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Sample records for ab initio predictions

  1. Ab Initio Protein Structure Prediction Using Pathway Models

    Christopher Bystroff

    2006-04-01

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

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

    Spencer, Matt; Eickholt, Jesse; Cheng, Jianlin

    2014-01-01

    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% 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 atte...

  3. Predicting materials for solar energy conversion: ab-initio spectroscopy of heterogeneous interfaces

    Galli, Giulia

    We will discuss some progress in predicting materials for solar energy conversion using ab initio calculations, in particular we will focus on heterogeneous interfaces between photo-electrodes and water and between nanocomposites. We will also address the problem of building much needed tighter connections between computational and laboratory experiments.

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

    Binosi, Daniele; Papavassiliou, Joannis; Roberts, Craig D

    2014-01-01

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

  5. Prediction of adsorption of small molecules in porous materials based on ab initio force field method

    2008-01-01

    Computational prediction of adsorption of small molecules in porous materials has great impact on the basic and applied research in chemical engineering and material sciences. In this work,we report an approach based on grand canonical ensemble Monte Carlo(GCMC) simulations and ab initio force fields. We calculated the adsorption curves of ammonia in ZSM-5 zeolite and hydrogen in MOF-5(a metal-organic-framework material). The predictions agree well with experimental data. Because the predictions are based on the first principle force fields,this approach can be used for the adsorption prediction of new molecules or materials without experimental data as guidance.

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

    Jepsen, Peter Uhd; Clark, Stewart J.

    2007-01-01

    We use a combination of experimental THz time-domain spectroscopy and ab-initio density functional perturbative theory to accurately predict the terahertz vibrational spectrum of molecules in the crystalline phase. Our calculations show that distinct vibrational modes found in solid-state materials...... are best described as phonon modes with strong coupling to the intramolecular degrees of freedom. Hence a computational method taking the periodicity of the crystal lattice as well as intramolecular motion into account is a prerequisite for the correct prediction of vibrational modes in such materials....

  7. 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.

  8. Novel high-pressure phase of ZrO{sub 2}: An ab initio prediction

    Durandurdu, Murat, E-mail: murat.durandurdu@agu.edu.tr

    2015-10-15

    The high-pressure behavior of the orthorhombic cotunnite type ZrO{sub 2} is explored using an ab initio constant pressure technique. For the first time, a novel hexagonal phase (Ni{sub 2}In type) within P6{sub 3}/mmc symmetry is predicted through the simulation. The Ni{sub 2}In type crystal is the densest high-pressure phase of ZrO{sub 2} proposed so far and has not been observed in other metal dioxides at high pressure before. The phase transformation is accompanied by a small volume drop and likely to occur around 380 GPa in experiment. - Graphical abstract: Post-cotunnite Ni{sub 2}In type hexagonal phase forms in zirconia at high pressure. - Highlights: • A post-cotunnite phase is predicted for ZrO{sub 2} through an ab initio simulation. • Cotunnite ZrO{sub 2} adopts the Ni{sub 2}In type structure at high pressure. • The Ni{sub 2}In type structure is the densest high-pressure phase of ZrO{sub 2} proposed so far. • The preferred mechanism in ZrO{sub 2} differs from the other metal dioxides.

  9. Novel high-pressure phase of ZrO2: An ab initio prediction

    The high-pressure behavior of the orthorhombic cotunnite type ZrO2 is explored using an ab initio constant pressure technique. For the first time, a novel hexagonal phase (Ni2In type) within P63/mmc symmetry is predicted through the simulation. The Ni2In type crystal is the densest high-pressure phase of ZrO2 proposed so far and has not been observed in other metal dioxides at high pressure before. The phase transformation is accompanied by a small volume drop and likely to occur around 380 GPa in experiment. - Graphical abstract: Post-cotunnite Ni2In type hexagonal phase forms in zirconia at high pressure. - Highlights: • A post-cotunnite phase is predicted for ZrO2 through an ab initio simulation. • Cotunnite ZrO2 adopts the Ni2In type structure at high pressure. • The Ni2In type structure is the densest high-pressure phase of ZrO2 proposed so far. • The preferred mechanism in ZrO2 differs from the other metal dioxides

  10. Realization of prediction of materials properties by ab initio computer simulation

    Yoshiyuki Kawazoe

    2003-01-01

    Ab initio treatment is becoming realistic to predict physical, chemical, and even mechanical properties of academically and industrially interesting materials. There is, however, some limitation in size and time of the system up to the order of several hundred atoms and ∼ 1 pico second, even if we use the fastest supercomputer efficiently. Therefore, it is very difficult to simulate realistic materials with grain boundaries and important reactions like diffusion in materials. To improve this situation, two ways have been invented. One way is to upgrade approximations to match the necessary levels according to inhomogeneous electron gas theory beyond the present day standard, i.e. local density approximation (LDA). The reason is simply that the system we are interested in is composed of many particles interacting with Coulomb forces governed by quantum mechanics. (Complete knowledge is available, and only what we should do is to make better approximations to explain the phenomena!). Another is to extract the necessary parameters from the ab initio calculations on systems with limited number of atoms, and apply these results into cluster variation, direct, or any other sophisticated methods based on classical concepts such as statistical mechanics. In this paper, several typical examples recently worked out by our research group are introduced to indicate that these methodologies are actually possible to be successfully used to predict materials properties before experiments based on the present day state-of-art supercomputing systems. It includes scientific visualization of the results of ab initio molecular dynamics simulation on atom insertion process to C60 and to carbon nanotube, tight-binding calculation of single electron conductance properties in nanotube to create nano-scale diode virtually by computer, which will be a base of future nanoscale electric device in nanometer size, Li + H reaction without Born–Oppenheimer approximation, structural phase

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

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

    2013-01-01

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

  12. Ab initio prediction of electronic, transport and bulk properties of Li2S

    Malozovsky, Yuriy; Franklin, Lashounda; Ekuma, Chinedu; Bagayoko, Diola

    2015-08-01

    In this paper, we present results from ab initio, self-consistent, local density approximation (LDA) calculations of electronic and related properties of cubic antifluorite (anti-CaF2) lithium sulfide (Li2S). Our nonrelativistic computations implemented the linear combination of atomic orbital (LCAO) formalism following the Bagayoko, Zhao and Williams method, as enhanced by Ekuma and Franklin (BZW-EF). Consequently, using several self-consistent calculations with increasing basis sets, we searched for the smallest basis set that yields the absolute minima of the occupied energies. The outcomes of the calculation with this basis set, called the optimal basis set, have the full physical content of density functional theory (DFT). Our calculated indirect band gap, from Γ to X, is 3.723 eV, for the low temperature experimental lattice constant of 5.689 Å. The predicted indirect band gap of 3.702 eV is obtained for the computationally determined equilibrium lattice constant of 5.651 Å. We have also calculated the total density of states (DOS) and partial densities of states (pDOS), electron and hole effective masses and the bulk modulus of Li2S. Due to a lack of experimental results, most of the calculated ones reported here are predictions for this material suspected of exhibiting a high temperature superconductivity similar to that of MgB2.

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

    Martin Alberto JM

    2009-01-01

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

  14. Optimizing weights of protein energy function to improve ab initio protein structure prediction

    Wang, Chao; Liu, Juntao; Zhang, Haicang; Ling, Bin; Li, Shuai Cheng; Zheng, Wei-Mou; Bu, Dongbo

    2013-01-01

    Predicting protein 3D structure from amino acid sequence remains as a challenge in the field of computational biology. If protein structure homologues are not found, one has to construct 3D structural conformations from the very beginning by the so-called ab initio approach, using some empirical energy functions. A successful algorithm in this category, Rosetta, creates an ensemble of decoy conformations by assembling selected best short fragments of known protein structures and then recognizes the native state as the highly populated one with a very low energy. Typically, an energy function is a combination of a variety of terms characterizing different structural features, say hydrophobic interactions, van der Waals force, hydrogen bonding, etc. It is critical for an energy function to be capable to distinguish native-like conformations from non-native ones and to drive most initial conformations assembled from fragments to a native-like one in a conformation search process. In this paper we propose a linea...

  15. Predictive Nuclear Many-Body Theory with Ab Initio Methods: A Brief Survey and A Look Ahead

    Hergert, Heiko

    2015-10-01

    The reach of ab initio many-body techniques has increased tremendously in recent years, owing to new developments in many-body theory as well as advances in their numerical implementation. Coupled Cluster, Self-Consistent Green's Function, and In-Medium Similarity Renormalization Group (IM-SRG) calculations are routinely performed for isotopes in the A ~ 100 region. Moreover, these techniques have been extended to tackle open-shell nuclei, either directly or through the auxiliary step of deriving valence-space interactions for use with existing Shell Model technology. One of the most powerful aspects of ab initio methods is their capability to provide results for energies and other observables with systematic uncertainties. Together with new accurate nuclear forces (and operators) derived from Chiral Effective Field Theory, they provide a consistent framework--and a road map--for a predictive description of nuclei. This will have a critical impact on the search for the limits of nuclear existence, tests of fundamental symmetries (e.g., the search for neutrinoless double beta decay), our understanding of quenching and effective charges in phenomenological Shell Model calculations etc. Using the Multi-Reference IM-SRG as a representative example, I will survey the current capabilities of ab initio methods with an emphasis on uncertainty quantification, highlight successes in the description of ground-state properties and spectra, and preview upcoming developments like the construction of consistent transition operators.

  16. Vibronic spectra predictions for open shell molecules - usefulness and limitations of ab initio calculations, assessed on alkali trimers

    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)

  17. Ab-Initio Molecular Dynamics

    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.

  18. Reactive wetting properties of TiO2 nanoparticles predicted by ab initio molecular dynamics simulations

    Brandt, Erik G.; Agosta, Lorenzo; Lyubartsev, Alexander P.

    2016-07-01

    Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity.Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity. Electronic supplementary information (ESI) available: Simulation data on equilibration of energies and structures (root-mean-square-deviations and

  19. Ab-Initio Description and Prediction of Properties of Carbon-Based and Other Non-Metallic Materials

    Bagayoko, D.; Zhao, G. L.; Hasan, S.

    2001-01-01

    We have resolved the long-standing problem consisting of 30%-50% theoretical underestimates of the band gaps of non-metallic materials. We describe the Bagayoko, Zhao, and Williams (BZW) method that rigorously circumvents the basis-set and variational effect presumed to be a cause of these underestimates. We present ab-initio, computational results that are in agreement with experiment for diamond (C), silicon (Si), silicon carbides (3C-SiC and 4H-SiC), and other semiconductors (GaN, BaTiO3, AlN, ZnSe, ZnO). We illustrate the predictive capability of the BZW method in the case of the newly discovered cubic phase of silicon nitride (c-Si3N4) and of selected carbon nanotabes [(10,0), and (8,4)]. Our conclusion underscores the inescapable need for the BZW method in ab-initio calculations that employ a basis set in a variational approach. Current nanoscale trends amplify this need. We estimate that the potential impact of applications of the BZW method in advancing our understanding of nonmetallic materials, in informing experiment, and particularly in guiding device design and fabrication is simply priceless.

  20. Ab initio RNA folding

    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding. (topical review)

  1. Ab initio RNA folding

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-01

    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.

  2. Semi-empirical correction of ab initio harmonic properties by scaling factors: a validated uncertainty model for calibration and prediction

    Pernot, Pascal

    2010-01-01

    Bayesian Model Calibration is used to revisit the problem of scaling factor calibration for semi-empirical correction of ab initio harmonic properties (e.g. vibrational frequencies and zero-point energies). A particular attention is devoted to the evaluation of scaling factor uncertainty, and to its effect on the accuracy of scaled properties. We argue that in most cases of interest the standard calibration model is not statistically valid, in the sense that it is not able to fit experimental calibration data within their uncertainty limits. This impairs any attempt to use the results of the standard model for uncertainty analysis and/or uncertainty propagation. We propose to include a stochastic term in the calibration model to account for model inadequacy. This new model is validated in the Bayesian Model Calibration framework. We provide explicit formulae for prediction uncertainty in typical limit cases: large and small calibration sets of data with negligible measurement uncertainty, and datasets with la...

  3. Prediction of possible CaMnO3 modifications using an ab initio minimization data-mining approach.

    Zagorac, Jelena; Zagorac, Dejan; Zarubica, Aleksandra; Schön, J Christian; Djuris, Katarina; Matovic, Branko

    2014-10-01

    We have performed a crystal structure prediction study of CaMnO3 focusing on structures generated by octahedral tilting according to group-subgroup relations from the ideal perovskite type (Pm\\overline 3 m), which is the aristotype of the experimentally known CaMnO3 compound in the Pnma space group. Furthermore, additional structure candidates have been obtained using data mining. For each of the structure candidates, a local optimization on the ab initio level using density-functional theory (LDA, hybrid B3LYP) and the Hartree--Fock (HF) method was performed, and we find that several of the modifications may be experimentally accessible. In the high-pressure regime, we identify a post-perovskite phase in the CaIrO3 type, not previously observed in CaMnO3. Similarly, calculations at effective negative pressure predict a phase transition from the orthorhombic perovskite to an ilmenite-type (FeTiO3) modification of CaMnO3. PMID:25274514

  4. Prediction of B1 to B10 phase transition in LuN under pressure: An ab-initio investigation

    Sahoo, B. D.; Mukherjee, D.; Joshi, K. D.; Kaushik, T. C.; Gupta, Satish C.

    2016-05-01

    Ab-initio total energy calculations have been performed in lutetium nitride (LuN) as a function of hydrostatic compression to understand the high pressure behavior of this compound. Our calculations predict a phase transition from ambient rocksalt type structure (B1 phase) to a tetragonal structure (B10 phase) at ~ 240 GPa. The phase transition has been identified as first order in nature with volume discontinuity of ~ 6%. The predicted high pressure phase has been found to be stable up to at least 400 GPa, the maximum pressure up to which calculations have been performed.Further, to substantiate the results of static lattice calculations analysis of lattice dynamic stability of B1 and B10 phase has been carried out at different pressures. Apart from this, we have analyzed the lattice dynamic stability CsCl type (B2) phase around the 240 GPa, the pressure reported for B1 to B2 transition in previous all-electron calculations by Gupta et al. 2013. We find that the B2 structure is lattice dynamically unstable at this pressure and remains unstable up to ~ 400 GPa, ruling out the possibility of B1 to B2 phase transition at least up to ~ 400 GPa. Further, the theoretically determined equation of state has been utilized to derive various physical quantities such as zero pressure equilibrium volume, bulk modulus, and pressure derivative of bulk modulus of B1 phase at ambient conditions.

  5. Accuracy of ab initio methods in predicting the crystal structures of metals: review of 80 binary alloys

    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...

  6. Guiding ab initio calculations by alchemical derivatives

    to Baben, M.; Achenbach, J. O.; von Lilienfeld, O. A.

    2016-03-01

    We assess the concept of alchemical transformations for predicting how a further and not-tested change in composition would change materials properties. This might help to guide ab initio calculations through multidimensional property-composition spaces. Equilibrium volumes, bulk moduli, and relative lattice stability of fcc and bcc 4d transition metals Zr, Nb, Mo, Tc, Ru, Rh, Pd, and Ag are calculated using density functional theory. Alchemical derivatives predict qualitative trends in lattice stability while equilibrium volumes and bulk moduli are predicted with less than 9% and 28% deviation, respectively. Predicted changes in equilibrium volume and bulk moduli for binary and ternary mixtures of Rh-Pd-Ag are in qualitative agreement even for predicted bulk modulus changes as large as +100% or -50%. Based on these results, it is suggested that alchemical transformations could be meaningful for enhanced sampling in the context of virtual high-throughput materials screening projects.

  7. Ab initio prediction of equilibrium boron isotope fractionation between minerals and aqueous fluids at high P and T

    Kowalski, Piotr M.; Wunder, Bernd; Jahn, Sandro

    2013-01-01

    Over the last decade experimental studies have shown a large B isotope fractionation between materials carrying boron incorporated in trigonally and tetrahedrally coordinated sites, but the mechanisms responsible for producing the observed isotopic signatures are poorly known. In order to understand the boron isotope fractionation processes and to obtain a better interpretation of the experimental data and isotopic signatures observed in natural samples, we use first principles calculations based on density functional theory in conjunction with ab initio molecular dynamics and a new pseudofrequency analysis method to investigate the B isotope fractionation between B-bearing minerals (such as tourmaline and micas) and aqueous fluids containing HBO and HBO4- species. We confirm the experimental finding that the isotope fractionation is mainly driven by the coordination of the fractionating boron atoms and have found in addition that the strength of the produced isotopic signature is strongly correlated with the Bsbnd O bond length. We also demonstrate the ability of our computational scheme to predict the isotopic signatures of fluids at extreme pressures by showing the consistency of computed pressure-dependent β factors with the measured pressure shifts of the Bsbnd O vibrational frequencies of HBO and HBO4- in aqueous fluid. The comparison of the predicted with measured fractionation factors between boromuscovite and neutral fluid confirms the existence of the admixture of tetrahedral boron species in neutral fluid at high P and T found experimentally, which also explains the inconsistency between the various measurements on the tourmaline-mica system reported in the literature. Our investigation shows that the calculated equilibrium isotope fractionation factors have an accuracy comparable to the experiments and give unique and valuable insight into the processes governing the isotope fractionation mechanisms on the atomic scale.

  8. The pure rotational spectrum of ruthenium monocarbide, RuC, and relativistic ab initio predictions

    Wang, Fang; Steimle, Timothy C.; Adam, Allan G. [Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604 (United States); Cheng, Lan; Stanton, John F. [Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712 (United States)

    2013-11-07

    The J = 1 ← J = 0 and J = 2 ← J = 1 rotational transitions of ruthenium monocarbide, RuC, have been recorded using the separated field pump/probe microwave optical double resonance technique and analyzed to determine the fine and hyperfine parameters for the X{sup 1}Σ{sup +} state. The {sup 101}Ru(I = 5/2) electric quadrupole parameter, eq{sub 0}Q, and nuclear spin-rotation interaction parameter, C{sub I}{sup eff}, were determined to be 433.19(8) MHz and −0.049(6) MHz, respectively. The equilibrium bond distance, r{sub e}, was determined to be 1.605485(2) Å. Hartree-Fock and coupled-cluster calculations were carried out for the properties of the X{sup 1}Σ{sup +} state. Electron-correlation effects are pronounced for all properties studied. It is shown that (a) the moderate scalar-relativistic contribution to eq{sub 0}Q is entirely due to the coupling between scalar-relativistic and electron-correlation effects, (b) the spin-free exact two-component theory in its one-electron variant offers a reliable and efficient treatment of scalar-relativistic effects, and (c) non-relativistic theory performs quite well for the prediction of C{sub I}{sup elec}, provided that electron correlation is treated accurately.

  9. Oxidation- and organic-molecule-induced changes of the Si surface optical anisotropy: ab initio predictions

    In the last couple of years there has been much methodological and computational progress in the modelling of optical properties from first principles. Reflectance anisotropy spectra (RAS) can now be calculated with true predictive power and can thus be used to draw conclusions directly on the surface geometry. In the present work we study two potentially very interesting applications for RAS: the oxidation of Si(001) and the functionalization of the Si surface with organic molecules. Our calculations confirm experimental indications that the polarity of the interface-induced optical anisotropy is reversed layer by layer with increasing oxide thickness. The oscillation of the RAS amplitude should thus allow for the quantitative monitoring of the vertical progression of the oxidation. Our results for Si(001) surfaces modified by cyclopentene and 9,10-phenanthrenequinone adsorption show a strong sensitivity of the RAS signal with respect to the adsorption geometry. Comparison with experimental data shows that cyclopentene most probably adsorbs via a cycloaddition reaction with the Si surface dimers, while phenanthrenequinone seems to adsorb across two Si dimers

  10. Use of ab initio quantum chemical methods in battery technology

    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.

  11. 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

  12. Ab initio prediction of equilibrium boron isotope fractionation between minerals and aqueous fluids at high P and T

    Kowalski, Piotr M; Jahn, Sandro

    2012-01-01

    Over the last decade experimental studies have shown a large B isotope fractionation between materials carrying boron incorporated in trigonally and tetrahedrally coordinated sites, but the mechanisms responsible for producing the observed isotopic signatures are poorly known. In order to understand the boron isotope fractionation processes and to obtain a better interpretation of the experimental data and isotopic signatures observed in natural samples, we use first principles calculations based on density functional theory in conjunction with ab initio molecular dynamics and a new pseudofrequency analysis method to investigate the B isotope fractionation between B-bearing minerals (such as tourmaline and micas) and aqueous fluids containing H_3BO_3 and H_4BO_4- species. We confirm the experimental finding that the isotope fractionation is mainly driven by the coordination of the fractionating boron atoms and have found in addition that the strength of the produced isotopic signature is strongly correlated w...

  13. Towards new horizons in ab initio nuclear structure theory

    We review recent advances in ab initio nuclear structure theory, which have changed the horizons of this field. Starting from chiral effective field theory to construct the nuclear Hamiltonian and the similarity renormalization group to further soften it, we address several many-body approaches that have seen major developments over the past few years. We show that the domain of ab initio nuclear structure theory has been pushed well beyond the p-shell and that quantitative QCD-based predictions are becoming possible all the way from the proton to the neutron drip line up into the medium-mass regime. (authors)

  14. P-V Relation for Mercuric Calcogenides: Ab Initio Method

    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.

  15. Ab initio gene identification in metagenomic sequences.

    Zhu, Wenhan; Lomsadze, Alexandre; Borodovsky, Mark

    2010-07-01

    We describe an algorithm for gene identification in DNA sequences derived from shotgun sequencing of microbial communities. Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered by uncertainty in model parameters. While several machine learning approaches could be proposed to bypass this difficulty, one effective method is to estimate parameters from dependencies, formed in evolution, between frequencies of oligonucleotides in protein-coding regions and genome nucleotide composition. Original version of the method was proposed in 1999 and has been used since for (i) reconstructing codon frequency vector needed for gene finding in viral genomes and (ii) initializing parameters of self-training gene finding algorithms. With advent of new prokaryotic genomes en masse it became possible to enhance the original approach by using direct polynomial and logistic approximations of oligonucleotide frequencies, as well as by separating models for bacteria and archaea. These advances have increased the accuracy of model reconstruction and, subsequently, gene prediction. We describe the refined method and assess its accuracy on known prokaryotic genomes split into short sequences. Also, we show that as a result of application of the new method, several thousands of new genes could be added to existing annotations of several human and mouse gut metagenomes. PMID:20403810

  16. Ab initio mass tensor molecular dynamics

    Tsuchida, Eiji

    2010-01-01

    Mass tensor molecular dynamics was first introduced by Bennett [J. Comput. Phys. 19, 267 (1975)] for efficient sampling of phase space through the use of generalized atomic masses. Here, we show how to apply this method to ab initio molecular dynamics simulations with minimal computational overhead. Test calculations on liquid water show a threefold reduction in computational effort without making the fixed geometry approximation. We also present a simple recipe for estimating the optimal ato...

  17. Discovering chemistry with an ab initio nanoreactor

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

    2014-01-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerat...

  18. Ab initio vel ex eventu. II

    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.

  19. 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.

  20. Prediction of new stable structure, promising electronic and thermodynamic properties of MoS3: Ab initio calculations

    Pan, Yong; Guan, Weiming

    2016-09-01

    MoS3 has attracted considerable attention as potential hydrogen storage material due to the interaction between the hydrogen and unsaturated sulfur atoms. However, its structure and physical properties are unknown. By means of first-principles approach and Inorganic crystal structure Database (ISCD), we systematically investigated the structure, relevant physical and thermodynamic properties of MoS3. Phonon dispersion, electronic structure, band structure and heat capacity are calculated in detail. We predicted the orthorhombic B2ab (SrS3-type) and tetragonal P-421m (BaS3-type) structures of MoS3, which prefers to form the SrS3-type (Space group: B2ab, No.41) structure at the ground state. High pressure results in structural transition from SrS3-type structure to BaS3-type structure. This sulfide exhibits a degree of metallic behavior. The calculated heat capacity of MoS3 with SrS3-type structure is about of 39 J/(mol·K).

  1. Ab initio no core full configuration approach for light nuclei

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

    2015-10-01

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

  2. Germacrene D Cyclization: An Ab Initio Investigation

    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.

  3. Ab initio calculations of material strength

    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 ČR IAA1041302; GA ČR GA202/03/1351; GA MŠk OC 523.90 Institutional research plan: CEZ:AV0Z2041904 Keywords : ab initio calculations * electronic structure * theoretical tensile strength Subject RIV: BM - Solid Matter Physics ; Magnetism

  4. Ab Initio Molecular Dynamics: A Virtual Laboratory

    Hobbi Mobarhan, Milad

    2014-01-01

    In this thesis, we perform ab initio molecular dynamics (MD) simulations at the Hartree-Fock level, where the forces are computed on-the-fly using the Born-Oppenheimer approximation. The theory behind the Hartree-Fock method is discussed in detail and an implementation of this method based on Gaussian basis functions is explained. We also demonstrate how to calculate the analytic energy derivatives needed for obtaining the forces acting on the nuclei. Hartree-Fock calculations on the ground s...

  5. Ab Initio Nuclear Structure Theory: From Few to Many

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

  6. Understanding phonon transport in thermoelectric materials using ab initio approaches

    Broido, David

    Good thermoelectric materials have low phonon thermal conductivity, kph. Accurate theories to describe kph are important components in developing predictive models of thermoelectric efficiency that can help guide synthesis and measurement efforts. We have developed ab initio approaches to calculate kph, in which phonon modes and phonon scattering rates are computed using interatomic force constants determined from density functional theory, and a full solution of the Boltzmann transport equation for phonons is implemented. A recent approach to calculate interatomic force constants using ab initio molecular dynamics has yielded a good description of the thermal properties of Bi2Te3. But, the complexity of new promising candidate thermoelectric materials introduces computational challenges in assessing their thermal properties. An example is germanane, a germanium based hydrogen-terminated layered semiconductor, which we will discuss in this talk.

  7. Ab Initio No-Core Shell Model

    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

  8. Ab Initio No-Core Shell Model

    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 (χEFT) 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

  9. Ab initio non-relativistic spin dynamics

    Ding, Feizhi; Goings, Joshua J.; Li, Xiaosong, E-mail: xsli@uw.edu [Department of Chemistry, University of Washington, Seattle, Washington 98195 (United States); Frisch, Michael J. [Gaussian, Inc., 340 Quinnipiac St, Bldg 40, Wallingford, Connecticut 06492 (United States)

    2014-12-07

    Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li{sub 3} molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.

  10. Ab initio calculations of reactions with light nuclei

    Quaglioni, Sofia; Hupin, Guillaume; Calci, Angelo; Navrátil, Petr; Roth, Robert

    2016-03-01

    An 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 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 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 ranges.

  11. Kopplung von Dichtefunktional- und ab-initio-Methoden

    Goll, Erich

    2008-01-01

    Im Rahmen der Doktorarbeit wurde untersucht, inwieweit die Kopplung von Dichtefunktionalmethoden und ab-initio-Korrelationsmethoden der Quantenchemie eine Verbesserung bezüglich beider Grenzmethoden erbringt. Die Kopplung erfolgt durch eine Aufspaltung des interelektronischen Hamiltonoperators (abstoßende Coulombwechselwirkung). Die kurzreichweitige Wechselwirkung wird mit Dichtefunktionaltheorie behandelt, die langreichweitige mit Hilfe von ab-initio-Methoden. Diese Aufteilung soll dazu dien...

  12. 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.

  13. Ab Initio Path to Heavy Nuclei

    Binder, Sven; Calci, Angelo; Roth, Robert

    2014-01-01

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

  14. Operator evolution for ab initio nuclear theory

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

    2014-01-01

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

  15. Discovering chemistry with an ab initio nanoreactor

    Martinez, Todd

    Traditional approaches for modeling chemical reaction networks such as those involved in combustion have focused on identifying individual reactions and using theoretical approaches to explore the underlying mechanisms. Recent advances involving graphical processing units (GPUs), commodity products developed for the videogaming industry, have made it possible to consider a distinct approach wherein one attempts to discover chemical reactions and mechanisms. We provide a brief summary of these developments and then discuss the concept behind the ``ab initio nanoreactor'' which explores the space of possible chemical reactions and molecular species for a given stoichiometry. The nanoreactor concept is exemplified with an example to the Urey-Miller reaction network which has been previously advanced as a potential model for prebiotic chemistry. We briefly discuss some of the future directions envisioned for the development of this nanoreactor concept.

  16. Ab initio molar volumes and Gaussian radii.

    Parsons, Drew F; Ninham, Barry W

    2009-02-12

    Ab initio molar volumes are calculated and used to derive radii for ions and neutral molecules using a spatially diffuse model of the electron distribution with Gaussian spread. The Gaussian radii obtained can be used for computation of nonelectrostatic ion-ion dispersion forces that underlie Hofmeister specific ion effects. Equivalent hard-sphere radii are also derived, and these are in reasonable agreement with crystalline ionic radii. The Born electrostatic self-energy is derived for a Gaussian model of the electronic charge distribution. It is shown that the ionic volumes used in electrostatic calculations of strongly hydrated cosmotropic ions ought best to include the first hydration shell. Ionic volumes for weakly hydrated chaotropic metal cations should exclude electron overlap (in electrostatic calculations). Spherical radii are calculated as well as nonisotropic ellipsoidal radii for nonspherical ions, via their nonisotropic static polarizability tensors. PMID:19140766

  17. Ab initio alpha-alpha scattering.

    Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G

    2015-12-01

    Processes such as the scattering of alpha particles ((4)He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei--nuclei with even and equal numbers of protons and neutrons--is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the 'adiabatic projection method' to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of

  18. Ab initio alpha-alpha scattering

    Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A.; Luu, Thomas; Meißner, Ulf-G.

    2015-12-01

    Processes such as the scattering of alpha particles (4He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei—nuclei with even and equal numbers of protons and neutrons—is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the ‘adiabatic projection method’ to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of

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

    Tao, Kun

    2012-01-05

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

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

    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...... 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...

  1. On the hierarchical parallelization of ab initio simulations

    Ruiz-Barragan, Sergi; Shiga, Motoyuki

    2016-01-01

    A hierarchical parallelization has been implemented in a new unified code PIMD-SMASH for ab initio simulation where the replicas and the Born-Oppenheimer forces are parallelized. It is demonstrated that ab initio path integral molecular dynamics simulations can be carried out very efficiently for systems up to a few tens of water molecules. The code was then used to study a Diels-Alder reaction of cyclopentadiene and butenone by ab initio string method. A reduction in the reaction energy barrier is found in the presence of hydrogen-bonded water, in accordance with experiment.

  2. Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates

    Chaka, Anne M.; Felmy, Andrew R.

    2014-03-28

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

  3. Ab initio two-component Ehrenfest dynamics

    We present an ab initio two-component Ehrenfest-based mixed quantum/classical molecular dynamics method to describe the effect of nuclear motion on the electron spin dynamics (and vice versa) in molecular systems. The two-component time-dependent non-collinear density functional theory is used for the propagation of spin-polarized electrons while the nuclei are treated classically. We use a three-time-step algorithm for the numerical integration of the coupled equations of motion, namely, the velocity Verlet for nuclear motion, the nuclear-position-dependent midpoint Fock update, and the modified midpoint and unitary transformation method for electronic propagation. As a test case, the method is applied to the dissociation of H2 and O2. In contrast to conventional Ehrenfest dynamics, this two-component approach provides a first principles description of the dynamics of non-collinear (e.g., spin-frustrated) magnetic materials, as well as the proper description of spin-state crossover, spin-rotation, and spin-flip dynamics by relaxing the constraint on spin configuration. This method also holds potential for applications to spin transport in molecular or even nanoscale magnetic devices

  4. Ab-initio study of thermoelectricity of layered tellurium compounds

    Ibarra Hernández, Wilfredo

    2015-01-01

    In this thesis, we explore the electronic, dynamic and thermoelectric properties of different tellurium-based compounds. We perform ab-initio calculations within the Vienna Ab-initio Simulation Package (VASP) that works in the framework of Density Functional Theory (DFT). For the thermoelectric properties, we use the Boltztrap code that solves the Boltzmann Transport Equations (BTE) for electrons within the Constant Relaxation Time Approximation (CRTA). This computational pa...

  5. Toward ab initio density functional theory for nuclei

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

    2009-01-01

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

  6. Quantum chemical ab initio prediction of proton exchange barriers between CH4 and different H-zeolites.

    Tuma, Christian; Sauer, Joachim

    2015-09-14

    A hybrid MP2:DFT (second-order Møller-Plesset perturbation theory-density functional theory) method that combines MP2 calculations for cluster models with DFT calculations for the full periodic structure is used to localize minima and transition structures for proton jumps at different Brønsted sites in different frameworks (chabazite, faujasite, ferrierite, and ZSM-5) and at different crystallographic positions of a given framework. The MP2 limit for the periodic structures is obtained by extrapolating the results of a series of cluster models of increasing size. A coupled-cluster (CCSD(T)) correction to MP2 energies is calculated for cluster models consisting of three tetrahedra. For the adsorption energies, this difference is small, between 0.1 and 0.9 kJ/mol, but for the intrinsic proton exchange barriers, this difference makes a significant (10.85 ± 0.25 kJ/mol) and almost constant contribution across different systems. The total values of the adsorption energies vary between 22 and 34 kJ/mol, whereas the total proton exchange energy barriers fall in the narrow range of 152-156 kJ/mol. After adding nuclear motion contributions (harmonic approximation, 298 K), intrinsic enthalpy barriers between 134 and 141 kJ/mol and apparent energy barriers between 105 and 118 kJ/mol are predicted for the different sites examined for the different frameworks. These predictions are consistent with experimental results available for faujasite, ferrierite, and ZSM-5. PMID:26374003

  7. Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

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

    1995-01-01

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

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

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

    2011-10-12

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

  9. Ab initio calculations of grain boundaries in bcc metals

    Scheiber, Daniel; Pippan, Reinhard; Puschnig, Peter; Romaner, Lorenz

    2016-03-01

    In this study, we compute grain boundary (GB) properties for a large set of GBs in bcc transition metals with a special focus on W, Mo and Fe using ab initio density functional theory (DFT) and semi-empirical second nearest neighbour modified embedded atom method (2NN-MEAM) potentials. The GB properties include GB energies, surface energies, GB excess volume and work of separation, which we analyse and then compare to experimental data. We find that the used 2NN-MEAM potentials can predict general trends of GB properties, but do not always reproduce the GB ground state structure and energy found with DFT. In particular, our results explain the experimental finding that W and Mo prefer intergranular fracture, while other bcc metals prefer transgranular cleavage.

  10. Ab initio electronic stopping power of protons in bulk materials

    Shukri, Abdullah Atef; Bruneval, Fabien; Reining, Lucia

    2016-01-01

    The electronic stopping power is a crucial quantity for ion irradiation: it governs the deposited heat, the damage profile, and the implantation depth. Whereas experimental data are readily available for elemental solids, the data are much more scarce for compounds. Here we develop a fully ab initio computational scheme based on linear response time-dependent density-functional theory to predict the random electronic stopping power (RESP) of materials without any empirical fitting. We show that the calculated RESP compares well with experimental data, when at full convergence, with the inclusion of the core states and of the exchange correlation. We evaluate the unexpectedly limited magnitude of the nonlinear terms in the RESP by comparing with other approaches based on the time propagation of time-dependent density-functional theory. Finally, we check the validity of a few empirical rules of thumbs that are commonly used to estimate the electronic stopping power.

