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...
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...
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
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)
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.
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.
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...
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.
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.
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.
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.
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.
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.
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 approach to the ion stopping power at the plasma-solid interface
Bonitz, Michael; Schlünzen, Niclas; Wulff, Lasse; Joost, Jan-Philip; Balzer, Karsten
2016-10-01
The energy loss of ions in solids is of key relevance for many applications of plasmas, ranging from plasma technology to fusion. Standard approaches are based on density functional theory or SRIM simulations, however, the applicability range and accuracy of these results are difficult to assess, in particular, for low energies. Here we present an independent approach that is based on ab initio nonequilibrium Green functions theory, e.g. that allows to incorporate electronic correlations effects of the solid. We present the first application of this method to low-temperature plasmas, concentrating on proton and alpha-particle stopping in a graphene layer. In addition to the stopping power we present time-dependent results for the local electron density, the spectral function and the photoemission spectrum that is directly accessible in optical, UV or x-ray diagnostics. http://www.itap.uni-kiel.de/theo-physik/bonitz/.
An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics.
Nakamura, Makoto; Obata, Masao; Morishita, Tetsuya; Oda, Tatsuki
2014-05-14
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields.
Sumner, Isaiah; Iyengar, Srinivasan S
2007-10-18
We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.
A fragment-based approach towards $\\it{ab-initio}$ treatment of polymeric materials
RESHMA S PINGALE; SUBHASH S PINGALE; ANJALI KSHIRSAGAR
2017-07-01
The broad range of applications of $\\pi$-conjugated polymeric materials in industries such as automobiles, textiles, packaging, medical etc. have led to their extensive studies in both academic and industrial fields. Predicting the structure of these polymers is important for the study of their properties. The present work uses a ‘divide and conquer’-type approach for the $\\it{ab-initio}$ studies of these polymeric systems. The method employs a fragmentation technique with independent fragment optimization for obtaining optimized geometries of the oligomers of various polymeric materials such as polyfuran, polypyrrole, polythiophene and other such $\\pi$-conjugated polymers. A few test calculations performed in the study provide fair concurrence between the energies and the HOMO–LUMO energy gaps obtained using the fragmentation-based approach with those obtained using the full optimization of the whole oligomer. Also, a significant reduction in time complexity occurs for the present fragment-based approach compared to the parent system optimization. The results are encouraging and prompt for studies of large polymeric materials.
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).
Molecular tailoring approach: a route for ab initio treatment of large clusters.
Sahu, Nityananda; Gadre, Shridhar R
2014-09-16
Conspectus Chemistry on the scale of molecular clusters may be dramatically different from that in the macroscopic bulk. Greater understanding of chemistry in this size regime could greatly influence fields such as materials science and atmospheric and environmental chemistry. Recent advances in experimental techniques and computational resources have led to accurate investigations of the energies and spectral properties of weakly bonded molecular clusters. These have enabled researchers to learn how the physicochemical properties evolve from individual molecules to bulk materials and to understand the growth patterns of clusters. Experimental techniques such as infrared, microwave, and photoelectron spectroscopy are the most popular and powerful tools for probing molecular clusters. In general, these experimental techniques do not directly reveal the atomistic details of the clusters but provide data from which the structural details need to be unearthed. Furthermore, the resolution of the spectral properties of energetically close cluster conformers can be prohibitively difficult. Thus, these investigations of molecular aggregates require a combination of experiments and theory. On the theoretical front, researchers have been actively engaged in quantum chemical ab initio calculations as well as simulation-based studies for the last few decades. To obtain reliable results, there is a need to use correlated methods such as Møller-Plesset second order method, coupled cluster theory, or dispersion corrected density functional theory. However, due to nonlinear scaling of these methods, optimizing the geometry of large clusters still remains a formidable quantum chemistry challenge. Fragment-based methods, such as divide-and-conquer, molecular tailoring approach (MTA), fragment molecular orbitals, and generalized energy-based fragmentation approach, provide alternatives for overcoming the scaling problem for spatially extended molecular systems. Within MTA, a large
Zeng, Xiancheng; Hu, Hao; Hu, Xiangqian; Cohen, Aron J; Yang, Weitao
2008-03-28
Electron transfer (ET) reactions are one of the most important processes in chemistry and biology. Because of the quantum nature of the processes and the complicated roles of the solvent, theoretical study of ET processes is challenging. To simulate ET processes at the electronic level, we have developed an efficient density functional theory (DFT) quantum mechanical (QM)/molecular mechanical (MM) approach that uses the fractional number of electrons as the order parameter to calculate the redox free energy of ET reactions in solution. We applied this method to study the ET reactions of the aqueous metal complexes Fe(H(2)O)(6)(2+/3+) and Ru(H(2)O)(6)(2+/3+). The calculated oxidation potentials, 5.82 eV for Fe(II/III) and 5.14 eV for Ru(II/III), agree well with the experimental data, 5.50 and 4.96 eV, for iron and ruthenium, respectively. Furthermore, we have constructed the diabatic free energy surfaces from histogram analysis based on the molecular dynamics trajectories. The resulting reorganization energy and the diabatic activation energy also show good agreement with experimental data. Our calculations show that using the fractional number of electrons (FNE) as the order parameter in the thermodynamic integration process leads to efficient sampling and validate the ab initio QM/MM approach in the calculation of redox free energies.
A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.
Spencer, Matt; Eickholt, Jesse; Jianlin Cheng
2015-01-01
Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80 percent and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test dataset of 198 proteins, achieving a Q3 accuracy of 80.7 percent and a Sov accuracy of 74.2 percent.
Yue, Yutao; Chachiyo, Teepanis; Rodriguez, Jorge H.
2007-03-01
The direct application of ab-initio methods (Hartree-Fock or density functional theory) to study complete biomolecules has been impossible due to the huge computational cost of fully quantum mechanical calculations. As an initial step towards overcoming this problem, we implemented an ab-initio-based method to predict geometric structures of large metalloproteins using the principle of ``divide and conquer.'' The method has been applied to small test systems showing satisfactory agreement with all-atom ab initio calculations. We have successfully applied the divide and conquer approach to partially optimize the geometry of a ligand-enzyme system, namely NO binding to nitric-oxide reductases (NOR, P450nor). NOR is a metalloenzyme that catalyzes the reduction of NO to N2O. To compare our results with all atom calculations we studied a biochemically relevant subsystem (375 atoms) of the ligand-enzyme complex. The deviation between the divide and conquer geometry and the all atom partial geometry optimization is minor, on order of 10-1 å for bond lengths. The computational cost of the method is moderately expensive making its application to large (bio) molecules plausible. Supported by NSF CAREER Award CHE-0349189 (JHR).
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.
TOUCHSTONE II: a new approach to ab initio protein structure prediction.
Zhang, Yang; Kolinski, Andrzej; Skolnick, Jeffrey
2003-08-01
We have developed a new combined approach for ab initio protein structure prediction. The protein conformation is described as a lattice chain connecting C(alpha) atoms, with attached C(beta) atoms and side-chain centers of mass. The model force field includes various short-range and long-range knowledge-based potentials derived from a statistical analysis of the regularities of protein structures. The combination of these energy terms is optimized through the maximization of correlation for 30 x 60,000 decoys between the root mean square deviation (RMSD) to native and energies, as well as the energy gap between native and the decoy ensemble. To accelerate the conformational search, a newly developed parallel hyperbolic sampling algorithm with a composite movement set is used in the Monte Carlo simulation processes. We exploit this strategy to successfully fold 41/100 small proteins (36 approximately 120 residues) with predicted structures having a RMSD from native below 6.5 A in the top five cluster centroids. To fold larger-size proteins as well as to improve the folding yield of small proteins, we incorporate into the basic force field side-chain contact predictions from our threading program PROSPECTOR where homologous proteins were excluded from the data base. With these threading-based restraints, the program can fold 83/125 test proteins (36 approximately 174 residues) with structures having a RMSD to native below 6.5 A in the top five cluster centroids. This shows the significant improvement of folding by using predicted tertiary restraints, especially when the accuracy of side-chain contact prediction is >20%. For native fold selection, we introduce quantities dependent on the cluster density and the combination of energy and free energy, which show a higher discriminative power to select the native structure than the previously used cluster energy or cluster size, and which can be used in native structure identification in blind simulations. These
Ab initio study of transport properties in defected carbon nanotubes: an O(N) approach
Biel, Blanca; GarcIa-Vidal, F J; Flores, Fernando [Departamento de Fisica Teorica de la Materia Condensada, Universidad Autonoma de Madrid, E-28049 Madrid (Spain); Rubio, Angel [European Theoretical Spectroscopy Facility (ETSF), Departamento de Fisica de Materiales, Universidad PaIs Vasco, Edificio Korta, Avenida Tolosa 72, 20018 San Sebastian (Spain)], E-mail: blanca.biel@cea.fr
2008-07-23
A combination of ab initio simulations and linear-scaling Green's functions techniques is used to analyze the transport properties of long (up to 1 {mu}m) carbon nanotubes with realistic disorder. The energetics and the influence of single defects (monovacancies and divacancies) on the electronic and transport properties of single-walled armchair carbon nanotubes are analyzed as a function of the tube diameter by means of the local orbital first-principles Fireball code. Efficient O(N) Green's functions techniques framed within the Landauer-Buettiker formalism allow a statistical study of the nanotube conductance averaged over a large sample of defected tubes and thus extraction of the nanotube localization length. The cases of zero and room temperature are both addressed.
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...
Short-range order in ab initio computer generated amorphous and liquid Cu–Zr alloys: A new approach
Galván-Colín, Jonathan, E-mail: jgcolin@ciencias.unam.mx [Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Apartado Postal 70-360, México, D.F. 04510, México (Mexico); Valladares, Ariel A., E-mail: valladar@unam.mx [Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Apartado Postal 70-360, México, D.F. 04510, México (Mexico); Valladares, Renela M.; Valladares, Alexander [Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-542, México, D.F. 04510, México (Mexico)
2015-10-15
Using ab initio molecular dynamics and a new approach based on the undermelt-quench method we generated amorphous and liquid samples of Cu{sub x}Zr{sub 100−x} (x=64, 50, 36) alloys. We characterized the topology of our resulting structures by means of the pair distribution function and the bond-angle distribution; a coordination number distribution was also calculated. Our results for both amorphous and liquids agree well with experiment. Dependence of short-range order with the concentration is reported. We found that icosahedron-like geometry plays a major role whenever the alloys are Cu-rich or Zr-rich disregarding if the samples are amorphous or liquid. The validation of these results, in turn would let us calculate other properties so far disregarded in the literature.
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.
Lee, Jeehye
2010-01-01
We present the first systematic {\\em ab initio} study of anti-ferrodistortive (AFD) order in Ruddlesden-Popper (RP) phases of strontium titanate, Sr$_{1+n}$Ti$_n$O$_{3n+1}$, as a function of both compressive epitaxial strain and phase number $n$. We find all RP phases to exhibit AFD order under a significant range of strains, recovering the bulk AFD order as $\\sim 1/n^2$. A Ginzburg-Landau Hamiltonian generalized to include inter-octahedral interactions reproduces our {\\em ab initio} results well, opening a pathway to understanding other nanostructured perovskite systems.
Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W
2016-08-25
Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and
Gorelik, Tatiana E; van de Streek, Jacco; Kilbinger, Andreas F M
2012-01-01
Ab-initio crystal structure analysis of organic materials from electron diffraction data is presented. The data were collected using the automated electron diffraction tomography (ADT) technique. The structure solution and refinement route is first validated on the basis of the known crystal stru...
Ab-initio study of magnetic properties and phase transitions in Ga (Mn) N with Monte Carlo approach
Sbai, Y.; Ait Raiss, A.; Salmani, E. [LMPHE (URAC 12), Faculty of Science, Mohammed V University, Av. Ibn Batouta, Rabat (Morocco); Bahmad, L., E-mail: Bahmad@fsr.ac.ma [LMPHE (URAC 12), Faculty of Science, Mohammed V University, Av. Ibn Batouta, Rabat (Morocco); Benyoussef, A. [LMPHE (URAC 12), Faculty of Science, Mohammed V University, Av. Ibn Batouta, Rabat (Morocco); Institute of Nanomaterials and Nanotechnologies, MAScIR, Rabat (Morocco); Hassan II Academy of Science and Technology, Rabat (Morocco)
2015-12-15
On the basis of ab-initio calculations and Monte Carlo simulations the magnetic and electronic properties of Gallium nitride (GaN) doped with the transition metal Manganese (Mn) were studied. The ab initio calculations were done using the AKAI–KKR–CPA method within the Local Density Approximation (LDA) approximation. We doped our Diluted Magnetic Semiconductor (DMS), with different concentrations of magnetic impurities Mn and plotted the density of state (DOS) for each one. Showing a half-metallic behavior and ferromagnetic state especially for Ga{sub 0.95}Mn{sub 0.05}N making this DMS a strong candidate for spintronic applications. Moreover, the magnetization and susceptibility of our system as a function of the temperature has been calculated and give for various system size L to study the size effect. In addition, the transition temperature was deduced from the peak of the susceptibility. The Ab initio results are in good agreement with literature especially for (x=0.05) of Mn which gives the most interesting results. - Highlights: • The AKAI–KKR–CPA method has been applied to study the doped compound GaN:Mn. • The local density approximation (LDA) has been applied. • The ab-initio calculations have been performed. • The density of states (DOS) have been plotted for differents doping concentrations, using Monte Carlo simulations.
Fediai, Artem; Ryndyk, Dmitry A.; Cuniberti, Gianaurelio
2016-10-01
Up to now, the electrical properties of the contacts between 3D metals and 2D materials have never been computed at a fully ab initio level due to the huge number of atomic orbitals involved in a current path from an electrode to a pristine 2D material. As a result, there are still numerous open questions and controversial theories on the electrical properties of systems with 3D/2D interfaces—for example, the current path and the contact length scalability. Our work provides a first-principles solution to this long-standing problem with the use of the modular approach, a method which rigorously combines a Green function formalism with the density functional theory (DFT) for this particular contact type. The modular approach is a general approach valid for any 3D/2D contact. As an example, we apply it to the most investigated among 3D/2D contacts—metal/graphene contacts—and show its abilities and consistency by comparison with existing experimental data. As it is applicable to any 3D/2D interface, the modular approach allows the engineering of 3D/2D contacts with the pre-defined electrical properties.
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.
Structure and dynamics of La(III) in aqueous solution An ab initio QM/MM MD approach
Hofer, Thomas S.; Scharnagl, Harald; Randolf, Bernhard R.; Rode, Bernd M.
2006-08-01
Ab initio QM/MM MD simulations have allowed to clarify some of the ambiguities arising from various studies on the hydrated La(III) ion. Both nine- and ten-coordinated hydrates co-exist and interchange in a dissociative process on the nano- or even subnanosecond scale, and thus much faster than any other trivalent main group or transition metal ions. The weak ion-ligand bond (53 N/m) supplies a reasonable explanation for it. The simulation results for La(III) are also compared to those for the isoelectronic ions Cs(I) and Ba(II) obtained by the same ab initio MD procedure, leading to conclusions on the influence of central ion charge on structural and dynamic properties of hydrate complexes.
Luo, Ye, E-mail: xw111luoye@gmail.com; Sorella, Sandro, E-mail: sorella@sissa.it [International School for Advanced Studies (SISSA), and CRS Democritos, CNR-INFM, Via Bonomea 265, I-34136 Trieste (Italy); Zen, Andrea, E-mail: zen.andrea.x@gmail.com [Dipartimento di Fisica, Università di Roma “La Sapienza,” Piazzale Aldo Moro 2, I-00185 Rome (Italy)
2014-11-21
We present a systematic study of a recently developed ab initio simulation scheme based on molecular dynamics and quantum Monte Carlo. In this approach, a damped Langevin molecular dynamics is employed by using a statistical evaluation of the forces acting on each atom by means of quantum Monte Carlo. This allows the use of an highly correlated wave function parametrized by several variational parameters and describing quite accurately the Born-Oppenheimer energy surface, as long as these parameters are determined at the minimum energy condition. However, in a statistical method both the minimization method and the evaluation of the atomic forces are affected by the statistical noise. In this work, we study systematically the accuracy and reliability of this scheme by targeting the vibrational frequencies of simple molecules such as the water monomer, hydrogen sulfide, sulfur dioxide, ammonia, and phosphine. We show that all sources of systematic errors can be controlled and reliable frequencies can be obtained with a reasonable computational effort. This work provides convincing evidence that this molecular dynamics scheme can be safely applied also to realistic systems containing several atoms.
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
Xie, Binbin; Liu, Lihong; Cui, Ganglong; Fang, Wei-Hai, E-mail: fangwh@bnu.edu.cn [Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875 (China); Cao, Jun [Guizhou Provincial Key Laboratory of Computational Nano-material Science, Guizhou Normal College, Guiyang 550018 (China); Feng, Wei; Li, Xin-qi [Department of Physics, Beijing Normal University, Beijing 100875 (China)
2015-11-21
In this work, the recently introduced quantum trajectory mean-field (QTMF) approach is implemented and employed to explore photodissociation dynamics of diazirinone (N{sub 2}CO), which are based on the high-level ab initio calculation. For comparison, the photodissociation process has been simulated as well with the fewest-switches surface hopping (FSSH) and the ab initio multiple spawning (AIMS) methods. Overall, the dynamical behavior predicted by the three methods is consistent. The N{sub 2}CO photodissociation at λ > 335 nm is an ultrafast process and the two C—N bonds are broken in a stepwise way, giving birth to CO and N{sub 2} as the final products in the ground state. Meanwhile, some noticeable differences were found in the QTMF, FSSH, and AIMS simulated time constants for fission of the C—N bonds, excited-state lifetime, and nonadiabatic transition ratios in different intersection regions. These have been discussed in detail. The present study provides a clear evidence that direct ab initio QTMF approach is one of the reliable tools for simulating nonadiabatic dynamics processes.
