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Sample records for ab initio simulations

  1. On the hierarchical parallelization of ab initio simulations

    Ruiz-Barragan, Sergi; Shiga, Motoyuki

    2016-01-01

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

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

    Sharipov, Felix; Strapasson, José L

    2012-09-01

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

  3. Ab initio simulation of helium inside carbon nanotubes

    In present work we consider the complex behaviour of quantum liquids like liquid He-4 inside carbon nanotubes. Interactions between helium atoms and carbon atoms of the short-length atomistic model and model with periodical boundary conditions of carbon nanotube were studied via ab initio quantum simulations. Effects of geometrical confinement of the tube on the He behaviour inside CNT (13,0) have been explored. Nanotubes with typical average diameter of 10 angstroms are under consideration.

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

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

    1996-01-01

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

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

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

  6. Ab initio simulations of peptide-mineral interactions

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

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

  7. Ab initio simulations on rutile-based titania nanowires

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

    2012-08-01

    The rod symmetry groups for monoperiodic (1D) nanostructures have been applied for construction of models for bulk-like TiO2 nanowires (NWs) cut from a rutile-based 3D crystal along the chosen [001] and [110] directions of crystallographic axes. In this study, we have considered nanowires described by both the Ti-atom centered rotation axes as well as the hollow site centered axes passing through the interstitial positions between the Ti and O atoms closest to the axes. The most stable [001]-oriented TiO2 NWs with rhombic cross sections are found to display the energetically preferable {110} facets only while the nanowires with quasi-square sections across the [110] axis are formed by the alternating { 1bar 10 } and {001} facets. For simulations on rutile-based nanowires possessing different diameters for each NW type, we have performed large-scale ab initio Density Functional Theory (DFT) and hybrid DFT-Hartree Fock (DFT-HF) calculations with total geometry optimization within the Generalized Gradient Approximation (GGA) in the form of the Perdew-Becke-Ernzenhof (PBE) exchange-correlation functionals (PBE and PBE0, respectively), using the formalism of linear combination of localized atomic functions (LCAO). We have simulated both structural and electronic properties of TiO2 NWs depending both on orientation and position of symmetry axes as well as on diameter and morphology of nanowires.

  8. 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...

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

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

    2008-12-05

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

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

    Tsuchida, Eiji

    2016-08-01

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

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

    Tsuchida, Eiji

    2014-01-01

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

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

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

    2014-01-01

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

  13. 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...

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

    Timko, Jeff; Kuyucak, Serdar

    2012-11-01

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

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

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

  16. Ab-initio molecular dynamics simulation of liquid water by Quantum Monte Carlo

    Zen, Andrea; Mazzola, Guglielmo; Guidoni, Leonardo; Sorella, Sandro

    2014-01-01

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

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

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

    2015-04-14

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

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

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

    1994-01-01

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

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

    The structural and dynamical properties of liquid ethanol (C2H5OH) at ambient conditions have been studied by ab initio molecular dynamics simulations using a large supercell containing 125 molecules (1125 atoms). The results obtained from a trajectory of 10 ps are found to be in good agreement with available experimental data. Without sacrificing accuracy, the computational cost of simulations is reduced by more than a factor of four by the linear scaling algorithm based on the augmented orbital minimization method

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

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

    2015-02-27

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

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

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

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

    Tsuchida, Eiji

    2015-01-01

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

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

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

    2008-01-01

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

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

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

    2013-01-01

    This work is devoted to the \\textit{ab initio} calculation of transport and optical properties of aluminum. The calculation is based on the quantum molecular dynamics simulation, density functional theory and the Kubo-Greenwood formula. Mainly the calculations are performed for liquid aluminum at near-normal densities for the temperatures from melting up to 20000 K. The results on dynamic electrical conductivity, static electrical conductivity and thermal conductivity are obtained and compare...

  5. 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.

  6. First results of ab initio simulations of scintillation detector characteristics

    We describe a new Monte-Carlo-simulation which models output signals of scintillator-photomultiplier tube (PMT) pairs . For the whole simulation from the initial photon-cascade within the scintillator to the final pulse as it is digitized at the output of the PMT only values from the scintillator's and PMT's technical manuals are used, no parameters need to be adapted. We find an excellent agreement between sampled and simulated signals. This allows to determine the influence of single parameters independent from the others. With a special focus on positron lifetime as well as perturbed angular correlation spectrometers, which have high demands on the γ-photon incidence time determination's accuracy, the influence of the tts-parameter on the detector's overall time resolution was studied in detail.

  7. Thermodynamics of water modeled using ab initio simulations

    Weber, Valéry

    2010-01-01

    We regularize the potential distribution framework to calculate the excess free energy of liquid water simulated with the BLYP-D density functional. The calculated free energy is in fair agreement with experiments but the excess internal energy and hence also the excess entropy are not. Our work emphasizes the importance of thermodynamic characterization in assessing the quality of electron density functionals in describing liquid water and hydration phenomena.

  8. Ab Initio Simulation Beryllium in Solid Molecular Hydrogen: Elastic Constant

    Guerrero, Carlo L.; Perlado, Jose M.

    2016-03-01

    In systems of inertial confinement fusion targets Deuterium-Tritium are manufactured with a solid layer, it must have specific properties to increase the efficiency of ignition. Currently there have been some proposals to model the phases of hydrogen isotopes and hence their high pressure, but these works do not allow explaining some of the structures present at the solid phase change effect of increased pressure. By means of simulation with first principles methods and Quantum Molecular Dynamics, we compare the structural difference of solid molecular hydrogen pure and solid molecular hydrogen with beryllium, watching beryllium inclusion in solid hydrogen matrix, we obtain several differences in mechanical properties, in particular elastic constants. For C11 the difference between hydrogen and hydrogen with beryllium is 37.56%. This may produce a non-uniform initial compression and decreased efficiency of ignition.

  9. Ab initio based force field and molecular dynamics simulations of crystalline TATB.

    Gee, Richard H; Roszak, Szczepan; Balasubramanian, Krishnan; Fried, Laurence E

    2004-04-15

    An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally. PMID:15267608

  10. Acidity of clay edges from ab-initio simulations

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

  11. Specific interactions between amyloid-β peptide and curcumin derivatives: Ab initio molecular simulations

    Ishimura, Hiromi; Kadoya, Ryushi; Suzuki, Tomoya; Murakawa, Takeru; Shulga, Sergiy; Kurita, Noriyuki

    2015-07-01

    Alzheimer's disease is caused by accumulation of amyloid-β (Aβ) peptides in a brain. To suppress the production of Aβ peptides, it is effective to inhibit the cleavage of amyloid precursor protein (APP) by secretases. However, because the secretases also play important roles to produce vital proteins for human body, inhibitors for the secretases may have side effects. To propose new agents for protecting the cleavage site of APP from the attacking of the γ-secretase, we have investigated here the specific interactions between a short APP peptide and curcumin derivatives, using protein-ligand docking as well as ab initio molecular simulations.

  12. Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol

    Pham, Thi Nu; Ono, Shota; Ohno, Kaoru

    2016-04-01

    Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronic excited state configuration.

  13. 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.

  14. Ab initio simulation of effects of structural singularities in aerogel absorption potential

    In the present work simulation of Van der Waals potential between helium atom and part of silica aerogel strand by means of ab initio methods was performed. Cell with alpha quartz structure was used as building block of aerogel strand, because it is the most stable structure at low temperature, and only the surface layer of aerogel has been considered. For modeling absorption potential field in plane, summation of potential from individual building blocks has been provided. Two dimensional Van der Waals energy field was calculated for different geometries of aerogel strands. A rather deep potential well has been found in the corner formed due to aerogel strand crossing.

  15. AB-INITIO SIMULATION OF ELECTRONIC FEATURES OF HYPERFINE RARE EARTH OXIDE FILMS FOR SENSORY NANOSYSTEMS

    A. V. Gulay

    2014-01-01

    Full Text Available Ab-Initio simulation of electronic features of sensoring nanomaterials based on rare earth oxides has been made by the example of yttrium oxide. The simulation method for thin films of nanometer scale consisted in the simulation of the material layer of the thickness equal to unit crystal cell size has been proposed within the VASP simulation package. The atomic bond breakdown in the crystal along one of the coordinate axes is simulated by the increase of a distance between the atomic layers along this axis up to values at which the value of free energy is stabilized. It has been found that the valence and conductivity bands are not revealed explicitly and the band gap is not formed in the hyperfine rare earth oxide film (at the film thickness close to 1 nm. In fact the hyperfine rare earth oxide film loses dielectric properties which were exhibited clear enough in continuum.

  16. Structure and Raman spectra in cryolitic melts: simulations with an ab initio interaction potential.

    Cikit, Serpil; Akdeniz, Zehra; Madden, Paul A

    2014-01-30

    The Raman spectra of cryolitic melts have been calculated from molecular dynamics computer simulations using a polarizable ionic potential obtained by force-fitting to ab initio electronic structure calculations. Simulations which made use of this ab initio derived polarizable interaction potential reproduced the structure and dynamical properties of crystalline cryolite, Na3AlF6, rather well. The transferability of the potential model from solid state to the molten state is tested by comparing results for the Raman spectra of melts of various compositions with those previously obtained with empirically developed potentials and with experimental data. The shapes of the spectra and their evolution with composition in the mixtures conform quite well to those seen experimentally, and we discuss the relationship between the bands seen in the spectra and the vibrational modes of the AlFn((3–n)) coordination complexes which are found in the NaF/AlF3 mixtures. The simulations thus enable a link between the structure of the melt as derived through Raman spectroscopy and through diffraction experiments. We report results for quantities which relate to the degree of cross-linking between these coordination complexes and the diffusive properties of ions. PMID:24432905

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

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

  18. Liquid chloroform structure from computer simulation with a full ab initio intermolecular interaction potential

    We have calculated the intermolecular interaction energies of the chloroform dimer in 12 orientations using the second-order Møller-Plesset perturbation theory. Single point energies of important geometries were calibrated by the coupled cluster with single and double and perturbative triple excitation method. Dunning's correlation consistent basis sets up to aug-cc-pVQZ have been employed in extrapolating the interaction energies to the complete basis set limit values. With the ab initio potential data we constructed a 5-site force field model for molecular dynamics simulations. We compared the simulation results with recent experiments and obtained quantitative agreements for the detailed atomwise radial distribution functions. Our results were also consistent with previous results using empirical force fields with polarization effects. Moreover, the calculated diffusion coefficients reproduced the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with existing empirical force fields for liquid chloroform

  19. Accelerating Ab Initio Path Integral Simulations via Imaginary Multiple-Timestepping.

    Cheng, Xiaolu; Herr, Jonathan D; Steele, Ryan P

    2016-04-12

    This work investigates the use of multiple-timestep schemes in imaginary time for computationally efficient ab initio equilibrium path integral simulations of quantum molecular motion. In the simplest formulation, only every n(th) path integral replica is computed at the target level of electronic structure theory, whereas the remaining low-level replicas still account for nuclear motion quantum effects with a more computationally economical theory. Motivated by recent developments for multiple-timestep techniques in real-time classical molecular dynamics, both 1-electron (atomic-orbital basis set) and 2-electron (electron correlation) truncations are shown to be effective. Structural distributions and thermodynamic averages are tested for representative analytic potentials and ab initio molecular examples. Target quantum chemistry methods include density functional theory and second-order Møller-Plesset perturbation theory, although any level of theory is formally amenable to this framework. For a standard two-level splitting, computational speedups of 1.6-4.0x are observed when using a 4-fold reduction in time slices; an 8-fold reduction is feasible in some cases. Multitiered options further reduce computational requirements and suggest that quantum mechanical motion could potentially be obtained at a cost not significantly different from the cost of classical simulations. PMID:26966920

  20. Dissociation dynamics of ethylene molecules on a Ni cluster using ab initio molecular dynamics simulations

    Shimamura, K.; Shibuta, Y.; Ohmura, S.; Arifin, R.; Shimojo, F.

    2016-04-01

    The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed.

  1. Dissociation dynamics of ethylene molecules on a Ni cluster using ab initio molecular dynamics simulations

    The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed. (paper)

  2. Ab initio molecular dynamics simulations of ion–solid interactions in zirconate pyrochlores

    In this study, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A2Zr2O7, A = La, Nd and Sm). It shows that both cations and anions in Nd2Zr2O7 and Sm2Zr2O7 are generally more likely to be displaced than those in La2Zr2O7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd2Zr2O7 and Sm2Zr2O7 are lower than those in La2Zr2O7. These results suggest that the order–disorder structural transition more easily occurs in Nd2Zr2O7 and Sm2Zr2O7 resulting in a defect-fluorite structure, which agrees well with experimental observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present results may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores

  3. Ab initio simulations for the ion-ion structure factor of warm dense aluminum.

    Rüter, Hannes R; Redmer, Ronald

    2014-04-11

    We perform ab initio simulations based on finite-temperature density functional theory in order to determine the static and dynamic ion-ion structure factor in aluminum. We calculate the dynamic structure factor via the intermediate scattering function and extract the dispersion relation for the collective excitations. The results are compared with available experimental x-ray scattering data. Very good agreement is obtained for the liquid metal domain. In addition we perform simulations for warm dense aluminum in order to obtain the ion dynamics in this strongly correlated quantum regime. We determine the sound velocity for both liquid and warm dense aluminum which can be checked experimentally using narrow-bandwidth free electron laser radiation. PMID:24765982

  4. 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.

  5. Decarboxylation of furfural on Pd(111): Ab initio molecular dynamics simulations

    Xue, Wenhua; Dang, Hongli; Shields, Darwin; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

    2013-03-01

    Furfural conversion over metal catalysts plays an important role in the studies of biomass-derived feedstocks. We report ab initio molecular dynamics simulations for the decarboxylation process of furfural on the palladium surface at finite temperatures. We observed and analyzed the atomic-scale dynamics of furfural on the Pd(111) surface and the fluctuations of the bondlengths between the atoms in furfural. We found that the dominant bonding structure is the parallel structure in which the furfural plane, while slightly distorted, is parallel to the Pd surface. Analysis of the bondlength fluctuations indicates that the C-H bond is the aldehyde group of a furfural molecule is likely to be broken first, while the C =O bond has a tendency to be isolated as CO. Our results show that the reaction of decarbonylation dominates, consistent with the experimental measurements. Supported by DOE (DE-SC0004600). Simulations and calculations were performed on XSEDE's and NERSC's supercomputers.

  6. Hydrogen-Water Mixtures in Giant Planet Interiors Studied with Ab Initio Simulations

    Soubiran, Francois

    2015-01-01

    We study water-hydrogen mixtures under planetary interior conditions using ab initio molecular dynamics simulations. We determine the thermodynamic properties of various water-hydrogen mixing ratios at temperatures of 2000 and 6000 K for pressures of a few tens of GPa. These conditions are relevant for ice giant planets and for the outer envelope of the gas giants. We find that at 2000 K the mixture is in a molecular regime, while at 6000 K the dissociation of hydrogen and water is important and affects the thermodynamic properties. We study the structure of the liquid and analyze the radial distribution function. We provide estimates for the transport properties, diffusion and viscosity, based on autocorrelation functions. We obtained viscosity estimates of the order of a few tenths of mPa.s for the conditions under consideration. These results are relevant for dynamo simulations of ice giant planets.

  7. i-PI: A Python interface for ab initio path integral molecular dynamics simulations

    Ceriotti, Michele; Manolopoulos, David E

    2014-01-01

    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.

  8. 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

  9. 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

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

    Knyazev, D V

    2013-01-01

    This work is devoted to the \\textit{ab initio} calculation of transport and optical properties of aluminum. The calculation is based on the quantum molecular dynamics simulation, density functional theory and the Kubo-Greenwood formula. Mainly the calculations are performed for liquid aluminum at near-normal densities for the temperatures from melting up to 20000 K. The results on dynamic electrical conductivity, static electrical conductivity and thermal conductivity are obtained and compared with available reference and experimental data and the calculations of other authors. The influence of the technical parameters on the results is investigated in detail. The error of static electrical conductivity calculation is estimated to be about 20%; more accurate results require bigger number of atoms.

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

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

    2010-07-01

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

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

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

    2013-01-01

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

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

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

    2013-01-01

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

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

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

    2015-01-01

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

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

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

    2016-07-01

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

  16. Ab-Initio Molecular Dynamics

    Kühne, Thomas D

    2012-01-01

    Computer simulations and molecular dynamics in particular, is a very powerful method to provide detailed and essentially exact informations of classical many-body problems. With the advent of \\textit{ab-initio} molecular dynamics, where the forces are computed on-the-fly by accurate electronic structure calculations, the scope of either method has been greatly extended. This new approach, which unifies Newton's and Schr\\"odinger's equations, allows for complex simulations without relying on any adjustable parameter. This review is intended to outline the basic principles as well as a survey of the field. Beginning with the derivation of Born-Oppenheimer molecular dynamics, the Car-Parrinello method as well as novel hybrid scheme that unifies best of either approach are discussed. The predictive power is demonstrated by a series of applications ranging from insulators to semiconductors and even metals in condensed phases.

  17. 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.)

