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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

    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.

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

    PubMed

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

    2015-12-01

    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 the study of the enzymatic reaction catalyzed by acetylcholinesterase. We carried out density functional theory calculations for a quantum-mechanical (QM) subsystem consisting of 612 atoms with an O(N) complexity finite-difference approach. The QM subsystem 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 show two energy barriers along the reaction coordinate for the enzyme-catalyzed acylation of acetylcholine. The second barrier (8.5 kcal/mol) is rate-limiting for the acylation reaction and in good agreement with experiment. PMID:26642985

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

    DOE PAGES

    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

  4. Linear-scaling first-principles molecular dynamics of complex biological systems with the Conquest code

    NASA Astrophysics Data System (ADS)

    Otsuka, Takao; Taiji, Makoto; Bowler, David R.; Miyazaki, Tsuyoshi

    2016-11-01

    The recent progress of linear-scaling or O(N) methods in density functional theory (DFT) is remarkable. In this paper, we show that all-atom molecular dynamics simulations of complex biological systems based on DFT are now possible using our linear-scaling DFT code Conquest. We first overview the calculation methods used in Conquest and explain the method introduced recently to realise efficient and robust first-principles molecular dynamics (FPMD) with O(N) DFT. Then, we show that we can perform reliable all-atom FPMD simulations of a hydrated DNA model containing about 3400 atoms. We also report that the velocity scaling method is both reliable and useful for controlling the temperature of the FPMD simulation of this system. From these results, we conclude that reliable FPMD simulations of complex biological systems are now possible with Conquest.

  5. Practical algorithms to facilitate large-scale first-principles molecular dynamics

    NASA Astrophysics Data System (ADS)

    Gygi, François; Duchemin, Ivan; Donadio, Davide; Galli, Giulia

    2009-07-01

    Running First-Principles Molecular Dynamics (FPMD) simulations on large parallel platforms presents a number of practical challenges related to the large size of the datasets generated during simulations and to the lack of flexibility of parallel FPMD codes for the implementation of new algorithms. In this paper, we present two approaches implemented in the Qbox code, that alleviate these problems and facilitate large-scale FPMD simulations. We first describe a parallel I/O strategy based on MPI-IO that fully exploits the performance of parallel file systems. We also describe the implementation of a client-server interface that enables coupled quantum-classical computations in which the quantum simulation run by Qbox is "driven" by another application. This feature can be used to couple FPMD simulations with other simulation methods such as e.g. Path Integral Monte Carlo, thermodynamic integration or replica exchange dynamics.

  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 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

  10. 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.

  11. 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.

  12. 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.

  13. Spin Crossover in Ferropericlase from First-Principles Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Holmström, E.; Stixrude, L.

    2015-03-01

    Ferropericlase, (Mg,Fe)O, is the second-most abundant mineral of Earth's lower mantle. With increasing pressure, the Fe ions in the material begin to collapse from a magnetic to nonmagnetic spin state. We present a finite-temperature first-principles phase diagram of this spin crossover, finding a broad pressure range with coexisting magnetic and nonmagnetic ions due to favorable enthalpy of mixing of the two. Furthermore, we find the electrical conductivity of the mineral to reach semimetallic values inside Earth.

  14. Spin crossover in ferropericlase from first-principles molecular dynamics.

    PubMed

    Holmström, E; Stixrude, L

    2015-03-20

    Ferropericlase, (Mg,Fe)O, is the second-most abundant mineral of Earth's lower mantle. With increasing pressure, the Fe ions in the material begin to collapse from a magnetic to nonmagnetic spin state. We present a finite-temperature first-principles phase diagram of this spin crossover, finding a broad pressure range with coexisting magnetic and nonmagnetic ions due to favorable enthalpy of mixing of the two. Furthermore, we find the electrical conductivity of the mineral to reach semimetallic values inside Earth. PMID:25839305

  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.

  16. 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

  17. 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.

  18. 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.

  19. 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).

  20. 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.

  1. ATOMIC AND MOLECULAR PHYSICS: First Principles Simulation of Molecular Oxygen Adsorption on SiC Nanotubes

    NASA Astrophysics Data System (ADS)

    Ganji, M. D.; Ahaz, B.

    2010-04-01

    We study the binding of molecular oxygen to a (5, 0) single walled SiC nanotube, by means of density functional calculations. The center of a hexagon of silicon and carbon atoms in sites on SiCNT surfaces is the most stable adsorption site for O2 molecule, with a binding energy of -38.22 eV and an average Si-O binding distance of 1.698 Å. We have also tested the stability of the O2-adsorbed SiCNT/CNT with ab initio molecular dynamics simulation which have been carried out at room temperature. Furthermore, the adsorption of O2 on the single walled carbon nanotubes has been investigated. Our first-principles calculations predict that the O2 adsorptive capability of silicon carbide nanotubes is much better than that of carbon nanotubes. This might have potential for gas detection and energy storage.

  2. 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})

  3. Cold melting of Li under pressure: Perspectives from first-principles molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Xia, Weiyi; Gao, Weiwei; Gao, Xiang; Zhang, Peihong

    Despite much work (experiment and theory), the pressure-dependent melting temperature of Li is still under debate. In particular, there is still controversy and significant uncertainty in determining the melting temperature of Li at pressures around 50 GPa. An earlier report suggests that Li melts at as low as 190 K between 40 and 64 GPa. Such a low melting temperature is not likely unless quantum effects of lattice vibration play a significant role. Later experiment, on the other hand, reports that Li melts above 300 K under pressured up to 64 GPa and does not seem to support the view that lattice quantum effects to play any important role. In this talk, we will present results from large-scale (large systems and long simulation times) first-principles molecular dynamics simulations and phonon free energy calculations, aiming at resolving some of the issues. This work is supported by US NSF under Grant No. DMR-0946404 and DMR-1506669. Work at Beijing CSRC is supported by the National Natural Science Foundation of China (Grant No. 11328401).

  4. 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.

  5. 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

  6. First-principles-based multiscale, multiparadigm molecular mechanics and dynamics methods for describing complex chemical processes.

    PubMed

    Jaramillo-Botero, Andres; Nielsen, Robert; Abrol, Ravi; Su, Julius; Pascal, Tod; Mueller, Jonathan; Goddard, William A

    2012-01-01

    We expect that systematic and seamless computational upscaling and downscaling for modeling, predicting, or optimizing material and system properties and behavior with atomistic resolution will eventually be sufficiently accurate and practical that it will transform the mode of development in the materials, chemical, catalysis, and Pharma industries. However, despite truly dramatic progress in methods, software, and hardware, this goal remains elusive, particularly for systems that exhibit inherently complex chemistry under normal or extreme conditions of temperature, pressure, radiation, and others. We describe here some of the significant progress towards solving these problems via a general multiscale, multiparadigm strategy based on first-principles quantum mechanics (QM), and the development of breakthrough methods for treating reaction processes, excited electronic states, and weak bonding effects on the conformational dynamics of large-scale molecular systems. These methods have resulted directly from filling in the physical and chemical gaps in existing theoretical and computational models, within the multiscale, multiparadigm strategy. To illustrate the procedure we demonstrate the application and transferability of such methods on an ample set of challenging problems that span multiple fields, system length- and timescales, and that lay beyond the realm of existing computational or, in some case, experimental approaches, including understanding the solvation effects on the reactivity of organic and organometallic structures, predicting transmembrane protein structures, understanding carbon nanotube nucleation and growth, understanding the effects of electronic excitations in materials subjected to extreme conditions of temperature and pressure, following the dynamics and energetics of long-term conformational evolution of DNA macromolecules, and predicting the long-term mechanisms involved in enhancing the mechanical response of polymer-based hydrogels.

  7. Understanding surface acidity of gibbsite with first principles molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Liu, Xiandong; Cheng, Jun; Sprik, Michiel; Lu, Xiancai; Wang, Rucheng

    2013-11-01

    In this paper, we report a first principles molecular dynamics (FPMD) study of the acid-base chemistry of gibbsite. With FPMD based vertical energy gap technique, the acidity constants of the sites on the basal surface (i.e. (0 0 1)) and the edge surface (1 0 0) are derived and the results overall indicate that l(OH2)2 groups on the edge surface are the major acidic sites. The free-energy calculation indicates that both the 6-fold (i.e. Al(OH2)2) and 5-fold (i.e. Al(OH2)) coordination states of edge Al atoms are probable with the former being much more stable. The 6-fold forms have very similar 1st and 2nd acidity constants in 9.0-10.0, which agrees with the experimental PZC (point of zero charge) range. The 5-fold forms have a very low pKa of about 2.0, which indicates that its common form is Al(OH) within normal pH range. The doubly coordinated site (i.e. Al2(OH)) on the edge surface has a very high pKa of about 13.0, indicating that the proton dissociation rarely happens. For the basal surface, the hydroxyl groups almost do not have contribution to the acid-base chemistry of gibbsite. On this surface, some OHs keep orientation parallel to the surface and therefore they can only perform as proton acceptors. However, their protonated states have very low pKas of around 1.3. The other OHs have an extremely high pKa (about 22.0), indicating no dissociation in common pH. Overall, this study provides atomic-scale understanding on the acid-base chemistry of gibbsite and the derived interfacial structures and acidity constants form a basis for future research on the interfacial processes of Al-hydroxides.

  8. 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.

  9. 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

  10. 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

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

    NASA Astrophysics Data System (ADS)

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

    2009-06-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    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.

  13. 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

  14. 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

  15. 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

    2016-10-01

    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.

  16. 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.

  17. Length dependence of electron transport through molecular wires--a first principles perspective.

    PubMed

    Khoo, Khoong Hong; Chen, Yifeng; Li, Suchun; Quek, Su Ying

    2015-01-01

    One-dimensional wires constitute a fundamental building block in nanoscale electronics. However, truly one-dimensional metallic wires do not exist due to Peierls distortion. Molecular wires come close to being stable one-dimensional wires, but are typically semiconductors, with charge transport occurring via tunneling or thermally-activated hopping. In this review, we discuss electron transport through molecular wires, from a theoretical, quantum mechanical perspective based on first principles. We focus specifically on the off-resonant tunneling regime, applicable to shorter molecular wires (<∼4-5 nm) where quantum mechanics dictates electron transport. Here, conductance decays exponentially with the wire length, with an exponential decay constant, beta, that is independent of temperature. Different levels of first principles theory are discussed, starting with the computational workhorse - density functional theory (DFT), and moving on to many-electron GW methods as well as GW-inspired DFT + Sigma calculations. These different levels of theory are applied in two major computational frameworks - complex band structure (CBS) calculations to estimate the tunneling decay constant, beta, and Landauer-Buttiker transport calculations that consider explicitly the effects of contact geometry, and compute the transmission spectra directly. In general, for the same level of theory, the Landauer-Buttiker calculations give more quantitative values of beta than the CBS calculations. However, the CBS calculations have a long history and are particularly useful for quick estimates of beta. Comparing different levels of theory, it is clear that GW and DFT + Sigma calculations give significantly improved agreement with experiment compared to DFT, especially for the conductance values. Quantitative agreement can also be obtained for the Seebeck coefficient - another independent probe of electron transport. This excellent agreement provides confirmative evidence of off

  18. 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.

  19. 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

  20. 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.

  1. Inelastic Electron Tunneling Spectroscopy in Molecular Electronic Devices from First-Principles

    NASA Astrophysics Data System (ADS)

    Ji, Tao

    In this thesis, we present the first-principle calculations of inelastic electron tunneling spectroscopy(IETS) in single molecular break junctions. In a two-probe electrode-molecule-electrode setup, density functional theory(DFT) is used for the construction of the Hamiltonian and the Keldysh non-equilibrium Green's function(NEGF) technique will be employed for determining the electron density in non-equilibrium system conditions. Total energy functional, atomic forces and Hessian matrix can be obtained in the DFT-NEGF formalism and self-consistent Born approximation(SCBA) is used to integrate the molecular vibrations (phonons) into the framework once the phonon spectra and eigenvectors are calculated from the dynamic matrix. Geometry optimization schemes will also be discussed as an indispensable part of the formalism as the equilibrium condition is crucial to correctly calculate the phonon properties of the system. To overcome the numerical difficulties, especially the large computational time demand of the electron-phonon coupling problem, we develop a numerical approximation for the electron self-energy due to phonons and the error is controlled within numerical precision. Besides, a direct IETS second order I-V derivative expression is derived to reduce the error of numerical differentiation under reasonable assumptions. These two approximations greatly reduce the computation requirement and make the calculation feasible within current numerical capability. As the application of the DFT-NEGF-SCBA formalism, we calculate the IETS of the gold-octanedithiol(ODT) molecular junction. The I-V curve, conductance and IETS from ab-inito calculations are compared directly to experiments. A microscopic understanding of the electron-phonon coupling mechanism in the molecular tunneling junctions is explained in this example. In addition, comparisons of the hydrogen-dissociative and hydrogen-non-dissociative ODT junctions as well as the different charge transfer behaviors

  2. First-Principles Determination of Molecular Conformations of Indolizidine (−)-235B′ in Solution

    PubMed Central

    Zheng, Fang; Dwoskin, Linda P.; Crooks, Peter A.; Zhan, Chang-Guo

    2009-01-01

    Indolizidine (−)-235B′ is a particularly interesting natural product, as it is the currently known, most potent and subtype-selective open-channel blocker of the α4β2 nicotinic acetylcholine receptor (nAChR). In the current study, extensive first-principles electronic structure calculations have been carried out in order to determine the stable molecular conformations and their relative free energies of the protonated and deprotonated states of (−)-235B′ in the gas phase, in chloroform, and in aqueous solution. The 1H and 13C NMR chemical shifts calculated using the computationally determined dominant molecular conformation of the deprotonated state are all consistent with available experimental NMR spectra of (−)-235B′ in chloroform, which suggests that the computationally determined molecular conformations are reasonable. Our computational results reveal for the first time that two geminal H atoms on carbon-3 (C3) of (−)-235B′ have remarkably different chemical shifts (i.e. 3.24 and 2.03 ppm). The computational results help one to better understand and analyze the experimental 1H NMR spectra of (−)-235B′. The finding of remarkably different chemical shifts of two C3 geminal H atoms in a certain molecular conformation of (−)-235B′ may also be valuable in analysis of NMR spectra of other related ring-containing compounds. In addition, the pKa of (−)-235B′ in aqueous solution is predicted to be ~9.7. All of the computational results provide a solid basis for future studies of the microscopic and phenomenological binding of various receptor proteins with the protonated and deprotonated structures of this unique open-channel blocker of α4β2 nAChRs. This computational study also demonstrates how one can appropriately use computational modeling and spectroscopic analysis to address the structural and spectroscopic problems that cannot be addressed by experiments alone. PMID:20161506

  3. Molecular and electronic structure of the peptide subunit of Geobacter sulfurreducens conductive pili from first principles.

    PubMed

    Feliciano, Gustavo T; da Silva, Antonio J R; Reguera, Gemma; Artacho, Emilio

    2012-08-01

    The respiration of metal oxides by the bacterium Geobacter sulfurreducens requires the assembly of a small peptide (the GS pilin) into conductive filaments termed pili. We gained insights into the contribution of the GS pilin to the pilus conductivity by developing a homology model and performing molecular dynamics simulations of the pilin peptide in vacuo and in solution. The results were consistent with a predominantly helical peptide containing the conserved α-helix region required for pilin assembly but carrying a short carboxy-terminal random-coiled segment rather than the large globular head of other bacterial pilins. The electronic structure of the pilin was also explored from first principles and revealed a biphasic charge distribution along the pilin and a low electronic HOMO-LUMO gap, even in a wet environment. The low electronic band gap was the result of strong electrostatic fields generated by the alignment of the peptide bond dipoles in the pilin's α-helix and by charges from ions in solution and amino acids in the protein. The electronic structure also revealed some level of orbital delocalization in regions of the pilin containing aromatic amino acids and in spatial regions of high resonance where the HOMO and LUMO states are, which could provide an optimal environment for the hopping of electrons under thermal fluctuations. Hence, the structural and electronic features of the pilin revealed in these studies support the notion of a pilin peptide environment optimized for electron conduction. PMID:22779741

  4. 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.

  5. First-principles molecular dynamics modeling of the molten fluoride salt with Cr solute

    NASA Astrophysics Data System (ADS)

    Nam, H. O.; Bengtson, A.; Vörtler, K.; Saha, S.; Sakidja, R.; Morgan, D.

    2014-06-01

    Fluoride salts and their interactions with metals are of wide interest for the nuclear community. In this work, first-principles molecular dynamics (FPMD) was employed to study both pure molten fluoride salt and fluoride salt with dissolved solute Cr ions (a common corrosion product) at high temperature (823-1423 K). Two types of molten fluoride salts, namely flibe (LiF-BeF2) and flinak (LiF-NaF-KF), with the Cr0, Cr2+ and Cr3+ ions were chosen as a target system for the FPMD modeling. The prediction of thermo-kinetic properties of pure fluoride salt, such as the equilibrium volume, density, bulk modulus, coefficient of thermal expansion, and self-diffusion coefficient, provide useful extensions of existing data and verify the accuracy of the FPMD simulation in modeling of fluoride salts. The FPMD modeling of solute Cr in fluoride salt shows the effect of Cr valence on diffusivity and local structure in the salt.

  6. First principles study on the electronic transport properties of C60 and B80 molecular bridges

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    The electronic transport properties of molecular bridges constructed by C60 and B80 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 C60, monomer B80 is a good conductor arising from the charge transfer from the leads to the molecule, while the dimer (B80)2 and (C60)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 (B80)2 and (C60)2 display poor conductivity, the heterogeneous dimer B80C60 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 (B80)2 and (C60)2 can be significantly improved by electron doping, for example, by doping C in (B80)2 and doping N in (C60)2.

  7. 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

  8. 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).

  9. Free energies of binding from large-scale first-principles quantum mechanical calculations: application to ligand hydration energies.

    PubMed

    Fox, Stephen J; Pittock, Chris; Tautermann, Christofer S; Fox, Thomas; Christ, Clara; Malcolm, N O J; Essex, Jonathan W; Skylaris, Chris-Kriton

    2013-08-15

    Schemes of increasing sophistication for obtaining free energies of binding have been developed over the years, where configurational sampling is used to include the all-important entropic contributions to the free energies. However, the quality of the results will also depend on the accuracy with which the intermolecular interactions are computed at each molecular configuration. In this context, the energy change associated with the rearrangement of electrons (electronic polarization and charge transfer) upon binding is a very important effect. Classical molecular mechanics force fields do not take this effect into account explicitly, and polarizable force fields and semiempirical quantum or hybrid quantum-classical (QM/MM) calculations are increasingly employed (at higher computational cost) to compute intermolecular interactions in free-energy schemes. In this work, we investigate the use of large-scale quantum mechanical calculations from first-principles as a way of fully taking into account electronic effects in free-energy calculations. We employ a one-step free-energy perturbation (FEP) scheme from a molecular mechanical (MM) potential to a quantum mechanical (QM) potential as a correction to thermodynamic integration calculations within the MM potential. We use this approach to calculate relative free energies of hydration of small aromatic molecules. Our quantum calculations are performed on multiple configurations from classical molecular dynamics simulations. The quantum energy of each configuration is obtained from density functional theory calculations with a near-complete psinc basis set on over 600 atoms using the ONETEP program.