Many-body effects on the electronic and optical properties of Si nanowires from ab initio approaches
Palummo, M.; Del Sole, R. [European Theoretical Spectroscopy Facility (ETSF), CNR-INFM-SMC, Roma (Italy); Dipartimento di Fisica - Universita di Roma, ' Tor Vergata' , Roma (Italy); Ossicini, S. [European Theoretical Spectroscopy Facility (ETSF), Reggio Emilia (Italy); Dipartimento di Scienze e Metodi dell' Ingegneria, Universita di Modena e Reggio Emilia (Italy)
2010-08-15
The study of semiconducting nanowires is one of the most rapidly growing research areas in materials science and nanotechnology, not only from the point of view of the possible applications, but also regarding the use of the latest developments in the theory. In this paper, we review the general ab initio many-body theory and methods and resume some of our very recent results regarding the structural, electronic, and optical properties of Silicon nanowires (Si-NWs), outlining both the reached achievements and some of the technical aspects necessary to obtain them. (Abstract Copyright [2010], Wiley Periodicals, Inc.)
Nam, Kwangho
2014-10-14
Development of multiscale ab initio quantum mechanical and molecular mechanical (AI-QM/MM) method for periodic boundary molecular dynamics (MD) simulations and their acceleration by multiple time step approach are described. The developed method achieves accuracy and efficiency by integrating the AI-QM/MM level of theory and the previously developed semiempirical (SE) QM/MM-Ewald sum method [J. Chem. Theory Comput. 2005, 1, 2] extended to the smooth particle-mesh Ewald (PME) summation method. In the developed methods, the total energy of the simulated system is evaluated at the SE-QM/MM-PME level of theory to include long-range QM/MM electrostatic interactions, which is then corrected on the fly using the AI-QM/MM level of theory within the real space cutoff. The resulting energy expression enables decomposition of total forces applied to each atom into forces determined at the low-level SE-QM/MM method and correction forces at the AI-QM/MM level, to integrate the system using the reversible reference system propagator algorithm. The resulting method achieves a substantial speed-up of the entire calculation by minimizing the number of time-consuming energy and gradient evaluations at the AI-QM/MM level. Test calculations show that the developed multiple time step AI-QM/MM method yields MD trajectories and potential of mean force profiles comparable to single time step QM/MM results. The developed method, together with message passing interface (MPI) parallelization, accelerates the present AI-QM/MM MD simulations about 30-fold relative to the speed of single-core AI-QM/MM simulations for the molecular systems tested in the present work, making the method less than one order slower than the SE-QM/MM methods under periodic boundary conditions.
Purcell factor for a cylindrical nanocavity: ab initio analytical approach: reply
Bordo, V.
2014-01-01
The comment by Sun et al. [J. Opt. Soc. Am. B 31, 175 (2014)] on my paper [J. Opt. Soc. Am. B 29, 1799 (2012)] is shown here to be due to a lack of understanding of the approach developed in my papers. (C) 2014 Optical Society of America...
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.
Ab-initio Hamiltonian approach to light nuclei and to quantum field theory
J P Vary; H Honkanen; Jun Li; P Maris; A M Shirokov; S J Brodsky; A Harindranath; G F De Teramond; E G Ng; C Yang; M Sosonkina
2010-07-01
Nuclear structure physics is on the threshold of confronting several long-standing problems such as the origin of shell structure from basic nucleon–nucleon and three-nucleon interactions. At the same time those interactions are being developed with increasing contact to QCD, the underlying theory of the strong interactions, using effective field theory. The motivation is clear – QCD offers the promise of great predictive power spanning phenomena on multiple scales from quarks and gluons to nuclear structure. However, new tools that involve non-perturbative methods are required to build bridges from one scale to the next. We present an overview of recent theoretical and computational progress with a Hamiltonian approach to build these bridges and provide illustrative results for the nuclear structure of light nuclei and quantum field theory.
Guilhon, I.; Bechstedt, F.; Botti, Silvana; Marques, M.; Teles, L. K.
2017-06-01
We study the incomplete oxidation of graphene or reduction of graphene oxide for hydroxyl and epoxy oxidant groups. While in wet oxidation hydroxyl groups are favorable, in a drier environment an oxygen atom can bridge two neighboring carbon atoms. We model composition variations and structural disorder within a statistical theory, the generalized quasichemical approximation, combined with density functional theory calculations of the local atomic geometries. A generalization of the statistical approach is developed to account for the antiparallel orientation of hydroxyl groups and a fourfold coordination of C atoms. The theoretical framework enables a thermodynamic treatment of graphene oxide as a function of oxygen content, allowing us to derive temperature-composition phase diagrams and investigate possible clustering and segregation. The resulting geometries, local and average electronic structures, and optical absorption spectra are discussed and compared with available experimental data.
A field-theoretic approach to linear scaling \\textit{ab-initio} molecular dynamics
Richters, Dorothee; Kühne, Thomas D
2012-01-01
We present a field-theoretic method suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is solved by means of a properly modified Langevin equation. The predictive power of this approach is illustrated using the example of liquid methane under extreme conditions.
Miyamoto, Yoshiyuki; Zhang, Hong; Rubio, Angel
2012-06-05
Nanoscale molecular confinement substantially modifies the functionality and electronic properties of encapsulated molecules. Many works have approached this problem from the perspective of quantifying ground-state molecular changes, but little is known about the nonequilibrium dynamics of encapsulated molecular system. In this letter, we report an analysis of the nonequilibrium dynamics of acetylene (C(2)H(2)) inside a semiconducting carbon nanotube (CNT). An ultrashort high-intense laser pulse (2 fs width and 10(15) W/cm(2) intensity) brings the systems out of equilibrium. This process is modeled by comprehensive first-principles time-dependent density-functional simulations. When encapsulated, acetylene dimer, unlike a single acetylene molecule, exhibits correlated vibrational dynamics (C-C bond rotation and H-C-C bending) that is markedly different from the dynamics observed in the gas phase. This result highlights the role of CNT in modulating the optical electric field within the tube. At longer simulation timescales (> 20 fs) in the largest-diameter tube studied here [CNT(14,0)], we observe synchronized rotation about the C-C axes in the dimer and ultimately ejection of one of the four hydrogen atoms. Our results illustrate the richness of photochemical phenomena in confined geometries.
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.
Hicks, L.D.; Fry, A.J.; Kurzweil, V.C. [Wesleyan Univ., Middletown, CT (United States). Hall-Atwater Lab.
2004-12-15
The electron affinities (EAs) of a training set of 29 monosubstituted benzalacetophenones (chalcones) were computed at the ab initio density functional B3LYP/6-31G* level of theory. The EAs and experimental reduction potentials of the training set are highly linearly correlated (correlation coefficient of 0.969 and standard deviation of 10.8 mV). An additional 72 di-, tri-, and tetrasubstituted chalcones were then synthesized. Their reduction potentials were predicted from computed EAs using the linear correlation derived from the training set. Agreement between the experimental and computed reduction potentials is remarkably good, with a standard deviation of less than 22 mV for this very large set of substances whose potentials extend over a range of almost 700 mV. (Author)
Bertoldi, Dalía S.; Ramos, Susana B.; Guillermet, Armando Fernández
2017-08-01
We present a theoretical analysis of the equation of state (EOS) of metals using a quasi-harmonic Einstein model with a dimensionless cohesive energy versus distance function (F(z)) involving the Wigner-Seitz radius and a material-dependent scaling length, as suggested in classical works by Rose, Ferrante, Smith and collaborators. Using this model, and ;universal; values for the function and its first and second derivatives at the equilibrium distance (z=0), three general interrelations between EOS parameters and the cohesive energy are obtained. The first correlation involves the bulk modulus, and the second, the thermal expansion coefficient. In order to test these results an extensive database is developed, which involves available experimental data, and results of current ab initio density-functional-theory calculations using the VASP code. In particular, the 0 K values for volume, bulk modulus, its pressure derivative, and the cohesive energy of 27 elements belonging to the first (Sc, Ti, V, Cr, Fe, Co, Ni, Cu, Zn), second (Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd) and third (Hf, Ta, W, Re, Os, Ir, Pt, Au) transition row of the Periodic Table are calculated ab initio and used to test the present results. The third correlation obtained, allows an evaluation of the third derivative of F(z) at z=0 for the current elements. With this new information, a discussion is presented of the possibility of finding a ;universal; F(z) versus z function able to account accurately for the pressure derivative of the bulk modulus of the transition elements.
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.
Reeh, S; Kasprzak, M; Klusmann, C D; Stalf, F; Music, D; Ekholm, M; Abrikosov, I A; Schneider, J M
2013-06-19
The elastic properties of fcc Fe-Mn-X (X = Cr, Co, Ni, Cu) alloys with additions of up to 8 at.% X were studied by combinatorial thin film growth and characterization and by ab initio calculations using the disordered local moments (DLM) approach. The lattice parameter and Young's modulus values change only marginally with X. The calculations and experiments are in good agreement. We demonstrate that the elastic properties of transition metal alloyed Fe-Mn can be predicted by the DLM model.
Accurate ab initio spin densities
Boguslawski, Katharina; Legeza, Örs; Reiher, Markus
2012-01-01
We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys. 2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CA...
de Melo, Pedro Miguel M. C.; Marini, Andrea
2016-04-01
We present a full ab initio description of the coupled out-of-equilibrium dynamics of photons, phonons, and electrons. In the present approach, the quantized nature of the electromagnetic field as well as of the nuclear oscillations is fully taken into account. The result is a set of integrodifferential equations, written on the Keldysh contour, for the Green's functions of electrons, phonons, and photons where the different kinds of interactions are merged together. We then concentrate on the electronic dynamics in order to reduce the problem to a computationally feasible approach. By using the generalized Baym-Kadanoff ansatz and the completed collision approximation, we introduce a series of efficient but controllable approximations. In this way, we reduce all equations to a set of decoupled equations for the density matrix that describe all kinds of static and dynamical correlations. The final result is a coherent, general, and inclusive scheme to calculate several physical quantities: carrier dynamics, transient photoabsorption, and light emission, all of which include, at the same time, electron-electron, electron-phonon, and electron-photon interactions. We further discuss how all these observables can be easily calculated within the present scheme using a fully atomistic ab initio approach.
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.
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.
Prediction of possible CaMnO3 modifications using an ab initio minimization data-mining approach.
Zagorac, Jelena; Zagorac, Dejan; Zarubica, Aleksandra; Schön, J Christian; Djuris, Katarina; Matovic, Branko
2014-10-01
We have performed a crystal structure prediction study of CaMnO3 focusing on structures generated by octahedral tilting according to group-subgroup relations from the ideal perovskite type (Pm\\overline 3 m), which is the aristotype of the experimentally known CaMnO3 compound in the Pnma space group. Furthermore, additional structure candidates have been obtained using data mining. For each of the structure candidates, a local optimization on the ab initio level using density-functional theory (LDA, hybrid B3LYP) and the Hartree--Fock (HF) method was performed, and we find that several of the modifications may be experimentally accessible. In the high-pressure regime, we identify a post-perovskite phase in the CaIrO3 type, not previously observed in CaMnO3. Similarly, calculations at effective negative pressure predict a phase transition from the orthorhombic perovskite to an ilmenite-type (FeTiO3) modification of CaMnO3.
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.
Pohl, Gábor; Beke, Tamás; Borbély, János; Perczel, András
2006-11-15
Because of their great flexibility and strength resistance, both spider silks and silkworm silks are of increasing scientific and commercial interest. Despite numerous spectroscopic and theoretical studies, several structural properties at the atomic level have yet to be identified. The present theoretical investigation focuses on these issues by studying three silk-like model peptides: (AG)(64), [(AG)(4)EG](16), and [(AG)(4)PEG](16), using a Lego-type approach to construct these polypeptides. On the basis of these examples it is shown that thermoneutral isodesmic reactions and ab initio calculations provide a capable method to investigate structural properties of repetitive polypeptides. The most probable overall fold schema of these molecules with respect to the type of embedded hairpin structures were determined at the ab initio level of theory (RHF/6-311++G(d,p)//RHF/3-21G). Further on, analysis is carried out on the possible hairpin and turn regions and on their effect on the global fold. In the case of the (AG)(64) model peptide, the optimal beta-sheet/turn ratio was also determined, which provided good support for experimental observations. In addition, lateral shearing of a hairpin "folding unit" was investigated at the quantum chemical level to explain the mechanical properties of spider silk. The unique mechanical characteristics of silk bio-compounds are now investigated at the atomic level.
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.
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...
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.
Josefsson, Ida; Kunnus, Kristjan; Schreck, Simon; Foehlisch, Alexander; de Groot, Frank; Wernet, Philippe; Odelius, Michael
2012-01-01
A new ab initio approach to the calculation of X-ray spectra is demonstrated. It combines a high-level quantum chemical description of the chemical interactions and local atomic multiplet effects. We show here calculated L-edge X-ray absorption (XA) and resonant inelastic X-ray scattering spectra fo
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.
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.
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.
Nishioka, Hirotaka; Ando, Koji
2011-05-28
By making use of an ab initio fragment-based electronic structure method, fragment molecular orbital-linear combination of MOs of the fragments (FMO-LCMO), developed by Tsuneyuki et al. [Chem. Phys. Lett. 476, 104 (2009)], we propose a novel approach to describe long-distance electron transfer (ET) in large system. The FMO-LCMO method produces one-electron Hamiltonian of whole system using the output of the FMO calculation with computational cost much lower than conventional all-electron calculations. Diagonalizing the FMO-LCMO Hamiltonian matrix, the molecular orbitals (MOs) of the whole system can be described by the LCMOs. In our approach, electronic coupling T(DA) of ET is calculated from the energy splitting of the frontier MOs of whole system or perturbation method in terms of the FMO-LCMO Hamiltonian matrix. Moreover, taking into account only the valence MOs of the fragments, we can considerably reduce computational cost to evaluate T(DA). Our approach was tested on four different kinds of model ET systems with non-covalent stacks of methane, non-covalent stacks of benzene, trans-alkanes, and alanine polypeptides as their bridge molecules, respectively. As a result, it reproduced reasonable T(DA) for all cases compared to the reference all-electron calculations. Furthermore, the tunneling pathway at fragment-based resolution was obtained from the tunneling current method with the FMO-LCMO Hamiltonian matrix.
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.
Kowalski, Piotr M
2011-01-01
The mass-dependent equilibrium stable isotope fractionation between different materials is an important geochemical process. Here we present an efficient method to compute the isotope fractionation between complex minerals and fluids at high pressure, P, and temperature, T, representative for the Earth's crust and mantle. The method is tested by computation of the equilibrium fractionation of lithium isotopes between aqueous fluids and various Li bearing minerals such as staurolite, spodumene and mica. We are able to correctly predict the direction of the isotope fractionation as observed in the experiments. On the quantitative level the computed fractionation factors agree within 1.0 permil with the experimental values indicating predictive power of ab initio methods. We show that with ab initio methods we are able to investigate the underlying mechanisms driving the equilibrium isotope fractionation process, such as coordination of the fractionating elements, their bond strengths to the neighboring atoms, c...
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 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.
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...
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.
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.
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.
Ricca, Alessandra; Bauschlicher, Charles W.; Langhoff, Stephen R. (Technical Monitor)
1994-01-01
Density functional theory (DFT) is found to give a better description of the geometries and vibrational frequencies of FeL and FeL(sup +) systems than second order Moller Plesset perturbation theory (MP2). Namely, the DFT correctly predicts the shift in the CO vibrational frequency between free CO and the Sigma(sup -) state of FeCO and yields a good result for the Fe-C distance in the quartet states of FeCH4(+) 4 These are properties where the MP2 results are unsatisfactory. Thus DFT appears to be an excellent approach for optimizing the geometries and computing the zero-point energies of systems containing first transition row atoms. Because the DFT approach is biased in favor of the 3d(exp 7) occupation, whereas the more traditional approaches are biased in favor of the 3d(exp 6) occupation, differences are found in the relative ordering of states. It is shown that if the dissociation is computed to the most appropriate atomic asymptote and corrected to the ground state asymptote using the experimental separations, the DFT results are in good agreement with high levels of theory. The energetics at the DFT level are much superior to the MP2 and in most cases in good agreement with high levels of theory.
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 ...
Asimow, P. D.; Caracas, R.; Wolf, A. S.; Harvey, J. P.
2016-12-01
To find inner core compositions (X) consistent with geophysical data, we need phase relations of multicomponent metallic systems at high pressure (P) and temperature (T); the stable phase at a given (P,T,X) determines the physical properties. Given the difficulty of experiments under inner core conditions, reliable computations of such phase relations are needed. Despite advances in computational methods and computing power, challenges include proper treatment of solid solutions with their continuous variation in composition and ordering phenomena. We consider here how to predict phase diagrams from thermodynamic models of partly ordered solid solution phases calibrated with density functional theory to obtain static enthalpy (H) and volume (V), density functional perturbation theory and quasiharmonic approximation for vibrational heat capacity, and three approaches to solution theory to parameterize mixing properties. This approach is applied to B2 and HCP structures in the system Fe-FeSi for comparison to experimental data such as Fischer et al. (2013). We computed H and V of 7 compositions across the Fe-FeSi binary for both B2 and HCP structures, every 20 or 40 GPa from 0 to 400 GPa. We used supercells with up to 24 atoms to explore multiple configurations of the atoms. The H differences among clustered, random, and ordered arrangments of the atoms are neither so small as to imply random mixing nor so large that one configuration will dominate. We computed phonon density of states of at least three compositions for each structure in order to define vibrational heat capacity across each binary using ideal mixing and to test this approximation. We then used three different approaches to solid solution theory to fit the mixing properties: (1) Asymmetric regular solution theory, with (P,T)-dependent Margules parameters to describe the excess H but assuming ideal one-site entropy (S) of mixing; (2) the quasichemical model, accounting for optimized Fe-Si pair
Solomon, Gemma C; Reimers, Jeffrey R; Hush, Noel S
2004-10-01
A priori evaluations, using Hartree-Fock self-consistent-field (SCF) theory or density-functional theory (DFT), of the current passing between two electrodes through a single bridging molecule result in predicted conductivities that may be up to one to two orders of magnitude larger than observed ones. We demonstrate that this is, in part, often due to the improper application of the computational methods. Conductivity is shown to arise from tunneling between junction states of the electrodes through the molecule; these states are inherently either quasi two-fold or four-fold degenerate and always comprise the (highest occupied molecular orbital) HOMO band at the Fermi energy of the system. Frequently, in previous cluster based molecular conduction calculations, closed-shell SCF or Kohn-Sham DFT methods have been applied to systems that we demonstrate to be intrinsically open shell in nature. Such calculations are shown to induce artificial HOMO-LUMO (LUMO-lowest unoccupied molecular orbital) band splittings that Landauer-based formalisms for steady-state conduction interpret as arising from extremely rapid through-molecule tunneling at the Fermi energy, hence, overestimating the low-voltage conductivity. It is demonstrated that these shortcomings can be eliminated, dramatically reducing calculated current magnitudes, through the alternate use of electronic-structure calculations based on the spin-restricted open-shell formalism and related multiconfigurational SCF of DFT approaches. Further, we demonstrate that most anomalies arising in DFT implementations arise through the use of hybrid density functionals such as B3LYP. While the enhanced band-gap properties of these functionals have made them the defacto standard in molecular conductivity calculations, we demonstrate that it also makes them particularly susceptible to open-shell anomalies.