  18. Ab Initio Cosmological Simulations of CR7 as an Active Black Hole

    Smidt, Joseph; Johnson, Jarrett L

    2016-01-01

    We present the first ab initio cosmological simulations of a CR7-like object which approximately reproduce the observed line widths and strengths. In our model, CR7 is powered by a massive (2.23 x 10^7 M_Sun), accreting (0.25 Eddington) supermassive black hole (BH). Our model takes into account multi-dimensional effects, X-ray feedback, secondary ionizations and primordial chemistry. We estimate Ly-alpha line widths by post-processing simulation output with Monte Carlo radiative transfer and calculate emissivity contributions from radiative recombination and collisional excitation. We find the luminosities in the Lyman-alpha and He II 1640 angstrom lines to be 5.0 x 10^44 and 2.4 x 10^43 erg/s, respectively, in agreement with the observed values of > 8.3 x 10^43 and 2.0 x 10^43 erg/s. We also find that the black hole heats the halo and renders it unable to produce stars as required to keep the halo metal free. These results demonstrate the viability of the BH hypothesis for CR7 in a cosmological context. Assu...

  19. 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.

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

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

  1. 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.

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

    Belousov, Roman; Prencipe, Mauro

    2014-01-01

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

  3. Resolving the HONO formation mechanism in the ionosphere via ab initio molecular dynamic simulations.

    He, Rongxing; Li, Lei; Zhong, Jie; Zhu, Chongqin; Francisco, Joseph S; Zeng, Xiao Cheng

    2016-04-26

    Solar emission produces copious nitrosonium ions (NO(+)) in the D layer of the ionosphere, 60 to 90 km above the Earth's surface. NO(+) is believed to transfer its charge to water clusters in that region, leading to the formation of gaseous nitrous acid (HONO) and protonated water cluster. The dynamics of this reaction at the ionospheric temperature (200-220 K) and the associated mechanistic details are largely unknown. Using ab initio molecular dynamics (AIMD) simulations and transition-state search, key structures of the water hydrates-tetrahydrate NO(+)(H2O)4 and pentahydrate NO(+)(H2O)5-are identified and shown to be responsible for HONO formation in the ionosphere. The critical tetrahydrate NO(+)(H2O)4 exhibits a chain-like structure through which all of the lowest-energy isomers must go. However, most lowest-energy isomers of pentahydrate NO(+)(H2O)5 can be converted to the HONO-containing product, encountering very low barriers, via a chain-like or a three-armed, star-like structure. Although these structures are not the global minima, at 220 K, most lowest-energy NO(+)(H2O)4 and NO(+)(H2O)5 isomers tend to channel through these highly populated isomers toward HONO formation. PMID:27071120

  4. Ab initio simulations of H2 in Li-doped carbon nanotube systems

    Because of their unique structure, it has been proposed that carbon nanotube ropes may well provide an ideal container for the storage of molecular hydrogen. Indeed, there has been some experimental evidence of enhanced hydrogen uptake in doped Li and other alkali metal systems (Chen et al 1999 Science 285 91). We have therefore addressed this issue of hydrogen storage in Li-doped graphite and carbon nanotube systems theoretically with ab initio simulations. Our results find no evidence for such enhanced storage, based on the induced structural changes. In addition, we have also investigated the diffusion barriers for hydrogen to enter into nanotube interiors, both in the presence and absence of topological defects. Even if nanotube interiors are made accessible, the hydrogen uptake remains modest, i.e., less than 3.5 wt%. Mechanically or chemically processing nanotubes is therefore not likely to lead to greatly increased hydrogen storage. Even with its limitation, because of the use of the LDA and GGA approaches, the current investigation must be regarded as a means in the search for proper media that can successfully enhance hydrogen storage

  5. 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.

  6. Axisymmetric Ab Initio Core-Collapse Supernova Simulations of 12-25 M_sol Stars

    Bruenn, Stephen W; Hix, W Raphael; Lentz, Eric J; Messer, O E Bronson; Lingerfelt, Eric J; Blondin, John M; Endeve, Eirik; Marronetti, Pedro; Yakunin, Konstantin N

    2012-01-01

    We present an overview of four ab initio axisymmetric core-collapse supernova simulations employing detailed spectral neutrino transport computed with our CHIMERA code and initiated from Woosley & Heger (2007) progenitors of mass 12, 15, 20, and 25 M_sol. All four models exhibit shock revival over \\sim 200 ms (leading to the possibility of explosion), driven by neutrino energy deposition. Hydrodynamic instabilities that impart substantial asymmetries to the shock aid these revivals, with convection appearing first in the 12 M_sol model and the standing accretion shock instability (SASI) appearing first in the 25 M_sol model. Three of the models have developed pronounced prolate morphologies (the 20 M_sol model has remained approximately spherical). By 500 ms after bounce the mean shock radii in all four models exceed 3,000 km and the diagnostic explosion energies are 0.33, 0.66, 0.65, and 0.70 Bethe (B = $10^{51}$ ergs) for the 12, 15, 20, and 25 M_sol models, respectively, and are increasing. The three l...

  7. Self-Healing of Stone—Wales Defects in Boron Nitride Monolayer by Irradiation: Ab Initio Molecular Dynamics Simulations

    We show an effective method of healing the Stone—Wales (SW) defects through low energy electron irradiation using ab initio molecular dynamics simulation. The SW defects can be healed by irradiation through bond rotation. Although the healing energy shows an anisotropic behavior, it is lower than the displacement threshold energy. The healing of the SW defect through electron irradiation can be effectively used in other sp2-bonded materials

  8. Benzene dimer: Dynamic structure and thermodynamics derived from on-the-fly ab initio DFT-D molecular dynamic simulations

    Řezáč, Jan; Hobza, Pavel

    2008-01-01

    Roč. 4, č. 11 (2008), s. 1835-1840. ISSN 1549-9618 R&D Projects: GA MŠk LC512; GA AV ČR IAA400550510 Institutional research plan: CEZ:AV0Z40550506 Keywords : benzene dimer * dynamic structure * on-the fly ab initio DFT-D molecular dynamic simulation Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.274, year: 2008

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

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

  10. Continuum-atomistic simulation of picosecond laser heating of copper with electron heat capacity from ab initio calculation

    Ji, Pengfei

    2016-01-01

    On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provide a general way that is accessible to other metals in laser heating.

  11. Diffusion within α-CuI studied using ab initio molecular dynamics simulations

    The structure and dynamics of superionic α-CuI are studied in detail by means of ab initio Born-Oppenheimer molecular dynamics simulations. The extreme cation disorder and a soft immobile face centred cubic sublattice are evident from the highly diffuse atomic density profiles. The Cu-Cu pair distribution function and distribution of Cu-I-Cu bond angles possess distinct peaks at 2.6 A and 60 deg. respectively, which are markedly lower than the values expected from the average cationic density, pointing to the presence of pronounced short-range copper-copper correlations. Comparison with lattice static calculations shows that these correlations and the marked shift in the cationic density profile in the (111) directions are associated with a locally distorted cation sublattice, and that the movements within the tetrahedral cavities involve rapid jumps into and out of shallow basins on the system potential energy surface. On average, the iodines are surrounded by three coppers within their first coordination shell, with the fourth copper being located in a transition zone between two neighbouring iodine cavities. However, time-resolved analysis reveals that the local structure actually involves a mixture of threefold-, fourfold- and fivefold-coordinated iodines. Examination of the ionic trajectories shows that the copper ions jump rapidly to nearest neighbouring tetrahedral cavities (aligned in the (100) directions) following a markedly curved trajectory and often involving short-lived (∼1 ps) interstitial positions. The nature of the correlated diffusion underlying the unusually high fraction of coppers with short residence time can be attributed to the presence of a large number of 'unsuccessful' jumps and the likelihood of cooperative motion of pairs of coppers. The calculated diffusion coefficient at 750 K, DCu = 2.8 x 10-5 cm2 s-1, is in excellent agreement with that found experimentally.

  12. Diffusion within α-CuI studied using ab initio molecular dynamics simulations

    Mohn, Chris E.; Stølen, Svein; Hull, Stephen

    2009-08-01

    The structure and dynamics of superionic α-CuI are studied in detail by means of ab initio Born-Oppenheimer molecular dynamics simulations. The extreme cation disorder and a soft immobile face centred cubic sublattice are evident from the highly diffuse atomic density profiles. The Cu-Cu pair distribution function and distribution of Cu-I-Cu bond angles possess distinct peaks at 2.6 Å and 60° respectively, which are markedly lower than the values expected from the average cationic density, pointing to the presence of pronounced short-range copper-copper correlations. Comparison with lattice static calculations shows that these correlations and the marked shift in the cationic density profile in the lang111rang directions are associated with a locally distorted cation sublattice, and that the movements within the tetrahedral cavities involve rapid jumps into and out of shallow basins on the system potential energy surface. On average, the iodines are surrounded by three coppers within their first coordination shell, with the fourth copper being located in a transition zone between two neighbouring iodine cavities. However, time-resolved analysis reveals that the local structure actually involves a mixture of threefold-, fourfold- and fivefold-coordinated iodines. Examination of the ionic trajectories shows that the copper ions jump rapidly to nearest neighbouring tetrahedral cavities (aligned in the lang100rang directions) following a markedly curved trajectory and often involving short-lived (~1 ps) interstitial positions. The nature of the correlated diffusion underlying the unusually high fraction of coppers with short residence time can be attributed to the presence of a large number of 'unsuccessful' jumps and the likelihood of cooperative motion of pairs of coppers. The calculated diffusion coefficient at 750 K, DCu = 2.8 × 10-5 cm2 s-1, is in excellent agreement with that found experimentally.

  13. Axisymmetric Ab Initio Core-Collapse Supernova Simulations of 12--25 Solar Mass Stars

    Bruenn, S. W. [Florida Atlantic University; Mezzacappa, Anthony [ORNL; Hix, William Raphael [ORNL; Lentz, E. J. [University of Tennessee, Knoxville (UTK) & Oak Ridge National Laboratory (ORNL); Messer, Bronson [ORNL; Lingerfelt, Eric J [ORNL; Blondin, J. M. [North Carolina State University; Endeve, Eirik [ORNL; Marronetti, Pedro [Florida Atlantic University; Yakunin, Konstantin [Florida Atlantic University

    2013-01-01

    We present an overview of four ab initio axisymmetric core-collapse supernova simulations employing detailed spectral neutrino transport computed with our CHIMERA code and initiated from Woosley & Heger (2007) progenitors of mass 12, 15, 20, and 25 M_sun. All four models exhibit shock revival over ~ 200 ms (leading to the possibility of explosion), driven by neutrino energy deposition. Hydrodynamic instabilities that impart substantial asymmetries to the shock aid these revivals, with convection appearing first in the 12 solar mass model and the standing accretion shock instability (SASI) appearing first in the 25 solar mass model. Three of the models have developed pronounced prolate morphologies (the 20 solar mass model has remained approximately spherical). By 500 ms after bounce the mean shock radii in all four models exceed 3,000 km and the diagnostic explosion energies are 0.33, 0.66, 0.65, and 0.70 Bethe (B=10^{51} ergs) for the 12, 15, 20, and 25 solar mass models, respectively, and are increasing. The three least massive of our models are already sufficiently energetic to completely unbind the envelopes of their progenitors (i.e., to explode), as evidenced by our best estimate of their explosion energies, which first become positive at 320, 380, and 440 ms after bounce. By 850 ms the 12 solar mass diagnostic explosion energy has saturated at 0.38 B, and our estimate for the final kinetic energy of the ejecta is ~ 0.3 B, which is comparable to observations for lower-mass progenitors.

  14. Ab initio quantum Monte Carlo simulations of the uniform electron gas without fixed nodes

    Groth, S.; Schoof, T.; Dornheim, T.; Bonitz, M.

    2016-02-01

    The uniform electron gas (UEG) at finite temperature is of key relevance for many applications in the warm dense matter regime, e.g., dense plasmas and laser excited solids. Also, the quality of density functional theory calculations crucially relies on the availability of accurate data for the exchange-correlation energy. Recently, results for N =33 spin-polarized electrons at high density, rs=r ¯/aB≲4 , and low temperature have been obtained with the configuration path integral Monte Carlo (CPIMC) method [T. Schoof et al., Phys. Rev. Lett. 115, 130402 (2015), 10.1103/PhysRevLett.115.130402]. To achieve these results, the original CPIMC algorithm [T. Schoof et al., Contrib. Plasma Phys. 51, 687 (2011), 10.1002/ctpp.201100012] had to be further optimized to cope with the fermion sign problem (FSP). It is the purpose of this paper to give detailed information on the manifestation of the FSP in CPIMC simulations of the UEG and to demonstrate how it can be turned into a controllable convergence problem. In addition, we present new thermodynamic results for higher temperatures. Finally, to overcome the limitations of CPIMC towards strong coupling, we invoke an independent method—the recently developed permutation blocking path integral Monte Carlo approach [T. Dornheim et al., J. Chem. Phys. 143, 204101 (2015), 10.1063/1.4936145]. The combination of both approaches is able to yield ab initio data for the UEG over the entire density range, above a temperature of about one half of the Fermi temperature. Comparison with restricted path integral Monte Carlo data [E. W. Brown et al., Phys. Rev. Lett. 110, 146405 (2013), 10.1103/PhysRevLett.110.146405] allows us to quantify the systematic error arising from the free particle nodes.

  15. Light Condensation and Localization in Disordered Photonic Media: Theory and Large Scale ab initio Simulations

    Toth, Laszlo Daniel

    2013-05-07

    Disordered photonics is the study of light in random media. In a disordered photonic medium, multiple scattering of light and coherence, together with the fundamental principle of reciprocity, produce a wide range of interesting phenomena, such as enhanced backscattering and Anderson localization of light. They are also responsible for the existence of modes in these random systems. It is known that analogous processes to Bose-Einstein condensation can occur in classical wave systems, too. Classical condensation has been studied in several contexts in photonics: pulse formation in lasers, mode-locking theory and coherent emission of disordered lasers. All these systems have the common theme of possessing a large ensemble of waves or modes, together with nonlinearity, dispersion or gain. In this work, we study light condensation and its connection with light localization in a disordered, passive dielectric medium. We develop a theory for the modes inside the disordered resonator, which combines the Feshbach projection technique with spin-glass theory and statistical physics. In particular, starting from the Maxwell’s equations, we map the system to a spherical p-spin model with p = 2. The spins are replaced by modes and the temperature is related to the fluctuations in the environment. We study the equilibrium thermodynamics of the system in a general framework and show that two distinct phases exist: a paramagnetic phase, where all the modes are randomly oscillating and a condensed phase, where the energy condensates on a single mode. The thermodynamic quantities can be explicitly interpreted and can also be computed from the disorder-averaged time domain correlation function. We launch an ab initio simulation campaign using our own code and the Shaheen supercomputer to test the theoretical predictions. We construct photonic samples of varying disorder and find computationally relevant ways to obtain the thermodynamic quantities. We observe the phase transition

  16. Structure and mechanical properties of cement and intermetallic compounds via ab-initio simulations

    Dharmawardhana, Chamila Chathuranga

    Calcium silicate hydrates comprise a class of minerals formed synthetically during Portland cement hydration or naturally through various geological processes. The importance of these minerals is immense since they are the primary binding phases for Portland cement derived construction materials. Efforts spanning centuries have been devoted to understand the structural aspects of cohesion in these minerals. In recent years, the focus has progressively turned to atomic level comprehension. Structurally these minerals can range from crystalline to highly disordered amorphous phases. This thesis focuses upon unraveling the nature of chemical bonding in a large subset of calcium silicate hydrate (CSH) crystals. Thus their electronic structure was calculated and bonding mechanisms were investigated quantitatively. Results highlight a wide range of contributions from each type of bonding (Si-O, Ca-O, O-H and hydrogen bond) with respect to silicate polymerization, crystal symmetry, water and OH content. Consequently, total bond order density (TBOD) was designated as the overall single criterion for characterizing crystal cohesion. The TBOD categorization indicates that a rarely known orthorhombic phase Suolunite is closest to the ideal composition and structure of cement. Present work finds the relationship of partial bond order density (PBOD) of each bond species, especially HBs to the mechanical properties of CSH crystals. This can be used as a basis to validate existing C-S-H models and to build improved ones. This work goes further and validates the recently proposed models (2014) for C-S-H (I) phase on the same basis of proposed electronic structure parameters. Then the respective Calcium aluminosilicate hydrates C-A-S-H (I) phase models are proposed. Finally, these results lead to improved interpretations and construction of realistic atomistic models of cement hydrates. Ab initio molecular dynamics (AIMD) could be vital to solve critical problems in complex

  17. A method for the extraction of the voltage-dependent quantum capacitance of carbon nanotubes using ab initio simulations

    In this paper, a method to obtain the quantum capacitance of carbon nanotubes (CNTs) using ab initio simulations is presented. As an example of the usage of the proposed method, the quantum capacitance of a metallic (6,6) CNT section is calculated. The quantum capacitance is extracted for various bias voltages applied to metallic CNT interconnects in the range 0-2.5 V, which is the operating voltage range of VLSI circuits. The obtained quantum capacitance values are found to be in good agreement with the experimental values. The average Fermi velocity of electrons dependent on the bias voltage is also obtained and plotted.

  18. Theoretical design of a novel copper doped gold cluster supported on graphene utilizing ab initio molecular dynamics simulations

    Ab initio molecular dynamics simulations have been used to inspect the adsorption of O2 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 O2 and consequently widens the reaction channel for the adsorption process. Conversely, a pure Au cluster on the same graphene support is inactive for the O2 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

  19. Orbital free ab initio molecular dynamics simulation study of some static and dynamic properties of liquid noble metals

    G.M. Bhuiyan

    2012-10-01

    Full Text Available Several static and dynamic properties of liquid Cu, Ag and Au at thermodynamic states near their respective melting points, have been evaluated by means of the orbital free ab-initio molecular dynamics simulation method. The calculated static structure shows good agreement with the available X-ray and neutron diffraction data. As for the dynamic properties, the calculated dynamic structure factors point to the existence of collective density excitations along with a positive dispersion for l-Cu and l-Ag. Several transport coefficients have been obtained which show a reasonable agreement with the available experimental data.