  10. Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; Schwegler, Eric

    2016-10-01

    Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na+, K+, and Cl- ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. Geometry and energetics of DNA basepairs and triplets from first principles quantum molecular relaxations.

    PubMed Central

    Lewis, J P; Sankey, O F

    1995-01-01

    A first principles model for calculating hydrogen bonding interactions, previously applied to water, is here applied to the more difficult problem of interactions between DNA bases. We first consider the energetics and geometry for the A-T and the G-C basepairs, comparing our results to other calculated results as well as to experiment. Next, we study the interactions of isomorphic DNA base triplet structures, which are important because of their suggested role in the recombination process. We find that energetically the third base in the triplet tends to favor a position along the dyadic axis, where it is hydrogen bonded to both bases in the duplex. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 PMID:8519960

  16. 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.

  17. 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

  18. 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.

  19. First principles calculation of oxygen K edge absorption spectrum of acetic acid: Relationship between the spectrum and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Matsui, Yoshiki; Mizoguchi, Teruyasu

    2016-04-01

    First principles calculation of the oxygen K-edge absorption near-edge structure of liquid acetic acid was performed to investigate the relationship between the spectrum and the molecular dynamics in a liquid. The single and double bonded oxygens gave strong peaks at different energies. A liquid model constructed using a molecular dynamics simulation reproduced the experimental spectrum. We revealed that the effect of the dynamic behavior of molecules in a liquid clearly appears in the particular peak from a single-bond oxygen. The relationship between the bonding nature and the dynamic information of a molecule in a spectrum was determined and presented.

  20. 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.

  1. ATOMIC AND MOLECULAR PHYSICS: First-Principles Study on Native Defect Complexes in InN

    NASA Astrophysics Data System (ADS)

    Zhao, Feng-Qi; Shi, Jun-Jie; Yang, Mao

    2010-01-01

    We present first-principles calculations of the formation energy of different native defects and their complexes in wurtzite InN using density-functional theory and the pseudopotential plane-wave method. Our calculations are aimed in the three cases: N/In = 1, N/In > 1 (N-rich), and N/In < 1 (In-rich). Our results indicate that the antisite defect has the lowest formation energy under N/In = 1. The formation energy of nitrogen interstitial (nitrogen vacancy) defect is significantly low under the N-rich (In-rich) condition. Thus the antisite defect is an important defect if N/In = 1, and the nitrogen interstitial (nitrogen vacancy) defect is a vital defect under the N-rich (In-rich) condition. The atomic site relaxation around the nitrogen interstitial and vacancy is investigated. Our calculations show that the nitrogen vacancy cannot be observed although it is one of the most important defects in InN. Our results are confirmed by experiments.

  2. Communication: Hydration structure and polarization of heavy alkali ions: A first principles molecular dynamics study of Rb+ and Cs+

    NASA Astrophysics Data System (ADS)

    Ikeda, Takashi; Boero, Mauro

    2012-07-01

    Hydration structure and polarization of Rb+ and Cs+ in liquid water at ambient conditions were studied by first principles molecular dynamics. Our systematic analysis of the relevant electronic structures, based on maximally localized Wannier functions, revealed that the dipole moment of H2O molecules in the first solvation shell of the ions slightly increases with increasing the atomic number. We also found that the polarization of heavy alkali ions, particularly Cs+, tends to stabilize a peculiar asymmetric hydration structure with relevant consequences in the extraction of the harmful 137Cs resulting from nuclear wastes.

  3. Large magnetoresistance of paracyclophane-based molecular tunnel junctions: A first-principles study

    SciTech Connect

    Tao, L. L.; Liang, S. H.; Liu, D. P.; Han, X. F.

    2013-12-07

    We report a theoretical study of magnetoresistance and spin-polarized transport of a series of paracyclophane-based molecular tunnel junctions. We predict that the molecular tunnel junction using [2.2]-paracyclophane barrier has the desired low resistance area product in combination with high magnetoresistance ratio. In addition, we find the spin-polarized conductance decreases exponentially with increasing the molecular length, indicating a nonresonant tunneling mechanism. In particular, the characteristic decay constant can be theoretically evaluated from the complex band structure of periodic paracyclophane molecule. The spin-polarized transport mechanism is systematically analyzed.

  4. 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.

  5. First-principles calculation on the conductance of ruthenium-quasi cumulene-ruthenium molecular junctions

    NASA Astrophysics Data System (ADS)

    Ning, Jing; Shen, Xin; Shen, Zi-Yong; Zhao, Xing-Yu; Hou, Shi-Min

    2009-09-01

    The conductance of a family of ruthenium-quasi cumulene-ruthenium molecular junctions including different numbers of carbon atoms, both in even numbers and odd numbers, are investigated using a fully self-consistent ab initio approach which combines the non-equilibrium Green’s function formalism with density functional theory. Our calculations demonstrate that although the overall transport properties of the Ru-quasi cumulene-Ru junctions with an even number of carbon atoms are different from those of the junctions with an odd number of carbon atoms, the difference between the corresponding current-voltage ( I-V) characteristics of these molecular junctions declines to lesser than 16% when the voltage goes up. In each group, the molecular junctions give a large transmission around the Fermi level since the Ru-C π bonds can extend the π conjugation of the carbon chains into the Ru electrodes, and their I-V characteristics are almost linear and independent of the chain length, illustrating potential applications as conducting molecular wires in future molecular electronic devices and circuits.

  6. Electrolysis of water in the diffusion layer: first-principles molecular dynamics simulation.

    PubMed

    Hofbauer, Florian; Frank, Irmgard

    2012-01-01

    With Car-Parrinello molecular dynamics simulations the elementary reaction steps of the electrolysis of bulk water are investigated. To simulate the reactions occurring near the anode and near the cathode, electrons are removed or added, respectively. The study focuses on the reactions in pure water. Effects depending on a particular electrode surface or a particular electrolyte are ignored. Under anodic conditions, the reaction continues till molecular oxygen is formed, under cathodic conditions the formation of molecular hydrogen is observed. In addition the formation of hydrogen peroxide is observed as an intermediate of the anodic reaction. The simulations demonstrate that the electrochemistry of oxygen formation without direct electrode contact can be explained by radical reactions in a solvent. These reactions may involve the intermediate formation of ions. The hydrogen formation is governed by rapid proton transfers between water molecules. PMID:22162243

  7. First-principles mobility calculations and atomic-scale interface roughness in nanoscale structures.

    PubMed

    Evans, M H; Zhang, X-G; Joannopoulos, J D; Pantelides, S T

    2005-09-01

    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.

  8. 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.

  9. First-principles molecular dynamics simulations of NH4(+) and CH3COO(-) adsorption at the aqueous quartz interface.

    PubMed

    Wright, Louise B; Walsh, Tiffany R

    2012-12-14

    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.

  10. First-principles studies on switching properties of azobenzene based molecular device

    NASA Astrophysics Data System (ADS)

    Dhivya, G.; Nagarajan, V.; Chandiramouli, R.

    2016-09-01

    The switching behavior of cis and trans-azobenzene molecular device is studied using DFT method in combination with non-equilibrium Green's function. The peak maximum is found to be more in the density of states spectrum for trans-azobenzene device rather than cis-azobenzene device due to direct link of two phenyl group by Ndbnd N bonds. The current voltage characteristics clearly show the closed configuration of cis-azobenzene and open configuration of trans-azobenzene, which is attributed through the HOMO and LUMO level of cis and trans isomers. The observations of the present work give an insight on switching behavior of azobenzene based molecular device in the atomistic level.

  11. 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.

  12. 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.

  13. First-Principles Electronic Structure Studies of the Current-Voltage Characteristics of Molecular Nanostructures

    NASA Astrophysics Data System (ADS)

    Pati, Ranjit; Karna, Shashi P.

    2001-03-01

    Recent advancements in the experimental measurement of conductance across a single molecule(M. A. Reed et al, Science, 278) , 252 (1997). have generated great deal of interest in the feasibility of molecular electronic devices. A successful realization of molecule based electronic devices rests on a detailed understanding of the physical principles underlying controlled transport of electron/hole across molecular units. In order to develop such a fundamental understanding, we have investigated current-voltage characteristics of metal atom (Ag, Au) substituted 1,4-dithiobenzene within Green's function approach according to Datta and coworkers( W. Tian et al, J. Chem. Phys., 109), 2874 (1998).. Ab initio Hamiltonian matrix elements are used to construct the Green's function. The calculated conductance spectrum for the molecule with S bonded to Au atoms qualitatively agrees with the experiment^1. However, large quantitative difference between the calculated and measured conductance is noted. The Au and Ag bonded 1,4-dithiobenzene molecules exhibit marked difference in their resistance and conductance spectra. The conductance of the Ag-bonded molecule is calculated to be about 1.5 times larger than that bonded with Au.

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

    PubMed

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

    2016-01-21

    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.

  15. Semiclassical Monte Carlo: a first principles approach to non-adiabatic molecular dynamics.

    PubMed

    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.

  16. 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.

  17. Semiclassical Monte Carlo: a first principles approach to non-adiabatic molecular dynamics.

    PubMed

    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. PMID:25399126

  18. 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.

  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. A fully first-principles approach to the Molecular Kondo problem

    NASA Astrophysics Data System (ADS)

    Soriano, Maria; Jacob, David; Palacios, Juan José; Atomelix Team

    2015-03-01

    There has been a great effort in recent years to understand the emerging Kondo-like resonances in different magnetic molecules such as MnPc. Theoretical approaches based on atomic models have proven to be very useful for the study of this phenomenon when the magnetic moment is essentially localized on a magnetic atom. Nevertheless the Kondo effect can arise in pure carbon-based systems as has been demonstrated experimentally in fullerenes and carbon nanotubes. In this communication we present a multiorbital Anderson model where the orbitals are not atomic but molecular orbitals. This model is fully obtained from Density Functional Theory calculation in combination with Green's functions methodologies. Standard impurity solver techniques are used to solve the model which is applied to fullerenes and other nanographene structures.

  1. First principles study on the molecular structure and vibrational spectra of ketoprofen

    NASA Astrophysics Data System (ADS)

    Liu, Lekun; Gao, Hongwei

    2012-11-01

    The aim of this work was to compare the performance of different DFT methods at different basis sets in predicting geometry and vibration spectrum of ketoprofen. The molecular geometry and vibrational frequencies of ketoprofen have been calculated using five different density function theory (DFT) methods, including LSDA, B3LYP, mPW1PW91, B3PW91 and HCTH, with various basis sets, including 6-311G, 6-311+G, 6-311++G, 6-311+G (d, p) and 6-311++G (2d, 2p). The results indicate that mPW1PW91/6-311++G (2d, 2p) level is clearly superior to all the remaining density functional methods in predicting the bond lengths and bond angles of ketoprofen. Mean absolute deviations between the calculated harmonic and observed fundamental vibration frequencies for each method shows that LSDA/6-311G method is the best to predict vibrational spectra of ketoprofen comparing other DFT methods.

  2. 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.

  3. 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).

  4. Large-scale first principles configuration interaction calculations of optical absorption in aluminum clusters.

    PubMed

    Shinde, Ravindra; Shukla, Alok

    2014-10-14

    We report the linear optical absorption spectra of aluminum clusters Aln (n = 2-5) involving valence transitions, computed using the large-scale all-electron configuration interaction (CI) methodology. Several low-lying isomers of each cluster were considered, and their geometries were optimized at the coupled-cluster singles-doubles (CCSD) level of theory. With these optimized ground-state geometries, excited states of different clusters were computed using the multi-reference singles-doubles configuration-interaction (MRSDCI) approach, which includes electron correlation effects at a sophisticated level. These CI wave functions were used to compute the transition dipole matrix elements connecting the ground and various excited states of different clusters, and thus their photoabsorption spectra. The convergence of our results with respect to the basis sets, and the size of the CI expansion, was carefully examined. Our results were found to be significantly different as compared to those obtained using time-dependent density functional theory (TDDFT) [Deshpande et al. Phys. Rev. B: Condens. Matter Mater. Phys., 2003, 68, 035428]. When compared to the available experimental data for the isomers of Al2 and Al3, our results are in very good agreement as far as important peak positions are concerned. The contribution of configurations to many body wave functions of various excited states suggests that in most cases optical excitations involved are collective, and plasmonic in nature. PMID:25162600

  5. 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.

  6. 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

    2016-02-19

    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.

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

    DOE PAGES

    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

  8. Low-temperature phases of dense hydrogen and deuterium by first-principles path-integral molecular dynamics

    NASA Astrophysics Data System (ADS)

    Torrent, Marc; Geneste, Gregory

    2012-02-01

    The low-temperature phases of dense hydrogen and deuterium have been investigated using first-principles path-integral molecular dynamics, a technique that we have recently implemented in the ABINIT code and that allows to account for the quantum fluctuations of atomic nuclei. A massively parallelized scheme is applied to produce trajectories of several tens of thousands steps using a 64-atom supercell and a Trotter number of 64. The so-called phases I, II and III are studied and compared to the structures proposed in the literature. The quantum fluctuations produce configurational disorder and are shown to systematically enhance the symmetry of the system: a continuous gain of symmetry in the angular density of probability of the molecules is found from classical particles to quantum D2 and finally to quantum H2. Particular emphasis is made on the ``broken-symmetry'' phase (phase II).

  9. Catalytic hydrogenation of cresol: first-principles density-functional calculations and ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Li, Yaping; Liu, Zhimin; Jentoft, Friederike; Wang, Sanwu

    2015-03-01

    Biomass is an important renewable energy resource. Cresol is one of components in crude bio-oil generated from biomass, and hydrogenation of cresol is often involved in the upgrading process. We studied catalytic hydrogenation of cresol on the Pt(111) surface with and without the presence of water. In particular, we used first-principles density-functional theory and ab initio molecular dynamics simulations to obtain adsorption geometries, binding energies, reaction energies, activation energies, and reaction pathways for hydrogenation of cresol with possible products of 2-methylcyclohexanone and 2-methylcyclohexanol. Our theoretical results are used to explain the available experimental measurements, which show a strong influence of water. Supported by DOE (DE-SC0004600). This research used the supercomputer resources at NERSC, of XSEDE, at TACC and at the Tandy Supercomputing Center.

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. Protection of DNA against low-energy electrons by amino acids: a first-principles molecular dynamics study.

    PubMed

    Gu, Bin; Smyth, Maeve; Kohanoff, Jorge

    2014-11-28

    Using first-principles molecular dynamics simulations, we have investigated the notion that amino acids can play a protective role when DNA is exposed to excess electrons produced by ionizing radiation. In this study we focus on the interaction of glycine with the DNA nucleobase thymine. We studied thymine-glycine dimers and a condensed phase model consisting of one thymine molecule solvated in amorphous glycine. Our results show that the amino acid acts as a protective agent for the nucleobase in two ways. If the excess electron is initially captured by the thymine, then a proton is transferred in a barrier-less way from a neighboring hydrogen-bonded glycine. This stabilizes the excess electron by reducing the net partial charge on the thymine. In the second mechanism the excess electron is captured by a glycine, which acts as a electron scavenger that prevents electron localization in DNA. Both these mechanisms introduce obstacles to further reactions of the excess electron within a DNA strand, e.g. by raising the free energy barrier associated with strand breaks.

  15. 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.

  16. 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}.

  17. The mechanism of hydrogen uptake in [NiFe] hydrogenase: first-principles molecular dynamics investigation of a model compound.

    PubMed

    Furlan, Sara; La Penna, Giovanni

    2012-01-01

    The recent discovery of a model compounds of [NiFe] hydrogenase that catalyzes the heterolytic cleavage of the H(2) molecule into a proton and a stable hydride in water solution under room conditions opened up the possibility to understand the mechanism of H(2) uptake by this peculiar class of enzymes. The simplest model compound belongs to the class of NiRu bimetallic cationic complexes mimicking, in water solution and at room conditions, the hydrogenase active site. By using first-principles molecular dynamics computer simulations, in the Car-Parrinello scheme, we investigated models including the water solvent and nitrate counterions. Several simulations, starting from different initial configurations, provided information on the first step of the H(2) cleavage: (1) the pathway of H(2) approach towards the active site; (2) the role of the ruthenium-bonded water molecule in providing a base that extracts the proton from the activated H(2) molecule; (3) the minor role of Ni in activating the H(2) molecule and its role in stabilizing the hydride produced. PMID:21892688

  18. 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.

  19. 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)

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

    DOE PAGES

    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

  1. 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).

  2. 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

  3. 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

  4. 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.

  5. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    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.

  7. 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

  8. Aluminum conducts better than copper at the atomic scale: a first-principles study of metallic atomic wires.

    PubMed

    Simbeck, Adam J; Lanzillo, Nick; Kharche, Neerav; Verstraete, Matthieu J; Nayak, Saroj K

    2012-12-21

    Using a first-principles density functional method, we have studied the electronic structure, electron-phonon coupling, and quantum transport properties of atomic wires of Ag, Al, Au, and Cu. Non-equilibrium Green's function-based transport studies of finite atomic wires suggest that the conductivity of Al atomic wires is higher than that of Ag, Au, and Cu in contrast to the bulk where Al has the lowest conductivity among these systems. This is attributed to the higher number of eigenchannels in Al wires, which becomes the determining factor in the ballistic limit. On the basis of density functional perturbation theory, we find that the electron-phonon coupling constant of the Al atomic wire is lowest among the four metals studied, and more importantly, that the value is reduced by a factor of 50 compared to the bulk. PMID:23083218

  9. 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.

  10. 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.

  11. First principles molecular dynamics simulation of a task-specific ionic liquid based on silver-olefin complex: atomistic insights into a separation process.

    PubMed

    Jiang, De-en; Dai, Sheng

    2008-08-21

    First principles molecular dynamics based on density functional theory is applied to a hypothetical ionic liquid whose cations and anions are silver-ethylene complex [Ag(C2H4)2+] and tetrafluoroborate [BF4-], respectively. This ionic liquid represents a group of task-specific silver complex-based ionic liquids synthesized recently. Molecular dynamics simulations at two temperatures are performed for five picoseconds. Events of association, dissociation, exchange, and recombination of ethylene with silver cation are found. A mechanism of ethylene transfer similar to the Grotthus type of proton transfer in water is identified, where a silver cation accepts one ethylene molecule and donates another to a neighboring silver cation. This mechanism may contribute to fast transport of olefins through ionic liquid membranes based on silver complexes for olefin/paraffin separation.

  12. 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.

  13. Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol

    NASA Astrophysics Data System (ADS)

    Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele

    2016-09-01

    Molecular crystals often exist in multiple competing polymorphs, showing significantly different physicochemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form, a real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenges inherent in the development of a quantitative and predictive framework to model molecular crystals. However, it also indicates which of the components of the free energy can benefit from a cancellation of errors that can redeem the predictive power of approximate models, and suggests simple steps that could be taken to improve the reliability of ab initio crystal structure prediction.

  14. Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol.

    PubMed

    Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele

    2016-09-01

    Molecular crystals often exist in multiple competing polymorphs, showing significantly different physicochemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form, a real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenges inherent in the development of a quantitative and predictive framework to model molecular crystals. However, it also indicates which of the components of the free energy can benefit from a cancellation of errors that can redeem the predictive power of approximate models, and suggests simple steps that could be taken to improve the reliability of ab initio crystal structure prediction. PMID:27661700

  15. 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.

