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Sample records for scaling first-principles molecular

  1. Large-Scale First-Principles Molecular Dynamics Simulations with Electrostatic Embedding: Application to Acetylcholinesterase Catalysis

    DOE PAGESBeta

    Fattebert, Jean-Luc; Lau, Edmond Y.; Bennion, Brian J.; Huang, Patrick; Lightstone, Felice C.

    2015-10-22

    Enzymes are complicated solvated systems that typically require many atoms to simulate their function with any degree of accuracy. We have recently developed numerical techniques for large scale First-Principles molecular dynamics simulations and applied them to study the enzymatic reaction catalyzed by acetylcholinesterase. We carried out Density functional theory calculations for a quantum mechanical (QM) sub- system consisting of 612 atoms with an O(N) complexity finite-difference approach. The QM sub-system is embedded inside an external potential field representing the electrostatic effect due to the environment. We obtained finite temperature sampling by First-Principles molecular dynamics for the acylation reaction of acetylcholinemore » catalyzed by acetylcholinesterase. Our calculations shows two energies barriers along the reaction coordinate for the enzyme catalyzed acylation of acetylcholine. In conclusion, the second barrier (8.5 kcal/mole) is rate-limiting for the acylation reaction and in good agreement with experiment.« less

  2. Large-Scale First-Principles Molecular Dynamics Simulations with Electrostatic Embedding: Application to Acetylcholinesterase Catalysis

    SciTech Connect

    Fattebert, Jean-Luc; Lau, Edmond Y.; Bennion, Brian J.; Huang, Patrick; Lightstone, Felice C.

    2015-10-22

    Enzymes are complicated solvated systems that typically require many atoms to simulate their function with any degree of accuracy. We have recently developed numerical techniques for large scale First-Principles molecular dynamics simulations and applied them to study the enzymatic reaction catalyzed by acetylcholinesterase. We carried out Density functional theory calculations for a quantum mechanical (QM) sub- system consisting of 612 atoms with an O(N) complexity finite-difference approach. The QM sub-system is embedded inside an external potential field representing the electrostatic effect due to the environment. We obtained finite temperature sampling by First-Principles molecular dynamics for the acylation reaction of acetylcholine catalyzed by acetylcholinesterase. Our calculations shows two energies barriers along the reaction coordinate for the enzyme catalyzed acylation of acetylcholine. In conclusion, the second barrier (8.5 kcal/mole) is rate-limiting for the acylation reaction and in good agreement with experiment.

  3. Stable and Efficient Linear Scaling First-Principles Molecular Dynamics for 10000+ Atoms.

    PubMed

    Arita, Michiaki; Bowler, David R; Miyazaki, Tsuyoshi

    2014-12-01

    The recent progress of linear-scaling or O(N) methods in density functional theory (DFT) is remarkable. Given this, we might expect that first-principles molecular dynamics (FPMD) simulations based on DFT could treat more realistic and complex systems using the O(N) technique. However, very few examples of O(N) FPMD simulations exist to date, and information on the accuracy and reliability of the simulations is very limited. In this paper, we show that efficient and robust O(N) FPMD simulations are now possible by the combination of the extended Lagrangian Born-Oppenheimer molecular dynamics method, which was recently proposed by Niklasson ( Phys. Rev. Lett. 2008 , 100 , 123004 ), and the density matrix method as an O(N) technique. Using our linear-scaling DFT code Conquest, we investigate the reliable calculation conditions for accurate O(N) FPMD and demonstrate that we are now able to do practical, reliable self-consistent FPMD simulations of a very large system containing 32768 atoms. PMID:26583225

  4. Large-Scale First-Principles Molecular Dynamics Simulations on the BlueGene/L Platform using the Qbox Code

    SciTech Connect

    Gygi, F; Draeger, E W; de Supinski, B R; Yates, R K; Franchetti, F; Kral, S; Lorenz, J; Ueberhuber, C; Gunnels, J A; Sexton, J C

    2005-04-25

    We demonstrate that the Qbox code supports unprecedented large-scale First-Principles Molecular Dynamics (FPMD) applications on the BlueGene/L supercomputer. Qbox is an FPMD implementation specifically designed for large-scale parallel platforms such as BlueGene/L. Strong scaling tests for a Materials Science application show an 86% scaling efficiency between 1024 and 32,768 CPUs. Measurements of performance by means of hardware counters show that 37% of the peak FPU performance can be attained.

  5. Large-Scale First-Principles Molecular Dynamics Simulations on the BlueGene/L Platform using the Qbox Code

    SciTech Connect

    Gygi, F; Draeger, E; de Supinski, B; Yates, R K; Franchetti, F; Kral, S; Lorenz, J; Ueberhueber, C; Gunnels, J A; Sexton, J

    2006-01-04

    First-Principles Molecular Dynamics (FPMD) is an accurate, atomistic simulation approach that is routinely applied to a variety of areas including solid-state physics, chemistry, biochemistry and nanotechnology. FPMD enables one to perform predictive materials simulations, as no empirical or adjustable parameters are used to describe a given system. Instead, a quantum mechanical description of electrons is obtained by solving the Kohn-Sham equations within a pseudopotential plane-wave formalism. This rigorous first-principles treatment of electronic structure is computationally expensive and limits the size of tractable systems to a few hundred atoms on most currently available parallel computers. Developed specifically for large parallel systems at LLNL's Center for Applied Scientific Computing, the Qbox implementation of the FPMD method shows unprecedented performance and scaling on BlueGene/L.

  6. A Scalable O(N) Algorithm for Large-Scale Parallel First-Principles Molecular Dynamics Simulations

    SciTech Connect

    Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

    2014-01-01

    Traditional algorithms for first-principles molecular dynamics (FPMD) simulations only gain a modest capability increase from current petascale computers, due to their O(N3) complexity and their heavy use of global communications. To address this issue, we are developing a truly scalable O(N) complexity FPMD algorithm, based on density functional theory (DFT), which avoids global communications. The computational model uses a general nonorthogonal orbital formulation for the DFT energy functional, which requires knowledge of selected elements of the inverse of the associated overlap matrix. We present a scalable algorithm for approximately computing selected entries of the inverse of the overlap matrix, based on an approximate inverse technique, by inverting local blocks corresponding to principal submatrices of the global overlap matrix. The new FPMD algorithm exploits sparsity and uses nearest neighbor communication to provide a computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic orbitals are confined, and a cutoff beyond which the entries of the overlap matrix can be omitted when computing selected entries of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to O(100K) atoms on O(100K) processors, with a wall-clock time of O(1) minute per molecular dynamics time step.

  7. First Principles Quantitative Modeling of Molecular Devices

    NASA Astrophysics Data System (ADS)

    Ning, Zhanyu

    In this thesis, we report theoretical investigations of nonlinear and nonequilibrium quantum electronic transport properties of molecular transport junctions from atomistic first principles. The aim is to seek not only qualitative but also quantitative understanding of the corresponding experimental data. At present, the challenges to quantitative theoretical work in molecular electronics include two most important questions: (i) what is the proper atomic model for the experimental devices? (ii) how to accurately determine quantum transport properties without any phenomenological parameters? Our research is centered on these questions. We have systematically calculated atomic structures of the molecular transport junctions by performing total energy structural relaxation using density functional theory (DFT). Our quantum transport calculations were carried out by implementing DFT within the framework of Keldysh non-equilibrium Green's functions (NEGF). The calculated data are directly compared with the corresponding experimental measurements. Our general conclusion is that quantitative comparison with experimental data can be made if the device contacts are correctly determined. We calculated properties of nonequilibrium spin injection from Ni contacts to octane-thiolate films which form a molecular spintronic system. The first principles results allow us to establish a clear physical picture of how spins are injected from the Ni contacts through the Ni-molecule linkage to the molecule, why tunnel magnetoresistance is rapidly reduced by the applied bias in an asymmetric manner, and to what extent ab initio transport theory can make quantitative comparisons to the corresponding experimental data. We found that extremely careful sampling of the two-dimensional Brillouin zone of the Ni surface is crucial for accurate results in such a spintronic system. We investigated the role of contact formation and its resulting structures to quantum transport in several molecular

  8. Towards a Molecular Scale Understanding of Surface Chemistry and Photocatalysis on Metal Oxides: Surface Science Experiments and First Principles Theory

    SciTech Connect

    Diebold, Ulrike

    2015-01-29

    This project has provided an increased understanding of molecular processes and structure-activity relationships in photocatalytic systems. This could ultimately lead to guidelines on how to make TiO2-based photocatalytic systems more efficient. This directly relates to the Program’s mission to develop a mechanistic understanding of chemical reactions that pertain to environmental remediation and pollution control; energy production (photoelectrochemical and production of hydrogen); and novel materials synthesis.

  9. First principles molecular dynamics of molten NaCl

    NASA Astrophysics Data System (ADS)

    Galamba, N.; Costa Cabral, B. J.

    2007-03-01

    First principles Hellmann-Feynman molecular dynamics (HFMD) results for molten NaCl at a single state point are reported. The effect of induction forces on the structure and dynamics of the system is studied by comparison of the partial radial distribution functions and the velocity and force autocorrelation functions with those calculated from classical MD based on rigid-ion and shell-model potentials. The first principles results reproduce the main structural features of the molten salt observed experimentally, whereas they are incorrectly described by both rigid-ion and shell-model potentials. Moreover, HFMD Green-Kubo self-diffusion coefficients are in closer agreement with experimental data than those predicted by classical MD. A comprehensive discussion of MD results for molten NaCl based on different ab initio parametrized polarizable interionic potentials is also given.

  10. First-principles semiclassical initial value representation molecular dynamics.

    PubMed

    Ceotto, Michele; Atahan, Sule; Shim, Sangwoo; Tantardini, Gian Franco; Aspuru-Guzik, Alán

    2009-05-28

    In this work, we explore the use of the semiclassical initial value representation (SC-IVR) method with first-principles electronic structure approaches to carry out classical molecular dynamics. The proposed approach can extract the vibrational power spectrum of carbon dioxide from a single trajectory providing numerical results that agree with experiment and quantum calculations. The computational demands of the method are comparable to those of classical single-trajectory calculations, while describing uniquely quantum features such as the zero-point energy and Fermi resonances. The method can also be used to identify symmetry properties of given vibrational peaks and investigate vibrational couplings by selected classical trajectories. The accuracy of the method degrades for the reproduction of anharmonic shifts for high-energy vibrational levels. PMID:19440613

  11. First principles molecular dynamics without self-consistent field optimization

    SciTech Connect

    Souvatzis, Petros; Niklasson, Anders M. N.

    2014-01-28

    We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations.

  12. First principles molecular dynamics study of filled ice hydrogen hydrate.

    PubMed

    Zhang, Jingyun; Kuo, Jer-Lai; Iitaka, Toshiaki

    2012-08-28

    We investigated structural changes, phase diagram, and vibrational properties of hydrogen hydrate in filled-ice phase C(2) by using first principles molecular dynamics simulation. It was found that the experimentally reported "cubic" structure is unstable at low temperature and/or high pressure: The "cubic" structure reflects the symmetry at high (room) temperature where the hydrogen bond network is disordered and the hydrogen molecules are orientationally disordered due to thermal rotation. In this sense, the "cubic" symmetry would definitely be lowered at low temperature where the hydrogen bond network and the hydrogen molecules are expected to be ordered. At room temperature and below 30 GPa, it is the thermal effects that play an essential role in stabilizing the structure in "cubic" symmetry. Above 60 GPa, the hydrogen bonds in the framework would be symmetrized and the hydrogen bond order-disorder transition would disappear. These results also suggest the phase behavior of other filled-ice hydrates. In the case of rare gas hydrate, there would be no guest molecules' rotation-nonrotation transition since the guest molecules keep their spherical symmetry at any temperature. On the contrary methane hydrate MH-III would show complex transitions due to the lower symmetry of the guest molecule. These results would encourage further experimental studies, especially nuclear magnetic resonance spectroscopy and neutron scattering, on the phases of filled-ice hydrates at high pressures and/or low temperatures. PMID:22938248

  13. First principles molecular dynamics study of filled ice hydrogen hydrate

    NASA Astrophysics Data System (ADS)

    Zhang, Jingyun; Kuo, Jer-Lai; Iitaka, Toshiaki

    2012-08-01

    We investigated structural changes, phase diagram, and vibrational properties of hydrogen hydrate in filled-ice phase C2 by using first principles molecular dynamics simulation. It was found that the experimentally reported "cubic" structure is unstable at low temperature and/or high pressure: The "cubic" structure reflects the symmetry at high (room) temperature where the hydrogen bond network is disordered and the hydrogen molecules are orientationally disordered due to thermal rotation. In this sense, the "cubic" symmetry would definitely be lowered at low temperature where the hydrogen bond network and the hydrogen molecules are expected to be ordered. At room temperature and below 30 GPa, it is the thermal effects that play an essential role in stabilizing the structure in "cubic" symmetry. Above 60 GPa, the hydrogen bonds in the framework would be symmetrized and the hydrogen bond order-disorder transition would disappear. These results also suggest the phase behavior of other filled-ice hydrates. In the case of rare gas hydrate, there would be no guest molecules' rotation-nonrotation transition since the guest molecules keep their spherical symmetry at any temperature. On the contrary methane hydrate MH-III would show complex transitions due to the lower symmetry of the guest molecule. These results would encourage further experimental studies, especially nuclear magnetic resonance spectroscopy and neutron scattering, on the phases of filled-ice hydrates at high pressures and/or low temperatures.

  14. Excited-State Properties of Molecular Solids from First Principles

    NASA Astrophysics Data System (ADS)

    Kronik, Leeor; Neaton, Jeffrey B.

    2016-05-01

    Molecular solids have attracted attention recently in the context of organic (opto)electronics. These materials exhibit unique charge carrier generation and transport phenomena that are distinct from those of conventional semiconductors. Understanding these phenomena is fundamental to optoelectronics and requires a detailed description of the excited-state properties of molecular solids. Recent advances in many-body perturbation theory (MBPT) and density functional theory (DFT) have made such description possible and have revealed many surprising electronic and optical properties of molecular crystals. Here, we review this progress. We summarize the salient aspects of MBPT and DFT as well as various properties that can be described by these methods. These properties include the fundamental gap and its renormalization, hybridization and band dispersion, singlet and triplet excitations, optical spectra, and excitonic properties. For each, we present concrete examples, a comparison to experiments, and a critical discussion.

  15. Excited-State Properties of Molecular Solids from First Principles.

    PubMed

    Kronik, Leeor; Neaton, Jeffrey B

    2016-05-27

    Molecular solids have attracted attention recently in the context of organic (opto)electronics. These materials exhibit unique charge carrier generation and transport phenomena that are distinct from those of conventional semiconductors. Understanding these phenomena is fundamental to optoelectronics and requires a detailed description of the excited-state properties of molecular solids. Recent advances in many-body perturbation theory (MBPT) and density functional theory (DFT) have made such description possible and have revealed many surprising electronic and optical properties of molecular crystals. Here, we review this progress. We summarize the salient aspects of MBPT and DFT as well as various properties that can be described by these methods. These properties include the fundamental gap and its renormalization, hybridization and band dispersion, singlet and triplet excitations, optical spectra, and excitonic properties. For each, we present concrete examples, a comparison to experiments, and a critical discussion. PMID:27090844

  16. Extreme Scale Computing for First-Principles Plasma Physics Research

    SciTech Connect

    Chang, Choogn-Seock

    2011-10-12

    World superpowers are in the middle of the “Computnik” race. US Department of Energy (and National Nuclear Security Administration) wishes to launch exascale computer systems into the scientific (and national security) world by 2018. The objective is to solve important scientific problems and to predict the outcomes using the most fundamental scientific laws, which would not be possible otherwise. Being chosen into the next “frontier” group can be of great benefit to a scientific discipline. An extreme scale computer system requires different types of algorithms and programming philosophy from those we have been accustomed to. Only a handful of scientific codes are blessed to be capable of scalable usage of today’s largest computers in operation at petascale (using more than 100,000 cores concurrently). Fortunately, a few magnetic fusion codes are competing well in this race using the “first principles” gyrokinetic equations.These codes are beginning to study the fusion plasma dynamics in full-scale realistic diverted device geometry in natural nonlinear multiscale, including the large scale neoclassical and small scale turbulence physics, but excluding some ultra fast dynamics. In this talk, most of the above mentioned topics will be introduced at executive level. Representative properties of the extreme scale computers, modern programming exercises to take advantage of them, and different philosophies in the data flows and analyses will be presented. Examples of the multi-scale multi-physics scientific discoveries made possible by solving the gyrokinetic equations on extreme scale computers will be described. Future directions into “virtual tokamak experiments” will also be discussed.

  17. Dithiocarbamate anchoring in molecular wire junctions: a first principles study.

    PubMed

    Li, Zhenyu; Kosov, Daniel S

    2006-05-25

    Recent experimental realization [J. Am. Chem. Soc., 127 (2005) 7328] of various dithiocarbamate self-assembly on gold surface opens the possibility for use of dithiocarbamate linkers to anchor molecular wires to gold electrodes. In this paper, we explore this hypothesis computationally. We computed the electron transport properties of 4,4'-bipyridine (BP), 4,4'-bipyridinium-1,1'-bis(carbodithioate) (BPBC), 4-(4'-pyridyl)-peridium-1-carbodithioate (BPC) molecule junctions based on the density functional theory and nonequilibrium Green's functions. We demonstrated that the stronger molecule-electrode coupling associated with the conjugated dithiocarbamate linker broadens transmission resonances near the Fermi energy. The broadening effect along with the extension of the pi conjugation from the molecule to the gold electrodes lead to enhanced electrical conductance for BPBC molecule. The conductance enhancement factor is as large as 25 at applied voltage bias 1.0 V. Rectification behavior is predicted for BPC molecular wire junction, which has the asymmetric anchoring groups. PMID:16706444

  18. First principles modelling of contact resistance in molecular electronic devices.

    NASA Astrophysics Data System (ADS)

    Stokbro, Kurt; Taylor, Jeremy; Brandbyge, Mads

    2002-03-01

    We have used the TranSIESTA package[1,2] to investigate the contact resistance of gold-thiol bonds. The TranSIESTA package is a new density functional code employing local basis sets[3], combined with a non-equilibrium Greens function transport scheme. With this package we can calculate the selfconsistent electronic structure of a nanostructure coupled to 3-dimensional electrodes with different electrochemical potentials, using the same level of model chemistry for the electrodes as for the nanostructure. We have used the method to calculate the electron transport through DiThiol-Benzene (DTB) connected to gold electrodes. The transport properties have been calculated for a range of different molecule-electrode couplings, and I will discuss the influence of the coupling on the molecular conductance, and compare with experimental data. [1] M. Brandbyge, K. Stokbro, J. Taylor, J. L. Mozos, P. Ordejon, Material Research Society symposium proceedings volume 636, D9.25 (2000). [2] M. Brandbyge, K. Stokbro, J. Taylor, J. L. Mozos, P. Ordejon, Condmat 0110650 [3] SIESTA: D. Sanchez-Portal, P. Ordejon, E. Artacho and J. Soler, Int. J. Quantum Chem. 65, 453 (1997).

  19. Scaling First Principles Materials Science Codes to Thousands of Processors

    NASA Astrophysics Data System (ADS)

    Canning, Andrew; Raczkowski, David

    2004-03-01

    Modern supercomputers have been rapidly increasing in power in large part by using more processors rather than more powerful processors. The most powerful computer in the world at present as listed by www.top500.org is the Earth simulator in Japan (NEC SX6) which has 5120 vector processors and all the top 18 machines on the list have more than 1000 processors. In this talk I will present some novel computational algorithms for scaling up plane-wave based materials science codes to run on these large machines avoiding communication bottlenecks typical of these types of codes. I will present some performance results for some physical systems such as CdSe quantum dots on the IBM SP, Cray X1 and NEC SX6. (This work was supported by the Director, Office of Advanced Scientific Computing Research, Division of Mathematical, Information and Computational Sciences of the U.S. Department of Energy and the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under contract number DE-AC03-76SF00098)

  20. First Principle Molecular Dynamics Study of Melting in Silicon and Germanium

    NASA Astrophysics Data System (ADS)

    Wang, Xiaofei; Scandolo, Sandro; Car, Roberto

    2003-03-01

    We present a scheme to compute the phase diagrams of materials with Density Functional Theory (DFT). Our approach is based on first principle molecular dynamics simulations combined with the scaling algorithm proposed by M. Koning, A. Antonelli and S. Yip. (Phys. Rev. Lett. 83, 3973 (1999)) to improve the efficiency of thermodynamic integration techniques. This approach allows us to compute the free energy of a given material phase over a finite temperature range using a single simulation run. We have applied this scheme to study the melting transition in Silicon and Germanium, using both LDA and GGA approximations of density functional theory. Both approximations give qualitatively similar results. In the Silicon case, the calculated melting temperature is in better agreement with experiment when the GGA approximation is used.

  1. Protein-Protein Interactions from Linear-Scaling First Principles Quantum Mechanical Calculations

    NASA Astrophysics Data System (ADS)

    Cole, Daniel; Skylaris, Chris-Kriton; Rajendra, Eeson; Venkitaraman, Ashok; Payne, Mike

    2010-03-01

    A modification of the MM-PBSA technique for calculating binding affinities of biomolecular complexes is presented. Classical molecular dynamics is used to explore the motion of the extended interface between two peptides derived from the BRC4 repeat of BRCA2 and the eukaryotic recombinase RAD51. The resulting trajectory is sampled using the linear-scaling density functional theory code, onetep, to determine from first principles, and with high computational efficiency, the relative free energies of binding of the ˜2800 atom receptor-ligand complexes. This new method provides the basis for computational interrogation of protein-protein and protein-ligand interactions, within fields ranging from chemical biological studies to small molecule binding behaviour, with both unprecedented chemical accuracy and affordable computational expense.

  2. Protein-protein interactions from linear-scaling first-principles quantum-mechanical calculations

    NASA Astrophysics Data System (ADS)

    Cole, D. J.; Skylaris, C.-K.; Rajendra, E.; Venkitaraman, A. R.; Payne, M. C.

    2010-08-01

    A modification of the MM-PBSA technique for calculating binding affinities of biomolecular complexes is presented. Classical molecular dynamics is used to explore the motion of the extended interface between two peptides derived from the BRC4 repeat of BRCA2 and the eukaryotic recombinase RAD51. The resulting trajectory is sampled using the linear-scaling density functional theory code, onetep, to determine from first principles, and with high computational efficiency, the relative free energies of binding of the ~2800 atom receptor-ligand complexes. This new method provides the basis for computational interrogation of protein-protein and protein-ligand interactions within fields ranging from chemical biological studies to small-molecule binding behaviour, with both unprecedented chemical accuracy and affordable computational expense.

  3. Magnetic materials at finite temperatures: thermodynamics and combined spin and molecular dynamics derived from first principles calculations

    SciTech Connect

    Eisenbach, Markus; Perera, Meewanage Dilina N.; Landau, David P; Nicholson, Don M.; Yin, Junqi; Brown, Greg

    2015-01-01

    We present a unified approach to describe the combined behavior of the atomic and magnetic degrees of freedom in magnetic materials. Using Monte Carlo simulations directly combined with first principles the Curie temperature can be obtained ab initio in good agreement with experimental values. The large scale constrained first principles calculations have been used to construct effective potentials for both the atomic and magnetic degrees of freedom that allow the unified study of influence of phonon-magnon coupling on the thermodynamics and dynamics of magnetic systems. The MC calculations predict the specific heat of iron in near perfect agreement with experimental results from 300K to above Tc and allow the identification of the importance of the magnon-phonon interaction at the phase-transition. Further Molecular Dynamics and Spin Dynamics calculations elucidate the dynamics of this coupling and open the potential for quantitative and predictive descriptions of dynamic structure factors in magnetic materials using first principles-derived simulations.

  4. A method of orbital analysis for large-scale first-principles simulations

    SciTech Connect

    Ohwaki, Tsukuru; Otani, Minoru; Ozaki, Taisuke

    2014-06-28

    An efficient method of calculating the natural bond orbitals (NBOs) based on a truncation of the entire density matrix of a whole system is presented for large-scale density functional theory calculations. The method recovers an orbital picture for O(N) electronic structure methods which directly evaluate the density matrix without using Kohn-Sham orbitals, thus enabling quantitative analysis of chemical reactions in large-scale systems in the language of localized Lewis-type chemical bonds. With the density matrix calculated by either an exact diagonalization or O(N) method, the computational cost is O(1) for the calculation of NBOs associated with a local region where a chemical reaction takes place. As an illustration of the method, we demonstrate how an electronic structure in a local region of interest can be analyzed by NBOs in a large-scale first-principles molecular dynamics simulation for a liquid electrolyte bulk model (propylene carbonate + LiBF{sub 4})

  5. Determination of structure and properties of molecular crystals from first principles.

    PubMed

    Szalewicz, Krzysztof

    2014-11-18

    CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be

  6. High-temperature properties of thorium dioxide: A first-principles molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Nakamura, Hiroki; Machida, Masahiko

    2016-09-01

    Thorium has been considered a potential nuclear fuel for decades. To develop evaluation method for high-temperature properties of thorium dioxide as a candidate nuclear fuel, we perform first-principles molecular dynamics. The calculated enthalpy and thermal expansion agree well with the observed data. The Bredig transition temperature also coincides with experiments. Our results indicate that this method can provide reliable data of thermal properties of nuclear fuels.

  7. Redox condition in molten salts and solute behavior: A first-principles molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Nam, Hyo On; Morgan, Dane

    2015-10-01

    Molten salts technology is of significant interest for nuclear, solar, and other energy systems. In this work, first-principles molecular dynamics (FPMD) was used to model the solute behavior in eutectic LiCl-KCl and FLiBe (Li2BeF4) melts at 773 K and 973 K, respectively. The thermo-kinetic properties for solute systems such as the redox potential, solute diffusion coefficients and structural information surrounding the solute were predicted from FPMD modeling and the calculated properties are generally in agreement with the experiments. In particular, we formulate an approach to model redox energetics vs. chlorine (or fluorine) potential from first-principles approaches. This study develops approaches for, and demonstrates the capabilities of, FPMD to model solute properties in molten salts.

  8. First-Principles Molecular Dynamics Studies of Organometallic Complexes and Homogeneous Catalytic Processes.

    PubMed

    Vidossich, Pietro; Lledós, Agustí; Ujaque, Gregori

    2016-06-21

    Computational chemistry is a valuable aid to complement experimental studies of organometallic systems and their reactivity. It allows probing mechanistic hypotheses and investigating molecular structures, shedding light on the behavior and properties of molecular assemblies at the atomic scale. When approaching a chemical problem, the computational chemist has to decide on the theoretical approach needed to describe electron/nuclear interactions and the composition of the model used to approximate the actual system. Both factors determine the reliability of the modeling study. The community dedicated much effort to developing and improving the performance and accuracy of theoretical approaches for electronic structure calculations, on which the description of (inter)atomic interactions rely. Here, the importance of the model system used in computational studies is highlighted through examples from our recent research focused on organometallic systems and homogeneous catalytic processes. We show how the inclusion of explicit solvent allows the characterization of molecular events that would otherwise not be accessible in reduced model systems (clusters). These include the stabilization of nascent charged fragments via microscopic solvation (notably, hydrogen bonding), transfer of charge (protons) between distant fragments mediated by solvent molecules, and solvent coordination to unsaturated metal centers. Furthermore, when weak interactions are involved, we show how conformational and solvation properties of organometallic complexes are also affected by the explicit inclusion of solvent molecules. Such extended model systems may be treated under periodic boundary conditions, thus removing the cluster/continuum (or vacuum) boundary, and require a statistical mechanics simulation technique to sample the accessible configurational space. First-principles molecular dynamics, in which atomic forces are computed from electronic structure calculations (namely, density

  9. Multiple coherent states for first-principles semiclassical initial value representation molecular dynamics.

    PubMed

    Ceotto, Michele; Atahan, Sule; Tantardini, Gian Franco; Aspuru-Guzik, Alán

    2009-06-21

    A multiple coherent states implementation of the semiclassical approximation is introduced and employed to obtain the power spectra with a few classical trajectories. The method is integrated with the time-averaging semiclassical initial value representation to successfully reproduce anharmonicity and Fermi resonance splittings at a level of accuracy comparable to semiclassical simulations of thousands of trajectories. The method is tested on two different model systems with analytical potentials and implemented in conjunction with the first-principles molecular dynamics scheme to obtain the power spectrum for the carbon dioxide molecule. PMID:19548717

  10. First-Principles Molecular Dynamics Calculations of the Equation of State for Tantalum

    PubMed Central

    Ono, Shigeaki

    2009-01-01

    The equation of state of tantalum (Ta) has been investigated to 100 GPa and 3,000 K using the first-principles molecular dynamics method. A large volume dependence of the thermal pressure of Ta was revealed from the analysis of our data. A significant temperature dependence of the calculated effective Grüneisen parameters was confirmed at high pressures. This indicates that the conventional approach to analyze thermal properties using the Mie-Grüneisen approximation is likely to have a significant uncertainty in determining the equation of state for Ta, and that an intrinsic anharmonicity should be considered to analyze the equation of state. PMID:20057949

  11. Liquid-Liquid Phase Transformation in Silicon: Evidence from First-Principles Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Jakse, N.; Pasturel, A.

    2007-11-01

    We report results of first principles molecular dynamics simulations that confirm early speculations on the presence of liquid-liquid phase transition in undercooled silicon. However, we find that structural and electronic properties of both low-density liquid (LDL) and high-density liquid (HDL) phases are quite different from those obtained by empirical calculations, the difference being more pronounced for the HDL phase. The discrepancy between quantum and classical simulations is attributed to the inability of empirical potentials to describe changes in chemical bonds induced by density and temperature variations.

  12. Spin Crossover in Ferropericlase From First-Principles Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Holmstrom, E.; Stixrude, L. P.

    2013-12-01

    Ferropericlase is believed to be the second-most abundant mineral of the lower mantle of the Earth. It is experimentally known that with increasing pressure, the iron ions in the mineral begin to collapse from a high-spin to low-spin state. This spin crossover looks certain to have geophysical effects, and hence a good theoretical understanding of the phenomenon is necessary. Using first-principles molecular dynamics simulations in conjunction with thermodynamic integration, we construct a phase diagram of the spin crossover as a function of pressure and temperature. In addition, we predict that the mineral loses its electrically insulating character within the lower mantle.

  13. First-principles study of the electronic and molecular structure of protein nanotubes

    NASA Astrophysics Data System (ADS)

    Okamoto, Hajime; Takeda, Kyozaburo; Shiraishi, Kenji

    2001-09-01

    The electronic and molecular structures of protein nanotubes (PNT's) have been investigated theoretically by first-principles electronic structure calculations. The results have been discussed in comparison to those of the polypeptide open chains (POC's) and polypeptide closed rings (PCR's) in order to give a systematic understanding. Focusing on the intra-ring and inter-ring hydrogen bonds (HB's), we also investigate the PCR stacking mechanism. The present calculation reveals that PNT's are semiconductors and that an extra proton in the tube interior has the potential to be an electron acceptor.

  14. Crystalline and liquid Si3 N4 characterization by first-principles molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Mauri, Aurelio; Celino, Massimo; Castellani, Niccoló; Erbetta, Davide

    2011-05-01

    Silicon nitride (Si3 N4) has a wide range of engineering applications where its mechanical and electronic properties can be effectively exploited. In particular, in the microelectronics field, the amorphous silicon nitride films are widely used as charge storage layer in metal-alumina-nitrideoxide nonvolatile memory devices. Atomic structure of amorphous silicon nitride is characterized by an high concentration of traps that control the electric behavior of the final device by the trappingde-trapping mechanism of the electrical charge occurring in its traps. In order to have a deep understanding of the material properties and, in particular, the nature of the electrical active traps a detailed numerical characterization of the crystalline and liquid phases is mandatory. For these reasons first-principles molecular dynamics simulations are extensively employed to simulate the crystalline Si3 N4 in its crystalline and liquid phases. Good agreement with experimental results is obtained in terms of density and formation entalpy. Detailed characterization of c-Si3 N4 electronic properties is performed in terms of band structure and band gap. Then constant temperature and constant volume first-principles molecular dynamics is used to disorder a stoichiometric sample of Si3 N4 . Extensive molecular dynamics simulations are performed to obtain a reliable liquid sample whose atomic structure does not depend on the starting atomic configuration. Detailed characterization of the atomic structure is achieved in terms of radial distribution functions and total structure factor.

  15. Charge and spin transport in single and packed ruthenium-terpyridine molecular devices: Insight from first-principles calculations

    PubMed Central

    Morari, C.; Buimaga-Iarinca, L.; Rungger, I.; Sanvito, S.; Melinte, S.; Rignanese, G.-M.

    2016-01-01

    Using first-principles calculations, we study the electronic and transport properties of rutheniumterpyridine molecules sandwiched between two Au(111) electrodes. We analyse both single and packed molecular devices, more amenable to scaling and realistic integration approaches. The devices display all together robust negative differential resistance features at low bias voltages. Remarkably, the electrical control of the spin transport in the studied systems implies a subtle distribution of the magnetisation density within the biased devices and highlights the key role of the Au(111) electrical contacts. PMID:27550064

  16. Charge and spin transport in single and packed ruthenium-terpyridine molecular devices: Insight from first-principles calculations.

    PubMed

    Morari, C; Buimaga-Iarinca, L; Rungger, I; Sanvito, S; Melinte, S; Rignanese, G-M

    2016-01-01

    Using first-principles calculations, we study the electronic and transport properties of rutheniumterpyridine molecules sandwiched between two Au(111) electrodes. We analyse both single and packed molecular devices, more amenable to scaling and realistic integration approaches. The devices display all together robust negative differential resistance features at low bias voltages. Remarkably, the electrical control of the spin transport in the studied systems implies a subtle distribution of the magnetisation density within the biased devices and highlights the key role of the Au(111) electrical contacts. PMID:27550064

  17. Mechanisms of molecular doping of graphene: A first-principles study

    NASA Astrophysics Data System (ADS)

    Saha, Srijan Kumar; Chandrakanth, Reddy Ch.; Krishnamurthy, H. R.; Waghmare, U. V.

    2009-10-01

    Doping graphene with electron donating or accepting molecules is an interesting approach to introduce carriers into it, analogous to electrochemical doping accomplished in graphene when used in a field-effect transistor. Here, we use first-principles density-functional theory to determine changes in the electronic-structure and vibrational properties of graphene that arise from the adsorption of aromatic molecules such as aniline and nitrobenzene. Identifying the roles of various mechanisms of chemical interaction between graphene and a molecule, we bring out the contrast between electrochemical and molecular doping of graphene. Our estimates of various contributions to shifts in the Raman-active modes of graphene with molecular doping are fundamental to the possible use of Raman spectroscopy in (a) characterization of the nature and concentration of carriers in graphene with molecular doping, and (b) graphene-based chemical sensors.