  20. Solvation structure of glucosamine in aqueous solution as studied by Monte Carlo simulation using ab initio fitted potential

    Siraleartmukul, Krisana; Siriwong, Khatcharin; Remsungnen, Tawun; Muangsin, Nongnuj; Udomkichdecha, Werasak; Hannongbua, Supot

    2004-09-01

    The solvation structure of glucosamine in aqueous solution was investigated using Monte Carlo simulation at 298 K. The MCY rigid water model and ab initio glucosamine-water fitted potential were applied. The first hydration shell appears at 4.6 Å from the center of glucosamine with a coordination number of seven water molecules where one water lies in the ligand's plane while two and four of them are about 2-4 Å above and below the plane, respectively. Furthermore, the mobility distribution and orientation of the water molecules around the ligand have been intensively investigated and reported.

  1. Hydrogen Recombination and Dimer Formation on Graphite from Ab Initio Molecular Dynamics Simulations.

    Casolo, S; Tantardini, G F; Martinazzo, R

    2016-07-14

    We studied Eley-Rideal molecular hydrogen formation on graphite using ab initio molecular dynamics, in the energy range relevant for the chemistry of the interstellar medium and for terrestrial experiments employing cold plasma (0.02-1 eV). We found substantial projectile steering effects that prevent dimer formation at low energies, thereby ruling out any catalytic synthetic pathways that form hydrogen molecules. Ortho and para dimers do form efficiently thanks to preferential sticking, but only at energies that are too high to be relevant for the chemistry of the interstellar medium. Computed reaction cross sections and ro-vibrational product populations are in good agreement with available experimental data and capable of generating adsorbate configurations similar to those observed with scanning tunneling microscopy techniques. PMID:26905385

  2. Impact of oxygen on the 300-K isotherm of Laser Megajoule ablator using ab initio simulation

    Colin-Lalu, P.; Recoules, V.; Salin, G.; Huser, G.

    2015-11-01

    The ablator material for inertial confinement fusion (ICF) capsules on the Laser Mégajoule is a glow-discharge polymer (GDP) plastic. Its equation of state (EOS) is of primary importance for the design of such capsules, since it has direct consequences on shock timing and is essential to mitigate hydrodynamic instabilities. Using ab initio molecular dynamics (AIMD), we have investigated the 300-K isotherm of amorphous CH1.37O0.08 plastic, whose structure is close to GDP plastic. The 300-K isotherm, which is often used as a cold curve within tabular EOS, is an important contribution of the EOS in the multimegabar pressure range. AIMD results are compared to analytic models within tabular EOS, pointing out large discrepancies. In addition, we show that the effect of oxygen decreases 300-K isotherm pressure by 10%-15%. The implication of these observations is the ability to improve ICF target performance, which is essential to achieve fusion ignition.

  3. Ab initio simulations of doped single-walled carbon nanotube sensors

    Graphical abstract: Ab initio calculations used to study O-doped and N-doped SWNT within the framework of the DFT. We introduced new type of gas sensor that can detect the presence of H2, Cl2, NO, and CO molecules. Band-gap narrowing occurs when the nanotube is doped with oxygen or nitrogen atoms. We proposed a new methodology of designing reliable, sensitive, and selective nanotube sensors. Highlights: ►Ab initio calculations used to study O-doped and N-doped SWNT within the framework of the DFT. ► We introduced new type of gas sensor that can detect the presence of H2, Cl2, NO, and CO molecules. ►Band-gap narrowing occurs when the nanotube is doped with oxygen or nitrogen atoms. ► We proposed a new methodology of designing reliable, sensitive, and selective nanotube sensors. - Abstract: The interactions between oxygen and nitrogen atoms with single-walled carbon nanotubes were investigated for nanotubes with two different geometrical configurations using first-principle calculations within the framework of the density functional theory. We introduced a new type of toxic gas sensor that can detect the presence of H2, Cl2, CO, and NO molecules. We also demonstrated that the sensitivity of this device can be controlled by the concentration of the dopants on the surface of the nanotube. In addition, the transport properties of the doped nanotube were studied for different concentrations of oxygen or nitrogen atoms that were randomly distributed on the surface of the single-walled carbon nanotube. We observed that small amounts of dopants can modify the electronic and transport properties of the nanotube and can lend metallic properties to the nanotube. Band-gap narrowing occurs when the nanotube is doped with either oxygen or nitrogen atoms.

  4. Ambient-Potential Composite Ewald Method for ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulation.

    Giese, Timothy J; York, Darrin M

    2016-06-14

    A new approach for performing Particle Mesh Ewald in ab initio quantum mechanical/molecular mechanical (QM/MM) simulations with extended atomic orbital basis sets is presented. The new approach, the Ambient-Potential Composite Ewald (CEw) method, does not perform the QM/MM interaction with Mulliken charges nor electrostatically fit charges. Instead the nuclei and electron density interact directly with the MM environment, but in a manner that avoids the use of dense Fourier transform grids. By performing the electrostatics with the underlying QM density, the CEw method avoids self-consistent field instabilities that have been encountered with simple charge mapping procedures. Potential of mean force (PMF) profiles of the p-nitrophenyl phosphate dissociation reaction in explicit solvent are computed from PBE0/6-31G* QM/MM molecular dynamics simulations with various electrostatic protocols. The CEw profiles are shown to be stable with respect to real-space Ewald cutoff, whereas the PMFs computed from truncated and switched electrostatics produce artifacts. PBE0/6-311G**, AM1/d-PhoT, and DFTB2 QM/MM simulations are performed to generate two-dimensional PMF profiles of the phosphoryl transesterification reactions with ethoxide and phenoxide leaving groups. The semiempirical models incorrectly produce a concerted ethoxide mechanism, whereas PBE0 correctly produces a stepwise mechanism. The ab initio reaction barriers agree more closely to experiment than the semiempirical models. The failure of Mulliken-charge QM/MM-Ewald is analyzed. PMID:27171914

  5. High adsorption capacity of heavy metals on two-dimensional MXenes: an ab initio study with molecular dynamics simulation.

    Guo, Xun; Zhang, Xitong; Zhao, Shijun; Huang, Qing; Xue, Jianming

    2016-01-01

    Density functional theory (DFT) calculation is employed to study the adsorption properties of Pb and Cu on recently synthesized two-dimensional materials MXenes, including Ti3C2, V2C1 and Ti2C1. The influence of surface decoration with functional groups such as H, OH and F have also been investigated. Most of these studied MXenes exhibit excellent capability to adsorb Pb and Cu, especially the adsorption capacity of Pb on Ti2C1 is as high as 2560 mg g(-1). Both the binding energies and the adsorption capacities are sensitive to the functional groups attached to the MXenes' surface. Ab initio molecular dynamics (ab-init MD) simulation confirms that Ti2C1 remains stable at room temperature after adsorbing Pb atoms. Our calculations imply that these newly emerging two-dimensional MXenes are promising candidates for wastewater treatment and ion separation. PMID:26602974

  6. Ab initio mass tensor molecular dynamics

    Tsuchida, Eiji

    2010-01-01

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

  7. Ab initio molecular dynamics simulations for the role of hydrogen in catalytic reactions of furfural on Pd(111)

    Xue, Wenhua; Dang, Hongli; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

    2014-03-01

    In the study of catalytic reactions of biomass, furfural conversion over metal catalysts with the presence of hydrogen has attracted wide attention. We report ab initio molecular dynamics simulations for furfural and hydrogen on the Pd(111) surface at finite temperatures. The simulations demonstrate that the presence of hydrogen is important in promoting furfural conversion. In particular, hydrogen molecules dissociate rapidly on the Pd(111) surface. As a result of such dissociation, atomic hydrogen participates in the reactions with furfural. The simulations also provide detailed information about the possible reactions of hydrogen with furfural. Supported by DOE (DE-SC0004600). This research used the supercomputer resources of the XSEDE, the NERSC Center, and the Tandy Supercomputing Center.

  8. Orbital free ab initio simulations of liquid alkaline earth metals: from pseudopotential construction to structural and dynamic properties.

    Rio, Beatriz G del; González, Luis E

    2014-11-19

    We have performed a comprehensive study of the properties of liquid Be, Ca and Ba, through the use of orbital free ab initio simulations. To this end we have developed a force-matching method to construct the necessary local pseudopotentials from standard ab initio calculations. The structural magnitudes are analyzed, including the average and local structures and the dynamic properties are studied. We find several common features, like an asymmetric second peak in the structure factor, a large amount of local structures with five-fold symmetry, a quasi-universal behaviour of the single-particle dynamic properties and a large degree of positive dispersion in the propagation of collective density fluctuations, whose damping is dictated by slow thermal relaxations and fast viscoelastic ones. Some peculiarities in the dynamic properties are however observed, like a very high sound velocity and a large violation of the Stokes-Einstein relation for Be, or an extremely high positive dispersion and a large slope in the dispersion relation of shear waves at the onset of the wavevector region where they are supported for Ba. PMID:25347355

  9. Insights into photodissociation dynamics of acetaldehyde from ab initio calculations and molecular dynamics simulations

    In the present paper we report a theoretical study on mechanistic photodissociation of acetaldehyde (CH3CHO). Stationary structures for H2 and CO eliminations in the ground state (S0) have been optimized with density functional theory method, which is followed by the intrinsic reaction coordinate and ab initio molecular dynamics calculations to confirm the elimination mechanism. Equilibrium geometries, transition states, and intersection structures for the C-C and C-H dissociations in excited states were determined by the complete-active-space self-consistent field (CASSCF) method. Based on the CASSCF optimized structures, the potential energy profiles for the dissociations were refined by performing the single-point calculations using the multireference configuration interaction method. Upon the low-energy irradiation of CH3CHO (265 nm1 C-C bond fission following intersystem crossing from the S1 state is the predominant channel and the minor channel, the ground-state elimination to CH4+CO after internal conversion (IC) from S1 to S0, could not be excluded. With the photon energy increasing, another pathway of IC, achieved via an S1/S0 intersection point resulting from the S1 C-C bond fission, becomes accessible and increases the yield of CH4+CO.

  10. Ab initio van der waals interactions in simulations of water alter structure from mainly tetrahedral to high-density-like

    Møgelhøj, Andreas; Kelkkanen, Kari André; Wikfeldt, K Thor;

    2011-01-01

    The structure of liquid water at ambient conditions is studied in ab initio molecular dynamics simulations in the NVE ensemble using van der Waals (vdW) density-functional theory, i.e., using the new exchange-correlation functionals optPBE-vdW and vdW-DF2, where the latter has softer nonlocal...... protocol could cause the deviation. An O-O PCF consisting of a linear combination of 70% from vdW-DF2 and 30% from low-density liquid water, as extrapolated from experiments, reproduces near-quantitatively the experimental O-O PCF for ambient water. This suggests the possibility that the new functionals...... shows some resemblance with experiment for high-density water ( Soper , A. K. and Ricci , M. A. Phys. Rev. Lett. 2000 , 84 , 2881 ), but not directly with experiment for ambient water. Considering the accuracy of the new functionals for interaction energies, we investigate whether the simulation...

  11. Communication: Ab initio simulations of hydrogen-bonded ferroelectrics: Collective tunneling and the origin of geometrical isotope effects

    Ab initio simulations that account for nuclear quantum effects have been used to examine the order-disorder transition in squaric acid, a prototypical H-bonded antiferroelectric crystal. Our simulations reproduce the >100 K difference in transition temperature observed upon deuteration as well as the strong geometrical isotope effect observed on intermolecular separations within the crystal. We find that collective transfer of protons along the H-bonding chains – facilitated by quantum mechanical tunneling – is critical to the order-disorder transition and the geometrical isotope effect. This sheds light on the origin of isotope effects and the importance of tunneling in squaric acid which likely extends to other H-bonded ferroelectrics

  12. Highly scalable Ab initio genomic motif identification

    Marchand, Benoît

    2011-01-01

    We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

  13. SPASER as a complex system: femtosecond dynamics traced by ab-initio simulations

    Totero Gongora, Juan Sebastian

    2016-03-14

    Integrating coherent light sources at the nanoscale with spasers is one of the most promising applications of plasmonics. A spaser is a nano-plasmonic counterpart of a laser, with photons replaced by surface plasmon polaritons and the resonant cavity replaced by a nanoparticle supporting localized plasmonic modes. Despite the large body of experimental and theoretical studies, the understanding of the fundamental properties of the spaser emission is still challenging. In this work, we investigated the ultrafast dynamics of the emission from a core-shell spaser by developing a rigorous first-principle numerical model. Our results show that the spaser is a highly nonlinear system with many interacting degrees of freedom, whose emission sustain a rich manifold of different spatial phases. In the regime of strong interaction we observed that the spaser emission manifests an irreversible ergodic evolution, where energy is equally shared among all the available degrees of freedom. Under this condition, the spaser generates ultrafast vortex lasing modes that are spinning on the femtosecond scale, acquiring the character of a nanoparticle with an effective spin. Interestingly, the spin orientation is defined by spontaneous symmetry breaking induced by quantum noise, which is a fundamental component of our ab-initio model. This opens up interesting possibilities of achieving unidirectional emission from a perfectly spherical nanoparticle, stimulating a broad range of applications for nano-plasmonic lasers as unidirectional couplers, random information sources and novel form of photonics neural-networks. © (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

  14. Theoretical design of a novel copper doped gold cluster supported on graphene utilizing ab initio molecular dynamics simulations

    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.

  15. {\\em Ab initio} Quantum Monte Carlo simulation of the warm dense electron gas in the thermodynamic limit

    Dornheim, Tobias; Sjostrom, Travis; Malone, Fionn D; Foulkes, W M C; Bonitz, Michael

    2016-01-01

    We perform \\emph{ab initio} quantum Monte Carlo (QMC) simulations of the warm dense uniform electron gas in the thermodynamic limit. By combining QMC data with linear response theory we are able to remove finite-size errors from the potential energy over the entire warm dense regime, overcoming the deficiencies of the existing finite-size corrections by Brown \\emph{et al.}~[PRL \\textbf{110}, 146405 (2013)]. Extensive new QMC results for up to $N=1000$ electrons enable us to compute the potential energy $V$ and the exchange-correlation free energy $F_{xc}$ of the macroscopic electron gas with an unprecedented accuracy of $|\\Delta V|/|V|, |\\Delta F_{xc}|/|F|_{xc} \\sim 10^{-3}$. A comparison of our new data to the recent parametrization of $F_{xc}$ by Karasiev {\\em et al.} [PRL {\\bf 112}, 076403 (2014)] reveals significant inaccuracies of the latter.

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

    Ibarra Hernández, Wilfredo

    2015-01-01

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

  17. Argon Interaction with Gold Surfaces: Ab Initio-Assisted Determination of Pair Ar-Au Potentials for Molecular Dynamics Simulations.

    Grenier, Romain; To, Quy-Dong; de Lara-Castells, María Pilar; Léonard, Céline

    2015-07-01

    Global potentials for the interaction between the Ar atom and gold surfaces are investigated and Ar-Au pair potentials suitable for molecular dynamics simulations are derived. Using a periodic plane-wave representation of the electronic wave function, the nonlocal van-der-Waals vdW-DF2 and vdW-OptB86 approaches have been proved to describe better the interaction. These global interaction potentials have been decomposed to produce pair potentials. Then, the pair potentials have been compared with those derived by combining the dispersionless density functional dlDF for the repulsive part with an effective pairwise dispersion interaction. These repulsive potentials have been obtained from the decomposition of the repulsive interaction between the Ar atom and the Au2 and Au4 clusters and the dispersion coefficients have been evaluated by means of ab initio calculations on the Ar+Au2 complex using symmetry adapted perturbation theory. The pair potentials agree very well with those evaluated through periodic vdW-DF2 calculations. For benchmarking purposes, CCSD(T) calculations have also been performed for the ArAu and Ar+Au2 systems using large basis sets and extrapolations to the complete basis set limit. This work highlights that ab initio calculations using very small surface clusters can be used either as an independent cross-check to compare the performance of state-of-the-art vdW-corrected periodic DFT approaches or, directly, to calculate the pair potentials necessary in further molecular dynamics calculations. PMID:26046588

  18. Ab Initio Molecular Dynamics: A Virtual Laboratory

    Hobbi Mobarhan, Milad

    2014-01-01

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

  19. Insights on the atomistic origin of X and W photoluminescence lines in c-Si from ab initio simulations

    We have used atomistic simulations to identify and characterize interstitial defect cluster configurations candidate for W and X photoluminescence centers in crystalline Si. The configurational landscape of small self-interstitial defect clusters has been explored through nanosecond annealing and implantation recoil simulations using classical molecular dynamics. Among the large collection of defect configurations obtained, we have selected those defects with the trigonal symmetry of the W center, and the tetrahedral and tetragonal symmetry of the X center. These defect configurations have been characterized using ab initio simulations in terms of their donor levels, their local vibrational modes, the defect induced modifications of the electronic band structure, and the transition amplitudes at band edges. We have found that the so-called I 3-V is the most likely candidate for the W PL center. It has a donor level and local vibrational modes in better agreement with experiments, a lower formation energy, and stronger transition amplitudes than the so-called I 3-I, which was previously proposed as the W center. With respect to defect candidates for the X PL center, our calculations have shown that none of the analyzed defect candidates match all of the experimental characteristics of the X center. Although the Arai tetra-interstitial configuration previously proposed as the X center cannot be excluded, the other defect candidates for the X center found, I 3-C and I 3-X, cannot be discarded either. (paper)

  20. Ab initio non-relativistic spin dynamics

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

    2014-12-07

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

  1. Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations

    Mal-Soon Lee; B. Peter McGrail; Roger Rousseau; Vassiliki-Alexandra Glezakou

    2015-01-01

    The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is ent...