  16. First-principles molecular spin dynamics study on the magnetic structure of Mn-based alloys with Cu3Au-type crystal structure

    NASA Astrophysics Data System (ADS)

    Uchida, T.; Kakehashi, Y.; Kimura, N.

    2016-02-01

    The magnetic and electronic structures of Mn3Pt and Mn3Rh, which are three-dimensional frustrated itinerant magnets with a Cu3Au-type crystal structure, have been investigated by means of the first-principles Molecular Spin Dynamics (MSD) method. The theory is based on the first-principles tight-binding linear muffin-tin orbital Hamiltonian combined with the functional integral method and the isothermal MSD technique, and allows us to determine automatically the magnetic structures of itinerant magnets at finite temperatures. The MSD calculations using a self-consistent site-dependent effective medium show that below the Néel temperature Mn3Pt with fixed crystal structure (Cu3Au structure) and volume exhibits a second-order transition from a triangular structure to another noncollinear phase with increasing temperature. Mn3Rh, on the other hand, shows no sign of a phase transition up to the Néel temperature. We found that the Mn-Eg DOS peak, which is responsible for the ferromagnetic couplings among the second nearest-neighbor Mn local moments, develops at the Fermi energy (EF) around 350 K for Mn3Pt, while the peak development for Mn3Rh occurs with increasing temperature slightly above EF.

  17. 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

  18. 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.

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

    DOE PAGES

    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

  20. 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

  1. 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.

  2. Hybrid molecular dynamics and first-principles study on the work function of a Pt(111) electrode immersed in aqueous solution at room temperature

    NASA Astrophysics Data System (ADS)

    Duan, Sai; Xu, Xin; Tian, Zhong-Qun; Luo, Yi

    2012-07-01

    With a combined molecular dynamics simulation and first-principles calculations, we have investigated a metal surface immersed in aqueous solution at room temperature using a Pt(111) electrode as an example. With the inclusion of thermal average effects at room temperature, the calculated averaged work function is found to be in good agreement with the experimental measurements. The electron redistribution at the interface of the topmost Pt(111) slab layer and the first water layer plays an important role in controlling the work function. A broad distribution of calculated work functions caused by the thermal motions of the dipolar solvents is obtained from statistical sampling, which implies that the chemical reactivity of a metal electrode in aqueous solution is a dynamic property at least in the nanoscale. Such a microscopic understanding helps to understand the behavior of complex electrochemical double layers.

  3. 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.

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

    PubMed

    Rajput, Nav Nidhi; Qu, Xiaohui; 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 (Mg(2+) → 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.

  5. 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

  6. 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.

  7. 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.

  8. Indirect Attractions between Superionic Di-interstitial Protons on Mid-Oxygens in Water at Extreme Conditions: First-Principles Molecular Dynamics Study

    NASA Astrophysics Data System (ADS)

    Tsumuraya, Kazuo; Tasaka, Tomofumi; Nagayama, Hisashi; Tsumuraya, Mary I.; Tsumuraya, Masato

    2014-10-01

    The first principles molecular dynamics study enables us to elucidate attractions between the di-interstitial protons on mid-oxygens in superionic water at an extreme high pressure and the temperature. The present analyses elucidate the existence of inner and outer bonded interstitial protons around oxygens and reveal two types of attractions between the protons and oxygens in the water. One is a covalent attraction between them which induces a covalent bonded indirect attraction between the di-interstitial protons on the mid-oxygens. The other is a Coulomb attraction between them which induces a Coulomb type indirect attraction between the di-interstitial protons on the mid-oxygens. The indirect attractions decrease the impurity diffusion of the protons which reduces Haven's ratios of the protons in the water. The negligible amount of the instantaneously formed proton dimers indicates a failure of the caterpillar diffusion mechanism or the Frenkel-Kontorova model for the water. The incomplete electron transfer from the protons to the oxygens reduces the Coulomb atraction between the ionized oxygens and the protons which weakens the sublattice of the mobile protons with smaller mass and size than the oxygens.

  9. 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

  10. Liquid structures of water, methanol, and hydrogen fluoride at ambient conditions from first principles molecular dynamics simulations with a dispersion corrected density functional.

    PubMed

    McGrath, Matthew J; Kuo, I-Feng William; Siepmann, J Ilja

    2011-11-28

    Using first principles molecular dynamics simulations in the isobaric-isothermal ensemble (T = 300 K, p = 1 atm) with the Becke-Lee-Yang-Parr exchange/correlation functional and a dispersion correction due to Grimme, the hydrogen bonding networks of pure liquid water, methanol, and hydrogen fluoride are probed. Although an accurate density is found for water with this level of electronic structure theory, the average liquid densities for both hydrogen fluoride and methanol are overpredicted by 50 and 25%, respectively. The radial distribution functions indicate somewhat overstructured liquid phases for all three compounds. The number of hydrogen bonds per molecule in water is about twice as high as for methanol and hydrogen fluoride, though the ratio of cohesive energy over number of hydrogen bonds is lower for water. An analysis of the hydrogen-bonded aggregates revealed the presence of mostly linear chains in both hydrogen fluoride and methanol, with a few stable rings and chains spanning the simulation box in the case of hydrogen fluoride. Only an extremely small fraction of smaller clusters was found for water, indicating that its hydrogen bond network is significantly more extensive. A special form of water with on average about two hydrogen bonds per molecule yields a hydrogen-bonding environment significantly different from the other two compounds.

  11. 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.

  12. A comprehensive picture in the view of atomic scale on piezoelectricity of ZnO tunnel junctions: The first principles simulation

    NASA Astrophysics Data System (ADS)

    Zhang, Genghong; Chen, Weijin; Zhu, Jia; Jiang, Gelei; Sheng, Qiang; Wang, Biao; Zheng, Yue

    2016-06-01

    Piezoelectricity is closely related with the performance and application of piezoelectric devices. It is a crucial issue to understand its detailed fundamental for designing functional devices with more peculiar performances. Basing on the first principles simulations, the ZnO piezoelectric tunnel junction is taken as an example to systematically investigate its piezoelectricity (including the piezopotential energy, piezoelectric field, piezoelectric polarization and piezocharge) and explore their correlation. The comprehensive picture of the piezoelectricity in the ZnO tunnel junction is revealed at atomic scale and it is verified to be the intrinsic characteristic of ZnO barrier, independent of its terminated surface but dependent on its c axis orientation and the applied strain. In the case of the ZnO c axis pointing from right to left, an in-plane compressive strain will induce piezocharges (and a piezopotential energy drop) with positive and negative signs (negative and positive signs) emerging respectively at the left and right terminated surfaces of the ZnO barrier. Meanwhile a piezoelectric polarization (and a piezoelectric field) pointing from right to left (from left to right) are also induced throughout the ZnO barrier. All these piezoelectric physical quantities would reverse when the applied strain switches from compressive to tensile. This study provides an atomic level insight into the fundamental behavior of the piezoelectricity of the piezoelectric tunnel junction and should have very useful information for future designs of piezoelectric devices.

  13. 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.

  14. TS-1 from First Principles

    NASA Astrophysics Data System (ADS)

    Gamba, Aldo; Tabacchi, Gloria; Fois, Ettore

    2009-09-01

    First principles studies on periodic TS-1 models at Ti content corresponding to 1.35% and 2.7% in weight of TiO2 are presented. The problem of Ti preferential siting is addressed by using realistic models corresponding to the TS-1 unit cell [TiSi95O192] and adopting for the first time a periodic DFT approach, thus providing an energy scale for Ti in the different crystallographic sites in nondefective TS-1. The structure with Ti in site T3 is the most stable, followed by T4 (+0.3 kcal/mol); the less stable structure, corresponding to Ti in T1, is 5.6 kcal/mol higher in energy. The work has been extended to investigate models with two Ti's per unit cell [Ti2Si94O192] (2.7%). The possible existence of Ti-O-Ti bridges, formed by two corner-sharing TiO4 tetrahedra, is discussed. By using cluster models cut from the optimized periodic DFT structures, both vibrational (DFT) and electronic excitation spectra (TDDFT) have been calculated and favorably compared with the experimental data available on TS-1. Interesting features emerged from excitation spectra: (i) Isolated tetrahedral Ti sites show a Beer-Lambert behavior, with absorption intensity proportional to concentration. Such a behavior is gradually lost when two Ti's occupy sites close to each other. (ii) The UV-vis absorption in the 200-250 nm region can be associated with transitions from occupied states delocalized on the framework oxygens to empty d states localized on Ti. Such extended-states-to-local-states transitions may help the interpretation of the photovoltaic activity recently detected in Ti zeolites.

  15. 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.

  16. ATOMIC AND MOLECULAR PHYSICS: Synthesizing Metastable Rocksalt-Type MgTe Based on High-Pressure Solid-State Phase Transition: A First-Principles Study

    NASA Astrophysics Data System (ADS)

    Cai, Ying-Xiang; Xu, Rui

    2009-11-01

    The controllability of pressure-induced structural transformation in the hexagonal wurtzite-type MgTe is studied by a first-principles pseudopotential method within the generalized gradient approximation (GGA). Based on the transitional mechanisms of the wurtzite→—NiAs and the wurtzite→—rocksalt, a special method of loading biaxial pressure on the (010) and (001) planes of an orthorhombic cell is designed. At equal biaxial pressure of 2.75 GPa, an abrupt volume collapse is found and the WZ phase transforms into an orthorhombic phase with a tiny distortion. While the pressure decreases to zero, three lattice parameters a, b and c become equal and a metastable rocksalt-type MgTe is obtained.

  17. 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

  18. 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.

  19. 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.

  20. Coordination numbers of K(+) and Na(+) Ions inside the selectivity filter of the KcsA potassium channel: insights from first principles molecular dynamics.

    PubMed

    Bucher, Denis; Guidoni, Leonardo; Carloni, Paolo; Rothlisberger, Ursula

    2010-05-19

    Quantum mechanics/molecular mechanics (QM/MM) Car-Parrinello simulations were performed to estimate the coordination numbers of K(+) and Na(+) ions in the selectivity filter of the KcsA channel, and in water. At the DFT/BLYP level, K(+) ions were found to display an average coordination number of 6.6 in the filter, and 6.2 in water. Na(+) ions displayed an average coordination number of 5.2 in the filter, and 5.0 in water. A comparison was made with the average coordination numbers obtained from using classical molecular dynamics (6.7 for K(+) in the filter, 6.6 for K(+) in water, 6.0 for Na(+) in the filter, and 5.2 for Na(+) in water). The observation that different coordination numbers were displayed by the ions in QM/MM simulations and in classical molecular dynamics is relevant to the discussion of selectivity in K-channels.

  1. 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.

  2. 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.

  3. 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.

  4. On the absolute thermodynamics of water from computer simulations: A comparison of first-principles molecular dynamics, reactive and empirical force fields

    NASA Astrophysics Data System (ADS)

    Pascal, Tod A.; Schärf, Daniel; Jung, Yousung; Kühne, Thomas D.

    2012-12-01

    We present the absolute enthalpy, entropy, heat capacity, and free energy of liquid water at ambient conditions calculated by the two-phase thermodynamic method applied to ab initio, reactive and classical molecular dynamics simulations. We find that the absolute entropy and heat capacity of liquid water from ab initio molecular dynamics (AIMD) is underestimated, but falls within the range of the flexible empirical as well as the reactive force fields. The origin of the low absolute entropy of liquid water from AIMD simulations is due to an underestimation of the translational entropy by 20% and the rotational entropy by 40% compared to the TIP3P classical water model, consistent with previous studies that reports low diffusivity and increased ordering of liquid water from AIMD simulations. Classical MD simulations with rigid water models tend to be in better agreement with experiment (in particular TIP3P yielding the best agreement), although the TIP4P-ice water model, the only empirical force field that reproduces the experimental melting temperature, has the lowest entropy, perhaps expectedly. This reiterates the limitations of existing empirical water models in simultaneously capturing the thermodynamics of solid and liquid phases. We find that the quantum corrections to heat capacity of water can be as large as 60%. Although certain water models are computed to yield good absolute free energies of water compared to experiments, they are often due to the fortuitous enthalpy-entropy cancellation, but not necessarily due to the correct descriptions of enthalpy and entropy separately.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. Substrate distortion in the Michaelis complex of Bacillus 1,3-1,4-beta-glucanase. Insight from first principles molecular dynamics simulations.

    PubMed

    Biarnés, Xevi; Nieto, Joan; Planas, Antoni; Rovira, Carme

    2006-01-20

    The structure and dynamics of the enzyme-substrate complex of Bacillus 1,3-1,4-beta-glucanase, one of the most active glycoside hydrolases, is investigated by means of Car-Parrinello molecular dynamics simulations (CPMD) combined with force field molecular dynamics (QM/MM CPMD). It is found that the substrate sugar ring located at the -1 subsite adopts a distorted 1S3 skew-boat conformation upon binding to the enzyme. With respect to the undistorted 4C1 chair conformation, the 1S3 skew-boat conformation is characterized by: (a) an increase of charge at the anomeric carbon (C1), (b) an increase of the distance between C1 and the leaving group, and (c) a decrease of the intraring O5-C1 distance. Therefore, our results clearly show that the distorted conformation resembles both structurally and electronically the transition state of the reaction in which the substrate acquires oxocarbenium ion character, and the glycosidic bond is partially broken. Together with analysis of the substrate conformational dynamics, it is concluded that the main determinants of substrate distortion have a structural origin. To fit into the binding pocket, it is necessary that the aglycon leaving group is oriented toward the beta region, and the skew-boat conformation naturally fulfills this premise. Only when the aglycon is removed from the calculation the substrate recovers the all-chair conformation, in agreement with the recent determination of the enzyme product structure. The QM/MM protocol developed here is able to predict the conformational distortion of substrate binding in glycoside hydrolases because it accounts for polarization and charge reorganization at the -1 sugar ring. It thus provides a powerful tool to model E.S complexes for which experimental information is not yet available.

  12. Hydrogen transfer and hydration properties of H(n)PO4(3-n) (n=0-3) in water studied by first principles molecular dynamics simulations.

    PubMed

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

    2009-06-21

    Density functional theory Perdew-Burke-Ernzerhof [Perdew et al., Phys. Rev. Lett. 77, 3865 (1996)] molecular dynamics simulations of aqueous solutions of orthophosphate species H(n)PO(4)(3-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 PO(4)(3-), of the hydrogen phosphate anions, HPO(4)(2-) and H(2)PO(4)(-), and of the orthophosphoric acid, H(3)PO(4), in explicit water show that the process of proton transfer from H(n)PO(4)(3-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 H(n)PO(4)(3-n) and three water molecules. Analysis of the intermolecular H(n)PO(4)(3-n)-water structure shows that the PO(4)(3-) 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 PO(4)(3-), HPO(4)(2-), and H(2)PO(4)(-) 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 PO(4)(3-) to H(2)PO(4)(-). The strength and number of hydrogen bonds of PO(4)(3-), HPO(4)(2-), and H(2)PO(4)(-) 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 PO(4)(3-) to the hydrogenated H(2)PO(4)(-) species, explain the diminished effect on the structure of water with the increasing hydrogenation of the orthophosphate anions. PMID:19548734

  13. N-H⋯O versus O-H⋯O: density functional calculation and first principle molecular dynamics study on a quinoline-2-carboxamide N-oxide.

    PubMed

    Jezierska, Aneta

    2015-03-01

    N-oxide-type compounds are the object of current research interest due to the presence of resonance-assisted N-H⋯O hydrogen bonds. Here, the metric and spectroscopic parameters of N-methyl-quinoline-2-carboxamide 1-oxide were computed on the basis of density functional theory and Car-Parrinello molecular dynamics. Computations were performed in vacuo and in solid state; for both phases additional simulations with Grimme's dispersion correction were carried out. The approaches used were able to reproduce correctly the structural aspects of the studied compound and shed more light on the hydrogen bonding with special focus on bridge proton mobility. Proton transfer phenomena were found not to occur in the investigated compound, and the bridge proton was localized to the donor site. This observation is in agreement with the classical theory of the acidity of donor-acceptor sites. The presence of hydrogen bonding was confirmed using atoms-in-molecules theory. The computational results were compared with available experimental data. PMID:25690363

  14. 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.

  15. Understanding formation mechanism of ZnO diatomic chain and multi-shell structure using physical mechanics: Molecular dynamics and first-principle simulations?

    NASA Astrophysics Data System (ADS)

    Wang, BinBin; Wang, FengChao; Zhao, YaPu

    2012-06-01

    In this paper, the possibility of the monatomic chain (MC) formation for ZnO material was studied by molecular dynamics (MD) simulation. The process of MC formation and the effects of temperature, strain rate and size were studied extensively. The tensile process can be divided to be five stages and the ZnO diatomic chain (DC) can be found. The MD results show that most atoms in MC came from the original surface of ZnO nanowires (NWs). Temperature and strain rate are two important factors affecting the process, and both high temperature and low strain rate in a certain range would be beneficial to the formation of DC. Moreover, the effects of strain rate and temperature could attribute to the Arrhenius model and the energy release mechanism. Furthermore, multi-shell structure was found for the samples under tensile strain and the layer-layer distance was about 3 Å. Our studies based on density functional theory showed that the most stable structure of ZnO DC was confirmed to be linear, and the I-V curve was also got using ATK.

  16. 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.

  17. First-Principle Calculations of Large Fullerenes.

    PubMed

    Calaminici, Patrizia; Geudtner, Gerald; Köster, Andreas M

    2009-01-13

    State of-the-art density functional theory calculations have been performed for the large fullerenes C180, C240, C320, and C540 using the linear combination of Gaussian-type orbitals density functional theory (LCGTO-DFT) approach. For the calculations all-electron basis sets were employed. All fullerene structures were fully optimized without symmetry constrains. The analysis of the obtained structures as well as a study on the evolution of the bond lengths and calculated binding energies are presented. The fullerene results are compared to diamond and graphene which were calculated at the same level of theory. This represents the first systematic study on these large fullerenes based on nonsymmetry adapted first-principle calculations, and it demonstrates the capability of DFT calculations for energy and structure computations of large scale structures without any symmetry constraint.

  18. Accurate Thermal Conductivities from First Principles

    NASA Astrophysics Data System (ADS)

    Carbogno, Christian

    2015-03-01

    In spite of significant research efforts, a first-principles determination of the thermal conductivity at high temperatures has remained elusive. On the one hand, Boltzmann transport techniques that include anharmonic effects in the nuclear dynamics only perturbatively become inaccurate or inapplicable under such conditions. On the other hand, non-equilibrium molecular dynamics (MD) methods suffer from enormous finite-size artifacts in the computationally feasible supercells, which prevent an accurate extrapolation to the bulk limit of the thermal conductivity. In this work, we overcome this limitation by performing ab initio MD simulations in thermodynamic equilibrium that account for all orders of anharmonicity. The thermal conductivity is then assessed from the auto-correlation function of the heat flux using the Green-Kubo formalism. Foremost, we discuss the fundamental theory underlying a first-principles definition of the heat flux using the virial theorem. We validate our approach and in particular the techniques developed to overcome finite time and size effects, e.g., by inspecting silicon, the thermal conductivity of which is particularly challenging to converge. Furthermore, we use this framework to investigate the thermal conductivity of ZrO2, which is known for its high degree of anharmonicity. Our calculations shed light on the heat resistance mechanism active in this material, which eventually allows us to discuss how the thermal conductivity can be controlled by doping and co-doping. This work has been performed in collaboration with R. Ramprasad (University of Connecticut), C. G. Levi and C. G. Van de Walle (University of California Santa Barbara).

