Recent achievements in ab initio modelling of liquid water
Khaliullin, Rustam Z
2013-01-01
The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.
Ab initio modeling of small proteins by iterative TASSER simulations
Zhang Yang
2007-05-01
Full Text Available Abstract Background Predicting 3-dimensional protein structures from amino-acid sequences is an important unsolved problem in computational structural biology. The problem becomes relatively easier if close homologous proteins have been solved, as high-resolution models can be built by aligning target sequences to the solved homologous structures. However, for sequences without similar folds in the Protein Data Bank (PDB library, the models have to be predicted from scratch. Progress in the ab initio structure modeling is slow. The aim of this study was to extend the TASSER (threading/assembly/refinement method for the ab initio modeling and examine systemically its ability to fold small single-domain proteins. Results We developed I-TASSER by iteratively implementing the TASSER method, which is used in the folding test of three benchmarks of small proteins. First, data on 16 small proteins (α-root mean square deviation (RMSD of 3.8Å, with 6 of them having a Cα-RMSD α-RMSD α-RMSD of the I-TASSER models was 3.9Å, whereas it was 5.9Å using TOUCHSTONE-II software. Finally, 20 non-homologous small proteins (α-RMSD of 3.9Å was obtained for the third benchmark, with seven cases having a Cα-RMSD Conclusion Our simulation results show that I-TASSER can consistently predict the correct folds and sometimes high-resolution models for small single-domain proteins. Compared with other ab initio modeling methods such as ROSETTA and TOUCHSTONE II, the average performance of I-TASSER is either much better or is similar within a lower computational time. These data, together with the significant performance of automated I-TASSER server (the Zhang-Server in the 'free modeling' section of the recent Critical Assessment of Structure Prediction (CASP7 experiment, demonstrate new progresses in automated ab initio model generation. The I-TASSER server is freely available for academic users http://zhang.bioinformatics.ku.edu/I-TASSER.
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.
Ab initio thermodynamic model for magnesium carbonates and hydrates.
Chaka, Anne M; Felmy, Andrew R
2014-09-04
An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.
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...... as the fate of HOCO, determines the oxidation rate of formic acid. At lower temperatures HO2, formed from HOCO + O2, is an important chain carrier and modeling predictions become sensitive to the HOCHO + HO2 reaction. © 2014 The Combustion Institute....... on calculations with the kinetic model. Formic acid is consumed mainly by reaction with OH, yielding OCHO, which dissociates rapidly to CO2 + H, and HOCO, which may dissociate to CO + OH or CO2 + H, or react with H, OH, or O2 to form more stable products. The branching fraction of the HOCHO + OH reaction, as well...
Quantum plasmonics: from jellium models to ab initio calculations
Varas Alejandro
2016-08-01
Full Text Available Light-matter interaction in plasmonic nanostructures is often treated within the realm of classical optics. However, recent experimental findings show the need to go beyond the classical models to explain and predict the plasmonic response at the nanoscale. A prototypical system is a nanoparticle dimer, extensively studied using both classical and quantum prescriptions. However, only very recently, fully ab initio time-dependent density functional theory (TDDFT calculations of the optical response of these dimers have been carried out. Here, we review the recent work on the impact of the atomic structure on the optical properties of such systems. We show that TDDFT can be an invaluable tool to simulate the time evolution of plasmonic modes, providing fundamental understanding into the underlying microscopical mechanisms.
Ab initio calculations and modelling of atomic cluster structure
Solov'yov, Ilia; Lyalin, Andrey G.; Greiner, Walter
2004-01-01
The optimized structure and electronic properties of small sodium and magnesium clusters have been investigated using it ab initio theoretical methods based on density-functional theory and post-Hartree-Fock many-body perturbation theory accounting for all electrons in the system. A new theoretical...
Thermochemical data for CVD modeling from ab initio calculations
Ho, P. [Sandia National Labs., Albuquerque, NM (United States); Melius, C.F. [Sandia National Labs., Livermore, CA (United States)
1993-12-31
Ab initio electronic-structure calculations are combined with empirical bond-additivity corrections to yield thermochemical properties of gas-phase molecules. A self-consistent set of heats of formation for molecules in the Si-H, Si-H-Cl, Si-H-F, Si-N-H and Si-N-H-F systems is presented, along with preliminary values for some Si-O-C-H species.
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.
Ab initio modelling of boron related defects in amorphous silicon
Oliveira, Tiago A.; Torres, Vitor J.B. [Department of Physics, University of Aveiro, Campus Santiago, 3810-193 Aveiro (Portugal)
2012-10-15
We have modeled boron related point defects in amorphous silicon, using an ab initio method, the Density functional theory-pseudopotential code Aimpro. The boron atoms were embedded in 64 atom amorphous silicon cubic supercells. The calculations were performed using boron defects in 15 different supercells. These supercells were developed using a modified Wooten-Winer-Weaire bond switching mechanism. In average, the properties of the 15 supercells agree with the observed radial and bond angle distributions, as well the electronic and vibrational density of states and Raman spectra. In amorphous silicon it has been very hard to find real self-interstitials, since for almost all the tested configurations, the amorphous lattice relaxes overall. We found that substitutional boron prefers to be 4-fold coordinated. We find also an intrinsic hole-trap in the non-doped amorphous lattice, which may explain the low efficiency of boron doping. The local vibrational modes are, in average, higher than the correspondent crystalline values (copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)
Ab initio modeling of decomposition in iron based alloys
Gorbatov, O. I.; Gornostyrev, Yu. N.; Korzhavyi, P. A.; Ruban, A. V.
2016-12-01
This paper reviews recent progress in the field of ab initio based simulations of structure and properties of Fe-based alloys. We focus on thermodynamics of these alloys, their decomposition kinetics, and microstructure formation taking into account disorder of magnetic moments with temperature. We review modern theoretical tools which allow a consistent description of the electronic structure and energetics of random alloys with local magnetic moments that become totally or partially disordered when temperature increases. This approach gives a basis for an accurate finite-temperature description of alloys by calculating all the relevant contributions to the Gibbs energy from first-principles, including a configurational part as well as terms due to electronic, vibrational, and magnetic excitations. Applications of these theoretical approaches to the calculations of thermodynamics parameters at elevated temperatures (solution energies and effective interatomic interactions) are discussed including atomistic modeling of decomposition/clustering in Fe-based alloys. It provides a solid basis for understanding experimental data and for developing new steels for modern applications. The precipitation in Fe-Cu based alloys, the decomposition in Fe-Cr, and the short-range order formation in iron alloys with s-p elements are considered as examples.
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.
Keegan, Ronan M; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D; Rigden, Daniel J
2015-02-01
AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.
Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions.
Changlani, Hitesh J; Zheng, Huihuo; Wagner, Lucas K
2015-09-14
We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U(∗)/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.
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.
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)
Raman spectroscopy, ab-initio model calculations, and conformational, equilibria in ionic liquids
Berg, Rolf W.
2009-01-01
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...... systems in the future. A few examples will be discussed. Contents 12.1 Introduction...........307 12.2 Brief introduction to Raman spectroscopy ..............309 12.2.1 Basics .....................309 12.2.2 Experimental, fluorescence and fouriertransform- Raman spectroscopy instrumentation ...... 311 12.......3 Brief introduction to ab-initio model calculations .... 312 12.4 Case study on Raman spectroscopy and structure of imidazolium-based ionic liquids ..... 312 12.5 Raman spectra and structure of [C4C1Im]+ liquids ..... 315 12.6 Normal mode analysis and rotational isomerism of the [C4C1Im]+ cation...
Raman Spectroscopy and Ab-Initio Model Calculations on Ionic Liquids
Berg, Rolf W.
2007-01-01
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-methylimidazolium ([C4mim][X]) salts. The rotational isomerism of the [C4mim]þ cation is described: the presence of anti...... will be applied to many more systems in the future. A few examples will be discussed....
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.
McKemmish, Laura K; Tennyson, Jonathan
2016-01-01
Accurate knowledge of the rovibronic near-infrared and visible spectra of vanadium monoxide (VO) is very important for studies of cool stellar and hot planetary atmospheres. Here, the required ab initio dipole moment and spin-orbit coupling curves for VO are produced. This data forms the basis of a new VO line list considering 13 different electronic states and containing over 277 million transitions. Open shell transition, metal diatomics are challenging species to model through ab initio quantum mechanics due to the large number of low-lying electronic states, significant spin-orbit coupling and strong static and dynamic electron correlation. Multi-reference configuration interaction methodologies using orbitals from a complete active space self-consistent-field (CASSCF) calculation are the standard technique for these systems. We use different state-specific or minimal-state CASSCF orbitals for each electronic state to maximise the calculation accuracy. The off-diagonal dipole moment controls the intensity...
Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions
Changlani, Hitesh J.; Zheng, Huihuo; Wagner, Lucas K. [Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green St., Urbana, Illinois 61801 (United States)
2015-09-14
We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U{sup ∗}/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.
Ab initio calculations and modelling of atomic cluster structure
Solov'yov, Ilia; Lyalin, Andrey G.; Greiner, Walter
2004-01-01
framework for modelling the fusion process of noble gas clusters is presented. We report the striking correspondence of the peaks in the experimentally measured abundance mass spectra with the peaks in the size-dependence of the second derivative of the binding energy per atom calculated for the chain...... of the noble gas clusters up to 150 atoms....
Ab initio determination of kinetics for atomic layer deposition modeling
Remmers, Elizabeth M.
A first principles model is developed to describe the kinetics of atomic layer deposition (ALD) systems. This model requires no fitting parameters, as it is based on the reaction pathways, structures, and energetics obtained from quantum-chemical studies. Using transition state theory and partition functions from statistical mechanics, equilibrium constants and reaction rates can be calculated. Several tools were created in Python to aid in the calculation of these quantities, and this procedure was applied to two systems- zinc oxide deposition from diethyl zinc (DEZ) and water, and alumina deposition from trimethyl aluminum (TMA) and water. A Gauss-Jordan factorization is used to decompose the system dynamics, and the resulting systems of equations are solved numerically to obtain the temporal concentration profiles of these two deposition systems.
Arntsen, Christopher; Chen, Chen; Voth, Gregory A.
2017-09-01
We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly from ab initio molecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown to faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields.
Monte Carlo Shell Model for ab initio nuclear structure
Abe T.
2014-03-01
Full Text Available We report on our recent application of the Monte Carlo Shell Model to no-core calculations. At the initial stage of the application, we have performed benchmark calculations in the p-shell region. Results are compared with those in the Full Configuration Interaction and No-Core Full Configuration methods. These are found to be consistent with each other within quoted uncertainties when they could be quantified. The preliminary results in Nshell = 5 reveal the onset of systematic convergence pattern.
Trivacancy in silicon: A combined DLTS and ab-initio modeling study
Markevich, V. P.; Peaker, A. R.; Lastovskii, S. B.; Murin, L. I.; Coutinho, J.; Markevich, A. V.; Torres, V. J. B.; Briddon, P. R.; Dobaczewski, L.; Monakhov, E. V.; Svensson, B. G.
2009-12-01
Deep level transient spectroscopy and ab-initio modeling have been used for identification of energy levels and structure of trivacancy (V3) in Si. It is found that in the neutral charge state the V3 is bistable, with the "fourfold" configuration being lower in energy than the (1 1 0) planar configuration. V3 in the (1 1 0) planar configuration gives rise to two acceptor levels at Ec-0.36 eV and Ec-0.46 eV in the gap, while in the "fourfold" configuration the defect has trigonal symmetry and an acceptor level at Ec-0.075 eV.
Strubbe, David A.; Grossman, Jeffrey C.
Classical inter-atomic potentials can be successful at predicting the vibrations of materials at system sizes intractable by quantum methods. However, to predict Raman spectra, electrons must be re-introduced, for example via a bond-polarizability model which attributes the polarizability to cylindrically symmetrical inter-atomic bonds. Parameters in assumed functional forms are fit to experimental spectra, and then a Raman intensity can be computed for each mode. In the case of amorphous silicon, the existing models do not show satisfactory agreement with experimental spectra. To generate a more accurate and transferable bond-polarizability model, we have instead begun with ab initio calculated Raman tensors for a set of a-Si:H structures [DA Strubbe et al., arXiv:1511.01139]. This atomistic data set al.lows us to obtain parameters and functional forms for a general model, without confounding errors from the potentials. This Raman model can be used to study large structural models with relevance for photovoltaics, such as medium- and long-range order in a-Si:H, nanocrystalline Si, amorphous/crystalline interfaces, or a-Si:H nanowires, at sizes that would be inaccessible for ab initio calculations. We analyze the applicability of this approach to other materials systems.
Thermodynamic modeling of the Fe–Mo system coupled with experiments and ab initio calculations
Rajkumar, V.B.; Hari Kumar, K.C., E-mail: kchkumar@iitm.ac.in
2014-10-25
Highlights: • Gibbs energy functions for all stable phases in the Fe–Mo system obtained using Calphad method. • Ab initio calculation results are employed to improve Gibbs energy functions. • New experimental data have been incorporated in the optimization. • Thermochemical properties: energy of formation, cohesive energy. • Calculated values are compared with experimental results. - Abstract: In this paper we report the Gibbs energy functions for all stable phases in the Fe–Mo system obtained using Calphad method. Newly measured enthalpy increment data, tie-line data and liquidus data for selected compositions are used as input for the Gibbs energy modeling, along with carefully selected thermochemical and phase diagram data from literature. Further, ab initio generated energy of formation at 0 K for the intermetallic phases and end-members of the sublattice model for the μ phase and the σ phase are also used in the optimization of model parameters of the Gibbs energy functions. Calculated phase diagram and the thermochemical properties show good agreement with the experimental data.
Comparison between phenomenological and ab-initio reaction and relaxation models in DSMC
Sebastião, Israel B.; Kulakhmetov, Marat; Alexeenko, Alina
2016-11-01
New state-specific vibrational-translational energy exchange and dissociation models, based on ab-initio data, are implemented in direct simulation Monte Carlo (DSMC) method and compared to the established Larsen-Borgnakke (LB) and total collision energy (TCE) phenomenological models. For consistency, both the LB and TCE models are calibrated with QCT-calculated O2+O data. The model comparison test cases include 0-D thermochemical relaxation under adiabatic conditions and 1-D normal shockwave calculations. The results show that both the ME-QCT-VT and LB models can reproduce vibrational relaxation accurately but the TCE model is unable to reproduce nonequilibrium rates even when it is calibrated to accurate equilibrium rates. The new reaction model does capture QCT-calculated nonequilibrium rates. For all investigated cases, we discuss the prediction differences based on the new model features.
A set of molecular models based on quantum mechanical ab initio calculations and thermodynamic data
Eckl, Bernhard; Hasse, Hans
2009-01-01
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic data. The geometry of the molecular models is specified according to the atom positions determined by QM energy minimization. The electrostatic interactions are modeled by reducing the electron density distribution to point dipoles and point quadrupoles located in the center of mass of the molecules. Dispersive and repulsive interactions are described by Lennard-Jones sites, for which the parameters are iteratively optimized to experimental vapor-liquid equilibrium (VLE) data, i.e. vapor pressure, saturated liquid density, and enthalpy of vaporization of the considered substance. The proposed modeling strategy was applied to a sample set of ten molecules from different substance classes. New molecular models are presented for iso-butane, cyclohexane, formaldehyde, dimethyl...
Pernot, Pascal
2009-01-01
Bayesian Model Calibration is used to revisit the problem of scaling factor calibration for semi-empirical correction of ab initio calculations. A particular attention is devoted to uncertainty evaluation for scaling factors, and to their effect on prediction of observables involving scaled properties. We argue that linear models used for calibration of scaling factors are generally not statistically valid, in the sense that they are not able to fit calibration data within their uncertainty limits. Uncertainty evaluation and uncertainty propagation by statistical methods from such invalid models are doomed to failure. To relieve this problem, a stochastic function is included in the model to account for model inadequacy, according to the Bayesian Model Calibration approach. In this framework, we demonstrate that standard calibration summary statistics, as optimal scaling factor and root mean square, can be safely used for uncertainty propagation only when large calibration sets of precise data are used. For s...
Ji, Pengfei
2016-01-01
By combining ab initio quantum mechanics calculation and Drude model, electron temperature and lattice temperature dependent electron thermal conductivity is calculated and implemented into a multiscale model of laser material interaction, which couples the classical molecular dynamics and two-temperature model. The results indicated that the electron thermal conductivity obtained from ab initio calculation leads to faster thermal diffusion than that using the electron thermal conductivity from empirical determination, which further induces deeper melting region, larger number of density waves travelling inside the copper film and more various speeds of atomic clusters ablated from the irradiated film surface.
Minimal parameter implicit solvent model for ab initio electronic structure calculations
Dziedzic, Jacek; Skylaris, Chris-Kriton; Mostofi, Arash A; Payne, Mike C
2011-01-01
We present an implicit solvent model for ab initio electronic structure calculations which is fully self-consistent and is based on direct solution of the nonhomogeneous Poisson equation. The solute cavity is naturally defined in terms of an isosurface of the electronic density according to the formula of Fattebert and Gygi (J. Comp. Chem. 23, 6 (2002)). While this model depends on only two parameters, we demonstrate that by using appropriate boundary conditions and dispersion-repulsion contributions, solvation energies obtained for an extensive test set including neutral and charged molecules show dramatic improvement compared to existing models. Our approach is implemented in, but not restricted to, a linear-scaling density functional theory (DFT) framework, opening the path for self-consistent implicit solvent DFT calculations on systems of unprecedented size, which we demonstrate with calculations on a 2615-atom protein-ligand complex.
Tight-binding model for carbon nanotubes from ab initio calculations.
Correa, J D; da Silva, Antônio J R; Pacheco, M
2010-07-14
Here we present a parametrized tight-binding (TB) model to calculate the band structure of single-wall carbon nanotubes (SWNTs). On the basis of ab initio calculations we fit the band structure of nanotubes of different radii with results obtained with an orthogonal TB model to third neighbors, which includes the effects of orbital hybridization by means of a reduced set of parameters. The functional form for the dependence of these parameters on the radius of the tubes can be used to interpolate appropriate TB parameters for different SWNTs and to study the effects of curvature on their electronic properties. Additionally, we have shown that the model gives an appropriate description of the optical spectra of SWNTs, which can be useful for a proper assignation of SWNTs' specific chirality from optical absorption experiments.
Tunneling of electrons via rotor-stator molecular interfaces: combined ab initio and model study
Petreska, Irina; Pejov, Ljupco; Kocarev, Ljupco
2015-01-01
Tunneling of electrons through rotor-stator anthracene aldehyde molecular interfaces is studied with a combined ab initio and model approach. Molecular electronic structure calculated from first principles is utilized to model different shapes of tunneling barriers. Together with a rectangular barrier, we also consider a sinusoidal shape that captures the effects of the molecular internal structure more realistically. Quasiclassical approach with the Simmons' formula for current density is implemented. Special attention is paid on conformational dependence of the tunneling current. Our results confirm that the presence of the side aldehyde group enhances the interesting electronic properties of the pure anthracene molecule, making it a bistable system with geometry dependent transport properties. We also investigate the transition voltage and we show that confirmation dependent field emission could be observed in these molecular interfaces at realistically low voltages. The present study accompanies our previ...
A New Generation of Cool White Dwarf Atmosphere Models Using Ab Initio Calculations
Blouin, S.; Dufour, P.; Kowalski, P. M.
2017-03-01
Due to their high photospheric density, cool helium-rich white dwarfs (particularly DZ, DQpec and ultracool) are often poorly described by current atmosphere models. As part of our ongoing efforts to design atmosphere models suitable for all cool white dwarfs, we investigate how the ionization ratio of heavy elements and the H2-He collision-induced absorption (CIA) spectrum are altered under fluid-like densities. For the conditions encountered at the photosphere of cool helium-rich white dwarfs, our ab initio calculations show that the ionization of most metals is inhibited and that the H2-He CIA spectrum is significantly distorted for densities higher than 0.1 g/cm3.
A New Generation of Cool White Dwarf Atmosphere Models Using Ab Initio Calculations
Blouin, Simon; Kowalski, Piotr M
2016-01-01
Due to their high photospheric density, cool helium-rich white dwarfs (particularly DZ, DQpec and ultracool) are often poorly described by current atmosphere models. As part of our ongoing efforts to design atmosphere models suitable for all cool white dwarfs, we investigate how the ionization ratio of heavy elements and the H$_2$-He collision-induced absorption (CIA) spectrum are altered under fluid-like densities. For the conditions encountered at the photosphere of cool helium-rich white dwarfs, our ab initio calculations show that the ionization of most metals is inhibited and that the H$_2$-He CIA spectrum is significantly distorted for densities higher than 0.1 g/cm$^3$.
Olsson, P. A. T.; Kese, K.; Kroon, M.; Alvarez Holston, A.-M.
2015-06-01
In this work we report the results of an ab initio study of the transgranular fracture toughness and cleavage of brittle zirconium hydrides. We use the Griffith-Irwin relation to assess the fracture toughness using calculated surface energy and estimated isotropic Voigt-Reuss-Hill averages of the elastic constants. The calculated fracture toughness values are found to concur well with experimental data, which implies that fracture is dominated by cleavage failure. To investigate the cleavage energetics, we model the decohesion process. To describe the interplanar interaction we adopt Rose’s universal binding energy relation, which is found to reproduce the behaviour accurately. The modelling shows that the work of fracture and ductility decreases with increasing hydrogen content.
ZHANG Zhi-jie; LIU Yu-hua; L(U) Zhong-yuan; LI Ze-sheng
2009-01-01
The rotational isomeric state(RIS) model was constructed for poly(vinylidene chloride)(PVDC) based on quantum chemistry calculations. The statistical weighted parameters were obtained from RIS representations and ab initio energies of conformers for model molecules 2,2,4,4-tetrachloropentane(TCP) and 2,2,4,4,6, 6-hexachlorohep-tane(HCH). By employing the RIS method, the characteristic ratio C∞ was calculated for PVDC. The calculated cha-racteristic ratio for PVDC is in good agreement with experiment result. Additionally, we studied the influence of the statistical weighted parameters on C∞ by calculating δC∞/δlnw. According to the values of δC∞/δlnw, the effects of second-order Cl-CH2 pentane type interaction and Cl-Cl long range interaction on C∞ were found to be important. In contrast, first-order interaction is unimportant.
Ab initio energetics for modeling phase stability of the Np-U system
Xie, Wei; Chang, Y. Austin; Morgan, Dane
2016-10-01
The Np-U system has been rarely studied despite this alloy being a key binary subsystem of metallic nuclear fuels. This study aims to further the understanding of the phase stability of the Np-U system through ab initio calculations. We first examined an existing CALPHAD model based on available experimental phase boundary data. We then focused on phases of which the CALPHAD model reproduces reasonably the experimental data and examined if values of the effective Hubbard U (i.e., Ueff) parameter for Np and U fitted previously in the Np-Zr and U-Zr systems are also applicable to the Np-U system, using CALPHAD predicted enthalpies as references. We found that in general DFT + U predicts improved or at least similarly accurate enthalpies compared to standard DFT when the Ueff's used are within the ranges of single-structure optimized Ueff's (0.65-0.9 eV for Np and 1-1.5 eV for U)-for example, the multi-structure optimized Ueff's (0.9 eV for Np and 1.24 eV for U)-determined in our previous U-Zr and Np-Zr studies. Finally, we focused on the intermediate phase ζ(Np,U), which at present is poorly characterized by experiments and unsatisfactorily described in the CALPHAD model. Based on ab initio calculated formation enthalpies for ordered end members and the compound energy formalism, we predicted its site occupations as functions of composition and temperature. Our study demonstrated that Ueff's fitted for U and Np determined in the U-Zr and Np-Zr systems may be transferable to the Np-U system and also provided new prediction of the site occupations for ζ(Np,U), which may serve as reference for future experimental and modeling study of the Np-U system.
Ab Initio No Core Shell Model - Recent Results and Further Prospects
Vary, James P; Potter, Hugh; Caprio, Mark A; Smith, Robin; Binder, Sven; Calci, Angelo; Fischer, Sebastian; Langhammer, Joachim; Roth, Robert; Aktulga, Hasan Metin; Ng, Esmond; Yang, Chao; Oryspayev, Dossay; Sosonkina, Masha; Saule, Erik; Çatalyürek, Ümit
2015-01-01
There has been significant recent progress in solving the long-standing problems of how nuclear shell structure and collective motion emerge from underlying microscopic inter-nucleon interactions. We review a selection of recent significant results within the ab initio No Core Shell Model (NCSM) closely tied to three major factors enabling this progress: (1) improved nuclear interactions that accurately describe the experimental two-nucleon and three-nucleon interaction data; (2) advances in algorithms to simulate the quantum many-body problem with strong interactions; and (3) continued rapid development of high-performance computers now capable of performing $20 \\times 10^{15}$ floating point operations per second. We also comment on prospects for further developments.
Trivacancy in silicon: A combined DLTS and ab-initio modeling study
Markevich, V.P., E-mail: V.Markevich@manchester.ac.u [University of Manchester, Manchester M60 1QD (United Kingdom); Peaker, A.R. [University of Manchester, Manchester M60 1QD (United Kingdom); Lastovskii, S.B.; Murin, L.I. [Scientific-Practical Materials Research Center of NAS of Belarus, Minsk 220072 (Belarus); Coutinho, J.; Markevich, A.V.; Torres, V.J.B. [Department of Physics and I3N, University of Aveiro, 3810-193 Aveiro (Portugal); Briddon, P.R. [University of Newcastle upon Tyne, Newcastle upon Tyne NE1 7RU (United Kingdom); Dobaczewski, L. [Institute of Physics, Polish Academy of Sciences, 02-668 Warsaw (Poland); Monakhov, E.V.; Svensson, B.G. [Department of Physics, Oslo University, 0316 Oslo (Norway)
2009-12-15
Deep level transient spectroscopy and ab-initio modeling have been used for identification of energy levels and structure of trivacancy (V{sub 3}) in Si. It is found that in the neutral charge state the V{sub 3} is bistable, with the 'fourfold' configuration being lower in energy than the (1 1 0) planar configuration. V{sub 3} in the (1 1 0) planar configuration gives rise to two acceptor levels at E{sub c}-0.36 eV and E{sub c}-0.46 eV in the gap, while in the 'fourfold' configuration the defect has trigonal symmetry and an acceptor level at E{sub c}-0.075 eV.
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.
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.)
Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela
2015-06-17
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.
Lunts, Peter; Miller, Jonah; Schnetter, Erik; Kim, Yong Baek; Lee, Sung-Sik
2015-01-01
We apply the quantum renormalization group to construct a holographic dual for the U(N) vector model for complex bosons defined on a lattice. The bulk geometry becomes dynamical as the hopping amplitudes which determine connectivity of space are promoted to quantum variables. In the large N limit, the full bulk equations of motion for the dynamical hopping fields are numerically solved for finite systems. From finite size scaling, we show that different phases exhibit distinct geometric features in the bulk. In the insulating phase, the space gets fragmented into isolated islands deep inside the bulk, exhibiting ultra-locality. In the superfluid phase, the bulk exhibits a horizon beyond which the geometry becomes non-local. Right at the horizon, the hopping fields decay with a universal power-law in coordinate distance between sites, while they decay in slower power-laws with continuously varying exponents inside the horizon. At the critical point, the bulk exhibits a local geometry whose characteristic lengt...
Matching a surface complexation model with ab initio molecular dynamics: montmorillonite case
Kulik, D.A.; Churakov, S.V. [Paul Scherrer Institute, Nuclear Energy and Safety Dpt., Lab. for Waste Management, CH-5232 Villigen PSI (Switzerland)
2005-07-01
Speciation modelling of sorption on mineral-water interfaces is performed with help of surface complexation models (SCM), suitable for diluted suspensions that seem to reach adsorption equilibrium within laboratory times. Electrostatic SCMs need several input parameters even for a relatively simple oxide mineral surface. Moreover, the electrolyte ion adsorption constants in triple layer (TL) or basic Stern (BS) models depend on the inner layer capacitance density Cl, but clear physical understanding of this parameter is missing so far. SCMs can fit acidimetric or metal titration data well at quite different combinations of input parameters, and this fact casts doubt on any interpretation of fitted parameter values in terms of microscopic physicochemical mechanisms. The problem is even deeper in SCMs for clay minerals like montmorillonite having at least two surface types: the edges exposing different (aluminol and silanol) functional groups, and the basal siloxane planes with permanent charge and ion exchange. A feasible way to overcome the caveat of SCMs is seen nowadays in relying on crystallographic data and ab initio calculations to restrict the EDL setup, species stoichiometries, and input parameter values when constructing the adsorption model. The aim of this contribution is to discuss how recent advances in sample surface characterization an d in quantum-chemistry calculations for pyrophyllite can help in putting together a multi-site-surface electrostatic SCM for montmorillonite implemented in GEM approach. The quality of macroscopic model fits is checked against the titration data. (authors)
Jupiter models with improved ab initio hydrogen EOS (H-REOS.2)
Nettelmann, Nadine; Holst, Bastian; Redmer, Ronald
2011-01-01
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 used, and on model assumptions. We present an improved ab initio hydrogen equation of state, H-REOS.2 and compute the internal structure and thermal evolution of Jupiter within the standard three-layer approach. The advance over comparable previous Jupiter models (Nettelmann et al. 2008, ApJ 683, 1217) is that the new models are also consistent with the observed \\gtrsim 2 times solar heavy element abundances in Jupiter's atmosphere. Such models have a rock core mass Mcore=0-8 ME, total mass of heavy elements MZ=28-31 ME, a deep internal layer boundary at \\geq 4 Mbar, and a cooling time of 4.7 Gyrs when assuming homogeneous evolution. We also calculate two-layer models in the manner of Militzer et al. (2008), ApJ 688, L45, and find a comparable core mass but significantly higher envelope metallicity of 4.5 times ...
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...
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.
Ab initio derivation of multi-orbital extended Hubbard model for molecular crystals
Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu; Bonnet, Marie-Laure; Robert, Vincent
2012-01-01
From configuration interaction (CI) ab initio calculations, we derive an effective two-orbital extended Hubbard model based on the gerade (g) and ungerade (u) molecular orbitals (MOs) of the charge-transfer molecular conductor (TTM-TTP)I3 and the single-component molecular conductor [Au(tmdt)2]. First, by focusing on the isolated molecule, we determine the parameters for the model Hamiltonian so as to reproduce the CI Hamiltonian matrix. Next, we extend the analysis to two neighboring molecule pairs in the crystal and we perform similar calculations to evaluate the inter-molecular interactions. From the resulting tight-binding parameters, we analyze the band structure to confirm that two bands overlap and mix in together, supporting the multi-band feature. Furthermore, using a fragment decomposition, we derive the effective model based on the fragment MOs and show that the staking TTM-TTP molecules can be described by the zig-zag two-leg ladder with the inter-molecular transfer integral being larger than the intra-fragment transfer integral within the molecule. The inter-site interactions between the fragments follow a Coulomb law, supporting the fragment decomposition strategy.
Ab initio state-specific N2 + O dissociation and exchange modeling for molecular simulations
Luo, Han; Kulakhmetov, Marat; Alexeenko, Alina
2017-02-01
Quasi-classical trajectory (QCT) calculations are used in this work to calculate state-specific N2(X1Σ ) +O(3P ) →2 N(4S ) +O(3P ) dissociation and N2(X1Σ ) +O(3P ) →NO(X2Π ) +N(4S ) exchange cross sections and rates based on the 13A″ and 13A' ab initio potential energy surface by Gamallo et al. [J. Chem. Phys. 119, 2545-2556 (2003)]. The calculations consider translational energies up to 23 eV and temperatures between 1000 K and 20 000 K. Vibrational favoring is observed for dissociation reaction at the whole range of collision energies and for exchange reaction around the dissociation limit. For the same collision energy, cross sections for v = 30 are 4 to 6 times larger than those for the ground state. The exchange reaction has an effective activation energy that is dependent on the initial rovibrational level, which is different from dissociation reaction. In addition, the exchange cross sections have a maximum when the total collision energy (TCE) approaches dissociation energy. The calculations are used to generate compact QCT-derived state-specific dissociation (QCT-SSD) and QCT-derived state-specific exchange (QCT-SSE) models, which describe over 1 × 106 cross sections with about 150 model parameters. The models can be used directly within direct simulation Monte Carlo and computational fluid dynamics simulations. Rate constants predicted by the new models are compared to the experimental measurements, direct QCT calculations and predictions by other models that include: TCE model, Bose-Candler QCT-based exchange model, Macheret-Fridman dissociation model, Macheret's exchange model, and Park's two-temperature model. The new models match QCT-calculated and experimental rates within 30% under nonequilibrium conditions while other models under predict by over an order of magnitude under vibrationally-cold conditions.
Speciation of magnesium in monohydrocalcite: XANES, ab initio and geochemical modeling
Fukushi, Keisuke; Suzuki, Yuma; Kawano, Jun; Ohno, Takeshi; Ogawa, Masahiro; Yaji, Toyonari; Takahashi, Yoshio
2017-09-01
Monohydrocalcite (MHC: CaCO3·H2O), a rare carbonate mineral formed under surface conditions, is usually observed in nature as containing a variable amount of Mg, with a 0.007-0.45 Mg/Ca mole ratio. The variable Mg composition in MHC is anticipated as a promising proxy to assess paleo-hydrochemistry especially in saline lakes. Although the roles of Mg on the formation and stability of MHC have been studied intensively, the Mg speciation in MHC has remained unclear and controversial. This study examined Mg speciation in MHC using X-ray absorption near edge structure (XANES), ab initio molecular simulation, and geochemical modeling. Mg-XANES spectra of MHC with different Mg/Ca ratios prepared from mixing solutions of Na2CO3, CaCl2 and MgCl2 revealed that the Mg in MHC is a mixture of amorphous Mg carbonate (AMC) and other Mg containing phase. The contribution of AMC to total Mg is negatively correlated to the crystallinity of MHC. Results show that AMC might play a protective role in the crystallization and the transformation to stable calcium carbonates. Ab initio calculation of Mg2+ substitution into MHC showed that a limited amount of Mg2+ can be incorporated into the MHC structure. Six-fold coordination of Mg2+ is substituted for eight-fold coordination of Ca2+ in the MHC structure. The other type of Mg in MHC revealed from the XANES analyses most likely corresponds to the structural Mg in MHC. The contribution of the structural Mg is almost constant at 0.06 in Mg/Ca, representing the limit of solid solubility of Mg in MHC. The solubility products of the MHC with the limit of solid solubility of Mg and the AMC associated with MHC were estimated from the reacted solution compositions. Prediction of the Mg/Ca ratio as a function of the initial solution conditions using solubility reasonably reproduces the observed apparent Mg/Ca ratios in MHC from the present study and earlier studies. The apparent Mg/Ca ratio of MHC is useful to elucidate water chemistry
Tunneling of electrons via rotor-stator molecular interfaces: Combined ab initio and model study
Petreska, Irina; Ohanesjan, Vladimir; Pejov, Ljupčo; Kocarev, Ljupčo
2016-07-01
Tunneling of electrons through rotor-stator anthracene aldehyde molecular interfaces is studied with a combined ab initio and model approach. Molecular electronic structure calculated from first principles is utilized to model different shapes of tunneling barriers. Together with a rectangular barrier, we also consider a sinusoidal shape that captures the effects of the molecular internal structure more realistically. Quasiclassical approach with the Simmons' formula for current density is implemented. Special attention is paid on conformational dependence of the tunneling current. Our results confirm that the presence of the side aldehyde group enhances the interesting electronic properties of the pure anthracene molecule, making it a bistable system with geometry dependent transport properties. We also investigate the transition voltage and we show that conformation-dependent field emission could be observed in these molecular interfaces at realistically low voltages. The present study accompanies our previous work where we investigated the coherent transport via strongly coupled delocalized orbital by application of Non-equilibrium Green's Function Formalism.
Ab-initio molecular modeling of interfaces in tantalum-carbon system
Balani, Kantesh; Mungole, Tarang [Materials Science and Engineering, Indian Institute of Technology, Kanpur-208016 (India); Bakshi, Srinivasa Rao [Mechanical and Materials Engineering, Florida International University, Miami, Florida 33174 (United States); Metallurgical and Materials Engineering, Indian Institute of Technology Madras, Chennai 600036 (India); Agarwal, Arvind [Mechanical and Materials Engineering, Florida International University, Miami, Florida 33174 (United States)
2012-03-15
Processing of ultrahigh temperature TaC ceramic material with sintering additives of B{sub 4}C and reinforcement of carbon nanotubes (CNTs) gives rise to possible formation of several interfaces (Ta{sub 2}C-TaC, TaC-CNT, Ta{sub 2}C-CNT, TaB{sub 2}-TaC, and TaB{sub 2}-CNT) that could influence the resultant properties. Current work focuses on interfaces developed during spark plasma sintering of TaC-system and performing ab initio molecular modeling of the interfaces generated during processing of TaC-B{sub 4}C and TaC-CNT composites. The energy of the various interfaces has been evaluated and compared with TaC-Ta{sub 2}C interface. The iso-surface electronic contours are extracted from the calculations eliciting the enhanced stability of TaC-CNT interface by 72.2%. CNTs form stable interfaces with Ta{sub 2}C and TaB{sub 2} phases with a reduction in the energy by 35.8% and 40.4%, respectively. The computed Ta-C-B interfaces are also compared with experimentally observed interfaces in high resolution TEM images.
Beyond Born-Mayer: Improved models for short-range repulsion in ab initio force fields
Van Vleet, Mary J; Stone, Anthony J; Schmidt, J R
2016-01-01
Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones (${A}/{r^{12}}$) or Born-Mayer ($A\\exp(-Br)$) forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, and robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Finally, we show how this methodology can be adapted to yield the standard Born-Mayer functional for...
Can DNA-binding proteins of replisome tautomerize nucleotide bases? Ab initio model study.
Brovarets', Ol'ha O; Yurenko, Yevgen P; Dubey, Igor Ya; Hovorun, Dmytro M
2012-01-01
Ab initio quantum-chemical study of specific point contacts of replisome proteins with DNA modeled by acetic acid with canonical and mutagenic tautomers of DNA bases methylated at the glycosidic nitrogen atoms was performed in vacuo and continuum with a low dielectric constant (ϵ ∼ 4) corresponding to a hydrophobic interface of protein-nucleic acid interaction. All tautomerized complexes were found to be dynamically unstable, because the electronic energies of their back-reaction barriers do not exceed zero-point vibrational energies associated with the vibrational modes whose harmonic vibrational frequencies become imaginary in the transition states of the tautomerization reaction. Additionally, based on the physicochemical arguments, it was demonstrated that the effects of biomolecular environment cannot ensure dynamic stabilization. This result allows suggesting that hypothetically generated by DNA-binding proteins of replisome rare tautomers will have no impact on the total spontaneous mutation due to the low reverse barrier allowing a quick return to the canonical form.