  2. Ab initio molecular dynamics simulations of organic electrolytes, electrodes, and lithium ion transport for Li-ion batteries

    Kent, P. R. C.; Ganesh, P.; Jiang, De-En; Borodin, O.

    2012-02-01

    Optimizing the choice of electrolyte in lithium ion batteries and an understanding of the solid-electrolyte interphase (SEI) is required to optimize the balance between high-energy storage, high rate capability, and lifetime. We perform accurate ab initio molecular-dynamics simulations of common cyclic carbonates and LiPF6 to build solvation models which explain available Neutron and NMR spectroscopies. Our results corroborate why ethylene carbonate is a preferred choice for battery applications over propylene carbonate and how mixtures with dimethyl carbonate improve Li-ion diffusion. We study the role of functionalization of graphite-anode edges on the reducibility of the electrolyte and the ease of Li-ion intercalation at the initial stages of SEI formation. We find that oxygen terminated edges readily act as strong reductive sites, while hydrogen terminated edges are less reactive and allow faster Li diffusion. Orientational ordering of the solvent molecules precedes reduction at the interphase. Inorganic reductive components are seen to readily migrate to the anode edges, leading to increased surface passivation of the anode. We are currently quantifying Li-intercalation barriers across realistic SEI models, and progress along these lines will be presented.

  3. Novel structural features of CDK inhibition revealed by an ab initio computational method combined with dynamic simulations

    Heady, Lucy; Mancera, Ricardo L; Joyce, Sian; Venkitaraman, Ashok R; Artacho, Emilio; Skylaris, Chris-Kriton; Ciacchi, Lucio Colombi; Payne, Mike C

    2008-01-01

    The rational development of specific inhibitors for the ~500 protein kinases encoded in the human genome is impeded by a poor understanding of the structural basis for the activity and selectivity of small molecules that compete for ATP binding. Combining classical dynamic simulations with a novel ab initio computational approach linear-scalable to molecular interactions involving thousands of atoms, we have investigated the binding of five distinct inhibitors to the cyclin-dependent kinase CDK2. We report here that polarization and dynamic hydrogen bonding effects, so far undetected by crystallography, affect both their activity and selectivity. The effects arise from the specific solvation patterns of water molecules in the ATP binding pocket or the intermittent formation of hydrogen bonds during the dynamics of CDK/inhibitor interactions and explain the unexpectedly high potency of certain inhibitors such as 3-(3H-imidazol-4-ylmethylene)-5-methoxy-1,3-dihydro-indol-2-one (SU9516). The Lys89 residue in the ...

  4. Study on Exploration of Azeotropic Point of Pb-Sb Alloys by Vacuum Distillation and Ab Initio Molecular Dynamic Simulation

    Song, Bingyi; Jiang, Wenlong; Yang, Bin; Chen, Xiumin; Xu, Baoqiang; Kong, Lingxin; Liu, Dachun; Dai, Yongnian

    2016-07-01

    The possibility of the separation of Pb-Sb alloys by vacuum distillation was investigated theoretically. The results show that Pb and Sb can be separated by vacuum distillation. However, the experimental results show that vacuum distillation technique does not provide clear separation. According to the literature, Pb-Sb alloys belong to azeotropic compounds under some certain temperature; the experiment and computer simulation were carried out based on the exceptional condition so as to analyze the reason from the experiment and microstructure of Pb-Sb alloys perspective. The separation of Pb-Sb alloys by vacuum distillation was experimentally carried out to probe the azeotropic point. Also, the functions, such as partial radial distributions functions, the structure factor, mean square displacement, and the density of state, were calculated by ab-initio molecular dynamics for the representation of the structure and properties of Pb-Sb alloys with different composition of Sb. The experimental results indicate that there exists common volatilization for Pb-Sb alloys when Sb content is 16.5 wt pct. On the other hand, the calculation results show that there is an intense interaction between Pb and Sb when Sb content is 22 wt pct, which supports the experimental results although Sb content is slightly deviation.

  5. Ab initio molecular dynamics simulation of the atom packing and density of Al-Ni amorphous alloys

    2010-01-01

    Al-Ni alloys have better glass forming ability (GFA) than other Al-based alloys. However, the relationship among the atomic arrangement, glass transition, packing density and composition hasn’t been systematically studied. In this paper the ab initio molecular dynamics simulation (AIMD) was performed on the atom packing and density of AlxNi100-x (x=80, 83, 85, 86, 87 and 90) alloys. The pair correlation function and Voronoi tessellation indicated that there are obvious topological and chemical short-range orders in these alloys. The topological structure consists of Al-centered icosahedra like and Ni-centered tri-capped trigonal prism (TTP) like polyhedra. There is strong chemical short-range ordering between Al and Ni atoms indicated by the bond-length of Al-Ni pair shorter than the sum of the radii of Al and Ni atoms, which increases with the increasing of Ni content. It is shown that the densities of amorphous alloys don’t agree with the linear law with a peak at x=85. Based on the features of the structure and density, it is concluded that Al-Ni alloys at x=84–86 have high GFA, which can be extended to multi-component Al-based alloys.

  6. The Development of Explosions in Axisymmetric Ab Initio Core-collapse Supernova Simulations of 12-25 M Stars

    Bruenn, Stephen W.; Lentz, Eric J.; Hix, W. Raphael; Mezzacappa, Anthony; Harris, J. Austin; Messer, O. E. Bronson; Endeve, Eirik; Blondin, John M.; Chertkow, Merek Austin; Lingerfelt, Eric J.; Marronetti, Pedro; Yakunin, Konstantin N.

    2016-02-01

    We present four ab initio axisymmetric core-collapse supernova simulations initiated from 12, 15, 20, and 25 {M}⊙ zero-age main sequence progenitors. All of the simulations yield explosions and have been evolved for at least 1.2 s after core bounce and 1 s after material first becomes unbound. These simulations were computed with our Chimera code employing RbR spectral neutrino transport, special and general relativistic transport effects, and state-of-the-art neutrino interactions. Continuing the evolution beyond 1 s after core bounce allows the explosions to develop more fully and the processes involved in powering the explosions to become more clearly evident. We compute explosion energy estimates, including the negative gravitational binding energy of the stellar envelope outside the expanding shock, of 0.34, 0.88, 0.38, and 0.70 Bethe (B ≡ {10}51 erg) and increasing at 0.03, 0.15, 0.19, and 0.52 {\\text{B s}}-1, respectively, for the 12, 15, 20, and 25 {M}⊙ models at the endpoint of this report. We examine the growth of the explosion energy in our models through detailed analyses of the energy sources and flows. We discuss how the explosion energies may be subject to stochastic variations as exemplfied by the effect of the explosion geometry of the 20 {M}⊙ model in reducing its explosion energy. We compute the proto-neutron star masses and kick velocities. We compare our results for the explosion energies and ejected {}56{Ni} masses against some observational standards despite the large error bars in both models and observations.

  7. Ab initio implementation of quantum trajectory mean-field approach and dynamical simulation of the N{sub 2}CO photodissociation

    Xie, Binbin; Liu, Lihong; Cui, Ganglong; Fang, Wei-Hai, E-mail: fangwh@bnu.edu.cn [Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875 (China); Cao, Jun [Guizhou Provincial Key Laboratory of Computational Nano-material Science, Guizhou Normal College, Guiyang 550018 (China); Feng, Wei; Li, Xin-qi [Department of Physics, Beijing Normal University, Beijing 100875 (China)

    2015-11-21

    In this work, the recently introduced quantum trajectory mean-field (QTMF) approach is implemented and employed to explore photodissociation dynamics of diazirinone (N{sub 2}CO), which are based on the high-level ab initio calculation. For comparison, the photodissociation process has been simulated as well with the fewest-switches surface hopping (FSSH) and the ab initio multiple spawning (AIMS) methods. Overall, the dynamical behavior predicted by the three methods is consistent. The N{sub 2}CO photodissociation at λ > 335 nm is an ultrafast process and the two C—N bonds are broken in a stepwise way, giving birth to CO and N{sub 2} as the final products in the ground state. Meanwhile, some noticeable differences were found in the QTMF, FSSH, and AIMS simulated time constants for fission of the C—N bonds, excited-state lifetime, and nonadiabatic transition ratios in different intersection regions. These have been discussed in detail. The present study provides a clear evidence that direct ab initio QTMF approach is one of the reliable tools for simulating nonadiabatic dynamics processes.

  8. Core structure of screw dislocations in Fe from first-principles; Simulation ab initio des coeurs de dislocation vis dans le fer

    Ventelon, L

    2008-11-15

    The various methods appropriate for the simulation of dislocations within first-principles calculations have been set up, improved and compared between them. They have been applied to study screw dislocations in body-centered cubic iron using the SIESTA code. A non-degenerate core structure is obtained; its detailed analysis reveals a dilatation effect. Taking it into account in an anisotropic elasticity model, allows explaining the cell-size dependence of the energetics, obtained within the dipole approach. The Peierls potential obtained in ab initio suggests that the metastable core configuration at halfway position in the Peierls barrier, predicted by empirical potential, does not exist. We show how to construct tri-periodic cells optimized to study kinked dislocations. Using empirical potential, we demonstrate the feasibility of ab initio calculations of Peierls stress and kink formation. (author)

  9. Ab initio alpha-alpha scattering

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

    2015-12-01

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

  10. Ab initio alpha-alpha scattering.

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

    2015-12-01

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

  11. Ab initio valence calculations in chemistry

    Cook, D B

    1974-01-01

    Ab Initio Valence Calculations in Chemistry describes the theory and practice of ab initio valence calculations in chemistry and applies the ideas to a specific example, linear BeH2. Topics covered include the Schrödinger equation and the orbital approximation to atomic orbitals; molecular orbital and valence bond methods; practical molecular wave functions; and molecular integrals. Open shell systems, molecular symmetry, and localized descriptions of electronic structure are also discussed. This book is comprised of 13 chapters and begins by introducing the reader to the use of the Schrödinge

  12. AXISYMMETRIC AB INITIO CORE-COLLAPSE SUPERNOVA SIMULATIONS OF 12-25 M{sub Sun} STARS

    Bruenn, Stephen W.; Yakunin, Konstantin N. [Department of Physics, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991 (United States); Mezzacappa, Anthony; Hix, W. Raphael; Lingerfelt, Eric J. [Physics Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6354 (United States); Lentz, Eric J. [Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996-1200 (United States); Messer, O. E. Bronson [National Center for Computational Sciences, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6164 (United States); Blondin, John M. [Department of Physics, North Carolina State University, Raleigh, NC 27695-8202 (United States); Endeve, Eirik [Computer Science and Mathematics Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6164 (United States); Marronetti, Pedro, E-mail: bruenn@fau.edu [Physics Division, National Science Foundation, Arlington, VA 22207 (United States)

    2013-04-10

    We present an overview of four ab initio axisymmetric core-collapse supernova simulations employing detailed spectral neutrino transport computed with our CHIMERA code and initiated from Woosley and Heger progenitors of mass 12, 15, 20, and 25 M{sub Sun }. All four models exhibit shock revival over {approx}200 ms (leading to the possibility of explosion), driven by neutrino energy deposition. Hydrodynamic instabilities that impart substantial asymmetries to the shock aid these revivals, with convection appearing first in the 12 M{sub Sun} model and the standing accretion shock instability appearing first in the 25 M{sub Sun} model. Three of the models have developed pronounced prolate morphologies (the 20 M{sub Sun} model has remained approximately spherical). By 500 ms after bounce the mean shock radii in all four models exceed 3000 km and the diagnostic explosion energies are 0.33, 0.66, 0.65, and 0.70 Bethe (B = 10{sup 51} erg) for the 12, 15, 20, and 25 M{sub Sun} models, respectively, and are increasing. The three least massive of our models are already sufficiently energetic to completely unbind the envelopes of their progenitors (i.e., to explode), as evidenced by our best estimate of their explosion energies, which first become positive at 320, 380, and 440 ms after bounce. By 850 ms the 12 M{sub Sun} diagnostic explosion energy has saturated at 0.38 B, and our estimate for the final kinetic energy of the ejecta is {approx}0.3 B, which is comparable to observations for lower mass progenitors.

  13. Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations

    The dynamic properties of liquid B2O3 under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B2O3 shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8)

  14. Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations

    Ohmura, Satoshi; Nagaya, Kiyonobu; Yao, Makoto [Department of Physics, Kyoto University, Kyoto 606-8502 (Japan); Shimojo, Fuyuki [Department of Physics, Kumamoto University, Kumamoto 860-8555 (Japan)

    2015-08-17

    The dynamic properties of liquid B{sub 2}O{sub 3} under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B{sub 2}O{sub 3} shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8)

  15. Ab-initio Simulation Structure of the Compound La0.5Li0.5TiO3

    S.A. Kalkuta

    2012-12-01

    Full Text Available Crystal structure of the ion conductor La0.5Li0.5TiO3 with high-precision ab-initio method FLAPW was studied. Total energies of six model ordered structures of La0.5Li0.5TiO3 with different type of distribution of lanthanum and lithium atoms were calculated. Energetically favorable position of lithium ions was defined. Paths of motion of lithium ions in the lattice and energy barrier that lithium ions have to overcome with this motion were found.

  16. Ab-initio molecular dynamics simulation of hydrogen diffusion in $\\alpha$-iron

    Sanchez, J; Fullea García, José; Andrade Perdrix, Maria del Carmen; de Andres, P. L.

    2011-01-01

    First-principles atomistic molecular dynamics simulation in the micro-canonical and canonical ensembles has been used to study the diffusion of interstitial hydrogen in $\\alpha$-iron. Hydrogen to Iron ratios between $\\theta=1/16 and 1/2 have been considered by locating interstitial hydrogen atoms at random positions in a $2 \\times 2 \\times 2$ supercell. We find that the average optimum absorption site and the barrier for diffusion depend on the concentration of interestitials. Iron Debye temp...

  17. Ab Initio Simulations of Transition Metal Alloys: Towards the Multiscale Modeling

    Pourovskii, Leonid

    2003-01-01

    The present thesis concerns applications of first principles electronic structure calculations in conjunction with methods of statistical mechanics for simulations of transition metal alloys both in the bulk and at surfaces. A fully relativistic generalization of the exact muffin-tin orbitals (EMTO) method has been developed. The method accurately takes into account spin-orbit coupling and allows one to calculate orbital polarization and magneto-crystalline anisotropy in magnetic systems a...

  18. Ab initio simulation of the equation of state and kinetics of shocked water

    Goldman, Nir; Reed, Evan; Kuo, I-F W.; Fried, Larry; Mundy, Christopher J.; Curioni, Alessandro

    2009-03-28

    We report herein first principles simulations of water under shock loading of pressures from ca. 9 - 69 GPa. Accurate description of the chemical mechanism for the ionic conductivity at high pressures and temperatures is of particular importance to models of the planetary dynamo mechanism in Neptune and Uranus. Using a novel simulation technique for shock compression, we are able to make excellent comparison to the experimental results for the Hugoniot pressure, temperature and density final states. Our simulations resolve controversy regarding the molecular mechanism for electric conduction at high pressures along the shock Hugoniot. At the approximate intersection of the Hugoniot and Neptune isentrope we observe high concentrations of negatively charges species that contribute electronic states near the band gap. Our results provide a microscopic picture of the chemistry in planetary interiors, which could impact models of Neptune and Uranus. This work was supported by the US Department of Energy's Office of Basic Energy Sciences' Chemical Sciences program. Battelle operates Pacific Northwest National Laboratory for the US Department of Energy.

  19. 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.

  20. 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.

  1. Ab-initio simulation of the ionization and fragmentation of acetylene by strong femtosecond laser pulses

    The electron and nuclear dynamics of acetylene when interacting with strong short laser pulses has been simulated in the framework of real-space Time Dependent Density Functional Theory (TDDFT) and molecular dynamics. The stretching and dissociation of individual bonds are reported, and are shown to depend on the laser field intensity and orientation relative to the laser polarization. The ionization dynamics, including ionization from individual Kohn-Sham orbitals, is also reported. The orbital ionization dynamics are shown to vary with an increase in the intensity of the laser field

  2. Ab initio phenomenological simulation of the growth of large tumor cell populations

    Chignola, R; Milotti, E; Pellegrina, C D; Chignola, Roberto; Fabbro, Alessio Del; Milotti, Edoardo; Pellegrina, Chiara Dalla

    2007-01-01

    In a previous paper we have introduced a phenomenological model of cell metabolism and of the cell cycle to simulate the behavior of large tumor cell populations (Chignola R and Milotti E, Phys. Biol. 2 (2005) 8-22). Here we describe a refined and extended version of the model that includes some of the complex interactions between cells and their surrounding environment. The present version takes into consideration several additional energy-consuming biochemical pathways such as protein and DNA synthesis, the tuning of extracellular pH and of the cell membrane potential. The control of the cell cycle - that was previously modeled by means of ad hoc thresholds - has been directly addressed here by considering checkpoints from proteins that act as targets for phosphorylation on multiple sites. As simulated cells grow, they can now modify the chemical composition of the surrounding environment which in turn acts as a feedback mechanism to tune cell metabolism and hence cell proliferation: in this way we obtain g...