  19. 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

  20. High Pressure Hydrogen from First Principles

    NASA Astrophysics Data System (ADS)

    Morales, M. A.

    2014-12-01

    Typical approximations employed in first-principles simulations of high-pressure hydrogen involve the neglect of nuclear quantum effects (NQE) and the approximate treatment of electronic exchange and correlation, typically through a density functional theory (DFT) formulation. In this talk I'll present a detailed analysis of the influence of these approximations on the phase diagram of high-pressure hydrogen, with the goal of identifying the predictive capabilities of current methods and, at the same time, making accurate predictions in this important regime. We use a path integral formulation combined with density functional theory, which allows us to incorporate NQEs in a direct and controllable way. In addition, we use state-of-the-art quantum Monte Carlo calculations to benchmark the accuracy of more approximate mean-field electronic structure calculations based on DFT, and we use GW and hybrid DFT to calculate the optical properties of the solid and liquid phases near metallization. We present accurate predictions of the metal-insulator transition on the solid, including structural and optical properties of the molecular phase. This work was supported by the U.S. Department of Energy at the Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 and by LDRD Grant No. 13-LW-004.

  1. Intrinsic ferroelectric switching from first principles.

    PubMed

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

    2016-06-15

    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

  2. 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

  3. 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

  4. Toward control of the metal-organic interfacial electronic structure in molecular electronics: a first-principles study on self-assembled monolayers of pi-conjugated molecules on noble metals.

    PubMed

    Heimel, Georg; Romaner, Lorenz; Zojer, Egbert; Brédas, Jean-Luc

    2007-04-01

    Self-assembled monolayers (SAMs) of organic molecules provide an important tool to tune the work function of electrodes in plastic electronics and significantly improve device performance. Also, the energetic alignment of the frontier molecular orbitals in the SAM with the Fermi energy of a metal electrode dominates charge transport in single-molecule devices. On the basis of first-principles calculations on SAMs of pi-conjugated molecules on noble metals, we provide a detailed description of the mechanisms that give rise to and intrinsically link these interfacial phenomena at the atomic level. The docking chemistry on the metal side of the SAM determines the level alignment, while chemical modifications on the far side provide an additional, independent handle to modify the substrate work function; both aspects can be tuned over several eV. The comprehensive picture established in this work provides valuable guidelines for controlling charge-carrier injection in organic electronics and current-voltage characteristics in single-molecule devices.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. First principles simulations of nanoelectronic devices

    NASA Astrophysics Data System (ADS)

    Maassen, Jesse

    As the miniaturization of devices begins to reveal the atomic nature of materials, where chemical bonding and quantum effects are important, one must resort to a parameter-free theory for predictions. This thesis theoretically investigates the quantum transport properties of nanoelectronic devices using atomistic first principles. Our theoretical formalism employs density functional theory (DFT) in combination with Keldysh nonequilibrium Green's functions (NEGF). Self-consistently solving the DFT Hamiltonian with the NEGF charge density provides a way to simulate nonequilibrium systems without phenomenological parameters. This state-of-the-art technique was used to study three problems related to the field of nanoelectronics. First, we investigated the role of metallic contacts (Cu, Ni and Co) on the transport characteristics of graphene devices. With Cu, the graphene is simply electron-doped (Fermi level shift of ≈ -0.7 eV) which creates a unique signature in the conduction profile allowing one to extract the doping level. With Ni and Co, spin-dependent band gaps are formed in graphene's linear dispersion bands, thus leading to the prediction of high spin injection efficiencies reaching 60% and 80%, respectively. Second, we studied how controlled doping distributions in nano-scale Si transistors could suppress OFF-state leakage currents. By assuming the dopants (B and P) are confined in ≈ 1.1 nm regions in the channel, we discovered large conductance variations (GMAX/G MIN ˜ 105) as a function of the doping location. The largest fluctuations arise when the dopants are in the vicinity of the electrodes. Our results indicate that if the dopants are located away from the leads, a distance equal to 20% of the channel length, the tunneling current can be suppressed by a factor of 2 when compared to the case of uniform doping. Thus, controlled doping engineering is found to suppress device-to-device variations and lower the undesirable leakage current. Finally, we

  11. 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.

  12. 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.

  13. First-principles transversal DNA conductance deconstructed.

    PubMed

    Zhang, X-G; Krstić, Predrag S; Zikić, Radomir; Wells, Jack C; Fuentes-Cabrera, Miguel

    2006-07-01

    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 its distance to the electrode, and the larger its conductance. Because the geometrical factors are difficult to control in an experiment, the direct-current measurements across DNA with gold contact electrodes may not be a convenient approach to DNA sequencing.

  14. 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.

  15. First Principles-Based Calculations of Free Energy of Binding: Application to Ligand Binding in a Self-Assembling Superstructure.

    PubMed

    Fox, Stephen; Wallnoefer, Hannes G; Fox, Thomas; Tautermann, Christofer S; Skylaris, Chris-Kriton

    2011-04-12

    The accurate prediction of ligand binding affinities to a protein remains a desirable goal of computational biochemistry. Many available methods use molecular mechanics (MM) to describe the system, however, MM force fields cannot fully describe the complex interactions involved in binding, specifically electron transfer and polarization. First principles approaches can fully account for these interactions, and with the development of linear-scaling first principles programs, it is now viable to apply first principles calculations to systems containing tens of thousands of atoms. In this paper, a quantum mechanical Poisson-Boltzmann surface area approach is applied to a model of a protein-ligand binding cavity, the "tennis ball" dimer. Results obtained from this approach demonstrate considerable improvement over conventional molecular mechanics Poisson-Boltzmann surface area due to the more accurate description of the interactions in the system. For the first principles calculations in this study, the linear-scaling density functional theory program ONETEP is used, allowing the approach to be applied to receptor-ligand complexes of pharmaceutical interest that typically include thousands of atoms.

  16. First-principles quantum chemistry in the life sciences.

    PubMed

    van Mourik, Tanja

    2004-12-15

    The area of computational quantum chemistry, which applies the principles of quantum mechanics to molecular and condensed systems, has developed drastically over the last decades, due to both increased computer power and the efficient implementation of quantum chemical methods in readily available computer programs. Because of this, accurate computational techniques can now be applied to much larger systems than before, bringing the area of biochemistry within the scope of electronic-structure quantum chemical methods. The rapid pace of progress of quantum chemistry makes it a very exciting research field; calculations that are too computationally expensive today may be feasible in a few months' time! This article reviews the current application of 'first-principles' quantum chemistry in biochemical and life sciences research, and discusses its future potential. The current capability of first-principles quantum chemistry is illustrated in a brief examination of computational studies on neurotransmitters, helical peptides, and DNA complexes.

  17. 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

  18. First principles semiclassical calculations of vibrational eigenfunctions

    NASA Astrophysics Data System (ADS)

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

    2011-06-01

    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 CO2 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.

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

    DOE PAGES

    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

  20. 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.

  1. 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

  2. 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.

  3. First principles studies of multiferroic materials.

    PubMed

    Picozzi, Silvia; Ederer, Claude

    2009-07-29

    Multiferroics, materials where spontaneous long-range magnetic and dipolar orders coexist, represent an attractive class of compounds, which combine rich and fascinating fundamental physics with a technologically appealing potential for applications in the general area of spintronics. Ab initio calculations have significantly contributed to recent progress in this area, by elucidating different mechanisms for multiferroicity and providing essential information on various compounds where these effects are manifestly at play. In particular, here we present examples of density-functional theory investigations for two main classes of materials: (a) multiferroics where ferroelectricity is driven by hybridization or purely structural effects, with BiFeO(3) as the prototype material, and (b) multiferroics where ferroelectricity is driven by correlation effects and is strongly linked to electronic degrees of freedom such as spin-, charge-, or orbital-ordering, with rare-earth manganites as prototypes. As for the first class of multiferroics, first principles calculations are shown to provide an accurate qualitative and quantitative description of the physics in BiFeO(3), ranging from the prediction of large ferroelectric polarization and weak ferromagnetism, over the effect of epitaxial strain, to the identification of possible scenarios for coupling between ferroelectric and magnetic order. For the second class of multiferroics, ab initio calculations have shown that, in those cases where spin-ordering breaks inversion symmetry (e.g. in antiferromagnetic E-type HoMnO(3)), the magnetically induced ferroelectric polarization can be as large as a few µC cm(-2). The examples presented point the way to several possible avenues for future research: on the technological side, first principles simulations can contribute to a rational materials design, aimed at identifying spintronic materials that exhibit ferromagnetism and ferroelectricity at or above room temperature. On

  4. 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.

  5. 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.

  6. 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.

  7. First-principles studies of boron nanostructures

    NASA Astrophysics Data System (ADS)

    Lau, Kah Chun

    Boron is an 'electron deficient' element which has a rather fascinating chemical versatility. In the solid state, the elemental boron has neither a pure covalent nor a pure metallic character. As a result, its vast structural dimensionality and peculiar bonding features hold a unique place among other elements in the periodic table. In order to understand and properly describe these unusual bonding features, a detailed and systematic theoretical study is needed. In this work, I will show that some of the qualitative features of boron nanostructures, including clusters, sheets and nanotubes can easily be extracted from the results of first principles calculations based on density functional theory. Specifically, the size-dependent evolution of topological structures and bonding characteristics of boron clusters, Bn will be discussed. Based on the scenario observed in the boron clusters, the unique properties of boron sheets and boron nanotubes will be described. Moreover, the ballistic electron transport in single-walled boron nanotube relative to that of single-walled carbon nanotubes will be considered. It is expected that the theoretical results obtained in the present thesis will initiate further studies on boron nanostructures, which will be helpful in understanding, designing and realizing boron-based nanoscale devices.

  8. 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

  9. Elasticity of serpentine: first principles investigation

    NASA Astrophysics Data System (ADS)

    Tsuchiya, J.; Tsuchiya, T.; Katayama, I.; Usui, Y.

    2009-12-01

    Serpentine is formed by reaction between peridotite and water which is released from hydrous mineral in subducting slab under pressure. Partially serpentinized peridotite may be a significant reservoir for water in the subducted cold slab and is considered to play an important role in subduction zone processes such as generation of arc magmatism. Precise determination of elastic properties of serpentine is essential for estimating the degree of serpentinization, and is important for investigating the transporting processes of water into deep Earth interior. Several studies on the degree of serpentinization have been reported so far based on limited experimental data on elasticity of serpentine (e.g. Bostock et al. 2002; Carlon and Miller 2003). Here we investigate by first principles calculation, the detailed structures and elastic properties of lizardite and antigorite which are lower and higher temperature polymorphs of serpentine up to 10 GPa at 2 GPa interval, and discuss the difference of compression mechanism and elasticity between these polymorphs. Our calculations are based on density functional theory within generalized gradient approximation for exchange correlation functional. We calculated the crystal structure and elasticity of antigorite m=16 polysome which contains 273 atoms in primitive cell (Capitani and Mellini 2006). We found the bulk modulus of antigorite and lizardite are almost same at ambient pressure, but they show significant difference at high pressure conditions. On the other hand, antigorite always has a few % larger shear modulus than lizardite presumably because of corrugated layer structure of antigorite. Combining the data from the present ab initio calculations, and seismological observations for the velocity and anisotropy structures of subduction zones, we analyzed the degree of serpentinization and possible water content in subducting slabs.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. First-Principles Thermoelasticity of Beryllium

    NASA Astrophysics Data System (ADS)

    Legrand, Ph.; Robert, G.

    2009-12-01

    The temperature dependence α of the shear modulus in beryllium is calculated using two different methods within the framework of Density Functional Theory. In Density Function Perturbation Theory, the usual technique to determine the values of elastic constants at T = 0 K is to access the temperature-dependence of the elastic constants through phonon calculations. The elastic constants are then combined to give the Voigt-Reuss-Hill shear modulus for each phase (hcp and bcc). In Quantum Molecular Dynamics, through a certainly crude assumption, we connect the ratio of mean square displacements at around melting temperature to the temperature-dependence of the shear modulus. With both techniques, we obtain α = 0.24±0.14, in good agreement with the model of D. L. Preston and D. C. Wallace [Solid State Comm; 81 277 (1992)].

  2. 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).

  3. 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.

  4. 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 PAGES

    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

  5. 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.

  6. 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.

  7. 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

  8. Exact results and open questions in first principle functional RG

    SciTech Connect

    Le Doussal, Pierre

    2010-01-15

    Some aspects of the functional RG (FRG) approach to pinned elastic manifolds (of internal dimension d) at finite temperature T > 0 are reviewed and reexamined in this much expanded version of Le Doussal (2006) . The particle limit d = 0 provides a test for the theory: there the FRG is equivalent to the decaying Burgers equation, with viscosity {nu} {approx} T-both being formally irrelevant. An outstanding question in FRG, i.e. how temperature regularizes the otherwise singular flow of T = 0 FRG, maps to the viscous layer regularization of inertial range Burgers turbulence (i.e. to the construction of the inviscid limit). Analogy between Kolmogorov scaling and FRG cumulant scaling is discussed. First, multi-loop FRG corrections are examined and the direct loop expansion at T > 0 is shown to fail already in d = 0, a hierarchy of ERG equations being then required (introduced in Balents and Le Doussal (2005) ). Next we prove that the FRG function R(u) and higher cumulants defined from the field theory can be obtained for any d from moments of a renormalized potential defined in an sliding harmonic well. This allows to measure the fixed point function R(u) in numerics and experiments. In d = 0 the beta function (of the inviscid limit) is obtained from first principles to four loop. For Sinai model (uncorrelated Burgers initial velocities) the ERG hierarchy can be solved and the exact function R(u) is obtained. Connections to exact solutions for the statistics of shocks in Burgers and to ballistic aggregation are detailed. A relation is established between the size distribution of shocks and the one for droplets. A droplet solution to the ERG functional hierarchy is found for any d, and the form of R(u) in the thermal boundary layer is related to droplet probabilities. These being known for the d = 0 Sinai model the function R(u) is obtained there at any T. Consistency of the {epsilon}=4-d expansion in one and two loop FRG is studied from first principles, and connected

  9. 67th Mosbacher Kolloquium: Protein Design: From First Principles to Biomedical Applications.

    PubMed

    Spieler, Valerie; Lühmann, Tessa

    2016-07-15

    The 67th Mosbacher Kolloquium of the German Society for Biochemistry and Molecular Biology (GBM) with the topic "Protein Design-From First Principles to Biomedical Application" took place from March 31 to April 2 in Mosbach, Germany. Highlights of the colloquium are presented here.

  10. High-Pressure Hydrogen from First-Principles

    NASA Astrophysics Data System (ADS)

    Morales, Miguel A.

    2014-03-01

    The main approximations typically employed in first-principles simulations of high-pressure hydrogen are the neglect of nuclear quantum effects (NQE) and the approximate treatment of electronic exchange and correlation, typically through a density functional theory (DFT) formulation. In this talk I'll present a detailed analysis of the influence of these approximations on the phase diagram of high-pressure hydrogen, with the goal of identifying the predictive capabilities of current methods and, at the same time, making accurate predictions in this important regime. We use a path integral formulation combined with density functional theory, which allows us to incorporate NQEs in a direct and controllable way. In addition, we use state-of-the-art quantum Monte Carlo calculations to benchmark the accuracy of more approximate mean-field electronic structure calculations based on DFT, and we use GW and hybrid DFT to calculate the optical properties of the solid and liquid phases near metallization. We present accurate predictions of the metal-insulator transition on the solid, including structural and optical properties of the molecular phase. MAM was supported by the U.S. Department of Energy at the Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 and by LDRD Grant No. 13-LW-004.

  11. First-principles studies of atomic dynamics in tetrahedrite thermoelectrics

    NASA Astrophysics Data System (ADS)

    Li, Junchao; Zhu, Mengze; Abernathy, Douglas L.; Ke, Xianglin; Morelli, Donald T.; Lai, Wei

    2016-10-01

    Cu12Sb4S13-based tetrahedrites are high-performance thermoelectrics that contain earth-abundant and environmentally friendly elements. At present, the mechanistic understanding of their low lattice thermal conductivity (<1 W m-1 K-1 at 300 K) remains limited. This work applies first-principles molecular dynamics simulations, along with inelastic neutron scattering (INS) experiments, to study the incoherent and coherent atomic dynamics in Cu10.5NiZn0.5Sb4S13, in order to deepen our insight into mechanisms of anomalous dynamic behavior and low lattice thermal conductivity in tetrahedrites. Our study of incoherent dynamics reveals the anomalous "phonon softening upon cooling" behavior commonly observed in inelastic neutron scattering data. By examining the dynamic Cu-Sb distances inside the Sb[CuS3]Sb cage, we ascribe softening to the decreased anharmonic "rattling" of Cu in the cage. On the other hand, our study of coherent dynamics reveals that acoustic modes are confined in a small region of dynamic scattering space, which we hypothesize leads to a minimum phonon mean free path. By assuming a Debye model, we obtain a lattice minimum thermal conductivity value consistent with experiments. We believe this study furthers our understanding of the atomic dynamics of tetrahedrite thermoelectrics and will more generally help shed light on the origin of intrinsically low lattice thermal conductivity in these and other structurally similar materials.

