules from its peroxide end, with the methyl group remaining hydrophobic for up to five water molecules. Ab initio quantum chemical computations on MHP⋯(H2O)n, [n =1-5] are performed at second order Møller-Plesset (MP2) perturbation theory employing the basis sets 6-31G(d,p) and 6-311++G(2d,2p) to study the cluster formation of MHP with water molecules from its peroxide end and hydrophobic hydration due to the methyl group. Successive addition of water molecules alters the hydrogen bonding pattern, which leads to changes in overall cluster geometry and in turn to IR vibrational frequency shifts. Molecular co-operativity in these clusters is gauged directly through a detailed many-body interaction energy analysis. Molecular electrostatic potential maps are shown to have a bearing on predicting further growth of these clusters, which is duly corroborated through sample calculations for MHP⋯(H2O)8. Further, a continuum solvation model calculation for energetically stable clusters suggests that this study should serve as a precursor for pathways to aqueous solvation of MHP.
A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.
Spencer, Matt; Eickholt, Jesse; Jianlin Cheng
2015-01-01
Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80 percent and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test dataset of 198 proteins, achieving a Q3 accuracy of 80.7 percent and a Sov accuracy of 74.2 percent. PMID:25750595
AN AB INITIO MODEL FOR COSMIC-RAY MODULATION
Energy Technology Data Exchange (ETDEWEB)
Engelbrecht, N. E.; Burger, R. A. [Center for Space Research, North-West University, Potchefstroom 2520 (South Africa)
2013-07-20
A proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays (CRs) is of vital importance for a better understanding of CR modulation in the heliosphere. This study presents an ab initio model for CR modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for solar minimum heliospheric conditions, utilizing boundary values chosen so that model results are in reasonable agreement with spacecraft observations of turbulence quantities in the solar ecliptic plane and along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modeled slab and two-dimensional (2D) turbulence energy spectra. The modeled 2D spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers. There currently exist no models or observations for the wavenumber where this drop-off occurs, and it is considered to be the only free parameter in this study. The modeled spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on CR drifts are modeled in a self-consistent way, also employing a recently developed model for wavy current sheet drift. The resulting diffusion and drift coefficients are applied to the study of galactic CR protons and antiprotons using a 3D, steady-state CR modulation code, and sample solutions in fair to good agreement with multiple spacecraft observations are presented.
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 electron diffraction and ab initio investigation of cyclopropylisothiocyanate
Durig, J. R.; Sullivan, J. F.; Berry, R. J.; Cradock, Stephen
1987-04-01
The molecular structure of cyclopropylisothiocyanate, c-C3H5NCS, has been investigated at 35 °C by gas phase electron diffraction. Two distinct conformers, trans and cis, were identified with the isomeric proportion being 72±5% trans at this temperature. The structural parameters were determined by combining the electron diffraction data with the previously published rotational constants. A quadratic force field was used to calculate vibrational corrections. The important distances (r*av,Å) and angles (?*av, deg) with their uncertainties in parentheses were determined to be for the trans conformer: r(C1-C2)=1.520(3), r(C2-C3) =1.515(3), r(N=C)=1.193(3), r(C=S)=1.574(3), r(C1-N)=1.387(5), r(C-H) =1.072(5), ?C1NC=149.1(15), ?C2C1N=118.9(6), ?HCH=115.0(fixed), ?C2C1H=117.35(fixed), and ?NCS=177.7(20), whereas those that differed for the cis conformer were found to be: r(C1-N)=1.413(5), ?C1NC=150.8(17), and ?C2C1N=116.2(15). The rms amplitudes of vibration with their associated uncertainties have been determined for some of the distances. In addition, the geometry has been calculated by ab initio Hartree-Fock gradient calculations with geometry optimization at the STO-3G level and it is found that the computed structure is in reasonable agreement to the one derived from the electron diffraction experiment. Features of the structure are compared with those of similar molecules and discussed.
Ab initio quantum transport calculations using plane waves
Garcia-Lekue, A.; Vergniory, M. G.; Jiang, X. W.; Wang, L. W.
2015-08-01
We present an ab initio method to calculate elastic quantum transport at the nanoscale. The method is based on a combination of density functional theory using plane wave nonlocal pseudopotentials and the use of auxiliary periodic boundary conditions to obtain the scattering states. The method can be applied to any applied bias voltage and the charge density and potential profile can either be calculated self-consistently, or using an approximated self-consistent field (SCF) approach. Based on the scattering states one can straightforwardly calculate the transmission coefficients and the corresponding electronic current. The overall scheme allows us to obtain accurate and numerically stable solutions for the elastic transport, with a computational time similar to that of a ground state calculation. This method is particularly suitable for calculations of tunneling currents through vacuum, that some of the nonequilibrium Greens function (NEGF) approaches based on atomic basis sets might have difficulty to deal with. Several examples are provided using this method from electron tunneling, to molecular electronics, to electronic devices: (i) On a Au nanojunction, the tunneling current dependence on the electrode-electrode distance is investigated. (ii) The tunneling through field emission resonances (FERs) is studied via an accurate description of the surface vacuum states. (iii) Based on quantum transport calculations, we have designed a molecular conformational switch, which can turn on and off a molecular junction by applying a perpendicular electric field. (iv) Finally, we have used the method to simulate tunnel field-effect transistors (TFETs) based on two-dimensional transition-metal dichalcogenides (TMDCs), where we have studied the performance and scaling limits of such nanodevices and proposed atomic doping to enhance the transistor performance.
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.
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)
International Nuclear Information System (INIS)
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
An ab initio-based Er–He interatomic potential in hcp Er
Energy Technology Data Exchange (ETDEWEB)
Yang, Li; ye, Yeting; Fan, K. M.; Shen, Huahai; Peng, Shuming; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei
2014-09-01
We have developed an empirical erbium-helium (Er-He) potential by fitting to the results calculated from ab initio method. Based on the electronic hybridization between Er and He atoms, an s-band model, along with a repulsive pair potential, has been derived to describe the Er-He interaction. The atomic configurations and the formation energies of single He defects, small He interstitial clusters (Hen) and He-vacancy (HenV ) clusters obtained by ab initio calculations are used as the fitting database. The binding energies and relative stabilities of the HnVm clusters are studied by the present potential and compared with the ab initio calculations. The Er-He potential is also applied to study the migration of He in hcp-Er at different temperatures, and He clustering is found to occur at 600 K in hcp Er crystal, which may be due to the anisotropic migration behavior of He interstitials.
Shear stiffness in nanolaminar Ti3SiC2 challenges ab initio calculations
International Nuclear Information System (INIS)
Nanolaminates such as the Mn+1AXn (MAX) phases are a material class with ab initio derived elasticity tensors published for over 250 compounds. We have for the first time experimentally determined the full elasticity tensor of the archetype MAX phase, Ti3SiC2, using polycrystalline samples and in situ neutron diffraction. The experimental elastic constants show extreme shear stiffness, with c44 more than five times greater than expected for an isotropic material. Such shear stiffness is quite rare in hexagonal materials and strongly contradicts the predictions of all published MAX phase elastic constants derived from ab initio calculations. It is concluded that second order properties such as elastic moduli derived from ab initio calculations require careful experimental verification. The diffraction technique used currently provides the only method of verification for the elasticity tensor for the majority of new materials where single crystals are not available. (fast track communication)
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.
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.
Estudo da geometria da uréia por métodos ab initio e simulação computacional de líquidos
Cirino José Jair Vianna; Bertran Celso Aparecido
2002-01-01
A study was carried out on the urea geometries using ab initio calculation and Monte Carlo computational simulation of liquids. The ab initio calculated results showed that urea has a non-planar conformation in the gas phase in which the hydrogen atoms are out of the plane formed by the heavy atoms. Free energies associated to the rotation of the amino groups of urea in water were obtained using the Monte Carlo method in which the thermodynamic perturbation theory is implemented. The magnitud...
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 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...
Ultralong-Range Rydberg Cs2 Molecules Investigated at the Ab Initio Level of Theory
Ji, Ting; Liu, Xiaomeng; Yang, Yonggang; Zhao, Jianming
2015-08-01
Rydberg molecules have been extensively investigated recently owing to rapid developments in ultracold experiments, which pave the way for their preparation. Many Rydberg molecules formed by alkali atoms, such as Rb2 and Cs2, have been produced and studied experimentally on the basis of good sources of corresponding cold atoms. On the other hand, quantitative theoretical investigations on Rydberg molecules, such as at the ab initio level, are still scarce. Very recently, an efficient method of studying Rydberg molecules at the ab initio level has been proposed. Following this method, we studied the potential energy curves and vibrational energy levels of Rydberg Cs2 molecules.
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.
Experimental IR, Raman and ab initio molecular orbital study of the 4-methylbenzenesulfonate anion
Ristova, M.; Pejov, L.; Žugi?, M.; Šoptrajanov, B.
1999-05-01
The 4-methylbenzenesulfonate ( p-toluenesulfonate) anion was studied by ab initio quantum chemical methods, and the IR and Raman spectra of oxonium p-toluenesulfonate were recorded. The geometry of the anion was fully optimized at the HF SCF/3-21+G(d) level of theory. The theoretically predicted structure was in very good agreement with the crystallographic results. Harmonic vibrational analysis was performed for the optimized structure (at the same level of theory). The predicted harmonic vibrational frequencies based on the ab initio force field were shown to be very valuable for an accurate assignment of the internal vibrational modes of the anion in 4-methylbenzenesulfonate salts.
Ab initio Molecular Dynamics Simulations of Water Under Static and Shock Compressed Conditions
Energy Technology Data Exchange (ETDEWEB)
Goldman, N; Fried, L E; Mundy, C J; Kuo, I W; Curioni, A; Reed, E
2007-07-25
We report herein a series of ab initio simulations of water under both static and shocked conditions. We have calculated the coherent x-ray scattering intensity of several phases of water under high pressure, using ab initio Density Functional Theory (DFT). We provide new atomic scattering form factors for water at extreme conditions, which take into account frequently neglected changes in ionic charge and electron delocalization. We have also simulated liquid water undergoing shock loading of velocities from 5-11 km/s using the Multi-Scale Shock Technique (MSST). We show that Density Functional Theory (DFT) molecular dynamics results compare extremely well to experiments on the water shock Hugoniot.
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...
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)
Silicate-Metal Partitioning of Trace Elements: An Exploratory Ab Initio Molecular Dynamics Study
Künzel, D.; Jahn, S.
2014-12-01
Partition coefficients of trace elements are very important for the reconstruction of Earth formation and evolution processes. As such processes typically take place at extreme conditions of pressure and temperature, it is still challenging to obtain experimental data. However, recent developments in super-computing facilities and in computational methods have made it possible to obtain supplementing information on melts and element partitioning from ab initio atomistic calculations. The model system used in this pilot study consists of two different melts: a simple Fe-Ni alloy representing the metal and a silicate phase with a varying ratio of Fe and Mg ((Fe,Mg)2SiO4). Traces of Ni or Cr are added to each system. Molecular dynamics simulations based on density functional theory are initially run at 2500 K and ambient pressure, using the CPMD and CP2K software packages. Conditions are chosen so that the results can be compared to available experimental data in order to assess the feasibility of the approach and the quality of its results. However, preliminary results at increased pressure and temperature conditions that are more relevant for core formation will be presented as well. The results of the calculations include information on the melt structure, such as coordination environment, nearest neighbor distance and x-ray diffraction structure factors. The calculations at ambient pressure show that the behavior of Ni atoms in the silicate melt shows similarities to Mg and differs clearly from Fe. First results with a Cr trace show that it resembles Fe rather than Ni. Furthermore, thermodynamic integration is able to provide thermodynamic information about the exchange of trace elements between both phases. It is possible to obtain the energy difference connected to this exchange, which can then be used to estimate partition factors. First results on the Ni partitioning will be presented.
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 molecular dynamics simulation on temperature-dependent properties of Al-Si liquid alloy
International Nuclear Information System (INIS)
We have carried out ab initio molecular dynamics simulations on Al-15% Si liquid alloy at different temperatures. The temperature dependences of energy, volume, diffusion coefficient and structure factor have been studied. The theoretical structure factors are in agreement with the experimental data. The obtained results suggest that the structure properties near 1100 K have different behaviour from that at higher temperature
Modelling of carbohydrate–aromatic interactions: ab initio energetics and force field performance.
Czech Academy of Sciences Publication Activity Database
Spiwok, V.; Lipovová, P.; Skálová, Tereza; Vondrá?ková, Eva; Dohnálek, Jan; Hašek, Jind?ich; Králová, B.
2005-01-01
Ro?. 19, ?. 12 (2005), s. 887-901. ISSN 0920-654X R&D Projects: GA ?R GA204/02/0843; GA AV ?R KJB500500512 Institutional research plan: CEZ:AV0Z40500505 Keywords : ab initio * carbohydrate recognition * C-H/.pi. interactions Subject RIV: CD - Macromolecular Chemistry Impact factor: 2.082, year: 2005
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
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: 4.465, year: 2014
Czech Academy of Sciences Publication Activity Database
Hemzalová, P.; Friák, Martin; Šob, Mojmír; Ma, D.; Udyansky, A.; Raabe, D.; Neugebauer, J.
2013-01-01
Ro?. 88, ?. 17 (2013), Art. no. 174103. ISSN 1098-0121 R&D Projects: GA ?R(CZ) GAP108/12/0311; GA ?R GD106/09/H035; GA AV ?R IAA100100920 Institutional support: RVO:68081723 Keywords : nitrides * ab initio * thermodynamics * elasticity Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.664, year: 2013
DNA oligonucleotide-cis-platin Binding: Ab initio interpretation of the vibrational spectra.
Czech Academy of Sciences Publication Activity Database
Andrushchenko, Valery; Wieser, H.; Bou?, Petr
2007-01-01
Ro?. 111, ?. 39 (2007), s. 9714-9723. ISSN 1089-5639 R&D Projects: GA AV ?R IAA400550702; GA ?R GA202/07/0732 Institutional research plan: CEZ:AV0Z40550506 Keywords : cis-platin * DNA * vibrational spektra * ab initio Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.918, year: 2007
Unraveling the structure of the h-BN/Rh(111) nanomesh with ab initio calculations
Laskowski, R.; Blaha, P.
2008-02-01
The properties of a single layer of h-BN on top of a Rh(111) surface are discussed in terms of an ab initio generated force field approach as well as by direct ab initio density-functional theory (DFT) calculations. A single-layer model for the h-BN/Rh(111) nanomesh, in contrast to a previously considered (incomplete) double-layer model of h-BN, can explain the experimental data. The main focus of this work is to compare a force field approach described earlier in (Laskowski et al 2007 Phys. Rev. Lett. 98 106802) with direct ab initio calculations. The calculated geometry of the h-BN layer is very similar to the structure predicted by the force field approach. The ab initio calculated density of states projected on N-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.
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
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
An ab initio investigation of the effects of 2-exo and endo substituents on norbornane
Seidl, Peter Rudolf; Leal, Katia Z.; Tostes, José Glauco R.; Taft, C. A.; Hammond, Brian L.; Lester, W. A., Jr.
1988-06-01
Ab initio calculations using the STO-3G basis set and optimized geometries by MM2 and MNDO are used to investigate the charge distribution of norbornane bicyclo-[2.2.1]-heptane with 2-exo and endo substituents (methyl, ethyl, hydroxyl). The calculated net atomic charges using geometries obtained by both methods are analyzed.
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 : ion s * water cluster * methanol * ab initio calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.784, year: 2008
Calibration of the isomer shift for iodine resonant transition by ab initio calculations.
Czech Academy of Sciences Publication Activity Database
Wdowik, U. D.; Legut, Dominik; Ruebenbauer, K.
2010-01-01
Ro?. 114, ?. 26 (2010), s. 7146-7152. ISSN 1089-5639 Institutional research plan: CEZ:AV0Z20410507 Keywords : ab initio * isomer shift of iodine * calibration * I127 * I129 Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.732, year: 2010
Ab Initio Study of C14 Fe-Mo Laves Compounds.
Czech Academy of Sciences Publication Activity Database
Houserová, Jana; Šob, Mojmír
Prague, 2004. s. 71. [CONDENSED MATTER DIVISION of the European Physical Society /20./. 19.07.2004-23.07.2004, Prague] 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
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
High accuracy ab initio calculations on reactions of OH with 1-alkenes. The case of propene.
Czech Academy of Sciences Publication Activity Database
Izsák, R.; Szöri, Milan; Knowles, P. J.; Viskolcz, B.
2009-01-01
Ro?. 5, ?. 9 (2009), s. 2313-2321. ISSN 1549-9618 Institutional research plan: CEZ:AV0Z40550506 Keywords : multireference ab initio calculations * OH-addition * H-abstraction by OH Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.804, year: 2009
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…
Czech Academy of Sciences Publication Activity Database
Slaví?ek, Petr; Fárník, Michal
2011-01-01
Ro?. 13, ?. 26 (2011), s. 12123-12137. ISSN 1463-9076 R&D Projects: GA ?R GA203/09/0422; GA ?R GAP208/11/0161 Institutional research plan: CEZ:AV0Z40400503 Keywords : photochemistry * hydrogen bonded heterocycles * ab initio methods Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.573, year: 2011
Finite-Temperature Magnetism of Transition Metals: An ab initio Dynamical Mean-Field Theory
International Nuclear Information System (INIS)
We present an ab initio quantum theory of the finite-temperature magnetism of iron and nickel. A recently developed technique which combines dynamical mean-field theory with realistic electronic structure methods successfully describes the many-body features of the one electron spectra and the observed magnetic moments below and above the Curie temperature
Finite-Temperature Magnetism of Transition Metals: An ab initio Dynamical Mean-Field Theory
Energy Technology Data Exchange (ETDEWEB)
Lichtenstein, A. I.; Katsnelson, M. I.; Kotliar, G.
2001-08-06
We present an ab initio quantum theory of the finite-temperature magnetism of iron and nickel. A recently developed technique which combines dynamical mean-field theory with realistic electronic structure methods successfully describes the many-body features of the one electron spectra and the observed magnetic moments below and above the Curie temperature.
Ab initio study of one-dimensional disorder on III-V semiconductor surfaces.
Czech Academy of Sciences Publication Activity Database
Romanyuk, Olexandr; Grosse, F.; Braun, W.
2010-01-01
Ro?. 7, ?. 2 (2010), s. 330-333. ISSN 1862-6351 R&D Projects: GA AV ?R KAN300100802 Grant ostatní: German Resarch Fondation(DE) GZ:436 TSE 113/62/0-1 Institutional research plan: CEZ:AV0Z10100521 Keywords : atomic disorder * ab initio * semiconductor * reconstruction Subject RIV: BM - Solid Matter Physics ; Magnetism
Ab initio Nuclear structure Theory with chiral two- plus three-nucleon interactions
International Nuclear Information System (INIS)
Low-energy nuclear theory has entered an era of ab initio nuclear structure and reaction calculations based on input from QCD. One of the most promising paths from QCD to nuclear observables employs Hamiltonians constructed within chiral effective field theory as consistent starting point for precise ab initio nuclear structure and reaction studies. However, the full inclusion of chiral two- plus three-nucleon (NN+3N) interactions in exact and approximate many-body calculations still poses a formidable challenge. We discuss recent developments towards this goal, ranging from consistent Similarity Renormalization Group evolutions of NN+3N Hamiltonians to large-scale ab initio calculations for ground states and spectra in the Importance-Truncated No-Core Shell Model with full 3N interactions. We highlight recent achievements and discuss open issues and future perspectives for nuclear structure theory with QCD-based interactions. Moreover, we discuss successful steps towards merging ab initio structure and reaction theory and show applications to low-energy reactions in the p-shell relevant for astrophysics.
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).
Advances in the ab initio description of nuclear three-cluster systems
Romero-Redondo, Carolina; Navrátil, Petr; Hupin, Guillaume
2015-01-01
We introduce the extension of the ab initio no-core shell model with continuum to describe three-body cluster systems. We present results for the ground state of 6He and show improvements with respect to the description obtained within the no-core shell model and the no-core shell model/resonating group methods.
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)
Oila, Adrian; Lung, Chi; Bull, Steve
2014-01-01
The elastic properties of eta-Fe2C (eta carbide) have been determined from ab initio density functional theory (DFT) calculations using the generalized gradient approximation (GGA). The isotropic polycrystalline elastic modulus of eta-Fe2C has been calculated as the average of anisotropic single-crystal elastic constants determined from the ab initio simulations. The calculated polycrystalline elastic modulus was used to compute the elastic modulus of a case carburised gear ...
ORLANDO, Roberto
1991-01-01
This paper presents a new theoretical technique for the study of defects in crystals. The methods is based on an ab-initio Hartree-Fock perturbed-cluster (PC) scheme1. A prerequisite for this technique is the availability of a model for the host, perfect crystal, that must be obtained with the same Hamiltonian and the same computational conditions (basis set, accuracy etc.). This information is provided by CRYSTAL, an ab-initio periodic Hartree-Fock code2.
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.