  18. First-Principle Molecular Dynamics of Sliding Diamond Surfaces: Tribochemical Reactions with Water and Load Effects

    NASA Astrophysics Data System (ADS)

    Righi, Maria Clelia; Zilibotti, Giovanna; Corni, Stefano; Ferrario, Mauro; Bertoni, Carlo Maria

    2016-05-01

    Ab initio molecular dynamics offers an unexpected tool to understand many aspects of complex and macroscopic phenomena, like friction, lubrication, and surface passivation through chemical reactions induced by load and confinement, as found in recent works (Zilibotti et al., in Phys. Rev. Lett. 111:146101, 2013; De Barros Bouchet et al., J Phys Chem C 116:6966, 2012). Here we review the results of first-principle molecular dynamics simulations of diamond interfaces interacting with water molecules, at different concentrations. We found that the molecular confinement induced by the applied load promotes water dissociation. The consequent surface passivation prevents the formation of carbon bonds across the interface, reducing adhesion and friction. The possibility to extend the use of an atomistic approach to understand the kinetics of tribochemical reactions and their effects on friction will also be discussed.

  19. Terahertz spectra of biotin based on first principle, molecular mechanical, and hybrid simulations.

    PubMed

    Bykhovski, Alexei; Woolard, Dwight

    2013-07-01

    Terahertz (THz) absorption of biotin was simulated using the first principle and the density functional theory (DFT) both in the harmonic approximation and with corrections for the anharmonicity. Anharmonicity corrections were calculated using two different approaches. First, the perturbation theory-based first principle calculations were performed to include third- and fourth-order anharmonicity corrections in atomic displacements to harmonic vibrational states. Second, the atom-centered density matrix propagation molecular dynamics model that provides a good energy conservation was used to calculate the atomic trajectories, velocities, and a dipole moment time history of biotin at low and room temperatures. Predicted low-THz lines agree well with the experimental spectra. The influence of the polyethylene (PE) matrix embedment on the THz spectra of biotin at the nanoscale was studied using the developed hybrid DFT/molecular mechanical approach. While PE is almost transparent at THz frequencies, additional low-THz lines are predicted in the biotin/PE system, which reflects a dynamic interaction between biotin and a surrounding PE cavity. PMID:25055303

  20. Three-dimensional diffusion of molecular hydrogen in graphdiyne: a first-principles study

    NASA Astrophysics Data System (ADS)

    Zhang, Hongyu; Zhao, Xiaoyang; Zhang, Meng; Luo, Youhua; Li, Guihua; Zhao, Mingwen

    2013-12-01

    First-principles calculations with van der Waals correction included are carried out to investigate the intercalation and diffusion of molecular hydrogen in single-layer and bulk graphdiyne, which is crucial for understanding and improving the hydrogen storage capacity of graphdiyne. Different intercalation sites and hydrogen molecular orientations have been considered and compared. It is found that configurations with the axis of the hydrogen molecule parallel to graphdiyne layers are favoured. In contrast to graphite where hydrogen diffusion is restricted within the interlayer space, the unique porous structure of graphdiyne enables three-dimensional diffusion of hydrogen (in-plane diffusion and out-plane diffusion) with moderate energy barriers, thus ensuring easy hydrogen loading and unloading. The in-plane diffusion barriers largely depend on the interlayer distance, whereas the interlayer spacing has little effect on the out-plane diffusion barriers. This experimentally available novel carbon allotrope is expected to find applications in hydrogen storage.

  1. Tuning the electron transport of molecular junctions by chemically functionalizing anchoring groups: First-principles study

    NASA Astrophysics Data System (ADS)

    Tsukamoto, Shigeru; Caciuc, Vasile; Atodiresei, Nicolae; Blügel, Stefan

    2012-06-01

    In this first-principles study, we present density-functional calculations of the electronic structures and electron transport properties of organic molecular junctions with several anchoring groups containing atoms with different electronegativities, i.e., benzenediboronate (BDB), benzenedicarboxylate (BDC), and dinitrobenzene (DNB) molecular junctions sandwiched between two Cu(110) electrodes. The electronic-structure calculations exhibit a significant difference in the density of states not only at the anchoring groups but also at the aromatic rings of the molecular junctions, suggesting that the electron transport is specific for each system. Our transport calculations show that the BDB and DNB molecular junctions have finite electron transmissions at the zero-bias limit while the BDC molecular junction has a negligible electron transmission. Moreover, for the BDB and DNB systems, the electron transmission channels around the Fermi energy reveal fingerprint features, which provide specific functionalities for the molecular junctions. Therefore, our theoretical results demonstrate the possibility to precisely tune the electron transport properties of molecular junctions by engineering the anchoring groups at the single-atom level.

  2. Rotation of water molecules in plastic phase at extreme conditions from first principles molecular dynamics method

    NASA Astrophysics Data System (ADS)

    Tasaka, Tomofumi; Tsumuraya, Kazuo

    2014-03-01

    Water has a variety of polymorphs in wide ranges of temperature and pressure. Ice VII phase transforms to ice X with increased pressure. However the ice VII transforms to a superionic phase at higher temperatures around 2000K and pressure 30GPa in which the protons migrate in the body centered cubic lattice of oxygens. The ice VII transforms into rotator phase (so called plastic phase at lower temperatures around 600K and 5 to 50GPa. The formation of the phase has been confirmed only with the empirical potentials, whereas the experimental confirmation has been postponed until now. The present study elucidates the mechanism of the rotation of the water molecules and the correlation between the molecules during the rotation with the first principles molecular dynamics method. The water molecules rotate around each oxygen atom to conserve the ice VII positions of the protons.

  3. First Principles Molecular Modeling of Sensing Material Selection for Hybrid Biomimetic Nanosensors

    NASA Astrophysics Data System (ADS)

    Blanco, Mario; McAlpine, Michael C.; Heath, James R.

    Hybrid biomimetic nanosensors use selective polymeric and biological materials that integrate flexible recognition moieties with nanometer size transducers. These sensors have the potential to offer the building blocks for a universal sensing platform. Their vast range of chemistries and high conformational flexibility present both a problem and an opportunity. Nonetheless, it has been shown that oligopeptide aptamers from sequenced genes can be robust substrates for the selective recognition of specific chemical species. Here we present first principles molecular modeling approaches tailored to peptide sequences suitable for the selective discrimination of small molecules on nanowire arrays. The modeling strategy is fully atomistic. The excellent performance of these sensors, their potential biocompatibility combined with advanced mechanistic modeling studies, could potentially lead to applications such as: unobtrusive implantable medical sensors for disease diagnostics, light weight multi-purpose sensing devices for aerospace applications, ubiquitous environmental monitoring devices in urban and rural areas, and inexpensive smart packaging materials for active in-situ food safety labeling.

  4. Spin crossover in ferropericlase from first-principles molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Holmstrom, Eero; Stixrude, Lars

    2014-05-01

    Ferropericlase is the second-most abundant mineral of the lower mantle of the Earth. It is experimentally known that with increasing pressure, the iron ions in the mineral begin to collapse from a high-spin to low-spin state. This spin crossover alters various properties of the material, and hence a good theoretical understanding of the phenomenon is necessary. Using first-principles molecular dynamics simulations in conjunction with thermodynamic integration, we construct a phase diagram of the spin crossover as a function of pressure and temperature. In addition, we present the thermal equation of state of the mineral up to 140 GPa and 4000 K, and predict that the electrical conductivity of ferropericlase reaches semi-metallic values within the lower mantle.

  5. First principles molecular dynamics study of nitrogen vacancy complexes in boronitrene.

    PubMed

    Ukpong, A M; Chetty, N

    2012-07-01

    We present the results of first principles molecular dynamics simulations of nitrogen vacancy complexes in monolayer hexagonal boron nitride. The threshold for local structure reconstruction is found to be sensitive to the presence of a substitutional carbon impurity. We show that activated nitrogen dynamics triggers the annihilation of defects in the layer through formation of Stone-Wales-type structures. The lowest energy state of nitrogen vacancy complexes is negatively charged and spin polarized. Using the divacancy complex, we show that their formation induces spontaneous magnetic moments, which is tunable by electron or hole injection. The Fermi level s-resonant defect state is identified as a unique signature of the ground state of the divacancy complex. Due to their ability to enhance structural cohesion, only the divacancy and the nitrogen vacancy carbon-antisite complexes are able to suppress the Fermi level resonant defect state to open a gap between the conduction and valence bands. PMID:22677800

  6. Accurate and Scalable O(N) Algorithm for First-Principles Molecular-Dynamics Computations on Large Parallel Computers

    SciTech Connect

    Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

    2014-01-01

    We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7x10-4 Ha/Bohr.

  7. Accurate and Scalable O(N) Algorithm for First-Principles Molecular-Dynamics Computations on Large Parallel Computers

    NASA Astrophysics Data System (ADS)

    Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

    2014-01-01

    We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7×10-4 Ha/Bohr.

  8. A First Principles Molecular Dynamics Study Of Calcium Ion In Water

    SciTech Connect

    Lightstone, F; Schwegler, E; Allesch, M; Gygi, F; Galli, G

    2005-01-28

    In this work we report on Car-Parrinello simulations of the divalent calcium ion in water, aimed at understanding the structure of the hydration shell and at comparing theoretical results with a series of recent experiments. Our paper shows some of the progress in the investigation of aqueous solutions brought about by the advent of ab initio molecular dynamics and highlights the importance of accessing subtle details of ion-water interactions from first-principles. Calcium plays a vital role in many biological systems, including signal transduction, blood clotting and cell division. In particular, calcium ions are known to interact strongly with proteins as they tend to bind well to both negatively charged (e.g. in aspartate and glutamate) and uncharged oxygens (e.g. in main-chain carbonyls). The ability of calcium to coordinate multiple ligands (from 6 to 8 oxygen atoms) with an asymmetric coordination shell enables it to cross-link different segments of a protein and induce large conformational changes. The great biochemical importance of the calcium ion has led to a number of studies to determine its hydration shell and its preferred coordination number in water. Experimental studies have used a variety of techniques, including XRD, EXAFS, and neutron diffraction to elucidate the coordination of Ca{sup 2+} in water. The range of coordination numbers (n{sub C}) inferred by X-ray diffraction studies varies from 6 to 8, and is consistent with that reported in EXAFS experiments (8 and 7.2). A wider range of values (6 to 10) was found in early neutron diffraction studies, depending on concentration, while a more recent measurement by Badyal, et al. reports a value close to 7. In addition to experimental measurements, many theoretical studies have been carried out to investigate the solvation of Ca{sup 2+} in water and have also reported a wide range of coordination numbers. Most of the classical molecular dynamics (MD) and QM/MM simulations report n{sub C} in the

  9. Electronic stopping in liquid water from first principles: An application of large-scale real-time TDDFT simulations

    NASA Astrophysics Data System (ADS)

    Reeves, Kyle; Yao, Yi; Kanai, Yosuke

    Electronic stopping describes the transfer of energy from a highly-energetic charged particle to electrons in a material. This process induces massive electronic excitations via interaction between the material and the highly localized electric field from the charged particle. Understanding this phenomenon in condensed matter systems under proton irradiation has implications in various modern technologies. First-principles simulations, based on our recently-developed large-scale real-time time-dependent density functional theory approach, provide a detailed description of how electrons are excited via a non-equilibrium energy transfer from protons on the attosecond time scale. We apply this computational approach to the important case of liquid water under proton irradiation. Our work reveals several key features of the excitation dynamics at the mesoscopic and molecular levels which support a clearer understanding of the water radiolysis mechanism under proton irradiation. Importantly, we will demonstrate a first-principles determination of the energy transfer rate, (i.e. electronic stopping power) in liquid water, and a comparison to existing empirical models will be presented. We will conclude by discussing how the exchange-correlation approximation influences the calculation of the electronic stopping power.

  10. First-principles quantum simulations of dissociation of molecular condensates: Atom correlations in momentum space

    SciTech Connect

    Savage, C. M.; Schwenn, P. E.; Kheruntsyan, K. V.

    2006-09-15

    We investigate the quantum many-body dynamics of dissociation of a Bose-Einstein condensate of molecular dimers into pairs of constituent bosonic atoms and analyze the resulting atom-atom correlations. The quantum fields of both the molecules and atoms are simulated from first principles in three dimensions using the positive-P representation method. This allows us to provide an exact treatment of the molecular field depletion and s-wave scattering interactions between the particles, as well as to extend the analysis to nonuniform systems. In the simplest uniform case, we find that the major source of atom-atom decorrelation is atom-atom recombination which produces molecules outside the initially occupied condensate mode. The unwanted molecules are formed from dissociated atom pairs with nonopposite momenta. The net effect of this process--which becomes increasingly significant for dissociation durations corresponding to more than about 40% conversion--is to reduce the atom-atom correlations. In addition, for nonuniform systems we find that mode mixing due to inhomogeneity can result in further degradation of the correlation signal. We characterize the correlation strength via the degree of squeezing of particle number-difference fluctuations in a certain momentum-space volume and show that the correlation strength can be increased if the signals are binned into larger counting volumes.

  11. First principle molecular dynamics simulation of hydrous modal basalt melt structure

    NASA Astrophysics Data System (ADS)

    Karki, B. B.; Bajgain, S. K.

    2012-12-01

    We have performed the first principle molecular dynamics simulation of hydrous model basalt to investigate its structural properties over wide ranges of pressure (0-100 GPa) and temperature (2200-6000 K) ranges. Our initial results show that all partial radial distribution functions represent well-defined peaks with decreased amplitudes compared to those in pure basalt liquid. The mean Si-O (Al-O) coordination number at the reference volume of 3422.47 Å3 is ~ 3.9 (4.8) at the ambient pressure and 3000 K. The coordination increases with increasing pressure but varies only a little with temperature though the abundances of various coordination species are highly sensitive to both pressure and temperature. We find that isolated structures of water component dominate in lower pressure, which consists of hydroxyl, water molecule, O-H-O bridging, and four-atom (O-H-O-H and H-O-H-O) groups. At higher pressures, extended structures (five or more O and H atoms) are formed. The effects of water on melt depolymerization, compressibility and dynamical properties will also be examined.

  12. Coupled molecular-dynamics and first-principle transport calculations of metal/oxide/metal heterostructures

    NASA Astrophysics Data System (ADS)

    Zapol, Peter; Karpeyev, Dmitry; Maheshwari, Ketan; Zhong, Xiaoliang; Narayanan, Badri; Sankaranarayanan, Subramanian; Wilde, Michael; Heinonen, Olle; Rungger, Ivan

    2015-03-01

    The electronic conduction in Hf-oxide heterostructures for use in, e.g., resistive switching devices, depends sensitively on local oxygen stoichiometry and interactions at interfaces with metal electrodes. In order to model the electronic structure of different disordered configurations near interfaces, we have combined molecular dynamics (MD) simulations with first-principle based non-equilibrium Green's functions (NEGF) methods, including self-interaction corrections. We have developed an approach to generating automated workflows that combine MD and NEGF computations over many parameter values using the Swift parallel scripting language. A sequence of software tools transforms the result of one calculation into the input of the next allowing for a high-throughput concurrent parameter sweep. MD simulations generate systems with quenched disorder, which are then directly fed to NEGF and on to postprocessing. Different computations can be run on different computer platforms matching the computational load to the hardware resources. We will demonstrate results for metal-HfO2-metal heterostructures obtained using this workflow. Argonne National Laboratory's work was supported under U.S. Department of Energy Contract DE-AC02-06CH11357.

  13. First-principles molecular dynamics of liquid alkali metals based on the quantal hypernetted chain theory

    NASA Astrophysics Data System (ADS)

    Kambayashi, Shaw; Chihara, Junzo

    1996-06-01

    A first-principles molecular dynamics (MD) scheme is presented on the basis of the density-functional (DF) theory with use of the the quantal hypernetted chain (QHNC) approximation. The DF theory brings about exact expressions for the ion-electron and ion-ion radial distribution functions (RDF) of an electron-ion mixture as a model of a simple liquid metal. These exact expressions prove that an ion-electron mixture can be treated as a one-component liquid interacting only via a pairwise interaction in the evaluation of the ion-ion RDF, and provide a set of integral equations: one is an exact integral equation for the ion-ion RDF and another for an effective ion-ion interaction, which depends on the ion configuration specified by the ion-ion RDF. Hence, after some approximations are introduced, the MD simulation can be performed to get the ion-ion RDF using the ion-ion interaction determined so as to be consistent to the ion-ion RDF: the MD simulation and the procedure to determine the effective interaction from the QHNC equation are performed iteratively. This MD simulation coupled with the QHNC equation (QHNC-MD method) for the effective interaction provides a first-principles calculation of structures of simple liquid metal: the ion-ion and electron-ion RDF's, the charge distributions of an ion and a pseudoatom, the effective ion-ion interaction and the ion-ion bridge function are evaluated in a self-consistent manner from the atomic number as the only input. We have applied this QHNC-MD method to Li, Na, K, Rb, and Cs near the melting temperature using up to 16 000 particles for the MD simulation. It is found that the convergence of the effective ion-ion interaction is fast enough for practical application to alkali metals; two MD runs are enough for convergence within accuracy of 3 to 4 digits, if the initial effective potential is properly set up. The structure factors, thus obtained, show excellent agreement with the experimental data observed by x-ray and

  14. Current rectification by self-assembled molecular quantum dots from first principles

    NASA Astrophysics Data System (ADS)

    Larade, Brian; Bratkovsky, Alexander

    2003-03-01

    We present results of first-principles calculations of the current rectification by self-assembled molecular quantum dots. Molecules of that kind should be synthesized with a central conjugated (narrow band-gap) part, and two peripheral saturated (wide band-gap) barrier groups of substantially different lengths L1 and L_2. The peripheral groups must end with chemical Â"anchorÂ" groups, enabling attachment of the molecule to the electrodes. In such molecules, if they are not longer than about 2-3 nm, the electron transport is likely to proceed by resonant tunneling through molecular orbitals (MO) centered on the conjugated part of the molecule (Â"quantum dotÂ") [1,2]. Generally, either LUMO (lowest unoccupied MO) or HOMO (highest occupied MO) will be most transparent to the tunneling electrons because of their different coupling to electrodes. We have studied (i) single benzene ring C6H6 [2] and (ii) naphthalene C10H8, separated from gold electrodes by alkane chains of different lengths with the use of the non-equilibrium Green's function method and self-consistent density-functional theory. The results show significant changes in electron density and potential distribution in the vicinity of molecule-electrode contact. In the case of a naphthalene quantum dot, separated from electrodes by asymmetric alkane groups (CH2)2 and (CH2)6, the I-V curve shows current rectification on the order of ˜ 10^2. [1] A.M. Bratkovsky and P.E. Kornilovitch, Phys. Rev. B (2002), to be published. [2] P. E. Kornilovitch, A.M. Bratkovsky, and R.S. Williams, Phys. Rev. B 66, 165436 (2002).

  15. Electrostatic embedding in large-scale first principles quantum mechanical calculations on biomolecules.

    PubMed

    Fox, Stephen J; Pittock, Chris; Fox, Thomas; Tautermann, Christofer S; Malcolm, Noj; Skylaris, Chris-Kriton

    2011-12-14

    Biomolecular simulations with atomistic detail are often required to describe interactions with chemical accuracy for applications such as the calculation of free energies of binding or chemical reactions in enzymes. Force fields are typically used for this task but these rely on extensive parameterisation which in cases can lead to limited accuracy and transferability, for example for ligands with unusual functional groups. These limitations can be overcome with first principles calculations with methods such as density functional theory (DFT) but at a much higher computational cost. The use of electrostatic embedding can significantly reduce this cost by representing a portion of the simulated system in terms of highly localised charge distributions. These classical charge distributions are electrostatically coupled with the quantum system and represent the effect of the environment in which the quantum system is embedded. In this paper we describe and evaluate such an embedding scheme in which the polarisation of the electronic density by the embedding charges occurs self-consistently during the calculation of the density. We have implemented this scheme in a linear-scaling DFT program as our aim is to treat with DFT entire biomolecules (such as proteins) and large portions of the solvent. We test this approach in the calculation of interaction energies of ligands with biomolecules and solvent and investigate under what conditions these can be obtained with the same level of accuracy as when the entire system is described by DFT, for a variety of neutral and charged species. PMID:22168680

  16. An accurate and scalable O(N) algorithm for First-Principles Molecular Dynamics computations on petascale computers and beyond

    NASA Astrophysics Data System (ADS)

    Osei-Kuffuor, Daniel; Fattebert, Jean-Luc

    2014-03-01

    We present a truly scalable First-Principles Molecular Dynamics algorithm with O(N) complexity and fully controllable accuracy, capable of simulating systems of sizes that were previously impossible with this degree of accuracy. By avoiding global communication, we have extended W. Kohn's condensed matter ``nearsightedness'' principle to a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wavefunctions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 100,000 atoms on 100,000 processors, with a wall-clock time of the order of one minute per molecular dynamics time step. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  17. First Principles Study of Double Photoionization of H2 UsingExterior Complex Scaling

    SciTech Connect

    Rescigno, Thomas N.; Vanroose, Wim; Horner, Daniel A.; Martin,Fernando; McCurdy, C. William

    2006-07-21

    Exterior complex scaling provides a practical path forfirst-principles studies of atomic and molecular ionizationproblemssince it avoids explicit enforcement of asymptotic boundary conditionsfor 3-body Coulomb breakup. We have used the method of exterior complexscaling, implemented with both the discrete variable representation andB-splines, to obtain the first-order wave function for molecular hydrogencorresponding to a single photon having been absorbed by a correlatedinitial state. These wave functions are used to construct convergedtriple differential cross sections for double photoionization of alignedH2 molecules.

  18. Stiffness of Diphenylalanine-Based Molecular Solids from First Principles Calculations

    NASA Astrophysics Data System (ADS)

    Azuri, Ido; Hod, Oded; Gazit, Ehud; Kronik, Leeor

    2013-03-01

    Diphenylalanine-based peptide nanotubes were found to be unexpectedly stiff, with a Young modulus of 19 GPa. Here, we calculate the Young modulus from first principles, using density functional theory with dispersive corrections. This allows us to show that at least half of the stiffness of the material comes from dispersive interactions and to identify the nature of the interactions that contribute most to the stiffness. This presents a general strategy for the analysis of bioinspired functional materials.

  19. Molecular adsorption study of nicotine and caffeine on single-walled carbon nanotubes from first principles

    NASA Astrophysics Data System (ADS)

    Lee, Hyung-June; Kim, Gunn; Kwon, Young-Kyun

    2013-08-01

    Using first-principles calculations, we investigate the electronic structures and binding properties of nicotine and caffeine adsorbed on single-walled carbon nanotubes to determine whether CNTs are appropriate for filtering or sensing nicotine and caffeine molecules. We find that caffeine adsorbs more strongly than nicotine. The different binding characteristics are discussed by analyzing the modification of the electronic structure of the molecule-adsorbed CNTs. We also calculate the quantum conductance of the CNTs in the presence of nicotine or caffeine adsorbates and demonstrate that the influence of caffeine is stronger than nicotine on the conductance of the host CNT.

  20. First principles investigations of electronic structure and transport properties of graphitic structures and single molecular junctions

    NASA Astrophysics Data System (ADS)

    Owens, Jonathan R.

    In this work, we first present two powerful methods for understanding the electronic, structural, conducting, and energetic properties of nano-materials: density functional theory (DFT) and quantum transport. The basics of the theory and background of both methods are discussed thoroughly. After establishing a firm foundation, we turn our attention to using these tools to solve practical problems, often in collaboration with experimental colleagues. The first two projects pertain to nitrogen doping in graphene nanoribbons (GNRs). We study nitrogen doping in two different schema: concentration-based (N_x-doped) and structural based (N_2. {AA}-doped). Concentration based doping is explored in the context of experimental measurements of IV curves on GNRs with differing dopant concentrations. These results show a shift towards semi-conducting behavior with an increase in dopant concentration. We combine first principles calculations (DFT) and transport calculations in the Landauer formalism to compute the density-of-states (DOS) and transport curves for various dopant concentrations (0.46%, 1.39%, 1.89%, and 2.31%), which corroborate the experimental observations. The N_2. {AA}-doped GNR study was inspired by experimental observation of an atomically precise nitrogen doping scheme in bulk graphene. Experimental STM images, combined with simulated STM images, revealed that the majority (80%) of doping sites consist of nitrogen atoms on neighboring sites of the same sublattice (A) in graphene, hence N_2. {AA} doping. We examine this doping scheme applied to zigzag and armchair GNRs under different orientations of the dopants. We present spin-resolved charge densities, energetics, transport, DOS, and simulated STM images for all four systems studied. Our results show the possibility of spin-filtered devices and the STM images provide an aid in helping experimentalist identify the dopant patterns, if these GNRs are fabricated. We next venture to explain different observed

  1. First principles investigations of electronic structure and transport properties of graphitic structures and single molecular junctions

    NASA Astrophysics Data System (ADS)

    Owens, Jonathan R.

    In this work, we first present two powerful methods for understanding the electronic, structural, conducting, and energetic properties of nano-materials: density functional theory (DFT) and quantum transport. The basics of the theory and background of both methods are discussed thoroughly. After establishing a firm foundation, we turn our attention to using these tools to solve practical problems, often in collaboration with experimental colleagues. The first two projects pertain to nitrogen doping in graphene nanoribbons (GNRs). We study nitrogen doping in two different schema: concentration-based (N_x-doped) and structural based (N_2. {AA}-doped). Concentration based doping is explored in the context of experimental measurements of IV curves on GNRs with differing dopant concentrations. These results show a shift towards semi-conducting behavior with an increase in dopant concentration. We combine first principles calculations (DFT) and transport calculations in the Landauer formalism to compute the density-of-states (DOS) and transport curves for various dopant concentrations (0.46%, 1.39%, 1.89%, and 2.31%), which corroborate the experimental observations. The N_2. {AA}-doped GNR study was inspired by experimental observation of an atomically precise nitrogen doping scheme in bulk graphene. Experimental STM images, combined with simulated STM images, revealed that the majority (80%) of doping sites consist of nitrogen atoms on neighboring sites of the same sublattice (A) in graphene, hence N_2. {AA} doping. We examine this doping scheme applied to zigzag and armchair GNRs under different orientations of the dopants. We present spin-resolved charge densities, energetics, transport, DOS, and simulated STM images for all four systems studied. Our results show the possibility of spin-filtered devices and the STM images provide an aid in helping experimentalist identify the dopant patterns, if these GNRs are fabricated. We next venture to explain different observed

  2. A unified electrostatic and cavitation model for first-principles molecular dynamics in solution

    NASA Astrophysics Data System (ADS)

    Scherlis, Damián A.; Fattebert, Jean-Luc; Gygi, François; Cococcioni, Matteo; Marzari, Nicola

    2006-02-01

    The electrostatic continuum solvent model developed by [Fattebert and Gygi J. Comput. Chem. 23, 662 (2002); Int. J. Quantum Chem. 93, 139 (2003)] is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. Our model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. We apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon.

  3. A unified electrostatic and cavitation model for first-principles molecular dynamics in solution

    SciTech Connect

    Scherlis, D A; Fattebert, J; Gygi, F; Cococcioni, M; Marzari, N

    2005-11-14

    The electrostatic continuum solvent model developed by Fattebert and Gygi is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. The model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution, and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. They apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon.

  4. A first principle particle mesh method for solution SAXS of large bio-molecular systems

    NASA Astrophysics Data System (ADS)

    Marchi, Massimo

    2016-07-01

    This paper will show that the solution small angle X-ray scattering (SAXS) intensity of globular and membrane proteins can be efficiently and accurately computed from molecular dynamics trajectories using 3D fast Fourier transforms (FFTs). A suitable particle meshing interpolation, similar to the one used in smooth particle mesh Ewald for electrostatic energies and forces, was combined with a uniform solvent density FFT padding scheme to obtain a convenient SAXS spectral resolution. The CPU time scaling of the method, as a function of system size, is highly favorable and its application to large systems such as solutions of solvated membrane proteins is computationally undemanding. Differently from other approaches, all contributions from the simulation cell are included. This means that the subtraction of the buffer from the solution scattering intensity is straightforward and devoid of artifact due to ad hoc definitions of proximal and distal solvent intensity contributions.

  5. A first principle particle mesh method for solution SAXS of large bio-molecular systems.

    PubMed

    Marchi, Massimo

    2016-07-28

    This paper will show that the solution small angle X-ray scattering (SAXS) intensity of globular and membrane proteins can be efficiently and accurately computed from molecular dynamics trajectories using 3D fast Fourier transforms (FFTs). A suitable particle meshing interpolation, similar to the one used in smooth particle mesh Ewald for electrostatic energies and forces, was combined with a uniform solvent density FFT padding scheme to obtain a convenient SAXS spectral resolution. The CPU time scaling of the method, as a function of system size, is highly favorable and its application to large systems such as solutions of solvated membrane proteins is computationally undemanding. Differently from other approaches, all contributions from the simulation cell are included. This means that the subtraction of the buffer from the solution scattering intensity is straightforward and devoid of artifact due to ad hoc definitions of proximal and distal solvent intensity contributions. PMID:27475396

  6. Liquid-Liquid Phase Transitions of Phosphorus via Constant-Pressure First-Principles Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Morishita, Tetsuya

    2001-09-01

    Pressure-induced phase transitions in liquid phosphorus have been studied by constant-pressure first-principles molecular dynamics simulations. By compressing a low-pressure liquid which consists of the tetrahedral P4 molecules, a structural phase transition from the molecular to polymeric liquid (a high-pressure phase) observed in the recent experiment by Katayama et al. [Nature (London) 403, 170 (2000)] was successfully realized. It is found that this transition is caused by a breakup of the tetrahedral molecules with large volume contraction. The same transition is also realized by heating. This indicates that only the polymeric liquid can stably exist at high temperature.

  7. First Principles Investigation of the C3 Coefficients for Molecular Adsorption on Transition Metal Surfaces

    NASA Astrophysics Data System (ADS)

    Kara, Abdelkader; Matos, Jeronimo; Yildirim, Handan

    2015-03-01

    C6 coefficients are used to investigate the strength of the long-range interactions for weakly interacting dimers as a function of separation distance. These coefficients are useful both as a measure for the accuracy of the various van der Waals (vdW) inclusive methods as well as reference for use in large-scale molecular dynamics simulations. In the case of molecule-surface interaction, the C3 coefficient is the counterpart to the C6 coefficient that is used for testing the interaction of dimers. We will present the results of the vdW inclusive density functional theory (DFT) calculations evaluating the C3 coefficients for the adsorption of M/X(110) and X(111), with X: Ag, Au, Cu, Pt, Pd, Ni, Rh and M: Benzene, Thiophene, Sexithiophene, Pentacene and Olympicene, as described by the PBE exchange-correlation functional and the self-consistent vdW-DF, optimized vdW-DFs and vdW-DF2 functionals. Work supported by the U.S. Department of Energy Basic Energy Science under Contract No. DE-FG02-11ER16243.

  8. Thermal desorption of molecular oxygen from SnO2 (110) surface: Insights from first-principles calculations

    NASA Astrophysics Data System (ADS)

    Golovanov, Viacheslav; Golovanova, Viktoria; Rantala, Tapio T.

    2016-02-01

    First-principles density functional theory calculations in the generalized gradient approximation, with plane wave basis set and pseudopotentials, have been used to investigate the desorption pathways of molecular oxygen species adsorbed on the SnO2 (110) surface. Energetics of the thermodynamically favored precursors is studied in dependence on the surface charge provided either by surface defects or by donor type impurities from the near-surface region. The resonant desorption modes of O2 molecules are examined in the framework of ab initio atomic thermodynamics and relationship of these results to experimental observations is discussed.

  9. Controlling Electronic Structures by Irradiation in Single-walled SiC Nanotubes: A First-Principles Molecular Dynamics Study

    SciTech Connect

    Wang, Zhiguo; Gao, Fei; Li , Jingbo; Zu, Xiaotao T.; Weber, William J.

    2009-02-18

    Using first principles molecular dynamics simulations, the displacement threshold energy and defect configurations are determined in SiC nanotubes. The simulation results reveal that a rich variety of defect structures (vacancies, Stone-Wales defects, and antisite defects) are formed with threshold energies of from 11 to 64 eV. The threshold energy shows an anisotropic behavior and exhibits a dramatic decrease with decreasing tube diameter. The electronic structure can be altered by the defects formed by irradiation, which suggests that the electron irradiation may be a way to use defect engineering to tailor electronic properties of SiC nanotubes.

  10. Structure of liquid phosphorus: A liquid-liquid phase transition via constant-pressure first-principles molecular dynamics

    NASA Astrophysics Data System (ADS)

    Morishita, Tetsuya

    2001-12-01

    Constant-pressure first-principles molecular dynamics simulations have been carried out to study structural phase transitions of liquid black phosphorus. By compressing the tetrahedral molecular liquid (a low-pressure phase), a structural phase transition from the molecular to polymeric liquid (a high-pressure phase) was successfully realized just as observed in the recent experiment by Katayama et al. [Nature 170 (2000) 403]. Structural properties in the polymeric liquid were investigated and it is found that the covalent p-state bonds are dominant within the first nearest neighbors of each atom. However, further compression of the polymeric liquid shows that the covalent bonding is weakened as pressure is increased. As a result, liquid phosphorus becomes similar to the simple liquid in which atoms form a close-packed structure at very high pressure.

  11. First-principles molecular dynamics simulations of NH_4^+ and CH3COO- adsorption at the aqueous quartz interface

    NASA Astrophysics Data System (ADS)

    Wright, Louise B.; Walsh, Tiffany R.

    2012-12-01

    The ability to exert molecular-level control at the aqueous interface between biomolecules and inorganic substrates is pivotal to advancing applications ranging from sustainable manufacturing to targeted therapeutics. Progress is hindered by a lack of structural information of these interfaces with atomic resolution. Molecular simulation is one approach to obtain such data, but can be limited by the reliability of the force-field used. First-principles simulations, in principle, can provide insights into such aqueous interfaces, but are resource-intensive, limiting previous first-principles studies to approximate the environment of liquid water. Here, we use Car-Parrinello simulations to investigate adsorption of two charged adsorbates that are functional groups common to all amino-acids—ethanoate and ammonium—at the interface between hydroxylated quartz and liquid water, directly incorporating full solvation effects at the interface. Our findings reveal the stable character of carboxylate-quartz binding, as well as the surprisingly indifferent nature of ammonium-quartz interactions, in liquid water.

  12. Scaling laws for ignition at the National Ignition Facility from first principles.

    PubMed

    Cheng, Baolian; Kwan, Thomas J T; Wang, Yi-Ming; Batha, Steven H

    2013-10-01

    We have developed an analytical physics model from fundamental physics principles and used the reduced one-dimensional model to derive a thermonuclear ignition criterion and implosion energy scaling laws applicable to inertial confinement fusion capsules. The scaling laws relate the fuel pressure and the minimum implosion energy required for ignition to the peak implosion velocity and the equation of state of the pusher and the hot fuel. When a specific low-entropy adiabat path is used for the cold fuel, our scaling laws recover the ignition threshold factor dependence on the implosion velocity, but when a high-entropy adiabat path is chosen, the model agrees with recent measurements. PMID:24229109

  13. First-Principles Mobility Calculations and Atomic-Scale Interface Roughness in Nanoscale Structures

    SciTech Connect

    Evans, Matthew H; Zhang, Xiaoguang; Joannopoulos, J. D.; Pantelides, Sokrates T

    2005-01-01

    Calculations of mobilities have so far been carried out using approximate methods that suppress atomic-scale detail. Such approaches break down in nanoscale structures. Here we report the development of a method to calculate mobilities using atomic-scale models of the structures and density functional theory at various levels of sophistication and accuracy. The method is used to calculate the effect of atomic-scale roughness on electron mobilities in ultrathin double-gate silicon-on-insulator structures. The results elucidate the origin of the significant reduction in mobility observed in ultrathin structures at low electron densities.