  12. Revising Intramolecular Photoinduced Electron Transfer (PET) from First-Principles.

    PubMed

    Escudero, Daniel

    2016-09-20

    Photoinduced electron transfer (PET) plays relevant roles in many areas of chemistry, including charge separation processes in photovoltaics, natural and artificial photosynthesis, and photoluminescence sensors and switches. As in many other photochemical scenarios, the structural and energetic factors play relevant roles in determining the rates and efficiencies of PET and its competitive photodeactivation processes. Particularly, in the field of fluorescent sensors and switches, intramolecular PET is believed (in many cases without compelling experimental proof) to be responsible of the quench of fluorescence. There is an increasing experimental interest in fluorophore's molecular design and on achieving optimal excitation/emission spectra, excitation coefficients, and fluorescence quantum yields (importantly for bioimaging purposes), but less efforts are devoted to fundamental mechanistic studies. In this Account, I revise the origins of the fluorescence quenching in some of these systems with state-of-the-art quantum chemical tools. These studies go beyond the common strategy of analyzing frontier orbital energy diagrams and performing PET thermodynamics calculations. Instead, the potential energy surfaces (PESs) of the lowest-lying excited states are explored with time-dependent density functional theory (TD-DFT) and complete active space self-consistent field (CASSCF) calculations and the radiative and nonradiative decay rates from the involved excited states are computed from first-principles using a thermal vibration correlation function formalism. With such a strategy, this work reveals the real origins of the fluorescence quenching, herein entitled as dark-state quenching. Dark states (those that do not absorb or emit light) are often elusive to experiments and thus, computational investigations can provide novel insights into the actual photodeactivation mechanisms. The success of the dark-state quenching mechanism is demonstrated for a wide variety of

  13. Revising Intramolecular Photoinduced Electron Transfer (PET) from First-Principles.

    PubMed

    Escudero, Daniel

    2016-09-20

    Photoinduced electron transfer (PET) plays relevant roles in many areas of chemistry, including charge separation processes in photovoltaics, natural and artificial photosynthesis, and photoluminescence sensors and switches. As in many other photochemical scenarios, the structural and energetic factors play relevant roles in determining the rates and efficiencies of PET and its competitive photodeactivation processes. Particularly, in the field of fluorescent sensors and switches, intramolecular PET is believed (in many cases without compelling experimental proof) to be responsible of the quench of fluorescence. There is an increasing experimental interest in fluorophore's molecular design and on achieving optimal excitation/emission spectra, excitation coefficients, and fluorescence quantum yields (importantly for bioimaging purposes), but less efforts are devoted to fundamental mechanistic studies. In this Account, I revise the origins of the fluorescence quenching in some of these systems with state-of-the-art quantum chemical tools. These studies go beyond the common strategy of analyzing frontier orbital energy diagrams and performing PET thermodynamics calculations. Instead, the potential energy surfaces (PESs) of the lowest-lying excited states are explored with time-dependent density functional theory (TD-DFT) and complete active space self-consistent field (CASSCF) calculations and the radiative and nonradiative decay rates from the involved excited states are computed from first-principles using a thermal vibration correlation function formalism. With such a strategy, this work reveals the real origins of the fluorescence quenching, herein entitled as dark-state quenching. Dark states (those that do not absorb or emit light) are often elusive to experiments and thus, computational investigations can provide novel insights into the actual photodeactivation mechanisms. The success of the dark-state quenching mechanism is demonstrated for a wide variety of

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. First-Principles Study on Dynamic Electron-Transport Property through Low Dimensional System

    NASA Astrophysics Data System (ADS)

    Egami, Yoshiyuki; Hirose, Kikuji

    We present an investigation of electron-transport in a low-dimensional system using a time-dependent first-principles simulator. The response time for the peaks in the transmission curve of a molecular chain system is discussed. Two types of resonant-tunneling channels with different responses to changes in the conformation are observed. It is found that one of the channels plays a minor role in the contribution to the electron transport because of its poor response.

  4. 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

  5. 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

  6. Vibrational spectral diffusion and hydrogen bond dynamics in heavy water from first principles.

    PubMed

    Mallik, Bhabani S; Semparithi, A; Chandra, Amalendu

    2008-06-12

    We present a first-principles theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in heavy water without using any empirical model potentials. The calculations are based on ab initio molecular dynamics simulations for trajectory generation and a time series analysis using the wavelet method for frequency calculations. It is found that, in deuterated water, although a one-to-one relation does not exist between the instantaneous frequency of an OD bond and the distance of its associated hydrogen bond, such a relation does hold on average. The dynamics of spectral diffusion is investigated by means of frequency-time correlation and spectral hole dynamics calculations. Both of these functions are found to have a short-time decay with a time scale of approximately 100 fs corresponding to dynamics of intact hydrogen bonds and a slower long-time decay with a time constant of approximately 2 ps corresponding to lifetimes of hydrogen bonds. The connection of the slower time scale to the dynamics of local structural relaxation is also discussed. The dynamics of hydrogen bond making is shown to have a rather fast time scale of approximately 100 fs; hence, it can also contribute to the short-time dynamics of spectral diffusion. A damped oscillation is also found at around 150-200 fs, which is shown to have come from underdamped intermolecular vibrations of a hydrogen-bonded water pair. Such assignments are confirmed by independent calculations of power spectra of intermolecular motion and hydrogen bond kinetics using the population correlation function formalism. The details of the time constants of frequency correlations and spectral shifts are found to depend on the frequencies of chosen OD bonds and are analyzed in terms of the dynamics of hydrogen bonds of varying strengths and also of free non-hydrogen-bonded OD groups.

  7. Oxygen plasma etching of graphene: A first-principles dynamical inspection of the reaction mechanisms and related activation barriers

    NASA Astrophysics Data System (ADS)

    Koizumi, Kenichi; Boero, Mauro; Shigeta, Yasuteru; Oshiyama, Atsushi; Dept. of Applied Physics Team; Institute of Physics and Chemistry of Strasbourg (IPCMS) Collaboration; Department Of Materials Engineering Science Collaboration

    2013-03-01

    Oxygen plasma etching is a crucial step in the fabrication of electronic circuits and has recently received a renovated interest in view of the realization of carbon-based nanodevices. In an attempt at unraveling the atomic-scale details and to provide guidelines for the control of the etching processes mechanisms, we inspected the possible reaction pathways via reactive first principles simulations. These processes involve breaking and formation of several chemical bonds and are characterized by different free-energy barriers. Free-energy sampling techniques (metadynamics and blue moon), used to enhance the standard Car-Parrinello molecular dynamics, provide us a detailed microscopic picture of the etching of graphene surfaces and a comprehensive scenario of the activation barriers involved in the various steps. MEXT, Japan - contract N. 22104005

  8. 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.

  9. First-Principles Modeling of Multiferroic RMn2O5

    NASA Astrophysics Data System (ADS)

    Cao, Kun; Guo, Guang-Can; Vanderbilt, David; He, Lixin

    2009-12-01

    We investigate the phase diagrams of RMn2O5 via a first-principles effective-Hamiltonian method. We are able to reproduce the most important features of the complicated magnetic and ferroelectric phase transitions. The calculated polarization as a function of temperature agrees very well with experiments. The dielectric-constant step at the commensurate-to-incommensurate magnetic phase transition is well reproduced. The microscopic mechanisms for the phase transitions are discussed.

  10. Adherence of Model Molecules to Silica Surfaces: First Principle Calculations

    NASA Astrophysics Data System (ADS)

    Nuñez, Matías; Prado, Miguel Oscar

    The adherence of "model molecules" methylene blue and eosine Y ("positive" and "negatively" charged respectively) to crystal SiO2 surfaces is studied from first principle calculations at the DFT level. Adsorption energies are calculated which follow the experimental threads obtained elsewhere (Rivera et al., 2013). We study the quantum nature of the electronic charge transfer between the surface and the molecules, showing the localized and delocalized patterns associated to the repulsive and attractive case respectively.

  11. 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.

  12. Conformational structures of a decapeptide validated by first principles calculations and cold ion spectroscopy.

    PubMed

    Roy, Tapta Kanchan; Kopysov, Vladimir; Nagornova, Natalia S; Rizzo, Thomas R; Boyarkin, Oleg V; Gerber, R Benny

    2015-05-18

    Calculated structures of the two most stable conformers of a protonated decapeptide gramicidin S in the gas phase have been validated by comparing the vibrational spectra, calculated from first- principles and measured in a wide spectral range using infrared (IR)-UV double resonance cold ion spectroscopy. All the 522 vibrational modes of each conformer were calculated quantum mechanically and compared with the experiment without any recourse to an empirical scaling. The study demonstrates that first-principles calculations, when accounting for vibrational anharmonicity, can reproduce high-resolution experimental spectra well enough for validating structures of molecules as large as of 200 atoms. The validated accurate structures of the peptide may serve as templates for in silico drug design and absolute calibration of ion mobility measurements.

  13. 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.

  14. Harmonic phonon theory for calculating thermal conductivity spectrum from first-principles dispersion relations

    NASA Astrophysics Data System (ADS)

    Shiga, Takuma; Aketo, Daisuke; Feng, Lei; Shiomi, Junichiro

    2016-05-01

    In recent years, nanostructuring of dielectric and semiconducting crystals has enhanced controllability of their thermal conductivity. To carry out computational materials search for nanostructured materials with desirable thermal conductivity, a key property is the thermal conductivity spectrum of the original single crystal, which determines the appropriate length scale of nanostructures and mutual adaptability of different kinds of nanostructures. Although the first-principles phonon transport calculations have become accessible, the anharmonic lattice dynamics calculations are still expensive to scan many materials. To this end, we have developed an empirical model that describes the thermal conductivity spectrum in terms only of harmonic phonon properties and bulk thermal conductivity. The model was tested for several crystals with different structures and thermal conductivities, and was confirmed to reproduce the overall profiles of thermal conductivity spectra and their accumulation functions obtained by the first-principles anharmonic calculations.

  15. Ethanol adsorption on the Si (111) surface: First principles study

    NASA Astrophysics Data System (ADS)

    Gavrilenko, Alexander V.; Bonner, Carl E.; Gavrilenko, Vladimir I.

    2012-03-01

    Equilibrium atomic configurations and electron energy structure of ethanol adsorbed on the Si (111) surface are studied by the first principles density functional theory. Geometry optimization is performed by the total energy minimization method. Equilibrium atomic geometries of ethanol, both undissociated and dissociated, on the Si (111) surface are found and analysed. Reaction pathways and predicted transition states are discussed in comparison with available experimental data in terms of the feasibility of the reactions occurring. Analysis of atom and orbital resolved projected density of states indicates substantial modifications of the Si surface valence and conduction electron bands due to the adsorption of ethanol affecting the electronic properties of the surface.

  16. First-principles study of graphene - carbon nanotube contacts

    NASA Astrophysics Data System (ADS)

    Cook, Brandon; Varga, Kalman

    2012-02-01

    The electron transport properties of carbon nanotube -- graphene junctions are investigated with first-principles total energy and electron transport calculations. By combining the advantageous material properties of graphene and nanotubes one can create all carbon hybrid architectures with properties that are particularly well suited to applications. The p-type Schottky barrier height is calculated in model junctions with (8,0) and (10,0) nanotubes in a top-contact configuration. Results indicate a lower barrier in carbon nanotube -- graphene junctions than in other carbon nanotue -- metal systems.

  17. First-principles study of NO adsorbed Ni(100) surface.

    PubMed

    Mu, X; Sun, X; Li, H M; Ding, Z J

    2010-11-01

    The geometric, electronic and magnetic properties of NO molecules adsorbed on the Ni(100) surface are investigated by the first-principles calculation on the basis of the density functional theory (DFT). The NO molecules are predicted to be chemisorbed at hollow site with an upright configuration at 0.125 ML and 0.5 ML coverages. After adsorption, the magnetic moment is significantly suppressed for surface Ni atom and almost quenched for NO molecule. This behavior can be reasonably explained by the difference of the backdonation process between the spin-up and spin-down electronic states, which is demonstrated by the spin-resolved differential charge density map.

  18. Electromagnetic Response of 12C: A First-Principles Calculation

    NASA Astrophysics Data System (ADS)

    Lovato, A.; Gandolfi, S.; Carlson, J.; Pieper, Steven C.; Schiavilla, R.

    2016-08-01

    The longitudinal and transverse electromagnetic response functions of 12C are computed in a "first-principles" Green's function Monte Carlo calculation, based on realistic two- and three-nucleon interactions and associated one- and two-body currents. We find excellent agreement between theory and experiment and, in particular, no evidence for the quenching of the measured versus calculated longitudinal response. This is further corroborated by a reanalysis of the Coulomb sum rule, in which the contributions from the low-lying Jπ=2+, 02+ (Hoyle), and 4+ states in 12 are accounted for explicitly in evaluating the total inelastic strength.

  19. Electromagnetic Response of ^{12}C: A First-Principles Calculation.

    PubMed

    Lovato, A; Gandolfi, S; Carlson, J; Pieper, Steven C; Schiavilla, R

    2016-08-19

    The longitudinal and transverse electromagnetic response functions of ^{12}C are computed in a "first-principles" Green's function Monte Carlo calculation, based on realistic two- and three-nucleon interactions and associated one- and two-body currents. We find excellent agreement between theory and experiment and, in particular, no evidence for the quenching of the measured versus calculated longitudinal response. This is further corroborated by a reanalysis of the Coulomb sum rule, in which the contributions from the low-lying J^{π}=2^{+}, 0_{2}^{+} (Hoyle), and 4^{+} states in ^{12}C are accounted for explicitly in evaluating the total inelastic strength. PMID:27588850

  20. Diffusion in thorium carbide: A first-principles study

    NASA Astrophysics Data System (ADS)

    Pérez Daroca, D.; Llois, A. M.; Mosca, H. O.

    2015-12-01

    The prediction of the behavior of Th compounds under irradiation is an important issue for the upcoming Generation-IV nuclear reactors. The study of self-diffusion and hetero-diffusion is a central key to fulfill this goal. As a first approach, we obtained, by means of first-principles methods, migration and activation energies of Th and C atoms self-diffusion and diffusion of He atoms in ThC. We also calculate diffusion coefficients as a function of temperature.

  1. Oxygen diffusion in hcp metals from first principles

    NASA Astrophysics Data System (ADS)

    Wu, Henry H.; Wisesa, Pandu; Trinkle, Dallas R.

    2016-07-01

    Oxygen interstitial site energies and migration barriers in 15 hexagonal close-packed (hcp) metals have been calculated with first-principles density functional theory. Multiple hcp systems show a preference for the hexahedral site over the tetrahedral site, as well as a stable crowdion site. More surprisingly, in more than half of the hcp systems, the oxygen does not choose the large octahedral interstitial as its ground state. We explain this result based on the effective valence of the metal from crystal-field splitting and the c /a ratio. Diffusion constants for oxygen in all 15 hcp systems are calculated from analytically derived diffusion equations and match available experimental data.

  2. Comparative study of Ti and Ni clusters from first principles

    SciTech Connect

    Lee, B; Lee, G W

    2007-08-20

    Icosahedral clusters in Ti and Ni are studied with first-principles density functional calculations. We find significant distortion on the Ti icosahedron caused by the strong interaction between surface atoms on the icosahedron but not between the center atom and surface atoms, whereas no such distortion is observed on Ni clusters. In addition, distortion becomes more severe when atoms are added to the Ti13 cluster resulting in short bonds. Such distorted icosahedra having short bonds are essentially to explain the structure factor of Ti liquid obtained in experiment.

  3. First-principles theory of multipolar order in neptunium dioxide

    NASA Astrophysics Data System (ADS)

    Suzuki, M.-T.; Magnani, N.; Oppeneer, P. M.

    2010-12-01

    We provide a first-principles, materials-specific theory of multipolar order and superexchange in NpO2 by means of a noncollinear local-density approximation +U (LDA+U) method. Our calculations offer a precise microscopic description of the triple- q antiferro ordered phase in the absence of any dipolar moment. We find that, while the most common nondipolar degrees of freedom (e.g., electric quadrupoles and magnetic octupoles) are active in the ordered phase, both the usually neglected higher-order multipoles (electric hexadecapoles and magnetic triakontadipoles) have at least an equally significant effect.

  4. Derivation of instanton rate theory from first principles

    NASA Astrophysics Data System (ADS)

    Richardson, Jeremy O.

    2016-03-01

    Instanton rate theory is used to study tunneling events in a wide range of systems including low-temperature chemical reactions. Despite many successful applications, the method has never been obtained from first principles, relying instead on the "Im F" premise. In this paper, the same expression for the rate of barrier penetration at finite temperature is rederived from quantum scattering theory [W. H. Miller, S. D. Schwartz, and J. W. Tromp, J. Chem. Phys. 79, 4889 (1983)] using a semiclassical Green's function formalism. This justifies the instanton approach and provides a route to deriving the rate of other processes.

  5. Accurately Predicting Complex Reaction Kinetics from First Principles

    NASA Astrophysics Data System (ADS)

    Green, William

    Many important systems contain a multitude of reactive chemical species, some of which react on a timescale faster than collisional thermalization, i.e. they never achieve a Boltzmann energy distribution. Usually it is impossible to fully elucidate the processes by experiments alone. Here we report recent progress toward predicting the time-evolving composition of these systems a priori: how unexpected reactions can be discovered on the computer, how reaction rates are computed from first principles, and how the many individual reactions are efficiently combined into a predictive simulation for the whole system. Some experimental tests of the a priori predictions are also presented.

  6. Collective Modes in Light Nuclei from First Principles

    NASA Astrophysics Data System (ADS)

    Dytrych, T.; Launey, K. D.; Draayer, J. P.; Maris, P.; Vary, J. P.; Saule, E.; Catalyurek, U.; Sosonkina, M.; Langr, D.; Caprio, M. A.

    2013-12-01

    Results for ab initio no-core shell model calculations in a symmetry-adapted SU(3)-based coupling scheme demonstrate that collective modes in light nuclei emerge from first principles. The low-lying states of Li6, Be8, and He6 are shown to exhibit orderly patterns that favor spatial configurations with strong quadrupole deformation and complementary low intrinsic spin values, a picture that is consistent with the nuclear symplectic model. The results also suggest a pragmatic path forward to accommodate deformation-driven collective features in ab initio analyses when they dominate the nuclear landscape.

  7. First-Principles Calculation of forces and phonons in solid

    NASA Astrophysics Data System (ADS)

    Ning, Zhenhua; Shelton, William

    We have developed a multiple scattering theory approach to calculate Hellmann-Feynman forces and phonons via the calculation of the force constant and dynamical matrix. To demonstrate the accuracy and validity of our approach we compare with the ELK code, which is a full potential Linear Augmented Plane Wave (FLAPW) based method. As we will show our forces and phonon dispersion curves are in good agreement with the FLAPW code. This work lays the foundation for developing a first principles approach for calculation of phonons in substitutionally disordered materials.

  8. Large impurity effects in rubrene crystals: First-principles calculations

    SciTech Connect

    Tsetseris, L.; Pantelides, Sokrates T.

    2008-01-01

    Carrier mobilities of rubrene films are among the highest values reported for any organic semiconductor. Here, we probe with first-principles calculations the sensitivity of rubrene crystals on impurities. We find that isolated oxygen impurities create distinct peaks in the electronic density of states consistent with observations of defect levels in rubrene and that increased O content changes the position and shape of rubrene energy bands significantly. We also establish a dual role of hydrogen as individual H species and H impurity pairs create and annihilate deep carrier traps, respectively. The results are relevant to the performance and reliability of rubrene-based devices.

  9. First-principles thermoelasticity of bcc iron under pressure

    NASA Astrophysics Data System (ADS)

    Sha, Xianwei; Cohen, R. E.

    2006-12-01

    We investigate the elastic and isotropic aggregate properties of ferromagnetic bcc iron as a function of temperature and pressure by computing the Helmholtz free energies for the volume-conserving strained structures using the first-principles linear response linear-muffin-tin-orbital method and the generalized-gradient approximation. We include the electronic excitation contributions to the free energy from the band structures, and phonon contributions from quasiharmonic lattice dynamics. We make detailed comparisons between our calculated elastic moduli and their temperature and pressure dependences with available experimental and theoretical data. The isotropic aggregate sound velocities obtained based on the calculated elastic moduli agree with available ultrasonic and diamond-anvil-cell data. Birch’s law, which assumes a linear increase in sound velocity with increasing atomic density, fails for bcc Fe under extreme conditions. First-principles linear-response lattice dynamics is shown to provide a tractable approach to examine the elasticity of transition metals at high pressures and high temperatures.

  10. First-principles opacity table of warm dense deuterium for inertial-confinement-fusion applications

    NASA Astrophysics Data System (ADS)

    Hu, S. X.; Collins, L. A.; Goncharov, V. N.; Boehly, T. R.; Epstein, R.; McCrory, R. L.; Skupsky, S.