  11. Ab initio electronic structure and optical conductivity of bismuth tellurohalides

    Schwalbe, Sebastian; Starke, Ronald; Schober, Giulio A H; Kortus, Jens

    2016-01-01

    We investigate the electronic structure, dielectric and optical properties of bismuth tellurohalides BiTeX (X = I, Cl, Br) by means of all-electron density functional theory. In particular, we present the ab initio conductivities and dielectric tensors calculated over a wide frequency range, and compare our results with the recent measurements by Akrap et al. , Makhnev et al. , and Rusinov et al. . We show how the low-frequency branch of the optical conductivity can be used to identify characteristic intra- and interband transitions between the Rashba spin-split bands in all three bismuth tellurohalides. We further calculate the refractive indices and dielectric constants, which in turn are systematically compared to previous predictions and measurements. We expect that our quantitative analysis will contribute to the general assessment of bulk Rashba materials for their potential use in spintronics devices.

  12. Highly anisotropic thermal conductivity of arsenene: An ab initio study

    Zeraati, Majid; Vaez Allaei, S. Mehdi; Abdolhosseini Sarsari, I.; Pourfath, Mahdi; Donadio, Davide

    2016-02-01

    Elemental two-dimensional (2D) materials exhibit intriguing heat transport and phononic properties. Here we have investigated the lattice thermal conductivity of newly proposed arsenene, the 2D honeycomb structure of arsenic, using ab initio calculations. Solving the Boltzmann transport equation for phonons, we predict a highly anisotropic thermal conductivity of 30.4 and 7.8 W/mK along the zigzag and armchair directions, respectively, at room temperature. Our calculations reveal that phonons with mean free paths between 20 nm and 1 μ m provide the main contribution to the large thermal conductivity in the zigzag direction; mean free paths of phonons contributing to heat transport in the armchair directions range between 20 and 100 nm. The obtained anisotropic thermal conductivity and feasibility of synthesis, in addition to high electron mobility reported elsewhere, make arsenene a promising material for nanoelectronic applications and thermal management.

  13. Ab initio engineering of materials with stacked hexagonal tin frameworks

    Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.

    2016-01-01

    The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator. PMID:27387140

  14. Ab initio Potential Energy Surface for H-H2

    Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

    1993-01-01

    Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

  15. Ab initio simulation of transport phenomena in rarefied gases.

    Sharipov, Felix; Strapasson, José L

    2012-09-01

    Ab initio potentials are implemented into the direct simulation Monte Carlo (DSMC) method. Such an implementation allows us to model transport phenomena in rarefied gases without any fitting parameter of intermolecular collisions usually extracted from experimental data. Applying the method proposed by Sharipov and Strapasson [Phys. Fluids 24, 011703 (2012)], the use of ab initio potentials in the DSMC requires the same computational efforts as the widely used potentials such as hard spheres, variable hard sphere, variable soft spheres, etc. At the same time, the ab initio potentials provide more reliable results than any other one. As an example, the transport coefficients of a binary mixture He-Ar, viz., viscosity, thermal conductivity, and thermal diffusion factor, have been calculated for several values of the mole fraction. PMID:23030889

  16. 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.

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

    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.

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

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

    2015-01-01

    Roč. 73, AUG (2015), s. 127-158. ISSN 0079-6425 R&D Projects: GA ČR(CZ) GAP108/12/0311 Institutional support: RVO:68081723 Keywords : Ab initio methods * Elastic moduli * Intrinsic hardness * Stability analysis * Theoretical strength * Intrinsic brittleness/ductility Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 27.417, year: 2014

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

    Bak, Börge; Jansen, Peter; Stafast, Herbert

    1975-01-01

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

  20. Relaxation of Small Molecules: an ab initio Study

    CAO Yi-Gang; JIAO Zheng-Kuan; A. Antons; K. Schroeder; S. Blügel2

    2002-01-01

    Using an ab initio total energy and force method, we have relaxed several group IV and group V elementalclusters, in detail the arsenic and antimony dimers, silicon, phosphorus, arsenic and antimony tetramers. The obtainedbond lengths and cohesive energies are more accurate than other calculating methods, and in excellent agreement withthe experimental results.

  1. Ab initio study of phase equilibria in TiCx

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

    2002-01-01

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

  2. State of the art for ab initio vs empirical potentials for predicting 6e$^{-}$ excited state molecular energies: Application to Li$_{2}\\left(b,1^{3}\\Pi_{u}\\right)$

    Dattani, Nikesh S

    2015-01-01

    We build the first analytic empirical potential for the most deeply bound $\\mbox{Li}_{2}$ state: $b\\left(1^{3}\\Pi_{u}\\right)$. Our potential is based on experimental energy transitions covering $v=0-34$, and very high precision theoretical long-range constants. It provides high accuracy predictions up to $v=100$ which pave the way for high-precision long-range measurements, and hopefully an eventual resolution of the age old discrepancy between experiment and theory for the $\\mbox{Li}\\left(2^{2}S\\right)+\\mbox{Li}\\left(2^{2}P\\right)$ $C_{3}$ value. State of the art ab initio calculations predict vibrational energy spacings that are all in at most 0.8 cm$^{-1}$ disagreement with the empirical potential.

  3. Ab initio molecular dynamics calculations of ion hydration free energies

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

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

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

    2007-02-01

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

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

    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

  6. Serine Proteases an Ab Initio Molecular Dynamics Study

    De Santis, L

    1999-01-01

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

  7. 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...

  8. Ab-initio calculations on melting of thorium

    Mukherjee, D.; Sahoo, B. D.; Joshi, K. D.; Kaushik, T. C.; Gupta, Satish C.

    2016-05-01

    Ab-initio molecular dynamics study has been performed on face centered cubic structured thorium to determine its melting temperature at room pressure. The ion-electron interaction potential energy calculated as a function of temperature for three volumes (a0)3 and (1.02a0)3 and (1.04a0)3 increases gradually with temperature and undergoes a sharp jump at ~2200 K, ~2100 K and ~1800 K, respectively. Here, a0 = 5.043 Å is the equilibrium lattice parameter at 0 K obtained from ab-initio calculations. These jumps in interaction energy are treated as due to the onset of melting and corresponding temperatures as melting point. The melting point of 2100 K is close to the experimental value of 2023K. Further, the same has been verified by plotting the atomic arrangement evolved at various temperatures and corresponding pair correlation functions.

  9. Ab initio evaluations of the He solubility in liquid Li

    Sedano, Luis A. [EURATOM-CIEMAT Assoc., Materials for Fusion Program, Bd. 43 P0.04, Avda. Complutense 22, 28040 Madrid (Spain)]. E-mail: luis.sedano@ciemat.es; Hassanein, Ahmed [Argonne Nat. Lab, 9700 South Class Av., Argonne, IL (United States)]. E-mail: hassanein@anl.gov; Sanz, Javier [ETSII-UNED, c/Juan del Rosal, 12, 28040 Madrid (E) (Spain)]. E-mail: jsanz@ind.UNED.es

    2005-11-15

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

  10. Engineering Room-temperature Superconductors Via ab-initio Calculations

    Gulian, Mamikon; Melkonyan, Gurgen; Gulian, Armen

    The BCS, or bosonic model of superconductivity, as Little and Ginzburg have first argued, can bring in superconductivity at room temperatures in the case of high-enough frequency of bosonic mode. It was further elucidated by Kirzhnitset al., that the condition for existence of high-temperature superconductivity is closely related to negative values of the real part of the dielectric function at finite values of the reciprocal lattice vectors. In view of these findings, the task is to calculate the dielectric function for real materials. Then the poles of this function will indicate the existence of bosonic excitations which can serve as a "glue" for Cooper pairing, and if the frequency is high enough, and the dielectric matrix is simultaneously negative, this material is a good candidate for very high-Tc superconductivity. Thus, our approach is to elaborate a methodology of ab-initio calculation of the dielectric function of various materials, and then point out appropriate candidates. We used the powerful codes (TDDF with the DP package in conjunction with ABINIT) for computing dielectric responses at finite values of the wave vectors in the reciprocal lattice space. Though our report is concerned with the particular problem of superconductivity, the application range of the data processing methodology is much wider. The ability to compute the dielectric function of existing and still non-existing (though being predicted!) materials will have many more repercussions not only in fundamental sciences but also in technology and industry.

  11. Molexpl: a tool for ab initio data exploration and visualization

    Wang, Xueying; Onofrio, Nicolas,; Strachan, Alejandro

    2015-01-01

    Density functional theory (DFT) based on ab initio theory, is a powerful method to resolve the electronic structure of atoms, molecules and solids. However, in practical, DFT is limited to few hundreds of atoms. To overcome this limitation, researchers have developed empirical interatomic potentials implemented in molecular dynamics (MD) simulations. MD ignores the movements of electrons and describes bonding and non-bonding interaction as a function of the distance between atoms called force...

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

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

    1996-01-01

    The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting transition to a metallic state. In contrast to ordinary liquid silicon, the new liquid is characterized by a high coordination number and a strong reduction of covalent bonding effects.

  13. Towards an ab initio description of magnetism in ionic solids

    Illas, F.; Casanovas, J.; García-Bach, M. A.; Caballol, R.; Castell, O.

    1993-11-01

    The physical contributions to the KNiF3 magnetic exchange coupling integral have been obtained from specially designed ab initio cluster model calculations. Three important mechanisms have been identified. These are the delocalization of the magnetic orbitals into the anion ``p'' band, the variational contribution of the second-order interactions, and the many-body terms ``hidden'' in the two-body operator and the Heisenberg Hamiltonian.

  14. Ab initio simulation of helium inside carbon nanotubes

    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.

  15. The density matrix renormalization group for ab initio quantum chemistry

    Wouters, Sebastian

    2015-01-01

    During the past 15 years, the density matrix renormalization group (DMRG) has become increasingly important for ab initio quantum chemistry. It is used as a numerically exact solver for highly correlated regions in molecules. While the method works extremely well for one-dimensional systems, the correlated regions of interest are often far from one-dimensional. In this introductory talk, I will discuss the DMRG algorithm from a quantum information perspective, how quantum information theory h...

  16. Ab Initio Modeling of Ecosystems with Artificial Life

    Adami, C.

    2002-01-01

    Artificial Life provides the opportunity to study the emergence and evolution of simple ecosystems in real time. We give an overview of the advantages and limitations of such an approach, as well as its relation to individual-based modeling techniques. The Digital Life system Avida is introduced and prospects for experiments with ab initio evolution (evolution "from scratch"), maintenance, as well as stability of ecosystems are discussed.

  17. P-V Relation for Mercuric Calcogenides: Ab Initio Method

    G. Misra; S. Tenguria; Gautam, M.

    2011-01-01

    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 a...

  18. Structure models: from shell model to ab initio methods

    Bacca, Sonia

    2016-01-01

    A brief review of models to describe nuclear structure and reactions properties is presented, starting from the historical shell model picture and encompassing modern ab initio approaches. A selection of recent theoretical results on observables for exotic light and medium-mass nuclei is shown. Emphasis is given to the comparison with experiment and to what can be learned about three-body forces and continuum properties.

  19. Ab-initio calculations for dilute magnetic semiconductors

    Belhadji, Brahim

    2008-01-01

    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 approximatio...

  20. GAUSSIAN 76: An ab initio Molecular Orbital Program

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

    1978-01-01

    Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type Gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans.

  1. GAUSSIAN 76: an ab initio molecular orbital program

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

    1978-06-01

    Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans.

  2. Der halbunendliche Kristall - Elektronische und optische Eigenschaften ab-initio

    Brodersen, Sven

    2002-01-01

    Es werden die elektronischen und optischen Eigenschaften eines kristallinen Festkörpers unter Berücksichtigung der Oberfläche mit ab-initio Methoden berechnet. Die Behandlung der Oberflächeneffekte in einer Halbraum-Geometrie erzwingt die Darstellung der Wellenfunktionen und der Dielektrischen Funktion (DK) in einer lokalen Basis. Anhand von Volumenkristallen wird die Effizienz von LCAO- Basisfunktionen demonstriert. Die Erweiterung der atomaren Orbitale mit unbesetzten Orbitalen und 'off-sit...

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

    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).

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

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

    2014-09-28

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

  5. Ab initio calculations for industrial materials engineering: successes and challenges

    Wimmer, Erich; Freeman, Clive; Christensen, Mikael; Wolf, Walter; Saxe, Paul [Materials Design, Inc., PO Box 2000, Angel Fire, NM 87710 (United States); Najafabadi, Reza; Young Jr, George A; Ballard, Jake D; Angeliu, Thomas M; Vollmer, James [Knolls Atomic Power Laboratory, PO Box 1072, Schenectady, NY 12301-1072 (United States); Chambers, James J; Niimi, Hiroaki; Shaw, Judy B, E-mail: ewimmer@materialsdesign.co [Advanced CMOS, Texas Instruments Incorporated, Dallas, TX 75243 (United States)

    2010-09-29

    Computational materials science based on ab initio calculations has become an important partner to experiment. This is demonstrated here for the effect of impurities and alloying elements on the strength of a Zr twist grain boundary, the dissociative adsorption and diffusion of iodine on a zirconium surface, the diffusion of oxygen atoms in a Ni twist grain boundary and in bulk Ni, and the dependence of the work function of a TiN-HfO{sub 2} junction on the replacement of N by O atoms. In all of these cases, computations provide atomic-scale understanding as well as quantitative materials property data of value to industrial research and development. There are two key challenges in applying ab initio calculations, namely a higher accuracy in the electronic energy and the efficient exploration of large parts of the configurational space. While progress in these areas is fueled by advances in computer hardware, innovative theoretical concepts combined with systematic large-scale computations will be needed to realize the full potential of ab initio calculations for industrial applications.

  6. Ab initio calculations for industrial materials engineering: successes and challenges

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

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

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

  8. A Complete and Accurate Ab Initio Repeat Finding Algorithm.

    Lian, Shuaibin; Chen, Xinwu; Wang, Peng; Zhang, Xiaoli; Dai, Xianhua

    2016-03-01

    It has become clear that repetitive sequences have played multiple roles in eukaryotic genome evolution including increasing genetic diversity through mutation, changes in gene expression and facilitating generation of novel genes. However, identification of repetitive elements can be difficult in the ab initio manner. Currently, some classical ab initio tools of finding repeats have already presented and compared. The completeness and accuracy of detecting repeats of them are little pool. To this end, we proposed a new ab initio repeat finding tool, named HashRepeatFinder, which is based on hash index and word counting. Furthermore, we assessed the performances of HashRepeatFinder with other two famous tools, such as RepeatScout and Repeatfinder, in human genome data hg19. The results indicated the following three conclusions: (1) The completeness of HashRepeatFinder is the best one among these three compared tools in almost all chromosomes, especially in chr9 (8 times of RepeatScout, 10 times of Repeatfinder); (2) in terms of detecting large repeats, HashRepeatFinder also performed best in all chromosomes, especially in chr3 (24 times of RepeatScout and 250 times of Repeatfinder) and chr19 (12 times of RepeatScout and 60 times of Repeatfinder); (3) in terms of accuracy, HashRepeatFinder can merge the abundant repeats with high accuracy. PMID:26272474

  9. 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.

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

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

    2014-08-07

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

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

    The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several 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.

  12. An ab initio study of plutonium oxides surfaces

    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 β-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)

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

    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.

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

    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)

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

    Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems

  16. 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.

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

    Zen, Andrea, E-mail: a.zen@ucl.ac.uk [Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome (Italy); London Centre for Nanotechnology, University College London, London WC1E 6BT (United Kingdom); Luo, Ye, E-mail: xw111luoye@gmail.com; Mazzola, Guglielmo, E-mail: gmazzola@phys.ethz.ch; Sorella, Sandro, E-mail: sorella@sissa.it [SISSA–International School for Advanced Studies, Via Bonomea 26, 34136 Trieste (Italy); Democritos Simulation Center CNR–IOM Istituto Officina dei Materiali, 34151 Trieste (Italy); Guidoni, Leonardo, E-mail: leonardo.guidoni@univaq.it [Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome (Italy); Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’ Aquila, via Vetoio, 67100 L’ Aquila (Italy)

    2015-04-14

    Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.

  18. Ab initio vibrations in nonequilibrium nanowires

    We review recent results on electronic and thermal transport in two different quasi one-dimensional systems: Silicon nanowires (SiNW) and atomic gold chains. For SiNW's we compute the ballistic electronic and thermal transport properties on equal footing, allowing us to make quantitative predictions for the thermoelectric properties, while for the atomic gold chains we evaluate microscopically the damping of the vibrations, due to the coupling of the chain atoms to the modes in the bulk contacts. Both approaches are based on the combination of density-functional theory, and nonequilibrium Green's functions.

  19. Projector augmented wave method: ab initio molecular dynamics with full wave functions

    Peter E Blöchl; Clemens J Först; Johannes Schimpl

    2003-01-01

    A brief introduction to the projector augmented wave method is given and recent developments are reviewed. The projector augmented wave method is an all-electron method for efficient ab initio molecular dynamics simulations with full wave functions. It extends and combines the traditions of existing augmented wave methods and the pseudopotential approach. Without sacrificing efficiency, the PAW method avoids transferability problems of the pseudopotential approach and it has been valuable to predict properties that depend on the full wave functions.

  20. Ab initio no-core shell model with continuum

    Navratil, Petr

    2008-04-01

    The ab initio no-core shell model (NCSM) is a many-body approach to nuclear structure of light nuclei. The NCSM adopts an effective interaction theory to transform fundamental inter-nucleon interactions into effective interactions for a specified nucleus in a selected harmonic oscillator basis space [1]. The method is capable of predicting nuclear structure from inter-nucleon forces derived from quantum chromodynamics by means of chiral effective field theory [2]. NCSM extensions to the microscopic description of nuclear reactions are now under development. In my talk, I will first discuss our recent calculations of the ^4He total photo-absorption cross section using two- and three-nucleon interactions from chiral effective field theory [3]. I will then outline our effort to augment the NCSM by the resonating group method (RGM) technique to develop a new method capable of describing simultaneously both bound states and nuclear reactions on light nuclei [4]. This approach, which preserves translational symmetry and the Pauli principle, will allow us to calculate cross sections of reactions important for astrophysics and describe weakly-bound systems from first principles. I will present our first phase shift results for neutron scattering off ^3H, ^4He and ^7Li and proton scattering off ^3He, ^4He and ^7Be using realistic nucleon-nucleon potentials. 3mm [1] P. Navr'atil, J. P. Vary and B. R. Barrett, Phys. Rev. C 62, 054311 (2000). [2] P. Navr'atil and V. G. Gueorguiev and J. P. Vary, W. E. Ormand and A. Nogga, Phys. Rev. Lett. 99, 042501 (2007). [3] S. Quaglioni and P. Navr'atil, Phys. Lett. B 652, 370 (2007). [4] S. Quaglioni and P. Navr'atil, arXiv:0712.0855.

  1. Ab-initio study of napthelene based conducting polymer

    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.

  2. Ab-initio study of napthelene based conducting polymer

    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

  3. Equations of state of heavy metals: ab initio approaches

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

  4. Ab initio study of neutron drops with chiral Hamiltonians

    H.D. Potter

    2014-12-01

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

  5. Ab initio calculation of tensile strength in iron

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

    2003-01-01

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

  6. Ab initio study of neutron drops with chiral Hamiltonians

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

  7. Ab initio vibrational and dielectric properties of Y V O

    Vali, R.

    2009-10-01

    For the yttrium orthovanadate Y V O with a tetragonal zircon-type structure, the first complete set of Raman-active and IR-active phonon modes has been calculated using ab initio density functional perturbation theory. The calculated IR reflectivity spectra are in good agreement with available experimental data. We report the calculated frequencies of three Raman-active modes that could not be detected experimentally and a new assignment of the experimental Raman data. The contributions of each IR-active phonon modes to static dielectric tensor have been determined.

  8. 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.

  9. Ab initio structure determination via powder X-ray diffraction

    Digamber G Porob; T N Guru Row

    2001-10-01

    Structure determination by powder X-ray diffraction data has gone through a recent surge since it has become important to get to the structural information of materials which do not yield good quality single crystals. Although the method of structure completion when once the starting model is provided is facile through the Rietveld refinement technique, the structure solution ab initio os still not push-button technology. In this article a survey of the recent development in this area is provided with an illustration of the structure determination of -NaBi3V2O10.

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

    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.

  11. In pursuit of the ab initio limit for conformational energy prototypes

    Császár, Attila G.; Allen, Wesley D.; Schaefer, Henry F.

    1998-06-01

    The convergence of ab initio predictions to the one- and n-particle limits has been systematically explored for several conformational energy prototypes: the inversion barriers of ammonia, water, and isocyanic acid, the torsional barrier of ethane, the E/Z rotamer separation of formic acid, and the barrier to linearity of silicon dicarbide. Explicit ab initio results were obtained with atomic-orbital basis sets as large as [7s6p5d4f3g2h1i/6s5p4d3f2g1h] and electron correlation treatments as extensive as fifth-order Møller-Plesset perturbation theory (MP5), the full coupled-cluster method through triple excitations (CCSDT), and Brueckner doubles theory including perturbational corrections for both triple and quadruple excitations [BD(TQ)]. Subsequently, basis set and electron correlation extrapolation schemes were invoked to gauge any further variations in arriving at the ab initio limit. Physical effects which are tacitly neglected in most theoretical work have also been quantified by computations of non-Born-Oppenheimer (BODC), relativistic, and core correlation shifts of relative energies. Instructive conclusions are drawn for the pursuit of spectroscopic accuracy in theoretical conformational analyses, and precise predictions for the key energetic quantities of the molecular prototypes are advanced.

  12. AB INITIO SIMULATIONS FOR MATERIAL PROPERTIES ALONG THE JUPITER ADIABAT

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

  13. Three-cluster dynamics within an ab initio framework

    Quaglioni, S; Navrátil, P

    2013-01-01

    We introduce a fully antisymmetrized treatment of three-cluster dynamics within the ab initio framework of the no-core shell model/resonating-group method (NCSM/RGM). Energy-independent non-local interactions among the three nuclear fragments are obtained from realistic nucleon-nucleon interactions and consistent ab initio many-body wave functions of the clusters. The three-cluster Schr\\"odinger equation is solved with bound-state boundary conditions by means of the hyperspherical-harmonic method on a Lagrange mesh. We discuss the formalism in detail and give algebraic expressions for systems of two single nucleons plus a nucleus. Using a soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we apply the method to an $^4$He+$n+n$ description of $^6$He and compare the results to experiment and to a six-body diagonalization of the Hamiltonian performed within the harmonic-oscillator expansions of the NCSM. Differences between the two calculations provide a measure of core ($^4$He) pola...

  14. Unified ab initio approaches to nuclear structure and reactions

    Navrátil, Petr; Quaglioni, Sofia; Hupin, Guillaume; Romero-Redondo, Carolina; Calci, Angelo

    2016-05-01

    The description of nuclei starting from the constituent nucleons and the realistic interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of the nuclear forces, with two-, three- and possibly higher many-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD-employing Hamiltonians constructed within chiral effective field theory. After a brief overview of the field, we focus on ab initio many-body approaches—built upon the no-core shell model—that are capable of simultaneously describing both bound and scattering nuclear states, and present results for resonances in light nuclei, reactions important for astrophysics and fusion research. In particular, we review recent calculations of resonances in the 6He halo nucleus, of five- and six-nucleon scattering, and an investigation of the role of chiral three-nucleon interactions in the structure of 9Be. Further, we discuss applications to the 7Be {({{p}},γ )}8{{B}} radiative capture. Finally, we highlight our efforts to describe transfer reactions including the 3H{({{d}},{{n}})}4He fusion.

  15. Unified ab initio approaches to nuclear structure and reactions

    Navratil, Petr; Hupin, Guillaume; Romero-Redondo, Carolina; Calci, Angelo

    2016-01-01

    The description of nuclei starting from the constituent nucleons and the realistic interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of the nuclear forces, with two-, three- and possibly higher many-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in {\\em ab initio} nuclear structure and reaction calculations based on input from QCD-employing Hamiltonians constructed within chiral effective field theory. After a brief overview of the field, we focus on ab initio many-body approaches - built upon the No-Core Shell Model - that are capable of simultaneously describing both bound and scattering nuclear states, and present results for resonances in light nuclei, reactions important for astrophysics and fusion research. In particular, we review recent calculations of resonances in the $^6$He halo nucleus, of five- and six...

  16. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    Elenewski, Justin E.; Hackett, John C, E-mail: jchackett@vcu.edu [Department of Physiology and Biophysics and The Massey Cancer Center, School of Medicine, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23219-1540 (United States)

    2015-02-14

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

  17. Ab initio quantum dynamics using coupled-cluster

    Kvaal, Simen

    2012-01-01

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

  18. Ab initio study of the transition-metal carbene cations

    李吉海; 冯大诚; 冯圣玉

    1999-01-01

    The geometries and bonding characteristics of the first-row transition-metal carbene cations MCH2+ were investigated by ab initio molecular orbital theory (HF/LANL2DZ). All of MCH2+ are coplanar. In the closed shell structures the C bonds to M with double bonds; while in the open shell structures the partial double bonds are formed, because one of the σ and π orbitals is singly occupied. It is mainly the π-type overlap between the 2px orbital of C and 4px, 3dxz, orbitals of M+ that forms the π orbitals. The dissociation energies of C—M bond appear in periodic trend from Sc to Cu. Most of the calculated bond dissociation energies are close to the experimental ones.

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

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-01-01

    We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world. PMID:27434308

  20. Transport coefficients in diamond from ab-initio calculations

    Löfâs, Henrik; Grigoriev, Anton; Isberg, Jan; Ahuja, Rajeev

    2013-03-01

    By combining the Boltzmann transport equation with ab-initio electronic structure calculations, we obtain transport coefficients for boron-doped diamond. We find the temperature dependence of the resistivity and the hall coefficients in good agreement with experimental measurements. Doping in the samples is treated via the rigid band approximation and scattering is treated in the relaxation time approximation. In contrast to previous results, the acoustic phonon scattering is the dominating scattering mechanism for the considered doping range. At room temperature, we find the thermopower, S, in the range 1-1.6 mV/K and the power factor, S2σ, in the range 0.004-0.16 μW /cm K2.

  1. Ab-initio melting curve and principal Hugoniot of tantalum

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

  2. Ab initio methods for electron-molecule collisions

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

  3. Relativistic ab initio calculations for ion-atom collisions

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

  4. Ab Initio Calculations of Co Shielding in Model Complexes

    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.

  5. Ab initio H2O in realistic hydrophilic confinement.

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

    2014-12-15

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

  6. Ab initio design of laser pulse for controlling photochemical reactions

    With high level ab initio description of molecule-field interaction, we have developed an optimal control algorithm for manipulating molecular transformation and quantum populations. High order molecule-field interactions are fully taken into account through the use of electric-nuclear Born-Oppenheimer (ENBO) approximation. The present algorithm is demonstrated on the control of molecular post-pulse (transient)alignment and orientation. High degrees of alignment and orientation are achieved in a vibrationally selective manner by optimized infrared laser pulses of duration on the order one rotational period of molecule. To reveal the control mechanism behind the complicated optimal pulses, an analytical pulse design method is developed within the ENBO approximation, which is based on a two-state treatment of the dynamics in a Floquet picture. This analytical method is also illustrated on the control of the alignment of homonuclear diatomics. (author)

  7. Efficient Ab initio Modeling of Random Multicomponent Alloys

    Jiang, Chao; Uberuaga, Blas P.

    2016-03-01

    We present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multicomponent alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high-entropy alloy chemistries. The SSOS method developed here can be broadly useful for the rapid computational design of multicomponent materials, especially those with a large number of alloying elements, a challenging problem for other approaches.

  8. Molecular ion LiHe+: ab initio study

    Highlights: ► Excited electronic states of LiHe+ are studied. ► Potential energy curves of thirteen states are calculated. ► Dipole moment and transition dipole moment functions are determined. ► Basic spectroscopic properties of the electronic states are derived. - Abstract: High level ab initio calculations are performed on the molecular ion LiHe+. Potential energy curves for the low-lying singlet and triplet electronic states are calculated using the multi-reference configuration interaction and single-reference coupled cluster methods with large basis sets. The corresponding dipole moments and transition dipole moments functions are also determined. The basic spectroscopic properties and excitation energies of the electronic states are derived from rovibrational bound state calculations.

  9. Ab initio potential energy surface and rovibrational states of HBO

    Ha, Tae-Kyu; Makarewicz, Jan

    1999-01-01

    The potential energy surface describing the large-amplitude motion of H around the BO core in the HBO molecule has been determined from ab initio calculations. This surface has been sampled by a set of 170 grid points from a two-dimensional space defined by the stretching and the bending coordinates of the H nucleus. At each grid point, the BO bond length has been optimized using the second-order Møller-Plesset perturbation theory with the basis set aug-cc-pVTZ. The surface has a local minimum for the linear as well as the bent configuration of HBO. A low energy barrier to the linear configuration BOH causes a large-amplitude motion and a strong rovibrational interaction in the molecule. Its rovibrational dynamics is different from the dynamics in bent or quasilinear triatomic molecules.

  10. Ab initio quantum dynamics using coupled-cluster.

    Kvaal, Simen

    2012-05-21

    The curse of dimensionality (COD) limits the current state-of-the-art ab initio propagation methods for non-relativistic quantum mechanics to relatively few particles. For stationary structure calculations, the coupled-cluster (CC) method overcomes the COD in the sense that the method scales polynomially with the number of particles while still being size-consistent and extensive. We generalize the CC method to the time domain while allowing the single-particle functions to vary in an adaptive fashion as well, thereby creating a highly flexible, polynomially scaling approximation to the time-dependent Schrödinger equation. The method inherits size-consistency and extensivity from the CC method. The method is dubbed orbital-adaptive time-dependent coupled-cluster, and is a hierarchy of approximations to the now standard multi-configurational time-dependent Hartree method for fermions. A numerical experiment is also given. PMID:22612082

  11. 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...

  12. An Efficient Approach to Ab Initio Monte Carlo Simulation

    Leiding, Jeff

    2013-01-01

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

  13. Interatomic Coulombic decay widths of helium trimer: Ab initio calculations

    Kolorenč, Přemysl, E-mail: kolorenc@mbox.troja.mff.cuni.cz [Charles University in Prague, Faculty of Mathematics and Physics, Institute of Theoretical Physics, V Holešovičkách 2, 180 00 Prague (Czech Republic); Sisourat, Nicolas [Sorbonne Universités, UPMC Univ Paris 06, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); CNRS, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France)

    2015-12-14

    We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green’s function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states.

  14. Pressure dependence of magnetic coupling in ionic solids from ab initio cluster model calculations

    Casanovas, Jordi; Illas, Francesc

    1994-11-01

    The dependence of the magnetic coupling constant, J, with the pressure has been studied by an ab initio cluster model approach in a typical ionic solid such as KNiF3. By computing J at different values of the lattice parameter R, we predict a power law of the form ‖J‖≊R-n with 10.5

  15. Superior thermal conductivity and extremely high mechanical strength in polyethylene chains from {\\it ab initio} calculation

    Jiang, Jin-Wu; Zhao, Junhua; Zhou, Kun; Rabczuk, Timon

    2012-01-01

    The upper limit of the thermal conductivity and the mechanical strength are predicted for the polyethylene chain, by performing the {\\it ab initio} calculation and applying the quantum mechanical non-equilibrium Green's function approach. Specially, there are two main findings from our calculation: (1). the thermal conductivity can reach a high value of 310 W/K/m in a 100 nm polyethylene chain at room temperature; (2). the Young's modulus in the polyethylene chain is as high as 374.5 GPa, and...

  16. Ab-initio GMR and current-induced torques in Au/Cr multilayers

    Haney, P. M.; Waldron, D; Duine, R. A.; Nunez, A. S.; Guo, H; MacDonald, A.H.

    2006-01-01

    We report on an {\\em ab-initio} study of giant magnetoresistance (GMR) and current-induced-torques (CITs) in Cr/Au multilayers that is based on non-equilibrium Green's functions and spin density functional theory. We find substantial GMR due primarily to a spin-dependent resonance centered at the Cr/Au interface and predict that the CITs are strong enough to switch the antiferromagnetic order parameter at current-densities $\\sim 100$ times smaller than typical ferromagnetic metal circuit swit...

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

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

    2014-09-16

    Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling

  18. The particle-in-cell model for ab initio thermodynamics: implications for the elastic anisotropy of the Earth's inner core

    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 gives an incorrect t...

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

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

    2007-01-01

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

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

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

    2014-01-01

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

  1. Ab Initio Studies of Halogen and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

    Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

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

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

  3. Ab initio electronic transport model with explicit solution to the linearized Boltzmann transport equation

    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.

  4. Volumic omit maps in ab initio dual-space phasing.

    Oszlányi, Gábor; Sütő, András

    2016-07-01

    Alternating-projection-type dual-space algorithms have a clear construction, but are susceptible to stagnation and, thus, inefficient for solving the phase problem ab initio. To improve this behaviour new omit maps are introduced, which are real-space perturbations applied periodically during the iteration process. The omit maps are called volumic, because they delete some predetermined subvolume of the unit cell without searching for atomic regions or analysing the electron density in any other way. The basic algorithms of positivity, histogram matching and low-density elimination are tested by their solution statistics. It is concluded that, while all these algorithms based on weak constraints are practically useless in their pure forms, appropriate volumic omit maps can transform them to practically useful methods. In addition, the efficiency of the already useful reflector-type charge-flipping algorithm can be further improved. It is important that these results are obtained by using non-sharpened structure factors and without any weighting scheme or reciprocal-space perturbation. The mathematical background of volumic omit maps and their expected applications are also discussed. PMID:27357850

  5. Ab initio simulations of peptide-mineral interactions

    Hug, Susanna; Hunter, Graeme K.; Goldberg, Harvey; Karttunen, Mikko

    We performed Car-Parrinello Molecular Dynamics (CPMD) simulations of two amino acids, aspartic acid (Asp) and phophoserine (pSer), on a calcium oxalate monohydrate (COM) surface as a model of the interactions of phosphoproteins with biominerals. In our earlier work using in vitro experiments and classical Molecular Dynamics (MD) simulations we have demonstrated the importance of phosphorylation of serine on the interactions of osteopontin (OPN) with COM. We used configurations from our previous classical MD simulations as a starting point for the ab initio simulations. In the case of Asp we found that the α-carboxyl and amine groups form temporary close contacts with the surface. For the dipeptide Asp-pSer the carboxyl groups form permanent close contacts with the surface and the distances of its other functional groups do not vary much. We show how the interaction of carboxyl groups with COM crystal is established and confirm the importance of phosphorylation in mediating the interactions between COM surfaces and OPN.

  6. Ab initio transport across bismuth selenide surface barriers

    Narayan, Awadhesh

    2014-11-24

    © 2014 American Physical Society. We investigate the effect of potential barriers in the form of step edges on the scattering properties of Bi2Se3(111) topological surface states by means of large-scale ab initio transport simulations. Our results demonstrate the suppression of perfect backscattering, while all other scattering processes, which do not entail a complete spin and momentum reversal, are allowed. Furthermore, we find that the spin of the surface state develops an out-of-plane component as it traverses the barrier. Our calculations reveal the existence of quasibound states in the vicinity of the surface barriers, which appear in the form of an enhanced density of states in the energy window corresponding to the topological state. For double barriers we demonstrate the formation of quantum well states. To complement our first-principles results we construct a two-dimensional low-energy effective model and illustrate its shortcomings. Our findings are discussed in the context of a number of recent experimental works.