{\\it Ab initio} nuclear structure - the large sparse matrix eigenvalue problem
Vary, James P; Ng, Esmond; Yang, Chao; Sosonkina, Masha
2009-01-01
The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several {\\it ab initio} methods have now emerged that provide nearly exact solutions for some nuclear properties. The {\\it ab initio} no core shell model (NCSM) and the no core full configuration (NCFC) method, frame this quantum many-particle problem as a large sparse matrix eigenvalue problem where one evaluates the Hamiltonian matrix in a basis space consisting of many-fermion Slater determinants and then solves for a set of the lowest eigenvalues and their associated eigenvectors. The resulting eigenvectors are employed to evaluate a set of experimental quantities to test the underlying potential. For fundamental problems of interest, the matrix dimension often exceeds $10^{10}$ and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. We survey recent results and advances in solving t...
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.
Matrix-isolation and ab initio study of HXeCCH complexed with acetylene
Domanskaya, Alexandra; Kobzarenko, Alexey V.; Tsivion, Ehud; Khriachtchev, Leonid; Feldman, Vladimir I.; Benny Gerber, R.; Räsänen, Markku
2009-10-01
The HXeCCH ⋯H 2C 2 complex has been characterized by IR spectroscopy in a xenon matrix and ab initio calculations. This species exhibits a blue shift of the H sbnd Xe stretching mode (19-28 cm -1) in comparison with the HXeCCH monomer, which indicates stabilization of the H sbnd Xe bond upon complexation. The complex results from annealing-induced diffusion of acetylene molecules above 50 K to isolated HXeCCH formed at lower temperature. In addition, a weak absorption with a blue shift of +51 cm -1 was tentatively assigned to the HXeCCH complex with two acetylene molecules. These experimental observations are supported by ab initio calculations.
Ab Initio Many-Body Calculations Of Nucleon-Nucleus Scattering
Energy Technology Data Exchange (ETDEWEB)
Quaglioni, S; Navratil, P
2008-12-17
We develop a new ab initio many-body approach capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group method with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters. This approach preserves translational symmetry and Pauli principle. We outline technical details and present phase shift results for neutron scattering on {sup 3}H, {sup 4}He and {sup 10}Be and proton scattering on {sup 3,4}He, using realistic nucleon-nucleon (NN) potentials. Our A = 4 scattering results are compared to earlier ab initio calculations. We find that the CD-Bonn NN potential in particular provides an excellent description of nucleon-{sup 4}He S-wave phase shifts. We demonstrate that a proper treatment of the coupling to the n-{sup 10}Be continuum is successful in explaining the parity-inverted ground state in {sup 11}Be.
Ab initio calculations of excitons in AlN and Elliott's model
Laskowski, Robert; Christensen, Niels Egede
2006-08-01
The optical absorption and excitonic properties of wurtzite AlN are investigated by means of an ab initio approach taking into account electron-hole correlations. This is done by solving the Bethe-Salpeter equation, using the results of density functional theory calculations as a starting point. The main focus is on the calculation of excitonic spectra near the conduction-band edge. The response is dominated by the exciton A formed out of excitations from valence ?7 band. The n-2 quantum-number dependence of the energies in Elliott’s model fits rather well the ab initio calculations whereas the n-3 decay of the intensities is less obvious for the calculated oscillator strengths.
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 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.
An ab initio reinvestigation of the geometric and electronic structure of boron trioxide
International Nuclear Information System (INIS)
In an attempt to resolve the controversy over the structure of the boron trioxide (B2O3) molecule an ab initio molecular orbital study employing a minimal STO-3G basis set with complete geometry optimization is reported. Our results indicate that B2O3 is a planar w shaped molecule with a rather small inversion barrier around the central atom and a quite important coupling between BOB and OBO angles. The computed bond distances are consistent with previous electron diffraction results, whereas the apex angle is in better agreement with the most recent IR study. The results obtained by the MNDO method are in good agreement with the ab initio ones. The electronic structure of B2O3 is discussed by means of Walsh diagrams and Mulliken population analysis. (orig.)
Hammes-Schiffer, Sharon; Andersen, Hans C.
1993-07-01
We present two new methods for molecular dynamics simulations based on general Hartree-Fock (GHF) theory. The first method involves approximating ab initio STO-3G matrix elements with fitting functions to enable faster computation of the energy and forces for molecular dynamics simulations. The implementation of this method includes a frozen-core approximation. The second method involves developing semiempirical potentials by reparametrizing the fitting functions obtained in the first method to fit experimental data. This second method enables us to reproduce experimental quantities with only the computational effort of an STO-3G calculation. We successfully applied both of these methods in conjunction with the Car-Parrinello ab initio molecular dynamics method to the geometry optimization of lithium clusters, cationic and neutral, of up to five atoms.
Csányi, G; Ismail-Beigi, S; Arias, T A; Csanyi, Gabor; Engeness, Torkel D.; Ismail-Beigi, Sohrab
2000-01-01
Based on {\\em ab initio} calculation, we propose a new structure for the fundamental excitation of the reconstructed 30$^\\circ$ partial dislocation in silicon. This soliton has a rare structure involving a five-fold coordinated atom near the dislocation core. The unique electronic structure of this defect is consistent with the electron spin resonance signature of the hitherto enigmatic thermally stable R center of plastically deformed silicon. We present the first {\\em ab initio} determination of the free energy of the soliton, which is also in agreement with the experimental observation. This identification suggests the possibility of an experimental determination of the density of solitons, a key defect in understanding the plastic flow of the material.
Ab initio modelling of vacancy–solute dragging in dilute irradiated iron-based alloys
International Nuclear Information System (INIS)
The formation of solute–defect nanoclusters in RPV steels is the main cause of radiation induced embrittlement. Solute atoms may diffuse in the alloy by a vacancy drag mechanism, depending on the strength of interaction with point defects. A multifrequency model based on ab initio computed migration barriers was applied in order to investigate the possibility of solute drag in iron-based bcc binary alloys containing Ni, Cr, Cu or Mn, and the obtained solute diffusion coefficients were compared with previous experiments. The results show that Ni is expected to be dragged at temperatures below approximately 900 K, while Cr and Mn are not involved in the dragging mechanism. As for Cu, the results are controversial because the computed migration barriers are strongly affected by the particular choice of the ab initio method
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.
Ab initio calculation of valley splitting in monolayer \\delta-doped phosphorus in silicon
Drumm, Daniel W; Per, Manolo C; Russo, Salvy P; Hollenberg, Lloyd C L
2012-01-01
The differences in energy between electronic bands due to valley splitting are of paramount importance in interpreting transport spectroscopy experiments on state-of-the-art quantum devices defined by scanning tunneling microscope lithography. We develop a plane-wave density functional theory description of these systems which is size-limited due to computational tractability. We then develop a less resource-intensive alternative via localized basis functions, retaining the physics of the plane-wave description, and extend this model beyond the capability of plane-wave methods to determine the ab initio valley splitting of well-isolated \\delta-layers. In obtaining agreement between plane-wave and delocalized methods, we show that the valley splitting has been overestimated in previous ab initio calculations by more than 50%.
A global ab initio potential for HCN/HNC, exact vibrational energies, and comparison to experiment
Bentley, Joseph A.; Bowman, Joel M.; Gazdy, Bela; Lee, Timothy J.; Dateo, Christopher E.
1992-01-01
An ab initio (i.e., from first principles) calculation of vibrational energies of HCN and HNC is reported. The vibrational calculations were done with a new potential derived from a fit to 1124 ab initio electronic energies which were calculated using the highly accurate CCSD(T) coupled-cluster method in conjunction with a large atomic natural orbital basis set. The properties of this potential are presented, and the vibrational calculations are compared to experiment for 54 vibrational transitions, 39 of which are for zero total angular momentum, J = 0, and 15 of which are for J = 1. The level of agreement with experiment is unprecedented for a triatomic with two nonhydrogen atoms, and demonstrates the capability of the latest computational methods to give reliable predictions on a strongly bound triatomic molecule at very high levels of vibrational excitation.
Large-scale ab initio configuration interaction calculations for light nuclei
International Nuclear Information System (INIS)
In ab-initio Configuration Interaction calculations, the nuclear wavefunction is expanded in Slater determinants of single-nucleon wavefunctions and the many-body Schrodinger equation becomes a large sparse matrix problem. The challenge is to reach numerical convergence to within quantified numerical uncertainties for physical observables using finite truncations of the infinite-dimensional basis space. We discuss strategies for constructing and solving the resulting large sparse matrix eigenvalue problems on current multicore computer architectures. Several of these strategies have been implemented in the code MFDn, a hybrid MPI/OpenMP Fortran code for ab-initio nuclear structure calculations that can scale to 100,000 cores and more. Finally, we will conclude with some recent results for 12C including emerging collective phenomena such as rotational band structures using SRG evolved chiral N3LO interactions.
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.
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.
Implicit infinite lattice summations for real space ab initio correlation methods
Albrecht, M
2005-01-01
We suggest a local wave function based ab initio correlation method for infinite periodic systems, which can describe both the near range as well as the long range correlation effects coherently in the same scheme. Specifically, this work introduces a formalism which allows to describe the long range polarization cloud around a quasi particle in a solid explicitly in the formalism of local wave function based ab initio descriptions. To this end we reformulate the infinite lattice summation underlying the quantum chemistry formula to second order in a closed analytic form employing the elliptic theta function of the third kind. All formulas and manipulations are developed explicitely in full detail and a first numeric example demonstrates the principle idea. Good results for the long range polarization effects in LiH and LiF are found in agreement with earlier estimates.
Improved DSAM measurements in ^10Be as a test of Ab-Initio calculations
McCutchan, E. A.; Lister, C. J.; Carpenter, M. P.; Janssens, R. V. F.; Khoo, T. L.; Lauritsen, T.; Seweryniak, D.; Stefanescu, I.; Zhu, S.
2008-10-01
Recent ab-initio calculations in light nuclei have emphasized the significance of 3-body forces. In the A = 10 systems, the inclusion of 3-body forces inverts the sequence of states, which has been attributed to the important contribution of the 3-body interaction to the overall spin orbit force. To challenge these latest calculations, a new generation of improved DSAM measurements is necessary to precisely (FMA) and ? rays measured with Gammasphere, the combination allowing for the collection of very clean ?-ray spectra and the elimination of cascade feeding. Preliminary results of the experiment will be presented and discussed in terms of recent ab-initio calculations. This research is supported by the DOE Office of Nuclear Physics under contract DE-AC02-06CH11357.
Vibrational properties of a sodium tetrasilicate glass: Ab initio versus Classical Force Fields
Ispas, S; De Wispelaere, S; Kob, W
2003-01-01
We compare some vibrational properties of a sodium tetrasilicate (Na$_{2}$Si$_{4}$O$_{9}$) glass model generated by molecular dynamics simulations. The vibrational study has been carried out using a classical valence force fields approach as well as an {\\it ab initio} approach in the framework of the density functional theory. The total and partial vibrational densities of states (VDOS) are presented, and some characteristics of the vibrational modes (participation ratios, correlation lengths) are determined using both approaches. We find that the shapes of the two calculated VDOS as well as those of their corresponding partial VDOS are quite similar, especially for a low-frequency band below 550 cm${}^{-1}$. For the intermediate- and high-frequency ranges, we observe larger discrepencies between the two calculations. Polarized Raman spectra are also calculated from the {\\it ab initio} and the valence-force-field eigenvectors in the bond-polarizability approximation. We find an overall agreement between the c...
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 parametrisation of the 14 band k·p Hamiltonian: Zinc blende study
International Nuclear Information System (INIS)
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 parametrisation, 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 parameterized using this method, at greatly reduced cost in comparison to GW methods.
Interface structure of graphene on SiC: an ab initio and STM approach
International Nuclear Information System (INIS)
High temperature treatment of SiC surfaces is a well-established technique for producing graphene directly on top of an insulating substrate. In this domain an important question is the influence of the substrate on the atomic and electronic structure of the graphene layers. This requires a detailed investigation of the interactions at the graphene-SiC interface. Surface science techniques and ab initio calculations are well suited for that purpose. In this paper, we present a brief review of the recent investigations performed in this domain by scanning tunnelling microscopy (STM) and ab initio simulations. It is largely based on the work performed in our group, but it also provides a survey of the literature in these fields. Both the so-called Si and C face of the hexagonal 6H(4H)SiC{0 0 0 1} substrates will be considered, as they show markedly different types of behaviour.
Constant pressure ab initio molecular dynamics with discrete variable representation basis sets
Ma, Zhonghua; Tuckerman, Mark
2010-11-01
The use of discrete variable representation (DVR) basis sets within ab initio molecular dynamics calculations allows the latter to be performed with converged energies and, more importantly, converged forces. In this paper, we show how to carry out ab initio molecular dynamics calculations in the isothermal-isobaric ensemble with fully flexible simulation boxes within the DVR basis set framework. In particular, we derive the appropriate DVR based expression for the pressure tensor when the electronic structure is represented using Kohn-Sham density functional theory, and we examine the convergence of this expression as a function of the basis set size. An illustrative example using 64 silicon atoms in a fully flexible box using a combination of the Martyna-Tobias-Klein [Martyna et al., J. Chem. Phys. 101, 4177 (1994)] and Car-Parrinello [Car and Parinello, Phys. Rev. Lett. 55, 2471 (1985)] algorithms is presented to demonstrate the efficacy of the approach.
Ab initio investigation of light-induced relativistic spin-flip effects in magneto-optics
Mondal, Ritwik; Berritta, Marco; Carva, Karel; Oppeneer, Peter M.
2015-05-01
Excitation of a metallic ferromagnet such as Ni with an intensive femtosecond laser pulse causes an ultrafast demagnetization within approximately 300 fs. It was proposed that the ultrafast demagnetization measured in femtosecond magneto-optical experiments could be due to relativistic light-induced processes. We perform an ab initio investigation of the influence of relativistic effects on the magneto-optical response of Ni. To this end, first, we develop a response theory formulation of the additional appearing ultrarelativistic terms in the Foldy-Wouthuysen transformed Dirac Hamiltonian due to the electromagnetic field, and second, we compute the influence of relativistic light-induced spin-flip transitions on the magneto-optics. Our ab initio calculations of relativistic spin-flip optical excitations predict that these can give only a very small contribution (?0.1 %) to the laser-induced magnetization change in Ni.
DFT and ab initio quantum chemical studies on p-cyanobenzoic acid
Arjunan, V.; Rani, T.; Varalakshmy, L.; Mohan, S.; Tedlamelekot, F.
2011-05-01
The Fourier transform infrared (FTIR) and FT-Raman spectra of p-cyanobenzoic acid (CBA) have been recorded in the range 4000-400 and 4000-100 cm -1, respectively. The complete vibrational assignment and analysis of the fundamental modes of the compound were carried out using the observed FTIR and FT-Raman data. The vibrational frequencies determined experimentally were compared with theoretical wavenumbers obtained from ab initio HF and DFT-B3LYP gradient calculations employing 6-31G**, 6-311++G** and cc-pVTZ basis sets for the optimised geometry of the compound. The geometry and normal modes of vibration obtained from the HF and DFT methods are in good agreement with the experimental data. The normal coordinate analysis was also carried out with ab initio force fields utilising Wilson's FG matrix method. The interactions of cyano and carboxylic acid groups with the skeletal vibrational modes were investigated.
Reddy, M Rami; Singh, U C; Erion, Mark D
2007-01-30
A free energy perturbation (FEP) method was developed that uses ab initio quantum mechanics (QM) for treating the solute molecules and molecular mechanics (MM) for treating the surroundings. Like our earlier results using AM1 semi empirical QMs, the ab initio QM/MM-based FEP method was shown to accurately calculate relative solvation free energies for a diverse set of small molecules that differ significantly in structure, aromaticity, hydrogen bonding potential, and electron density. Accuracy was similar to or better than conventional FEP methods. The QM/MM-based methods eliminate the need for time-consuming development of MM force field parameters, which are frequently required for drug-like molecules containing structural motifs not adequately described by MM. Future automation of the method and parallelization of the code for Linux 128/256/512 clusters is expected to enhance the speed and increase its use for drug design and lead optimization. PMID:17186484
An
Fossey John S; Chen Wenbo; Wang Xin; Wang Yan-Fang; Yuan Xiu-Xiang; Wong Ning-Bew
2010-01-01
Abstract Background Hydration is a universal phenomenon in nature. The interactions between biomolecules and water of hydration play a pivotal role in molecular biology. 2-Thioxanthine (2TX), a thio-modified nucleic acid base, is of significant interest as a DNA inhibitor yet its interactions with hydration water have not been investigated either computationally or experimentally. Here in, we reported an ab initio study of the hydration of 2TX, revealing water can form seven hydrated complexe...
Influence of the ab-initio nd cross sections in the critical heavy-water benchmarks
Morillon, B; Carbonell, J
2013-01-01
The n-d elastic and breakup cross sections are computed by solving the three-body Faddeev equations for realistic and semi-realistic Nucleon-Nucleon potentials. These cross sections are inserted in the Monte Carlo simulation of the nuclear processes considered in the International Handbook of Evaluated Criticality Safety Benchmark Experiments (ICSBEP). The results obtained using thes ab initio n-d cross sections are compared with those provided by the most renown international libraries.
Gao, Haiyuan; Xu, Yang; Li, Meijiao; Guo, Zhendong; Chen, Hongshen; Jin, Zhonghe; Yu, Bin
2011-01-01
Electronic transport properties of monolayer graphene with extreme physical bending up to 90o angle are studied using ab Initio first-principle calculations. The importance of key structural parameters including step height, curvature radius and bending angle are discussed how they modify the transport properties of the deformed graphene sheet comparing to the corresponding flat ones. The local density of state reveals that energy state modification caused by the physical be...
Ab initio I-V characteristics of short C-20 chains
DEFF Research Database (Denmark)
Roland, C.; Larade, B.
2002-01-01
We have calculated the I-V characteristics of short chains of C-20 molecular cages between Al and Au leads with an ab initio formalism. The results indicate that a linear chain of such molecules acts primarily as metallic nanowires. The transmission, however, depends sensitively both on the orientation and distance between the individual C-20 molecules. Transport through the molecular chains is accompanied by a significant amount of charge transfer, which remains localized at the electrode/molecular interface.
Electronic structure of superconducting gallium-doped germanium from ab-initio calculations
Lebegue, S.
2009-01-01
Using ab-initio calculations, we study the electronic structure of gallium-doped germanium, which was found recently to be a superconductor, with a critical temperature of 0.5 Kelvins, and a particularly low density of Cooper pairs. The calculations of the electronic properties reveal that no sign of an impurity band is observed, and that the Fermi level lies in the valence band of Germanium. Moreover, the calculation of the phonon frequencies shows that a new mode associate...
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.
Hugouvieux, Virginie; Farhi, Emmanuel; Mark R. Johnson; Juranyi, Fanni; Bourges, Philippe; Kob, Walter
2007-01-01
We report the first measurements of the dynamics of liquid germanium (l-Ge) by quasi-elastic neutron scattering on time-of-flight and triple-axis spectrometers. These results are compared with simulation data of the structure and dynamics of l-Ge which have been obtained with ab initio density functional theory methods. The simulations accurately reproduce previous results from elastic and inelastic scattering experiments, as well as the q-dependence of the width of the quas...
Direct ab initio MD simulation of silver ion diffusion in chalcogenide glasses
Tafen, De Nyago; Drabold, D. A.; Mitkova, M.
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 g...
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
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
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
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
Ab Initio No Core Shell Model - Recent Results and Further Prospects
Vary, James P.(Department of Physics and Astronomy, Iowa State University, Ames, IA, 50011, USA); Maris, Pieter(Department of Physics and Astronomy, Iowa State University, Ames, IA, 50011, USA); Potter, Hugh; Caprio, Mark A.; Smith, Robin; Binder, Sven(Institut für Kernphysik, Technische Universität Darmstadt, Schlossgartenstr. 2, 64289 Darmstadt, Germany); Calci, Angelo(Institut für Kernphysik, Technische Universität Darmstadt, Schlossgartenstr. 2, 64289 Darmstadt, Germany); Fischer, Sebastian; Langhammer, Joachim(Institut für Kernphysik, Technische Universität Darmstadt, Schlossgartenstr. 2, 64289 Darmstadt, Germany); Roth, Robert(Institut für Kernphysik, Technische Universität Darmstadt, Schlossgartenstr. 2, 64289 Darmstadt, Germany); Aktulga, Hasan Metin; Ng, Esmond; Yang, Chao; Oryspayev, Dossay; Sosonkina, Masha
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...
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 investigation of the melting line of nitrogen at high pressure
Donadio, Davide; Spanu, Leonardo; Duchemin, Ivan; Gygi, Francois; Galli, Giulia
2010-01-01
Understanding the behavior of molecular systems under pressure is a fundamental problem in condensed matter physics. In the case of nitrogen, the determination of the phase diagram and in particular of the melting line, are largely open problems. Two independent experiments have reported the presence of a maximum in the nitrogen melting curve, below 90 GPa, however the position and the interpretation of the origin of such maximum differ. By means of ab initio molecular dynam...