    2014-09-01

    Accurate knowledge of the optical properties of a warm dense deuterium-tritium (DT) mixture is important for reliable design of inertial confinement fusion (ICF) implosions using radiation-hydrodynamics simulations. The opacity of a warm dense DT shell essentially determines how much radiation from hot coronal plasmas can be deposited in the DT fuel of an imploding capsule. Even for the simplest species of hydrogen, the accurate calculation of their opacities remains a challenge in the warm-dense matter regime because strong-coupling and quantum effects play an important role in such plasmas. With quantum-molecular-dynamics (QMD) simulations, we have derived a first-principles opacity table (FPOT) of deuterium (and the DT mixture by mass scaling) for a wide range of densities from ρD=0.5 to 673.518g/cm3 and temperatures from T=5000K up to the Fermi temperature TF for each density. Compared with results from the astrophysics opacity table (AOT) currently used in our hydrocodes, the FPOT of deuterium from our QMD calculations has shown a significant increase in opacity for strongly coupled and degenerate plasma conditions by a factor of 3-100 in the ICF-relevant photon-energy range. As conditions approach those of classical plasma, the opacity from the FPOT converges to the corresponding values of the AOT. By implementing the FPOT of deuterium and the DT mixture into our hydrocodes, we have performed radiation-hydrodynamics simulations for low-adiabat cryogenic DT implosions on the OMEGA laser and for direct-drive-ignition designs for the National Ignition Facility. The simulation results using the FPOT show that the target performance (in terms of neutron yield and energy gain) could vary from ˜10% up to a factor of ˜2 depending on the adiabat of the imploding DT capsule; the lower the adiabat, the more variation is seen in the prediction of target performance when compared to the AOT modeling.

  11. First-principle approach to rescale the dynamics of simulated coarse-grained macromolecular liquids

    NASA Astrophysics Data System (ADS)

    Lyubimov, I.; Guenza, M. G.

    2011-09-01

    We present a detailed derivation and testing of our approach to rescale the dynamics of mesoscale simulations of coarse-grained polymer melts (I. Y. Lyubimov, J. McCarty, A. Clark, and M. G. Guenza, J. Chem. Phys.JCPSA60021-960610.1063/1.3450301 132, 224903 (2010)). Starting from the first-principle Liouville equation and applying the Mori-Zwanzig projection operator technique, we derive the generalized Langevin equations (GLEs) for the coarse-grained representations of the liquid. The chosen slow variables in the projection operators define the length scale of coarse graining. Each polymer is represented at two levels of coarse graining: monomeric as a bead-and-spring model and molecular as a soft colloid. In the long-time regime where the center-of-mass follows Brownian motion and the internal dynamics is completely relaxed, the two descriptions must be equivalent. By enforcing this formal relation we derive from the GLEs the analytical rescaling factors to be applied to dynamical data in the coarse-grained representation to recover the monomeric description. Change in entropy and change in friction are the two corrections to be accounted for to compensate the effects of coarse graining on the polymer dynamics. The solution of the memory functions in the coarse-grained representations provides the dynamical rescaling of the friction coefficient. The calculation of the internal degrees of freedom provides the correction of the change in entropy due to coarse graining. The resulting rescaling formalism is a function of the coarse-grained model and thermodynamic parameters of the system simulated. The rescaled dynamics obtained from mesoscale simulations of polyethylene, represented as soft-colloidal particles, by applying our rescaling approach shows a good agreement with data of translational diffusion measured experimentally and from simulations. The proposed method is used to predict self-diffusion coefficients of new polyethylene samples.

  12. Effects of interlayer screening and temperature on dielectric functions of graphene by first-principles

    NASA Astrophysics Data System (ADS)

    Yang, J. Y.; Liu, L. H.

    2016-07-01

    The dielectric functions of few-layer graphene and the related temperature dependence are investigated from the atomic scale using first-principles calculations. Compared with ellipsometry experiments in the spectral range of 190-2500 nm, the normalized optical constants of mono-layer graphene demonstrate good agreement and further validate first-principles calculations. To interpret dielectric function of mono-layer graphene, the electronic band structure and density of states are analyzed. By comparing dielectric functions of mono-, bi-, and tri-layer graphene, it shows that interlayer screening strengthens intraband transition and greatly enhances the absorption peak located around 1 eV. The strengthened optical absorption is intrinsically caused by the increasing electron states near the Fermi level. To investigate temperature effect, the first-principles calculations and lattice dynamics are combined. The lattice vibration enhances parallel optical absorption peak around 1 eV and induces redshift. Moreover, it is observed that the van der Waals force plays a key role in keeping the interlayer distance stable during dynamics simulations.

  13. All-carbon nanoswitch based on C70 molecule: A first principles study

    NASA Astrophysics Data System (ADS)

    OuYang, Fangping; Xu, Hui; Fan, Toujiao

    2007-09-01

    We have demonstrated the electron transport properties of an all-carbon molecular junction based on the C70 molecule connecting with two armchair single-wall carbon nanotubes using first principles transport calculations. It is shown that the Landauer conductance of this carbon hybrid system can be tuned within several orders of magnitude not only by changing the orientation of the C70 molecule but also by rotating one of the tubes around the symmetry axis of the system at fixed distances. This fact could make this pure-carbon molecular system a possible candidate for a nanoelectronic switching device. Moreover, we have also studied the nitrogen doping effect of such a molecular device. The results reveal that molecular configuration selection and nitrogen doping would play important roles in such switching devices.

  14. First-Principles Informed Thermodynamics of CRUD Deposition

    NASA Astrophysics Data System (ADS)

    O'Brien, Christopher John

    The recent emphasis in the United States on developing abundant domestic sources of energy, together with an increasing awareness of the environmental hazards of fossil fuels, has led to a fresh look at the challenges of nuclear energy within the science and engineering community. One of these challenges is controlling the precipitation of porous oxide deposits onto the nuclear fuel rod cladding from the primary coolant during operation of pressurized light-water reactors (PWRs). These deposits, called CRUD (an acronym for Chalk River Unidentified Deposits), are a major concern to reactor operation because they reduce fuel lifetime and efficiency by reducing heat transfer to the coolant, promote corrosion, and depress neutron flux. This dissertation provides fundamental insights into the process by which CRUD is formed in PWRs by providing a framework linking the results of first-principles calculations to experimental data. The technique developed to facilitate the investigation is referred to as Density Functional Theory (DFT) referenced semi-empirical thermodynamics; It links 0K first-principles calculations with high temperature thermodynamics by redefining the reference chemical potentials of the constituent elements. The technique permits aqueous chemistry to be incorporated into thermodynamic calculations and allows for the prediction of temperature and pressure dependent free energies of materials that are experimentally inaccessible or have not yet been measured. The ability to extend accurate first-principles calculations to high temperatures and aqueous environments allows the stability of crystal surfaces, calculated with DFT techniques, to be predicted at conditions representative of an operating PWR. Accurate values of surface energies are used in fulfilling the principal goal of this dissertation, which is to investigate the aqueous thermodynamics of formation of nickel oxide (NiO) and nickel ferrite (NiFe 2O4) crystallites as representative CRUD

  15. Explorative First-Principles Simulation Study of Mineral - Melt Trace Element Partitioning Behavior

    NASA Astrophysics Data System (ADS)

    Wagner, J.; Jahn, S.

    2014-12-01

    Knowledge of trace element partition coefficients is crucial for a range of geoscientific applications. Obtaining the necessary experimental data is still a challenging and time consuming task, as the relevant processes typically take place under extreme P/T conditions. In this study, we explore a molecular scale simulation approach to predict mineral-melt partitioning. We use first principles molecular dynamics to investigate the rare earth element Y in the system garnet - melt, with focus on the influence of the melt. To predict the free energy change of the exchange reaction when Y is distributed between two phases, the method of thermodynamic integration is employed. Here we use an alchemical transmutation by which the identity (here expressed by its pseudopotential parameters) of a major element is gradually changed, in our case from 100% Al to 100% Y. The free energy change in turn enables us to predict the phase Y will partition into, as has been done previously for a CaO-Al2O3-SiO2-Y2O3 model system, employing classical force field simulations1. A major advantage of a molecular dynamics approach is that simulations contain information about the melt structure itself, thus enabling us to link observations to structural changes, e.g. a shift of average Y-O coordination number as a function of network connectivity. We choose a garnet-rich peridotite and a mid-ocean ridge basalt as starting compositions. After both melts are equilibrated at 3000 K and ambient pressure, we perform the thermodynamic integration and compare the free energy of the exchange reaction. The first results suggest that it is possible to at least qualitatively predict the behavior of Y in the two model systems, as compared to experimental findings. We will discuss the potential of the method to make quantitative predictions and how the effect of P and T can be evaluated. Potentially, this new tool may allow us to make predictions for almost any composition and condition available to

  16. Magnetization of iron clusters from first-principles calculations

    NASA Astrophysics Data System (ADS)

    Chelikowsky, James R.; Tiago, Murilo L.; Li, Shen; Alemany, Manuel M. G.; Zhou, Yunkai; Saad, Yousef

    2006-03-01

    The magnetic moment of Fe clusters as function of number of atoms has been observed to show a slow decrease from the isolated atom value (4 Bohr magnetons) to its bulk value of 2.2 Bohr magnetons per atom. In addition, a series of peaks has been observed, for which the causes are not yet fully understood (see Billas, Chatelain, and de Heer, Science, 1994). We analyze the dependence of total magnetic moment, local magnetic moment, cohesive energy and other physical quantities in iron clusters Fen ( 1 < n < 250 ), and compare these results with available experimental data. We use a real-space method, pseudopotentials and first-principles DFT to obtain the properties of the cluster in its ground state. Calculations are done using the PARSEC code ( www.ices.utexas.edu/parsec ). We also discuss some of the recently developed capabilities of PARSEC.

  17. Hadron Phenomenology from First-Principle QCD Studies

    NASA Astrophysics Data System (ADS)

    Papavassiliou, Joannis

    2016-06-01

    The form of the kernel that controls the dynamics of the Bethe-Salpeter equations is essential for obtaining quantitatively accurate predictions for the observable properties of hadrons. In the present work we briefly review the basic physical concepts and field-theoretic techniques employed in a first-principle derivation of a universal (process-independent) component of this kernel. This "top-down" approach combines nonperturbative ingredients obtained from lattice simulations and Dyson-Schwinger equations, and furnishes a renormalization-group invariant quark-gluon interaction strength, which is in excellent agreement with the corresponding quantity obtained from a systematic "bottom-up" treatment, where bound-state data are fitted within a well-defined truncation scheme.

  18. First-principles study of interface doping in ferroelectric junctions.

    PubMed

    Wang, Pin-Zhi; Cai, Tian-Yi; Ju, Sheng; Wu, Yin-Zhong

    2016-04-11

    Effect of atomic monolayer insertion on the performance of ferroelectric tunneling junction is investigated in SrRuO3/BaTiO3/SrRuO3 heterostrucutures. Based on first-principles calculations, the atomic displacement, orbital occupancy, and ferroelectric polarization are studied. It is found that the ferroelectricity is enhanced when a (AlO2)(-) monolayer is inserted between the electrode SRO and the barrier BTO, where the relatively high mobility of doped holes effectively screen ferroelectric polarization. On the other hand, for the case of (LaO)(+) inserted layer, the doped electrons resides at the both sides of middle ferroelectric barrier, making the ferroelectricity unfavorable. Our findings provide an alternative avenue to improve the performance of ferroelectric tunneling junctions.

  19. Accurate first principles model potentials for intermolecular interactions.

    PubMed

    Gordon, Mark S; Smith, Quentin A; Xu, Peng; Slipchenko, Lyudmila V

    2013-01-01

    The general effective fragment potential (EFP) method provides model potentials for any molecule that is derived from first principles, with no empirically fitted parameters. The EFP method has been interfaced with most currently used ab initio single-reference and multireference quantum mechanics (QM) methods, ranging from Hartree-Fock and coupled cluster theory to multireference perturbation theory. The most recent innovations in the EFP model have been to make the computationally expensive charge transfer term much more efficient and to interface the general EFP dispersion and exchange repulsion interactions with QM methods. Following a summary of the method and its implementation in generally available computer programs, these most recent new developments are discussed.

  20. First-principles study of point defects in thorium carbide

    NASA Astrophysics Data System (ADS)

    Pérez Daroca, D.; Jaroszewicz, S.; Llois, A. M.; Mosca, H. O.

    2014-11-01

    Thorium-based materials are currently being investigated in relation with their potential utilization in Generation-IV reactors as nuclear fuels. One of the most important issues to be studied is their behavior under irradiation. A first approach to this goal is the study of point defects. By means of first-principles calculations within the framework of density functional theory, we study the stability and formation energies of vacancies, interstitials and Frenkel pairs in thorium carbide. We find that C isolated vacancies are the most likely defects, while C interstitials are energetically favored as compared to Th ones. These kind of results for ThC, to the best authors' knowledge, have not been obtained previously, neither experimentally, nor theoretically. For this reason, we compare with results on other compounds with the same NaCl-type structure.

  1. First principle study of manganese doped cadmium sulphide sheet

    SciTech Connect

    Kumar, Sanjeev; Kumar, Ashok; Ahluwalia, P. K.

    2014-04-24

    First-principle electronic structure calculations for cadmium sulphide (CdS) sheet in hexagonal phase, with Manganese substitution and addition, as well as including the Cd defects, are investigated. The lattice constants calculated for CdS sheet agrees fairly well with results reported for thin films experimentally. The calculations of total spin density of states and partial density of states in different cases shows substantial magnetic dipole moments acquired by the sheet. A magnetic dipole moment 5.00612 μ{sub B} and band gap of the order 1 eV are found when cadmium atom is replaced by Manganese. The magnetism acquired by the sheet makes it functionally important candidate in many applications.

  2. Diffusion of aluminium in MgO from first principles

    NASA Astrophysics Data System (ADS)

    Ammann, M. W.; Brodholt, J. P.; Dobson, D. P.

    2012-06-01

    We have calculated the diffusivity of aluminium in periclase, MgO, under pressures relevant to deep planetary interiors from first principles. We reconcile differences between experimental migration enthalpies and those obtained with previous theoretical studies by finding a lower energy saddle point for the aluminium atom migration. Previous studies did not recognise a bifurcation at the saddle point. We also explain differences between experimental and theoretical binding enthalpies of an aluminium with a magnesium vacancy. We find that binding enthalpies continuously increase with decreasing aluminium concentrations, such that the difference between experimental and theoretical binding energies can be attributed to differing concentrations. We also find that binding energies increase with pressure as the permittivity decreases. Aluminium therefore not only causes extrinsic vacancy formation but also binds some of them, effectively removing them for magnesium diffusion. We discuss the implications for how other 3+ ions affect diffusion in oxides and silicates.

  3. Two Dimensional Ice from First Principles: Structures and Phase Transitions.

    PubMed

    Chen, Ji; Schusteritsch, Georg; Pickard, Chris J; Salzmann, Christoph G; Michaelides, Angelos

    2016-01-15

    Despite relevance to disparate areas such as cloud microphysics and tribology, major gaps in the understanding of the structures and phase transitions of low-dimensional water ice remain. Here, we report a first principles study of confined 2D ice as a function of pressure. We find that at ambient pressure hexagonal and pentagonal monolayer structures are the two lowest enthalpy phases identified. Upon mild compression, the pentagonal structure becomes the most stable and persists up to ∼2  GPa, at which point the square and rhombic phases are stable. The square phase agrees with recent experimental observations of square ice confined within graphene sheets. This work provides a fresh perspective on 2D confined ice, highlighting the sensitivity of the structures observed to both the confining pressure and the width.

  4. Point defects in thorium nitride: A first-principles study

    NASA Astrophysics Data System (ADS)

    Pérez Daroca, D.; Llois, A. M.; Mosca, H. O.

    2016-11-01

    Thorium and its compounds (carbides and nitrides) are being investigated as possible materials to be used as nuclear fuels for Generation-IV reactors. As a first step in the research of these materials under irradiation, we study the formation energies and stability of point defects in thorium nitride by means of first-principles calculations within the framework of density functional theory. We focus on vacancies, interstitials, Frenkel pairs and Schottky defects. We found that N and Th vacancies have almost the same formation energy and that the most energetically favorable defects of all studied in this work are N interstitials. These kind of results for ThN, to the best authors' knowledge, have not been obtained previously, neither experimentally, nor theoretically.

  5. Defects in AIN/GaN Superlattice: First Principle Calculations.

    PubMed

    Rao, Xue; Wang, Ru-Zhi; Cao, Juexian; Yan, Hui

    2016-01-01

    In this paper we investigate the atomic configurations, electronic structure and formation energies of native point defects, (such as vacancies and self-interstitials), in an AIN/GaN superlattice (SL) constructed on a wurtzite structure along a [0001] growth direction. Comprehensive first-principle calculations based on the density functional theory (DFT) are used. Cation and anion vacancies in the neutral charge state are calculated. For the native defects, the results showed that the most favorable configurations are the cation vacancies at the interface of the SL, or the anion vacancies in the GaN wells. Considering the formation energies of different vacancies, the results show that the nitrogen vacancy has the lowest formation energy, indicating that they are significantly the most stable configuration, and thus should be expected to be the major defect in a AIN/GaN superlattice. PMID:27398499

  6. First-principles study of high explosive decomposition energetics

    SciTech Connect

    Wu, C J

    1998-08-21

    The mechanism of the gas phase unimolecular decomposition of hexahydro-1,3,5,- trinitro- 1,3,5,-triazine (RDX) has been investigated using first principles gradient corrected density functional theory. Our results show that the dominant reaction channel is the N-NO* bond rupture, which has a barrier of 34.2 kcal/mol at the B- PW9 l/cc-pVDZ level and is 18.3 kcal/mol lower than that of the concerted ring fission to three methylenenitramine molecules. In addition, we have carried out a systematic study of homolytic bond dissociation energies of 14 other high explosives at the B-PW91/D95V level. We find that the correlation between the weakest bond strength and high explosive sensitivity is strong

  7. First-principles study of 2D electride : Gadolinium carbide

    NASA Astrophysics Data System (ADS)

    Nandadasa, Chandani; Kim, Seong-Gon; Kim, Sungho; Kim, Sung Wng

    Electrides are an exclusive class of ionic compounds in which some electrons are occupying crystal voids instead of attaching to specific atoms or bonds. Using first-principles density functional theory calculations, we study structural, electronic and magnetic properties of Gd2C. The theoretically predicted structure of Gd2C is in good agreement with the available experimental data. Energy band diagram of Gd2C shows that they are crossing the Fermi level. Projected electronic density of states plots indicate that the interstitial sites are the main contributor to the density of states at the Fermi level. Charge of individual atoms including interstitial site are obtained using Bader analysis. Magnetic properties of Gd2C is determined from magnetization density plots. Work functions of Gd2C are determined for (001) and (100) surfaces with the technique of macroscopic average of electrostatic potential with the Fermi energy of bulk.