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.
Liu, Hanchao; Wang, Yimin; Bowman, Joel M. [Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322 (United States)
2015-05-21
The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H{sub 2}O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0–4000 cm{sup −1} is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.
Liu, Hanchao; Wang, Yimin; Bowman, Joel M
2015-05-21
The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm(-1) is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.
Timoshenko, Janis; Shivhare, Atal; Scott, Robert W J; Lu, Deyu; Frenkel, Anatoly I
2016-07-20
We adopted ab initio X-ray absorption near edge structure (XANES) modeling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modeling, where the candidate structures are known, and the inverse modeling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by revealing the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.
Ran, Shi-Ju
2016-05-01
In this work, a simple and fundamental numeric scheme dubbed as ab initio optimization principle (AOP) is proposed for the ground states of translational invariant strongly correlated quantum lattice models. The idea is to transform a nondeterministic-polynomial-hard ground-state simulation with infinite degrees of freedom into a single optimization problem of a local function with finite number of physical and ancillary degrees of freedom. This work contributes mainly in the following aspects: (1) AOP provides a simple and efficient scheme to simulate the ground state by solving a local optimization problem. Its solution contains two kinds of boundary states, one of which play the role of the entanglement bath that mimics the interactions between a supercell and the infinite environment, and the other gives the ground state in a tensor network (TN) form. (2) In the sense of TN, a novel decomposition named as tensor ring decomposition (TRD) is proposed to implement AOP. Instead of following the contraction-truncation scheme used by many existing TN-based algorithms, TRD solves the contraction of a uniform TN in an opposite way by encoding the contraction in a set of self-consistent equations that automatically reconstruct the whole TN, making the simulation simple and unified; (3) AOP inherits and develops the ideas of different well-established methods, including the density matrix renormalization group (DMRG), infinite time-evolving block decimation (iTEBD), network contractor dynamics, density matrix embedding theory, etc., providing a unified perspective that is previously missing in this fields. (4) AOP as well as TRD give novel implications to existing TN-based algorithms: A modified iTEBD is suggested and the two-dimensional (2D) AOP is argued to be an intrinsic 2D extension of DMRG that is based on infinite projected entangled pair state. This paper is focused on one-dimensional quantum models to present AOP. The benchmark is given on a transverse Ising
Lucas, G
2006-10-15
The behaviour of silicon carbide under irradiation has been studied using classical and ab initio simulations, focusing on the nano scale elementary processes. First, we have been interested in the calculation of threshold displacement energies, which are difficult to determine both experimentally and theoretically, and also the associated Frenkel pairs. In the framework of this thesis, we have carried out simulations in classical and ab initio molecular dynamics. For the classical approach, two types of potentials have been used: the Tersoff potential, which led to non satisfactory results, and a new one which has been developed during this thesis. This potential allows a better modelling of SiC under irradiation than most of the empirical potentials available for SiC. It is based on the EDIP potential, initially developed to describe defects in silicon, that we have generalized to SiC. For the ab initio approach, the feasibility of the calculations has been validated and average energies of 19 eV for the C and 38 eV for the Si sublattices have been determined, close to the values empirically used in the fusion community. The results obtained with the new potential EDIP are globally in agreement with those values. Finally, the elementary processes involved in the crystal recovery have been studied by calculating the stability of the created Frenkel pairs and determining possible recombination mechanisms with the nudged elastic band method. (author)
Ab initio modeling of radiation damage in MgF{sub 2} crystals
Abuova, F.U. [L. N. Gumilyov Eurasian National University, 3 Munaitpasova Str., Astana (Kazakhstan); Kotomin, E.A., E-mail: kotomin@latnet.lv [Institute of Solid State Physics, University of Latvia, 8 Kengaraga Str., LV-1063, Riga (Latvia); Lisitsyn, V.M. [Tomsk Polytechnical University, Tomsk 634003 (Russian Federation); Akilbekov, A.T. [L. N. Gumilyov Eurasian National University, 3 Munaitpasova Str., Astana (Kazakhstan); Piskunov, S. [Institute of Solid State Physics, University of Latvia, 8 Kengaraga Str., LV-1063, Riga (Latvia)
2014-05-01
MgF{sub 2} with a rutile structure is important radiation-resistant material with numerous applications due to its transparency from vacuum ultraviolet to infrared range of photon energies. We present and discuss the results of calculations for basic radiation defects in this crystal. The study is based on the large scale ab initio DFT calculations using hybrid B3PW exchange–correlation functional and atomic basis set. We analyzed the electronic structure, atomic displacements, charge density distribution as well as defect formation energies using large supercells. We compared properties of close and well separated F−H (Frenkel) defect pairs as well as individual defects. We simulated also formation and energetic preference of inert F{sub 2} interstitial molecules as sinks of mobile interstitial fluorine atoms which is relevant for material radiation stability. We discussed also diffusion of the primary electronic defects—F centers.
Ab initio atomic recombination reaction energetics on model heat shield surfaces
Senese, Fredrick; Ake, Robert
1992-01-01
Ab initio quantum mechanical calculations on small hydration complexes involving the nitrate anion are reported. The self-consistent field method with accurate basis sets has been applied to compute completely optimized equilibrium geometries, vibrational frequencies, thermochemical parameters, and stable site labilities of complexes involving 1, 2, and 3 waters. The most stable geometries in the first hydration shell involve in-plane waters bridging pairs of nitrate oxygens with two equal and bent hydrogen bonds. A second extremely labile local minimum involves out-of-plane waters with a single hydrogen bond and lies about 2 kcal/mol higher. The potential in the region of the second minimum is extremely flat and qualitatively sensitive to changes in the basis set; it does not correspond to a true equilibrium structure.
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.
Lister, C.J. [Department of Physics, University of Massachusetts, Lowell, Lowell MA 01854 (United States); McCutchan, E.A. [National Nuclear Data Center, Brookhaven National Laboratory, Upton, NY 11973-5000 (United States)
2014-06-15
A new generation of ab-initio calculations, based on realistic two- and three-body forces, is having a profound impact on our view of how nuclei work. To improve the numerical methods, and the parameterization of 3-body forces, new precise data are needed. Electromagnetic transitions are very sensitive to the dynamics which drive mixing between configurations. We have made a series of precise (< 3%) measurements of electromagnetic transitions in the A=10 nuclei {sup 10}C and {sup 10}Be by using the Doppler Shift Attenuation method carefully. Many interesting features can be reproduced including the strong α clustering. New measurements on {sup 8}Be and {sup 12}Be highlight the interplay between the alpha clusters and their valence neutrons.
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...
Sharma, Anshuman [Materials Science Program, University of Wisconsin-Madison, 1509, University Avenue, Madison, WI 53706 (United States); Zhang Chuan [CompuTherm LLC, 437 S. Yellowstone Dr., Suite 217, Madison, WI 53719 (United States); Chang, Y. Austin [Materials Science Program, University of Wisconsin-Madison, 1509, University Avenue, Madison, WI 53706 (United States); Department of Materials Science and Engineering, University of Wisconsin-Madison, 1509, University Avenue, Madison, WI 53706 (United States); Knoeppel, Ray [A.O. Smith Corporate Technology Centre, 12100, West Park Place, Milwaukee, WI 53224 (United States); Morgan, Dane, E-mail: ddmorgan@wisc.ed [Materials Science Program, University of Wisconsin-Madison, 1509, University Avenue, Madison, WI 53706 (United States); Department of Materials Science and Engineering, University of Wisconsin-Madison, 1509, University Avenue, Madison, WI 53706 (United States)
2011-05-15
Research highlights: {yields} Effect of alloying on the corrosion activity of sacrificial Al anodes. {yields} Sn in solid solution form is a key alloying element for activation of Al anodes. {yields} Ternary additions that increase Sn solubility decrease the potential of Al alloys. {yields} Elements bigger than Al expand the Al lattice and allow more Sn to dissolve in Al. {yields} Large ternary dopants can reduce Sn's solubility in Al if they form compounds with Sn. - Abstract: This work summarizes the experimental literature to date on Al-alloy sacrificial anodes and shows that the presence of Sn as an alloying element in solid solution form consistently debases the alloy corrosion potential. This study then assesses the lattice expander theory, which states that lattice-expanding dopants can be used to increase Sn solubility in Al and thereby reduce passivation. The thermodynamic effects on Sn solubility of lattice expanders (Ga, Mg, Zr, In and Bi) are predicted with ab-initio methods. Our results support lattice expander theory although we demonstrate that Sn solubility can decrease by alloying with even large dopants if they form compounds with Sn.
Neukirch, Amanda; Nei, Wanyi; Pedesseau, Laurent; Even, Jacky; Katan, Claudine; Mohite, Aditya; Tretiak, Segrei
2015-03-01
The need for an inexpensive, clean, and plentiful source of energy has generated large amounts of research in an assortment of solution processed organic and hybrid organic-inorganic solar cells. A relative newcomer to the field of solution processed photovoltaics is the lead halide perovskite solar cell. In the past 5 years, the efficiencies of devices made from this material have increased from 3.5% to nearly 20%. Despite the rapid development of organic-inorganic perovskite solar cells, a thorough understanding of the fundamental photophysical processes driving the high performance of these devices is not well understood. I am using state-of-the-art ab initio computational techniques in order to characterize the properties at the interface of perovskite devices in order to aide in materials design and device engineering. I will present an in-depth analysis of the electronic and optical properties of bulk and surface states of pure and mixed halide systems. The high-level static quantum mechanical calculations, including spin-orbit-coupling and the many body GW approach, identify the key electronic states involved in photoinduced dynamics. This knowledge provides important information on how the optical properties change with variations to the system. Supported by the DOE, the LANL LDRD program XW11, and CNLS.
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
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.
Jose Ángel Silva-Guillén
2016-10-01
Full Text Available Semiconducting transition metal dichalcogenides present a complex electronic band structure with a rich orbital contribution to their valence and conduction bands. The possibility to consider the electronic states from a tight-binding model is highly useful for the calculation of many physical properties, for which first principle calculations are more demanding in computational terms when having a large number of atoms. Here, we present a set of Slater–Koster parameters for a tight-binding model that accurately reproduce the structure and the orbital character of the valence and conduction bands of single layer MX 2 , where M = Mo, W and X = S, Se. The fit of the analytical tight-binding Hamiltonian is done based on band structure from ab initio calculations. The model is used to calculate the optical conductivity of the different compounds from the Kubo formula.
Stirling, András; Nair, Nisanth N; Lledós, Agustí; Ujaque, Gregori
2014-07-21
We present here a review of the mechanistic studies of the Wacker process stressing the long controversy about the key reaction steps. We give an overview of the previous experimental and theoretical studies on the topic. Then we describe the importance of the most recent Ab Initio Molecular Dynamics (AIMD) calculations in modelling organometallic reactivity in water. As a prototypical example of homogeneous catalytic reactions, the Wacker process poses serious challenges to modelling. The adequate description of the multiple role of the water solvent is very difficult by using static quantum chemical approaches including cluster and continuum solvent models. In contrast, such reaction systems are suitable for AIMD, and by combining with rare event sampling techniques, the method provides reaction mechanisms and the corresponding free energy profiles. The review also highlights how AIMD has helped to obtain a novel understanding of the mechanism and kinetics of the Wacker process.
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...
Yuryeva, E. I. [Ural Branch of the Russian Academy of Sciences, Institute of Solid State Chemistry (Russian Federation); Oshtrakh, M. I., E-mail: oshtrakh@mail.utnet.ru [Ural State Technical University - UPI, Division of Applied Biophysics, Faculty of Physical Techniques and Devices for Quality Control (Russian Federation)
2005-09-15
Ab initio X{alpha} discrete variation method was used for calculation of quadrupole splitting for the rough heme models in {alpha}- and {beta}-subunits of tetrameric deoxyhemoglobin accounting small stereochemical variations. The differences of theoretical values of quadrupole splitting for these heme models were obtained.
KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.
2014-01-01
We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421
Forssén, C.; Caurier, E.; Navrátil, P.
2009-02-01
Recently, charge radii and ground-state electromagnetic moments of Li and Be isotopes were measured precisely. We have performed large-scale ab initio no-core shell model calculations for these isotopes using high-precision nucleon-nucleon potentials. The isotopic trends of our computed charge radii and quadrupole and magnetic-dipole moments are in good agreement with experimental results with the exception of the Li11 charge radius. The magnetic moments are in particular well described, whereas the absolute magnitudes of the quadrupole moments are about 10% too small. The small magnitude of the Li6 quadrupole moment is reproduced, and with the CD-Bonn NN potential, also its correct sign.
Ab initio joint density-functional theory of solvated electrodes, with model and explicit solvation
Arias, Tomas
2015-03-01
First-principles guided design of improved electrochemical systems has the potential for great societal impact by making non-fossil-fuel systems economically viable. Potential applications include improvements in fuel-cells, solar-fuel systems (``artificial photosynthesis''), supercapacitors and batteries. Economical fuel-cell systems would enable zero-carbon footprint transportation, solar-fuel systems would directly convert sunlight and water into hydrogen fuel for such fuel-cell vehicles, supercapacitors would enable nearly full recovery of energy lost during vehicle braking thus extending electric vehicle range and acceptance, and economical high-capacity batteries would be central to mitigating the indeterminacy of renewable resources such as wind and solar. Central to the operation of all of the above electrochemical systems is the electrode-electrolyte interface, whose underlying physics is quite rich, yet remains remarkably poorly understood. The essential underlying technical challenge to the first principles studies which could explore this physics is the need to properly represent simultaneously both the interaction between electron-transfer events at the electrode, which demand a quantum mechanical description, and multiscale phenomena in the liquid environment such as the electrochemical double layer (ECDL) and its associated shielding, which demand a statistical description. A direct ab initio approach to this challenge would, in principle, require statistical sampling and thousands of repetitions of already computationally demanding quantum mechanical calculations. This talk will begin with a brief review of a recent advance, joint density-functional theory (JDFT), which allows for a fully rigorous and, in principle, exact representation of the thermodynamic equilibrium between a system described at the quantum-mechanical level and a liquid environment, but without the need for costly sampling. We then shall demonstrate how this approach applies in
Bruning, W.; Feil, D.
1992-01-01
An algorithm for calculating the scattering factors of atomic fragments in molecules as defined by the Stockholder recipe is presented. This method allows the calculation, from ab initio molecular wave functions, of structure factors including individual anisotropic atomic temperature factors. These
Resonance and Aromaticity : An Ab Initio Valence Bond Approach
Rashid, Zahid; van Lenthe, Joop H.; Havenith, Remco W. A.
2012-01-01
Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB wav
Ab-Initio Theory of Charge Transport in Organic Crystals
Hannewald, K.; Bobbert, P. A.
2005-06-01
A theory of charge transport in organic crystals is presented. Using a Holstein-Peierls model, an explicit expression for the charge-carrier mobilities as a function of temperature is obtained. Calculating all material parameters from ab initio calculations, the theory is applied to oligo-acene crystals and a brief comparison to experiment is given.
Reciprocity Theorems for Ab Initio Force Calculations
Wei, C; Mele, E J; Rappe, A M; Lewis, Steven P.; Rappe, Andrew M.
1996-01-01
We present a method for calculating ab initio interatomic forces which scales quadratically with the size of the system and provides a physically transparent representation of the force in terms of the spatial variation of the electronic charge density. The method is based on a reciprocity theorem for evaluating an effective potential acting on a charged ion in the core of each atom. We illustrate the method with calculations for diatomic molecules.
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...
Highly scalable Ab initio genomic motif identification
Marchand, Benoit
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.
Ab initio Bogoliubov coupled cluster theory
Signoracci, Angelo; Hagen, Gaute; Duguet, Thomas
2014-09-01
Coupled cluster (CC) theory has become a standard method in nuclear theory for realistic ab initio calculations of medium mass nuclei, but remains limited by its requirement of a Slater determinant reference state which reasonably approximates the nuclear system of interest. Extensions of the method, such as equation-of-motion CC, permit the calculation of nuclei with one or two nucleons added or removed from a doubly magic core, yet still only a few dozen nuclei are accessible with modern computational restrictions. In order to extend the applicability of ab initio methods to open-shell systems, the superfluid nature of nuclei must be taken into account. By utilizing Bogoliubov algebra and employing spontaneous symmetry breaking with respect to particle number conservation, superfluid systems can be treated by a single reference state. An ab initio theory to include correlations on top of a Bogoliubov reference state has been developed in the guise of standard CC theory. The formalism and first results of this Bogoliubov coupled cluster theory will be presented to demonstrate the applicability of the method.
Large-basis ab initio no-core shell model and its application to {sup 12}C
Navratil, P.; Vary, J. P.; Barrett, B. R.
2000-11-01
We present the framework for the ab initio no-core nuclear shell model and apply it to obtain properties of {sup 12}C. We derive two-body effective interactions microscopically for specific model spaces from the realistic CD-Bonn and the Argonne V8' nucleon-nucleon (NN) potentials. We then evaluate binding energies, excitation spectra, radii, and electromagnetic transitions in the 0{Dirac_h}{Omega}, 2{Dirac_h}{Omega}, and 4{Dirac_h}{Omega} model spaces for the positive-parity states and the 1{Dirac_h}{Omega}, 3{Dirac_h}{Omega}, and 5{Dirac_h}{Omega} model spaces for the negative-parity states. Dependence on the model-space size, on the harmonic-oscillator frequency, and on the type of the NN potential, used for the effective interaction derivation, are studied. In addition, electromagnetic and weak neutral elastic charge form factors are calculated in the impulse approximation. Sensitivity of the form-factor ratios to the strangeness one-body form-factor parameters and to the influence of isospin-symmetry violation is evaluated and discussed. Agreement between theory and experiment is favorable for many observables, while others require yet larger model spaces and/or three-body forces. The limitations of the present results are easily understood by virtue of the trends established and previous phenomenological results.
Ab initio phonon scattering by dislocations
Wang, Tao; Carrete, Jesús; van Roekeghem, Ambroise; Mingo, Natalio; Madsen, Georg K. H.
2017-06-01
Heat management in thermoelectric and power devices as well as in random access memories poses a grand challenge and can make the difference between a working and an abandoned device design. Despite the prevalence of dislocations in all these technologies, the modeling of their thermal resistance is based on 50-year-old analytical approximations, whose simplicity was driven by practical limitations rather than physical insight. We introduce an efficient ab initio approach based on Green's functions computed by two-dimensional reciprocal space integration. By combining elasticity theory and density functional theory, we calculate the scattering strength of a 90∘ misfit edge dislocation in Si. Because of the breakdown of the Born approximation, earlier literature models fail, even qualitatively. We find that a dislocation density larger than 109cm-2 is necessary to substantially influence thermal conductivity at room temperature and above. We quantify how much of the reduction of thermal conductivity measured in nanograined samples can be explained by realistic dislocation concentrations.
Konstantinou, Konstantinos; Sushko, Peter V; Duffy, Dorothy M
2016-09-21
The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5-(B2O3)10-(Na2O)15-(CaO)15-(MoO3)2.5 and (SiO2)57.3-(B2O3)20-(Na2O)6.8-(Li2O)13.4-(MoO3)2.5, were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations.
Olsson, Paer
2004-04-01
The efficiency of fast neutron reactors, such as for fusion, breeding and transmutation, depend strongly on the neutron radiation resistance of the materials used in the reactors. The binary Fe-Cr alloy, which has many attractive properties in this regard, is the base for the best steels of today which are, however, still not up to the required standards. Therefore, substantial effort has been devoted to finding new materials that can cope with the demands better. Experimental studies must be complemented with extensive theoretical modelling in order to understand the effects that different alloying elements has on the resistance properties of materials. To this end, the first steps of multi-scale modelling has been taken, starting out with ab initio calculations of the electronic structure of the complete concentration range range of the disordered binary Fe-C alloy. The mixing enthalpy of Fe-Cr has been quantitatively predicted and has, together with data from literature, been used in order to fit two sets of interatomic potentials for the purpose of simulating defect evolution with molecular dynamics and kinetic Monte-Carlo codes. These dedicated Fe-Cr alloy potentials are new and represent important additions to the pure element potentials that can be found in literature.
Superconductivity and its mechanism in an ab initio model for electron-doped LaFeAsO.
Misawa, Takahiro; Imada, Masatoshi
2014-12-22
Two families of high-temperature superconductors whose critical temperatures are higher than 50 K are known. One are the copper oxides and the other are the iron-based superconductors. Comparisons of mechanisms between these two in terms of common ground as well as distinctions will greatly help in searching for higher T(c) superconductors. However, studies on mechanisms for the iron family based on first principles calculations are few. Here we first show that superconductivity emerges in the state-of-the-art numerical calculations for an ab initio multi-orbital model of an electron-doped iron-based superconductor LaFeAsO, in accordance with experimental observations. Then the mechanism of the superconductivity is identified as enhanced uniform density fluctuations by one-to-one correspondence with the instability towards inhomogeneity driven by first-order antiferromagnetic and nematic transitions. Despite many differences, certain common features with the copper oxides are also discovered in terms of the underlying orbital-selective Mottness found in the iron family.
Spin-orbit decomposition of ab initio wavefunctions
Johnson, Calvin W
2014-01-01
Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum $j$, leading to $j$-$j$ coupling, phenomenological models suggested decades ago that for $0p$-shell nuclides a simpler picture can be realized via coupling of total spin $S$ and total orbital angular momentum $L$. I revisit this idea with large-basis, no-core shell model (NCSM) calculations using modern \\textit{ab initio} two-body interactions, and dissect the resulting wavefunctions into their component $L$- and $S$-components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly fifty years and six orders of magnitude in basis dimensions. I suggest $L$-$S$ may be a useful tool for analyzing \\textit{ab initio} wavefunctions of light nuclei, for example in the case of rotational bands.
Spin-orbit decomposition of ab initio nuclear wave functions
Johnson, Calvin W.
2015-03-01
Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum j , leading to j -j coupling, decades ago phenomenological models suggested that a simpler picture for 0 p -shell nuclides can be realized via coupling of the total spin S and total orbital angular momentum L . I revisit this idea with large-basis, no-core shell-model calculations using modern ab initio two-body interactions and dissect the resulting wave functions into their component L - and S -components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly 50 years and six orders of magnitude in basis dimensions. I suggest that L -S decomposition may be a useful tool for analyzing ab initio wave functions of light nuclei, for example, in the case of rotational bands.
Swerts, Ben; Chibotaru, Liviu F; Lindh, Roland; Seijo, Luis; Barandiaran, Zoila; Clima, Sergiu; Pierloot, Kristin; Hendrickx, Marc F A
2008-04-01
In this article, we present a fragment model potential approach for the description of the crystalline environment as an extension of the use of embedding ab initio model potentials (AIMPs). The biggest limitation of the embedding AIMP method is the spherical nature of its model potentials. This poses problems as soon as the method is applied to crystals containing strongly covalently bonded structures with highly nonspherical electron densities. The newly proposed method addresses this problem by keeping the full electron density as its model potential, thus allowing one to group sets of covalently bonded atoms into fragments. The implementation in the MOLCAS 7.0 quantum chemistry package of the new method, which we call the embedding fragment ab inito model potential method (embedding FAIMP), is reported here, together with results of CASSCF/CASPT2 calculations. The developed methodology is applied for two test problems: (i) the investigation of the lowest ligand field states (2)A1 and (2)B1 of the Cr(V) defect in the YVO4 crystal and (ii) the investigation of the lowest ligand field and ligand-metal charge transfer (LMCT) states at the Mn(II) substitutional impurity doped into CaCO3. Comparison with similar calculations involving AIMPs for all environmental atoms, including those from covalently bounded units, shows that the FAIMP treatment of the YVO4 units surrounding the CrO4(3-) cluster increases the excitation energy (2)B1 → (2)A1 by ca. 1000 cm(-1) at the CASSCF level of calculation. In the case of the Mn(CO3)6(10-) cluster, the FAIMP treatment of the CO3(2-) units of the environment give smaller corrections, of ca. 100 cm(-1), for the ligand-field excitation energies, which is explained by the larger ligands of this cluster. However, the correction for the energy of the lowest LMCT transition is found to be ca. 600 cm(-1) for the CASSCF and ca. 1300 cm(-1) for the CASPT2 calculation.
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.
Wong, Kin-Yiu; Xu, Yuqing; York, Darrin M
2014-06-30
Detailed understandings of the reaction mechanisms of RNA catalysis in various environments can have profound importance for many applications, ranging from the design of new biotechnologies to the unraveling of the evolutionary origin of life. An integral step in the nucleolytic RNA catalysis is self-cleavage of RNA strands by 2'-O-transphosphorylation. Key to elucidating a reaction mechanism is determining the molecular structure and bonding characteristics of transition state. A direct and powerful probe of transition state is measuring isotope effects on biochemical reactions, particularly if we can reproduce isotope effect values from quantum calculations. This article significantly extends the scope of our previous joint experimental and theoretical work in examining isotope effects on enzymatic and nonenzymatic 2'-O-transphosphorylation reaction models that mimic reactions catalyzed by RNA enzymes (ribozymes), and protein enzymes such as ribonuclease A (RNase A). Native reactions are studied, as well as reactions with thio substitutions representing chemical modifications often used in experiments to probe mechanism. Here, we report and compare results from eight levels of electronic-structure calculations for constructing the potential energy surfaces in kinetic and equilibrium isotope effects (KIE and EIE) computations, including a "gold-standard" coupled-cluster level of theory [CCSD(T)]. In addition to the widely used Bigeleisen equation for estimating KIE and EIE values, internuclear anharmonicity and quantum tunneling effects were also computed using our recently developed ab initio path-integral method, that is, automated integration-free path-integral method. The results of this work establish an important set of benchmarks that serve to guide calculations of KIE and EIE for RNA catalysis. Copyright © 2014 Wiley Periodicals, Inc.
Churakov, S.V
2005-03-01
Pyrophyllite, Al{sub 2}[Si{sub 4}O{sub 10}](OH){sub 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-OH{sub 2} 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)
Ciofi degli Atti, Claudio; Mezzetti, Chiara Benedetta; Morita, Hiko
2017-04-01
Background: Two-nucleon (2 N ) short-range correlations (SRC) in nuclei have been recently thoroughly investigated, both theoretically and experimentally and the study of three-nucleon (3 N ) SRC, which could provide important information on short-range hadronic structure, is underway. Novel theoretical ideas concerning 2 N and 3 N SRC are put forward in the present paper. Purpose: The general features of a microscopic one-nucleon spectral function which includes the effects of both 2 N and 3 N SRC and its comparison with ab initio spectral functions of the three-nucleon systems are illustrated. Methods: A microscopic and parameter-free one-nucleon spectral function expressed in terms of a convolution integral involving ab initio relative and center-of-mass (c.m.) momentum distributions of a 2 N pair and aimed at describing two- and three-nucleon short-range correlations, is obtained by using: (i) the two-nucleon momentum distributions obtained within ab initio approaches based upon nucleon-nucleon interactions of the Argonne family; (ii) the exact relation between one- and two-nucleon momentum distributions; (iii) the fundamental property of factorization of the nuclear wave function at short internucleon ranges. Results: The comparison between the ab initio spectral function of 3He and the one based upon the convolution integral shows that when the latter contains only two-nucleon short-range correlations the removal energy location of the peaks and the region around them exhibited by the ab initio spectral function are correctly predicted, unlike the case of the high and low removal energy tails; the inclusion of the effects of three-nucleon correlations brings the convolution model spectral function in much better agreement with the ab initio one; it is also found that whereas the three-nucleon short-range correlations dominate the high energy removal energy tail of the spectral function, their effects on the one-nucleon momentum distribution are almost one
Phenylalanine ab initio models for the simulation of skin natural moisturizing factor
Carvalho, B. G.; Raniero, L. J.; Martin, A. A.; Favero, P. P.
2013-04-01
In this study, we evaluated models that can be used to simulate amino acids in biological environments via density functional theory (DFT). The goal was to obtain realistic representations that combine computational economy and result quality when compared to experimental data. We increased the complexity of the models by using a model of an amino acid in a vacuum, followed by a water-solvated amino acid model. To consider pH variation, we simulated zwitterionic and nonionic amino acid configurations. The amino acid chosen for testing was phenylalanine, an aromatic amino acid present in high concentrations in the natural moisturizing factor of skin that plays a fundamental role in ultraviolet protection and vitiligo disease. To validate the models, vibrational modes and electronic properties were calculated and compared to experimental results.
Symplectic Symmetry and the Ab Initio No-Core Shell Model
Draayer, Jerry P.; Dytrych, Tomas; Sviratcheva, Kristina D.; Bahri, Chairul; /Louisiana State U.; Vary, James P.; /Iowa State U. /LLNL, Livermore /SLAC
2007-03-14
The symplectic symmetry of eigenstates for the 0{sub gs}{sup +} in {sup 16}O and the 0{sub gs}{sup +} and lowest 2{sup +} and 4{sup +} configurations of {sup 12}C that are well-converged within the framework of the no-core shell model with the JISP16 realistic interaction is examined. These states are found to project at the 85-90% level onto very few symplectic representations including the most deformed configuration, which confirms the importance of a symplectic no-core shell model and reaffirms the relevance of the Elliott SU(3) model upon which the symplectic scheme is built.
Evidence for Symplectic Symmetry in Ab Initio No-Core Shell Model Results for Light Nuclei
Dytrych, Tomas; Sviratcheva, Kristina D.; Bahri, Chairul; Draayer, Jerry P.; /Louisiana State U.; Vary, James P.; /Iowa State U. /LLNL, Livermore /SLAC
2007-04-24
Clear evidence for symplectic symmetry in low-lying states of {sup 12}C and {sup 16}O is reported. Eigenstates of {sup 12}C and {sup 16}O, determined within the framework of the no-core shell model using the JISP16 NN realistic interaction, typically project at the 85-90% level onto a few of the most deformed symplectic basis states that span only a small fraction of the full model space. The results are nearly independent of whether the bare or renormalized effective interactions are used in the analysis. The outcome confirms Elliott's SU(3) model which underpins the symplectic scheme, and above all, points to the relevance of a symplectic no-core shell model that can reproduce experimental B(E2) values without effective charges as well as deformed spatial modes associated with clustering phenomena in nuclei.
Ab Initio Study of 40Ca with an Importance Truncated No-Core Shell Model
Roth, R; Navratil, P
2007-05-22
We propose an importance truncation scheme for the no-core shell model, which enables converged calculations for nuclei well beyond the p-shell. It is based on an a priori measure for the importance of individual basis states constructed by means of many-body perturbation theory. Only the physically relevant states of the no-core model space are considered, which leads to a dramatic reduction of the basis dimension. We analyze the validity and efficiency of this truncation scheme using different realistic nucleon-nucleon interactions and compare to conventional no-core shell model calculations for {sup 4}He and {sup 16}O. Then, we present the first converged calculations for the ground state of {sup 40}Ca within no-core model spaces including up to 16{h_bar}{Omega}-excitations using realistic low-momentum interactions. The scheme is universal and can be easily applied to other quantum many-body problems.
Ab initio alpha-alpha scattering
Elhatisari, Serdar; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G
2015-01-01
Processes involving alpha particles and alpha-like nuclei comprise a major part of stellar nucleosynthesis and hypothesized mechanisms for thermonuclear supernovae. In an effort towards understanding alpha processes from first principles, we describe in this letter the first ab initio calculation of alpha-alpha scattering. We use lattice effective field theory to describe the low-energy interactions of nucleons and apply a technique called the adiabatic projection method to reduce the eight-body system to an effective two-cluster system. We find good agreement between lattice results and experimental phase shifts for S-wave and D-wave scattering. The computational scaling with particle number suggests that alpha processes involving heavier nuclei are also within reach in the near future.
An ab initio study of hydroxylated graphane
Buonocore, Francesco; Capasso, Andrea; Lisi, Nicola
2017-09-01
Graphene-based derivatives with covalent functionalization and well-defined stoichiometry are highly desirable in view of their application as functional surfaces. Here, we have evaluated by ab initio calculations the energy of formation and the phase diagram of hydroxylated graphane structures, i.e., fully functionalized graphene derivatives coordinated with -H and -OH groups. We compared these structures to different hydrogenated and non-hydrogenated graphene oxide derivatives, with high level of epoxide and hydroxyl groups functionalization. Based on our calculations, stable phases of hydroxylated graphane with low and high contents of hydrogen are demonstrated for high oxygen and hydrogen partial pressure, respectively. Stable phases of graphene oxide with a mixed carbon hybridization are also found. Notably, the synthesis of hydroxylated graphane has been recently reported in the literature.
Giant magnetoresistance An ab-initio description
Binder, J
2000-01-01
A new theoretical concept to study the microscopic origin of Giant Magnetoresistance (GMR) from first principles is presented. The method is based on ab-initio electronic structure calculations within the spin density functional theory using a Screened KORRINGA-KOHNROSTOKER method. Scattering at impurity atoms in the multilayers is described by means of a GREEN's-function method. The scattering potentials are calculated self-consistently. The transport properties are treated quasi-classically solving the BOLTZMANN equation including the electronic structure of the layered system and the anisotropic scattering. The solution of the BOLTZMANN equation is performed iteratively taking into account both scattering out and scattering in terms (vertex corrections). The method is applied to Co/Cu and Fe/Cr multilayers. Trends of scattering cross sections, residual resistivities and GMR ratios are discussed for various transition metal impurities at different positions in the Co/Cu or Fe/Cr multilayers. Furthermore the...
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-12-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor—a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.
Ab Initio 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).
SurfKin: an ab initio kinetic code for modeling surface reactions.
Le, Thong Nguyen-Minh; Liu, Bin; Huynh, Lam K
2014-10-05
In this article, we describe a C/C++ program called SurfKin (Surface Kinetics) to construct microkinetic mechanisms for modeling gas-surface reactions. Thermodynamic properties of reaction species are estimated based on density functional theory calculations and statistical mechanics. Rate constants for elementary steps (including adsorption, desorption, and chemical reactions on surfaces) are calculated using the classical collision theory and transition state theory. Methane decomposition and water-gas shift reaction on Ni(111) surface were chosen as test cases to validate the code implementations. The good agreement with literature data suggests this is a powerful tool to facilitate the analysis of complex reactions on surfaces, and thus it helps to effectively construct detailed microkinetic mechanisms for such surface reactions. SurfKin also opens a possibility for designing nanoscale model catalysts.
Effective Operators Within the Ab Initio No-Core Shell Model
Stetcu, I; Barrett, B R; Navratil, P; Vary, J P
2004-11-30
We implement an effective operator formalism for general one- and two-body operators, obtaining results consistent with the no-core shell model (NCSM) wave functions. The Argonne V8' nucleon-nucleon potential was used in order to obtain realistic wave functions for {sup 4}He, {sup 6}Li and {sup 12}C. In the NCSM formalism, we compute electromagnetic properties using the two-body cluster approximation for the effective operators and obtain results which are sensitive to the range of the bare operator. To illuminate the dependence on the range, we employ a Gaussian two-body operator of variable range, finding weak renormalization of long range operators (e.g., quadrupole) in a fixed model space. This is understood in terms of the two-body cluster approximation which accounts mainly for short-range correlations. Consequently, short range operators, such as the relative kinetic energy, will be well renormalized in the two-body cluster approximation.
Evarestov, RA
2015-01-01
This book deals with the theoretical and computational simulation of monoperiodic nanostructures for different classes of inorganic substances. These simulations are related to their synthesis and experimental studies. A theoretical formalism is developed to describe 1D nanostructures with symmetric shapes and morphologies. Three types of models are considered for this aim: (i) nanotubes (rolled from 2D nanolayers and described within the formalism of line symmetry groups); (ii) nanoribbons (obtained from 2D nanolayers by their cutting along the chosen direction of translation); (iii) nanowire
Ab Initio Approach to the Non-Perturbative Scalar Yukawa Model
Li, Yang; Maris, P; Vary, J P
2015-01-01
We report on the first non-perturbative calculation of the quenched scalar Yukawa model in the four-body Fock sector truncation. The light-front Hamiltonian approach with a Fock sector dependent renormalization is applied. We study the Fock sector contribution and the electromagnetic form factor in the non-perturbative region. We find that the one- and two-body contributions dominate the Fock space up to coupling $\\alpha\\approx 1.7$. By comparing with lower Fock sector truncations, we show that the form factor converges with respect to the Fock sector expansion. As we approach the coupling $\\alpha \\approx 2.2$, we discover that the four-body contribution rises rapidly and overtakes the two- and three-body contributions.
Ab initio approach to the non-perturbative scalar Yukawa model
Yang Li
2015-09-01
Full Text Available We report on the first non-perturbative calculation of the scalar Yukawa model in the single-nucleon sector up to four-body Fock sector truncation (one “scalar nucleon” and three “scalar pions”. The light-front Hamiltonian approach with a systematic non-perturbative renormalization is applied. We study the n-body norms and the electromagnetic form factor. We find that the one- and two-body contributions dominate up to coupling α≈1.7. As we approach the coupling α≈2.2, we discover that the four-body contribution rises rapidly and overtakes the two- and three-body contributions. By comparing with lower sector truncations, we show that the form factor converges with respect to the Fock sector expansion.
Vu, M.; Massey, M.; Huang, P.
2015-12-01
The speciation of aqueous uranium ions is an important factor in predicting its mobility and fate in the environment. Two major controls on speciation are pH and the presence of complexing ligands. For the case of aqueous uranyl, UO22+(aq), some common complexes include uranyl-hydroxy, uranyl-carbonato, and uranyl-calcium-carbonato complexes, all of which differ in chemical reactivity and mobility. Uranyl-silicate complexes are also known but remain poorly characterized. In this work, we studied uranyl speciation in a series of aqueous solutions of 0.1 mM uranyl and 2 mM silicate with pH ranging from 4 to 7. Extended X-Ray Absorption Fine Structure (EXAFS) spectra of these samples were recorded at the Stanford Synchrotron Radiation Lightsource (SLAC National Accelerator Laboratory). Of particular note are the uranyl and silicate concentrations employed in our experiments, which are lower than conditions in previously reported EXAFS studies and approach conditions in natural groundwater systems. Preliminary analyses of EXAFS data indicate that uranyl speciation changes across the pH range, consistent with published thermodynamic data that suggest uranyl-silicate complexes may be important for pH ~ 5 and below, while uranyl-carbonato complexes become dominant at circumneutral pH. To guide the interpretation of the EXAFS data, molecular-scale simulations were carried out using density functional theory. We considered two classes of models: (i) hydrated clusters, and (ii) ab initio molecular dynamics simulations of 3D-periodic models involving uranyl and silicate in water. These calculations reveal that at pH ~ 5, the uranyl speciation is the [UO2(H2O)4H3SiO4]+ complex formed by the substitution of an equatorial uranyl water with a monodentate silicate ligand. The evidence from experiments and simulations provide a consistent picture for the uranyl-silicate complex, which may be important in the transport of uranyl in acidic, silicate-rich waters.