Ab initio study of antiphase boundaries and stacking faults in L12 and DO22 compounds
DEFF Research Database (Denmark)
Rosengaard, N. M.; Skriver, Hans Lomholt
1994-01-01
We have performed ab initio calculations of the energies of antiphase boundaries as well as complex and superlattice intrinsic stacking faults in nine intermetallic compounds observed in the face-centered-cubic L1(2) and DO22 structures. The calculations were performed by means of a Green's function technique based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations.
Base pairing motifs involving 1,8-naphthyridine: an ab initio study.
Czech Academy of Sciences Publication Activity Database
Czernek, Ji?í
2006-01-01
Ro?. 7, - (2006), s. 124-127. ISBN 90-6764-443-9. ISSN 1573-4196. [International Conference on Computational Methods in Sciences and Engineering. Chania, Crete, 27.10.2006-01.11.2006] R&D Projects: GA AV ?R KJB400500602; GA AV ?R 1ET400500402 Institutional research plan: CEZ:AV0Z40500505 Keywords : ab initio * electron correlation * MP2 Subject RIV: CD - Macromolecular Chemistry
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...
Ab initio calculations for S=-2, A=4-6 s-shell hypernuclei with strangeness
International Nuclear Information System (INIS)
We describe full-coupled-channel ab initio calculations for S=-2, A=4-6 s-shell hypernuclei. The wave function includes explicit ??, ??, ?? and ?? channels. Minnesota ??, D2' ?? and Nijmegen model D (or F) simulated ?? interactions are used. Bound state solutions of the ?? hypernuclei, ??4H, ??5H, ??5He and ??6He, are obtained. This is the first attempt to explore the few-body problem of the full-coupled channel scheme for these systems. (author)
Pair potentials for alumina from ab initio results on the Al2O3 molecule
International Nuclear Information System (INIS)
We use results from an ab initio investigation by Chang et al. on energetically low-lying stationary points of the Al2O3 molecule to determine interionic potentials for the Al-O, O-O and Al-Al pairs. Our results are discussed in the perspective of previous studies of the condensed phases of alumina, with special regard to the structure of its molten state. (author)
Ab initio excited states calculations of Kr3+, probing semi-empirical modelling.
Czech Academy of Sciences Publication Activity Database
Milko, Petr; Kalus, R.; Paidarová, Ivana; Hrušák, Jan; Gadéa, F. X.
-, 23 June (2009), s. 25. ISSN 1432-2234 R&D Projects: GA AV ?R IAA100400501 Institutional research plan: CEZ:AV0Z40400503 Keywords : cluster modelling * rare gas ions * ab initio potential energie * evaporation energies Subject RIV: CF - Physical ; Theoretical Chemistry http://www.springerlink.com/content/100493/?Content+Status=Accepted&sort=p_OnlineDate&sortorder=desc&v=condensed&o=20
Dislocation constriction and cross-slip in Al and Ag: an ab initio study
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 c...
Ab initio study of C14 Laves phase in Fe-based systems.
Czech Academy of Sciences Publication Activity Database
Houserová, Jana; Šob, Mojmír
Praha : Department of metal physics, Charles University, 2005. [International symposium on physics of materials /10./. 30.08.2005-02.09.2005, Praha] R&D Projects: GA ?R(CZ) GP106/03/P002; GA ?R(CZ) GA202/03/1351; GA AV ?R(CZ) IAA1041302 Institutional research plan: CEZ:AV0Z2041904 Keywords : Laves phase * Fe-based systems * ab initio Subject RIV: BM - Solid Matter Physics ; Magnetism
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...
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
Ab initio strategy for muon site assignment in wide band gap fluorides
Bernardini, F.; Bonfa, P.; Massidda, S.; De Renzi, R.
2013-01-01
We report on an ab initio strategy based on Density Functional Theory to identify the muon sites. Two issues must be carefully addressed, muon delocalization about candidate interstitial sites and local structural relaxation of the atomic positions due to $\\mu^+$-sample interaction. Here, we report on the validation of our strategy on two wide band gap materials, LiF and YF3, where localization issues are important because of the interplay between muon localization and latti...
Ab initio theory of Cr$_2$O$_3$ surface chemistry in solution
Petrosyan, S.; Rigos, A. A.; Arias, T. A.
2004-01-01
Using a new form of density functional theory for the {\\em ab initio} description of electronic systems in contact with a dielectric environment, we present the first detailed study of the impact of a solvent on the surface chemistry of Cr$_2$O$_3$, the passivating layer of stainless steel alloys. Compared to vacuum, we predict that the presence of water has little impact on the adsorption of chloride ions to the oxygen-terminated surface but a dramatic effect on the binding...
Ab initio molecular dynamics simulations with linear scaling: application to liquid ethanol
International Nuclear Information System (INIS)
The structural and dynamical properties of liquid ethanol (C2H5OH) at ambient conditions have been studied by ab initio molecular dynamics simulations using a large supercell containing 125 molecules (1125 atoms). The results obtained from a trajectory of 10 ps are found to be in good agreement with available experimental data. Without sacrificing accuracy, the computational cost of simulations is reduced by more than a factor of four by the linear scaling algorithm based on the augmented orbital minimization method
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.
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 ...
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
Vibrational properties of a sodium tetrasilicate glass: Ab initio versus Classical Force Fields
Ispas, S.; Zotov, N.; De Wispelaere, S.; Kob, W.
2003-01-01
We have determined the vibrational properties of a sodium tetrasilicate (Na$_{2}$Si$_{4}$O$_{9}$) glass model generated by molecular dynamics simulations. The study has been carried out using a classical valence force fields approach as well as an {\\it ab initio} approach in the framework of the density functional theory. The total and partial vibrational densities of states (VDOS) are presented, as well as some characteristics of the vibrational modes (participation ratios,...
A set of molecular models based on quantum mechanical ab initio calculations and thermodynamic data
Eckl, Bernhard; Vrabec, Jadran; 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 po...
GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders
Majoros, William H; Pertea, Mihaela; Antonescu, Corina; Salzberg, Steven L.
2003-01-01
We present three programs for ab initio gene prediction in eukaryotes: Exonomy, Unveil and GlimmerM. Exonomy is a 23-state Generalized Hidden Markov Model (GHMM), Unveil is a 283-state standard Hidden Markov Model (HMM) and GlimmerM is a previously-described genefinder which utilizes decision trees and Interpolated Markov Models (IMMs). All three are readily re-trainable for new organisms and have been found to perform well compared to other genefinders. Results are presented for Arabidopsis ...
Ab initio study of the TiO$_2$ Rutile(110)/Fe interface
Gruenebohm, Anna; Herper, Heike C.; Entel, Peter
2013-01-01
Adsorption of Fe on the rutile (110)-surface is investigated by means of {\\it ab initio} density functional theory calculations. We discuss the deposition of single Fe atoms, an increasing Fe coverage, as well as the adsorption of small Fe clusters. It is shown that the different interface structures found in experiment can be understood in terms of the adsorption of the Fe atoms landing first on the rutile surface. On the one hand, strong interface bonds form if single Fe a...
Ozaki, Taisuke
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 lar...
Experimental IR study and ab initio modelling of ethylene adsorption in a MFI - type host zeolite
Zvereva-Loëte, Natalia; Ballandras, Anthony; Weber, Guy; ROTGER, Maud; Boudon, Vincent
2009-01-01
Abstract Different ab initio methods and experimental results are used to investigate the effect of the adsorption of one ethylene molecule on silicalite-1, a MFI type zeolite. We used simplified models to simulate a portion of a straight or sinusoidal channel of silicalite-1 at a quantum level. The calculated absorption spectra of the models are qualitatively in good agreement with the experimental FTIR spectrum of silicalite-1. Additionally we simulate the FTIR spectrum of the ...
Ab initio simulations and STM-images for Co/Pt(110) surfaces.
Czech Academy of Sciences Publication Activity Database
Máca, František; Hofer, W. A.; Redinger, J.
482-485, - (2001), s. 844-849. ISSN 0039-6028. [ECOSS-19. Madrid, 05.09.2000-08.09.2000] R&D Projects: GA MŠk OC P3.80 Institutional research plan: CEZ:A02/98:Z1-010-914 Keywords : STM -images * Co/Pt(110) * ab initio simulation Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.189, year: 2001
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)
Structure, electronic, and optical properties of TiO 2 atomic clusters: An ab initio study
Chiodo, Letizia; Romero, A. H.; Rubio Secades, Ángel
2011-01-01
Atomic clusters of TiO 2 are modeled by means of state-of-the-art techniques to characterize their structural, electronic and optical properties. We combine ab initio molecular dynamics, static density functional theory, time-dependent density functional theory, and many body techniques, to provide a deep and comprehensive characterization of these systems. TiO 2 clusters can be considered as the starting seeds for the synthesis of larger nanostructures, which are of technological interest in...
Advances and applications in the FIREBALL ab initio tight-binding molecular-dynamics formalism.
Czech Academy of Sciences Publication Activity Database
Lewis, J.P.; Jelínek, Pavel; Ortega, J.; Demkov, A.A.; Trabada, D.G.; Haycock, B.; Wang, H.; Adams, G.; Tomfohr, J.K.; Abad, E.; Wang, Ho.; Drabold, D.A.
2011-01-01
Ro?. 248, ?. 9 (2011), 1989-2007. ISSN 0370-1972 R&D Projects: GA ?R GA202/09/0545; GA ?R GAP204/10/0952 Grant ostatní: AV?R(CZ) M100100904 Institutional research plan: CEZ:AV0Z10100521 Keywords : DFT * ab initio molecular-dynamics Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.316, year: 2011
Ab initio GW electron-electron interaction effects in Quantum Transport
Darancet, Pierre; FERRETTI, ANDREA; Mayou, Didier; Olevano, Valerio
2006-01-01
We present an ab initio approach to electronic transport in nanoscale systems which includes electronic correlations through the GW approximation. With respect to Landauer approaches based on density-functional theory (DFT), we introduce a physical quasiparticle electronic-structure into a non-equilibrium Green's function theory framework. We use an equilibrium non-selfconsistent $G^0W^0$ self-energy considering both full non-hermiticity and dynamical effects. The method is ...
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.
Ab initio nuclear structure and reactions with chiral three-body forces
International Nuclear Information System (INIS)
One major ambition of ab initio nuclear theory is the description of nuclear-structure and reaction observables on equal footing. This is accomplished by combining the no-core shell model (NCSM) with the resonating-group method (RGM) to a unified ab initio approach to bound and continuum states, which is developed further to the no-core shell model with continuum (NCSMC). We present the formal developments to include three-nucleon interactions in both the NCSM/RGM and NCSMC formalism. This provides the possibility to assess the predictive power of chiral two- and three-nucleon forces in the variety of scattering observables. We study three-nucleon force effects on phase-shifts, cross sections and analyzing powers in first ab-initio studies of nucleon-4He scattering with chiral two- and three-nucleon forces. Finally, we focus on heavier target nuclei using the NCSMC, e.g., in neutron-8Be scattering and study the impact of the continuum on the spectrum of 9Be.
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)
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)
Structures of 13-atom clusters of fcc transition metals by ab initio and semiempirical calculations
Longo, R. C.; Gallego, L. J.
2006-11-01
We report the results of ab initio calculations of the structures and magnetic moments of Ni13 , Pd13 , Pt13 , Cu13 , Ag13 , and Au13 that were performed using a density-functional method that employs linear combinations of pseudoatomic orbitals as basis sets (SIESTA). Our structural results for Pt13 , Cu13 , Ag13 , and Au13 show that a buckled biplanar structure (BBP) is more stable than the icosahedral configuration, in keeping with results obtained recently by Chang and Chou [Phys. Rev. Lett. 93, 133401 (2004)] using the Vienna ab initio simulation package with a plane-wave basis. However, for Ni13 and Pd13 we found that the icosahedral structure is more stable than BBP. For all these clusters, two semiempirical methods based on spherically symmetric potentials both found the icosahedral structure to be the more stable, while the modified embedded atom model method, which uses a direction-dependent potential, found BBP to be the more stable structure. When low-energy structures found in recent ab initio studies of Pt13 , Cu13 , and Au13 other than Chang and Chou were optimized with SIESTA, those reported for Pt13 and Cu13 were found to be less stable than BBP, but the two-dimensional planar configuration reported for Au13 proved to be more stable than BBP.
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.
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)
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...
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
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.
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
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...
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.
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.)
Ab initio calculation of the spectrum and structure of $^{16}$O
Epelbaum, Evgeny; Lähde, Timo A; Lee, Dean; Meißner, Ulf-G; Rupak, Gautam
2013-01-01
We present ab initio lattice calculations of the low-energy even-parity states of $^{16}$O using chiral nuclear effective field theory. We find good agreement with the empirical energy spectrum, and with the electromagnetic properties and transition rates. For the ground state, we find that the nucleons are arranged in a tetrahedral configuration of alpha clusters. For the first excited spin-0 state, we find that the predominant structure is a square configuration of alpha clusters, with rotational excitations that include the first spin-2 state.
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.
Ramsdellite-structured LiTiO 2: A new phase predicted from ab initio calculations
Koudriachova, M. V.
2008-06-01
A new phase of highly lithiated titania with potential application as an anode in Li-rechargeable batteries is predicted on the basis of ab initio calculations. This phase has a composition LiTiO2 and may be accessed through electrochemical lithiation of ramsdellite-structured TiO2 at the lowest potential reported for titanium dioxide based materials. The potential remains constant over a wide range of Li-concentrations. The new phase is metastable with respect to a tetragonally distorted rock salt structure, which hitherto has been the only known polymorph of LiTiO2.
Hydrogen-enhanced local plasticity in aluminum an ab initio study
Lu, G; Kioussis, N; Kaxiras, E; Lu, Gang; Zhang, Qing; Kioussis, Nicholas; Kaxiras, Efthimios
2001-01-01
Dislocation core properties of Al with and without H impurities are studied using the Peierls-Nabarro model with parameters determined by ab initio calculations. We find that H not only facilitates dislocation emission from the crack tip but also enhances dislocation mobility dramatically, leading to macroscopically softening and thinning of the material ahead of the crack tip. We observe strong binding between H and dislocation cores, with the binding energy depending on dislocation character. This dependence can directly affect the mechanical properties of Al by inhibiting dislocation cross-slip and developing slip planarity.
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.
Ab Initio calculation of band gap renormalization in highly excited GaAs
Spataru, C D; Louie, S G; Spataru, Catalin D.; Benedict, Lorin X.; Louie, Steven G.
2004-01-01
We present ab initio quasiparticle self-energy calculations in crystalline GaAs for cases of intense electronic excitation (~ 10% of valence electrons excited into conduction band), relevant for high-intensity ultra-short pulsed laser experiments. Calculations are performed using an out-of-equilibrium generalization of the GW approximation based on the Keldysh Green's function approach. Our results indicate that while the band gap is a sensitive function of the amount of excitation, it is not possible to induce complete band gap closure in this system by purely electronic means.
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
International Nuclear Information System (INIS)
A general method for the energy-adjustment of accurate relativistic ab initio pseudopotentials to be used in one-, two- or four-component quantum chemical valence-only calculations of the electronic structure and spectra of heavy-element compounds is discussed. The described pseudopotential scheme is completely based on quantum chemical observables, i.e., all parameters are determined by a least-squares adjustment to total valence energies of a multitude of many-electron states from corresponding atomic all-electron calculations. The presentation will include several examples of theoretical investigations of heavy-element compounds, many of them containing lanthanide or actinide atoms
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 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...
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.
Heavy Metal Compounds and Hydrogen Storage Materials from Ab Initio Calculations
Sun, Weiwei
2013-01-01
In principle, most of the properties of solids can be determined by their electronic structures. So the understanding of electronic structures is essential. This thesis presents two classes of materials using ab initio method based on density functional theory. One is heavy metal compounds like Ta2AlC, ThO and the other one is hydrogen storage material namely MgH2 surfaces. The study of correlation and relativistic effects in Ta2AlC are presented. Based on our results, Ta2AlC is a weakly corr...
Ab initio calculations of elastic properties of Ru1-xNixAl superalloys
Bleskov, I. D.; Smirnova, E. A.; Vekilov, Yu. Kh.; Korzhavyi, P. A.; Johansson, B.; Katsnelson, M.; Vitos, L.; Abrikosov, I. A.; Isaev, E. I.
2009-04-01
Ab initio total energy calculations based on the exact muffin-tin orbitals method, combined with the coherent potential approximation, have been used to study the thermodynamical and elastic properties of substitutional refractory Ru1-xNixAl alloys. We have found that the elastic constants C' and C11 exhibit pronounced peculiarities near the concentration of about 40 at. % Ni, which we ascribe to electronic topological transitions. Our suggestion is supported by the Fermi surface calculations in the whole concentration range. Results of our calculations show that one can design Ru-Ni-Al alloys substituting Ru by Ni (up to 40 at. %) with almost invariable elastic constants and reduced density.
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.
Electronic structure and transport in graphene/haeckelite hybrids: an ab initio study
Zhu, Zhen; Fthenakis, Zacharias G.; Tománek, David
2015-09-01
We combine ab initio density functional theory (DFT) structural studies with DFT-based nonequilibrium Green's function calculations to investigate how the presence of non-hexagonal rings affects electronic transport in graphitic structures. We find that infinite monolayers, finite-width nanoribbons, and nanotubes formed of 5–8 haeckelite with only 5- and 8-membered rings are generally more conductive than their graphene-based counterparts. The presence of haeckelite defect lines in the perfect graphitic structure, a model of grain boundaries in CVD-grown graphene, increases the electronic conductivity and renders it highly anisotropic.
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
Ab initio theory of Cr$_2$O$_3$ surface chemistry in solution
Petrosyan, S; Arias, T A
2004-01-01
Using a new form of density functional theory for the {\\em ab initio} description of electronic systems in contact with a dielectric environment, we present the first detailed study of the impact of a solvent on the surface chemistry of Cr$_2$O$_3$, the passivating layer of stainless steel alloys. Compared to vacuum, we predict that the presence of water has little impact on the adsorption of chloride ions to the oxygen-terminated surface but a dramatic effect on the binding of hydrogen to that surface. These results indicate that the dielectric screening properties of water are important to the passivating effects of the oxygen-terminated surface.
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.
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.
Ab-Initio Calculation of the Metal-Insulator Transition in Lithium rings
Paulus, Beate; Rosciszewski, Krzysztof; Fulde, Peter; Stoll, Hermann
2004-01-01
We study how the Mott metal-insulator transition (MIT) is affected when we have to deal with electrons with different angular momentum quantum numbers. For that purpose we apply ab-initio quantum-chemical methods to lithium rings in order to investigate the analogue of a MIT. By changing the interatomic distance we analyse the character of the many-body wavefunction and discuss the importance of the $s-p$ orbital quasi-degeneracy within the metallic regime. The charge gap (i...
Ab initio calculations of Curie temperatures in GdX compounds
Energy Technology Data Exchange (ETDEWEB)
Rusz, Jan [Department of Electronic Structures, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2 (Czech Republic)]. E-mail: rusz@mag.mff.cuni.cz; Turek, Ilja [Department of Electronic Structures, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2 (Czech Republic); Divis, Martin [Department of Electronic Structures, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2 (Czech Republic)
2006-02-09
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.
Carbon Nanotube with Square Cross-section: An Ab Initio Investigation
Autreto, P A S; Flores, M Z S; Galvao, D S; 10.1063/1.348323
2010-01-01
Recently, Lagos et al. (Nature Nanotechnology 4, 149 (2009)) reported the discovery of the smallest possible silver square cross-section nanotube. A natural question is whether similar carbon nanotubes can exist. In this work we report ab initio results for the structural, stability and electronic properties for such hypothetical structures. Our results show that stable (or at least metastable) structures are possible with metallic properties. They also show that these structures can be obtained by a direct interconversion from SWNT(2,2). Large finite cubane-like oligomers, topologically related to these new tubes were also investigated.
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
Site occupancy trend of Co in Ni2MnIn: Ab initio approach
Pal, Soumyadipta; Mahadevan, Priya; Biswas, C.
2015-06-01
The trend of site occupation of Co at Ni sites of Ni2MnIn system is studied in austenitic phase having L21 structure by ab initio density functional theory (DFT) calculation. The Co atoms prefer to be at Ni sites rather than Mn site and are ferromagetically coupled with Ni and Mn. The ground state has tetragonal structure for Ni1.5Co0.5MnIn and Ni1.25Co0.75MnIn. The Co tends to form cluster.
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
Ab-initio prediction of materials properties with CRYSTAL: MOF-5 as a case study
DOVESI, Roberto; ROETTI, Carla; Civalleri, Bartolomeo; NAPOLI, Francesco
2006-01-01
MOF-5 is by far the most relevant member of the new class of metal - organic framework materials and has been adopted as a case study to show that reliable ab initio prediction of materials properties of complex systems can be obtained by means of a solid state computational tool like the CRYSTAL code. Structure, electronic properties and vibrational frequencies of MOF-5 computed at the B3LYP level of theory are reported and discussed. Animations representing MOF-5 vibrations are available at...
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.
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
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.