  8. First-principles study of thermal properties of borophene.

    PubMed

    Sun, Hongyi; Li, Qingfang; Wan, X G

    2016-06-01

    Very recently, a new single-element two-dimensional (2D) material borophene was successfully grown on a silver surface under pristine ultrahigh vacuum conditions which attracts tremendous interest. In this paper, the lattice thermal conductivity, phonon lifetimes, thermal expansion and temperature dependent elastic moduli of borophene are systematically studied by using first-principles. Our simulations show that borophene possesses unique thermal properties. Strong phonon-phonon scattering is found in borophene, which results in its unexpectedly low lattice thermal conductivity. Thermal expansion coefficients along both the armchair and zigzag directions of borophene show impressive negative values. More strikingly, the elastic moduli are sizably strengthened as temperature increases, and the negative in-plane Poisson's ratios are found along both the armchair and zigzag directions at around 120 K. The mechanisms of these unique thermal properties are also discussed in this paper. PMID:27188523

  9. Modeling of Co overlayers on Pd (111) from first principles

    NASA Astrophysics Data System (ADS)

    Uba, S.; Uba, L.; Antonov, V. N.

    2007-04-01

    The electronic, magnetic and magneto-optical properties of Co overlayers on Pd (1 1 1) substrate have been investigated by ab initio band structure calculations within the spin-polarized relativistic linear muffin-thin orbitals (LMTO) method and supercell approach. The role of the Co-Pd interface structure, the number of the Co atomic layers ( n Co ), as well as the spin-orbit interaction and induced Pd spin polarization, in formation of magneto-optical response of the structures for [ n CoCo/Pd (1 1 1)] system is shown. The sign reversal of the polar Kerr rotation obtained theoretically with decreasing thickness of Co overlayers agrees well with experiment. We will demonstrate the effectiveness of the extended numeric modeling of magneto-optical properties from first principles.

  10. First-Principles Theoretical Analysis of Carbon Allotropes and Nanostructures

    NASA Astrophysics Data System (ADS)

    Singh, Tejinder; Behr, Michael J.; Aydil, Eray S.; Maroudas, Dimitrios

    2008-03-01

    We analyze the various crystalline phases of C observed upon exposing carbon nanotubes to H2 plasmas, which produces an amorphous carbon matrix with carbon nanocrystalls embedded in it. Structural characterization with electron diffraction and high-resolution TEM yields three distinct crystalline phases of C consistent with a fcc lattice with lattice parameter a = 4.25 å, a bcc lattice with a = 3.0 å, and a diamond lattice with a = 3.57 å. Using first-principles density functional theory (DFT) calculations, we have analyzed the structure of several allotropes of pure carbon and we discuss our results in the context of the experimental findings. In addition, we consider the possibility of H incorporation in these C phases. According to our DFT calculations, incorporation at proper concentrations of H in interstitial sites of cubic phases of C provides interpretations for the experimentally observed crystalline C phases.

  11. Electromagnetic response of C12 : A first-principles calculation

    DOE PAGES

    Lovato, A.; Gandolfi, S.; Carlson, J.; Pieper, Steven C.; Schiavilla, R.

    2016-08-15

    Here, the longitudinal and transverse electromagnetic response functions ofmore » $$^{12}$$C are computed in a ``first-principles'' Green's function Monte Carlo calculation, based on realistic two- and three-nucleon interactions and associated one- and two-body currents. We find excellent agreement between theory and experiment and, in particular, no evidence for the quenching of measured versus calculated longitudinal response. This is further corroborated by a re-analysis of the Coulomb sum rule, in which the contributions from the low-lying $$J^\\pi\\,$$=$$\\, 2^+$$, $0^+$ (Hoyle), and $4^+$ states in $$^{12}$$C are accounted for explicitly in evaluating the total inelastic strength.« less

  12. First-principles study of interface doping in ferroelectric junctions

    PubMed Central

    Wang, Pin-Zhi; Cai, Tian-Yi; Ju, Sheng; Wu, Yin-Zhong

    2016-01-01

    Effect of atomic monolayer insertion on the performance of ferroelectric tunneling junction is investigated in SrRuO3/BaTiO3/SrRuO3 heterostrucutures. Based on first-principles calculations, the atomic displacement, orbital occupancy, and ferroelectric polarization are studied. It is found that the ferroelectricity is enhanced when a (AlO2)− monolayer is inserted between the electrode SRO and the barrier BTO, where the relatively high mobility of doped holes effectively screen ferroelectric polarization. On the other hand, for the case of (LaO)+ inserted layer, the doped electrons resides at the both sides of middle ferroelectric barrier, making the ferroelectricity unfavorable. Our findings provide an alternative avenue to improve the performance of ferroelectric tunneling junctions. PMID:27063704

  13. A metallic superhard boron carbide: first-principles calculations.

    PubMed

    Ma, Mengdong; Yang, Bingchao; Li, Zihe; Hu, Meng; Wang, Qianqian; Cui, Lin; Yu, Dongli; He, Julong

    2015-04-21

    A monoclinic BC3 phase (denoted M-BC3) has been predicted using first principles calculations. The M-BC3 structure is formed by alternately stacking sequences of metallic BC-layers and insulating C atom layers, thus, the structure exhibits two-dimensional conductivity. Its stability has been confirmed by our calculations of the total energy, elastic constants, and phonon frequencies. The pressure of phase transition from graphite-like BC3 to M-BC3 is calculated to be 9.3 GPa, and the theoretical Vickers hardness of M-BC3 is 43.8 GPa, this value indicates that the compound is a potentially superhard material. By comparing Raman spectral calculations of M-BC3 and previously proposed structures with the experimental data, we speculate that the experimentally synthesized BC3 crystal may simultaneously contain M-BC3 and Pmma-b phases.

  14. Electronic Stopping Power in LiF from First Principles

    SciTech Connect

    Pruneda, J. M.; Sanchez-Portal, D.; Artacho, Emilio

    2007-12-07

    Using time-dependent density-functional theory we calculate from first principles the rate of energy transfer from a moving proton or antiproton to the electrons of an insulating material, LiF. The behavior of the electronic stopping power versus projectile velocity displays an effective threshold velocity of {approx}0.2 a.u. for the proton, consistent with recent experimental observations, and also for the antiproton. The calculated proton/antiproton stopping-power ratio is {approx}2.4 at velocities slightly above the threshold (v{approx}0.4 a.u.), as compared to the experimental value of 2.1. The projectile energy loss mechanism is observed to be extremely local.

  15. Towards a first-principles thermodynamics of solids

    SciTech Connect

    de Fontaine, D.; Wolverton, C.

    1992-08-01

    Total energy density-functional methods have made it possible to calculate, from first principles, such important properties as cohesive energies, lattice constants and elastic moduli for elemental crystals and perfectly ordered compounds. Real solids are imperfect, however, so that lattice vibrations and compositional disorder lead to entropy contributions, vibrational and configurational. When these effects are included in an appropriate manner, properties of real crystals can be computed ab initio as a function of temperature and concentration. Consequently, it is possible to obtain, virtually from the knowledge of atomic numbers alone, such basic thermodynamic properties as free energies, entropies, heats of formation, and lattice parameters for stable and metastable phases, leading, for example, to the successful computation of certain classes of phase diagrams. Recent progress in the field will be reviewed. Application is made to the Pd-Rh-V system.

  16. First-principles investigation of PVDF and its copolymers

    NASA Astrophysics Data System (ADS)

    Ranjan, V.; Yu, Liping; Buongiorno Nardelli, Marco; Bernholc, J.

    2009-03-01

    Recently, PVDF and its copolymers have generated significant interest due to their electroactive properties [1] and potential for ultra-high energy-storage applications [2]. In this talk, we present the results of first-principles calculations of stable phases and dielectric properties of different copolymers and terpolymers of PVDF at varying concentrations. Our results show that at very high concentrations of Chloro-trifluoroethylene (CTFE), PVDF/CTFE displays sharp transitions between non-polar (α) and polar (β) phases. On the contrary, the same transitions in copolymers with trifluoroethylene (TrFE) and tetrafluoroethylene (TeFE) are not sharp and happen at lower concentrations. We discuss the interplay of copolymer admixture on the dielectric properties of PVDF and discuss the suitability of copolymers for energy storage and electroactive applications. [1] S. G. Lu et al., App. Phys. Lett. 93, 042905 (2008). [2] V. Ranjan et al., Phys. Rev. Lett. 99, 047801 (2007).

  17. Carbon-rich icosahedral boron carbide designed from first principles

    SciTech Connect

    Jay, Antoine; Vast, Nathalie; Sjakste, Jelena; Duparc, Olivier Hardouin

    2014-07-21

    The carbon-rich boron-carbide (B{sub 11}C)C-C has been designed from first principles within the density functional theory. With respect to the most common boron carbide at 20% carbon concentration B{sub 4}C, the structural modification consists in removing boron atoms from the chains linking (B{sub 11}C) icosahedra. With C-C instead of C-B-C chains, the formation of vacancies is shown to be hindered, leading to enhanced mechanical strength with respect to B{sub 4}C. The phonon frequencies and elastic constants turn out to prove the stability of the carbon-rich phase, and important fingerprints for its characterization have been identified.

  18. NMR shifts for polycyclic aromatic hydrocarbons from first-principles

    SciTech Connect

    Thonhauser, Timo; Ceresoli, Davide; Marzari, Nicola N.

    2009-09-03

    We present first-principles, density-functional theory calculations of the NMR chemical shifts for polycyclic aromatic hydrocarbons, starting with benzene and increasing sizes up to the one- and two-dimensional infinite limits of graphene ribbons and sheets. Our calculations are performed using a combination of the recently developed theory of orbital magnetization in solids, and a novel approach to NMR calculations where chemical shifts are obtained from the derivative of the orbital magnetization with respect to a microscopic, localized magnetic dipole. Using these methods we study on equal footing the 1H and 13C shifts in benzene, pyrene, coronene, in naphthalene, anthracene, naphthacene, and pentacene, and finally in graphene, graphite, and an infinite graphene ribbon. Our results show very good agreement with experiments and allow us to characterize the trends for the chemical shifts as a function of system size.

  19. Two Dimensional Ice from First Principles: Structures and Phase Transitions

    NASA Astrophysics Data System (ADS)

    Chen, Ji; Schusteritsch, Georg; Pickard, Chris J.; Salzmann, Christoph G.; Michaelides, Angelos

    2016-01-01

    Despite relevance to disparate areas such as cloud microphysics and tribology, major gaps in the understanding of the structures and phase transitions of low-dimensional water ice remain. Here, we report a first principles study of confined 2D ice as a function of pressure. We find that at ambient pressure hexagonal and pentagonal monolayer structures are the two lowest enthalpy phases identified. Upon mild compression, the pentagonal structure becomes the most stable and persists up to ˜2 GPa , at which point the square and rhombic phases are stable. The square phase agrees with recent experimental observations of square ice confined within graphene sheets. This work provides a fresh perspective on 2D confined ice, highlighting the sensitivity of the structures observed to both the confining pressure and the width.

  20. 2D ice from first principles: structures and phase transitions

    NASA Astrophysics Data System (ADS)

    Chen, Ji; Schusteritsch, Georg; Pickard, Chris J.; Salzmann, Christoph G.; Michaelides, Angelos

    Despite relevance to disparate areas such as cloud microphysics and tribology, major gaps in the understanding of the structures and phase transitions of low-dimensional water ice remain. Here we report a first principles study of confined 2D ice as a function of pressure. We find that at ambient pressure hexagonal and pentagonal monolayer structures are the two lowest enthalpy phases identified. Upon mild compression the pentagonal structure becomes the most stable and persists up to ca. 2 GPa at which point square and rhombic phases are stable. The square phase agrees with recent experimental observations of square ice confined within graphene sheets. We also find a double layer AA stacked square ice phase, which clarifies the difference between experimental observations and earlier force field simulations. This work provides a fresh perspective on 2D confined ice, highlighting the sensitivity of the structures observed to both the confining pressure and width.

  1. Stability of hydrogenated graphene: a first-principles study

    DOE PAGES

    Yi, Ding; Yang, Liu; Xie, Shijie; Saxena, Avadh

    2015-02-10

    In order to explain the disagreement between present theoretical and experimental investigations on the stability of hydrogenated graphene, we have systematically studied hydrogenated graphene with different configurations from the consideration of single-side and double-side adsorption using first-principles calculations. Both binding energy and formation energy are calculated to characterize the stability of the system. It is found that single-side hydrogenated graphene is always unstable. However, for double-side hydrogenation, some configurations are stable due to the increased carbon–carbon sp3 hybridization compared to single-side hydrogenation. Furthermore, it is found that the system is energetically favorable when an equal number of hydrogen atoms aremore » adsorbed on each side of the graphene.« less

  2. Stability of hydrogenated graphene: a first-principles study

    SciTech Connect

    Yi, Ding; Yang, Liu; Xie, Shijie; Saxena, Avadh

    2015-02-10

    In order to explain the disagreement between present theoretical and experimental investigations on the stability of hydrogenated graphene, we have systematically studied hydrogenated graphene with different configurations from the consideration of single-side and double-side adsorption using first-principles calculations. Both binding energy and formation energy are calculated to characterize the stability of the system. It is found that single-side hydrogenated graphene is always unstable. However, for double-side hydrogenation, some configurations are stable due to the increased carbon–carbon sp3 hybridization compared to single-side hydrogenation. Furthermore, it is found that the system is energetically favorable when an equal number of hydrogen atoms are adsorbed on each side of the graphene.

  3. Two Dimensional Ice from First Principles: Structures and Phase Transitions.

    PubMed

    Chen, Ji; Schusteritsch, Georg; Pickard, Chris J; Salzmann, Christoph G; Michaelides, Angelos

    2016-01-15

    Despite relevance to disparate areas such as cloud microphysics and tribology, major gaps in the understanding of the structures and phase transitions of low-dimensional water ice remain. Here, we report a first principles study of confined 2D ice as a function of pressure. We find that at ambient pressure hexagonal and pentagonal monolayer structures are the two lowest enthalpy phases identified. Upon mild compression, the pentagonal structure becomes the most stable and persists up to ∼2  GPa, at which point the square and rhombic phases are stable. The square phase agrees with recent experimental observations of square ice confined within graphene sheets. This work provides a fresh perspective on 2D confined ice, highlighting the sensitivity of the structures observed to both the confining pressure and the width. PMID:26824547

  4. First-principles simulations of electrostatic interactions between dust grains

    SciTech Connect

    Itou, H. Amano, T.; Hoshino, M.

    2014-12-15

    We investigated the electrostatic interaction between two identical dust grains of an infinite mass immersed in homogeneous plasma by employing first-principles N-body simulations combined with the Ewald method. We specifically tested the possibility of an attractive force due to overlapping Debye spheres (ODSs), as was suggested by Resendes et al. [Phys. Lett. A 239, 181–186 (1998)]. Our simulation results demonstrate that the electrostatic interaction is repulsive and even stronger than the standard Yukawa potential. We showed that the measured electric field acting on the grain is highly consistent with a model electrostatic potential around a single isolated grain that takes into account a correction due to the orbital motion limited theory. Our result is qualitatively consistent with the counterargument suggested by Markes and Williams [Phys. Lett. A 278, 152–158 (2000)], indicating the absence of the ODS attractive force.

  5. First-Principles Prediction of Liquid/Liquid Interfacial Tension.

    PubMed

    Andersson, M P; Bennetzen, M V; Klamt, A; Stipp, S L S

    2014-08-12

    The interfacial tension between two liquids is the free energy per unit surface area required to create that interface. Interfacial tension is a determining factor for two-phase liquid behavior in a wide variety of systems ranging from water flooding in oil recovery processes and remediation of groundwater aquifers contaminated by chlorinated solvents to drug delivery and a host of industrial processes. Here, we present a model for predicting interfacial tension from first principles using density functional theory calculations. Our model requires no experimental input and is applicable to liquid/liquid systems of arbitrary compositions. The consistency of the predictions with experimental data is significant for binary, ternary, and multicomponent water/organic compound systems, which offers confidence in using the model to predict behavior where no data exists. The method is fast and can be used as a screening technique as well as to extend experimental data into conditions where measurements are technically too difficult, time consuming, or impossible.

  6. First Principles Investigations of Technologically and Environmentally Important Nano-structured Materials and Devices

    NASA Astrophysics Data System (ADS)

    Paul, Sujata

    In the course of my PhD I have worked on a broad range of problems using simulations from first principles: from catalysis and chemical reactions at surfaces and on nanostructures, characterization of carbon-based systems and devices, and surface and interface physics. My research activities focused on the application of ab-initio electronic structure techniques to the theoretical study of important aspects of the physics and chemistry of materials for energy and environmental applications and nano-electronic devices. A common theme of my research is the computational study of chemical reactions of environmentally important molecules (CO, CO2) using high performance simulations. In particular, my principal aim was to design novel nano-structured functional catalytic surfaces and interfaces for environmentally relevant remediation and recycling reactions, with particular attention to the management of carbon dioxide. We have studied the carbon-mediated partial sequestration and selective oxidation of carbon monoxide (CO), both in the presence and absence of hydrogen, on graphitic edges. Using first-principles calculations we have studied several reactions of CO with carbon nanostructures, where the active sites can be regenerated by the deposition of carbon decomposed from the reactant (CO) to make the reactions self-sustained. Using statistical mechanics, we have also studied the conditions under which the conversion of CO to graphene and carbon dioxide is thermodynamically favorable, both in the presence and in the absence of hydrogen. These results are a first step toward the development of processes for the carbon-mediated partial sequestration and selective oxidation of CO in a hydrogen atmosphere. We have elucidated the atomic scale mechanisms of activation and reduction of carbon dioxide on specifically designed catalytic surfaces via the rational manipulation of the surface properties that can be achieved by combining transition metal thin films on oxide

  7. Molecular scale electronics: syntheses and testing

    NASA Astrophysics Data System (ADS)

    Reinerth, William A.; Jones, LeRoy, II; Burgin, Timothy P.; Zhou, Chong-wu; Muller, C. J.; Deshpande, M. R.; Reed, Mark A.; Tour, James M.

    1998-09-01

    This paper describes four significant breakthroughs in the syntheses and testing of molecular scale electronic devices. The 16-mer of oligo(2-dodecylphenylene ethynylene) was prepared on Merrifields resin using the iterative divergent/convergent approach which significantly streamlines the preparation of this molecular scale wire. The formation of self-assembled monolayers and multilayers on gold surfaces of rigid rod conjugated oligomers that have thiol, 0957-4484/9/3/016/img11-dithiol, thioacetyl, or 0957-4484/9/3/016/img11-dithioacetyl end groups have been studied. The direct observation of charge transport through molecules of benzene-1, 4-dithiol, which have been self-assembled onto two facing gold electrodes, has been achieved. Finally, we report initial studies into what effect varying the molecular alligator clip has on the molecule scale wire's conductivity.