  7. Accurate ab initio vibrational energies of methyl chloride

    Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH335Cl and CH337Cl. The respective PESs, CBS-35 HL, and CBS-37 HL, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY 3Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35 HL and CBS-37 HL PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm−1, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH3Cl without empirical refinement of the respective PESs

  8. Accurate ab initio vibrational energies of methyl chloride

    Owens, Alec, E-mail: owens@mpi-muelheim.mpg.de [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany); Department of Physics and Astronomy, University College London, Gower Street, WC1E 6BT London (United Kingdom); Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan [Department of Physics and Astronomy, University College London, Gower Street, WC1E 6BT London (United Kingdom); Thiel, Walter [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany)

    2015-06-28

    Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH{sub 3}{sup 35}Cl and CH{sub 3}{sup 37}Cl. The respective PESs, CBS-35{sup  HL}, and CBS-37{sup  HL}, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY {sub 3}Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35{sup  HL} and CBS-37{sup  HL} PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm{sup −1}, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH{sub 3}Cl without empirical refinement of the respective PESs.

  9. Ab-initio calculations for dilute magnetic semiconductors

    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.)

  10. Ab initio no-core solutions for $^6$Li

    Shin, Ik Jae; Maris, Pieter; Vary, James P; Forssén, Christian; Rotureau, Jimmy; Michel, Nicolas

    2016-01-01

    We solve for properties of $^6$Li in the ab initio No-Core Full Configuration approach and we separately solve for its ground state and $J^{\\pi}=2_{2}^{+}$ resonance with the Gamow Shell Model in the Berggren basis. We employ both the JISP16 and chiral NNLO$_{opt}$ realistic nucleon-nucleon interactions and investigate the ground state energy, excitation energies, point proton root-mean-square radius and a suite of electroweak observables. We also extend and test methods to extrapolate the ground state energy, point proton root-mean-square radius, and electric quadrupole moment. We attain improved estimates of these observables in the No-Core Full Configuration approach by using basis spaces up through N$_{max}$=18 that enable more definitive comparisons with experiment. Using the Density Matrix Renormalization Group approach with the JISP16 interaction, we find that we can significantly improve the convergence of the Gamow Shell Model treatment of the $^6$Li ground state and $J^{\\pi}=2_{2}^{+}$ resonance by ...

  11. Ab initio studies of phoshorene island single electron transistor.

    Ray, S J; Venkata Kamalakar, M; Chowdhury, R

    2016-05-18

    Phosphorene is a newly unveiled two-dimensional crystal with immense potential for nanoelectronic and optoelectronic applications. Its unique electronic structure and two dimensionality also present opportunities for single electron devices. Here we report the behaviour of a single electron transistor (SET) made of a phosphorene island, explored for the first time using ab initio calculations. We find that the band gap and the charging energy decrease monotonically with increasing layer numbers due to weak quantum confinement. When compared to two other novel 2D crystals such as graphene and MoS2, our investigation reveals larger adsorption energies of gas molecules on phosphorene, which indicates better a sensing ability. The calculated charge stability diagrams show distinct changes in the presence of an individual molecule which can be applied to detect the presence of different molecules with sensitivity at a single molecular level. The higher charging energies of the molecules within the SET display operational viability at room temperature, which is promising for possible ultra sensitive detection applications. PMID:27093536

  12. Ab initio studies of phosphorene island single electron transistor

    Ray, S. J.; Venkata Kamalakar, M.; Chowdhury, R.

    2016-05-01

    Phosphorene is a newly unveiled two-dimensional crystal with immense potential for nanoelectronic and optoelectronic applications. Its unique electronic structure and two dimensionality also present opportunities for single electron devices. Here we report the behaviour of a single electron transistor (SET) made of a phosphorene island, explored for the first time using ab initio calculations. We find that the band gap and the charging energy decrease monotonically with increasing layer numbers due to weak quantum confinement. When compared to two other novel 2D crystals such as graphene and MoS2, our investigation reveals larger adsorption energies of gas molecules on phosphorene, which indicates better a sensing ability. The calculated charge stability diagrams show distinct changes in the presence of an individual molecule which can be applied to detect the presence of different molecules with sensitivity at a single molecular level. The higher charging energies of the molecules within the SET display operational viability at room temperature, which is promising for possible ultra sensitive detection applications.

  13. Ab initio study of MoS2 nanotube bundles

    Verstraete, Matthieu; Charlier, Jean-Christophe

    2003-07-01

    Recently, the synthesis of a new phase of MoS2I1/3 stoichiometry was reported [M. Remskar, A. Mrzel, Z. Skraba, A. Jesih, M. Ceh, J. Demšar, P. Stadelmann, F. Lévy, and D. Mihailovic, Science 292, 479 (2001)]. Electron microscope images and diffraction data were interpreted to indicate bundles of sub-nanometer-diameter single-wall MoS2 nanotubes. After experimental characterization, the structure was attributed to an assembly of “armchair” nanotubes with interstitial iodine. Using first-principles total-energy calculations, bundles of MoS2 nanotubes with different topologies and stoichiometries are investigated. All of the systems are strongly metallic. Configurations with “zigzag” structures are found to be more stable energetically than the “armchair” ones, though all of the structures have similar stabilities. After relaxation, there remain several candidates which give a lattice parameter in relative agreement with experiment. Further, spin-polarized calculations indicate that a structure with armchair tubes iodine atoms in their center acquires a very large spontaneous magnetic moment of 12μB, while the other structures are nonmagnetic. Our ab initio calculations show that in most of the other structures, the tubes are very strongly bound together, and that the compounds should be considered as a crystal, rather than as a bundle of tubes in the habitual sense.

  14. Exploring the free energy surface using ab initio molecular dynamics

    Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

    2016-04-01

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.

  15. Exploring the free energy surface using ab initio molecular dynamics.

    Samanta, Amit; Morales, Miguel A; Schwegler, Eric

    2016-04-28

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti. PMID:27131525

  16. Ab initio study of optical excitations in VO2

    Coulter, John; Gali, Adam; Manousakis, Efstratios

    2014-03-01

    Motivated by recent experimental efforts to fabricate p-n junctions from transition metal oxides (TMOs) and a recent theoretical study claiming TMOs to be good absorbers and promising materials for efficient carrier multiplication, we study the optical properties of a prototypical TMO, the insulator M1 phase of vanadium dioxide (VO2), by ab initio methods. We applied the Bethe-Salpeter equations (BSE) to calculate the optical properties, starting from self-consistent GW quasi-particle energy levels and states. In contrast to expectations, the exciton binding energy obtained by BSE is in good agreement with the experiment. We find that the electron-electron interaction is very strong which makes this material promising for efficient carrier multiplication that might lead to an enhanced efficiency in photo-voltaics applications. To illustrate this more quantitatively, we calculated the impact ionization rate within the independent quasiparticle approximation, and find that the rate is significantly higher than silicon in the region of highest solar intensity, due to the strong multiple carrier excitations.

  17. Ab initio simulations on rutile-based titania nanowires

    Zhukovskii, Yu F.; Evarestov, R. A.

    2012-08-01

    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 { 1bar 10 } 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.

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

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

  19. Experimental, ab initio and density functional theory studies on sulfadiazine

    Ogruc-Ildiz, Gulce; Akyuz, Sevim; Ozel, Aysen E.

    2009-04-01

    In the present study, combined experimental and computational study on molecular vibrations of free sulfadiazine has been reported. The theoretically possible stable conformers of free sulfadiazine molecule in electronically ground state were searched by means of torsion potential energy surfaces scan studies through C1 sbnd C7 sbnd S8 sbnd N8, C7 sbnd S8 sbnd N9 sbnd C10 and S8 sbnd N9 sbnd C10 sbnd N11 dihedral angles, at both semi-empirical PM3 and B3LYP/3-21G levels of theory. The final geometrical parameters for the obtained stable conformers were determined by means of geometry optimization carried out at ab initio HF/6-31G++(d,p) and DFT/B3LYP/6-31G++(d,p) theory levels. The harmonic and anharmonic vibrational wavenumbers and IR intensities were calculated at the same theory levels used in geometry optimization. The modes of the fundamental vibrations were characterized depending on their the total energy distribution (TED%). In order to fit the calculated harmonic wavenumbers to experimental ones, dual scale factors were used. The experimental infrared and Raman spectra of sulfadiazine in solid phase have been measured and compared with the calculated vibrational spectra of each conformer.

  20. Explicit Polarization (X-Pol) Potential Using ab Initio Molecular Orbital Theory and Density Functional Theory†

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

    2009-01-01

    The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree—Fo...

  1. Realistic modelling of water/solid interfaces from ab Initio molecular dynamics

    Tocci, G.

    2014-01-01

    Water/solid interfaces are of utmost importance to a number of technological processes. Theoretical studies, based on ab initio approaches are suitable to unveil processes occurring at water/solid interfaces and can therefore be instrumental to delineate guidelines to improve the efficiency of these processes. In this thesis we study several systems of current interest using ab initio methods based on density functional theory (DFT). By going often beyond the use of standard DFT methods and a...

  2. Ab Initio Computation of Dynamical Properties: Pressure Broadening

    Wiesenfeld, Laurent; Drouin, Brian

    2014-06-01

    Rotational spectroscopy of polar molecules is the main observational tool in many areas of astrophysics, for gases of low densities (n ˜ 102 - 108 cm-3). Spectral line shapes in astrophysical media are largely dominated by turbulence-induced Doppler effects and natural line broadening are negligible. However line broadening remains an important tool for denser gases, like planetary high atmospheres. Understanding the excitation schemes of polar molecules requires the knowledge of excitation transfer rate due to collisional excitation, between the polar molecule and the ambient gas, usually H2. Transport properties in ionized media also require a precise knowledge of momentum transfer rates by elastic collisions. In order to assess the theoretically computed cross section and energy/momentum transfer rates, direct absolute experiments are scarce. The best way is to measure not individual scattering events but rather the global effect of the buffer gas, thanks to the pressure broadening cross sections, whose magnitude can be measured without any scaling parameters. At low temperatures, both elastic and inelastic scattering amplitudes are tested. At higher temperature, depending on the interaction strength, only inelastic scattering cross section are shown to play a significant role 1 ,2. Thanks to the advances of computer capabilities, it has become practical to compute spectral line parameters fromab initio quantum chemistry. In particular, the theory of rotational line broadening is readily incorporated into scattering quantum dynamical theory, like close-coupling schemes. The only approximations used in the computation are the isolated collision/isolated line approximations. We compute the non-binding interaction potential with high precision quantum chemistry and fit the resulting ab initio points onto a suitable functional. We have recently computed several such systems, for molecules in H2 buffer gas: H2O,3 H2CO,4 HCO+ .5 Detailed computations taking into

  3. Ab initio design of elastically isotropic TiZrNbMoVx high-entropy alloys

    Highlights: • The refractory high-entropy alloys are studied with ab initio theory. • We study the effect of alloying elements on the elastic parameters. • We propose an criterion of elastically isotropic refractory high-entropy alloys. - Abstract: The TiZrVNb and TiZrNbMoVx (x = 0–1.5) high-entropy alloys (HEAs) are single-phase solid solutions having the body centered cubic crystallographic structure. Here we use the ab initio exact muffin-tin orbitals method in combination with the coherent potential approximation to study the equilibrium bulk properties of the above refractory HEAs. We provide a detailed investigation of the effect of alloying elements on the electronic structure and elastic parameters. Our results indicate that vanadium enhances the anisotropy of TiZrNbMoVx. As an application of the present theoretical database, we verify the often quoted correlation between the valence electron concentration (VEC) and the micro-mechanical properties in the case of multi-component alloys. Furthermore, we predict that the present HEAs become elastically isotropic for VEC∼4.72

  4. 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.

  5. Lithium Insertion In Silicon Nanowires: An ab Initio Study

    Zhang, Qianfan

    2010-09-08

    The ultrahigh specific lithium ion storage capacity of Si nanowires (SiNWs) has been demonstrated recently and has opened up exciting opportunities for energy storage. However, a systematic theoretical study on lithium insertion in SiNWs remains a challenge, and as a result, understanding of the fundamental interaction and microscopic dynamics during lithium insertion is still lacking. This paper focuses on the study of single Li atom insertion into SiNWs with different sizes and axis orientations by using full ab initio calculations. We show that the binding energy of interstitial Li increases as the SiNW diameter grows. The binding energies at different insertion sites, which can be classified as surface, intermediate, and core sites, are quite different. We find that surface sites are energetically the most favorable insertion positions and that intermediate sites are the most unfavorable insertion positions. Compared with the other growth directions, the [110] SiNWs with different diameters always present the highest binding energies on various insertion locations, which indicates that [110] SiNWs are more favorable by Li doping. Furthermore, we study Li diffusion inside SiNWs. The results show that the Li surface diffusion has a much higher chance to occur than the surface to core diffusion, which is consistent with the experimental observation that the Li insertion in SiNWs is layer by layer from surface to inner region. After overcoming a large barrier crossing surface-to-intermediate region, the diffusion toward center has a higher possibility to occur than the inverse process. © 2010 American Chemical Society.

  6. Ab-initio molecular dynamics for metallic systems

    This thesis deals with the problem of performing first-principles electronic structure calculations in metallic systems, with the goal of bringing ab-initio quantum-mechanical molecular dynamics simulations for these systems to the same level of computational cost, efficiency and accuracy that are now obtained for semiconductors and insulators. The problem is first reviewed from the theoretical and methodological point of view, with a presentation of the current state of research. In particular, the formulation of the electronic structure problem as a Density-Functional-Theory constrained minimization is examined in detail, as well as the description of metallic systems via generalized electronic free energy functionals. A novel reformulation of the problem is here proposed, using the language of Ensemble Density Functional Theory, and a variational realization of it is developed and implemented. The dramatic improvement in the efficiency for the convergence to the electronic ground-state is discussed and explained. The role of the fictitious electronic temperature is examined, as well as its contribution to controlling the errors originating from inadequate sampling of the Brillouin Zone. The associated systematic errors are also examined, and non-selfconsistent and self-consistent estimates for these errors in the energies and the ionic forces are made explicit. The novel technique of cold smearing is introduced. The new method of Ensemble Density Functional Theory, in conjunction with the cold smearing, is shown to reach the proposed goal of greatly improving our current efficiency and accuracy for molecular dynamics simulations, making them affordable at the level of currently available computational power. The method is applied to the study of the finite temperature properties of bulk aluminium and aluminium surfaces, to identify the microscopical processes that give rise to the premelting of the (110) surface and to show evidence for the different phase

  7. Cosmic-ray modulation: an ab initio approach

    A better understanding of cosmic-ray modulation in the heliosphere can only be gained through a proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays. We present an ab initio model for cosmic-ray modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for periods of minimum solar activity, utilizing boundary values chosen so that model results are in fair to good agreement with spacecraft observations of turbulence quantities, not only in the solar ecliptic plane but also along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modelled slab and 2D turbulence energy spectra. The latter spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers commencing at the 2D outerscale. There currently exist no models or observations for this quantity, and it is the only free parameter in this study. The modelled turbulence spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on cosmic-ray drifts are modelled in a self-consistent way, employing a recently developed model for drift along the wavy current sheet. The resulting diffusion coefficients and drift expressions are applied to the study of galactic cosmic-ray protons and antiprotons using a three dimensional, steady-state cosmic-ray modulation code, and sample solutions in fair agreement with multiple spacecraft observations are presented. (author)

  8. Ab initio spectroscopic characterization of borane, BH, in its X1Σ+ electronic state.

    Koput, Jacek

    2015-11-15

    The accurate potential energy and electric dipole moment functions of borane, BH, in its X1Σ+ electronic state have been determined from ab initio calculations using the multireference averaged coupled-pair functional method in conjunction with the correlation-consistent core-valence basis sets up to septuple-zeta quality. The higher-order electron correlation, scalar relativistic, adiabatic, and nonadiabatic effects were discussed. Vibration-rotation energy levels of the (11)BH, (11)BD, (10)BH, and (10)BD isotopologues were predicted to near "spectroscopic" accuracy. For the main isotopologue (11)BH, the adiabatic dissociation energy D0 and the effective equilibrium internuclear distance r(e) were predicted to be 28,469 ± 10 cm(-1) and 1.23214 ± 0.0001 Å, respectively. PMID:26444679

  9. Modeling and Ab initio Calculations of Thermal Transport in Si-Based Clathrates and Solar Perovskites

    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.

  10. Lattice thermal conductivity of UO2 using ab-initio and classical molecular dynamics

    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

  11. An investigation of ab initio shell-model interactions derived by no-core shell model

    Wang, XiaoBao; Dong, GuoXiang; Li, QingFeng; Shen, CaiWan; Yu, ShaoYing

    2016-09-01

    The microscopic shell-model effective interactions are mainly based on the many-body perturbation theory (MBPT), the first work of which can be traced to Brown and Kuo's first attempt in 1966, derived from the Hamada-Johnston nucleon-nucleon potential. However, the convergence of the MBPT is still unclear. On the other hand, ab initio theories, such as Green's function Monte Carlo (GFMC), no-core shell model (NCSM), and coupled-cluster theory with single and double excitations (CCSD), have made many progress in recent years. However, due to the increasing demanding of computing resources, these ab initio applications are usually limited to nuclei with mass up to A = 16. Recently, people have realized the ab initio construction of valence-space effective interactions, which is obtained through a second-time renormalization, or to be more exactly, projecting the full-manybody Hamiltonian into core, one-body, and two-body cluster parts. In this paper, we present the investigation of such ab initio shell-model interactions, by the recent derived sd-shell effective interactions based on effective J-matrix Inverse Scattering Potential (JISP) and chiral effective-field theory (EFT) through NCSM. In this work, we have seen the similarity between the ab initio shellmodel interactions and the interactions obtained by MBPT or by empirical fitting. Without the inclusion of three-body (3-bd) force, the ab initio shell-model interactions still share similar defects with the microscopic interactions by MBPT, i.e., T = 1 channel is more attractive while T = 0 channel is more repulsive than empirical interactions. The progress to include more many-body correlations and 3-bd force is still badly needed, to see whether such efforts of ab initio shell-model interactions can reach similar precision as the interactions fitted to experimental data.

  12. Transport and optical properties of warm dense aluminum in the two-temperature regime: Ab initio calculation and semiempirical approximation

    Knyazev, D. V.; Levashov, P. R.

    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. ...

  13. Calculation of intermolecular potentials for H{sub 2}−H{sub 2} and H{sub 2}−O{sub 2} dimers ab initio and prediction of second virial coefficients

    Pham Van, Tat [Faculty of Science and Technology, Hoa Sen University (Viet Nam); Deiters, Ulrich K. [Institute of Physical Chemistry, University of Cologne, Luxemburger Str. 116, D-50939 Köln (Germany)

    2015-08-18

    Highlights: • We construct the angular orientations of dimers H{sub 2}−H{sub 2} and H{sub 2}−O{sub 2}. • We calculate the ab initio intermolecular interaction energies for all built orientations. • Extrapolating the interaction energies to the complete basis set limit aug-cc-pV23Z. • We develop two 5-site ab initio intermolecular potentials of dimers H{sub 2}−H{sub 2}, H{sub 2}−O{sub 2}. • Calculating the virial coefficients of dimer H{sub 2}−H{sub 2} and H{sub 2}−O{sub 2}. - Abstract: The intermolecular interaction potentials of the dimers H{sub 2}−H{sub 2} and H{sub 2}−O{sub 2} were calculated from quantum mechanics, using coupled-cluster theory CCSD(T) and correlation-consistent basis sets aug-cc-pVmZ (m = 2, 3); the results were extrapolated to the basis set limit aug-cc-pV23Z. The interaction energies were corrected for the basis set superposition error with the counterpoise scheme. For comparison also Møller–Plesset perturbation theory (at levels 2–4) with the basis sets aug-cc-pVTZ were considered, but the results proved inferior. The quantum mechanical results were used to construct analytical pair potential functions. From these functions the second virial coefficients of hydrogen and the cross virial coefficients of the hydrogen–oxygen system were obtained by integration; in both cases corrections for quantum effects were included. The results agree well with experimental data, if available, or with empirical correlations.

  14. Ground and excited states of doubly open-shell nuclei from ab initio valence-space Hamiltonians

    Stroberg, S R; Holt, J D; Bogner, S K; Schwenk, A

    2015-01-01

    We present ab initio predictions for ground and excited states of doubly open-shell fluorine and neon isotopes based on chiral two- and three-nucleon interactions. We use the in-medium similarity renormalization group, in both flow-equation and Magnus formulations, to derive mass-dependent sd valence-space Hamiltonians. The experimental ground-state energies are reproduced through neutron number N=14, beyond which a new targeted normal-ordering procedure improves agreement with data and large-scale multi-reference calculations. For spectroscopy, we focus on neutron-rich 23-26F and 24-26Ne isotopes near N=14,16 magic numbers. In all cases we find an agreement with experiment competitive with established phenomenology. Moreover, yrast states are well described in 20Ne and 24Mg, providing an ab initio description of deformation in the medium-mass region.

  15. Ab initio calculation of molecular energies including parity violating interactions

    A new approach, RHF-CIS, based on the perturbation of the ground state RHF wave function by the CIS excitations, has been implemented for evaluation of energy of parity violating interaction in molecules, Epv. The earlier approach, RHF-SDE, was based on the perturbation of the RHF ground states by the single-determinant ''excitations'' (SDE). The results obtained show the dramatic difference between Epv values in the RHF-CIS framework and those in the RHF-SDE framework: the Epv values of the RHF-CIS formalism are more than one order of magnitude greater compared to the RHF-SDE formalism as well as the corresponding tensor components. The maximal total value obtained for hydrogen peroxide in the RHF-CIS framework is 3.661 X 10-19 EH (DZ** basis set) while the maximal Epv value for the RHF-SDE formalism is just 3.635 X 10-20 EH (TZ basis set). It is remarkable that both in the RFH-CIS and in the RHF-SDE approaches the diagonal tensor components of Epv strictly follow the geometry of a molecule and are always different from zero at chiral conformations. The zeros of the total Epv at chiral geometries are now found to be the results of the interplay between the diagonal tensor components values. We have carried out exhaustive analysis of the RHF-SDE formalism and found that it is not sufficiently accurate for studies of Epv. To this end, we have completely reproduced the previous work, which has been done in the RHF-SDE frame-work, and developed it further, studying how the RHF-SDE results vary when changing size and quality of basis sets. This last resource does not save the RHF-SDE formalism for evaluations of Epv from the general failure. Packages of FORTRAN routines called ENWEAK/RHFSDE-93 and ENWEAK/RHFCIS-94 have been developed which run on top of an ab initio MO package. We used 6-31G and 6-31G**, DZ and DZ**, TZ and TZ**, and (10s, 6p,**) basis sets. We will discuss the importance of the present results for possible measurement of the parity violating energy

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

    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.

  17. Coordination modes and bonding of sulfur oxides on transition metal surfaces: combined ab initio and BOC-MP results

    Seller, Harrell; Shustorovich, Evgeny

    1996-02-01

    Binding energies for sulfur oxides, SO x, x = 1-3, have been determined for several coordination modes on silver, gold and palladium surfaces employing ab initio quantum chemical methods and the bond order conservation Morse potential (BOC-MP) method. SO 2 coordination was studied in the most detail. In general the agreement between the BOC-MP and ab initio binding energies is good for the (111) surfaces of silver and palladium with both methods predicting that, in the zero coverage limit, di-coordination via S,O and O,O will be more favorable energetically than mono-coordination via S. In the case of chemisorption on the Pd (110) surface the two methods agree well for the cases in which there are formulas for the BOC-MP binding energies. In going from the (111) surfaces to the (110) surfaces of silver and palladium the ab initio calculations predict that the preferred chemisorption site shifts from the bridge site to the hollow site. On the silver surfaces the net charge transferred to the adsorbate as judged from the Mulliken populations correlates roughly with the binding energy. No significant charge transfer was found on the palladium surfaces. Our SO 2 chemisorption calculations indicate that the work functions of the metal surfaces examined should increase upon mono-S adsorption, increase to a lesser extent upon di S,O adsorption and may even decrease upon di O,O adsorption. Ab initio calculations provide evidence of the existence of SO 2 surface dimers. The binding energy predicted by the BOC-MP model for SO 3 in the bridging site agrees well with the ab initio result for SO 3 di-coordinated in the long bridge of the Ag(110) surface. The methods yield similar predictions for the case of SO on silver. Our modeling provides a coherent picture consistent with many aspects of the experimental literature. We present some model predictions, particularly the di O,O coordination mode for SO 2, that require verification experimentally.

  18. Ab Initio Study of BiFeO3: Thermodynamic Stability Conditions.

    Heifets, E; Kotomin, E A; Bagaturyants, A A; Maier, J

    2015-07-16

    BiFeO3 is investigated intensively, mainly as a multiferroic material. In this paper, the state-of-the-art ab initio hybrid functional approach with atomic basis sets was employed for a study of the stability range of BiFeO3 with respect to its decomposition into binary oxides and elementary metals, as a function of temperature and oxygen partial pressure. The calculated atomic and electronic structure of BiFeO3 was compared with previous LDA+U calculations using plane-wave basis sets. Based on performed calculations, the phase diagram was constructed, which allows us to predict the stability region of stoichiometric BiFeO3. PMID:26266871

  19. High-pressure physical properties of magnesium silicate post-perovskite from ab initio calculations

    Zi-Jiang Liu; Xiao-Wei Sun; Cai-Rong Zhang; Jian-Bu Hu; Ling-Cang Cai; Qi-Feng Chen

    2012-08-01

    The structure, thermodynamic and elastic properties of magnesium silicate (MgSiO3) post-perovskite at high pressure are investigated with quasi-harmonic Debye model and ab initio method based on the density functional theory (DFT). The calculated structural parameters of MgSiO3 post-perovskite are consistent with the available experimental results and the recent theoretical results. The Debye temperature, heat capacity and thermal expansion coefficient at high pressures and temperatures are predicted using the quasi-harmonic Debye model. The elastic constants are calculated using stress–strain relations. A complete elastic tensor of MgSiO3 post-perovskite is determined in the wide pressure range. The calculated elastic anisotropic factors and directional bulk modulus show that MgSiO3 post-perovskite possesses high elastic anisotropy.

  20. Ab Initio Calculation of Structure and Thermodynamic Properties of Zintl Aluminide SrAl2

    Fu, Zhi-Jian; Jia, Li-Jun; Xia, Ji-Hong; Tang, Ke; Li, Zhao-Hong; Sun, Xiao-Wei; Chen, Qi-Feng

    2015-12-01

    The structural and thermodynamic properties of the orthorhombic and cubic structure SrAl2 at pressure and temperature are investigated by using the ab initio plane-wave pseudopotential density functional theory methodwithin the generalised gradient approximation (GGA). The calculated lattice parameters are in agreement with the available experimental data and other theoretical results. The phase transition predicted takes place at 0.5 GPa from the orthorhombic to the cubic structure at zero temperature. The thermodynamic properties of the zinc-blende structure SrAl2 are calculated by the quasi-harmonic Debye model. The pressure-volume relationship and the variations inthe thermal expansion α are obtained systematically in the pressure and temperature ranges of 0-5 GPa and 0-500 K, respectively.

  1. Extend of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches

    Rosenow, Phil

    2016-01-01

    The extent of hydrogen coverage of the Si(001)c(4x2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even if corrections by the Einstein model for surface vibrations are considered. The on-set of H2 desorption from the fully hydrogenated surface is predicted to occur at temperatures around 750 K. Strong changes in hydrogen coverage are found between 1000 and 1200 K in good agreement with previous reflectance anisotropy spectroscopy experiments. These findings allow a rational choice for the surface state in the computationa...

  2. Study of the atomic rare gas behaviour by ab initio calculations

    The atomic behaviour of helium and krypton in uranium dioxide has been studied using an ab initio simulation technique. Incorporation energies and solution energies of these two rare gases have been calculated. Krypton atoms are found to be insoluble in this nuclear fuel whatever the trap considered and their presence in the lattice induces swelling when they are located in interstitial sites or in oxygen vacancies. Due to its small atomic size, the predicted helium behaviour is very different. Indeed, helium is found to be soluble in stoichiometric and hyper-stoichiometric uranium dioxide in the presence of uranium vacancies or divacancies constituted by one uranium and one oxygen vacancy. Moreover helium atoms induce a lattice parameter contraction except in interstitial sites where a slight expansion is calculated. (author)

  3. Ab-initio calculations of electronic, transport, and structural properties of boron phosphide

    Ejembi, J. I.; Nwigboji, I. H.; Franklin, L.; Malozovsky, Y.; Zhao, G. L.; Bagayoko, D., E-mail: diola-bagayoko@subr.edu [Department of Physics, Southern University and A and M College, Baton Rouge, Louisiana 70813 (United States)

    2014-09-14

    We present results from ab-initio, self-consistent density functional theory calculations of electronic and related properties of zinc blende boron phosphide (zb-BP). We employed a local density approximation potential and implemented the linear combination of atomic orbitals formalism. This technique follows the Bagayoko, Zhao, and Williams method, as enhanced by the work of Ekuma and Franklin. The results include electronic energy bands, densities of states, and effective masses. The calculated band gap of 2.02 eV, for the room temperature lattice constant of a=4.5383 Å, is in excellent agreement with the experimental value of 2.02±0.05 eV. Our result for the bulk modulus, 155.7 GPa, agrees with experiment (152–155 GPa). Our predictions for the equilibrium lattice constant and the corresponding band gap, for very low temperatures, are 4.5269 Å and 2.01 eV, respectively.

  4. Ab initio phonon coupling and optical response of hot electrons in plasmonic metals

    Brown, Ana M; Narang, Prineha; Goddard, William A; Atwater, Harry A

    2016-01-01

    Ultrafast laser measurements probe the non-equilibrium dynamics of excited electrons in metals with increasing temporal resolution. Electronic structure calculations can provide a detailed microscopic understanding of hot electron dynamics, but a parameter-free description of pump-probe measurements has not yet been possible, despite intensive research, because of the phenomenological treatment of electron-phonon interactions. We present ab initio predictions of the electron-temperature dependent heat capacities and electron-phonon coupling coefficients of plasmonic metals. We find substantial differences from free-electron and semi-empirical estimates, especially in noble metals above transient electron temperatures of 2000 K, because of the previously-neglected strong dependence of electron-phonon matrix elements on electron energy. We also present first-principles calculations of the electron-temperature dependent dielectric response of hot electrons in plasmonic metals, including direct interband and phon...

  5. Accelerated ab-initio Molecular Dynamics: probing the weak dispersive forces in dense liquid hydrogen

    Sorella, Sandro

    2016-01-01

    We propose an ab-initio molecular dynamics method, capable to reduce dramatically the autocorrelation time required for the simulation of classical and quantum particles at finite temperature. The method is based on an efficient implementation of a first order Langevin dynamics modified by means of a suitable, position dependent acceleration matrix $S$. Here we apply this technique, within a Quantum Monte Carlo (QMC) based wavefuntion approach and within the Born-Oppheneimer approximation, for determining the phase diagram of high-pressure Hydrogen with simulations much longer than the autocorrelation time. With the proposed method, we are able to equilibrate in few hundreds steps even close to the liquid-liquid phase transition (LLT). Within our approach we find that the LLT transition is consistent with recent density functionals predicting a much larger transition pressures when the long range dispersive forces are taken into account.

  6. Charge Transfer in FeO: A combined Molecular-Dynamics and Ab Initio Study

    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

  7. Efficient ab initio free energy calculations by classically assisted trajectory sampling

    Wilson, Hugh F.

    2015-12-01

    A method for efficiently performing ab initio free energy calculations based on coupling constant thermodynamic integration is demonstrated. By the use of Boltzmann-weighted sums over states generated from a classical ensemble, the free energy difference between the classical and ab initio ensembles is readily available without the need for time-consuming integration over molecular dynamics trajectories. Convergence and errors in this scheme are discussed and characterised in terms of a quantity representing the degree of misfit between the classical and ab initio systems. Smaller but still substantial efficiency gains over molecular dynamics are also demonstrated for the calculation of average properties such as pressure and total energy for systems in equilibrium.

  8. Ab initio calculations of phosphorus and arsenic clustering parameters for the improvement of process simulation models

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

    2008-12-05

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

  9. Electrical resistivity of NaPb compound-forming liquid alloy using ab initio pseudopotentials

    Anil Thakur; N S Negi; P K Ahluwalla

    2005-08-01

    The study of electrical resistivity of compound-forming liquid alloy, NaPb, is presented as a function of concentration. Hard sphere diameters of Na and Pb are obtained through the interionic pair potentials evaluated using Troullier and Martins ab initio pseudopotential, which have been used to calculate the partial structure factors (). Considering the liquid alloy to be a ternary mixture, Ziman formula, modified for complex formation has been used for calculating resistivity of binary liquid alloys. Form factors are calculated using ab initio pseudopotentials. The results suggest that Ziman formalism, when used with ab initio pseudopotentials, are quite successful in explaining the electrical resistivity data of compound-forming binary liquid alloys.

  10. An Efficient Time-Stepping Scheme for Ab Initio Molecular Dynamics Simulations

    Tsuchida, Eiji

    2016-08-01

    In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. We also propose several extensions of the algorithm required for use in ab initio molecular dynamics. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2× performance gain over the standard Verlet method for a given accuracy. We also show how to generate a canonical ensemble within this approach.

  11. Matrix Product Operators, Matrix Product States, and ab initio Density Matrix Renormalization Group algorithms

    Chan, Garnet Kin-Lic; Nakatani, Naoki; Li, Zhendong; White, Steven R

    2016-01-01

    Current descriptions of the ab initio DMRG algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab-initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational par...

  12. Accurate evaluation of magnetic coupling between atoms with numerous open shells: An ab initio method

    Gellé, A.; Varignon, J.; Lepetit, M.-B.

    2009-11-01

    We propose a new ab initio method designed for the accurate calculation of effective exchange integrals between atoms with numerous open shells. This method applies to ferromagnetic as well as antiferromagnetic exchange, direct or ligand-mediated exchange. Test calculations on high spin transition metal oxides such as KNiF3, Ba2CoS3 or YMnO3 exhibit a very good accuracy compared either to the best ab initio calculations —when those are feasible— and with experimental evaluations.

  13. Ab initio calculations versus polarized neutron diffraction for the spin density of free radicals

    The determination of the magnetization distribution using polarized neutron diffraction has played a key role during the last twenty years in the field of molecular magnetism. This distribution can also be obtained by first principle ab initio calculations. Such calculations always rely on approximations and the question that arises is to know whether the obtained results are reliable enough to represent accurately the properties of these molecules. The comparison between polarized neutron experimental results and ab initio calculations has turned to provide stringent tests for these methods. In the resent article a comparison between experimental and theoretical results is made and is illustrated by examples based on magnetic free radicals. (author)

  14. Ab initio implementation of quantum trajectory mean-field approach and dynamical simulation of the N2CO photodissociation

    In this work, the recently introduced quantum trajectory mean-field (QTMF) approach is implemented and employed to explore photodissociation dynamics of diazirinone (N2CO), which are based on the high-level ab initio calculation. For comparison, the photodissociation process has been simulated as well with the fewest-switches surface hopping (FSSH) and the ab initio multiple spawning (AIMS) methods. Overall, the dynamical behavior predicted by the three methods is consistent. The N2CO photodissociation at λ > 335 nm is an ultrafast process and the two C—N bonds are broken in a stepwise way, giving birth to CO and N2 as the final products in the ground state. Meanwhile, some noticeable differences were found in the QTMF, FSSH, and AIMS simulated time constants for fission of the C—N bonds, excited-state lifetime, and nonadiabatic transition ratios in different intersection regions. These have been discussed in detail. The present study provides a clear evidence that direct ab initio QTMF approach is one of the reliable tools for simulating nonadiabatic dynamics processes

  15. Multi-scale modeling of materials: from ab-initio calculations to kinetic simulations; Modelisation multiechelle des materiaux de l'ab-initio a la cinetique

    Willaime, F. [Division de l' energie nucleaire, CEA Centre de Saclay, 91191 Gif-sur-Yvette (France); Deutsch, T.; Pochet, P. [INAC, Direction des sciences de la matiere, CEA Centre de Grenoble, 38054 Grenoble Cedex 9 (France)

    2010-07-01

    Ab-initio calculation methods, for the purposes of computing electronic structures, have made it possible, since the early nineties, to simulate the properties of perfect crystalline materials (materials free of any defect). By improving such methods, and with the increasing power of supercomputers, it has now become feasible to simulate the properties of elementary defects, which may seldom be accessed directly through experiments. This has opened up a vast, fruitful field of multi-scale simulations, where such data yield the basis for realistic simulations of the kinetics of materials evolution. The kinetic Monte-Carlo method thus provides the means to model phenomena acting at the scale of a second, or even of a year. In the issue of self-diffusion in silicon, multi-scale simulation has been successful in predicting an asymmetrical behaviour: a speeding up of vacancy diffusion under compression and a tailing off under tension, and conversely, a speeding up of interstitial diffusion under tension and a falling off under compression. Multi-scale modeling has also been successful in simulating irradiation defects in iron. (A.C.)