Quantum chemistry the development of ab initio methods in molecular electronic structure theory
Schaefer III, Henry F
2004-01-01
This guide is guaranteed to prove of keen interest to the broad spectrum of experimental chemists who use electronic structure theory to assist in the interpretation of their laboratory findings. A list of 150 landmark papers in ab initio molecular electronic structure methods, it features the first page of each paper (which usually encompasses the abstract and introduction). Its primary focus is methodology, rather than the examination of particular chemical problems, and the selected papers either present new and important methods or illustrate the effectiveness of existing methods in predi
Electron-scattering form factors for 6Li in the ab initio symmetry-guided framework
T. Dytrych; Hayes, A. C.; K. D. Launey; 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 frame...
Ab initio many-body calculations of deuteron-He4 scattering and Li6 states
Navrátil, Petr; Quaglioni, Sofia
2011-04-01
We extend the ab initio no-core shell model/resonating-group method (NCSM/RGM) to projectile-target binary-cluster states where the projectile is a deuteron. We discuss the formalism in detail and give algebraic expressions for the integration kernels. Using a soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we calculate deuteron-He4 scattering and investigate Li6 bound and unbound states. Virtual three-body breakup effects are obtained in an approximated way by including excited pseudostates of the deuteron in the calculation. We compare our results to experiment and to a standard NCSM calculation for Li6.
Estudo ab-initio da a-alanina em meio aquoso
Sambrano Júlio Ricardo; Souza Aguinaldo Robinson de; Queralt Joaquim Josep; Andrés Juan; Longo Elson
1999-01-01
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 elec...
Simple synthesis, structure and ab initio study of 1,4-benzodiazepine-2,5-diones
Jadidi, Khosrow; Aryan, Reza; Mehrdad, Morteza; Lügger, Thomas; Ekkehardt Hahn, F.; Ng, Seik Weng
2004-04-01
A simple procedure for the synthesis of pyrido[2,1-c][1,4] benzodiazepine-6,12-dione ( 1) and 1,4-benzodiazepine-2,5-diones ( 2a- 2d), using microwave irradiation and/or conventional heating is reported. The configuration of 1 was determined by single-crystal X-ray diffraction. A detailed ab initio B3LYP/6-31G* calculation of structural parameters and substituent effects on ring inversion barriers (? G#) and also free energy differences (? G0) for benzodiazepines are reported.
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
Time-dependent Born charges of lithium borate melts by ab initio molecular dynamics
Ohkubo, Takahiro; Tsuchida, Eiji; Iwadate, Yasuhiko
2014-09-01
We present time-dependent Born effective charges of B and O in lithium borate melts determined by ab initio molecular dynamics (AIMD) simulations. The Born charge, based on polarization theory, is calculated from all atoms at each time step of the AIMD run. The time-averaged charge distributions are obtained for specific chemical species such as three-coordinated B, four-coordinated B, bridging O (Ob) and, non-bridging O (Onb). Ob and Onb have similar time-averaged charge distributions, indicating that positively charged Li+ is compensated not only by Onb but also by the glass network of the melt as a whole.
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
Ab-initio calculations for the structural properties of Zr-Nb alloys
Directory of Open Access Journals (Sweden)
V.O. Kharchenko
2013-03-01
Full Text Available Ab-initio calculations for the structural properties of Zr-Nb alloys at different values of the niobium concentration are done at zero temperature. Different cases for Zr-Nb alloys with unit cells having BCC and HCP structures are considered. Optimal values of the lattice constants are obtained. Critical value for the niobium concentration corresponding to the structural transformation HCP ? BCC at zero temperature is defined. Electronic densities of states for two different structures with niobium concentrations 12.5% and 25% having HCP and BCC structures, accordingly, are studied.
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.
Hydriding and dehydriding energies of PuHx from ab initio calculations
Yang, Yu; Zhang, Ping
2015-08-01
Based on ab initio calculations within the density-functional theory (DFT) + U theoretical formalism, we systematically study the electronic properties of different PuHx compounds. We successfully obtain the antiferromagnetic ground state for PuH2 and the ferromagnetic ground state for PuH3. In combination with chemical potential calculations, we obtain the hydriding and dehydriding energies for PuHx compounds at different temperatures, which accord well with available experimental results. The equilibrium hydrogen pressure along the hydriding and dehydriding processes is presented and carefully analyzed.
José Jair Vianna Cirino; Celso Aparecido Bertran
2002-01-01
A study was carried out on the urea geometries using ab initio calculation and Monte Carlo computational simulation of liquids. The ab initio calculated results showed that urea has a non-planar conformation in the gas phase in which the hydrogen atoms are out of the plane formed by the heavy atoms. Free energies associated to the rotation of the amino groups of urea in water were obtained using the Monte Carlo method in which the thermodynamic perturbation theory is implemented. The magnitud...
Scientific Electronic Library Online (English)
José Jair Vianna, Cirino; Celso Aparecido, Bertran.
2002-05-01
Full Text Available [...] Abstract in english 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.
Klevets, Ivan; Bryk, Taras
2014-12-01
Electron-ion structure factors, calculated in ab initio molecular dynamics simulations, are reported for several binary liquids with different kinds of chemical bonding: metallic liquid alloy Bi-Pb, molten salt RbF, and liquid water. We derive analytical expressions for the long-wavelength asymptotes of the partial electron-ion structure factors of binary systems and show that the analytical results are in good agreement with the ab initio simulation data. The long-wavelength behaviour of the total charge structure factors for the three binary liquids is discussed. PMID:25481149
International Nuclear Information System (INIS)
Ab initio molecular orbital calculations on the structure and stability of the nitrate and sulfate complexes of uranyl (UO22+) and plutonyl (PuO22+) using effective core potentials are reported. It is found that the binding energy of sulfate is greater than that of nitrate to both uranyl and plutonyl, with a slight preference for plutonyl. A method of decomposing the binding energy into electrostatic, Pauli repulsion, polarization, and charge-transfer components is described which predicts that electrostatic forces are dominant. A simple molecular mechanics potential is developed by using this finding, which is successful in reproducing the ab initio results. 38 refs., 2 figs., 6 tabs
Palacios Clemente, Pablo; Aguilera Bonet, Irene; Wahnón 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...
Ab initio predictions of the structures and spectra of some simple thiosulfeno (XS2) free radicals
International Nuclear Information System (INIS)
Ab initio theory with split-valence plus polarization function and larger basis sets at the self-consistent field (SCF) and second order Moller--Plesset (UMP2) levels was used to predict the geometries and spectroscopic parameters for the ground and first excited electronic states of the HS2, FS2, and ClS2 free radicals. The ground-state species are predicted to be bent and may be described as having a sulfur--sulfur double bond, a sulfur-substituent single bond, and an unpaired electron which is delocalized principally over the sulfur centers. The first electronic transition involves an (n,?*) electron promotion which leads to a longer S--S bond, smaller bond angle, and greater localization of the unpaired electron on the terminal sulfur atom. The adiabatic transition energies are predicted to be at ?6700, 13 700, and 10 600 cm-1 for HS2, FS2, and ClS2, respectively. The theoretical results are in good agreement with the rather limited amount of experimental data available. These ab initio predictions provide critical information to aid in future experimental studies of the matrix isolation or gas-phase spectra of the thiosulfeno radicals
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)
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 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.
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.
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.
Ab initio quantum-enhanced optical phase estimation using real-time feedback control
DEFF Research Database (Denmark)
Berni, Adriano; Gehring, Tobias
2015-01-01
Optical phase estimation is a vital measurement strategy that is used to perform accurate measurements of various physical quantities including length, velocity and displacements(1,2). The precision of such measurements can be greatly enhanced by the use of entangled or squeezed states of light as demonstrated in a variety of different optical systems(3-8). Most of these accounts, however, deal with the measurement of a very small shift of an already known phase, which is in stark contrast to ab initio phase estimation where the initial phase is unknown(9-12). Here, we report on the realization of a quantum-enhanced and fully deterministic ab initio phase estimation protocol based on real-time feedback control. Using robust squeezed states of light combined with a real-time Bayesian adaptive estimation algorithm, we demonstrate deterministic phase estimation with a precision beyond the quantum shot noise limit. The demonstrated protocol opens up new opportunities for quantum microscopy, quantum metrology and quantum information processing.
An Ab Initio Approach Towards Engineering Fischer-Tropsch Surface Chemistry
Energy Technology Data Exchange (ETDEWEB)
Matthew Neurock
2005-06-13
As petroleum prices continue to rise and the United States seeks to reduce its dependency on foreign oil, there is a renewed interest in the research and development of more efficient and alternative energy sources, such as fuel cells. One approach is to utilize processes that can produce long-chain hydrocarbons from other sources. One such reaction is Fischer-Tropsch synthesis. Fischer-Tropsch synthesis is a process by which syngas (CO and H{sub 2}) is converted to higher molecular weight hydrocarbons. The reaction involves a complex set of bond-breaking and bond-making reactions, such as CO and H{sub 2} activation, hydrocarbon hydrogenation reactions, and hydrocarbon coupling reactions. This report details our initial construction of an ab initio based kinetic Monte Carlo code that can be used to begin to simulate Fischer-Tropsch synthesis over model Co(0001) surfaces. The code is based on a stochastic kinetic formalism that allows us to explicitly track the transformation of all reactants, intermediates and products. The intrinsic kinetics for the simulations were derived from the ab initio results that we reported in previous year summaries.
Ab initio calculation of the rotational spectrum of methane vibrational ground state
Cassam-Chenaï, P.; Liévin, J.
2012-05-01
In a previous article we have introduced an alternative perturbation scheme to the traditional one starting from the harmonic oscillator, rigid rotator Hamiltonian, to find approximate solutions of the spectral problem for rotation-vibration molecular Hamiltonians. The convergence of our method for the methane vibrational ground state rotational energy levels was quicker than that of the traditional method, as expected, and our predictions were quantitative. In this second article, we study the convergence of the ab initio calculation of effective dipole moments for methane within the same theoretical frame. The first order of perturbation when applied to the electric dipole moment operator of a spherical top gives the expression used in previous spectroscopic studies. Higher orders of perturbation give corrections corresponding to higher centrifugal distortion contributions and are calculated accurately for the first time. Two potential energy surfaces of the literature have been used for solving the anharmonic vibrational problem by means of the vibrational mean field configuration interaction approach. Two corresponding dipole moment surfaces were calculated in this work at a high level of theory. The predicted intensities agree better with recent experimental values than their empirical fit. This suggests that our ab initio dipole moment surface and effective dipole moment operator are both highly accurate.
Boese, A D; Martin, J M L; Marx, D; Chandra, Amalendu; Martin, Jan M.L.; Marx, Dominik
2003-01-01
The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without resorting to experiment. The global minimum of eclipsed C_s symmetry is characterized by a significantly bent hydrogen bond which deviates from linearity by about 20 degrees. In addition, the so-called cyclic C_{2h} structure is extremely close in energy on an overall flat potential energy surface. It is demonstrated that none of the currently available (GGA, meta--GGA, and hybrid) density functionals satisfactorily describe the structure and relative energies of this nonlinear hydrogen bond. We present a novel density functional, HCTH/407+, designed to describe this sort of hydrogen bond quantitatively on the level of the dimer, contrary to e.g. the widely used BLYP functional. This improved functional is employed in Car-Parrinello ab initio molecular dynamics simulations of liq...
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.
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
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
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.
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.
Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics
International Nuclear Information System (INIS)
Techniques from gauge-field theory are employed to derive an alternative formulation of the Car-Parrinello ab initio molecular-dynamics method that allows maximally localized Wannier orbitals to be generated dynamically as the calculation proceeds. In particular, the Car-Parrinello Lagrangian is mapped onto an SU(n) non-Abelian gauge-field theory and the fictitious kinetic energy in the Car-Parrinello Lagrangian is modified to yield a fully gauge-invariant form. The Dirac gauge-fixing method is then employed to derive a set of equations of motion that automatically maintain orbital locality by restricting the orbitals to remain in the 'Wannier gauge'. An approximate algorithm for integrating the equations of motion that is stable and maintains orbital locality is then developed based on the exact equations of motion. It is shown in a realistic application (64 water molecules plus one hydrogen-chloride molecule in a periodic box) that orbital locality can be maintained with only a modest increase in CPU time. The ability to keep orbitals localized in an ab initio molecular-dynamics calculation is a crucial ingredient in the development of emerging linear scaling approaches
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...
Ab initio, density functional theory and structural studies of 4-amino-2-methylquinoline
Arjunan, V.; Saravanan, I.; Ravindran, P.; Mohan, S.
2009-10-01
The Fourier transform infrared (FTIR) and FT-Raman spectra of 4-amino-2-methylquinoline (AMQ) have been recorded in the range 4000-400 and 4000-100 cm -1, respectively. The experimental vibrational frequency was compared with the wavenumbers obtained theoretically by ab initio HF and DFT-B3LYP gradient calculations employing the standard 6-31G** and high level 6-311++G** basis sets for optimised geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compounds were carried out using the experimental FTIR and FT-Raman data, and quantum mechanical studies. The geometry and normal modes of vibration obtained from the HF and DFT methods are in good agreement with the experimental data. The potential energy distribution of the fundamental modes was calculated with ab initio force fields utilising Wilson's FG matrix method. The NH -? interactions and the influence of amino and methyl groups on the skeletal modes are investigated.
Arjunan, V.; Mohan, S.; Ravindran, P.; Mythili, C. V.
2009-05-01
The Fourier transform infrared (FTIR) and FT-Raman spectra of 7-bromo-5-chloro-8-hydroxyquinoline (BCHQ) have been measured in the range 4000-400 and 4000-100 cm -1, respectively. Complete vibrational assignment and analysis of the fundamental modes of the compound were carried out using the observed FTIR and FT-Raman data. The geometry was optimised without any symmetry constrains using the DFT/B3LYP and HF methods with 6-31G** basis set. The vibrational frequencies which were determined experimentally are compared with those obtained theoretically from ab initio HF and density functional theory (DFT) gradient calculations employing the HF/6-31G** and B3LYP/6-31G** methods for the optimised geometry of the compound. The structural parameters and normal modes of vibration obtained from HF and DFT methods are in good agreement with the experimental data. Normal coordinate analysis was also carried out with ab initio force fields utilising Wilson's FG matrix method.
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...
Phase diagrams from ab-initio calculations: Re-W and Fe-B
International Nuclear Information System (INIS)
The CALPHAD (CaLculation of Phase Diagrams) method relies on Gibbs energy databases and is of limited predictive power in cases where only limited experimental data is available for constructing the Gibbs energy databases. This is problematic for, e.g., the calculation of the phase transformation kinetics within phase field simulations that not only require the thermodynamic equilibrium data but also information on metastable phases. Such information is difficult to obtain directly from experiment but ab-initio calculations may supplement experimental databases as they comprise metastable phases and arbitrary chemical compositions. We present simulations for two prototypical systems: Re-W and Fe-B. For both systems we calculate the heat of formation for an extensive set of structures using ab-initio calculations and employ the total energies in CALPHAD in order to determine the corresponding phase diagrams. We account for the configurational entropy within the Bragg-Williams approximation and neglect the phenomenological excess-term that is commonly used in CALPHAD as well as the contribution of phonons and electronic excitations to the free energy. According to our calculations the complex intermetallic phases in Re-W are stabilized by the configurational entropy. For Fe-B, we calculate metastable and stable phase diagrams including recently predicted new stable phases.
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.
Complexation of Cu + in Hydrothermal NaCl Brines: Ab initio molecular dynamics and energetics
Sherman, David M.
2007-02-01
Chloride complexation of Cu + controls the solubility of copper(I) oxide and sulfide ore minerals in hydrothermal and diagenetic fluids. Solubility measurements and optical spectra of high temperature CuCl solutions have been interpreted as indicating the formation of CuCl, CuCl2-, CuCl32- and CuCl43- complexes. However, no other monovalent cation forms tri- and tetrachloro complexes. EXAFS spectra of high temperature Cu-Cl solutions, moreover, appear to show only CuCl and CuCl2- complexes at T > 100 °C. To reconcile these results, I investigated the nature and stability of Cu-Cl complexes using ab initio cluster calculations and ab initio (Car-Parrinello) molecular dynamics simulations for CuCl-NaCl-H 2O systems at 25 to 450 °C. Ab initio molecular dynamic simulations of 1 m CuCl in a 4 m Cl solution give a stable CuCl3- complex at 25 °C over 4 ps but show that the third Cl - is weakly bound. When the temperature is increased along the liquid-vapour saturation curve to 125 °C, the CuCl32- complex dissociates into CuCl2-and Cl -; only CuCl2- forms at 325 °C and 1 kbar. Even in a 15.6 m Cl brine at 450 °C, only the CuCl2- complex forms over a 4 ps simulation run. Cluster calculations with a static dielectric continuum solvation field (COSMO) were used in an attempt directly estimate free energies of complex formation in aqueous solution. Consistent with the MD simulations, the CuCl32- complex is slightly stable at 25 °C but decreases in stability with decreasing dielectric constant ( ?). The CuCl42- complex is predicted to be unstable at 25 °C and becomes increasingly unstable with decreasing dielectric constant. In hydrothermal fluids ( ? 125 °C, even in NaCl-saturated brines. The high-temperature ( T > 125 °C) optical spectra of CuCl solutions and solubility measurements of Cu minerals in Cl-brines need to be reinterpreted in terms of only the CuCl and CuCl2- complexes.
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
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
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
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: 1.370, year: 2014
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
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
Ab initio study of formation energy and magnetism of sigma phase in Cr–Fe and Cr–Co systems.
Czech Academy of Sciences Publication Activity Database
Pavl?, Jana; V?eš?ál, J.; Šob, Mojmír
2010-01-01
Ro?. 18, ?. 2 (2010), s. 212-220. ISSN 0966-9795 Institutional research plan: CEZ:AV0Z20410507 Keywords : ab initio calculations of sigma phases * energy of formation * magnetism Subject RIV: BJ - Thermodynamics Impact factor: 2.327, year: 2010
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
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 prediction of pressure-induced structural phase transition of superconducting FeSe
Rahman, Gul; Kim, In Gee; Freeman, Arthur J.
2012-01-01
External pressure driven phase transitions of FeSe are predicted using \\textit{ab initio} calculations. The calculations reveal that $\\alpha$-FeSe takes transitions to NiAs-type, MnP-type, and CsCl-type FeSe. Transitions from NiAs-type to MnP-type and CsCl-type FeSe is also predicted. MnP-type FeSe is also found to be able to transform to CsCl-type FeSe, which is easier from $\\alpha$-FeSe than the transition to MnP-type FeSe, but comparable to the transition from NiAs-type F...
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 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 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 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...
Nelson, Tammie; Zhang, Bo; Prezhdo, Oleg
2010-03-01
We report an ab initio study of the interaction of two nucleobases, cytosine and adenine, with a novel graphene nanopore device for detecting the base sequence of a single-stranded nucleic acid (ssDNA or RNA). The nucleobases were inserted into a pore in a graphene nanoribbon, and the electrical current and conductance spectra were calculated as functions of voltage applied across the nanoribbon. The conductance spectra and charge densities were analyzed in the presence of each nucleobase in the graphene nanopore. The results indicate that, due to significant differences in the conductance spectra, the proposed device has adequate sensitivity to discriminate between different nucleotides. Moreover, we show that the nucleotide conductance spectra is not affected by its orientation inside the graphene nanopore. The proposed technique may be extremely useful for real applications in developing ultrafast, low cost DNA sequencing methods.
Characterization of amorphous In2O3: An ab initio molecular dynamics study
International Nuclear Information System (INIS)
In this work, we report on the structural and electronic properties of amorphous In2O3 obtained with ab initio molecular dynamics. Our results show crystal-like short range InO6 polyhedra having average In-O distance consistent with x-ray spectroscopy data. Structural disorder yields band tailing and localized states, which are responsible of a strong reduction of the electronic gap. Most importantly, the appearance of a peculiar O-O bond imparts n-type character to the amorphous compound and provides contribution for interpreting spectroscopic measurements on indium based oxidized systems. Our findings portray characteristic features to attribute transparent semiconductive properties to amorphous In2O3.
Structural properties of iron nitride on Cu(100): An ab-initio molecular dynamics study
Heryadi, Dodi
2011-01-01
Due to their potential applications in magnetic storage devices, iron nitrides have been a subject of numerous experimental and theoretical investigations. Thin films of iron nitride have been successfully grown on different substrates. To study the structural properties of a single monolayer film of FeN we have performed an ab-initio molecular dynamics simulation of its formation on a Cu(100) substrate. The iron nitride layer formed in our simulation shows a p4gm(2x2) reconstructed surface, in agreement with experimental results. In addition to its structural properties, we are also able to determine the magnetization of this thin film. Our results show that one monolayer of iron nitride on Cu(100) is ferromagnetic with a magnetic moment of 1.67 ? B. © 2011 Materials Research Society.