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 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 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...
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.
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.
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.
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 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.
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.)
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...
Kozlov, S V; Stolyarov, A V
2016-01-01
We performed a diabatization of the mutually perturbed $1^1\\Pi$ and $2^1\\Pi$ states of KRb based on both electronic structure calculation and direct coupled-channel deperturbation analysis of experimental energies. The potential energy curves (PECs) of the diabatic states and their scalar coupling were constructed from the \\textit{ab initio} adiabatic PECs by analytically integrating the radial $\\langle \\psi_1^{ad}|\\partial /\\partial R|\\psi_2^{ad}\\rangle$ matrix element obtained by a finite-difference method. The diabatic potentials and electronic coupling function were refined by the least squares fitting of the rovibronic termvalues of the $1^1\\Pi\\sim 2^1\\Pi$ complex. The empirical PECs combined with the coupling function as well as the diabatized spin-orbit coupling and transition dipole matrix elements are useful for further deperturbation treatment of both singlet and triplet states manifold.
Vladimir Sokolovskiy
2014-09-01
Full Text Available The complex magnetic and structural properties of Co-doped Ni-Mn-Ga Heusler alloys have been investigated by using a combination of first-principles calculations and classical Monte Carlo simulations. We have restricted the investigations to systems with 0, 5 and 9 at% Co. Ab initio calculations show the presence of the ferrimagnetic order of austenite and martensite depending on the composition, where the excess Mn atoms on Ga sites show reversed spin configurations. Stable ferrimagnetic martensite is found for systems with 0 (5 at% Co and a c=a ratio of 1.31 (1.28, respectively, leading to a strong competition of ferro- and antiferro-magnetic exchange interactions between nearest neighbor Mn atoms. The Monte Carlo simulations with ab initio exchange coupling constants as input parameters allow one to discuss the behavior at finite temperatures and to determine magnetic transition temperatures. The Curie temperature of austenite is found to increase with Co, while the Curie temperature of martensite decreases with increasing Co content. This behavior can be attributed to the stronger Co-Mn, Mn-Mn and Mn-Ni exchange coupling constants in austenite compared to the corresponding ones in martensite. The crossover from a direct to inverse magnetocaloric effect in Ni-Mn-Ga due to the substitution of Ni by Co leads to the appearance of a “paramagnetic gap” in the martensitic phase. Doping with In increases the magnetic jump at the martensitic transition temperature. The simulated magnetic and magnetocaloric properties of Co- and In-doped Ni-Mn-Ga alloys are in good qualitative agreement with the available experimental data.
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).
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 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.
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.
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...
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.
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.
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).
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.
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.
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 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).
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.
Sylvetsky, Nitai; Peterson, Kirk A.; Karton, Amir; Martin, Jan M. L.
2016-06-01
In the context of high-accuracy computational thermochemistry, the valence coupled cluster with all singles and doubles (CCSD) correlation component of molecular atomization energies presents the most severe basis set convergence problem, followed by the (T) component. In the present paper, we make a detailed comparison, for an expanded version of the W4-11 thermochemistry benchmark, between, on the one hand, orbital-based CCSD/AV{5,6}Z + d and CCSD/ACV{5,6}Z extrapolation, and on the other hand CCSD-F12b calculations with cc-pVQZ-F12 and cc-pV5Z-F12 basis sets. This latter basis set, now available for H-He, B-Ne, and Al-Ar, is shown to be very close to the basis set limit. Apparent differences (which can reach 0.35 kcal/mol for systems like CCl4) between orbital-based and CCSD-F12b basis set limits disappear if basis sets with additional radial flexibility, such as ACV{5,6}Z, are used for the orbital calculation. Counterpoise calculations reveal that, while total atomization energies with V5Z-F12 basis sets are nearly free of BSSE, orbital calculations have significant BSSE even with AV(6 + d)Z basis sets, leading to non-negligible differences between raw and counterpoise-corrected extrapolated limits. This latter problem is greatly reduced by switching to ACV{5,6}Z core-valence basis sets, or simply adding an additional zeta to just the valence orbitals. Previous reports that all-electron approaches like HEAT (high-accuracy extrapolated ab-initio thermochemistry) lead to different CCSD(T) limits than "valence limit + CV correction" approaches like Feller-Peterson-Dixon and Weizmann-4 (W4) theory can be rationalized in terms of the greater radial flexibility of core-valence basis sets. For (T) corrections, conventional CCSD(T)/AV{Q,5}Z + d calculations are found to be superior to scaled or extrapolated CCSD(T)-F12b calculations of similar cost. For a W4-F12 protocol, we recommend obtaining the Hartree-Fock and valence CCSD components from CCSD-F12b/cc-pV{Q,5}Z-F12
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 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}.
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.
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.
Ab initio vibrations in nonequilibrium nanowires
Jauho, Antti-Pekka; Engelund, Mads; Markussen, T
2010-01-01
We review recent results on electronic and thermal transport in two different quasi one-dimensional systems: Silicon nanowires (SiNW) and atomic gold chains. For SiNW's we compute the ballistic electronic and thermal transport properties on equal footing, allowing us to make quantitative predicti......We review recent results on electronic and thermal transport in two different quasi one-dimensional systems: Silicon nanowires (SiNW) and atomic gold chains. For SiNW's we compute the ballistic electronic and thermal transport properties on equal footing, allowing us to make quantitative...... predictions for the thermoelectric properties, while for the atomic gold chains we evaluate microscopically the damping of the vibrations, due to the coupling of the chain atoms to the modes in the bulk contacts. Both approaches are based on the combination of density-functional theory, and nonequilibrium...... Green's functions....
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.
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.
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 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...
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...
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 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.
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.
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.
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.
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
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.
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.
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.
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.
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.
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.
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., 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.
Geng, Hua Y.
2015-02-01
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model-the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of rs = 0.912.
Ab initio nuclear structure and reactions with chiral three-body forces
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.
The Crystal Structure of Impurity Centers Tm^{2+} and Eu^{2+} in SrCl2: Ab Initio Calculations
Chernyshev, V. A.; Serdcev, A. V.; Petrov, V. P.; Nikiforov, A. E.
2016-12-01
Ab initio calculations of the impurity centers Tm^{2+} thulium and europium Eu^{2+} in SrCl2 and MeF2 (Me = Ca, Sr, Ba) were carried out at low (zero) temperature. The crystal structure of impurity centers was investigated. Charge density maps show that the bonds formed by the rare-earth ions have an ionic character. The crystal structures, lattice dynamics, and band structures of MeF2 and SrCl2 were calculated at low temperature. Ab initio calculations were performed in periodic CRYSTAL code within the framework of the MO LCAO approach by using hybrid DFT functionals.
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.
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 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.
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 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...
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.
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.
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.
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.
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.
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.
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.
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.
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
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)
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.
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.
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.
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.
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 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 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 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
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.
Marsalek, Ondrej; Markland, Thomas E
2016-02-07
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 ring polymer contraction 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 protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.
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.
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.)
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.)
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 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.
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 ...
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.
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
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...
Galler, Anna; Gunacker, Patrik; Tomczak, Jan; Thunström, Patrik; Held, Karsten
Recently, approaches such as the dynamical vertex approximation (D ΓA) or the dual-fermion method have been developed. These diagrammatic approaches are going beyond dynamical mean field theory (DMFT) by including nonlocal electronic correlations on all length scales as well as the local DMFT correlations. Here we present our efforts to extend the D ΓA methodology to ab-initio materials calculations (ab-initio D ΓA). Our approach is a unifying framework which includes both GW and DMFT-type of diagrams, but also important nonlocal correlations beyond, e.g. nonlocal spin fluctuations. In our multi-band implementation we are using a worm sampling technique within continuous-time quantum Monte Carlo in the hybridization expansion to obtain the DMFT vertex, from which we construct the reducible vertex function using the two particle-hole ladders. As a first application we show results for transition metal oxides. Support by the ERC project AbinitioDGA (306447) is acknowledged.
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
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.
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).
Ab initio many-body calculations of nucleon-nucleus scattering
Quaglioni, Sofia; Navrátil, Petr
2009-04-01
We develop a new ab initio many-body approach capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group method with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters. This approach preserves translational symmetry and the Pauli principle. We outline technical details and present phase-shift results for neutron scattering on H3, He4, and Be10 and proton scattering on He3,4, using realistic nucleon-nucleon (NN) potentials. Our A=4 scattering results are compared to earlier ab initio calculations. We find that the CD-Bonn NN potential in particular provides an excellent description of nucleon-He4S-wave phase shifts. In contrast, the experimental nucleon-He4P-wave phase shifts are not well reproduced by any NN potential we use. We demonstrate that a proper treatment of the coupling to the n-Be10 continuum is successful in explaining the parity-inverted ground state in Be11.
Ab initio many-body calculations of nucleon-nucleus scattering
Quaglioni, Sofia
2009-01-01
We develop a new ab initio many-body approach capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group method with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters. This approach preserves translational symmetry and Pauli principle. We outline technical details and present phase shift results for neutron scattering on 3H, 4He and 10Be and proton scattering on 3He and 4He, using realistic nucleon-nucleon (NN) potentials. Our A=4 scattering results are compared to earlier ab initio calculations. We find that the CD-Bonn NN potential in particular provides an excellent description of nucleon-4He S-wave phase shifts. On the contrary, the experimental nucleon-4He P-wave phase shifts are not well reproduced by any NN potential we use. We demonstrate that a proper treatment of the coupling to the n-10Be continuum is successful in explaining the parity-inverted ground state in 11Be.
Tanha, Matteus; Cappiello, Alex; Gordon, Geoffrey J; Yaron, David J
2013-01-01
A means to take advantage of molecular similarity to lower the computational cost of electronic structure theory is proposed, in which parameters are embedded into a low-cost, low-level (LL) ab initio theory and adjusted to obtain agreement with a higher level (HL) ab initio theory. This approach is explored by training such a model on data for ethane and testing the resulting model on methane, propane and butane. The electronic distribution of the molecules is varied by placing them in strong electrostatic environments consisting of random charges placed on the corners of a cube. The results find that parameters embedded in HF/STO-3G theory can be adjusted to obtain agreement, to within about 2 kcal/mol, with results of HF/6-31G theory. Obtaining this level of agreement requires the use of parameters that are functions of the bond lengths, atomic charges, and bond orders within the molecules. The argument is made that this approach provides a well-controlled means to take advantage of molecular similarity in...
Ab initio interaction potentials for X and B excited states of He-I{sub 2} for studying dynamics
Prosmiti, Rita; Garcia-Gutierrez, Leonor; Delgado-Tellez, Laura; Valdes, Alvaro; Villarreal, Pablo; Delgado-Barrio, Gerardo, E-mail: rita@imaff.cfmac.csic.e [Instituto de Fisica Fundamental (CSIC), Serrano 123, 28006 Madrid (Spain)
2009-11-01
Ab initio CCSD(T) and MRCI approaches were employed to construct potential energy surfaces of the ground and the B electronic excited states of He-I{sub 2} complex, while full quantum mechanical methods were applied to study its spectroscopy and dynamics. A description of the approach adopted, together with the results obtained and their comparison with recent experimental data, as well as further improvements are presented.
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.
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.
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.
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 electronic structure, magnetism, and magnetocrystalline anisotropy of UGa2
Diviš, Martin; Richter, Manuel; Eschrig, Helmut; Steinbeck, Lutz
1996-04-01
Ab initio electronic structure calculations for the intermetallic compound UGa2 were performed using an optimized linear combination of atomic orbitals method based on the local spin density approximation. Three separate calculations were done treating the uranium 5f states as band states and as localized states with occupation two and three, respectively. In the itinerant approach, spin and orbital moments, magnetocrystalline anisotropy, and the Sommerfeld constant were calculated and found to deviate significantly from the related experimental data. In the localized approach, crystal field parameters were obtained for the 5f states, which have been treated by self-interaction corrected local-density theory. This approach with 5f2 occupation is shown to provide reasonable results for the anisotropy of the susceptibility, for the field dependence of the magnetic moments, and for the Sommerfeld constant.
{ital Ab initio} electronic structure, magnetism, and magnetocrystalline anisotropy of UGa{sub 2}
Divis, M. [Department of Metal Physics, Charles University, Ke Karlovu 5, 121 16 Prague 2 (Czech Republic)]|[Max-Planck-Gesellschaft, Research Group ``Electron Systems,`` University of Technology, D-01062 Dresden (Germany); Richter, M.; Eschrig, H.; Steinbeck, L. [Max-Planck-Gesellschaft, Research Group ``Electron Systems,`` University of Technology, D-01062 Dresden (Germany)
1996-04-01
{ital Ab} {ital initio} electronic structure calculations for the intermetallic compound UGa{sub 2} were performed using an optimized linear combination of atomic orbitals method based on the local spin density approximation. Three separate calculations were done treating the uranium 5{ital f} states as band states and as localized states with occupation two and three, respectively. In the itinerant approach, spin and orbital moments, magnetocrystalline anisotropy, and the Sommerfeld constant were calculated and found to deviate significantly from the related experimental data. In the localized approach, crystal field parameters were obtained for the 5{ital f} states, which have been treated by self-interaction corrected local-density theory. This approach with 5{ital f}{sup 2} occupation is shown to provide reasonable results for the anisotropy of the susceptibility, for the field dependence of the magnetic moments, and for the Sommerfeld constant. {copyright} {ital 1996 The American Physical Society.}
A unified scheme for ab initio molecular orbital theory and path integral molecular dynamics
Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi
2001-11-01
We present a general approach for accurate calculation of chemical substances which treats both nuclei and electrons quantum mechanically, adopting ab initio molecular orbital theory for the electronic structure and path integral molecular dynamics for the nuclei. The present approach enables the evaluation of physical quantities dependent on the nuclear configuration as well as the electronic structure, within the framework of Born-Oppenheimer adiabatic approximation. As an application, we give the path integral formulation of electric response properties—dipole moment and polarizability, which characterize the changes both in electronic structure and nuclear configuration at a given temperature when uniform electrostatic field is present. We also demonstrate the calculation of a water molecule using the present approach and the result of temperature and isotope effects is discussed.
Steinmann, Casper; Fedorov, Dmitri G; Jensen, Jan H
2013-01-01
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be [Formula: see text] kcal mol(-1) for MP2/cc-pVDZ and [Formula: see text] for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively.
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)
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...
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...
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.
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.
Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data
White, Andrew D.; Knight, Chris; Hocky, Glen M.; Voth, Gregory A.
2017-01-01
Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties of systems such as water due to inaccuracies in the underlying electronic density functionals. This shortcoming is often addressed by added empirical corrections and/or increasing the simulation temperature. We present here a maximum-entropy approach to directly incorporate limited experimental data via a minimal bias. Biased AIMD simulations of water and an excess proton in water are shown to give significantly improved properties both for observables which were biased to match experimental data and for unbiased observables. This approach also yields new physical insight into inaccuracies in the underlying density functional theory as utilized in the unbiased AIMD.
M. P. Polak
2016-01-01
Full Text Available Structural and elastic properties of AlNxP1-x, a novel semiconductor alloy, are studied from the first principles in both zinc-blende and wurtzite structures. Performances of the finite difference (FD method and the density functional perturbation theory (DFPT are tested and compared. Both of these methods are applied to two different approaches of alloy simulation, a supercell of 16 and 32 atoms (for zinc-blende and wurtzite structures, resp. and the alchemical mixing (AM method, where the pseudopotentials are mixed in an appropriate way to form an alloy. All elastic properties, including the elastic tensors, elastic moduli, Poisson’s ratio, B/G, and relaxation coefficient, as well as lattice parameters are calculated using all said methods. Conclusions about the use of the approaches investigated in this paper and about their performance are drawn. In addition, in both crystal structures, the band gap is studied in the whole composition range using the MBJLDA functional. The band gap bowings are unusually high, which confirms earlier reports.
Exchange interaction in pyrochlore vanadates Lu2V2O7 and Y2V2O7: Ab initio approach
Nazipov, D. V.; Nikiforov, A. E.; Chernyshev, V. A.
2016-10-01
The exchange interaction in vanadates with the pyrochlore structure, namely, Lu2V2O7 and Y2V2O7, has been investigated using the first-principles approach. The isotropic exchange coupling constants have been determined. The calculations have been performed within the unrestricted Hartree-Fock (UHF) approximation, as well as in the framework of the density functional theory (DFT), using hybrid functionals. It has been shown that, in the description of the exchange interaction in the compounds under investigation, the nonlocal Hartree-Fock exchange should be taken into account. The splitting patterns of the 3 d 1 level of the V4+ ion in the crystal field have been obtained within the model approach. The calculation has been carried out in the approximation of point charges taking into account the spin-orbit interaction. It has been revealed that the "orbital liquid" state cannot be observed in the compounds under investigation, because the exchange interaction energy is significantly less than the energy spacing between the ground state and the first excited state. The orbital ordering has been analyzed, and the spin density maps have been constructed.
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)
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.
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...
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.
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.