None, None
2016-01-01
The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5 – (B2O3)10 – (Na2O)15 – (CaO)15 – (MoO3)2.5 and (SiO2)57.3 – (B2O3)20 – (Na2O)6.8 – (Li2O)13.4 – (MoO3)2.5 , were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations. K.K. was supported through the Impact Studentship scheme at UCL co-funded by the IHI Corporation and UCL. P.V.S. thanks the Royal Society, which supported preliminary work on this project, and the Laboratory Directed Research and Development program at PNNL, a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy. Via our membership of the UK's HEC Materials Chemistry Consortium, which is funded by EPSRC (EP/L000202), this work used the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk).
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.
Heats of Segregation of BCC Binaries from ab Initio and Quantum Approximate Calculations
Good, Brian S.
2004-01-01
We compare dilute-limit heats of segregation for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent LMTO-based parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation, while the ab initio calculations are performed without relaxation. Results are discussed within the context of a segregation model driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.
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.
Spin-orbit decomposition of ab initio wavefunctions
Johnson, Calvin W.
2014-01-01
Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum $j$, leading to $j$-$j$ coupling, phenomenological models suggested decades ago that for $0p$-shell nuclides a simpler picture can be realized via coupling of total spin $S$ and total orbital angular momentum $L$. I revisit this idea with large-basis, no-core shell model (NCSM) calculations using modern \\textit{ab initio} two-body interactions, and dissect the resulti...
Reply to Comment on "Ab Initio Study of 40Ca with an Importance Truncated No-Core Shell Model"
Roth, R; Navratil, P
2008-01-04
In their comment on our recent Letter [1] Dean et al. [2] criticize the calculations for the ground-state energy of {sup 40}Ca within the importance truncated no-core shell model (NCSM). In particular they address the role of configurations beyond the 3p3h level, which have not been included in the {sup 40}Ca calculations for large N{sub max} {h_bar}{Omega} model spaces. Before responding to this point, the following general statements are in order. For the atomic nucleus as a self-bound system, translational invariance is an important symmetry. The only possibility to preserve translational invariance when working with a Slater determinant basis is to use the harmonic oscillator (HO) basis in conjunction with a basis truncation according to the total HO excitation energy, i.e. N{sub max} {h_bar}{Omega}, as done in the ab initio NCSM. This is important not only for obtaining proper binding or excitation energies, but also for a correct extraction of physical wavefunctions. The spurious center-of-mass components can be exactly removed only if the HO basis and the N{sub max} {h_bar}{Omega} truncation are employed. The minimal violation of the translational invariance was one of the main motivations for developing the importance-truncation scheme introduced in the Letter. In this scheme, we start with the complete N{sub max} {h_bar}{Omega} HO basis space and select important configurations via perturbation theory. All symmetries are under control and our importance-truncated NCSM calculations are completely variational and provide an upper bound of the ground-state energy of the system. The restriction to the 3p3h level, made for computational reasons in the N{sub max} > 8 calculations for {sup 40}Ca, is not inherent to the importance truncation scheme. The explicit inclusion of 4p4h configurations--though computationally more demanding--is straight-forward, even for the largest N{sub max} {h_bar}{Omega} model spaces discussed. To demonstrate this fact we have
Castin, N.; Messina, L.; Domain, C.; Pasianot, R. C.; Olsson, P.
2017-06-01
We significantly improve the physical models underlying atomistic Monte Carlo (MC) simulations, through the use of ab initio fitted high-dimensional neural network potentials (NNPs). In this way, we can incorporate energetics derived from density functional theory (DFT) in MC, and avoid using empirical potentials that are very challenging to design for complex alloys. We take significant steps forward from a recent work where artificial neural networks (ANNs), exclusively trained on DFT vacancy migration energies, were used to perform kinetic MC simulations of Cu precipitation in Fe. Here, a more extensive transfer of knowledge from DFT to our cohesive model is achieved via the fitting of NNPs, aimed at accurately mimicking the most important aspects of the ab initio predictions. Rigid-lattice potentials are designed to monitor the evolution during the simulation of the system energy, thus taking care of the thermodynamic aspects of the model. In addition, other ANNs are designed to evaluate the activation energies associated with the MC events (migration towards first-nearest-neighbor positions of single point defects), thereby providing an accurate kinetic modeling. Because our methodology inherently requires the calculation of a substantial amount of reference data, we design as well lattice-free potentials, aimed at replacing the very costly DFT method with an approximate, yet accurate and considerably more computationally efficient, potential. The binary FeCu and FeCr alloys are taken as sample applications considering the extensive literature covering these systems.
Badaut, V.
2010-07-15
Among the many radionuclides contained in high-level nuclear waste, {sup 79}Se was identified as a potential threat to the safety of long term underground storage. However, siderite (FeCO{sub 3}) is known to form upon corrosion of the waste container, and the impact of this mineral on the fate of selenium was not accounted for. In this work, the interactions between selenium oxyanions - selenate and selenite - and siderite were investigated. To this end, both experimental characterizations (solution chemistry, X-ray Absorption Spectroscopy - XAS) and theoretical studies (ab initio modelling using Density Functional Theory - DFT) were performed. Selenite and selenate ({<=} 10{sup 3} M) retention experiments by siderite suspensions (75 g/L) at neutral pH in reducing glovebox (5 % H{sub 2}) showed that selenite is quantitatively immobilized by siderite after 48 h of reaction time, when selenate is only partly immobilized after 10 days. In the selenite case, XAS showed that immobilized selenium is initially present as Se(IV) probably sorbed on siderite surface. After 10 days of reaction, selenite ions are quantitatively reduced and form poorly crystalline elementary selenium. Selenite retention and reduction kinetics are therefore distinct. On the other hand, the fraction of immobilized selenate retained in the solid fraction does not appear to be significantly reduced over the probed timescale (10 days). For a better understanding of the reduction mechanism of selenite ions by siderite, the properties of bulk and perfect surfaces of siderite were modelled using DFT. We suggest that the properties of the valence electrons can be correctly described only if the symmetry of the fundamental state electronic density is lower than the experimental crystallographic symmetry. We then show that the retention of simple molecules as O{sub 2} or H{sub 2}O on siderite and magnesite (10{sup -14}) perfect surfaces (perfect cleavage plane, whose surface energy is the lowest according
Ab initio calculation of the Hoyle state
Epelbaum, Evgeny; Lee, Dean; Meißner, Ulf-G
2011-01-01
The Hoyle state plays a crucial role in the hydrogen burning of stars heavier than our sun and in the production of carbon and other elements necessary for life. This excited state of the carbon-12 nucleus was postulated by Hoyle^{1} as a necessary ingredient for the fusion of three alpha particles to produce carbon at stellar temperatures. Although the Hoyle state was seen experimentally more than a half century ago^{2,3}, nuclear theorists have not yet uncovered the nature of this state from first principles. In this letter we report the first ab initio calculation of the low-lying states of carbon-12 using supercomputer lattice simulations and a theoretical framework known as effective field theory. In addition to the ground state and excited spin-2 state, we find a resonance at -85(3) MeV with all of properties of the Hoyle state and in agreement with the experimentally observed energy. These lattice simulations provide insight into the structure of this unique state and new clues as to the amount of fine...
Ab initio phase diagram of iridium
Burakovsky, L.; Burakovsky, N.; Cawkwell, M. J.; Preston, D. L.; Errandonea, D.; Simak, S. I.
2016-09-01
The phase diagram of iridium is investigated using the Z methodology. The Z methodology is a technique for phase diagram studies that combines the direct Z method for the computation of melting curves and the inverse Z method for the calculation of solid-solid phase boundaries. In the direct Z method, the solid phases along the melting curve are determined by comparing the solid-liquid equilibrium boundaries of candidate crystal structures. The inverse Z method involves quenching the liquid into the most stable solid phase at various temperatures and pressures to locate a solid-solid boundary. Although excellent agreement with the available experimental data (to ≲65 GPa) is found for the equation of state (EOS) of Ir, it is the third-order Birch-Murnaghan EOS with B0'=5 rather than the more widely accepted B0'=4 that describes our ab initio data to higher pressure (P ) . Our results suggest the existence of a random-stacking hexagonal close-packed structure of iridium at high P . We offer an explanation for the 14-layer hexagonal structure observed in experiments by Cerenius and Dubrovinsky.
Phonocatalysis. An ab initio simulation experiment
Kwangnam Kim
2016-06-01
Full Text Available Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF6 on h-BN surface leads to formation of XeF4 and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.
Ab initio materials physics and microscopic electrodynamics of media
2016-01-01
We argue that the amazing progress of first-principles materials physics necessitates a revision of the Standard Approach to electrodynamics of media. We hence subject this Standard Approach to a thorough critique, which shows both its inherent conceptual problems and its practical inapplicability to modern ab initio calculations. We then go on to show that the common practice in ab initio materials physics has overcome these difficulties by taking a different, microscopic approach to electro...
Balan, Etienne; Lazzeri, M.; Mauri, F.; Calas, G.
2007-01-01
We review here some recent applications of ab initio calculations to the modelling of spectroscopic and energetic properties of minerals, which are key components of lateritic soils or govern their geochemical properties. Quantum mechanical ab initio calculations are based on density functional theory and density functional perturbation theory. Among the minerals investigated, zircon is a typical resistant primary mineral. Its resistance to weathering is at the origin of the peculiar geochemi...
Benchmarks of the ab initio FCI, MCSM and NCFC methods
Abe, T; Otsuka, T; Shimizu, N; Utsuno, Y; Vary, J P
2012-01-01
We report ab initio no-core solutions for properties of light nuclei with three different approaches in order to assess the accuracy and convergence rates of each method. Full Configuration Interaction (FCI), Monte Carlo Shell Model (MCSM) and No Core Full Configuration (NCFC) approaches are solved separately for the ground state energy and other properties of seven light nuclei using the realistic JISP16 nucleon-nucleon interaction. The results are consistent among the different approaches. The methods differ significantly in how the required computational resources scale with increasing particle number for a given accuracy.
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.
Hydrogen Desorption from Mg Hydride: An Ab Initio Study
Simone Giusepponi
2012-07-01
Full Text Available Hydrogen desorption from hydride matrix is still an open field of research. By means of accurate first-principle molecular dynamics (MD simulations an Mg–MgH2 interface is selected, studied and characterized. Electronic structure calculations are used to determine the equilibrium properties and the behavior of the surfaces in terms of structural deformations and total energy considerations. Furthermore, extensive ab-initio molecular dynamics simulations are performed at several temperatures to characterize the desorption process at the interface. The numerical model successfully reproduces the experimental desorption temperature for the hydride.
Hyla, M.
2017-01-01
Network-forming As2(S/Se)m nanoclusters are employed to recognize expected variations in a vicinity of some remarkable compositions in binary As-Se/S glassy systems accepted as signatures of optimally constrained intermediate topological phases in earlier temperature-modulated differential scanning calorimetry experiments. The ab initio quantum chemical calculations performed using the cation-interlinking network cluster approach show similar oscillating character in tendency to local chemical decomposition but obvious step-like behavior in preference to global phase separation on boundary chemical compounds (pure chalcogen and stoichiometric arsenic chalcogenides). The onsets of stability are defined for chalcogen-rich glasses, these being connected with As2Se5 ( Z = 2.29) and As2S6 ( Z = 2.25) nanoclusters for As-Se and As-S glasses, respectively. The physical aging effects result preferentially from global phase separation in As-S glass system due to high localization of covalent bonding and local demixing on neighboring As2Sem+1 and As2Sem-1 nanoclusters in As-Se system. These nanoclusters well explain the lower limits of reversibility windows in temperature-modulated differential scanning calorimetry, but they cannot be accepted as signatures of topological phase transitions in respect to the rigidity theory.
Atomistic and Ab initio modeling of CaAl2O4 high-pressure polymorphs under Earth's mantle conditions
Eremin, N. N.; Grechanovsky, A. E.; Marchenko, E. I.
2016-05-01
Semi-empirical and ab initio theoretical investigation of crystal structure geometry, interatomic distances, phase densities and elastic properties for some CaAl2O4 phases under pressures up to 200 GPa was performed. Two independent simulation methods predicted the appearance of a still unknown super-dense CaAl2O4 modification. In this structure, the Al coordination polyhedron might be described as distorted one with seven vertices. Ca atoms were situated inside polyhedra with ten vertices and Ca-O distances from 1.96 to 2.49 Å. It became the densest modification under pressures of 170 GPa (density functional theory prediction) or 150 GPa (semi-empirical prediction). Both approaches indicated that this super-dense CaAl2O4 modification with a "stuffed α-PbO2" type structure could be a probable candidate for mutual accumulation of Ca and Al in the lower mantle. The existence of this phase can be verified experimentally using high pressure techniques.
Cottom, J.; Gruber, G.; Hadley, P.; Koch, M.; Pobegen, G.; Aichinger, T.; Shluger, A.
2016-05-01
Electrically detected magnetic resonance (EDMR) is a powerful technique for the observation and categorization of paramagnetic defects within semiconductors. The interpretation of the recorded EDMR spectra has long proved to be challenging. Here, defect spectra are identified by comparing EDMR measurements with extensive ab initio calculations. The defect identification is based upon the defect symmetry and the form of the hyperfine (HF) structure. A full description is given of how an accurate spectrum can be generated from the theoretical data by considering some thousand individual HF contributions out of some billion possibilities. This approach is illustrated with a defect observed in nitrogen implanted silicon carbide (SiC). Nitrogen implantation is a high energy process that gives rise to a high defect concentration. The majority of these defects are removed during the dopant activation anneal, shifting the interstitial nitrogen to the desired substitutional lattice sites, where they act as shallow donors. EDMR shows that a deep-level defect persists after the dopant activation anneal. This defect is characterized as having a g c ∥ B = 2.0054 ( 4 ) and g c ⊥ B = 2.0006 ( 4 ) , with pronounced hyperfine shoulder peaks with a 13 G peak to peak separation. The nitrogen at a carbon site next to a silicon vacancy ( N C V Si ) center is identified as the persistent deep-level defect responsible for the observed EDMR signal and the associated dopant deactivation.
Gebrerufael, Eskendr; Hergert, Heiko; Roth, Robert
2016-01-01
We merge two successful ab initio nuclear-structure methods, the no-core shell model (NCSM) and the multi-reference in-medium similarity renormalization group (IM-SRG) to define a new many-body approach for the comprehensive description of ground and excited states of closed and open-shell nuclei. Building on the key advantages of the two methods---the decoupling of excitations at the many-body level in the IM-SRG and the access to arbitrary nuclei, eigenstates, and observables in the NCSM---their combination enables fully converged no-core calculations for an unprecedented range of nuclei and observables at moderate computational cost. We present applications in the carbon and oxygen isotopic chains, where conventional NCSM calculations are still feasible and provide an important benchmark. The efficiency and rapid convergence of the new approach make it ideally suited for ab initio studies of the complete spectroscopy of nuclei up into the medium-mass regime.
Gebrerufael, Eskendr; Vobig, Klaus; Hergert, Heiko; Roth, Robert
2017-04-14
We merge two successful ab initio nuclear-structure methods, the no-core shell model (NCSM) and the multireference in-medium similarity renormalization group (IM-SRG) to define a new many-body approach for the comprehensive description of ground and excited states of closed and open-shell nuclei. Building on the key advantages of the two methods-the decoupling of excitations at the many-body level in the IM-SRG and the access to arbitrary nuclei, eigenstates, and observables in the NCSM-their combination enables fully converged no-core calculations for an unprecedented range of nuclei and observables at moderate computational cost. We present applications in the carbon and oxygen isotopic chains, where conventional NCSM calculations are still feasible and provide an important benchmark. The efficiency and rapid convergence of the new approach make it ideally suited for ab initio studies of the complete spectroscopy of nuclei up into the medium-mass regime.
Nattino, Francesco; Galparsoro, Oihana; Costanzo, Francesca; Díez Muiño, Ricardo; Alducin, Maite; Kroes, Geert-Jan
2016-06-01
Accurately modeling surface temperature and surface motion effects is necessary to study molecule-surface reactions in which the energy dissipation to surface phonons can largely affect the observables of interest. We present here a critical comparison of two methods that allow to model such effects, namely, the ab initio molecular dynamics (AIMD) method and the generalized Langevin oscillator (GLO) model, using the dissociation of N2 on W(110) as a benchmark. AIMD is highly accurate as the surface atoms are explicitly part of the dynamics, but this advantage comes with a large computational cost. The GLO model is much more computationally convenient, but accounts for lattice motion effects in a very approximate way. Results show that, despite its simplicity, the GLO model is able to capture the physics of the system to a large extent, returning dissociation probabilities which are in better agreement with AIMD than static-surface results. Furthermore, the GLO model and the AIMD method predict very similar energy transfer to the lattice degrees of freedom in the non-reactive events, and similar dissociation dynamics.
Leszek Bober
2012-05-01
Full Text Available Pharmacological and physicochemical classification of the furan and thiophene amide derivatives by multiple regression analysis and partial least square (PLS based on semi-empirical ab initio molecular modeling studies and high-performance liquid chromatography (HPLC retention data is proposed. Structural parameters obtained from the PCM (Polarizable Continuum Model method and the literature values of biological activity (antiproliferative for the A431 cells expressed as LD_{50} of the examined furan and thiophene derivatives was used to search for relationships. It was tested how variable molecular modeling conditions considered together, with or without HPLC retention data, allow evaluation of the structural recognition of furan and thiophene derivatives with respect to their pharmacological properties.
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.
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...
Ab initio calculations of reactions of light nuclei
Hupin, Guillaume; Quaglioni, Sofia; Navrátil, Petr
2017-09-01
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 as a support tool for accurate evaluations of crucial reaction data for nuclear astrophysics, fusion-energy research, and other applications. We present an efficient many-body approach to nuclear bound and scattering states alike, known as the ab initio no-core shell model with continuum. In this approach, 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. We show that predictive results for nucleon and deuterium scattering on 4He nuclei can be obtained from the direct solution of the Schröedinger equation with modern nuclear potentials.
Liu, Haiyan; Lu, Zhenyu; Cisneros, G Andres; Yang, Weitao
2004-07-08
The determination of reaction paths for enzyme systems remains a great challenge for current computational methods. In this paper we present an efficient method for the determination of minimum energy reaction paths with the ab initio quantum mechanical/molecular mechanical approach. Our method is based on an adaptation of the path optimization procedure by Ayala and Schlegel for small molecules in gas phase, the iterative quantum mechanical/molecular mechanical (QM/MM) optimization method developed earlier in our laboratory and the introduction of a new metric defining the distance between different structures in the configuration space. In this method we represent the reaction path by a discrete set of structures. For each structure we partition the atoms into a core set that usually includes the QM subsystem and an environment set that usually includes the MM subsystem. These two sets are optimized iteratively: the core set is optimized to approximate the reaction path while the environment set is optimized to the corresponding energy minimum. In the optimization of the core set of atoms for the reaction path, we introduce a new metric to define the distances between the points on the reaction path, which excludes the soft degrees of freedom from the environment set and includes extra weights on coordinates describing chemical changes. Because the reaction path is represented by discrete structures and the optimization for each can be performed individually with very limited coupling, our method can be executed in a natural and efficient parallelization, with each processor handling one of the structures. We demonstrate the applicability and efficiency of our method by testing it on two systems previously studied by our group, triosephosphate isomerase and 4-oxalocrotonate tautomerase. In both cases the minimum energy paths for both enzymes agree with the previously reported paths.
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.
Hovell, Ian; Monte, Marisa de Mello; Coelho, Roberto Rodrigues [Centro de Tecnologia Mineral (CETEM), Rio de Janeiro, RJ (Brazil); Souza, Andre Lopes de [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Escola de Quimica
2004-07-01
In this work a proposed methodology of the characterization of organic sulphur compounds is proposed in agreement with its functionality for the elucidation of asphaltenic structures that contain sulphur. Theoretical Infrared spectra of organic sulphur compounds were modelled using quantum mechanical ab initio Hartree-Fock calculations. Using these spectra it is possible to identify the frequency corresponding to the vibrational transition of the C-S bond of the organic sulphur compounds studied. The experimental IR spectra were studied, of these same compounds, and their respective C-S bond frequencies were obtained. A good comparison was obtained when the theoretical vibrational frequencies when compared with the experimental vibrational frequencies. Finally, this proposed methodology was applied to the experimental deconvoluted DRIFTS, and theoretical spectra of an asphaltene from Brazilian VR's, with the elucidation of the organic sulphur that is present in the average molecule. (author)
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.
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.
Gas phase ion chemistry of coumarins: ab initio calculations used to ...
Gas phase ion chemistry of coumarins: ab initio calculations used to justify ... and quadrupole mass spectrometer (qMS) coupled to a gas chromatograph is ... Ab Initio calculations, Electron ionization, Positive chemical ionization, Negative ...
High-throughput ab-initio dilute solute diffusion database
Wu, Henry; Mayeshiba, Tam; Morgan, Dane
2016-07-01
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.
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 tr
Ab initio study of alanine polypeptide chain twisting
Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.
2006-01-01
chains. These particular degrees of freedom are essential for the characterization of the proteins folding process. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined...
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.
Ab initio interatomic potentials and the thermodynamic properties of fluids
Vlasiuk, Maryna; Sadus, Richard J.
2017-07-01
Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.
Bicanonical ab Initio Molecular Dynamics for Open Systems.
Frenzel, Johannes; Meyer, Bernd; Marx, Dominik
2017-08-08
Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.
Structural flexibility of DABCO. Ab initio and DFT benchmark study
Nizovtsev, Anton S.; Ryzhikov, Maxim R.; Kozlova, Svetlana G.
2017-01-01
The energy and structural parameters of 1,4-diazabicyclo[2.2.2]octane (DABCO) obtained by various DFT methods are examined versus ab initio and experimental data. The features of twisting potentials of DABCO and closely-related species (1-azabicyclo[2.2.2]octane and bicyclo[2.2.2]octane) are discussed in light of computational schemes applied.
Electron Transport through Polyene Junctions in between Carbon Nanotubes: an Ab Initio Realization
Chen, Yiing-Rei; Chen, Kai-Yu; Dou, Kun-Peng; Tai, Jung-Shen; Lee, Hsin-Han; Kaun, Chao-Cheng
With both ab initio and tight-binding model calculations, we study a system of polyene bridged armchair carbon nanotube electrodes, considering one-polyene and two-polyene cases, to address aspects of quantum transport through junctions with multiple conjugated molecules. The ab initio results of the two-polyene cases not only show the interference effect in transmission, but also the sensitive dependence of such effect on the combination of relative contact sites, which agrees nicely with the tight-binding model. Moreover, we show that the discrepancy mainly brought by ab initio relaxation provides an insight into the influence upon transmission spectra, from the junction's geometry, bonding and effective potential. This work was supported by the Ministry of Science and Technology of the Republic of China under Grant Nos. 99-2112-M-003-012-MY2 and 103-2622-E-002-031, and the National Center for Theoretical Sciences of Taiwan.
Levesque, M.
2010-11-15
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
Xu, Dong; Zhang, Jian; Roy, Ambrish; Zhang, Yang
2011-01-01
I-TASSER is an automated pipeline for protein tertiary structure prediction using multiple threading alignments and iterative structure assembly simulations. In CASP9 experiments, two new algorithms, QUARK and fragment-guided molecular dynamics (FG-MD), were added to the I-TASSER pipeline for improving the structural modeling accuracy. QUARK is a de novo structure prediction algorithm used for structure modeling of proteins that lack detectable template structures. For distantly homologous targets, QUARK models are found useful as a reference structure for selecting good threading alignments and guiding the I-TASSER structure assembly simulations. FG-MD is an atomic-level structural refinement program that uses structural fragments collected from the PDB structures to guide molecular dynamics simulation and improve the local structure of predicted model, including hydrogen-bonding networks, torsion angles, and steric clashes. Despite considerable progress in both the template-based and template-free structure modeling, significant improvements on protein target classification, domain parsing, model selection, and ab initio folding of β-proteins are still needed to further improve the I-TASSER pipeline. Copyright © 2011 Wiley-Liss, Inc.
Ventelon, L. [CEA Saclay, Dept. des Materiaux pour le Nucleaire (DEN/DANS/DMN/SRMP), 91 - Gif-sur-Yvette (France)
2008-07-01
In the framework of the multi scale simulation of metals and alloys plasticity, the aim of this study is to develop a methodology of ab initio dislocations study and to apply it to the [111] screw dislocation in the bc iron. (A.L.B.)
New ab initio based pair potential for accurate simulation of phase transitions in ZnO
Wang, Shuaiwei; Fan, Zhaochuan; Koster, Rik S.; Fang, Changming; Van Huis, Marijn A.; Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W.; Vlugt, Thijs J H
2014-01-01
A set of interatomic pair potentials is developed for ZnO based on the partially charged rigid ion model (PCRIM). The derivation of the potentials combines lattice inversion, empirical fitting, and ab initio energy surface fitting. We show that, despite the low number of parameters in this model (8)
Ab initio modeling of steady-state and time-dependent charge transport in hole-only α-NPD devices
Liu, Feilong; Massé, Andrea; Friederich, Pascal; Symalla, Franz; Nitsche, Robert; Wenzel, Wolfgang; Coehoorn, Reinder; Bobbert, Peter A.
2016-12-01
We present an ab initio modeling study of steady-state and time-dependent charge transport in hole-only devices of the amorphous molecular semiconductor α-NPD [N ,N'-Di(1 -naphthyl)-N ,N'-diphenyl-(1 ,1'-biphenyl)-4 ,4'-diamine] . The study is based on the microscopic information obtained from atomistic simulations of the morphology and density functional theory calculations of the molecular hole energies, reorganization energies, and transfer integrals. Using stochastic approaches, the microscopic information obtained in simulation boxes at a length scale of ˜10 nm is expanded and employed in one-dimensional (1D) and three-dimensional (3D) master-equation modeling of the charge transport at the device scale of ˜100 nm. Without any fit parameter, predicted current density-voltage and impedance spectroscopy data obtained with the 3D modeling are in very good agreement with measured data on devices with different α-NPD layer thicknesses in a wide range of temperatures, bias voltages, and frequencies. Similarly good results are obtained with the computationally much more efficient 1D modeling after optimizing a hopping prefactor.
The density matrix renormalization group for ab initio quantum chemistry
Wouters, Sebastian
2014-01-01
During the past 15 years, the density matrix renormalization group (DMRG) has become increasingly important for ab initio quantum chemistry. Its underlying wavefunction ansatz, the matrix product state (MPS), is a low-rank decomposition of the full configuration interaction tensor. The virtual dimension of the MPS, the rank of the decomposition, controls the size of the corner of the many-body Hilbert space that can be reached with the ansatz. This parameter can be systematically increased until numerical convergence is reached. The MPS ansatz naturally captures exponentially decaying correlation functions. Therefore DMRG works extremely well for noncritical one-dimensional systems. The active orbital spaces in quantum chemistry are however often far from one-dimensional, and relatively large virtual dimensions are required to use DMRG for ab initio quantum chemistry (QC-DMRG). The QC-DMRG algorithm, its computational cost, and its properties are discussed. Two important aspects to reduce the computational co...
High Level Ab Initio Kinetics as a Tool for Astrochemistry
Klippenstein, Stephen
2015-05-01
We will survey the application of ab initio theoretical kinetics to reactions of importance to astrochemistry. Illustrative examples will be taken from our calculations for (i) interstellar chemistry, (ii) Titan's atmospheric chemistry, and (iii) the chemistry of extrasolar giant planets. The accuracy of various aspects of the calculations will be summarized including (i) the underlying ab initio electronic structure calculations, (ii) the treatment of the high pressure recombination process, and (iii) the treatment of the pressure dependence of the kinetics. The applications will consider the chemistry of phosphorous on giant planets, the kinetics of water dimerization, the chemistry of nitrogen on Titan's atmosphere, as well as various reactions of interstellar chemistry interest such as the recombination of OH with H, and O(3P) reacting with C2H5, CH2, and CCS. Chemical Sciences and Engineering Division.
Toward the Ab-initio Description of Medium Mass Nuclei
Barbieri, C; Soma, V; Duguet, T; Navratil, P
2012-01-01
As ab-initio calculations of atomic nuclei enter the A=40-100 mass range, a great challenge is how to approach the vast majority of open-shell (degenerate) isotopes. We add realistic three-nucleon interactions to the state of the art many-body Green's function theory of closed-shells, and find that physics of neutron driplines is reproduced with very good quality. Further, we introduce the Gorkov formalism to extend ab-initio theory to semi-magic, fully open-shell, isotopes. Proof-of-principle calculations for Ca-44 and Ni-74 confirm that this approach is indeed feasible. Combining these two advances (open-shells and three-nucleon interactions) requires longer, technical, work but it is otherwise within reach.
Ab initio theories for light nuclei and neutron stars
Gezerlis, Alexandros
2016-09-01
In this talk I will touch upon several features of modern ab initio low-energy nuclear theory. I will start by discussing what ``ab initio'' means in this context. Specifically, I will spend some time going over nucleon-nucleon and three-nucleon interactions and their connections with the underlying theory of Quantum Chromodynamics. I will then show how these interactions are used to describe light nuclei using essentially exact few-body methods. I will then discuss heavier systems, especially those of astrophysical relevance, as well as the methods used to tackle them. This work was supported by the Natural Sciences and Engineering Research Council (NSERC) of Canada and the Canada Foundation for Innovation (CFI).
Study of Nuclear Clustering from an Ab Initio Perspective
Kravvaris, Konstantinos; Volya, Alexander
2017-08-01
We put forward a new ab initio approach that seamlessly bridges the structure, clustering, and reactions aspects of the nuclear quantum many-body problem. The configuration interaction technique combined with the resonating group method based on a harmonic oscillator basis allows us to treat the reaction and multiclustering dynamics in a translationally invariant way and preserve the Pauli principle. Our presentation includes studies of Be,108 and an exploration of 3 α clustering in 12C.
Ab initio calculation of tight-binding parameters
McMahan, A.K.; Klepeis, J.E.
1997-12-01
We calculate ab initio values of tight-binding parameters for the f- electron metal Ce and various phases of Si, from local-density functional one-electron Hamiltonian and overlap matrix elements. Our approach allows us to unambiguously test the validity of the common minimal basis and two-center approximations as well as to determine the degree of transferability of both nonorthogonal and orthogonal hopping parameters in the cases considered.
Uniaxial Phase Transition in Si : Ab initio Calculations
Cheng, C.
2002-01-01
Based on a previously proposed thermodynamic analysis, we study the relative stabilities of five Si phases under uniaxial compression using ab initio methods. The five phases are diamond, beta-tin, sh, sc, and hcp structures. The possible phase-transition patterns were investigated by considering the phase transitions between any two chosen phases of the five phases. By analyzing the different conributions to the relative pahse stability, we identified the most important factors in reducing t...
Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry
2015-07-15
144306 (2010)] and the cubic -‐ spline -‐fitted PES reported by Xu, Xie, Zhang, Lin, and Guo...SUBTITLE 13. SUPPLEMENTARY NOTES 12. DISTRIBUTION AVAILIBILITY STATEMENT 6. AUTHORS 7. PERFORMING ORGANIZATION NAMES AND ADDRESSES 15. SUBJECT TERMS b ...accurate global PESs and for direct dynamics simulations using interpolating moving least squares (IMLS) that guarantee high fidelity to ab initio data. A
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.
Nuclear forces and ab initio calculations of atomic nuclei
Meißner, Ulf-G.
2014-01-01
Nuclear forces and the nuclear many-body problem have been some of Gerry Brown's main topics in his so productive life as a theoretical physicist. In this talk, I outline how Gerry's work laid the foundations of the modern theory of nuclear forces and ab initio calculations of atomic nuclei. I also present some recent developments obtained in the framework of nuclear lattice simulations.
Ab initio calculation of the potential bubble nucleus 34Si
Duguet, T.; Somà, V.; Lecluse, S.; Barbieri, C.; Navrátil, P.
2017-03-01
Background: The possibility that an unconventional depletion (referred to as a "bubble") occurs in the center of the charge density distribution of certain nuclei due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. Based on a mean-field rationale, a correlation between the occurrence of such a semibubble and an anomalously weak splitting between low angular-momentum spin-orbit partners has been further conjectured. Energy density functional and valence-space shell model calculations have been performed to identify and characterize the best candidates, among which 34Si appears as a particularly interesting case. While the experimental determination of the charge density distribution of the unstable 34Si is currently out of reach, (d ,p ) experiments on this nucleus have been performed recently to test the correlation between the presence of a bubble and an anomalously weak 1 /2--3 /2- splitting in the spectrum of 35Si as compared to 37S. Purpose: We study the potential bubble structure of 34Si on the basis of the state-of-the-art ab initio self-consistent Green's function many-body method. Methods: We perform the first ab initio calculations of 34Si and 36S. In addition to binding energies, the first observables of interest are the charge density distribution and the charge root-mean-square radius for which experimental data exist in 36S. The next observable of interest is the low-lying spectroscopy of 35Si and 37S obtained from (d ,p ) experiments along with the spectroscopy of 33Al and 35P obtained from knock-out experiments. The interpretation in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input internucleon interactions. The convergence of the results with respect to the truncation of the many-body expansion, i.e., with respect to
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.
Makhov, Dmitry V; Glover, William J; Martinez, Todd J; Shalashilin, Dmitrii V
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.
Ab initio molecular dynamics using hybrid density functionals
Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost
2008-06-01
Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.
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.
Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott (Michigan); (Kansas); (HWMRI)
2012-02-13
Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-{angstrom} C{alpha} root mean square deviation [RMSD]) the high-resolution (1.8-{angstrom}) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur.
The Hydration Structure of Carbon Monoxide by Ab Initio Methods
Awoonor-Williams, Ernest
2016-01-01
The solvation of carbon monoxide (CO) in liquid water is important for understanding its toxicological effects and biochemical roles. In this paper, we use ab initio molecular dynamics (AIMD) and CCSD(T)-F12 calculations to assess the accuracy of the Straub and Karplus molecular mechanical (MM) model for CO(aq). The CCSD(T)-F12 CO--H2O potential energy surfaces show that the most stable structure corresponds to water donating a hydrogen bond to the C center. The MM-calculated surface it incorrectly predicts that the O atom is a stronger hydrogen bond acceptor than the C atom. The AIMD simulations indicate that CO is solvated like a hydrophobic solute, with very limited hydrogen bonding with water. The MM model tends to overestimate the degree of hydrogen bonding and overestimates the atomic radius of the C atom. The calculated Gibbs energy of hydration is in good agreement with experiment (9.3 kJ/mol calc. vs 10.7 kJ/mol exptl.). The calculated diffusivity of CO(aq) in TIP3P-model water was 5.19 x 10-5 cm2/s ...
Bernard, St
1998-12-31
The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H{sub 2}){sub 2} which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author) 109 refs.
Ab initio 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}.
Cosmic-Ray Modulation: an Ab Initio Approach
Engelbrecht, N. E.; Burger, R. A.
2014-10-01
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.
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.
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.
Ab initio thermodynamic results for warm dense matter
Bonitz, Michael
2016-10-01
Warm dense matter (WDM) - an exotic state where electrons are quantum degenerate and ions may be strongly correlated - is ubiquitous in dense astrophysical plasmas and highly compressed laboratory systems including inertial fusion. Accurate theoretical predictions require precision thermodynamic data for the electron gas at high density and finite temperature around the Fermi temperature. First such data have been obtained by restricted path integral Monte Carlo (restricted PIMC) simulations and transformed into analytical fits for the free energy. Such results are also key input for novel finite temperature density functional theory. However, the RPIMC data of Ref. 1 are limited to moderate densities, and even there turned out to be surprisingly inaccurate, which is a consequence of the fermion sign problem. These problems were recently overcome by the development of alternative QMC approaches in Kiel (configuration PIMC and permutation blocking PIMC) and Imperial College (Density matrix QMC). The three methods have their strengths and limitations in complementary parameter regions and provide highly accurate thermodynamic data for the electronic contributions in WDM. While the original results were obtained for small particle numbers, recently accurate finite size corrections were derived allowing to compute ab initio thermodynamic data with an unprecedented accuracy of better than 0.3 percent. This provides the final step for the use as benchmark data for experiments and models of Warm dense matter. Co-authors: T. Schoof, S. Groth, T. Dornheim, F. D. Malone, M. Foulkes, and T. Sjostroem, Funded by: DFG via SFB-TR24 and project BO1366-10.
Local Environment Distribution in Ab Initio Liquid Water
Santra, Biswajit; Distasio, Robert A., Jr.; Car, Roberto
2013-03-01
We have analyzed the distribution of local environments in liquid water at ambient conditions and its inherent potential energy surface (IPES) based on state-of-the-art ab initio molecular dynamics simulations performed on 128 molecules implementing hybrid PBE0 exchange [PRB 79, 085102 (2009)] and van der Waals (vdW) interactions [PRL 102, 073005 (2009)]. The local environments of molecules are characterized in terms of the local structure index (LSI) [JCP 104, 7671 (1996)] which is able to distinguish high- and low-density molecular environments. In agreement with simulations based on model potentials, we find that the distribution of LSI is unimodal at ambient conditions and bimodal in the IPES, consistent with the existence of polymorphism in amorphous phases of water. At ambient conditions spatial LSI fluctuations extend up to ~7 Å and their dynamical correlation decays on a time scale of ~3 ps, as found for density fluctuations in a recent study [PRL 106, 037801 (2011)]. DOE: DE-SC0008626, DOE: DE-SC0005180, NSF: CHE-0956500
Liu, Peng; Johansson, Viktor; Trilaksana, Herri; Rosdahl, Jan; Andersson, Gunther G; Kloo, Lars
2017-06-14
The organization of dye molecules in the dye layer adsorbed on the semiconductor substrate in dye-sensitized solar cells has been studied using a combination of theoretical methods and experimental techniques. The model system is based on the simple D-π-A dye L0, which has been chemically modified by substituting the acceptor group CN with Br (L0Br) to offer better X-ray contrast. Experimental EXAFS data based on the Br K-edge backscattering show no obvious difference between dye-sensitized titania powder and titania film samples, thus allowing model systems to be based on powder slurries. Ab initio molecular dynamic (aiMD) calculations have been performed to extract less biased information from the experimental EXASF data. Using the aiMD calculation as input, the EXAFS structural models can be generated a priori that match the experimental data. Our study shows that the L0Br dye adsorbs in the trans-L0Br configuration and that adsorption involves both a proximity to other L0Br dye molecules and the titanium atoms in the TiO2 substrate. These results indicate direct coordination of the dye molecules to the TiO2 surface in contrast to previous results on metal-organic dyes. The molecular coverage of L0Br on mesoporous TiO2 was also estimated using NICIS spectroscopy. The NICISS results emphasized that the L0Br dye on nanoporous titania mainly forms monolayers with a small contribution of multilayer coverage.