Ab initio calculations on magnetism induced by composite defects in magnesium oxide
Energy Technology Data Exchange (ETDEWEB)
Zhang, Yao-Fang [Department of Physics, Tianjin Polytechnic University, Tianjin 300384 (China); College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300071 (China); Feng, Min [School of Physics, Nankai University, Tianjin 300071 (China); Shao, Bin [Department of Physics, Tsinghua University, Beijing 100084 (China); Lu, Yuan; Zuo, Xu, E-mail: xzuonku@gmail.com [College of Electronic Information and Optical Engineering, Nankai University, Tianjin 300071 (China); Liu, Hong [Office of International Academic Exchanges, Nankai University, Tianjin 300071 (China)
2014-05-07
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.
Crystal structure and ab initio calculations of a cyano-carbamimidic acid ethyl ester
Van Hecke, Kristof; Thi Ngan, Vu; Nockemann, Peter; Thijs, Ben; Tho Nguyen, Minh; Binnemans, Koen; Van Meervelt, Luc
2008-08-01
The structure of one tautomer (amine form) of cyano-carbamimidic acid ethyl ester or (amino-ethoxy-methylidene)aminoformonitrile (CAS: 13947-84-7) was determined by single crystal X-ray diffraction. Ab initio quantum chemical calculations at the B3LYP, MP2 and G3 levels were performed to investigate the stability and the formation of the different tautomers and conformers. The calculations indicate that the amine form is the more stable tautomer, showing a high degree of electron conjugation. The most stable amine conformer located by the calculations corresponds to the crystallized structure. On the contrary, in the less stable imine form, the conjugation is separated by a N2-C2 single bond.
Prediction of toxicity of nitrobenzenes using ab initio and least squares support vector machines
Energy Technology Data Exchange (ETDEWEB)
Niazi, Ali [Department of Chemistry, Faculty of Sciences, Azad University of Arak, Arak (Iran, Islamic Republic of)], E-mail: ali.niazi@gmail.com; Jameh-Bozorghi, Saeed; Nori-Shargh, Davood [Department of Chemistry, Faculty of Sciences, Azad University of Arak, Arak (Iran, Islamic Republic of)
2008-03-01
A quantitative structure-property relationship (QSPR) study is suggested for the prediction of toxicity (IGC{sub 50}) 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 IGC{sub 50} 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 (IGC{sub 50}) 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.
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)
Hugouvieux, V; Johnson, M R; Juranyi, F; Bourges, P; Kob, W; Hugouvieux, Virginie; Farhi, Emmanuel; Johnson, Mark R.; Juranyi, Fanni; Bourges, Philippe; Kob, Walter
2007-01-01
We report the first measurements of the dynamics of liquid germanium (l-Ge) by quasi-elastic neutron scattering on time-of-flight and triple-axis spectrometers. These results are compared with simulation data of the structure and dynamics of l-Ge which have been obtained with ab initio density functional theory methods. The simulations accurately reproduce previous results from elastic and inelastic scattering experiments, as well as the q-dependence of the width of the quasi-elastic signal of the new experimental data. In order to understand some special features of the structure of the liquid we have also simulated amorphous Ge. Overall we find that the atomistic model represents accurately the average structure of real l-Ge as well as the time dependent structural fluctuations. The new quasi-elastic neutron scattering data allows us to investigate to what extent simple theoretical models can be used to describe diffusion in l-Ge.
Ab initio molecular-dynamics simulation of liquid AsxSe1-x alloys
International Nuclear Information System (INIS)
Ab initio molecular-dynamics simulations have been used to investigate the structure and dynamics properties of the liquid AsxSe1-x at four compositions x=0.2, 0.4, 0.5, and 0.6. We present results for the static structure factors, frequency spectra, and the electronic density of states. The results for the structure factor are in good agreement with the available experimental data. The vibrational density of states has two distinct bands for all compositions; the lower-energy band shifts to higher frequency while the higher-energy band shifts to lower frequency as the number of As atoms increases. The electronic density of states show that the liquid As2Se3 has semiconducting properties; increase or decrease As atoms will reduce the semiconducting character of the sample
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...
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.
Ab initio study of topological surface states of Sb (111) surface with magnetic impurities
Han, Jinhee; Lee, Hyungjun; Choi, Hyoung Joon
2013-03-01
We study effects of magnetic impurities on topological surface state of Sb (111) surface by using an ab-initio pseudopotential density-functional method. We have implemented the spin-orbit interaction into the SIESTA code in a form of additional fully non-local projectors. To calculate surface band structures, we use a slab of Sb using a 4x4 supercell containing 20 atomic layers. In particular, we compare Fe impurities with Mn impurities, whose atoms have larger magnetic moments, and compare interstitial impurities with substitutional impurities for each atom. To understand the impurity effects on the topological surface states, we simulate ARPES spectra and calculate projected density of states of impurity near Fermi level. This work was supported by NRF of KOREA (Grant No. 2011-0018306) and KISTI supercomputing center (Project No. KSC-2012-C2-14).
Ab initio molecular dynamics study of the hydrogen diffusion in sodium and lithium hydrides
Ramzan, M.; Ahuja, R.
2009-07-01
Light weight complex metal hydrides, sodium hydride (NaH), and lithium hydride (LiH) are the last step materials during hydrogen release process of alanates and borates, which are promising candidates for hydrogen storage. We report ab initio molecular dynamics (MD) calculations based on density functional theory to study the hydrogen-deuterium exchange in NaH and LiH. We predict the single hydrogen-deuterium exchange in NaH and LiH and calculate the self-diffusion constants, ?D?NaH?1.46×10-9 m2 s-1 of deuterium in NaH at 420 K and ?D?LiH?1.49×10-9 m2 s-1 of deuterium in LiH at 550 K, which are in good agreement with the experimental values.
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.
Ab Initio Molecular-Dynamics Simulation of Neuromorphic Computing in Phase-Change Memory Materials.
Skelton, Jonathan M; Loke, Desmond; Lee, Taehoon; Elliott, Stephen R
2015-07-01
We present an in silico study of the neuromorphic-computing behavior of the prototypical phase-change material, Ge2Sb2Te5, using ab initio molecular-dynamics simulations. Stepwise changes in structural order in response to temperature pulses of varying length and duration are observed, and a good reproduction of the spike-timing-dependent plasticity observed in nanoelectronic synapses is demonstrated. Short above-melting pulses lead to instantaneous loss of structural and chemical order, followed by delayed partial recovery upon structural relaxation. We also investigate the link between structural order and electrical and optical properties. These results pave the way toward a first-principles understanding of phase-change physics beyond binary switching. PMID:26040531
A matrix isolation and ab initio study of the hydrogen bonded complexes of acetylene with pyridine
Sundararajan, K.; Sankaran, K.; Viswanathan, K. S.
2005-01-01
Hydrogen bonded complexes of acetylene and pyridine were studied using matrix isolation spectroscopy and ab initio computations. The adduct was formed by depositing acetylene and pyridine in an argon matrix and a 1:1 C 2H 2-NC 5H 5 complex was identified using infrared spectroscopy. Formation of the adduct was evidenced from the shifts in the vibrational frequencies of C 2H 2 in the complex compared with that of free C 2H 2. The molecular structure, vibrational frequencies and stabilization energies of the complex were computed at the HF/6-31++G** and B3LYP/6-31++G** levels. We located one minimum on the potential surface, corresponding to a strongly bound C 2H 2-NC 5H 5 n-? complex. Both experimental and computational data indicated that C 2H 2 acts as a proton donor and C 5H 5N as a proton acceptor.
International Nuclear Information System (INIS)
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.
He, Yuping
2015-03-01
We present calculations of the thermal transport coefficients of Si-based clathrates and solar perovskites, as obtained from ab initio calculations and models, where all input parameters derived from first principles. We elucidated the physical mechanisms responsible for the measured low thermal conductivity in Si-based clatherates and predicted their electronic properties and mobilities, which were later confirmed experimentally. We also predicted that by appropriately tuning the carrier concentration, the thermoelectric figure of merit of Sn and Pb based perovskites may reach values ranging between 1 and 2, which could possibly be further increased by optimizing the lattice thermal conductivity through engineering perovskite superlattices. Work done in collaboration with Prof. G. Galli, and supported by DOE/BES Grant No. DE-FG0206ER46262.
Structural evolution in high-pressure amorphous CO2 from ab initio molecular dynamics
Plašienka, Dušan; MartoÅák, Roman
2014-04-01
By employing ab initio molecular dynamics simulations at constant pressure we investigated the behavior of amorphous carbon dioxide between 0 and 100 GPa and 200 and 500 K. We focused on the 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 state. During the simulations we observed a spectrum of amorphous forms between two limiting polymeric forms with different proportions of three- and four-coordinated carbon atoms. Besides that we also found a mixed molecular-polymeric form that shows pronounced metastability at certain conditions. The observed behavior suggests CO2 as a possible candidate for polyamorphism. We discuss the structural and physical properties of the observed amorphous forms as well as their relation to crystalline phases.
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...
Olsson, P. A. T.; Kese, K.; Kroon, M.; Alvarez Holston, A.-M.
2015-06-01
In this work we report the results of an ab initio study of the transgranular fracture toughness and cleavage of brittle zirconium hydrides. We use the Griffith–Irwin relation to assess the fracture toughness using calculated surface energy and estimated isotropic Voigt–Reuss–Hill averages of the elastic constants. The calculated fracture toughness values are found to concur well with experimental data, which implies that fracture is dominated by cleavage failure. To investigate the cleavage energetics, we model the decohesion process. To describe the interplanar interaction we adopt Rose’s universal binding energy relation, which is found to reproduce the behaviour accurately. The modelling shows that the work of fracture and ductility decreases with increasing hydrogen content.
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 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.
Ab initio calculations of electron affinity and ionization potential of carbon nanotubes
International Nuclear Information System (INIS)
By combining ab initio all-electron localized orbital and pseudopotential plane-wave approaches we report on calculations of the electron affinity (EA) and the ionization potential (IP) of (5, 5) and (7, 0) single-wall carbon nanotubes. The role played by finite-size effects and nanotube termination has been analysed by comparing several hydrogen-passivated and not passivated nanotube segments. The dependence of the EA and IP on both the quantum confinement effect, due to the nanotube finite length, and the charge accumulation on the edges, is studied in detail. Also, the EA and IP are compared to the energies of the lowest unoccupied and highest occupied states, respectively, upon increasing the nanotube length. We report a slow convergence with respect to the number of atoms. The effect of nanotube packing in arrays on the electronic properties is eventually elucidated as a function of the intertube distance
Pressure-induced semimetallic behavior of calcium from ab initio calculations
Magnitskaya, M. V.; Matsko, N. L.; Baturin, V. S.; Uspenskii, Yu A.
2014-05-01
A loss of metallic properties in fcc calcium under high pressure is studied ab initio using the density functional theory (DFT) and GW approximation. It is found that a more correct description of many-electron effects given by GW method does not provide significant changes in the behavior of electronic spectrum in comparison with DFT approach. We note that the obtained width of (pseudo)gap is highly sensitive to the k-point sampling used for density of states calculation. The analysis of fcc calcium's band structure at p ~ 20 GPa shows that the crossing of bands at the Fermi level is removed if the spin-orbit coupling is taken into account.
Ab initio studies of hyperconjugation effects on charge distribution in tetracyclododecane alcohols
Tostes, J. Glauco R.; Seidl, Peter Rudolf; Soto, M. M.; De M. Carneiro, J. W.; Lie, S. K.; Taft, C. A.; Brown, W.; Lester, W. A., Jr.
1995-05-01
Ab initio calculations using the STO-3G, 6-31G, and 6-31G ?? basis sets are used to investigate charge distribution in tetracyclododecane alcohols. The calculated net atomic charges using fully optimized geometries indicate that certain carbon and hydrogen atoms in the proximity of a nonbonding oxygen lone pair are more negatively charged and the carbon-carbon and carbon-hydrogen bonds are longer. Analysis of these charges and bond lengths as well as atomic orbital populations suggests that the differences between charge distribution on carbon and hydrogen atoms adjacent to the hydroxyl group and their corresponding carbon-carbon and carbon-hydrogen bond lengths can be explained in terms of hyperconjugation.
The reaction pathway for the hydration of ketenimine by water dimer. An Ab initio study
Nguyen, Minh Tho; Hegarty, Anthony F.
The reaction pathway for the hydration of the ketenimine CH 2?C?NH by H 2O and (H 20) 2 has been investigated by ab initio methods using STO-3G and 4-31G basis sets, optimized geometries of stationary points being determined by the gradient method. The preferred reaction is with the water dimer which, although it enters the transition state correctly oriented for proton transfer to the ?-carbon, does not actually transfer this proton until after the transition state. The reaction is calculated (4-31G) to have an activation barrier of 22 kcal/mole, most of which arises due to the deformation of ketenimine and water dimer. The reaction with water monomer is far less favoured (activation barrier 67 kcal/ mole using the same basis set).
Ab initio investigation of geometric and electronic structure of BF3OOH- anion
International Nuclear Information System (INIS)
Results are presented from ab initio calculations of the geometric and electronic structure and the barriers to rotation of the BF3OOH- anion. It is established that the optimal structure of the anion is that with coordination of the hydroperoxo group in the cis form, which is stabilized by an intramolecular hydrogen bond OOH...F. The barrier to internal rotation of the OH groups around the O-O bond, in the STO-3G basis, is 3.5 kcal/mole. The barrier to rotation O1O2H has been calculated to be 5.5 kcal/mole (STO-3G basis) and 11.8 kcal/mole (4-31G basis), which is comparable with the energy of the F...H hydrogen bond
Taft, C. A.; Seidl, Peter Rudolf; Tostes, J. Glauco R.; Lie, S. K.; De M. Carneiro, J. W.; Lester, W. A., Jr.
1996-01-01
Ab initio calculations using fully optimized geometries are used to generalize hyperconjugation effects in a representative series of eight polycyclic alcohols. The systems studied include tetra-, penta- and hexa-cyclic structures with varying degrees of tension, due to compression and stretching of carbon-carbon and carbon-hydrogen bonds, and of distortion from normal bond angles as well to differences in van der Waals interactions. These findings indicate, in general, that carbon and hydrogen atoms with the proper spatial alignment relative to a nonbonding oxygen lone pair follow the same general trends as small acyclic alcohols. Results from minimum STO-3G basis-set calculations and the hyperconjugation model can generally distinguish clearly the subtleties of charge and bond length distributions observed in the various conformations of all the polycyclic alcohols investigated.
Ab initio calculations of the electronic and optical properties of germanium selenide
International Nuclear Information System (INIS)
We have performed an ab initio calculation of the germanium selenide electronic structure, adopting the LDA and GGA approximations for the exchange-correlation potential within the DFT. These calculations have been carried out with and without the inclusion of the spin-orbit interaction. The subtle changes it produces in the band structure, the density of states and the optical properties have been discussed. Also, we propose the s-Ge state contribution at the edge of the valence band as having an important role. Based on our electronic structure, we discuss germanium selenide experimental core spectra and optical properties. We found excellent agreement between our results and available experimental core spectra data, and our calculated optical functions of GeSe explain the origin of the optical transitions, comparing them satisfactorily against existing experimental data
All-electron ab initio investigations of the electronic states of the NiC molecule
DEFF Research Database (Denmark)
Shim, Irene; Gingerich, Karl. A.
1999-01-01
The low-lying electronic states of NiC are investigated by all-electron ab initio multi-configuration self-consistent-field (CASSCF) calculations including relativistic corrections. The electronic structure of NiC is interpreted as perturbed antiferromagnetic couplings of the localized angular momenta of F-4(g) Ni+ and S-4(u) C-. The predicted ground state, (1)Sigma(+), is well separated from the dense manifold of excited states by an energy gap of 6465 cm(-1). Multi-reference configuration-interaction (MRCI) calculations result in r(e) = 1.621 Angstrom and omega(e) = 874 cm(-1) agreeing well with new experimental data by Brugh and Morse. D-e is determined as 2.76 eV, and D-0 as 2.70 eV. (C) 1999 Elsevier Science B.V. All rights reserved.
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
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 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 study of the uranyl oxide hydrates: a proton transfer mediated by water
International Nuclear Information System (INIS)
We present a first-principles study of the UO3·n(H2O) uranyl oxide hydrates, namely, schoepite (n = 2.25), metaschoepite (n = 2) and dehydrated metaschoepite (n = 1.75), which appear as the alteration U(VI) products of aqueous corrosion of nuclear fuel. For these compounds, the calculated enthalpy of formation is in good agreement with calorimetry and solubility measurements. We discuss the key electronic state factors behind the phase stability of uranyl oxide hydrates. An unexplored proton-transfer mechanism, which produces the H3O hydronium ions in UO3·nH2O, has been studied using ab initio molecular dynamics simulations at room temperature. For the hydronium ion, a very short lifetime of around 20 fs has been suggested
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.
An ab initio investigation of some hydrogen-bonded complexes of methanol and dimethylamine
Bricknell, Bradley C.; Ford, Thomas A.
2010-05-01
The hydrogen-bonded molecular complexes formed between methanol and dimethylamine, as proton donors, and the series of proton acceptors trimethylamine, dimethyl ether, methyl fluoride, trimethyl phosphine, dimethyl sulphide and methyl chloride, have been studied by means of ab initio molecular orbital theory, at the second order level of Møller-Plesset perturbation theory, and using the 6-311++G(d,p) basis set. The properties determined were the molecular structures, the interaction energies and the vibrational spectra. The results show that, based on the trends in the values of these properties, the order of strength of interaction per proton donor is methanol > dimethylamine and the order per proton acceptor is trimethylamine > dimethyl ether > methyl fluoride for the first row bases and trimethyl phosphine > dimethyl sulphide > methyl chloride for the second row. The first row proton acceptors consistently form stronger hydrogen-bonded complexes than their counterparts from the second row.
Buczek, P.; Borisov, V.; Bersier, C.; Ostanin, S.; Sandratskii, L.; Staunton, J. B.; Gross, E. K. U.; Mertig, I.; Ernst, A.
2012-02-01
et al. Motivated by a experimental reports on possible high temperature superconductivity in palladium hydride [Tripodi ,Physica C 388-389, 571 (2003)], we present a first principle study of spin fluctuations, electron-phonon coupling and critical temperature in PdHx, 0 generally believed [Berk & Schrieffer, Phys. Rev. Lett., 17, 433 (1966)] that the ferromagnetic-like paramagnons of Pd are destructive for the conventional, i.e. s-wave, superconductivity. We describe them using linear response time dependent density functional theory, recently implemented to study complex metals [Buczek ,Phys. Rev. Lett. 105, 097205 (2010)] . We find that hydrogenation suppresses the intense spin fluctuations of pure Pd, driving it away from a magnetic critical point. Under the assumption of s-wave pairing, this could lead to the formation of the superconducting state. The ab-initio estimated electron-phonon coupling is strong enough to support superconductivity. Please look for the complementary contribution of Christophe Bersier.
Ab initio intermolecular potential energy surface and thermophysical properties of nitrous oxide
Crusius, Johann-Philipp; Hellmann, Robert; Hassel, Egon; Bich, Eckard
2015-06-01
We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N2O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N2O-N2O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N2O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data.
Ln3+(NO3)n complexes studied using ab-initio quantum chemical calculations
International Nuclear Information System (INIS)
The structures and interaction energies of Ln3+(NO3-)n complexes have been studied using ab initio Hartree-Fock method for La3+, Eu3+ and Lu3+ cations with one to three nitrates in gas phase. The interaction energy between one cation and one bidentate nitrate is 20 to 30 kCal/mol greater than that with one monodentate nitrate. This value is quite lower than the interaction between a cation and one water molecule (about 90 kCal/mol), which could come and complete the hydration sphere of the cation when nitrate's coordination-type moves from bidentate to monodentate. The first studies on these systems with five water molecules in the hydration sphere show changes in the coordination type of nitrates or moves of water molecules in the second sphere. (authors)
Ab initio calculations for dissociative hydrogen adsorption on lithium oxide surfaces
International Nuclear Information System (INIS)
Dissociative hydrogen chemisorption on the Li2O surfaces of the (100), (110) and (111) planes has been investigated with ab initio Hartree-Fock calculations. Calculations for unrelaxed crystal Li2O structures indicated that except for the (100) surface, the (110) and (111) surfaces are stable. Results on the heterolytic sites of n-layer (110) (where n?2) slabs and three-layer (111) slabs suggest that dissociative hydrogen chemisorption is endothermic. For a one-layer (110) slab at 100% surface coverage, the dissociative hydrogen chemisorption is exothermic, forming OH- and Li+H-Li+. This results also indicate that the low coordination environment in surface step structure, such as kinks and ledges, may play an important role in the hydrogen chemisorption process. On the homolytic sites of the (110) and (111) surfaces, there is no hydrogen chemisorption. ((orig.))
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
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.
Ab initio molecular dynamics study of the hydration of the formohydroxamate anion.