  14. First-principles molecular dynamics simulations at solid-liquid interfaces with a continuum solvent.

    PubMed

    Sánchez, Verónica M; Sued, Mariela; Scherlis, Damián A

    2009-11-01

    Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such a continuum approach in a density functional theory framework using plane-wave basis sets and periodic boundary conditions. Our work stems from a recent model designed for Car-Parrinello simulations of quantum solutes in a dielectric medium [D. A. Scherlis et al., J. Chem. Phys. 124, 074103 (2006)], for which the permittivity of the solvent is defined as a function of the electronic density of the solute. This strategy turns out to be inadequate for systems extended in two dimensions: the dependence of the dielectric function on the electronic density introduces a new term in the Kohn-Sham potential, which becomes unphysically large at the interfacial region, seriously affecting the convergence of the self-consistent calculations. If the dielectric medium is properly redefined as a function of the atomic coordinates, a good convergence is obtained and the constant of motion is conserved during the molecular dynamics simulations. The Poisson problem is solved using a multigrid method, and in this way Car-Parrinello molecular dynamics simulations of solid-liquid interfaces can be performed at a very moderate computational cost. This scheme is employed to investigate the acid-base equilibrium at the TiO(2)-water interface. The aqueous behavior of titania surfaces has stimulated a large amount of experimental research, but many open questions remain concerning the molecular mechanisms determining the chemistry of the interface. Here we make an attempt to answer some of them, putting to the test our continuum model. PMID:19894999

  15. Polymorphism and Elastic Response of Molecular Materials from First Principles: How Hard Can it Be?

    NASA Astrophysics Data System (ADS)

    Reilly, Anthony; Tkatchenko, Alexandre

    2014-03-01

    Molecular materials are of great fundamental and applied importance in science and industry, with numerous applications in pharmaceuticals, electronics, sensing, and catalysis. A key challenge for theory has been the prediction of their stability, polymorphism and response to perturbations. While pairwise models of van der Waals (vdW) interactions have improved the ability of density functional theory (DFT) to model these systems, substantial quantitative and even qualitative failures remain. In this contribution we show how a many-body description of vdW interactions can dramatically improve the accuracy of DFT for molecular materials, yielding quantitative description of stabilities and polymorphism for these challenging systems. Moreover, the role of many-body vdW interactions goes beyond stabilities to response properties. In particular, we have studied the elastic properties of a series of molecular crystals, finding that many-body vdW interactions can account for up to 30% of the elastic response, leading to quantitative and qualitative changes in elastic behavior. We will illustrate these crucial effects with the challenging case of the polymorphs of aspirin, leading to a better understanding of the conflicting experimental and theoretical studies of this system.

  16. First principles investigations of vinazene molecule and molecular crystal: a prospective candidate for organic photovoltaic applications.

    PubMed

    Mohamad, Mazmira; Ahmed, Rashid; Shaari, Amirudin; Goumri-Said, Souraya

    2015-02-01

    Escalating demand for sustainable energy resources, because of the rapid exhaustion of conventional energy resources as well as to maintain the environmental level of carbon dioxide (CO2) to avoid its adverse effect on the climate, has led to the exploitation of photovoltaic technology manifold more than ever. In this regard organic materials have attracted great attention on account of demonstrating their potential to harvest solar energy at an affordable rate for photovoltaic technology. 2-vinyl-4,5-dicyanoimidazole (vinazene) is considered as a suitable material over the fullerenes for photovoltaic applications because of its particular chemical and physical nature. In the present study, DFT approaches are employed to provide an exposition of optoelectronic properties of vinazene molecule and molecular crystal. To gain insight into its properties, different forms of exchange correlation energy functional/potential such as LDA, GGA, BLYP, and BL3YP are used. Calculated electronic structure of vinazene molecule has been displayed via HOMO-LUMO isosurfaces, whereas electronic structure of the vinazene molecular crystal, via electronic band structure, is presented. The calculated electronic and optical properties were analyzed and compared as well. Our results endorse vinazene as a suitable material for organic photovoltaic applications. PMID:25631921

  17. Anisotropy induced Kondo splitting in a mechanically stretched molecular junction: A first-principles based study

    NASA Astrophysics Data System (ADS)

    Wang, Xiaoli; Hou, Dong; Zheng, Xiao; Yan, YiJing

    2016-01-01

    The magnetic anisotropy and Kondo phenomena in a mechanically stretched magnetic molecular junction are investigated by combining the density functional theory (DFT) and hierarchical equations of motion (HEOM) approach. The system is comprised of a magnetic complex Co(tpy-SH)2 sandwiched between adjacent gold electrodes, which is mechanically stretched in experiments done by Parks et al. [Science 328, 1370 (2010)]. The electronic structure and mechanical property of the stretched system are investigated via the DFT calculations. The HEOM approach is then employed to characterize the Kondo resonance features, based on the Anderson impurity model parameterized from the DFT results. It is confirmed that the ground state prefers the S = 1 local spin state. The structural properties, the magnetic anisotropy, and corresponding Kondo peak splitting in the axial stretching process are systematically evaluated. The results reveal that the strong electron correlations and the local magnetic properties of the molecule magnet are very sensitive to structural distortion. This work demonstrates that the combined DFT+HEOM approach could be useful in understanding and designing mechanically controlled molecular junctions.

  18. Semiclassical Monte Carlo: A first principles approach to non-adiabatic molecular dynamics

    SciTech Connect

    White, Alexander J.; Gorshkov, Vyacheslav N.; Wang, Ruixi; Tretiak, Sergei; Mozyrsky, Dmitry

    2014-11-14

    Modeling the dynamics of photophysical and (photo)chemical reactions in extended molecular systems is a new frontier for quantum chemistry. Many dynamical phenomena, such as intersystem crossing, non-radiative relaxation, and charge and energy transfer, require a non-adiabatic description which incorporate transitions between electronic states. Additionally, these dynamics are often highly sensitive to quantum coherences and interference effects. Several methods exist to simulate non-adiabatic dynamics; however, they are typically either too expensive to be applied to large molecular systems (10's-100's of atoms), or they are based on ad hoc schemes which may include severe approximations due to inconsistencies in classical and quantum mechanics. We present, in detail, an algorithm based on Monte Carlo sampling of the semiclassical time-dependent wavefunction that involves running simple surface hopping dynamics, followed by a post-processing step which adds little cost. The method requires only a few quantities from quantum chemistry calculations, can systematically be improved, and provides excellent agreement with exact quantum mechanical results. Here we show excellent agreement with exact solutions for scattering results of standard test problems. Additionally, we find that convergence of the wavefunction is controlled by complex valued phase factors, the size of the non-adiabatic coupling region, and the choice of sampling function. These results help in determining the range of applicability of the method, and provide a starting point for further improvement.

  19. Semiclassical Monte Carlo: A first principles approach to non-adiabatic molecular dynamics

    NASA Astrophysics Data System (ADS)

    White, Alexander J.; Gorshkov, Vyacheslav N.; Wang, Ruixi; Tretiak, Sergei; Mozyrsky, Dmitry

    2014-11-01

    Modeling the dynamics of photophysical and (photo)chemical reactions in extended molecular systems is a new frontier for quantum chemistry. Many dynamical phenomena, such as intersystem crossing, non-radiative relaxation, and charge and energy transfer, require a non-adiabatic description which incorporate transitions between electronic states. Additionally, these dynamics are often highly sensitive to quantum coherences and interference effects. Several methods exist to simulate non-adiabatic dynamics; however, they are typically either too expensive to be applied to large molecular systems (10's-100's of atoms), or they are based on ad hoc schemes which may include severe approximations due to inconsistencies in classical and quantum mechanics. We present, in detail, an algorithm based on Monte Carlo sampling of the semiclassical time-dependent wavefunction that involves running simple surface hopping dynamics, followed by a post-processing step which adds little cost. The method requires only a few quantities from quantum chemistry calculations, can systematically be improved, and provides excellent agreement with exact quantum mechanical results. Here we show excellent agreement with exact solutions for scattering results of standard test problems. Additionally, we find that convergence of the wavefunction is controlled by complex valued phase factors, the size of the non-adiabatic coupling region, and the choice of sampling function. These results help in determining the range of applicability of the method, and provide a starting point for further improvement.

  20. First-principles calculation and molecular dynamics simulation of fracture behavior of VN layers under uniaxial tension

    NASA Astrophysics Data System (ADS)

    Fu, Tao; Peng, Xianghe; Zhao, Yinbo; Feng, Chao; Tang, Shan; Hu, Ning; Wang, Zhongchang

    2015-05-01

    We develop the second nearest-neighbor modified embedded atom method (2NN MEAM) potential for vanadium nitride (VN) in terms of the individual vanadium and nitrogen. The potential parameters are determined by fitting the cohesive energy, lattice parameter, and elastic constants of the VN with the NaCl-type structure, which are obtained by first-principles calculations. We find that the developed potentials can be used to describe the fundamental physical properties of the V-N system with other lattice structures. The calculated tensile stress-strain curves of the VN layers by first principles agree with those obtained by molecular dynamic simulations, validating the use of the developed potential. The bond breaking and its growth and coalescence are found to play an important role in the formation of fracture. We also find that temperature influences markedly the breaking of bonds, which can be attributed to the deviation of atoms from their equilibrium positions due to the thermal activated vibration, or to the superposition of the thermal energy to the deformation energy. Moreover, no dislocations and slips are found throughout the deformation process.

  1. First-principles molecular dynamics simulation of the Ca2UO2(CO3)3 complex in water.

    PubMed

    Priest, Chad; Tian, Ziqi; Jiang, De-En

    2016-06-14

    Recent experiments have shown that the neutral Ca2UO2(CO3)3 complex is the dominant species of uranium in many uranyl-containing streams. However, the structure and solvation of such a species in water has not been investigated from first principles. Herein we present a first principles molecular dynamics perspective of the Ca2UO2(CO3)3 complex in water based on density functional theory and Born-Oppenheimer approximation. We find that the Ca2UO2(CO3)3 complex is very stable in our simulation timeframe for three different concentrations considered and that the key distances from our simulation are in good agreement with the experimental data from extended X-ray absorption fine structure (EXAFS) spectroscopy. More important, we find that the two Ca ions bind differently in the complex, as a result of the hydrogen-bonding network around the whole complex. This finding invites confirmation from time-resolved EXAFS and has implications in understanding the dissociative equilibrium of the Ca2UO2(CO3)3 complex in water. PMID:26901265

  2. Electronic processes in fast thermite chemical reactions: A first-principles molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Shimojo, Fuyuki; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya

    2008-06-01

    Rapid reaction of a molten metal with an oxide is the key to understanding recently discovered fast reactions in nanothermite composites. We have investigated the thermite reaction of Fe2O3 with aluminum by molecular dynamics simulations with interatomic forces calculated quantum mechanically in the framework of the density functional theory. A redox reaction to form iron metal and Al2O3 initiates with the rapid formation of Al-O bonds at the interface within 1 ps, followed by the propagation of the combustion front with a velocity of 70 m/s for at least 5 ps at 2000 K. The reaction time for an oxygen atom to change character from Fe2O3 type to Al2O3 type at the interface is estimated to be 1.7±0.9ps , and bond-overlap population analysis has been used to calculate reaction rates.

  3. Electronic processes in fast thermite chemical reactions: a first-principles molecular dynamics study.

    PubMed

    Shimojo, Fuyuki; Nakano, Aiichiro; Kalia, Rajiv K; Vashishta, Priya

    2008-06-01

    Rapid reaction of a molten metal with an oxide is the key to understanding recently discovered fast reactions in nanothermite composites. We have investigated the thermite reaction of Fe2O3 with aluminum by molecular dynamics simulations with interatomic forces calculated quantum mechanically in the framework of the density functional theory. A redox reaction to form iron metal and Al2O3 initiates with the rapid formation of Al-O bonds at the interface within 1 ps, followed by the propagation of the combustion front with a velocity of 70 m/s for at least 5 ps at 2000 K. The reaction time for an oxygen atom to change character from Fe2O3 type to Al2O3 type at the interface is estimated to be 1.7+/-0.9 ps , and bond-overlap population analysis has been used to calculate reaction rates. PMID:18643332

  4. Large-Scale Computations Leading to a First-Principles Approach to Nuclear Structure

    SciTech Connect

    Ormand, W E; Navratil, P

    2003-08-18

    We report on large-scale applications of the ab initio, no-core shell model with the primary goal of achieving an accurate description of nuclear structure from the fundamental inter-nucleon interactions. In particular, we show that realistic two-nucleon interactions are inadequate to describe the low-lying structure of {sup 10}B, and that realistic three-nucleon interactions are essential.

  5. Solvation of Na^+ in water from first-principles molecular dynamics

    NASA Astrophysics Data System (ADS)

    White, J. A.; Schwegler, E.; Galli, G.; Gygi, F.

    2000-03-01

    We have carried out ab initio molecular dynamics (MD) simulations of the Na^+ ion in water with an MD cell containing a single alkali ion and 53 water molecules. The electron-electron and electron-ion interactions were modeled by density functional theory with a generalized gradient approximation for the exchange-correlation functional. The computed radial distribution functions, coordination numbers, and angular distributions are consistent with available experimental data. The first solvation shell contains 5.2±0.6 water molecules, with some waters occasionally exchanging with those of the second shell. The computed Na^+ hydration number is larger than that from calculations for water clusters surrounding an Na^+ ion, but is consistent with that derived from x-ray measurements. Our results also indicate that the first hydration shell is better defined for Na^+ than for K^+ [1], as indicated by the first minimum in the Na-O pair distribution function. [1] L.M. Ramaniah, M. Bernasconi, and M. Parrinello, J. Chem. Phys. 111, 1587 (1999). This work was performed for DOE under contract W-7405-ENG-48.

  6. Transport processes at alpha-quartz-water interfaces: insights from first-principles molecular dynamics simulations.

    PubMed

    Adeagbo, Waheed A; Doltsinis, Nikos L; Klevakina, Ksenia; Renner, Jörg

    2008-05-16

    Car-Parrinello molecular dynamics (CP-MD) simulations are performed at high temperature and pressure to investigate chemical interactions and transport processes at the alpha-quartz-water interface. The model system initially consists of a periodically repeated quartz slab with O-terminated and Si-terminated (1000) surfaces sandwiching a film of liquid water. At a temperature of 1000 K and a pressure of 0.3 GPa, dissociation of H(2)O molecules into H(+) and OH(-) is observed at the Si-terminated surface. The OH(-) fragments immediately bind chemically to the Si-terminated surface while Grotthus-type proton diffusion through the water film leads to protonation of the O-terminated surface. Eventually, both surfaces are fully hydroxylated and no further chemical reactions are observed. Due to the confinement between the two hydroxylated quartz surfaces, water diffusion is reduced by about one third in comparison to bulk water. Diffusion properties of dissolved SiO(2) present as Si(OH)(4) in the water film are also studied. We do not observe strong interactions between the hydroxylated quartz surfaces and the Si(OH)(4) molecule as would have been indicated by a substantial lowering of the Si(OH)(4) diffusion coefficient along the surface. No spontaneous dissolution of quartz is observed. To study the mechanism of dissolution, constrained CP-MD simulations are done. The associated free energy profile is calculated by thermodynamic integration along the reaction coordinate. Dissolution is a stepwise process in which two Si--O bonds are successively broken. Each bond breaking between a silicon atom at the surface and an oxygen atom belonging to the quartz lattice is accompanied by the formation of a new Si--O bond between the silicon atom and a water molecule. The latter loses a proton in the process which eventually leads to protonation of the oxygen atom in the cleaved quartz Si--O bond. The final solute species is Si(OH)(4). PMID:18404743

  7. High resolution transmission electron microscope Imaging and first-principles simulations of atomic-scale features in graphene membrane

    NASA Astrophysics Data System (ADS)

    Wang, Wei; Bhandari, Sagar; Yi, Wei; Bell, David; Westervelt, Robert; Kaxiras, Efthimios

    2012-02-01

    Ultra-thin membranes such as graphene[1] are of great importance for basic science and technology applications. Graphene sets the ultimate limit of thinness, demonstrating that a free-standing single atomic layer not only exists but can be extremely stable and strong [2--4]. However, both theory [5, 6] and experiments [3, 7] suggest that the existence of graphene relies on intrinsic ripples that suppress the long-wavelength thermal fluctuations which otherwise spontaneously destroy long range order in a two dimensional system. Here we show direct imaging of the atomic features in graphene including the ripples resolved using monochromatic aberration-corrected transmission electron microscopy (TEM). We compare the images observed in TEM with simulated images based on an accurate first-principles total potential. We show that these atomic scale features can be mapped through accurate first-principles simulations into high resolution TEM contrast. [1] Geim, A. K. & Novoselov, K. S. Nat. Mater. 6, 183-191, (2007). [2] Novoselov, K. S.et al. Science 306, 666-669, (2004). [3] Meyer, J. C. et al. Nature 446, 60-63, (2007). [4] Lee, C., Wei, X. D., Kysar, J. W. & Hone, J. Science 321, 385-388, (2008). [5] Nelson, D. R. & Peliti, L. J Phys-Paris 48, 1085-1092, (1987). [6] Fasolino, A., Los, J. H. & Katsnelson, M. I. Nat. Mater. 6, 858-861, (2007). [7] Meyer, J. C. et al. Solid State Commun. 143, 101-109, (2007).

  8. Molecular Theory of Detonation Initiation: Insight from First Principles Modeling of the Decomposition Mechanisms of Organic Nitro Energetic Materials.

    PubMed

    Tsyshevsky, Roman V; Sharia, Onise; Kuklja, Maija M

    2016-01-01

    This review presents a concept, which assumes that thermal decomposition processes play a major role in defining the sensitivity of organic energetic materials to detonation initiation. As a science and engineering community we are still far away from having a comprehensive molecular detonation initiation theory in a widely agreed upon form. However, recent advances in experimental and theoretical methods allow for a constructive and rigorous approach to design and test the theory or at least some of its fundamental building blocks. In this review, we analyzed a set of select experimental and theoretical articles, which were augmented by our own first principles modeling and simulations, to reveal new trends in energetic materials and to refine known existing correlations between their structures, properties, and functions. Our consideration is intentionally limited to the processes of thermally stimulated chemical reactions at the earliest stage of decomposition of molecules and materials containing defects. PMID:26907231

  9. Biased interface between solid ion conductor LiBH{sub 4} and lithium metal: A first principles molecular dynamics study

    SciTech Connect

    Ikeshoji, Tamio; Ando, Yasunobu; Otani, Minoru; Tsuchida, Eiji; Takagi, Shigeyuki; Matsuo, Motoaki; Orimo, Shin-ichi

    2013-09-23

    We use first-principles molecular dynamics to study the electrochemical solid-solid interface between lithium metal and lithium electrolyte LiBH{sub 4}. An external bias is applied by using an effective screening medium. We observe large polarization in the LiBH{sub 4}, because the lithium cations in LiBH{sub 4} are shifted more on one side of the double-well potential of Li{sup +}. This results in a large potential drop in the interface region and a large double-layer capacity corresponding to ca. 70 μF/cm{sup 2}. H-coordination to the Li atoms plays an important role in the charge-transfer reaction and ion transfer.

  10. Molecular Theory of Detonation Initiation: Insight from First Principles Modeling of the Decomposition Mechanisms of Organic Nitro Energetic Materials

    DOE PAGESBeta

    Tsyshevsky, Roman; Sharia, Onise; Kuklja, Maija

    2016-02-19

    Our review presents a concept, which assumes that thermal decomposition processes play a major role in defining the sensitivity of organic energetic materials to detonation initiation. As a science and engineering community we are still far away from having a comprehensive molecular detonation initiation theory in a widely agreed upon form. However, recent advances in experimental and theoretical methods allow for a constructive and rigorous approach to design and test the theory or at least some of its fundamental building blocks. In this review, we analyzed a set of select experimental and theoretical articles, which were augmented by our ownmore » first principles modeling and simulations, to reveal new trends in energetic materials and to refine known existing correlations between their structures, properties, and functions. Lastly, our consideration is intentionally limited to the processes of thermally stimulated chemical reactions at the earliest stage of decomposition of molecules and materials containing defects.« less

  11. Interaction of gas molecules with crystalline polymer separation membranes: Atomic-scale modeling and first-principles calculations

    SciTech Connect

    Sergey N. Rashkeev; Eric S. Peterson

    2011-11-01

    Carbon dioxide (CO2)-induced plasticization can significantly decrease the gas separation performance of membranes in high-temperature or high pressure conditions, such as industrial methane (CH4) separations. In this paper, we investigated the crystalline phase of three polymers (polybenzimidazole (PBI), Bis(isobutylcarboxy)polybenzimidazole (PBI-Butyl), and KaptonTM) and interactions between gas molecules (CO2 and N2) and these polymers. A novel, molecular dynamics (MD) based, computational technique was employed to find unknown crystalline structures of these polymer materials. The interaction of CO2 and N2 gases with these crystals was studied by first-principles calculations and by classical MD simulations. The results showed that the packing structure and the interlayer coupling in polymer crystals determine the permeability and diffusivity of gas molecules. This methodology also allows prediction of plastic swelling in these materials caused by gas molecules absorbed in the polymer matrix.

  12. First-principles molecular dynamics study of water dissociation on the γ-U(1 0 0) surface.

    PubMed

    Yang, Yu; Zhang, Ping

    2015-05-01

    Based on first-principles molecular dynamics simulations at finite temperatures, we systematically study the adsorption and dissociation of water molecules on the γ-U(1 0 0) surface. We predict that water molecules spontaneously dissociate upon approaching the native γ-U(1 0 0) surface. The dissociation results from electronic interactions between surface uranium 6d states and 1b2, 3a1, and 1b1 molecular orbitals of water. With segregated Nb atoms existing on the surface, adsorbing water molecules also dissociate spontaneously because Nb 3d electronic states can also interact with the molecular orbitals similarly. After dissociation, the isolated hydrogen atoms are found to diffuse fast on both the γ-U surface and that with a surface substitutional Nb atom, which is very similar to the 'Hot-Atom' dissociation of oxygen molecules on the Al(1 1 1) surface. From a series of consecutive molecular dynamics simulations, we further reveal that on both the γ-U surface and that with a surface substitutional Nb atom, one surface U atom will be pulled out to form the U-O-U structure after dissociative adsorption of 0.44 ML water molecules. This result indicates that oxide nucleus can form at low coverage of water adsorption on the two surfaces. PMID:25835568

  13. First-principles molecular dynamics study of water dissociation on the γ-U(1 0 0) surface

    NASA Astrophysics Data System (ADS)

    Yang, Yu; Zhang, Ping

    2015-05-01

    Based on first-principles molecular dynamics simulations at finite temperatures, we systematically study the adsorption and dissociation of water molecules on the γ-U(1 0 0) surface. We predict that water molecules spontaneously dissociate upon approaching the native γ-U(1 0 0) surface. The dissociation results from electronic interactions between surface uranium 6d states and 1b2, 3a1, and 1b1 molecular orbitals of water. With segregated Nb atoms existing on the surface, adsorbing water molecules also dissociate spontaneously because Nb 3d electronic states can also interact with the molecular orbitals similarly. After dissociation, the isolated hydrogen atoms are found to diffuse fast on both the γ-U surface and that with a surface substitutional Nb atom, which is very similar to the ‘Hot-Atom’ dissociation of oxygen molecules on the Al(1 1 1) surface. From a series of consecutive molecular dynamics simulations, we further reveal that on both the γ-U surface and that with a surface substitutional Nb atom, one surface U atom will be pulled out to form the U-O-U structure after dissociative adsorption of 0.44 ML water molecules. This result indicates that oxide nucleus can form at low coverage of water adsorption on the two surfaces.

  14. First-Principles Quantum Dynamics of Singlet Fission: Coherent versus Thermally Activated Mechanisms Governed by Molecular π Stacking.

    PubMed

    Tamura, Hiroyuki; Huix-Rotllant, Miquel; Burghardt, Irene; Olivier, Yoann; Beljonne, David

    2015-09-01

    Singlet excitons in π-stacked molecular crystals can split into two triplet excitons in a process called singlet fission that opens a route to carrier multiplication in photovoltaics. To resolve controversies about the mechanism of singlet fission, we have developed a first principles nonadiabatic quantum dynamical model that reveals the critical role of molecular stacking symmetry and provides a unified picture of coherent versus thermally activated singlet fission mechanisms in different acenes. The slip-stacked equilibrium packing structure of pentacene derivatives is found to enhance ultrafast singlet fission mediated by a coherent superexchange mechanism via higher-lying charge transfer states. By contrast, the electronic couplings for singlet fission strictly vanish at the C(2h) symmetric equilibrium π stacking of rubrene. In this case, singlet fission is driven by excitations of symmetry-breaking intermolecular vibrations, rationalizing the experimentally observed temperature dependence. Design rules for optimal singlet fission materials therefore need to account for the interplay of molecular π-stacking symmetry and phonon-induced coherent or thermally activated mechanisms. PMID:26382701

  15. First-Principles Quantum Dynamics of Singlet Fission: Coherent versus Thermally Activated Mechanisms Governed by Molecular π Stacking

    NASA Astrophysics Data System (ADS)

    Tamura, Hiroyuki; Huix-Rotllant, Miquel; Burghardt, Irene; Olivier, Yoann; Beljonne, David

    2015-09-01

    Singlet excitons in π -stacked molecular crystals can split into two triplet excitons in a process called singlet fission that opens a route to carrier multiplication in photovoltaics. To resolve controversies about the mechanism of singlet fission, we have developed a first principles nonadiabatic quantum dynamical model that reveals the critical role of molecular stacking symmetry and provides a unified picture of coherent versus thermally activated singlet fission mechanisms in different acenes. The slip-stacked equilibrium packing structure of pentacene derivatives is found to enhance ultrafast singlet fission mediated by a coherent superexchange mechanism via higher-lying charge transfer states. By contrast, the electronic couplings for singlet fission strictly vanish at the C2 h symmetric equilibrium π stacking of rubrene. In this case, singlet fission is driven by excitations of symmetry-breaking intermolecular vibrations, rationalizing the experimentally observed temperature dependence. Design rules for optimal singlet fission materials therefore need to account for the interplay of molecular π -stacking symmetry and phonon-induced coherent or thermally activated mechanisms.

  16. Enhanced reactivity of nanoenergetic materials: A first-principles molecular dynamics study based on divide-and-conquer density functional theory

    NASA Astrophysics Data System (ADS)

    Shimojo, Fuyuki; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya

    2009-07-01

    Integration of nanowires and nanoparticles of energetic materials into semiconducting structures is giving birth to "nanoenergetics-on-a-chip" technology. Understanding and controlling the reactions of nanoenergetic materials pose a theoretical challenge for combining quantum-mechanical accuracy with large scales to capture nanostructural effects. Recent developments in linear-scaling density functional theory have set a stage for first-principles molecular dynamics simulation of thermite reaction at an Al /Fe2O3 interface. Here, we report the finding of a concerted metal-oxygen flip mechanism that enhances mass diffusion and reaction rate at the interface. This mechanism leads to two-stage reactions, which may explain recent experimental observation in thermite nanowire arrays.

  17. Exploring adsorption and desorption characteristics of molecular hydrogen on neutral and charged Mg nanoclusters: A first principles study

    NASA Astrophysics Data System (ADS)

    Banerjee, Paramita; Chandrakumar, K. R. S.; Das, G. P.

    2016-05-01

    To surmount the limitations of bulk MgH2 for the purpose of hydrogen storage, we report here, a detailed first principles density functional theory (DFT) based study on the structure and stability of neutral (Mgm) and positively charged (Mgm+) Mg nanoclusters of different sizes (m = 2, 4, 8 and 12) and their interaction with molecular hydrogen (H2). Our results demonstrate that H2 is weakly bound to the Mg nanoclusters through van der Waals interactions. Incorporation of Grimme's dispersion correction (D3) in the DFT based exchange-correlation functionals leads to improved accuracy of H2 interaction energy (IE) values that fall within an energy window (between physisorption and chemisorption) desirable for hydrogen storage. Energy decomposition analysis reveals the significance of polarization energy for these Mg-H2 binding. Ab-initio molecular dynamics simulation shows that complete dehydrogenation from these Mg nanoclusters occur at ∼100 °C which is a significant improvement over bulk MgH2 (∼300 °C).

  18. First-principles study of hydrogen-bonded molecular conductor κ -H3(Cat-EDT-TTF/ST)2

    NASA Astrophysics Data System (ADS)

    Tsumuraya, Takao; Seo, Hitoshi; Kato, Reizo; Miyazaki, Tsuyoshi

    2015-07-01

    We theoretically study hydrogen-bonded molecular conductors synthesized recently, κ -H3(Cat-EDT-TTF) 2 and its diselena analog, κ -H3(Cat-EDT-ST) 2, by first-principles density functional theory calculations. In these crystals, two H(Cat-EDT-TTF/ST) units share a hydrogen atom with a short O-H-O hydrogen bond. The calculated band structure near the Fermi level shows a quasi-two-dimensional character with a rather large interlayer dispersion due to the absence of insulating layers, in contrast with conventional molecular conductors. We discuss effective low-energy models based on H(Cat-EDT-TTF/ST) units and its dimers, respectively, where the microscopic character of the orbitals composing them are analyzed. Furthermore, we find a stable structure which is different from the experimentally determined structure, where the shared hydrogen atom becomes localized to one of the oxygen atoms, in which charge disproportionation between the two types of H(Cat-EDT-TTF) units is associated. The calculated potential energy surface for the H atom is very shallow near the minimum points; therefore the probability of the H atom can be delocalized between the two O atoms.

  19. First-principles molecular dynamics study of glassy GeS2: Atomic structure and bonding properties

    NASA Astrophysics Data System (ADS)

    Celino, M.; Le Roux, S.; Ori, G.; Coasne, B.; Bouzid, A.; Boero, M.; Massobrio, C.

    2013-11-01

    The structure of glassy GeS2 is studied in the framework of density functional theory, by using a fully self-consistent first-principles molecular dynamics (FPMD) scheme. A comparative analysis is performed with previous molecular dynamics data obtained within the Harris functional (HFMD) total energy approach. The calculated total neutron structure factor exhibits an unprecedented agreement with the experimental counterpart. In particular, the height of the first sharp diffraction peak (FSDP) improves considerably upon the HFMD results. Both the Ge and the S subnetworks are affected by a consistent number of miscoordinations, coexisting with the main tetrahedral structural motif. Glassy GeS2 features a short-range order quite similar to the one found in glassy GeSe2, a notable exception being the larger number of edge-sharing connections. An electronic structure localization analysis, based on the Wannier functions formalism, provides evidence of a more enhanced ionic character in glassy GeS2 when compared to glassy GeSe2.

  20. Structural, dynamic, electronic, and vibrational properties of flexible, intermediate, and stressed rigid As-Se glasses and liquids from first principles molecular dynamics

    SciTech Connect

    Bauchy, M.; Kachmar, A.; Micoulaut, M.

    2014-11-21

    The structural, vibrational, electronic, and dynamic properties of amorphous and liquid As{sub x}Se{sub 1-x} (0.10 First Principles Molecular Dynamics. Within the above range of compositions, thresholds, and anomalies are found in the behavior of reciprocal and real space properties that can be correlated to the experimental location of the Boolchand intermediate phase in these glassy networks, observed at 0.27 scale fingerprints for the onset of rigidity within the network, while also providing a much more complex picture than the one derived from mean-field approaches of stiffness transitions.

  1. Structural, dynamic, electronic, and vibrational properties of flexible, intermediate, and stressed rigid As-Se glasses and liquids from first principles molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bauchy, M.; Kachmar, A.; Micoulaut, M.

    2014-11-01

    The structural, vibrational, electronic, and dynamic properties of amorphous and liquid AsxSe1-x (0.10 First Principles Molecular Dynamics. Within the above range of compositions, thresholds, and anomalies are found in the behavior of reciprocal and real space properties that can be correlated to the experimental location of the Boolchand intermediate phase in these glassy networks, observed at 0.27 scale fingerprints for the onset of rigidity within the network, while also providing a much more complex picture than the one derived from mean-field approaches of stiffness transitions.

  2. Lithium ion solvation and diffusion in bulk organic electrolytes from first-principles and classical reactive molecular dynamics.

    PubMed

    Ong, Mitchell T; Verners, Osvalds; Draeger, Erik W; van Duin, Adri C T; Lordi, Vincenzo; Pask, John E

    2015-01-29

    Lithium-ion battery performance is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact both the solvation and diffusivity of Li ions. In this work, we used first-principles molecular dynamics to examine the solvation and diffusion of Li ions in the bulk organic solvents ethylene carbonate (EC), ethyl methyl carbonate (EMC), and a mixture of EC and EMC. We found that Li ions are solvated by either carbonyl or ether oxygen atoms of the solvents and sometimes by the PF6(-) anion. Li(+) prefers a tetrahedrally coordinated first solvation shell regardless of which species are involved, with the specific preferred solvation structure dependent on the organic solvent. In addition, we calculated Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in the linear carbonate EMC compared to the cyclic carbonate EC. The magnitude of the diffusion coefficient correlates with the strength of Li(+) solvation. Corresponding analysis for the PF6(-) anion shows greater diffusivity associated with a weakly bound, poorly defined first solvation shell. These results can be used to aid in the design of new electrolytes to improve Li-ion battery performance. PMID:25523643

  3. First principles study on the electronic transport properties of C{sub 60} and B{sub 80} molecular bridges

    SciTech Connect

    Zheng, X. H. Hao, H.; Lan, J.; Wang, X. L.; Shi, X. Q.; Zeng, Z.

    2014-08-21

    The electronic transport properties of molecular bridges constructed by C{sub 60} and B{sub 80} molecules which have the same symmetry are investigated by first principles calculations combined with a non-equilibrium Green's function technique. It is found that, like C{sub 60}, monomer B{sub 80} is a good conductor arising from the charge transfer from the leads to the molecule, while the dimer (B{sub 80}){sub 2} and (C{sub 60}){sub 2} are both insulators due to the potential barrier formed at the molecule-molecule interface. Our further study shows that, although both the homogeneous dimer (B{sub 80}){sub 2} and (C{sub 60}){sub 2} display poor conductivity, the heterogeneous dimer B{sub 80}C{sub 60} shows a very high conductance as a result from the decreased HOMO-LUMO gap and the excess charge redistribution. Finally, we find that the conductivity of both (B{sub 80}){sub 2} and (C{sub 60}){sub 2} can be significantly improved by electron doping, for example, by doping C in (B{sub 80}){sub 2} and doping N in (C{sub 60}){sub 2}.

  4. First-principles molecular dynamics simulations of condensed-phase V-type nerve agent reaction pathways and energy barriers.