  3. Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations

    We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling’s iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step

  4. Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations

    Schiffmann, Florian; VandeVondele, Joost, E-mail: Joost.VandeVondele@mat.ethz.ch [Nanoscale Simulations, Department of Materials, ETH Zürich, Wolfgang-Pauli-Str. 27, CH-8093 Zürich (Switzerland)

    2015-06-28

    We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling’s iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.

  5. Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations.

    Schiffmann, Florian; VandeVondele, Joost

    2015-06-28

    We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling's iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step. PMID:26133420

  6. Ab initio simulations on migration paths of interstitial oxygen in corundum

    Zhukovskii, Yuri F.; Platonenko, Alexander; Piskunov, Sergei; Kotomin, Eugene A.

    2016-05-01

    Ionizing radiation produces in Al2O3 (corundum) crystals primary Frenkel pairs of complementary defects (in oxygen sublattice these are oxygen vacancies and interstitial oxygen ions, VO - Oi). The interstitial Oi atoms begin to migrate above certain temperature and create the dumbbell pairs with regular oxygen atoms (Oreg - Oi). We have calculated the optimal dumbbell configurations and optimized further migration paths (i.e., Oi interstitial can break the bond with one Oreg atom and moves towards another, one of four next-neighbor Oreg atoms). To simulate all possible Oi migration trajectories, we have performed large-scale hybrid DFT-LCAO PBE0 calculations on 2 × 2 × 1 supercells of defective α-Al2O3 crystals using CRYSTAL14 computer code. The limiting barrier height for oxygen interstitial 3D migration is estimated as 1.3 eV.

  7. Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations

    Schiffmann, Florian; VandeVondele, Joost

    2015-06-01

    We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling's iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.

  8. Ab initio simulations of subatomic resolution images in noncontact atomic force microscopy

    Kim, Minjung; Chelikowsky, James R.

    2015-03-01

    Direct imaging of polycyclic aromatic molecules with a subatomic resolution has recently been achieved with noncontact atomic force microscopy (nc-AFM). Specifically, nc-AFM employing a CO functionalized tip has provided details of the chemical bond in aromatic molecules, including the discrimination of bond order. However, the underlying physics of such high resolution imaging remains problematic. By employing new, efficient algorithms based on real space pseudopotentials, we calculate the forces between the nc-AFM tip and specimen. We simulate images of planar organic molecules with two different approaches: 1) with a chemically inert tip and 2) with a CO functionalized tip. We find dramatic differences in the resulting images, which are consistent with recent experimental work. Our work is supported by the DOE under DOE/DE-FG02-06ER46286 and by the Welch Foundation under Grant F-1837. Computational resources were provided by NERSC and XSEDE.

  9. Ab Initio Petaflop-scale Particle-in-Cell Simulation of Laser-Plasma Interaction

    Albright, Brian

    2008-11-01

    Large three-dimensional (3D) particle-in-cell (PIC) simulations have been performed using the VPIC code on some of the world's largest supercomputers, including the Roadrunner supercomputer, the first machine capable of a petaflop/s. These simulations have revealed the complex physical mechanisms underlying laser-plasma interactions and show an emerging universal picture of nonlinear saturation of LPI in the kinetic regime. Moreover, with the advent of peta-scale computing, we are entering an era of ``at-scale'' modeling necessary to understand the essential nonlinearity of LPI in solitary laser speckles, the building-blocks of multi-speckle beams. Under NIF-relevant conditions, stimulated Raman scattering (SRS) vs. speckle intensity shows a sharp onset at a threshold intensity (below linear estimates) and saturation at higher intensity, as validated in Trident experiments. Wavefront bowing of electron plasma waves (EPW) from trapped electron nonlinear frequency shift and amplitude-dependent damping is observed in 3D. This is followed by trapped particle modulational instability, which evolves nonlinearly into self-focusing, rapid transverse EPW phase variation, increased loss of trapped electrons, and EPW damping. In 3D, EPW turbulence may also exhibit loss of coherence through azimuthal filamentation. This reduction of source coherence for backscattered light and increased damping limit how much backscatter can obtain in a speckle. In addition, 3D modeling of novel ultraintense laser-ion acceleration mechanisms will be shown. Collaborators: L. Yin, K. J. Bowers, B. Bergen, D. S. Montgomery, J. L. Kline, H. A. Rose, B. M. Hegelich, K. A. Flippo, J. C. Fern'andez.

  10. Comprehensive ab initio simulations of turbulence in ITER-relevant fusion plasmas

    Jenko, Frank

    2014-07-01

    The astonishing improvements achieved in supercomputing capabilities over the past two decades have allowed groundbreaking new insights into the physics of plasma turbulence. Even though much has been learned already, fundamental challenges related to predicting the performance of future fusion reactors still remain. In particular, today's fusion experiments routinely achieve a transition to a high-confinement mode (H-mode) with a strong transport barrier at the plasma boundary. Understanding the formation conditions of this barrier and its characteristic size and height are crucial to predicting the efficiency of future fusion reactors, but a fully consistent numerical treatment has still been lacking up to now. A main challenge in the treatment of such barriers is their extreme profile variation, implying their susceptibility to finite-size effects. Global simulation capabilities such as demonstrated within the framework of the present project are thus essential in order to understand the dynamics of the edge transport barrier. Both present and future projects employing the GENE code will build on the experience established within this SuperMUC project and tackle this challenging issue. Another increasingly important field relates to turbulence studies in stellarators, which represent an alternative machine design for future fusion applications. With its newly developed capability of studying turbulence in stellarator geometry (i.e. retaining magnetic geometry variations within a magnetic surface), the GENE code is uniquely suited for this problem. With the new German stellarator experiment Wendelstein 7-X nearing completion, existing predictions already made with GENE for stellarator turbulence will be put to the test, and possibilities for validation will emerge. Due to the complex magnetic geometry, stellarator turbulence simulations have extreme computational requirements and will thus continue to challenge the available supercomputing capabilities also

  11. 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, ...

  12. Infrared Spectroscopy of N-Methylacetamide Revisited by ab Initio Molecular Dynamics Simulations.

    Gaigeot, M P; Vuilleumier, R; Sprik, M; Borgis, D

    2005-09-01

    The density functional theory based molecular dynamics simulation method ("Car-Parrinello") was applied in a numerical study of the electronic properties, hydrogen bonding, and infrared spectroscopy of the trans and cis isomer of N-methylacetamide in aqueous solution. A detailed analysis of the electronic structure of the solvated molecules, in terms of localized Wannier functions and Born atomic charges, is presented. Two schemes for the computation of the solute infrared absorption spectrum are investigated:  In the first method the spectrum is determined by Fourier transforming the time correlation function of the solute dipole as determined from the Wannier function analysis. The second method uses instead the molecular current-current correlation function computed from the Born charges and atomic velocities. The resulting spectral properties of trans- and cis-NMA are carefully compared to each other and to experimental results. We find that the two solvated isomers can be clearly distinguished by their infrared spectral profile in the 1000-2000 cm(-)(1) range. PMID:26641894

  13. Derivatization and diffusive motion of molecular fullerenes: Ab initio and atomistic simulations

    Berdiyorov, G., E-mail: gberdiyorov@qf.org.qa; Tabet, N. [Qatar Environment and Energy Research Institute (QEERI), Hamad Ben Khalifa University (HBKU), Qatar Foundation, P.O. Box 5825, Doha (Qatar); Harrabi, K. [Department of Physics, King Fahd University of Petroleum and Minerals, 31261 Dhahran (Saudi Arabia); Mehmood, U.; Hussein, I. A. [Department of Chemical Engineering, King Fahd University of Petroleum and Minerals, 31261 Dharan (Saudi Arabia); Peeters, F. M. [Departement Fysica, Universiteit Antwerpen, Groenenborgerlaan 171, B-2020 Antwerpen (Belgium); Zhang, J. [Department of Materials and London Centre for Nanotechnology, Imperial College London, SW7 2AZ London (United Kingdom); McLachlan, M. A. [Department of Materials and Centre for Plastic Electronics, Imperial College London, SW7 2AZ London (United Kingdom)

    2015-07-14

    Using first principles density functional theory in combination with the nonequilibrium Green's function formalism, we study the effect of derivatization on the electronic and transport properties of C{sub 60} fullerene. As a typical example, we consider [6,6]-phenyl-C{sub 61}-butyric acid methyl ester (PCBM), which forms one of the most efficient organic photovoltaic materials in combination with electron donating polymers. Extra peaks are observed in the density of states (DOS) due to the formation of new electronic states localized at/near the attached molecule. Despite such peculiar behavior in the DOS of an isolated molecule, derivatization does not have a pronounced effect on the electronic transport properties of the fullerene molecular junctions. Both C{sub 60} and PCBM show the same response to finite voltage biasing with new features in the transmission spectrum due to voltage induced delocalization of some electronic states. We also study the diffusive motion of molecular fullerenes in ethanol solvent and inside poly(3-hexylthiophene) lamella using reactive molecular dynamics simulations. We found that the mobility of the fullerene reduces considerably due to derivatization; the diffusion coefficient of C{sub 60} is an order of magnitude larger than the one for PCBM.

  14. Derivatization and diffusive motion of molecular fullerenes: Ab initio and atomistic simulations

    Using first principles density functional theory in combination with the nonequilibrium Green's function formalism, we study the effect of derivatization on the electronic and transport properties of C60 fullerene. As a typical example, we consider [6,6]-phenyl-C61-butyric acid methyl ester (PCBM), which forms one of the most efficient organic photovoltaic materials in combination with electron donating polymers. Extra peaks are observed in the density of states (DOS) due to the formation of new electronic states localized at/near the attached molecule. Despite such peculiar behavior in the DOS of an isolated molecule, derivatization does not have a pronounced effect on the electronic transport properties of the fullerene molecular junctions. Both C60 and PCBM show the same response to finite voltage biasing with new features in the transmission spectrum due to voltage induced delocalization of some electronic states. We also study the diffusive motion of molecular fullerenes in ethanol solvent and inside poly(3-hexylthiophene) lamella using reactive molecular dynamics simulations. We found that the mobility of the fullerene reduces considerably due to derivatization; the diffusion coefficient of C60 is an order of magnitude larger than the one for PCBM

  15. Hydroxyl-functionalized 1-(2-hydroxyethyl)-3-methyl imidazolium ionic liquids: thermodynamic and structural properties using molecular dynamics simulations and ab initio calculations.

    Fakhraee, Mostafa; Zandkarimi, Borna; Salari, Hadi; Gholami, Mohammad Reza

    2014-12-11

    The influences of hydroxyl functional group (-OH) on the thermodynamic and structural properties of ionic liquids (ILs) composed of 1-(2-Hydroxyethyl)-3-methyl imidazolium ([C2OHmim](+)) cation and the six different conventional anions, including [Cl](-), [NO3](-), [BF4](-), [PF6](-), [TfO](-), and [Tf2N](-) have been extensively investigated using classical molecular dynamics (MD) simulations combined with ab initio calculations over a wide range of temperature (298-550 K). The volumetric thermodynamic properties, enthalpy of vaporization, cohesive energy density, Hildebrand solubility parameter, and heat capacity at constant pressure were estimated at desired temperature. The simulated densities were in good agreement with the experimental data with a slight overestimation. The interionic interaction of selected ILs was also computed using both the MD simulations and ab initio calculations. It was found that the highest association of cation and anion is attributed to [C2OHmim][Cl] followed by [C2OHmim][NO3], and [C2OHmim][Tf2N] with the bulkiest anion has the weakest interionic interaction among chosen ILs. The similar trend of interactions energies was nearly observed from cohesive energy density results. Additional structural details were comprehensively yielded by calculating radial distribution functions (RDFs) and spatial distribution function (SDFs) at 358 K. The most stable configurations of isolated and dimer ion pairs of these ILs were in excellent consistency with RDFs and SDFs results. Significant changes in arrangement of anions around the [C2OHmim](+) cation in comparison with conventional imidazolium-based ILs can be inferred from the MD simulations and ab initio results. Also, microscopic structural properties disclosed that the most strong cation-cation interaction is ascribed to the hydroxyl-functionalized ILs composed of bulkier anions, whereas ILs incorporating [Cl](-) and [NO3](-) anions are mainly involved in cation-anion interactions. The

  16. Structure and Dynamics of the Instantaneous Water/Vapor Interface Revisited by Path-Integral and Ab-Initio Molecular Dynamics Simulations

    Kessler, Jan; Spura, Thomas; Karhan, Kristof; Partovi-Azar, Pouya; Hassanali, Ali A; Kühne, Thomas D

    2015-01-01

    The structure and dynamics of the water/vapor interface is revisited by means of path-integral and second-generation Car-Parrinello ab-initio molecular dynamics simulations in conjunction with an instantaneous surface definition [A. P. Willard and D. Chandler, J. Phys. Chem. B 114, 1954 (2010)]. In agreement with previous studies, we find that one of the OH bonds of the water molecules in the topmost layer is pointing out of the water into the vapor phase, while the orientation of the underlying layer is reversed. Therebetween, an additional water layer is detected, where the molecules are aligned parallel to the instantaneous water surface.

  17. Speciation and thermodynamic properties of zinc in sulfur-rich hydrothermal fluids: Insights from ab initio molecular dynamics simulations and X-ray absorption spectroscopy

    Mei, Yuan; Etschmann, Barbara; Liu, Weihua; Sherman, David M.; Testemale, Denis; Brugger, Joël

    2016-04-01

    Chlorine and sulfur are the main elements involved in the complexing of metals in ore-forming fluids. The nature and thermodynamic properties of the Zn(II)-Cl complexes have been investigated by previous experimental and theoretical studies and are now well established up to high temperatures (600 °C). In contrast, the role of bisulfide complexes for zinc speciation in sulfur-bearing fluids remains poorly known, and a better understanding of Zn(II)-HS complexation is required for modeling zinc transport in magmatic and metamorphic fluids and for optimizing the hydrometallurgical processing of sulfide ores. We have conducted ab initio molecular dynamics (MD) simulations to calculate the speciation of Zn(II)-HS complexes from ambient to hydrothermal-magmatic conditions (25-600 °C, up to 2000 bar). These theoretical calculations were complemented by X-ray absorption spectroscopy (XAS) measurements of Zn(II) in HS--rich solutions at 200-500 °C and 600-1000 bar. The speciation and geometrical properties predicted by the ab initio MD simulations and the in situ XAS data are in excellent agreement. Upon heating from room temperature to 250 °C, Zn(II) speciation in HS--rich solutions shows a transition from the sixfold octahedral hexaaquo complex [Zn(H2O)6]2+ to fourfold tetrahedral [Zn(HS)n(H2O)4-n]2-n complexes (n = 1-4). Ab initio MD simulations also show that at temperatures > 250 °C, the threefold trigonal-planar [Zn(HS)3]- complex becomes increasingly stable, and predominates in S-rich solutions; in contrast, chloro-complexes display a tetrahedral geometry at 25-500 °C, while trigonal planar ZnCl3- predominates at temperatures > 500 °C. The stability constants of Zn(II)-HS complexes were calculated by thermodynamic integration of constrained ab initio MD simulations at 200, 350 and 600 °C. The stability constants generated from this study predict that zinc can be transported by HS- at high temperature in reduced, neutral to alkaline solutions, while Zn

  18. Proposal for an inhibitor of Alzheimer's disease blocking aggregation of amyloid-β peptides: ab initio molecular simulations

    Aggregation of amyloid-β (Aβ) peptides is believed to play a key role in the mechanism of molecular pathogenesis of Alzheimer's disease (AD). To inhibit the aggregation and prevent AD, numerous compounds have been synthesized. A previous experimental study elucidated that a triazine derivative AA3E2 has anti-amyloidogenic ability, while a triazine derivative AA3D2 having a different substituent has no inhibitory effect. However, the reason for this remarkable difference in the ability cannot be explained by the chemical structures of these derivatives. In the present study, we present stable structures of the solvated complexes with Aβ and AA3E2/AA3D2 obtained by classical molecular mechanics method. The specific interactions between Aβ and AA3E2/AA3D2 in the complexes are investigated by ab initio fragment molecular orbital calculations. Based on the results obtained, we attempt to propose new potent inhibitors for the Aβ aggregation.

  19. Ab initio simulation of copper dopants and vacancies in the lead-free ferroelectric potassium sodium niobate

    Lead-free ferroelectric ceramics, for instance the perovskite potassium sodium niobate (KNN), are regarded as potential future alternatives to the widely used lead zirconate titanate (PZT) for piezoelectric applications. These materials can be doped with various elements in order to optimize their ferroelectric properties for the respective application. In the case of KNN, copper oxide can be added during processing as a sintering aid. In this work, the influence of metal impurities on the ferroelectric properties of KNN is investigated for the example of Cu. By means of ab initio density functional theory, we determined the prevailing point defect types and the preferred lattice sites of Cu dopants for different processing conditions, and the stability of dopant-vacancy complexes. In order to study the influence of point defects on switching the ferroelectric polarization of KNN, we investigated the effect of Cu on the energy needed for switching between different polarization directions.

  20. 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...

  1. Ab initio vel ex eventu. II

    Thiessen, P. A.; Treder, H.-J.