Energy Technology Data Exchange (ETDEWEB)
Leung, Kevin
2006-01-01
We apply ab initio molecular dynamics (AIMD) to study the hydration structures and electronic properties of the formohydroxamate anion in liquid water. We consider the cis- nitrogen-deprotonated, cis- oxygen-deprotonated, and trans- oxygen-deprotonated formohydroxamate tautomers. They form an average of 6.3, 6.9, and 6.0 hydrogen bonds with water molecules, respectively. The predicted pair correlation functions and time dependence of the hydration numbers suggest that water is highly structured around the nominally negatively charged oxime oxygen in O-deprotonated tautomers but significantly less so around the nitrogen atom in the N-deprotonated species. Wannier function analysis suggests that, in the O-deprotonated anions, the negative charge is concentrated on the oxime oxygen, while in the N-deprotonated case, it is partially delocalized between the nitrogen and the adjoining oxime oxygen atom.
Water-mediated tautomerization of cytosine to the rare imino form: An ab initio dynamics study
Energy Technology Data Exchange (ETDEWEB)
Fogarasi, Geza [Institute of Chemistry, Eotvos University, H-1518 Budapest, Pf. 32. (Hungary)], E-mail: fg@chem.elte.hu
2008-06-16
Tautomerism in nucleotide bases is one of the possible mechanisms of mutation of DNA. In spite of numerous studies on the structure and energy of cytosine tautomers, little information is available on the process of proton transfer itself. We present here Born-Oppenheimer dynamics calculations, with the potential surface obtained 'on the fly' from ab initio quantum chemistry (QC) and the atoms moving classically. In search for water-mediated tautomerization the monohydrated complex was studied, running about 300 trajectories each of 3000-5000 points of 1 fs steps. One single trajectory has been found to lead to tautomerization. Although the QC method used in the simulations was inevitably modest (B3LYP/3-21G), higher-level test calculations along the same trajectory suggest that the simulation grasped the basic mechanism of proton transfer: a concerted, synchronous process characterized by strong coupling between the motions of the two participating hydrogen atoms.
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.
Isomerism of OBe3F3+ cation: an ab initio study
International Nuclear Information System (INIS)
Ab initio MP2/6-31G*/HF/6-31G*+ZPE(HF/6-31G*) calculations of the potential energy surface in the vicinity of stationary points and the pathways of intramolecular rearrangements between low-lying structures of the OBe3F3+ cation detected in the mass spectra of ?4-Be4O(CF3COO)6 were carried out. Ten stable isomers with di- and tricoordinate oxygen atoms were localized. The relative energies of six structures lie in the range 0-8 kcal mol-1 and those of the rest four structures lie in the range 20-40 kcal mol-1. two most favorable isomers are a planar C2, isomer and a pyramidal C3 isomer
Ab initio study of one-dimensional disorder on III-V semiconductor surfaces
Energy Technology Data Exchange (ETDEWEB)
Romanyuk, O. [Institute of Physics, Academy of Sciences of the Czech Republic, Cukrovarnicka 10, 162 00 Prague 6 (Czech Republic); Grosse, F.; Braun, W. [Paul-Drude-Institut fuer Festkoerperelektronik, Hausvogteiplatz 5-7, 10117 Berlin (Germany)
2010-02-15
Atomic disorder on GaSb(001) and GaAs(001) surfaces is studied by ab initio calculations within density functional theory (DFT). Surface energies are computed for GaSb(001) {beta} (4 x 3), {beta} (4 x 3)A{sub 1}, (4 x 6), and GaAs(001) {beta} 2(2 x 4), c (4 x 4) reconstructions. The computed energy differences do not exceed 1 meV / (1 x 1) which is in agreement with observed one-dimensional disorder on GaSb(001) and GaAs(001) surfaces at elevated temperatures for {beta} and {beta} 2 stoichiometries, respectively. Deviations in bond lengths due to disorder with respect to the ordered ground state phases are calculated (copyright 2010 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)
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.
Ab initio MRD CI calculations on the cesium hydride (CsH) molecule
International Nuclear Information System (INIS)
Ab initio multi-reference configuration interaction (MRD CI) calculations were carried out for the potential energy curves of the first 17 electronic states of the CsH molecule up to large bond distances (20 bohr). The 1?+ states were also calculated by means of relativistic all-electron SCF and CI using the spin-free no-pair operator with external field projectors. For the low-lying states, the spectroscopic parameters were determined. Dipole moments as well as the transition dipole moments: ?(X1?+?A1?+), ?(X1?+?B1?+), ?(A1?+?B1?+), were also calculated. Non-relativistic and relativistic results are compared. An analysis of the interactions in the 1,3?+ states is also proposed. (orig.)
Lattice thermal conductivity of UO2 using ab-initio and classical molecular dynamics
Kim, Hyoungchul; Kim, Moo Hwan; Kaviany, Massoud
2014-03-01
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.
Ab-initio Hartree-Fock study of tritium desorption from Li{sub 2}O
Energy Technology Data Exchange (ETDEWEB)
Taniguchi, Masaki; Tanaka, Satoru [Tokyo Univ. (Japan). Faculty of Engineering
1998-03-01
Dissociative adsorption of hydrogen on Li{sub 2}O (110) surface has been investigated with ab-initio Hartree-Fock quantum chemical calculation technique. Heat of adsorption and potential energy surface for H{sub 2} dissociative adsorption was evaluated by calculating the total energy of the system. Calculation results on adsorption heat indicated that H{sub 2} adsorption is endothermic. However, when oxygen vacancy exists adjacent to the adsorption sites, heat of adsorption energy became less endothermic and the activation energy required to dissociate the H-H bonding was smaller than that for the terrace site. This is considered to be caused by the excess charge localized near the defect. (author)
Bessac, Fabienne; Hoyau, Sophie; Maynau, Daniel
2005-09-01
Thanks to the use of localized orbitals and the subsequent possibility of neglecting long-range interactions, the linear-scaling methods have allowed to treat large systems at ab initio level. However, the limitation of the number of active orbitals in a complete active space self consistent-field (CASSCF) calculation remains unchanged. The method presented in this paper suggests to divide the system into fragments containing only a small number of active orbitals. Starting from a guess wave function, each orbital is optimized in its corresponding fragment, in the presence of the other fragments. Once all the fragments have been treated, a new set of orbitals is obtained. The process is iterated until convergence. At the end of the calculation, a set of active orbitals is obtained, which is close to the exact CASSCF solution, and an accurate CASSCF energy can be estimated. PMID:16178587
Electronic states of lithium passivated germanium nanowires: An ab-initio study
Energy Technology Data Exchange (ETDEWEB)
Trejo, A.; Carvajal, E.; Vázquez-Medina, R.; Cruz-Irisson, M. [Instituto Politécnico Nacional, ESIME-Culhuacan, Av. Santa Ana 1000, 04430 D.F. (Mexico)
2014-05-15
A study of the electronic and structural properties of germanium nanowires (GeNWs) was performed using the ab-initio Density Functional Theory within the generalized gradient approximation where electron-ion interactions are described by ultrasoft pseudopotentials. To study the effects of the lithium in the surface of the GeNWs we compare the electronic band structures of Hydrogen passivated GeNWs with those of partial and totally Li passivated GeNWs. The nanowires were constructed in the [001], [111] and [110] directions, using the supercell model to create different wire diameters. The results show that in the case of partial Li passivation there are localized orbitals near the valence band maximum, which would create a p-doped-kind of state. The total Li passivation created metallic states for all the wires.
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.
Tunneling of electrons via rotor-stator molecular interfaces: combined ab initio and model study
Petreska, Irina; Pejov, Ljupco; Kocarev, Ljupco
2015-01-01
Tunneling of electrons through rotor-stator anthracene aldehyde molecular interfaces is studied with a combined ab initio and model approach. Molecular electronic structure calculated from first principles is utilized to model different shapes of tunneling barriers. Together with a rectangular barrier, we also consider a sinusoidal shape that captures the effects of the molecular internal structure more realistically. Quasiclassical approach with the Simmons' formula for current density is implemented. Special attention is paid on conformational dependence of the tunneling current. Our results confirm that the presence of the side aldehyde group enhances the interesting electronic properties of the pure anthracene molecule, making it a bistable system with geometry dependent transport properties. We also investigate the transition voltage and we show that confirmation dependent field emission could be observed in these molecular interfaces at realistically low voltages. The present study accompanies our previ...
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.
Theoretical ab initio study the hydrogen bonding nature of the A:T base pair
International Nuclear Information System (INIS)
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
Theoretical AB initio study of the hydrogen bonding nature of the A:T base pair
International Nuclear Information System (INIS)
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 (B3LYP). 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
Ab initio intermolecular potential energy surface and thermophysical properties of nitrous oxide.
Crusius, Johann-Philipp; Hellmann, Robert; Hassel, Egon; Bich, Eckard
2015-06-28
We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N2O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N2O-N2O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N2O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data. PMID:26133428
International Nuclear Information System (INIS)
The determination of the molecular structure of molecules is of fundamental importance in chemistry. X-rays and electron diffraction methods constitute in important tools for the elucidation of the molecular structure of systems in the solid state and gas phase, respectively. The use of quantum mechanical molecular orbital ab initio methods offer an alternative for conformational analysis studies. Comparison between theoretical results and those obtained experimentally in the gas phase can make a significant contribution for an unambiguous determination of the geometrical parameters. In this article the determination for an unambiguous determination of the geometrical parameters. In this article the determination of the molecular structure of the cyclooctane molecule by electron diffraction in the gas phase an initio calculations will be addressed, providing an example of a comparative analysis of theoretical and experimental predictions. (author)
Iftimie, R; Schofield, J P; Iftimie, Radu; Salahub, Dennis; Schofield, Jeremy
2003-01-01
In this article, we propose an efficient method for sampling the relevant state space in condensed phase reactions. In the present method, the reaction is described by solving the electronic Schr\\"{o}dinger equation for the solute atoms in the presence of explicit solvent molecules. The sampling algorithm uses a molecular mechanics guiding potential in combination with simulated tempering ideas and allows thorough exploration of the solvent state space in the context of an ab initio calculation even when the dielectric relaxation time of the solvent is long. The method is applied to the study of the double proton transfer reaction that takes place between a molecule of acetic acid and a molecule of methanol in tetrahydrofuran. It is demonstrated that calculations of rates of chemical transformations occurring in solvents of medium polarity can be performed with an increase in the cpu time of factors ranging from 4 to 15 with respect to gas-phase calculations.
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.
Dynamic decomposition of aliphatic molecules on Al(111) from ab initio molecular dynamics
International Nuclear Information System (INIS)
Ab initio molecular dynamics based on density functional theory within the generalized gradient approximation was used to explore decomposition on Al(111) of butanol-alcohol and butanoic-acid, two important boundary additives in Al processing. Each molecule was oriented with its functional group closest to the surface and then given an initial velocity toward the surface. Decomposition occurred upon collision with Al(111) resulting in the formation of adhered fragments that represent the very initial stages in additive film formation during plastic deformation where nascent Al is liberated. Bonding interactions over the simulation time frames were explored with contours of the electron localization function. Results of the simulations were compared with existing experimental studies of chemical decomposition on clean Al surfaces and found to be in qualitative accord. The effects of other initial molecular orientations on decomposition were explored in ancillary calculations where the molecules were rotated through 90 deg. and 180 deg. prior to collision with Al(111)
Static and dynamic structures of liquid tin at high pressure from ab initio molecular dynamics
Munejiri, S.; Shimojo, F.; Hoshino, K.
2012-09-01
Static and dynamic structures of liquid Sn were studied by ab initio molecular-dynamics simulations from a state near the melting point (573 K, 0 GPa) to one at higher temperature and pressure (1273 K, 14 GPa). The calculated static structures are in good agreement with the experimental data for a wide range of temperatures and pressures. The dynamic structure factors also agree reasonably well with the available experimental data. Though a cage effect and a transverse mode exist near the melting point, they tend to fade out with increasing temperature. On the other hand, at high pressure, we found that the cage effect and the transverse mode recover even at high temperature. We have also confirmed that a mixing effect exists; that is, when a transverse collective mode occurs in liquid Sn, it also produces a longitudinal mode with a frequency similar to itself. This mixing effect is crucially important for experimental observations of transverse modes.
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.
Electronic states of lithium passivated germanium nanowires: An ab-initio study
International Nuclear Information System (INIS)
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
Atomic carbon chains as spin-transmitters: An ab initio transport study
DEFF Research Database (Denmark)
Fürst, Joachim Alexander; Brandbyge, Mads
2010-01-01
An atomic carbon chain joining two graphene flakes was recently realized in a ground-breaking experiment by Jin et al. (Phys. Rev. Lett., 102 (2009) 205501). We present ab initio results for the electron transport properties of such chains and demonstrate complete spin-polarization of the transmission in large energy ranges. The effect is due to the spin-polarized zig-zag edge terminating each graphene flake causing a spin-splitting of the graphene pi(z) bands, and the chain states. Transmission occurs when the graphene p-states resonate with similar states in the strongly hybridized edges and chain. This effect should in general hold for any p-conjugated molecules bridging the zig-zag edges of graphene electrodes. The polarization of the transmission can be controlled by chemically or mechanically modifying the molecule, or by applying an electrical gate.
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...
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.
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.
International Nuclear Information System (INIS)
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
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.
Ab initio calculation of the ion feature in x-ray Thomson scattering.
Plagemann, Kai-Uwe; Rüter, Hannes R; Bornath, Thomas; Shihab, Mohammed; Desjarlais, Michael P; Fortmann, Carsten; Glenzer, Siegfried H; Redmer, Ronald
2015-07-01
The spectrum of x-ray Thomson scattering is proportional to the dynamic structure factor. An important contribution is the ion feature which describes elastic scattering of x rays off electrons. We apply an ab initio method for the calculation of the form factor of bound electrons, the slope of the screening cloud of free electrons, and the ion-ion structure factor in warm dense beryllium. With the presented method we can calculate the ion feature from first principles. These results will facilitate a better understanding of x-ray scattering in warm dense matter and an accurate measurement of ion temperatures which would allow determining nonequilibrium conditions, e.g., along shock propagation. PMID:26274290
Ab initio calculation of the ion feature in x-ray Thomson scattering
Plagemann, Kai-Uwe; Rüter, Hannes R.; Bornath, Thomas; Shihab, Mohammed; Desjarlais, Michael P.; Fortmann, Carsten; Glenzer, Siegfried H.; Redmer, Ronald
2015-07-01
The spectrum of x-ray Thomson scattering is proportional to the dynamic structure factor. An important contribution is the ion feature which describes elastic scattering of x rays off electrons. We apply an ab initio method for the calculation of the form factor of bound electrons, the slope of the screening cloud of free electrons, and the ion-ion structure factor in warm dense beryllium. With the presented method we can calculate the ion feature from first principles. These results will facilitate a better understanding of x-ray scattering in warm dense matter and an accurate measurement of ion temperatures which would allow determining nonequilibrium conditions, e.g., along shock propagation.
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. PMID:25871229
International Nuclear Information System (INIS)
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 investigation of the switching behavior of the dithiole-benzene nano-molecular wire
International Nuclear Information System (INIS)
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
Modern Ab Initio Approaches and Applications in Few-Nucleon Physics with A \\ge 4
Leidemann, Winfried
2012-01-01
We present an overview of the evolution of ab initio methods for few-nucleon systems with A \\ge 4, tracing the progress made that today allows precision calculations for these systems. First a succinct description of the diverse approaches is given. In order to identify analogies and differences the methods are grouped according to different formulations of the quantum mechanical many-body problem. Various significant applications from the past and present are described. We discuss the results with emphasis on the developments following the original implementations of the approaches. In particular we highlight benchmark results which represent important milestones towards setting an ever growing standard for theoretical calculations. This is relevant for meaningful comparisons with experimental data. Such comparisons may reveal whether a specific force model is appropriate for the description of nuclear dynamics.
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.
Prediction of toxicity of nitrobenzenes using ab initio and least squares support vector machines
International Nuclear Information System (INIS)
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
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.
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 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.
Excitons in Carbon Nanotubes: An Ab Initio Symmetry-Based Approach
Chang, Eric; Bussi, Giovanni; Ruini, Alice; Molinari, Elisa
2004-05-01
The optical absorption spectrum of the carbon (4,2) nanotube is computed using an ab initio many-body approach which takes into account excitonic effects. We develop a new method involving a local basis set which is symmetric with respect to the screw-symmetry of the tube. Such a method has the advantages of scaling faster than plane-wave methods and allowing for a precise determination of the symmetry character of the single-particle states, two-particle excitations, and selection rules. The binding energy of the lowest, optically active states is approximately 0.8eV. The corresponding exciton wave functions are delocalized along the circumference of the tube and localized in the direction of the tube axis.
Excitons in carbon nanotubes: an ab initio symmetry-based approach
Chang, E; Ruini, A; Molinari, E; Chang, Eric; Bussi, Giovanni; Ruini, Alice; Molinari, Elisa
2004-01-01
The optical absorption spectrum of the carbon (4,2) nanotube is computed using an ab-initio many-body approach which takes into account excitonic effects. We develop a new method involving a local basis set which is symmetric with respect to the screw symmetry of the tube. Such a method has the advantages of scaling faster than plane-wave methods and allowing for a precise determination of the symmetry character of the single particle states, two-particle excitations, and selection rules. The binding energy of the lowest, optically active states is approximately 0.8 eV. The corresponding exciton wavefunctions are delocalized along the circumference of the tube and localized in the direction of the tube axis.
Directory of Open Access Journals (Sweden)
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 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
Charge Transfer in FeO: A combined Molecular-Dynamics and Ab Initio Study
International Nuclear Information System (INIS)
Molecular dynamics simulations and ab initio electronic structure calculations were carried out to determine the rate of charge transfer in stoichiometric w-stite (FeO). The charge transfer of interest occurs by II/III valence interchange between nearest-neighbor Fe atoms, with the Fe(III) constituting a ''hole'' electronic defect. There are two possible nearest-neighbor charge transfers in the FeO lattice, which occur between edge-sharing or corner-sharing FeO6 octahedra. Molecular dynamics simulations predict charge transfer rates of 3.7x1011 and 1.9x109 s-1 for the edge and corner transfers, respectively, in good agreement with those calculated using an ab initio cluster approach (1.6x1011 and 8.0x108 s-1, respectively). The calculated rates are also similar to those along basal and c-axis directions in hematite (?-Fe2O3) determined previously. Therefore, as is the case for hematite, w-stite is predicted to show anisotropic electrical conductivity. Our findings indicate that a rigid ion model does not give acceptable results, thus showing the need to account for the change in polarizability of the system upon charge transfer. Our model achieves this by using a simple mechanical shell model. By calculating the electronic coupling matrix elements for many transition state configurations obtained from the molecular dynamics simulations, we found evidence that the position of the bridging oxygen atoms can greatly affect the amount electronic coupling between the donor and acceptor states. Finally, we address the effect of oxygen vacancies on the charge transfer. It was found that an oxygen vacancy not only creates a driving force for holes to transport away from the vacancy (or equivalently for electrons to diffuse toward the vacancy) but also lowers the free energy barriers for charge transfer. In addition, the reorganization energy significantly differed from the non-defective case in a small radius around the defect
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.
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)
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.
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.
Energy Technology Data Exchange (ETDEWEB)
Rohrer, J; Ruberto, C; Hyldgaard, P, E-mail: rohrer@chalmers.s [BioNano Systems Laboratory, Department of Microtechnology, MC2, Chalmers University of Technology, SE-412 96 Gothenburg (Sweden)
2010-01-13
We present a strategy to identify energetically favourable oxide structures in thin-film geometries. Thin-film candidate configurations are constructed from a pool of sublattices of stable and metastable oxide bulk phases. Favourable stoichiometric compositions and atomic geometries are identified by comparing total and Gibbs free energies of the relaxed configurations. This strategy is illustrated for thin-film alumina on TiC, materials which are commonly fabricated by chemical vapour deposition (CVD) and used as wear-resistant multilayer coatings. Based on the standard implementation of ab initio thermodynamics, with an assumption of equilibrium between molecular O{sub 2} and the oxide, we predict a stability preference of TiC/alumina configurations that show no binding across the interface. This result is seemingly in conflict with the wear-resistant character of the material and points towards a need for extending standard ab initio thermodynamics to account for relevant growth environments.
International Nuclear Information System (INIS)
We present a strategy to identify energetically favourable oxide structures in thin-film geometries. Thin-film candidate configurations are constructed from a pool of sublattices of stable and metastable oxide bulk phases. Favourable stoichiometric compositions and atomic geometries are identified by comparing total and Gibbs free energies of the relaxed configurations. This strategy is illustrated for thin-film alumina on TiC, materials which are commonly fabricated by chemical vapour deposition (CVD) and used as wear-resistant multilayer coatings. Based on the standard implementation of ab initio thermodynamics, with an assumption of equilibrium between molecular O2 and the oxide, we predict a stability preference of TiC/alumina configurations that show no binding across the interface. This result is seemingly in conflict with the wear-resistant character of the material and points towards a need for extending standard ab initio thermodynamics to account for relevant growth environments.
Du, A. J.; Smith, Sean C.; Lu, G. Q.