  16. Deuteron-induced nucleon transfer reactions within an ab initio framework: First application to p -shell nuclei

    Raimondi, Francesco; Hupin, Guillaume; Navrátil, Petr; Quaglioni, Sofia

    2016-05-01

    Background: Low-energy transfer reactions in which a proton is stripped from a deuteron projectile and dropped into a target play a crucial role in the formation of nuclei in both primordial and stellar nucleosynthesis, as well as in the study of exotic nuclei using radioactive beam facilities and inverse kinematics. Ab initio approaches have been successfully applied to describe the 3H (d ,n )4He and 3He(d ,p )4He fusion processes. Purpose: An ab initio treatment of transfer reactions would also be desirable for heavier targets. In this work, we extend the ab initio description of (d ,p ) reactions to processes with light p -shell nuclei. As a first application, we study the elastic scattering of deuterium on 7Li and the 7Li(d ,p )8Li transfer reaction based on a two-body Hamiltonian. Methods: We use the no-core shell model to compute the wave functions of the nuclei involved in the reaction, and describe the dynamics between targets and projectiles with the help of microscopic-cluster states in the spirit of the resonating group method. Results: The shapes of the excitation functions for deuterons impinging on 7Li are qualitatively reproduced up to the deuteron breakup energy. The interplay between d -7Li and p -8Li particle-decay channels determines some features of the 9Be spectrum above the d +7Li threshold. Our prediction for the parity of the 17.298 MeV resonance is at odds with the experimental assignment. Conclusions: Deuteron stripping reactions with p -shell targets can now be computed ab initio, but calculations are very demanding. A quantitative description of the 7Li(d ,p )8Li reaction will require further work to include the effect of three-nucleon forces and additional decay channels and to improve the convergence rate of our calculations.

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

    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)

  18. Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

    John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

    2016-04-01

    We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

  19. Quantum Ring-Polymer Contraction Method: Including nuclear quantum effects at no additional computational cost in comparison to ab-initio molecular dynamics

    John, Chris; Habershon, Scott; Kühne, Thomas D

    2015-01-01

    We present a simple and accurate computational method, which facilitates ab-initio path-integral molecular dynamics simulations, where the quantum mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions. This development permits to routinely include nuclear quantum effects in ab-initio molecular dynamics simulations.

  20. Stiffness and toughness prediction of Co–Fe–Ta–B metallic glasses, alloyed with Y, Zr, Nb, Mo, Hf, W, C, N and O by ab initio molecular dynamics.

    Schnabel, Volker; Evertz, Simon; Rueß, Holger; Music, Denis; Schneider, Jochen M

    2015-03-18

    Ab initio molecular dynamics simulations are used to systematically explore the influence of alloying on the stiffness and plasticity of Co–Fe–Ta–B metallic glasses. The Co(43.5)Ta(6.1)B(50.4) metallic glass studied in this work, with a Young’s modulus of 295 GPa, is the stiffest metallic glass known in literature. From the analysis of the density of the states it is suggested that the very large stiffness is due to strong covalent metal to boron bonding. Furthermore it has been observed that by alloying with Y, Zr, Nb, Mo, Hf, W, C, N and O the bulk to shear modulus ratio can be varied from 2.08 to 2.82. As noted by Lewandowski et al (2005 Phil. Mag. Lett.85 77) a brittle to plastic transition for metallic glasses can be identified in the range of 2.33 to 2.44. Hence, it is evident that the whole range from brittle to plastic behaviour can be covered,with the systems studied in this work. This evolution from brittle to plastic behaviour can be attributed to a change from predominately covalent to predominately metallic bond character. PMID:25710383

  1. Electronic states and nature of bonding of the molecule PdGe by all electron ab initio HF–CI calculations and mass spectrometric equilibrium experiments

    Shim, Irene; Kingcade, Joseph E. , Jr.; Gingerich, Karl A.

    1986-01-01

    In the present work we present all-electron ab initio Hartree–Fock (HF) and configuration interaction (CI) calculations of six electronic states of the PdGe molecule. The molecule is predicted to have a 3Pi ground state and two low-lying excited states 3Sigma− and 1Sigma+. The electronic structure...

  2. Ab initio gene identification: prokaryote genome annotation with GeneScan and GLIMMER

    Gautam Aggarwal; Ramakrishna Ramaswamy

    2002-02-01

    We compare the annotation of three complete genomes using the ab initio methods of gene identification GeneScan and GLIMMER. The annotation given in GenBank, the standard against which these are compared, has been made using GeneMark. We find a number of novel genes which are predicted by both methods used here, as well as a number of genes that are predicted by GeneMark, but are not identified by either of the nonconsensus methods that we have used. The three organisms studied here are all prokaryotic species with fairly compact genomes. The Fourier measure forms the basis for an efficient non-consensus method for gene prediction, and the algorithm GeneScan exploits this measure. We have bench-marked this program as well as GLIMMER using 3 complete prokaryotic genomes. An effort has also been made to study the limitations of these techniques for complete genome analysis. GeneScan and GLIMMER are of comparable accuracy insofar as gene-identification is concerned, with sensitivities and specificities typically greater than 0.9. The number of false predictions (both positive and negative) is higher for GeneScan as compared to GLIMMER, but in a significant number of cases, similar results are provided by the two techniques. This suggests that there could be some as-yet unidentified additional genes in these three genomes, and also that some of the putative identifications made hitherto might require re-evaluation. All these cases are discussed in detail.

  3. Ab-initio modeling of an anion $C_{60}^-$ pseudopotential for fullerene-based compounds

    Vrubel, I I; Ivanov, V K

    2015-01-01

    A pseudopotential of $C_{60}^-$ has been constructed from ab-initio quantum-mechanical calculations. Since the obtained pseudopotential can be easily fitted by rather simple analytical approximation it can be effectively used both in classical and quantum molecular dynamics of fullerene-based compounds.

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

    Gazda, Daniel; Gal, A.

    2016-01-01

    Roč. 116, č. 12 (2016), s. 122501. ISSN 0031-9007 R&D Projects: GA ČR(CZ) GA15-04301S Institutional support: RVO:61389005 Keywords : ab initio * shell model * four-body calculations Subject RIV: BE - Theoretical Physics Impact factor: 7.512, year: 2014

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

    Shim, Irene; Gingerich, Karl. A.

    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...

  6. Ab initio charge-carrier mobility model for amorphous molecular semiconductors

    Massé, Andrea; Friederich, Pascal; Symalla, Franz; Liu, Feilong; Nitsche, Robert; Coehoorn, Reinder; Wenzel, Wolfgang; Bobbert, Peter A.

    2016-05-01

    Accurate charge-carrier mobility models of amorphous organic molecular semiconductors are essential to describe the electrical properties of devices based on these materials. The disordered nature of these semiconductors leads to percolative charge transport with a large characteristic length scale, posing a challenge to the development of such models from ab initio simulations. Here, we develop an ab initio mobility model using a four-step procedure. First, the amorphous morphology together with its energy disorder and intermolecular charge-transfer integrals are obtained from ab initio simulations in a small box. Next, the ab initio information is used to set up a stochastic model for the morphology and transfer integrals. This stochastic model is then employed to generate a large simulation box with modeled morphology and transfer integrals, which can fully capture the percolative charge transport. Finally, the charge-carrier mobility in this simulation box is calculated by solving a master equation, yielding a mobility function depending on temperature, carrier concentration, and electric field. We demonstrate the procedure for hole transport in two important molecular semiconductors, α -NPD and TCTA. In contrast to a previous study, we conclude that spatial correlations in the energy disorder are unimportant for α -NPD. We apply our mobility model to two types of hole-only α -NPD devices and find that the experimental temperature-dependent current density-voltage characteristics of all devices can be well described by only slightly decreasing the simulated energy disorder strength.

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

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

    2014-01-01

    Roč. 118, č. 35 (2014), s. 7507-7515. ISSN 1089-5639 R&D Projects: GA ČR GBP208/12/G016 Institutional support: RVO:61388963 Keywords : hydrated electron * optical spectrum * ab initio molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.693, year: 2014

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

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

    2012-01-01

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

  9. Ab initio calculation of the lifetimes of 4p and 3d levels of Ca+

    We have done an ab initio calculation based on the Brueckner approximation for the lifetimes of 4p2P and 3d2D levels of Ca+. The results of the Brueckner approximation differ from experiment by 2.5%. With leading third-order corrections included, our results agree with the latest accurate experiment within a 1% difference

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

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

    2010-01-01

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

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

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

    2006-01-01

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

  12. Ab initio study of long-period superstructures in close-packed A3B compounds

    Rosengaard, N. M.; Skriver, Hans Lomholt

    1994-01-01

    We have performed ab initio calculations of the stability of one-dimensional long-period superstructures in Cu3Pd, Cu3Al, and Ag3Mg by means of an interface Green's function technique based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations. The...

  13. Mechanisms for catalytic carbon nanofiber growth studied by ab initio density functional theory calculations

    Abild-Pedersen, Frank; Nørskov, Jens Kehlet; Rostrup-Nielsen, Jens;

    2006-01-01

    Mechanisms and energetics of graphene growth catalyzed by nickel nanoclusters were studied using ab initio density functional theory calculations. It is demonstrated that nickel step-edge sites act as the preferential growth centers for graphene layers on the nickel surface. Carbon is transported...

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

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

    2013-01-01

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

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

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

    2013-01-01

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

  16. Stabilization of Ab Initio Molecular Dynamics Simulations at Large Time Steps

    Tsuchida, Eiji

    2014-01-01

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

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

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

    2009-01-01

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

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

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

    2014-01-01

    Roč. 70, MAY (2014), s. 92-104. ISSN 1359-6454 Grant 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

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

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

    2002-01-01

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

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

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

    2014-01-01

    In the midst of the epitaxial circuitry revolution in silicon technology, we look ahead to the next paradigm shift: effective use of the third dimension - in particular, its combination with epitaxial technology. We perform ab initio calculations of atomically thin epitaxial bilayers in silicon, ...

  1. Raman and ab initio studies of simple and binary 1-alkyl-3-methylimidazolium ionic liquids

    Berg, R.W.; Deetlefs, M.; Seddon, K.R.;

    2005-01-01

    Raman spectra of the ionic liquids, 1-butyl-3-methylimidazolium hexafluorophosphate ([C(4)mim][PF6]), 1-hexyl-3-methylimidazolium chloride ([C(6)mim]Cl), and 1-hexyl-3-methylimidazolium hexafluorophosphate ([C(6)mim][PF6]), and binary mixtures thereof, have been assigned using ab initio MP2...

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

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

    2015-01-01

    Roč. 85, FEB (2015), s. 53-66. ISSN 1359-6454 Institutional support: RVO:68081723 Keywords : Solid-solution strengthening * DFT * Peierls–Nabarro model * Ab initio * Al alloy s Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 4.465, year: 2014

  3. Ab initio Nuclear structure Theory with chiral two- plus three-nucleon interactions

    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.

  4. Ab Initio Calculations of Deuterium Isotope Effects on Chemical Shifts of Salt-Bridged Lysines

    Ullah, Saif; Ishimoto, Takayoshi; Williamson, Mike P.;

    2011-01-01

    Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation. This me...

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

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

    1996-10-01

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

  6. Ab Initio Studies of Chlorine Oxide and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

    Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of chlorine oxide and nitrogen oxide species will be demonstrated by presentation of some example studies. In particular the geometrical structures, vibrational spectra, and heats of formation Of ClNO2, CisClONO, and trans-ClONO are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the ab initio results are shown to fill in the gaps and to resolve the experimental controversy. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of ClONO2, HONO2, ClOOC17 ClOOH, and HOOH will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of the experimental studies.

  7. Ab initio ground state phenylacetylene-argon intermolecular potential energy surface and rovibrational spectrum

    Cybulski, Hubert; Fernandez, Berta; Henriksen, Christian; Felker, Peter M.

    2012-01-01

    We evaluate the phenylacetylene-argon intermolecular potential energy surface by fitting a representative number of ab initio interaction energies to an analytic function. These energies are calculated at a grid of intermolecular geometries, using the CCSD(T) method and the aug-cc-pVDZ basis set...

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

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

    2014-01-01

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

  9. Ab Initio Investigations of the C2F4S Isomers and of Their Interconversions

    Shim, Irene; Vallano-Lorenzo, Sandra; Lisbona-Martin, Pilar;

    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...

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

    Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms. PMID:27394094

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

    Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R.

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

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

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

    2003-01-01

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

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

    Timko, Jeff; Kuyucak, Serdar

    2012-11-01

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

  14. Direct molecular simulation of nitrogen dissociation based on an ab initio potential energy surface

    Valentini, Paolo, E-mail: vale0142@umn.edu; Schwartzentruber, Thomas E., E-mail: schwart@aem.umn.edu; Bender, Jason D., E-mail: jbender73@gmail.com; Nompelis, Ioannis, E-mail: nompelis@umn.edu; Candler, Graham V., E-mail: candler@umn.edu [Department of Aerospace Engineering and Mechanics, College of Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (United States)

    2015-08-15

    The direct molecular simulation (DMS) approach is used to predict the internal energy relaxation and dissociation dynamics of high-temperature nitrogen. An ab initio potential energy surface (PES) is used to calculate the dynamics of two interacting nitrogen molecules by providing forces between the four atoms. In the near-equilibrium limit, it is shown that DMS reproduces the results obtained from well-established quasiclassical trajectory (QCT) analysis, verifying the validity of the approach. DMS is used to predict the vibrational relaxation time constant for N{sub 2}–N{sub 2} collisions and its temperature dependence, which are in close agreement with existing experiments and theory. Using both QCT and DMS with the same PES, we find that dissociation significantly depletes the upper vibrational energy levels. As a result, across a wide temperature range, the dissociation rate is found to be approximately 4–5 times lower compared to the rates computed using QCT with Boltzmann energy distributions. DMS calculations predict a quasi-steady-state distribution of rotational and vibrational energies in which the rate of depletion of high-energy states due to dissociation is balanced by their rate of repopulation due to collisional processes. The DMS approach simulates the evolution of internal energy distributions and their coupling to dissociation without the need to precompute rates or cross sections for all possible energy transitions. These benchmark results could be used to develop new computational fluid dynamics models for high-enthalpy flow applications.

  15. Direct molecular simulation of nitrogen dissociation based on an ab initio potential energy surface

    The direct molecular simulation (DMS) approach is used to predict the internal energy relaxation and dissociation dynamics of high-temperature nitrogen. An ab initio potential energy surface (PES) is used to calculate the dynamics of two interacting nitrogen molecules by providing forces between the four atoms. In the near-equilibrium limit, it is shown that DMS reproduces the results obtained from well-established quasiclassical trajectory (QCT) analysis, verifying the validity of the approach. DMS is used to predict the vibrational relaxation time constant for N2–N2 collisions and its temperature dependence, which are in close agreement with existing experiments and theory. Using both QCT and DMS with the same PES, we find that dissociation significantly depletes the upper vibrational energy levels. As a result, across a wide temperature range, the dissociation rate is found to be approximately 4–5 times lower compared to the rates computed using QCT with Boltzmann energy distributions. DMS calculations predict a quasi-steady-state distribution of rotational and vibrational energies in which the rate of depletion of high-energy states due to dissociation is balanced by their rate of repopulation due to collisional processes. The DMS approach simulates the evolution of internal energy distributions and their coupling to dissociation without the need to precompute rates or cross sections for all possible energy transitions. These benchmark results could be used to develop new computational fluid dynamics models for high-enthalpy flow applications

  16. Relaxation of Small Molecules:an ab initio Study

    CAOYi-Gang; A.Antons; 等

    2002-01-01

    Using an ab inito total energy and force method,we have relaxed several group IV and group V elemental clusters,in detail the arsenic and antimony dimers,silicon,phosphorus,arsenic and antimony tetraners,The obtained bond lengths and cohesive energies are more accurate than other calculating methods,and in excellent agreement with the experimental results.

  17. Ab initio kinetics studies of hydrogen atom abstraction from methyl propanoate.

    Tan, Ting; Yang, Xueliang; Ju, Yiguang; Carter, Emily A

    2016-02-14

    The kinetics of hydrogen abstraction by five radicals (H, CH3, O((3)P), OH, and HO2) from a biodiesel surrogate, methyl propanoate (MP), is theoretically investigated. We employ high-level ab initio quantum chemistry methods, coupled-cluster singles and doubles with perturbative triples correction (CCSD(T)) and multi-reference singles and doubles configuration interaction (MRSDCI) with the Davidson-Silver (DS) correction, and obtain chemically accurate reaction energetics. Overall, MRSDCI + DS predicts comparable energetics to CCSD(T) for MP + H/CH3/O/OH. The rate constants are computed using transition state theory (TST-Rice-Ramsperger-Kassel-Marcus theory) in conjunction with the separable-hindered-rotor approximation, variable reaction coordinate TST, and the multi-structure all-structure (MS-AS) approach. A simplified method, semi-multi-structure, is also employed for MP + OH/HO2, and the rate coefficients with this less expensive method are in good agreement with the results obtained with the MS-AS method. The fitted modified Arrhenius expressions are provided over a temperature range of 250 to 2000 K. The predicted rate coefficients for MP + OH agree remarkably well with experimental data over a wide temperature range. Branching ratio analysis of all the studied reactions shows that abstractions of the secondary H atoms within MP are expected to dominate the consumption of fuel at low temperatures, and the contributions of abstractions from the two methyl groups increase with temperature for all abstracting radicals. PMID:26796249

  18. Ab initio Mechanism Study on the Reaction of Chlorine Atom with Formic Acid

    于海涛; 付宏刚; 等

    2003-01-01

    The potential energy surface(PES) for the reaction of Cl atom with HCOOH is predicted using ab initio molecular orbital calculation methods at UQCIDS(T,full)6-311++G(3df,2p)//UMP2(full)/6-311+G(d,P) level of theory with zero-point vibrational energy (ZPVE) correction.The calculated results show that the reaction mechanism of Cl atom with formic acid is a C-site hydrogen abstraction reaction from cis-HOC(H)O molecule by Cl atom with a 3.73kJ/mol reaction barrier height,leading to the formation of cis-HOCO radical which will reacts with Cl atom or other molecules in such a reaction system.Because the reaction barrier height of O-site hydrogen abstraction reaction from cis-HOC(H)O molecule by Cl atom which leads to the formation of HCO2 radical is 67.95kJ/mol,it is a secondary reaction channel in experiment,This is in good agreement with the prediction based on the previous experiments.

  19. Ab-Initio Computations of Electronic and Related Properties of cubic Lithium Selenide (Li2Se)

    Goita, Abdoulaye; Nwigboji, Ifeanyi H.; Malozovsky, Yuriy; Bagayoko, Diola

    We present theoretical predictions, from ab-initio, self-consistent calculations, of electronic and related properties of cubic lithium selenide (Li2Se). We employed a local density approximation (LDA) potential and the linear combination of atomic orbitals (LCAO). We performed the computations following the Bagayoko, Zhao, and Williams (BZW) method, as enhanced by Ekuma and Franklin (BZW-EF). Our results include electronic energies, total and partial densities of states, effective masses, and the bulk modulus. The theoretical equilibrium lattice constant is 5.882 Å. We found cubic Li2Se to have a direct band gap of 4.363 eV (prediction), at Γ. This gap is 4.065 eV for a room temperature lattice constant of 6.017 Å. The calculated bulk modulus is 31.377 GPa. Acknowledgments: This work was funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award No. DE- NA0002630), LaSPACE, and LONI-SUBR.

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

    Allen, B. Danette; Alexandrov, Natalia

    2016-01-01

    Incremental approaches to air transportation system development inherit current architectural constraints, which, in turn, place hard bounds on system capacity, efficiency of performance, and complexity. To enable airspace operations of the future, a clean-slate (ab initio) airspace design(s) must be considered. This ab initio National Airspace System (NAS) must be capable of accommodating increased traffic density, a broader diversity of aircraft, and on-demand mobility. System and subsystem designs should scale to accommodate the inevitable demand for airspace services that include large numbers of autonomous Unmanned Aerial Vehicles and a paradigm shift in general aviation (e.g., personal air vehicles) in addition to more traditional aerial vehicles such as commercial jetliners and weather balloons. The complex and adaptive nature of ab initio designs for the future NAS requires new approaches to validation, adding a significant physical experimentation component to analytical and simulation tools. In addition to software modeling and simulation, the ability to exercise system solutions in a flight environment will be an essential aspect of validation. The NASA Langley Research Center (LaRC) Autonomy Incubator seeks to develop a flight simulation infrastructure for ab initio modeling and simulation that assumes no specific NAS architecture and models vehicle-to-vehicle behavior to examine interactions and emergent behaviors among hundreds of intelligent aerial agents exhibiting collaborative, cooperative, coordinative, selfish, and malicious behaviors. The air transportation system of the future will be a complex adaptive system (CAS) characterized by complex and sometimes unpredictable (or unpredicted) behaviors that result from temporal and spatial interactions among large numbers of participants. A CAS not only evolves with a changing environment and adapts to it, it is closely coupled to all systems that constitute the environment. Thus, the ecosystem that

  1. Ab initio STM and STS simulations on magnetic and nonmagnetic metallic surfaces

    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.)

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

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

    2015-02-27

    The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

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

    The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA

  4. Liquid Be, Ca and Ba. An orbital-free ab-initio molecular dynamics study

    Several static and dynamic properties of liquid beryllium (l-Be), liquid calcium (l-Ca) and liquid barium (l-Ba) near their triple point have been evaluated by the orbital-free ab initio molecular dynamics method (OF-AIMD), where the interaction between valence electrons and ions is described by means of local pseudopotentials. These local pseudopotentials used were constructed through a force-matching process with those obtained from a Kohn-Sham ab initio molecular dynamics study (KS-AIMD) of a reduced system with non-local pseudopotentials. The calculated static structures show good agreement with the available experimental data, including an asymmetric second peak in the structure factor which has been linked to the existence of a marked icosahedral short-range order in the liquid. As for the dynamic properties, we obtain collective density excitations whose associated dispersion relations exhibit a positive dispersion

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

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

    2014-08-01

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

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

    Zaharieva, Roussislava

    subject of studies of the shock or thermally induced chemical reactions of the two solids comprising these reactive materials, from first principles, is a relatively new field of study. The published literature on ab initio techniques or quantum mechanics based approaches consists of the ab initio or ab initio-molecular dynamics studies in related fields that contain a solid and a gas. One such study in the literature involves a gas and a solid. This is an investigation of the adsorption of gasses such as carbon monoxide (CO) on Tungsten. The motivation for these studies is to synthesize alternate or synthetic fuel technology by Fischer-Tropsch process. In this thesis these studies are first to establish the procedure for solid-solid reaction and then to extend that to consider the effects of mechanical strain and temperature on the binding energy and chemisorptions of CO on tungsten. Then in this thesis, similar studies are also conducted on the effect of mechanical strain and temperature on the binding energies of Titanium and hydrogen. The motivations are again to understand the method and extend the method to such solid-solid reactions. A second motivation is to seek strained conditions that favor hydrogen storage and strain conditions that release hydrogen easily when needed. Following the establishment of ab initio and ab initio studies of chemical reactions between a solid and a gas, the next step of research is to study thermally induced chemical reaction between two solids (Ni+Al). Thus, specific new studies of the thesis are as follows: (1) Ab initio Studies of Binding energies associated with chemisorption of (a) CO on W surfaces (111, and 100) at elevated temperatures and strains and (b) adsorption of hydrogen in titanium base. (2) Equations of state of mixtures of reactive material structures from ab initio methods. (3) Ab initio studies of the reaction initiation, transition states and reaction products of intermetallic mixtures of (Ni+Al) at elevated

  7. Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.

    Kulczycka-Mierzejewska, Katarzyna; Trylska, Joanna; Sadlej, Joanna

    2016-01-01

    Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born-Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations. PMID:26733483

  8. Ab initio calculations on the magnetic properties of transition metal complexes

    We present a protocol for the ab initio determination of the magnetic properties of mono- and polynuclear transition metal compounds. First, we obtain the low lying electronic states by multireference methods. Then, we include spin-orbit coupling and an external magnetic field for the determination of zero-field splitting and g-tensors. For the polynuclear complexes the magnetic exchange coupling constants are determined by a modified complete active space self consistent field method. Based on the results of the ab initio calculations, magnetic data such as magnetic susceptibility or magnetization are simulated and compared to experimental data. The results obtained for the polynuclear complexes are further analysed by calculations on model complexes where part of the magnetic centers are substituted by diamagnetic ions. The methods are applied to different Co and Ni containing transition metal complexes

  9. Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

    Sharma, Nalini; Ahluwalia, P. K. [Department of Physics, Himachal Pradesh University, Shimla(HP)-171005 (India); Thakur, Anil [Department of Physics, Govt. P. G. College Solan (HP)-173212 (India)

    2015-05-15

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.

  10. Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg10In90, Hg30In70, Hg50In50, Hg70In30 and Hg90In10) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys

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

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

    2013-01-01

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

  12. Emergent properties of nuclei from ab initio coupled-cluster calculations

    Hagen, G; Hjorth-Jensen, M; Papenbrock, T

    2016-01-01

    Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. This endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. This paper reviews some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO$_{\\rm sat}$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to $^{56}$Ni. We derive an efficient scheme for including continuum effects in coupled-clust...

  13. Ab initio calculations on twisted graphene/hBN: Electronic structure and STM image simulation

    Correa, J. D.; Cisternas, E.

    2016-09-01

    By performing ab initio calculations we obtained theoretical scanning tunneling microscopy (STM) images and studied the electronic properties of graphene on a hexagonal boron-nitrite (hBN) layer. Three different stack configurations and four twisted angles were considered. All calculations were performed using density functional theory, including van der Waals interactions as implemented in the SIESTA ab initio package. Our results show that the electronic structure of graphene is preserved, although some small changes are induced by the interaction with the hBN layer, particularly in the total density of states at 1.5 eV under the Fermi level. When layers present a twisted angle, the density of states shows several van Hove singularities under the Fermi level, which are associated to moiré patterns observed in theoretical STM images.

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

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

    2011-01-01

    For the first time, the differences between the spectra of amphetamine and amphetamine-H+ and between different conformers are thoroughly studied by ab initio model calculations, and Raman and surface-enhanced Raman spectroscopy (SERS) spectra are measured for different species of amphetamine....... The spectra of amphetamine and amphetamine-H+ sampleswere obtained and assigned according to a comparison of the experimental spectra and the ab initio MO calculations, performed using the Gaussian 03W program (Gaussian, Inc., Pittsburgh, PA). The analyses were based on complete geometry minimization...... with internal bonds (sulfates, hydrogen phosphates, etc.) need to be taken into account when employing these spectra for identification purposes. These results also show how Raman spectroscopy can assist the forensic community in drug profiling studies. Furthermore, because their spectra are different...

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

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

  16. Properties of metals during the heating by intense laser irradiation using ab initio simulations

    Holst, Bastian; Recoules, Vanina; Torrent, Marc; Mazevet, Stephane

    2011-10-01

    Ultrashort laser pulses irradiating a target heat the electrons to very high temperatures. In contrast, the ionic lattice is unaffected on the time scale of the laser pulse since the heat capacity of electrons is much smaller than that of the lattice. This non-equilibrium system can be described as a composition of two subsystems: one consisting of hot electrons and the other of an ionic lattice at low temperature. We studied the effect of this intense electronic excitations on the optical properties of gold using ab initio simulations. We additionally use ab initio linear response to compute the phonon spectrum and the electron-phonon coupling constant within Density Functional Theory for several electronic temperatures of few eV. LULI, Ecole Polytechnique, CNRS, CEA, UPMC, 91128 Palaiseau, France.

  17. A fully ab initio potential energy surface for ClH2 reactive system

    2000-01-01

    An ab initio analytical potential energy surface called BW3 for the ClH2 reactive system is presented. The fit of this surface is based on about 1 200 ab initio energy points, computed with multi-reference configuration interaction(MRCI) and scaling external correlation (SEC) method and a very large basis set. The precision in the fit is very high. The BW3 surface could reproduce correctly the dissociation energy of H2 and HCl, and the endothermicity of the Cl + H2 abstraction reaction. For the Cl + H2 abstraction reaction, the saddle point of BW3 lies in collinear geometries, and the barrier height is 32.84 kJ/mol; for the H + ClH exchange reaction, the barrier of BW3 is also linear, with a height of 77.40 kJ/mol.

  18. A fully ab initio potential energy surface for C1H2 reactive system

    边文生; 刘成卜; H.J.Werner

    2000-01-01

    An ab initio analytical potential energy surface called BW3 for the CIH2 reactive system is presented. The fit of this surface is based on about 1 200 ab initio energy points, computed with multi-reference configuration interaction(MRCI) and scaling external correlation (SEC) method and a very large basis set. The precision in the fit is very high. The BW3 surface could reproduce correctly the dissociation energy of H2 and HCI, and the endothermicity of the Cl + H2 abstraction reaction. For the Cl + H2 abstraction reaction, the saddle point of BW3 lies in collinear geometries, and the barrier height is 32.84 kJ/mol; for the H + CIH exchange reaction, the barrier of BW3 is also linear, with a height of 77.40 kJ/mol.

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

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

    2016-05-01

    Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg10In90, Hg30In70,. Hg50In50, Hg70In30, and Hg90Pb10) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.

  20. Melting of sodium under high pressure. An ab-initio study

    González, D. J.; González, L. E. [Departamento de Física Teórica, Atómica y Optica, Universidad de Valladolid, 47011 Valladolid (Spain)

    2015-08-17

    We report ab-initio molecular dynamics simulations of dense liquid/solid sodium for a pressure range from 0 to 100 GPa. The simulations have been performed with the orbital free ab-initio molecular dynamics method which, by using the electron density as the basic variable, allows to perform simulations with large samples and for long runs. The calculated melting curve shows a maximum at a pressure ≈ 30 GPa and it is followed by a long, steep decrease. These features are in good agreement with the experimental data. For various pressures along the melting curve, we have calculated several liquid static properties (pair distribution functions, static structure factors and short-range order parameters) in order to analyze the structural effects of pressure.

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

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

    2004-01-01

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

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

    Berg, Rolf W.

    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...... 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...... 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 [C4...

  3. Implementation of a vector potential method in an ab initio Hartree-Fock code

    Tevekeliyska, Violina; Springborg, Michael; Champagne, Benoît; Kirtman, Bernard

    2012-12-01

    For extended systems exposed to an external, electrostatic field, the presence of the field leads to an extra term (E⃗. P⃗) to the Hamiltonian, where E⃗ is the field vector and P⃗ is the polarization of the system of interest. In order to find out how a polymer chain responds to an external electric perturbation, a field with a charge and a current term for the polarization is added to an ab initio Hartree-Fock Hamiltonian. The polarization expression is taken from an efficient vector potential approach (VPA) [1] for calculating electronic and nuclear responses of infinite periodic systems to finite electric fields and is implemented in the ab initio LCAO-SCF algorithm [3], which computes band structure of regular or helical polymers, taking into account the one-dimensional translational symmetry. A smoothing procedure for numerical differentiation of the orbital coefficients is used in order to calculate self-consistently the charge flow contribution to the polarization.

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

    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.

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

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

  6. {\\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...

  7. Experimental studies and ab initio calculations on characteristics of the C state of SF2 radical

    SF2 radicals were generated by a pulsed dc discharge in the mixture gas beam of SF2 and Ar. The (2+1) resonance-enhanced multiphoton ionization (REMPI) excitation spectroscopy of SF2 radical was obtained between 325 and 365 nm. The SF+ ion signals were also observed in the same wavelength range. The analysis shows that the spectrum can be assigned as the two-photon resonant excitation of SF2 radical (B-tilde1 B1 and (C-tilde1 A1 states). And also, ab initio calculations suggest that the C-tilde state is a bonding state with Rydberg characteristic. The potential energy surfaces (PESs) of SF2 and SF2+ by ab initio calculations suggest that SF+ ions originate from dissociation processes of excited SF2+ ions. (author)

  8. An efficient time-stepping scheme for ab initio molecular dynamics simulations

    Tsuchida, Eiji

    2015-01-01

    In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2x performance gain over the standard Verlet method for a given accuracy.

  9. Ab initio modelling of the behaviour of point defects and fission products in nuclear fuel

    The aim of this work is to determine precisely the mechanisms of formation and migration of defects and fission products as well as the associated energies. Examples on uranium dioxide UO2 (standard nuclear fuel) and on uranium carbide UC (potential fuel for new generation reactors) are given. The obtained results are discussed and compared with the experimental results carried out. The ab initio method used is the Projector Augmented-Wave (PAW) method based on the density functional theory. The particular electronic properties of actinides are especially studied because, on account of their 5f orbitals more or less localized around the nucleus, it is difficult to model the actinide compounds by the DFT method. In particular, the modelling of the exchange-correlation interaction of the 5f electrons of UO2 requires approximations (as GGA+U) beyond those more currently used in ab initio calculations (LDA or GGA). (O.M.)

  10. Ab initio molecular dynamics with nuclear quantum effects at classical cost: ring polymer contraction for density functional theory

    Marsalek, Ondrej

    2015-01-01

    Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ab initio ring polymer contraction (AI-RPC) scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive pro...

  11. Hydrogen adsorption in ZIF-7: A DFT and ab-initio molecular dynamics study

    Dixit, Mudit; Major, Dan Thomas; Pal, Sourav

    2016-05-01

    Primary H2 adsorption sites in a zeolitic imidazolate framework, ZIF-7, are identified using ab-initio density functional theory (DFT) based molecular dynamics annealing simulations. The simulations suggest several low energy adsorption sites. The effect of light transition metal decoration on hydrogen storage properties was studied. Our ab-intio DFT calculations illustrate that decorating the ZIF with Sc increases both the number of H2 molecules, as well as the H2 binding energy. The binding energy (∼25 kJ/mol per H2) at 8H2 loading in the pore, suggests that Sc-ZIFs can be potential candidates for hydrogen storage.

  12. Ab initio study of the unusual thermal transport properties of boron arsenide and related materials

    Broido, D. A.; Lindsay, L.; Reinecke, T. L.