Ab initio study of the low-lying electronic states of the CaO molecule
Khalil, Hossain; Brites, Vincent; Quere, Frederic Le [Universite Paris-Est, Laboratoire de Modelisation et Simulation Multi Echelle, UMR 8208 CNRS, Batiment Lavoisier, 5 boulevard Descartes, Champs sur Marne, 77454 Marne-la-Vallee, Cedex 2 (France); Leonard, Celine, E-mail: celine.leonard@univ-paris-est.fr [Universite Paris-Est, Laboratoire de Modelisation et Simulation Multi Echelle, UMR 8208 CNRS, Batiment Lavoisier, 5 boulevard Descartes, Champs sur Marne, 77454 Marne-la-Vallee, Cedex 2 (France)
2011-07-28
Graphical abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X{sup 1}{Sigma}{sup +}, a{sup 3}{Pi}, A'{sup 1{Pi}}, b{sup 3}{Sigma}{sup +} and A{sup 1}{Sigma}{sup +}, and the corresponding dipole moment functions have been determined using internally contracted multi-reference configuration interaction approaches. The spectroscopic constants associated with these electronic states are compared to experimental values. The corresponding electronic wavefunctions have also been analyzed using the dipole moment functions. Display Omitted Highlights: {yields} The five lowest electronic states of Cao have been determined ab initio at a high level of accuracy. {yields} Large active space, core-valence correlation and configuration interaction are required. {yields} The multi-configurational nature of the electronic ground state is confirmed as well as its monovalent and divalent ionic nature using dipole moment analysis. {yields} These interacting potentials will serve for future obtention of spin-rovibronic levels. - Abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X{sup 1}{Sigma}{sup +}, a{sup 3}{Pi}, A'{sup 1}{Pi}, b{sup 3}{Sigma}{sup +} and A{sup 1
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.
Borges, P. D., E-mail: pdborges@gmail.com, E-mail: lscolfaro@txstate.edu; Scolfaro, L., E-mail: pdborges@gmail.com, E-mail: lscolfaro@txstate.edu [Department of Physics, Texas State University, San Marcos, Texas 78666 (United States)
2014-12-14
The thermoelectric properties of indium nitride in the most stable wurtzite phase (w-InN) as a function of electron and hole concentrations and temperature were studied by solving the semiclassical Boltzmann transport equations in conjunction with ab initio electronic structure calculations, within Density Functional Theory. Based on maximally localized Wannier function basis set and the ab initio band energies, results for the Seebeck coefficient are presented and compared with available experimental data for n-type as well as p-type systems. Also, theoretical results for electric conductivity and power factor are presented. Most cases showed good agreement between the calculated properties and experimental data for w-InN unintentionally and p-type doped with magnesium. Our predictions for temperature and concentration dependences of electrical conductivity and power factor revealed a promising use of InN for intermediate and high temperature thermoelectric applications. The rigid band approach and constant scattering time approximation were utilized in the calculations.
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.
Malbon, Christopher L.; Zhu, Xiaolei; Guo, Hua; Yarkony, David R.
2016-12-01
For two electronic states coupled by conical intersections, the line integral of the derivative coupling can be used to construct a complex-valued multiplicative phase factor that makes the real-valued adiabatic electronic wave function single-valued, provided that the curl of the derivative coupling is zero. Unfortunately for ab initio determined wave functions, the curl is never rigorously zero. However, when the wave functions are determined from a coupled two diabatic state Hamiltonian Hd (fit to ab initio data), the resulting derivative couplings are by construction curl free, except at points of conical intersection. In this work we focus on a recently introduced diabatization scheme that produces the Hd by fitting ab initio determined energies, energy gradients, and derivative couplings to the corresponding Hd determined quantities in a least squares sense, producing a removable approximation to the ab initio determined derivative coupling. This approach and related numerical issues associated with the nonremovable ab initio derivative couplings are illustrated using a full 33-dimensional representation of phenol photodissociation. The use of this approach to provide a general framework for treating the molecular Aharonov Bohm effect is demonstrated.
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.
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 intermolecular potential energy surface and thermophysical properties of nitrous oxide
Crusius, Johann-Philipp, E-mail: johann-philipp.crusius@uni-rostock.de; Hassel, Egon [Lehrstuhl für Technische Thermodynamik, Universität Rostock, 18059 Rostock (Germany); Hellmann, Robert, E-mail: robert.hellmann@uni-rostock.de; Bich, Eckard [Institut für Chemie, Universität Rostock, 18059 Rostock (Germany)
2015-06-28
We present an analytical intermolecular potential energy surface (PES) for two rigid nitrous oxide (N{sub 2}O) molecules derived from high-level quantum-chemical ab initio calculations. Interaction energies for 2018 N{sub 2}O–N{sub 2}O configurations were computed utilizing the counterpoise-corrected supermolecular approach at the CCSD(T) level of theory using basis sets up to aug-cc-pVQZ supplemented with bond functions. A site-site potential function with seven sites per N{sub 2}O molecule was fitted to the pair interaction energies. We validated our PES by computing the second virial coefficient as well as shear viscosity and thermal conductivity in the dilute-gas limit. The values of these properties are substantiated by the best experimental data.
Hydrogen bond dynamics in liquid water: Ab initio molecular dynamics simulation
Kim, Cheolhee; Kim, Eunae [College of Pharmacy, Chosun University, Gwangju (Korea, Republic of); Yeom, Min Sun [Korea Institute of Science and Technology Information, Daejeon (Korea, Republic of)
2016-01-15
The effect of intermolecular interaction on the distribution of the harmonic vibrational frequencies of water molecules was investigated through ab initio molecular dynamics simulations based on the Born-Oppenheimer approach. For single water, the effect of the dynamics of the oxygen atom in single water and the simulation time step on the frequency distribution were examined. The distributions of the OH stretching and HOH bending vibrational frequencies of liquid water were compared to those of single water. The probability distributions of the change in OH bond length and the lifetime of the dangling OH bond were also obtained. The distribution of the frequencies was strongly affected by the long lifetime of the dangling OH bond, resulting in the formation of hydrogen bonds between water molecules.
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...
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.
Ab-initio calculations on two-electron ions in strongly coupled plasma environment
Bhattacharyya, S; Mukherjee, T K
2015-01-01
In this work, the controversy between the interpretations of recent measurements on dense aluminum plasma created with Linac coherent light sources (LCLS) X-ray free electron laser (FEL) and Orion laser has been addressed. In both kind of experiments, helium-like and hydrogen-like spectral lines are used for plasma diagnostics . However, there exist no precise theoretical calculations for He-like ions within dense plasma environment. The strong need for an accurate theoretical estimates for spectral properties of He-like ions in strongly coupled plasma environment leads us to perform ab initio calculations in the framework of Rayleigh-Ritz variation principle in Hylleraas coordinates where ion-sphere potential is used. An approach to resolve the long-drawn problem of numerical instability for evaluating two-electron integrals with extended basis inside a finite domain is presented here. The present values of electron densities corresponding to disappearance of different spectral lines obtained within the fram...
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.
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.
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.
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)
Despoja, Vito; Djordjević, Tijana; Karbunar, Lazar; Radović, Ivan; Mišković, Zoran L.
2017-08-01
The propagator of a dynamically screened Coulomb interaction W in a sandwichlike structure consisting of two graphene layers separated by a slab of Al2O3 (or vacuum) is derived from single-layer graphene response functions and by using a local dielectric function for the bulk Al2O3 . The response function of graphene is obtained using two approaches within the random phase approximation (RPA): an ab initio method that includes all electronic bands in graphene and a computationally less demanding method based on the massless Dirac fermion (MDF) approximation for the low-energy excitations of electrons in the π bands. The propagator W is used to derive an expression for the effective dielectric function of our sandwich structure, which is relevant for the reflection electron energy loss spectroscopy of its surface. Focusing on the range of frequencies from THz to mid-infrared, special attention is paid to finding an accurate optical limit in the ab initio method, where the response function is expressed in terms of a frequency-dependent conductivity of graphene. It was shown that the optical limit suffices for describing hybridization between the Dirac plasmons in graphene layers and the Fuchs-Kliewer phonons in both surfaces of the Al2O3 slab, and that the spectra obtained from both the ab initio method and the MDF approximation in the optical limit agree perfectly well for wave numbers up to about 0.1 nm-1. Going beyond the optical limit, the agreement between the full ab initio method and the MDF approximation was found to extend to wave numbers up to about 0.3 nm-1 for doped graphene layers with the Fermi energy of 0.2 eV.
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.
Heuvel, Willem Van den; Soncini, Alessandro
2015-01-01
We present an ab initio methodology dedicated to the determination of the electronic structure and magnetic properties of ground and low-lying excited states, i.e., the crystal field levels, in lanthanide(III) complexes. Currently, the most popular and successful ab initio approach is the CASSCF/RASSI-SO method, consisting of the optimization of multiple complete active space self-consistent field (CASSCF) spin eigenfunctions, followed by full diagonalization of the spin--orbit coupling (SOC) Hamiltonian in the basis of the CASSCF spin states featuring spin-dependent orbitals. Based on two simple observations valid for Ln(III) complexes, namely: (i) CASSCF 4f atomic orbitals are expected to change very little when optimized for different multiconfigurational states belonging to the 4f-electronic configuration, (ii) due to strong SOC the total spin is not a good quantum number, we propose here an efficient ab initio strategy which completely avoids any multiconfigurational calculation, by optimizing a unique s...
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...
Martin Alberto JM
2009-01-01
Full Text Available Abstract Background Prediction of protein structures from their sequences is still one of the open grand challenges of computational biology. Some approaches to protein structure prediction, especially ab initio ones, rely to some extent on the prediction of residue contact maps. Residue contact map predictions have been assessed at the CASP competition for several years now. Although it has been shown that exact contact maps generally yield correct three-dimensional structures, this is true only at a relatively low resolution (3–4 Å from the native structure. Another known weakness of contact maps is that they are generally predicted ab initio, that is not exploiting information about potential homologues of known structure. Results We introduce a new class of distance restraints for protein structures: multi-class distance maps. We show that Cα trace reconstructions based on 4-class native maps are significantly better than those from residue contact maps. We then build two predictors of 4-class maps based on recursive neural networks: one ab initio, or relying on the sequence and on evolutionary information; one template-based, or in which homology information to known structures is provided as a further input. We show that virtually any level of sequence similarity to structural templates (down to less than 10% yields more accurate 4-class maps than the ab initio predictor. We show that template-based predictions by recursive neural networks are consistently better than the best template and than a number of combinations of the best available templates. We also extract binary residue contact maps at an 8 Å threshold (as per CASP assessment from the 4-class predictors and show that the template-based version is also more accurate than the best template and consistently better than the ab initio one, down to very low levels of sequence identity to structural templates. Furthermore, we test both ab-initio and template-based 8
Ab-initio simulations of materials using VASP: Density-functional theory and beyond.
Hafner, Jürgen
2008-10-01
During the past decade, computer simulations based on a quantum-mechanical description of the interactions between electrons and between electrons and atomic nuclei have developed an increasingly important impact on solid-state physics and chemistry and on materials science-promoting not only a deeper understanding, but also the possibility to contribute significantly to materials design for future technologies. This development is based on two important columns: (i) The improved description of electronic many-body effects within density-functional theory (DFT) and the upcoming post-DFT methods. (ii) The implementation of the new functionals and many-body techniques within highly efficient, stable, and versatile computer codes, which allow to exploit the potential of modern computer architectures. In this review, I discuss the implementation of various DFT functionals [local-density approximation (LDA), generalized gradient approximation (GGA), meta-GGA, hybrid functional mixing DFT, and exact (Hartree-Fock) exchange] and post-DFT approaches [DFT + U for strong electronic correlations in narrow bands, many-body perturbation theory (GW) for quasiparticle spectra, dynamical correlation effects via the adiabatic-connection fluctuation-dissipation theorem (AC-FDT)] in the Vienna ab initio simulation package VASP. VASP is a plane-wave all-electron code using the projector-augmented wave method to describe the electron-core interaction. The code uses fast iterative techniques for the diagonalization of the DFT Hamiltonian and allows to perform total-energy calculations and structural optimizations for systems with thousands of atoms and ab initio molecular dynamics simulations for ensembles with a few hundred atoms extending over several tens of ps. Applications in many different areas (structure and phase stability, mechanical and dynamical properties, liquids, glasses and quasicrystals, magnetism and magnetic nanostructures, semiconductors and insulators, surfaces
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 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.
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.
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.
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.
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 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
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.
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.
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.
Simulating ionic thermal trasport by equilibrium ab-initio molecular dynamics
Marcolongo, Aris; Umari, Paolo; Baroni, Stefano
2014-03-01
The Green-Kubo approach to thermal transport is often considered to be incompatible with ab-initio molecular dynamics (AIMD) because a suitable quantum-mechanical definition of the heat current is not readily available, due to the ill-definedness of the microscopic energy density to which it is related by the continuity equation. We argue that a similar difficulty actually exists in classical mechanics as well, and we address the conditions that have to be fulfilled in order for the physically well defined transport coefficients to be independent of the ill defined microscopic energy density from which they derive. We then provide two alternative approaches to calculating thermal conductivites from equilibrium AIMD. The first is based on the Green-Kubo formula, supplemented with an expression for the energy current, which is a generalization of Thouless' expression for the adiabatic charge current. The second approach, which avoids the recourse to an energy current altogether, rests on an efficient and accurate extrapolation to infinite wavelengths of the energy-density time correlation functions. The two methods are compared on a simple classical test bed, and their implementation in AIMD is demonstrated with the calculation of the thermal conductivity of simple fluids.
Ab Initio Excited States from the In-Medium Similarity Renormalization Group
Parzuchowski, N M; Bogner, S K
2016-01-01
We present two new methods for performing \\emph{ab initio} calculations of excited states for closed-shell systems within the in-medium similarity renormalization group (IMSRG) framework. Both are based on combining the IMSRG with simple many-body methods commonly used to target excited states, such as the Tamm-Dancoff approximation (TDA) and equations-of-motion (EOM) techniques. In the first approach, a two-step sequential IMSRG transformation is used to drive the Hamiltonian to a form where a simple TDA calculation (i.e., diagonalization in the space of $1$p$1$h excitations) becomes exact for a subset of eigenvalues. In the second approach, equations-of-motion (EOM) techniques are applied to the ground-state-decoupled IMSRG Hamiltonian to access excited states. We perform proof-of-principle calculations for parabolic quantum dots in two-dimensions and the closed shell nuclei $^{16}$O and $^{22}$O. We find that the TDA-IMSRG approach gives better accuracy than the EOM-IMSRG when calculations converge, but is...
Zhu, L.; Yao, K. L.; Liu, Z. L.
2007-10-01
Ab initio computations within the full potential linearized augmented plane wave method with the generalized gradient approximation plus Hubbard potential approach were applied in the study of the electronic structures of the compound [Gd2(mal)3(H2O)6] . The present calculations show that the major part of the spin magnetic moment is from Gd(III) ions, and the origin of the ferromagnetic intermolecular interaction of the two interacting Gd(III) ions comes from the spin polarization effect through the oxo-carboxylato and carboxylato bridges. By analysis of the band structure, we find that the compound has a metallic property.
Hyeon-Deuk, Kim; Prezhdo, Oleg V
2011-04-13
We developed time-domain ab initio simulation of Auger phenomena, including multiple exciton generation (MEG) and recombination (MER). It is the first approach describing phonon-assisted processes and early dynamics. MEG starts below the electronic threshold, strongly accelerating with energy. Ligands are particularly important to phonon-assisted MEG, which therefore can be probed with infrared spectroscopy. Short-time gaussian component gives 5-10% of MEG, justifying rate theories that assume exponential dynamics. MER is preceded by electron-phonon relaxation to low energies.
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.
Pollet, Rodolphe; Bonnet, Célia S; Retailleau, Pascal; Durand, Philippe; Tóth, Éva
2017-03-27
The proton-exchange process between water and a carbamate has been studied experimentally and theoretically in a lanthanide-based paramagnetic chemical exchange saturation transfer agent endowed with potential multimodality detection capabilities (optical imaging, or T1 MRI for the Gd(III) analogue). In addition to an in-depth structural analysis by a combined approach (using X-ray crystallography, NMR, and molecular dynamics), our ab initio simulation in aqueous solution sheds light on the reaction mechanism for this proton exchange, which involves structural Grotthuss diffusion.
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.)
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.
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 theory of exchange interactions and the Curie temperature of bulk Gd
Turek, I; Bihlmayer, G; Bluegel, S
2003-01-01
An ab initio approach to the magnetic properties of bulk hexagonal Gd is developed that is based on the local spin-density approximation with the 4f electrons treated as localized core electrons. The effective one-electron problem is solved using the tight-binding linear muffin-tin orbital method in the atomic-sphere approximation with the valence basis consisting of s-, p-and d-type orbitals. The approach leads to a correct description of the ground-state properties like the stability of the ferromagnetic structure, the magnetic moment and the equilibrium lattice constant. Application of a real-space Green-function formalism yields the exchange pair interactions between distant neighbours that are inevitable for quantitative studies of magnetic excitations. The distance dependence and anisotropy of the exchange pair interactions are presented and the Curie temperature in the mean-field approximation is evaluated. The obtained value of 334 K is in much better agreement with the experimental value of 293 K tha...
Ab initio calculation of optical constants from visible to x-ray energies
Prange, M. P.; Rivas, G.; Ankudinov, A. L.; Rehr, J. J.
2004-03-01
We present a semi-automated approach for ab initio calculations of optical constants of materials from the visible to the hard x-ray energies. The approach is based on a generalization of the real space Green's formalism implemented in the FEFF8 spectroscopy code to include optical spectra. The method includes self-consistent potentials, core-hole and self-energy effects, inelastic losses and a full- or high order multiple-scattering. The procedure is based on calculations of the imaginary part of the dielectric function ɛ2 summed over all edges, from which other optical constants are derived using Kramers-Kronig transforms and analytical relations. These constants include the complex index of refraction, the real part of the dielectric function, and energy loss spectra. In contrast to standard atomic tables, the calculations include solid-state corrections, such as fine structure, Debye-Waller factors, lifetime broadening, etc. Typical results for several materials are presented and compared with experiment.
{\\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...
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.
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.
[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.