    PubMed

    Gee, Richard H; Kuo, I-Feng W; Chinn, Sarah C; Raber, Ellen

    2012-03-14

    Computational studies of condensed-phase chemical reactions are challenging in part because of complexities in understanding the effects of the solvent environment on the reacting chemical species. Such studies are further complicated due to the demanding computational resources required to implement high-level ab initio quantum chemical methods when considering the solvent explicitly. Here, we use first-principles molecular dynamics simulations to examine condensed-phase decontamination reactions of V-type nerve agents in an explicit aqueous solvent. Our results include a detailed study of hydrolysis, base-hydrolysis, and nucleophilic oxidation of both VX and R-VX, as well as their protonated counterparts (i.e., VXH(+) and R-VXH(+)). The decontamination mechanisms and chemical reaction energy barriers, as determined from our simulations, are found to be in good agreement with experiment. The results demonstrate the applicability of using such simulations to assist in understanding new decontamination technologies or other applications that require computational screening of condensed-phase chemical reaction mechanisms. PMID:22298156

  5. Anharmonic lattice dynamics of Ag2O studied by inelastic neutron scattering and first-principles molecular dynamics simulations

    SciTech Connect

    Lan, Tian; Li, Chen; Niedziela, Jennifer L; Smith, Hillary; Abernathy, Douglas L; Rossman, George; Fultz, B.

    2014-01-01

    Inelastic neutron scattering measurements on silver oxide (Ag2O) with the cuprite structure were performed at temperatures from 40 to 400 K, and Fourier transform far-infrared spectra were measured from 100 to 300 K. The measured phonon densities of states and the infrared spectra showed unusually large energy shifts with temperature, and large linewidth broadenings. First principles molecular dynamics (MD) calculations were performed at various temperatures, successfully accounting for the negative thermal expansion (NTE) and local dynamics. Using the Fourier-transformed velocity autocorrelation method, the MD calculations reproduced the large anharmonic effects of Ag2O, and were in excellent agreement with the neutron scattering data. The quasiharmonic approximation (QHA) was less successful in accounting for much of the phonon behavior. The QHA could account for some of the NTE below 250 K, although not at higher temperatures. Strong anharmonic effects were found for both phonons and for the NTE. The lifetime broadenings of Ag2O were explained by anharmonic perturbation theory, which showed rich interactions between the Ag-dominated modes and the O-dominated modes in both up- and down-conversion processes.

  6. A first principles molecular dynamics study of lithium atom solvation in binary liquid mixture of water and ammonia: Structural, electronic, and dynamical properties

    NASA Astrophysics Data System (ADS)

    Pratihar, Subha; Chandra, Amalendu

    2011-01-01

    The preferential solvation of solutes in mixed solvent systems is an interesting phenomenon that plays important roles in solubility and kinetics. In the present study, solvation of a lithium atom in aqueous ammonia solution has been investigated from first principles molecular dynamics simulations. Solvation of alkali metal atoms, like lithium, in aqueous and ammonia media is particularly interesting because the alkali metal atoms release their valence electrons in these media so as to produce solvated electrons and metal counterions. In the present work, first principles simulations are performed employing the Car-Parrinello molecular dynamics method. Spontaneous ionization of the Li atom is found to occur in the mixed solvent system. From the radial distribution functions, it is found that the Li ^+ ion is preferentially solvated by water and the coordination number is mostly four in its first solvation shell and exchange of water molecules between the first and second solvation shells is essentially negligible in the time scale of our simulations. The Li ^+ ion and the unbound electron are well separated and screened by the polar solvent molecules. Also the unbound electron is primarily captured by the hydrogens of water molecules. The diffusion rates of Li ^+ ion and water molecules in its first solvation shell are found to be rather slow. In the bulk phase, the diffusion of water is found to be slower than that of ammonia molecules because of strong ammonia-water hydrogen bonds that participate in solvating ammonia molecules in the mixture. The ratio of first and second rank orientational correlation functions deviate from 3, which suggests a deviation from the ideal Debye-type orientational diffusion. It is found that the hydrogen bond lifetimes of ammonia-ammonia pairs is very short. However, ammonia-water H-bonds are found to be quite strong when ammonia acts as an acceptor and these hydrogen bonds are found to live longer than even water-water hydrogen

  7. Adsorption and diffusion of Ru adatoms on Ru(0001)-supported graphene: Large-scale first-principles calculations

    SciTech Connect

    Han, Yong; Evans, James W.

    2015-10-28

    Large-scale first-principles density functional theory calculations are performed to investigate the adsorption and diffusion of Ru adatoms on monolayer graphene (G) supported on Ru(0001). The G sheet exhibits a periodic moiré-cell superstructure due to lattice mismatch. Within a moiré cell, there are three distinct regions: fcc, hcp, and mound, in which the C{sub 6}-ring center is above a fcc site, a hcp site, and a surface Ru atom of Ru(0001), respectively. The adsorption energy of a Ru adatom is evaluated at specific sites in these distinct regions. We find the strongest binding at an adsorption site above a C atom in the fcc region, next strongest in the hcp region, then the fcc-hcp boundary (ridge) between these regions, and the weakest binding in the mound region. Behavior is similar to that observed from small-unit-cell calculations of Habenicht et al. [Top. Catal. 57, 69 (2014)], which differ from previous large-scale calculations. We determine the minimum-energy path for local diffusion near the center of the fcc region and obtain a local diffusion barrier of ∼0.48 eV. We also estimate a significantly lower local diffusion barrier in the ridge region. These barriers and information on the adsorption energy variation facilitate development of a realistic model for the global potential energy surface for Ru adatoms. This in turn enables simulation studies elucidating diffusion-mediated directed-assembly of Ru nanoclusters during deposition of Ru on G/Ru(0001)

  8. Adsorption and diffusion of Ru adatoms on Ru(0001)-supported graphene: Large-scale first-principles calculations

    DOE PAGESBeta

    Han, Yong; Evans, James W.

    2015-10-27

    Large-scale first-principles density functional theory calculations are performed to investigate the adsorption and diffusion of Ru adatoms on monolayer graphene (G) supported on Ru(0001). The G sheet exhibits a periodic moiré-cell superstructure due to lattice mismatch. Within a moiré cell, there are three distinct regions: fcc, hcp, and mound, in which the C6-ring center is above a fcc site, a hcp site, and a surface Ru atom of Ru(0001), respectively. The adsorption energy of a Ru adatom is evaluated at specific sites in these distinct regions. We find the strongest binding at an adsorption site above a C atom inmore » the fcc region, next strongest in the hcp region, then the fcc-hcp boundary (ridge) between these regions, and the weakest binding in the mound region. Behavior is similar to that observed from small-unit-cell calculations of Habenicht et al. [Top. Catal. 57, 69 (2014)], which differ from previous large-scale calculations. We determine the minimum-energy path for local diffusion near the center of the fcc region and obtain a local diffusion barrier of ~0.48 eV. We also estimate a significantly lower local diffusion barrier in the ridge region. These barriers and information on the adsorption energy variation facilitate development of a realistic model for the global potential energy surface for Ru adatoms. Furthermore, this in turn enables simulation studies elucidating diffusion-mediated directed-assembly of Ru nanoclusters during deposition of Ru on G/Ru(0001).« less

  9. Adsorption and diffusion of Ru adatoms on Ru(0001)-supported graphene: Large-scale first-principles calculations

    SciTech Connect

    Han, Yong; Evans, James W.

    2015-10-27

    Large-scale first-principles density functional theory calculations are performed to investigate the adsorption and diffusion of Ru adatoms on monolayer graphene (G) supported on Ru(0001). The G sheet exhibits a periodic moiré-cell superstructure due to lattice mismatch. Within a moiré cell, there are three distinct regions: fcc, hcp, and mound, in which the C6-ring center is above a fcc site, a hcp site, and a surface Ru atom of Ru(0001), respectively. The adsorption energy of a Ru adatom is evaluated at specific sites in these distinct regions. We find the strongest binding at an adsorption site above a C atom in the fcc region, next strongest in the hcp region, then the fcc-hcp boundary (ridge) between these regions, and the weakest binding in the mound region. Behavior is similar to that observed from small-unit-cell calculations of Habenicht et al. [Top. Catal. 57, 69 (2014)], which differ from previous large-scale calculations. We determine the minimum-energy path for local diffusion near the center of the fcc region and obtain a local diffusion barrier of ~0.48 eV. We also estimate a significantly lower local diffusion barrier in the ridge region. These barriers and information on the adsorption energy variation facilitate development of a realistic model for the global potential energy surface for Ru adatoms. Furthermore, this in turn enables simulation studies elucidating diffusion-mediated directed-assembly of Ru nanoclusters during deposition of Ru on G/Ru(0001).

  10. Carbon and other light element contents in the Earth’s core based on first-principles molecular dynamics

    PubMed Central

    Zhang, Yigang; Yin, Qing-Zhu

    2012-01-01

    Carbon (C) is one of the candidate light elements proposed to account for the density deficit of the Earth’s core. In addition, C significantly affects siderophile and chalcophile element partitioning between metal and silicate and thus the distribution of these elements in the Earth’s core and mantle. Derivation of the accretion and core–mantle segregation history of the Earth requires, therefore, an accurate knowledge of the C abundance in the Earth’s core. Previous estimates of the C content of the core differ by a factor of ∼20 due to differences in assumptions and methods, and because the metal–silicate partition coefficient of C was previously unknown. Here we use two-phase first-principles molecular dynamics to derive this partition coefficient of C between liquid iron and silicate melt. We calculate a value of 9 ± 3 at 3,200 K and 40 GPa. Using this partition coefficient and the most recent estimates of bulk Earth or mantle C contents, we infer that the Earth’s core contains 0.1–0.7 wt% of C. Carbon thus plays a moderate role in the density deficit of the core and in the distribution of siderophile and chalcophile elements during core–mantle segregation processes. The partition coefficients of nitrogen (N), hydrogen, helium, phosphorus, magnesium, oxygen, and silicon are also inferred and found to be in close agreement with experiments and other geochemical constraints. Contents of these elements in the core derived from applying these partition coefficients match those derived by using the cosmochemical volatility curve and geochemical mass balance arguments. N is an exception, indicating its retention in a mantle phase instead of in the core. PMID:23150591

  11. Carbon and other light element contents in the Earth's core based on first-principles molecular dynamics.

    PubMed

    Zhang, Yigang; Yin, Qing-Zhu

    2012-11-27

    Carbon (C) is one of the candidate light elements proposed to account for the density deficit of the Earth's core. In addition, C significantly affects siderophile and chalcophile element partitioning between metal and silicate and thus the distribution of these elements in the Earth's core and mantle. Derivation of the accretion and core-mantle segregation history of the Earth requires, therefore, an accurate knowledge of the C abundance in the Earth's core. Previous estimates of the C content of the core differ by a factor of ∼20 due to differences in assumptions and methods, and because the metal-silicate partition coefficient of C was previously unknown. Here we use two-phase first-principles molecular dynamics to derive this partition coefficient of C between liquid iron and silicate melt. We calculate a value of 9 ± 3 at 3,200 K and 40 GPa. Using this partition coefficient and the most recent estimates of bulk Earth or mantle C contents, we infer that the Earth's core contains 0.1-0.7 wt% of C. Carbon thus plays a moderate role in the density deficit of the core and in the distribution of siderophile and chalcophile elements during core-mantle segregation processes. The partition coefficients of nitrogen (N), hydrogen, helium, phosphorus, magnesium, oxygen, and silicon are also inferred and found to be in close agreement with experiments and other geochemical constraints. Contents of these elements in the core derived from applying these partition coefficients match those derived by using the cosmochemical volatility curve and geochemical mass balance arguments. N is an exception, indicating its retention in a mantle phase instead of in the core. PMID:23150591

  12. First principles molecular dynamics of molten NaI: Structure, self-diffusion, polarization effects, and charge transfer

    NASA Astrophysics Data System (ADS)

    Galamba, N.; Costa Cabral, B. J.

    2007-09-01

    The structure and self-diffusion of NaI and NaCl at temperatures close to their melting points are studied by first principles Hellmann-Feynman molecular dynamics (HFMD). The results are compared with classical MD using rigid-ion (RI) and shell-model (ShM) interionic potentials. HFMD for NaCl was reported before at a higher temperature [N. Galamba and B. J. Costa Cabral, J. Chem. Phys. 126, 124502 (2007)]. The main differences between the structures predicted by HFMD and RI MD for NaI concern the cation-cation and the anion-cation pair correlation functions. A ShM which allows only for the polarization of I- reproduces the main features of the HFMD structure of NaI. The inclusion of polarization effects for both ionic species leads to a more structured ionic liquid, although a good agreement with HFMD is also observed. HFMD Green-Kubo self-diffusion coefficients are larger than those obtained from RI and ShM simulations. A qualitative study of charge transfer in molten NaI and NaCl was also carried out with the Hirshfeld charge partitioning method. Charge transfer in molten NaI is comparable to that in NaCl, and results for NaCl at two temperatures support the view that the magnitude of charge transfer is weakly state dependent for ionic systems. Finally, Hirshfeld charge distributions indicate that differences between RI and HFMD results are mainly related to polarization effects, while the influence of charge transfer fluctuations is minimal for these systems.

  13. Chemical reaction dynamics of PeCB and TCDD decomposition: A tight-binding quantum chemical molecular dynamics study with first-principles parameterization

    NASA Astrophysics Data System (ADS)

    Suzuki, Ai; Selvam, Parasuraman; Kusagaya, Tomonori; Takami, Seiichi; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira

    The decomposition reaction dynamics of 2,3,4,4',5-penta-chlorinated biphenyl (2,3,4,4',5-PeCB), 3,3',4,4',5-penta-chlorinated biphenyl (3,3',4,4',5-PeCB), and 2,3,7,8-tetra-chlorinated dibenzo-p-dioxin (2,3,7,8-TCDD) was clarified for the first time at atomic and electronic levels, using our novel tight-binding quantum chemical molecular dynamics method with first-principles parameterization. The calculation speed of our new method is over 5000 times faster than that of the conventional first-principles molecular dynamics method. We confirmed that the structure, energy, and electronic states of the above molecules calculated by our new method are quantitatively consistent with those by first-principles calculations. After the confirmation of our methodology, we investigated the decomposition reaction dynamics of the above molecules and the calculated dynamic behaviors indicate that the oxidation of the 2,3,4,4',5-PeCB, 3,3',4,4',5-PeCB, and 2,3,7,8-TCDD proceeds through an epoxide intermediate, which is in good agreement with the previous experimental reports and consistent with our static density functional theory calculations. These results proved that our new tight-binding quantum chemical molecular dynamics method with first-principles parameterization is an effective tool to clarify the chemical reaction dynamics at reaction temperatures.

  14. Silver in geological fluids from in situ X-ray absorption spectroscopy and first-principles molecular dynamics

    NASA Astrophysics Data System (ADS)

    Pokrovski, Gleb S.; Roux, Jacques; Ferlat, Guillaume; Jonchiere, Romain; Seitsonen, Ari P.; Vuilleumier, Rodolphe; Hazemann, Jean-Louis

    2013-04-01

    The molecular structure and stability of species formed by silver in aqueous saline solutions typical of hydrothermal settings were quantified using in situ X-ray absorption spectroscopy (XAS) measurements, quantum-chemical modeling of near-edge absorption spectra (XANES) and extended fine structure spectra (EXAFS), and first-principles molecular dynamics (FPMD). Results show that in nitrate-bearing acidic solutions to at least 200 °C, silver speciation is dominated by the hydrated Ag+ cation surrounded by 4-6 water molecules in its nearest coordination shell with mean Ag-O distances of 2.32 ± 0.02 Å. In NaCl-bearing acidic aqueous solutions of total Cl concentration from 0.7 to 5.9 mol/kg H2O (m) at temperatures from 200 to 450 °C and pressures to 750 bar, the dominant species are the di-chloride complex AgCl2- with Ag-Cl distances of 2.40 ± 0.02 Å and Cl-Ag-Cl angle of 160 ± 10°, and the tri-chloride complex AgCl32- of a triangular structure and mean Ag-Cl distances of 2.60 ± 0.05 Å. With increasing temperature, the contribution of the tri-chloride species decreases from ˜50% of total dissolved Ag in the most concentrated solution (5.9m Cl) at 200 °C to less than 10-20% at supercritical temperatures for all investigated solutions, so that AgCl2- becomes by far the dominant Ag-bearing species at conditions typical of hydrothermal-magmatic fluids. Both di- and tri-chloride species exhibit outer-sphere interactions with the solvent as shown by the detection, using FPMD modeling, of H2O, Cl-, and Na+ at distances of 3-4 Å from the silver atom. The species fractions derived from XAS and FPMD analyses, and total AgCl(s) solubilities, measured in situ in this work from the absorption edge height of XAS spectra, are in accord with thermodynamic predictions using the stability constants of AgCl2- and AgCl32- from Akinfiev and Zotov (2001) and Zotov et al. (1995), respectively, which are based on extensive previous AgCl(s) solubility measurements. These data

  15. Light Elements in the Core and Equilibration Degree with Silicate Mantle: Perspective from First-Principles Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Yin, Q.; Zhang, Y.

    2012-12-01

    The degree of chemical equilibration (hereafter as Ke), defined as the cumulative mass fraction of the metalic core in equilibrium with the silicate mantle during the Earth accretion processes, greatly influences determination of the timing of the Earth core formation [1]. If Ke is larger than ~0.4, Hf-W chronology implies a fast accretion in less than 30 Myr for the Earth. Otherwise, Hf-W data can only be used to constrain the Ke instead of timing [1]. Here we use the two-phase first-principles molecular dynamics (FPMD) [2] to constrain the solubility of light elements in liquid iron in equilibration with silicate melt at temperatures from 2500 to 4200 K, pressures from 20 to 120 GPa, and two compositions simplified from the "O-bearing" and "Si-bearing" bulk Earth model compositions of McDonough [3]. The solubility data are then used in the simulations of the many possible accretion scenarios of the Earth as outlined in [4], considering magma ocean depth, homogeneous vs heterogeneous accretion etc. For each accretion route, we calculate the effective core-mantle equilibration degree (Ke), where Kei and Wi are the core-mantle equilibration degree and the accreted mass fraction of the ith step, respectively. The successful Ke are selected based on the criterion that the resulting Earth's core must meet the required density deficit [5]. The Ke in those successful simulations are all found to be larger than 0.57, implying that the core-mantle differentiation has to occur early [1], within 30 millions years from the beginning of the solar system as originally stated [6]. Additional simulations (all at 3200 K and 40 GPa) are also made to calculate the partition coefficients of several other light elements. Combined with the bulk Earth compositions of these elements [3], it is found Si, O, and S are the major light elements in the core while C, P, Mg, H, N, and He are the minor elements in the core. We show [7] that FPMD calculations lend strong support to the classical

  16. First-Principle Framework for Total Charging Energies in Electrocatalytic Materials and Charge-Responsive Molecular Binding at Gas-Surface Interfaces.

    PubMed

    Tan, Xin; Tahini, Hassan A; Seal, Prasenjit; Smith, Sean C

    2016-05-01

    Heterogeneous charge-responsive molecular binding to electrocatalytic materials has been predicted in several recent works. This phenomenon offers the possibility of using voltage to manipulate the strength of the binding interaction with the target gas molecule and thereby circumvent thermochemistry constraints, which inhibit achieving both efficient binding and facile release of important targets such as CO2 and H2. Stability analysis of such charge-induced molecular adsorption has been beyond the reach of existing first-principle approaches. Here, we draw on concepts from semiconductor physics and density functional theory to develop a first principle theoretical approach that allows calculation of the change in total energy of the supercell due to charging. Coupled with the calculated adsorption energy of gas molecules at any given charge, this allows a complete description of the energetics of the charge-induced molecular adsorption process. Using CO2 molecular adsorption onto negatively charged h-BN (wide-gap semiconductor) and g-C4N3 (half metal) as example cases, our analysis reveals that - while adsorption is exothermic after charge is introduced - the overall adsorption processes are not intrinsically spontaneous due to the energetic cost of charging the materials. The energies needed to overcome the barriers of these processes are 2.10 and 0.43 eV for h-BN and g-C4N3, respectively. This first principle approach opens up new pathways for a more complete description of charge-induced and electrocatalytic processes. PMID:27067063

  17. Structure of amorphous GeSe9 by neutron diffraction and first-principles molecular dynamics: Impact of trajectory sampling and size effects.

    PubMed

    Le Roux, Sébastien; Bouzid, Assil; Kim, Kye Yeop; Han, Seungwu; Zeidler, Anita; Salmon, Philip S; Massobrio, Carlo

    2016-08-28

    The structure of glassy GeSe9 was investigated by combining neutron diffraction with density-functional-theory-based first-principles molecular dynamics. In the simulations, three different models of N = 260 atoms were prepared by sampling three independent temporal trajectories, and the glass structures were found to be substantially different from those obtained for models in which smaller numbers of atoms or more rapid quench rates were employed. In particular, the overall network structure is based on Sen chains that are cross-linked by Ge(Se4)1/2 tetrahedra, where the latter are predominantly corner as opposed to edge sharing. The occurrence of a substantial proportion of Ge-Se-Se connections does not support a model in which the material is phase separated into Se-rich and GeSe2-rich domains. The appearance of a first-sharp diffraction peak in the Bhatia-Thornton concentration-concentration partial structure factor does, however, indicate a non-uniform distribution of the Ge-centered structural motifs on an intermediate length scale. PMID:27586930

  18. First-principles studies on vacancy-modified interstitial diffusion mechanism of oxygen in nickel, associated with large-scale atomic simulation techniques

    SciTech Connect

    Fang, H. Z.; Shang, S. L.; Wang, Y.; Liu, Z. K.; Alfonso, D.; Alman, D. E.; Shin, Y. K.; Zou, C. Y.; Duin, A. C. T. van; Lei, Y. K.; Wang, G. F.

    2014-01-28

    This paper is concerned with the prediction of oxygen diffusivities in fcc nickel from first-principles calculations and large-scale atomic simulations. Considering only the interstitial octahedral to tetrahedral to octahedral minimum energy pathway for oxygen diffusion in fcc lattice, greatly underestimates the migration barrier and overestimates the diffusivities by several orders of magnitude. The results indicate that vacancies in the Ni-lattice significantly impact the migration barrier of oxygen in nickel. Incorporation of the effect of vacancies results in predicted diffusivities consistent with available experimental data. First-principles calculations show that at high temperatures the vacancy concentration is comparable to the oxygen solubility, and there is a strong binding energy and a redistribution of charge density between the oxygen atom and vacancy. Consequently, there is a strong attraction between the oxygen and vacancy in the Ni lattice, which impacts diffusion.

  19. First-principles study of the variation of electron transport in a single molecular junction with the length of the molecular wire

    NASA Astrophysics Data System (ADS)

    Pal, Partha Pratim; Pati, Ranjit

    2010-07-01

    We report a first-principles study of quantum transport in a prototype two-terminal device consisting of a molecular nanowire acting as an inter-connect between two gold electrodes. The wire is composed of a series of bicyclo[1.1.1]pentane (BCP) cage-units. The length of the wire (L) is increased by sequentially increasing the number of BCP cage units in the wire from 1 to 3. A two terminal model device is made out of each of the three wires. A parameter free, nonequilibrium Green’s function approach, in which the bias effect is explicitly included within a many body framework, is used to calculate the current-voltage characteristics of each of the devices. In the low bias regime that is considered in our study, the molecular devices are found to exhibit Ohmic behavior with resistances of 0.12, 1.4, and 6.5μΩ for the wires containing one, two, and three cages respectively. Thus the conductance value, Gc , which is the reciprocal of resistance, decreases as e-βL with a decay constant (β) of 0.59Å-1 . This observed variation of conductance with the length of the wire is in excellent agreement with the earlier reported exponential decay feature of the electron transfer rate predicted from the electron transfer coupling matrix values obtained using the two-state Marcus-Hush model and the Koopman’s theorem approximation. The downright suppression of the computed electrical current for a bias up to 0.4 V in the longest wire can be exploited in designing a three terminal molecular transistor; this molecular wire could potentially be used as a throttle to avoid leakage gate current.

  20. A perfect wetting of Mg monolayer on Ag(111) under atomic scale investigation: First principles calculations, scanning tunneling microscopy, and Auger spectroscopy

    NASA Astrophysics Data System (ADS)

    Migaou, Amani; Sarpi, Brice; Guiltat, Mathilde; Payen, Kevin; Daineche, Rachid; Landa, Georges; Vizzini, Sébastien; Hémeryck, Anne

    2016-05-01

    First principles calculations, scanning tunneling microscopy, and Auger spectroscopy experiments of the adsorption of Mg on Ag(111) substrate are conducted. This detailed study reveals that an atomic scale controlled deposition of a metallic Mg monolayer perfectly wets the silver substrate without any alloy formation at the interface at room temperature. A liquid-like behavior of the Mg species on the Ag substrate is highlighted as no dot formation is observed when coverage increases. Finally a layer-by-layer growth mode of Mg on Ag(111) can be predicted, thanks to density functional theory calculations as observed experimentally.

  1. A perfect wetting of Mg monolayer on Ag(111) under atomic scale investigation: First principles calculations, scanning tunneling microscopy, and Auger spectroscopy.

    PubMed

    Migaou, Amani; Sarpi, Brice; Guiltat, Mathilde; Payen, Kevin; Daineche, Rachid; Landa, Georges; Vizzini, Sébastien; Hémeryck, Anne

    2016-05-21

    First principles calculations, scanning tunneling microscopy, and Auger spectroscopy experiments of the adsorption of Mg on Ag(111) substrate are conducted. This detailed study reveals that an atomic scale controlled deposition of a metallic Mg monolayer perfectly wets the silver substrate without any alloy formation at the interface at room temperature. A liquid-like behavior of the Mg species on the Ag substrate is highlighted as no dot formation is observed when coverage increases. Finally a layer-by-layer growth mode of Mg on Ag(111) can be predicted, thanks to density functional theory calculations as observed experimentally. PMID:27208966

  2. Homocoordination preference in NaCs and LiNa liquid alloys by first principles molecular dynamics

    NASA Astrophysics Data System (ADS)

    Costa Cabral, B. J.; Martins, J. L.

    1999-09-01

    We present structural and dynamics results based on Hellman-Feynman molecular dynamics for the liquid phase of the NaCs alloy at two Na concentrations (cNa=0.6 and 0.8) and for the Li0.61Na0.39 zero alloy at two temperatures (T=590 K and 690 K). For NaCs the calculated structure factor S(k) is in very good agreement with data from neutron scattering experiments and the partial structure factors are compared to semiexperimental, theoretical and classical molecular dynamics predictions. We predict similar values for the self-diffusion coefficients of Na and Cs atoms in the Na0.6Cs0.4 alloy. For LiNa the concentration-concentration structure factor is in good agreement with experimental data and our results for the dynamics are compared with data from classical molecular dynamics simulations.

  3. Dissociative versus molecular adsorption of phenol on Si(100)2×1 : A first-principles calculation

    NASA Astrophysics Data System (ADS)

    Carbone, Marilena; Meloni, Simone; Caminiti, Ruggero

    2007-08-01

    We investigated the competitive adsorption of a bifunctional molecule, phenol, on Si(100)2×1 by ab initio calculations. We performed geometry optimizations of phenol adsorbed either molecularly or dissociatively, on five possible sites (top, bridge, valley bridge, cave, and pedestal), in the low coverage regime. We found that the dissociative adsorption of phenol on top of a silicon dimer is the most favorable adsorption configuration. In the group of dissociative adsorption the phenol initially placed on the bridge or the valley-bridge sites ends up as a toplike local minima. The pedestal and cave sites remain as low-adsorption energy “open” sites. In the group of molecular adsorption, a higher adsorption energy is associated to the adsorption through an addition reaction and loss of the aromatic character (bridge, valley-bridge, and pedestal sites). Standard butterfly or diagonal butterfly are the corresponding optimized geometries. Retention of aromatic character and lower adsorption energy are associated to the adsorption on the top and cave sites. The ordering of adsorption sites according to the adsorption energy shows a mixture of the dissociative and the molecular sites. In the case of adsorption on the top site, the adsorption energies after a rotation of the phenoxy fragment along the bonding axis and hydrogen migration on the surface are very similar. The bend of the phenoxy fragment on the surface, instead, is not favored (the adsorption energy is 1.004eV lower compared to the vertical position). Different electron density maps were calculated for different adsorption sites and modes. Finally, we investigated the possibility that molecularly adsorbed phenol behaves as a precursor for the dissociative one by nudged elastic band calculations. We found a barrier of the same order of magnitude of the thermodynamic energy at room temperature for the conversion of the valley-bridge molecular into the top dissociative site.

  4. First Principles Calculations of the Double Photoionization ofAtoms and Molecules using B-splines and Exterior Complex Scaling

    SciTech Connect

    Martin, Fernando; Horner, Daniel A.; Vanroose, Wim; Rescigno,Thomas N.; McCurdy, C. William

    2005-11-04

    We report a fully ab initio implementation of exterior complex scaling in B-splines to evaluate total, singly and triply differential cross sections in double photoionization problems. Results for He and H{sub 2} double photoionization are presented and compared with experiment.

  5. Multi-scale First-Principles Modeling of Three-Phase System of Polymer Electrolyte Membrane Fuel Cel

    SciTech Connect

    Brunello, Giuseppe; Choi, Ji; Harvey, David; Jang, Seung

    2012-07-01

    The three-phase system consisting of Nafion, graphite and platinum in the presence of water is studied using molecule dynamics simulation. The force fields describing the molecular interaction between the components in the system are developed to reproduce the energies calculated from density functional theory modeling. The configuration of such complicated three-phase system is predicted through MD simulations. The nanophase-segregation and transport properties are investigated from the equilibrium state. The coverage of the electrolyte on the platinum surface and the dissolution of oxygen are analyzed.

  6. Influence of Boron Substitution on Conductance of Pyridine- and Pentane-Based Molecular Single Electron Transistors: First-Principles Analysis

    NASA Astrophysics Data System (ADS)

    Srivastava, Anurag; Santhibhushan, B.; Sharma, Vikash; Kaur, Kamalpreet; Shahzad Khan, Md.; Marathe, Madura; De Sarkar, Abir; Shahid Khan, Mohd.

    2016-04-01

    We have investigated the modeling of boron-substituted molecular single-electron transistor (SET), under the influence of a weak coupling regime of Coulomb blockade between source and drain metal electrodes. The SET consists of a single organic molecule (pyridine/pentane/1,2-azaborine/butylborane) placed over the dielectric, with boron (B) as a substituent. The impact of B-substitution on pyridine and pentane molecules in isolated, as well as SET, environments has been analyzed by using density functional theory-based ab initio packages Atomistix toolkit-Virtual NanoLab and Gaussian03. The performance of proposed SETs was analyzed through charging energies, total energy as a function of gate potential and charge stability diagrams. The analysis confirms that the B-substituted pentane (butylborane) and the boron-substituted pyridine (1,2-azaborine) show remarkably improved conductance in SET environment in comparison to simple pyridine and pentane molecules.

  7. Sticking to (first) principles: quantum molecular dynamics and Bayesian probabilistic methods to simulate aquatic pollutant absorption spectra.

    PubMed

    Trerayapiwat, Kasidet; Ricke, Nathan; Cohen, Peter; Poblete, Alex; Rudel, Holly; Eustis, Soren N

    2016-08-10

    This work explores the relationship between theoretically predicted excitation energies and experimental molar absorption spectra as they pertain to environmental aquatic photochemistry. An overview of pertinent Quantum Chemical descriptions of sunlight-driven electronic transitions in organic pollutants is presented. Second, a combined molecular dynamics (MD), time-dependent density functional theory (TD-DFT) analysis of the ultraviolet to visible (UV-Vis) absorption spectra of six model organic compounds is presented alongside accurate experimental data. The functional relationship between the experimentally observed molar absorption spectrum and the discrete quantum transitions is examined. A rigorous comparison of the accuracy of the theoretical transition energies (ΔES0→Sn) and oscillator strength (fS0→Sn) is afforded by the probabilistic convolution and deconvolution procedure described. This method of deconvolution of experimental spectra using a Gaussian Mixture Model combined with Bayesian Information Criteria (BIC) to determine the mean (μ) and standard deviation (σ) as well as the number of observed singlet to singlet transition energy state distributions. This procedure allows a direct comparison of the one-electron (quantum) transitions that are the result of quantum chemical calculations and the ensemble of non-adiabatic quantum states that produce the macroscopic effect of a molar absorption spectrum. Poor agreement between the vertical excitation energies produced from TD-DFT calculations with five different functionals (CAM-B3LYP, PBE0, M06-2X, BP86, and LC-BLYP) suggest a failure of the theory to capture the low energy, environmentally important, electronic transitions in our model organic pollutants. However, the method of explicit-solvation of the organic solute using the quantum Effective Fragment Potential (EFP) in a density functional molecular dynamics trajectory simulation shows promise as a robust model of the hydrated organic

  8. First-principles molecular dynamics study of the structure and dynamic behavior of liquid Li4BN3H10

    NASA Astrophysics Data System (ADS)

    Farrell, David E.; Shin, Dongwon; Wolverton, C.

    2009-12-01

    We have applied density-functional theory based ab initio molecular dynamics to examine Li4BN3H10 at temperatures both above and below the experimental melting point. We examine the structure of the liquid, diffusivity, vibrational spectra and compare to both experimental data and analogous properties from solid-state calculations. We find the following: (1) the liquid state, like the solid state, is primarily a mixture of Li+ , BH4- , and NH2- with ionic interactions between the BH4- and NH2- anions and the Li+ cations. (2) We observe the reaction of two amide anions exchanging hydrogen to form ammonia and an imide anion: 2NH2-→NH3+NH2- . (3) The liquid demonstrates wide bond-angle distributions in the BH4- and NH2- units and thus these anionic units are not simply rigid complexes. (4) The Li+ sublattice disorders before the anionic sublattices and the liquid exhibits very fast Li+ diffusion. We calculate the activation energy and pre-exponential factor for Li+ diffusivity in the liquid to be ˜20kJ/mol and 15×10-4cm2/s , respectively. (5) Finally, we find that the liquid contains the same generic types of vibrational modes as the solid, however the lower-frequency anionic vibration and rotation modes become more prominent with increasing temperature.

  9. Prediction of the Chapman-Jouguet chemical equilibrium state in a detonation wave from first principles based reactive molecular dynamics.

    PubMed

    Guo, Dezhou; Zybin, Sergey V; An, Qi; Goddard, William A; Huang, Fenglei

    2016-01-21

    The combustion or detonation of reacting materials at high temperature and pressure can be characterized by the Chapman-Jouguet (CJ) state that describes the chemical equilibrium of the products at the end of the reaction zone of the detonation wave for sustained detonation. This provides the critical properties and product kinetics for input to macroscale continuum simulations of energetic materials. We propose the ReaxFF Reactive Dynamics to CJ point protocol (Rx2CJ) for predicting the CJ state parameters, providing the means to predict the performance of new materials prior to synthesis and characterization, allowing the simulation based design to be done in silico. Our Rx2CJ method is based on atomistic reactive molecular dynamics (RMD) using the QM-derived ReaxFF force field. We validate this method here by predicting the CJ point and detonation products for three typical energetic materials. We find good agreement between the predicted and experimental detonation velocities, indicating that this method can reliably predict the CJ state using modest levels of computation. PMID:26688211

  10. First-principles path-integral molecular dynamics study of diffusion process of hydrogen in face-centered cubic metals

    NASA Astrophysics Data System (ADS)

    Kimizuka, Hajime; Ogata, Shigenobu

    We investigated the H diffusivity in face-centered cubic Pd and Al by performing path-integral molecular dynamics (PIMD) modeling in the framework of density functional theory (DFT); in our calculations, we took nuclear quantum effects into consideration. The DFT results showed that the H-migration barriers (Em) in Pd and Al exhibited similar values (approximately 0.16 eV), while the H atoms were stable at octahedral (O) sites for Pd and at tetrahedral (T) sites for Al. The PIMD-based free-energy profiles for H migration between the O-site and T-site were evaluated using the thermodynamic integration of the centroid forces at 150-600 K. We confirmed that the quantum effects significantly affected the Em and the difference between the energies of the H atom at the O-site and the T-site (EO - T); The Em and EO - T values in Pd at 300 K increased by 32% and 98%, respectively, relative to the classical limit. On the other hand, the Em and ET - O (i.e., -EO - T) values in Al at 300 K decreased by 3% and 41%, respectively. This suggested that the quantum nature of H nuclei was essential for understanding the H-diffusion kinetics in these metals even above ambient temperature.