    2013-12-01

    Recently, using a first principles approach, we predicted that zinc blende boron arsenide (BAs) will have an ultrahigh lattice thermal conductivity, κ, of over 2000 Wm-1K-1 at room temperature (RT), comparable to that of diamond. Here, we provide a detailed ab initio examination of phonon thermal transport in boron arsenide, contrasting its unconventional behavior with that of other related materials, including the zinc blende crystals boron nitride (BN), boron phosphide, boron antimonide, and gallium nitride (GaN). The unusual vibrational properties of BAs contribute to its weak phonon-phonon scattering and phonon-isotope scattering, which are responsible for its exceptionally high κ. The thermal conductivity of BAs has contributions from phonons with anomalously large mean free paths (˜2 μm), two to three times those of diamond and BN. This makes κ in BAs sensitive to phonon scattering from crystal boundaries. An order of magnitude smaller RT thermal conductivity in a similar material, zinc blende GaN, is connected to more separated acoustic phonon branches, larger anharmonic force constants, and a large isotope mixture on the heavy rather than the light constituent atom. The striking difference in κ for BAs and GaN demonstrates the importance of using a microscopic first principles thermal transport approach for calculating κ. BAs also has an advantageous RT coefficient of thermal expansion, which, combined with the high κ value, suggests that it is a promising material for use in thermal management applications.

  13. Ab initio atomistic thermodynamics study on the oxidation mechanism of binary and ternary alloy surfaces

    Utilizing a combination of ab initio density-functional theory and thermodynamics formalism, we have established the microscopic mechanisms for oxidation of the binary and ternary alloy surfaces and provided a clear explanation for the experimental results of the oxidation. We construct three-dimensional surface phase diagrams (SPDs) for oxygen adsorption on three different Nb-X(110) (X = Ti, Al or Si) binary alloy surfaces. On the basis of the obtained SPDs, we conclude a general microscopic mechanism for the thermodynamic oxidation, that is, under O-rich conditions, a uniform single-phase SPD (type I) and a nonuniform double-phase SPD (type II) correspond to the sustained complete selective oxidation and the non-sustained partial selective oxidation by adding the X element, respectively. Furthermore, by revealing the framework of thermodynamics for the oxidation mechanism of ternary alloys through the comparison of the surface energies of two separated binary alloys, we provide an understanding for the selective oxidation behavior of the Nb ternary alloy surfaces. Using these general microscopic mechanisms, one could predict the oxidation behavior of any binary and multi-component alloy surfaces based on thermodynamics considerations

  14. Ab initio study of Cr interactions with point defects in bcc Fe

    Full text of publication follows. Ferritic martensitic steels are candidate structural materials for fast neutron reactors, and in particular high-Cr reduced-activation steels. In Fe-Cr alloys, Cr plays a major role in the radiation-induced evolution of the mechanical properties. Using ab initio calculations based on density functional theory, the properties of Cr in α-Fe have been investigated. The intrinsic point defect formation energies were found to be larger in model bcc Cr as compared to those in ferromagnetic bcc Fe. The interactions of Cr with point defects (vacancy and self interstitials) have been characterised. Single Cr atoms interact weakly with vacancies but significantly with self-interstitial atoms. Mixed interstitials of any interstitial symmetry are bound. Configurations where two Cr atoms are in nearest neighbour position are generally unfavourable in bcc Fe except when they are a part of a interstitial complex. Mixed interstitials do not have as strong directional stability as pure Fe interstitials have. The effects on the results using the atom description scheme of either the ultrasoft pseudo-potential (USPP) or the projector augmented wave (PAW) formalisms are connected to the differences in local magnetic moments that the two methods predict. As expected for the Fe-Cr system, the results obtained using the PAW method are more reliable than the ones obtained with USPP. (authors)

  15. Ab initio calculations of the forbidden Bragg reflections energy spectra in wurtzites versus temperature.

    Oreshko, A P; Ovchinnikova, E N; Beutier, G; Collins, S P; Nisbet, G; Kolchinskaya, A M; Dmitrienko, V E

    2012-06-20

    Thermal-motion induced (TMI) scattering is caused by the influence of atomic displacements on electronic states in crystals and strongly depends on temperature. It corresponds to dipole-dipole resonant x-ray scattering, but is usually accompanied by dipole-quadrupole scattering. The phenomenological theory supposes the dipole-quadrupole term to be temperature independent (TI). As a result, the transformation of the energy spectra with temperature observed experimentally in ZnO and GaN corresponds to the interference between the TMI and TI terms. In the present paper the direct confirmation of this theoretical prediction is given. Ab initio molecular dynamics was used to simulate the sets of atomic sites at various temperatures followed by quantum mechanical calculation of resonant Bragg reflection energy spectra. The results of simulation are in excellent coincidence with experimental energy spectra of forbidden reflections and confirm the earlier phenomenological conjecture about the interference between the TI dipole-quadrupole and TMI dipole-dipole contributions to the resonant atomic factor. PMID:22627099

  16. Extent of hydrogen coverage of Si(001) under chemical vapor deposition conditions from ab initio approaches

    Rosenow, Phil; Tonner, Ralf

    2016-05-01

    The extent of hydrogen coverage of the Si(001) c(4 × 2) surface in the presence of hydrogen gas has been studied with dispersion corrected density functional theory. Electronic energy contributions are well described using a hybrid functional. The temperature dependence of the coverage in thermodynamic equilibrium was studied computing the phonon spectrum in a supercell approach. As an approximation to these demanding computations, an interpolated phonon approach was found to give comparable accuracy. The simpler ab initio thermodynamic approach is not accurate enough for the system studied, even if corrections by the Einstein model for surface vibrations are considered. The on-set of H2 desorption from the fully hydrogenated surface is predicted to occur at temperatures around 750 K. Strong changes in hydrogen coverage are found between 1000 and 1200 K in good agreement with previous reflectance anisotropy spectroscopy experiments. These findings allow a rational choice for the surface state in the computational treatment of chemical reactions under typical metal organic vapor phase epitaxy conditions on Si(001).

  17. Ab initio calculation of the electronic absorption spectrum of liquid water

    The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O–H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase

  18. Stacking fault energy of face-centered cubic metals: thermodynamic and ab initio approaches.

    Li, Ruihuan; Lu, Song; Kim, Dongyoo; Schönecker, Stephan; Zhao, Jijun; Kwon, Se Kyun; Vitos, Levente

    2016-10-01

    The formation energy of the interface between face-centered cubic (fcc) and hexagonal close packed (hcp) structures is a key parameter in determining the stacking fault energy (SFE) of fcc metals and alloys using thermodynamic calculations. It is often assumed that the contribution of the planar fault energy to the SFE has the same order of magnitude as the bulk part, and thus the lack of precise information about it can become the limiting factor in thermodynamic predictions. Here, we differentiate between the interfacial energy for the coherent fcc(1 1 1)/hcp(0 0 0 1) interface and the 'pseudo-interfacial energy' that enters the thermodynamic expression for the SFE. Using first-principles calculations, we determine the coherent and pseudo-interfacial energies for six elemental metals (Al, Ni, Cu, Ag, Pt, and Au) and three paramagnetic Fe-Cr-Ni alloys. Our results show that the two interfacial energies significantly differ from each other. We observe a strong chemistry dependence for both interfacial energies. The calculated pseudo-interfacial energies for the Fe-Cr-Ni steels agree well with the available literature data. We discuss the effects of strain on the description of planar faults via thermodynamic and ab initio approaches. PMID:27484794

  19. Ab initio calculation of the electronic absorption spectrum of liquid water

    Martiniano, Hugo F. M. C.; Galamba, Nuno [Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa (Portugal); Cabral, Benedito J. Costa, E-mail: ben@cii.fc.ul.pt [Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa (Portugal); Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa (Portugal); Instituto de Física da Universidade de São Paulo, CP 66318, 05314-970 São Paulo, SP (Brazil)

    2014-04-28

    The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O–H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.

  20. Why does bromine square palladium off? An ab initio study of brominated palladium and its nanomorphology.

    Yoo, Su-Hyun; Lee, Ji-Hwan; Delley, Bernard; Soon, Aloysius

    2014-09-14

    A first-principles description and prediction of brominated nanocrystals of Pd is presented. In particular, we conducted an extensive study of the adsorption behaviour of Br on various Pd surfaces (including both low and high Miller-index surfaces) as a function of its surface coverage. By coupling our calculated surface energies with ab initio (electrochemical) thermodynamics and the Gibbs-Wulff shape model, we find that the relative stability of the Pd surfaces is strongly modified by Br, allowing high Miller-index surfaces of Pd (namely the (210) surface) to become competitively favourable at moderate concentrations of Br. We also show that Pd nanoparticles assume a cube-like crystal shape at high concentrations of Br, exposing mainly the (100) facets with a Br surface coverage of 0.5 ML. This not only confirms and explains recent solution synthesis results, but also provides a quantitative atomic picture of the exposed surface facets, which is crucial in understanding the local surface chemistry of shape-controlled nanoparticles for better nanocatalyst design. PMID:25075669

  1. Ab initio computational study of vincristine as a biological active compound: NMR and NBO analyses

    Shiva Joohari

    2015-06-01

    Full Text Available Vincristine is a biological active alkaloid that has been used clinically against a variety of neoplasms. In the current study we have theoretically investigated the magnetic properties of titled compound to predict physical and chemical properties of vincristine as a biological inhibitor. Ab initio computation using HF and B3LYP with 3-21G(d and 6-31G(d level of theory have been performed and then magnetic shielding tensor (, ppm, shielding asymmetry (, magnetic shielding anisotropy (aniso, ppm, the skew of a tensor (K, chemical shift anisotropy ( and chemical shift ( were calculated to indicate the details of the interaction mechanism between microtubules and vincristine. Moreover, EHOMO, ELUMO and Ebg were evaluated. The maximum and minimum values of Ebg were found in HF/3-21g and B3LYP/3-21g respectively. It was also uggested that O24, O37, O49 and O55 with minimum values of iso, are active sites of titled compound. Furthermore the calculated chemical shifts were compared with experimental data in DMSO and CDCl3 solvents.

  2. JUPITER MODELS WITH IMPROVED AB INITIO HYDROGEN EQUATION OF STATE (H-REOS.2)

    The amount and distribution of heavy elements in Jupiter gives indications on the process of its formation and evolution. Core mass and metallicity predictions, however, depend on the equations of state (EOSs) used and on model assumptions. We present an improved ab initio hydrogen EOS, H-REOS.2, and compute the internal structure and thermal evolution of Jupiter within the standard three-layer approach. The advance over our previous Jupiter models with H-REOS.1 by Nettelmann et al. is that the new models are also consistent with the observed ∼> 2 times solar heavy element abundances in Jupiter's atmosphere. Such models have a rock core mass Mc = 0-8 M⊕, total mass of heavy elements MZ = 28-32 M⊕, a deep internal layer boundary at ≥4 Mbar, and a cooling time of 4.4-5.0 Gyr when assuming homogeneous evolution. We also calculate two-layer models in the manner of Militzer et al. and find a comparable large core of 16-21 M⊕, out of which ∼11 M⊕ is helium, but a significantly higher envelope metallicity of 4.5 times solar. According to our preferred three-layer models, neither the characteristic frequency (ν0 ∼ 156 μHz) nor the normalized moment of inertia (λ ∼0.276) is sensitive to the core mass but accurate measurements could well help to rule out some classes of models.

  3. Ab initio studies of transition metal complexes and related electron transfer properties

    Ab initio electronic structure calculations have been carried out for various aquo and ammine complexes of Fe, Co, and Ru in their 2+ and 3+ oxidation states. The results of these calculations are used as assessing a variety of factors controlling electron transfer kinetics including the charge-state dependence of various inner shell geometrical parameters and associated vibrational frequencies (metal-ligand and intra-ligand and intra-ligand stretching modes, and librational modes), and the dependence of electron transfer matrix elements on the nature of the ligand and the metal orbital type (/sup t/2/sub g/ vs. e/sub g/). The charge-state dependence of the OH bond lengths in hexa-aquo ions is predicted to yield H/D isotope effects (i.e., fractionation between bulk and first shell water), which should be detectable by neutron scattering experiments on appropriate aqueous solutions. The relationship between these thermodynamic isotope effects, which depend critically on strong OH triple bond O hydrogen bonding between first and second-shell water molecules, and kinetic H/D isotope effects in electron exchange involving hexa-aquo ions will be discussed

  4. Ab initio Stellar Astrophysics: Reliable Modeling of Cool White Dwarf Atmospheres

    Kowalski, Piotr M

    2010-01-01

    Over the last decade {\\it ab initio} modeling of material properties has become widespread in diverse fields of research. It has proved to be a powerful tool for predicting various properties of matter under extreme conditions. We apply modern computational chemistry and materials science methods, including density functional theory (DFT), to solve lingering problems in the modeling of the dense atmospheres of cool white dwarfs ($T_{\\rm eff}\\rm <7000 \\, K$). Our work on the revision and improvements of the absorption mechanisms in the hydrogen and helium dominated atmospheres resulted in a new set of atmosphere models. By inclusion of the Ly-$\\rm \\alpha$ red wing opacity we successfully fitted the entire spectral energy distributions of known cool DA stars. In the subsequent work we fitted the majority of the coolest stars with hydrogen-rich models. This finding challenges our understanding of the spectral evolution of cool white dwarfs. We discuss a few examples, including the cool companion to the pulsar...

  5. Ab initio calculation of the electronic absorption spectrum of liquid water

    Martiniano, Hugo F. M. C.; Galamba, Nuno; Cabral, Benedito J. Costa

    2014-04-01

    The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O-H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.

  6. The role of anharmonicity in the ab-initio phase diagram of calcium

    di Gennaro, Marco; Saha, Srijan Kumar; Verstraete, Matthieu Jean

    2013-03-01

    In the 32-119 GPa pressure range and at room temperature, a simple cubic phase was reported for calcium in many different experiments. Standard linear response theory, both within density functional perturbation theory and frozen phonon calculations, presents dynamical instabilities for simple cubic in the whole pressure range. Many other possible candidate phases, as well as several possible stabilization mechanisms for simple cubic phase, have been proposed as the result of ab-initio predictions but the role of temperature on the relative stability of the different phases has not been investigated systematically. We revisit the stability of three candidate phases of calcium for the intermediate pressure range and for various value of temperatures, taking explicitly into account thermal corrections relative to electronic as well as phononic entropy and anharmonic contributions. This corrects the discrepancies among previous theoretical results and experiments, and presents a different picture of the temperature driven phase transition, which results from dynamical anharmonic stabilization of simple cubic and de-stabilization of the tetragonal phase. Transport quantities are calculated in the stabilized phases, to provide additional points of comparison with experiments.

  7. Role of Dynamical Instability in the Ab Initio Phase Diagram of Calcium

    Di Gennaro, Marco; Saha, Srijan Kumar; Verstraete, Matthieu J.

    2013-07-01

    In the 32-119 GPa pressure range and at room temperature, a simple cubic phase was reported for calcium in many different experiments. Standard linear response theory, both within density functional perturbation theory and frozen phonon calculations, presents dynamical instabilities for the simple cubic structure in the whole pressure range. Many other possible candidate phases, as well as several possible stabilization mechanisms for the simple cubic phase, have been proposed as the result of ab initio predictions but the role of temperature on the relative stability of the different phases has not been systematically investigated. We revisit the stability of the three most important candidate phases of calcium for the intermediate pressure range and for various temperatures, taking explicitly into account thermal corrections relative to electronic as well as phononic entropy and anharmonic contributions. This corrects the discrepancies among previous theoretical results and experiments and presents a different picture of the temperature driven phase transition, which results from dynamical anharmonic stabilization of simple cubic and destabilization of the tetragonal phase.

  8. Ab Initio Enhanced calphad Modeling of Actinide-Rich Nuclear Fuels

    The process of fuel recycling is central to the Advanced Fuel Cycle Initiative (AFCI), where plutonium and the minor actinides (MA) Am, Np, and Cm are extracted from spent fuel and fabricated into new fuel for a fast reactor. Metallic alloys of U-Pu-Zr-MA are leading candidates for fast reactor fuels and are the current basis for fast spectrum metal fuels in a fully recycled closed fuel cycle. Safe and optimal use of these fuels will require knowledge of their multicomponent phase stability and thermodynamics (Gibbs free energies). In additional to their use as nuclear fuels, U-Pu-Zr-MA contain elements and alloy phases that pose fundamental questions about electronic structure and energetics at the forefront of modern many-body electron theory. This project will validate state-of-the-art electronic structure approaches for these alloys and use the resulting energetics to model U-Pu-Zr-MA phase stability. In order to keep the work scope practical, researchers will focus on only U-Pu-Zr-m), leaving Cm for later study. The overall objectives of this project are to: Provide a thermodynamic model for U-Pu-Zr-MA for improving and controlling reactor fuels; and, Develop and validate an ab initio approach for predicting actinide alloy energetics for thermodynamic modeling

  9. Ab initio calculations for the far infrared collision induced absorption by N2 gas.

    Bussery-Honvault, Béatrice; Hartmann, Jean-Michel

    2014-02-01

    We present (far-infrared) Collision Induced Absorption (CIA) spectra calculations for pure gaseous N2 made for the first time, from first-principles. They were carried out using classical molecular dynamics simulations based on ab initio predictions of both the intermolecular potential and the induced-dipole moment. These calculations reproduce satisfactory well the experimental values (intensity and band profile) with agreement within 3% at 149 K. With respect to results obtained with only the long range (asymptotic) dipole moment (DM), including the short range overlap contribution improves the band intensity and profile at 149 K, but it deteriorates them at 296 K. The results show that the relative contribution of the short range DM to the band intensity is typically around 10%. We have also examined the sensitivity of the calculated CIA to the intermolecular potential anisotropy, providing a test of the so-called isotropic approximation used up to now in all N2 CIA calculations. As all these effects interfere simultaneously with quantitatively similar influences (around 10%), it is rather difficult to assert which one could explain remaining deviations with the experimental results. Furthermore, the rather large uncertainties and sometimes inconsistencies of the available measurements forbid any definitive conclusion, stressing the need for new experiments. PMID:24511942

  10. Ab initio atomistic thermodynamics study on the oxidation mechanism of binary and ternary alloy surfaces

    Liu, Shi-Yu, E-mail: buaasyliu@gmail.com [College of Physics and Electronic Information Science, Tianjin Normal University, Tianjin 300387 (China); Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong (China); Liu, Shiyang [Institute of Information Optics, Zhejiang Normal University, Jinhua, Zhejiang 321004 (China); Li, De-Jun [College of Physics and Electronic Information Science, Tianjin Normal University, Tianjin 300387 (China); Wang, Sanwu, E-mail: sanwu-wang@utulsa.edu [Department of Physics and Engineering Physics, The University of Tulsa, Tulsa, Oklahoma 74104 (United States); Guo, Jing; Shen, Yaogen, E-mail: meshen@cityu.edu.hk [Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong (China)

    2015-02-14

    Utilizing a combination of ab initio density-functional theory and thermodynamics formalism, we have established the microscopic mechanisms for oxidation of the binary and ternary alloy surfaces and provided a clear explanation for the experimental results of the oxidation. We construct three-dimensional surface phase diagrams (SPDs) for oxygen adsorption on three different Nb-X(110) (X = Ti, Al or Si) binary alloy surfaces. On the basis of the obtained SPDs, we conclude a general microscopic mechanism for the thermodynamic oxidation, that is, under O-rich conditions, a uniform single-phase SPD (type I) and a nonuniform double-phase SPD (type II) correspond to the sustained complete selective oxidation and the non-sustained partial selective oxidation by adding the X element, respectively. Furthermore, by revealing the framework of thermodynamics for the oxidation mechanism of ternary alloys through the comparison of the surface energies of two separated binary alloys, we provide an understanding for the selective oxidation behavior of the Nb ternary alloy surfaces. Using these general microscopic mechanisms, one could predict the oxidation behavior of any binary and multi-component alloy surfaces based on thermodynamics considerations.

  11. A theoretical study of benzaldehyde derivatives as tyrosinase inhibitors using Ab initio calculated NQCC parameters

    Marjan Rafiee

    2015-09-01

    Full Text Available Tyrosinase is a multifunctional copper-containing enzyme. It can catalyze two distinct reactions of melanin synthesis and benzaldehyde derivatives, which are potential tyrosinase inhibitors. To find the relationships between charge distributions of benzaldehyde and their pharmaceutical behavior, the present study aimed at investigating nuclear quadrupole coupling constants of quadrupolare nuclei in the functional benzaldehyde group and calculating some its derivatives. In addition, the differences between the electronic structures of various derivatives of this depigmenting drug were examined. All ab initio calculations were carried out using Gaussian 03. The results predicted benzaldehyde derivatives to be bicentral inhibitors; nevertheless, the oxygen or hydrogen contents of the aldehyde group were not found to be the only active sites. Furthermore with the presence of the aldehyde group, the terminal methoxy group in C4 was found to contribute to tyrosinase inhibitory activities. In addition, an oxygen atom with high charge density in the side chain was found to play an important role in its inhibitory effect.

  12. Using ab initio calculations in designing bcc Mg-Li alloys for ultra-lightweight applications

    Ab initio calculations are becoming increasingly useful to engineers interested in designing new alloys, because these calculations are able to accurately predict basic material properties only knowing the atomic composition of the material. In this paper, single crystal elastic constants of 11 bcc Mg-Li alloys are calculated using density functional theory (DFT) and compared with available experimental data. Based on DFT determined properties, engineering parameters such as the ratio of bulk modulus over shear modulus (B/G) and the ratio of Young's modulus over mass density (Y/ρ) are calculated. Analysis of B/G and Y/ρ shows that bcc Mg-Li alloys with 30-50 at.% Li offer the most potential as lightweight structural material. Compared with fcc Al-Li alloys, bcc Mg-Li alloys have a lower B/G ratio, but a comparable Y/ρ ratio. An Ashby map containing Y/ρ vs B/G shows that it is not possible to increase both Y/ρ and B/G by changing only the composition of a binary alloy

  13. Ab initio studies on the lattice thermal conductivity of silicon clathrate frameworks II and VIII

    Härkönen, Ville J.; Karttunen, Antti J.

    2016-01-01

    The lattice thermal conductivities of silicon clathrate frameworks II and VIII are investigated by using ab initio lattice dynamics and an iterative solution of the linearized Boltzmann transport equation (BTE) for phonons. Within the temperature range 100-350 K, the clathrate structures II and VIII were found to have lower lattice thermal conductivity values than the silicon diamond structure (d -Si) by factors of 1/2 and 1/3, respectively. The main reason for the lower lattice thermal conductivity of the clathrate structure II in comparison to d -Si was found to be the harmonic phonon spectra, while in the case of the clathrate structure VIII, the difference is mainly due to the harmonic phonon spectra and partly due to the shorter relaxation times of phonons. In the studied clathrate frameworks, the anharmonic effects have larger impact on the lattice thermal conductivity than the size of the unit cell. For the structure II, the predicted lattice thermal conductivity differs approximately by a factor of 20 from the previous experimental results obtained for a polycrystalline sample at room temperature.

  14. Ab Initio Enhanced calphad Modeling of Actinide-Rich Nuclear Fuels

    Morgan, Dane [Univ. of Wisconsin, Madison, WI (United States); Yang, Yong Austin [Univ. of Wisconsin, Madison, WI (United States)

    2013-10-28

    The process of fuel recycling is central to the Advanced Fuel Cycle Initiative (AFCI), where plutonium and the minor actinides (MA) Am, Np, and Cm are extracted from spent fuel and fabricated into new fuel for a fast reactor. Metallic alloys of U-Pu-Zr-MA are leading candidates for fast reactor fuels and are the current basis for fast spectrum metal fuels in a fully recycled closed fuel cycle. Safe and optimal use of these fuels will require knowledge of their multicomponent phase stability and thermodynamics (Gibbs free energies). In additional to their use as nuclear fuels, U-Pu-Zr-MA contain elements and alloy phases that pose fundamental questions about electronic structure and energetics at the forefront of modern many-body electron theory. This project will validate state-of-the-art electronic structure approaches for these alloys and use the resulting energetics to model U-Pu-Zr-MA phase stability. In order to keep the work scope practical, researchers will focus on only U-Pu-Zr-{Np,Am}, leaving Cm for later study. The overall objectives of this project are to: Provide a thermodynamic model for U-Pu-Zr-MA for improving and controlling reactor fuels; and, Develop and validate an ab initio approach for predicting actinide alloy energetics for thermodynamic modeling.

  15. Anomalous structural dynamics in liquid Al80Cu20: An ab initio molecular dynamics study

    In this work, the structural dynamics of liquid Al80Cu20 is systematically investigated in terms of the evolution of its atomic structure, diffusivity, viscosity and fragility through ab initio molecular dynamics simulations. In addition to using pair correlation functions and coordination numbers, the various local ordered clusters are characterized comprehensively by Honeycutt-Anderson bond pairs and Voronoi polyhedra. Compared to the self diffusivity of pure liquid Cu, the tracer diffusion coefficients of Cu in liquid Al80Cu20 are increased, in agreement with the results measured by quasielastic neutron-scattering (QENS). Although the interdiffusion coefficients predicted by Darken’s equation match well to those obtained from the viscosity measurements via the Stokes-Einstein relation, they are smaller than those measured by QENS or X-ray radiography, indicative of an anomalous nature of the structural dynamics, dominated by the local ordered clusters in liquid Al80Cu20. Furthermore, Vogel–Fulcher–Tammann fitting results indicate that the liquid Al80Cu20 can be classified into a strong liquid. The deformation electron density shows that the intrinsic tetrahedral-type bonds in FCC Al and Cu are transformed into an amorphous type in liquid Al80Cu20. The present work provides insights into the understanding of structural dynamics and the kinetic properties of such metallic melts

  16. Ferromagnetic ordering of Cr and Fe doped p-type diamond: An ab initio study

    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 μB) and 33.3 meV (1.0 μB), 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

  17. Ab initio pseudopotential studies of cubic BC2N under high pressure

    We present the results of a systematic study of the structural, electronic, and vibrational properties of various cubic BC2N phases under high pressure. Ab initio pseudopotential total-energy and phonon calculations have been carried out to examine the changes in the structural parameters, bonding behaviours, band structures, and dynamic instabilities caused by phonon softening in these phases. We find that an experimentally synthesized high-density phase of cubic BC2N exhibits outstanding stability in the structural and electronic properties up to very high pressures. On the other hand, another experimentally identified phase with lower density and lower symmetry undergoes a dramatic structural transformation with a volume and bond-length collapse and a concomitant semi-metal to semiconductor transition. A third phase is predicted to be favourable over the above-mentioned lower-density phase by the enthalpy calculations. However, the dynamic phonon calculations reveal that it develops imaginary phonon modes and, therefore, is unstable in the experimental pressure range. The calculations indicate that its synthesis may be achieved at reduced pressures. These results provide a comprehensive understanding for the high-pressure behaviour of the cubic BC2N phases and reveal their interesting properties that can be verified by experiments

  18. Ab Initio Studies on Hematite Surface and the Adsorption of Phosphate

    Swati Chaudhury; Chandrika Varadachari; Kunal Ghosh

    2014-01-01

    This investigation explores the ab initio DFT method for understanding surface structure of hematite and the nature and energetics of phosphate adsorption. Using the full potential linearized plane wave method (FP-LAPW), we derived the structure and energies of various magnetic forms of hematite. The antiferromagnetic (AFM) form was observed to be the most stable. Hematite surfaces with Fe-termination, O-termination, or OH-termination were studied. The OH-terminated surface was the most stabl...

  19. Investigation of metal-insulator like transition through the ab initio density matrix renormalization group approach

    Fertitta, E.; Paulus, B.; 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 or...

  20. Modelling of carbohydrate–aromatic interactions: ab initio energetics and force field performance

    Spiwok, V.; Lipovová, P.; Skálová, Tereza; Vondráčková, Eva; Dohnálek, Jan; Hašek, Jindřich; Králová, B.

    2005-01-01

    Roč. 19, č. 12 (2005), s. 887-901. ISSN 0920-654X R&D Projects: GA ČR GA204/02/0843; GA AV ČR 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

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

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

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

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

    We have performed ab initio calculations of positron distribution, ACAR and lifetime in the quasi-one-dimensional organic conductor TTF-TCNQ. The electronic structure is obtained within the LDA, while the positron state is calculated either with the LDA or with the GGA. Except the positron lifetime, differences between the LDA and GGA results are rather small. The obtained results are compared with our previous experiments and calculations.

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

    Ishibashi, Shoji; Kohyama, Masanori

    2000-06-01

    We have performed ab initio calculations of positron distribution, ACAR and lifetime in the quasi-one-dimensional organic conductor TTF-TCNQ. The electronic structure is obtained within the LDA, while the positron state is calculated either with the LDA or with the GGA. Except the positron lifetime, differences between the LDA and GGA results are rather small. The obtained results are compared with our previous experiments and calculations.

  4. How Is Acetylcholinesterase Phosphonylated by Soman? An Ab Initio QM/MM Molecular Dynamics Study

    Sirin, Gulseher Sarah; Zhang, Yingkai

    2014-01-01

    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 characteriz...

  5. Ab Initio Study on the Anti-HIV Activities of Hydroxyflavones

    ZHANG Yu

    2005-01-01

    Flavone and 95 hydroxyflavones have been studied with ab initio method, and their total energies, atomic charges, dipole moments, multipole moments, molecular orbital compositions, orbital energies etc. were obtained. Among them the relationship between total atomic charges and activities against HIV is basically in accordance with the experimental results. The beneficial references are provided for the extraction and synthesis of strong active anti-HIV medicines.

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

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

    2008-01-01

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

  7. \\textit{Ab initio} calculation of transport and optical properties of aluminum: influence of simulation parameters

    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 obtained and compare...

  8. Large scale ab initio calculations based on three levels of parallelization

    Bottin, François; Leroux, Stéphane; Knyazev, Andrew; Zérah, Gilles

    2007-01-01

    We suggest and implement a parallelization scheme based on an efficient multiband eigenvalue solver, called the locally optimal block preconditioned conjugate gradient LOBPCG method, and using an optimized three-dimensional (3D) fast Fourier transform (FFT) in the ab initio}plane-wave code ABINIT. In addition to the standard data partitioning over processors corresponding to different k-points, we introduce data partitioning with respect to blocks of bands as well as spatial partitioning in t...

  9. Ab initio study of one-dimensional disorder on III-V semiconductor surfaces

    Romanyuk, Olexandr; Grosse, F.; Braun, W.

    2010-01-01

    Roč. 7, č. 2 (2010), s. 330-333. ISSN 1862-6351 R&D Projects: GA AV ČR 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

  10. Ab initio study of antiphase boundaries and stacking faults in L12 and DO22 compounds

    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 funct......'s function technique based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations....

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

    Káňa, Tomáš; Šob, Mojmír; Vitek, V.

    2011-01-01

    Roč. 19, č. 7 (2011), s. 919-926. ISSN 0966-9795 R&D Projects: GA AV ČR 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

  12. Ab initio study on the magnetostructural properties of MnAs

    Sanvito, Stefano; RUNGGER, IVAN

    2006-01-01

    The magnetic and structural properties of MnAs are studied with ab initio methods, and by mapping total energies onto a Heisenberg model. The stability of the different phases is found to depend mainly on the volume and on the amount of magnetic order, confirming previous experimental findings and phenomenological models. It is generally found that for large lattice constants the ferromagnetic state is favored, whereas for small lattice constants different antiferromagnetic states can be stab...

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

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

    2003-01-01

    Roč. 68, č. 18 (2003), s. 184101-1 - 181101-10. ISSN 0163-1829 R&D Projects: GA AV ČR IAA1041302; GA ČR GA202/03/1351; GA MŠk OC 523.90 Institutional research plan: CEZ:AV0Z2041904 Keywords : ab initio calculations * electronic structure * theoretical tensile strength Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 2.962, year: 2003

  14. Capillary affinity electrophoresis and ab initio calculation studies on complexation of valinomycin with Na+ ion

    Ehala, Sille; Dybal, Jiří; Makrlík, E.; Kašička, Václav

    2009-01-01

    Roč. 32, č. 4 (2009), s. 597-604. ISSN 1615-9306 R&D Projects: GA ČR(CZ) GA203/06/1044; GA ČR(CZ) GA203/08/1428; GA AV ČR 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

  15. Ab initio study of thermodynamic, electronic, magnetic, structural, and elastic properties of Ni4N allotropes

    Hemzalová, P.; Friák, Martin; Šob, Mojmír; Ma, D.; Udyansky, A.; Raabe, D.; Neugebauer, J.

    2013-01-01

    Roč. 88, č. 17 (2013), Art. no. 174103. ISSN 1098-0121 R&D Projects: GA ČR(CZ) GAP108/12/0311; GA ČR GD106/09/H035; GA AV ČR IAA100100920 Institutional support: RVO:68081723 Keywords : nitrides * ab initio * thermodynamics * elasticity Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 3.664, year: 2013

  16. On limits of ab initio calculations of pairing gap in nuclei

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

    2010-01-01

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

  17. Equations of state of magnesium perovskite and postperovskite: diagnostics from ab initio simulations

    Belousov, Roman; Prencipe, Mauro

    2014-01-01

    The isothermal compression of magnesium perovskite and postperovskite is examined through the F-f plot and the diagnostic plot of Vinet universal model theoretically from the ab initio quantum-mechanical calculations at the hybrid Hartree-Fock / Density Functional Theory level. A purely numerical approach, first time applied in this paper, shows that the discrepancies largely observed between studies on the perovskite and criticized in geophysical applications are due to the inadequate choice...

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

    Turek, Ilja; Kudrnovsky, Josef; Drchal, Vaclav

    2011-01-01

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

  19. Ab initio simulations of liquid NaSn alloys: Zintl anions and network formation

    Schoene, M.; Kaschner, R.; Seifert, G

    1994-01-01

    Using the Car-Parrinello technique, ab initio molecular dynamics simulations are performed for liquid NaSn alloys in five different compositions (20, 40, 50, 57 and 80 % sodium). The obtained structure factors agree well with the data from neutron scattering experiments. The measured prepeak in the structure factor is reproduced qualitatively for most compositions. The calculated and measured positions of all peaks show the same trend as function of the composition.\\\\ The dynamic simulations ...

  20. Ab initio molecular dynamics study of liquid sodium and cesium up to critical point

    Yuryev, Anatoly A. [Institute of Metallurgy of Ural Branch of the Russian Academy of Sciences, Amundsen st. 101,620016, Yekaterinburg (Russian Federation); Ural Federal University, Vira st. 19, 620002, Yekaterinburg (Russian Federation); Gelchinski, Boris R. [Institute of Metallurgy of Ural Branch of the Russian Academy of Sciences, Amundsen st. 101,620016, Yekaterinburg (Russian Federation)

    2015-08-17

    Ab initio modeling of liquid metals Na and K is carried out using the program SIESTA. We have determined the parameters of the model (the optimal step, the number of particles, the initial state etc) and calculated a wide range of properties: the total energy, pair correlation function, coefficient of self-diffusion, heat capacity, statistics of Voronoi polyhedra, the density of electronic states up to the critical temperature.

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

    Fürst, Joachim Alexander; J Hashemi; Markussen, Troels; Brandbyge, Mads; Jauho, Antti-Pekka; Nieminen, R. M.

    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...

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

    Fürst, J. A.; J Hashemi; Markussen, T.; Brandbyge, M.; Jauho, A.P.; Nieminen, Risto M.

    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...

  3. Ab initio studies on the lattice thermal conductivity of silicon clathrate frameworks II and VIII

    Härkönen, Ville J.; Karttunen, Antti J.