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.
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.
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.
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...
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.
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%.
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.
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...
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.
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%.
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.
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.
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.
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....
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....
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 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....
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.
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.
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.
360⁰ -View of Quantum Theory and Ab Initio Simulation at Extreme Conditions: 2014 Sanibel Symposium
Cheng, Hai-Ping [Univ. of Florida, Gainesville, FL (United States)
2016-09-02
The Sanibel Symposium 2014 was held February 16-21, 2014, at the King and Prince, St. Simons Island, GA. It was successful in bringing condensed-matter physicists and quantum chemists together productively to drive the emergence of those specialties. The Symposium had a significant role in preparing a whole generation of quantum theorists. The 54th Sanibel meeting looked to the future in two ways. We had 360⁰-View sessions to honor the exceptional contributions of Rodney Bartlett (70), Bill Butler (70), Yngve Öhrn (80), Fritz Schaefer (70), and Malcolm Stocks (70). The work of these five has greatly impacted several generations of quantum chemists and condensed matter physicists. The “360⁰” is the sum of their ages. More significantly, it symbolizes a panoramic view of critical developments and accomplishments in theoretical and computational chemistry and physics oriented toward the future. Thus, two of the eight 360⁰-View sessions focused specifically on younger scientists. The 360⁰-View program was the major component of the 2014 Sanibel meeting. Another four sessions included a sub-symposium on ab initio Simulations at Extreme Conditions, with focus on getting past the barriers of present-day Born-Oppenheimer molecular dynamics by advances in finite-temperature density functional theory, orbital-free DFT, and new all-numerical approaches.
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)
SGO: A fast engine for ab initio atomic structure global optimization by differential evolution
Chen, Zhanghui; Jia, Weile; Jiang, Xiangwei; Li, Shu-Shen; Wang, Lin-Wang
2017-10-01
As the high throughout calculations and material genome approaches become more and more popular in material science, the search for optimal ways to predict atomic global minimum structure is a high research priority. This paper presents a fast method for global search of atomic structures at ab initio level. The structures global optimization (SGO) engine consists of a high-efficiency differential evolution algorithm, accelerated local relaxation methods and a plane-wave density functional theory code running on GPU machines. The purpose is to show what can be achieved by combining the superior algorithms at the different levels of the searching scheme. SGO can search the global-minimum configurations of crystals, two-dimensional materials and quantum clusters without prior symmetry restriction in a relatively short time (half or several hours for systems with less than 25 atoms), thus making such a task a routine calculation. Comparisons with other existing methods such as minima hopping and genetic algorithm are provided. One motivation of our study is to investigate the properties of magnetic systems in different phases. The SGO engine is capable of surveying the local minima surrounding the global minimum, which provides the information for the overall energy landscape of a given system. Using this capability we have found several new configurations for testing systems, explored their energy landscape, and demonstrated that the magnetic moment of metal clusters fluctuates strongly in different local minima.
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.
Structural insights and ab initio sequencing within the DING proteins family
Elias, Mikael, E-mail: mikael.elias@weizmann.ac.il [Weizmann Institute of Science, Rehovot (Israel); Liebschner, Dorothee [CRM2, Nancy Université (France); Gotthard, Guillaume; Chabriere, Eric [AFMB, Université Aix-Marseille II (France)
2011-01-01
DING proteins constitute a recently discovered protein family that is ubiquitous in eukaryotes. The structural insights and the physiological involvements of these intriguing proteins are hereby deciphered. DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated.
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 transport calculations of molecular wires with electron-phonon couplings
Hirose, Kenji; Kobayashi, Nobuhiko
2009-03-01
Understanding of electron transport through nanostructures becomes important with the advancement of fabrication process to construct atomic-scale devices. Due to the drastic change of transport properties by contact conditions to electrodes in local electric fields, first-principles calculation approaches are indispensable to understand and characterize the transport properties of nanometer-scale molecular devices. Here we study the transport properties of molecular wires between metallic electrodes, especially focusing on the effects of contacts to electrodes and of the electron-phonon interactions. We use an ab initio calculation method based on the scattering waves, which are obtained by the recursion-transfer-matrix (RTM) method, combined with non-equilibrium Green's function (NEGF) method including the electron-phonon scatterings. We find that conductance shows exponential behaviors as a function of the length of molecular wires due to tunneling process determined by the HOMO-LUMO energy gap. From the voltage drop behaviors inside the molecular wires, we show that the contact resistances are dominant source for the bias drop and thus are related to local heating. We will present the electron-phonon coupling effects at contact on the inelastic scattering and discuss on the local heating and local temperature, comparing them with those of metallic atomic wires.
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 ...
An ab initio study of the polytypism in InP
Dacal, Luis C. O.; Cantarero, A.
2016-09-01
The existence of polytypism in semiconductor nanostructures gives rise to the appearance of stacking faults which many times can be treated as quantum wells. In some cases, despite of a careful growth, the polytypism can be hardly avoided. In this work, we perform an ab initio study of zincblende stacking faults in a wurtzite InP system, using the supercell approach and taking the limit of low density of narrow stacking faults regions. Our results confirm the type II band alignment between the phases, producing a reliable qualitative description of the band gap evolution along the growth axis. These results show an spacial asymmetry in the zincblende quantum wells, that is expected due to the fact that the wurtzite stacking sequence (ABAB) is part of the zincblende one (ABCABC), but with an unexpected asymmetry between the valence and the conduction bands. We also present results for the complex dielectric function, clearly showing the influence of the stacking on the homostructure values and surprisingly proving that the correspondent bulk results can be used to reproduce the polytypism even in the limit we considered.
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.
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...
Optimizing weights of protein energy function to improve ab initio protein structure prediction
Wang, Chao; Liu, Juntao; Zhang, Haicang; Ling, Bin; Li, Shuai Cheng; Zheng, Wei-Mou; Bu, Dongbo
2013-01-01
Predicting protein 3D structure from amino acid sequence remains as a challenge in the field of computational biology. If protein structure homologues are not found, one has to construct 3D structural conformations from the very beginning by the so-called ab initio approach, using some empirical energy functions. A successful algorithm in this category, Rosetta, creates an ensemble of decoy conformations by assembling selected best short fragments of known protein structures and then recognizes the native state as the highly populated one with a very low energy. Typically, an energy function is a combination of a variety of terms characterizing different structural features, say hydrophobic interactions, van der Waals force, hydrogen bonding, etc. It is critical for an energy function to be capable to distinguish native-like conformations from non-native ones and to drive most initial conformations assembled from fragments to a native-like one in a conformation search process. In this paper we propose a linea...
Ab initio carbon capture in open-site metal-organic frameworks
Dzubak, Allison L.; Lin, Li-Chiang; Kim, Jihan; Swisher, Joseph A.; Poloni, Roberta; Maximoff, Sergey N.; Smit, Berend; Gagliardi, Laura
2012-10-01
During the formation of metal-organic frameworks (MOFs), metal centres can coordinate with the intended organic linkers, but also with solvent molecules. In this case, subsequent activation by removal of the solvent molecules creates unsaturated ‘open’ metal sites known to have a strong affinity for CO2 molecules, but their interactions are still poorly understood. Common force fields typically underestimate by as much as two orders of magnitude the adsorption of CO2 in open-site Mg-MOF-74, which has emerged as a promising MOF for CO2 capture. Here we present a systematic procedure to generate force fields using high-level quantum chemical calculations. Monte Carlo simulations based on an ab initio force field generated for CO2 in Mg-MOF-74 shed some light on the interpretation of thermodynamic data from flue gas in this material. The force field describes accurately the chemistry of the open metal sites, and is transferable to other structures. This approach may serve in molecular simulations in general and in the study of fluid-solid interactions.
360⁰ -View of Quantum Theory and Ab Initio Simulation at Extreme Conditions: 2014 Sanibel Symposium
Cheng, Hai-Ping [Univ. of Florida, Gainesville, FL (United States)
2016-09-02
The Sanibel Symposium 2014 was held February 16-21 2014 at the King and Prince, St. Simons Island, GA. It was successful in bringing condensed-matter physicists and quantum chemists together productively to drive the emergence of those specialties. The Symposium had a significant role in preparing a whole generation of quantum theorists. The 54th Sanibel meeting looked to the future in two ways. We had 360⁰-View sessions to honor the exceptional contributions of Rodney Bartlett (70), Bill Butler (70), Yngve Öhrn (80), Fritz Schaefer (70), and Malcolm Stocks (70). The work of these five has greatly impacted several generations of quantum chemists and condensed matter physicists. The “360⁰” is the sum of their ages. More significantly, it symbolizes a panoramic view of critical developments and accomplishments in theoretical and computational chemistry and physics oriented toward the future. Thus, two of the eight 360⁰-View sessions focused specifically on younger scientists. The 360⁰-View program was the major component of the 2014 Sanibel meeting. Another four sessions included a sub-symposium on ab initio Simulations at Extreme Conditions, with focus on getting past the barriers of present-day Born-Oppenheimer molecular dynamics by advances in finite-temperature density functional theory, orbital-free DFT, and new all-numerical approaches.
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.
Ab initio study of structural, electronic, and thermal properties of Pt1-xPdx alloys
Ahmed, Shabbir; Zafar, Muhammad; Shakil, M.; Choudhary, M. A.; Hashmi, Muhammad Raza-Ur-Rehman
2017-01-01
We report a systematic theoretical study of Pt1-xPdx alloys using ab initio density functional theory (DFT) by pseudo potential method. We have used super cell approach to investigate structural, electronic and thermal properties of Platinum (Pt), Palladium (Pd) and their alloys Pt1-xPdx(x = 0.00, 0.25, 0.50, 0.75, 1.00). The calculated lattice constants and bulk moduli are in good agreement with available literature data. The results of electronic properties revealed that the alloys are metallic in nature. The thermal properties were investigated through density functional perturbation theory (DFPT) and quasi-harmonic approximation. The contribution to the free energy from the lattice vibration was calculated using the phonon densities of states (DOS) derived by means of the linear-response theory. The DFPT with quasi-harmonic approximation methods was applied to determine the phonon DOS and thermal quantities i.e., the Debye temperatures, vibration energy, entropy and constant-volume specific heat.
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.
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 ro-vibronic spectroscopy of SiCCl (X{sup ~2}Π)
Brites, Vincent [Université d’Evry Val d’Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE CNRS UMR 8587, Boulevard F. Mitterrand, 91025 Evry Cedex (France); Mitrushchenkov, Alexander O.; Léonard, Céline, E-mail: celine.leonard@u-pem.fr [Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée (France); Peterson, Kirk A. [Department of Chemistry, Washington State University, Pullman, Washington 99164 (United States)
2014-07-21
The full dimensional potential energy surfaces of the {sup 2}A{sup ′} and {sup 2}A{sup ′′} electronic components of X{sup ~2}Π SiCCl have been computed using the explicitly correlated coupled cluster method, UCCSD(T)-F12b, combined with a composite approach taking into account basis set incompleteness, core-valence correlation, scalar relativity, and higher order excitations. The spin-orbit and dipole moment surfaces have also been computed ab initio. The ro-vibronic energy levels and absorption spectrum at 5 K have been determined from variational calculations. The influence of each correction on the fundamental frequencies is discussed. An assignment is proposed for bands observed in the LIF experiment of Smith et al. [J. Chem. Phys. 117, 6446 (2002)]. The overall agreement between the experimental and calculated ro-vibronic levels is better than 7 cm{sup −1} which is comparable with the 10–20 cm{sup −1} resolution of the emission spectrum.
Ab initio carbon capture in open-site metal-organic frameworks.
Dzubak, Allison L; Lin, Li-Chiang; Kim, Jihan; Swisher, Joseph A; Poloni, Roberta; Maximoff, Sergey N; Smit, Berend; Gagliardi, Laura
2012-10-01
During the formation of metal-organic frameworks (MOFs), metal centres can coordinate with the intended organic linkers, but also with solvent molecules. In this case, subsequent activation by removal of the solvent molecules creates unsaturated 'open' metal sites known to have a strong affinity for CO(2) molecules, but their interactions are still poorly understood. Common force fields typically underestimate by as much as two orders of magnitude the adsorption of CO(2) in open-site Mg-MOF-74, which has emerged as a promising MOF for CO(2) capture. Here we present a systematic procedure to generate force fields using high-level quantum chemical calculations. Monte Carlo simulations based on an ab initio force field generated for CO(2) in Mg-MOF-74 shed some light on the interpretation of thermodynamic data from flue gas in this material. The force field describes accurately the chemistry of the open metal sites, and is transferable to other structures. This approach may serve in molecular simulations in general and in the study of fluid-solid interactions.
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.
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 description of continuum effects in A=11 exotic systems with chiral NN+3N forces
Calci, Angelo; Navratil, Petr; Roth, Robert; Dohet-Eraly, Jeremy; Quaglioni, Sofia; Hupin, Guillaume
2016-09-01
Based on the fundamental symmetries of QCD, chiral effective field theory (EFT) provides two- (NN), three- (3N) and many-nucleon interactions in a consistent and systematically improvable scheme. The rapid developments to construct divers families of chiral NN+3N interactions and the conceptual and technical improvements of ab initio many-body approaches pose a great opportunity for nuclear physics. By studying particular interesting phenomena in nuclear structure and reaction observables one can discriminate between different forces and study the predictive power of chiral EFT. The accurate description of the 11Be nucleus, in particular, the ground-state parity inversion and exceptionally strong E1 transition between its two bound states constitute an enormous challenge for the developments of nuclear forces and many-body approaches. We present a sensitivity analysis of structure and reaction observables to different NN+3N interactions in 11Be and n+10Be as well as the mirror p+10C scattering using the ab initio NCSM with continuum (NCSMC). Supported by the U.S. Department of Energy, Office of Science, Office of Nuclear Physics, under Work Proposal No. SCW1158. TRIUMF receives federal funding via a contribution agreement with the National Research Council of Canada.
The ab initio calculation of spectra of open shell diatomic molecules
Tennyson, Jonathan; Lodi, Lorenzo; McKemmish, Laura K.; Yurchenko, Sergei N.
2016-05-01
The spectra (rotational, rotation-vibrational or electronic) of diatomic molecules due to transitions involving only closed-shell (1Σ ) 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 perturbed spectra of even greater 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 ab initio approach; these areas are ultracold chemistry and the astrophysics of ‘cool’ stars, brown dwarfs and most recently extrasolar planets. However, the complex electronic structure of these molecules combined with the accuracy requirements of high-resolution spectroscopy render such an approach particularly challenging. This review describes recent progress in developing methods for directly solving the effective Schrödinger equation for open-shell diatomic molecules, with a focus on molecules containing a transtion metal. It considers four aspects of the problem: (i) the electronic structure problem; (ii) non-perturbative treatments of the curve couplings; (iii) the solution of the nuclear motion Schrödinger equation; (iv) the generation of accurate electric dipole transition intensities. Examples of applications are used to illustrate these issues.
Ab initio calculation of the NMR shielding constants for histamine
Mazurek, A. P.; Dobrowolski, J. Cz.; Sadlej, J.
1997-12-01
The gage-independent atomic orbital (GIAO) approach is used within the coupled Hartree-Fock approximation to compute the 1H, 13C and 15N NMR shielding constants in two tautomeric forms of both the histamine molecule and its protonated form. An analysis of the results shows that the protonation on the end of the chain changes its nitrogen shielding constants of the pyridine and pyrrole type. These changes are much higher for the N(3)-H than for the N(1)-H tautomer.
Hoy, Erik P.; Mazziotti, David A., E-mail: damazz@uchicago.edu [Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637 (United States)
2015-08-14
Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.
Hoy, Erik P; Mazziotti, David A
2015-08-14
Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.
An ab initio electronic transport database for inorganic materials
Ricci, Francesco; Chen, Wei; Aydemir, Umut; Snyder, G. Jeffrey; Rignanese, Gian-Marco; Jain, Anubhav; Hautier, Geoffroy
2017-07-01
Electronic transport in materials is governed by a series of tensorial properties such as conductivity, Seebeck coefficient, and effective mass. These quantities are paramount to the understanding of materials in many fields from thermoelectrics to electronics and photovoltaics. Transport properties can be calculated from a material's band structure using the Boltzmann transport theory framework. We present here the largest computational database of electronic transport properties based on a large set of 48,000 materials originating from the Materials Project database. Our results were obtained through the interpolation approach developed in the BoltzTraP software, assuming a constant relaxation time. We present the workflow to generate the data, the data validation procedure, and the database structure. Our aim is to target the large community of scientists developing materials selection strategies and performing studies involving transport properties.
Ab initio Calculations of Optical Properties of Clusters
Shinde, Ravindra
2016-01-01
We have performed systematic large-scale all-electron correlated calculations on boron Bn, aluminum Aln and magnesium Mgn clusters (n=2--5), to study their linear optical absorption spectra. Several possible isomers of each cluster were considered, and their geometries were optimized at the coupled-cluster singles doubles (CCSD) level of theory. Using the optimized ground-state geometries, excited states of different clusters were computed using the multi-reference singles-doubles configuration interaction (MRSDCI) approach, which includes electron correlation effects at a sophisticated level. These CI wavefunctions were used to compute the transition dipole matrix elements connecting the ground and various excited states of different clusters, eventually leading to their linear absorption spectra. The convergence of our results with respect to the basis sets, and the size of the CI expansion was carefully examined. Isomers of a given cluster show a distinct signature spectrum, indicating a strong structure p...
Organic/inorganic hybrid materials: challenges for ab initio methodology.