    Jedes initium wird durch experimenta crucis zum eventus. Jedes theoretisch interpretierbare ex-eventu-Resultat führt auf ein neues Initium. Gerade dies ist die gemeinsame Aussage von Atomistik, Quantenmechanik und Relativitätstheorie.Translated AbstractAb initio vel ex eventu. IIEvery initium becomes an eventus by experimenta crucis. Every theoretically interpretable ex-eventu result leads to a new initium. Right this is the joint assertion of atomism, quantum mechanics, and relativity.

  2. Simulation of NEXAFS spectra of a photo-reactive copolymer with considerably large monomer units: An ab initio molecular orbital study

    We performed the simulation of near edge X-ray absorption fine structure (NEXAFS) spectra of a photo-reactive copolymer with considerably large monomer units by ab initio molecular orbital calculation, in order to explain the spectral change induced by irradiation of the linearly polarized near ultra-violet (LPNUV) light. The 'building block approach' is applied for the theoretical calculation to calculate the core-excited states of the polymer with such large monomer units; the monomer unit is divided into subunits, whose core-excited states are calculated individually, and the results are summed up to simulate the spectra of the polymer. With the result of the simulation, the peaks in the observed spectra were assigned. The spectral change after the LPNUV-irradiation is attributed to the change in the electronic structure caused by the breakdown of the π-conjugation system of chalconyl group after photo-dimerization

  3. 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.

  4. A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation.

    Okamoto, Takuya; Yamada, Kenta; Koyano, Yoshiyuki; Asada, Toshio; Koga, Nobuaki; Nagaoka, Masataka

    2011-04-15

    For applying to a number of theoretical methodologies based on an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics method connecting AMBER9 with GAUSSIAN03, we have developed an AMBER-GAUSSIAN interface (AG-IF), which can be one of the simplest architectures. In the AG-IF, only a few subroutines addition is necessary to retrieve the QM/MM energy and forces, obtained by GAUSSIAN, for solving a set of Newtonian equations of motion in AMBER. It is, therefore, easy to be modified for individual applications since AG-IF utilizes most of those functions originally equipped not only in AMBER but also in GAUSSIAN. In the present minimal implementation, only AMBER is modified, whereas GAUSSIAN is left unchanged. Moreover, a different method of calculating electrostatic forces of MM atoms interacting with QM region is proposed. Using the AG-IF, we also demonstrate three examples of application: (i) the QM versus MM comparison in the radial distribution function, (ii) the free energy gradient method, and (iii) the charge from interaction energy and forces. PMID:20949515

  5. Nonlinear elastic effects in phase field crystal and amplitude equations: Comparison to ab initio simulations of bcc metals and graphene

    Hüter, Claas; Friák, Martin; Weikamp, Marc; Neugebauer, Jörg; Goldenfeld, Nigel; Svendsen, Bob; Spatschek, Robert

    2016-06-01

    We investigate nonlinear elastic deformations in the phase field crystal model and derived amplitude equation formulations. Two sources of nonlinearity are found, one of them is based on geometric nonlinearity expressed through a finite strain tensor. This strain tensor is based on the inverse right Cauchy-Green deformation tensor and correctly describes the strain dependence of the stiffness for anisotropic and isotropic behavior. In isotropic one- and two-dimensional situations, the elastic energy can be expressed equivalently through the left deformation tensor. The predicted isotropic low-temperature nonlinear elastic effects are directly related to the Birch-Murnaghan equation of state with bulk modulus derivative K'=4 for bcc. A two-dimensional generalization suggests K2D '=5 . These predictions are in agreement with ab initio results for large strain bulk deformations of various bcc elements and graphene. Physical nonlinearity arises if the strain dependence of the density wave amplitudes is taken into account and leads to elastic weakening. For anisotropic deformation, the magnitudes of the amplitudes depend on their relative orientation to the applied strain.

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

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

    2011-01-01

    Mercuric Calcogenides found many applications in electronic and optical devices as semiconducting materials. An equation of state provides useful information about the relationship between pressure (P), volume (V) and temperature (T) that helps to understand the behaviour of materials under the effect of high pressure and high temperature. The present paper sheds light on the electronic structure of Mercuric Calcogenides by simulating its electronic properties through ab initio method. This a...

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

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

    2015-01-01

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

  8. Diffusion of point defects, nucleation of dislocation loops, and effect of hydrogen in hcp-Zr: Ab initio and classical simulations

    Highlights: • Simulations of point defects in alpha-Zr using ab initio and forcefield methods. • Anisotropic strain dependent diffusion for interstitials and vacancies. • Explanation of pre-breakaway irradiation growth. • Interstitial nanoclusters cause expansion in 〈a〉, vacancy clusters contract 〈c〉. • H atoms diffuse isotropically, attracted to vacancy defects. - Abstract: Diffusion of point defects, nucleation of dislocation loops, and the associated dimensional changes of pure and H-loaded hcp-Zr have been investigated by a combination of ab initio calculations and classical simulations. Vacancy diffusion is computed to be anisotropic with Dvac,basal = 8.6 × 10−6 e−Q/(RT) (m2/s) and Dvac,axial = 9.9 × 10−6 e−Q/(RT) (m2/s), Q = 69 and 72 kJ/mol for basal and axial diffusion, respectively. At 550 K vacancy diffusion is about twice as fast in the basal plane as in a direction parallel to the c-axis. Diffusion of self-interstitials is found to be considerably faster and anisotropic involving collective atomic motions. At 550 K diffusion occurs predominantly in the a-directions, but this anisotropy diminishes with increasing temperature. Furthermore, the diffusion anisotropy is very dependent on the local strain (c/a ratio). Interstitial H atoms are found to diffuse isotropically with DH = 1.1 × 10−7 e−42/(RT) (m2/s). These results are consistent with experimental data and other theoretical studies. Molecular dynamics simulations at 550 K with periodic injection of vacancies and self-interstitial atoms reveal the formation of small nanoclusters, which are sufficient to cause a net expansion of the lattice in the a-directions driven by clusters of self-interstitials and a smaller contraction in the c-direction involving nanoclusters of vacancies. This is consistent with and can explain experimental data of irradiation growth. Energy minimizations show that vacancy c-loops can collapse into stacking-fault pyramids and, somewhat

  9. Diffusion of point defects, nucleation of dislocation loops, and effect of hydrogen in hcp-Zr: Ab initio and classical simulations

    Christensen, M., E-mail: mchristensen@materialsdesign.com [Materials Design, Inc., 6 First National Place, Angel Fire, NM 87710 (United States); Wolf, W.; Freeman, C.; Wimmer, E. [Materials Design, Inc., 6 First National Place, Angel Fire, NM 87710 (United States); Adamson, R.B. [Zircology Plus, 36848 Montecito Dr, Fremont, CA 94536 (United States); Hallstadius, L. [Westinghouse Electric Sweden AB, SE-721 63 Västerås (Sweden); Cantonwine, P.E. [Global Nuclear Fuel – Americas, P.O. Box 780, M/C F12, Wilmington, NC 28402 (United States); Mader, E.V. [Electric Power Research Institute (EPRI), 3420 Hillview Ave, Palo Alto, CA 94303 (United States)

    2015-05-15

    Highlights: • Simulations of point defects in alpha-Zr using ab initio and forcefield methods. • Anisotropic strain dependent diffusion for interstitials and vacancies. • Explanation of pre-breakaway irradiation growth. • Interstitial nanoclusters cause expansion in 〈a〉, vacancy clusters contract 〈c〉. • H atoms diffuse isotropically, attracted to vacancy defects. - Abstract: Diffusion of point defects, nucleation of dislocation loops, and the associated dimensional changes of pure and H-loaded hcp-Zr have been investigated by a combination of ab initio calculations and classical simulations. Vacancy diffusion is computed to be anisotropic with D{sub vac,basal} = 8.6 × 10{sup −6} e{sup −Q/(RT)} (m{sup 2}/s) and D{sub vac,axial} = 9.9 × 10{sup −6} e{sup −Q/(RT)} (m{sup 2}/s), Q = 69 and 72 kJ/mol for basal and axial diffusion, respectively. At 550 K vacancy diffusion is about twice as fast in the basal plane as in a direction parallel to the c-axis. Diffusion of self-interstitials is found to be considerably faster and anisotropic involving collective atomic motions. At 550 K diffusion occurs predominantly in the a-directions, but this anisotropy diminishes with increasing temperature. Furthermore, the diffusion anisotropy is very dependent on the local strain (c/a ratio). Interstitial H atoms are found to diffuse isotropically with D{sub H} = 1.1 × 10{sup −7} e{sup −42/(RT)} (m{sup 2}/s). These results are consistent with experimental data and other theoretical studies. Molecular dynamics simulations at 550 K with periodic injection of vacancies and self-interstitial atoms reveal the formation of small nanoclusters, which are sufficient to cause a net expansion of the lattice in the a-directions driven by clusters of self-interstitials and a smaller contraction in the c-direction involving nanoclusters of vacancies. This is consistent with and can explain experimental data of irradiation growth. Energy minimizations show that vacancy

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

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

    2015-10-01

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

  11. Atomic packing and diffusion in Fe85Si2B9P4 amorphous alloy analyzed by ab initio molecular dynamics simulation

    In the work reported in this paper, ab initio molecular dynamics simulation was performed on Fe85Si2B9P4 amorphous alloy. Preferred atomic environment of the elements was analyzed with Voronoi polyhedrons. It showed that B and P atoms prefer less neighbors compared with Fe and Si, making them structurally incompatible with Fe rich structure and repulsive to the formation of α-Fe. However, due to the low bonding energy of B and P caused by low coordination number, the diffusion rates of them were considerably large, resulting in the requirement of fast annealing for achieving optimum nano-crystallization for its soft magnetic property. The simulation work also indicates that diffusion rate in amorphous alloy is largely determined by bonding energy rather than atomic size

  12. Ab initio calculations of material strength

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

    Tokyo : The Japan Society of Mechanical Engineers, 2003, s. 467-475. [International Symposium on Micro-Mechanical Engineering - Heat Transfer, Fluid Dynamics, Reliability and Mechanotronics.. Tsuchiura and Tsukuba (JP), 01.12.2003-03.12.2003] R&D Projects: GA AV ČR IAA1041302; GA ČR GA202/03/1351; GA MŠk OC 523.90 Institutional research plan: CEZ:AV0Z2041904 Keywords : ab initio calculations * electronic structure * theoretical tensile strength Subject RIV: BM - Solid Matter Physics ; Magnetism

  13. Germacrene D Cyclization: An Ab Initio Investigation

    William N. Setzer

    2008-01-01

    Full Text Available Essential oils that contain large concentrations of germacrene D are typically accompanied by cadinane sesquiterpenoids. The acid-catalyzed cyclization of germacrene D to give cadinane and selinane sesquiterpenes has been computationally investigated using both density functional (B3LYP/6-31G* and post Hartree-Fock (MP2/6-31G** ab initio methods. The calculated energies are in general agreement with experimentally observed product distributions, both from acid-catalyzed cyclizations as well as distribution of the compounds in essential oils.

  14. Strong Influence of Coadsorbate Interaction on CO Desorption Dynamics on Ru(0001) Probed by Ultrafast X-Ray Spectroscopy and Ab Initio Simulations

    Xin, H; LaRue, J.; Mercurio, G; Hieke, F.; Nordlund, D.; Schlotter, W. F.; Dakovski, G. L.; Minitti, M. P.; Föhlisch, A.; Wolf, M.(University of Notre Dame, Notre Dame, USA); Wurth, W.; H. Ogasawara; Öberg, H.; Nørskov, J. K.; Öström, H.

    2015-01-01

    Strong Influence of Coadsorbate Interaction on CO Desorption Dynamics on Ru(0001) Probed by Ultrafast X-Ray Spectroscopy and Ab Initio Simulations H. Xin,1,2 J. LaRue,1 H. Öberg,3 M. Beye,1,4 M. Dell’Angela,5 J. J. Turner,6 J. Gladh,3 M. L. Ng,1 J. A. Sellberg,1,3 S. Kaya,1 G. Mercurio,5 F. Hieke,5 D. Nordlund,7 W. F. Schlotter,6 G. L. Dakovski,6 M. P. Minitti,6 A. Föhlisch,4,8 M. Wolf,9 W. Wurth,5,10 H. Ogasawara,7 J. K. Nørskov,1,2 H. Öström,3 L. G. M. Pettersson,3 A. Nilsson,1,...

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

    Goll, Erich

    2008-01-01

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

  16. Mechanistic Insights into Radical-Mediated Oxidation of Tryptophan from ab Initio Quantum Chemistry Calculations and QM/MM Molecular Dynamics Simulations.

    Wood, Geoffrey P F; Sreedhara, Alavattam; Moore, Jamie M; Wang, John; Trout, Bernhardt L

    2016-05-12

    An assessment of the mechanisms of (•)OH and (•)OOH radical-mediated oxidation of tryptophan was performed using density functional theory calculations and ab initio plane-wave Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics simulations. For the (•)OH reactions, addition to the pyrrole ring at position 2 is the most favored site with a barrierless reaction in the gas phase. The subsequent degradation of this adduct through a H atom transfer to water was intermittently observed in aqueous-phase molecular dynamics simulations. For the (•)OOH reactions, addition to the pyrrole ring at position 2 is the most favored pathway, in contrast to the situation in the model system ethylene, where concerted addition to the double bond is preferred. From the (•)OOH position 2 adduct QM/MM simulations show that formation of oxy-3-indolanaline occurs readily in an aqueous environment. The observed transformation starts from an initial rupture of the O-O bond followed by a H atom transfer with the accompanying loss of an (•)OH radical to solution. Finally, classical molecular dynamics simulations were performed to equate observed differential oxidation rates of various tryptophan residues in monoclonal antibody fragments. It was found that simple parameters derived from simulation correlate well with the experimental data. PMID:27082439

  17. Ab Initio Path to Heavy Nuclei

    Binder, Sven; Calci, Angelo; Roth, Robert

    2014-01-01

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

  18. Guiding ab initio calculations by alchemical derivatives

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

    2016-03-01

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

  19. Ab initio molar volumes and Gaussian radii.

    Parsons, Drew F; Ninham, Barry W

    2009-02-12

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

  20. 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.

  1. 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...

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

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

    2009-01-01

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

  3. Efficient solution of Poisson's equation using discrete variable representation basis sets for Car-Parrinello ab initio molecular dynamics simulations with cluster boundary conditions.

    Lee, Hee-Seung; Tuckerman, Mark E

    2008-12-14

    An efficient computational approach to perform Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations under cluster (free) boundary conditions is presented. The general approach builds upon a recent real-space CPAIMD formalism using discrete variable representation (DVR) basis sets [Y. Liu et al., Phys. Rev. B 12, 125110 (2003); H.-S. Lee and M. E. Tuckerman, J. Phys. Chem. A 110, 5549 (2006)]. In order to satisfy cluster boundary conditions, a DVR based on sinc functions is utilized to expand the Kohn-Sham orbitals and electron density. Poisson's equation is solved in order to calculate the Hartree potential via an integral representation of the 1/r singularity. Excellent convergence properties are achieved with respect to the number of grid points (or DVR functions) and the size of the simulation cell. A straightforward implementation of the present approach leads to near linear scaling [O(N(4/3))] of the computational cost with respect to the system size (N) for the solution of Poisson's equation. The accuracy and stability of CPAIMD simulations based on sinc DVR are tested for a model problem as well as for N(2) and a water dimer. PMID:19071908

  4. The Development of Explosions in Axisymmetric Ab Initio Core-Collapse Supernova Simulations of 12-25 $M_\\odot$ Stars

    Bruenn, Stephen W; Hix, W Raphael; Mezzacappa, Anthony; Harris, James Austin; Messer, O E Bronson; Endeve, Eirik; Blondin, John M; Chertkow, Merek Austin; Lingerfelt, Eric J; Marronetti, Pedro; Yakunin, Konstantin N

    2014-01-01

    We present four ab initio axisymmetric core-collapse supernova simulations for 12, 15, 20, and 25 $M_\\odot$ progenitors. All of the simulations yield explosions and have been evolved for at least 1.2 seconds after core bounce and 1 second after material first becomes unbound. Simulations were computed with our Chimera code employing spectral neutrino transport, special and general relativistic transport effects, and state-of-the-art neutrino interactions. Continuing the evolution beyond 1 second allows explosions to develop more fully and the processes powering the explosions to become more clearly evident. We compute explosion energy estimates, including the binding energy of the stellar envelope outside the shock, of 0.34, 0.88, 0.38, and 0.70 B ($10^{51}$ ergs) and increasing at 0.03, 0.15, 0.19, and 0.52 B s$^{-1}$, respectively, for the 12, 15, 20, and 25 $M_\\odot$ models. Three models developed pronounced prolate shock morphologies, while the 20 $M_\\odot$ model, though exhibiting lobes and accretion str...

  5. Spatial distribution of rare-earth ions and GaS4 tetrahedra in chalcogenide glasses studied via laser spectroscopy and ab initio molecular dynamics simulation

    Lee, T. H.; Simdyankin, S. I.; Hegedus, J.; Heo, J.; Elliott, S. R.