Ab Initio Studies of Metal Hexaboride Materials
Schmidt, Kevin M.
Metal hexaborides are refractory ceramics with several qualities relevant to materials design, such as low work functions, high hardness, low thermal expansion coefficients, and high melting points, among many other properties of interest for industrial applications. Thermal and mechanical stability is a common feature provided by the covalently-bonded network boron atoms, and electronic properties can vary significantly with the resident metal. While these materials are currently employed as electron emitters and abrasives, promising uses of these materials also include catalytic applications for chemical dissociation reactions of various molecules such as hydrogen, water and carbon monoxide, for example. However, these extensions require a thorough understanding of particular mechanical and electronic properties. This dissertation is a collection of studies focused on understanding the behavior of metal hexaboride materials using computational modeling methods to investigate materials properties of these from both classical and quantum mechanical points of view. Classical modeling is performed using molecular dynamics methods with interatomic potentials obtained from density functional theory (DFT) calculations. Atomic mean-square displacements from the quasi-harmonic approximation and lattice energetic data are produced with DFT for developing the potentials. A generalized method was also developed for the inversion of cohesive energy curves of crystalline materials; pairwise interatomic potentials are extracted using detailed geometrical descriptions of the atomic interactions and a list of atomic displacements and degeneracies. The surface structure of metal hexaborides is studied with DFT using several model geometries to describe the terminal cation layouts, and these provide a basis for further studies on metal hexaboride interactions with hydrogen. The surface electronic structure calculations show that segregated regions of metal and boron
Efficient conformational space exploration in ab initio protein folding simulation.
Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A Z M Dayem; Rahman, M Sohel
2015-08-01
Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic-polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency.
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, Ti......3C2, and Ti6C5) are found to be ground state configurations. Their stability has been verified by full-potential total energy calculations of the fully relaxed structures....
Accelerating Ab Initio Nuclear Physics Calculations with GPUs
Potter, Hugh; Maris, Pieter; Sosonkina, Masha; Vary, James; Binder, Sven; Calci, Angelo; Langhammer, Joachim; Roth, Robert; Çatalyürek, Ümit; Saule, Erik
2014-01-01
This paper describes some applications of GPU acceleration in ab initio nuclear structure calculations. Specifically, we discuss GPU acceleration of the software package MFDn, a parallel nuclear structure eigensolver. We modify the matrix construction stage to run partly on the GPU. On the Titan supercomputer at the Oak Ridge Leadership Computing Facility, this produces a speedup of approximately 2.2x - 2.7x for the matrix construction stage and 1.2x - 1.4x for the entire run.
Ab initio 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......, investigating the fundamental electronic properties of monolayer pairs. Quantitative band splittings and the electronic density are presented, along with effects of the layers’ relative alignment and comments on disordered systems, and for the first time, the effective electronic widths of such device...
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.
Ab-initio study of transition metal hydrides
Sharma, Ramesh [Dept. of Physics, Feroze Gandhi Insititute of Engineering and Technology, Raebareli-229001 (India); Shukla, Seema, E-mail: sharma.yamini62@gmail.com; Dwivedi, Shalini, E-mail: sharma.yamini62@gmail.com; Sharma, Yamini, E-mail: sharma.yamini62@gmail.com [Theoretical Condensed Matter Physics Laboratory, Dept. of Physics Feroze Gandhi College, Raebareli-229001 (India)
2014-04-24
We have performed ab initio self consistent calculations based on Full potential linearized augmented plane wave (FP-LAPW) method to investigate the optical and thermal properties of yttrium hydrides. From the band structure and density of states, the optical absorption spectra and specific heats have been calculated. The band structure of Yttrium metal changes dramatically due to hybridization of Y sp orbitals with H s orbitals and there is a net charge transfer from metal to hydrogen site. The electrical resistivity and specific heats of yttrium hydrides are lowered but the thermal conductivity is slightly enhanced due to increase in scattering from hydrogen sites.
Morphing ab initio potential energy curve of beryllium monohydride
Špirko, Vladimír
2016-12-01
Effective (mass-dependent) potential energy curves of the ground electronic states of 9BeH, 9BeD, and 9BeT are constructed by morphing a very accurate MR-ACPF ab initio potential of Koput (2011) within the framework of the reduced potential energy curve approach of Jenč (1983). The morphing is performed by fitting the RPC parameters to available experimental ro-vibrational data. The resulting potential energy curves provide a fairly quantitative reproduction of the fitted data. This allows for a reliable prediction of the so-far unobserved molecular states in terms of only a small number of fitting parameters.
A numerical ab initio study of harmonic generation from a ring-shaped model molecule in laser fields
Bauer, D
2001-01-01
When a laser pulse impinges on a molecule which is invariant under certain symmetry operations selection rules for harmonic generation (HG) arise. In other words: symmetry controls which channels are open for the deposition and emission of laser energy---with the possible application of filtering or amplification. We review the derivation of HG selection rules and study numerically the interaction of laser pulses with an effectively one-dimensional ring-shaped model molecule. The harmonic yields obtained from that model and their dependence on laser frequency and intensity are discussed. In a real experiment obvious candidates for such molecules are benzene, other aromatic compounds, or even nanotubes.
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
Resonance and aromaticity: an ab initio valence bond approach.
Rashid, Zahid; van Lenthe, Joop H; Havenith, Remco W A
2012-05-17
Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB wave function for each system was constructed using a linear combination of the VB structures (spin functions), which closely resemble the Kekulé valence structures, and two types of orbitals, that is, strictly atomic (local) and delocalized atomic (delocal) p-orbitals, were used to describe the π-system. It is found that the Pauling-Wheland's resonance energy with nonorthogonal structures decreases, while the same with orthogonalized structures and the total mean resonance energy (the sum of the weighted off-diagonal contributions in the Hamiltonian matrix of orthogonalized structures) increase when delocal orbitals are used as compared to local p-orbitals. Analysis of the interactions between the different structures of a system shows that the resonance in the 6π electrons conjugated circuits have the largest contributions to the resonance energy. The VBSCF calculations also show that the extra stability of phenanthrene, a kinked benzenoid, as compared to its linear counterpart, anthracene, is a consequence of the resonance in the π-system rather than the H-H interaction in the bay region as suggested previously. Finally, the empirical parameters for the resonance interactions between different 4n+2 or 4n π electrons conjugated circuits, used in Randić's conjugated circuits theory or Herdon's semi-emprical VB approach, are quantified. These parameters have to be scaled by the structure coefficients (weights) of the contributing structures.
Ab initio calculations of ^12C and neutron drops
Pieper, Steven C.
2009-10-01
Ab initio calculations of nuclei, which treat a nucleus as a system of A nucleons interacting by realistic two- and three-nucleon forces, have made tremendous progress in the last 15 years. This is a result of better Hamiltonians, rapidly increasing computer power, and new or improved many-body methods. Three methods are principally being used: Green's function Monte Carlo (GFMC), no-core shell model, and coupled cluster. In the limit of large computer resources, all three methods produce exact eigenvalues of a given nuclear Hamiltonian. With DOE SciDAC and INCITE support, all three methods are using the largest computers available today. Under the UNEDF SciDAC grant, the Argonne GFMC program was modified to efficiently use more than 2000 processors. E. Lusk (Argonne), R.M. Butler (Middle Tennessee State U.) and I have developed an Asynchronous Dynamic Load-Balancing (ADLB) library. In addition all the cores in a node are used via OpenMP as one ADLB/MPI client. In this way we obtain very good scalability up to 30,000 processors on Argonne's IBM Blue Gene/P. Two systems of particular interest that require this computer power are ^12C and neutron drops. V.R. Pandharipande (UIUC, deceased), J. Carlson (LANL), R.B. Wiringa (Argonne), and I have developed new trial wave functions that explicitly contain the three-alpha particle structure of ^12C. These are being used with the Argonne V18 and Illinois-7 potentials which reproduce the energies of 51 states in 3energy-density functionals.
Bernard, S.; Jollet, F.; Jomard, G.; Siberchicot, B.; Torrent, M.; Zerah, G.; Amadon, B.; Bouchet, J.; Richard, N.; Robert, G. [CEA Bruyeres-le-Chatel, 91 (France)
2005-07-01
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)
Finite Elements in Ab Initio Electronic-Structure Calulations
Pask, J. E.; Sterne, P. A.
Over the course of the past two decades, the density functional theory (DFT) (see e.g., [1]) of Hohenberg, Kohn, and Sham has proven to be an accurate and reliable basis for the understanding and prediction of a wide range of materials properties from first principles (ab initio), with no experimental input or empirical parameters. However, the solution of the Kohn-Sham equations of DFT is a formidable task and this has limited the range of physical systems which can be investigated by such rigorous, quantum mechanical means. In order to extend the interpretive and predictive power of such quantum mechanical theories further into the domain of "real materials", involving nonstoichiometric deviations, defects, grain boundaries, surfaces, interfaces, and the like; robust and efficient methods for the solution of the associated quantum mechanical equations are critical. The finite-element (FE) method (see e.g., [2]) is a general method for the solution of partial differential and integral equations which has found wide application in diverse fields ranging from particle physics to civil engineering. Here, we discuss its application to large-scale ab initio electronic-structure calculations.
Ho, Ming-Hsun; Rousseau, Roger; Roberts, John A. S.; Wiedner, Eric S.; Dupuis, Michel; DuBois, Daniel L.; Bullock, R. Morris; Raugei, Simone
2015-09-04
Design of fast, efficient electrocatalysts for energy production and energy utilization requires a systematic approach to predict and tune the energetics of reaction intermediates and the kinetic barriers between them as well as to tune reaction conditions (e.g., concentration of reactants, acidity of the reaction medium, and applied electric potential). Thermodynamics schemes based on the knowledge of pKa values, hydride donor ability, redox potentials, and other relevant thermodynamic properties have been demonstrated to be very effective for exploring possible reaction pathways. We seek to identify high-energy intermediates, which may represent a catalytic bottleneck, and low-energy intermediates, which may represent a thermodynamic sink. In this study, working on a well-established Ni-based bioinspired electrocatalyst for H2 production, we performed a detailed kinetic analysis of the catalytic pathways to assess the limitations of our current (standard state) thermodynamic analysis with respect to prediction of optimal catalyst performance. To this end, we developed a microkinetic model based on extensive ab initio simulations. The model was validated against available experimental data, and it reproduces remarkably well the observed turnover rate as a function of the acid concentration and catalytic conditions, providing valuable information on the main factors limiting catalysis. Using this kinetic analysis as a reference, we show that indeed a purely thermodynamic analysis of the possible reaction pathways provides us with valuable information, such as a qualitative picture of the species involved during catalysis, identification of the possible branching points, and the origin of the observed overpotential, which are critical insights for electrocatalyst design. However, a significant limitation of this approach is understanding how these insights relate to rate, which is an equally critical piece of information. Taking our analysis a step further, we show
Whitfield, T. W.; Crain, J.; Martyna, G. J.
2006-03-01
In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.
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.
2013-02-01
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%.
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
2013-02-27
: 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%.
Optical and other material properties of SiO2 from ab initio studies
Warmbier, Robert; Mohammed, Faris; Quandt, Alexander
2014-07-01
The optical properties of photonic devices largely depend on the dielectric properties of the underlying materials. We apply modern ab initio methods to study crystalline SiO2 phases, which serve as toy models for amorphous glass. We discuss the dielectric response from the infrared to the VIS/UV, which is crucial for glass based photonic applications. Low density silica, like cristobalite, may provide a good basis for high transmission optical devices.
Lattice dynamics of wurtzite CdS: Neutron scattering and ab-initio calculations
Debernardi, A.; Pyka, N. M.; Göbel, A.; Ruf, T.; Lauck, R.; Kramp, S.; Cardona, M.
1997-08-01
We have measured the phonon dispersion of wurtzite CdS by inelastic neutron scattering in a single crystal made from the nonabsorbing isotope 114Cd. One of the two silent B 1-modes occurs at 3.96 THz ( k = 0 ). It is significantly lower and less dispersive than so far assumed. Previous semiempirical lattice dynamical models need to be reanalyzed. However, the observed dispersion branches compare favorably with an ab-initio calculation.
Ab initio molecular dynamics simulations of the Li4F4 cluster
Heidenreich, A.; Sauer, J.
1995-12-01
Molecular dynamics simulations have been performed directly on the ab initio potential energy surface of Li4F4, which was generated within the Hartree-Fock approximation using a Gaussian basis set (split valence contraction). Trajectories at different temperatures yield the temperature dependence of the infrared spectra and the photoelectron spectra. For the infrared spectra comparison is made with MD results using a shell model ion pair potential function.
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)
{\\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...
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.
Ab initio calculations on the magnetic properties of transition metal complexes
Bodenstein, Tilmann; Fink, Karin [Karlsruhe Institute of Technology, Institute of Nanotechnology, POB 3640, 76021 Karlsruhe (Germany)
2015-12-31
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.
Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi
2004-01-01
An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.
Ab initio nuclear structure and reactions with chiral three-body forces
Langhammer, Joachim; Roth, Robert; Calci, Angelo [Institut fuer Kernphysik - Theoriezentrum, TU Darmstadt (Germany); Navratil, Petr [TRIUMF, Vancouver (Canada)
2014-07-01
One major ambition of ab initio nuclear theory is the description of nuclear-structure and reaction observables on equal footing. This is accomplished by combining the no-core shell model (NCSM) with the resonating-group method (RGM) to a unified ab initio approach to bound and continuum states, which is developed further to the no-core shell model with continuum (NCSMC). We present the formal developments to include three-nucleon interactions in both the NCSM/RGM and NCSMC formalism. This provides the possibility to assess the predictive power of chiral two- and three-nucleon forces in the variety of scattering observables. We study three-nucleon force effects on phase-shifts, cross sections and analyzing powers in first ab-initio studies of nucleon-{sup 4}He scattering with chiral two- and three-nucleon forces. Finally, we focus on heavier target nuclei using the NCSMC, e.g., in neutron-{sup 8}Be scattering and study the impact of the continuum on the spectrum of {sup 9}Be.
Ab initio study of alanine polypeptide chains twisting
Solovyov, I A; Solovyov, A V; Yakubovitch, A V; Greiner, Walter; Solov'yov, Andrey V.; Solov'yov, Ilia A.; Yakubovitch, Alexander V.
2005-01-01
We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable corres...
A Review on Ab Initio Approaches for Multielectron Dynamics
Ishikawa, Kenichi L
2015-01-01
In parallel with the evolution of femtosecond and attosecond laser as well as free-electron laser technology, a variety of theoretical methods have been developed to describe the behavior of atoms, molecules, clusters, and solids under the action of those laser pulses. Here we review major ab initio wave-function-based numerical approaches to simulate multielectron dynamics in atoms and molecules driven by intense long-wavelength and/or ultrashort short-wavelength laser pulses. Direct solution of the time-dependent Schr\\"odinger equation (TDSE), though its applicability is limited to He, ${\\rm H}_2$, and Li, can provide an exact description and has been greatly contributing to the understanding of dynamical electron-electron correlation. Multiconfiguration self-consistent-field (MCSCF) approach offers a flexible framework from which a variety of methods can be derived to treat both atoms and molecules, with possibility to systematically control the accuracy. The equations of motion of configuration interactio...
Ab initio Molecular Dynamics Study on Small Carbon Nanotubes
叶林晖; 刘邦贵; 王鼎盛
2001-01-01
Ab initio molecular dynamics simulations are performed on small single wall nanotubes. By structural relaxation,the equilibrium C-C bond lengths and bond angles are determined. Our result shows that for both zigzag and armchair nanotubes there are two nonequivalent bond lengths. One bond stretches from that of the graphene sheet, while the other shrinks. Small variations on bond angles are also shown. Energy bands are calculated for the optimized structures. It is found that the intrinsic curvature of the very small nanotube greatly modifies the energy band which can no longer be well described in the tight-binding zone-folding picture. In our calculation very small nanotubes are metallic. The energy per atom fits quite well with the relation of E(R) = E0 + f/R2 even for the extreme small radius. The implications of the results on the properties of small nanotubes are discussed.
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...
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.
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.
Ab initio dynamical exchange interactions in frustrated antiferromagnets
Simoni, Jacopo; Stamenova, Maria; Sanvito, Stefano
2017-08-01
The ultrafast response to an optical pulse excitation of the spin-spin exchange interaction in transition metal antiferromagnets is studied within the framework of the time-dependent spin-density functional theory. We propose a formulation for the full dynamical exchange interaction, which is nonlocal in space, and it is derived starting from ab initio arguments. Then, we investigate the effect of the laser pulse on the onset of the dynamical process. It is found that we can distinguish two types of excitations, both activated immediately after the action of the laser pulse. While the first one can be associated to a Stoner-like excitation and involves the transfer of spin from one site to another, the second one is related to the ultrafast modification of a Heisenberg-like exchange interaction and can trigger the formation of spin waves in the first few hundred femtoseconds of the time evolution.
Ab initio investigation of the mechanical properties of copper
Liu Yue-Lin; Gui Li-Jiang; Jin Shuo
2012-01-01
Employing the ab initio total energy method based on the density functional theory with the generalized gradient approximation,we have systematically investigated the theoretical mechanical properties of copper (Cu).The theoretical tensile strengths are calculated to be 25.3 GPa,5.9 GPa,and 37.6 GPa for the fcc Cu single crystal in the [001],[110],and [111] directions,respectively.Among the three directions,the [110] direction is the weakest one due to the occurrence of structure transition at the lower strain and the weakest interaction of atoms between the (110) planes,while the [111] direction is the strongest direction because of the strongest interaction of atoms between the (111) planes.In terms of the elastic constants of Cu single crystal,we also estimate some mechanical quantities of polycrystalline Cu,including bulk modulus B,shear modulus G,Young's modulus Ep,and Poisson's ratio v.
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)
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.
The ab-initio density matrix renormalization group in practice.
Olivares-Amaya, Roberto; Hu, Weifeng; Nakatani, Naoki; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic
2015-01-21
The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.
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.
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.
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...
Geng, Hua Y.
2015-02-01
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model-the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of rs = 0.912.
A NASSOUR
2016-09-01
In the present paper, an empirical embedded atom method (EAM) potential for gold–silicon (Au–Si) is developed by fitting to ab initio force (the ‘force matching’ method) and experimental data. The force database is generated within ab initio molecular dynamics (AIMD). The database includes liquid phase at various temperatures. Classical molecular dynamics simulations are performed to examine structural, coordination numbers, structure factors and dynamic properties of Au$_{81}$Si$_{19}$ alloy, with the interaction described via EAM model. The results are in good agreement with AIMD simulations and experimental data.
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.
Ab initio path integral ring polymer molecular dynamics: Vibrational spectra of molecules
Shiga, Motoyuki; Nakayama, Akira
2008-01-01
The path integral ring polymer molecular dynamics method is combined with 'on-the-fly' ab initio electronic structure calculations and applied to vibrational spectra of small molecules, LiH and H 2O, at the room temperature. The results are compared with those of the numerically exact solution and ab initio path integral centroid molecular dynamics calculation. The peak positions in the calculated spectra are found to be reasonable, showing the red-shift due to potential anharmonicity. This unification enables the investigation of real-time quantum dynamics of chemically complex molecular systems on the ab initio Born-Oppenheimer potential energy surface.
Ab initio many-body calculations of the 4He photo-absorption cross section
Schuster, Micah D; Johnson, Calvin W; Jurgenson, Eric D; Navratil, Petr
2013-01-01
A major goal of nuclear theory is to make quantitative calculations of low-energy nuclear observables starting from microscopic internucleon forces. Computationally, this is complicated by the large model spaces needed to reach convergence in many-body approaches, such as the no-core shell model (NCSM). In recent years, the similarity renormalization group (SRG) has provided a powerful and versatile means to soften interactions for ab initio structure calculations, thus leading to convergence within smaller model spaces. Here we compute the 4He total photo absorption cross section and study, for the first time, the consistency of the SRG approach in a continuum observable.
Messina, Luca; Castin, Nicolas; Domain, Christophe; Olsson, Pär
2017-02-01
The quality of kinetic Monte Carlo (KMC) simulations of microstructure evolution in alloys relies on the parametrization of point-defect migration rates, which are complex functions of the local chemical composition and can be calculated accurately with ab initio methods. However, constructing reliable models that ensure the best possible transfer of physical information from ab initio to KMC is a challenging task. This work presents an innovative approach, where the transition rates are predicted by artificial neural networks trained on a database of 2000 migration barriers, obtained with density functional theory (DFT) in place of interatomic potentials. The method is tested on copper precipitation in thermally aged iron alloys, by means of a hybrid atomistic-object KMC model. For the object part of the model, the stability and mobility properties of copper-vacancy clusters are analyzed by means of independent atomistic KMC simulations, driven by the same neural networks. The cluster diffusion coefficients and mean free paths are found to increase with size, confirming the dominant role of coarsening of medium- and large-sized clusters in the precipitation kinetics. The evolution under thermal aging is in better agreement with experiments with respect to a previous interatomic-potential model, especially concerning the experiment time scales. However, the model underestimates the solubility of copper in iron due to the excessively high solution energy predicted by the chosen DFT method. Nevertheless, this work proves the capability of neural networks to transfer complex ab initio physical properties to higher-scale models, and facilitates the extension to systems with increasing chemical complexity, setting the ground for reliable microstructure evolution simulations in a wide range of alloys and applications.
Zhang, Yang
2014-02-01
We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. Copyright © 2013 Wiley Periodicals, Inc.
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
Ab initio quasiparticle energies in 2H, 4H, and 6H SiC
Ummels, R. T. M.; Bobbert, P. A.; van Haeringen, W.
1998-09-01
Ab initio quasiparticle energies are calculated for the 2H, 4H, and 6H polytypes of SiC within the GW approximation for the self-energy. The starting point is a calculation within the pseudopotential local-density approximation framework. The calculated fundamental gaps of 3.15, 3.35, and 3.24 eV for 2H, 4H, and 6H SiC, respectively, show very good agreement with experimental data. The energy dependence of the screened interaction is modeled by a plasmon pole model from which the plasmon band structures are obtained.
Ab initio study of the thermopower of biphenyl-based single-molecule junctions
Bürkle, M.; Zotti, L. A.; Viljas, J. K.; Vonlanthen, D.; Mishchenko, A.; Wandlowski, T.; Mayor, M.; Schön, G.; Pauly, F.
2012-09-01
By employing ab initio electronic-structure calculations combined with the nonequilibrium Green's function technique, we study the dependence of the thermopower Q on the conformation in biphenyl-based single-molecule junctions. For the series of experimentally available biphenyl molecules, alkyl side chains allow us to gradually adjust the torsion angle ϕ between the two phenyl rings from 0∘ to 90∘ and to control in this way the degree of π-electron conjugation. Studying different anchoring groups and binding positions, our theory predicts that the absolute values of the thermopower decrease slightly towards larger torsion angles, following an a+bcos2ϕ dependence. The anchoring group determines the sign of Q and a,b simultaneously. Sulfur and amine groups give rise to Q,a,b>0, while for cyano, Q,a,bbinding positions can lead to substantial variations of the thermopower mostly due to changes in the alignment of the frontier molecular orbital levels and the Fermi energy. We explain our ab initio results in terms of a π-orbital tight-binding model and a minimal two-level model, which describes the pair of hybridizing frontier orbital states on the two phenyl rings. The variations of the thermopower with ϕ seem to be within experimental resolution.
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....
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.
Ab initio simulations of pseudomorphic silicene and germanene bidimensional heterostructures
Debernardi, Alberto; Marchetti, Luigi
2016-06-01
Among the novel two-dimensional (2D) materials, silicene and germanene, which are two honeycomb crystal structures composed of a monolayer of Si and Ge, respectively, have attracted the attention of material scientists because they combine the advantages of the new 2D ultimate-scaled electronics with their compatibility with industrial processes presently based on Si and Ge. We envisage pseudomorphic lateral heterostructures based on ribbons of silicene and germanene, which are the 2D analogs of conventional 3D Si/Ge superlattices and quantum wells. In spite of the considerable lattice mismatch (˜4 % ) between free-standing silicene and germanene, our ab initio simulations predict that, considering striped 2D lateral heterostructures made by alternating silicene and germanene ribbons of constant width, the silicene/germanene junction remains pseudomorphic—i.e., it maintains lattice-matched edges—up to critical ribbon widths that can reach some tens of nanometers. Such critical widths are one order of magnitude larger than the critical thickness measured in 3D pseudomorphic Si/Ge heterostructures and the resolution of state-of-the-art lithography, thus enabling the possibility of lithography patterned silicene/germanene junctions. We computed how the strain produced by the pseudomorphic growth modifies the crystal structure and electronic bands of the ribbons, providing a mechanism for band-structure engineering. Our results pave the way for lithography patterned lateral heterostructures that can serve as the building blocks of novel 2D electronics.
Ab initio studies of niobium defects in uranium
Xiang, S; Huang, H; Hsiung, L
2007-06-01
Uranium (U), with the addition of small amount of niobium (Nb), is stainless. The Nb is fully miscible with the high temperature phase of U and tends to segregate upon cooling below 647 C. The starting point of segregation is the configuration of Nb substitutional or interstitial defects. Using density-functional-theory based ab initio calculations, the authors find that the formation energy of a single vacancy is 1.08 eV, that of Nb substitution is 0.59 eV, that of Nb interstitial at octahedral site is 1.58 eV, and that of Nb interstitial at tetrahedral site is 2.35 eV; all with reference to a reservoir of {gamma} phase U and pure Nb. The formation energy of Nb defects correlates with the local perturbation of electron distribution; higher formation energy to larger perturbation. Based on this study, Nb atoms thermodynamically prefer to occupy substitutional sites in {gamma} phase U, and they prefer to be in individual substitutional defects than clusters.
Melting curves of metals by ab initio calculations
Minakov, Dmitry; Levashov, Pavel
2015-06-01
In this work we used several ab initio approaches to reproduce melting curves and discussed their abilities, advantages and drawbacks. We used quasiharmonic appoximation and Lindemann criterion to build melting curves in wide region of pressures. This approach allows to calculate the total free energy of electrons and phonons, so it is possible to obtain all thermodynamic properties in the crystalline state. We also used quantum molecular dynamics simulations to investigate melting at various pressures. We explored the size-effect of the heat until it melts (HUM) method in detail. Special attention was paid to resolve the boundaries of the melting region on density. All calculations were performed for aluminum, copper and gold. Results were in good agreement with available experimental data. Also we studied the influence of electronic temperature on melting curves. It turned out that the melting temperature increased with the rise of electron temperature at normal density and had non-monotonic behavior at higher densities. This work is supported by the Ministry of Education and Science of the Russian Federation (Project No. 3.522.2014/K).
An efficient approach to ab initio Monte Carlo simulation.
Leiding, Jeff; Coe, Joshua D
2014-01-21
We present a Nested Markov chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, was used to substantially decorrelate configurations at which the potential of interest was evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure was maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature β(0)), which was otherwise unconstrained. Local density approximation results are presented for shocked states of argon at pressures from 4 to 60 GPa, where-depending on the quality of the reference system potential-acceptance probabilities were enhanced by factors of 1.2-28 relative to unoptimized NMC. The optimization procedure compensated strongly for reference potential shortcomings, as evidenced by significantly higher speedups when using a reference potential of lower quality. The efficiency of optimized NMC is shown to be competitive with that of standard ab initio molecular dynamics in the canonical ensemble.
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.)
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.
Ab initio calculation of the potential bubble nucleus $^{34}$Si
Duguet, T; Lecluse, S; Barbieri, C; Navrátil, P
2016-01-01
The possibility that an unconventional depletion in the center of the charge density distribution of certain nuclei occurs due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. We report on ab initio self-consistent Green's function calculations of one of such candidates, $^{34}$Si, together with its Z+2 neighbour $^{36}$S. Binding energies, rms radii and density distributions of the two nuclei as well as low-lying spectroscopy of $^{35}$Si, $^{37}$S, $^{33}$Al and $^{35}$P are discussed. The interpretation of one-nucleon removal and addition spectra in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input inter-nucleon interactions. The prediction regarding the (non-)existence of the bubble structure in $^{34}$Si varies significantly with the nuclear Hamiltonian used. However, demandin...
Rational design of electrolyte components by ab initio calculations
Johansson, Patrik; Jacobsson, Per [Department of Applied Physics, Chalmers University of Technology, SE-412 96 Goeteborg (Sweden)
2006-02-28
This paper is a small review of the use of computer simulations and especially the use of standard quantum-mechanical ab initio electronic structure calculations to rationally design and investigate different choices of chemicals/systems for lithium battery electrolytes. Covered systems and strategies to enhance the performance of electrolytes will range from assisting the interpretation of vibrational spectroscopy experiments over development of potentials for molecular dynamics simulations, to the design of new lithium salts and the lithium ion coordination in liquid, polymer, and gel polymer electrolytes. Examples of studied properties include the vibrational spectra of anions and ion pairs to characterize the nature and extent of the interactions present, the lithium ion affinities of anions, important for the salt solvation and the ability to provide a high concentration of charge carriers, the HOMO energies of the anions to estimate the stability versus oxidation, the anion volumes that correlate to the anion mobility, the lithium ion coordination and dynamics to reveal the limiting steps of lithium ion transport, etc. (author)
Ab initio predictions of the symmetry energy and recent constraints
Sammarruca, Francesca
2017-01-01
The symmetry energy plays a crucial role in the structure and the dynamics of neutron-rich systems, including the formation of neutron skins, the location of neutron drip lines, as well as intriguing correlations with the structure of compact stars. With experimental efforts in progress or being planned to shed light on the less known aspects of the nuclear chart, microscopic predictions based on ab initio approaches are very important. In recent years, chiral effective field theory has become popular because of its firm connection with quantum chromodynamics and its systematic approach to the development of nuclear forces. Predictions of the symmetry energy obtained from modern chiral interactions will be discussed in the light of recent empirical constraints extracted from heavy ion collisions at 400 MeV per nucleon at GSI. Applications of our equations of state to neutron-rich systems will also be discussed, with particular emphasis on neutron skins, which are sensitive to the density dependence of the symmetry energy.
Ab initio calculations of the absorption spectrum of chalcone
Oumi, Manabu; Maurice, David; Head-Gordon, Martin
1999-03-01
The excitation energies and excited states of trans-chalcone ( trans-( s-cis)-1,3-diphenylpropenone), and several related molecules ( trans-( s-cis)-3-phenylpropenal, s-cis-1-phenylpropenone, propenal, trans-( s-cis)-1-(4-hydroxyphenyl)-3-phenylpropenone, trans-( s-cis)3-(4-hydroxyphenyl)-1-phenylpropenone) have been calculated using single reference ab initio molecular orbital methods, and characterized by attachment-detachment density analysis. The results suggest assignments for the lowest three electronic transitions observed experimentally for trans-( s-cis)-chalcone in solution. The extent of localization of the electronic transitions is established by calculations on the excited states of trans-( s-cis)-3-phenylpropenal, s-cis-1-phenylpropenone and propenal, as well as analysis of the chalcone calculations. Contrary to some previous work, none of these excitations are strongly delocalized over the entire molecule. Calculated substituent shifts for the hydroxy chalcones are in qualitative agreement with experimental data, and support the localized interpretation of the main π→ π* transition.
Local structure analysis in ab initio liquid water
Santra, Biswajit; DiStasio, Robert A., Jr.; Martelli, Fausto; Car, Roberto
2015-09-01
Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion (vdW) interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively agrees with experiment. In this work, we have used the local structure index (LSI) order parameter to analyse the local structure in such highly accurate ab initio liquid water. At ambient conditions, the LSI probability distribution, P(I ), was unimodal with most water molecules characterised by more disordered high-density-like local environments. With thermal excitations removed, the resultant bimodal P(I ) in the inherent potential energy surface (IPES) exhibited a 3:1 ratio between high-density- and low-density-like molecules, with the latter forming small connected clusters amid the predominant population. By considering the spatial correlations and hydrogen bond network topologies among water molecules with the same LSI identities, we demonstrate that the signatures of the experimentally observed low- and high-density amorphous phases of ice are present in the IPES of ambient liquid water. Analysis of the LSI autocorrelation function uncovered a persistence time of ∼ 4 ps - a finding consistent with the fact that natural thermal fluctuations are responsible for transitions between these distinct yet transient local aqueous environments in ambient liquid water.
An ab initio Non-Equilibrium Green Function Approach to Charge Transport: Dithiolethine
Alexander Schnurpfeil; SONG Bo; Martin Albrecht
2006-01-01
@@ We present a novel ab initio non-equilibrium approach to calculate the current across a molecular junction. The method rests on a wavefunction-based full ab initio description of the central region of the junction combined with a tight binding approximation for the electrodes in the frame of the Keldysh Green function formalism. Our procedure is demonstrated for a dithiolethine molecule located between silver electrodes. The main conducting channel is identified and the full current-voltage characteristic is calculated.
Fowler, P. W.; Peebles, S. A.; Legon, A. C.; Sadlej, A. J.
1996-07-01
The generalised polarisabilities describing the response to an applied field of the electric field gradients at the nuclei of BrCl are calculated ab initio using the correlated CCSD(T) method with relativistic corrections estimated by the Douglas-Kroll 'no-pair' model. The magnitudes of 86.9 and 42.3 α0-1 for the electric field derivatives of the gradients at Br and Cl include substantial and opposing correlation and relativistic corrections amounting to -12% and -16% of the respective non-relativistic self-consistent-field values. Relevance of the calculations to the Townes-Dailey model of the measured nuclear quadrupole coupling constants of complexes B ⋯ BrCl of BrCl with a base B is discussed.
Accurate calculation of the p Ka of trifluoroacetic acid using high-level ab initio calculations
Namazian, Mansoor; Zakery, Maryam; Noorbala, Mohammad R.; Coote, Michelle L.
2008-01-01
The p Ka value of trifluoroacetic acid has been successfully calculated using high-level ab initio methods such as G3 and CBS-QB3. Solvation energies have been calculated using CPCM continuum model of solvation at the HF and B3-LYP levels of theory with various basis sets. Excellent agreement with experiment (to within 0.4 p Ka units) was obtained using CPCM solvation energies at the B3-LYP/6-31+G(d) level (or larger) in conjunction with CBS-QB3 or G3 gas-phase energies of trifluoroacetic acid and its anion.
S. Tolosa
2013-01-01
Full Text Available A procedure for the theoretical study of chemical reactions in solution by means of molecular dynamics simulations of aqueous solution at infinite dilution is described using ab initio solute-solvent potentials and TIP3P water model to describe the interactions. The procedure is applied to the study of neutral hydrolysis of various molecules (HCONH2, HNCO, HCNHNH2, and HCOOCH3 via concerted and water-assisted mechanisms. We used the solvent as a reaction coordinate and the free energy curves for the calculation of the properties related with the reaction mechanism, namely, reaction and activation energies.
Charge carrier motion in disordered conjugated polymers: a multiscale ab-initio study
Vukmirovic, Nenad; Wang, Lin-Wang
2009-11-10
We developed an ab-initio multiscale method for simulation of carrier transport in large disordered systems, based on direct calculation of electronic states and electron-phonon coupling constants. It enabled us to obtain the never seen before rich microscopic details of carrier motion in conjugated polymers, which led us to question several assumptions of phenomenological models, widely used in such systems. The macroscopic mobility of disordered poly(3- hexylthiophene) (P3HT) polymer, extracted from our simulation, is in agreement with experimental results from the literature.
Curchod, Basile F. E.; Rauer, Clemens; Marquetand, Philipp; González, Leticia; Martínez, Todd J.
2016-03-01
Full multiple spawning is a formally exact method to describe the excited-state dynamics of molecular systems beyond the Born-Oppenheimer approximation. However, it has been limited until now to the description of radiationless transitions taking place between electronic states with the same spin multiplicity. This Communication presents a generalization of the full and ab initio multiple spawning methods to both internal conversion (mediated by nonadiabatic coupling terms) and intersystem crossing events (triggered by spin-orbit coupling matrix elements) based on a spin-diabatic representation. The results of two numerical applications, a model system and the deactivation of thioformaldehyde, validate the presented formalism and its implementation.
Nechaev, I. A.; Krasovskii, E. E.
2016-11-01
We present a method to microscopically derive a small-size k .p Hamiltonian in a Hilbert space spanned by physically chosen ab initio spinor wave functions. Without imposing any complementary symmetry constraints, our formalism equally treats three- and two-dimensional systems and simultaneously yields the Hamiltonian parameters and the true Z2 topological invariant. We consider bulk crystals and thin films of Bi2Se3 , Bi2Te3 , and Sb2Te3 . It turns out that the effective continuous k .p models with open boundary conditions often incorrectly predict the topological character of thin films.
Ab initio research on DNA base alkylation by the β-position metabolite of methylethylnitrosamine
ZHAO Lijiao; ZHONG Rugang; YUAN Xiaolong; CUI Yasong; DAI Qianhuan
2004-01-01
Ab initio calculation is carried out to study the different supposed mechanisms of DNA base alkylation by β-sulphate-nitrosamines at RHF/6-31G(d) and MP2/6-31G(d)levels. Full geometric structure optimization is done for all reactants, intermediates, products and transition states. The activation energy and IRC are obtained. The results show that the anchimeric assistant effect promotes the alkylation of DNA base by β-sulphate-nitrosamines. Solvent calculation is carried out with Onsager model of SCRF method at the same level. The results indicate that the activation energy is decreased obviously in water.
Ashcraft, Robert W; Raman, Sumathy; Green, William H
2007-10-18
Ab initio molecular orbital calculations were performed and thermochemical parameters estimated for 46 species involved in the oxidation of hydroxylamine in aqueous nitric acid solution. Solution-phase properties were estimated using the several levels of theory in Gaussian03 and using COSMOtherm. The use of computational chemistry calculations for the estimation of physical properties and constants in solution is addressed. The connection between the pseudochemical potential of Ben-Naim and the traditional standard state-based thermochemistry is shown, and the connection of these ideas to computational chemistry results is established. This theoretical framework provides a basis for the practical use of the solution-phase computational chemistry estimates for real systems, without the implicit assumptions that often hide the nuances of solution-phase thermochemistry. The effect of nonidealities and a method to account for them is also discussed. A method is presented for estimating the solvation enthalpy and entropy for dilute aqueous solutions based on the solvation free energy from the ab initio calculations. The accuracy of the estimated thermochemical parameters was determined through comparison with (i) enthalpies of formation in the gas phase and in solution, (ii) Henry's law data for aqueous solutions, and (iii) various reaction equilibria in aqueous solution. Typical mean absolute deviations (MAD) for the solvation free energy in room-temperature water appear to be ~1.5 kcal/mol for most methods investigated. The MAD for computed enthalpies of formation in solution was 1.5-3 kcal/mol, depending on the methodology employed and the type of species (ion, radical, closed-shell) being computed. This work provides a relatively simple and unambiguous approach that can be used to estimate the thermochemical parameters needed to build detailed ab initio kinetic models of systems in aqueous solution. Technical challenges that limit the accuracy of the estimates are
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...