Draxl, Claudia; Nabok, Dmitrii; Hannewald, Karsten
2014-11-18
CONSPECTUS: Organic/inorganic hybrid structures are most exciting since one can expect new properties that are absent in either of their building blocks. They open new perspectives toward the design and tailoring of materials with desired features and functions. Prerequisite for real progress is, however, the in-depth understanding of what happens on the atomic and electronic scale. In this respect, hybrid materials pose a challenge for electronic-structure theory. Methods that proved useful for describing one side may not be applicable for the other one, and they are likely to fail for the interfaces. In this Account, we address the question to what extent we can quantitatively describe hybrid materials and where we even miss a qualitative description. We note that we are dealing with extended systems and thus adopt a solid-state approach. Therefore, density-functional theory (DFT) and many-body perturbation theory (MBPT), the GW approach for charged and the Bethe-Salpeter equation for neutral excitations, are our methods of choice. We give a brief summary of the used methodology, focusing on those aspects where problems can be expected when materials of different character meet at an interface. These issues are then taken up when discussing hybrid materials. We argue when and why, for example, standard DFT may fall short when it comes to the electronic structure of organic/metal interfaces or where the framework of MBPT can or must take over. Selected examples of organic/inorganic interfaces, structural properties, electronic bands, optical excitation spectra, and charge-transport properties as obtained from DFT and MBPT highlight which properties can be reliably computed for such materials. The crucial role of van der Waals forces is shown for sexiphenyl films, where the subtle interplay between intermolecular and molecule-substrate interactions is decisive for growth and morphologies. With a PTCDA monolayer on metal surfaces we discuss the performance of DFT in
Unified ab initio treatment of attosecond photoionization and Compton scattering
Yudin, G. L.; Bondar, D. I.; Patchkovskii, S.; Corkum, P. B.; Bandrauk, A. D.
2009-10-01
We present a new theoretical approach to attosecond laser-assisted photo- and Compton ionization. Attosecond x-ray absorption and scattering are described by \\hat{\\mathscr{S}}^{(1,2)} -matrices, which are coherent superpositions of 'monochromatic' \\skew{3}\\hat{S}^{(1,2)} -matrices in a laser-modified Furry representation. Besides refining the existing theory of the soft x-ray photoelectron attosecond streak camera and spectral phase interferometry (ASC and ASPI), we formulate a theory of hard x-ray photoelectron and Compton ASC and ASPI. The resulting scheme has a simple structure and leads to closed-form expressions for ionization amplitudes. We investigate Compton electron interference in the separable Coulomb-Volkov continuum with both Coulomb and laser fields treated non-perturbatively. We find that at laser-field intensities below 1013 Wcm-2 normalized Compton lines almost coincide with the lines obtained in the laser-free regime. At higher intensities, attosecond interferences survive integration over electron momenta, and feature prominently in the Compton lines themselves. We define a regime where the electron ground-state density can be measured with controllable accuracy in an attosecond time interval. The new theory provides a firm basis for extracting photo- and Compton electron phases and atomic and molecular wavefunctions from experimental data.
Ab initio Sternheimer-GW method for quasiparticle calculations
Lambert, Henry; Giustino, Feliciano
2014-03-01
The GW method has emerged as the standard computational tool for investigating electronic excitations in bulk and nanoscale systems. Recently significant efforts have been devoted to extending the range of applicability of the GW method. With this aim, Ref. introduced the Sternheimer-GW method, reformulating the standard GW approach so that no unoccupied electronic states are required in the calculations. Here we present the implementation of the Sternheimer-GW method using planewaves and norm-conserving pseudopotentials. In our method we calculate the complete position- and energy-dependent GW self-energy operator, and as a by-product we obtain the entire G0W0 quasiparticle spectral function. We have validated our method by calculating the quasiparticle band structures of standard semiconductors and insulators (Si, SiC, diamond, LiCl) and by comparing the results with previous GW calculations. This method is currently being used for investigating the electronic structure of novel materials of reduced dimensionality. This work was supported by the ERC under the EU FP7/ERC Grant No. 239578 and by the UK EPSRC Grant No. EP/J009857/1.
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 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.
Le Page, Yvon; Saxe, Paul
2002-03-01
A symmetry-general approach for the least-squares, therefore precise, extraction of elastic coefficients for strained materials is reported. It analyzes stresses calculated ab initio for properly selected strains. The problem, its implementation, and its solution strategy all differ radically from a previous energy-strain approach that we published last year, but the normal equations turn out to be amenable to the same constrainment scheme that makes both approaches symmetry general. The symmetry considerations governing the automated selection of appropriately strained models and their Cartesian systems are detailed. The extension to materials under general stress is discussed and implemented. VASP was used for ab initio calculation of stresses. A comprehensive range of examples includes a triclinic material (kyanite) and simple materials with a range of symmetries at zero pressure, MgO under hydrostatic pressure, Ti4As3 under [001] uniaxial strain, and Si under [001] uniaxial stress. The MgO case agrees with recent experimental work including elastic coefficients as well as their first and second derivatives. The curves of elastic coefficients for Si show a gradual increase in the 33 compliance coefficient, leading to a collapse of the material at -11.7 GPa, compared with -12.0 GPa experimentally. Interpretation of results for Be using two approximations [local density (LDA), generalized gradient (GGA)], two approaches (stress strain and energy strain), two potential types (projector augmented wave and ultrasoft), and two quantum engines (VASP and ORESTES) expose the utmost importance of the cell data used for the elastic calculations and the lesser importance of the other factors. For stiffness at relaxed cell data, differences are shown to originate mostly in the considerable overestimation of the residual compressive stresses at x-ray cell data by LDA, resulting in a smaller relaxed cell, thus larger values for diagonal stiffness coefficients. The symmetry
Ab Initio Many-Body Calculations of n-3H, n-4He, p-{3,4}He, and n-10Be Scattering
Quaglioni, Sofia
2008-01-01
We develop a new ab initio many-body approach capable of describing simultaneously both bound and scattering states in light nuclei, by combining the resonating-group method with the use of realistic interactions, and a microscopic and consistent description of the nucleon clusters. This approach preserves translational symmetry and Pauli principle. We present phase shifts for neutron scattering on 3H, 4He and 10Be and proton scattering on {3,4}He, using realistic nucleon-nucleon potentials. Our A=4 scattering results are compared to earlier ab initio calculations. We demonstrate that a proper treatment of the coupling to the n-10Be continuum is essential to explain the parity-inverted ground state in 11Be.
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.
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.
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.
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...
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
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.
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...
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.
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
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.
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.
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)
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.
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 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.
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 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 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.
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.
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.
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.
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
Partovi-Azar, Pouya
2015-01-01
We present a computational method to accurately calculate Raman spectra from first principles with an at least one order of magnitude higher efficiency. This scheme thus allows to routinely calculate finite-temperature Raman spectra "on-the-fly" by means of \\textit{ab-initio} molecular dynamics simulations. To demonstrate the predictive power of this approach we investigate the effect of hydrophobic and hydrophilic solutes in water solution on the infrared and Raman spectra.
Towards a rational design of ruthenium CO2 hydrogenation catalysts by Ab initio metadynamics.
Urakawa, Atsushi; Iannuzzi, Marcella; Hutter, Jürg; Baiker, Alfons
2007-01-01
Complete reaction pathways relevant to CO2 hydrogenation by using a homogeneous ruthenium dihydride catalyst ([Ru(dmpe)2H2], dmpe=Me2PCH2CH2PMe2) have been investigated by ab initio metadynamics. This approach has allowed reaction intermediates to be identified and free-energy profiles to be calculated, which provide new insights into the experimentally observed reaction pathway. Our simulations indicate that CO2 insertion, which leads to the formation of formate complexes, proceeds by a concerted insertion mechanism. It is a rapid and direct process with a relatively low activation barrier, which is in agreement with experimental observations. Subsequent H2 insertion into the formate--Ru complex, which leads to the formation of formic acid, instead occurs via an intermediate [Ru(eta2-H2)] complex in which the molecular hydrogen coordinates to the ruthenium center and interacts weakly with the formate group. This step has been identified as the rate-limiting step. The reaction completes by hydrogen transfer from the [Ru(eta2-H2)] complex to the formate oxygen atom, which forms a dihydrogen-bonded Ru--HHO(CHO) complex. The activation energy for the H2 insertion step is lower for the trans isomer than for the cis isomer. A simple measure of the catalytic activity was proposed based on the structure of the transition state of the identified rate-limiting step. From this measure, the relationship between catalysts with different ligands and their experimental catalytic activities can be explained.
Baima, Jacopo; Ferrabone, Matteo; Orlando, Roberto; Erba, Alessandro; Dovesi, Roberto
2016-02-01
The phonon dispersion and thermodynamic properties of pyrope ({Mg}_3{Al}_2{Si}_3{O}_{12}) and grossular ({Ca}_3{Al}_2{Si}_3{O}_{12} ) have been computed by using an ab initio quantum mechanical approach, an all-electron variational Gaussian-type basis set and the B3LYP hybrid functional, as implemented in the Crystal program. Dispersion effects in the phonon bands have been simulated by using supercells of increasing size, containing 80, 160, 320, 640, 1280 and 2160 atoms, corresponding to 1, 2, 4, 8, 16 and 27 {k} points in the first Brillouin zone. Phonon band structures, density of states and corresponding inelastic neutron scattering spectra are reported. Full convergence of the various thermodynamic properties, in particular entropy ( S) and specific heat at constant volume (CV), with the number of {k} points is achieved with 27 {k} points. The very regular behavior of the S( T) and CV(T) curves as a function of the number of {k} points, determined by high numerical stability of the code, permits extrapolation to an infinite number of {k} points. The limiting value differs from the 27-{k} case by only 0.40 % at 100 K for S (the difference decreasing to 0.11 % at 1000 K) and by 0.29 % (0.05 % at 1000 K) for CV. The agreement with the experimental data is rather satisfactory. We also address the problem of the relative entropy of pyrope and grossular, a still debated question. Our lattice dynamical calculations correctly describe the larger entropy of pyrope than grossular by taking into account merely vibrational contributions and without invoking "static disorder" of the Mg ions in dodecahedral sites. However, as the computed entropy difference is found to be larger than the experimental one by a factor of 2-3, present calculations cannot exclude possible thermally induced structural changes, which could lead to further conformational contributions to the entropy.
Electronic absorption and resonance Raman spectroscopy from ab initio quantum molecular dynamics
Ben-Nun, M.; Martinez, T.J.
1999-12-09
The absorption and resonance Raman excitation profiles of ethylene following {pi} {yields} {pi}* excitation and taking full account of anharmonicity and Duschinsky rotation effects are calculated from first principles molecular dynamics using the ab initio multiple spawning (AIMS) method and a correlation function approach. The AIMS method solves the nuclear and electronic Schroedinger equations simultaneously and it associates a unique nuclear wave function with each electronic state. The compound absorption spectrum has a full width at half maximum of 9,800 and 1,300 cm{sup {minus}1} (in agreement with the experimental value, 9,500 cm{sup {minus}1}) and a high-frequency structure spaced by 800 and 10 cm{sup {minus}1}, attributed to C{double{underscore}bond}C stretching. The resonance Raman excitation profile exhibits fundamental activity in all totally symmetric modes with the C{double{underscore}bond}C stretching mode being the most dominant. In addition, overtone activity is observed in the torsional motion, out-of-plane wagging motions and the out-of-plane rocking motions. The activity is consistent with the observation that the first excited state is twisted and one of the CH{sub 2} groups is pyramidalized. The coordinate dependence of the electronic transition dipole is investigated, and they find that it depends very strongly on the torsional coordinate and less so on the pyramidalization and C{double{underscore}bond}C stretching coordinates. However, within the approximations used in this paper this dependence does not influence the spectra significantly and the Condon approximation is quite accurate.
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.
Phonon spectra of elpasolites Cs2NaRF6 (R=Y,Yb): Ab initio calculations
Chernyshev, Vladimir; Petrov, Vladislav; Nikiforov, Anatoliy; Zakiryanov, Dmitriy
2015-12-01
The influence of hydrostatic pressure on structure and dynamics of a crystal lattice of elpasolites Cs2NaYbF6 and Cs2NaYF6 (S.G. 225) within ab initio approach is investigated. Frequencies and irreducible representations (irreps) of phonon modes are determined. Elastic constants are calculated. The calculations are carried out within MO LCAO approach using DFT method with hybrid functionalities of B3LYP and PBE0 in CRYSTAL09 periodic code. For the description of rare earth ion the pseudopotential replacing internal orbitals including 4f orbitals was used. External 5s and 5p orbitals defining chemical bond were described by valence basis sets.
Phonon spectra of elpasolites Cs{sub 2}NaRF{sub 6} (R=Y,Yb): Ab initio calculations
Chernyshev, Vladimir, E-mail: Vladimir.Chernyshev@urfu.ru; Petrov, Vladislav; Nikiforov, Anatoliy; Zakiryanov, Dmitriy [Ural Federal University, Ekaterinburg (Russian Federation)
2015-12-07
The influence of hydrostatic pressure on structure and dynamics of a crystal lattice of elpasolites Cs{sub 2}NaYbF{sub 6} and Cs{sub 2}NaYF{sub 6} (S.G. 225) within ab initio approach is investigated. Frequencies and irreducible representations (irreps) of phonon modes are determined. Elastic constants are calculated. The calculations are carried out within MO LCAO approach using DFT method with hybrid functionalities of B3LYP and PBE0 in CRYSTAL09 periodic code. For the description of rare earth ion the pseudopotential replacing internal orbitals including 4f orbitals was used. External 5s and 5p orbitals defining chemical bond were described by valence basis sets.
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.
1989-01-01
Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F + H2 yields HF + H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.
Ab initio intermolecular potential energy surface of He-LiH
鄢国森; 杨明晖; 谢代前
1997-01-01
The intermolecular potential energy surface of He-LiH complex was studied using the full-electronic complete forth-order Miller-Plesset perturbation (MPPT) method.In ab initio calculations,the bond length of LiH was fixed at 0 159 5 nm.The potential has two local minima of Vm=-179.93 cm for the linear He LiH geormetrv at Rm=0.227 nm and Vm=-10.44 cm-1 for the linear He-HL1 geometry at Rm=0.516 nm The potemal exhibits strong anisotropy The analytic potential function with 31 parameters was determined by fitting to the calculated ab,mtio potentials The influence of variation of LiH bond length on the potential energy surface was also studied
Sumner, Isaiah; Iyengar, Srinivasan S
2008-08-07
We discuss hybrid quantum-mechanics/molecular-mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) generalizations to our recently developed quantum wavepacket ab initio molecular dynamics methodology for simultaneous dynamics of electrons and nuclei. The approach is a synergy between a quantum wavepacket dynamics, ab initio molecular dynamics, and the ONIOM scheme. We utilize this method to include nuclear quantum effects arising from a portion of the system along with a simultaneous description of the electronic structure. The generalizations provided here make the approach a potentially viable alternative for large systems. The quantum wavepacket dynamics is performed on a grid using a banded, sparse, and Toeplitz representation of the discrete free propagator, known as the "distributed approximating functional." Grid-based potential surfaces for wavepacket dynamics are constructed using an empirical valence bond generalization of ONIOM and further computational gains are achieved through the use of our recently introduced time-dependent deterministic sampling technique. The ab initio molecular dynamics is achieved using Born-Oppenheimer dynamics. All components of the methodology, namely, quantum dynamics and ONIOM molecular dynamics, are harnessed together using a time-dependent Hartree-like procedure. We benchmark the approach through the study of structural and vibrational properties of molecular, hydrogen bonded clusters inclusive of electronic, dynamical, temperature, and critical quantum nuclear effects. The vibrational properties are constructed through a velocity/flux correlation function formalism introduced by us in an earlier publication.
Xiong, L H; Yoo, H; Lou, H B; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z; Xie, H L; Xiao, T Q; Jeon, S; Lee, G W
2015-01-28
X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al(75)Cu(25) alloy have been performed from 800 to 1600 K. Experimental and ab initio molecular dynamics simulation results match well with each other. No abnormal changes were experimentally detected in the specific heat capacity over total hemispheric emissivity and density curves in the studied temperature range for a bulk liquid Al(75)Cu(25) alloy measured by the electrostatic levitation technique. The structure factors gained by the ab initio molecular dynamics simulation precisely coincide with the experimental data. The atomic structure analyzed by the Honeycutt-Andersen index and Voronoi tessellation methods shows that icosahedral-like atomic clusters prevail in the liquid Al(75)Cu(25) alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al(75)Cu(25) alloy in the studied temperature range.
Ventelon, L
2008-11-15
The various methods appropriate for the simulation of dislocations within first-principles calculations have been set up, improved and compared between them. They have been applied to study screw dislocations in body-centered cubic iron using the SIESTA code. A non-degenerate core structure is obtained; its detailed analysis reveals a dilatation effect. Taking it into account in an anisotropic elasticity model, allows explaining the cell-size dependence of the energetics, obtained within the dipole approach. The Peierls potential obtained in ab initio suggests that the metastable core configuration at halfway position in the Peierls barrier, predicted by empirical potential, does not exist. We show how to construct tri-periodic cells optimized to study kinked dislocations. Using empirical potential, we demonstrate the feasibility of ab initio calculations of Peierls stress and kink formation. (author)
Espinosa-Garcia, Joaquin; Rangel, Cipriano; Suleimanov, Yury V
2017-07-26
We have developed an analytical full-dimensional potential energy surface, named PES-2017, for the gas-phase hydrogen abstraction reaction between the cyano radical and methane. This surface is fitted using high-level ab initio information as input. Using the PES-2017 surface, a kinetics study was performed via two theoretical approaches: variational transition-state theory with multidimensional tunnelling (VTST-MT) and ring polymer molecular dynamics (RPMD). The results are compared with the experimental data. In the whole temperature range analysed, 300-1500 K, both theories agree within a factor of kinetic isotope effects are important, reproducing the scarce experimental evidence. The good agreement with the ab initio information used in the fitting process (self-consistency test) and with the kinetic behaviour in a wide temperature range gives confidence and strength to the new surface.
Lawson, John W.; Bauschlicher, Charles W.; Daw, Murray
2011-01-01
Refractory materials such as metallic borides, often considered as ultra high temperature ceramics (UHTC), are characterized by high melting point, high hardness, and good chemical inertness. These materials have many applications which require high temperature materials that can operate with no or limited oxidation. Ab initio, first principles methods are the most accurate modeling approaches available and represent a parameter free description of the material based on the quantum mechanical equations. Using these methods, many of the intrinsic properties of these material can be obtained. We performed ab initio calculations based on density functional theory for the UHTC materials ZrB2 and HfB2. Computational results are presented for structural information (lattice constants, bond lengths, etc), electronic structure (bonding motifs, densities of states, band structure, etc), thermal quantities (phonon spectra, phonon densities of states, specific heat), as well as information about point defects such as vacancy and antisite formation energies.