    2015-01-01

    The lattice thermal conductivities of silicon clathrate frameworks II and VIII are investigated by using ab initio lattice dynamics and iterative solution of the linearized Boltzmann transport equation(BTE) for phonons. Within the temperature range 100-350 K, the clathrate structures II and VIII were found to have lower lattice thermal conductivity values than silicon diamond structure (d-Si) by factors of 1/2 and 1/5, respectively. The main reason for the lower lattice thermal conductivity o...

  4. Surface Tension of Ab Initio Liquid Water at the Water-Air Interface

    Nagata, Yuki; Ohto, Tatsuhiko; Bonn, Mischa; Kühne, Thomas D.

    2016-01-01

    We report calculations of the surface tension of the water-air interface using ab initio molecular dynamics (AIMD) simulations. We investigate the simulation cell size dependence of the surface tension of water from force field molecular dynamics (MD) simulations, which show that the calculated surface tension increases with increasing simulation cell size, thereby illustrating that a correction for finite size effects is required for the small system used in the AIMD simulation. The AIMD sim...

  5. Photochemistry of hydrogen bonded heterocycles probed by photodissociation experiments and ab initio methods

    Slavíček, Petr; Fárník, Michal

    2011-01-01

    Roč. 13, č. 26 (2011), s. 12123-12137. ISSN 1463-9076 R&D Projects: GA ČR GA203/09/0422; GA ČR 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

  6. Ab initio studies of the kinetic isotope effect of the CH4 + OH atmospheric reaction

    Lasaga, Antonio C.; Gibbs, G. V.

    1991-07-01

    High level ab initio calculations have been carried out on the C-13 - C-12 kinetic isotope effect of the CH4 + OH reaction in the atmosphere. The results agree quite well with both the absolute value of the isotope effect and the temperature dependence of the effect, based on new experimental data. The calculated kinetic isotope effect supports a bigger effect of biomass burning on the methane global budget.

  7. The onset of ion solvation by ab initio calculations: Comparison of water and methanol

    Pluhařová, Eva; Jungwirth, Pavel

    2008-01-01

    Roč. 73, 6/7 (2008), s. 733-744. ISSN 0010-0765 R&D Projects: GA MŠk LC512; GA ČR GA203/07/1006 Institutional research plan: CEZ:AV0Z40550506 Keywords : ions * water cluster * methanol * ab initio calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.784, year: 2008

  8. Hyperfine tensors of nitrogen-vacancy center in diamond from \\emph{ab initio} calculations

    Gali, Adam

    2009-01-01

    We determine and analyze the charge and spin density distributions of nitrogen-vacancy (N-V) center in diamond for both the ground and excited states by \\emph{ab initio} supercell calculations. We show that the hyperfine tensor of $^{15}$N nuclear spin is negative and strongly anisotropic in the excited state, in contrast to previous models used extensively to explain electron spin resonance measurements. In addition, we detect a significant redistribution of the spin density due to excitatio...

  9. Ab InitioStudy of Hot Carriers in the First Picosecond after Sunlight Absorption in Silicon

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

    2014-01-01

    Hot carrier thermalization is a major source of efficiency loss in solar cells. Because of the subpicosecond time scale and complex physics involved, a microscopic characterization of hot carriers is challenging even for the simplest materials. We develop and apply an ab initio approach based on density functional theory and many-body perturbation theory to investigate hot carriers in semiconductors. Our calculations include electron-electron and electron-phonon interactions, and require no e...

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

    Blomqvist, Andreas

    2010-01-01

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

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

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

    2007-01-01

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

  12. Ab initio molecular dynamics simulations with linear scaling: application to liquid ethanol

    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

  13. Ab Initio Quality NMR Parameters in Solid-State Materials Using a High-Dimensional Neural-Network Representation.

    Cuny, Jérôme; Xie, Yu; Pickard, Chris J; Hassanali, Ali A

    2016-02-01

    Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful experimental tools to probe the local atomic order of a wide range of solid-state compounds. However, due to the complexity of the related spectra, in particular for amorphous materials, their interpretation in terms of structural information is often challenging. These difficulties can be overcome by combining molecular dynamics simulations to generate realistic structural models with an ab initio evaluation of the corresponding chemical shift and quadrupolar coupling tensors. However, due to computational constraints, this approach is limited to relatively small system sizes which, for amorphous materials, prevents an adequate statistical sampling of the distribution of the local environments that is required to quantitatively describe the system. In this work, we present an approach to efficiently and accurately predict the NMR parameters of very large systems. This is achieved by using a high-dimensional neural-network representation of NMR parameters that are calculated using an ab initio formalism. To illustrate the potential of this approach, we applied this neural-network NMR (NN-NMR) method on the (17)O and (29)Si quadrupolar coupling and chemical shift parameters of various crystalline silica polymorphs and silica glasses. This approach is, in principal, general and has the potential to be applied to predict the NMR properties of various materials. PMID:26730889

  14. Temperature dependent surface relaxation for Al(110) and Mg(10-10) studied by orbital free ab initio molecular dynamics

    Gonzalez, Luis E.; Gonzalez, David J

    2006-01-01

    We have performed orbital free ab initio molecular dynamics simulations in order to study the thermal behaviour of two open surfaces of solid metallic systems, namely the (110) face of fcc Al and the (10-10) face of hcp Mg. Our results reproduce qualitatively both the experimental measurements and previous ab initio calculations performed with the more costly Kohn-Sham approach of Density Functional Theory. These calculations can be viewed as a validation test of the orbital free method for s...

  15. Ab-initio chemical potentials of solid and liquid solutions and the chemistry of the Earth's core

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

    2001-01-01

    A general set of methods is presented for calculating chemical potentials in solid and liquid mixtures using {\\em ab initio} techniques based on density functional theory (DFT). The methods are designed to give an {\\em ab initio} approach to treating chemical equilibrium between coexisting solid and liquid solutions, and particularly the partitioning ratio of solutes between such solutions. For the liquid phase, the methods are based on the general technique of thermodynamic integration, appl...

  16. Theoretical study of silicon carbide under irradiation at the nano scale: classical and ab initio modelling

    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)

  17. Ab initio studies of magnetism in the iron chalcogenides FeTe and FeSe

    The iron chalcogenides FeTe and FeSe belong to the family of iron-based superconductors. We study the magnetism in these compounds in the normal state using the ab initio downfolding scheme developed for strongly correlated electron systems. In deriving ab initio low-energy effective models, we employ the constrained GW method to eliminate the double counting of electron correlations originating from the exchange correlations already taken into account in the density functional theory. By solving the derived ab initio effective models, we reveal that the elimination of the double counting is important in reproducing the bicollinear antiferromagnetic order in FeTe, as is observed in experiments. We also show that the elimination of the double counting induces a unique degeneracy of several magnetic orders in FeSe, which may explain the absence of the magnetic ordering. We discuss the relationship between the degeneracy and the recently found puzzling phenomena in FeSe as well as the magnetic ordering found under pressure. (author)

  18. Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

    Geng, Hua Y

    2014-01-01

    A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model, the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4 fold for a two-level implementation, and can be increased to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibration...

  19. 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.

  20. The particle-in-cell model for ab initio thermodynamics: implications for the elastic anisotropy of the Earth's inner core

    Gannarelli, C M S; 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 gives an incorrect treatment of anharmonic lattice vibrations. In addition, our assessment does not support recent PIC-based predictions that the hexagonal c/a ratio increases strongly with increasing temperature, and we point out that this casts doubt on a proposed re-interpretation of the elastic anisotropy of the inner core.

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

    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

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

    Zaharieva, Roussislava; Hanagud, Sathya

    2009-06-01

    Shock-induced and shock assisted chemical reactions of intermetallic mixtures are studied by many researchers, using both experimental and theoretical techniques. The theoretical studies are primarily at continuum scales. The model frameworks include mixture theories and meso-scale models of grains of porous mixtures. The reaction models vary from equilibrium thermodynamic model to several non-equilibrium thermodynamic models. The shock-effects are primarily studied using appropriate conservation equations and numerical techniques to integrate the equations. All these models require material constants from experiments and estimates of transition states. Thus, the objective of this paper is to present studies based on ab initio techniques. The ab inito studies, to date, use ab inito molecular dynamics. This paper presents a study that uses shock pressures, and associated temperatures as starting variables. Then intermetallic mixtures are modeled as slabs. The required shock stresses are created by straining the lattice. Then, ab initio binding energy calculations are used to examine the stability of the reactions. Binding energies are obtained for different strain components super imposed on uniform compression and finite temperatures. Then, vibrational frequencies and nudge elastic band techniques are used to study reactivity and transition states. Examples include Ni and Al.

  3. Verification of Anderson Superexchange in MnO via Magnetic Pair Distribution Function Analysis and ab initio Theory

    Frandsen, Benjamin A.; Brunelli, Michela; Page, Katharine; Uemura, Yasutomo J.; Staunton, Julie B.; Billinge, Simon J. L.

    2016-05-01

    We present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ˜1 nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominated by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. The Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory.

  4. A theoretical-spectroscopy, ab initio-based study of the electronic ground state of 121SbH3

    For the stibine isotopologue 121SbH3, we report improved theoretical calculations of the vibrational energies below 8000 cm-1 and simulations of the rovibrational spectrum in the 0-8000 cm-1 region. The calculations are based on a refined ab initio potential energy surface and on a new dipole moment surface obtained at the coupled cluster CCSD(T) level. The theoretical results are compared with the available experimental data in order to validate the ab initio surfaces and the TROVE computational method [Yurchenko SN, Thiel W, Jensen P. J Mol Spectrosc 2007;245:126-40] for calculating rovibrational energies and simulating rovibrational spectra of arbitrary molecules in isolated electronic states. A number of predicted vibrational energies of 121SbH3 are provided in order to stimulate new experimental investigations of stibine. The local-mode character of the vibrations in stibine is demonstrated through an analysis of the results in terms of local-mode theory.

  5. Conformational Characteristics of Poly(tetrafluoroethylene) (PTFE) Based Upon Ab Initio Electronic Structure Calculations on Model Molecules

    Smith, Grant D.; Jaffe, R. L.; Yoon, D. Y.; Arnold, James O. (Technical Monitor)

    1994-01-01

    Conformational energy contours of perfluoroalkanes, determined from ab initio calculations, confirm the well-known spitting of trans states into two minima at plus or minus 17 degrees but also show that the gauche states split as well, with minima at plus or minus 124 degrees and plus or minus 84 in order to relieve steric crowding. The directions of such split distortions from the perfectly staggered states are strongly coupled for adjacent pairs of bonds in a manner identical to the intradyad pair for poly (isobutylene) chains. These conformational characteristics are fully represented by a six-state rotational isomeric state (RIS) model for PTFE comprised of t(+), t(-), g(sup +)+, g(sup +)-, g(sup -) + and g(sup -)-states, located at the split energy minima. The resultant 6 x 6 statistical weight matrix is described by first-order interaction parameters for the g+(+) (ca. 0.6 kcal/mol) and g+- (ca. 2.0 kcal/mol) states, and second order parameters for the g(sup +)+g(sup +)+ (ca 0.6 kcal/mol) and g(sup +)+g(sup -)+ (ca. 1.0 kcal/mol) states. This six-state RIS model, without adjustment of the geometric or energy parameters as determined from the ab initio calculations, predicts the unperturbed chain dimensions and the fraction of gauche bonds as a function of temperature for PTFE in good agreement with available experimental values.

  6. Ab-Initio Modelling Of Surface Site Reactivity And Fluid Transport In Clay Minerals Case Study: Pyrophyllite

    Pyrophyllite, Al2[Si4O10](OH)2, is the simplest structural prototype for 2:1 dioctahedral phyllosilicate. Because the net electric charge in pyrophyllite is zero, it is the best candidate for investigating the non electrostatic contribution to sorption and transport phenomena in clays. Using ab-initio simulations, we have investigated the reactivity and structure of the water-solid interface on the basal plane and edge sites of pyrophyllite. The calculations predict slightly hydrophobic behaviour of the basal plane. For the high water coverage (100), (110) and (-110), lateral facets have a lower energy than for the (010), (130) and (-130) surfaces. Analysis of the surface reactivity reveals that the =Al-OH groups are most easily protonated on the (010), (130) and (-130) facets. The =Al-O-Si= sites will be protonated on the (100), (130), (110), (-110) and (-130) surfaces. The =Al-OH2 complexes are more easily de-protonated than the =Si-OH and =Al-OH sites. A spontaneous, reversible exchange of the protons between the solution and the edge sites has been observed in ab-initio molecular dynamics simulations at 300 K. Such near-surface proton diffusion may result in a significant contribution to the diffusion coefficients measured in neutron scattering experiments. (author)

  7. Verification of Anderson Superexchange in MnO via Magnetic Pair Distribution Function Analysis and ab initio Theory.

    Frandsen, Benjamin A; Brunelli, Michela; Page, Katharine; Uemura, Yasutomo J; Staunton, Julie B; Billinge, Simon J L

    2016-05-13

    We present a temperature-dependent atomic and magnetic pair distribution function (PDF) analysis of neutron total scattering measurements of antiferromagnetic MnO, an archetypal strongly correlated transition-metal oxide. The known antiferromagnetic ground-state structure fits the low-temperature data closely with refined parameters that agree with conventional techniques, confirming the reliability of the newly developed magnetic PDF method. The measurements performed in the paramagnetic phase reveal significant short-range magnetic correlations on a ∼1  nm length scale that differ substantially from the low-temperature long-range spin arrangement. Ab initio calculations using a self-interaction-corrected local spin density approximation of density functional theory predict magnetic interactions dominated by Anderson superexchange and reproduce the measured short-range magnetic correlations to a high degree of accuracy. Further calculations simulating an additional contribution from a direct exchange interaction show much worse agreement with the data. The Anderson superexchange model for MnO is thus verified by experimentation and confirmed by ab initio theory. PMID:27232042

  8. Ab initio design of elastically isotropic TiZrNbMoV{sub x} high-entropy alloys

    Tian, Fuyang, E-mail: fuytian@gmail.com [Applied Materials Physics, Department of Materials Science and Engineering, Royal Institute of Technology, Stockholm SE-100 44 (Sweden); Institute for Applied Physics, University of Science and Technology Beijing, Beijing 100083 (China); Varga, Lajos Karoly [Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, P.O. Box 49, H-1525 Budapest (Hungary); Chen, Nanxian [Institute for Applied Physics, University of Science and Technology Beijing, Beijing 100083 (China); Department of Physics, Tsinghua University, Beijing 100084 (China); Shen, Jiang [Institute for Applied Physics, University of Science and Technology Beijing, Beijing 100083 (China); Vitos, Levente [Applied Materials Physics, Department of Materials Science and Engineering, Royal Institute of Technology, Stockholm SE-100 44 (Sweden); Institute for Solid State Physics and Optics, Wigner Research Centre for Physics, Hungarian Academy of Sciences, P.O. Box 49, H-1525 Budapest (Hungary); Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, Box 516, SE-751210 Uppsala (Sweden)

    2014-06-25

    Highlights: • The refractory high-entropy alloys are studied with ab initio theory. • We study the effect of alloying elements on the elastic parameters. • We propose an criterion of elastically isotropic refractory high-entropy alloys. - Abstract: The TiZrVNb and TiZrNbMoV{sub x} (x = 0–1.5) high-entropy alloys (HEAs) are single-phase solid solutions having the body centered cubic crystallographic structure. Here we use the ab initio exact muffin-tin orbitals method in combination with the coherent potential approximation to study the equilibrium bulk properties of the above refractory HEAs. We provide a detailed investigation of the effect of alloying elements on the electronic structure and elastic parameters. Our results indicate that vanadium enhances the anisotropy of TiZrNbMoV{sub x}. As an application of the present theoretical database, we verify the often quoted correlation between the valence electron concentration (VEC) and the micro-mechanical properties in the case of multi-component alloys. Furthermore, we predict that the present HEAs become elastically isotropic for VEC∼4.72.

  9. Periodic arrays of intercalated atoms in twisted bilayer graphene: An ab initio investigation

    Miwa, R. H.; Venezuela, P.; Morell, Eric Suárez

    2015-09-01

    We have performed an ab initio investigation of transition metals (TMs =Mo ,Ru ,Co ,andPt ) embedded in twisted bilayer graphene (tBG) layers. Our total energy results reveal that, triggered by the misalignment between the graphene layers, Mo and Ru atoms may form a quasiperiodic (triangular) array of intercalated atoms. In contrast, the formation of those structures is not expected for the other TMs, the Co and Pt atoms. The net magnetic moment (m ) of Mo and Ru atoms may be quenched upon intercalation, depending on the stacking region (AA or AB). For instance, we find a magnetic moment of 0.3 μB(1.8 μB) for Ru atoms intercalated between the AA (AB) regions of the stacked twisted layers. Through simulated scanning tunneling microscopy (STM) images, we verify that the presence of intercalated TMs can be identified by the formation of bright (hexagonal) spots lying on the graphene surface.

  10. An ab initio cluster study of the structure of the Si(001) surface

    Ab initio calculations, employing double zeta plus polarization (DZP) basis sets and generalized valence bond (GVB) wave functions, have been performed on clusters of varying size, to investigate the utility of such clusters as prototypes for the study of silicon surfaces, and to investigate the effect of the level of theory used on predicted results. This work builds on landmark papers by Goddard in 1982 and Paulus in 1998 that demonstrate that a single reference wave function description of the silicon dimer bond is incorrect, and that a multireference description results in a symmetric dimer in a silicon cluster containing one dimer. In this work, it is shown that the imposition of arbitrary geometrical constraints (fixing subsurface atoms at lattice positions) on cluster models of the Si(100) surface can also lead to nonphysical results. Calculations on the largest clusters, without geometrical constraints, reveal that surface rearrangement due to dimer bond formation is ''felt'' several layers into the bulk. The predicted subsurface displacements compare favorably to experiment. Thus, small clusters, such as Si9H12, cannot adequately represent bulk behavior. Vibrational analysis shows that dimer buckling modes require minimal excitation energy, so the experimental observation of buckled dimers on silicon surfaces may reflect the ease with which a symmetric dimer can be perturbed from its minimum energy structure. In the study of surface reconstruction and relaxation, and the associated issue of the buckling of dimer surfaces, it is critical to use adequate wave functions. As shown in this work and previously by Goddard and Paulus, this generally means that multireference treatments are needed to correctly treat the dangling bonds. (c) 2000 American Institute of Physics

  11. Six low-strain zinc-blende half metals: An ab initio investigation

    Pask, J. E.; Yang, L. H.; Fong, C. Y.; Pickett, W. E.; Dag, S.

    2003-06-01

    A class of spintronic materials, the zinc-blende (ZB) half metals, has recently been synthesized in thin-film form. We apply all-electron and pseudopotential ab initio methods to investigate the electronic and structural properties of ZB Mn and Cr pnictides and carbides, and find six compounds to be half metallic at or near their respective equilibrium lattice constants, making them excellent candidates for growth at low strain. Based on these findings, we further propose substrates on which the growth may be accomplished with minimum strain. Our findings are supported by the recent successful synthesis of ZB CrAs on GaAs and ZB CrSb on GaSb, where our predicted equilibrium lattice constants are within 0.5% of the lattice constants of the substrates on which the growth was accomplished. We confirm previous theoretical results for ZB MnAs, but find ZB MnSb to be half metallic at its equilibrium lattice constant, whereas previous work has found it to be only nearly so. We report here two low-strain half metallic ZB compounds, CrP and MnC, and suggest appropriate substrates for each. Unlike the other five compounds, we predict ZB MnC to become/remain half metallic with compression rather than expansion, and to exhibit metallicity in the minority- rather than majority-spin channel. These fundamentally different properties of MnC can be connected to substantially greater p-d hybridization and d-d overlap, and correspondingly larger bonding-antibonding splitting and smaller exchange splitting. We examine the relative stability of each of the six ZB compounds against NiAs and MnP structures, and find stabilities for the compounds not yet grown comparable to those already grown.

  12. An ab initio study of complexes between ethylene and ozone

    McKee, M.L. (Auburn Univ., AL (USA)); Rohlfing, C.M. (Sandia National Labs., Livermore, CA (USA))

    1989-03-29

    A series of complexes between ethylene and ozone have been examined at the SCF, MP2, and MP4(SDTQ) levels of theory within a split-valence-plus-polarization basis. The conformational nature of the primary ozonide (PO) is determined to be an O-envelope, and the theoretically predicted geometry is in excellent agreement with a recently reported microwave structure. The binding energy of PO at correlated levels is computed to be slightly less than 50 kcal/mol, which is also in very good agreement with thermochemical estimates. Five other weakly bound complexes and the transition state to PO have also been investigated.

  13. Ab initio study of hydrogen adsorption in MOF-5.

    Sillar, Kaido; Hofmann, Alexander; Sauer, Joachim

    2009-03-25

    Metal-organic frameworks (MOFs) are promising adsorbents for hydrogen storage. Density functional theory and second-order Møller-Plesset perturbation theory (MP2) are used to calculate the interaction energies between H(2) and individual structural elements of the MOF-5 framework. The strongest interaction, DeltaH(77) = -7.1 kJ/mol, is found for the alpha-site of the OZn(4)(O(2)Ph)(6) nodes. We show that dispersion interactions and zero-point vibrational energies must be taken into account. Comparison of calculations done under periodic boundary conditions for the complete structure with those done for finite models cut from the MOF-5 framework shows that the interactions with H(2) originate mainly from the local environment around the adsorption site. When used within a Multi-Langmuir model, the MP2 results reproduce measured adsorption isotherms (the predicted amount is 6 wt % at 77 K and 40 bar) if we assume that the H(2) molecules preserve their rotational degrees of freedom in the adsorbed state. This allows to discriminate between different isotherms measured for different MOF-5 samples and to reliably predict isotherms for new MOF structures. PMID:19253977

  14. A systematic benchmark of the ab initio Bethe-Salpeter equation approach for low-lying optical excitations of small organic molecules

    Bruneval, Fabien; Hamed, Samia M.; Neaton, Jeffrey B.

    2015-01-01

    The predictive power of the ab initio Bethe-Salpeter equation (BSE) approach, rigorously based on many-body Green's function theory but incorporating information from density functional theory, has already been demonstrated for the optical gaps and spectra of solid-state systems. Interest in photoactive hybrid organic/inorganic systems has recently increased, and so has the use of the BSE for computing neutral excitations of organic molecules. However, no systematic benchmarks of the BSE for ...

  15. Spectra of barium, radium, and element 120; application of the combined correlation potential, singles-doubles, and configuration interaction ab initio method

    Ginges, J S M

    2015-01-01

    We apply a version of the recently developed approach combining the correlation potential, linearized singles-doubles coupled-cluster, and the configuration interaction methods to the spectra of the heavy alkaline earths barium, radium, and element 120. Quantum electrodynamics radiative corrections are included. We have found unprecedented agreement between ab initio theory and experiment for the spectra of barium and radium, and we make accurate predictions for missing and unreliable data for all three atoms.

  16. Spectra of barium, radium, and element 120; application of the combined correlation potential, singles-doubles, and configuration interaction ab initio method

    Ginges, J. S. M.; Dzuba, V. A.

    2015-01-01

    We apply a version of the recently developed approach combining the correlation potential, linearized singles-doubles coupled-cluster, and the configuration interaction methods to the spectra of the heavy alkaline earths barium, radium, and element 120. Quantum electrodynamics radiative corrections are included. We have found unprecedented agreement between ab initio theory and experiment for the spectra of barium and radium, and we make accurate predictions for missing and unreliable data fo...

  17. Efficient "on-the-fly" calculation of Raman spectra from \\textit{ab-initio} molecular dynamics: Application to hydrophobic/hydrophilic solutes in bulk water

    Partovi-Azar, Pouya

    2015-01-01

    We present a computational method to accurately calculate Raman spectra from first principles with an at least one order of magnitude higher efficiency. This scheme thus allows to routinely calculate finite-temperature Raman spectra "on-the-fly" by means of \\textit{ab-initio} molecular dynamics simulations. To demonstrate the predictive power of this approach we investigate the effect of hydrophobic and hydrophilic solutes in water solution on the infrared and Raman spectra.

  18. Electronically Excited States of Vitamin B12: Benchmark Calculations Including Time-Dependent Density Functional Theory and Correlated Ab Initio Methods

    Kornobis, Karina; Kumar, Neeraj; Wong, Bryan M.; Lodowski, Piotr; Jaworska, Maria; Andruniów, Tadeusz; Rudd, Kenneth; Kozlowski, Pawel M.

    2011-01-01

    Time-dependent density functional theory (TD-DFT) and correlated ab initio methods have been applied to the electronically excited states of vitamin B12 (cyanocobalamin or CNCbl). Different experimental techniques have been used to probe the excited states of CNCbl, revealing many issues that remain poorly understood from an electronic structure point of view. Due to its efficient scaling with size, TD-DFT emerges as one of the most practical tools that can be used to predict the electronic p...

  19. Ab Initio Calculations Of Nuclear Reactions And Exotic Nuclei

    Quaglioni, S. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2014-05-05

    Our ultimate goal is to develop a fundamental theory and efficient computational tools to describe dynamic processes between nuclei and to use such tools toward supporting several DOE milestones by: 1) performing predictive calculations of difficult-to-measure landmark reactions for nuclear astrophysics, such as those driving the neutrino signature of our sun; 2) improving our understanding of the structure of nuclei near the neutron drip line, which will be the focus of the DOE’s Facility for Rare Isotope Beams (FRIB) being constructed at Michigan State University; but also 3) helping to reveal the true nature of the nuclear force. Furthermore, these theoretical developments will support plasma diagnostic efforts at facilities dedicated to the development of terrestrial fusion energy.

  20. Ab Initio Calculations Of Nuclear Reactions And Exotic Nuclei

    Our ultimate goal is to develop a fundamental theory and efficient computational tools to describe dynamic processes between nuclei and to use such tools toward supporting several DOE milestones by: 1) performing predictive calculations of difficult-to-measure landmark reactions for nuclear astrophysics, such as those driving the neutrino signature of our sun; 2) improving our understanding of the structure of nuclei near the neutron drip line, which will be the focus of the DOE's Facility for Rare Isotope Beams (FRIB) being constructed at Michigan State University; but also 3) helping to reveal the true nature of the nuclear force. Furthermore, these theoretical developments will support plasma diagnostic efforts at facilities dedicated to the development of terrestrial fusion energy.

  1. The energy computation paradox and ab initio protein folding.

    John C Faver

    Full Text Available The routine prediction of three-dimensional protein structure from sequence remains a challenge in computational biochemistry. It has been intuited that calculated energies from physics-based scoring functions are able to distinguish native from nonnative folds based on previous performance with small proteins and that conformational sampling is the fundamental bottleneck to successful folding. We demonstrate that as protein size increases, errors in the computed energies become a significant problem. We show, by using error probability density functions, that physics-based scores contain significant systematic and random errors relative to accurate reference energies. These errors propagate throughout an entire protein and distort its energy landscape to such an extent that modern scoring functions should have little chance of success in finding the free energy minima of large proteins. Nonetheless, by understanding errors in physics-based score functions, they can be reduced in a post-hoc manner, improving accuracy in energy computation and fold discrimination.

  2. Ab initio calculation of the neutron-proton mass difference

    CERN. Geneva

    2015-01-01

    The existence and stability of atoms relies on the fact that neutrons are more massive than protons. The mass difference is only 0.14% of the average and has significant astrophysical and cosmological implications. A slightly smaller or larger value would have led to a dramatically different universe. After an introduction to the problem and to lattice quantum chromodynamics (QCD), I will show how this difference can be computed precisely by carefully accounting for electromagnetic and mass isospin breaking effects in lattice computations. I will also report on results for splittings in the \\Sigma, \\Xi, D and \\Xi_{cc} isospin multiplets, some of which are predictions. The computations are performed in lattice QCD plus QED with four, non-degenerate quark flavors.

  3. Acidity of clay edges from ab-initio simulations

    Document available in extended abstract form only. One of the most important factor to understand and predict the sorption of cations on clay surfaces is the protonation state of the surface sites, which is difficult to determine experimentally. Indeed, titration provides a global measure only; it does not probe the status of different silanol (Si-OH) and aluminol sites (Al-OH and Al-OH2) present along the edges of clay sheets in the presence of water. A novel method has been recently designed to quantify the acidity of chemical species. This method allows to estimate pKa values from First Principles Molecular Dynamics by thermodynamic integration. We have applied it to the case of pyrophyllite clay edge sites. These calculations will allow us to subsequently perform classical Molecular Dynamic simulations with realistic surface structures (protonated/deprotonated sites) for natural clays in the presence of water. After presenting the method, we show its application to the (010) edge of pyrophyllite. We find that the most acidic group is Si-OH while the least acidic one is Al-OH, which never deprotonates in water because of its high pKa value (22.1). We further provide a microscopic understanding of the solvation structure and reactivity of the edges of neutral clays. In particular we address the tendency to deprotonation of the different reactive groups on the (010) face of pyrophyllite, showing the important role of solvation and its rearrangements after deprotonation. Finally, we compare our results to the one predicted by the empiric method MUSIC and the estimate from deprotonation energies in the vacuum, confirming the important role of solvation in both the protonated and deprotonated states. (authors)

  4. An Ab Initio Study on Silicon and Germanium Nanotubes

    Pradhan, Prachi

    2005-03-01

    First principles calculations using hybrid density functional theory have been performed to examine the electronic and geometric structure properties of single-walled silicon (SWSiNT) and germanium (SWGeNT) nanotubes. Finite clusters XmHn^ (X = Si or Ge) are used to model the nanotubes (e.g. the smallest SWSiNT is modeled as Si60H12). Hydrogen termination is done to simulate the effect of longer tubes as well as to take care of end effects. A pseudopotential basis set has been used for the silicon atoms^1 and complete geometry optimizations of the structures has been carried out using the Gaussian 03 suite of programs.^2 Computer simulations predict that the existence and stability of the nanotubes are highly dependent on the ratio of the sp^2 to sp^3 hybridization. Results will be presented on cohesive energies, HOMO- LUMO gaps, and other electronic structure properties and their dependence on the tube diameter. We will discuss the density of states (DOS) to explain the possible metallic or semi-conducting character of the tubes. Detailed comparisons with published data in the literature will also be presented. * Work supported, in part, by the Welch Foundation, Houston, Texas (Grant No. Y-1525). ^1 P. J. Hay and W. R. Wadt, J. Chem. Phys. 82, 270 (1985). ^2 Gaussian03, Revision A.1, M. J. Frisch et al., Gaussian Inc., Pittsburgh, PA , 2003.

  5. A Reasonable Ab Initio Cosmological Constant Without Holography

    Trout, Aaron D

    2012-01-01

    We give a well-motivated explanation for the origin of dark energy, claiming that it arises from a small residual negative scalar-curvature present even in empty spacetime. The vacuum has this residual curvature because spacetime is fundamentally discrete and there are more ways for a discrete geometry to have negative curvature than positive. We explicitly compute this effect in the well-known {\\em dynamical triangulations} (DT) model for quantum gravity and the predicted cosmological constant $\\Lambda$ agrees with observation. We begin by almost completely characterizing the DT-model's vacuum energies in dimension three. Remarkably, the energy gap between states comes in increments of [\\Delta\\mathcal{A} =\\frac{\\ell}{8\\mathcal{V}}] in natural units, where $\\ell$ is the "Planck length" in the model and $\\mathcal{V}$ is the volume of the universe. Then, using only vacua in the $N$ energy levels nearest zero, where $N$ is the universe's radius in units of $\\ell$, we apply our model to the current co-moving spat...

  6. Structure of the glass-forming metallic liquids by ab-initio and classical molecular dynamics, a case study: Quenching the Cu60Ti20Zr20 alloy

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

  7. Organic/inorganic hybrid materials: challenges for ab initio methodology.

    Draxl, Claudia; Nabok, Dmitrii; Hannewald, Karsten

    2014-11-18

    terms of interfacial electronic structure. We face the problem of a so far hidden variable, namely, electron-vibrational coupling, regarding level alignment at interfaces between organic and inorganic semiconductors. Poly(para-phenylene) adsorbed on graphene and encapsulated in carbon nanotubes represent case studies to demonstrate the impact of polarization effects and exciton delocalization in optoelectronic excitations, respectively. Polaron-induced band narrowing and its consequences for charge transport in organic crystals is exemplified for the HOMO bandwidth in naphthalene crystals. On the basis of these prototypical systems, we discuss what is missing to reach predictive power on a quantitative level for organic/inorganic hybrid materials and, thus, open a perspective toward the computational discovery of new materials for optoelectronic applications. PMID:25171272

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

    Tossell, J. A.

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

  9. Vacancy–solute interactions in ferromagnetic and paramagnetic bcc iron: Ab initio calculations

    Highlights: ► Interactions of vacancies with 3p, 3d, and 4d impurities in bcc Fe are calculated ab initio. ► Ferromagnetic and disordered paramagnetic states of the Fe matrix are considered. ► Three groups of impurities whose interactions with vacancies strongly depend on magnetic order. ► Compound-formers (Al, Si, P, S), insoluble elements (Cu, Ag), and magnetic elements (Mn, Co, Ni). ► The results are applied to interpret anomalies of vacancy trapping and impurity diffusion. - Abstract: Vacancy–solute interactions play a crucial role in diffusion-controlled processes, such as ordering or decomposition, which occur in alloys under heat treatment or under irradiation. Detailed knowledge of these interactions is important for predicting long-term behavior of nuclear materials (such as reactor steels and nuclear-waste containers) as well as for advancing our general understanding of kinetic processes in alloys. Using first-principles calculations based on the density functional theory and employing the locally self-consistent Green’s function technique, we develop a database of vacancy–solute interactions in dilute alloys of bcc Fe with 3p (Al, Si, P, S), 3d (Sc–Cu), and 4d (Y–Ag) elements. Unrelaxed interactions within the first three coordination shells have been computed in the ferromagnetic state as well as in the paramagnetic (disordered local moment) state of the iron matrix. Magnetism is found to have a strong effect on the vacancy–solute interactions. Implications of the obtained results for interpreting the effects of vacancy trapping and enhanced impurity diffusion are discussed.

  10. Reaction mechanisms and kinetics of the iminovinylidene radical with NO: Ab initio study

    Hsiao, Ming-Kai; Chung, Yi-Hua; Hung, Yu-Ming; Chen, Hui-Lung, E-mail: chl3@faculty.pccu.edu.tw [Department of Chemistry and Institute of Applied Chemistry, Chinese Culture University, Taipei 111, Taiwan (China)

    2014-05-28

    The nitric oxide (NO) is a notorious compound for polluting environment. Recent year, removing nitric oxide from the atmosphere becomes a focus of the investigation. In our work, we study the iminovinylidene (HNCC) radical reacted with NO molecule. The mechanism and kinetic for reaction of the HNCC radical with the NO molecule is investigated via considering the possible channels of the N and O atoms of NO attacking the N and C atoms of the HNCC based on the high level ab initio molecular orbital calculations in conjunction with variational TST and RRKM calculations. The species involved have been optimized at the B3LYP/6-311++G(3df,2p) level and their single-point energies are refined by the CCSD(T)/aug-cc-PVQZ//B3LYP/6-311++G(3df,2p) method. The calculated potential energy surfaces indicated that energetically the most favorable channel for the HNCC + NO reaction was predicted to be the formation of HNC+CNO (P8) product via the addition reaction of the C atom of HNCC radical and the N atom of NO with the head to head orientation. To rationalize the scenario of the calculated results, we also employ the Fukui functions and HSAB theory to seek for a possible explanation. In addition, the reaction rate constants were calculated using VariFlex code, and the results show that the total rate coefficient, k{sub total}, at Ar pressure 760 Torr can be represented with an equation: k{sub total} = 6.433 × 10{sup −11} T {sup 0.100} exp(0.275 kcal mol{sup −1}/RT) at T = 298–3000 K, in units of cm{sup 3} molecule{sup −1} s{sup −1}.