  11. The mechanism of the initial step of germanosilicate formation in solution: a first-principles molecular dynamics study.

    PubMed

    Trinh, Thuat T; Rozanska, Xavier; Delbecq, Françoise; Tuel, Alain; Sautet, Philippe

    2016-06-01

    The condensation reactions between Ge(OH)4 and Si(OH)4 units in solution are studied to understand the mechanism and stable species during the initial steps of the formation process of Ge containing zeolites under basic conditions. The free energy of formation of (OH)3Ge-O-Ge-(OH)2O(-), (OH)3Si-O-Si-(OH)2O(-), (OH)3Ge-O-Si-(OH)2O(-) and (OH)3Si-O-Ge-(OH)2O(-) dimers is calculated with ab initio molecular dynamics and thermodynamic integration, including an explicit description of the water solvent molecules. Calculations show that the attack of the conjugated base (Ge(OH)3O(-) and Si(OH)3O(-)) proceeds with a smaller barrier at the Ge center. In addition, the formation of the pure germanate dimer is more favorable than that of the germano-silicate structure. These results explain the experimental observation of Ge-Ge and Si-Ge dimer species in solutions, with a few Si-Si ones. PMID:27172391

  12. First-principles studies on molecular beam epitaxy growth of GaAs1-xBix

    DOE PAGESBeta

    Luo, Guangfu; Yang, Shujiang; Li, Jincheng; Arjmand, Mehrdad; Szlufarska, Izabela; Brown, April S.; Kuech, Thomas F.; Morgan, Dane

    2015-07-14

    We investigate the molecular beam epitaxy (MBE) growth of GaAs1-xBix film using density functional theory with spin-orbit coupling to understand the growth of this film, especially the mechanisms of Bi incorporation. We study the stable adsorption structures and kinetics of the incident molecules (As₂ molecule, Ga atom, Bi atom, and Bi₂ molecule) on the (2 x 1)-Gasub||Bi surface and a proposed q(1 x 1)-Gasub||AsAs surface has a quasi-(1 x 1) As layer above the Ga-terminated GaAs substrate and a randomly oriented As dimer layer on top. We obtain the desorption and diffusion barriers of the adsorbed molecules and also themore » reaction barriers of three key processes related to Bi evolution, namely, Bi incorporation, As/Bi exchange, and Bi clustering. The results help explain the experimentally observed dependence of Bi incorporation on the As/Ga ratio and growth temperature. Furthermore, we find that As₂ exchange with Bi of the (2 x 1)-Gasub||Bi surface is a key step controlling the kinetics of the Bi incorporation. Finally, we explore two possible methods to enhance the Bi incorporation, namely, replacing the MBE growth mode from codeposition of all fluxes with a sequential deposition of fluxes and applying asymmetric in-plane strain to the substrate.« less

  13. Thermodynamics of nano-scale precipitate-strengthened Fe-Cu and Al-transition-metal systems from first-principles calculations

    NASA Astrophysics Data System (ADS)

    Liu, Zhe

    The thermodynamic properties of two nano-scale precipitate-strengthened alloys, Fe-Cu and Al-TM(=Ti, Zr and Hf) systems, are investigated within framework of first-principles thermodynamics methods. In particular, thermodynamic properties of the metastable precipitate phases are calculated, where direct experimental measurements are not available. Atomic volumes, magnetic moments, mixing energies and elastic properties of bcc Fe1-xCux solid solutions are studied by first-principles calculations based on the cluster expansion (CE) framework. We introduce a generalization of the CE technique for the calculation of concentration-dependent elastic moduli in disordered phase. Calculated mixing energies, atomic volumes and magnetic moments agree well with measurements for metastable alloys prepared through non-equilibrium processing techniques. The variations of the bulk modulus B, shear moduli C44 and C', with respect to copper concentration are calculated for the disordered bcc phase. While the B and C44 are positive for all concentrations, C' is positive only for Cu concentrations less than 50 atomic%. The implications of present results are discussed in relation to the observed metastability of bcc Fe-Cu alloys, and the strengthening mechanism of nanoscale bcc precipitates in an alpha-Fe matrix. Vibrational entropy, which is often omitted in first-principles phase-diagram calculations, has been shown to be an essential contribution in the phase stability of many Al-based alloys. In this work, we study the effect of lattice vibrations on the solubility limit for Al-TM(=Ti, Zr and Hf) systems. We propose a transferable force constant approach (TFC), in which the relations between bond force constants, bond length and TM composition are assumed to be transferable among different structures, to substantially reduce the heavy computational expense associated with first-principles lattice dynamics calculations. Our results demonstrate that the TFC can predict the

  14. Large-scale first principles and tight-binding density functional theory calculations on hydrogen-passivated silicon nanorods

    NASA Astrophysics Data System (ADS)

    Zonias, Nicholas; Lagoudakis, Pavlos; Skylaris, Chris-Kriton

    2010-01-01

    We present a computational study by density functional theory (DFT) of entire silicon nanorods with up to 1648 atoms without any periodicity or symmetry imposed. The nanorods have been selected to have varying aspect ratios and levels of surface passivation with hydrogen. The structures of the nanorods have been optimized using a density functional tight-binding approach, while energies and electronic properties have been computed using linear-scaling DFT with plane-wave accuracy with the ONETEP (Skylaris et al 2005 J. Chem. Phys. 122 084119) program. The aspect ratio and surface passivation (1 × 1 and 2 × 1 reconstructions) along with the size of the nanorods which leads to quantum confinement along all three dimensions, significantly affect their electronic properties. The structures of the nanorods also show interesting behaviour as, depending on their characteristics, they can in certain areas retain the structure of bulk silicon while in other parts significantly deviate from it.

  15. Extended application of Kohn-Sham first-principles molecular dynamics method with plane wave approximation at high energy—From cold materials to hot dense plasmas

    NASA Astrophysics Data System (ADS)

    Zhang, Shen; Wang, Hongwei; Kang, Wei; Zhang, Ping; He, X. T.

    2016-04-01

    An extended first-principles molecular dynamics (FPMD) method based on Kohn-Sham scheme is proposed to elevate the temperature limit of the FPMD method in the calculation of dense plasmas. The extended method treats the wave functions of high energy electrons as plane waves analytically and thus expands the application of the FPMD method to the region of hot dense plasmas without suffering from the formidable computational costs. In addition, the extended method inherits the high accuracy of the Kohn-Sham scheme and keeps the information of electronic structures. This gives an edge to the extended method in the calculation of mixtures of plasmas composed of heterogeneous ions, high-Z dense plasmas, lowering of ionization potentials, X-ray absorption/emission spectra, and opacities, which are of particular interest to astrophysics, inertial confinement fusion engineering, and laboratory astrophysics.

  16. Rock-salt structure lithium deuteride formation in liquid lithium with high-concentrations of deuterium: a first-principles molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Chen, Mohan; Abrams, T.; Jaworski, M. A.; Carter, Emily A.

    2016-01-01

    Because of lithium’s possible use as a first wall material in a fusion reactor, a fundamental understanding of the interactions between liquid lithium (Li) and deuterium (D) is important. We predict structural and dynamical properties of liquid Li samples with high concentrations of D, as derived from first-principles molecular dynamics simulations. Liquid Li samples with four concentrations of inserted D atoms (LiDβ , β =0.25 , 0.50, 0.75, and 1.00) are studied at temperatures ranging from 470 to 1143 K. Densities, diffusivities, pair distribution functions, bond angle distribution functions, geometries, and charge transfer between Li and D atoms are calculated and analyzed. The analysis suggests liquid-solid phase transitions can occur at some concentrations and temperatures, forming rock-salt LiD within liquid Li. We also observe formation of some D2 molecules at high D concentrations.

  17. First-principles study of the nano-scaling effect on the electrochemical behavior in LiNi0.5Mn1.5O4

    NASA Astrophysics Data System (ADS)

    Lee, Eunseok; Persson, Kristin A.

    2013-10-01

    Nano-scaling of electrode materials is often used in battery applications to enhance performance, particularly relating to rate capability. However, for the high-voltage spinel LiNi0.5Mn1.5O4 conflicting results have been reported on the benefits of nano-scaling. In this study, we present first-principles calculations to investigate the effect of nano-scaling on LiNi0.5Mn1.5O4, specifically focusing on the roles and coupling between surface stability, cation ordering and phase behavior. We calculate and compare the surface energy for the low index facets (100), (110), and (111), and find that the most stable facet is dependent on the cation ordering at the surface layer. In this context, we predict a spontaneous surface reconstruction in the cation-ordered structure which leads to a deviation from the perfect surface cation ordering and results in an enhanced accessibility to solid solution behavior as a function of Li content. Our results imply that nano-scaling will be more beneficial for the cation-ordered structure, as compared to the disordered structure where the solid solution region is already intrinsically accessible for a broad range of Li concentrations.

  18. First-principles study of the nano-scaling effect on the electrochemical behavior in LiNi(0.5)Mn(1.5)O4.

    PubMed

    Lee, Eunseok; Persson, Kristin A

    2013-10-25

    Nano-scaling of electrode materials is often used in battery applications to enhance performance, particularly relating to rate capability. However, for the high-voltage spinel LiNi0.5Mn1.5O4 conflicting results have been reported on the benefits of nano-scaling. In this study, we present first-principles calculations to investigate the effect of nano-scaling on LiNi0.5Mn1.5O4, specifically focusing on the roles and coupling between surface stability, cation ordering and phase behavior. We calculate and compare the surface energy for the low index facets (100), (110), and (111), and find that the most stable facet is dependent on the cation ordering at the surface layer. In this context, we predict a spontaneous surface reconstruction in the cation-ordered structure which leads to a deviation from the perfect surface cation ordering and results in an enhanced accessibility to solid solution behavior as a function of Li content. Our results imply that nano-scaling will be more beneficial for the cation-ordered structure, as compared to the disordered structure where the solid solution region is already intrinsically accessible for a broad range of Li concentrations. PMID:24067535

  19. The coupling between stability and ion pair formation in magnesium electrolytes from first-principles quantum mechanics and classical molecular dynamics

    SciTech Connect

    Rajput, Nav Nidhi; Qu, Xiaohuui; Sa, Niya; Burrell, Anthony K.; Persson, Kristin A.

    2015-03-11

    In this work we uncover a novel effect between concentration dependent ion pair formation and anion stability at reducing potentials, e.g., at the metal anode. Through comprehensive calculations using both first-principles as well as well-benchmarked classical molecular dynamics over a matrix of electrolytes, covering solvents and salt anions with a broad range in chemistry, we elucidate systematic correlations between molecular level interactions and composite electrolyte properties, such as electrochemical stability, solvation structure, and dynamics. We find that Mg electrolytes are highly prone to ion pair formation, even at modest concentrations, for a wide range of solvents with different dielectric constants, which have implications for dynamics as well as charge transfer. Specifically, we observe that, at Mg metal potentials, the ion pair undergoes partial reduction at the Mg cation center (Mg2+ -> Mg+), which competes with the charge transfer mechanism and can activate the anion to render it susceptible to decomposition. Specifically, TFSI exhibits a significant bond weakening while paired with the transient, partially reduced Mg+. In contrast, BH4 and BF4 are shown to be chemically stable in a reduced ion pair configuration. Furthermore, we observe that higher order glymes as well as DMSO improve the solubility of Mg salts, but only the longer glyme chains reduce the dynamics of the ions in solution. This information provides critical design metrics for future electrolytes as it elucidates a close connection between bulk solvation and cathodic stability as well as the dynamics of the salt.

  20. Surface chemistry of copper metal and copper oxide atomic layer deposition from copper(ii) acetylacetonate: a combined first-principles and reactive molecular dynamics study.

    PubMed

    Hu, Xiao; Schuster, Jörg; Schulz, Stefan E; Gessner, Thomas

    2015-10-28

    Atomistic mechanisms for the atomic layer deposition using the Cu(acac)2 (acac = acetylacetonate) precursor are studied using first-principles calculations and reactive molecular dynamics simulations. The results show that Cu(acac)2 chemisorbs on the hollow site of the Cu(110) surface and decomposes easily into a Cu atom and the acac-ligands. A sequential dissociation and reduction of the Cu precursor [Cu(acac)2 → Cu(acac) → Cu] are observed. Further decomposition of the acac-ligand is unfavorable on the Cu surface. Thus additional adsorption of the precursors may be blocked by adsorbed ligands. Molecular hydrogen is found to be nonreactive towards Cu(acac)2 on Cu(110), whereas individual H atoms easily lead to bond breaking in the Cu precursor upon impact, and thus release the surface ligands into the gas-phase. On the other hand, water reacts with Cu(acac)2 on a Cu2O substrate through a ligand-exchange reaction, which produces gaseous H(acac) and surface OH species. Combustion reactions with the main by-products CO2 and H2O are observed during the reaction between Cu(acac)2 and ozone on the CuO surface. The reactivity of different co-reactants toward Cu(acac)2 follows the order H > O3 > H2O. PMID:26399423

  1. Functionalization-induced changes in the structural and physical properties of amorphous polyaniline: a first-principles and molecular dynamics study

    PubMed Central

    Chen, X. P.; Liang, Q. H.; Jiang, J. K.; Wong, Cell K. Y.; Leung, Stanley Y. Y.; Ye, H. Y.; Yang, D. G.; Ren, T. L.

    2016-01-01

    In this paper, we present a first-principles and molecular dynamics study to delineate the functionalization-induced changes in the local structure and the physical properties of amorphous polyaniline. The results of radial distribution function (RDF) demonstrate that introducing -SO3−Na+ groups at phenyl rings leads to the structural changes in both the intrachain and interchain ordering of polyaniline at shorter distances (≤5 Å). An unique RDF feature in 1.8–2.1 Å regions is usually observed in both the interchain and intrachain RDF profiles of the -SO3−Na+ substituted polymer (i.e. Na-SPANI). Comparative studies of the atom-atom pairs, bond structures, torsion angles and three-dimensional structures show that EB-PANI has much better intrachain ordering than that of Na-SPANI. In addition, investigation of the band gap, density of states (DOS), and absorption spectra indicates that the derivatization at ring do not substantially alter the inherent electronic properties but greatly change the optical properties of polyaniline. Furthermore, the computed diffusion coefficient of water in Na-SPANI is smaller than that of EB-PANI. On the other hand, the Na-SPANI shows a larger density than that of EB-PANI. The computed RDF profiles, band gaps, absorption spectra, and diffusion coefficients are in quantitative agreement with the experimental data. PMID:26857962

  2. Structure, electronic and magnetic properties of hexagonal boron nitride sheets doped by 5d transition metal atoms: First-principles calculations and molecular orbital analysis

    NASA Astrophysics Data System (ADS)

    Zhang, Zhaofu; Geng, Zhaohui; Cai, Danyun; Pan, Tongxi; Chen, Yixin; Dong, Liyuan; Zhou, Tiege

    2015-01-01

    A first-principles calculation based on density functional theory is carried out to reveal the geometry, electronic structures and magnetic properties of hexagonal boron nitride sheets (h-BNSs) doped by 5d transitional mental atoms (Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au and Hg) at boron-site (B5d) and nitrogen-site (N5d). Results of pure h-BNS, h-BNS with B vacancy (VB) and N vacancy (VN) are also given for comparison. It is shown that all the h-BNSs doped with 5d atoms possess a C3v local symmetry except for NLu and NHg which have a clear deviation. For the same 5d dopant, the binding energy of B5d is larger than that of N5d, which indicates the substitution of a 5d atom for B is preferred. The total densities of states are presented, where impurity energy levels exist. Besides, the total magnetic moments (TMMs) change regularly with the increment of the 5d atomic number. Theoretical analyses by molecular orbital under C3v symmetry explain the impurity energy levels and TMMs.

  3. Pressure-induced structural changes in the network-forming isostatic glass GeSe4: An investigation by neutron diffraction and first-principles molecular dynamics

    NASA Astrophysics Data System (ADS)

    Bouzid, Assil; Pizzey, Keiron J.; Zeidler, Anita; Ori, Guido; Boero, Mauro; Massobrio, Carlo; Klotz, Stefan; Fischer, Henry E.; Bull, Craig L.; Salmon, Philip S.

    2016-01-01

    The changes to the topological and chemical ordering in the network-forming isostatic glass GeSe4 are investigated at pressures up to ˜14.4 GPa by using a combination of neutron diffraction and first-principles molecular dynamics. The results show a network built from corner- and edge-sharing Ge(Se1 /2)4 tetrahedra, where linkages by Se2 dimers or longer Sen chains are prevalent. These linkages confer the network with a local flexibility that helps to retain the network connectivity at pressures up to ˜8 GPa, corresponding to a density increase of ˜37 % . The network reorganization at constant topology maintains a mean coordination number n ¯≃2.4 , the value expected from mean-field constraint-counting theory for a rigid stress-free network. Isostatic networks may therefore remain optimally constrained to avoid stress and retain their favorable glass-forming ability over a large density range. As the pressure is increased to around 13 GPa, corresponding to a density increase of ˜49 % , Ge(Se1 /2)4 tetrahedra remain as the predominant structural motifs, but there is an appearance of 5-fold coordinated Ge atoms and homopolar Ge-Ge bonds that accompany an increase in the fraction of 3-fold coordinated Se atoms. The band gap energy decreases with increasing pressure, and midgap states appear at pressures beyond ˜6.7 GPa. The latter originate from undercoordinated Se atoms that terminate broken Sen chains.

  4. Fundamental Reaction Pathway for Peptide Metabolism by Proteasome: Insights from First-principles Quantum Mechanical/Molecular Mechanical Free Energy Calculations

    PubMed Central

    Wei, Donghui; Fang, Lei; Tang, Mingsheng; Zhan, Chang-Guo

    2013-01-01

    Proteasome is the major component of the crucial nonlysosomal protein degradation pathway in the cells, but the detailed reaction pathway is unclear. In this study, first-principles quantum mechanical/molecular mechanical free energy calculations have been performed to explore, for the first time, possible reaction pathways for proteasomal proteolysis/hydrolysis of a representative peptide, succinyl-leucyl-leucyl-valyl-tyrosyl-7-amino-4-methylcoumarin (Suc-LLVY-AMC). The computational results reveal that the most favorable reaction pathway consists of six steps. The first is a water-assisted proton transfer within proteasome, activating Thr1-Oγ. The second is a nucleophilic attack on the carbonyl carbon of a Tyr residue of substrate by the negatively charged Thr1-Oγ, followed by the dissociation of the amine AMC (third step). The fourth step is a nucleophilic attack on the carbonyl carbon of the Tyr residue of substrate by a water molecule, accompanied by a proton transfer from the water molecule to Thr1-Nz. Then, Suc-LLVY is dissociated (fifth step), and Thr1 is regenerated via a direct proton transfer from Thr1-Nz to Thr1-Oγ. According to the calculated energetic results, the overall reaction energy barrier of the proteasomal hydrolysis is associated with the transition state (TS3b) for the third step involving a water-assisted proton transfer. The determined most favorable reaction pathway and the rate-determining step have provided a reasonable interpretation of the reported experimental observations concerning the substituent and isotopic effects on the kinetics. The calculated overall free energy barrier of 18.2 kcal/mol is close to the experimentally-derived activation free energy of ~18.3–19.4 kcal/mol, suggesting that the computational results are reasonable. PMID:24111489

  5. The solvation structure of Mg ions in dichloro complex solutions from first-principles molecular dynamics and simulated X-ray absorption spectra.

    PubMed

    Wan, Liwen F; Prendergast, David

    2014-10-15

    The knowledge of Mg solvation structure in the electrolyte is requisite to understand the transport behavior of Mg ions and their dissolution/deposition mechanism at electrolyte/electrode interfaces. In the first established rechargeable Mg-ion battery system [D. Aurbach et al. Nature 2000, 407, 724], the electrolyte is of the dichloro complex (DCC) solution family, Mg(AlCl2BuEt)2/THF, resulting from the reaction of Bu2Mg and EtAlCl2 with a molar ratio of 1:2. There is disagreement in the literature regarding the exact solvation structure of Mg ions in such solutions, i.e., whether Mg(2+) is tetra- or hexacoordinated by a combination of Cl(-) and THF. In this work, theoretical insight into the solvation complexes present is provided based on first-principles molecular dynamics simulations (FPMD). Both Mg monomer and dimer structures are considered in both neutral and positively charged states. We found that, at room temperature, the Mg(2+) ion tends to be tetracoordinated in the THF solution phase instead of hexacoordinated, which is the predominant solid-phase coordination. Simulating the X-ray absorption spectra (XAS) at the Mg K-edge by sampling our FPMD trajectories, our predicted solvation structure can be readily compared with experimental measurements. It is found that when changing from tetra- to hexacoordination, the onset of X-ray absorption should exhibit at least a 1 eV blue shift. We propose that this energy shift can be used to monitor changes in the Mg solvation sphere as it migrates through the electrolyte to electrolyte/electrode interfaces and to elucidate the mechanism of Mg dissolution/deposition. PMID:25243732

  6. First principle thousand atom quantum dot calculations

    SciTech Connect

    Wang, Lin-Wang; Li, Jingbo

    2004-03-30

    A charge patching method and an idealized surface passivation are used to calculate the single electronic states of IV-IV, III-V, II-VI semiconductor quantum dots up to a thousand atoms. This approach scales linearly and has a 1000 fold speed-up compared to direct first principle methods with a cost of eigen energy error of about 20 meV. The calculated quantum dot band gaps are parametrized for future references.

  7. First-principles calculations of novel materials

    NASA Astrophysics Data System (ADS)

    Sun, Jifeng

    Computational material simulation is becoming more and more important as a branch of material science. Depending on the scale of the systems, there are many simulation methods, i.e. first-principles calculation (or ab-initio), molecular dynamics, mesoscale methods and continuum methods. Among them, first-principles calculation, which involves density functional theory (DFT) and based on quantum mechanics, has become to be a reliable tool in condensed matter physics. DFT is a single-electron approximation in solving the many-body problems. Intrinsically speaking, both DFT and ab-initio belong to the first-principles calculation since the theoretical background of ab-initio is Hartree-Fock (HF) approximation and both are aimed at solving the Schrodinger equation of the many-body system using the self-consistent field (SCF) method and calculating the ground state properties. The difference is that DFT introduces parameters either from experiments or from other molecular dynamic (MD) calculations to approximate the expressions of the exchange-correlation terms. The exchange term is accurately calculated but the correlation term is neglected in HF. In this dissertation, DFT based first-principles calculations were performed for all the novel materials and interesting materials introduced. Specifically, the DFT theory together with the rationale behind related properties (e.g. electronic, optical, defect, thermoelectric, magnetic) are introduced in Chapter 2. Starting from Chapter 3 to Chapter 5, several representative materials were studied. In particular, a new semiconducting oxytelluride, Ba2TeO is studied in Chapter 3. Our calculations indicate a direct semiconducting character with a band gap value of 2.43 eV, which agrees well with the optical experiment (˜ 2.93 eV). Moreover, the optical and defects properties of Ba2TeO are also systematically investigated with a view to understanding its potential as an optoelectronic or transparent conducting material. We find

  8. Compositional dependence of the local structure of Se{sub x}Te{sub 1-x} alloys: Electron energy-loss spectra, real-space multiple-scattering calculations, and first-principles molecular dynamics

    SciTech Connect

    Katcho, N. A.; Lomba, E.; Urones-Garrote, E.; Otero-Diaz, L. C.; Landa-Canovas, A. R.

    2006-06-01

    In this work we present an investigation on the composition dependence of the local structure in Se{sub x}Te{sub 1-x} crystalline alloys analyzing their experimental energy-loss spectra with the aid of a real-space multiple-scattering modeling approach and first-principles molecular dynamics. The concourse of this latter technique is essential for a proper modeling of the alloy spectra. From our results, it can be inferred that Se{sub x}Te{sub 1-x} alloys exhibit a high degree of substitutional disorder ruling out the existence of fully ordered alternating copolymer chains of Se and Te atoms.

  9. Compositional dependence of the local structure of SexTe1-x alloys: Electron energy-loss spectra, real-space multiple-scattering calculations, and first-principles molecular dynamics

    NASA Astrophysics Data System (ADS)

    Katcho, N. A.; Lomba, E.; Urones-Garrote, E.; Landa-Cánovas, A. R.; Otero-Díaz, L. C.

    2006-06-01

    In this work we present an investigation on the composition dependence of the local structure in SexTe1-x crystalline alloys analyzing their experimental energy-loss spectra with the aid of a real-space multiple-scattering modeling approach and first-principles molecular dynamics. The concourse of this latter technique is essential for a proper modeling of the alloy spectra. From our results, it can be inferred that SexTe1-x alloys exhibit a high degree of substitutional disorder ruling out the existence of fully ordered alternating copolymer chains of Se and Te atoms.

  10. Culturing conceptions: From first principles

    NASA Astrophysics Data System (ADS)

    Roth, Wolff-Michael; Lee, Yew Jin; Hwang, Sungwon

    2008-07-01

    Over the past three decades, science educators have accumulated a vast amount of information on conceptions--variously defined as beliefs, ontologies, cognitive structures, mental models, or frameworks--that generally (at least initially) have been derived from interviews about certain topics. During the same time period, cultural studies has emerged as a field in which everyday social practices are interrogated with the objective to understand culture in all its complexity. Science educators have however yet to ask themselves what it would mean to consider the possession of conceptions as well as conceptual change from the perspective of cultural studies. The purpose of this article is thus to articulate in and through the analysis of an interview about natural phenomenon the first principles of such a cultural approach to scientific conceptions. Our bottom-up approach in fact leads us to develop the kind of analyses and theories that have become widespread in cultural studies. This promises to generate less presupposing and more parsimonious explanations of this core issue within science education than if conceptions are supposed to be structures inhabiting the human mind.

  11. First-principles simulations of thiophene oligomers

    NASA Astrophysics Data System (ADS)

    Scherlis, Damian; Marzari, Nicola

    2003-03-01

    Conducting polymers, extensively investigated for their use in electronic and nanotechnology applications, have recently gained prominence for their possible use as molecular actuators in mechanical and bioengineering devices. We have focused our efforts on thiophene-based compounds, a class of materials that can be designed for high stress generation and large linear displacement (actuation strain), ideally outperforming mammalian muscle. Key features for the development of these materials are the microscopic binding properties of thiophene and thiophene oligomers stacks, where applied electric fields lead to oxidation and enhanced pi-pi bonding. We have completed the structural studies of neutral and charged oligothiophene dimers, in the search for efficient dimerization mechanisms. A comparison between different density-functional and quantum-chemistry approaches is critically presented, as are solvation effects, described in this work with a combination of first-principles molecular dynamics and a QM/MM approach for the solvating medium.

  12. Modeling the material strength and equations of state of beta-HMX from both first-principles calculations and molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Peng, Qing; Wang, Guangyu; Liu, G. R.; de, Suvranu

    2015-06-01

    We investigate the elastic constants and equations of state (EOS) of the β-polymorph of cyclotetramethylene tetranitramine (HMX) energetic molecular crystal using density functional theory (DFT) calculations. The combination of vdW-DF2 van der Waals functionals and PBE exchange-correlation functionals gives optimized results. The DFT results are used to optimize the Reactive Force Field (ReaxFF). The material strength and EOS of beta-HMX at finite temperatures are then predicted from ReaxFF molecular dynamics simulations. Our results suggest that the optimized ReaxFF predicts the mechanics and EOS of beta-HMX well. The authors would like to acknowledge the generous financial support from the Defense Threat Reduction Agency (DTRA) Grant # HDTRA1-13-1-0025.

  13. Coarse Grained Approach to First Principles Modeling of Radiation Cascade in Large Fe Supercells

    NASA Astrophysics Data System (ADS)

    Odbadrakh, Kh; Nicholson, D. M.; Rusanu, A.; Samolyuk, G. D.; Stoller, R. E.; Zhang, X.-G.; Stocks, G. M.

    2012-12-01

    Classical Molecular Dynamics (MD) simulations characterizing dislocations and radiation damage typically treat 105-107 atoms. First principles techniques employed to understand systems at an atomistic level are not practical for such large systems consisting of millions of atoms. We present an efficient coarse grained (CG) approach to calculate local electronic and magnetic properties of large MD-generated structures from the first principles. Local atomic magnetic moments in crystalline Fe are perturbed by the presence of radiation generated vacancies and interstitials. The effects are most pronounced near the defect cores and decay slowly as the strain field of the defects decrease with distance. We develop the CG technique based on the Locally Self-consistent Multiple Scattering (LSMS) method that exploits the near-sightedness of the electron Green function. The atomic positions were determined by MD with an embedded atom force field. The local moments in the neighborhood of the defect cores are calculated with first-principles based on full local structure information. Atoms in the rest of the system are modeled by representative atoms with approximated properties. The calculations result in local moments near the defect centers with first-principles accuracy, while capturing coarse-grained details of local moments at greater length scales. This CG approach makes these large scale structures amenable to first principles study.

  14. Investigation of hydrogen bonds and temperature effects on the water monolayer adsorption on rutile TiO 2 (110) by first-principles molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Sebbari, K.; Domain, C.; Roques, J.; Perron, H.; Simoni, E.; Catalette, H.

    2011-07-01

    Density Functional Theory (DFT), based on both static and Born-Oppenheimer Molecular Dynamics approaches, has been used to investigate the effect of hydrogen bonds and temperature on the water monolayer adsorption on the rutile TiO2 (110) face. It was demonstrated that the difference between some previous theoretical results and experimental data is due to too slim slab thickness model and/or too small surface area. According to the present static calculations, water monolayer adsorbs molecularly on the five-fold titanium atoms of an optimised five-layer slab thickness, due to the stabilising lateral hydrogen bonds between molecules. From the molecular dynamics simulations, two adsorption mechanisms were described as a function of temperature. Finally, it was pointed out that the dynamics of water adsorption is strongly influenced by the structural model used. When temperature increases, the monolayer dissociates gradually. However, because of the periodic boundary conditions, the 1 × 1 surface unit needs to be extended to at least 2 × 5 to get an accurate representation of the monolayer dissociation ratio. In these conditions, this ratio is around 20%, 25% and 33% at 270, 350 and 425 K, respectively.

  15. First-principles molecular-dynamics simulation of biphenyl under strong laser pulses by time-dependent density-functional theory

    NASA Astrophysics Data System (ADS)

    Haruyama, Jun; Hu, Chunping; Watanabe, Kazuyuki

    2012-06-01

    The femtosecond laser reaction dynamics of the 3,5-difluoro-3',5'-dibromo-biphenyl (DFDBrBPh) molecule is investigated using time-dependent density-functional theory combined with molecular-dynamics (TDDFT-MD) simulation. This work is based on a recent experiment that monitored torsional motion of the DFDBrBPh molecule by femtosecond time-resolved Coulomb explosion imaging [Madsen , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.102.073007 102, 073007 (2009)]. The results confirm that the probe pulse triggers a Coulomb explosion and the kick pulse induces the torsional motion of two phenyl rings, using the experimental settings of the lasers. The Coulomb explosion dynamics simulation verifies that the F and Br atoms dissociate to the ion detector while maintaining their initial alignment with respect to the phenyl rings, which is the fundamental basis of Coulomb explosion imaging of molecular torsion. Furthermore, the period and amplitude of the torsional motion obtained by the simulation are consistent with the experimental values. This validates the ability of the TDDFT-MD method to reveal the underlying mechanism of experimentally observed molecular torsional dynamics.

  16. Time-dependent first-principles approaches to PV materials

    SciTech Connect

    Miyamoto, Yoshiyuki

    2013-12-10

    Computational scheme for designing photovoltaic (PV) materials is presented. First-principles electron dynamics of photo-excitation and subsequent electron-hole splitting is performed based on the time-dependent density functional theory. Photo-induced enhancement of dipole moment was observed in a polar crystal and a donor-acceptor molecular pair. These experiences will pave a way to design PV material from first-principles simulations.

  17. First-Principles pH Theory

    NASA Astrophysics Data System (ADS)

    Kim, Yong-Hyun; Zhang, S. B.

    2006-03-01

    Despite being one of the most important macroscopic measures and a long history even before the quantum mechanics, the concept of pH has rarely been mentioned in microscopic theories, nor being incorporated computationally into first-principles theory of aqueous solutions. Here, we formulate a theory for the pH dependence of solution formation energy by introducing the proton chemical potential as the microscopic counterpart of pH in atomistic solution models. Within the theory, the general acid-base chemistry can be cast in a simple pictorial representation. We adopt density-functional molecular dynamics to demonstrate the usefulness of the method by studying a number of solution systems including water, small solute molecules such as NH3 and HCOOH, and more complex amino acids with several functional groups. For pure water, we calculated the auto- ionization constant to be 13.2 with a 95 % accuracy. For other solutes, the calculated dissociation constants, i.e., the so- called pKa, are also in reasonable agreement with experiments. Our first-principles pH theory can be readily applied to broad solution chemistry problems such as redox reactions.

  18. B40 fullerene as a highly sensitive molecular device for NH3 detection at low bias: a first-principles study.

    PubMed

    Lin, Bin; Dong, Huilong; Du, Chunmiao; Hou, Tingjun; Lin, Haiping; Li, Youyong

    2016-02-19

    The adsorption of small molecules (NH3, N2, H2 and CH4) on all-boron fullerene B40 is investigated by density functional theory (DFT) and the non-equilibrium Green's function (NEGF) for its potential application in the field of single-molecular gas sensors. The high adsorption energies (-1.09 to -0.75 eV) of NH3 on different adsorption sites of the B40 surface indicate that NH3 strongly chemisorbs to B40. The charge transfer induced by the NH3 adsorption results in a modification of the density of states (DOS) of B40 near the Fermi level, and therefore changes its electronic transport properties. For all possible adsorption sites, the adsorption of NH3 exclusively leads to a decrease of the conductance of B40. Taking into consideration that the non-polar gas molecules (e.g. N2, H2 and CH4) are only physisorbed and show negligible effect on the conductance properties of B40, we would expect that B40 can be used as a single-molecular gas sensor to distinguish NH3 from non-polar gas molecules at low bias. PMID:26775574

  19. Uranyl ion interaction at the water/NiO(100) interface: A predictive investigation by first-principles molecular dynamic simulations

    NASA Astrophysics Data System (ADS)

    Sebbari, Karim; Roques, Jérôme; Domain, Christophe; Simoni, Eric

    2012-10-01

    The behavior of the UO22+ uranyl ion at the water/NiO(100) interface was investigated for the first time using Born-Oppenheimer molecular dynamic simulations with the spin polarized DFT + U extension. A water/NiO(100) interface model was first optimized on a defect-free five layers slab thickness, proposed as a reliable surface model, with an explicit treatment of the solvent. Water molecules are adsorbed with a well-defined structure in a thickness of about 4 Å above the surface. The first layer, adsorbed on nickel atoms, remains mainly in molecular form but can partly dissociate at 293 K. Considering low acidic conditions, a bidentate uranyl ion complex was characterized on two surface oxygen species (arising from water molecules adsorption on nickel atoms) with d_{U{-O}_{adsorption}}= 2.39 Å. This complex is stable at 293 K due to iono-covalent bonds with an estimated charge transfer of 0.58 electron from the surface to the uranyl ion.