Renison, C Alicia; Fernandes, Kyle D; Naidoo, Kevin J
2015-07-05
This article describes an extension of the quantum supercharger library (QSL) to perform quantum mechanical (QM) gradient and optimization calculations as well as hybrid QM and molecular mechanical (QM/MM) molecular dynamics simulations. The integral derivatives are, after the two-electron integrals, the most computationally expensive part of the aforementioned calculations/simulations. Algorithms are presented for accelerating the one- and two-electron integral derivatives on a graphical processing unit (GPU). It is shown that a Hartree-Fock ab initio gradient calculation is up to 9.3X faster on a single GPU compared with a single central processing unit running an optimized serial version of GAMESS-UK, which uses the efficient Schlegel method for s- and l-orbitals. Benchmark QM and QM/MM molecular dynamics simulations are performed on cellobiose in vacuo and in a 39 Å water sphere (45 QM atoms and 24843 point charges, respectively) using the 6-31G basis set. The QSL can perform 9.7 ps/day of ab initio QM dynamics and 6.4 ps/day of QM/MM dynamics on a single GPU in full double precision. © 2015 Wiley Periodicals, Inc.
Kimberg, Victor, E-mail: victor.kimberg@pks.mpi.de [Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, 01187 Dresden (Germany); Miron, Catalin, E-mail: miron@synchrotron-soleil.fr [Synchrotron SOLEIL, l’Orme des Merisiers, Saint-Aubin, BP 48, FR-91192 Gif-sur-Yvette Cedex (France)
2014-08-15
Highlights: • Some studies related to the vibrational wave functions mapping phenomenon are reviewed. • The core-excited vibrational wave functions were mapped using dissociative and bound final states. • High-resolution experimental data is accompanied by ab initio calculations. • The mapping phenomenon allows one to extract constants of the molecular potentials. • The mapping techniques are general and can be applied for the study of many systems. - Abstract: The recent development of high brightness 3{sup rd} generation soft X-ray sources and high energy resolution electron spectrometers made it possible to accurately trace quantum phenomena associated to the vibrational dynamics in core-excited molecules. The present paper reviews the recent results on mapping of vibrational wave functions and molecular potentials based on electron spectroscopy. We discuss and compare the mapping phenomena in various systems, stressing the advantages of the resonant X-ray scattering for studying of the nuclear dynamics and spectroscopic constants of small molecules. The experimental results discussed in the paper are most often accompanied by state-of-the-art ab initio calculations allowing for a deeper understanding of the quantum effects. Besides its fundamental interest, the vibrational wave function mapping is shown to be useful for the analysis of core- and valence-excited molecular states based on the reflection principle.
Boese, A D; Martin, J M L; Marx, D; Chandra, Amalendu; Martin, Jan M.L.; Marx, Dominik
2003-01-01
The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without resorting to experiment. The global minimum of eclipsed C_s symmetry is characterized by a significantly bent hydrogen bond which deviates from linearity by about 20 degrees. In addition, the so-called cyclic C_{2h} structure is extremely close in energy on an overall flat potential energy surface. It is demonstrated that none of the currently available (GGA, meta--GGA, and hybrid) density functionals satisfactorily describe the structure and relative energies of this nonlinear hydrogen bond. We present a novel density functional, HCTH/407+, designed to describe this sort of hydrogen bond quantitatively on the level of the dimer, contrary to e.g. the widely used BLYP functional. This improved functional is employed in Car-Parrinello ab initio molecular dynamics simulations of liq...
Ab initio quantum Monte Carlo calculations of ground-state properties of manganese's oxides
Sharma, Vinit; Krogel, Jaron T.; Kent, P. R. C.; Reboredo, Fernando A.
One of the critical scientific challenges of contemporary research is to obtain an accurate theoretical description of the electronic properties of strongly correlated systems such as transition metal oxides and rare-earth compounds, since state-of-art ab-initio methods based on approximate density functionals are not always sufficiently accurate. Quantum Monte Carlo (QMC) methods, which use statistical sampling to evaluate many-body wave functions, have the potential to answer this challenge. Owing to the few fundamental approximations made and the direct treatment of electron correlation, QMC methods are among the most accurate electronic structure methods available to date. We assess the accuracy of the diffusion Monte Carlo method in the case of rocksalt manganese oxide (MnO). We study the electronic properties of this strongly-correlated oxide, which has been identified as a suitable candidate for many applications ranging from catalysts to electronic devices. ``This work was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division.'' Ab initio quantum Monte Carlo calculations of ground-state properties of manganese's oxides.
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.
smyRNA: a novel Ab initio ncRNA gene finder.
Raheleh Salari
Full Text Available BACKGROUND: Non-coding RNAs (ncRNAs have important functional roles in the cell: for example, they regulate gene expression by means of establishing stable joint structures with target mRNAs via complementary sequence motifs. Sequence motifs are also important determinants of the structure of ncRNAs. Although ncRNAs are abundant, discovering novel ncRNAs on genome sequences has proven to be a hard task; in particular past attempts for ab initio ncRNA search mostly failed with the exception of tools that can identify micro RNAs. METHODOLOGY/PRINCIPAL FINDINGS: We present a very general ab initio ncRNA gene finder that exploits differential distributions of sequence motifs between ncRNAs and background genome sequences. CONCLUSIONS/SIGNIFICANCE: Our method, once trained on a set of ncRNAs from a given species, can be applied to a genome sequences of other organisms to find not only ncRNAs homologous to those in the training set but also others that potentially belong to novel (and perhaps unknown ncRNA families. AVAILABILITY: (http://compbio.cs.sfu.ca/taverna/smyrna.
Ab initio study of the structural properties of acetonitrile-water mixtures
Chen, Jinfan; Sit, Patrick H.-L.
2015-08-01
Structural properties of acetonitrile and acetonitrile-water mixtures are studied using Density Functional Theory (DFT) and ab initio molecular dynamics simulations. Stable molecular clusters consisted of several water and acetonitrile molecules are identified to provide microscopic understanding of the interaction among water and acetonitrile molecules. Ab initio molecular dynamics simulations are performed to study the liquid structure at the finite temperature. Three mixing compositions in which the mole fraction of acetonitrile equals 0.109, 0.5 and 0.891 are studied. These compositions correspond to three distinct structural regimes. At the 0.109 and 0.891 mole fraction of acetonitrile, the majority species are mostly connected among themselves and the minority species are either isolated or forming small clusters without disrupting the network of the majority species. At the 0.5 mole fraction of acetonitrile, large water and acetonitrile clusters persist throughout the simulation, exhibiting the microheterogeneous behavior in acetonitrile-water mixtures in the mid-range mixing ratio.
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...
Ab initio study of structural, electronic, and thermal properties of Ir1-xRhx alloys
Sh. Ahmed
2015-06-01
Full Text Available The structural, electronic, mechanical and thermal properties of Ir1-xRhx alloys was studied systematically using ab initio density functional theory at different concentration (x = 0.00, 0.25, 0.50, 0.75, 1.00. The Special Quasirandom Structure method was used to make the alloys with FCC structure with four atoms per unit cell. The ground state properties such as lattice constant and bulk modulus were calculated to find the equilibrium atomic position for stable alloys. The calculated ground state properties are in good agreement with the experimental and previously presented other theoretical data. The electronic band structure and density of states were calculated to study the electronic properties for these alloys at different concentration. The electronic properties substantiate metallic behavior of alloys. The first principle density functional perturbation theory as implemented in quasiharmonic approximation was used for the calculation of thermal properties. We have calculated the thermal properties such the Debye temperatures, vibration energy, entropy, constant-volume specific heat and internal energy. The ab initio linear-response method was used for phonon densities of states calculations.
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.
Novel high-pressure phase of ZrO{sub 2}: An ab initio prediction
Durandurdu, Murat, E-mail: murat.durandurdu@agu.edu.tr
2015-10-15
The high-pressure behavior of the orthorhombic cotunnite type ZrO{sub 2} is explored using an ab initio constant pressure technique. For the first time, a novel hexagonal phase (Ni{sub 2}In type) within P6{sub 3}/mmc symmetry is predicted through the simulation. The Ni{sub 2}In type crystal is the densest high-pressure phase of ZrO{sub 2} proposed so far and has not been observed in other metal dioxides at high pressure before. The phase transformation is accompanied by a small volume drop and likely to occur around 380 GPa in experiment. - Graphical abstract: Post-cotunnite Ni{sub 2}In type hexagonal phase forms in zirconia at high pressure. - Highlights: • A post-cotunnite phase is predicted for ZrO{sub 2} through an ab initio simulation. • Cotunnite ZrO{sub 2} adopts the Ni{sub 2}In type structure at high pressure. • The Ni{sub 2}In type structure is the densest high-pressure phase of ZrO{sub 2} proposed so far. • The preferred mechanism in ZrO{sub 2} differs from the other metal dioxides.
Ab initio simulations of phase stability and martensitic transitions in NiTi
Haskins, Justin B.; Thompson, Alexander E.; Lawson, John W.
2016-12-01
For NiTi-based alloys, the shape memory effect is governed by a transition from a low-temperature martensite phase to a high-temperature austenite phase. Despite considerable experimental and computational work, basic questions regarding the stability of the phases and the martensitic phase transition remain unclear even for the simple case of binary, equiatomic NiTi. We perform ab initio molecular dynamics simulations to describe the temperature-dependent behavior of NiTi and resolve several of these outstanding issues. Structural correlation functions and finite temperature phonon spectra are evaluated to determine phase stability. We show that finite temperature, entropic effects stabilize the experimentally observed martensite (B19') and austenite (B2) phases while destabilizing the theoretically predicted (B33) phase. Free energy computations based on ab initio thermodynamic integration confirm these results and permit estimates of the transition temperature between the phases. In addition to the martensitic phase transition, we predict a new transition between the B33 and B19' phases. The role of defects in suppressing phase transformation temperatures is discussed.
Ab Initio Simulations of Temperature Dependent Phase Stability and Martensitic Transitions in NiTi
Haskins, Justin B.; Thompson, Alexander E.; Lawson, John W.
2016-01-01
For NiTi based alloys, the shape memory effect is governed by a transition from a low-temperature martensite phase to a high-temperature austenite phase. Despite considerable experimental and computational work, basic questions regarding the stability of the phases and the martensitic phase transition remain unclear even for the simple case of binary, equiatomic NiTi. We perform ab initio molecular dynamics simulations to describe the temperature-dependent behavior of NiTi and resolve several of these outstanding issues. Structural correlation functions and finite temperature phonon spectra are evaluated to determine phase stability. In particular, we show that finite temperature, entropic effects stabilize the experimentally observed martensite (B19') and austenite (B2) phases while destabilizing the theoretically predicted (B33) phase. Free energy computations based on ab initio thermodynamic integration confirm these results and permit estimates of the transition temperature between the phases. In addition to the martensitic phase transition, we predict a new transition between the B33 and B19' phases. The role of defects in suppressing these phase transformations is discussed.
Higher-order elastic constants and megabar pressure effects of bcc tungsten: Ab initio calculations
Vekilov, Yu. Kh.; Krasilnikov, O. M.; Lugovskoy, A. V.; Lozovik, Yu. E.
2016-09-01
The general method for the calculation of n th (n ≥2 ) order elastic constants of the loaded crystal is given in the framework of the nonlinear elasticity theory. For the crystals of cubic symmetry under hydrostatic compression, the two schemes of calculation of the elastic constants of second, third, and fourth order from energy-finite strain relations and stress-finite strain relations are implemented. Both techniques are applied for the calculation of elastic constants of orders from second to fourth to the bcc phase of tungsten at a 0-600 GPa pressure range. The energy and stress at the various pressures and deformations are obtained ab initio in the framework of projector augmented wave+generalized gradient approximation (PAW+GGA) method, as implemented in Vienna Ab initio Simulation Package (VASP) code. Using the obtained results, we found the pressure dependence of Grüneisen parameters for long-wave acoustic modes in this interval. The Lamé constants of second and third order were estimated for polycrystalline tungsten. The proposed method is applicable for crystals with arbitrary symmetry.
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.
Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces
Herron, Jeffrey A.; Morikawa, Yoshitada; Mavrikakis, Manos
2016-08-01
Using ab initio molecular dynamics as implemented in periodic, self-consistent (generalized gradient approximation Perdew-Burke-Ernzerhof) density functional theory, we investigated the mechanism of methanol electrooxidation on Pt(111). We investigated the role of water solvation and electrode potential on the energetics of the first proton transfer step, methanol electrooxidation to methoxy (CH3O) or hydroxymethyl (CH2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), whereas the binding energies of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrained ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Water solvation reduces the barriers for both C-H and O-H bond activation steps with respect to their vapor-phase values, although the effect is more pronounced for C-H bond activation, due to less disruption of the hydrogen bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased or uncharged Pt(111). However, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.
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}.
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.
Ab initio determination of an extended Heisenberg Hamiltonian in CuO{sub 2} layers
Calzado, C.J.; Malrieu, J.P. [Lab. de Physique Quantique, IRSAMC, Univ. Paul Sabatier, Toulouse (France)
2001-06-01
Accurate ab initio calculations on embedded Cu{sub 4}O{sub 12} square clusters, fragments of the La{sub 2}CuO{sub 4} lattice, confirm a value of the nearest neighbor antiferromagnetic coupling (J = 124 meV) previously obtained from ab initio calculations on bicentric clusters and in good agreement with experiment. These calculations predict non negligible antiferromagnetic second-neighbor interaction (J' = 6.5 meV) and four-spin cyclic exchange (K = 14 meV), which may affect the thermodynamic and spectroscopic properties of these materials. The dependence of the magnetic coupling on local lattice distortions has also been investigated. Among them the best candidate to induce a spin-phonon effect seems to be the movement of the Cu atoms, changing the Cu-Cu distance, for which the variation of the nearest neighbor magnetic coupling with the Cu-O distance is {delta}J/{delta}d{sub Cu} {sub -} {sub O} {proportional_to} 1700 cm {sup -1} A {sup -1}. (orig.)
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 calculation of oxygen self-diffusion coefficient in uranium dioxide UO2
Dorado, Boris; Garcia, Philippe; Torrent, Marc
Uranium dioxide UO2 is the most widely used nuclear fuel worldwide and its atomic transport properties are relevant to practically all engineering aspects of the material. Although transport properties have already been studied in UO2 by means of first-principles calculations, the ab initio determination of self-diffusion coefficients has up to now remained unreachable because the relevant computational tools were neither available or adapted. The present work reports our results related to the ab initio calculation of the oxygen self-diffusion coefficient in UO2. We first determine the Gibbs free energies of formation of oxygen charged defects by calculating both the electronic and vibrational (hence entropic) contributions. Then, we use the transition state theory in order to compute the effective jump frequency of the defects, which in turn provides us with the value of the pre-exponential factor. The results are compared to self-diffusion data obtained experimentally with a careful monitoring of the relevant thermodynamic conditions (oxygen partial pressure, temperature, impurity content).
Duffy, Daniel J.; Quenneville, Jason; Baumbaugh, T. M.; Kitchener, S. A.; McCormick, R. K.; Dormady, C. N.; Croce, T. A.; Navabi, A.; Stidham, Howard D.; Hsu, Shaw L.; Guirgis, Gamil A.; Deng, Shiping; Durig, James R.
2004-02-01
Ab initio calculations are reported for three of four possible conformers of 1,3-dichloropropane. The fourth conformer, with C s symmetry, has a predicted enthalpy difference of more than 1500 cm -1 from the most stable conformer from each calculation regardless of the basis set used, so there is little chance of observing it. Thus, there is no evidence in the infrared or Raman spectrum of the presence of a fourth conformer. The order of stability given by the ab initio calculations is C 2(GG)>C 1(AG)>C 2v(AA)>C s(GG'), where A indicates the anti form for one of the CH 2Cl groups and G indicates the gauche conformation for the other CH 2Cl group relative to the plane of the carbon atoms. Almost every band observed can be confidently assigned to one or another of the conformers. Many observed bands proved to be of a composite nature, with several nearly coincident vibrations of different conformers contributing to the band contour. Nonetheless, a complete assignment of fundamentals is possible for the most stable C 2 conformer, and 5 of the fundamentals of the C 2v conformer and 13 those of the C 1 conformer can be confidently assigned.
Abe, K.; Ito, K.; Suezawa, H.; Hirota, M.; Nishio, M.
1986-10-01
Conformations of a series of acyclic alcohols (CH/sub 3/CH(R)CH(OH)CH/sub 3/, CH/sub 3/CH(R)CH(OH)CH(R')CH/sub 3/, and CH/sub 3/CH(R)CH(OH)Bu/sup t/) were studied (1) by measuring vicinal H-H coupling constants (/sup 3/JH-H), (2) by lanthanoid-induced shift (LIS) analysis, (3) by molecular mechanics calculations (MM2), and (4) by ab initio (STO-3G, 4-31G geometry optimization) calculations. In the case of conformationally flexible alcohols as exemplified by 2-butanol and 3-pentanol, population of conformers determined by the LIS method do not agree with those determined by the /sup 3/JH-H, MM2, and ab initio methods. The discrepancy comes from the fact that the LIS measurement gives the most stable conformation of the alcohol in the LSR-alcohol complex and not of the free alcohol. In some flexible molecules, the most stable conformer in the complex can be different from that of the free molecule. In general, the conformational equilibrium is shifted by coordination of the shift reagent to the conformer whose alkyl chain stretches opposite to the direction of the coordination site of the shift reagent. 21 references, 1 figure, 6 tables.
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.