Thermodynamic assessment of the Ho–Te system supported by ab initio calculations
Ghamri, H.; Belgacem-Bouzida, A. [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria); Djaballah, Y., E-mail: ydjaballah@yahoo.fr [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria); Hidoussi, A. [Laboratoire d’étude Physico-Chimique des Matériaux, Département de Physique, Faculté des Sciences, Université de Batna, Rue Chahid Boukhlouf, 05000 Batna (Algeria)
2013-03-05
Highlights: ► We calculated enthalpies of formation of the HoTe and Ho{sub 2}Te{sub 5} compounds by using ab initio method. ► We modeled the Gibbs energy of the HoTe intermediate phase for the first time. ► The thermodynamic parameters of the all phases existing in the system were determined. ► The complete phase diagram of the system (Ho–Te) is calculated. -- Abstract: The phase diagram of the Ho–Te binary system has been assessed by using the CALPHAD (Calculation of Phase Diagrams) method on the basis of the experimental data of the phase equilibria and enthalpies of formation from ab initio electronic-structure calculations within the framework of density-functional theory. Reasonable models were constructed for all the phases of the system. The liquid phase was described as the substitutional solution model with excess energy expressed by Redlich–Kister polynomial. The compounds Ho{sub 2}Te{sub 5} and HoTe{sub 3} were expressed as stoichiometric phases. The (HoTe) phase was modeled by two-sublattices; (Ho,Va){sub 1}(Te){sub 1}. A consistent set of thermodynamic parameters has been derived, and calculated phase diagram was compared with the experimental data. A good agreement between the calculated results and experimental data was obtained.
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.
Aupiais, J; Bonin, L; Den Auwer, C; Moisy, P; Siberchicot, B; Topin, S
2016-03-07
In the case of an accidental nuclear event, contamination of human bodies by actinide elements may occur. Such elements have the particularity to exhibit both radiological and chemical toxicities that may induce severe damages at several levels, depending on the biokinetics of the element. In order to eliminate the actinide elements before they are stored in target organs (liver, kidneys, or bone, depending on the element), sequestering agents must be quickly injected. However, to date, there is still no ideal sequestering agent, despite the recent interest in this topic due to contamination concerns. DTPA (diethylene triamine pentaacetic acid) is currently generating interest for the development of oral or alternative self-administrable forms. Although biokinetics data are mostly available, molecular scale characterization of actinide-DTPA complexes is still scarce. Nevertheless, strong interest is growing in the characterization of An(IV)DTPA(-) complexes at the molecular level because this opens the way for predicting the stability constants of unknown systems or even for developing new analytical strategies aimed at better and more selective decorporation. For this purpose, Extended X-ray Absorption Fine Structure (EXAFS) and Ab Initio Molecular Dynamics (AIMD) investigations were undertaken and compared with capillary electrophoresis (CE) used in a very unusual way. Indeed, it is commonly believed that CE is incapable of extracting structural information. In capillary electrophoresis, the electrophoretic mobility of an ion is a function of its charge and size. Despite very similar ratios, partial separations between An(IV)DTPA(-) species (An(IV) = Th, U, Np, Pu) were obtained. A linear relationship between the electrophoretic mobility and the actinide--oxygen distance calculated by AIMD was evidenced. As an example, the interpolated U-O distances in U(IV)DTPA(-) from CE-ICPMS experiments, EXAFS, AIMD, and the relationship between the stability constants and
Ab initio calculations of the optical properties of crystalline and liquid InSb
Sano, Haruyuki, E-mail: h-sano@ishikawa-nct.ac.jp [National Institute of Technology, Ishikawa College, Kitacyujo, Tsubata, Ishikawa 929-0392 (Japan); Mizutani, Goro [School of Materials Science, Japan Advanced Institute of Science and Technology, Tatsunokuchi, Ishikawa 923-1292 (Japan)
2015-11-15
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.
Ab initio molecular dynamics study of collective dynamics in liquid Tl: Thermo-viscoelastic analysis
Bryk, Taras; Demchuk, Taras
2017-08-01
We studied collective dynamics of pure liquid metal Tl using a combination of ab initio molecular dynamics (AIMD) simulations and a thermoviscoelastic model applied to calculations of dynamic eigenmodes and dispersion of collective excitations in particular. We found that for liquid Tl at ambient pressure the transverse current spectral functions obtained directly in ab initio simulations for wave numbers larger than first pseudo-Brillouin-zone boundary contain two low-and high-frequency peaks that is an evidence of emergence of the unusually high-frequency transverse modes as it was observed before in liquid Li at very high pressures. The thermo-viscoelastic dynamic model shows perfect reproduction of the simulation-derived longitudinal current autocorrelation functions, and the acoustic eigenmodes are in nice agreement with the peaks of the longitudinal current spectral functions up to the first pseudo-Brillouin-zone boundary. The deviation of the dynamic eigenmodes from peak positions at higher wave numbers gives evidence of L-T coupling effects.
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}.
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...
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.
Ulian, Gianfranco; Valdrè, Giovanni, E-mail: giovanni.valdre@unibo.it [Dipartimento di Scienze Biologiche e Geologico-Ambientali, Centro di Ricerca Interdisciplinare di Biomineralogia, Cristallografia e Biomateriali, Università di Bologna “Alma Mater Studiorum” Piazza di Porta San Donato 1, 40126 Bologna (Italy); Tosoni, Sergio [Departament de Química Física and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, C/ Martí i Franquès 1, E-08028 Barcelona (Spain)
2013-11-28
The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, and phonon properties of a model layer silicate, talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO/B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum.
Kihara, D; Lu, H; Kolinski, A; Skolnick, J
2001-08-28
The successful prediction of protein structure from amino acid sequence requires two features: an efficient conformational search algorithm and an energy function with a global minimum in the native state. As a step toward addressing both issues, a threading-based method of secondary and tertiary restraint prediction has been developed and applied to ab initio folding. Such restraints are derived by extracting consensus contacts and local secondary structure from at least weakly scoring structures that, in some cases, can lack any global similarity to the sequence of interest. Furthermore, to generate representative protein structures, a reduced lattice-based protein model is used with replica exchange Monte Carlo to explore conformational space. We report results on the application of this methodology, termed TOUCHSTONE, to 65 proteins whose lengths range from 39 to 146 residues. For 47 (40) proteins, a cluster centroid whose rms deviation from native is below 6.5 (5) A is found in one of the five lowest energy centroids. The number of correctly predicted proteins increases to 50 when atomic detail is added and a knowledge-based atomic potential is combined with clustered and nonclustered structures for candidate selection. The combination of the ratio of the relative number of contacts to the protein length and the number of clusters generated by the folding algorithm is a reliable indicator of the likelihood of successful fold prediction, thereby opening the way for genome-scale ab initio folding.
Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei
Dytrych, T. [Academy of Sciences of the Czech Republic (ASCR), Prague (Czech Republic); Louisiana State Univ., Baton Rouge, LA (United States); Maris, Pieter [Iowa State Univ., Ames, IA (United States); Launey, K. D. [Louisiana State Univ., Baton Rouge, LA (United States); Draayer, J. P. [Louisiana State Univ., Baton Rouge, LA (United States); Vary, James [Iowa State Univ., Ames, IA (United States); Langr, D. [Czech Technical Univ., Prague (Czech Republic); Aerospace Research and Test Establishment, Prague (Czech Republic); Saule, E. [Univ. of North Carolina, Charlotte, NC (United States); Caprio, M. A. [Univ. of Notre Dame, IN (United States); Catalyurek, U. [The Ohio State Univ., Columbus, OH (United States). Dept. of Electrical and Computer Engineering; Sosonkina, M. [Old Dominion Univ., Norfolk, VA (United States)
2016-06-09
We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for ^{6}Li and ^{12}C in large harmonic oscillator model spaces and SU(3)-selected subspaces. We demonstrate LSU3shell's strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and signi cant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis a ords memory savings in calculations of states with a fixed total angular momentum in large model spaces while exactly preserving translational invariance.
Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei
Dytrych, T; Launey, K D; Draayer, J P; Vary, J P; Langr, D; Saule, E; Caprio, M A; Catalyurek, U; Sosonkina, M
2016-01-01
We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for 6Li and 12C in large harmonic oscillator model spaces and SU(3)-selected subspaces. We demonstrate LSU3shell's strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and significant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis affords memory savings in calculations of states with a fixed total angular momentum in large model spaces while exactly preserving translational invariance.
Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei
Dytrych, T.; Maris, P.; Launey, K. D.; Draayer, J. P.; Vary, J. P.; Langr, D.; Saule, E.; Caprio, M. A.; Catalyurek, U.; Sosonkina, M.
2016-10-01
We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for 6Li and 12C in large harmonic oscillator model spaces and SU3-selected subspaces. We demonstrate LSU3shell's strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and significant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis affords memory savings in calculations of states with a fixed total angular momentum in large model spaces while exactly preserving translational invariance.
Wiengarten, Tobias; Engelbrecht, Eugene; Fichtner, Horst; Kleimann, Jens; Scherer, Klaus
2016-01-01
We extend a two-component model for the evolution of fluctuations in the solar wind plasma so that it is fully three-dimensional (3D) and also coupled self-consistently to the large-scale magnetohydrodynamic (MHD) equations describing the background solar wind. The two classes of fluctuations considered are a high-frequency parallel-propagating wave-like piece and a low-frequency quasi-two-dimensional component. For both components, the nonlinear dynamics is dominanted by quasi-perpendicular spectral cascades of energy. Driving of the fluctuations, by, for example, velocity shear and pickup ions, is included. Numerical solutions to the new model are obtained using the Cronos framework, and validated against previous simpler models. Comparing results from the new model with spacecraft measurements, we find improved agreement relative to earlier models that employ prescribed background solar wind fields. Finally, the new results for the wave-like and quasi-two-dimensional fluctuations are used to calculate ab i...
Ionescu, Andrei R; Whitfield, Dennis M; Zgierski, Marek Z; Nukada, Tomoo
2006-12-29
We present a constrained ab initio molecular dynamics method that allows the modeling of the conformational interconversions of glycopyranosyl oxacarbenium ions. The model was successfully tested by estimating the barriers to ring inversion for two 4-substituted tetrahydropyranosyl oxacarbenium ions. The model was further extended to predict the pathways that connect the (4)H(3) half-chair conformation of 2,3,4,6-tetra-O-methyl-d-glucopyranosyl cation to its inverted (5)S(1) conformation and the (4)H(3) half-chair conformation of 2,3,4,6-tetra-O-methyl-d-mannopyranosyl cation to its inverted (3)E conformation. The modeled interconversion pathways reconcile a large body of experimental work on the acid-catalyzed hydrolysis of glycosides and the mechanisms of a number of glucosidases and mannosidases.
Prediction of toxicity of nitrobenzenes using ab initio and least squares support vector machines
Niazi, Ali [Department of Chemistry, Faculty of Sciences, Azad University of Arak, Arak (Iran, Islamic Republic of)], E-mail: ali.niazi@gmail.com; Jameh-Bozorghi, Saeed; Nori-Shargh, Davood [Department of Chemistry, Faculty of Sciences, Azad University of Arak, Arak (Iran, Islamic Republic of)
2008-03-01
A quantitative structure-property relationship (QSPR) study is suggested for the prediction of toxicity (IGC{sub 50}) of nitrobenzenes. Ab initio theory was used to calculate some quantum chemical descriptors including electrostatic potentials and local charges at each atom, HOMO and LUMO energies, etc. Modeling of the IGC{sub 50} of nitrobenzenes as a function of molecular structures was established by means of the least squares support vector machines (LS-SVM). This model was applied for the prediction of the toxicity (IGC{sub 50}) of nitrobenzenes, which were not in the modeling procedure. The resulted model showed high prediction ability with root mean square error of prediction of 0.0049 for LS-SVM. Results have shown that the introduction of LS-SVM for quantum chemical descriptors drastically enhances the ability of prediction in QSAR studies superior to multiple linear regression and partial least squares.
Ab initio study of perovskite type oxide materials for solid oxide fuel cells
Lee, Yueh-Lin
2011-12-01
Perovskite type oxides form a family of materials of significant interest for cathodes and electrolytes of solid oxide fuel cells (SOFCs). These perovskites not only are active catalysts for surface oxygen reduction (OR) reactions but also allow incorporating the spilt oxygen monomers into their bulk, an unusual and poorly understood catalytic mechanism that couples surface and bulk properties. The OR mechanisms can be influenced strongly by defects in perovskite oxides, composition, and surface defect structures. This thesis work initiates a first step in developing a general strategy based on first-principles calculations for detailed control of oxygen vacancy content, transport rates of surface and bulk oxygen species, and surface/interfacial reaction kinetics. Ab initio density functional theory methods are used to model properties relevant for the OR reactions on SOFC cathodes. Three main research thrusts, which focus on bulk defect chemistry, surface defect structures and surface energetics, and surface catalytic properties, are carried to investigate different level of material chemistry for improved understanding of key physics/factors that govern SOFC cathode OR activity. In the study of bulk defect chemistry, an ab initio based defect model is developed for modeling defect chemistry of LaMnO 3 under SOFC conditions. The model suggests an important role for defect interactions, which are typically excluded in previous defect models. In the study of surface defect structures and surface energetics, it is shown that defect energies change dramatically (1˜2 eV lower) from bulk values near surfaces. Based on the existing bulk defect model with the calculated ab initio surface defect energetics, we predict the (001) MnO 2 surface oxygen vacancy concentration of (La0.9Sr0.1 )MnO3 is about 5˜6 order magnitude higher than that of the bulk under typical SOFC conditions. Finally, for surface catalytic properties, we show that area specific resistance, oxygen
Becerra Romero, David Camilo
2010-01-01
La tesis se enfoca en el problema de la predicción de estructuras de proteínas, uno de los problemas más importantes abordados por la bioinformática y la biología molecular. El problema básico consiste en la predicción de la estructura tridimensional de una proteína dada su secuencia de amino-ácidos. De forma particular, en éste trabajo se presenta una aproximación ab-initio, multi-objetivo y paralela para la predicción de estructuras de proteínas a un nivel atómico. El modelo propuesto incor...
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...
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.
Virtual synthesis of crystals using ab initio MD: Case study on LiFePO4
Mishra, S. B.; Nanda, B. R. K.
2017-05-01
Molecular dynamics simulation technique is fairly successful in studying the structural aspects and dynamics of fluids. Here we study the ability of ab initio molecular dynamics (ab initio MD) to carry out virtual experiments to synthesize new crystalline materials and to predict their structures. For this purpose the olivine phosphate LiFePO4 (LFPO) is used as an example. As transition metal oxides in general are stabilized with layered geometry, we carried out ab initio MD simulations over a hypothetical layered configuration consisting of alternate LiPO2 and FeO2 layers. With intermittent steps of electron minimization, the resulted equilibrium lattice consist of PO4 tetrahedra and distorted Fe-O complexes similar to the one observed in the experimental lattice.
Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11.
Zhang, Wenxuan; Yang, Jianyi; He, Baoji; Walker, Sara Elizabeth; Zhang, Hongjiu; Govindarajoo, Brandon; Virtanen, Jouko; Xue, Zhidong; Shen, Hong-Bin; Zhang, Yang
2016-09-01
We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score = 0.736 and RMSD = 2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline, weakly scoring threading templates are re-ordered by the structural similarity to the ab initio folding models, which are then reassembled by I-TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I-TASSER pipeline with a TM-score above 0.4. The robustness of the I-TASSER pipeline can stem from the composite fragment-assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long-range beta-strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. Proteins 2016; 84(Suppl 1):76-86. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.
The Ab Initio Studies of NO Chemisorption on TiO2(110) Surface
无
1999-01-01
The studies of NO chemisorption on TiO2(110) surface are the base of research to NO decomposed to N2O on TiO2 surface. In this paper, 12 kinds of possible models of NO adsorbed on TiO2 perfect and defect surface were calculated by use of ab initio cluster method. We carried out optimization of the geometry, calculation of the chemisorption energy and analysis of the Mulliken population to those adsorption models. According to the calculation results, it can be got that the adsorbed decomposition of NO on defect surface is more advantageous and M6 and M12 are the important models to NO chemisorption and decomposition on TiO2 surface.
Ab initio determination of coarse-grained interactions in double stranded DNA
Hsu, Chia Wei; Fyta, Maria; Lakatos, Greg; Melchionna, Simone; Kaxiras, Efthimios
2012-02-01
We derive the coarse-grained interactions between DNA nucleotides from ab initio calculations using density functional theory (DFT). The interactions take into account the base and sequence specificity, and are decomposed into physically distinct contributions. The interactions energies calculated from DFT for a wide range of configurations are fitted to simple analytical expressions for use in the coarse-grained model, which reduces each nucleotide into two sites. This non-empirical model accurately yields structural properties of B-DNA even in extreme conditions, and predicts persistence length in excellent agreement with experiments. The model enables quantitative an efficient investigations of the dynamics of long DNA strands in various environments, making it possible to reach microsecond time scales and beyond.
Binding of TNT to amplifying fluorescent polymers: an ab initio and molecular dynamics study.
Enlow, Mark A
2012-03-01
Molecular modeling techniques were employed to study the interaction of trinitrotoluene with an amplifying fluorescent polymer used in explosive sensor devices. The pentiptycene moiety present in these polymers appears to be the most energetically favorable binding site for trinitrotoluene. Surface features of the polymer suggest that the small cavity feature of the pentiptycene moiety may be more available for binding to analyte compounds due to steric crowding about the large cavity. Binding energies between model binding sites of the polymer and various analyte compounds were more rigorously estimated by semiempirical and ab initio techniques. Binding energies were found to be largest with trinitrotoluene and other nitroaromatic compounds. Electrostatic and π-stacking interactions between trinitrotoluene and the model host were investigated by studying a series of modified host compounds.
Valencia, Hubert; Kangawa, Yoshihiro; Kakimoto, Koichi
2015-12-01
GaAs(100) c(4×4) surfaces were examined by ab initio calculations, under As2, H2 and N2 gas mixed conditions as a model for GaAs1-xNx vapor-phase epitaxy (VPE) on GaAs(100). Using a simple model consisting of As2 and H2 molecules adsorptions and As/N atom substitutions, it was shown to be possible to examine the crystal growth behavior considering the relative stability of the resulting surfaces against the chemical potential of As2, H2 and N2 gases. Such simple model allows us to draw a picture of the temperature and pressure stability domains for each surfaces that can be linked to specific growth conditions, directly. We found that, using this simple model, it is possible to explain the different N-incorporation regimes observed experimentally at different temperatures, and to predict the transition temperature between these regimes. Additionally, a rational explanation of N-incorporation ratio for each of these regimes is provided. Our model should then lead to a better comprehension and control of the experimental conditions needed to realize a high quality VPE of GaAs1-xNx.
Valencia, Hubert; Kangawa, Yoshihiro; Kakimoto, Koichi
2017-06-01
Using ab initio calculations, a simple model for GaAs1-xNx vapor-phase epitaxy on (100) surface of GaAs was created. By studying As2 and H2 molecules adsorptions and As/N atom substitutions on (100) GaAs surfaces, we obtain a relative stability diagram of all stable surfaces under varying As2, H2, and N2 conditions. We previously proved that this model could describe the vapor-phase epitaxy of GaAs1-x Nx with simple, fully decomposed, precursors. In this paper, we show that in more complex reaction conditions using monomethylhydrazine (MMHy), and dimethylhydrazine (DMHy), it is still possible to use our model to obtain an accurate description of the temperature and pressure stability domains for each surfaces, linked to chemical beam epitaxy (CBE) growth conditions. Moreover, the different N-incorporation regimes observed experimentally at different temperature can be explain and predict by our model. The use of MMHy and DMHy precursors can also be rationalized. Our model should then help to better understand the conditions needed to obtain an high quality GaAs1-xNx using vapor-phase epitaxy.
Ramos de Debiaggi, S., E-mail: susana.ramos@fain.uncoma.edu.ar [Facultad de Ingeniería, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquén (Argentina); Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas – CONICET-UNCo (Argentina); González Lemus, N.V. [Facultad de Ingeniería, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquén (Argentina); Deluque Toro, C. [Grupo de Nuevos Materiales, Universidad de la Guajira, Riohacha (Colombia); Fernández Guillermet, A. [CONICET - Instituto Balseiro, Centro Atómico Bariloche, Avda. Bustillo 9500, 8400 Bariloche (Argentina)
2015-01-15
Highlights: • A DFT study of the compounds involved in CALPHAD modeling of the Ni–In–Sn (hP6) phase. • Several three-sublattice compounds of Ni, In, Sn and vacancies are studied ab initio. • Structural, cohesive and thermodynamic properties and the electronic DOS are reported. • Trends in calculated properties are correlated with changes in electronic structure. • A picture of the chemical bonding trends for these s-p/d type compounds is discussed. - Abstract: The thermodynamic modeling of non-stoichiometric, multisublattice intermetallic phases using the Compound-Energy Formalism (CEF) involves the determination of parameters representing the Gibbs energy (G{sub m}) of binary compounds, the so-called “end-member compounds” (EMCs), which are often metastable or hypothetical. In current CALPHAD (i.e., “Calculation of Phase Diagrams”) work, these quantities are treated as free parameters to be determined by searching for the best fit to the available information in the optimization procedure. The general purpose of this paper is to propose a theoretical approach to the study of the EMCs which makes use of density-functional-theory (DFT) ab initio calculations. The present method is applied to the EMCs involved in the CEF modeling of the non-stoichiometric (hP6) Ni{sub 2}In-structure type phase of the Ni–In and Ni–In–Sn systems using the three-sublattice models (Ni){sub 1}(Ni,Va){sub 1}(In,Ni){sub 1} and (Ni,Va){sub 1}(Ni,Va){sub 1}(In,Ni,Sn){sub 1}, respectively. By means of systematic ab initio projected augmented waves (PAW) calculations using the VASP code we study the EMCs involved in the CEF formulations of the G{sub m} for this phase in the binary and the ternary systems. Specifically, we study the twelve EMCs corresponding to the following sublattice occupations: (Ni){sub 1}(Ni){sub 1}(In){sub 1}, which is usually described as Ni:Ni:In (i.e., a compound with formula “Ni{sub 2}In”), Ni:Ni:Ni (i.e., “Ni{sub 3}”), Ni:Ni:Sn (
X-ray absorption Debye-Waller factors from ab initio molecular dynamics
Vila, F. D.; Lindahl, V. E.; Rehr, J. J.
2012-01-01
An ab initio equation of motion method is introduced to calculate the temperature-dependent mean-square vibrational amplitudes σ2 which appear in the Debye-Waller factors in x-ray absorption, x-ray scattering, and related spectra. The approach avoids explicit calculations of phonon modes, and is based instead on calculations of the displacement-displacement time correlation function from ab initio density functional theory molecular dynamics simulations. The method also yields the vibrational density of states and thermal quantities such as the lattice free energy. Illustrations of the method are presented for a number of systems and compared with other methods and experiment.
Ab Initio Calculation on Self-Assembled Base-Functionalized Single-Walled Carbon Nanotubes
SONG Chen; XIA Yue-Yuan; ZHAO Ming-Wen; LIU Xiang-Dong; LI Ji-Ling; LI Li-Juan; LI Feng; HUANG Bo-Da
2006-01-01
@@ We perform ab initio calculations on the self-assembled base-functionalized single-walled carbon nanotubes (SWNTs) which exhibit the quasi-1D ‘ladder’ structure. The optimized configuration in the ab initio calculation is very similar to that obtainedfrom molecular dynamics simulation. We also calculate the electronic structures of the self-assembled base-functionalized SWNTs that exhibit distinct difference from the single-branch base-functionalized SWNT with a localized state lying just below the Fermi level, which may result from the coupling interaction between the bases accompanied by the self-assembly behaviour.
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......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...
Ab initio quantum-enhanced optical phase estimation using real-time feedback control
Berni, Adriano; Gehring, Tobias; Nielsen, Bo Melholt
2015-01-01
as demonstrated in a variety of different optical systems(3-8). Most of these accounts, however, deal with the measurement of a very small shift of an already known phase, which is in stark contrast to ab initio phase estimation where the initial phase is unknown(9-12). Here, we report on the realization...... of a quantum-enhanced and fully deterministic ab initio phase estimation protocol based on real-time feedback control. Using robust squeezed states of light combined with a real-time Bayesian adaptive estimation algorithm, we demonstrate deterministic phase estimation with a precision beyond the quantum shot...
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 orien......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...
Lopuszynski, Michal; Majewski, Jacek A.
2007-01-01
We present theoretical studies for the third-order elastic constants $C_{ijk}$ in zinc-blende nitrides AlN, GaN, and InN. Our predictions for these compounds are based on detailed ab initio calculations of strain-energy and strain-stress relations in the framework of the density functional theory. To judge the computational accuracy, we compare the ab initio calculated results for $C_{ijk}$ with experimental data available for Si and GaAs. We also underline the relation of the third-order ela...
An ab initio study on single electron transfer between ClO2 and phenol
崔崇威; 黄君礼
2004-01-01
The SET mechanism between chlorine dioxide (ClO2 ) and phenol was studied by using ab initio method at 4-31G* level. Geometries of the reactants, intermediate and products of the reaction were optimized and the single point energy calculations of the species were performed. The relative structure data of the reactants, intermediate and products are given. The SET mechanism between ClO2 and phenol was confirmed by ab initio calculations. The reaction is exothermic about 200. 88 k J/mol.
Ab initio theory of charge-carrier conduction in ultrapure organic crystals
Hannewald, K.; Bobbert, P. A.
2004-08-01
We present an ab initio description of charge-carrier mobilities in organic molecular crystals of high purity. Our approach is based on Holstein's original concept of small-polaron bands but generalized with respect to the inclusion of nonlocal electron-phonon coupling. By means of an explicit expression for the mobilities as a function of temperature in combination with ab initio calculations of the material parameters, we demonstrate the predictive power of our theory by applying it to naphthalene. The results show a good qualitative agreement with experiment and provide insight into the difference between electron and hole mobilities as well as their peculiar algebraic and anisotropic temperature dependencies.
2001-01-01
The adsorption of H And S2- species on Pd (100) has been studied with ab initio, density-functional calculations and electrochemical methods. A cluster of five Pd atoms with a frozen geometry described the surface. The computational calculations were performed through the GAUSSIAN94 program, and the basis functions adapted to a pseudo-potential obtained by using the Generator Coordinate Method adapted to the this program. Using the cyclic voltammetry technique through a Model 283 Potentiostat...
Many-body ab initio study of antiferromagnetic {Cr7M } molecular rings
Chiesa, A.; Carretta, S.; Santini, P.; Amoretti, G.; Pavarini, E.
2016-12-01
Antiferromagnetic molecular rings are widely studied both for fundamental quantum-mechanical issues and for technological applications, particularly in the field of quantum information processing. Here we present a detailed first-principles study of two families—purple and green—of {Cr7M } antiferromagnetic rings, where M is a divalent transition metal ion (M =Ni2 + , Mn2 +, and Zn2 +). We employ a recently developed flexible and efficient scheme to build ab initio system-specific Hubbard models. From such many-body models we systematically derive the low-energy effective spin Hamiltonian for the rings. Our approach allows us to calculate isotropic as well as anisotropic terms of the spin Hamiltonian, without any a priori assumption on its form. For each compound we calculate magnetic exchange couplings, zero-field splitting tensors, and gyromagnetic tensors, finding good agreement with experimental results.
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.
A-dependence of the Spectra of the F Isotopes from ab initio Calculations
Barrett, Bruce R.; Dikmen, Erdal; Maris, Pieter; Vary, James P.; Shirokov, Andrey M.
2016-03-01
Using a succession of Okubo-Lee-Suzuki transformations within the No Core Shell Model (NCSM) formalism, we derive an ab initio, non-perturbative procedure for calculating the input for standard shell-model (SSM) calculations within one major shell. We have used this approach for calculating the spectra of the F isotopes from A=18 to A=25, so as to study the A-dependence of the results. In particular, we are interested in seeing if the theoretical input is weak enough, so that a single set of two-body effective interactions can be used for all of the F isotopes investigated. We will present results from SSM calculations based on input obtained with the JISP16 nucleon-nucleon interaction in an initial 4 ℏΩ NCSM basis space. This work supported in part by TUBITAK-BIDEB, the US DOE, the US NSF, NERSC, and the Russian Ministry of Education and Science.
Ab initio determination of coarse-grained interactions in double-stranded DNA
Hsu, Chia Wei; Fyta, Maria; Lakatos, Greg; Melchionna, Simone; Kaxiras, Efthimios
2012-09-01
We derive the coarse-grained interactions between DNA nucleotides from ab initio total-energy calculations based on density functional theory (DFT). The interactions take into account base and sequence specificity, and are decomposed into physically distinct contributions that include hydrogen bonding, stacking interactions, backbone, and backbone-base interactions. The interaction energies of each contribution are calculated from DFT for a wide range of configurations and are fitted by simple analytical expressions for use in the coarse-grained model, which reduces each nucleotide into two sites. This model is not derived from experimental data, yet it successfully reproduces the stable B-DNA structure and gives good predictions for the persistence length. It may be used to realistically probe dynamics of DNA strands in various environments at the μs time scale and the μm length scale.
reaxFF Reactive Force Field for Disulfide Mechanochemistry, Fitted to Multireference ab Initio Data.
Müller, Julian; Hartke, Bernd
2016-08-09
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.
HCO+ dissociation in a strong laser field: An ab initio classical trajectory study
Lee, Suk Kyoung; Li, Wen; Bernhard Schlegel, H.
2012-05-01
We have investigated the photodissociation of HCO+ in a strong field with a wavelength of 10 μm using ab initio molecular dynamics. Classical trajectories were calculated at three field intensities. At 2.9 × 1014 W/cm2 and phase ϕ = 0, protons have two distinct dissociation times, mainly due to the reorientation of HCO+ relative to the field direction prior to dissociation. The kinetic energy distribution at this intensity agrees with Wardlaw's wagging tail model, suggesting that dissociation occurs through barrier-suppression. At 1.7 × 1014 and 8.8 × 1013 W/cm2, barrier suppression is incomplete and the maximum kinetic energy is less than predicted by the wagging tail model.
van der Horst, J.-W.; Bobbert, P. A.; de Jong, P. H. L.; Michels, M. A. J.; Brocks, G.; Kelly, P. J.
2000-06-01
We calculate the electronic and optical excitations of polythiophene using the GW (G stands for one-electron Green function, W for the screened Coulomb interaction) approximation for the electronic self-energy, and include excitonic effects by solving the electron-hole Bethe-Salpeter equation. Two different situations are studied: excitations on isolated chains and excitations on chains in crystalline polythiophene. The dielectric tensor for the crystalline situation is obtained by modeling the polymer chains as polarizable line objects, with a long-wavelength polarizability tensor obtained from the ab initio polarizability function of the isolated chain. With this model dielectric tensor we construct a screened interaction for the crystalline case, including both intra- and interchain screening. In the crystalline situation both the quasiparticle band gap and the exciton binding energies are drastically reduced in comparison with the isolated chain. However, the optical gap is hardly affected. We expect this result to be relevant for conjugated polymers in general.
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
Ab Initio and Analytic Intermolecular Potentials for Ar–CH3OH
Tasic, Uros; Alexeev, Yuri; Vayner, Grigoriy; Crawford, T Daniel; Windus, Theresa L.; Hase, William L.
2006-09-20
Ab initio calculations at the CCSD(T)/aug-cc-pVTZ level of theory were used to characterize the Ar–CH₃y6tOH intermolecular potential energy surface (PES). Potential energy curves were calculated for four different Ar + CH₃OH orientations and used to derive an analytic function for the intermolecular PES. A sum of Ar–C, Ar–O, Ar–H(C), and Ar–H(O) two-body potentials gives an excellent fit to these potential energy curves up to 100 kcal mol¯¹, and adding an additional r¯¹n term to the Buckingham two-body potential results in only a minor improvement in the fit. Three Ar–CH₃OH van der Waals minima were found from the CCSD(T)/aug-cc-pVTZ//MP2/aug-cc-pVTZ calculations. The structure of the global minimum is in overall good agreement with experiment (X.-C. Tan, L. Sun and R. L. Kuczkowski, J. Mol. Spectrosc., 1995, 171, 248). It is T-shaped with the hydroxyl H-atom syn with respect to Ar. Extrapolated to the complete basis set (CBS) limit, the global minimum has a well depth of 0.72 kcal mol¯¹ with basis set superposition error (BSSE) correction. The aug-cc-pVTZ basis set gives a well depth only 0.10 kcal mol¯¹ smaller than this value. The well depths of the other two minima are within 0.16 kcal mol¯¹ of the global minimum. The analytic Ar–CH₃OH intermolecular potential also identifies these three minima as the only van der Waals minima and the structures predicted by the analytic potential are similar to the ab initio structures. The analytic potential identifies the same global minimum and the predicted well depths for the minima are within 0.05 kcal mol¯1 of the ab initio values. Combining this Ar–CH₃OH intermolecular potential with a potential for a OH-terminated alkylthiolate self-assembled monolayer surface (i.e., HO-SAM) provides a potential to model Ar + HO-SAM collisions.
Knyazev, D V
2014-01-01
This work is devoted to the investigation of transport and optical properties of liquid aluminum in the two-temperature case. At first optical properties, static electrical and thermal conductivities were obtained in the \\textit{ab initio} calculation. The \\textit{ab initio} calculation is based on the quantum molecular dynamics, density functional theory and the Kubo-Greenwood formula. The semiempirical approximation was constructed based on the results of the \\textit{ab initio} caculation. The approximation yields the dependences $\\sigma_{1_\\mathrm{DC}}\\propto1/T_i^{0.25}$ and $K\\propto T_e/T_i^{0.25}$ for the static electrical conductivity and thermal conductivity, respectively. The approximation is valid for liquid aluminum at $\\rho=2.70$~g/cm$^3$, 3~kK~$\\leq T_i\\leq T_e\\leq20$~kK. Our results are well described by the Drude model with the effective relaxation time $\\tau\\propto T_i^{-0.25}$. We have compared our results with a number of other models. They are all reduced in the low-temperature limit to th...
Probing defects and correlations in the hydrogen-bond network of ab initio water
Gasparotto, Piero; Ceriotti, Michele
2016-01-01
The hydrogen-bond network of water is characterized by the presence of coordination defects relative to the ideal tetrahedral network of ice, whose fluctuations determine the static and time-dependent properties of the liquid. Because of topological constraints, such defects do not come alone, but are highly correlated coming in a plethora of different pairs. Here we discuss in detail such correlations in the case of ab initio water models and show that they have interesting similarities to regular and defective solid phases of water. Although defect correlations involve deviations from idealized tetrahedrality, they can still be regarded as weaker hydrogen bonds that retain a high degree of directionality. We also investigate how the structure and population of coordination defects is affected by approximations to the inter-atomic potential, finding that in most cases, the qualitative features of the hydrogen bond network are remarkably robust.
Ab initio calculation of the growth of Te nanorods and Bi2Te3 nanoplatelets
Tian Xiao-Qing; Du Shi-Xuan; Gao Hong-Jun
2008-01-01
In this paper the growth mechanism of a Te/Bi2Te3 novel structure is studied by ab-initio calculations.The results show that the growth of Te nanorods is determined by the adsorption energy of Te atoms on different crystalline Te surfaces.The adsorption energy of Te on the Te (001) surface is 3.29 eV,which is about 0.25 eV higher than that of Te on the Te (110).This energy difference makes the preferential growth direction along the ＜ 001＞ direction.In addition,the higher surface energy of Bi2Te3 (110) and the lattice misfit between crystalline Bi2Te3 and Te along ＜ 001＞ direction are considered to explain the growth of the Bi2Te3 nanoplatelets,in which Volmer-Weber model is used.The theoretical results axe in agreement with experimental observation.
Ab initio calculation of structure and thermodynamic properties of Zintl aluminide SrAl{sub 2}
Fu, Zhi-Jian [Chongqing Key Laboratory of Micro/Nano Materials Engineering and Technology, Chongqing (China); Chongqing Univ. of Arts and Sciences (China). School of Electrical and Electronic Engineering; China Academy of Engineering Physics (CAEP), Mianyang, Sichuan (China). National Key Lab. of Shock Wave and Detonation Physics; Jia, Li-Jun [Chongqing Univ. of Arts and Sciences Library (China); Xia, Ji-Hong; Tang, Ke; Li, Zhao-Hong [Chongqing Univ. of Arts and Sciences (China). School of Electrical and Electronic Engineering; Sun, Xiao-Wei [Lanzhou Jiaotong Univ. (China). School of Mathematics and Physics; Chen, Qi-Feng [China Academy of Engineering Physics (CAEP), Mianyang, Sichuan (China). National Key Lab. of Shock Wave and Detonation Physics
2015-07-01
The structural and thermodynamic properties of the orthorhombic and cubic structure SrAl{sub 2} at pressure and temperature are investigated by using the ab initio plane-wave pseudopotential density functional theory method within 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 SrAl{sub 2} are calculated by the quasi-harmonic Debye model. The pressure-volume relationship and the variations in the thermal expansion a are obtained systematically in the pressure and temperature ranges of 0-5 GPa and 0-500 K, respectively.
The {\\it ab initio} calculation of spectra of open shell diatomic molecules
Tennyson, Jonathan; McKemmish, Laura K; Yurchenko, Sergei N
2016-01-01
The spectra (rotational, rotation-vibrational or electronic) of diatomic molecules due to transitions involving only closed-shell ($^1\\Sigma$) electronic states follow very regular, simple patterns and their theoretical analysis is usually straightforward. On the other hand, open-shell electronic states lead to more complicated spectral patterns and, moreover, often appear as a manifold of closely lying electronic states, leading to perturbations with even larger complexity. This is especially true when at least one of the atoms is a transition metal. Traditionally these complex cases have been analysed using approaches based on perturbation theory, with semi-empirical parameters determined by fitting to spectral data. Recently the needs of two rather diverse scientific areas have driven the demand for improved theoretical models of open-shell diatomic systems based on an \\emph{ab initio} approach, these areas are ultracold chemistry and the astrophysics of "cool" stars, brown dwarfs and most recently extraso...
Trends in magnetism of free Rh clusters via relativistic ab-initio calculations.