    2010-03-01

    The spatial distribution of Nd3+ ions and GaS4 tetrahedral units in Nd-doped Ge-As-Ga-S glasses has been studied by laser spectroscopy and ab initio molecular dynamics (MD) simulations. A sharp increase in Nd3+ fluorescence intensities and lifetimes was observed with increasing Ga content, and attributed to the formation of tightly bound Nd3+ clusters in Ga-free glasses and the subsequent dissolution of such clusters upon Ga doping. A large modification in Nd3+ sites was also identified from low-temperature site-selective excitation spectra, suggesting preferential spatial correlations between Nd3+ and GaS4 tetrahedra even at low Ga-doping levels. MD simulations of these materials in the liquid state showed a tendency for Ga cluster formation as well as spatial correlations between Nd and Ga atoms consistent with the experimental results. On the basis of this result, a comprehensive structural model for Nd- and Ga-doped sulfide glasses is proposed.

  6. Ab initio two-component Ehrenfest dynamics

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

  7. Ab initio gene identification in metagenomic sequences.

    Zhu, Wenhan; Lomsadze, Alexandre; Borodovsky, Mark

    2010-07-01

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

  8. Toward ab initio density functional theory for nuclei

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

    2009-01-01

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

  9. 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.

  10. Effects of spin orbital coupling on atomic and electronic structures in Al2Cu and Al2Au crystal and liquid phases via ab initio molecular dynamics simulations

    Highlights: • The SOC effect affects the cohesion energy of crystal phase. • The effect of SOC was reduced due to random local atomic structures in liquids. • The local geometrical structures also affect the melting points. • Both SOC effect and local atomic structures are important for melting point difference. - Abstract: The origin of different melting points between Al2Cu and Al2Au has been studied using ab initio molecular dynamics simulations. Cohesive energy, electronic structures and structure information of both crystal and liquid phases have been analyzed. It is found that spin orbital coupling (SOC) plays an important role on the cohesive energy of crystal phase, consistent with the different melting points of these two alloys. Whereas, it seems that SOC has no effect on the formation energy and structure of liquid phase. Possible mechanism of reduced SOC effect at liquid phase is proposed. Our results are helpful to understand the glass formation ability difference between Al2Cu and Al2Au

  11. Strong influence of coadsorbate interaction on CO desorption dynamics on Ru(0001) probed by ultrafast x-ray spectroscopy and ab initio simulations

    Xin, H. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); LaRue, J. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Oberg, H. [Stockholm Univ., Stockholm (Sweden); Beye, M. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Dell' Angela, M. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); Turner, J. J. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Gladh, J. [Stockholm Univ., Stockholm (Sweden); Ng, M. L. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Sellberg, J. A. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Kaya, S. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Mercurio, G. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); Hieke, F. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); Nordlund, D. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Schlotter, W. F. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Dakovski, G. L. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Minitti, M. P. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Fohlisch, A. [Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Univ. Potsdam, Potsdam (Germany); Wolf, M. [Fritz-Haber Institute of the Max-Planck-Society, Berlin (Germany); Wurth, W. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); DESY Photon Science, Hamburg (Germany); Ogasawara, H. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Norskov, J. K. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); Ostrom, H. [Stockholm Univ., Stockholm (Sweden); Pettersson, L. G. M. [Stockholm Univ., Stockholm (Sweden); Nilsson, A. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stockholm Univ., Stockholm (Sweden); Ablid-Pedersen, F. [SLAC National Accelerator Lab., Menlo Park, CA (United States)

    2015-04-16

    We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distribution and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.

  12. Stimulated Raman signals at conical intersections: Ab initio surface hopping simulation protocol with direct propagation of the nuclear wave function

    Femtosecond Stimulated Raman Spectroscopy (FSRS) signals that monitor the excited state conical intersections dynamics of acrolein are simulated. An effective time dependent Hamiltonian for two C—H vibrational marker bands is constructed on the fly using a local mode expansion combined with a semi-classical surface hopping simulation protocol. The signals are obtained by a direct forward and backward propagation of the vibrational wave function on a numerical grid. Earlier work is extended to fully incorporate the anharmonicities and intermode couplings

  13. 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.

  14. Ab Initio No-Core Shell Model

    A long-standing goal of nuclear theory is to determine the properties of atomic nuclei based on the fundamental interactions among the protons and neutrons (i.e., nucleons). By adopting nucleon-nucleon (NN), three-nucleon (NNN) and higher-nucleon interactions determined from either meson-exchange theory or QCD, with couplings fixed by few-body systems, we preserve the predictive power of nuclear theory. This foundation enables tests of nature's fundamental symmetries and offers new vistas for the full range of complex nuclear phenomena. Basic questions that drive our quest for a microscopic predictive theory of nuclear phenomena include: (1) What controls nuclear saturation; (2) How the nuclear shell model emerges from the underlying theory; (3) What are the properties of nuclei with extreme neutron/proton ratios; (4) Can we predict useful cross sections that cannot be measured; (5) Can nuclei provide precision tests of the fundamental laws of nature; and (6) Under what conditions do we need QCD to describe nuclear structure, among others. Along with other ab initio nuclear theory groups, we have pursued these questions with meson-theoretical NN interactions, such as CD-Bonn and Argonne V18, that were tuned to provide high-quality descriptions of the NN scattering phase shifts and deuteron properties. We then add meson-theoretic NNN interactions such as the Tucson-Melbourne or Urbana IX interactions. More recently, we have adopted realistic NN and NNN interactions with ties to QCD. Chiral perturbation theory within effective field theory (χEFT) provides us with a promising bridge between QCD and hadronic systems. In this approach one works consistently with systems of increasing nucleon number and makes use of the explicit and spontaneous breaking of chiral symmetry to expand the strong interaction in terms of a dimensionless constant, the ratio of a generic small momentum divided by the chiral symmetry breaking scale taken to be about 1 GeV/c. The resulting NN

  15. Ab Initio No-Core Shell Model

    Barrett, B R; Navratil, P; Vary, J P

    2011-04-11

    A long-standing goal of nuclear theory is to determine the properties of atomic nuclei based on the fundamental interactions among the protons and neutrons (i.e., nucleons). By adopting nucleon-nucleon (NN), three-nucleon (NNN) and higher-nucleon interactions determined from either meson-exchange theory or QCD, with couplings fixed by few-body systems, we preserve the predictive power of nuclear theory. This foundation enables tests of nature's fundamental symmetries and offers new vistas for the full range of complex nuclear phenomena. Basic questions that drive our quest for a microscopic predictive theory of nuclear phenomena include: (1) What controls nuclear saturation; (2) How the nuclear shell model emerges from the underlying theory; (3) What are the properties of nuclei with extreme neutron/proton ratios; (4) Can we predict useful cross sections that cannot be measured; (5) Can nuclei provide precision tests of the fundamental laws of nature; and (6) Under what conditions do we need QCD to describe nuclear structure, among others. Along with other ab initio nuclear theory groups, we have pursued these questions with meson-theoretical NN interactions, such as CD-Bonn and Argonne V18, that were tuned to provide high-quality descriptions of the NN scattering phase shifts and deuteron properties. We then add meson-theoretic NNN interactions such as the Tucson-Melbourne or Urbana IX interactions. More recently, we have adopted realistic NN and NNN interactions with ties to QCD. Chiral perturbation theory within effective field theory ({chi}EFT) provides us with a promising bridge between QCD and hadronic systems. In this approach one works consistently with systems of increasing nucleon number and makes use of the explicit and spontaneous breaking of chiral symmetry to expand the strong interaction in terms of a dimensionless constant, the ratio of a generic small momentum divided by the chiral symmetry breaking scale taken to be about 1 GeV/c. The

  16. Quasielastic neutron scattering measurements and ab initio MD-simulations on single ion motions in molten NaF

    Demmel, F. [ISIS Facility, Rutherford Appleton Laboratory, Didcot OX11 0QX (United Kingdom); Mukhopadhyay, S. [ISIS Facility, Rutherford Appleton Laboratory, Didcot OX11 0QX (United Kingdom); Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ (United Kingdom)

    2016-01-07

    The ionic stochastic motions in the molten alkali halide NaF are investigated by quasielastic neutron scattering and first principles molecular dynamics simulation. Quasielastic neutron scattering was employed to extract the diffusion behavior of the sodium ions in the melt. An extensive first principles based simulation on a box of up to 512 particles has been performed to complement the experimental data. From that large box, a smaller 64-particle box has then been simulated over a runtime of 60 ps. A good agreement between calculated and neutron data on the level of spectral shape has been obtained. The obtained sodium diffusion coefficients agree very well. The simulation predicts a fluorine diffusion coefficient similar to the sodium one. Applying the Nernst-Einstein equation, a remarkable large cross correlation between both ions can be deduced. The velocity cross correlations demonstrate a positive correlation between the ions over a period of 0.1 ps. That strong correlation is evidence that the unlike ions do not move completely statistically independent and have a strong association over a short period of time.

  17. Thermal effects on CH$_3$NH$_3$PbI$_3$ perovskite from ab-initio molecular dynamics simulations

    Carignano, Marcelo A; Hutter, Jürg

    2014-01-01

    We present a molecular dynamics simulation study of CH$_3$NH$_3$PbI$_3$ based on forces calculated from density functional theory. The simulation were performed on model systems having 8 and 27 unit cells, and for a total simulation time of 40 ps in each case. Analysis of the finite size effects, in particular the mobility of the organic component, suggests that the smaller system is over correlated through the long range electrostatic interaction. In the larger system this finite size artifact is relaxed producing a more reliable description of the anisotropic rotational behavior of the methyl ammonium molecules. The thermal effects on the optical properties of the system were also analyzed. The HOMO-LUMO energy gap fluctuates around its central value with a standard deviation of approximately 0.1 eV. The projected density of states consistently place the Fermi level on the $p$ orbitals of the I atoms, and the lowest virtual state on $p$ orbitals of the Pb atoms throughout the whole simulation trajectory.

  18. Quasielastic neutron scattering measurements and ab initio MD-simulations on single ion motions in molten NaF

    Demmel, F.; Mukhopadhyay, S.

    2016-01-01

    The ionic stochastic motions in the molten alkali halide NaF are investigated by quasielastic neutron scattering and first principles molecular dynamics simulation. Quasielastic neutron scattering was employed to extract the diffusion behavior of the sodium ions in the melt. An extensive first principles based simulation on a box of up to 512 particles has been performed to complement the experimental data. From that large box, a smaller 64-particle box has then been simulated over a runtime of 60 ps. A good agreement between calculated and neutron data on the level of spectral shape has been obtained. The obtained sodium diffusion coefficients agree very well. The simulation predicts a fluorine diffusion coefficient similar to the sodium one. Applying the Nernst-Einstein equation, a remarkable large cross correlation between both ions can be deduced. The velocity cross correlations demonstrate a positive correlation between the ions over a period of 0.1 ps. That strong correlation is evidence that the unlike ions do not move completely statistically independent and have a strong association over a short period of time.

  19. Quasielastic neutron scattering measurements and ab initio MD-simulations on single ion motions in molten NaF

    The ionic stochastic motions in the molten alkali halide NaF are investigated by quasielastic neutron scattering and first principles molecular dynamics simulation. Quasielastic neutron scattering was employed to extract the diffusion behavior of the sodium ions in the melt. An extensive first principles based simulation on a box of up to 512 particles has been performed to complement the experimental data. From that large box, a smaller 64-particle box has then been simulated over a runtime of 60 ps. A good agreement between calculated and neutron data on the level of spectral shape has been obtained. The obtained sodium diffusion coefficients agree very well. The simulation predicts a fluorine diffusion coefficient similar to the sodium one. Applying the Nernst-Einstein equation, a remarkable large cross correlation between both ions can be deduced. The velocity cross correlations demonstrate a positive correlation between the ions over a period of 0.1 ps. That strong correlation is evidence that the unlike ions do not move completely statistically independent and have a strong association over a short period of time

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

    Marsalek, Ondrej

    2015-01-01

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

  1. Synthesis, characterization and RHF/ab initio simulations of 2-amino-1,3,4-thiadiazole and its annulated ring junction pyrimidine derivatives

    Wafaa S. Hamama

    2013-01-01

    Full Text Available Michael addition reaction of the 2-amino-1,3,4-thiadiazole to chalcone as biselectrophile afforded 5,7-diphenyl-6-[1,3-diphenylpropan-1-on-3-yl][1,3,4]thiadiazolo[3,2-a]pyrimidine (3 instead of 5,7-diphenyl-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidine (5 via further Michael addition at C5 in pyrimidine moiety. The structure 3 was established through the aspect of ab initio calculations, elemental analysis and spectral data.

  2. Synthesis, characterization and RHF/ab initio simulations of 2-amino-1,3,4-thiadiazole and its annulated ring junction pyrimidine derivatives

    Wafaa S. Hamama; Gouda, Moustafa A.; Mamdouh S. Soliman; Badr, Marwa H.; Zoorob, Hanafi H.

    2013-01-01

    Michael addition reaction of the 2-amino-1,3,4-thiadiazole to chalcone as biselectrophile afforded 5,7-diphenyl-6-[1,3-diphenylpropan-1-on-3-yl][1,3,4]thiadiazolo[3,2-a]pyrimidine (3) instead of 5,7-diphenyl-5H-[1,3,4]thiadiazolo[3,2-a]pyrimidine (5) via further Michael addition at C5 in pyrimidine moiety. The structure 3 was established through the aspect of ab initio calculations, elemental analysis and spectral data.

  3. Ab-initio simulations of higher Miller index Si:SiO2 interfaces for fin field effect transistor and nanowire transistors

    Models of three representative higher Miller index interfaces, Si(310):SiO2, Si(410):SiO2, and Si(331):SiO2, have been built by an ab-initio molecular dynamics method. We show that each interface can be made as a fully bonded network without any defects and has a reasonable electronic structure for use in fin field effect transistors or gate-all-around nanowire devices. The differences in numbers of oxygen bridges are attributed to the intermediate sub-oxide components and the atomic step structure. The interface bonding schemes to passivate different densities of dangling bonds on different facets are also analyzed

  4. Optical-induced electrical current in diamond switched by femtosecond–attosecond laser pulses by ab initio simulations

    The electric current has been switched in diamond by a dual-laser field with an attosecond pulse train and a femtosecond laser, respectively serving to excite and drive electrons. The optical-induced current is simulated by the developed method based on the time-dependent density functional theory. The electric current is induced within several attoseconds with the diamond’s conductivity increased by 16∼23 orders of magnitude. Our work opens the way to extending electronic signal processing from the present gigahertz domain into the exahertz domain. (paper)

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

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-01-01

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

  6. 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...

  7. An ab initio path integral Monte Carlo simulation method for molecules and clusters application to $Li_4$ and $Li_{5}^{+}$

    Weht, R; Estrin, D A; Chakravarty, C; Weht, Ruben O.; Kohanoff, Jorge; Estrin, Dario A.; Chakravarty, Charusita

    1998-01-01

    A novel method for simulating the statistical mechanics of molecular systems in which both nuclear and electronic degrees of freedom are treated quantum mechanically is presented. The scheme combines a path integral description of the nuclear variables with a first-principles adiabatic description of the electronic structure. The electronic problem is solved for the ground state within a density functional approach, with the electronic orbitals expanded in a localized (Gaussian) basis set. The discretized path integral is computed by a Metropolis Monte Carlo sampling technique on the normal modes of the isomorphic ring-polymer. An effective short-time action correct to order small Lithium clusters, namely Li$_4$ and Li$_5^+$. Structural and electronic properties computed within this fully quantum-mechanical scheme are presented and compared to those obtained within the classical nuclei approximation. Quantum delocalization effects are significant but tunneling turns out to be irrelevant at low temperatures.

  8. Ab initio calculations on SCl2 and low-lying cationic states of SCl2+: Franck-Condon simulation of the UV photoelectron spectrum of SCl2

    Mok, Daniel K. W.; Chau, Foo-tim; Lee, Edmond P. F.; Dyke, John M.

    2006-09-01

    Geometry optimization calculations were carried out on the X˜A11 state of SCl2 and the X˜B12, ÃB22, B˜A12, C˜A12, D˜A22, and ẼB22 states of SCl2+ at the restricted-spin coupled-cluster single-double plus perturbative triple excitation [RCCSD(T)] level with basis sets of up to the augmented correlation-consistent polarized quintuple-zeta [aug-cc-pV(5+d )Z] quality. Effects of core electron correlation, basis set extension to the complete basis set limit, and relativistic contributions on computed minimum-energy geometrical parameters and/or relative electronic energies were also investigated. RCCSD(T) potential energy functions (PEFs) were calculated for the X˜A11 state of SCl2 and the low-lying states of SCl2+ listed above employing the aug-cc-pV(5+d )Z basis set. Anharmonic vibrational wave functions of these neutral and cationic states of SCl2, and Franck-Condon (FC) factors of the lowest four one-electron allowed neutral photoionizations were computed employing the RCCSD(T )/aug-cc-pV(5+d)Z PEFs. Calculated FC factors with allowance for the Duschinsky rotation and anharmonicity were used to simulate the first four photoelectron (PE) bands of SCl2. The agreement between simulated and observed He I PE spectra reported by Colton et al. [J. Electron Spectrosc. Relat. Phenom. 3, 345 (1974)] and Solouki et al. [Chem. Phys. Lett. 26, 20 (1974)] is excellent. However, our FC spectral simulations indicate that the first observed vibrational component in the first PE band of SCl2 is a "hot" band arising from the SCl2+X˜B12(0,0,0)←SCl2X˜A11(1,0,0) ionization. Consequently, the experimental adiabatic ionization energy of SCl2 is revised to 9.55±0.01eV, in excellent agreement with results obtained from state-of-the-art ab initio calculations in this work.

  9. Ab initio simulation of ammonia monohydrate (NH3ṡH2O) and ammonium hydroxide (NH4OH)

    Fortes, A. D.; Brodholt, J. P.; Wood, I. G.; Vočadlo, L.; Jenkins, H. D. B.