Erba, A., E-mail: alessandro.erba@unito.it; Mahmoud, A.; Dovesi, R. [Dipartimento di Chimica and Centre of Excellence NIS (Nanostructured Interfaces and Surfaces), Università di Torino, via Giuria 5, IT-10125 Torino (Italy); Belmonte, D. [DISTAV, Università di Genova, Corso Europa 26, 16132 Genoa (Italy)
2014-03-28
A computational strategy is devised for the accurate ab initio simulation of elastic properties of crystalline materials under pressure. The proposed scheme, based on the evaluation of the analytical stress tensor and on the automated computation of pressure-dependent elastic stiffness constants, is implemented in the CRYSTAL solid state quantum-chemical program. Elastic constants and related properties (bulk, shear and Young moduli, directional seismic wave velocities, elastic anisotropy index, Poisson's ratio, etc.) can be computed for crystals of any space group of symmetry. We apply such a technique to the study of high-pressure elastic properties of three silicate garnet end-members (namely, pyrope, grossular, and andradite) which are of great geophysical interest, being among the most important rock-forming minerals. The reliability of this theoretical approach is proved by comparing with available experimental measurements. The description of high-pressure properties provided by several equations of state is also critically discussed.
Paulla, Kirti K.; Hassan, Ahmed J.; Knick, Cory R.; Farajian, Amir A.
2014-03-01
Molecules adsorption on graphene nanoribbons (GNRs) can be used to engineer and make use of their properties for applications such as energy storage and sensors. We investigate adsorption characteristics by considering nitrogen dioxide as a sample molecule for assessing nanosensor functionality of GNRs. Using ab initio modeling, energetics of various adsorption possibilities are determined and their rate constants are calculated and compared. Nonbonding and weak sp3 adsorptions at the hydrogen-terminated edges are shown to be more feasible than center adsorptions. This shows increased reactivity compared to graphene. Calculated quantum transport responses upon molecules adsorption indicate possibility of sensing extremely low nitrogen dioxide concentrations. Possible approaches for improving gas nanosensor functionality of GNRs are discussed. Reference: RSC Advances, 2013, DOI: 10.1039/c3ra46372a. This research was supported by the National Science Foundation Grant ECCS-0925939.
Salim de Amorim, H.; Amaral, M.R. do [Instituto de Fisica, Universidade Federal do Rio de Janeiro, CP 68528, 21495-970 Rio de Janeiro (Brazil); Pattison, P. [Institute of Crystallography, BSP, University of Laussane, CH-1015, Laussane (Switzerland); Pereira L, I.; Mendes, J.C. [Departamento de Geologia, Universidade Federal do Rio de Janeiro, 21949-900, Rio de Janeiro (Brazil)
2002-07-01
The structure of ammonium azide (NH{sub 4})N{sub 3} was (re-)determined ab initio from x-ray powder diffraction experiment using synchrotron radiation. We tried to detail and comment the different steps involved in the structure determination. The compound crystallize in the orthorhombic Pmna space group (no.53) with a = 8.937(1) A, b= 3.8070(5) A, c = 8.664(1) A, V = 294.79(7) A{sup 3}; Z= 4. It was possible to locate and refine the hydrogen coordinates, in two different approaches, and to establish the H-bonds. The final structural parameters are in good agreement with previous results based on three-dimensional neutron diffraction. (Author)
Monteiro, Norberto K V; Firme, Caio L
2014-03-06
The hydrogen-hydrogen (H-H) bond or hydrogen-hydrogen bonding is formed by the interaction between a pair of identical or similar hydrogen atoms that are close to electrical neutrality and it yields a stabilizing contribution to the overall molecular energy. This work provides new, important information regarding hydrogen-hydrogen bonds. We report that stability of alkane complexes and boiling point of alkanes are directly related to H-H bond, which means that intermolecular interactions between alkane chains are directional H-H bond, not nondirectional induced dipole-induced dipole. Moreover, we show the existence of intramolecular H-H bonds in highly branched alkanes playing a secondary role in their increased stabilities in comparison with linear or less branched isomers. These results were accomplished by different approaches: density functional theory (DFT), ab initio, quantum theory of atoms in molecules (QTAIM), and electron localization function (ELF).
Koizumi, Kenichi; Nobusada, Katsuyuki [Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki 444-8585 (Japan); Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520 (Japan); Boero, Mauro [Institut de Physique et Chimie des Matériaux de Strasbourg UMR 7504, University of Strasbourg and CNRS, 23 rue du Loess, F-67034 Strasbourg (France)
2015-12-31
Ab initio molecular dynamics simulations have been used to inspect the adsorption of O{sub 2} to a small gold-copper alloy cluster supported on graphene. The exposed Cu atom in this cluster acts as a crucial attractive site for the approaching of O{sub 2} and consequently widens the reaction channel for the adsorption process. Conversely, a pure Au cluster on the same graphene support is inactive for the O{sub 2} adsorption because the corresponding reaction channel for the adsorption is very narrow. These results clearly indicate that doping a different metal to the Au cluster is a way to enhance the oxygen adsorption and to promote catalytic reactions.
Cerdeira, M. A.; Palacios, S. L.; González, C.; Fernández-Pello, D.; Iglesias, R.
2016-09-01
The formation, binding and migration energetics of helium clusters inside a niobium crystal have been analysed via ab initio simulations. The effect of placing several He atoms within an n-vacancy previously formed or as interstitials inside the initial perfect bulk matrix has been studied. DFT-based results show that He atoms prefer to aggregate forming small clusters at n-vacancy sites rather than at interstitial positions in the perfect crystal. The minimum formation energy is found when NHe is equal to the number of vacancies, n. It follows that vacancies act as almost perfect traps for He atoms, as is well known for other metals. The migration barriers of He atoms inside vacancies increase considerably when compared to what happens for vacancies alone. A secondary consequence is that the full set of energies obtained will be highly relevant as an input for new approaches to KMC simulations of defects in Nb.
Ab initio treatment of ion-induced charge transfer dynamics of isolated 2-deoxy-D-ribose.
Bacchus-Montabonel, Marie-Christine
2014-08-21
Modeling-induced radiation damage in biological systems, in particular, in DNA building blocks, is of major concern in cancer therapy studies. Ion-induced charge-transfer dynamics may indeed be involved in proton and hadrontherapy treatments. We have thus performed a theoretical approach of the charge-transfer dynamics in collision of C(4+) ions and protons with isolated 2-deoxy-D-ribose in a wide collision energy range by means of ab initio quantum chemistry molecular methods. The comparison of both projectile ions has been performed with regard to previous theoretical and experimental results. The charge transfer appears markedly less efficient with the 2-deoxy-D-ribose target than that with pyrimidine nucleobases, which would induce an enhancement of the fragmentation process in agreement with experimental measurements. The mechanism has been analyzed with regard to inner orbital excitations, and qualitative tendencies have been pointed out for studies on DNA buiding block damage.
Sun, Tao; Zhang, Dong-Bo; Wentzcovitch, Renata M.
2014-03-01
The stability of cubic CaSiO3 perovskite (CaPv) at high temperatures and pressures is investigated by vibrational normal-mode analysis. We compute power spectra of mode autocorrelation functions using a recently developed hybrid approach combining ab initio molecular dynamics with lattice dynamics. These power spectra, together with the probability distributions of atomic displacements, indicate that cubic CaPv is stabilized at T ˜600 K and P ˜ 26 GPa. We then utilize the concept of phonon quasiparticles to characterize the vibrational properties of cubic CaPv at high temperature and obtain anharmonic phonon dispersions through the whole Brillouin zone. Such temperature-dependent phonon dispersions pave the way for more accurate calculations of free-energy, thermodynamic, and thermoelastic properties of cubic CaPv at Earth's lower mantle conditions.
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.
Ko, Hsin-Yu; Distasio, Robert A., Jr.; Santra, Biswajit; Car, Roberto
2014-03-01
Pyridine has recently been investigated as a potentially effective material for use in artificial light harvesting.In this work, we propose the use of ab initio molecular dynamics (AIMD) to gain valuable physical insight into the artificial photosynthetic processes occurring in condensed-phase pyridine, the study of which has been limited to semi-empirical force fields to date.For this purpose, we introduce an accurate and efficient AIMD method, based on density functional theory (DFT) and a self-consistent pairwise description of van der Waals (vdW) interactions, for use in finite temperature and pressure (NPT) simulations on pyridine and several pyridine-like molecular crystals (PLMCs). Utilizing this approach, we demonstrate that vdW forces play a crucial role in the theoretical prediction of the structure and density of pyridine and PLMCs, and therefore must be accounted for in studies of these potential alternative energy materials. DOE: DE-SC0008626, NSF: DMS-1065894.
Kawashima, Yukio; Tachikawa, Masanori
2013-05-01
Ab initio path integral molecular dynamics simulation was performed to understand the nuclear quantum effect on the hydrogen bond of hydrogen malonate anion. Static calculation predicted the proton transfer barrier as 0.12 kcal/mol. Conventional ab initio molecular dynamics simulation at 300 K found proton distribution with a double peak on the proton transfer coordinate. Inclusion of thermal effect alone elongates the hydrogen bond length, which increases the barrier height. Inclusion of nuclear quantum effect washes out this barrier, and distributes a single broad peak in the center. H/D isotope effect on the proton transfer is also discussed.
AB initio calculations of the structure and stability of the non-rigid LiBF 4 molecule
Zakzhevzskii, V. G.; Boldyrev, A. I.; Charkin, O. P.
1980-07-01
Ab initio calculations of the potential energy surface, equilibrium geometry and energetic stability of the non-rigid LiBF4 molecule have been performed using the basis sets of Roos and Siegbahn, and Huzinaga and Dunning in a doublezeta contraction. The results are compared with similar ab initio data for LiBH 4, LiAlH 4, LiBeH -4, LiCH +4, Li 2 F 2, and LiBeF 3 ‡The geometry of the most disadvantageous configuration (m) was not optimized completely
Kedziera, Dariusz; Mentel, Łukasz; Żuchowski, Piotr S.; Knoop, Steven
2015-06-01
We have obtained accurate ab initio +4Σ quartet potentials for the diatomic metastable triplet helium+alkali-metal (Li, Na, K, Rb) systems, using all-electron restricted open-shell coupled cluster singles and doubles with noniterative triples corrections CCSD(T) calculations and accurate calculations of the long-range C6 coefficients. These potentials provide accurate ab initio quartet scattering lengths, which for these many-electron systems is possible, because of the small reduced masses and shallow potentials that result in a small amount of bound states. Our results are relevant for ultracold metastable triplet helium+alkali-metal mixture experiments.
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.
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.)
Stavretis, Shelby E; Atanasov, Mihail; Podlesnyak, Andrey A; Hunter, Seth C; Neese, Frank; Xue, Zi-Ling
2015-10-19
experimentally deduced trend. D parameters from CASSCF and NEVPT2 results have been calibrated against those from the INS data, yielding a predictive power of these approaches. Methods to improve the quantitative agreement between ab initio calculated and experimental D and spectroscopic transitions for high-spin Fe(III) complexes are proposed.
An analysis of hydrated proton diffusion in ab initio molecular dynamics
Tse, Ying-Lung Steve; Voth, Gregory A., E-mail: gavoth@uchicago.edu [Department of Chemistry, James Franck Institute, and Computation Institute, University of Chicago, Chicago, Illinois 60637 (United States); Knight, Chris [Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439 (United States)
2015-01-07
A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ∼2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP–D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300–330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and after successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions
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
An analysis of hydrated proton diffusion in ab initio molecular dynamics
Tse, Ying-Lung Steve; Knight, Chris; Voth, Gregory A.
2015-01-01
A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ˜2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP-D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300-330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and after successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions. Furthermore
Realization of prediction of materials properties by ab initio computer simulation
Yoshiyuki Kawazoe
2003-01-01
Ab initio treatment is becoming realistic to predict physical, chemical, and even mechanical properties of academically and industrially interesting materials. There is, however, some limitation in size and time of the system up to the order of several hundred atoms and ∼ 1 pico second, even if we use the fastest supercomputer efficiently. Therefore, it is very difficult to simulate realistic materials with grain boundaries and important reactions like diffusion in materials. To improve this situation, two ways have been invented. One way is to upgrade approximations to match the necessary levels according to inhomogeneous electron gas theory beyond the present day standard, i.e. local density approximation (LDA). The reason is simply that the system we are interested in is composed of many particles interacting with Coulomb forces governed by quantum mechanics. (Complete knowledge is available, and only what we should do is to make better approximations to explain the phenomena!). Another is to extract the necessary parameters from the ab initio calculations on systems with limited number of atoms, and apply these results into cluster variation, direct, or any other sophisticated methods based on classical concepts such as statistical mechanics. In this paper, several typical examples recently worked out by our research group are introduced to indicate that these methodologies are actually possible to be successfully used to predict materials properties before experiments based on the present day state-of-art supercomputing systems. It includes scientific visualization of the results of ab initio molecular dynamics simulation on atom insertion process to C60 and to carbon nanotube, tight-binding calculation of single electron conductance properties in nanotube to create nano-scale diode virtually by computer, which will be a base of future nanoscale electric device in nanometer size, Li + H reaction without Born–Oppenheimer approximation, structural phase
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.
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
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
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.
Giovannetti, Gianluca; Brocks, Geert; Brink, van den Jeroen
2008-01-01
We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic mome
Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi
2000-12-01
We present an accurate calculational scheme for many-body systems composed of electrons and nuclei, by path integral molecular dynamics technique combined with the ab initio molecular orbital theory. Based upon the scheme, the simulation of a water molecule at room temperature is demonstrated, applying all-electron calculation at the Hartree-Fock level of theory.
Berg, Rolf W.
-H-Br] [ref 2] and (3) the 1-methylimidazolium ethano-ate, [mim-H-O2CCH3] found [ref 3] to have a less likely existence in the vapor of the corresponding liquid in ampouls at ~200°C (Fig. 2). Experimental Raman results will be compared to ab initio calculated spectra. Fig. 1. Likely gaseous ion pair molecule...
Fishchuk, A.V.; Groenenboom, G.C.; Avoird, A. van der
2006-01-01
Bound energy levels and properties of the Cl((2)p)-HF complex were obtained from full three-dimensional (3D) calculations, with the use of the ab initio computed diabatic potential surfaces from the preceding paper and the inclusion of spin-orbit coupling. For a better understanding of the dynamics
Åstrand, P.-O.; Bak, K.L.; Sauer, S.P.A.
2001-01-01
The two lowest singlet excitation energies of 26 2-imidazolyl-2-thiazolylazo compounds have been investigated by ab initio methods within the second-order polarization propagator approximation (SOPPA). Various combinations of 4- and 5-substituents at both the imidazole and thiazole units have bee...
Giovannetti, G.; Brocks, G.; van den Brink, J.
2008-01-01
We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic
2011-01-01
The geometric, electronic structure, effect of the substitution, and structure physical-chemistry relationship for oxazoles derivatives have been studied by ab initio and DFT theory. In the present work, the calculated values, namely, net charges, bond lengths, dipole moments, electron affinities, heats of formation, and QSAR properties are reported and discussed in terms of the reactivity of oxazole derivatives.
Giovannetti, G.; Brocks, G.; van den Brink, J.
2008-01-01
We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic mome
Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.
1997-01-01
The method of ab initio molecular dynamics, based on finite-temperature density-functional theory, is used to simulate laser heating of crystalline silicon. We found that a high concentration of excited electrons dramatically weakens the covalent bonding. As a result the system undergoes a melting t
Salah Belaidi
2011-01-01
Full Text Available The geometric, electronic structure, effect of the substitution, and structure physical-chemistry relationship for oxazoles derivatives have been studied by ab initio and DFT theory. In the present work, the calculated values, namely, net charges, bond lengths, dipole moments, electron affinities, heats of formation, and QSAR properties are reported and discussed in terms of the reactivity of oxazole derivatives.
Iftimie, R; Schofield, J P; Iftimie, Radu; Salahub, Dennis; Schofield, Jeremy
2003-01-01
In this article, we propose an efficient method for sampling the relevant state space in condensed phase reactions. In the present method, the reaction is described by solving the electronic Schr\\"{o}dinger equation for the solute atoms in the presence of explicit solvent molecules. The sampling algorithm uses a molecular mechanics guiding potential in combination with simulated tempering ideas and allows thorough exploration of the solvent state space in the context of an ab initio calculation even when the dielectric relaxation time of the solvent is long. The method is applied to the study of the double proton transfer reaction that takes place between a molecule of acetic acid and a molecule of methanol in tetrahydrofuran. It is demonstrated that calculations of rates of chemical transformations occurring in solvents of medium polarity can be performed with an increase in the cpu time of factors ranging from 4 to 15 with respect to gas-phase calculations.
Ab Initio 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.
Barbosa, Marcelo
A review about the nuclear properties, namely the nuclear moments (magnetic dipole moment and electric quadrupole moment) and their interaction with electromagnetic fields external to the nucleus (hyperfine interactions), as well as the angular distribution of radiation produced by $\\gamma$-decay, is presented. A detailed description about the theory of Perturbed Angular Correlations was done, including the comparison between $\\gamma-\\gamma$- correlations and $e^{-}- \\gamma$ correlations. For dynamic nuclear interactions, an introduction to the theory of stochastic states in PAC was performed. We focused on ab-initio implementation of observables for analyzing fluctuating quadrupole hyperfine interactions on time dependent perturbed angular correlations experiments. The development of computacional codes solving the full problem, adapted to fit data obtained on single crystals or polycrystals for two-state transient fields with any axial symmetry and orientation was the main purpose of this work. The final pa...
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 study of pressure induced structural and electronic properties in TmPo
Makode, Chandrabhan, E-mail: cbmakode@gmail.com; Pataiya, Jagdish; Sanyal, Sankar P. [Department of Physics, Barkatullah University, Bhopal-462026 (India); Panwar, Y. S.; Aynyas, Mahendra [Department of Physics, C.S.A. Govt. P.G. College, Sehore-466001 (India)
2015-06-24
We report an ab initio calculation of pressure induced structural phase transition and electronic properties of Thulium Polonide (TmPo).The total energy as a function of volume is obtained by means of self-consistent tight binding linear muffin-tin-orbital (TB-LMTO) method within the local density approximation (LDA). It is found that TmPo is stable in NaCl-type (B{sub 1}-phase) structure to CsCl-type (B{sub 2}-phase) structure of this compound in the pressure range of 7.0 GPa. We also calculate the lattice parameter (a{sub 0}), bulk modulus (B{sub 0}), band structure and density of states. From energy diagram it is observed that TmPo exhibit metallic behavior. The calculated values of equilibrium lattice parameter and bulk modulus are in general good agreement.