  11. Optical properties of surfaces with supercell ab initio calculations: Local-field effects

    Tancogne-Dejean, Nicolas; Giorgetti, Christine; Véniard, Valérie

    2015-12-01

    Surface optical and electronic properties are crucial for material science and have implications in fields as various as nanotechnology, nonlinear optics, and spectroscopies. In particular, the huge variation of electronic density perpendicular to the surface is expected to play a key role in absorption due to local-field effects. Numerous state-of-the-art theoretical and numerical ab initio formalisms developed for studying these properties are based on supercell approaches, in reciprocal space, due to their efficiency. In this paper, we show that the standard scheme fails for the out-of-plane optical response of the surface. This response is interpreted using the "effective-medium theory" with vacuum and also in terms of interaction between replicas, as the supercell approach implies a periodicity which is absent in the real system. We propose an alternative formulation, also based on the supercell, for computing the macroscopic dielectric function. Application to the clean Si(001) 2 ×1 surface allows us to present the effect of the local fields for both peak positions and line shape on the bulk and surface contributions. It shows how local fields built up for the in-plane and out-of-plane dielectric responses of the surface. In addition to their conceptual impact, our results explain why the standard approach gives reliable predictions for the in-plane components, leading to correct reflectance anisotropy spectra. Our scheme can be further generalized to other low-dimensional geometries, such as clusters or nanowires, and open the way to nonlinear optics for surfaces.

  12. The electronic structure of wurtzite and zincblende AlN: an ab initio comparative study

    This work deals with the electronic properties, in different crystal phases, of AlN (wurtzite and zincblende) compounds computed using an all electron ab initio linearized augmented plane wave method. Results include band structure, total and partial density of states, charge density and the ionicity factor. Most of the calculated band parameters, of direct bandgap, total- and upper-valence bandwidths and antisymmetric gap for wurtzite-AlN are close to those of c-AlN to within 1%. The charge distributions have similar features, meaning that AlN has the same ionicity factor in both structures. (author)

  13. Benchmarking ab initio binding energies of hydrogen-bonded molecular clusters based on FTIR spectroscopy

    Bork, Nicolai Christian; Du, Lin; Reiman, Heidi;

    2014-01-01

    Gibbs free binding energies in molecular complexes and clusters based on gas phase FTIR spectroscopy. The acetonitrile-HCl molecular complex is identified via its redshifted H-Cl stretching vibrational mode. We determine the Gibbs free binding energy, ΔG°295 K, to between 4.8 and 7.9 kJ mol(-1) and......Models of formation and growth of atmospheric aerosols are highly dependent on accurate cluster binding energies. These are most often calculated by ab initio electronic structure methods but remain associated with significant uncertainties. We present a computational benchmarking study of the...

  14. Ab initio molecular orbital calculations on ion pair-water complexes of metal halides and oxides

    Mohandas, P; Singh, S.; Chandrasekhar, J

    1994-01-01

    Ab initio MO calculations are performed on a series of ion-molecular and ion pair-molecular complexes of H2O + MX (MX = LiF, LiCl, NaCl, BeO and MgO) systems. BSSE-corrected stabilization energies, optimized geometrical parameters, internal force constants and harmonic vibrational frequencies have been evaluated for all the structures of interest. The trends observed in the geometrical parameters and other properties calculated for the mono-hydrated contact ion pair complexes parallel those c...

  15. 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

  16. Transport coefficients of helium-argon mixture based on ab initio potential.

    Sharipov, Felix; Benites, Victor J

    2015-10-21

    The viscosity, thermal conductivity, diffusion coefficient, and thermal diffusion factor of helium-argon mixtures are calculated for a wide range of temperature and for various mole fractions up to the 12th order of the Sonine polynomial expansion with an ab initio intermolecular potential. The calculated values for these transport coefficients are compared with other data available in the open literature. The comparison shows that the obtained transport coefficients of helium-argon mixture have the best accuracy for the moment. PMID:26493894

  17. Real-space ab-initio electronic structure calculations using SfePy

    Cimrman, R.; Novák, Matyáš; Kolman, Radek; Vackář, Jiří

    Plzeň: University of West Bohemia, 2015 - (Adámek, V.). s. 21-22 ISBN 978-80-261-0568-8. [Computational Mechanics 2015 /31./- conference with international participation /31./. 09.11.2015-11.11.2015, Špičák] R&D Projects: GA ČR(CZ) GAP108/11/0853; GA ČR(CZ) GAP101/12/2315 Institutional support: RVO:61388998 ; RVO:68378271 Keywords : real-space ab-initio electronic structure calculations * finite element method * isogeometric analysis Subject RIV: BE - Theoretical Physics

  18. Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol

    Pham, Thi Nu; Ono, Shota; Ohno, Kaoru

    2016-04-01

    Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronic excited state configuration.

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

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

  20. Structure and lattice dynamics of PrFe3(BO3)4: Ab initio calculation

    Chernyshev, V. A.; Nikiforov, A. E.; Petrov, V. P.

    2016-06-01

    The crystal structure and phonon spectrum of PrFe3(BO3)4 are ab initio calculated in the context of the density functional theory. The ion coordinates in the unit cell of a crystal and the lattice parameters are evaluated from the calculations. The types and frequencies of the fundamental vibrations, as well as the line intensities of the IR spectrum, are determined. The elastic constants of the crystal are calculated. A "seed" frequency of the vibration strongly interacting with the electron excitation on the praseodymium ion is obtained for low-frequency A 2 mode. The calculated results are in agreement with the known experimental data.

  1. Elastic Properties of CaSiO3 Perovskite from ab initio Molecular Dynamics

    Shigeaki Ono

    2013-01-01

    Ab initio molecular dynamics simulations were performed to investigate the elasticity of cubic CaSiO3 perovskite at high pressure and temperature. All three independent elastic constants for cubic CaSiO3 perovskite, C11, C12, and C44, were calculated from the computation of stress generated by small strains. The elastic constants were used to estimate the moduli and seismic wave velocities at the high pressure and high temperature characteristic of the Earth’s interior. The dependence of temp...

  2. Ab initio calculations of 14N and 15N hyperfine structures

    Jönsson, P; Nemouchi, M; Godefroid, M

    2010-01-01

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

  3. Efficient Use of an Adapting Database of Ab Initio Calculations To Generate Accurate Newtonian Dynamics.

    Shaughnessy, M C; Jones, R E

    2016-02-01

    We develop and demonstrate a method to efficiently use density functional calculations to drive classical dynamics of complex atomic and molecular systems. The method has the potential to scale to systems and time scales unreachable with current ab initio molecular dynamics schemes. It relies on an adapting dataset of independently computed Hellmann-Feynman forces for atomic configurations endowed with a distance metric. The metric on configurations enables fast database lookup and robust interpolation of the stored forces. We discuss mechanisms for the database to adapt to the needs of the evolving dynamics, while maintaining accuracy, and other extensions of the basic algorithm. PMID:26669825

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

    Yu, Hua-Gen

    2011-08-01

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

  5. Ab initio study of beryllium-decorated fullerenes for hydrogen storage

    Lee, Hoonkyung; Huang, Bing; Duan, Wenhui; Ihm, Jisoon

    2010-01-01

    We have found that a beryllium (Be) atom on nanostructured materials with H2 molecules generates a Kubas-like dihydrogen complex [H. Lee et al. arXiv:1002.2247v1 (2010)]. Here, we investigate the feasibility of Be-decorated fullerenes for hydrogen storage using ab initio calculations. We find that the aggregation of Be atoms on pristine fullerenes is energetically preferred, resulting in the dissociation of the dihydrogen. In contrast, for boron (B)-doped fullerenes, Be atoms prefer to be ind...

  6. Paired-permanent approach for VB theory (II) -An ab initio spin-free VB program

    2001-01-01

    Paired-permanent approach for VB theory is extensively developed. Canonical expan sion of a paired-permanent is deduced. Furthermore, it is shown that a paired-permanent may be expressed in terms of the products of sub-paired-permanents of any given order and their corre sponding minors. An ab initio spin-free valence bond program, called Xiamen, is implemented by using paired-permanent approach. Test calculation shows that Xiamen package is more efficient than some other programs based on the traditional VB algorithm, and it provides a new practical tool for quantum chemistry.

  7. Ab initio based force field and molecular dynamics simulations of crystalline TATB.

    Gee, Richard H; Roszak, Szczepan; Balasubramanian, Krishnan; Fried, Laurence E

    2004-04-15

    An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally. PMID:15267608

  8. Ab initio studies of ionization potentials of hydrated hydroxide and hydronium

    Swartz, Charles W

    2013-01-01

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

  9. smyRNA: A Novel Ab Initio ncRNA Gene Finder

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

    2009-01-01

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

  10. Steady state Ab-initio Theory of Lasers with Injected Signals

    Cerjan, Alexander; Stone, A. Douglas

    2013-01-01

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

  11. Exploring proton transfer in 1,2,3-triazole-triazolium dimer with ab initio method

    Li, Ailin; Yan, Tianying; Shen, Panwen [Department of Material Chemistry, Institute of New Energy Material Chemistry, Nankai University, Tianjin, 300071 (China)

    2011-02-01

    Ab initio calculations are utilized to search for transition state structures for proton transfer in the 1,2,3-triazole-triazolium complexes on the basis of optimized dimers. The result suggests six transition state structures for single proton transfer in the complexes, most of which are coplanar. The energy barriers, between different stable and transition states structures with zero point energy (ZPE) corrections, show that proton transfer occurs at room temperature with coplanar configuration that has the lowest energy. The results clearly support that reorientation gives triazole flexibility for proton transfer. (author)

  12. Improved Ab Initio Molecular Dynamics by Minimal Biasing with Experimental Data

    White, Andrew D; Hocky, Glen M; Voth, Gregory A

    2016-01-01

    Accounting for electrons and nuclei simultaneously is a key goal of computer simulation via ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce the properties of systems such as water due to inaccuracies in the underlying electronic density functionals, shortcomings that are often addressed by added empirical corrections and/or increasing the simulation temperature. We present here a maximum-entropy-based approach to directly incorporate limited experimental data via a minimal bias. The biased AIMD simulations of both water and of an excess proton in water are shown to give significantly improved properties for both the biased and unbiased observables.

  13. Ab Initio Calculations of Elastic Constants of Li2O under Pressure

    LI Xiao-Feng; CHEN Xiang-Rong; JI Guang-Fu; MENG Chuan-Min

    2006-01-01

    @@ We investigate the equilibrium lattice constant, bulk modulus, elastic constants and Debye temperature of Li2 O under pressure by using ab initio unrestricted Hartree-Fock (HF) linear combination of atomic orbital (LCAO) periodic approach. The obtained results at zero pressure are well consistent with the available experimental data and other theoretical results. It is found that the elastic constants C11, C12 and C44 and bulk modulus B increase monotonously as pressure increases. Also, the anisotropy will weaken and the Debye temperature will rise with pressure increasing.

  14. 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

  15. Ab initio adiabatic and quasidiabatic potential energy surfaces of H++ CN system

    Bhargava Anusuri; Sanjay Kumar

    2016-02-01

    We present restricted geometry (collinear and perpendicular approaches of proton) ab initio three dimensional potential energy surfaces for H++ CN system. The calculations were performed at the internally contracted multi-reference configuration interaction level of theory using Dunning’s correlation consistent polarized valence triple zeta basis set. Adiabatic and quasidiabatic surfaces have been computed for the ground and the first excited electronic states. Nonadiabatic effects arising from radial coupling have been analyzed in terms of nonadiabatic coupling matrix elements and coupling potentials.

  16. Site occupancy trend of Co in Ni2MnIn: Ab initio approach

    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

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

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

  18. Structural Features of Boron-Doped Si(113) Surfaces Simulated by ab initio Calculations

    LIAO Long-Zhong; LIU Zheng-Hui; ZHANG Zhao-Hui

    2008-01-01

    Based on ab initio calculations, boron-doped Si(113) surfaces have been simulated and atomic structures of the surfaces have been proposed. It has been determined that surface features of empty and filled states that are separately localized at pentamers and adatoms indicates a low surface density of B atoms, while it is attributed to heavy doping of B atoms at the second layer that pentamers and adatoms are both present in an image of scanning tunnelling microscopy. B doping at the second layer should be balanced by adsorbed B or Si atoms beside the adatoms and inserted B interstitials below the adatoms.

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

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

  20. Phonon spectrum of lead oxychloride Pb3O2Cl2: Ab initio calculation and experiment

    Zakir'yanov, D. O.; Chernyshev, V. A.; Zakir'yanova, I. D.

    2016-02-01

    IR and Raman spectra of Pb3O2Cl2 in the range of 50-600 cm-1 have been detected for the first time. Ab initio calculations of the crystal structure and the phonon spectrum of Pb3O2Cl2 in the framework of LCAO approach have been performed by the Hartree-Fock method and in the framework of the density functional theory with the use of hybrid functionals. The results of calculations have made it possible to interpret the experimental vibration spectra and reveal silent modes, which do not manifest themselves in these spectra but influence the optical properties of the crystal.

  1. Ionization of aqueous cations: Photoelectron spectroscopy and ab initio calculations of protonated imidazole

    Jagoda-Cwiklik, Barbara; Slavíček, P.; Nolting, D.; Winter, B.; Jungwirth, Pavel

    2008-01-01

    Roč. 112, č. 25 (2008), s. 7355-7358. ISSN 1520-6106 R&D Projects: GA MŠk LC512; GA ČR GA203/07/1006 Grant ostatní: DFG(DE) WI1327/3-1; GA ČR(CZ) GP203/07/P449 Institutional research plan: CEZ:AV0Z40550506 Keywords : protenated imidazole * ab initio calculations * photoelectron spectroscopy Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.189, year: 2008

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

    We study the nuclear quadrupole interaction at the nitrogen sites in the molecular and crystalline phases of the imidazole compound. We use PAW which is a state-of-the-art method to calculate the electronic structure and electric field gradient at the nucleus in the framework of the density functional theory. The quadrupole frequencies at both imino and amino N sites are in excellent agreement with measurements. This is the first time that the electric field gradient at crystalline imidazole is correctly treated by an ab initio theoretical approach.

  3. Experimental and ab initio DFT calculated Raman Spectrum of Sudan I, a Red Dye

    Kunov-Kruse, Andreas Jonas; Kristensen, Steffen Buus; Liu, Chuan;

    2011-01-01

    . Comparison was made with other azo dyes in the literature on natural, abundant plant pigments. The results show that there is a possibility in foodstuff analysis to distinguish Sudan I from other dyes by using Raman spectroscopy with more than one laser wavelength for resonance enhancement of the different......The red dye Sudan I was investigated by Raman spectroscopy using different excitation wavelengths (1064, 532 and 244 nm). A calculation of the Raman spectrum based on quantum mechanical ab initio density functional theory (DFT) was made using the RB3LYP method with the 3-21G and 6-311+G(d,p) basis...

  4. Specific interactions between amyloid-β peptide and curcumin derivatives: Ab initio molecular simulations

    Ishimura, Hiromi; Kadoya, Ryushi; Suzuki, Tomoya; Murakawa, Takeru; Shulga, Sergiy; Kurita, Noriyuki

    2015-07-01

    Alzheimer's disease is caused by accumulation of amyloid-β (Aβ) peptides in a brain. To suppress the production of Aβ peptides, it is effective to inhibit the cleavage of amyloid precursor protein (APP) by secretases. However, because the secretases also play important roles to produce vital proteins for human body, inhibitors for the secretases may have side effects. To propose new agents for protecting the cleavage site of APP from the attacking of the γ-secretase, we have investigated here the specific interactions between a short APP peptide and curcumin derivatives, using protein-ligand docking as well as ab initio molecular simulations.

  5. Sinteza, spektroskopska karakterizacija i ab initio istraživanje tioanaloga spirohidantoina

    Marin MARINOV; Minchev, Stoyan; Stoyanov, Neyko; Ivanova, Galya; Spassova, Milena; Enchev, Venelin

    2005-01-01

    Ditioanalozi cikloalkan-spiro-5-hidantoina pripravljeni su reakcijama odgovarajućih spirohidantoina i Lawesson-ovoga reagensa ili P4S10. Sintetizirani su i cikloalkan-spiro-5-(2-tiohidantoini) i cikloalkan-spiro-5- -(4-tiohidantoini), uporabom različitih reakcijskih putova. Strukture dobivenih spojeva potvrđene su 1H, 13C NMR i IR spektroskopijom. Nelinearne molekularne karakteristike predviđene su kvantno-kemijskim računima na ab initio razini. U svim proučavanim strukturama, s povećanjem za...

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

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

  7. Ab initio scaling laws for the formation energy of nanosized interstitial defect clusters in iron, tungsten, and vanadium

    Alexander, R.; Marinica, M.-C.; Proville, L.; Willaime, F.; Arakawa, K.; Gilbert, M. R.; Dudarev, S. L.

    2016-07-01

    The size limitation of ab initio calculations impedes first-principles simulations of crystal defects at nanometer sizes. Considering clusters of self-interstitial atoms as a paradigm for such crystal defects, we have developed an ab initio-accuracy model to predict formation energies of defect clusters with various geometries and sizes. Our discrete-continuum model combines the discrete nature of energetics of interstitial clusters and continuum elasticity for a crystalline solid matrix. The model is then applied to interstitial dislocation loops with and 1 /2 Burgers vectors, and to C15 clusters in body-centered-cubic crystals Fe, W, and V, to determine their relative stabilities as a function of size. We find that in Fe the C15 clusters were more stable than dislocation loops if the number of self-interstitial atoms involved was fewer than 51, which corresponds to a C15 cluster with a diameter of 1.5 nm. In V and W, the 1 /2 loops represent the most stable configurations for all defect sizes, which is at odds with predictions derived from simulations performed using some empirical interatomic potentials. Further, the formation energies predicted by the discrete-continuum model are reparametrized by a simple analytical expression giving the formation energy of self-interstitial clusters as a function of their size. The analytical scaling laws are valid over a very broad range of defect sizes, and they can be used in multiscale techniques including kinetic Monte Carlo simulations and cluster dynamics or dislocation dynamics studies.

  8. Core structure of screw dislocations in Fe from first-principles; Simulation ab initio des coeurs de dislocation vis dans le fer

    Ventelon, L

    2008-11-15

    The various methods appropriate for the simulation of dislocations within first-principles calculations have been set up, improved and compared between them. They have been applied to study screw dislocations in body-centered cubic iron using the SIESTA code. A non-degenerate core structure is obtained; its detailed analysis reveals a dilatation effect. Taking it into account in an anisotropic elasticity model, allows explaining the cell-size dependence of the energetics, obtained within the dipole approach. The Peierls potential obtained in ab initio suggests that the metastable core configuration at halfway position in the Peierls barrier, predicted by empirical potential, does not exist. We show how to construct tri-periodic cells optimized to study kinked dislocations. Using empirical potential, we demonstrate the feasibility of ab initio calculations of Peierls stress and kink formation. (author)

  9. Quasiparticle electronic structure and optical absorption of diamond nanoparticles from ab initio many-body perturbation theory

    The excited states of small-diameter diamond nanoparticles in the gas phase are studied using the GW method and Bethe-Salpeter equation (BSE) within the ab initio many-body perturbation theory. The calculated ionization potentials and optical gaps are in agreement with experimental results, with the average error about 0.2 eV. The electron affinity is negative and the lowest unoccupied molecular orbital is rather delocalized. Precise determination of the electron affinity requires one to take the off-diagonal matrix elements of the self-energy operator into account in the GW calculation. BSE calculations predict a large exciton binding energy which is an order of magnitude larger than that in the bulk diamond

  10. Performance of the major semiempirical, ab initio, and DFT methods for isomerization enthalpies of linear to branched heptanes.

    Rayne, Sierra; Forest, Kaya

    2016-06-01

    The gas phase standard state (298.15 K, 1 atm) isomerization enthalpy (ΔisomH°(g)) prediction performance of the major semiempirical, ab initio, and density functional levels of theory for environmentally relevant transformations was investigated using the linear to branched heptanes as a representative case study. The M062X density functional, MP2 (and higher) levels of Moller-Plesset perturbation theory, and the CBS and Gaussian-n composite methods are well suited for investigating the thermodynamic properties of environmentally interesting isomerizations, although the M062X functional may not be appropriate for all systems. Where large molecular systems prohibit the use of higher levels of theory, the PM6 and PDDG semiempirical methods may offer an appropriate computational cost-accuracy compromise. PMID:26979512

  11. Ab initio theory of magnetic-field-induced odd-frequency two-band superconductivity in MgB2

    Aperis, Alex; Maldonado, Pablo; Oppeneer, Peter M.

    2015-08-01

    We develop the anisotropic Eliashberg framework for superconductivity in the presence of an applied magnetic field. Using as input the ab initio calculated electron and phonon band structures and electron-phonon coupling, we solve self-consistently the anisotropic Eliashberg equations for the archetypal superconductor MgB2. We find two self-consistent solutions, time-even two-band superconductivity, as well as unconventional time-odd s -wave spin triplet two-band superconductivity emerging with applied field. We provide the full momentum, frequency, and spin-resolved dependence and magnetic field-temperature phase diagrams of the time-even and time-odd superconducting pair amplitudes and predict fingerprints of this novel odd-frequency state in tunneling experiments.

  12. The (Lb)S1 0 transition of phenylpropyne and phenylacetylene: an experimental and ab initio study

    This work describes the first excited singlet electronic state, Lb, of phenylpropyne (PPR) and phenylacetylene (PA). Ab initio calculations have been performed for the geometry and normal modes in the S0 and S1 states. One-photon and two-photon S1 0 spectra of jet cooled samples have been examined (REMPI detection) and a detailed vibronic analysis has been carried out for PPR and PA. The origin band of PPR (λ = 279.64 nm) is one order of magnitude weaker than the origin band (λ = 278.63 nm) of PA and the acetylenic modes are greatly reduced by the H → CH3 substitution. These changes and the parallel PPR-PA comparison provided a way for secure vibronic assignment in both molecules, which was also aided by theoretical predictions

  13. Ab initio many-body calculation of the 7Be(p,gamma)8B radiative capture

    Navratil, Petr; Quaglioni, Sofia

    2011-01-01

    We apply the ab initio no-core shell model/resonating group method (NCSM/RGM) approach to calculate the cross section of the 7Be(p,gamma)8B radiative capture. This reaction is important for understanding the solar neutrino flux. Starting from a selected similarity-transformed chiral nucleon-nucleon interaction that accurately describes two-nucleon data, we performed parameter-free many-body calculations that simultaneously predict both the normalization and the shape of the S-factor. We study the dependence on the number of 7Be eigenstates included in the coupled-channel equations and on the size of the harmonic oscillator basis used for the expansion of the eigenstates and of the localized parts of the integration kernels. Our S-factor result at zero energy is on the lower side of, but consistent with, the latest evaluation.

  14. Fingerprints of antiaromaticity in the negative ion (Li_3Al_4)^- via an ab initio quantum-chemical study

    Grassi, A; Angilella, G G N; March, N H; Pucci, R

    2012-01-01

    Fingerprints of antiaromaticity in the negative ion (Li_3Al_4)^-, this species being realizable via a laser vaporization technique, are revealed by means of an ab initio quantum-chemical investigation. First, the ground-state equilibrium geometry of this ion is predicted. Also, the characteristics of the HOMO are studied, both for the square and the rectangular Al_4 geometry in two low-lying isomers of the negative ion. There is no particular sensitivity to the change in geometry of the Al_4 configuration. Therefore, we have calculated theoretically chemical shifts, which contain remarkable fingerprints of antiaromaticity. As to future directions, some comments are added in relation to the Shannon entropy.

  15. Constructing ab initio and empirical potential energy surfaces for water Infrared spectrum; Vibrational and rotational energy levels; Born- Oppenheimer surface

    Kain, J S

    2001-01-01

    The infrared spectrum of water is possibly one of the most well studied and yet portions of it are still poorly understood. Recently, significant advances have been made in assigning water spectra using variational nuclear calculations. The major factor determining the accuracy of ro-vibrational spectra of water is the accuracy of the underlying Potential Energy Surface. Even the most accurate ab initio Potential Energy Surface does not reproduce the Born-Oppenheimer surface to sufficient accuracy for spectroscopic studies. Furthermore, effects beyond this model such as the adiabatic correction, the relativistic correction and the non-adiabatic correction have to be considered. This thesis includes a discussion on how the relativistic correction was calculated, for the water molecule, from first-order perturbation theory. The relativistic correction improved vibrational stretching motion while making the prediction of the bending modes far worse. For rotational motion the relativistic effect had an increasing...

  16. Toward spectroscopically accurate global ab initio potential energy surface for the acetylene-vinylidene isomerization

    Han, Huixian [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States); School of Physics, Northwest University, Xi’an, Shaanxi 710069 (China); Li, Anyang; Guo, Hua, E-mail: hguo@unm.edu [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States)

    2014-12-28

    A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S{sub 0}) electronic state has been constructed by fitting ∼37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm{sup −1}. The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies up to 12 700 cm{sup −1} above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction.

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

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

    2014-12-01

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

  18. Structure and Raman spectra in cryolitic melts: simulations with an ab initio interaction potential.

    Cikit, Serpil; Akdeniz, Zehra; Madden, Paul A

    2014-01-30

    The Raman spectra of cryolitic melts have been calculated from molecular dynamics computer simulations using a polarizable ionic potential obtained by force-fitting to ab initio electronic structure calculations. Simulations which made use of this ab initio derived polarizable interaction potential reproduced the structure and dynamical properties of crystalline cryolite, Na3AlF6, rather well. The transferability of the potential model from solid state to the molten state is tested by comparing results for the Raman spectra of melts of various compositions with those previously obtained with empirically developed potentials and with experimental data. The shapes of the spectra and their evolution with composition in the mixtures conform quite well to those seen experimentally, and we discuss the relationship between the bands seen in the spectra and the vibrational modes of the AlFn((3–n)) coordination complexes which are found in the NaF/AlF3 mixtures. The simulations thus enable a link between the structure of the melt as derived through Raman spectroscopy and through diffraction experiments. We report results for quantities which relate to the degree of cross-linking between these coordination complexes and the diffusive properties of ions. PMID:24432905

  19. Estudio ab initio del mecanismo de la reacción HSO + O3

    Nebot Gil, I.

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

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

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

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

    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...

  2. From ab initio quantum chemistry to molecular dynamics: The delicate case of hydrogen bonding in ammonia

    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...

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

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

    1991-01-01

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

  4. Vibrational spectroscopic investigations, ab initio and DFT studies on 7-bromo-5-chloro-8-hydroxyquinoline

    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.

  5. 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 -π interactions and the influence of amino and methyl groups on the skeletal modes are investigated.

  6. Ab initio calculation of the ro-vibrational spectrum of H2F+

    Kyuberis, Aleksandra A.; Lodi, Lorenzo; Zobov, Nikolai F.; Polyansky, Oleg L.

    2015-10-01

    An ab initio study of the rotation-vibrational spectrum of the electronic ground state of the (gas-phase) fluoronium ion H2F+ is presented. A new potential energy surface (PES) and a new dipole moment surface (DMS) were produced and used to compute rotation-vibrational energy levels, line positions and line intensities. Our computations achieve an accuracy of 0.15 cm-1 for the fundamental vibrational frequencies, which is about 50 times more accurate than previous ab initio results. The computed room-temperature line list should facilitate the experimental observations of new H2F+ lines, in particular of yet unobserved overtone transitions. The H2F+ molecular ion, which is isoelectronic to water, has a non-linear equilibrium geometry but a low-energy barrier to linearity at about 6000 cm-1. As a result the effects of so-called quantum monodromy become apparent already at low bending excitations. An analysis of excited bends in terms of quantum monodromy is presented.

  7. Voltage-dependent parameter extraction for graphene nanoribbon interconnect model through ab initio approach

    This paper presents electrical parameter extraction for metallic graphene nanoribbon (GNR) interconnects utilizing ab initio approach. Unlike the studies taking the kinetic inductance, quantum capacitance and Fermi velocity as constant values, voltage-dependencies of these parameters are obtained for GNR transmission line model. The variations of the kinetic energy and the current by the applied voltage are taken as bases for voltage-dependent kinetic inductance calculation. Quantum capacitance and the Fermi velocity are also computed from the kinetic inductance variation. It is concluded that voltage-dependencies of the kinetic inductance and the quantum capacitance have to be taken into account for accurate GNR modelling in nanoelectronic design. - Highlights: • Metallic graphene nanoribbon interconnects are studied using ab initio approach. • Variations of the kinetic inductance (LK) and the current are obtained. • Voltage-dependency of the kinetic inductance is extracted. • The variations of quantum capacitance (CQ) and Fermi velocity are calculated. • LK and CQ change by 34% in the voltage range of 0–1 V

  8. Accelerating Ab Initio Path Integral Simulations via Imaginary Multiple-Timestepping.

    Cheng, Xiaolu; Herr, Jonathan D; Steele, Ryan P

    2016-04-12

    This work investigates the use of multiple-timestep schemes in imaginary time for computationally efficient ab initio equilibrium path integral simulations of quantum molecular motion. In the simplest formulation, only every n(th) path integral replica is computed at the target level of electronic structure theory, whereas the remaining low-level replicas still account for nuclear motion quantum effects with a more computationally economical theory. Motivated by recent developments for multiple-timestep techniques in real-time classical molecular dynamics, both 1-electron (atomic-orbital basis set) and 2-electron (electron correlation) truncations are shown to be effective. Structural distributions and thermodynamic averages are tested for representative analytic potentials and ab initio molecular examples. Target quantum chemistry methods include density functional theory and second-order Møller-Plesset perturbation theory, although any level of theory is formally amenable to this framework. For a standard two-level splitting, computational speedups of 1.6-4.0x are observed when using a 4-fold reduction in time slices; an 8-fold reduction is feasible in some cases. Multitiered options further reduce computational requirements and suggest that quantum mechanical motion could potentially be obtained at a cost not significantly different from the cost of classical simulations. PMID:26966920

  9. Ab initio modeling of plasticity in HCP metals: pure zirconium and titanium and effect of oxygen

    We performed atomistic simulations to determine screw dislocations properties in pure zirconium and titanium and to explain the hardening effect attributed to oxygen alloying in both hexagonal close-packed transition metals. We used two energetic models: ab initio calculations based on the density functional theory and calculations with an empirical potential. The complete energetic profile of the screw dislocation when gliding in the different slip planes is obtained in pure Zr. Our calculations reveal the existence of a metastable configuration of the screw dislocation partially spread in the first order pyramidal plane. This configuration is responsible for the cross slip of screw dislocations from prismatic planes, the easiest glide planes, to pyramidal or basal planes. This energy profile is affected by oxygen addition. Ab initio calculations reveal two main effects: oxygen enhances pyramidal cross slip by modifying the dislocation core structure, and pins the dislocation in its metastable sessile configuration. The same modeling approach is applied to titanium. In pure Ti, the same configurations of the screw dislocation in Zr are obtained, but with different energy levels. This leads to a different gliding mechanism. The same way as in Zr, oxygen enhances pyramidal glide in Ti by modifying the dislocation core structure. Besides, oxygen atom lowers the energy of the metastable configuration but not enough to pin the dislocation in this sessile configuration. (author)

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

    Forssén, C; Ormand, W E; Caurier, E

    2004-01-01

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

  11. Ab initio many-body calculations of nucleon-nucleus scattering

    Quaglioni, Sofia

    2009-01-01

    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 3H, 4He and 10Be and proton scattering on 3He and 4He, 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-4He S-wave phase shifts. On the contrary, the experimental nucleon-4He P-wave phase shifts are not well reproduced by any NN potential we use. We demonstrate that a proper treatment of the coupling to the n-10Be continuum is successful in explaining the parity-inverted ground state in 11Be.

  12. Quantum supercharger library: hyper-parallel integral derivatives algorithms for ab initio QM/MM dynamics.

    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

  13. 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...

  14. Emergent properties of nuclei from ab initio coupled-cluster calculations

    Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; Papenbrock, T.

    2016-06-01

    Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. This endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. This paper reviews some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO{}{{sat}} is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon–nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. The coupling to the continuum impacts the energies of the {J}π =1/{2}-,3/{2}-,7/{2}-,3/{2}+ states in {}{17,23,25}O, and—contrary to naive shell-model expectations—the level ordering of the {J}π =3/{2}+,5/{2}+,9/{2}+ states in {}{53,55,61}Ca. ).

  15. Voltage-dependent parameter extraction for graphene nanoribbon interconnect model through ab initio approach

    Yamacli, Serhan, E-mail: syamacli@nny.edu.tr

    2014-07-01

    This paper presents electrical parameter extraction for metallic graphene nanoribbon (GNR) interconnects utilizing ab initio approach. Unlike the studies taking the kinetic inductance, quantum capacitance and Fermi velocity as constant values, voltage-dependencies of these parameters are obtained for GNR transmission line model. The variations of the kinetic energy and the current by the applied voltage are taken as bases for voltage-dependent kinetic inductance calculation. Quantum capacitance and the Fermi velocity are also computed from the kinetic inductance variation. It is concluded that voltage-dependencies of the kinetic inductance and the quantum capacitance have to be taken into account for accurate GNR modelling in nanoelectronic design. - Highlights: • Metallic graphene nanoribbon interconnects are studied using ab initio approach. • Variations of the kinetic inductance (L{sub K}) and the current are obtained. • Voltage-dependency of the kinetic inductance is extracted. • The variations of quantum capacitance (C{sub Q}) and Fermi velocity are calculated. • L{sub K} and C{sub Q} change by 34% in the voltage range of 0–1 V.

  16. Toward spectroscopically accurate global ab initio potential energy surface for the acetylene-vinylidene isomerization

    A new full-dimensional global potential energy surface (PES) for the acetylene-vinylidene isomerization on the ground (S0) electronic state has been constructed by fitting ∼37 000 high-level ab initio points using the permutation invariant polynomial-neural network method with a root mean square error of 9.54 cm−1. The geometries and harmonic vibrational frequencies of acetylene, vinylidene, and all other stationary points (two distinct transition states and one secondary minimum in between) have been determined on this PES. Furthermore, acetylene vibrational energy levels have been calculated using the Lanczos algorithm with an exact (J = 0) Hamiltonian. The vibrational energies up to 12 700 cm−1 above the zero-point energy are in excellent agreement with the experimentally derived effective Hamiltonians, suggesting that the PES is approaching spectroscopic accuracy. In addition, analyses of the wavefunctions confirm the experimentally observed emergence of the local bending and counter-rotational modes in the highly excited bending vibrational states. The reproduction of the experimentally derived effective Hamiltonians for highly excited bending states signals the coming of age for the ab initio based PES, which can now be trusted for studying the isomerization reaction

  17. Ab initio many-body calculations of light nuclei neutron and proton scattering

    Quaglioni, Sofia

    2008-10-01

    One of the greatest challenges of nuclear physics today is the development of a quantitative microscopic theory of low-energy reactions on light nuclei. At the same time, technical progress on the theoretical front is urgent to match the major experimental advances in the study of exotic nuclei at the radioactive beam facilities. We build a new ab initio many-body approachootnotetextS. Quaglioni and P. Navratil, arXiv:0804.1560. capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group methodootnotetextY. C. Tang et al., Phys. Rep. 47, 167 (1978); K. Langanke and H. Friedrich, Advances in Nuclear Physics, chapter 4., Plenum, New York, 1987. with the ab initio no-core shell model.ootnotetextP. Navratil, J. P. Vary, and B. R. Barrett, Phys. Rev. Lett. 84, 5728 (2000); Phys. Rev. C 62, 054311 (2000).. In this way, we complement a microscopic-cluster technique with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters, while preserving Pauli principle and translational symmetry. I will present results for neutron and proton scattering on light nuclei, including n- and p-^4He phase shifts, and low-lying states of one-neutron halo p-shell nuclei, obtained using realistic nucleon-nucleon potentials. In particular, I will address the parity inversion of the ^11Be ground state.