2007-04-01
Ab initio spin-polarized density functional theory calculations are performed to explore the effect of single Na vacancy on NaAlH4(001) surface on the initial dehydrogenation kinetics. The authors found that two Al-H bond lengths become elongated and weakened due to the presence of a Na vacancy on the NaAlH4(001) surface. Spontaneous recombination from the surface to form molecular hydrogen is observed in the spin-polarized ab initio molecular dynamics simulation. The authors' results indicate that surface Na vacancies play a critical role in accelerating the dehydrogenation kinetics in sodium alanate. The understanding gained here will aid in the rational design and development of complex hydride materials for hydrogen storage.
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
Gorenstein, D G; Luxon, B A; Findlay, J B
1977-03-01
CNDO and ab initio calculations on the dimethyl phosphate monoanion demonstrate that geometry optimization can dramatically alter the relative energies of the conformational isomers of the phosphate ester. Thus, with geometry optimization (particularly of the diester RO-P-OR bond angle) the energy differences between the gauche-gauche, gauche-trans, and trans-trans conformations is less than 1 kcal/mol rather than approximately 7 kcal/mol previously reported. A torsional energy map for the two ester torsional angles which includes ester bond angle optimization is presented. Ab initio (STO-3G level) and CNDO calculations confirm the strong coupling of the diester RO-P-OR bond angle to the torsional conformation. PMID:849444
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.
Directory of Open Access Journals (Sweden)
Martin Alberto JM
2009-01-01
Full Text Available Abstract Background Prediction of protein structures from their sequences is still one of the open grand challenges of computational biology. Some approaches to protein structure prediction, especially ab initio ones, rely to some extent on the prediction of residue contact maps. Residue contact map predictions have been assessed at the CASP competition for several years now. Although it has been shown that exact contact maps generally yield correct three-dimensional structures, this is true only at a relatively low resolution (3–4 Å from the native structure. Another known weakness of contact maps is that they are generally predicted ab initio, that is not exploiting information about potential homologues of known structure. Results We introduce a new class of distance restraints for protein structures: multi-class distance maps. We show that 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/.
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
Time-domain ab initio studies of photoinduced electron dynamics in nanoscale semiconductors
Prezhdo, Oleg
2010-03-01
Design of novel materials for energy harvesting and storage requires an understanding of the dynamical response on the nanometer scale. We have developed state-of-the-art non-adiabatic molecular dynamics techniques and implemented them within time-dependent density functional theory in order to model the ultrafast processes in these materials at the atomistic level and in real time. Quantum dots (QD) are quasi-zero dimensional structures with a unique combination of molecular and bulk properties. As a result, QDs exhibit new physical phenomena such as the electron-phonon relaxation bottleneck and carrier multiplication, which have the potential to greatly increase solar cell efficiencies. Photoinduced charge separation across molecular/bulk interfaces drives the dye-sensitized semiconductor solar cell. A subject of active research, it creates many challenges due to the stark differences between the quantum states of molecular and periodic systems, as well as the different sets of theories and experimental tools used by physicists and chemists. Our time-domain atomistic simulations create a detailed picture of these materials. By comparing and contrasting their properties, we provide a unifying description of quantum dynamics on the nanometer scale, resolve several highly debated issues, and generate theoretical guidelines for development of novel systems for energy harvesting and storage. [4pt] [1] O. V. Prezhdo ``Photoinduced dynamics in semiconductor quantum-dots: insights from time-domain ab initio studies'', Acc. Chem. Res., available online.[0pt] [2] O. V. Prezhdo, W. R. Duncan, V. V. Prezhdo, ``Photoinduced electron dynamics at semiconductor interfaces: a time-domain ab initio prospective'', Prog. Surf. Science, 84, 39 (2009).[0pt] [3] O. V. Prezhdo, et al., ``Dynamics of the photoexcited electron at the chromophore-semiconductor interface'', Acc. Chem. Res., 41, 339 (2008).[0pt] [4] W. R. Duncan, O. V. Prezhdo, ``Theoretical studies of photoinduced electron transfer in dye-sensitized TiO2'', Review, Ann. Rev. Phys. Chem., 58, 143 (2007).[0pt] [5] C. F. Craig, W. R. Duncan, O. V. Prezhdo ``Trajectory surface hopping in the time-dependent Kohn-Sham theory for electron-nuclear dynamics'', Phys. Rev. Lett., 95 163001 (2005).
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)
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.)
Ab initio static and molecular dynamics studies of helium behavior in beryllium
Vladimirov, P. V.; Moeslang, A.
2013-11-01
Beryllium is an effective neutron multiplier material widely exploited in nuclear applications. It will be used in the helium-cooled beryllium pebble bed of fusion reactor blankets for increasing the efficiency of tritium production. Macroscopic effects of irradiation (e.g., swelling) on beryllium are greatly influenced by accumulated transmutation helium. Atomic scale simulations of beryllium behavior under irradiation are necessary for understanding the basic mechanisms and reliable prediction of microstructural changes. In this study, we investigate the behavior of interstitial and substitutional helium, its diffusion pathways and interaction with point defects present in irradiated beryllium by means of static and molecular dynamics ab initio simulations. It was shown that a mixed dumbbell consisting of self-interstitial and helium atoms represents the ground-state configuration for interstitial helium. At low temperatures, the mixed dumbbell migrates in the basal plane through a series of in-basal-plane rotations, while at higher temperatures it jumps also between adjacent basal planes. It was revealed that, as in many other metals, interstitial helium atoms are bound to each other (Eb˜1eV). In beryllium, two mixed dumbbells meet each other so that helium atoms are the nearest neighbors, whereas the helium pair can be oriented either in- or out-of-basal plane. Diffusion modes of the pair are discussed. In addition, it was found that helium is very strongly bound to vacancies: the binding energy of more than 3 eV found by static ab initio calculations suggests that helium is unlikely to be released from a mono-vacancy at temperatures below the melting point. As has been shown previously, vacancy clusters are unstable in beryllium. This study shows that the addition of helium stabilizes di-vacancies. Thus, it is confirmed that the presence of transmutation gas is necessary for the development of a porous microstructure in beryllium. NVT ensemble means that the number of particles (N) and system volume (V) are constant and the ensemble has a well-defined temperature (T).
Ab initio density functional theory study of strain effects on ferroelectricity at PbTiO3 surfaces
Umeno, Y.; Shimada, T.; Kitamura, T; Elsässer, C.
2006-01-01
The PbTiO3 surface structure with ferroelectric (FE) polarization parallel to the surface and its response to tangential strain have been studied using ab initio density functional theory calculations with the local density approximation. We find (110)-oriented ferroelectricity is more stable than (100)-oriented under zero and nonzero strain in both TiO2 and PbO terminations. Tensile strain enhances the FE distortion and suppresses the antiferrodistortive rotation, while the opposite trend is...
Czech Academy of Sciences Publication Activity Database
Sychrovský, Vladimír; Bud?šínský, Miloš; Benda, Ladislav; Špirko, Vladimír; Voká?ová, Zuzana; Šebestík, Jaroslav; Bou?, Petr
2008-01-01
Ro?. 112, ?. 6 (2008), s. 1796-1805. ISSN 1520-6106 R&D Projects: GA ?R GA203/06/0420; GA ?R GA202/07/0732; GA AV ?R IAA400550702; GA AV ?R IAA400550701; GA MŠk LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : NMR * ab initio * dipeptide Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.189, year: 2008
Czech Academy of Sciences Publication Activity Database
?urík, Roman; Šulc, M.
2010-01-01
Ro?. 43, ?. 17 (2010), s. 175205. ISSN 0953-4075 R&D Projects: GA MŠk(CZ) OC10046; GA MŠk OC09079; GA AV ?R KJB400400803; GA ?R GA202/08/0631 Institutional research plan: CEZ:AV0Z40400503 Keywords : Ab initio calculations * Commonly used * DFT potential Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.902, year: 2010
Rasim, Karsten
2011-01-01
Cette thèse porte sur une étude de matériaux oxydes fortement désordonnés de type Brownmillerite et présentant diverses substitutions. Les aspects les plus étudiés sont la conductivité protonique des phases hydratées ainsi que les propriétés structurales des composés anhydres. L'étude repose majoritairement sur des calculs de type DFT (réalisés de manière statique à 0 K et à température élevée en utilisant la dynamique moléculaire ab initio). Elle est complétée de mesures XANES (spectroscopie...
Curtarolo, S; Ceder, G; Curtarolo, Stefano; Morgan, Dane; Ceder, Gerbrand
2005-01-01
Predicting and characterizing the crystal structure of materials is a key problem in materials research and development. We report the results of ab initio LDA/GGA computations for the following systems: AgAu, AgCd, AgMg, AgMo*, AgNa, AgNb*, AgPd, AgRh*, AgRu*, AgTc*, AgTi, AgY, AgZr, AlSc, AuCd, AuMo*, AuNb, AuPd, AuPt*, AuRh*, AuRu*, AuSc, AuTc*, AuTi, AuY, AuZr, CdMo*, CdNb*, CdPd, CdPt, CdRh, CdRu*, CdTc*, CdTi, CdY, CdZr, CrMg*, MoNb, MoPd, MoPt, MoRh, MoRu, MoTc*, MoTi, MoY*, MoZr, NbPd, NbPt, NbRh, NbRu, NbTc, NbY*, NbZr*, PdPt, PdRh*, PdRu*, PdTc, PdTi, PdY, PdZr, PtRh, PtRu, PtY, PtTc, PtTi, PtZr, RhRu, RhTc, RhTi, RhY, RhZr, RuTi, RuTc, RuY, RuZr, TcTi, TcY, TcZr, TiZr*, YZr* (*= systems in which the ab initio method predicts that no compounds are stable). A detailed comparison to experimental data confirms the high accuracy with which ab initio methods can predict ground states. Keywords: Binary Alloys, Ab initio, Intermetallics, Transition Metals, StructureAluminum, Cadmium, Gold, Magnesium, Molyb...
Paulus, Beate; Rosciszewski, Krzysztof
2004-01-01
Solid mercury in the rhombohedral structure is unbound within the self-consistent field (Hartree-Fock) approximation. The metallic binding is entirely due to electronic correlations. We determine the cohesive energy of solid mercury within an ab-initio many-body expansion for the correlation part. Electronic correlations in the $5d$ shell contribute about half to the cohesive energy. Relativistic effects are found to be very important. Very good agreement with the experiment...
DEFF Research Database (Denmark)
Pedersen, Kim Vestergaard; Christensen, Henrik
2004-01-01
Trichlorothioacetyl chloride 1, tetrachlorothiirane 2, and trichloroethenesulfenyl chloride 3 and the equilibria between them have been investigated by ab initio Hartree-Fock (HF), Møller-Plesset second order perturbation (MP2) calculations, and by Gaussian-3 theory, G3(MP2). The transition states of the isomerization reactions have been identified. Also investigated were possible reactions leading to the isomers and their possible decomposition products. The results show that the unobserved isomerization reactions are feasible.
Weak interactions in Graphane/BN systems under static electric fields—A periodic ab-initio study.
Steinkasserer, Lukas Eugen Marsoner; Gaston, Nicola; Paulus, Beate
2015-04-21
Ab-initio calculations via periodic Hartree-Fock (HF) and local second-order Møller-Plesset perturbation theory (LMP2) are used to investigate the adsorption properties of combined Graphane/boron nitride systems and their response to static electric fields. It is shown how the latter can be used to alter both structural as well as electronic properties of these systems. PMID:25903899
Application of Ab initio Results in Prediction of the Phase Diagram in the Co-Mo system.
Czech Academy of Sciences Publication Activity Database
Houserová, Jana; V?eš?ál, J.; Šob, Mojmír
Brno : Masarykova univerzita v Brn?, 2004, s. 59. ISBN 80-210-3319-3. [Workshop of Physical Chemists and Electrochemists /4./. Brno (CZ), 02.02.2004] R&D Projects: GA ?R GP106/03/P002; GA ?R GA106/02/0877 Institutional research plan: CEZ:AV0Z2041904 Keywords : ab initio calculations * sigma phase * phase diagram Subject RIV: BM - Solid Matter Physics ; Magnetism
Czech Academy of Sciences Publication Activity Database
?ezá?, Jan; Hobza, Pavel
2008-01-01
Ro?. 4, ?. 11 (2008), s. 1835-1840. ISSN 1549-9618 R&D Projects: GA MŠk LC512; GA AV ?R IAA400550510 Institutional research plan: CEZ:AV0Z40550506 Keywords : benzene dimer * dynamic structure * on-the fly ab initio DFT-D molecular dynamic simulation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.274, year: 2008
Ismail-Beigi, S; Ismail-Beigi, Sohrab
2000-01-01
We report the first ab initio density-functional study of screw dislocations cores in the bcc transition metals Mo and Ta. Our results suggest a new picture of bcc plasticity with symmetric and compact dislocation cores, contrary to the presently accepted picture based on continuum and interatomic potentials. Core energy scales in this new picture are in much better agreement with the Peierls energy barriers to dislocation motion suggested by experiments.
Ab-Initio Calculated Energetics of Sigma Phase in Mo-Fe and Mo-Co Systems.
Czech Academy of Sciences Publication Activity Database
Houserová, Jana; Šob, Mojmír; V?eš?ál, J.
Brno : Brno University of Technology, Faculty of Mechanical Engeneering, 2003, s. 242-243. [JUNIORMAT'03 /4./. Brno (CZ), 23.09.2003-24.09.2003] R&D Projects: GA ?R GP106/03/P002; GA ?R GA106/02/0877 Institutional research plan: CEZ:AV0Z2041904 Keywords : sigma phase * thermodynamic ? ab initio methods Subject RIV: BM - Solid Matter Physics ; Magnetism
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-...
Victora, Andrea; Möller, Heiko M.; Exner, Thomas E
2014-01-01
NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on...
Ab initio study of InxGa(1-x)N - performance of the alchemical mixing approximation
Scharoch, P.; M. J. Winiarski; Polak, M. P.
2014-01-01
The alchemical mixing approximation which is the ab initio pseudopotential specific implementation of the virtual crystal approximation (VCA), offered in the ABINIT package, has been employed to study the wurtzite (WZ) and zinc blende (ZB) InxGa(1-x)N alloy from first principles. The investigations were focused on structural properties (the equilibrium geometries), elastic properties (elastic constants and their pressure derivatives), and on the band-gap. Owing to the ABINIT...
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...
Ab initio study of magnetic structure and chemical reactivity of Cr2O3 and its (0001) surface
Cline, J. A.; Rigos, A. A.; Arias, T. A.
1999-01-01
We present the first ab initio density functional theory study of the oxygen-terminated Cr2O3 (0001) surface within the local spin-density approximation (LSDA). We find that spin plays a critical role for even the most basic properties of Cr2O3 such as the structure and mechanical response of the bulk material. The surface exhibits strong relaxations and changes in electronic and magnetic structure with important implications for the chemical reactivity and unusual spin-depe...
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...
Lesinski, T.; Bennaceur, K.; Duguet, T; Meyer, J.
2006-01-01
We study the effect of the splitting of neutron and proton effective masses with isospin asymmetry on the properties of the Skyrme energy density functional. We discuss the ability of the latter to predict observable of infinite matter and finite nuclei, paying particular attention to controlling the agreement with ab-initio predictions of the spin-isospin content of the nuclear equation of state, as well as diagnosing the onset of finite size instabilities, which we find to...
Czech Academy of Sciences Publication Activity Database
Jelínek, Pavel; Pérez, R.; Ortega, J.; Flores, F.
2008-01-01
Ro?. 77, ?. 11 (2008), 115447/1-115447/11. ISSN 1098-0121 R&D Projects: GA AV ?R KAN400100701; GA AV ?R IAA100100616; GA MŠk 1K05020; GA AV ?R IAA1010413 Institutional research plan: CEZ:AV0Z10100521 Keywords : electronic transport in nanoscale materials and structures * ab initio calculations of adsorbate structure and reactions * nanoscale contacts Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.322, year: 2008
Ab Initio Studies on the Preferred Site of Protonation in Cytisine in the Gas Phase and Water
MaÃ…Â‚gorzata Darowska; ElÃ…Â¼bieta GÃƒÂ³rnicka; Mariusz Makowski; Ewa D. RaczyÃ…Â„ska
2005-01-01
Abstract: Ab initio calculations (HF, MP2, DFT for isolated and PCM for solvated molecules) were performed for cytisine (1) and its model compounds: N-methyl-2-pyridone (2) and piperidine (3). Among three heteroatomic functions (carbonyl oxygen, pyridone and piperidine nitrogens) considered as the possible sites of protonation in 1, surprisingly the carbonyl oxygen takes preferentially the proton in the gas phase whereas in water the piperidine nitrogen is firstly protonated. For model compou...
DiStasio Jr, Robert A.; Santra, Biswajit; Li, Zhaofeng; Wu, Xifan; Car, Roberto
2014-01-01
In this work, we report the results of a series of density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations of ambient liquid water using a hierarchy of exchange-correlation (XC) functionals to investigate the individual and collective effects of exact exchange (Exx), via the PBE0 hybrid functional, non-local vdW/dispersion interactions, via a fully self-consistent density-dependent dispersion correction, and approximate nuclear quantum effects (...
Ismail-Beigi, Sohrab; Arias, T. A.
1999-01-01
We report the first ab initio density-functional study of screw dislocations cores in the bcc transition metals Mo and Ta. Our results suggest a new picture of bcc plasticity with symmetric and compact dislocation cores, contrary to the presently accepted picture based on continuum and interatomic potentials. Core energy scales in this new picture are in much better agreement with the Peierls energy barriers to dislocation motion suggested by experiments.
Gannarelli, C. M. S.; Alfe, D.; Gillan, M. J.
2003-01-01
We assess the quantitative accuracy of the particle-in-cell (PIC) approximation used in recent ab initio predictions of the thermodynamic properties of hexagonal-close-packed iron at the conditions of the Earth's inner core. The assessment is made by comparing PIC predictions for a range of thermodynamic properties with the results of more exact calculations that avoid the PIC approximation. It is shown that PIC gives very accurate results for some properties, but that it gi...
Taylor, J; Guo, H.; WANG, J
2000-01-01
We present an {\\it ab initio} analysis of electron conduction through a $C_{60}$ molecular device. Charge transfer from the device electrodes to the molecular region is found to play a crucial role in aligning the lowest unoccupied molecular orbital (LUMO) of the $C_{60}$ to the Fermi level of the electrodes. This alignment induces a substantial device conductance of $\\sim 2.2 \\times (2e^2/h)$. A gate potential can inhibit charge transfer and introduce a conductance gap near...
Mönnich, A.; Lange, J; Bauer , M.; Aeschlimann, M.; Nechaev, I. A.; Zhukov, V. P.; Echenique, P. M.; Chulkov, E. V.
2006-01-01
We have studied the relaxation dynamics of optically excited electrons in molybdenum and rhodium by means of time resolved two-photon photoemission spectroscopy (TR-2PPE) and ab initio electron self-energy calculations performed within the GW and GW+T approximations. Both theoretical approaches reproduce qualitatively the experimentally observed trends and differences in the lifetimes of excited electrons in molybdenum and rhodium. For excitation energies exceeding the Fermi...
International Nuclear Information System (INIS)
Full text: The usefulness of standard ab initio techniques, such as coupled-cluster or multi-reference approaches, for the prediction of vibronic spectra is discussed using the example of K3 and Rb3 alkali-metal clusters. These exotic molecules, can be formed in their lowest-energy spin state (the doublet) by standard molecular beam methods; their weakly bound quartet state is easily stabilized on the surface of cold (0.4 K) helium nanodroplets. Both spin multiplicities have been characterized spectroscopically, and are good candidates to assess the quality of ab initio methods for electronic-structure calculations. The following characteristics make alkali trimers interesting in this respect: they are multi-electron systems, of moderate size, and include heavy atoms. Correlation energy and relativistic effects thus play an equally essential role for the molecular binding; at the same time, the system remains tractable by computationally expensive high-level methods. The symmetry properties of alkali trimers, in either spin multiplicity, makes them prime examples for the E.e Jahn-Teller effect, where a doubly-degenerate electronic state interacts with the doubly-degenerate vibrational mode of the system. By least-squares-fits of the ab initio points we extract parameters for the analytical description of the potential energy surfaces of several electronic states. We calculate vibronic spectra where the Jahn-Teller distortion as well as spin-orbit coupling are accounted for, which we compare with the available experimental data. (author)
Heuvel, Willem Van den; Soncini, Alessandro
2015-01-01
We present an ab initio methodology dedicated to the determination of the electronic structure and magnetic properties of ground and low-lying excited states, i.e., the crystal field levels, in lanthanide(III) complexes. Currently, the most popular and successful ab initio approach is the CASSCF/RASSI-SO method, consisting of the optimization of multiple complete active space self-consistent field (CASSCF) spin eigenfunctions, followed by full diagonalization of the spin--orbit coupling (SOC) Hamiltonian in the basis of the CASSCF spin states featuring spin-dependent orbitals. Based on two simple observations valid for Ln(III) complexes, namely: (i) CASSCF 4f atomic orbitals are expected to change very little when optimized for different multiconfigurational states belonging to the 4f-electronic configuration, (ii) due to strong SOC the total spin is not a good quantum number, we propose here an efficient ab initio strategy which completely avoids any multiconfigurational calculation, by optimizing a unique s...