  20. B40 fullerene as a highly sensitive molecular device for NH3 detection at low bias: a first-principles study

    NASA Astrophysics Data System (ADS)

    Lin, Bin; Dong, Huilong; Du, Chunmiao; Hou, Tingjun; Lin, Haiping; Li, Youyong

    2016-02-01

    The adsorption of small molecules (NH3, N2, H2 and CH4) on all-boron fullerene B40 is investigated by density functional theory (DFT) and the non-equilibrium Green’s function (NEGF) for its potential application in the field of single-molecular gas sensors. The high adsorption energies (-1.09 to -0.75 eV) of NH3 on different adsorption sites of the B40 surface indicate that NH3 strongly chemisorbs to B40. The charge transfer induced by the NH3 adsorption results in a modification of the density of states (DOS) of B40 near the Fermi level, and therefore changes its electronic transport properties. For all possible adsorption sites, the adsorption of NH3 exclusively leads to a decrease of the conductance of B40. Taking into consideration that the non-polar gas molecules (e.g. N2, H2 and CH4) are only physisorbed and show negligible effect on the conductance properties of B40, we would expect that B40 can be used as a single-molecular gas sensor to distinguish NH3 from non-polar gas molecules at low bias.

  1. Uranyl ion interaction at the water/NiO(100) interface: A predictive investigation by first-principles molecular dynamic simulations

    SciTech Connect

    Sebbari, Karim; Roques, Jerome; Simoni, Eric; Domain, Christophe

    2012-10-28

    The behavior of the UO{sub 2}{sup 2+} uranyl ion at the water/NiO(100) interface was investigated for the first time using Born-Oppenheimer molecular dynamic simulations with the spin polarized DFT +U extension. A water/NiO(100) interface model was first optimized on a defect-free five layers slab thickness, proposed as a reliable surface model, with an explicit treatment of the solvent. Water molecules are adsorbed with a well-defined structure in a thickness of about 4 A above the surface. The first layer, adsorbed on nickel atoms, remains mainly in molecular form but can partly dissociate at 293 K. Considering low acidic conditions, a bidentate uranyl ion complex was characterized on two surface oxygen species (arising from water molecules adsorption on nickel atoms) with d{sub U-O{sub a{sub d{sub s{sub o{sub r{sub p{sub t{sub i{sub o{sub n}}}}}}}}}}}=2.39 A. This complex is stable at 293 K due to iono-covalent bonds with an estimated charge transfer of 0.58 electron from the surface to the uranyl ion.

  2. First-principles molecular dynamics simulations of uranyl ion interaction at the water/rutile TiO2(110) interface

    NASA Astrophysics Data System (ADS)

    Sebbari, K.; Roques, J.; Simoni, E.; Domain, C.; Perron, H.; Catalette, H.

    2012-08-01

    The effects of temperature and solvation on uranyl ion adsorption at the water/rutile TiO2(110) interface are investigated by Density Functional Theory (DFT) in both static and Born-Oppenheimer molecular dynamics approaches. According to experimental observations, uranyl ion can form two surface complexes in a pH range from 1.5 to 4.5. Based on these observations, the structures of the complexes at 293 K are first calculated in agreement with vacuum static calculations. Then, an increase in temperature (293 to 425 K) induces the reinforcement of uranyl ion adsorption due to the release of water molecules from the solvation shell of uranyl ion. Finally, temperature can modify the nature of the surface species.

  3. Small Atomic Orbital Basis Set First-Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources.

    PubMed

    Sure, Rebecca; Brandenburg, Jan Gerit; Grimme, Stefan

    2016-04-01

    In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods. PMID:27308221

  4. Conformation-dependent Molecular Orientation Deduced from First-principles Modeling of Oligo(ethylene glycol)-terminated and Amide Group Containing Alkanethiolates Self-assembled on Gold

    NASA Astrophysics Data System (ADS)

    Malysheva, L.; Onipko, A.; Valiokas, R.; Liedberg, B.

    2005-09-01

    We report orientation angles for the alkyl chain, amide group, and oligo(ethylene glycol) (OEG) portion within self-assembled monolayers (SAMs) of OEG-terminated and amide containing alkanethiolates which, depending on the OEG length and substrate temperature, display unique conformations — all-trans or helical. Optimized geometries of the molecular constituents, characteristic vibration frequencies and transition dipole moments are obtained by using DFT methods with gradient corrections. These ab initio data are subsequently used to simulate infrared reflection-absorption (RA) spectra associated with different conformations and orientations. The obtained results have generated a deeper knowledge of the internal SAM structure, which is crucial for understanding phase and folding characteristics, interaction with water and ultimately the protein repellent properties of OEG-containing SAMs.

  5. Hydrogen transfer and hydration properties of HnPO43-n (n=0-3) in water studied by first principles molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Tang, Emilia; Di Tommaso, Devis; de Leeuw, Nora H.

    2009-06-01

    Density functional theory Perdew-Burke-Ernzerhof [Perdew et al., Phys. Rev. Lett. 77, 3865 (1996)] molecular dynamics simulations of aqueous solutions of orthophosphate species HnPO43-n (n =0-3) provide new insights into hydrogen transfer and intermolecular and hydration properties of these important aqueous species. Extensive Car-Parrinello molecular dynamics simulations of the orthophosphate ion PO43-, of the hydrogen phosphate anions, HPO42- and H2PO4-, and of the orthophosphoric acid, H3PO4, in explicit water show that the process of proton transfer from HnPO43-n to the surrounding water molecules is very fast, less than 1 ps, and indicate that the dehydrogenation occurs through a concerted proton hopping mechanism, which involves HnPO43-n and three water molecules. Analysis of the intermolecular HnPO43-n-water structure shows that the PO43- anions have a significant effect on the H-bonding network of bulk water and the presence of P-O- moieties induce the formation of new types of H-H interactions around this orthophosphate. Calculated probability distributions of the coordination numbers of the first hydration shell of PO43-, HPO42-, and H2PO4- show that these phosphate species display a flexible first coordination shell (between 7 and 13 water molecules) and that the flexibility increases on going from PO43- to H2PO4-. The strength and number of hydrogen bonds of PO43-, HPO42-, and H2PO4- are determined through a detailed analysis of the structural correlation functions. In particular, the H-bond interactions between the oxygen atoms of the phosphates and the surrounding water molecules, which decrease on going from PO43- to the hydrogenated H2PO4- species, explain the diminished effect on the structure of water with the increasing hydrogenation of the orthophosphate anions.

  6. Chamber Clearing First Principles Modeling

    SciTech Connect

    Loosmore, G

    2009-06-09

    LIFE fusion is designed to generate 37.5 MJ of energy per shot, at 13.3 Hz, for a total average fusion power of 500 MW. The energy from each shot is partitioned among neutrons ({approx}78%), x-rays ({approx}12%), and ions ({approx}10%). First wall heating is dominated by x-rays and debris because the neutron mean free path is much longer than the wall thickness. Ion implantation in the first wall also causes damage such as blistering if not prevented. To moderate the peak-pulse heating, the LIFE fusion chamber is filled with a gas (such as xenon) to reduce the peak-pulse heat load. The debris ions and majority of the x-rays stop in the gas, which re-radiates this energy over a longer timescale (allowing time for heat conduction to cool the first wall sufficiently to avoid damage). After a shot, because of the x-ray and ion deposition, the chamber fill gas is hot and turbulent and contains debris ions. The debris needs to be removed. The ions increase the gas density, may cluster or form aerosols, and can interfere with the propagation of the laser beams to the target for the next shot. Moreover, the tritium and high-Z hohlraum debris needs to be recovered for reuse. Additionally, the cryogenic target needs to survive transport through the gas mixture to the chamber center. Hence, it will be necessary to clear the chamber of the hot contaminated gas mixture and refill it with a cool, clean gas between shots. The refilling process may create density gradients that could interfere with beam propagation, so the fluid dynamics must be studied carefully. This paper describes an analytic modeling effort to study the clearing and refilling process for the LIFE fusion chamber. The models used here are derived from first principles and balances of mass and energy, with the intent of providing a first estimate of clearing rates, clearing times, fractional removal of ions, equilibrated chamber temperatures, and equilibrated ion concentrations for the chamber. These can be used

  7. [UO2(NH3)5]Br2·NH3: synthesis, crystal structure, and speciation in liquid ammonia solution by first-principles molecular dynamics simulations.

    PubMed

    Woidy, Patrick; Bühl, Michael; Kraus, Florian

    2015-04-28

    Pentaammine dioxido uranium(VI) dibromide ammonia (1/1), [UO2(NH3)5]Br2·NH3, was synthesized in the form of yellow crystals by the reaction of uranyl bromide, UO2Br2, with dry liquid ammonia. The compound crystallizes orthorhombic in space group Cmcm and is isotypic to [UO2(NH3)5]Cl2·NH3 with a = 13.2499(2), b = 10.5536(1), c = 8.9126(1) Å, V = 1246.29(3) Å(3) and Z = 4 at 123 K. The UO2(2+) cation is coordinated by five ammine ligands and the coordination polyhedron can be best described as pentagonal bipyramid. Car-Parrinello molecular dynamics simulations are reported for [UO2(NH3)5](2+) in the gas phase and in liquid NH3 solution (using the BLYP density functional). According to free-energy simulations, solvation by ammonia has only a small effect on the uranyl-NH3 bond strength. PMID:25797497

  8. A first principles molecular dynamics study of the solvation structure and migration kinetics of an excess proton and a hydroxide ion in binary water-ammonia mixtures

    NASA Astrophysics Data System (ADS)

    Bankura, Arindam; Chandra, Amalendu

    2012-03-01

    We have investigated the solvation structure and migration kinetics of an excess proton and a hydroxide ion in water-ammonia mixed liquids of varying composition by means of ab initio molecular dynamics simulations. The excess proton is always found to be attached to an ammonia molecule to form the ammonium ion. Migration of the excess proton is found to occur very occasionally from one ammonia to the other but no proton transfer to a water molecule is observed during the entire simulations. Also, when the ammonium ion is solvated in water only, its hydrogen bond dynamics and rotation are found to occur at a faster rate than those in water-ammonia mixtures. For water-ammonia mixtures containing a proton less, the defect is found to stay like the hydroxide ion. For these systems, occasional proton transfer is found to occur only through the hydrogen bonded chains of water molecules in these water-ammonia mixtures. No proton transfer is found to take place from an ammonia molecule. The presence of ammonia molecules makes the realization of proper presolvated state of the hydroxide ion to accept a proton a more difficult process and, as a result, the rate of proton transfer and migration kinetics of the hydroxide ion in water-ammonia mixtures are found to be slower than that in liquid water and these rates are found to slow down further with increase of ammonia concentration.

  9. First-principles studies on molecular beam epitaxy growth of GaAs1-xBix

    SciTech Connect

    Luo, Guangfu; Yang, Shujiang; Li, Jincheng; Arjmand, Mehrdad; Szlufarska, Izabela; Brown, April S.; Kuech, Thomas F.; Morgan, Dane

    2015-07-14

    We investigate the molecular beam epitaxy (MBE) growth of GaAs1-xBix film using density functional theory with spin-orbit coupling to understand the growth of this film, especially the mechanisms of Bi incorporation. We study the stable adsorption structures and kinetics of the incident molecules (As₂ molecule, Ga atom, Bi atom, and Bi₂ molecule) on the (2 x 1)-Gasub||Bi surface and a proposed q(1 x 1)-Gasub||AsAs surface has a quasi-(1 x 1) As layer above the Ga-terminated GaAs substrate and a randomly oriented As dimer layer on top. We obtain the desorption and diffusion barriers of the adsorbed molecules and also the reaction barriers of three key processes related to Bi evolution, namely, Bi incorporation, As/Bi exchange, and Bi clustering. The results help explain the experimentally observed dependence of Bi incorporation on the As/Ga ratio and growth temperature. Furthermore, we find that As₂ exchange with Bi of the (2 x 1)-Gasub||Bi surface is a key step controlling the kinetics of the Bi incorporation. Finally, we explore two possible methods to enhance the Bi incorporation, namely, replacing the MBE growth mode from codeposition of all fluxes with a sequential deposition of fluxes and applying asymmetric in-plane strain to the substrate.

  10. Phonon-phonon interactions: First principles theory

    SciTech Connect

    Gibbons, T. M.; Bebek, M. B.; Kang, By.; Stanley, C. M.; Estreicher, S. K.

    2015-08-28

    We present the details of a method to perform molecular-dynamics (MD) simulations without thermostat and with very small temperature fluctuations ±ΔT starting with MD step 1. It involves preparing the supercell at the time t = 0 in physically correct microstates using the eigenvectors of the dynamical matrix. Each initial microstate corresponds to a different distribution of kinetic and potential energies for each vibrational mode (the total energy of each microstate is the same). Averaging the MD runs over many initial microstates further reduces ΔT. The electronic states are obtained using first-principles theory (density-functional theory in periodic supercells). Three applications are discussed: the lifetime and decay of vibrational excitations, the isotope dependence of thermal conductivities, and the flow of heat at an interface.

  11. Iron diffusion from first principles calculations

    NASA Astrophysics Data System (ADS)

    Wann, E.; Ammann, M. W.; Vocadlo, L.; Wood, I. G.; Lord, O. T.; Brodholt, J. P.; Dobson, D. P.

    2013-12-01

    The cores of Earth and other terrestrial planets are made up largely of iron1 and it is therefore very important to understand iron's physical properties. Chemical diffusion is one such property and is central to many processes, such as crystal growth, and viscosity. Debate still surrounds the explanation for the seismologically observed anisotropy of the inner core2, and hypotheses include convection3, anisotropic growth4 and dendritic growth5, all of which depend on diffusion. In addition to this, the main deformation mechanism at the inner-outer core boundary is believed to be diffusion creep6. It is clear, therefore, that to gain a comprehensive understanding of the core, a thorough understanding of diffusion is necessary. The extremely high pressures and temperatures of the Earth's core make experiments at these conditions a challenge. Low-temperature and low-pressure experimental data must be extrapolated across a very wide gap to reach the relevant conditions, resulting in very poorly constrained values for diffusivity and viscosity. In addition to these dangers of extrapolation, preliminary results show that magnetisation plays a major role in the activation energies for diffusion at low pressures therefore creating a break down in homologous scaling to high pressures. First principles calculations provide a means of investigating diffusivity at core conditions, have already been shown to be in very good agreement with experiments7, and will certainly provide a better estimate for diffusivity than extrapolation. Here, we present first principles simulations of self-diffusion in solid iron for the FCC, BCC and HCP structures at core conditions in addition to low-temperature and low-pressure calculations relevant to experimental data. 1. Birch, F. Density and composition of mantle and core. Journal of Geophysical Research 69, 4377-4388 (1964). 2. Irving, J. C. E. & Deuss, A. Hemispherical structure in inner core velocity anisotropy. Journal of Geophysical

  12. First principles nonequilibrium plasma mixing

    NASA Astrophysics Data System (ADS)

    Ticknor, C.; Herring, S. D.; Lambert, F.; Collins, L. A.; Kress, J. D.

    2014-01-01

    We have performed nonequilibrium classical and quantum-mechanical molecular dynamics simulations that follow the interpenetration of deuterium-tritium (DT) and carbon (C) components through an interface initially in hydrostatic and thermal equilibrium. We concentrate on the warm, dense matter regime with initial densities of 2.5-5.5 g/cm3 and temperatures from 10 to 100 eV. The classical treatment employs a Yukawa pair-potential with the parameters adjusted to the plasma conditions, and the quantum treatment rests on an orbital-free density functional theory at the Thomas-Fermi-Dirac level. For times greater than about a picosecond, the component concentrations evolve in accordance with Fick's law for a classically diffusing fluid with the motion, though, described by the mutual diffusion coefficient of the mixed system rather than the self-diffusion of the individual components. For shorter times, microscopic processes control the clearly non-Fickian dynamics and require a detailed representation of the electron probability density in space and time.

  13. Intrinsic ferroelectric switching from first principles

    NASA Astrophysics Data System (ADS)

    Liu, Shi; Grinberg, Ilya; Rappe, Andrew M.

    2016-06-01

    The existence of domain walls, which separate regions of different polarization, can influence the dielectric, piezoelectric, pyroelectric and electronic properties of ferroelectric materials. In particular, domain-wall motion is crucial for polarization switching, which is characterized by the hysteresis loop that is a signature feature of ferroelectric materials. Experimentally, the observed dynamics of polarization switching and domain-wall motion are usually explained as the behaviour of an elastic interface pinned by a random potential that is generated by defects, which appear to be strongly sample-dependent and affected by various elastic, microstructural and other extrinsic effects. Theoretically, connecting the zero-kelvin, first-principles-based, microscopic quantities of a sample with finite-temperature, macroscopic properties such as the coercive field is critical for material design and device performance; and the lack of such a connection has prevented the use of techniques based on ab initio calculations for high-throughput computational materials discovery. Here we use molecular dynamics simulations of 90° domain walls (separating domains with orthogonal polarization directions) in the ferroelectric material PbTiO3 to provide microscopic insights that enable the construction of a simple, universal, nucleation-and-growth-based analytical model that quantifies the dynamics of many types of domain walls in various ferroelectrics. We then predict the temperature and frequency dependence of hysteresis loops and coercive fields at finite temperatures from first principles. We find that, even in the absence of defects, the intrinsic temperature and field dependence of the domain-wall velocity can be described with a nonlinear creep-like region and a depinning-like region. Our model enables quantitative estimation of coercive fields, which agree well with experimental results for ceramics and thin films. This agreement between model and experiment suggests

  14. Intrinsic ferroelectric switching from first principles.

    PubMed

    Liu, Shi; Grinberg, Ilya; Rappe, Andrew M

    2016-06-16

    The existence of domain walls, which separate regions of different polarization, can influence the dielectric, piezoelectric, pyroelectric and electronic properties of ferroelectric materials. In particular, domain-wall motion is crucial for polarization switching, which is characterized by the hysteresis loop that is a signature feature of ferroelectric materials. Experimentally, the observed dynamics of polarization switching and domain-wall motion are usually explained as the behaviour of an elastic interface pinned by a random potential that is generated by defects, which appear to be strongly sample-dependent and affected by various elastic, microstructural and other extrinsic effects. Theoretically, connecting the zero-kelvin, first-principles-based, microscopic quantities of a sample with finite-temperature, macroscopic properties such as the coercive field is critical for material design and device performance; and the lack of such a connection has prevented the use of techniques based on ab initio calculations for high-throughput computational materials discovery. Here we use molecular dynamics simulations of 90° domain walls (separating domains with orthogonal polarization directions) in the ferroelectric material PbTiO3 to provide microscopic insights that enable the construction of a simple, universal, nucleation-and-growth-based analytical model that quantifies the dynamics of many types of domain walls in various ferroelectrics. We then predict the temperature and frequency dependence of hysteresis loops and coercive fields at finite temperatures from first principles. We find that, even in the absence of defects, the intrinsic temperature and field dependence of the domain-wall velocity can be described with a nonlinear creep-like region and a depinning-like region. Our model enables quantitative estimation of coercive fields, which agree well with experimental results for ceramics and thin films. This agreement between model and experiment suggests

  15. First principles model of carbonate compaction creep

    NASA Astrophysics Data System (ADS)

    Keszthelyi, Daniel; Dysthe, Dag Kristian; Jamtveit, Bjørn

    2016-05-01

    Rocks under compressional stress conditions are subject to long-term creep deformation. From first principles we develop a simple micromechanical model of creep in rocks under compressional stress that combines microscopic fracturing and pressure solution. This model was then upscaled by a statistical mechanical approach to predict strain rate at core and reservoir scale. The model uses no fitting parameter and has few input parameters: effective stress, temperature, water saturation porosity, and material parameters. Material parameters are porosity, pore size distribution, Young's modulus, interfacial energy of wet calcite, the dissolution, and precipitation rates of calcite, and the diffusion rate of calcium carbonate, all of which are independently measurable without performing any type of deformation or creep test. Existing long-term creep experiments were used to test the model which successfully predicts the magnitude of the resulting strain rate under very different effective stress, temperature, and water saturation conditions. The model was used to predict the observed compaction of a producing chalk reservoir.

  16. Materials Databases Infrastructure Constructed by First Principles Calculations: A Review

    SciTech Connect

    Lin, Lianshan

    2015-10-13

    The First Principles calculations, especially the calculation based on High-Throughput Density Functional Theory, have been widely accepted as the major tools in atom scale materials design. The emerging super computers, along with the powerful First Principles calculations, have accumulated hundreds of thousands of crystal and compound records. The exponential growing of computational materials information urges the development of the materials databases, which not only provide unlimited storage for the daily increasing data, but still keep the efficiency in data storage, management, query, presentation and manipulation. This review covers the most cutting edge materials databases in materials design, and their hot applications such as in fuel cells. By comparing the advantages and drawbacks of these high-throughput First Principles materials databases, the optimized computational framework can be identified to fit the needs of fuel cell applications. The further development of high-throughput DFT materials database, which in essence accelerates the materials innovation, is discussed in the summary as well.

  17. A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: Multi-center molecular Ornstein–Zernike self-consistent field approach

    SciTech Connect

    Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

    2015-07-07

    In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein–Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple S{sub N}2 reaction (Cl{sup −} + CH{sub 3}Cl → ClCH{sub 3} + Cl{sup −}) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

  18. A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: Multi-center molecular Ornstein-Zernike self-consistent field approach

    NASA Astrophysics Data System (ADS)

    Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

    2015-07-01

    In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl- + CH3Cl → ClCH3 + Cl-) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

  19. A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: multi-center molecular Ornstein-Zernike self-consistent field approach.

    PubMed

    Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

    2015-07-01

    In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl(-) + CH3Cl → ClCH3 + Cl(-)) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF. PMID:26156461

  20. Description of charge conjugation from first principles

    SciTech Connect

    Lujan-Peschard, C.; Napsuciale, M.

    2006-09-25

    We construct the charge conjugation operator as a unitary automorphism in the spinor space ((1/2), 0) + (0 (1/2)) from first principles. We calculate its eigenspinors and derive the equation of motion they satisfy. The mapping associated to charge conjugation is constructed from parity eigenstates which are considered as particle and antiparticle.

  1. First-principles calculation of dielectric response in molecule-based materials.

    PubMed

    Heitzer, Henry M; Marks, Tobin J; Ratner, Mark A

    2013-07-01

    The dielectric properties of materials are of fundamental significance to many chemical processes and the functioning of numerous solid-state device technologies. While experimental methods for measuring bulk dielectric constants are well-established, far less is known, either experimentally or theoretically, about the origin of dielectric response at the molecular/multimolecular scale. In this contribution we report the implementation of an accurate first-principles approach to calculating the dielectric response of molecular systems. We assess the accuracy of the method by reproducing the experimental dielectric constants of several bulk π-electron materials and demonstrating the ability of the method to capture dielectric properties as a function of frequency and molecular orientation in representative arrays of substituted aromatic derivatives. The role of molecular alignment and packing density on dielectric response is also examined, showing that the local dielectric behavior of molecular assemblies can diverge significantly from that of the bulk material. PMID:23734640

  2. Interface Structure Prediction from First-Principles

    SciTech Connect

    Zhao, Xin; Shu, Qiang; Nguyen, Manh Cuong; Wang, Yangang; Ji, Min; Xiang, Hongjun; Ho, Kai-Ming; Gong, Xingao; Wang, Cai-Zhuang

    2014-05-08

    Information about the atomic structures at solid–solid interfaces is crucial for understanding and predicting the performance of materials. Due to the complexity of the interfaces, it is very challenging to resolve their atomic structures using either experimental techniques or computer simulations. In this paper, we present an efficient first-principles computational method for interface structure prediction based on an adaptive genetic algorithm. This approach significantly reduces the computational cost, while retaining the accuracy of first-principles prediction. The method is applied to the investigation of both stoichiometric and nonstoichiometric SrTiO3 Σ3(112)[1¯10] grain boundaries with unit cell containing up to 200 atoms. Several novel low-energy structures are discovered, which provide fresh insights into the structure and stability of the grain boundaries.

  3. First-principles transversal DNA conductance deconstructed

    SciTech Connect

    Zhang, Xiaoguang; Krstic, Predrag; Zikic, Radomir; Wells, Jack C; Fuentes-Cabrera, Miguel A

    2006-01-01

    First-principles calculation of the transverse conductance across DNA fragments placed between gold nanoelectrodes, reveals that such conductance describes electron tunneling that depends critically on geometrical rather than electronic-structure properties. By factoring the first-principles result into two simple and approximately independent tunneling factors, we show that the conductances of the A, C, G, and T fragments differ only because of their sizes: the larger is the DNA base, the smaller is the distance that separates the electrode from the corresponding molecule, and the larger is its conductance. Because the geometrical factors are difficult to control in an experiment, the DC-current measurements across DNA may not be a convenient approach to DNA sequencing.

  4. First principles determination of dislocation properties.

    SciTech Connect

    Hamilton, John C.

    2003-12-01

    This report details the work accomplished on first principles determination of dislocation properties. It contains an introduction and three chapters detailing three major accomplishments. First, we have used first principle calculations to determine the shear strength of an aluminum twin boundary. We find it to be remarkably small ({approx}17 mJ/m{sup 2}). This unexpected result is explained and will likely pertain for many other grain boundaries. Second, we have proven that the conventional explanation for finite grain boundary facets is wrong for a particular aluminum grain boundary. Instead of finite facets being stabilized by grain boundary stress, we find them to originate from kinetic effects. Finally we report on a new application of the Frenkel-Kontorova model to understand reconstructions of (100) type surfaces. In addition to the commonly accepted formation of rectangular dislocation arrays, we find numerous other possible solutions to the model including hexagonal reconstructions and a clock-rotated structure.

  5. First principles semiclassical calculations of vibrational eigenfunctions.

    PubMed

    Ceotto, Michele; Valleau, Stéphanie; Tantardini, Gian Franco; Aspuru-Guzik, Alán

    2011-06-21

    Vibrational eigenfunctions are calculated on-the-fly using semiclassical methods in conjunction with ab initio density functional theory classical trajectories. Various semiclassical approximations based on the time-dependent representation of the eigenfunctions are tested on an analytical potential describing the chemisorption of CO on Cu(100). Then, first principles semiclassical vibrational eigenfunctions are calculated for the CO(2) molecule and its accuracy evaluated. The multiple coherent states initial value representations semiclassical method recently developed by us has shown with only six ab initio trajectories to evaluate eigenvalues and eigenfunctions at the accuracy level of thousands trajectory semiclassical initial value representation simulations. PMID:21837839

  6. First principles calculations for lithiated manganese oxides.

    SciTech Connect

    Prasad, R.

    1998-12-23

    First principles calculations within the local-spin-density-functional theory (LSDFF) framework are presented of densities of electronic states for MnO, LiMnO{sub 2} in the monoclinic and orthorhombic structures, cubic LiMn{sub 2}O{sub 4} spinel and {lambda}-MnO{sub 2} (delithiated spinel), all in antiferromagnetic spin configurations. The changes in energy spectra as the Mn oxidation state varies between 2+ and 4+ are illustrated. Preliminary calculations for Co-doped LiMnO{sub 2} are presented, and the destabilization of a monoclinic relative to a rhombohedral structure is discussed.

  7. Atomistic models of hydrogenated amorphous silicon nitride from first principles

    NASA Astrophysics Data System (ADS)

    Jarolimek, K.; de Groot, R. A.; de Wijs, G. A.; Zeman, M.

    2010-11-01

    We present a theoretical study of hydrogenated amorphous silicon nitride (a-SiNx:H) , with equal concentrations of Si and N atoms (x=1) , for two considerably different densities (2.0 and 3.0g/cm3 ). Densities and hydrogen concentration were chosen according to experimental data. Using first-principles molecular-dynamics within density-functional theory the models were generated by cooling from the liquid. Where both models have a short-range order resembling that of crystalline Si3N4 because of their different densities and hydrogen concentrations they show marked differences at longer length scales. The low-density nitride forms a percolating network of voids with the internal surfaces passivated by hydrogen. Although some voids are still present for the high-density nitride, this material has a much denser and uniform space filling. The structure factors reveal some tendency for the nonstoichiometric high-density nitride to phase separate into nitrogen rich and poor areas. For our slowest cooling rate (0.023 K/fs) we obtain models with a modest number of defect states, where the low (high) density nitride favors undercoordinated (overcoordinated) defects. Analysis of the structural defects and electronic density of states shows that there is no direct one-to-one correspondence between the structural defects and states in the gap. There are several structural defects that do not contribute to in-gap states and there are in-gap states that do only have little to no contributions from (atoms in) structural defects. Finally an estimation of the size and cooling rate effects on the amorphous network is reported.

  8. Materials Databases Infrastructure Constructed by First Principles Calculations: A Review

    DOE PAGESBeta

    Lin, Lianshan

    2015-10-13

    The First Principles calculations, especially the calculation based on High-Throughput Density Functional Theory, have been widely accepted as the major tools in atom scale materials design. The emerging super computers, along with the powerful First Principles calculations, have accumulated hundreds of thousands of crystal and compound records. The exponential growing of computational materials information urges the development of the materials databases, which not only provide unlimited storage for the daily increasing data, but still keep the efficiency in data storage, management, query, presentation and manipulation. This review covers the most cutting edge materials databases in materials design, and their hotmore » applications such as in fuel cells. By comparing the advantages and drawbacks of these high-throughput First Principles materials databases, the optimized computational framework can be identified to fit the needs of fuel cell applications. The further development of high-throughput DFT materials database, which in essence accelerates the materials innovation, is discussed in the summary as well.« less

  9. First-principles study of complex material systems

    NASA Astrophysics Data System (ADS)

    He, Lixin

    This thesis covers several topics concerning the study of complex materials systems by first-principles methods. It contains four chapters. A brief, introductory motivation of this work will be given in Chapter 1. In Chapter 2, I will give a short overview of the first-principles methods, including density-functional theory (DFT), planewave pseudopotential methods, and the Berry-phase theory of polarization in crystallines insulators. I then discuss in detail the locality and exponential decay properties of Wannier functions and of related quantities such as the density matrix, and their application in linear-scaling algorithms. In Chapter 3, I investigate the interaction of oxygen vacancies and 180° domain walls in tetragonal PbTiO3 using first-principles methods. Our calculations indicate that the oxygen vacancies have a lower formation energy in the domain wall than in the bulk, thereby confirming the tendency of these defects to migrate to, and pin, the domain walls. The pinning energies are reported for each of the three possible orientations of the original Ti--O--Ti bonds, and attempts to model the results with simple continuum models are discussed. CaCu3Ti4O12 (CCTO) has attracted a lot of attention recently because it was found to have an enormous dielectric response over a very wide temperature range. In Chapter 4, I study the electronic and lattice structure, and the lattice dynamical properties, of this system. Our first-principles calculations together with experimental results point towards an extrinsic mechanism as the origin of the unusual dielectric response.

  10. First principles studies on anatase surfaces

    NASA Astrophysics Data System (ADS)

    Selcuk, Sencer

    TiO2 is one of the most widely studied metal oxides from both the fundamental and the technological points of view. A variety of applications have already been developed in the fields of energy production, environmental remediation, and electronics. Still, it is considered to have a high potential for further improvement and continues to be of great interest. This thesis describes our theoretical studies on the structural and electronic properties of anatase surfaces, and their (photo)chemical behavior. Recently much attention has been focused on anatase crystals synthesized by hydrofluoric acid assisted methods. These crystals exhibit a high percentage of {001} facets, generally considered to be highly reactive. We used first principles methods to investigate the structure of these facets, which is not yet well understood. Our results suggest that (001) surfaces exhibit the bulk-terminated structure when in contact with concentrated HF solutions. However, 1x4-reconstructed surfaces, as observed in UHV, become always more stable at the typical temperatures used to clean the as-prepared crystals in experiments. Since the reconstructed surfaces are only weakly reactive, we predict that synthetic anatase crystals with dominant {001} facets should not exhibit enhanced photocatalytic activity. Understanding how defects in solids interact with external electric fields is important for technological applications such as memristor devices. We studied the influence of an external electric field on the formation energies and diffusion barriers of the surface and the subsurface oxygen vacancies at the anatase (101) surface from first principles. Our results show that the applied field can have a significant influence on the relative stabilities of these defects, whereas the effect on the subsurface-to-surface defect migration is found to be relatively minor. Charge carriers play a key role in the transport properties and the surface chemistry of TiO2. Understanding their

  11. Numerical inductance calculations based on first principles.

    PubMed

    Shatz, Lisa F; Christensen, Craig W

    2014-01-01

    A method of calculating inductances based on first principles is presented, which has the advantage over the more popular simulators in that fundamental formulas are explicitly used so that a deeper understanding of the inductance calculation is obtained with no need for explicit discretization of the inductor. It also has the advantage over the traditional method of formulas or table lookups in that it can be used for a wider range of configurations. It relies on the use of fast computers with a sophisticated mathematical computing language such as Mathematica to perform the required integration numerically so that the researcher can focus on the physics of the inductance calculation and not on the numerical integration. PMID:25402467

  12. Safeguards First Principle Initiative (SFPI) Cost Model

    SciTech Connect

    Mary Alice Price

    2010-07-11

    The Nevada Test Site (NTS) began operating Material Control and Accountability (MC&A) under the Safeguards First Principle Initiative (SFPI), a risk-based and cost-effective program, in December 2006. The NTS SFPI Comprehensive Assessment of Safeguards Systems (COMPASS) Model is made up of specific elements (MC&A plan, graded safeguards, accounting systems, measurements, containment, surveillance, physical inventories, shipper/receiver differences, assessments/performance tests) and various sub-elements, which are each assigned effectiveness and contribution factors that when weighted and rated reflect the health of the MC&A program. The MC&A Cost Model, using an Excel workbook, calculates budget and/or actual costs using these same elements/sub-elements resulting in total costs and effectiveness costs per element/sub-element. These calculations allow management to identify how costs are distributed for each element/sub-element. The Cost Model, as part of the SFPI program review process, enables management to determine if spending is appropriate for each element/sub-element.

  13. First principle study of sodium decorated graphyne

    NASA Astrophysics Data System (ADS)

    Sarkar, Utpal; Bhattacharya, Barnali; Seriani, Nicola

    2015-11-01

    We present first-principles calculations of the electronic properties of Na-decorated graphyne. This structure of the graphyne family is a direct band gap semiconductor with a band gap of 0.44 eV in absence of sodium, but Na-decorated graphyne compounds are metallic, and can then be employed as carbon-based conductors. Metallization is due to charge donation from sodium to carbon. Pristine graphyne is more stable than Na-decorated graphyne, therefore is seems probable that, if this material should be employed as electrode in Na-ion batteries, it would lead to the formation of metallic sodium rather than well dispersed sodium ions. On the other side, this property might be useful if graphyne is employed in water desalination. Finally, the abrupt change from a semiconducting to a metallic state in presence of a small amount of sodium might be exploited in electronics, e.g. for the production of smooth metal-semiconductor interfaces through spatially selective deposition of sodium.