Šipr, O; Ebert, H; Minár, J
2015-02-11
A fully relativistic ab-initio study on free Rh clusters of 13-135 atoms is performed to identify general trends concerning their magnetism and to check whether concepts which proved to be useful in interpreting magnetism of 3d metals are applicable to magnetism of 4d systems. We found that there is no systematic relation between local magnetic moments and coordination numbers. On the other hand, the Stoner model appears well-suited both as a criterion for the onset of magnetism and as a guide for the dependence of local magnetic moments on the site-resolved density of states at the Fermi level. Large orbital magnetic moments antiparallel to spin magnetic moments were found for some sites. The intra-atomic magnetic dipole Tz term can be quite large at certain sites but as a whole it is unlikely to affect the interpretation of x-ray magnetic circular dichroism experiments based on the sum rules.
Ab initio research of stopping power for energetic ions in solids
He, Bin, E-mail: hebin-rc@163.com; Meng, Xu-Jun; Wang, Jian-Guo
2017-03-01
A new physical scenario is suggested to estimate the stopping power of energetic α particles in solid-density Be, Na, and Al at room temperature in an ab initio way based on the average atom model. In the scenario the stopping power is caused by the transition of free electrons to higher energy states and the ionization of bound electrons of the atom. Our results are found generally in good agreement with the recommended data in Al, Be and Na as well as the experimental data in Al. A comparison of energy loss with the recent experiment of protons in Be indicates that the scenario is more reasonable than the local density approximation in this case.
Ab initio research of stopping power for energetic ions in solids
He, Bin; Meng, Xu-Jun; Wang, Jian-Guo
2017-03-01
A new physical scenario is suggested to estimate the stopping power of energetic α particles in solid-density Be, Na, and Al at room temperature in an ab initio way based on the average atom model. In the scenario the stopping power is caused by the transition of free electrons to higher energy states and the ionization of bound electrons of the atom. Our results are found generally in good agreement with the recommended data in Al, Be and Na as well as the experimental data in Al. A comparison of energy loss with the recent experiment of protons in Be indicates that the scenario is more reasonable than the local density approximation in this case.
Ab initio electron scattering cross-sections and transport in liquid xenon
Boyle, G. J.; McEachran, R. P.; Cocks, D. G.; Brunger, M. J.; Buckman, S. J.; Dujko, S.; White, R. D.
2016-09-01
Ab initio fully differential cross-sections for electron scattering in liquid xenon are developed from a solution of the Dirac-Fock scattering equations, using a recently developed framework (Boyle et al 2015 J. Chem. Phys. 142 154507) which considers multipole polarizabilities, a non-local treatment of exchange, and screening and coherent scattering effects. A multi-term solution of Boltzmann’s equation accounting for the full anisotropic nature of the differential cross-section is used to calculate transport properties of excess electrons in liquid xenon. The results were found to agree to within 25% of the measured mobilities and characteristic energies over the reduced field range of 10-4-1 Td. The accuracies are comparable to those achieved in the gas phase. A simple model, informed by highly accurate gas-phase cross-sections, is presented to improve the liquid cross-sections, which was found to enhance the accuracy of the transport coefficient calculations.
A room temperature CO$_2$ line list with ab initio computed intensities
Zak, Emil; Polyansky, Oleg L; Lodi, Lorenzo; Zobov, Nikolay F; Tashkun, Sergey A; Perevalov, Valery I
2016-01-01
Atmospheric carbon dioxide concentrations are being closely monitored by remote sensing experiments which rely on knowing line intensities with an uncertainty of 0.5% or better. We report a theoretical study providing rotation-vibration line intensities substantially within the required accuracy based on the use of a highly accurate {\\it ab initio} dipole moment surface (DMS). The theoretical model developed is used to compute CO$_2$ intensities with uncertainty estimates informed by cross comparing line lists calculated using pairs of potential energy surfaces (PES) and DMS's of similar high quality. This yields lines sensitivities which are utilized in reliability analysis of our results. The final outcome is compared to recent accurate measurements as well as the HITRAN2012 database. Transition frequencies are obtained from effective Hamiltonian calculations to produce a comprehensive line list covering all $^{12}$C$^{16}$O$_2$ transitions below 8000 cm$^{-1}$ and stronger than 10$^{-30}$ cm / molecule at ...
Ab initio contribution to the study of complexes formed during dilute FeCu alloys radiation
Becquart, C S
2003-01-01
Cu plays an important role in the embrittlement of pressure vessel steels under radiation and entities containing both Cu atoms and vacancies seem to appear as a consequence of displacement cascades. The characterisation of the stability as well as the migration of small Cu-vacancy complexes is thus necessary to understand and simulate the formation of these entities. For instance, cascade ageing studied by kinetic Monte Carlo or by rate theory models requires a good characterisation of such complexes which are parameters for these methods. We have investigated, by ab initio calculations based on the density functional theory, point defects and small defects in dilute FeCu alloys. The structure of small Cu clusters and Cu-vacancy complexes has been determined, as well as their formation and binding energies. Their relative stability is discussed. Vacancy migration energies in the presence of Cu atoms have been calculated and analysed. All the results are compared to the figures obtained with empirical interat...
Ab initio determination of effective electron-phonon coupling factor in copper
Ji, Pengfei; Zhang, Yuwen
2016-04-01
The electron temperature Te dependent electron density of states g (ε), Fermi-Dirac distribution f (ε), and electron-phonon spectral function α2 F (Ω) are computed as prerequisites before achieving effective electron-phonon coupling factor Ge-ph. The obtained Ge-ph is implemented into a molecular dynamics (MD) and two-temperature model (TTM) coupled simulation of femtosecond laser heating. By monitoring temperature evolutions of electron and lattice subsystems, the result utilizing Ge-ph from ab initio calculation shows a faster decrease of Te and increase of Tl than those using Ge-ph from phenomenological treatment. The approach of calculating Ge-ph and its implementation into MD-TTM simulation is applicable to other metals.
Ab initio determination of effective electron-phonon coupling factor in copper
Ji, Pengfei
2016-01-01
The electron temperature T_e dependent electron density of states g({\\epsilon}), Fermi-Dirac distribution f({\\epsilon}), and electron-phonon spectral function {\\alpha}^2 F({\\Omega}) are computed as prerequisites before achieving effective electron-phonon coupling factor. The obtained is implemented into a molecular dynamics (MD) and two-temperature model (TTM) coupled simulation of femtosecond laser heating. By monitoring temperature evolutions of electron and lattice subsystems, the result utilizing G_(e-ph) from ab initio calculation, shows a faster decrease of T_e and increase of T_l than those using G_(e-ph) from phenomenological treatment. The approach of calculating G_(e-ph) and its implementation into MD-TTM simulation is applicable to other metals.
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...
Ab initio study of heterojunction discontinuities in the ZnO/Cu2O system
Zemzemi, M.; Alaya, S.; Ben Ayadi, Z.
2014-06-01
Solar cells based on transparent conductive oxides such as ZnO/Cu2O constitute a very advanced way to build high-performance cells. In this work, we are interested in the characterization of the interface through nanoscale modeling based on ab initio approaches (density functional theory, local density approximation, and pseudopotential). This work aims to build a supercell containing a heterojunction ZnO/Cu2O and study the structural properties and the discontinuity of the valence band (band offset) from a semiconducting to another phase. We build a zinc oxide in the wurtzite structure along [0001] on which we place the copper oxide in the hexagonal (CdI2-type) structure. We choose the method of Van de Walle and Martin to calculate the energy offset. This approach fits well the density functional theory. Our calculation of the band offset gives a value that corresponds to other experimental and theoretical values.
Impact of oxygen on the 300-K isotherm of Laser Megajoule ablator using ab initio simulation
Colin-Lalu, P.; Recoules, V.; Salin, G.; Huser, G.
2015-11-01
The ablator material for inertial confinement fusion (ICF) capsules on the Laser Mégajoule is a glow-discharge polymer (GDP) plastic. Its equation of state (EOS) is of primary importance for the design of such capsules, since it has direct consequences on shock timing and is essential to mitigate hydrodynamic instabilities. Using ab initio molecular dynamics (AIMD), we have investigated the 300-K isotherm of amorphous CH1.37O0.08 plastic, whose structure is close to GDP plastic. The 300-K isotherm, which is often used as a cold curve within tabular EOS, is an important contribution of the EOS in the multimegabar pressure range. AIMD results are compared to analytic models within tabular EOS, pointing out large discrepancies. In addition, we show that the effect of oxygen decreases 300-K isotherm pressure by 10%-15%. The implication of these observations is the ability to improve ICF target performance, which is essential to achieve fusion ignition.
Ab-initio investigation of ferroelectricity in asymmetrically layered magnetic perovskites
Hatt, Alison; Spaldin, Nicola
2007-03-01
In an effort to combine magnetism and ferroelectricity in a single material we are motivated to explore creative routes to ferroelectricity that allow the coexistence of magnetism. In this talk we present results from an ab-initio study of a system of asymmetrically layered magnetic perovskite oxides in which the asymmetric layering should induce a ferroelectric polarization. We investigate this prediction in a model system of La(Al,Fe,Cr)O3, and find that a large switchable ferroelectric polarization can indeed be obtained, although it does not originate from the asymmetric layering. We examine the forces driving polarization in this system, and propose two- and three-dimensional heteroepitaxy as a general route to stabilizing novel ferroelectrics and multiferroics.
Ab initio theory for current-induced molecular switching: Melamine on Cu(001)
Ohto, Tatsuhiko
2013-05-28
Melamine on Cu(001) is mechanically unstable under the current of a scanning tunneling microscope tip and can switch among configurations. However, these are not equally accessible, and the switching critical current depends on the bias polarity. In order to explain such rich phenomenology, we have developed a scheme to evaluate the evolution of the reaction paths and activation barriers as a function of bias, which is rooted in the nonequilibrium Green\\'s function method implemented within density functional theory. This, combined with the calculation of the inelastic electron tunneling spectroscopy signal, allows us to identify the vibrational modes promoting the observed molecular conformational changes. Finally, once our ab initio results are used within a resonance model, we are able to explain the details of the switching behavior, such as its dependence on the bias polarity, and the noninteger power relation between the reaction rate constants and both the bias voltage and the electric current. © 2013 American Physical Society.
An Ab-Initio Calculation of Raman Spectra of Binary Sodium Silicates
尤静林; 蒋国昌; 侯怀宇; 陈辉; 吴永全; 徐匡迪
2004-01-01
Raman spectra of binary sodium silicates are calculated by self-consistent field (SCF) molecular orbital ab initio calculation of the quantum chemical method with several poly silicon-oxygen tetrahedral model clusters when both the basis sets of 6-31 G and 6-31 G(d) are applied. The symmetric stretching vibrational frequency of non-bridging oxygen in a high frequency range and its Raman optical activity and scattering cross section are deduced and analysed. The correlation between this vibrational Raman shift and its microscopic environment of the silicon-oxygen tetrahedron is found based on interior stress of configuration, which depends on the connecting topology of adjacent silicon-oxygen tetrahedra (SiOT). A newly established empirical stress index of tetrahedron is introduced to elucidate the above relationship.
Bork, Nicolai Christian; Du, Lin; Reiman, Heidi;
2014-01-01
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......) and compare this range to predictions from several widely used electronic structure methods, including five density functionals, Møller-Plesset perturbation theory, and five coupled cluster methods up to CCSDT quality, considering also the D3 dispersion correctional scheme. With some exceptions, we find...... that most electronic structure methods overestimate ΔG°295 K. The effects of vibrational anharmonicity is approximated using scaling factors, reducing ΔG°295 K by ca. 1.8 kJ mol(-1), whereby ΔG°295 K predictions well within the experimental range can be obtained....
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...
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
van Setten, M.J.; de Wijs, G.A.; Popa, V.A.; Popa, V.A.; Brocks, G.
2005-01-01
Magnesium alanate Mg(AlH4)2 has recently raised interest as a potential material for hydrogen storage. We apply ab initio calculations to characterize structural, electronic and energetic properties of Mg(AlH4)2. Density functional theory calculations within the generalized gradient approximation
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...
Ab initio study of energy-level alignments in polymer-dye blends
Pasveer, W.F.; Bobbert, P.A.; Michels, M.A.J.; Langeveld-Voss, B.M.W.; Schoo, H.F.M.; Bastiaansen, J.J.A.M.
2003-01-01
Polymers with a small amount of dye blended in offer an attractive possibility to change the color of the emitted light by changing the dye. We present ab initio calculations within density-functional theory of the HOMO/ LUMO energies for dipyrrolomethane dyes, polyphenylenevinylene and polyfluorene
Cybulski, Hubert; Fernandez, Berta; Henriksen, Christian
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 ...
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...
Ab initio electronic-structure calculations on the Nb/Zr multilayer system
Leuken, H. v.; Czyżyk, M.T.; Springelkamp, F.; Groot, R.A. de
1990-01-01
Ab initio electronic-structure calculations are performed for the Nb/Zr metallic multilayer system in the coherent bcc structure and in the incoherent bcc/hcp structure, observed for small and larger modulation wavelengths, respectively. A new calculational scheme, the localized-spherical-wave
Dispersion Interactions between Rare Gas Atoms: Testing the London Equation Using ab Initio Methods
Halpern, Arthur M.
2011-01-01
A computational chemistry experiment is described in which students can use advanced ab initio quantum mechanical methods to test the ability of the London equation to account quantitatively for the attractive (dispersion) interactions between rare gas atoms. Using readily available electronic structure applications, students can calculate the…
An ab initio Valence Bond Study on Cyclopenta-Fused Naphthalenes and Fluoranthenes
Havenith, R.W.A.; van Lenthe, J.H.; Jenneskens, L.W.
2005-01-01
To probe the effect of external cyclopenta-fusion on a naphthalene core, ab initio valence bond (VB) calculations have been performed, using strictly atomic benzene p-orbitals and p-orbitals that are allowed to delocalize, on naphthalene (1), acenaphthylene (2), pyracylene (3), cyclopenta[b,c]-acena
Ab initio study of energy-level alignments in polymer-dye blends
Pasveer, W.F.; Bobbert, P.A.; Michels, M.A.J.; Langeveld-Voss, B.M.W.; Schoo, H.F.M.; Bastiaansen, J.J.A.M.
2003-01-01
Polymers with a small amount of dye blended in offer an attractive possibility to change the color of the emitted light by changing the dye. We present ab initio calculations within density-functional theory of the HOMO/ LUMO energies for dipyrrolomethane dyes, polyphenylenevinylene and
POLY-ANIONS IN LIQUID CSPB - AN AB-INITIO MOLECULAR-DYNAMICS SIMULATION
DEWIJS, GA; PASTORE, G; SELLONI, A; VANDERLUGT, W
1994-01-01
Most alkali-group-IV liquid alloys exhibit strong chemical effects leading to well-defined equiatomic compounds. This is generally explained by the survival of particular clusters of lead-''Zintl'' ions-in the liquid state. We report on an ab initio simulation of liquid CsPb, for which the chemical
The Pu–U–Am system: An ab initio informed CALPHAD thermodynamic study
Perron, A., E-mail: perron1@llnl.gov [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Turchi, P.E.A.; Landa, A.; Söderlind, P. [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Ravat, B.; Oudot, B.; Delaunay, F. [CEA-Centre de Valduc, 21120 Is sur Tille (France)
2015-03-15
Highlights: • The ab initio informed CALPHAD assessment of the Am–U system has been realized. • A strong tendency toward phase separation across the whole composition range is predicted. • The ab initio informed Pu–U–Am thermodynamic database has been developed. • The solubility of Am and U in the liquid phase is improved by adding Pu. • The δ-Pu (fcc) phase is strongly stabilized by Am, on the contrary to the bcc phase. - Abstract: Phase diagram and thermodynamic properties of the Am–U system, that are experimentally unknown, are calculated using the CALPHAD method with input from ab initio electronic-structure calculations for the fcc and bcc phases. A strong tendency toward phase separation across the whole composition range is predicted. In addition, ab initio informed Pu–U and Am–Pu thermodynamic assessments are combined to build a Pu–U–Am thermodynamic database. Regarding the Pu-rich corner of the ternary system, predictions indicate that Am acts as a powerful δ-Pu (fcc) stabilizer. In the U-rich corner, similar predictions are made but to a lesser extent. In both cases, the bcc phase is destabilized and the fcc phase is enhanced. Finally, results and methodology are discussed and compared with previous assessments and guidelines are provided for further experimental studies.
Ab initio calculations on the inclusion complexation of cyclobis(paraquat- p-phenylene)
Zhang, Ke-Chun; Liu, Lei; Mu, Ting-Wei; Guo, Qing-Xiang
2001-01-01
Semiempirical PM3, ab initio HF/3-21g ∗, and DFT B3LYP/6-31g ∗ calculations in vacuum and in solution were performed on the inclusion complexation of cyclobis(paraquat- p-phenylene) with nine symmetric aromatic substrates. A good correlation was found between the theoretical stabilization energies and experimental free energy changes upon complexation.
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 ene...
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...
Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules
Zhang, Hao; Lund, Ole; Nielsen, Morten
2010-01-01
potentials derived from the analysis of known protein structures; energetic evaluation of different peptide snapshots in a molecular dynamics simulation; and direct analysis of contacts made in known 3D structures of peptide:MHC complexes. These methods are ab initio in that they require structural data...
Relativistic ab initio spectroscopy study of forbidden lines of singly ionized zinc
Dixit, Gopal; Sahoo, Bijaya K.; Chaudhuri, Rajat K.; Majumder, Sonjoy
2009-01-01
The ab initio calculation has been carried out to study the astrophysically important forbidden electromagnetic transition rates of singly ionized zinc (Zn II). Electron correlations are considered to all orders using coupled-cluster theory in the relativistic framework. Calculated excitation energi
Relativistic ab initio spectroscopy study of forbidden lines of singly ionized zinc
Dixit, Gopal; Sahoo, Bijaya K.; Chaudhuri, Rajat K.; Majumder, Sonjoy
2009-01-01
The ab initio calculation has been carried out to study the astrophysically important forbidden electromagnetic transition rates of singly ionized zinc (Zn II). Electron correlations are considered to all orders using coupled-cluster theory in the relativistic framework. Calculated excitation
Setten, van M.J.; Wijs, de G.A.; Popa, V.A.; Brocks, G.
2005-01-01
Magnesium alanate Mg(AlH4)2 has recently raised interest as a potential material for hydrogen storage. We apply ab initio calculations to characterize structural, electronic and energetic properties of Mg(AlH4)2. Density functional theory calculations within the generalized gradient approximation (G
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...
Ab initio calculations on the structure of pyridine in its lowest triplet state
Buma, W.J.; Groenen, E.J.J.; Schmidt, J.
1990-01-01
Recently we have experimentally shown that pyridine-d5, as a guest in a single crystal of benzene-d6, adopts a boatlike structure upon excitation into the lowest triplet state T0. Here MRDCI ab initio calculations are presented that reveal that the observed nonplanarity of the molecule is not caused
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.
Computer simulation of acetonitrile and methanol with ab initio-based pair potentials
Hloucha, M.; Sum, A. K.; Sandler, S. I.
2000-10-01
This study address the adequacy of ab initio pair interaction energy potentials for the prediction of macroscopic properties. Recently, Bukowski et al. [J. Phys. Chem. A 103, 7322 (1999)] performed a comprehensive study of the potential energy surfaces for several pairs of molecules using symmetry-adapted perturbation theory. These ab initio energies were then fit to an appropriate site-site potential form. In an attempt to bridge the gap between ab initio interaction energy information and macroscopic properties prediction, we performed Gibbs ensemble Monte Carlo (GEMC) simulations using their developed pair potentials for acetonitrile and methanol. The simulations results show that the phase behavior of acetonitrile is well described by just the pair interaction potential. For methanol, on the other hand, pair interactions are insufficient to properly predict its vapor-liquid phase behavior, and its saturated liquid density. We also explored simplified forms for representing the ab initio interaction energies by refitting a selected range of the data to a site-site Lennard-Jones and to a modified Buckingham (exponential-6) potentials plus Coulombic interactions. These were also used in GEMC simulations in order to evaluate the quality and computational efficiency of these different potential forms. It was found that the phase behavior prediction for acetonitrile and methanol are highly dependent on the details of the interaction potentials developed.
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.
Ab Initio Calculations and Raman and SERS Spectral Analyses of Amphetamine Species
Berg, Rolf W.; Nørbygaard, Thomas; White, Peter C.
2011-01-01
. 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...
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
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.
Raimondi, Francesco; Navrátil, Petr; Quaglioni, Sofia
2016-01-01
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 $^3$H$(d,n)^4$He and $^3$He$(d,p)^4$He 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 $^7$Li and the ${}^{7}$Li($d$,$p$)${}^{8}$Li 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-clu...
Yao, Yongxin [Iowa State Univ., Ames, IA (United States)
2009-01-01
also plays an important role, as it may directly track the movement of every atom. Simulation time is a major limit for molecular dynamics, not only because of “slow” computer speed, but also because of the accumulation error in the numerical treatment of the motion equations. There is also a great concern about the reliability of the emperical potentials if using classical molecular dynamics. Ab initio methods based on density functional theory(DFT) do not have this problem, however, it suffers from small simulation cells and is more demanding computationally. When crystal phase is involved, size effect of the simulation cell is more pronounced since long-range elastic energy would be established. Simulation methods which are more efficient in computation but yet have similar reliability as the ab initio methods, like tight-binding method, are highly desirable. While the complexity of metallic glasses comes from the atomistic level, there is also a large field which deals with the complexity from electronic level. The only “ab initio” method applicable to solid state systems is density functional theory with local density approximation( LDA) or generalized gradient approximation(GGA) for the exchange-correlation energy. It is very successful for simple sp element, where it reaches an high accuracy for determining the surface reconstruction. However, there is a large class of materials with strong electron correlation, where DFT based on LDA or GGA fails in a fundamental way. An “ab initio” method which can generally apply to correlated materials, as LDA for simple sp element, is still to be developed. The thesis is prepared to address some of the above problems.
NestedMICA as an ab initio protein motif discovery tool
Down Thomas A
2008-01-01
Full Text Available Abstract Background Discovering overrepresented patterns in amino acid sequences is an important step in protein functional element identification. We adapted and extended NestedMICA, an ab initio motif finder originally developed for finding transcription binding site motifs, to find short protein signals, and compared its performance with another popular protein motif finder, MEME. NestedMICA, an open source protein motif discovery tool written in Java, is driven by a Monte Carlo technique called Nested Sampling. It uses multi-class sequence background models to represent different "uninteresting" parts of sequences that do not contain motifs of interest. In order to assess NestedMICA as a protein motif finder, we have tested it on synthetic datasets produced by spiking instances of known motifs into a randomly selected set of protein sequences. NestedMICA was also tested using a biologically-authentic test set, where we evaluated its performance with respect to varying sequence length. Results Generally NestedMICA recovered most of the short (3–9 amino acid long test protein motifs spiked into a test set of sequences at different frequencies. We showed that it can be used to find multiple motifs at the same time, too. In all the assessment experiments we carried out, its overall motif discovery performance was better than that of MEME. Conclusion NestedMICA proved itself to be a robust and sensitive ab initio protein motif finder, even for relatively short motifs that exist in only a small fraction of sequences. Availability NestedMICA is available under the Lesser GPL open-source license from: http://www.sanger.ac.uk/Software/analysis/nmica/
Timko, Jeff; Kuyucak, Serdar
2012-11-28
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.
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.
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.
Properties of Zr – 12.5 % Nb and Zr – 25 % Nb Alloys with hcp and bcc Lattices: ab-initio Modeling
V.O. Kharchenko
2012-06-01
Full Text Available Ab-initio calculations of the electronic structure for Zr – 12.5 % Nb and Zr – 25 % Nb alloys are done using density functional theory, method of linearized augmented plane-wave approximation and generalized gradient approximation. The structural and energetic properties, such as the electron densities, densities of states, energetically and X-ray spectra in the case of the hcp and bcc lattices are calculated. Optimal values for the lattice constants are found. The most favorable structure for each studied alloy is defined.
Axisymmetric Ab Initio Core-Collapse Supernova Simulations of 12-25 M_sol Stars
Bruenn, Stephen W; Hix, W Raphael; Lentz, Eric J; Messer, O E Bronson; Lingerfelt, Eric J; Blondin, John M; Endeve, Eirik; Marronetti, Pedro; Yakunin, Konstantin N
2012-01-01
We present an overview of four ab initio axisymmetric core-collapse supernova simulations employing detailed spectral neutrino transport computed with our CHIMERA code and initiated from Woosley & Heger (2007) progenitors of mass 12, 15, 20, and 25 M_sol. All four models exhibit shock revival over \\sim 200 ms (leading to the possibility of explosion), driven by neutrino energy deposition. Hydrodynamic instabilities that impart substantial asymmetries to the shock aid these revivals, with convection appearing first in the 12 M_sol model and the standing accretion shock instability (SASI) appearing first in the 25 M_sol model. Three of the models have developed pronounced prolate morphologies (the 20 M_sol model has remained approximately spherical). By 500 ms after bounce the mean shock radii in all four models exceed 3,000 km and the diagnostic explosion energies are 0.33, 0.66, 0.65, and 0.70 Bethe (B = $10^{51}$ ergs) for the 12, 15, 20, and 25 M_sol models, respectively, and are increasing. The three l...
Ab Initio Studies on the Preferred Site of Protonation in Cytisine in the Gas Phase and Water
MaÃ…Â‚gorzata Darowska
2005-01-01
Full Text Available Abstract: Ab initio calculations (HF, MP2, DFT for isolated and PCM for solvated molecules were performed for cytisine (1 and its model compounds: N-methyl-2-pyridone (2 and piperidine (3. Among three heteroatomic functions (carbonyl oxygen, pyridone and piperidine nitrogens considered as the possible sites of protonation in 1, surprisingly the carbonyl oxygen takes preferentially the proton in the gas phase whereas in water the piperidine nitrogen is firstly protonated. For model compounds, the piperidine nitrogen in 3 is more basic than the carbonyl oxygen in 2 in both, the gas phase and water.
Ji, Pengfei; Zhang, Yuwen
2016-03-01
On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provides a general way that is accessible to other metals in laser heating.
Ji, Pengfei
2016-01-01
On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provide a general way that is accessible to other metals in laser heating.
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.
[Photoelectron Spectra of CCl2-: Ab Initio Calculation and Franck-Condon Analysis].
Wu, Jun
2015-12-01
Geometry optimization and harmonic vibrational frequency calculations were performed on the X¹A₁ state of CCl₂ and X²B₁ state of CCl₂⁻ at the B3LYP, MP2, CCSD levels. Franck-Condon analysis and spectral simulations were carried out on the photoelectron band of CCl₂⁻ including Duschinsky effects. The simulated spectra obtained are in excellent agreement with the experiment. Note that Duschinsky effect between bending vibration and the symmetric stretch modes should be considered in the CCl₂ (X¹A₁)-CCl₂⁻ (X²B₁) photodetachment process. By combining ab initio calculations with Franck-Condon analyses, the assignment of spectrum observed is firmly established to the X¹A₁-X²B₁ photodetachment process of the CCl₂⁻ radical, and the recommended geometric parameters of which in the literature are confirmed again base on ab initio theory and IFCA process.
A highly accurate {\\it ab initio} potential energy surface for methane
Owens, Alec; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter
2016-01-01
A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art \\textit{ab initio} theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include: core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of $^{12}$CH$_4$ reproduced with a root-mean-square error of $0.70{\\,}$cm$^{-1}$. The computed \\textit{ab initio} equilibrium C{--}H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as $J$ (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the e...
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.
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.
Bridging a gap between continuum-QCD and ab initio predictions of hadron observables
Daniele Binosi
2015-03-01
Full Text Available Within contemporary hadron physics there are two common methods for determining the momentum-dependence of the interaction between quarks: the top-down approach, which works toward an ab initio computation of the interaction via direct analysis of the gauge-sector gap equations; and the bottom-up scheme, which aims to infer the interaction by fitting data within a well-defined truncation of those equations in the matter sector that are relevant to bound-state properties. We unite these two approaches by demonstrating that the renormalisation-group-invariant running-interaction predicted by contemporary analyses of QCD's gauge sector coincides with that required in order to describe ground-state hadron observables using a nonperturbative truncation of QCD's Dyson–Schwinger equations in the matter sector. This bridges a gap that had lain between nonperturbative continuum-QCD and the ab initio prediction of bound-state properties.
Low-temperature metallic liquid hydrogen: an ab-initio path-integral molecular dynamics perspective
Chen, Ji; Li, Xin-Zheng; Zhang, Qianfan; Probert, Matthew; Pickard, Chris; Needs, Richard; Michaelides, Angelos; Wang, Enge
2013-03-01
Experiments and computer simulations have shown that the melting temperature of solid hydrogen drops with pressure above about 65 GPa, suggesting that a low temperature liquid state might exist. It has also been suggested that this liquid state might be non-molecular and metallic, although evidence for such behaviour is lacking. Using a combination of ab initio path-integral molecular dynamics and the two-phase methods, we have simulated the melting of solid hydrogen under finite temperatures. We found an atomic solid phase from 500 to 800 GPa which melts at < 200 K. Beyond this and up to pressures of 1,200 GPa a metallic atomic liquid is stable at temperatures as low as 50 K. The quantum motion of the protons is critical to the low melting temperature in this system as ab initio simulations with classical nuclei lead to a considerably higher melting temperature of ~300 K across the entire pressure range considered.
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.
Liquid Be, Ca and Ba. An orbital-free ab-initio molecular dynamics study
Rio, B. G. del; González, L. E. [Departamento de Física Teórica, Atómica y Óptica, Universidad de Valladolid, 47011 Valladolid (Spain)
2015-08-17
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.
Ab initio simulations and neutron scattering studies of structure and dynamics in PdH
Totolici, I E
2001-01-01
The work presented in this PhD thesis is concerned with the interpretation of the neutron scattering measurements from the palladium hydrogen system by means of ab initio electronic structure calculations. The motivation of performing such calculations was due to recent neutron scattering studies on this system that showed a strong directional dependence to the dynamical structure factor together with a complex dependence on energy. Here we attempt to describe the origin of these features by ab initio simulations of the dynamical structure factor. The method assumes an adiabatic separation of the motion of the proton and palladium atoms. The proton wave functions are calculated by a direct solution of the associated single-particle Schroedinger equation using a plane wave basis set method and a mapping of the adiabatic surface. The Fourier components of the adiabatic potential are obtained from LDA pseudopotential calculations. Using Fermi's golden rule within the Born approximation we were then able to calcu...
Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo
Zen, Andrea, 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.
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.
An ab initio potential function for the ν13 vibrational mode of 1,3-butadiene
Senent, M. L.
1995-06-01
The restricted potential of the ν13 torsional mode of 1,3-butadiene has been determined from ab initio calculations. The relative energy and geometry of the second rotamer were calculated with the optimized couple cluster method with double substitutions. This ab initio level provides that the second stable structure attaches to a gauche form situated at 140.8°. The potential energy function was obtained by fitting to a symmetry-adapted Fourier series the total electronic energies of several selected conformations. These energies were calculated by the Möller-Plesset perturbation theory up to the second order (MP2) with full and partial optimization of the geometry. Torsional Raman band positions and fundamental frequencies were determined from the periodic potentials with a good agreement with experimental data. The convenience of performing fully optimized calculations to determine the restricted function is also refuted.
Interatomic potentials for Al and Ni from experimental data and ab initio calculations
Mishin, Y.; Farkas, D.; Miehl, M.J.; Papaconstantopoulos, D.A.
1999-07-01
New embedded-atom potentials for Al and Ni have been developed by fitting to both experimental data and the results of ab initio calculations. The ab initio data were obtained in the form of energies of different alternative computer-generated crystalline structures of these metals. The potentials accurately reproduce basic equilibrium properties of Al and Ni such as the elastic constants, phonon dispersion curves, vacancy formation and migration energies, stacking fault energies, and surface energies. The equilibrium energies of various alternative structures not included in the fitting database are calculated with these potentials. The results are compared with predictions of total-energy tight-binding calculations for the same structures. The embedded-atom potentials correctly reproduce the structural stability trends, which suggests that they are transferable to different local environments encountered in atomistic simulations of lattice defects.
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.
Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study.
Yang, Jianjun; Tse, John S
2011-11-17
The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated.
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...
Electrical Resistivity of Na-K Binary Liquid Alloy Using Ab-Initio Pseudopotentials
Anil Thakur; P. K. Ahluwalia
2005-01-01
@@ The study of electrical resistivity of simple binary liquid alloy Na-K is presented as a function of concentration.Hard sphere diameters of sodium (Na) and potassium (K) are obtained through the inter ionic pair potentials evaluated using Troullier and Martins ab-initio pseudopotentials, which have been used to calculate partial structure factors S(q). The Ziman formula for calculating resistivity of binary liquid alloys has been used. Form factors are calculated using ab-initio pseudopotentials. The results suggest that the first principle approach for calculating pseudopotentials with in the frame work of Ziman formalism is quite successful in explaining the electrical resistivity data of compound forming binary liquid alloys.
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.
Halasyamani, Shiv [Univ. of Houston, TX (United States); Fennie, Craig [Cornell Univ., Ithaca, NY (United States)
2016-11-03
We have focused on the synthesis, characterization, and ab initio theory on multi-functional mixed-metal fluorides. With funding from the DOE, we have successfully synthesized and characterized a variety of mixed metal fluoride materials.
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...
First fully ab initio potential energy surface of methane with a spectroscopic accuracy
Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.
2016-09-01
Full 9-dimensional ab initio potential energy surfaces for the methane molecule are constructed using extended electronic structure coupled-cluster calculations with various series of basis sets following increasing X cardinal numbers: cc-pVXZ (X = 3, 4, 5, 6), aug-cc-ACVXZ (X = 3, 4, 5), and cc-pCVXZ-F12 (X = 3, 4). High-order dynamic electron correlations including triple and quadrupole excitations as well as relativistic and diagonal Born-Oppenheimer breakdown corrections were accounted for. Analytical potential functions are parametrized as non-polynomial expansions in internal coordinates in irreducible tensor representation. Vibrational energy levels are reported using global variational nuclear motion calculations with exact kinetic energy operator and a full account of the tetrahedral symmetry of CH4. Our best ab initio surface including above-mentioned contributions provides the rms (obs.-calc.) errors of less than 0.11 cm-1 for vibrational band centers below 4700 cm-1, and ˜0.3 cm-1 for all 229 assigned experimentally determined vibrational levels up to the Icosad range <7900 cm-1 without empirically adjusted parameters. These results improve the accuracy of ab initio methane vibrational predictions by more than an order of magnitude with respect to previous works. This is an unprecedented accuracy of first-principles calculations of a five-atomic molecule for such a large data set. New ab initio potential results in significantly better band center predictions even in comparison with best available empirically corrected potential energy surfaces. The issues related to the basis set extrapolation and an additivity of various corrections at this level of accuracy are discussed.
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 its static and dynamic properties. The results obtained show good agreement with well established data, and, moreover, we were able to show significant changes within the structure depending on the system's temperature and density....
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.
Simulation of Ab Initio Molecular Dynamics of Shock Wave on Copper
张林; 蔡灵仓; 向士凯; 经福谦; 陈栋泉
2003-01-01
The relation between particle velocity Up, up to 4 km/s, and shock wave velocity Us in copper has been simulated with ab initio molecular dynamics. The simulated relationship without considering the correction of zero-point and finite temperature effects is Us = 4.23 + 1.53Up. After considering the correction the relation becomes Us = 4.08 + 1.53Up, which is consistent with the experimental result.
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...... bonding between the imidazolium headgroup and the anions, and the invariance of the essentially 50:50 mixture of the predominant conformers informs on the nature of glass formation in these systems....
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.
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....
Herbig, Alexander
2016-02-12
An ab-initio electronic structure method for substitutionally disordered real materials is developed within a pseudopotential density functional theory approach. The method is validated against exact diagonalization and for simple disordered CuZn alloys. The developed method is applied to iron-based superconductors. In particular, band renormalization effects due to various chemical substitutions in BaFe{sub 2}As{sub 2} are investigated and their Cooper pair breaking effects are compared.
Influence of the ab-initio nd cross sections in the critical heavy-water benchmarks
Morillon, B; Carbonell, J
2013-01-01
The n-d elastic and breakup cross sections are computed by solving the three-body Faddeev equations for realistic and semi-realistic Nucleon-Nucleon potentials. These cross sections are inserted in the Monte Carlo simulation of the nuclear processes considered in the International Handbook of Evaluated Criticality Safety Benchmark Experiments (ICSBEP). The results obtained using thes ab initio n-d cross sections are compared with those provided by the most renown international libraries.
Ab initio verification of the analytical R-matrix theory for strong field ionization
Torlina, Lisa; Morales, Felipe; Muller, H. G.; Smirnova, Olga
2014-10-01
We summarize the key aspects of the recently developed analytical R-matrix (ARM) theory for strong field ionization (Torlina and Smirnova 2012 Phys. Rev. A 86 043408; Kaushal and Smirnova 2013 Phys. Rev. A 88 013421), and present tests of this theory using ab initio numerical simulations for hydrogen and helium atoms in long circularly polarized laser pulses. We find excellent agreement between the predictions of ARM and the numerical calculations.
Steady state Ab-initio Theory of Lasers with Injected Signals
Cerjan, Alexander
2013-01-01
We present an ab-initio treatment of steady-state lasing with injected signals that treats both multimode lasing and spatial hole burning, and describes the transition to injection locking or partial locking in the multimode case. The theory shows that spatial hole burning causes a shift in the frequency of free-running laser modes away from the injection frequency, in contrast to standard approaches.
Yamaji, Youhei [Quantum-Phase Electronics Center, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-8656 (Japan)
2015-12-31
Recently, condensed-matter ab initio approaches to strongly correlated electrons confined in crystalline solids have been developed and applied to transition-metal oxides and molecular conductors. In this paper, an ab initio scheme based on constrained random phase approximations and localized Wannier orbitals is applied to a spin liquid candidate Na{sub 2}IrO{sub 3} and is shown to reproduce experimentally observed specific heat.
Geng, Hua Y., E-mail: huay.geng@gmail.com [National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, CAEP, P.O. Box 919-102, Mianyang, Sichuan, 621900 (China); Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY 14853 (United States)
2015-02-15
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.
Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation.
Yang, Lina; Minnich, Austin J
2017-03-14
Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials.