    2001-10-01

    We report the results of the first pseudopotential plane-wave simulations of the static properties of ammonia monohydrate phase I (AMH I) and ammonium hydroxide. Our calculated fourth-order logarithmic equation of state, at zero pressure and temperature, has molar volume, V0=36.38(3) cm3 mol-1, bulk modulus, K0=9.59(9) GPa, and the first derivative of the bulk modulus with respect to pressure, K0'=5.73(21). Both this and the lattice parameters are in very good agreement with experimental values. The monohydrate transforms, via a solid-state proton transfer reaction, to ammonium hydroxide (NH4OH) at 5.0(4) GPa. The equation of state of ammonium hydroxide is, V0=31.82(5) cm3 mol-1, K0=14.78(62) GPa, K0'=2.69(48). We calculate the reaction enthalpy, ΔH(NH4OH,s→NH3ṡH2O,s)=-14.8(5) kJ mol-1 at absolute zero, and thus estimate the enthalpy of formation, ΔfH⊖(NH4OH,s)=-356 kJ mol-1 at 298 K. This result places an upper limit of 84 kJ mol-1 on the barrier to rotation of the ammonium cation, and yields an average hydrogen bond enthalpy of ˜23 kJ mol-1.

  10. Towards new horizons in ab initio nuclear structure theory

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

  11. 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.

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

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

    2016-01-01

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

  13. 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.

  14. 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...

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

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

    2015-01-01

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

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

    Bak, Börge; Jansen, Peter; Stafast, Herbert

    1975-01-01

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

  17. 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.

  18. Temperature and compression effects on electron heat capacity and electron-phonon coupling in aluminum and beryllium: Insights from ab initio simulations

    Ultrafast laser experiments on metals usually induce a high electron temperature and a low ion temperature and, thus, an energy relaxation process. The electron heat capacity and electron-phonon coupling factor are crucial thermal quantities to describe this process. We perform ab initio theoretical studies to determine these thermal quantities and their dependence on density and electron temperature for the metals aluminum and beryllium. The heat capacity shows an approximately linear dependence on the temperature, similar to free electron gas, and the compression only slightly affects the capacity. The electron-phonon coupling factor increases with both temperature and density, and the change observed for beryllium is more obvious than that for aluminum. The connections between thermal quantities and electronic/atomic structures are discussed in detail, and the different behaviors of aluminum and beryllium are well explained

  19. Ab-initio simulations of higher Miller index Si:SiO{sub 2} interfaces for fin field effect transistor and nanowire transistors

    Li, Hongfei; Guo, Yuzheng; Robertson, John [Engineering Department, Cambridge University, Cambridge CB2 1PZ (United Kingdom); Okuno, Y. [Taiwan Semiconductor Manufacturing Company (TSMC), Hsinchu Science Park, Hsinchu, Taiwan (China)

    2016-02-07

    Models of three representative higher Miller index interfaces, Si(310):SiO{sub 2}, Si(410):SiO{sub 2}, and Si(331):SiO{sub 2}, have been built by an ab-initio molecular dynamics method. We show that each interface can be made as a fully bonded network without any defects and has a reasonable electronic structure for use in fin field effect transistors or gate-all-around nanowire devices. The differences in numbers of oxygen bridges are attributed to the intermediate sub-oxide components and the atomic step structure. The interface bonding schemes to passivate different densities of dangling bonds on different facets are also analyzed.

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

    Gonzalez, Luis E.; Gonzalez, David J

    2006-01-01

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

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

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

    2016-01-01

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

  2. 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}.

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

    Allen, B. Danette; Alexandrov, Natalia

    2016-01-01

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

  4. Ab-initio calculations on melting of thorium

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

    2016-05-01

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

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

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

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

    Broido, David

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

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

    Wouters, Sebastian

    2014-01-01

    During the past 15 years, the density matrix renormalization group (DMRG) has become increasingly important for ab initio quantum chemistry. Its underlying wavefunction ansatz, the matrix product state (MPS), is a low-rank decomposition of the full configuration interaction tensor. The virtual dimension of the MPS, the rank of the decomposition, controls the size of the corner of the many-body Hilbert space that can be reached with the ansatz. This parameter can be systematically increased until numerical convergence is reached. The MPS ansatz naturally captures exponentially decaying correlation functions. Therefore DMRG works extremely well for noncritical one-dimensional systems. The active orbital spaces in quantum chemistry are however often far from one-dimensional, and relatively large virtual dimensions are required to use DMRG for ab initio quantum chemistry (QC-DMRG). The QC-DMRG algorithm, its computational cost, and its properties are discussed. Two important aspects to reduce the computational co...

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

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

    2007-02-01

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

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

    We discuss some accuracy aspects inherent to ab initio electronic structure calculations in the understanding of nuclear quadrupole interactions. We use the projector augmented wave method to study the electric-field gradient (EFG) at both Sn and O sites in the prototype cases SnO and SnO2. The term ab initio is used in the standard context of the also called first principles methods in the framework of the Density Functional Theory. As the main contributions of EFG calculations to problems in condensed matter physics are related to structural characterizations on the atomic scale, we discuss the 'state of the art' on theoretical EFG calculations and make a brief critical review on the subject, calling attention to some fundamental theoretical aspects

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

    Sirin, Gulseher Sarah; Zhang, Yingkai

    2014-01-01

    Acetylcholinesterase (AChE) is a crucial enzyme in the cholinergic nerve system that hydrolyzes acetylcholine (ACh) and terminates synaptic signals by reducing the effective concentration of ACh in the synaptic clefts. Organophosphate compounds irreversibly inhibit AChEs, leading to irreparable damage to nerve cells. By employing Born–Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling, a state-of-the-art approach to simulate enzyme reactions, we have characteriz...

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

    Brodersen, Sven

    2002-01-01

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

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

    Wouters, Sebastian

    2015-01-01

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

  13. Ab Initio Modeling of Ecosystems with Artificial Life

    Adami, C.

    2002-01-01

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

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

    Bacca, Sonia

    2016-01-01

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

  15. Ab-initio calculations for dilute magnetic semiconductors

    Belhadji, Brahim

    2008-01-01

    This thesis focusses on ab-initio calculations for the electronic structure and the magnetic properties of dilute magnetic semiconductors (DMS). In particular we aim at the understanding of the complex exchange interactions in these systems. Our calculations are based on density functional theory, being ideally suited for a description of the material specific properties of the considered DMS. Moreover we use the KKR Green function method in connection with the coherent potential approximatio...

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

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

    1993-11-01

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

  17. GAUSSIAN 76: an ab initio molecular orbital program

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

    1978-06-01

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

  18. 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.

  19. 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.

  20. 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.)

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

    The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several ab initio methods have now emerged that provide nearly exact solutions for some nuclear properties. The ab initio no core shell model (NCSM) and the no core full configuration (NCFC) method, frame this quantum many-particle problem as a large sparse matrix eigenvalue problem where one evaluates the Hamiltonian matrix in a basis space consisting of many-fermion Slater determinants and then solves for a set of the lowest eigenvalues and their associated eigenvectors. The resulting eigenvectors are employed to evaluate a set of experimental quantities to test the underlying potential. For fundamental problems of interest, the matrix dimension often exceeds 1010 and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. We survey recent results and advances in solving this large sparse matrix eigenvalue problem. We also outline the challenges that lie ahead for achieving further breakthroughs in fundamental nuclear theory using these ab initio approaches.

  2. 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).

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

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

    2010-09-29

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

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

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

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

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

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

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

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

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

    2016-03-01

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

  8. Ab initio calculations of reactions with light nuclei

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

    2016-03-01

    An ab initio (i.e., from first principles) theoretical framework capable of providing a unified description of the structure and low-energy reaction properties of light nuclei is desirable to further our understanding of the fundamental interactions among nucleons, and provide accurate predictions of crucial reaction rates for nuclear astrophysics, fusion-energy research, and other applications. In this contribution we review ab initio calculations for nucleon and deuterium scattering on light nuclei starting from chiral two- and three-body Hamiltonians, obtained within the framework of the ab initio no-core shell model with continuum. This is a unified approach to nuclear bound and scattering states, in which square-integrable energy eigenstates of the A-nucleon system are coupled to (A-a)+a target-plus-projectile wave functions in the spirit of the resonating group method to obtain an efficient description of the many-body nuclear dynamics both at short and medium distances and at long ranges.

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

    Makhov, Dmitry V.; Glover, William J.; Martinez, Todd J.; Shalashilin, Dmitrii V.

    2014-08-01

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

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

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

    2014-08-07

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

  11. 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.

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

    Bernard, St

    1998-12-31

    The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H{sub 2}){sub 2} which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author) 109 refs.

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

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

    2016-05-01

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

  14. Atomic packing and diffusion in Fe{sub 85}Si{sub 2}B{sub 9}P{sub 4} amorphous alloy analyzed by ab initio molecular dynamics simulation

    Wang, Yaocen; Takeuchi, Akira; Makino, Akihiro [Institute for Material Research, Tohoku University, Sendai 980-8577 (Japan); Liang, Yunye [New Industry Creation Hatchery Center, Tohoku University, Sendai 980-8579 (Japan); Kawazoe, Yoshiyuki [New Industry Creation Hatchery Center, Tohoku University, Sendai 980-8579 (Japan); Kutateladze Institute of Thermophysics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk (Russian Federation)

    2015-05-07

    In the work reported in this paper, ab initio molecular dynamics simulation was performed on Fe{sub 85}Si{sub 2}B{sub 9}P{sub 4} amorphous alloy. Preferred atomic environment of the elements was analyzed with Voronoi polyhedrons. It showed that B and P atoms prefer less neighbors compared with Fe and Si, making them structurally incompatible with Fe rich structure and repulsive to the formation of α-Fe. However, due to the low bonding energy of B and P caused by low coordination number, the diffusion rates of them were considerably large, resulting in the requirement of fast annealing for achieving optimum nano-crystallization for its soft magnetic property. The simulation work also indicates that diffusion rate in amorphous alloy is largely determined by bonding energy rather than atomic size.

  15. Toward ab initio extremely metal poor stars

    Ritter, Jeremy S; Milosavljevic, Milos; Bromm, Volker

    2016-01-01

    Extremely metal poor stars have been the focus of much recent attention owing to the expectation that their chemical abundances can shed light on the metal and dust yields of the earliest supernovae. We present our most realistic simulation to date of the astrophysical pathway to the first metal enriched stars. We simulate the radiative and supernova hydrodynamic feedback of a 60 Msun Population III star starting from cosmological initial conditions realizing Gaussian density fluctuations. We follow the gravitational hydrodynamics of the supernova remnant at high spatial resolution through its freely-expanding, adiabatic, and radiative phases, until gas, now metal-enriched, has resumed runaway gravitational collapse. Our findings are surprising: while the Population III progenitor exploded with a low energy of 10^51 erg and injected an ample metal mass of 6 Msun, the first cloud to collapse after the supernova explosion is a dense surviving primordial cloud on which the supernova blastwave deposited metals on...

  16. Ab-initio molecular dynamics for metallic systems

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

  17. Toward ab initio extremely metal poor stars

    Ritter, Jeremy S.; Safranek-Shrader, Chalence; Milosavljević, Miloš; Bromm, Volker

    2016-09-01

    Extremely metal poor stars have been the focus of much recent attention owing to the expectation that their chemical abundances can shed light on the metal and dust yields of the earliest supernovae. We present our most realistic simulation to date of the astrophysical pathway to the first metal enriched stars. We simulate the radiative and supernova hydrodynamic feedback of a 60 M⊙ Population III star starting from cosmological initial conditions realizing Gaussian density fluctuations. We follow the gravitational hydrodynamics of the supernova remnant at high spatial resolution through its freely-expanding, adiabatic, and radiative phases, until gas, now metal-enriched, has resumed runaway gravitational collapse. Our findings are surprising: while the Population III progenitor exploded with a low energy of 1051 erg and injected an ample metal mass of 6 M⊙, the first cloud to collapse after the supernova explosion is a dense surviving primordial cloud on which the supernova blast wave deposited metals only superficially, in a thin, unresolved layer. The first metal-enriched stars can form at a very low metallicity, of only 2 - 5 × 10-4 Z⊙, and can inherit the parent cloud's highly elliptical, radially extended orbit in the dark matter gravitational potential.

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

    Blomqvist, Andreas

    2010-01-01

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

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

    Peter E Blöchl; Clemens J Först; Johannes Schimpl

    2003-01-01

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

  20. An ab initio study of plutonium oxides surfaces

    By means of first-principles calculations, we have studied the atomic structure as well as the thermodynamic stability of various plutonium dioxide surfaces in function of their environment (in terms of oxygen partial pressure and temperature). All these simulations have been performed with the ABINIT code. It is well known that DFT fails to describe correctly plutonium-based materials since 5f electrons in such systems are strongly correlated. In order to go beyond DFT, we have treated PuO2 and β-Pu2O3 in a DFT+U framework. We show that the couple of parameters (U,J) that works well for pure Pu is also well designed for describing ground state (GS) properties of these two oxides. The major improvement with respect with DFT is that we are able to predict an insulating GS in agreement with experiments. The presence of a gap in the DOS (Density of States) of plutonium oxides should play a significant role in the predicted surface reactivity. However, performing DFT+U calculations on surfaces of plutonium oxide from scratch was too ambitious. That is why we decided, as a first step, to study the stability of the (100), (110) and (111) surfaces of PuO2 in a DFT-GGA framework. For each of these orientations, we considered various terminations. These ab initio results have been introduced in a thermodynamic model which allows us to predict the relative stability of the different terminations as a function of temperature and oxygen partial pressure (pO2). We conclude that at room temperature and for pO2∼10 atm., the polar O2-(100) termination is favoured. The stabilization of such a polar stoichiometric surface is surprising and should be confirmed by DFT+U calculations before any final conclusion. (authors)

  1. Ab initio quantum transport calculations using plane waves

    Garcia-Lekue, A.; Vergniory, M. G.; Jiang, X. W.; Wang, L. W.

    2015-08-01

    We present an ab initio method to calculate elastic quantum transport at the nanoscale. The method is based on a combination of density functional theory using plane wave nonlocal pseudopotentials and the use of auxiliary periodic boundary conditions to obtain the scattering states. The method can be applied to any applied bias voltage and the charge density and potential profile can either be calculated self-consistently, or using an approximated self-consistent field (SCF) approach. Based on the scattering states one can straightforwardly calculate the transmission coefficients and the corresponding electronic current. The overall scheme allows us to obtain accurate and numerically stable solutions for the elastic transport, with a computational time similar to that of a ground state calculation. This method is particularly suitable for calculations of tunneling currents through vacuum, that some of the nonequilibrium Greens function (NEGF) approaches based on atomic basis sets might have difficulty to deal with. Several examples are provided using this method from electron tunneling, to molecular electronics, to electronic devices: (i) On a Au nanojunction, the tunneling current dependence on the electrode-electrode distance is investigated. (ii) The tunneling through field emission resonances (FERs) is studied via an accurate description of the surface vacuum states. (iii) Based on quantum transport calculations, we have designed a molecular conformational switch, which can turn on and off a molecular junction by applying a perpendicular electric field. (iv) Finally, we have used the method to simulate tunnel field-effect transistors (TFETs) based on two-dimensional transition-metal dichalcogenides (TMDCs), where we have studied the performance and scaling limits of such nanodevices and proposed atomic doping to enhance the transistor performance.

  2. 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.

  3. Ab initio study of neutron drops with chiral Hamiltonians

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

  4. 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.

  5. Ab initio calculation of tensile strength in iron

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

    2003-01-01

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

  6. Ab initio 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.

  7. Ab-initio study of napthelene based conducting polymer

    Ruhela, Ankur [Advanced Materials Research Group, Computational Nanoscience and Technology Lab (CNTL), ABV-Indian Institute of Information Technology and Management, Gwalior -474010, India and Amity Institute of Nanotechnology, Amity University, Noida-201303 (India); Kanchan, Reena, E-mail: reena.kanchan1977@gmail.com [Department of Chemistry, Jiwaji University, Gwalior-474001 (India); Srivastava, Anurag [Advanced Materials Research Group, Computational Nanoscience and Technology Lab (CNTL), ABV-Indian Institute of Information Technology and Management, Gwalior -474010 (India); Sinha, O. P. [Amity Institute of Nanotechnology, Amity University, Noida-201303 (India)

    2014-04-24

    In this paper, we have identified structural and electronic properties of conducting polymers by using DFT based ATK-VNL ab-initio tool. Naphthalene derivative structures were stabilized by varying the bond length between two atoms of the molecule C-N and C-C. We have also studied the molecular energy spectrum of naphthalene derivatives and found the HOMOLUMO for the same. A comparison of structural and electronic properties of naphthalene derivatives by attaching the functional group of amine, have been performed and found that they show good semi conducting properties.

  8. Ab-initio study of napthelene based conducting polymer

    In this paper, we have identified structural and electronic properties of conducting polymers by using DFT based ATK-VNL ab-initio tool. Naphthalene derivative structures were stabilized by varying the bond length between two atoms of the molecule C-N and C-C. We have also studied the molecular energy spectrum of naphthalene derivatives and found the HOMOLUMO for the same. A comparison of structural and electronic properties of naphthalene derivatives by attaching the functional group of amine, have been performed and found that they show good semi conducting properties

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

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

  10. Ab initio study of neutron drops with chiral Hamiltonians

    H.D. Potter

    2014-12-01

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