  14. Transition Metal Nitrides: A First Principles Study

    NASA Astrophysics Data System (ADS)

    Pathak, Ashish; Singh, A. K.

    2016-04-01

    The present work describes the structural stability and electronic and mechanical properties of transition metal nitrides (TmNs: B1 cubic structure (cF8, Fm ‾ overline 3 m)) using first principles density functional theory (DFT) within generalized gradient approximation (GGA). The lattice constant of TmNs increases with increasing the atomic radii of the transition metals. Stability of the TmNs decreases from IVB to VIB groups due to increase in formation energy/atom. The bonding characteristics of these nitrides have been explained based on electronic density of states and charge density. All the TmNs satisfy Born stability criteria in terms of elastic constants except CrN and MoN that do not exist in equilibrium binary phase diagrams. The groups IVB and V-VIB nitrides are associated with brittle and ductile behaviour based on G/B ratios, respectively. The estimated melting temperatures of these nitrides exhibit reasonably good agreement with calculated with B than those of the C11 for all nitrides.

  15. Methods for First-Principles Alloy Thermodynamics

    NASA Astrophysics Data System (ADS)

    van de Walle, Axel

    2013-11-01

    Traditional first-principles calculations excel at providing formation energies at absolute zero, but obtaining thermodynamic information at nonzero temperatures requires suitable sampling of all the excited states visited in thermodynamic equilibrium, which would be computationally prohibitive via brute-force quantum mechanical calculations alone. In the context of solid-state alloys, this issue can be addressed via the coarse-graining concept and the cluster expansion formalism. This process generates simple, effective Hamiltonians that accurately reproduce quantum mechanical calculation results and that can be used to efficiently sample configurational, vibrational, and electronic excitations and enable the prediction of thermodynamic properties at nonzero temperatures. Vibrational and electronic degrees of freedom are formally eliminated from the problem by writing the system's partition function in a nested form in which the inner sums can be readily evaluated to yield an effective Hamiltonian. The remaining outermost sum corresponds to atomic configurations and can be handled via Monte Carlo sampling driven by the resulting effective Hamiltonian, thereby delivering thermodynamic properties at nonzero temperatures. This article describes these techniques and their implementation in the alloy theoretic automated toolkit, an open-source software package. The methods are illustrated by applications to various alloy systems.

  16. THERMODYNAMIC MODELING AND FIRST-PRINCIPLES CALCULATIONS

    SciTech Connect

    Turchi, P; Abrikosov, I; Burton, B; Fries, S; Grimvall, G; Kaufman, L; Korzhavyi, P; Manga, R; Ohno, M; Pisch, A; Scott, A; Zhang, W

    2005-12-15

    The increased application of quantum mechanical-based methodologies to the study of alloy stability has required a re-assessment of the field. The focus is mainly on inorganic materials in the solid state. In a first part, after a brief overview of the so-called ab initio methods with their approximations, constraints, and limitations, recommendations are made for a good usage of first-principles codes with a set of qualifiers. Examples are given to illustrate the power and the limitations of ab initio codes. However, despite the ''success'' of these methodologies, thermodynamics of complex multi-component alloys, as used in engineering applications, requires a more versatile approach presently afforded within CALPHAD. Hence, in a second part, the links that presently exist between ab initio methodologies, experiments, and CALPHAD approach are examined with illustrations. Finally, the issues of dynamical instability and of the role of lattice vibrations that still constitute the subject of ample discussions within the CALPHAD community are revisited in the light of the current knowledge with a set of recommendations.

  17. First-principles investigation of electronic structures and properties of impurities in molecular solids and semiconductors: I. Muon and muonium in organic ferromagnets. II. Erbium in silicon-optoelectronic system

    NASA Astrophysics Data System (ADS)

    Jeong, Junho

    The first-principles Hartree-Fock theory is used to obtain the electronic structures and properties of three different systems. For the TEMPO system, the trapping sites were obtained near NO group site for muonium singlet and near chlorine and bridge nitrogen for muon. The calculated hyperfine interactions including relaxation and vibrational effect were used to compare the observed zero field muSR frequency 3.2 MHz. It has been concluded that the two trapping centers that can best explain the observed muSR frequency is trapped singlet muonium near the radical oxygen and a trapped muon site near the chlorine. The direction for the easy axis is determined to be the b-axis of the monoclinic lattice and also is obtained using the magnetic moment distributions in the ferromagnetic state in the absence of muon and muonium. The nuclear quadrupole coupling constants and asymmetry parameters (eta) have studied for the 35Cl, 17O, and 14N nuclei in the TEMPO system for the bare system and systems with trapped muon and muonium. Substantial influence of the muon and muonium on the coupling constants and eta for the nuclei close to the trapping sites have been observed for the systems with trapped muon and muonium. For the beta-NPNN, the observed muSR signal at zero field with frequency 2.1 MHz is assigned to the singlet muonium sites near the two oxygens of the two NO groups and the high frequency signal ascribed to an isotropic hyperfine constant of 400MHz is assigned to the trapped muon sites near the oxygen atoms of the NO groups. Er3+-Si material which emits 1.54 mum wavelength has led to interest in optoelectronic system. Using first-principles HF procedure, the locations of Er3+ in silicon cluster without codopant were determined. Since covalent radius of Er3+ is bigger than that of silicon, the first nearest and second nearest silicon of Er3+ for Hi (Er3+Si14H18), Ti (Er3+ Si10H16, Er3+Si26H 48), and Substitutional site (Er3+Si18H 36) applied relaxation effect. The

  18. Ziegler Natta heterogeneous catalysis by first principles computer experiments

    NASA Astrophysics Data System (ADS)

    Boero, M.; Parrinello, M.; Terakura, K.

    1999-09-01

    In this work we present a first attempt to study the polymerization process of ethylene in a realistic Ziegler-Natta heterogeneous system by means of first principles molecular dynamics. In particular, we simulate, in a very unbiased way, both the deposition of the catalyst TiCl 4 on the (110) active surface of a solid MgCl 2 support and the polymer chain formation. By using a constrained molecular dynamics approach, we work out the energetics and the reaction pathway of the polymerization process as it occurs in a laboratory or an industrial plant. The good agreement of the results of our simulations with the available experimental data indicates that these kinds of simulations can be used as a skilful approach to study the details of the reaction mechanism which are not accessible to experimental probes. This offers a tool to improve the production and/or to design reactants and products for practical use.

  19. Transversity from First Principles in QCD

    SciTech Connect

    Brodsky, Stanley J.; /SLAC /Southern Denmark U., CP3-Origins

    2012-02-16

    Transversity observables, such as the T-odd Sivers single-spin asymmetry measured in deep inelastic lepton scattering on polarized protons and the distributions which are measured in deeply virtual Compton scattering, provide important constraints on the fundamental quark and gluon structure of the proton. In this talk I discuss the challenge of computing these observables from first principles; i.e.; quantum chromodynamics, itself. A key step is the determination of the frame-independent light-front wavefunctions (LFWFs) of hadrons - the QCD eigensolutions which are analogs of the Schroedinger wavefunctions of atomic physics. The lensing effects of initial-state and final-state interactions, acting on LFWFs with different orbital angular momentum, lead to T-odd transversity observables such as the Sivers, Collins, and Boer-Mulders distributions. The lensing effect also leads to leading-twist phenomena which break leading-twist factorization such as the breakdown of the Lam-Tung relation in Drell-Yan reactions. A similar rescattering mechanism also leads to diffractive deep inelastic scattering, as well as nuclear shadowing and non-universal antishadowing. It is thus important to distinguish 'static' structure functions, the probability distributions computed the target hadron's light-front wavefunctions, versus 'dynamical' structure functions which include the effects of initial- and final-state rescattering. I also discuss related effects such as the J = 0 fixed pole contribution which appears in the real part of the virtual Compton amplitude. AdS/QCD, together with 'Light-Front Holography', provides a simple Lorentz-invariant color-confining approximation to QCD which is successful in accounting for light-quark meson and baryon spectroscopy as well as hadronic LFWFs.

  20. First principles investigation of substituted strontium hexaferrite

    NASA Astrophysics Data System (ADS)

    Dixit, Vivek

    This dissertation investigates how the magnetic properties of strontium hexaferrite change upon the substitution of foreign atoms at the Fe sites. Strontium hexaferrite, SrFe12O19, is a commonly used hard magnetic material and is produced in large quantities (around 500,000 tons per year). For different applications of strontium hexaferrite, its magnetic properties can be tuned by a proper substitution of the foreign atoms. Experimental screening for a proper substitution is a cost-intensive and time-consuming process, whereas computationally it can be done more efficiently. We used the 'density functional theory' a first principles based method to study substituted strontium hexaferrite. The site occupancies of the substituted atoms were estimated by calculating the substitution energies of different configurations. The formation probabilities of configurations were used to calculate the magnetic properties of substituted strontium hexaferrite. In the first study, Al-substituted strontium hexaferrite, SrFe12-x AlxO19 with x=0.5 and x=1.0 were investigated. It was found that at the annealing temperature the non-magnetic Al +3 ions preferentially replace Fe+3 ions from the 12 k and 2a sites. We found that the magnetization decreases and the magnetic anisotropy field increases as the fraction, x of the Al atoms increases. In the second study, SrFe12-xGaxO19 and SrFe12-xInxO19 with x=0.5 and x=1.0 were investigated. In the case of SrFe12-xGaxO19, the sites where Ga+3 ions prefer to enter are: 12 k, 2a, and 4f1. For SrFe12-xInxO19, In+3 ions most likely to occupy the 12k, 4f1 , and 4f2 sites. In both cases the magnetization was found to decrease slightly as the fraction of substituted atom increases. The magnetic anisotropy field increased for SrFe12-xGaxO 19, and decreased for SrFe12-xInxO19 as the concentration of substituted atoms increased. In the third study, 23 elements (M) were screened for their possible substitution in strontium hexaferrite, SrFe12-xMxO 19

  1. Adsorption of methylchloride on Si(100) from first principles

    NASA Astrophysics Data System (ADS)

    Romero, Aldo H.; Sbraccia, Carlo; Silvestrelli, Pier Luigi; Ancilotto, Francesco

    2003-07-01

    The chemisorption of methylchloride (CH3Cl) on Si(100) is studied from first principles. We find that, among a number of possible adsorption configurations, the lowest-energy structure is one in which the methylchloride molecule is dissociated into CH3 and Cl fragments which are bound to the two Si atoms of the same surface dimer. Our calculations show that dissociative chemisorption of methylchloride on Si(100) may proceed along different reaction paths characterized by different energy barriers that the system must overcome: some dissociation processes are mediated by a molecular precursor state and, at least in one case, we find that the dissociation process is nonactivated, in agreement with recent experimental findings. We have also generated, for many possible adsorption structures, theoretical scanning tunneling microscopy images which could facilitate the interpretation of experimental measurements.

  2. First Principles Dynamics of Photoexcited DNA and RNA Bases

    SciTech Connect

    Hudock, Hanneli R.; Levine, Benjamin G.; Thompson, Alexis L.; Martinez, Todd J.

    2007-12-26

    The reaction dynamics of excited electronic states in nucleic acid bases is a key process in DNA photodamage. Recent ultrafast spectroscopy experiments have shown multi-component decays of excited uracil and thymine, tentatively assigned to nonadiabatic transitions involving multiple electronic states. Using both quantum chemistry and first principles quantum molecular dynamics methods we show that a true minimum on the bright S{sub 2} electronic state is responsible for the first step which occurs on a femtosecond timescale. Thus the observed femtosecond decay does not correspond to surface crossing as previously thought. We suggest that subsequent barrier crossing to the minimal energy S{sub 2}/S{sub 1} conical intersection is responsible for the picosecond decay.

  3. First principles electron transport simulations in the Kondo regime

    NASA Astrophysics Data System (ADS)

    Rungger, Ivan; Radonjic, Milos; Appelt, Wilhelm; Chioncel, Liviu; Droghetti, Andrea

    When magnetic atoms, molecules or thin films are brought into contact with metals the electron-electron interaction leads to the appearance of the correlated Kondo state at low temperatures. In this talk we will present results for the electronic structure and conductance in the Kondo regime of recent STM and break junction experiments for stable radical molecules, which correspond to spin half molecular magnets. We will outline the methodological approach to evaluate the conductance of such systems from first principles, as implemented in the Smeagol electron transport code. The method combines the density functional theory (DFT) with Anderson impurity solvers within the continuum time quantum Monte Carlo (CTQMC) and numerical renormalization group (NRG) approaches.

  4. First-principles theory, coarse-grained models, and simulations of ferroelectrics.

    PubMed

    Waghmare, Umesh V

    2014-11-18

    CONSPECTUS: A ferroelectric crystal exhibits macroscopic electric dipole or polarization arising from spontaneous ordering of its atomic-scale dipoles that breaks inversion symmetry. Changes in applied pressure or electric field generate changes in electric polarization in a ferroelectric, defining its piezoelectric and dielectric properties, respectively, which make it useful as an electromechanical sensor and actuator in a number of applications. In addition, a characteristic of a ferroelectric is the presence of domains or states with different symmetry equivalent orientations of spontaneous polarization that are switchable with large enough applied electric field, a nonlinear property that makes it useful for applications in nonvolatile memory devices. Central to these properties of a ferroelectric are the phase transitions it undergoes as a function of temperature that involve lowering of the symmetry of its high temperature centrosymmetric paraelectric phase. Ferroelectricity arises from a delicate balance between short and long-range interatomic interactions, and hence the resulting properties are quite sensitive to chemistry, strains, and electric charges associated with its interface with substrate and electrodes. First-principles density functional theoretical (DFT) calculations have been very effective in capturing this and predicting material and environment specific properties of ferroelectrics, leading to fundamental insights into origins of ferroelectricity in oxides and chalcogenides uncovering a precise picture of electronic hybridization, topology, and mechanisms. However, use of DFT in molecular dynamics for detailed prediction of ferroelectric phase transitions and associated temperature dependent properties has been limited due to large length and time scales of the processes involved. To this end, it is quite appealing to start with input from DFT calculations and construct material-specific models that are realistic yet simple for use in

  5. Molecular dynamics and first-principles studies of structural change in 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) in crystalline state under high pressure: Comparison of hydrogen bond systems of TATB versus 1,3-diamino-2,4,6-trinitrobenzene (DATB)

    NASA Astrophysics Data System (ADS)

    Kohno, Yuji; Mori, Kazuki; Hiyoshi, Reiko I.; Takahashi, Osamu; Ueda, Kazuyoshi

    2016-06-01

    Classical molecular dynamics (MD) calculations were performed to reveal the effect of high pressure on the crystal structure of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), an insensitive energetic material. The primary simulation cell consisted of 54 molecules in a triclinic cell, corresponding to 27 unit cells obtained by replicating the experimentally determined unit cell. Inter- and intra-molecular hydrogen bonds were maintained in the range of 1.0 atm to 20.0 GPa as pressure was incremented by 0.5 GPa. The pressure dependence of the interlayer distances (h1) and farthest intermolecular distance (d1) between nitro groups in the TATB crystal's unit cell was investigated in the same range. h1 decreased monotonously from 3.50 to 2.90 Å as pressure increased to 20.0 GPa. However, d1 increased considerably with pressure up to 4.0 GPa, most remarkably between 2.0 and 4.0 GPa. Thus, a unique structural change occurred in TATB crystal in this range. On the other hand, 1,3-diamino-2,4,6-trinitrobenzene (DATB) crystal showed a unique structural change between 7.0 and 8.0 GPa. These discrepancies are attributed to the different network systems of hydrogen bonding of these two molecules. To validate the MD calculation results, we conducted first-principles calculations. MD and first-principles calculations showed good agreement with previous experimental results.

  6. Thermodynamics of Magnetic Systems from First Principles: WL-LSMS

    SciTech Connect

    Eisenbach, Markus; Zhou, Chenggang; Nicholson, Don M; Brown, Greg; Larkin, Jeffrey M; Schulthess, Thomas C

    2010-01-01

    Density Functional calculations have proven to be a powerful tool to study the ground state of many materials. For finite temperatures the situation is less ideal and one is often forced to rely on models with parameters either fitted to zero temperature first principles calculations or experimental results. This approach is especially unsatisfacory in inhomogeneous systems, nano particles, or other systems where the model parameters could vary significantly from one site to another. Here we describe a possible solution to this problem by combining classical Monte Carlo calculations the Wang-Landau method in this case with a firs principles electronic structure calculation, specifically our locally selfconsistent multiple scallering code (LSMS). The combined code shows superb scaling behavior on massively parallel computers. The code sustained 1.836 Petaflop/s on 223232 cores of the Cray XT5 jaguar system at Oak Ridge.

  7. Auger recombination in sodium-iodide scintillators from first principles

    SciTech Connect

    McAllister, Andrew; Åberg, Daniel; Schleife, André; Kioupakis, Emmanouil

    2015-04-06

    Scintillator radiation detectors suffer from low energy resolution that has been attributed to non-linear light yield response to the energy of the incident gamma rays. Auger recombination is a key non-radiative recombination channel that scales with the third power of the excitation density and may play a role in the non-proportionality problem of scintillators. In this work, we study direct and phonon-assisted Auger recombination in NaI using first-principles calculations. Our results show that phonon-assisted Auger recombination, mediated primarily by short-range phonon scattering, dominates at room temperature. We discuss our findings in light of the much larger values obtained by numerical fits to z-scan experiments.

  8. Vibrational and Thermophysical Properties of PETN from First Principles

    NASA Astrophysics Data System (ADS)

    Gonzalez, Joseph; Landerville, Aaron; Oleynik, Ivan

    2015-06-01

    Thermophysical properties are urgently sought as input for meso- and continuum-scale modeling of energetic materials (EMs). However, empirical data in this regard are often limited to specific pressures and temperatures. Such modeling of EMs can be greatly improved by inclusion of thermophysical properties over a wide range of pressures and temperatures, provided such data could be reliably obtained from theory. We demonstrate such a capability by calculating the equation of state, heat capacities, coefficients of thermal expansion, and Gruneissen parameters for pentaerythritol tetranitrate (PETN) using first-principles density functional theory, which includes proper description of van der Waals interactions and zero-point and thermal free energy contributions to pressure, the latter being calculated using the quasi-harmonic approximation. Further, we investigate the evolution of the vibration spectrum of PETN as a function of pressure.

  9. First principles modeling of grain boundaries in CdTe

    NASA Astrophysics Data System (ADS)

    Chan, Maria K. Y.; Sen, Fatih; Buurma, Christopher; Paulauskas, Tadas; Sun, Ce; Kim, Moon; Klie, Robert

    The role of extended defects is of significant interest for semiconductors, especially photovoltaics since energy conversion efficiencies are often affected by such defects. In particular, grain boundaries in CdTe photovoltaics are enigmatic since the achievable efficiencies of CdTe photovoltaics are higher in polycrystalline devices as compared to single crystalline devices. Yet, despite recent advances, the efficiency of poly-CdTe devices are still substantially below the theoretical maximum. We carry out an atomistic-level study using Scanning Transmission Electron Microscopy (STEM), together with first principles density functional theory (DFT) modeling, in order to understand the properties of specific bicrystals, i.e. artificial grain boundaries, constructed using wafer bonding. We discuss examples of bicrystals, including some involving large scale DFT calculations, and trends in defect and electronic properties. This work was funded by DOE SunShot BRIDGE program.

  10. Optimized Materials From First Principles Simulations: Are We There Yet?

    SciTech Connect

    Galli, G; Gygi, F

    2005-07-26

    In the past thirty years, the use of scientific computing has become pervasive in all disciplines: collection and interpretation of most experimental data is carried out using computers, and physical models in computable form, with various degrees of complexity and sophistication, are utilized in all fields of science. However, full prediction of physical and chemical phenomena based on the basic laws of Nature, using computer simulations, is a revolution still in the making, and it involves some formidable theoretical and computational challenges. We illustrate the progress and successes obtained in recent years in predicting fundamental properties of materials in condensed phases and at the nanoscale, using ab-initio, quantum simulations. We also discuss open issues related to the validation of the approximate, first principles theories used in large scale simulations, and the resulting complex interplay between computation and experiment. Finally, we describe some applications, with focus on nanostructures and liquids, both at ambient and under extreme conditions.

  11. Dissolved carbon in extreme conditions characterized by first principles simulations

    NASA Astrophysics Data System (ADS)

    Pan, Ding; Galli, Giulia

    One key component to understanding carbon transport in the Earth interior is the determination of the molecular species formed when carbon bearing materials are dissolved in water at extreme conditions. We used first principles molecular dynamics to investigate oxidized carbon in water at high pressure (P) and high temperature (T), up to the conditions of the Earth's upper mantle. Contrary to popular geochemistry models assuming that CO2 is the major carbon species present in water, we found that most of the dissolved carbon at 10 GPa and 1000 K is in the form of solvated CO32- and HCO3-anions. We also found that ion pairing between alkali metal cations and CO32- or HCO3-anions is greatly affected by P-T conditions, decreasing with pressure along an isotherm. Our study shows that it is crucial to take into account the specific molecular structure of water under extreme conditions and the changes in hydrogen bonding occurring at high P and T, in order to predict chemical reactions in dissolved carbon. Our findings also shed light on possible reduction mechanisms of CO2 when it is geologically stored, depending on the availability of water. The work is supported by the Sloan Foundation through the Deep Carbon Observatory.

  12. Transport Properties of Nanoscale Materials by First-principles Calculations

    NASA Astrophysics Data System (ADS)

    Mizuseki, Hiroshi; Belosludov, Rodion V.; Lee, S.-U.; Kawazoe, Yoshiyuki

    2009-03-01

    Molecular devices are potential candidates for the next step towards nanoelectronic technology. Our group has covered a wide range of nanoscale wires, which have potential application in molecular electronics using first-principles calculations and nonequilibrium Green's function formalism [1]. Our target materials are supramolecular enamel wires (covered wires) [2], connection between organic molecules and metal electrodes, self-assembled nanowires on silicon surface [3], porphyrin [4], phthalocyanine, metallocene [5], fused-ring thiophene molecules, length dependence of conductance in alkanedithiols and so on. Namely, we have investigated a relationship of the energy levels of delocalized frontier orbitals (HOMO and LUMO) and Fermi level of metal electrodes and estimate the electronic transport properties through atomic and molecular wires using Green's function approach. References [1] http://www-lab.imr.edu/˜mizuseki/nanowire.html [2] R. V. Belosludov, A. A. Farajian, H. Baba, H. Mizuseki, and Y. Kawazoe, Jpn. J. Appl. Phys., 44, 2823 (2005). [3] R. V. Belosludov, A. A. Farajian, H. Mizuseki, K. Miki, and Y. Kawazoe, Phys. Rev. B, 75, 113411 (2007). [4] S.-U. Lee, R. V. Belosludov, H. Mizuseki, and Y. Kawazoe, Small 4 (2008) 962. [5] S.-U Lee, R. V. Belosludov, H. Mizuseki, and Y. Kawazoe, J. Phys. Chem. C. 111 (2007) 15397.

  13. First-principles design of nanomachines.

    PubMed

    Banavar, Jayanth R; Cieplak, Marek; Hoang, Trinh Xuan; Maritan, Amos

    2009-04-28

    Learning from nature's amazing molecular machines, globular proteins, we present a framework for the predictive design of nanomachines. We show that the crucial ingredients for a chain molecule to behave as a machine are its inherent anisotropy and the coupling between the local Frenet coordinate reference frames of nearby monomers. We demonstrate that, even in the absence of heterogeneity, protein-like behavior is obtained for a simple chain molecule made up of just 30 hard spheres. This chain spontaneously switches between 2 distinct geometries, a single helix and a dual helix, merely because of thermal fluctuations. PMID:19359489

  14. First-principles design of nanomachines

    PubMed Central

    Banavar, Jayanth R.; Cieplak, Marek; Hoang, Trinh Xuan; Maritan, Amos

    2009-01-01

    Learning from nature's amazing molecular machines, globular proteins, we present a framework for the predictive design of nanomachines. We show that the crucial ingredients for a chain molecule to behave as a machine are its inherent anisotropy and the coupling between the local Frenet coordinate reference frames of nearby monomers. We demonstrate that, even in the absence of heterogeneity, protein-like behavior is obtained for a simple chain molecule made up of just 30 hard spheres. This chain spontaneously switches between 2 distinct geometries, a single helix and a dual helix, merely because of thermal fluctuations. PMID:19359489

  15. First Principles Simulations of Nanoparticle Solids

    NASA Astrophysics Data System (ADS)

    Greenwood, Arin; Vörös, Márton; Galli, Giulia

    Nanoparticle solids are gaining popularity as materials for optoelectronic devices such as solar cells. However, there is still much debate regarding the transport regime governing the charge carriers. To date, no comprehensive description of transport mechanisms in nanoparticle solids has been established, and there is a lack of computational studies predicting electron mobilities and transport rates at the ab initio level. In order to understand electron transport properties, it is an essential prerequisite to build realistic structural models of nanoparticle solids to use for prediction of electronic structure and eventually transport properties. Here we present Ab Initio Molecular Dynamics simulations of lead chalcogenide nanoparticles and surrounding ligands to extract relevant electronic structure properties for charge transport calculations. We tested the validity of recently observed ''band-like'' transport by assessing the formation of bands and their dependence on nanoparticle surface structure and ligands. Work supported by DOE-BES under DE-FG02-06ER46262.

  16. Ions in solutions: Determining their polarizabilities from first-principles

    NASA Astrophysics Data System (ADS)

    Molina, John J.; Lectez, Sébastien; Tazi, Sami; Salanne, Mathieu; Dufrêche, Jean-François; Roques, Jérôme; Simoni, Eric; Madden, Paul A.; Turq, Pierre

    2011-01-01

    Dipole polarizabilities of a series of ions in aqueous solutions are computed from first-principles. The procedure is based on the study of the linear response of the maximally localized Wannier functions to an applied external field, within density functional theory. For most monoatomic cations (Li ^+, Na ^+, K ^+, Rb ^+, Mg ^{2+}, Ca ^{2+} and Sr ^{2+}) the computed polarizabilities are the same as in the gas phase. For Cs ^+ and a series of anions (F ^-, Cl ^-, Br ^- and I ^-), environmental effects are observed, which reduce the polarizabilities in aqueous solutions with respect to their gas phase values. The polarizabilities of H ^+_(aq), OH ^-_(aq) have also been determined along an ab initio molecular dynamics simulation. We observe that the polarizability of a molecule instantaneously switches upon proton transfer events. Finally, we also computed the polarizability tensor in the case of a strongly anisotropic molecular ion, UO _2^{2+}. The results of these calculations will be useful in building interaction potentials that include polarization effects.

  17. First-principles stability study of clathrate hydrates under pressure

    NASA Astrophysics Data System (ADS)

    Thonhauser, Timo; Li, Qi; Kolb, Brian

    2010-03-01

    We present a first-principles DFT study of the structural stability of clathrate hydrates under pressure. These materials form under high pressure and low temperature and consist of polyhedral water cages that form an ice-like framework of hydrogen bonds. Clathrate hydrates can be filled with guest molecules such as methane or molecular hydrogen, in which case these materials and their stability are of interest for energy-storage solutions. Since the interactions between the water molecules themselves---but also between the water molecules and the guest molecules---is at least partly determined by van der Waals forces, we utilize the recently developed self-consistent van der Waals density functional vdW-DF (T. Thonhauser, V.R. Cooper, S. Li, A. Puzder, P. Hyldgaard, and D.C. Langreth, Phys. Rev. B 76, 125112 (2007)). For our simulations we consider the empty host lattice, as well as the host lattice filled with methane and molecular hydrogen, for pressures up to 1 GPa. Our results show that the system undergoes phase transitions from structure I to structure II and finally to structure H, in good agreement with experiment.

  18. The high pressure structure and equation of state of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) up to 20 GPa: X-ray diffraction measurements and first principles molecular dynamics simulations

    SciTech Connect

    Stavou, Elissaios; Manaa, M. Riad; Zaug, Joseph M.; Kuo, I-Feng W.; Pagoria, Philip F.; Crowhurst, Jonathan C.; Armstrong, Michael R.; Kalkan, Bora

    2015-10-14

    Recent theoretical studies of 2,6-diamino-3,5-dinitropyrazine-1-oxide (C4H4N6O5 Lawrence Livermore Molecule No. 105, LLM-105) report unreacted high pressure equations of state that include several structural phase transitions, between 8 and 50 GPa, while one published experimental study reports equation of state (EOS) data up to a pressure of 6 GPa with no observed transition. Here we report the results of a synchrotron-based X-ray diffraction study and also ambient temperature isobaric-isothermal atomistic molecular dynamics simulations of LLM-105 up to 20 GPa. We find that the ambient pressure phase remains stable up to 20 GPa; there is no indication of a pressure induced phase transition. We do find a prominent decrease in b-axis compressibility starting at approximately 13 GPa and attribute the stiffening to a critical length where inter-sheet distance becomes similar to the intermolecular distance within individual sheets. The ambient temperature isothermal equation of state was determined through refinements of measured X-ray diffraction patterns. The pressure-volume data were fit using various EOS models to yield bulk moduli with corresponding pressure derivatives. As a result, we find very good agreement between the experimental and theoretically derived EOS.

  19. The high pressure structure and equation of state of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) up to 20 GPa: X-ray diffraction measurements and first principles molecular dynamics simulations

    DOE PAGESBeta

    Stavou, Elissaios; Manaa, M. Riad; Zaug, Joseph M.; Kuo, I-Feng W.; Pagoria, Philip F.; Crowhurst, Jonathan C.; Armstrong, Michael R.; Kalkan, Bora

    2015-10-14

    Recent theoretical studies of 2,6-diamino-3,5-dinitropyrazine-1-oxide (C4H4N6O5 Lawrence Livermore Molecule No. 105, LLM-105) report unreacted high pressure equations of state that include several structural phase transitions, between 8 and 50 GPa, while one published experimental study reports equation of state (EOS) data up to a pressure of 6 GPa with no observed transition. Here we report the results of a synchrotron-based X-ray diffraction study and also ambient temperature isobaric-isothermal atomistic molecular dynamics simulations of LLM-105 up to 20 GPa. We find that the ambient pressure phase remains stable up to 20 GPa; there is no indication of a pressure induced phasemore » transition. We do find a prominent decrease in b-axis compressibility starting at approximately 13 GPa and attribute the stiffening to a critical length where inter-sheet distance becomes similar to the intermolecular distance within individual sheets. The ambient temperature isothermal equation of state was determined through refinements of measured X-ray diffraction patterns. The pressure-volume data were fit using various EOS models to yield bulk moduli with corresponding pressure derivatives. As a result, we find very good agreement between the experimental and theoretically derived EOS.« less

  20. The high pressure structure and equation of state of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) up to 20 GPa: X-ray diffraction measurements and first principles molecular dynamics simulations.

    PubMed

    Stavrou, Elissaios; Riad Manaa, M; Zaug, Joseph M; Kuo, I-Feng W; Pagoria, Philip F; Kalkan, Bora; Crowhurst, Jonathan C; Armstrong, Michael R

    2015-10-14

    Recent theoretical studies of 2,6-diamino-3,5-dinitropyrazine-1-oxide (C4H4N6O5 Lawrence Livermore Molecule No. 105, LLM-105) report unreacted high pressure equations of state that include several structural phase transitions, between 8 and 50 GPa, while one published experimental study reports equation of state (EOS) data up to a pressure of 6 GPa with no observed transition. Here we report the results of a synchrotron-based X-ray diffraction study and also ambient temperature isobaric-isothermal atomistic molecular dynamics simulations of LLM-105 up to 20 GPa. We find that the ambient pressure phase remains stable up to 20 GPa; there is no indication of a pressure induced phase transition. We do find a prominent decrease in b-axis compressibility starting at approximately 13 GPa and attribute the stiffening to a critical length where inter-sheet distance becomes similar to the intermolecular distance within individual sheets. The ambient temperature isothermal equation of state was determined through refinements of measured X-ray diffraction patterns. The pressure-volume data were fit using various EOS models to yield bulk moduli with corresponding pressure derivatives. We find very good agreement between the experimental and theoretically derived EOS. PMID:26472388

  1. The high pressure structure and equation of state of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) up to 20 GPa: X-ray diffraction measurements and first principles molecular dynamics simulations

    SciTech Connect

    Stavrou, Elissaios Riad Manaa, M. Zaug, Joseph M.; Kuo, I-Feng W.; Pagoria, Philip F.; Crowhurst, Jonathan C.; Armstrong, Michael R.; Kalkan, Bora

    2015-10-14

    Recent theoretical studies of 2,6-diamino-3,5-dinitropyrazine-1-oxide (C{sub 4}H{sub 4}N{sub 6}O{sub 5} Lawrence Livermore Molecule No. 105, LLM-105) report unreacted high pressure equations of state that include several structural phase transitions, between 8 and 50 GPa, while one published experimental study reports equation of state (EOS) data up to a pressure of 6 GPa with no observed transition. Here we report the results of a synchrotron-based X-ray diffraction study and also ambient temperature isobaric-isothermal atomistic molecular dynamics simulations of LLM-105 up to 20 GPa. We find that the ambient pressure phase remains stable up to 20 GPa; there is no indication of a pressure induced phase transition. We do find a prominent decrease in b-axis compressibility starting at approximately 13 GPa and attribute the stiffening to a critical length where inter-sheet distance becomes similar to the intermolecular distance within individual sheets. The ambient temperature isothermal equation of state was determined through refinements of measured X-ray diffraction patterns. The pressure-volume data were fit using various EOS models to yield bulk moduli with corresponding pressure derivatives. We find very good agreement between the experimental and theoretically derived EOS.

  2. The high pressure structure and equation of state of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) up to 20 GPa: X-ray diffraction measurements and first principles molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Stavrou, Elissaios; Riad Manaa, M.; Zaug, Joseph M.; Kuo, I.-Feng W.; Pagoria, Philip F.; Kalkan, Bora; Crowhurst, Jonathan C.; Armstrong, Michael R.

    2015-10-01

    Recent theoretical studies of 2,6-diamino-3,5-dinitropyrazine-1-oxide (C4H4N6O5 Lawrence Livermore Molecule No. 105, LLM-105) report unreacted high pressure equations of state that include several structural phase transitions, between 8 and 50 GPa, while one published experimental study reports equation of state (EOS) data up to a pressure of 6 GPa with no observed transition. Here we report the results of a synchrotron-based X-ray diffraction study and also ambient temperature isobaric-isothermal atomistic molecular dynamics simulations of LLM-105 up to 20 GPa. We find that the ambient pressure phase remains stable up to 20 GPa; there is no indication of a pressure induced phase transition. We do find a prominent decrease in b-axis compressibility starting at approximately 13 GPa and attribute the stiffening to a critical length where inter-sheet distance becomes similar to the intermolecular distance within individual sheets. The ambient temperature isothermal equation of state was determined through refinements of measured X-ray diffraction patterns. The pressure-volume data were fit using various EOS models to yield bulk moduli with corresponding pressure derivatives. We find very good agreement between the experimental and theoretically derived EOS.

  3. Towards Experimental Accuracy from the First Principles

    NASA Astrophysics Data System (ADS)

    Polyansky, O. L.; Lodi, L.; Tennyson, J.; Zobov, N. F.