An ab initio HCN/HNC rotational-vibrational line list and opacity function for astronomy
Harris, Gregory John
HCN/HNC is an important molecule which is found throughout the universe. For example HCN/HNC is known to exist in comets, planetary atmospheres and the interstellar medium. HCN is also an important opacity source in carbon rich stars (C-stars). HCN masers have been observed in the circumstellar material around these C-stars and also in galaxies. Jorgensen and co-workers investigated model carbon star atmospheres in which they included HCN as an opacity source. They found that including a HCN opacity function had a remarkable effect: the atmosphere expanded by five times and the pressure of the atmosphere in the surface layers dropped by one or two orders of magnitude. This suggests that a full and detailed treatment of the rotational-vibrational spectrum of HCN/HNC could have a profound effect on the models of carbon stars, this provides the main motivation in this work. The temperatures of the stars in which HCN is an important opacity source Teff = 2000 - 3000 K. If HCN and HNC are in thermodynamic equilibrium it would be expected that HNC as well as HCN are found in significant populations. The transition dipoles of the fundamental bands of HNC are more than twice as strong as their HCN counter parts. These factors mean that both HCN and HNC will be considered, which makes a semiglobal treatment of the [H,C,N] system necessary. In this thesis an ab initio HCN/HNC linelist, from which accurate spectra and opacity functions can be calculated, is computed. Within this thesis I present least squares fits for ab initio semiglobal potential energy, dipole moment, relativistic correction and adiabatic correction surfaces. The potential energy surface (PES) is morphed for HNC geometries of the potential to improve the HNC representation of the surface. The PES and dipole moment surface (DMS) are used to perform quantum mechanical nuclear motion (rotational-vibrational) calculations with the DVR3D suite of codes. Preliminary calculations are made to optimise a ro
Ab-initio optimization of the crystal structure ksi and ksi* in Al- Mn-Pd
Sanatana Bonilla, Alejandro [Universitaet Stuttgart (Germany). Institut fuer Theoretische und Angewandte Physik; Grupo de Sistemas Complejos, Universidad Antonio, Bogota (Colombia); Engel, Michael [Univ. of Michigan, Ann Arbor (United States); Trebin, Hans-Rainer [Universitaet Stuttgart (Germany). Institut fuer Theoretische und Angewandte Physik; Mihalkovic, Marek [Inst. of Physics, Slovak Academy of Sciences Bratslava (Slovakia)
2010-07-01
A structural model is given for two approximants, {xi} and {xi}{sup *}, of the decagonal Al-Mn-Pd phase. Both structures were shown to be completely described by two sorts of interpenetrating clusters, namely ''Distorted Bergman Cluster'' (DBC) and by ''Pseudo Mackay Cluster'' (PMC). On the basis of these two atomic clusters the two phases can be characterized as some simple periodic tiling of assembly of the column clusters projected onto the plane perpendicular to the 1.6 nm stacking axis. From crystallographic studies the skeleton of heavy atoms was fully described, whereas the inner shell from PMC was poorly detailed. The structural models have been investigated using ab initio and molecular dynamics numerical methods. For this study, suitable improved pair potentials were used in order to determine the ideal cluster structure and the interactions between adjacent clusters. Plausibility of the suggested structures was tested using competing crystalline phases obtained through convex hull calculations and allowing us to suggest a reliable atomic model for the inner shell of the PMC. 3.
Bereau, Tristan; von Lilienfeld, O Anatole
2015-01-01
Accurate predictions of van der Waals forces require faithful models of dispersion, permanent and induced multipole-moments, as well as penetration and repulsion. We introduce a universal combined physics- and data-driven model of dispersion and multipole-moment contributions, respectively. Atomic multipoles are estimated "on-the-fly" for any organic molecule in any conformation using a machine learning approach trained on quantum chemistry results for tens of thousands of atoms in varying chemical environments drawn from thousands of organic molecules. Globally neutral, cationic, and anionic molecular charge states can be treated with individual models. Dispersion interactions are included via recently-proposed classical many-body potentials. For nearly one thousand intermolecular dimers, this approximate van der Waals model is found to reach an accuracy similar to that of state-of-the-art force fields, while bypassing the need for parametrization. Estimates of cohesive energies for the benzene crystal confi...
Study on the effects of fluorine and oxygen deficiency on YBa2Cu3O7 by ab initio method
刘洪霖; 曹晓卫; 瞿丽曼; 陈念贻
1997-01-01
The calculations of clusters modeling the fluorine-doping and oxygen deficiency of YBa2Cu3O2,have been performed by the method of all-electron ab initio Hartree-Fock with self-consistent crystal field Results show that in CuO planes electric charge significantly increases,the chemical valence of Cu decreases and the covalent bonding of Cu-O greatly weakens owing to oxygen deficiency,while the effect of F restores the local electronic structure of YBa2Cu3O7 The reported opinion that F occupied the oxygen vacancy in Cu-O chains seems disputable according to the calculated bonding characteristics.
Luntz, A. C.; Kratzer, Peter
1996-01-01
Dynamical calculations are reported for D-2 dissociative chemisorption on and associative desorption from a Si(100) surface. These calculations use the dynamically relevant effective potential which is based on an ab initio potential energy surface for the ''pre-paired'' species. Three coordinates...... experimental findings. We discuss several possibilities for this disagreement, including experimental artifact, limitations in the dynamical model and even the possibility that electronically adiabatic dynamics involving the ''pre-paired'' species is not relevant to experiments on real systems. (C) 1996...
Kundu, Arpan; Sillar, Kaido; Sauer, Joachim
2017-06-15
Gibbs free energies of adsorption on individual sites and the lateral (adsorbate-adsorbate) interaction energies are obtained from quantum chemical ab initio methods and molecular statistics. They define a Grand Canonical Monte Carlo (GCMC) Hamiltonian for simulations of gas mixtures on a lattice of adsorption sites. Coadsorption of CO2 and CH4 at Mg(2+) sites in the pores of the metal-organic framework CPO-27-Mg (Mg-MOF-74) is studied as an example. Simulations with different approximations as made in widely used coadsorption models such as the ideal adsorbed solution theory (IAST) show their limitations in describing adsorption selectivities for binary mixtures.
Nikitin, Andrei; Champion, Jean Paul; Tyuterev, Vladimir
2012-01-01
The MIRS software for the modeling of ro-vibrational spectra of polyatomic molecules was considerably extended and improved. The original version (Nikitin, et al. JQSRT, 2003, pp. 239--249) was especially designed for separate or simultaneous treatments of complex band systems of polyatomic molecules. It was set up in the frame of effective polyad models by using algorithms based on advanced group theory algebra to take full account of symmetry properties. It has been successfully used for predictions and data fitting (positions and intensities) of numerous spectra of symmetric and spherical top molecules within the vibration extrapolation scheme. The new version offers more advanced possibilities for spectra calculations and modeling by getting rid of several previous limitations particularly for the size of polyads and the number of tensors involved. It allows dealing with overlapping polyads and includes more efficient and faster algorithms for the calculation of coefficients related to molecular symmetry ...
B. Ramos
2012-03-01
Full Text Available Molecular modeling is growing as a research tool in Chemical Engineering studies, as can be seen by a simple research on the latest publications in the field. Molecular investigations retrieve information on properties often accessible only by expensive and time-consuming experimental techniques, such as those involved in the study of radical-based chain reactions. In this work, different quantum chemical techniques were used to study phenol oxidation by hydroxyl radicals in Advanced Oxidation Processes used for wastewater treatment. The results obtained by applying a DFT-based model showed good agreement with experimental values available, as well as qualitative insights into the mechanism of the overall reaction chain. Solvation models were also tried, but were found to be limited for this reaction system within the considered theoretical level without further parameterization.
Ab initio and DFT Studies of Be(BH42
J. S. Al-Otaibi
2016-03-01
Full Text Available In this study, the Ab inito and DFT calculations of optimized geometries, energy and vibrational spectra for the Beryllium borohydride Be(BH42 at different levels are achieved by Hartre – Fock (HF, perturbation theory (MP2 and density functional theory (B3LYP methods. They utilize the 6-31G(d, 6-311G(d,p, 6-311+G(d,p and 6-311++G(d,p basis sets. The theoretical results showed that Beryllium borohydride with the D2d structure which contains two identical groups of double bridging hydrogen has the lowest energy at all levels. Consequently, this compound is considered as the most stable one and the results of IR and Raman Spectra at all levels support that. We found that both structures Cs, C3v have the structure of D2d kind at all levels. The values of bond lengths for these two structures are identical for the bond lengths to the structure D2d kind which confirms this theory.
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.)
Periodic Trends in Lanthanide Compounds through the Eyes of Multireference ab Initio Theory.
Aravena, Daniel; Atanasov, Mihail; Neese, Frank
2016-05-01
Regularities among electronic configurations for common oxidation states in lanthanide complexes and the low involvement of f orbitals in bonding result in the appearance of several periodic trends along the lanthanide series. These trends can be observed on relatively different properties, such as bonding distances or ionization potentials. Well-known concepts like the lanthanide contraction, the double-double (tetrad) effect, and the similar chemistry along the lanthanide series stem from these regularities. Periodic trends on structural and spectroscopic properties are examined through complete active space self-consistent field (CASSCF) followed by second-order N-electron valence perturbation theory (NEVPT2) including both scalar relativistic and spin-orbit coupling effects. Energies and wave functions from electronic structure calculations are further analyzed in terms of ab initio ligand field theory (AILFT), which allows one to rigorously extract angular overlap model ligand field, Racah, and spin-orbit coupling parameters directly from high-level ab initio calculations. We investigated the elpasolite Cs2NaLn(III)Cl6 (Ln(III) = Ce-Nd, Sm-Eu, Tb-Yb) crystals because these compounds have been synthesized for most Ln(III) ions. Cs2NaLn(III)Cl6 elpasolites have been also thoroughly characterized with respect to their spectroscopic properties, providing an exceptionally vast and systematic experimental database allowing one to analyze the periodic trends across the lanthanide series. Particular attention was devoted to the apparent discrepancy in metal-ligand covalency trends between theory and spectroscopy described in the literature. Consistent with earlier studies, natural population analysis indicates an increase in covalency along the series, while a decrease in both the nephelauxetic (Racah) and relativistic nephelauxetic (spin-orbit coupling) reduction with increasing atomic number is calculated. These apparently conflicting results are discussed on the
Enthalpy of the gas-phase CO2 + Mg reaction from ab initio total energies.
Lesar, Antonija; Prebil, Sasa; Hodoscek, Milan
2002-01-01
Various highly accurate ab initio composite methods of Gaussian-n (G1, G2, G3), their variations (G2(MP2), G3(MP2), G3//B3LYP, G3(MP2)//B3LYP), and complete basis set (CBS-Q, CBS-Q//B3LYP) series of models were applied to compute reaction enthalpies of the ground-state reaction of CO2 with Mg. All model chemistries predict highly endothermic reactions, with DeltaH(298) = 63.6-69.7 kcal x mol(-1). The difference between the calculated reaction enthalpies and the experimental value, evaluated with recommended experimental standard enthalpies of formation for products and reactants, is more than 20 kcal x mol(-1) for all methods. This difference originates in the incorrect experimental enthalpy of formation of gaseous MgO given in thermochemical databases. When the theoretical formation enthalpy for MgO calculated by a particular method is used, the deviation is reduced to 1.3 kcal x mol(-1). The performance of the methodologies used to calculate the heat of this particular reaction and the enthalpy of formation of MgO are discussed.
Chen, Chen; Arntsen, Christopher; Voth, Gregory A.
2017-10-01
Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.
Ab Initio Cosmological Simulations of CR7 as an Active Black Hole
Smidt, Joseph; Johnson, Jarrett L
2016-01-01
We present the first ab initio cosmological simulations of a CR7-like object which approximately reproduce the observed line widths and strengths. In our model, CR7 is powered by a massive (2.23 x 10^7 M_Sun), accreting (0.25 Eddington) supermassive black hole (BH). Our model takes into account multi-dimensional effects, X-ray feedback, secondary ionizations and primordial chemistry. We estimate Ly-alpha line widths by post-processing simulation output with Monte Carlo radiative transfer and calculate emissivity contributions from radiative recombination and collisional excitation. We find the luminosities in the Lyman-alpha and He II 1640 angstrom lines to be 5.0 x 10^44 and 2.4 x 10^43 erg/s, respectively, in agreement with the observed values of > 8.3 x 10^43 and 2.0 x 10^43 erg/s. We also find that the black hole heats the halo and renders it unable to produce stars as required to keep the halo metal free. These results demonstrate the viability of the BH hypothesis for CR7 in a cosmological context. Assu...
Misquitta, Alston J; Stone, Anthony J
2016-09-13
Creating accurate, analytic atom-atom potentials for small organic molecules from first principles can be a time-consuming and computationally intensive task, particularly if we also require them to include explicit polarization terms, which are essential in many systems. We describe how the CamCASP suite of programs can be used to generate such potentials using some of the most accurate electronic structure methods currently applicable. We derive the long-range terms from monomer properties and determine the short-range anisotropy parameters by a novel and robust method based on the iterated stockholder atom approach. Using these techniques, we develop distributed multipole models for the electrostatic, polarization, and dispersion interactions in the pyridine dimer and develop a series of many-body potentials for the pyridine system. Even the simplest of these potentials exhibits root mean square errors of only about 0.6 kJ mol(-1) for the low-energy pyridine dimers, significantly surpassing the best empirical potentials. Our best model is shown to support eight stable minima, four of which have not been reported before in the literature. Further, the functional form can be made systematically more elaborate so as to improve the accuracy without a significant increase in the human-time spent in their generation. We investigate the effects of anisotropy, rank of multipoles, and choice of polarizability and dispersion models.
Morrison, Adrian F; Herbert, John M
2015-11-05
We introduce a charge-embedding scheme for an excited-state quantum chemistry method aimed at weakly interacting molecular aggregates. The Hamiltonian matrix for the aggregate is constructed in a basis of direct products of configuration-state functions for the monomers, and diagonalization of this matrix affords excitation energies within ∼0.2 eV of the corresponding supersystem calculation. Both the basis states and the coupling matrix elements can be computed in a distributed way, resulting in an algorithm whose time-to-solution is independent of the number of chromophores, and we report calculations on systems with almost 55 000 basis functions using fewer than 450 processors. In a semiconducting organic nanotube, we find evidence of ultrafast, coherent dynamics followed by energy localization driven by static disorder. Truncation of the model system has a qualitative effect on the energy-transfer dynamics, demonstrating the importance of simulating an extended portion of the nanotube, which is not feasible using traditional quantum chemistry.
Phasha, MJ
2008-11-01
Full Text Available on the metastable phase formation of equilibrium immiscible Ti-Mg system studied by ab initio technique and mechanical milling MJ PHASHA1,2, M KASONDE1, P E NGOEPE1,2 1CSIR Materials Science and Manufacturing, PO Box 395, Pretoria, 0001 2Materials Modelling... to predict the possible metastable phases of A3B, AB and AB3 type in the Ti-Mg system, which has no alloy phase over the entire composition range. RESULTS CONCLUSION 1 The hypothetical crystalline structures of Ti-Mg system were successfully cal...
Axisymmetric Ab Initio Core-Collapse Supernova Simulations of 12--25 Solar Mass Stars
Bruenn, S. W. [Florida Atlantic University; Mezzacappa, Anthony [ORNL; Hix, William Raphael [ORNL; Lentz, E. J. [University of Tennessee, Knoxville (UTK) & Oak Ridge National Laboratory (ORNL); Messer, Bronson [ORNL; Lingerfelt, Eric J [ORNL; Blondin, J. M. [North Carolina State University; Endeve, Eirik [ORNL; Marronetti, Pedro [Florida Atlantic University; Yakunin, Konstantin [Florida Atlantic University
2013-01-01
We present an overview of four ab initio axisymmetric core-collapse supernova simulations employing detailed spectral neutrino transport computed with our CHIMERA code and initiated from Woosley & Heger (2007) progenitors of mass 12, 15, 20, and 25 M_sun. All four models exhibit shock revival over ~ 200 ms (leading to the possibility of explosion), driven by neutrino energy deposition. Hydrodynamic instabilities that impart substantial asymmetries to the shock aid these revivals, with convection appearing first in the 12 solar mass model and the standing accretion shock instability (SASI) appearing first in the 25 solar mass model. Three of the models have developed pronounced prolate morphologies (the 20 solar mass model has remained approximately spherical). By 500 ms after bounce the mean shock radii in all four models exceed 3,000 km and the diagnostic explosion energies are 0.33, 0.66, 0.65, and 0.70 Bethe (B=10^{51} ergs) for the 12, 15, 20, and 25 solar mass models, respectively, and are increasing. The three least massive of our models are already sufficiently energetic to completely unbind the envelopes of their progenitors (i.e., to explode), as evidenced by our best estimate of their explosion energies, which first become positive at 320, 380, and 440 ms after bounce. By 850 ms the 12 solar mass diagnostic explosion energy has saturated at 0.38 B, and our estimate for the final kinetic energy of the ejecta is ~ 0.3 B, which is comparable to observations for lower-mass progenitors.
Ab-initio electron scattering cross-sections and transport in liquid xenon
Boyle, Greg; Cocks, Daniel; Brunger, Michael; Buckman, Steve; Dujko, Sasa; White, Ron
2016-01-01
Ab-initio electron - liquid phase xenon fully differential cross-sections for electrons scattering in liquid xenon are developed from a solution of the Dirac-Fock scattering equations, using a recently developed framework [1] which considers multipole polarizabilities, a non-local treatment of exchange, and screening and coherent scattering effects. A multi-term solution of Boltzmann's equation accounting for the full anisotropic nature of the differential cross-section is used to calculate transport properties of excess electrons in liquid xenon. The results were found to agree to within 25% of the measured mobilities and characteristic energies over the reduced field range of 10^{-4} to 1 Td. The accuracies are comparable to those achieved in the gas phase. A simple model, informed by highly accurate gas-phase cross-sections, is presented to transform highly accurate gas-phase cross-sections to improve the liquid cross-sections, which was found to enhance the accuracy of the transport coefficient calculatio...
Ab initio molecular dynamics of the reaction of quercetin with superoxide radical
Lespade, Laure
2016-08-01
Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car-Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.
Fischer, Sean A.; Apra, Edoardo; Govind, Niranjan; Hess, Wayne P.; El-Khoury, Patrick Z.
2017-02-03
Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single molecule SERS spectra and selection rules is a challenging task, and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4’-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.
Steady-state ab initio laser theory for complex gain media.
Cerjan, Alexander; Chong, Y D; Stone, A Douglas
2015-03-09
We derive and test a generalization of the steady-state ab initio laser theory (SALT) to treat complex gain media. The generalized theory (C-SALT) is able to treat atomic and molecular gain media with diffusion and multiple lasing transitions, and semiconductor gain media in the free carrier approximation including fully the effect of Pauli blocking. The key assumption of the theory is stationarity of the level populations, which leads to coupled self-consistent equations for the populations and the lasing modes that fully include the effects of openness and non-linear spatial hole-burning. These equations can be solved efficiently for the steady-state lasing properties by a similar iteration procedure as in SALT, where a static gain medium with a single transition is assumed. The theory is tested by comparison to much less efficient finite difference time domain (FDTD) methods and excellent agreement is found. Using C-SALT to analyze the effects of varying gain diffusion constant we demonstrate a cross-over between the regime of strong spatial hole burning with multimode lasing to a regime of negligible spatial hole burning, leading to gain-clamping, and single mode lasing. The effect of spatially inhomogeneous pumping combined with diffusion is also studied and a relevant length scale for spatial inhomogeneity to persist under these conditions is determined. For the semiconductor gain model, we demonstrate the frequency shift due to Pauli blocking as the pumping strength changes.
Mehandzhiyski, Aleksandar Y; Riccardi, Enrico; van Erp, Titus S; Trinh, Thuat T; Grimes, Brian A
2015-08-20
The interaction between a carboxylate anion (deprotonated propanoic acid) and the divalent Mg(2+), Ca(2+), Sr(2+), Ba(2+) metal ions is studied via ab initio molecular dynamics. The main focus of the study is the selectivity of the carboxylate-metal ion interaction in aqueous solution. The interaction is modeled by explicitly accounting for the solvent molecules on a DFT level. The hydration energies of the metal ions along with their diffusion and mobility coefficients are determined and a trend correlated with their ionic radius is found. Subsequently, a series of 16 constrained molecular dynamics simulations for every ion is performed, and the interaction free energy is obtained from thermodynamic integration of the forces between the metal ion and the carboxylate ion. The results indicate that the magnesium ion interacts most strongly with the carboxylate, followed by calcium, strontium, and barium. Because the interaction free energy is not enough to explain the selectivity of the reaction observed experimentally, more detailed analysis is performed on the simulation trajectories to understand the steric changes in the reaction complex during dissociation. The solvent dynamics appear to play an important role during the dissociation of the complex and also in the observed selectivity behavior of the divalent ions.
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.
Ab initio calculation of the crystalline structure and IR spectrum of polymers: nylon 6 polymorphs.
Quarti, Claudio; Milani, Alberto; Civalleri, Bartolomeo; Orlando, Roberto; Castiglioni, Chiara
2012-07-19
State-of-the-art computational methods in solid-state chemistry were applied to predict the structural and spectroscopic properties of the α and γ crystalline polymorphs of nylon 6. Density functional theory calculations augmented with an empirical dispersion correction (DFT-D) were used for the optimization of the two different crystal structures and of the isolated chains, characterized by a different regular conformation and described as one-dimensional infinite chains. The structural parameters of both crystalline polymorphs were correctly predicted, and new insight into the interplay of conformational effects, hydrogen bonding, and van der Waals interactions in affecting the properties of the crystal structures of polyamides was obtained. The calculated infrared spectra were compared to experimental data; based on computed vibrational eigenvectors, assignment of the infrared absorptions of the two nylon 6 polymorphs was carried out and critically analyzed in light of previous investigations. On the basis of a comparison of the computed and experimental IR spectra, a set of marker bands was identified and proposed as a tool for detecting and quantifying the presence of a given polymorph in a real sample: several marker bands employed in the past were confirmed, whereas some of the previous assignments are criticized. In addition, some new marker bands are proposed. The results obtained demonstrate that accurate computational techniques are now affordable for polymers characterization, opening the way to several applications of ab initio modeling to the study of many families of polymeric materials.
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.
Ab initio lattice stability of fcc and hcp Fe-Mn random alloys.
Gebhardt, T; Music, D; Hallstedt, B; Ekholm, M; Abrikosov, I A; Vitos, L; Schneider, J M
2010-07-28
We have studied the lattice stability of face centred cubic (fcc) versus hexagonal close packed (hcp) Fe-Mn random alloys using ab initio calculations. In the calculations we considered the antiferromagnetic order of local moments, which for fcc alloys models the magnetic configuration of this phase at room temperature (below its Néel temperature) as well as their complete disorder, corresponding to paramagnetic fcc and hcp alloys. For both cases, the results are consistent with our thermodynamic calculations, obtained within the Calphad approach. For the room temperature magnetic configuration, the cross-over of the total energies of the hcp phase and the fcc phase of Fe-Mn alloys is at the expected Mn content, whereas for the magnetic configuration above the fcc Néel temperature, the hcp lattice is more stable within the whole composition range studied. The increase of the total energy difference between hcp and antiferromagnetic fcc due to additions of Mn as well as the stabilizing effect of antiferromagnetic ordering on the fcc phase are well displayed. These results are of relevance for understanding the deformation mechanisms of these random alloys.
Ab-initio calculation of the photonuclear cross section of $^{10}$B
Kruse, M K G; Johnson, C W
2015-01-01
We present for the first-time the photonuclear cross section of $^{10}$B calculated within the ab-initio No Core Shell Model framework. Realistic two-nucleon (NN) chiral forces up to next-to-next-to-next-order (N3LO), which have been softened by the similarity renormalization group method (SRG) to $\\lambda=2.02$ fm$^{-1}$, were utilized. The electric-dipole response function is calculated using the Lanczos method. The effects of the continuum were accounted for by including neutron escape widths derived from R-matrix theory. The calculated cross section agrees well with experimental data in terms of structure as well as in absolute peak height, $\\sigma_{\\rm max}=4.85~{\\rm mb}$ at photon energy $\\omega=23.61~{\\rm MeV}$, and integrated cross section $85.36\\, {\\rm MeV \\cdotp mb}$. We test the Brink hypothesis by calculating the electric-dipole response for the first five positive-parity states in $^{10}$B and verify that dipole excitations built upon the ground- and excited states have similar characteristics.
Morse-Smale Analysis of Ion Diffusion in Ab Initio Battery Materials Simulations
Gyulassy, Attila [Univ. of Utah, Salt Lake City, UT (United States); Knoll, Aaron [Univ. of Utah, Salt Lake City, UT (United States); Lau, Kah Chun [Argonne National Lab. (ANL), Argonne, IL (United States); Wang, Bei [Univ. of Utah, Salt Lake City, UT (United States); Bremer, Peer-Timo [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Papka, Michael [Argonne National Lab. (ANL), Argonne, IL (United States); Curtiss, Larry A [Argonne National Lab. (ANL), Argonne, IL (United States); Pascucci, Valerio [Univ. of Utah, Salt Lake City, UT (United States)
2017-06-03
Ab initio molecular dynamics (AIMD) simulations are increasingly useful in modeling, optimizing and synthesizing materials in energy sciences. In solving Schrödinger’s equation, they generate the electronic structure of the simulated atoms as a scalar field. However, methods for analyzing these volume data are not yet common in molecular visualization. The Morse-Smale complex is a proven, versatile tool for topological analysis of scalar fields. In this paper, we apply the discrete Morse-Smale complex to analysis of first-principles battery materials simulations. We consider a carbon nanosphere structure used in battery materials research, and employ Morse-Smale decomposition to determine the possible lithium ion diffusion paths within that structure. Our approach is novel in that it uses the wavefunction itself as opposed distance fields, and that we analyze the 1-skeleton of the Morse-Smale complex to reconstruct our diffusion paths. Furthermore, it is the first application where specific motifs in the graph structure of the complete 1-skeleton define features, namely carbon rings with specific valence. We compare our analysis of DFT data with that of a distance field approximation, and discuss implications on larger classical molecular dynamics simulations.
Amino acid anions in organic ionic compounds. An ab initio study of selected ion pairs.
Benedetto, A; Bodo, E; Gontrani, L; Ballone, P; Caminiti, R
2014-03-06
The combination of amino acids in their deprotonated and thus anionic form with a choline cation gives origin to a new and potentially important class of organic ionic compounds. A series of such neutral ion pairs has been investigated by first principle methods. The results reveal intriguing structural motives as well as regular patterns in the charge distribution and predict a number of vibrational and optical properties that could guide the experimental investigation of these compounds. The replacement of choline with its phosphocholine analogue causes the spontaneous reciprocal neutralization of cations and anions, taking place through the transfer of a proton between the two ions. Systems of this kind, therefore, provide a wide and easily accessible playground to probe the ionic/polar transition in organic systems, while the easy transfer of H(+) among neutral and ionic species points to their potential application as proton conductors. The analysis of the ab initio data highlights similarities as well as discrepancies from the rigid-ions force-field picture and suggests directions for the improvement of empirical models.
Ab initio study of Al(III) adsorption on stepped {100} surfaces of KDP crystals
Salter, E A; Wierzbicki, A; Land, T A
2004-04-01
Crystals of potassium dihydrogen phosphate (KH{sub 2}PO{sub 4}, KDP) are grown in large scale for use as nonlinear material in laser components. Traces of trivalent metal impurities are often added to the supernatant to achieve habit control during crystal growth, selectively inhibiting the growth of the {l_brace}100{r_brace} face. Model systems representing AlPO{sub 4}-doped KDP {l_brace}100{r_brace} stepped surfaces are prepared and studied using ab initio quantum methods. Results of Hartree-Fock partial optimizations are presented, including estimated energies of ion pair binding to the steps. We find that the PO{sub 4}{sup 3-} ion takes a position not unlike that of a standard phosphate in the crystal lattice, while the aluminum atom is displaced far from a K{sup +} ion position to establish coordinations with the PO{sub 4}{sup 3-} ion and to bind with another lattice-bound phosphate. Our optimized structures suggest that it is the formation of a fourth coordination of Al(III) to a third phosphate ion from solution, or perhaps from a nearby position in the lattice, that disrupts further deposition, pinning the steps.
Ab initio study of a Y-doped Σ31 grain boundary in alumina
2008-01-01
The atomic structures and energetics of clean and Y-doped general grain boundary (GB) Σ31/(0001) models in α-Al2O3 are studied by a series of high precision ab initio calculations. A large supercell with 700 atoms and periodic boundary conditions is adopted for undoped and Y-doped GB with different substitution sites and con-centrations. It is shown that Y atoms preferably segregate to the central column of the 7-member Al ring. This is explained as more favorable bond formation for Y in this position and lower GB energy. The calculated GB formation energy for the clean and Y-doped cases is respectively 3.99 and 3.67 J/m2. On the average, the GB region in Σ31 has a slightly lower charge density than the bulk crystalline region. In addtition, the GB induces a long ranged asymmetric electrostatic potential distri-bution on each side of the grain boundary.
Mechanism of GeSbTe phase change materials: an ab initio molecular dynamics study
Raty, Jean-Yves; Otjacques, Céline; Gaspard, Jean-Pierre; Bichara, Christophe
2008-03-01
Among phase change materials, Ge2Sb2Te5 (225) is one of the most successfully used in applications. Accepted models are based on EXAFS spectra and suppose a complete reorganization of bonds during amorphization, with Ge changing from sixfold to tetrahedral coordination. We perform ab initio MD simulations of the (225), (124) and (415) liquid alloys. We show that the crystalline, liquid and amorphous structure of these systems are similar, with very little sp3 hybridization around Ge atoms and a majority of p-sigma bonds. Using a set of quenched liquid configurations we reproduce the EXAFS measurements on the (225) composition and explain how the static Debye Waller factor due to the vacancies in the crystal phase leads to a cancellation of individual neighbors contribution to the EXAFS signal while in the amorphous, a larger coherence occurs, enhancing the EXAFS signal. The computed electrical conductivities of the three phases (cubic solid, liquid and amorphous) prove to be very different, accordingly with the experiment.
van der Linden, Marx Gomes; Ferreira, Diogo César; de Oliveira, Leandro Cristante; Onuchic, José N; de Araújo, Antônio F Pereira
2014-07-01
The three-dimensional structure of proteins is determined by their linear amino acid sequences but decipherment of the underlying protein folding code has remained elusive. Recent studies have suggested that burials, as expressed by atomic distances to the molecular center, are sufficiently informative for structural determination while potentially obtainable from sequences. Here we provide direct evidence for this distinctive role of burials in the folding code, demonstrating that burial propensities estimated from local sequence can indeed be used to fold globular proteins in ab initio simulations. We have used a statistical scheme based on a Hidden Markov Model (HMM) to classify all heavy atoms of a protein into a small number of burial atomic types depending on sequence context. Molecular dynamics simulations were then performed with a potential that forces all atoms of each type towards their predicted burial level, while simple geometric constraints were imposed on covalent structure and hydrogen bond formation. The correct folded conformation was obtained and distinguished in simulations that started from extended chains for a selection of structures comprising all three folding classes and high burial prediction quality. These results demonstrate that atomic burials can act as informational intermediates between sequence and structure, providing a new conceptual framework for improving structural prediction and understanding the fundamentals of protein folding.
Ab initio potential energy surface and bound states for the Kr-OCS complex.
Feng, Eryin; Sun, Chunyan; Yu, Chunhua; Shao, Xi; Huang, Wuying
2011-09-28
The first ab initio potential energy surface of the Kr-OCS complex is developed using the coupled-cluster singles and doubles with noniterative inclusion of connected triples [CCSD(T)]. The mixed basis sets, aug-cc-pVTZ for the O, C, and S atom, and aug-cc-pVQZ-PP for the Kr atom, with an additional (3s3p2d1f) set of midbond functions are used. A potential model is represented by an analytical function whose parameters are fitted numerically to the single point energies computed at 228 configurations. The potential has a T-shaped global minimum and a local linear minimum. The global minimum occurs at R = 7.146 a(0), θ = 105.0° with energy of -270.73 cm(-1). Bound state energies up to J = 9 are calculated for three isotopomers (82)Kr-OCS, (84)Kr-OCS, and (86)Kr-OCS. Analysis of the vibrational wavefunctions and energies suggests the complex can exist in two isomeric forms: T-shaped and quasi-linear. The calculated transition frequencies and spectroscopic constants of the three isotopomers are in good agreement with the experimental values.
Ab-Initio Based Computation of Rate Constants for Spin Forbidden Metalloprotein-Substrate Reactions
Ozkanlar, Abdullah; Rodriguez, Jorge H.
2007-03-01
Some chemical and biochemical reactions are non-adiabatic processes whereby the total spin angular momentum, before and after the reaction, is not conserved. These are named spin- forbidden reactions. The application of ab-initio methods, such as spin density functional theory (SDFT), to the prediction of rate constants is a challenging task of fundamental and practical importance. We apply non-adiabatic transition state theory (NA-TST) in conjuntion with SDFT to predict the rate constant of the spin- forbidden recombination of carbon monoxide with iron tetracarbonyl. To model the surface hopping probability between singlet and triplet states, the Landau-Zener formalism is used. The lowest energy point for singlet-triplet crossing, known as minimum energy crossing point (MECP), was located and used to compute, in a semi-quantum approach, reaction rate constants at 300 K. The predicted rates are in very good agreement with experiment. In addition, we present results for the spin- forbidden ligand binding reactions of iron-containing heme proteins such as myoglobin.
Band offset of the ZnO/Cu2O heterojunction from ab initio calculations
Zemzemi, M.; Alaya, S.
2013-12-01
The ZnO/Cu2O system has known a recent revival of interest in solar cells for its potential use as a heterojunction able to highly perform under visible light. In this work, we are interested on the characterization of the interface through nanoscale modelization based on ab initio (Density Functional Theory (DFT), Local Density Approximation (LDA), Generalized Gradient Approximation (GGA-PBE), and Pseudopotential (PP)). This work aims to build a supercell containing a heterojunction ZnO/Cu2O and study the structural properties and the discontinuity of the valence band (band offset) from a semiconductor to another. We built a zinc oxide in the wurtzite structure along the [0 0 0 1] on which we placed the copper oxide in the hexagonal structure (CdI2-type). We choose the method of Van de Walle and Martin to calculate the energy offset. This approach fits well with the DFT. Our calculations of the band offset gave us a value that corresponds to other experimental and theoretical values.
Catalytic reaction mechanism of L-lactate dehydrogenase: an ab initio study
侯若冰; 陈志达; 义祥辉; 卞江; 徐光宪
2000-01-01
Studies on the catalytic reaction mechanism of L-lactate dehydrogenase have been carried out by using quantum chemical ab initio calculation at HF/6-31G* level. It is found that the interconversion reaction of pyruvate to L-lactate is dominated by the hydride ion HR- transfer, and the transfers of the hydride ion HR and proton HR+ are a quasi-coupled process, in which the energy barrier of the transition state is about 168.37 kJ/mol. It is shown that the reactant complex is 87.61 kJ/mol lower, in energy, than the product complex. The most striking features in our calculated results are that pyridine ring of the model cofactor is a quasi-boat-like configuration in the transited state, which differs from a planar conformation in some previous semiempirical quantum chemical studies. On the other hand, the similarity in the structure and charge between the HR transfer process and the hydrogen bonding with lower barrier indicates that the HR transfer process occurs by means of an unusual manner. In addition,
High-level ab initio computations of the absorption spectra of organic iridium complexes.
Plasser, Felix; Dreuw, Andreas
2015-02-12
The excited states of fac-tris(phenylpyridinato)iridium [Ir(ppy)3] and the smaller model complex Ir(C3H4N)3 are computed using a number of high-level ab initio methods, including the recently implemented algebraic diagrammatic construction method to third-order ADC(3). A detailed description of the states is provided through advanced analysis methods, which allow a quantification of different charge transfer and orbital relaxation effects and give extended insight into the many-body wave functions. Compared to the ADC(3) benchmark an unexpected striking difference of ADC(2) is found for Ir(C3H4N)3, which derives from an overstabilization of charge transfer effects. Time-dependent density functional theory (TDDFT) using the B3LYP functional shows an analogous but less severe error for charge transfer states, whereas the ωB97 results are in good agreement with ADC(3). Multireference configuration interaction computations, which are in reasonable agreement with ADC(3), reveal that static correlation does not play a significant role. In the case of the larger Ir(ppy)3 complex, results at the TDDFT/B3LYP and TDDFT/ωB97 levels of theory are presented. Strong discrepancies between the two functionals, which are found with respect to the energies, characters, as well as the density of the low lying states, are discussed in detail and compared to experiment.
Ab initio Calculations of the Linear and Nonlinear Optical Properties of Amino Acids
Tokarz, D; Tuer, A; Cisek, R; Krouglov, S; Barzda, V, E-mail: virgis.barzda@utoronto.ca [Department of Chemical and Physical Sciences, Department of Chemistry, Department of Physics, and Institute for Optical Sciences, University of Toronto, 3359 Mississauga Road North, Mississauga, ON L5L 1C6 (Canada)
2010-11-01
A number of proteins can assemble into chiral structures that display strong nonlinear optical activity. For instance, proteins such as myosin and collagen exhibit intense second harmonic generation (SHG). A large number of experimental studies on the SHG of proteins have been conducted; however few predictive models have been proposed that reliably relate the macroscopic SHG properties to the amino acids present in the peptidic chain. In this study, the linear polarizability ({alpha}), first ({beta}) and second hyperpolarizability ({gamma}) of all twenty amino acids was investigated by time-dependent Hartree-Fock calculations under physiological conditions. Ab initio calculations were performed using the GAMESSUS computational chemistry package. We have found that the aromatic amino acids give rise to the largest mean {alpha}, {beta} and {gamma} values. With this finding, we hope to apply this method to protein structures in order to understand how second harmonic signal is generated from individual amino acids, as well as, recognize how manipulation of the secondary structure of proteins might enhance SHG and third harmonic generation (THG).
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).
X-ray absorption of liquid water studied by advanced ab initio methods
Sun, Zhaoru; Wang, Jianping; Kang, Wei; Car, Roberto; Wu, Xifan
Oxygen K-edge X-ray absorption spectra (XAS) provide a sensitive local probe of the H-bond structure of liquid water. Based on the static COHSEX approach, we computed the XAS spectra of liquid water from molecular structures generated by ab initio molecular dynamics (AIMD) simulations using a van der Waals (vdW) inclusive hybrid functional (PBE0) that gives ambient water structure in quantitative agreement with experiment [JCP 141, 084502 (2014)]. We find that good agreement between experimental and theoretical XAS requires both improved molecular modeling and excitation treatment. In our simulation the over-structured H-bond network resulting from GGA-AIMD is systematically reduced as the directional H-bond strength is lowered by the mitigated self-interaction error in PBE0 and the increased population of interstitial water molecules promoted by vdW interactions. The better H-bond structure in turn gives improved XAS spectra. Moreover, we find that the orbitals obtained from the self-consistent diagonalization of the self-energy are crucial in obtaining spectra that compare well with experiment. Doe SciDAC: DE-SC0008626 and DE-SC0008726.
Tyuterev, Vladimir G.; Kochanov, Roman V.; Tashkun, Sergey A.