Directory of Open Access Journals (Sweden)
Kamarulzaman Abdul Ghani
2014-04-01
Full Text Available 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 students were selected randomly. These students were diverse in their courses ranging from Medicine, Engineering to Geology and Dentistry among others. This study used questionnaire as the main research tool to collect information on the use of language learning strategies. The questionnaire consisted of three parts, namely the demographic data, the Arabic Language Learning Strategies and motivation. The results showed that as a whole, the students had used language learning strategies at a moderate level. Metaphysics strategy was the most frequently used strategy. Also, it was found that high-achieving students used the language learning strategies more often and frequently as compared to other students of different proficiency. The Pearson test also showed that there was a significant positive correlation between Language Learning Strategies and the proficiency in the Arabic Ab Initio language.
Knyazev, D V
2014-01-01
This work is devoted to the investigation of transport and optical properties of liquid aluminum in the two-temperature case. At first optical properties, static electrical and thermal conductivities were obtained in the \\textit{ab initio} calculation. The \\textit{ab initio} calculation is based on the quantum molecular dynamics, density functional theory and the Kubo-Greenwood formula. The semiempirical approximation was constructed based on the results of the \\textit{ab initio} caculation. The approximation yields the dependences $\\sigma_{1_\\mathrm{DC}}\\propto1/T_i^{0.25}$ and $K\\propto T_e/T_i^{0.25}$ for the static electrical conductivity and thermal conductivity, respectively. The approximation is valid for liquid aluminum at $\\rho=2.70$~g/cm$^3$, 3~kK~$\\leq T_i\\leq T_e\\leq20$~kK. Our results are well described by the Drude model with the effective relaxation time $\\tau\\propto T_i^{-0.25}$. We have compared our results with a number of other models. They are all reduced in the low-temperature limit to th...
Energy Technology Data Exchange (ETDEWEB)
Dane Morgan
2010-06-10
The project began March 13, 2006, allocated for three years, and received a one year extension from March 13, 2009 to March 12, 2010. It has now completed 48 of 48 total months. The project was focused on using ab initio methods to gain insights into radiation induced segregation (RIS) in Ni-Fe-Cr alloys. The project had the following key accomplishments • Development of a large database of ab initio energetics that can be used by many researchers in the future for increased understanding of this system. For example, we have the first calculations showing a dramatic stabilization effect of Cr-Cr interstitial dumbbells in Ni. • Prediction of both vacancy and interstitial diffusion constants for Ni-Cr and Ni-Fe for dilute Cr and Fe. This work included generalization of widely used multifrequency models to make use of ab initio derived energetics and thermodynamics. • Prediction of qualitative trends of RIS from vacancy and interstitial mechanisms, suggesting the two types of defect fluxes drive Cr RIS in opposite directions. • Detailed kinetic Monte Carlo modeling of diffusion by vacancy mechanism in Ni-Cr as a function of Cr concentration. The results demonstrate that Cr content can have a significant effect on RIS. • Development of a quantitative RIS transport model, including models for thermodynamic factors and boundary conditions.
International Nuclear Information System (INIS)
Graphical abstract: Completely new and accurate ab initio adiabatic and quasidiabatic potential energy surfaces for the ground and the first excited electronic states of the H+ + CO system have been obtained which are relevant for the coupling dynamics of the inelastic and charge transfer processes. - Abstract: Ab initio global adiabatic as well as quasidiabatic potential energy surfaces for the ground and the first excited electronic states of the H+ + CO system have been computed as a function of the Jacobi coordinates (R, r, ?) using Dunning's cc-pVTZ basis set at the internally contracted multi-reference (single and double) configuration interaction level of accuracy. In addition, nonadiabatic coupling matrix elements arising from radial motion, mixing angle and coupling potential have been computed using the ab initio procedure [Simah et al. (1999) ] for the purpose of dynamics study. The geometrical properties corresponding to the minimum energy of the bound HCO+ and HOC+ isomers have been obtained and compared with those predicted by previous theoretical and experimental results. The HCO+ has been found to be more stable than the HOC+. The minimum energy pathway in the ground electronic state for the isomerization process, HCO+ ? HOC+ has also been obtained as a function of ?.
Ab-Initio calculations including Van der Waals interactions: the SnS2 layered material
Seminóvski Pérez, Yohanna; Palacios Clemente, Pablo; Wahnon Benarroch, Perla; Grau-Crespo, Ricardo; Wahnón Benarroch, Perla
2012-01-01
Tin disulfide SnS2 was recently proposed as a high efficiency solar cell precursor [1]. The aim of this work is a deep study of the structural disposition of the most important polytipes of this layered material, not only describing the electronic correlation but also the interatomic Van der Waals interactions that is present between the layers. The two recent implementations to take Van der Waals interactions into account in the VASP code are the self-consistent Dion et al. [2] functional o...
International Nuclear Information System (INIS)
Ammoniated ammonium ions (NH4+·nNH3, n=0-6) were studied theoretically by molecular orbital calculations and experimentally by observing their formation and decomposition in a corona discharge-jet expansion process. Ab initio calculations were carried out by employing Gaussian 98 program, which gave optimized structures, binding energies, and wave numbers of the symmetric bending mode of the solvent ammonia molecule. Effects of the stagnation pressure of reactant gas and the diameter of the gas expanding pinhole were examined on the size distribution of NH4+·nNH3. It was found that the cluster size n in NH4+·nNH3 increased by one or remained unchanged in the jet expansion process. Effects of discharge current, the pinhole diameter and flight time were examined on the decomposition rate of the ammonia cluster ions. It was deduced that the internal energies of the cluster were mainly determined by the reactions involved in the cluster formation or decomposition. (author)
International Nuclear Information System (INIS)
We have studied the correlation between chemical composition, structure, chemical bonding and elastic properties of amorphous B6O based solids using ab initio molecular dynamics. These solids are of different chemical compositions, but the elasticity data appear to be a function of density. This is in agreement with previous experimental observations. As the density increases from 1.64 to 2.38 g cm-3, the elastic modulus increases from 74 to 253 GPa. This may be understood by analyzing the cohesive energy and the chemical bonding of these compounds. The cohesive energy decreases from -7.051 to -7.584 eV/atom in the elastic modulus range studied. On the basis of the electron density distributions, Mulliken analysis and radial distribution functions, icosahedral bonding is the dominating bonding type. C and N promote cross-linking of icosahedra and thus increase the density, while H hinders the cross-linking by forming OH groups. The presence of icosahedral bonding is independent of the density
Sub-monolayers of carbon on alpha-iron facets: an ab-initio study
Riikonen, S; Nieminen, R M
2010-01-01
Motivated by recent in situ studies of carbon nanotube growth from large transition-metal nanoparticles, we study various alpha-iron (ferrite) facets at different carbon concentrations using ab initio methods. The studied (110), (100) and (111) facets show qualitatively different behaviour when carbon concentration changes. In particular, adsorbed carbon atoms repel each other on the (110) facet, resulting in carbon dimer and graphitic material formation. Carbon on the (100) facet forms stable structures at concentrations of about 0.5 monolayer and at 1.0 monolayer this facet becomes unstable due to a frustration of the top layer iron atoms. The stability of the (111) facet is weakly affected by the amount of adsorbed carbon and its stability increases further with respect to the (100) facet with increasing carbon concentration. The exchange of carbon atoms between the surface and sub-surface regions on the (111) facet is easier than on the other facets and the formation of carbon dimers is exothermic. These ...
International Nuclear Information System (INIS)
The equilibrium lattice parameters, formation energy, and diffusion behavior of hydrogen atoms in vanadium hydrides with and without Ti substitution were calculated by ab initio calculations and quantum correction by zero point energy was achieved using phonon vibration calculations. The calculated formation energies indicated that Ti substitution induces instability in the vanadium hydrides and electron density calculations showed that hydrogen has strong electrochemical affinity with Ti. The diffusion behavior was examined by the nudged elastic band (NEB) method to investigate the transition states of the hydrides. It revealed that Ti substitution is shown to reduce the diffusion coefficient and this effect was decreased with increasing temperature. The results of this study are expected to provide useful guidelines for understanding hydrogen absorption and desorption properties of hydrogen storage materials. - Highlights: • Ti substitution expands any crystal structure of vanadium metal or hydride. • H atoms are repulsed by Ti atoms despite their high electrochemical affinity. • Strong electrochemical bonding between Ti and H lowers the formation energy. • Ti substitution reduces hydrogen diffusion by over 90% at room temperature
Ab initio Calculations of Electron-Impact Excitation Cross Sections for N2 Molecule
International Nuclear Information System (INIS)
One of the great difficulties in understanding nitrogen plasma elementary processes is the lack of an available database of the cross-sections of electron-impact excitations and radiations. Ab initio calculations of vibrational excitation cross sections for electron collisions with nitrogen molecules in low-lying states using similarity function approach, such as a-a', a-w, B-B' and B-W transition systems, are reported here for the first time. In the meantime, the average excitation energies of neighboring levels of these systems have been calculated. In order to obtain the cross sections, accurate spectroscopic constants and transition dipole moments have been investigated. Potential energy curves and other electronic transition dipole moments for the low-lying states of N2 have been re-evaluated using complete active space self-consistent field (CASSCF) approach with aug-cc-pVqZ basis set. The calculated cross-sections could provide a database for studying the elementary processes and the properties in N2 plasma. (low temperature plasma)
Ti adatom diffusion on TiN(001): Ab initio and classical molecular dynamics simulations
Sangiovanni, D. G.; Edström, D.; Hultman, L.; Petrov, I.; Greene, J. E.; Chirita, V.
2014-09-01
Ab initio and classical molecular dynamics (AIMD and CMD) simulations reveal that Ti adatoms on TiN(001) surfaces migrate between neighboring fourfold hollow sites primarily along in-plane channels. and single jumps, as well as double jump rates, obtained directly from MD runs as a function of temperature, are used to determine diffusion activation energies Ea, and attempt frequencies A, for the three preferred Ti adatom migration pathways on TiN(001). From transition rates Aexp[- Ea / (kBT)], we determine adatom surface distribution probabilities as a function of time, which are used to calculate adatom diffusion coefficients Ds(T). AIMD and CMD predictions are consistent and complementary. Using CMD, we investigate the effect on the adatom jump rate of varying the phonon wavelength degrees of freedom by progressively increasing the supercell size. We find that long-wavelength phonons significantly contribute to increasing adatom mobilities at temperatures ? 600 K, but not at higher temperatures. Finally, by directly tracking the Ti adatom mean-square displacement during CMD runs, we find that Ti adatom jumps are highly correlated on TiN(001), an effect that yields lower Ds values (Dscorr) than those estimated from uncorrelated transition probabilities. The temperature-dependent diffusion coefficient is Dscorr (T) = (4.5 × 10- 4 cm2 s- 1) exp[- 0.55 eV / (kBT)].
All electron ab initio investigations of the electronic states of the FeC molecule
DEFF Research Database (Denmark)
Shim, Irene; Gingerich, Karl A.
1999-01-01
The low lying electronic states of the molecule FeC have been investigated by performing all electron ab initio multi-configuration self-consistent-field (CASSCF) and multi reference configuration interaction (MRCI) calculations. The relativistic corrections for the one electron Darwin contact term and the relativistic mass-velocity correction have been determined in perturbation calculations. The electronic structure of the FeC molecule is interpreted as antiferromagnetic couplings of the localized angular momenta of the ions Fe+ and C resulting in a triple bond in the valence bond sense. The electronic ground state is confirmed as being 3 . The spectroscopic constants for the ground state and eleven excited states have been derived from the results of the MRCI calculations. The spectroscopic constants for the 3 ground state have been determined as re = 1.585 Å and e = 859 cm-1, and for the low-lying 1 state as re = 1.567 Å and e = 952 cm-1. The values for the ground state agree well with the available experimental data. The FeC molecule is polar with charge transfer from Fe to C. The dipole moment has been determined as 1.86 D in the 3 ground state and as 1.51 D in the 1 state. From the results of the MRCI calculations the dissociation energy, De, is determined as 2.79 eV, and D0 as 2.74 eV.
Laser spectroscopy and ab initio studies of metal-containing free radicals
Greetham, G M
2000-01-01
strontium-containing free radical is reported, that of SrCCH. This new excited electronic state is accessed by the orbitally-forbidden B-tilde' sup 2 DELTA-X-tilde sup 2 SIGMA sup + transition. Spin-orbit and vibrational structure have been seen in spectra of SrCCH and SrCCD and confirmed the assignment. Finally, observation of a new transition in an unidentified gallium-containing molecule is reported. Two progressions corresponding to two different vibrational modes of the molecule are seen in the spectrum. Potential spectral carriers, including Ga sub x clusters and other gallium-containing molecules formed by reaction with impurities, are discussed in an attempt to explain the observed spectrum. This work describes the use of laser spectroscopy and ab initio calculations in the investigation of several new electronic transitions in metal-containing free radicals. These free radicals were prepared in a supersonic jet by laser ablation of solid metal samples in the presence of appropriate precursor molecule...
Ab Initio Studies of the Unreconstructed Polar CdTe (111) Surface
Li, Jin; Gayles, Jacob; Kioussis, Nicholas; Zhang, Z.; Grein, C.; Aqariden, F.
2012-10-01
Ab initio electronic structure calculations were carried out for bulk cadmium telluride (CdTe) and the unreconstructed CdTe polar (111) Cd-terminated and ( bar{1}bar{1}bar{1} ) Te-terminated surfaces. The hybrid functional for the exchange and correlation potential improves the overall description of the electronic structure of bulk CdTe, by lowering Cd 4d states and hence reducing the Cd 4d-Te 5p hybridization. The Cd-Te interlayer distance of the Cd-terminated surface exhibits a dramatic contraction in contrast with the expansion of the Te-terminated surface, and the surface relaxations decrease as the slab thickness increases. The underlying mechanism of the convergence of the electrostatic potential energy, work function, and electric dipole moment of the polar surfaces as a function of slab thickness is surface electron rearrangement leading to charge transfer from the Te- to the Cd-terminated surfaces. The surface electric polarization induces an internal electric field in the slab, which in turn tilts the bands of the slab double layers, thus rendering the surface layers metallic. The electric field decreases with increasing slab thickness due to convergence of the difference of electrostatic potentials between the Cd- and Te-terminated surfaces.
Energy Technology Data Exchange (ETDEWEB)
Giuliani, A. [Synchrotron Soleil, DISCO beamline, L' Orme des Merisiers, 91 - Gif-sur-Yvette (France); Giuliani, A. [Cepia, Institut National de la Recherche Agronomique (INRA), 44 - Nantes (France); Limiao-Vieira, P. [Lisboa Univ. Nova, Lab. de Colisoes Atomicas e Moleculares, CEFITEC, Dept. de Fysica, Caparica (Portugal); Limao-Vieira, P.; Mason, N. [Open Univ., Centre of Molecular and Optical Sciences, Dept. of Physics and Astronomy, Milton Keynes, MK (United Kingdom); Duflot, D. [Lille Univ. des Sciences et Technologies, Lab. de Physique des Lasers, Atomes et Molecules (PhLAM), UMR CNRS 8523, Centre d' Etudes et de Recherches Lasers et Applications, CERLA, FR CNRS 2416, 59 - Villeneuve d' Ascq (France); Milosavljevic, A.R.; Marinkovic, B.P. [Laboratory for atomic collision processes, Institute of Physics, Belgrade, Serbia (Yugoslavia); Hoffmann, S.V. [Aarhus Univ., Institute for Storage Ring Facilities (Denmark); Delwiche, J.; Hubin-Franskin, M.J. [Liege Univ., Laboratoire de Spectroscopie d' Electrons Diffuses, Institut de Chimie (Belgium)
2009-01-15
The electronic spectroscopy of isolated tetrahydrofuran (THF) in the gas phase has been investigated using high-resolution photoabsorption spectroscopy in the 5.8 - 10.6 eV with absolute cross-section measurements derived. In addition, an electron energy loss spectrum was recorded at 100 eV and 10 degrees over the 5 - 11.4 eV range. The He(I) photoelectron spectrum was also collected to quantify ionisation energies in the 9 - 16.1 eV spectral region. These experiments are supported by the first high-level ab initio calculations performed on the excited states of the neutral molecule and on the ground state of the positive ion. The excellent agreement between the theoretical results and the measurements allows us to solve several discrepancies concerning the electronic state spectroscopy of THF. The present work reconsiders the question of the lowest energy conformers of the molecule and its population distribution at room temperature. (authors)
A nonlocal, ab initio model of dissociative electron attachment and vibrational excitation of NO
Energy Technology Data Exchange (ETDEWEB)
Trevisan, Cynthia S.; Houfek, Karel; Zhang, Zhiyong; Orel, Ann E.; McCurdy, C. William; Rescigno, Thomas N.
2005-02-01
We present the results of an ab initio study of elastic scattering and vibrational excitation of NO by electron impact in the low-energy (0-2 eV) region where the cross sections are dominated by resonance contributions. The 3Sigma-, 1Delta and 1Sigma+ NO- resonance lifetimes are taken from our earlier study [Phys. Rev. A 69, 062711 (2004)], but the resonance energies used here are obtained from new configuration-interaction studies. Here we employ a more elaborate nonlocal treatment of the nuclear dynamics, which is found to remedy the principal deficiencies of the local complex potential model we employed in our earlier study, and gives cross sections in better agreement with the most recent experiments. We also present cross sections for dissociative electron attachment to NO leading to groundstate products. The calculations show that, while the peak cross sections starting from NO in its ground vibrational state are very small, the cross sections are extremely sensitive to vibrational excitation of the target and should be readily observable for target NO molecules excited to v = 10 and above.
Vuilleumier, R; Guillot, B
2011-01-01
The structure around oxygen atoms of four silicate liquids (silica, rhyolite, a model basalt and enstatite) is evaluated by ab initio molecular dynamics simulation. Thanks to the use of maximally localized Wannier orbitals to represent the electronic ground state of the simulated system, one is able to quantify the redistribution of electronic density around oxygen atoms as a function of the cationic environment and melt composition. It is shown that the structure of the melt in the immediate vicinity of the oxygen atoms modulates the distribution of the Wannier orbitals associated with oxygen atoms. In particular the evaluation of the distances between the oxygen-core and the orbital Wannier centers and their evolution with the nature of the cation indicates that the Al-O bond in silicate melts is certainly less covalent than the Si-O bond while for the series Mg-O, Ca-O, Na-O and K-O the covalent character of the M-O bond diminishes rapidly to the benefit of the ionic character. Furthermore it is found that...
Ferromagnetic ordering of Cr and Fe doped p-type diamond: An ab initio study
International Nuclear Information System (INIS)
Ferromagnetic ordering of transition metal dopants in semiconductors holds the prospect of combining the capabilities of semiconductors and magnetic systems in single hybrid devices for spintronic applications. Various semiconductors have so far been considered for spintronic applications, but low Curie temperatures have hindered room temperature applications. We report ab initio DFT calculations on the stability and magnetic properties of Fe and Cr impurities in diamond, and show that their ground state magnetic ordering and stabilization energies depend strongly on the charge state and type of co-doping. We predict that divacancy Cr+2 and substitutional Fe+1 order ferromagnetically in p-type diamond, with magnetic stabilization energies (and magnetic moment per impurity ion) of 16.9 meV (2.5 ?B) and 33.3 meV (1.0 ?B), respectively. These magnetic stabilization energies are much larger than what has been achieved in other semiconductors at comparable impurity concentrations, including the archetypal dilute magnetic semiconductor GaAs:Mn. In addition, substitutional Fe+1 exhibits a strong half-metallic character, with the Fermi level crossing bands in only the spin down channel. These results, combined with diamond’s extreme properties, demonstrate that Cr or Fe dopedp-type diamond may successfully be considered in the search for room temperature spintronic materials
How Is Acetylcholinesterase Phosphonylated by Soman? An Ab Initio QM/MM Molecular Dynamics Study
2015-01-01
Acetylcholinesterase (AChE) is a crucial enzyme in the cholinergic nerve system that hydrolyzes acetylcholine (ACh) and terminates synaptic signals by reducing the effective concentration of ACh in the synaptic clefts. Organophosphate compounds irreversibly inhibit AChEs, leading to irreparable damage to nerve cells. By employing Born–Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling, a state-of-the-art approach to simulate enzyme reactions, we have characterized the covalent inhibition mechanism between AChE and the nerve toxin soman and determined its free energy profile for the first time. Our results indicate that phosphonylation of the catalytic serine by soman employs an addition–elimination mechanism, which is highly associative and stepwise: in the initial addition step, which is also rate-limiting, His440 acts as a general base to facilitate the nucleophilic attack of Ser200 on the soman’s phosphorus atom to form a trigonal bipyrimidal pentacovalent intermediate; in the subsequent elimination step, Try121 of the catalytic gorge stabilizes the leaving fluorine atom prior to its dissociation from the active site. Together with our previous characterization of the aging mechanism of soman inhibited AChE, our simulations have revealed detailed molecular mechanistic insights into the damaging function of the nerve agent soman. PMID:24786171