    2013-06-01

    Producing ab initio ro-vibrational energy levels of small, gas-phase molecules with an accuracy of 0.10 cm^{-1} would constitute a significant step forward in theoretical spectroscopy and would place calculated line positions considerably closer to typical experimental accuracy. Such an accuracy has been recently achieved for the H_3^+ molecular ion for line positions up to 17 000 cm ^{-1}. However, since H_3^+ is a two-electron system, the electronic structure methods used in this study are not applicable to larger molecules. A major breakthrough was reported in ref., where an accuracy of 0.10 cm^{-1} was achieved ab initio for seven water isotopologues. Calculated vibrational and rotational energy levels up to 15 000 cm^{-1} and J=25 resulted in a standard deviation of 0.08 cm^{-1} with respect to accurate reference data. As far as line intensities are concerned, we have already achieved for water a typical accuracy of 1% which supersedes average experimental accuracy. Our results are being actively extended along two major directions. First, there are clear indications that our results for water can be improved to an accuracy of the order of 0.01 cm^{-1} by further, detailed ab initio studies. Such level of accuracy would already be competitive with experimental results in some situations. A second, major, direction of study is the extension of such a 0.1 cm^{-1} accuracy to molecules containg more electrons or more than one non-hydrogen atom, or both. As examples of such developments we will present new results for CO, HCN and H_2S, as well as preliminary results for NH_3 and CH_4. O.L. Polyansky, A. Alijah, N.F. Zobov, I.I. Mizus, R. Ovsyannikov, J. Tennyson, L. Lodi, T. Szidarovszky and A.G. Csaszar, Phil. Trans. Royal Soc. London A, {370}, 5014-5027 (2012). O.L. Polyansky, R.I. Ovsyannikov, A.A. Kyuberis, L. Lodi, J. Tennyson and N.F. Zobov, J. Phys. Chem. A, (in press). L. Lodi, J. Tennyson and O.L. Polyansky, J. Chem. Phys. {135}, 034113 (2011).

  4. Materials corrosion and protection from first principles

    NASA Astrophysics Data System (ADS)

    Johnson, Donald F.

    suggests that alloying Fe with Si can be an effective means to limit uptake of these elements into steel. Spallation of protective layers on jet engine turbine blades is a problem that arises during thermal cycling. An alternative thermal barrier coating system involving MoSi2 is considered and calculations predict strong adhesion at the MoSi2/Ni interface. The interfacial bonding structure reveals a mixture of metallic and covalent cross-interface bonds. The adhesion energy is similar across all three MoSi2 facets studied. Upon exposure to oxygen, this MoSi2 alloy will form a strongly adhered oxide scale, which in turn may strongly adhere the heat shield material (yttria-stabilized zirconia), thereby potentially extending the lifetime of the barrier coating. Lastly, the interaction of hydrogen isotopes (fusion fuel) with tungsten (a proposed fusion reactor wall material) is examined. Exothermic dissociative adsorption is predicted, along with endothermic absorption and dissolution. Surface-to-subsurface diffusion energy barriers for H incorporation into bulk W are large and the corresponding outward diffusion barriers are very small. In bulk W, deep energetic traps (trapping multiple H atoms) are predicted at vacancy defects. Thus, under high neutron fluxes that will produce vacancies in W, H are predicted to collect at these vacancies. In turn, locally high concentrations of H at such vacancies will enhance decohesion of bulk W, consistent with observed blistering under deuterium implantation. Limiting vacancy formation may be key to the survival of W as a fusion reactor wall material.

  5. First Principles Calculations of Aqueous pKa Values for Organic and Inorganic Acids Using COSMO-RS Reveal an Inconsistency in the Slope of the pKa Scale.

    PubMed

    Klamt, Andreas; Eckert, Frank; Diedenhofen, Michael; Beck, Michael E

    2003-11-01

    The COSMO-RS method, a combination of the quantum chemical dielectric continuum solvation model COSMO with a statistical thermodynamics treatment for more realistic solvation (RS) simulations, has been used for the direct prediction of pKa constants of a large variety of 64 organic and inorganic acids. A highly significant correlation of r(2) = 0.984 with a standard deviation of only 0.49 between the calculated values of the free energies of dissociation and the experimental pKa values was found, without any special adjustment of the method. Thus, we have a theoretical a priori prediction method for pKa, which has the regression constant and the slope as only adjusted parameters. Such a method can be of great value in many areas of physical chemistry, especially in pharmaceutical and agrochemical industry. To our surprise, the slope of pKa vs ΔGdiss is only 58% of the theoretically expected value of 1/RTln(10). A careful analysis with respect to different contributions as well as a comparison with the work of other authors excludes the possibility that the discrepancy is due to weaknesses of the calculation method. Hence, we must conclude that the experimental pKa scale depends differently on the free energy of dissociation than generally assumed. PMID:26313337

  6. First-principles pressure-temperature phase diagrams in metals

    SciTech Connect

    Moriarty, J.A.

    1993-07-01

    Using interatomic potentials derived from first-principles generalized pseudopotential theory, finite-temperature phase transitions in both simple and transition metals can be studied through a combination of analytic statistical methods and molecular-dynamics simulation. In the prototype simple metal-Mg, where volume and pair forces adequately describe the energetics, a complete and accurate phase diagram has thereby been obtained to 60 GPa. A rapidly temperature-dependent hcp-bcc phase line is predicted which ends in a triple point on the melting curve near 4 GPa. In central transition metals such as Mo or Fe, on the other hand, the energetics are complicated by d-state interactions which give rise to both many-body angular forces and enhanced electron-thermal contributions. We have made a detailed study of these phenomena and their impact on melting in the prototype case of Mo and a full melting curve to 2 Mbar has been obtained. In the case of Fe, we are examining the high-pressure phase diagram and the question of whether or not there exists a high-pressure, high-temperature solid bcc phase, as has been speculated. To date, we have shown that the bcc structure is both thermodynamically and mechanically unstable at high pressure and zero temperature, with a large and increasing bcc-hcp energy difference under compression.

  7. First principles simulations of fluid water: The radial distribution functions

    NASA Astrophysics Data System (ADS)

    Ortega, José; Lewis, James P.; Sankey, Otto F.

    1997-03-01

    We apply a recently developed first principles but simplified molecular dynamics method to the simulation of water at different conditions. The computational simplicity of this method allows its application to systems containing a significant number of molecules, yet still taking explicitly into account the quantum electronic structure of the system. In the present work we simulate a system of 216 H2O molecules with periodic boundary conditions at two different densities (ρ=1.0 g/cm3 and ρ=0.72 g/cm3 and temperatures ranging from ˜300 K to ˜580 K. The effect of density and temperature on the structure of water is analyzed by means of the partial radial distribution functions gOO, gOH and gHH . We find an important reduction of the hydrogen-bond peak for water at the supercritical conditions ρ= 0.72 g/cm3, T=580 K, in good agreement with recent experimental results.

  8. First-Principles and Semi-Empirical Studies of Microclusters.

    NASA Astrophysics Data System (ADS)

    Chang, Audrey Young-Zee

    The structural, electronic and magnetic properties of clusters have been a subject of intense investigation in recent years, due to many advancements in theoretical and experimental techniques. Since the bonding of atoms in clusters is often different from in bulk, clusters may assume different shapes and structures as the size varies. They therefore provide a model for understanding the transition and structural formation of bulk materials. In this dissertation, two different approaches for pursuing cluster study are carried out: one is based on a realistic but semi-empirical method, the other is more of a first-principles type of calculation. In the first part, the implementation and application of a dynamics simulated annealing scheme, introduced by Car and Parrinello, to a semi-empirical tight-binding model for studying the silicon clusters is presented. In searching for the ground state structures, Langevin molecular dynamics is employed to allow relaxation of the nuclei. For small silicon clusters, Si_{n} (n <= 10), a preference of close-packed structure with binding energies depending on the size are found. Relatively stable structures are observed for clusters of size 4, 6 and 7 which are in accordance with the experimentally found "magic number". In the second part, the study of transition-metal chromium clusters via a first-principles, all-electron, linear combination of Gaussian orbitals method is presented. Transition -metal elements are characterized by having contracted valence d-orbitals containing up to ten electrons, which make them a highly correlated system. The many-electron effects attributed to interactions among these electrons are manifested rather dramatically through the observed magnetic ordering. In this study, the magnetic and structural properties of chromium clusters, (Cr_{n} n <= 9), are investigated based on density functional theory. In bulk, the bcc chromium crystal has a weak antiferromagnetic coupling due to Fermi surfaces

  9. First Principles Studies of ABO3 Perovskite Surfaces and Nanostructures

    NASA Astrophysics Data System (ADS)

    Pilania, Ghanshyam

    environment and processing conditions on the surface relaxations, local electronic structure and chemical reactivity. By combining our first principles computations with an in-house developed kMC simulation approach, we describe the thermodynamics, steady-state kinetics and the long-time and large-length scale behavior of the catalytically active (001) MnO2-terminated LaMnO3 surface in contact with an oxygen reservoir, as a function of temperature and partial pressure of oxygen. The results obtained are in excellent agreement with available experimental data in the literature.

  10. Order O (1) algorithm for first-principles transient current through open quantum systems

    NASA Astrophysics Data System (ADS)

    Cheung, King Tai; Yu, Zhizhou; Fu, Bin; Wang, Jian

    First principles transient current through molecular devices is known to be extremely time consuming with typical computational complexity T3N3 where N and T are the dimension of the scattering system and the number of time steps respectively. Various algorithms have been developed which eventually brings the complexity down to cTN3 , a linear scaling in T, where c is a large coefficient comparable to N. Here we provide an order O (1) algorithm that reduces it further to c1N3 +c2 TN2 where c1 and c2 are ~50 and 0.1 respectively. Hence for T < N , the transient calculation is independent of T, thus order O (1) is achieved. To make this happening four important ingredients are essential: (1). availability of exact solution based on non-equilibrium Green's function (NEGF) that goes beyond wideband limit; (2). the use of complex absorbing potential (CAP) so that all the pole of Green's function can be found; (3). the exact solution is separable between real space and time domain; (4). the exploit of Vandermonde matrix further reduces the scaling of TN2 to TlnTN for T > N . Benchmark calculation has been done on graphene nanoribbons using Tight-binding (TB) Hamiltonian with a huge speed up factor of 100 T , confirmed the O (1) scaling.

  11. A First-Principle Kinetic Theory of Meteor Plasma Formation

    NASA Astrophysics Data System (ADS)

    Dimant, Yakov; Oppenheim, Meers

    2015-11-01

    Every second millions of tiny meteoroids hit the Earth from space, vast majority too small to observe visually. However, radars detect the plasma they generate and use the collected data to characterize the incoming meteoroids and the atmosphere in which they disintegrate. This diagnostics requires a detailed quantitative understanding of formation of the meteor plasma. Fast-descending meteoroids become detectable to radars after they heat due to collisions with atmospheric molecules sufficiently and start ablating. The ablated material then collides into atmospheric molecules and forms plasma around the meteoroid. Reflection of radar pulses from this plasma produces a localized signal called a head echo. Using first principles, we have developed a consistent collisional kinetic theory of the near-meteoroid plasma. This theory shows that the meteoroid plasma develops over a length-scale close to the ion mean free path with a non-Maxwellian velocity distribution. The spatial distribution of the plasma density shows significant deviations from a Gaussian law usually employed in head-echo modeling. This analytical model will serve as a basis for more accurate quantitative interpretation of the head echo radar measurements. Work supported by NSF Grant 1244842.

  12. Properties of nanoscale dielectrics from first principles computations

    NASA Astrophysics Data System (ADS)

    Shi, Ning

    In recent years, dielectric materials of nanoscale dimensions have aroused considerable interest. We mention two examples. First, in the semiconductor industry, in order to keep pace with Moore's law scaling, the thickness of gate oxide dielectric material is reaching nanoscale dimensions. Second, the high energy density capacitor industry is currently considering dielectric composites with a polymer host matrix filled with inorganic dielectric nanoparticles or polarizable organic molecules. The driving force for the former application is high dielectric constants (or high-k), and those for the latter are high-k and/or high dielectric breakdown strengths. Thus, it is important to characterize the electronic and dielectric properties of materials in the nano-regime, where surface and interface effects naturally play a dominant role. The primary goal of this work is to determine the extent to which such surface/interface effects modify the dielectric constants, band edges, and dielectric breakdown strengths of systems with at least one of their dimensions in the nano-regime. Towards that end, we have developed new computational methodologies at the first principles (density functional) level of theory. These methods have then been applied to several relevant and critical nanoscale systems, including Si:SiO2 and Si:HfO2 heterojunctions, and polymeric composites containing Cu-phthalocyanine and SiO2 nanoparticles.

  13. First-principles investigation of graphene-metal interfaces

    NASA Astrophysics Data System (ADS)

    Ross, Andrew; Adamska, Lyudmyla; Lin, You; Oleynik, Ivan

    2011-03-01

    Epitaxial growth of graphene on Ni(111) substrates is one promising method of large-scale, high-quality graphene wafer production, due to the small lattice mismatch between these two materials. We present results of first-principles density functional theory (DFT) investigation of thestructural, electronic, and magnetic properties of graphene/Ni(111) interfaces relevant to experimental studies of graphene growth on nickel substrates. DFT calculations were performed to identify the favored interface geometries and binding sites for different interface configurations. Additional adlayers of Ni and Cu were either adsorbed on top of the graphene/metal interface, or placed between the graphene and substrate to model processes of metal intercalation. It was also found that the interaction between graphene/Ni(111) and the top Cu adlayer is much weaker compared to that for Ni adlayer. The atomic, electronic, and magnetic properties of these interfaces, including induced magnetic moments in graphene/Ni(111) and Cu,Ni/graphene/Ni(111) systems are also discussed. This work was supported by NSF REU supplement to the award CCF-0726842.

  14. First-Principles Monte Carlo Simulations of Reaction Equilibria in Compressed Vapors.

    PubMed

    Fetisov, Evgenii O; Kuo, I-Feng William; Knight, Chris; VandeVondele, Joost; Van Voorhis, Troy; Siepmann, J Ilja

    2016-06-22

    Predictive modeling of reaction equilibria presents one of the grand challenges in the field of molecular simulation. Difficulties in the study of such systems arise from the need (i) to accurately model both strong, short-ranged interactions leading to the formation of chemical bonds and weak interactions arising from the environment, and (ii) to sample the range of time scales involving frequent molecular collisions, slow diffusion, and infrequent reactive events. Here we present a novel reactive first-principles Monte Carlo (RxFPMC) approach that allows for investigation of reaction equilibria without the need to prespecify a set of chemical reactions and their ideal-gas equilibrium constants. We apply RxFPMC to investigate a nitrogen/oxygen mixture at T = 3000 K and p = 30 GPa, i.e., conditions that are present in atmospheric lightning strikes and explosions. The RxFPMC simulations show that the solvation environment leads to a significantly enhanced NO concentration that reaches a maximum when oxygen is present in slight excess. In addition, the RxFPMC simulations indicate the formation of NO2 and N2O in mole fractions approaching 1%, whereas N3 and O3 are not observed. The equilibrium distributions obtained from the RxFPMC simulations agree well with those from a thermochemical computer code parametrized to experimental data. PMID:27413785

  15. First-principles calculation of electronic stopping contributions from core electrons and off-channeling

    NASA Astrophysics Data System (ADS)

    Correa, Alfredo; Schleife, Andre; Kanai, Yosuke

    2014-03-01

    In order to understand the interaction of projectile atoms with targets under particle radiation in materials, e.g. in space applications or nuclear reactors, it is critical to investigate electronic and ionic contributions to stopping power. The goal of such efforts is detailed understanding of radiation damages as well as fundamental effects such as ion-electron interaction. While ionic stopping has been successfully modeled by molecular dynamics in the past, only recently a computational framework came within reach that is capable of accurately describing electronic stopping from first principles. Using our large-scale implementation of real-time time-dependent density functional theory in non-adiabatic Ehrenfest molecular dynamics, we are able to gain deep insight into electronic stopping for systems with hundreds of atoms and thousands of electrons, taking into account their quantum-mechanical electron-electron interaction. We discuss distinct contributions of valence and core electrons of aluminum target atoms to electronic stopping, and we study their importance for different projectile (hydrogen and helium atoms) velocities. There is striking influence of the stopping geometry especially for fast projectiles, and we find excellent agreement with experiment. Prepared by LLNL under Contract DE-AC52-07NA27344.

  16. First-Principles Monte Carlo Simulations of Reaction Equilibria in Compressed Vapors

    PubMed Central

    2016-01-01

    Predictive modeling of reaction equilibria presents one of the grand challenges in the field of molecular simulation. Difficulties in the study of such systems arise from the need (i) to accurately model both strong, short-ranged interactions leading to the formation of chemical bonds and weak interactions arising from the environment, and (ii) to sample the range of time scales involving frequent molecular collisions, slow diffusion, and infrequent reactive events. Here we present a novel reactive first-principles Monte Carlo (RxFPMC) approach that allows for investigation of reaction equilibria without the need to prespecify a set of chemical reactions and their ideal-gas equilibrium constants. We apply RxFPMC to investigate a nitrogen/oxygen mixture at T = 3000 K and p = 30 GPa, i.e., conditions that are present in atmospheric lightning strikes and explosions. The RxFPMC simulations show that the solvation environment leads to a significantly enhanced NO concentration that reaches a maximum when oxygen is present in slight excess. In addition, the RxFPMC simulations indicate the formation of NO2 and N2O in mole fractions approaching 1%, whereas N3 and O3 are not observed. The equilibrium distributions obtained from the RxFPMC simulations agree well with those from a thermochemical computer code parametrized to experimental data. PMID:27413785

  17. Thermal Conductivities in Solids from First Principles: Accurate Computations and Rapid Estimates

    NASA Astrophysics Data System (ADS)

    Carbogno, Christian; Scheffler, Matthias

    In spite of significant research efforts, a first-principles determination of the thermal conductivity κ at high temperatures has remained elusive. Boltzmann transport techniques that account for anharmonicity perturbatively become inaccurate under such conditions. Ab initio molecular dynamics (MD) techniques using the Green-Kubo (GK) formalism capture the full anharmonicity, but can become prohibitively costly to converge in time and size. We developed a formalism that accelerates such GK simulations by several orders of magnitude and that thus enables its application within the limited time and length scales accessible in ab initio MD. For this purpose, we determine the effective harmonic potential occurring during the MD, the associated temperature-dependent phonon properties and lifetimes. Interpolation in reciprocal and frequency space then allows to extrapolate to the macroscopic scale. For both force-field and ab initio MD, we validate this approach by computing κ for Si and ZrO2, two materials known for their particularly harmonic and anharmonic character. Eventually, we demonstrate how these techniques facilitate reasonable estimates of κ from existing MD calculations at virtually no additional computational cost.

  18. Monolayer II-VI semiconductors: A first-principles prediction

    NASA Astrophysics Data System (ADS)

    Zheng, Hui; Li, Xian-Bin; Chen, Nian-Ke; Xie, Sheng-Yi; Tian, Wei Quan; Chen, Yuanping; Xia, Hong; Zhang, S. B.; Sun, Hong-Bo

    2015-09-01

    A systematic study of 32 honeycomb monolayer II-VI semiconductors is carried out by first-principles methods. While none of the two-dimensional (2D) structures can be energetically stable, it appears that BeO, MgO, CaO, ZnO, CdO, CaS, SrS, SrSe, BaTe, and HgTe honeycomb monolayers have a good dynamic stability. The stability of the five oxides is consistent with the work published by Zhuang et al. [Appl. Phys. Lett. 103, 212102 (2013), 10.1063/1.4831972]. The rest of the compounds in the form of honeycomb are dynamically unstable, revealed by phonon calculations. In addition, according to the molecular dynamic (MD) simulation evolution from these unstable candidates, we also find two extra monolayers dynamically stable, which are tetragonal BaS [P 4 /n m m (129 ) ] and orthorhombic HgS [P 21/m (11 ) ] . The honeycomb monolayers exist in the form of either a planar perfect honeycomb or a low-buckled 2D layer, all of which possess a band gap and most of them are in the ultraviolet region. Interestingly, the dynamically stable SrSe has a gap near visible light, and displays exotic electronic properties with a flat top of the valence band, and hence has a strong spin polarization upon hole doping. The honeycomb HgTe has recently been reported to achieve a topological nontrivial phase under appropriate in-plane tensile strain and spin-orbital coupling (SOC) [J. Li et al., arXiv:1412.2528]. Some II-VI partners with less than 5 % lattice mismatch may be used to design novel 2D heterojunction devices. If synthesized, potential applications of these 2D II-VI families could include optoelectronics, spintronics, and strong correlated electronics.

  19. Magnetic Properties of Ni(2+)(aq) from First Principles.

    PubMed

    Mareš, Jiří; Liimatainen, Helmi; Pennanen, Teemu O; Vaara, Juha

    2011-10-11

    The aqueous solution of the Ni(2+) ion was investigated using a first principles molecular dynamics (FPMD) simulation based on periodic density-functional theory (DFT) calculations. Statistical averages of the magnetic properties corresponding to the triplet spin state of the ion, the hyperfine coupling, g and zero-field splitting tensors, as well as the resulting paramagnetic nuclear magnetic resonance (pNMR) shielding terms were calculated using DFT from instantaneous simulation snapshots extracted from the FPMD trajectory. We report comprehensive tests of the reliability of systematically selected DFT functionals for the properties. The isotropic nuclear shielding of the (17)O nuclei can be obtained with good predictive power. The accuracy of the calculated (1)H shieldings is limited by the fact that the spin-density on the proton sites is not reproduced reliably with the tested functionals, rendering the dominant Fermi contact isotropic shielding term less well-defined. On the other hand, the dominant spin-dipole term of the shielding anisotropy, which gives a practically vanishing isotropic contribution, can be obtained with good reliability for both the (1)H and (17)O nuclei. The anisotropic shielding tensor can be thus utilized reliably in the calculation of Curie-type paramagnetic relaxation. We discuss the evolution of the pNMR properties through the first and second solvation shells of the ion, toward the bulk solvent. The magnetic properties of the dominant, six-coordinated solution are compared to those of the metastable, 5-fold coordinated intermediate occurring in the dissociative exchange process. PMID:26598159

  20. Electron Exchange and Conduction in Nontronite from First-Principles

    SciTech Connect

    Alexandrov, Vitali Y.; Neumann, Anke; Scherer, Michelle; Rosso, Kevin M.

    2013-01-11

    Fe-bearing clay minerals serve as an important source and sink for electrons in redox reactions in various subsurface geochemical environments, and electron transfer (ET) properties of the Fe2+/Fe3+ redox couple play a decisive role in a variety of physicochemical processes involving clays. Here, we apply first-principles calculations using both periodic GGA+U planewave and Hartree-Fock molecular-cluster frameworks in conjuction with small polaron hopping approach and Marcus electron transfer theory to examine electron exchange mobilities in an Fe-rich smectite, taking nontronite as a case study. GGA+U calculations of the activation barrier for small-polaron migration provide rates of electron hopping that agree very well with values deduced from variable temperature Mössbauer data (M. V. Schaefer, et. al., Environ. Sci. Technol. 45, 540, (2011)), indicating a surprisingly fast electron mobility at room temperature. Based on molecular cluster calculations, we show that the state with tetrahedral Fe2+ ion in the nontronite lattice is about 0.9 eV higher than the one with octahedral Fe2+. Also, evaluation of the ET rates for the Fe2+/Fe3+ electron hopping in tetrahedral (TS) and octahedral sheets (OS), as well as across the sheets (TS–OS) shows that the dominant contribution to the bulk electronic conductivity should come from the ET within the OS. Deprotonation of structural OH groups mediating ET between the Fe ions in the OS is found to decrease the internal reorganization energy and to increase the magnitude of the electronic coupling matrix element, whereas protonation (to OH2 groups) has the opposite effect. Overall, our calculations suggest that the major factors affecting ET rates are the nature and structure of the nearest-neighbor local environment and the degree of covalency of the bonds between Fe and ligands mediating electron hops. The generally higher reorganization energy and weaker electronic coupling found in Fe-bearing clay minerals leads to

  1. Force field development from first principles for materials design

    NASA Astrophysics Data System (ADS)

    Chan, Maria; Kinaci, Alper; Narayanan, Badri; Sen, Fatih; Gray, Stephen; Davis, Michael; Sankaranaryanan, Subramanian

    2015-03-01

    The ability to perform accurate calculations efficiently is crucial for computational materials design. In this talk, we will discuss a stream-lined approach to force field development using first principles density functional theory training data and machine learning algorithms. We will also discuss the validation of this approach on precious metal nanoparticles.

  2. Transport and first-principles study of novel thermoelectric materials

    NASA Astrophysics Data System (ADS)

    Chi, Hang

    Thermoelectric materials can recover waste industrial heat and convert it to electricity as well as provide efficient local cooling of electronic devices. The efficiency of such environmentally responsible and exceptionally reliable solid state energy conversion is determined by the dimensionless figure-of-merit ZT = alpha2 sigmaT/kappa, where alpha is the Seebeck coefficient, sigma is the electrical conductivity, kappa is the thermal conductivity, and T is the absolute temperature. The goal of the thesis is to (i) illustrate the physics to achieve high ZT of advanced thermoelectric materials and (ii) explore fundamental structure and transport properties in novel condensed matter systems, via an approach combining comprehensive experimental techniques and state-of-the-art first-principles simulation methods. Thermo-galvanomagnetic transport coefficients are derived from Onsager's reciprocal relations and evaluated via solving Boltzmann transport equation using Fermi-Dirac statistics, under the relaxation time approximation. Such understanding provides insights on enhancing ZT through two physically intuitive and very effective routes: (i) improving power factor PF = alpha2sigma; and (ii) reducing thermal conductivity kappa, as demonstrated in the cases of Mg2Si1-xSnx solid solution and Ge/Te double substituted skutterudites CoSb3(1-x)Ge1.5x Te1.5x, respectively. Motivated by recent theoretical predictions of enhanced thermoelectric performance in highly mismatched alloys, ZnTe:N molecular beam epitaxy (MBE) films deposited on GaAs (100) substrates are carefully examined, which leads to a surprising discovery of significant phonon-drag thermopower (reaching 1-2 mV/K-1) at ~13 K. Further systematic study in Bi2Te3 MBE thin films grown on sapphire (0001) and/or BaF2 (111) substrates, reveal that the peak of phonon drag can be tuned by the choice of substrates with different Debye temperatures. Moreover, the detailed transport and structure studies of Bi2-xTl xTe3

  3. FIRST-PRINCIPLES APPROACHES TO THE STRUCTURE AND REACTIVITY OF ATMOSPHERICALLY RELEVANT AQUESOUS INTERFACES

    SciTech Connect

    Mundy, C; Kuo, I W

    2005-06-08

    successfully applied to studying the complex problems put forth by atmospheric chemists. To date, the majority of the molecular models of atmospherically relevant interfaces have been comprised of two genres of molecular models. The first is based on empirical interaction potentials. The use of an empirical interaction potential suffers from at least two shortcomings. First, empirical potentials are usually fit to reproduce bulk thermodynamic states, or gas phase spectroscopic data. Thus, without the explicit inclusion of charge transfer, it is not at all obvious that empirical potentials can faithfully reproduce the structure at a solid-vapor, or liquid-vapor interface where charge rearrangement is known to occur (see section 5). One solution is the empirical inclusion of polarization effects. These models are certainly an improvement, but still cannot offer insight into charge transfer processes and are usually difficult to parameterize. The other shortcoming of empirical models is that, in general, they cannot describe bond-making/breaking events, i.e. chemistry. In order to address chemistry one has to consider an ab initio (to be referred to as first-principles throughout the remaining text) approach to molecular modeling that explicitly treats the electronic degrees of freedom. First-principles modeling also give a direct link to spectroscopic data and chemistry, but at a large computational cost. The bottle-neck associated with first-principles modeling is usually determined by the level of electronic structure theory that one chooses to study a particular problem. High-level first-principles approaches, such as MP2, provide accurate representation of the electronic degrees of freedom but are only computationally tractable when applied to small system sizes (i.e. 10s of atoms). Nevertheless, this type of modeling has been extremely useful in deducing reaction mechanisms of atmospherically relevant chemistry that will be discussed in this review (see section 4). However

  4. Diagnosis: Reasoning from first principles and experiential knowledge

    NASA Technical Reports Server (NTRS)

    Williams, Linda J. F.; Lawler, Dennis G.

    1987-01-01

    Completeness, efficiency and autonomy are requirements for suture diagnostic reasoning systems. Methods for automating diagnostic reasoning systems include diagnosis from first principles (i.e., reasoning from a thorough description of structure and behavior) and diagnosis from experiential knowledge (i.e., reasoning from a set of examples obtained from experts). However, implementation of either as a single reasoning method fails to meet these requirements. The approach of combining reasoning from first principles and reasoning from experiential knowledge does address the requirements discussed above and can possibly ease some of the difficulties associated with knowledge acquisition by allowing developers to systematically enumerate a portion of the knowledge necessary to build the diagnosis program. The ability to enumerate knowledge systematically facilitates defining the program's scope, completeness, and competence and assists in bounding, controlling, and guiding the knowledge acquisition process.

  5. Hybrid first-principles/neural networks model for column flotation

    SciTech Connect

    Gupta, S.; Liu, P.H.; Svoronos, S.A.; Sharma, R.; Abdel-Khalek, N.A.; Cheng, Y.; El-Shall, H.

    1999-03-01

    A new model for phosphate column flotation is presented which for the first time relates the effects of operating variables such as frother concentration on column performance. This is a hybrid model that combines a first-principles model with artificial neural networks. The first-principles model is obtained from material balances on both phosphate particles and gangue (undesired material containing mostly silica). First-order rates of net attachment are assumed for both. Artificial neural networks relate the attachment rate constants to the operating variables. Experiments were conducted in a 6-in.-dia. (152-mm-dia.) laboratory column to provide data for neural network training and model validation. The model successfully predicts the effects of frother concentration, particle size, air flow rate and bubble diameter on grade and recovery.

  6. Understanding and Predicting Thiolated Gold Nanoclusters from First Principles

    SciTech Connect

    Jiang, Deen

    2010-01-01

    This is an exciting time for studying thiolated gold nanoclusters. Single crystal structures of Au{sub 102}(SR){sub 44} and Au{sub 25}(SR){sub 18}{sup -} (-SR being an organothiolate group) bring both surprises and excitement in this field. First principles density functional theory (DFT) simulations turn out to be an important tool to understand and predict thiolated gold nanoclusters. In this review, I summarize the progresses made by us and others in applying first principles DFT to thiolated gold nanoclusters, as inspired by the recent experiments. First, I will give some experimental background on synthesis of thiolated gold nanoclusters, followed by a description of the recent experimental breakthroughs. Then I will introduce the superatom complex concept as a way to understand the electronic structure of thiolated gold nanoclusters or smaller nanoparticles. Next, I will describe in detail how first principles DFT is used to understand the Au-thiolate interface, predict structures for Au{sub 38}(SR){sub 24}, screen good dopants for the Au{sub 25}(SR){sub 18}{sup -} cluster, design the smallest magic thiolated gold cluster, and demonstrate the need for the trimer protecting motif. I will conclude with a grand challenge: the real time monitoring of nucleation of thiolated gold nanoclusters.

  7. Evolutionary approach for determining first-principles hamiltonians

    NASA Astrophysics Data System (ADS)

    Hart, Gus L. W.; Blum, Volker; Walorski, Michael J.; Zunger, Alex

    2005-05-01

    Modern condensed-matter theory from first principles is highly successful when applied to materials of given structure-type or restricted unit-cell size. But this approach is limited where large cells or searches over millions of structure types become necessary. To treat these with first-principles accuracy, one 'coarse-grains' the many-particle Schrödinger equation into 'model hamiltonians' whose variables are configurational order parameters (atomic positions, spin and so on), connected by a few 'interaction parameters' obtained from a microscopic theory. But to construct a truly quantitative model hamiltonian, one must know just which types of interaction parameters to use, from possibly 106-108 alternative selections. Here we show how genetic algorithms, mimicking biological evolution ('survival of the fittest'), can be used to distil reliable model hamiltonian parameters from a database of first-principles calculations. We demonstrate this for a classic dilemma in solid-state physics, structural inorganic chemistry and metallurgy: how to predict the stable crystal structure of a compound given only its composition. The selection of leading parameters based on a genetic algorithm is general and easily applied to construct any other type of complex model hamiltonian from direct quantum-mechanical results.

  8. Evolutionary approach for determining first-principles hamiltonians.

    PubMed

    Hart, Gus L W; Blum, Volker; Walorski, Michael J; Zunger, Alex

    2005-05-01

    Modern condensed-matter theory from first principles is highly successful when applied to materials of given structure-type or restricted unit-cell size. But this approach is limited where large cells or searches over millions of structure types become necessary. To treat these with first-principles accuracy, one 'coarse-grains' the many-particle Schrodinger equation into 'model hamiltonians' whose variables are configurational order parameters (atomic positions, spin and so on), connected by a few 'interaction parameters' obtained from a microscopic theory. But to construct a truly quantitative model hamiltonian, one must know just which types of interaction parameters to use, from possibly 10(6)-10(8) alternative selections. Here we show how genetic algorithms, mimicking biological evolution ('survival of the fittest'), can be used to distil reliable model hamiltonian parameters from a database of first-principles calculations. We demonstrate this for a classic dilemma in solid-state physics, structural inorganic chemistry and metallurgy: how to predict the stable crystal structure of a compound given only its composition. The selection of leading parameters based on a genetic algorithm is general and easily applied to construct any other type of complex model hamiltonian from direct quantum-mechanical results. PMID:15834412

  9. Communication: Charge-transfer rate constants in zinc-porphyrin-porphyrin-derived dyads: A Fermi golden rule first-principles-based study

    SciTech Connect

    Manna, Arun K.; Dunietz, Barry D.

    2014-09-28

    We investigate photoinduced charge transfer (CT) processes within dyads consisting of porphyrin derivatives in which one ring ligates a Zn metal center and where the rings vary by their degree of conjugation. Using a first-principles approach, we show that molecular-scale means can tune CT rates through stabilization affected by the polar environment. Such means of CT tuning are important for achieving high efficiency optoelectronic applications using organic semiconducting materials. Our fully quantum mechanical scheme is necessary for reliably modeling the CT process across different regimes, in contrast to the pervading semi-classical Marcus picture that grossly underestimates transfer in the far-inverted regime.

  10. Equation of state for technetium from X-ray diffraction and first-principle calculations

    NASA Astrophysics Data System (ADS)

    Mast, Daniel S.; Kim, Eunja; Siska, Emily M.; Poineau, Frederic; Czerwinski, Kenneth R.; Lavina, Barbara; Forster, Paul M.

    2016-08-01

    The ambient temperature equation of state (EoS) of technetium metal has been measured by X-ray diffraction. The metal was compressed using a diamond anvil cell and using a 4:1 methanol-ethanol pressure transmitting medium. The maximum pressure achieved, as determined from the gold pressureEquation of state for technetium from X-ray diffraction and first-principle calculations scale, was 67 GPa. The compression data shows that the HCP phase of technetium is stable up to 67 GPa. The compression curve of technetium was also calculated using first-principles total-energy calculations. Utilizing a number of fitting strategies to compare the experimental and theoretical data it is determined that the Vinet equation of state with an ambient isothermal bulk modulus of B0T=288 GPa and a first pressure derivative of B‧=5.9(2) best represent the compression behavior of technetium metal.