  18. Ab initio many-body calculations of nucleon scattering on ^16O

    Navratil, Petr; Quaglioni, Sofia; Roth, Robert

    2008-10-01

    We develop a new ab initio many-body approachootnotetextS. Quaglioni and P. Navratil, arXiv:0804.1560. capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group methodootnotetextY. C. Tang et al., Phys. Rep. 47, 167 (1978); K. Langanke and H. Friedrich, Advances in Nuclear Physics, Plenum, New York, 1987. with the ab initio no-core shell model (NCSM).ootnotetextP. Navratil, J. P. Vary, and B. R. Barrett, Phys. Rev. Lett. 84, 5728 (2000); Phys. Rev. C 62, 054311 (2000). In this way, we complement a microscopic-cluster technique with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters, while preserving Pauli principle and translational symmetry. We will present results for low-energy nucleon scattering on ^16O and for A=17 bound states obtained using realistic nucleon-nucleon potentials. The ^16O wave functions are calculated within the importance-truncated NCSMootnotetextR. Roth and P. Navratil, Phys. Rev. Lett. 99, 092501 (2007). that allows the use of model spaces up to 18φ and ultimately enables to reach convergence of phase-shifts and other observables. Prepared by LLNL under Contract DE-AC52-07NA27344. Support from the U.S. DOE/SC/NP (Work Proposal No. SCW0498), and from the U. S. Department of Energy Grant DE-FC02-07ER41457 is acknowledged.

  19. Recent progress with large-scale ab initio calculations: the CONQUEST code

    Bowler, D. R.; Choudhury, R.; Gillan, M. J.; Miyazaki, T.

    While the success of density functional theory (DFT) has led to its use in a wide variety of fields such as physics, chemistry, materials science and biochemistry, it has long been recognised that conventional methods are very inefficient for large complex systems, because the memory requirements scale as N 2 and the cpu requirements as N 3 (where N is the number of atoms). The principles necessary to develop methods with linear scaling of the cpu and memory requirements with system size (O(N ) methods) have been established for more than ten years, but only recently have practical codes showing this scaling for DFT started to appear. We report recent progress in the development of the Conquest code, which performs O(N ) DFT calculations on parallel computers, and has a demonstrated ability to handle systems of over 10000 atoms. The code can be run at different levels of precision, ranging from empirical tight-binding, through ab initio tight-binding, to full ab initio , and techniques for calculating ionic forces in a consistent way at all levels of precision will be presented. Illustrations are given of practical Conquest calculations in the strained Ge/Si(001) system.

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

    This paper describes the tailored preparation of nearly identical lithium–manganese–oxide thin film cathodes with different global grain orientations. The thin films were synthesized by rf magnetron sputtering from a LiMn2O4-target in a pure argon plasma. Under appropriate processing conditions, thin films with a cubic spinel structure and a nearly similar density and surface topography but different grain orientation, i.e. (111)- and (440)-textured films, were achieved. The chemical composition was determined by inductively coupled plasma optical emission spectroscopy and carrier gas hot extraction. The constitution- and microstructure were evaluated by X-ray diffraction and Raman spectroscopy. The surface morphology and roughness were investigated by scanning electron and atomic force microscopy. The differently textured films represent an ideal model system for studying potential effects of grain orientation on the lithium ion diffusion and electrochemical behavior in LiMn2O4-based thin films. They are nearly identical in their chemical composition, atomic bonding behavior, surface-roughness, morphology and thickness. Our initial ab initio molecular dynamics data indicate that Li ion transport is faster in (111)-textured structure than in (440)-textured one. - Highlights: • Thin film model system of differently textured cubic Li–Mn–O spinels. • Investigation of the Li–Mn–O thin film mass density by X-ray reflectivity. • Ab initio molecular dynamics simulation on Li ion diffusion in LiMn2O4

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

    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

  2. Ab initio molecular dynamics simulations of ion–solid interactions in zirconate pyrochlores

    In this study, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A2Zr2O7, A = La, Nd and Sm). It shows that both cations and anions in Nd2Zr2O7 and Sm2Zr2O7 are generally more likely to be displaced than those in La2Zr2O7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd2Zr2O7 and Sm2Zr2O7 are lower than those in La2Zr2O7. These results suggest that the order–disorder structural transition more easily occurs in Nd2Zr2O7 and Sm2Zr2O7 resulting in a defect-fluorite structure, which agrees well with experimental observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present results may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores

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

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

    2014-06-01

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

  4. Ground state analytical ab initio intermolecular potential for the Cl{sub 2}-water system

    Hormain, Laureline; Monnerville, Maurice, E-mail: maurice.monnerville@univ-lille1.fr; Toubin, Céline; Duflot, Denis; Pouilly, Brigitte; Briquez, Stéphane [Laboratoire de Physique des Lasers Atomes et Molécules, Unité Mixte de Recherche (UMR) 8523, Université Lille I, Bât. P5, 59655 Villeneuve d’Ascq Cedex (France); Bernal-Uruchurtu, Margarita I.; Hernández-Lamoneda, Ramón [Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca 62209, México (Mexico)

    2015-04-14

    The chlorine/water interface is of crucial importance in the context of atmospheric chemistry. Modeling the structure and dynamics at this interface requires an accurate description of the interaction potential energy surfaces. We propose here an analytical intermolecular potential that reproduces the interaction between the Cl{sub 2} molecule and a water molecule. Our functional form is fitted to a set of high level ab initio data using the coupled-cluster single double (triple)/aug-cc-p-VTZ level of electronic structure theory for the Cl{sub 2} − H{sub 2}O complex. The potential fitted to reproduce the three minima structures of 1:1 complex is validated by the comparison of ab initio results of Cl{sub 2} interacting with an increasing number of water molecules. Finally, the model potential is used to study the physisorption of Cl{sub 2} on a perfectly ordered hexagonal ice slab. The calculated adsorption energy, in the range 0.27 eV, shows a good agreement with previous experimental results.

  5. Ab initio study on electron excitation and electron transfer in tryptophan-tyrosine system

    In this article, ab initio calculation has been performed to evaluate the transition energy of electronic excitation in tryptophan and tyrosine by using semiempirical molecular orbital method AM1 and complete active space self-consistent field method. The solvent effect has been considered by means of the conductor-like screening model. After geometric optimizations of isolated tryptophan and tyrosine, and their corresponding radicals and cations, reaction heat of these electron transfer reactions have been obtained by the means of complete active space self-consistent field method. The transition energies from the ground state, respectively, to the lowest excited state and to the lowest triplet state of these two amino acids are also calculated and compared with the experimentally observed values. The ionization potential and electron affinity are also calculated for tryptophan and tyrosine employing Koopmans' theorem and ab initio calculation. Compared with the experimental measurements, the theoretical results are found satisfactory. Theoretical results give good explanations on the experimental phenomena that N3· can preferably oxide the side chain of tryptophan residue and then the electron transfer from tyrosine residue to tryptophan residue follows in peptides involving tryptophan and tyrosine

  6. Ab initio calculations of the optical properties of crystalline and liquid InSb

    Ab initio calculations of the electronic and optical properties of InSb were performed for both the crystalline and liquid states. Two sets of atomic structure models for liquid InSb at 900 K were obtained by ab initio molecular dynamics simulations. To reduce the effect of structural peculiarities in the liquid models, an averaging of the two sets of the calculated electronic and optical properties corresponding to the two liquid models was performed. The calculated results indicate that, owing to the phase transition from crystal to liquid, the density of states around the Fermi level increases. As a result, the energy band gap opening near the Fermi level disappears. Consequently, the optical properties change from semiconductor to metallic behavior. Namely, owing to the melting of InSb, the interband transition peaks disappear and a Drude-like dispersion is observed in the optical dielectric functions. The optical absorption at a photon energy of 3.06 eV, which is used in Blu-ray Disc systems, increases owing to the melting of InSb. This increase in optical absorption is proposed to result from the increased optical transitions below 2 eV

  7. Magnetic Transitions in Iron Porphyrin Halides by Inelastic Neutron Scattering and Ab Initio Studies of Zero-Field Splittings.

    Stavretis, Shelby E; Atanasov, Mihail; Podlesnyak, Andrey A; Hunter, Seth C; Neese, Frank; Xue, Zi-Ling

    2015-10-19

    experimentally deduced trend. D parameters from CASSCF and NEVPT2 results have been calibrated against those from the INS data, yielding a predictive power of these approaches. Methods to improve the quantitative agreement between ab initio calculated and experimental D and spectroscopic transitions for high-spin Fe(III) complexes are proposed. PMID:26428688

  8. Magnetic Transitions in Iron Porphyrin Halides by Inelastic Neutron Scattering and Ab-initio Studies of Zero-Field Splittings

    parameters from CASSCF and NEVPT2 results have been calibrated against those from the INS data, yielding a predictive power of these approaches. Methods to improve the quantitative agreement between ab initio calculated and experimental D and spectroscopic transitions for high-spin Fe(III) complexes are proposed

  9. Ab initio interaction potentials and scattering lengths for ultracold mixtures of metastable helium and alkali-metal atoms

    Kedziera, Dariusz; Mentel, Łukasz; Żuchowski, Piotr S.; Knoop, Steven

    2015-06-01

    We have obtained accurate ab initio +4Σ quartet potentials for the diatomic metastable triplet helium+alkali-metal (Li, Na, K, Rb) systems, using all-electron restricted open-shell coupled cluster singles and doubles with noniterative triples corrections CCSD(T) calculations and accurate calculations of the long-range C6 coefficients. These potentials provide accurate ab initio quartet scattering lengths, which for these many-electron systems is possible, because of the small reduced masses and shallow potentials that result in a small amount of bound states. Our results are relevant for ultracold metastable triplet helium+alkali-metal mixture experiments.

  10. Unrestricted compact model potentials for ab initio embedded cluster calculations: Magnetic interactions in KNiF3

    Mejías, J. A.; Sanz, Javier Fernández

    1995-01-01

    Compact model potentials to introduce the effect of spin-dependent environments in ab initio embedded cluster calculations are reported. The groups forming the environment are described by unrestricted Hartree-Fock wave functions. The method is tested for the magnetic description of KNiF3 by using different model clusters. The cluster calculations are done at the unrestricted Hartree-Fock and unrestricted second-order perturbation levels. The obtained values are in excellent agreement with other more sophisticated ab initio calculations if some Ni-F delocalization is allowed. How the superexchange interaction is accounted for in our method is also discussed.

  11. A theoretical-spectroscopy, ab-initio-based study of the electronic ground state of 121SbH3

    Yurchenko, Sergei N.; Carvajal Zaera, Miguel; Yachmenev, Andrey; Thiel, Walter; Jensen, Per

    2010-01-01

    For the stibine isotopologue (SbH3)-Sb-121, we report improved theoretical calculations of the vibrational energies below 8000 cm- and simulations of the rovibrational spectrum in the 0-8000 cm(-1) region. The calculations are based on a refined ab initio potential energy surface and on a new dipole moment surface obtained at the coupled cluster CCSD(T) level. The theoretical results are compared with the available experimental data in order to validate the ab initio surfaces and the TROVE co...

  12. Ab initio ground and the first excited adiabatic and quasidiabatic potential energy surfaces of H + + CO system

    George, D. X. F.; Kumar, Sanjay

    2010-08-01

    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, γ) 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) [66

  13. The Crystal Structure of Impurity Centers Tm^{2+} and Eu^{2+} in SrCl2 : Ab Initio Calculations

    Chernyshev, V. A.; Serdcev, A. V.; Petrov, V. P.; Nikiforov, A. E.

    2016-01-01

    Ab initio calculations of the impurity centers Tm^{2+} thulium and europium Eu^{2+} in SrCl2 and MeF2 (Me = Ca, Sr, Ba) were carried out at low (zero) temperature. The crystal structure of impurity centers was investigated. Charge density maps show that the bonds formed by the rare-earth ions have an ionic character. The crystal structures, lattice dynamics, and band structures of MeF2 and SrCl2 were calculated at low temperature. Ab initio calculations were performed in periodic CRYSTAL code within the framework of the MO LCAO approach by using hybrid DFT functionals.

  14. Structural phase transitions in Ruddlesden-Popper phases of strontium titanate: {\\em ab initio} and inhomogeneous Ginzburg-Landau approaches

    Lee, Jeehye

    2010-01-01

    We present the first systematic {\\em ab initio} study of anti-ferrodistortive (AFD) order in Ruddlesden-Popper (RP) phases of strontium titanate, Sr$_{1+n}$Ti$_n$O$_{3n+1}$, as a function of both compressive epitaxial strain and phase number $n$. We find all RP phases to exhibit AFD order under a significant range of strains, recovering the bulk AFD order as $\\sim 1/n^2$. A Ginzburg-Landau Hamiltonian generalized to include inter-octahedral interactions reproduces our {\\em ab initio} results well, opening a pathway to understanding other nanostructured perovskite systems.

  15. Ab initio implementation of quantum trajectory mean-field approach and dynamical simulation of the N{sub 2}CO photodissociation

    Xie, Binbin; Liu, Lihong; Cui, Ganglong; Fang, Wei-Hai, E-mail: fangwh@bnu.edu.cn [Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875 (China); Cao, Jun [Guizhou Provincial Key Laboratory of Computational Nano-material Science, Guizhou Normal College, Guiyang 550018 (China); Feng, Wei; Li, Xin-qi [Department of Physics, Beijing Normal University, Beijing 100875 (China)

    2015-11-21

    In this work, the recently introduced quantum trajectory mean-field (QTMF) approach is implemented and employed to explore photodissociation dynamics of diazirinone (N{sub 2}CO), which are based on the high-level ab initio calculation. For comparison, the photodissociation process has been simulated as well with the fewest-switches surface hopping (FSSH) and the ab initio multiple spawning (AIMS) methods. Overall, the dynamical behavior predicted by the three methods is consistent. The N{sub 2}CO photodissociation at λ > 335 nm is an ultrafast process and the two C—N bonds are broken in a stepwise way, giving birth to CO and N{sub 2} as the final products in the ground state. Meanwhile, some noticeable differences were found in the QTMF, FSSH, and AIMS simulated time constants for fission of the C—N bonds, excited-state lifetime, and nonadiabatic transition ratios in different intersection regions. These have been discussed in detail. The present study provides a clear evidence that direct ab initio QTMF approach is one of the reliable tools for simulating nonadiabatic dynamics processes.

  16. Ab initio parameterization of a charge optimized many-body forcefield for Si-SiO2: Validation and thermal transport in nanostructures

    France-Lanord, Arthur; Soukiassian, Patrick; Glattli, Christian; Wimmer, Erich

    2016-03-01

    In an effort to extend the reach of current ab initio calculations to simulations requiring millions of configurations for complex systems such as heterostructures, we have parameterized the third-generation Charge Optimized Many-Body (COMB3) potential using solely ab initio total energies, forces, and stress tensors as input. The quality and the predictive power of the new forcefield are assessed by computing properties including the cohesive energy and density of SiO2 polymorphs, surface energies of alpha-quartz, and phonon densities of states of crystalline and amorphous phases of SiO2. Comparison with data from experiments, ab initio calculations, and molecular dynamics simulations using published forcefields including BKS (van Beest, Kramer, and van Santen), ReaxFF, and COMB2 demonstrates an overall improvement of the new parameterization. The computed temperature dependence of the thermal conductivity of crystalline alpha-quartz and the Kapitza resistance of the interface between crystalline Si(001) and amorphous silica is in excellent agreement with experiment, setting the stage for simulations of complex nanoscale heterostructures.

  17. An experimental and ab initio study of the electronic spectrum of the jet-cooled F2BO free radical

    We have studied the B~2A1–X~2B2 laser-induced fluorescence (LIF) spectrum of the jet-cooled F2BO radical for the first time. The transition consists of a strong 000 band at 446.5 nm and eight weak sequence bands to shorter wavelengths. Single vibronic level emission spectra obtained by laser excitation of individual levels of the B~ state exhibit two electronic transitions: a very weak, sparse B~–X~ band system in the 450–500 nm region and a stronger, more extensive set of B~2A1–A~2B1 bands in the 580–650 nm region. We have also performed a series of high level ab initio calculations to predict the electronic energies, molecular structures, vibrational frequencies, and rotational and spin-rotation constants in the X~2B2, A~2B1 and B~2A1 electronic states as an aid to the analysis of the experimental data. The theoretical results have been used as input for simulations of the rotationally resolved B~2A1–X~2B2 000 LIF band and Franck-Condon profiles of the LIF and single vibronic level emission spectra. The agreement between the simulations obtained with purely ab initio parameters and the experimental spectra validates the geometries calculated for the ground and excited states and the conclusion that the radical has C2v symmetry in the X~, A~, and B~ states. The spectra provide considerable new information about the vibrational energy levels of the X~ and A~ states, but very little for the B~ state, due to the very restrictive Franck-Condon factors in the LIF spectra

  18. Light Condensation and Localization in Disordered Photonic Media: Theory and Large Scale ab initio Simulations

    Toth, Laszlo Daniel

    2013-05-07

    Disordered photonics is the study of light in random media. In a disordered photonic medium, multiple scattering of light and coherence, together with the fundamental principle of reciprocity, produce a wide range of interesting phenomena, such as enhanced backscattering and Anderson localization of light. They are also responsible for the existence of modes in these random systems. It is known that analogous processes to Bose-Einstein condensation can occur in classical wave systems, too. Classical condensation has been studied in several contexts in photonics: pulse formation in lasers, mode-locking theory and coherent emission of disordered lasers. All these systems have the common theme of possessing a large ensemble of waves or modes, together with nonlinearity, dispersion or gain. In this work, we study light condensation and its connection with light localization in a disordered, passive dielectric medium. We develop a theory for the modes inside the disordered resonator, which combines the Feshbach projection technique with spin-glass theory and statistical physics. In particular, starting from the Maxwell’s equations, we map the system to a spherical p-spin model with p = 2. The spins are replaced by modes and the temperature is related to the fluctuations in the environment. We study the equilibrium thermodynamics of the system in a general framework and show that two distinct phases exist: a paramagnetic phase, where all the modes are randomly oscillating and a condensed phase, where the energy condensates on a single mode. The thermodynamic quantities can be explicitly interpreted and can also be computed from the disorder-averaged time domain correlation function. We launch an ab initio simulation campaign using our own code and the Shaheen supercomputer to test the theoretical predictions. We construct photonic samples of varying disorder and find computationally relevant ways to obtain the thermodynamic quantities. We observe the phase transition

  19. An Ab Initio Approach Towards Engineering Fischer-Tropsch Surface Chemistry

    Matthew Neurock

    2006-09-11

    One of the greatest societal challenges over the next decade is the production of cheap, renewable energy for the 10 billion people that inhabit the earth. This will require the development of various energy sources which will likely include fuels derived from methane, coal, and biomass and alternatives sources such as solar, wind and nuclear energy. One approach will be to synthesize gasoline and other fuels from simpler hydrocarbons such as CO derived from methane or other U.S. based sources such as coal. Syngas (CO and H{sub 2}) can be readily converted into higher molecular weight hydrocarbons through Fischer-Tropsch synthesis. Fischer-Tropsch (FT) synthesis involves the adsorption and the activation of CO and H{sub 2}, the subsequent propagation steps including hydrogenation and carbon-carbon coupling, followed by chain termination reactions. The current commercial catalysts are supported Co and Co-alloys particles. This project set out with the following objectives in mind: (1) understand the reaction mechanisms that control FT kinetics, (2) predict how the intrinsic metal-adsorbate bond affects the sequence of elementary steps in FT, (3) establish the effects of the reaction environment on catalytic activity and selectivity, (4) construct a first-principles based algorithm that can incorporate the detailed atomic surface structure and simulate the kinetics for the myriad of elementary pathways that make up FT chemistry, and (5) suggest a set of optimal features such as alloy composition and spatial configuration, oxide support, distribution of defect sites. As part of this effort we devoted a significant portion of time to develop an ab initio based kinetic Monte Carlo simulation which can be used to follow FT surface chemistry over different transition metal and alloy surfaces defined by the user. Over the life of this program, we have used theory and have developed and applied stochastic Monte Carlo simulations in order to establish the fundamental

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

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

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

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

    2014-03-01

    Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic

  2. Quantitative Comparison of a New Ab Initio Micrometeor Ablation Model with an Observationally Verifiable Standard Model

    Meisel, David D.; Szasz, Csilla; Kero, Johan

    2008-06-01

    The Arecibo UHF radar is able to detect the head-echos of micron-sized meteoroids up to velocities of 75 km/s over a height range of 80 140 km. Because of their small size there are many uncertainties involved in calculating their above atmosphere properties as needed for orbit determination. An ab initio model of meteor ablation has been devised that should work over the mass range 10-16 kg to 10-7 kg, but the faint end of this range cannot be observed by any other method and so direct verification is not possible. On the other hand, the EISCAT UHF radar system detects micrometeors in the high mass part of this range and its observations can be fit to a “standard” ablation model and calibrated to optical observations (Szasz et al. 2007). In this paper, we present a preliminary comparison of the two models, one observationally confirmable. Among the features of the ab initio model that are different from the “standard” model are: (1) uses the experimentally based low pressure vaporization theory of O’Hanlon (A users’s guide to vacuum technology, 2003) for ablation, (2) uses velocity dependent functions fit from experimental data on heat transfer, luminosity and ionization efficiencies measured by Friichtenicht and Becker (NASA Special Publication 319: 53, 1973) for micron sized particles, (3) assumes a density and temperature dependence of the micrometeoroids and ablation product specific heats, (4) assumes a density and size dependent value for the thermal emissivity and (5) uses a unified synthesis of experimental data for the most important meteoroid elements and their oxides through least square fits (as functions of temperature, density, and/or melting point) of the tables of thermodynamic parameters given in Weast (CRC Handbook of Physics and Chemistry, 1984), Gray (American Institute of Physics Handbook, 1972), and Cox (Allen’s Astrophysical Quantities 2000). This utilization of mostly experimentally determined data is the main reason for

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

    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, X1Σ+, a3Π, A'1Π, b3Σ+ and A1Σ+, and the corresponding dipole moment functions have been determined using internally contracted multi-reference configuration interaction approaches. The spectroscopic constants associated with these electronic states are compared to experimental values. The corresponding electronic wavefunctions have also been analyzed using the dipole moment functions. Display Omitted Highlights: → The five lowest electronic states of Cao have been determined ab initio at a high level of accuracy. → Large active space, core-valence correlation and configuration interaction are required. → The multi-configurational nature of the electronic ground state is confirmed as well as its monovalent and divalent ionic nature using dipole moment analysis. → These interacting potentials will serve for future obtention of spin-rovibronic levels. - Abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X1Σ+, a3Π, A'1Π, b3Σ+ and A1Σ+, and the corresponding dipole moment functions have been determined using internally contracted multi-reference configuration interaction approaches

  4. Comparative studies of the spectroscopy of CuCl2: DFT versus standard ab initio approaches.

    Ramírez-Solís, A; Poteau, R; Vela, A; Daudey, J P

    2005-04-22

    The X2Pi g-2Sigma g+, X2Pi g-2Delta g, X2Pi g-2Sigma u+, X2Pi g-2Pi u transitions on CuCl2 have been studied using several exchange-correlation functionals from the various types of density functional theory (DFT) approaches like local density approximation (LDA), generalized gradient approximation (GGA), hybrid and meta-GGA. The results are compared with the experience and with those coming from the most sophisticated nondynamic and dynamic electronic correlation treatments using the same relativistic effective core potentials and especially developed basis sets to study the electronic structure of the five lowest states and the corresponding vertical and adiabatic transition energies. The calculated transition energies for three of the hybrid functionals (B3LYP, B97-2, and PBE0) are in very good agreement with the benchmark ab initio results and experimental figures. All of the other functionals largely overestimate the X2Pi g-2Sigma g+ and X2Pi g-2Delta g transition energies, many of them even placing the 2Delta g ligand field state above the charge transfer 2Pi u and 2Sigma u+ states. The relative weight of the Hartree-Fock exchange in the definition of the functional used appears to play a key role in the accurate description of the LambdaSSigma density defined by the orientation of the 3d hole (sigma, pi, or delta) on Cu in the field of both chlorine atoms, but no simple connection of this weight with the quality of the spectra has been found. Mulliken charges and spin densities are carefully analyzed; a possible link between the extent of spin density on the metal for the X2Pi g state and the performance of the various functionals was observed, suggesting that those that lead to the largest values (close to 0.65) are the ones that best reproduce these four transitions. Most functionals lead to a remarkably low ionicity for the three ligand field states even for the best performing functionals, compared to the complete active space (SCF) (21, 14) ab initio

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

    Vlahos, Vasilios; Booske, John H.; Morgan, Dane

    2010-02-01

    Microwave, x-ray, and radio-frequency radiation sources require a cathode emitting electrons into vacuum. Thermionic B-type dispenser cathodes consist of BaxOz coatings on tungsten (W), where the surface coatings lower the W work function and enhance electron emission. The new and promising class of scandate cathodes modifies the B-type surface through inclusion of Sc, and their superior emissive properties are also believed to stem from the formation of a low work function surface alloy. In order to better understand these cathode systems, density-functional theory (DFT)-based ab initio modeling is used to explore the stability and work function of BaxScyOz on W(001) monolayer-type surface structures. It is demonstrated how surface depolarization effects can be calculated easily using ab initio calculations and fitted to an analytic depolarization equation. This approach enables the rapid extraction of the complete depolarization curve (work function versus coverage relation) from relatively few DFT calculations, useful for understanding and characterizing the emitting properties of novel cathode materials. It is generally believed that the B-type cathode has some concentration of Ba-O dimers on the W surface, although their structure is not known. Calculations suggest that tilted Ba-O dimers are the stable dimer surface configuration and can explain the observed work function reduction corresponding to various dimer coverages. Tilted Ba-O dimers represent a new surface coating structure not previously proposed for the activated B-type cathode. The thermodynamically stable phase of Ba and O on the W surface was identified to be the Ba0.25O configuration, possessing a significantly lower Φ value than any of the Ba-O dimer configurations investigated. The identification of a more stable Ba0.25O phase implies that if Ba-O dimers cover the surface of emitting B-type cathodes, then a nonequilibrium steady state must dominate the emitting surface. The identification of

  6. Manipulating magnetism and conductance of an adatom-molecule junction on a metal surface: An ab initio study

    Tao, Kun; Stepanyuk, V.S.; Bruno, P.;

    2008-01-01

    The state of the art ab initio calculations reveal the effect of a scanning tunneling microscopy tip on magnetic properties and conductance of a benzene-adatom sandwich on Cu(001). We concentrate on a benzene-Co system interacting with a Cr tip. Our studies give a clear evidence that magnetism an...

  7. Laves phases in the V-Zr system below room temperature: Stability analysis using ab initio results and phase digram

    Štrof, J.; Pavlů, Jana; Wdowik, U.; Buršík, Jiří; Šob, Mojmír; Vřešťál, Jan

    2014-01-01

    Roč. 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

  8. Ab-initio study of magnetic properties and phase transitions in Ga (Mn) N with Monte Carlo approach

    Sbai, Y.; Ait Raiss, A.; Salmani, E. [LMPHE (URAC 12), Faculty of Science, Mohammed V University, Av. Ibn Batouta, Rabat (Morocco); Bahmad, L., E-mail: Bahmad@fsr.ac.ma [LMPHE (URAC 12), Faculty of Science, Mohammed V University, Av. Ibn Batouta, Rabat (Morocco); Benyoussef, A. [LMPHE (URAC 12), Faculty of Science, Mohammed V University, Av. Ibn Batouta, Rabat (Morocco); Institute of Nanomaterials and Nanotechnologies, MAScIR, Rabat (Morocco); Hassan II Academy of Science and Technology, Rabat (Morocco)

    2015-12-15

    On the basis of ab-initio calculations and Monte Carlo simulations the magnetic and electronic properties of Gallium nitride (GaN) doped with the transition metal Manganese (Mn) were studied. The ab initio calculations were done using the AKAI–KKR–CPA method within the Local Density Approximation (LDA) approximation. We doped our Diluted Magnetic Semiconductor (DMS), with different concentrations of magnetic impurities Mn and plotted the density of state (DOS) for each one. Showing a half-metallic behavior and ferromagnetic state especially for Ga{sub 0.95}Mn{sub 0.05}N making this DMS a strong candidate for spintronic applications. Moreover, the magnetization and susceptibility of our system as a function of the temperature has been calculated and give for various system size L to study the size effect. In addition, the transition temperature was deduced from the peak of the susceptibility. The Ab initio results are in good agreement with literature especially for (x=0.05) of Mn which gives the most interesting results. - Highlights: • The AKAI–KKR–CPA method has been applied to study the doped compound GaN:Mn. • The local density approximation (LDA) has been applied. • The ab-initio calculations have been performed. • The density of states (DOS) have been plotted for differents doping concentrations, using Monte Carlo simulations.

  9. Structural, dynamical, electronic, and bonding properties of laser-heated silicon: An ab initio molecular-dynamics study

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

    1997-01-01

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

  10. Ab initio electronic structure and correlations in pristine and potassium-doped molecular crystals of copper phthalocyanine

    Giovannetti, Gianluca; Brocks, Geert; Brink, van den Jeroen

    2008-01-01

    We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic mome

  11. A Photoelectron Spectroscopy and ab initio Study of B3- and B4- Anions and Their Neutrals

    Zhai, Hua-Jin; Wang, Lai S.; Alexandrova, A N.; Boldyrev, Alexander I.; Zakrzewski, V G.

    2003-11-06

    The two smallest boron clusters (B3 and B4) in their neutral and anionic forms were studied by photoelectron spectroscopy and ab initio calculations. Vibrationally resolved photoelectron spectra were observed for B3- at three photon energies (355, 266, and 193 nm) and the electron affinity of B3 was measured to be+0.02 eV.

  12. Ab Initio Calculation of Vacancies and Interstitials in NiSi2

    WANG Tao; DAI Yong-Bing; OUYANG Si-Ke; WU Jian-Sheng; SHEN He-Sheng

    2004-01-01

    @@ An ab initio plane-wave ultrasoft pseudopotential method based on the generalized gradient approximations has been utilized to investigate the electronic structure, atomic geometry, formation energy to provide a better understanding of properties of Ni disilicide. The vacancy and interstitial formation energies largely depend on the atomic chemical potentials. The formation energies of vacancies Vsi and VNi are in the range of 0.04-0.56 eV and 1.25-2.3 eV, respectively and the formation energies of Si and Ni interstitials are 3.89-4.42 eV and 0.67-1.71 eV,respectively. The smaller Ni interstitial formation energy is in agreement with the experimental result that Ni interstitial atom is dominant diffusion species in NiSi2.

  13. Ab initio intermolecular potential energy surface and thermophysical properties of nitrous oxide

    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

  14. Hydrogen bond dynamics in liquid water: Ab initio molecular dynamics simulation

    Kim, Cheolhee; Kim, Eunae [College of Pharmacy, Chosun University, Gwangju (Korea, Republic of); Yeom, Min Sun [Korea Institute of Science and Technology Information, Daejeon (Korea, Republic of)

    2016-01-15

    The effect of intermolecular interaction on the distribution of the harmonic vibrational frequencies of water molecules was investigated through ab initio molecular dynamics simulations based on the Born-Oppenheimer approach. For single water, the effect of the dynamics of the oxygen atom in single water and the simulation time step on the frequency distribution were examined. The distributions of the OH stretching and HOH bending vibrational frequencies of liquid water were compared to those of single water. The probability distributions of the change in OH bond length and the lifetime of the dangling OH bond were also obtained. The distribution of the frequencies was strongly affected by the long lifetime of the dangling OH bond, resulting in the formation of hydrogen bonds between water molecules.

  15. Ab initio study of the electronic properties of the planar Ga5N5 cluster

    Zheng Hao-Ping; Hao Jing-An

    2005-01-01

    The first-principles, all electron, ab initio calculations have been performed for an the amazing stable planar structure of Ga5N5 cluster based on the density functional theory. Electronic structure, Electron affinity, ionization potential, and binding energy are obtained. No spin magnetic moment is found. The results show that the planar structure of the Ga5N5 cluster is stable. It is found that for the planar structure of Ga5N5 cluster, three nitrogen atoms in the N3 subunit bind together with large electon transfer although no free N3 can exist. This may be important to the stability of the planar structure of the Ga5N5 cluster which has the lowest ground-state energy.

  16. 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.

  17. AB INITIO Modeling of Thermomechanical Properties of Mo-Based Alloys for Fossil Energy Conversion

    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.

  18. ESTUDIO TEÓRICO DE LA MOLÉCULA DE HIDROGENO CALCULO AB-INITIO

    Quitián, N.

    2010-01-01

    Utilizando la técnica LCGO-SCF-MO (Combinación Lineal de los Orbitales Moleculares en Orbitales Gausianos, en el método del Campo Auto-Coherente), se determinaron las energías de orbital, la energía electrónica total, la energía de repulsión nuclear y la energía de Hartree-Fock de la molécula de hidrógeno en su estado fundamental, mediante un cálculo ab initio y utilizando una base de funciones gausianas. Los orbitales moleculares fueron desarrollados en términos de una función Is contraída p...

  19. reaxFF Reactive Force Field for Disulfide Mechanochemistry, Fitted to Multireference ab Initio Data.

    Müller, Julian; Hartke, Bernd

    2016-08-01

    Mechanochemistry, in particular in the form of single-molecule atomic force microscopy experiments, is difficult to model theoretically, for two reasons: Covalent bond breaking is not captured accurately by single-determinant, single-reference quantum chemistry methods, and experimental times of milliseconds or longer are hard to simulate with any approach. Reactive force fields have the potential to alleviate both problems, as demonstrated in this work: Using nondeterministic global parameter optimization by evolutionary algorithms, we have fitted a reaxFF force field to high-level multireference ab initio data for disulfides. The resulting force field can be used to reliably model large, multifunctional mechanochemistry units with disulfide bonds as designed breaking points. Explorative calculations show that a significant part of the time scale gap between AFM experiments and dynamical simulations can be bridged with this approach. PMID:27415976

  20. Ab Initio Studies on Hematite Surface and the Adsorption of Phosphate

    Swati Chaudhury

    2014-01-01

    Full Text Available This investigation explores the ab initio DFT method for understanding surface structure of hematite and the nature and energetics of phosphate adsorption. Using the full potential linearized plane wave method (FP-LAPW, we derived the structure and energies of various magnetic forms of hematite. The antiferromagnetic (AFM form was observed to be the most stable. Hematite surfaces with Fe-termination, O-termination, or OH-termination were studied. The OH-terminated surface was the most stable. Stability of hematite surfaces follows the order OH-termination > Fe-termination > O-termination. Thus, surface reaction with hematite would occur with the OH at the surface and not with Fe atoms. The structure of phosphate adsorbed on hematite was derived. Bonding is through the H atom of the OH at the surface. An alternative mechanism of phosphate adsorption on hematite has been derived. Adsorption energy is high and suggests chemisorption rather than physisorption of phosphate on hematite.