2017-02-01
Ab initio dipole moment surfaces (DMSs) of the ozone molecule are computed using the MRCI-SD method with AVQZ, AV5Z, and VQZ-F12 basis sets on a dense grid of about 1950 geometrical configurations. The analytical DMS representation used for the fit of ab initio points provides better behavior for large nuclear displacements than that of previous studies. Various DMS models were derived and tested. Vibration-rotation line intensities of 16O3 were calculated from these ab initio surfaces by the variational method using two different potential functions determined in our previous works. For the first time, a very good agreement of first principle calculations with the experiment was obtained for the line-by-line intensities in rotationally resolved ozone spectra in a large far- and mid-infrared range. This includes high overtone and combination bands up to Δ V = 6. A particular challenge was a correct description of the B-type bands (even Δ V3 values) that represented major difficulties for the previous ab initio investigations and for the empirical spectroscopic models. The major patterns of various B-type bands were correctly described without empirically adjusted dipole moment parameters. For the 10 μ m range, which is of key importance for the atmospheric ozone retrievals, our ab initio intensity results are within the experimental error margins. The theoretical values for the strongest lines of the ν3 band lie in general between two successive versions of HITRAN (HIgh-resolution molecular TRANsmission) empirical database that corresponded to most extended available sets of observations. The overall qualitative agreement in a large wavenumber range for rotationally resolved cold and hot ozone bands up to about 6000 cm-1 is achieved here for the first time. These calculations reveal that several weak bands are yet missing from available spectroscopic databases.
Tyuterev, Vladimir G; Kochanov, Roman V; Tashkun, Sergey A
2017-02-14
Ab initio dipole moment surfaces (DMSs) of the ozone molecule are computed using the MRCI-SD method with AVQZ, AV5Z, and VQZ-F12 basis sets on a dense grid of about 1950 geometrical configurations. The analytical DMS representation used for the fit of ab initio points provides better behavior for large nuclear displacements than that of previous studies. Various DMS models were derived and tested. Vibration-rotation line intensities of (16)O3 were calculated from these ab initio surfaces by the variational method using two different potential functions determined in our previous works. For the first time, a very good agreement of first principle calculations with the experiment was obtained for the line-by-line intensities in rotationally resolved ozone spectra in a large far- and mid-infrared range. This includes high overtone and combination bands up to ΔV = 6. A particular challenge was a correct description of the B-type bands (even ΔV3 values) that represented major difficulties for the previous ab initio investigations and for the empirical spectroscopic models. The major patterns of various B-type bands were correctly described without empirically adjusted dipole moment parameters. For the 10 μm range, which is of key importance for the atmospheric ozone retrievals, our ab initio intensity results are within the experimental error margins. The theoretical values for the strongest lines of the ν3 band lie in general between two successive versions of HITRAN (HIgh-resolution molecular TRANsmission) empirical database that corresponded to most extended available sets of observations. The overall qualitative agreement in a large wavenumber range for rotationally resolved cold and hot ozone bands up to about 6000 cm(-1) is achieved here for the first time. These calculations reveal that several weak bands are yet missing from available spectroscopic databases.
Wen, Jun, E-mail: wenjunkd@mail.ustc.edu.cn [School of Physics and Electric Engineering, Anqing Normal University, Anqing 246011 (China); Department of Physics, University of Science and Technology of China, Hefei 230026 (China); Reid, Michael F. [Department of Physics and Astronomy and MacDiarmid Institute for Advanced Materials and Nanotechnology, University of Canterbury, PB4800 Christchurch (New Zealand); Ning, Lixin [Department of Physics, Anhui Normal University, Wuhu 241000 (China); Zhang, Jie [School of Physics and Electric Engineering, Anqing Normal University, Anqing 246011 (China); Zhang, Yongfan [Department of Chemistry, Fuzhou University, Fuzhou, Fujian 350002 (China); Duan, Chang-Kui; Yin, Min [Department of Physics, University of Science and Technology of China, Hefei 230026 (China)
2014-08-01
Wavefunction-based ab-initio calculations of the electric-dipole moments of 4f{sup N}–4f{sup N} transitions of lanthanide ions are performed to extract the A{sub tp}{sup λ} intensity parameters. The extraction method is an extension of our earlier calculations of crystal-field (CF) parameters for lanthanide ions in crystals. The CASSCF/RASSI-SO (Complete-Active-Space Self-Consistent-Field/Restricted-Active-Space State-Interaction Spin-Orbit) calculations have been carried out on the chosen model system of CaF{sub 2}: Ce{sup 3+} with an interstitial fluoride ion (F{sub i}{sup −}) on z-axis (Ce{sup 3+} ion occupying the C{sub 4v} symmetry site). In consideration of the site symmetry and the coordination situation of Ce{sup 3+} ion at C{sub 4v} site in CaF{sub 2} as well as the superposition model (SM), the calculated intensity parameters for Ce{sup 3+} ion can be classified into three categories, and detailed discussions are then given. - Highlights: • Extraction of transition intensity parameters from ab-initio calculations. • CASSCF/RASSI-SO calculations are performed for Ce{sup 3+}-doped CaF{sub 2} crystal (C{sub 4v} case). • Extracted parameters are analyzed and compared with experiment and other calculation.
2014-12-01
Poly(aryl-ether-ether-ketone) as a Possible Metalized Film Capacitor Dielectric: Accurate Description of the Band Gap Through Ab Initio...Possible Metalized Film Capacitor Dielectric: Accurate Description of the Band Gap Through Ab Initio Calculation Janet Ho and Marco Olguin Sensors...a Possible Metalized Film Capacitor Dielectric: Accurate Description of the Band Gap Through Ab Initio Calculation 5a. CONTRACT NUMBER 5b. GRANT
Ab Initio Calculations for the Polarizabilities of Small Sulfur Clusters
BAI Yu-Lin; CHEN Xiang-Rong; CHENG Xiao-Hong; YANG Xiang-Dong
2005-01-01
@@ Polarizabilities of small Sn (n = 2-8) clusters are calculated by using the higher-order finite-difference pseudopotential density functional method in real space. We find that the polarizabilities of the clusters are considered to be higher than the value estimated from the "hard sphere" model using the bulk static dielectric constant.The computed polarizabilities per atom tend to decrease with the increasing cluster size. The polarizabilities are closely related to the HOMO-LUMO gaps and the geometrical configurations.
Ab Initio Study of Electronic States of Astrophysically Important Molecules
Valiev, R. R.; Berezhnoy, A. A.; Minaev, B. F.; Chernov, V. E.; Cherepanov, V. N.
2016-08-01
A study of electronic states of LiO, NaO, KO, MgO, and CaO molecules has been performed. Potential energy curves of the investigated molecules have been constructed within the framework of the XMC-QDPT2 method. Lifetimes and efficiencies of photolysis mechanisms of these monoxides have been estimated within the framework of an analytical model of photolysis. The results obtained show that oxides of the considered elements in the exospheres of the Moon and Mercury are destroyed by solar photons during the first ballistic flight.
Ab initio theory of helix <-> coil phase transition
Yakubovich, Alexander V.; Solov'yov, Ilia; Solov'yov, Andrey V.
2008-01-01
In this paper, we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix <-> random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory which is free of model parameters and is based solely ...... twisting. The suggested theory is general and with some modification can be applied for the description of phase transitions in other complex molecular systems (e.g. proteins, DNA, nanotubes, atomic clusters, fullerenes).......In this paper, we suggest a theoretical method based on the statistical mechanics for treating the alpha-helix random coil transition in alanine polypeptides. We consider this process as a first-order phase transition and develop a theory which is free of model parameters and is based solely...... on fundamental physical principles. It describes essential thermodynamical properties of the system such as heat capacity, the phase transition temperature and others from the analysis of the polypeptide potential energy surface calculated as a function of two dihedral angles, responsible for the polypeptide...
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.
Electronic Structure of Silicon Nanowires Matrix from Ab Initio Calculations.
Monastyrskii, Liubomyr S; Boyko, Yaroslav V; Sokolovskii, Bogdan S; Potashnyk, Vasylyna Ya
2016-12-01
An investigation of the model of porous silicon in the form of periodic set of silicon nanowires has been carried out. The electronic energy structure was studied using a first-principle band method-the method of pseudopotentials (ultrasoft potentials in the basis of plane waves) and linearized mode of the method of combined pseudopotentials. Due to the use of hybrid exchange-correlation potentials (B3LYP), the quantitative agreement of the calculated value of band gap in the bulk material with experimental data is achieved. The obtained results show that passivation of dangling bonds with hydrogen atoms leads to substantial transformation of electronic energy structure. At complete passivation of the dangling silicon bonds by hydrogen atoms, the band gap value takes the magnitude which substantially exceeds that for bulk silicon. The incomplete passivation gives rise to opposite effect when the band gap value decreases down the semimetallic range.
An ab-initio study of pyrrole and imidazole arylamides
Abramyan Ara M.
2013-01-01
Full Text Available Arylamide foldamers have been shown to have a number of biological and medicinal applications. For example, a class of pyrrole-imidazole polyamide foldamers is capable of binding specific DNA sequences and preventing development of various gene disorders, most importantly cancer. Molecular dynamics (MD simulations can provide crucial details in understanding the atomic level events related to foldamer/DNA binding. An important first step in the accurate simulation of these foldamer/DNA systems is the reparametrization of force field parameters for torsion around the aryl-amide bonds. Here we highlight our Density Functional Theory (DFT potential energy profiles and derived force field parameters for four aryl-amide bond types for the pyrrole and imidazole building blocks extensively used in foldamer design for the DNA-binding polyamides. These results contribute to developing of computational tools for an appropriate molecular modeling of pyrrole-imidazole polyamide/DNA binding, and provide an insight into the chemical factors that influence the flexibility of the pyrrole-imidazole polyamides, and their binding to DNA.
Ab Initio Calculations for the Surface Energy of Silver Nanoclusters
Medasani, Bharat; Vasiliev, Igor; Park, Young Ho
2007-03-01
We apply first principles computational methods to study the surface energy and the surface stress of silver nanoparticles. The structures, energies and lattice contractions of spherical Ag nanoclusters are calculated in the framework of density functional theory combined with the generalized gradient approximation. Our calculations predict the surface energies of Ag nanoclusters to be in the range of 1-2 J/m^2. These values are close to the bulk surface energy of silver, but are significantly lower than the recently reported value of 7.2 J/m^2 derived from the Kelvin equation for free Ag nanoparticles. From the lattice contraction and the nearest neighbor interatomic distance, we estimate the surface stress of the silver nanoclusters to be in the the range of 1-1.45 N/m. This result suggests that a liquid droplet model can be employed to evaluate the surface energy and the surface stress of Ag nanoparticles. K. K. Nanda et al., Phys. Rev. Lett. 91, 106102 (2003).
Ab initio calculation of chromium oxide containing Ti dopant
Maldonado, Frank [Grupo de Fisicoquimica de Materiales, Universidad Tecnica Particular de Loja, Apartado 11-01-608, Loja (Ecuador); Novillo, Corina [Escuela de Ingenieria Quimica, Universidad Tecnica Particular de Loja, Apartado 11-01-608, Loja (Ecuador); Stashans, Arvids, E-mail: arvids@utpl.edu.ec [Grupo de Fisicoquimica de Materiales, Universidad Tecnica Particular de Loja, Apartado 11-01-608, Loja (Ecuador)
2012-01-17
Highlights: Black-Right-Pointing-Pointer Microstructure changes in chromium oxide due to the Ti doping. Black-Right-Pointing-Pointer Discovery of magnetism in Ti-doped {alpha}-Cr{sub 2}O{sub 3} crystal. Black-Right-Pointing-Pointer Explanation of the origin of n-type electrical conductivity. Black-Right-Pointing-Pointer Detailed analysis of electronic properties and density of states. Black-Right-Pointing-Pointer As to authors' knowledge, Ti-doped crystal is studied for the first time by the DFT. - Abstract: First-principles computations based on the density functional theory within the generalised gradient approximation and introduced intra-atomic interaction term for strongly correlated electrons (DFT + U method) has been used in this work. Ti impurity doping in the {alpha}-Cr{sub 2}O{sub 3} crystal has been carried out considering single defect model within the periodic crystalline structure. Atomic displacements, Bader charges on atoms have been computed showing that Ti dopant converts the chemical bonding in its neighbourhood into more ionic one. The defect-local microstructure is such as there exist general tendency of atomic rearrangements away with respect to the Ti imperfection. It is found that defect incorporation produces some local changes upon the band structure of the material and also induces a metallic state. That implies n-type electrical conductivity in the Ti-doped {alpha}-Cr{sub 2}O{sub 3} crystals and relates our work directly to a number of experimental studies in this area. Our results provide evidence over change in magnetic moments in the vicinity of defect, which means that the chromium oxide doped with Ti impurity might not act as an antiferromagnetic substance.
Majumder, Moumita; Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker; Li, Jun; Guo, Hua; Manzhos, Sergei
2014-06-01
New potential energy surfaces for methane were constructed, represented as analytic fits to about 100,000 individual high-level ab initio data. Explicitly-correlated multireference data (MRCI-F12(AE)/CVQZ-F12) were computed using Molpro [1] and fit using multiple strategies. Fits with small to negligible errors were obtained using adaptations of the permutation-invariant-polynomials (PIP) approach [2,3] based on neural-networks (PIP-NN) [4,5] and the interpolative moving least squares (IMLS) fitting method [6] (PIP-IMLS). The PESs were used in full-dimensional vibrational calculations with an exact kinetic energy operator by representing the Hamiltonian in a basis of products of contracted bend and stretch functions and using a symmetry adapted Lanczos method to obtain eigenvalues and eigenvectors. Very close agreement with experiment was produced from the purely ab initio PESs. References 1- H.-J. Werner, P. J. Knowles, G. Knizia, 2012.1 ed. 2012, MOLPRO, a package of ab initio programs. see http://www.molpro.net. 2- Z. Xie and J. M. Bowman, J. Chem. Theory Comput 6, 26, 2010. 3- B. J. Braams and J. M. Bowman, Int. Rev. Phys. Chem. 28, 577, 2009. 4- J. Li, B. Jiang and Hua Guo, J. Chem. Phys. 139, 204103 (2013). 5- S Manzhos, X Wang, R Dawes and T Carrington, JPC A 110, 5295 (2006). 6- R. Dawes, X-G Wang, A.W. Jasper and T. Carrington Jr., J. Chem. Phys. 133, 134304 (2010).
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.
Razee, S.S.A.; Staunton, J.B. [Department of Physics, University of Warwick, Coventry (United Kingdom); Ginatempo, B.; Bruno, E. [Dipartimento di Fisica and Unita INFM, Universita di Messina, Messina (Italy); Pinski, F.J. [Department of Physics, University of Cincinnati, OH (United States)
2001-09-24
A theory is presented for describing the effects of annealing magnetic alloys in magnetic fields. It has an ab initio spin-polarized relativistic Korringa-Kohn-Rostoker coherent potential approximation (KKR-CPA) electronic structure basis and uses the framework of concentration waves. Alloys which would otherwise be soft magnets are found experimentally to develop directional chemical order and significant uniaxial anisotropy when annealed in magnetic fields. Our approach is able to provide a quantitative description of these effects together with the underlying electronic mechanisms. We describe applications to the soft magnetic alloys permalloy and FeCo. (author)
Ab initio calculation of the spectrum and structure of $^{16}$O
Epelbaum, Evgeny; Lähde, Timo A; Lee, Dean; Meißner, Ulf-G; Rupak, Gautam
2013-01-01
We present ab initio lattice calculations of the low-energy even-parity states of $^{16}$O using chiral nuclear effective field theory. We find good agreement with the empirical energy spectrum, and with the electromagnetic properties and transition rates. For the ground state, we find that the nucleons are arranged in a tetrahedral configuration of alpha clusters. For the first excited spin-0 state, we find that the predominant structure is a square configuration of alpha clusters, with rotational excitations that include the first spin-2 state.
Kubota, Yoshiyuki; Ohnuma, Toshiharu; Bučko, Tomáš
2017-03-01
The reaction of carbon dioxide (CO2) with aqueous 2-aminoethanol (MEA) has been investigated using both blue moon ensemble and metadynamics approaches combined with ab initio molecular dynamics (AIMD) simulations. The AIMD simulations predicted the spontaneous deprotonation of the intermediate compound, MEA zwitterion, and they were used to study two possible routes for subsequent proton transfer reactions: the formation of the protonated MEA and the formation of MEA carbamic acid. The free-energy curve depicted by blue moon ensemble technique supported the favorable deprotonation of MEA zwitterion. The overall free-energy profile showed the favorable formation of the ionic products of MEA carbamate ion and protonated MEA.
Heat capacities of xenotime-type ceramics: An accurate ab initio prediction
Ji, Yaqi; Beridze, George; Bosbach, Dirk; Kowalski, Piotr M.
2017-10-01
Because of ability to incorporate actinides into their structure, the lanthanide phosphate ceramics (LnPO4) are considered as potential matrices for the disposal of nuclear waste. Here we present highly reliable ab initio prediction of the variation of heat capacities and the standard entropies of these compounds in zircon structure along lanthanide series (Ln = Dy, …,Lu) and validate them against the existing experimental data. These data are helpful for assessment of thermodynamic parameters of these materials in the context of using them as matrices for immobilization of radionuclides for the purpose of nuclear waste management.
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.
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.
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.
Wang, Shidong; Wang, Zhao; Setyawan, Wahyu; Mingo, Natalio; Curtarolo, Stefano
2011-10-01
Several thousand compounds from the Inorganic Crystal Structure Database have been considered as nanograined, sintered-powder thermoelectrics with the high-throughput ab-initio AFLOW framework. Regression analysis unveils that the power factor is positively correlated with both the electronic band gap and the carrier effective mass, and that the probability of having large thermoelectric power factors increases with the increasing number of atoms per primitive cell. Avenues for further investigation are revealed by this work. These avenues include the role of experimental and theoretical databases in the development of novel materials.
无
2000-01-01
Ab initio method, under the effective core potential(ECP) approximation at HF/LANL2DZ level, has been employed to study the reaction mechanism of the carbonyl insertion of olefin hydroformylation catalyzed by a carbonyl cobalt HCo(CO)3. The two reaction paths have been discussed. The calculated potential energy barriers for the carbonyl migration and the ethyl group migration are 105.0 kJ/mol and 39.17 kJ/mol, respectively. The results indicate that the reaction path via ethyl migration is more energetically favorable than that via carbonyl insertion.
All-electron ab initio investigations of the electronic states of the NiC molecule
Shim, Irene; Gingerich, Karl. A.
1999-01-01
momenta of F-4(g) Ni+ and S-4(u) C-. The predicted ground state, (1)Sigma(+), is well separated from the dense manifold of excited states by an energy gap of 6465 cm(-1). Multi-reference configuration-interaction (MRCI) calculations result in r(e) = 1.621 Angstrom and omega(e) = 874 cm(-1) agreeing well......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...
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.
Monte Carlo methods in AB initio quantum chemistry quantum Monte Carlo for molecules
Lester, William A; Reynolds, PJ
1994-01-01
This book presents the basic theory and application of the Monte Carlo method to the electronic structure of atoms and molecules. It assumes no previous knowledge of the subject, only a knowledge of molecular quantum mechanics at the first-year graduate level. A working knowledge of traditional ab initio quantum chemistry is helpful, but not essential.Some distinguishing features of this book are: Clear exposition of the basic theory at a level to facilitate independent study. Discussion of the various versions of the theory: diffusion Monte Carlo, Green's function Monte Carlo, and release n
Ab initio 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.
Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method
Fujita, Takatoshi; Watanabe, Hirofumi; Tanaka, Shigenori
2009-10-01
We have developed an ab initio path integral molecular dynamics method based on the fragment molecular orbital method. This “FMO-PIMD” method can treat both nuclei and electrons quantum mechanically, and is useful to simulate large hydrogen-bonded systems with high accuracy. After a benchmark calculation for water monomer, water trimer and glycine pentamer have been studied using the FMO-PIMD method to investigate nuclear quantum effects on structure and molecular interactions. The applicability of the present approach is demonstrated through a number of test calculations.
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...... calculations. The previously reported anti and gauche forms of the [C(4)mim](+) cation have been observed, and this study reveals this to be a general feature of the long-chain I-alkyl derivatives. Analysis of mixtures Of [C(6)mim]Cl and [C(6)mim][PF6] has provided information on the nature of the hydrogen...
Ab-initio simulation of photoinduced transformation of small rings in amorphous silica
Bernasconi, D. Donadio M.
2004-01-01
We have studied the photoinduced transformation of small rings (3-membered) in amorphous silica by Car-Parrinello simulations. The process of ring opening leading to the formation of a couple of paramagnetic centers, namely an E' and a non-bridging-oxygen hole center (NBOHC), has been proposed experimentally to occur in silica exposed to F2 laser irradiation (at 7.9 eV). By using a new scheme for the simulation of rare events in ab-initio molecular dynamics (Iannuzzi, Laio and Parrinello, Phy...
Fürst, Joachim Alexander; Hashemi, J.; Markussen, Troels
2009-01-01
techniques and tight-binding calculations to illustrate these materials' transmission properties and give physical arguments to interpret the numerical results. Specifically, above the Fermi energy we find a strong reduction in electron transmission due to localized states in certain regions of the structure......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...
Xiao, H. Y.; Weber, W. J.; Zhang, Y.; Zu, X. T.; Li, S.
2015-01-01
The response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser, electron and ion irradiations. PMID:25660219
Atomic ionization of germanium by neutrinos from an ab initio approach
Chen, Jiunn-Wei [Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China); National Center for Theoretical Sciences and Leung Center for Cosmology and Particle Astrophysics, National Taiwan University, Taipei 10617, Taiwan (China); Chi, Hsin-Chang [Department of Physics, National Dong Hwa University, Shoufeng, Hualien 97401, Taiwan (China); Huang, Keh-Ning [Department of Physics, Sichuan University, Chengdu, Sichuan (China); Department of Physics, Fuzhou University, Fuzhou, Fujian (China); Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China); Liu, C.-P. [Department of Physics, National Dong Hwa University, Shoufeng, Hualien 97401, Taiwan (China); Shiao, Hao-Tse [Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China); Singh, Lakhwinder [Institute of Physics, Academia Sinica, Taipei 11529, Taiwan (China); Department of Physics, Banaras Hindu University, Varanasi 221005 (India); Wong, Henry T. [Institute of Physics, Academia Sinica, Taipei 11529, Taiwan (China); Wu, Chih-Liang; Wu, Chih-Pan [Department of Physics, National Taiwan University, Taipei 10617, Taiwan (China)
2014-04-04
An ab initio calculation of atomic ionization of germanium by neutrinos was carried out in the framework of multiconfiguration relativistic random phase approximation and benchmarked by related atomic structure and photoabsorption data. This improves over the conventional approach based on scattering off free electrons whose validity at sub-keV energy transfer is questionable. Limits on neutrino magnetic moments are derived using reactor neutrino data taken with low threshold germanium detectors. Future applications of these atomic techniques will greatly reduce the atomic uncertainties in low-energy neutrino and dark matter detections.
Temperature-Dependent Diffusion Coefficients from ab initio Computations: Hydrogen in Nickel
E Wimmer; W Wolf; J Sticht; P Saxe; C Geller; R Najafabadi; G Young
2006-03-16
The temperature-dependent mass diffusion coefficient is computed using transition state theory. Ab initio supercell phonon calculations of the entire system provide the attempt frequency, the activation enthalpy, and the activation entropy as a function of temperature. Effects due to thermal lattice expansion are included and found to be significant. Numerical results for the case of hydrogen in nickel demonstrate a strong temperature dependence of the migration enthalpy and entropy. Trapping in local minima along the diffusion path has a pronounced effect especially at low temperatures. The computed diffusion coefficients with and without trapping bracket the available experimental values over the entire temperature range between 0 and 1400 K.
Superconductivity in an expanded phase of ZnO: an ab initio study
Hapiuk, D.; Marques, M. A. L.; Mélinon, P.; Botti, S.; Masenelli, B.; Flores-Livas, J. A.
2015-04-01
It is known that covalent semiconductors become superconducting if conveniently doped with large concentration of impurities. In this article we investigate, using ab initio methods, if the same situation is possible for an ionic, large-band gap semiconductor such as ZnO. We concentrate on the cage-like sodalite phase, with very similar electronic and phononic properties as wurtzite ZnO, but allow for endohedral doping of the cages. We find that sodalite ZnO becomes superconducting for a variety of dopants, reaching a maximum critical temperature of 7 K. This value is comparable to the transition temperatures of doped silicon clathrates, cubic silicon, and diamond.
Novel silicon allotropes for photovoltaic applications from ab initio structure prediction
Amsler, Maximilian; Goedecker, Stefan; Botti, Silvana; Marques, Miguel A. L.
2015-03-01
Sophisticated structure prediction methods have been developed and become essential tools when theoretically designing new materials with desired properties. Their successful applications to many systems at various conditions and increasing computational power have strongly contributed to their popularity. However, an accurate prediction from ab initio calculations still remains an extremely challenging task. The Minima Hopping Method is a powerful tool to find low energy structures given only the chemical composition of a system and allows the prediction of structures at any boundary condition. I will present the results of our studies on low density silicon phases with potential use in photovoltaic applications.
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.
Ab initio molecular simulations on specific interactions between amyloid beta and monosaccharides
Nomura, Kazuya; Okamoto, Akisumi; Yano, Atsushi; Higai, Shin'ichi; Kondo, Takashi; Kamba, Seiji; Kurita, Noriyuki
2012-09-01
Aggregation of amyloid β (Aβ) peptides, which is a key pathogenetic event in Alzheimer's disease, can be caused by cell-surface saccharides. We here investigated stable structures of the solvated complexes of Aβ with some types of monosaccharides using molecular simulations based on protein-ligand docking and classical molecular mechanics methods. Moreover, the specific interactions between Aβ and the monosaccharides were elucidated at an electronic level by ab initio fragment molecular orbital calculations. Based on the results, we proposed which type of monosaccharide prefers to have large binding affinity to Aβ and inhibit the Aβ aggregation.
Ab-initio density functional theory study of a WO3 NH3-sensing mechanism
Hu Ming; Zhang Jie; Wang Wei-Dan; Qin Yu-Xiang
2011-01-01
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.
Simple synthesis, structure and ab initio study of 1,4-benzodiazepine-2,5-diones
Jadidi, Khosrow; Aryan, Reza; Mehrdad, Morteza; Lügger, Thomas; Ekkehardt Hahn, F.; Ng, Seik Weng
2004-04-01
A simple procedure for the synthesis of pyrido[2,1-c][1,4] benzodiazepine-6,12-dione ( 1) and 1,4-benzodiazepine-2,5-diones ( 2a- 2d), using microwave irradiation and/or conventional heating is reported. The configuration of 1 was determined by single-crystal X-ray diffraction. A detailed ab initio B3LYP/6-31G* calculation of structural parameters and substituent effects on ring inversion barriers (Δ G#) and also free energy differences (Δ G0) for benzodiazepines are reported.
Pietrucci, Fabio; Andreoni, Wanda
2011-08-19
Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.
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)
Paired-permanent approach for VB theory (II) -An ab initio spin-free VB program
无
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.
Ab initio studies on the mechanic and magnetic properties of PdHx
Cui Xin; Liang Xi-Xia; Wang Jian-Tao; Zhao Guo-Zhong
2011-01-01
Based on ab initio total energy calculations, the structural, electronic, mechanic, and magnetic properties of PdHx are investigated. It is found that bulk modulus of PdHx is larger than the metal Pd with the hydrogen storage except Pd4H2. The calculated results for the magnetic moments show that the hydrogen addition weakens the magnetic properties of the PdHx systems. A strong magneto-volume effect is found in PdHx structures as well as Pd. The transition from paramagnetism to ferromagnetism is discussed. The corresponding densities of states for both structures are also shown to understand the magnetic behaviour.
Ab initio study of the EFG at the N sites in imidazole
Brown Goncalves, Marcos, E-mail: browngon@if.usp.br [Universidade de Sao Paulo, Instituto de Fisica (Brazil); Di Felice, R. [National Center on Nanostructures and Biosystems at Surfaces (S3) of INFM-CNR (Italy); Poleshchuk, O. Kh. [Tomsk State Pedagogical University (Russian Federation); Petrilli, H. M. [Universidade de Sao Paulo, Instituto de Fisica (Brazil)
2008-01-15
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.
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...... replaced by ‘‘hydrogen atoms’’ having mass 15 and TRPES spectra were calculated. These showed an induction time of (108 10) fs which could directly be assigned to progress along a torsional mode leading to the intersection seam with the molecular ground state. In a stepladder-type approach, the close...
Ab-initio study of several static and dynamic properties of liquid palladium and platinum
González L. E.
2017-01-01
Full Text Available We report a study on several static and dynamic properties of liquid Pd and Pt metals at thermodynamic conditions near their respective triple points. The calculations have been carried out by an ab initio molecular dynamics simulation technique. Results are reported for several static structural magnitudes which are compared with the available X-ray diffraction. As for the dynamic properties, results have been obtained for both single and collective dynamical magnitudes as well as for some transport coeffcients which are compared with the corresponding experimental data.
Orbital free ab initio study of static and dynamic properties of some liquid transition metals
Bhuiyan G. M.
2017-01-01
Full Text Available Several static and dynamic properties of liquid transition metals Cr, Mn and Co are studied for the first time using the orbital free ab-initio molecular dynamics simulation (OF-AIMD. This method is based on the density functional theory (DFT which accounts for the electronic energy of the system whereas the interionic forces are derived from the electronic energy via the Hellman-Feynman theorem. The external energy functional is treated with a local pseudopotential. Results are reported for static structure factors, isothermal compressibility, diffusion coeffcients, sound velocity and viscosity and comparison is performed with the available experimental data and other theoretical calculations.
Ab-initio Study of Known and Hypothetical Metal-Organic Frameworks
Fuentes-Cabrera, Miguel; Nicholson, Don M.
2004-03-01
Rosi et al. [1] have found that microporous Metal-Organic Frameworks (MOF) materials are candidates for hydrogen storage applications. In particular, MOF-5 was found to adsorb hydrogen up to 4.5 weight percent at 78 kelvin and 1.0 weight percent at room temperature and pressure of 20 bar. We use ab-initio techniques to investigate hydrogen adsorption, stability, and the electronic properties of known and hypothetical Metal-Organic Frameworks. [1] N.L. Rosi, J. Eckert, M. Eddaoudi, D.T. Vodak, J. Kim, M. O'Keeffe, and O.M. Yaghi
Krisilov, A. V.; Lantsuzskaya, E. V.; Levina, A. M.
2017-01-01
Reduced ion mobility and scattering cross sections are calculated from experimentally obtained spectra of the ion mobility of linear aliphatic alcohols with carbon atom numbers from 2 to 9. A linear increase in the scattering cross sections as the molecular weight grows is found. According to the results from experiments and quantum chemical calculations, alcohol cluster ions do not form a compact structure. Neither are dipole moments compensated for during dimerization, in contrast to the aldehydes and ketones described earlier. It was concluded from ab initio calculations that charge delocalization in monomeric and dimeric ions of alcohols increases the dipole moment many times over.
Ab initio study of energy-level alignments in polymer-dye blends
Pasveer, W. F.; Bobbert, P. A.; Michels, M. A. J.; Langeveld-Voss, B. M. W.; Schoo, H. F. M.; Bastiaansen, J. J. A. M.
2003-11-01
Polymers with a small amount of dye blended in offer an attractive possibility to change the color of the emitted light by changing the dye. We present ab initio calculations within density-functional theory of the HOMO/LUMO energies for dipyrrolomethane dyes, polyphenylenevinylene and polyfluorene. Special attention is paid to the trends in these energies with variation of the sidegroups of the dyes as observed in cyclic-voltammetry measurements. From the energy-level alignments between dye and polymer we can understand and predict electron and hole trapping, crucial processes for the functioning of light-emitting devices based on these blends.
Ab initio MO study of reaction mechanism for carbonyl migration of Co complex
无
2000-01-01
Ab initio method under the effective core potential (ECP) approximation is employed to study the reaction mechanism of carbonyl migration of the cycle of olefin hydroformylation catalyzed by a carbonyl cobalt HCo(CO)3 at Hartree-Fock (HF) level. The structures of the reactant, transition state and product for the reaction are determined. The energy of each stationary point is corrected at MP2/LAN2DZ//LANL2DZ+ZPE (zero-point energy) level. The calculated activation barrier is 28.89 kJ/mol.
Ab initio study of the epitaxial growth of Ge on Si(100) surface
Milman, V.; Pennycook, S.J.; Jesson, D.E. [Oak Ridge National Lab., TN (United States); Payne, M.C.; Stich, I. [Cambridge Univ. (United Kingdom). Dept. of Physics
1993-11-01
We identify the binding sites for adsorption of a single Ge atom on the Si(100) surface using ab initio total energy calculations. The calculated diffusion barriers are in excellent agreement with experimental estimates. Using a large supercell we resolve the controversy regarding the binding geometry and migration path for the adatom, and investigate the influence of the adatom on the buckling of Si dimers. The adatom induces a buckling defect that is frequently observed using scanning tunneling microscopy (STM); therefore the study of single adatoms may be experimentally accessible.
An accurate potential energy curve for helium based on ab initio calculations
Janzen, A. R.; Aziz, R. A.
1997-07-01
Korona, Williams, Bukowski, Jeziorski, and Szalewicz [J. Chem. Phys. 106, 1 (1997)] constructed a completely ab initio potential for He2 by fitting their calculations using infinite order symmetry adapted perturbation theory at intermediate range, existing Green's function Monte Carlo calculations at short range and accurate dispersion coefficients at long range to a modified Tang-Toennies potential form. The potential with retardation added to the dipole-dipole dispersion is found to predict accurately a large set of microscopic and macroscopic experimental data. The potential with a significantly larger well depth than other recent potentials is judged to be the most accurate characterization of the helium interaction yet proposed.
Bogdanchikov, Georgii A.; Baklanov, Alexey V.
2017-01-01
Ab initio calculations have been carried out to investigate interaction of titanium dioxide TiO2 with oxygen O2 in ground triplet and excited singlet states. On a singlet potential energy surface (PES) formation of a stable compound of titanium peroxide TiO4 is revealed which should appear in reaction of TiO2 with singlet oxygen without activation barrier. This peroxide is lower in energy than the ground state of two individual molecules TiO2 + 3O2 by 34.6 kcal/mol. Location of conical intersection between triplet and singlet PESs of TiO2sbnd O2 is also investigated.
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.
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.
Ab initio study of spin-dependent transport in carbon nanotubes with iron and vanadium adatoms
Fürst, Joachim Alexander; Brandbyge, Mads; Jauho, Antti-Pekka
2008-01-01
We present an ab initio study of spin-dependent transport in armchair carbon nanotubes with transition metal adsorbates: iron or vanadium. The method based on density functional theory and nonequilibrium Green's functions is used to compute the electronic structure and zero-bias conductance...... (majority or minority) being scattered depends on the adsorbate and is explained in terms of d-state filling. We contrast the single-walled carbon nanotube results to the simpler case of the adsorbate on a flat graphene sheet with periodic boundary conditions and corresponding width in the zigzag direction...
Gao, Yi; Huang, Wei; Woodford, Jeffrey; Wang, Lai-Sheng; Zeng, Xiao Cheng
2009-07-15
We show that anion photoelectron spectroscopy can be a very sensitive probe for weak intermolecular interactions between gold anion and a noble-gas atom or other nonreactive molecule. High-level ab initio calculations support the measured trend of relatively weak intermolecular interactions among various gold anion-atom complexes. The interaction between Au(-) and H(2)O is much stronger, comparable to a strong hydrogen bond. The interaction between Au(-) and O(2) is weaker than that between Au(-) and a noble-gas atom (Ar, Kr, or Xe).
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
Suter, James L.; Kabalan, Lara; Khader, Mahmoud; Coveney, Peter V.
2015-11-01
Ab initio molecular dynamics simulations have been performed to gain an understanding of the interfacial microscopic structure and reactivity of fully hydrated clay edges. The models studied include both micropore and interlayer water. We identify acidic sites through dissociation mechanisms; the resulting ions can be stabilized by both micropore and interlayer water. We find clay edges possess a complex amphoteric behavior, which depends on the face under consideration and the location of isomorphic substitution. For the neutral (1 1 0) surface, we do not observe any dissociation on the timescale accessible. The edge terminating hydroxyl groups participate in a hydrogen bonded network of water molecules that spans the interlayer between periodic images of the clay framework. With isomorphic substitutions in the tetrahedral layer of the (1 1 0) clay edge, we find the adjacent exposed apical oxygen behaves as a Brönsted base and abstracts a proton from a nearby water molecule, which in turn removes a proton from an AlOH2 group. With isomorphic substitutions in the octahedral layer of the (1 1 0) clay edge the adjacent exposed apical oxygen atom does not abstract a proton from the water molecules, but increases the number of hydrogen bonded water molecules (from one to two). Acid treated clays are likely to have both sites protonated. The (0 1 0) surface does not have the same interfacial hydrogen bonding structure; it is much less stable and we observe dissociation of half the terminal SiOH groups (tbnd Sisbnd Osbnd H → tbnd Sisbnd O- + H+) in our models. The resulting anions are stabilized by solvation from both micropore and interlayer water molecules. This suggests that, when fully hydrated, the (0 1 0) surface can act as a Brönsted acid, even at neutral pH.
SPASER as a complex system: femtosecond dynamics traced by ab-initio simulations
Gongora, J. S. Totero
2016-03-14
Integrating coherent light sources at the nanoscale with spasers is one of the most promising applications of plasmonics. A spaser is a nano-plasmonic counterpart of a laser, with photons replaced by surface plasmon polaritons and the resonant cavity replaced by a nanoparticle supporting localized plasmonic modes. Despite the large body of experimental and theoretical studies, the understanding of the fundamental properties of the spaser emission is still challenging. In this work, we investigated the ultrafast dynamics of the emission from a core-shell spaser by developing a rigorous first-principle numerical model. Our results show that the spaser is a highly nonlinear system with many interacting degrees of freedom, whose emission sustain a rich manifold of different spatial phases. In the regime of strong interaction we observed that the spaser emission manifests an irreversible ergodic evolution, where energy is equally shared among all the available degrees of freedom. Under this condition, the spaser generates ultrafast vortex lasing modes that are spinning on the femtosecond scale, acquiring the character of a nanoparticle with an effective spin. Interestingly, the spin orientation is defined by spontaneous symmetry breaking induced by quantum noise, which is a fundamental component of our ab-initio model. This opens up interesting possibilities of achieving unidirectional emission from a perfectly spherical nanoparticle, stimulating a broad range of applications for nano-plasmonic lasers as unidirectional couplers, random information sources and novel form of photonics neural-networks. © (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.