  8. First-principles studies for understanding diverse high- Tc

    NASA Astrophysics Data System (ADS)

    Cheng, Hai-Ping

    2011-03-01

    In this talk, I survey results and insights gained from first-principles calculations on materials that exhibit superconducting behavior at temperatures higher than those characteristic of conventional BCS superconductors. These range from highly correlated cuprate Mott insulators as represented by the bismuth-strontium-calcium-copper-oxides (BSCCOs) to border-line itinerant-Mott systems such as the recently discovered 1111 and 122 pnictides. ultimate goal of our studies is to correlate Tc with specific material composition using detailed first-principles calculations in conjunction with many-body physics techniques via the critical step of constructing real-materials model Hamiltonians. By manipulating impurity doping, which plays a crucial role in the phase diagrams of high Tc materials, we hope to find guidance for designing candidate systems with Tc higher than ones currently known. BSCCO material, density functional calculations using a good generalized-gradient approximation (GGA) yield structural information that is correlated to the experimentally observed (STM) super-modulation and impurity peak in the high energy regime (~ 1 eV), even though the Kohn-Sham bands from such functionals fail to have a band gap. For FeAs-based high-Tc systems, DFT band-structure calculations provide a very good starting point for constructing model Hamiltonians for studies of spin fluctuation and electron pairing mechanisms. Fermi sheets that have been constructed using Wannier transformed Kohn-Sham states have provided critical information for understanding this family of superconducting materials. Analysis of the details of magnetic ordering, density of states, and 2D vs. 3D features in both the 1111 and 122 materials have been valuable in understanding sometimes perplexing experimental findings. Effects of Co impurities have been studied and fully analyzed as well., I will discuss persistent challenges related to calculations on the structure of the non-magnetic state Ba 1

  9. First-principles interpretation of core-level spectroscopy of photoelectrochemical materials and processes

    NASA Astrophysics Data System (ADS)

    Pemmaraju, Sri Chaitanya Das; Prendergast, David

    2014-03-01

    We present two case studies of first-principles theoretical methods applied in conjunction with experimental core-level spectroscopy measurements to investigate the electronic structure and dynamical processes in molecular and interfacial systems relevant to photoelectrochemical (PEC) technologies. In the first, we study the core-level and valence spectroscopies of two zinc(II)-porphyrin based Donor-pi-Acceptor (D-p-A) dyes using the occupancy-constrained excited electron and core-hole (XCH) approach and time-dependent density functional theory (TDDFT) simulations. In the second, we use constrained DFT and TDDFT to interpret measured transient core-level shifts in time-resolved femtosecond x-ray photoelectron spectroscopy, investigating the dynamics of the electron injection process from a N3 dye molecule chemisorbed onto a ZnO substrate. These studies illustrate the utility of first-principles methods in guiding the design of better PEC materials. This work was performed at the Molecular Foundry, LBNL, supported by the Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.

  10. First Principles Modeling of Phonon Heat Conduction in Nanoscale Crystalline Structures

    SciTech Connect

    Sandip Mazumder; Ju Li

    2010-06-30

    The inability to remove heat efficiently is currently one of the stumbling blocks toward further miniaturization and advancement of electronic, optoelectronic, and micro-electro-mechanical devices. In order to formulate better heat removal strategies and designs, it is first necessary to understand the fundamental mechanisms of heat transport in semiconductor thin films. Modeling techniques, based on first principles, can play the crucial role of filling gaps in our understanding by revealing information that experiments are incapable of. Heat conduction in crystalline semiconductor films occurs by lattice vibrations that result in the propagation of quanta of energy called phonons. If the mean free path of the traveling phonons is larger than the film thickness, thermodynamic equilibrium ceases to exist, and thus, the Fourier law of heat conduction is invalid. In this scenario, bulk thermal conductivity values, which are experimentally determined by inversion of the Fourier law itself, cannot be used for analysis. The Boltzmann Transport Equation (BTE) is a powerful tool to treat non-equilibrium heat transport in thin films. The BTE describes the evolution of the number density (or energy) distribution for phonons as a result of transport (or drift) and inter-phonon collisions. Drift causes the phonon energy distribution to deviate from equilibrium, while collisions tend to restore equilibrium. Prior to solution of the BTE, it is necessary to compute the lifetimes (or scattering rates) for phonons of all wave-vector and polarization. The lifetime of a phonon is the net result of its collisions with other phonons, which in turn is governed by the conservation of energy and momentum during the underlying collision processes. This research project contributed to the state-of-the-art in two ways: (1) by developing and demonstrating a calibration-free simple methodology to compute intrinsic phonon scattering (Normal and Umklapp processes) time scales with the inclusion

  11. First-principles calculations of gated adatoms on graphene

    NASA Astrophysics Data System (ADS)

    Chan, Kevin T.; Lee, Hoonkyung; Cohen, Marvin L.

    2011-03-01

    The two-dimensional surface of graphene is well-suited for adsorption of adatoms or molecules. The application of a gate voltage can be used to precisely control the electron concentration of the adsorbate-graphene system. Such control over electronic properties of adsorbates on graphene might have useful applications in areas such as catalysis and hydrogen storage. In this work, the gating of a variety of adatoms adsorbed on graphene is studied using first-principles calculations. We compute the projected density of states, local electrostatic potential, and charge density of the adatom-graphene system as a function of gate voltage. We demonstrate that adatoms on graphene can be ionized by gating, and that the ionization causes a sharp change in the electrostatic potential. Additional interesting features of our results are also discussed. This work was supported by NSF Grant No. DMR10-1006184 and DOE under Contract No. DE-AC02-05CH11231. Computational resources were provided by the IT Division at LBNL.

  12. Anisotropic intrinsic lattice thermal conductivity of phosphorene from first principles.

    PubMed

    Qin, Guangzhao; Yan, Qing-Bo; Qin, Zhenzhen; Yue, Sheng-Ying; Hu, Ming; Su, Gang

    2015-02-21

    Phosphorene, the single layer counterpart of black phosphorus, is a novel two-dimensional semiconductor with high carrier mobility and a large fundamental direct band gap, which has attracted tremendous interest recently. Its potential applications in nano-electronics and thermoelectrics call for fundamental study of the phonon transport. Here, we calculate the intrinsic lattice thermal conductivity of phosphorene by solving the phonon Boltzmann transport equation (BTE) based on first-principles calculations. The thermal conductivity of phosphorene at 300 K is 30.15 W m(-1) K(-1) (zigzag) and 13.65 W m(-1) K(-1) (armchair), showing an obvious anisotropy along different directions. The calculated thermal conductivity fits perfectly to the inverse relationship with temperature when the temperature is higher than Debye temperature (ΘD = 278.66 K). In comparison to graphene, the minor contribution around 5% of the ZA mode is responsible for the low thermal conductivity of phosphorene. In addition, the representative mean free path (MFP), a critical size for phonon transport, is also obtained.

  13. First principle investigation of isolated vacancy in (111) diamond surface

    NASA Astrophysics Data System (ADS)

    Hu, Wenhao; Flatté, Michael

    As the simplest intrinsic defect, isolated vacancy has been studied intensively theoretically and experimentally in diamond's bulk phase. Nevertheless, its correspondence in surface phase still lacks people's attention. Nitrogen vacancy center has become the most ideal candidates for solid states computing due to its long coherence time at room temperature. Resembling NV center, the isolated vacancy on surface exhibits a similar ambient potential and the same 3-fold rotational symmetry due to the asymmetry of surface, which implies a similar character in them. In our work, the isolated vacancy in clean and hydrogen terminated (111) surface of diamond are investigated from first principle perspective. Full potential LAPW method implemented in WIEN2K is exploited under GGA approximation. To evaluated the surface effect, the defect depth from topmost layer to fifth subsurface are considered with different slab thickness. By checking the spin density distribution and electronic structure, the hydrogen vacancy in H-terminated surface exhibit a spin-1/2 center with a 0/-1 transition level located in the middle of band gap. The -1/-2 transition level of carbon vacancy in the subsurface approaches the 0/-1 transition level implying the potential stability of spin-1 center. The work was supported by an AFOSR MURI.

  14. Incorporation of water in pyrope: a first principles study

    NASA Astrophysics Data System (ADS)

    Manga, V. R.; Mookherjee, M.; Muralidharan, K.

    2014-12-01

    Pyrope (Mg3Al2Si3O12) rich garnet is the most important secondary mineral phase with volume fractions ranging between 20 % in the shallow upper mantle to 40 % in the lower part of upper mantle. The volume fractions of garnet in subducted oceanic crusts are as high as 80 %. However, our understanding of the incorporation of water in garnet as proton defect is rather limited. Experimental studies conducted at pressures and temperatures relevant to the deep lower mantle have resulted in wide range of water contents ranging between 0 wt % to ~ 0.8 wt %. In a pyriolyte composition representative of the upper mantle, unlike olivine (Mg2SiO4), which remains largely iso-chemical upon compression, garnet undergoes solid solution with pyroxene (MgSiO3) and as a result there is a continuous evolution of the chemistry of garnet as a function of pressure. This complicates the analysis of proton defects using conventional thermodynamics expressing water solubility as a function of water fugacity, oxide activity, and activation volume. To circumvent this issue, we use first principles simulations to explore the relative energetics of the formation of protons in Mg, Al, and Si sites. Preliminary results at ambient conditions indicate positive enthalpy changes for the proton defects in all the sites, with silicon site being the most favorable. We intend to explore the effect of pressure and temperature on the defect formation energies. Acknowledgement- MM is supported by the US National Science Foundation grant (EAR-1250477).

  15. Oxygen transport in ceria: a first-principles study

    NASA Astrophysics Data System (ADS)

    Sergei, Simak

    2012-02-01

    Ceria (CeO2) is an important material for environmentally benign applications, ranging from solid-oxide fuel cells (SOFC) to oxygen storage [1-2]. The key characteristic needed to be improved is the mobility of oxygen ions. Optimization of ionic transport in ceria has been the topic of many studies. In particular, it has been discovered how the ionic conductivity in ceria might be improved by choosing the proper kind and concentration of dopants [3]. In this presentation we will approach the problem from a different direction by adjusting structural parameters of ceria via the change of external conditions. A systematic first-principles study of the energy landscape and kinetics of reduced ceria as a function of external parameters reveals a physically transparent way to improve oxygen transport in ceria. [4pt] [1] N. Skorodumova, S. Simak, B. Lundqvist, I. Abrikosov, and B. Johansson, Physical Review Letters 89, 14 (2002). [0pt] [2] A. Trovarelli, in Catalysis by Ceria and related materials (Imperial College Press, London, 2002). [0pt] [3] D. A. Andersson, S. I. Simak, N. V. Skorodumova, I. A.Abrikosov, and B. Johansson, Proceedings of the National Academy of Sciences of the United States of America 103, 3518 (2006).

  16. First principles modelling of oxygen impurities in UN nuclear fuels

    NASA Astrophysics Data System (ADS)

    Kotomin, E. A.; Mastrikov, Yu. A.

    2008-07-01

    We report results of first principles VASP supercell calculations of O impurity in UN fuels placed either at an interstitial tetrahedral position or as a substitution for a host N ion. In the latter case O perfectly fits into N site producing no lattice distortion. Such the O substitutional impurity only slightly affects the formation energies of U and N vacancies nearby. In both interstitial and substitutional positions O atom attracts the additional electron density and transforms into the negatively charged ion. Oxygen incorporation into pre-existing N vacancy is energetically more favourable than into the interstitial position. The O impurities produce an additional peak at the low energy side of N contribution to the DOS calculated for uranium mononitride which could be used for the O identification by means of the UPS spectroscopy. We compare also the DOS calculated for UN and hypothetical isostructural UO. Both O solution and incorporation energies are negative, indicating that O penetration into UN fuel is the energetically favourable. The migration energy of the interstitial O ion is estimated as 2.8 eV.

  17. First-principles prediction of disordering tendencies in complex oxides

    SciTech Connect

    Jiang, Chao; Stanek, Christopher R; Sickafus, Kurt E; Uberuaga, Blas P

    2008-01-01

    The disordering tendencies of a series of zirconate (A{sub 2}Zr{sub 2}O{sub 7}) , hafnate (A{sub 2}Hf{sub 2}O{sub 7}), titanate (A{sub 2}Ti{sub 2}O{sub 7}), and stannate (A{sub 2} Sn{sub 2}O{sub 7}) pyrochlores are predicted in this study using first-principles total energy calculations. To model the disordered (A{sub 1/2}B{sub 1/2})(O{sub 7/8}/V{sub 1/8}){sub 2} fluorite structure, we have developed an 88-atom two-sublattice special quasirandom structure (SQS) that closely reproduces the most important near-neighbor intra-sublattice and inter-sublattice pair correlation functions of the random alloy. From the calculated disordering energies, the order-disorder transition temperatures of those pyrochlores are further predicted and our results agree well with the existing experimental phase diagrams. It is clearly demonstrated that both size and electronic effects play an important role in determining the disordering tendencies of pyrochlore compounds.

  18. Auger recombination in scintillator materials from first principles

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    Scintillators convert high energy radiation into lower energy photons which are easier to detect and analyze. One of the uses of these devices is identifying radioactive materials being transported across national borders. However, scintillating materials have a non-proportional light yield in response to incident radiation, which makes this task difficult. One possible cause of the non-proportional light yield is non-radiative Auger recombination. Auger recombination can occur in two ways - direct and phonon-assisted. We have studied both types of Auger recombination from first principles in the common scintillating material sodium iodide. Our results indicate that the phonon-assisted process, assisted primarily by short-range optical phonons, dominates the direct process. The corresponding Auger coefficients are 5 . 6 +/- 0 . 3 ×10-32cm6s-1 for the phonon-assisted process versus 1 . 17 +/- 0 . 01 ×10-33cm6s-1 for the direct process. At higher electronic temperatures the direct Auger recombination rate increases but remains lower than the phonon-assisted rate. This research was supported by the National Science Foundation CAREER award through Grant No. DMR-1254314 and NA-22. Computational Resources provide by LLNL and DOE NERSC Facility.

  19. Semiconducting Graphene on Silicon from First-Principles Calculations.

    PubMed

    Dang, Xuejie; Dong, Huilong; Wang, Lu; Zhao, Yanfei; Guo, Zhenyu; Hou, Tingjun; Li, Youyong; Lee, Shuit-Tong

    2015-08-25

    Graphene is a semimetal with zero band gap, which makes it impossible to turn electric conduction off below a certain limit. Transformation of graphene into a semiconductor has attracted wide attention. Owing to compatibility with Si technology, graphene adsorbed on a Si substrate is particularly attractive for future applications. However, to date there is little theoretical work on band gap engineering in graphene and its integration with Si technology. Employing first-principles calculations, we study the electronic properties of monolayer and bilayer graphene adsorbed on clean and hydrogen (H)-passivated Si (111)/Si (100) surfaces. Our calculation shows that the interaction between monolayer graphene and a H-passivated Si surface is weak, with the band gap remaining negligible. For bilayer graphene adsorbed onto a H-passivated Si surface, the band gap opens up to 108 meV owing to asymmetry introduction. In contrast, the interaction between graphene and a clean Si surface is strong, leading to formation of chemical bonds and a large band gap of 272 meV. Our results provide guidance for device designs based on integrating graphene with Si technology.

  20. First principles statistical mechanics of alloys and magnetism

    NASA Astrophysics Data System (ADS)

    Eisenbach, Markus; Khan, Suffian N.; Li, Ying Wai

    Modern high performance computing resources are enabling the exploration of the statistical physics of phase spaces with increasing size and higher fidelity of the Hamiltonian of the systems. For selected systems, this now allows the combination of Density Functional based first principles calculations with classical Monte Carlo methods for parameter free, predictive thermodynamics of materials. We combine our locally selfconsistent real space multiple scattering method for solving the Kohn-Sham equation with Wang-Landau Monte-Carlo calculations (WL-LSMS). In the past we have applied this method to the calculation of Curie temperatures in magnetic materials. Here we will present direct calculations of the chemical order - disorder transitions in alloys. We present our calculated transition temperature for the chemical ordering in CuZn and the temperature dependence of the short-range order parameter and specific heat. Finally we will present the extension of the WL-LSMS method to magnetic alloys, thus allowing the investigation of the interplay of magnetism, structure and chemical order in ferrous alloys. This research was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Materials Science and Engineering Division and it used Oak Ridge Leadership Computing Facility resources at Oak Ridge National Laboratory.

  1. First principles calculation of finite temperature magnetism in Ni

    NASA Astrophysics Data System (ADS)

    Eisenbach, Markus; Yin, Junqi; Nicholson, Don M.; Li, Ying Wai

    2013-03-01

    We harnesses the computational power of massively parallel computers to calculate finite temperature magnetic properties by combining classical Monte-Carlo calculations with our first principles multiple scattering electronic structure code (LSMS) for constrained magnetic states. Our previous calculations of Fe and Fe3 C [J. Appl. Phys. 109, 07E138 (2011)] only considered fluctuations in the local moment directions. Recent advances, both in the understanding of the Wang-Landau method used in our calculations [Phys. Rev. E 84, 065702(R) (2011)] and more powerful computing resources have enabled us to investigate Ni where the fluctuation in the magnitude of the local magnetic moments is of importance equal to their directional fluctuations. Here we will present our recent results for Ni that axpands our method to an even wider class of 3d element based ferromagnets. This research was sponsored by the Offices of Basic Energy Science (M.E. and D.M.N) and the Office of Advanced Computing Research (J.Y. and Y.W.L) of the US Department of Energy. This research used resources of the Oak Ridge Leadership Computing Facility at Oak Ridge National Laboratory, which is supported by the Office of Science of the Department of Energy under contract DE-AC05-00OR22725.

  2. Predicted boron-carbide compounds: a first-principles study.

    PubMed

    Wang, De Yu; Yan, Qian; Wang, Bing; Wang, Yuan Xu; Yang, Jueming; Yang, Gui

    2014-06-14

    By using developed particle swarm optimization algorithm on crystal structural prediction, we have explored the possible crystal structures of B-C system. Their structures, stability, elastic properties, electronic structure, and chemical bonding have been investigated by first-principles calculations with density functional theory. The results show that all the predicted structures are mechanically and dynamically stable. An analysis of calculated enthalpy with pressure indicates that increasing of boron content will increase the stability of boron carbides under low pressure. Moreover, the boron carbides with rich carbon content become more stable under high pressure. The negative formation energy of predicted B5C indicates its high stability. The density of states of B5C show that it is p-type semiconducting. The calculated theoretical Vickers hardnesses of B-C exceed 40 GPa except B4C, BC, and BC4, indicating they are potential superhard materials. An analysis of Debye temperature and electronic localization function provides further understanding chemical and physical properties of boron carbide.

  3. Thermal conductivity of silicene from first-principles

    SciTech Connect

    Xie, Han; Bao, Hua E-mail: hua.bao@sjtu.edu.cn; Hu, Ming E-mail: hua.bao@sjtu.edu.cn

    2014-03-31

    Silicene, as a graphene-like two-dimensional material, now receives exceptional attention of a wide community of scientists and engineers beyond graphene. Despite extensive study on its electric property, little research has been done to accurately calculate the phonon transport of silicene so far. In this paper, thermal conductivity of monolayer silicene is predicted from first-principles method. At 300 K, the thermal conductivity of monolayer silicene is found to be 9.4 W/mK and much smaller than bulk silicon. The contributions from in-plane and out-of-plane vibrations to thermal conductivity are quantified, and the out-of-plane vibration contributes less than 10% of the overall thermal conductivity, which is different from the results of the similar studies on graphene. The difference is explained by the presence of small buckling, which breaks the reflectional symmetry of the structure. The flexural modes are thus not purely out-of-plane vibration and have strong scattering with other modes.

  4. First-principles Simulations and the Criticality of Calving Glaciers

    NASA Astrophysics Data System (ADS)

    Vallot, D.; Åström, J. A.; Schäfer, M.; Welty, E.; O'Neel, S.; Bartholomaus, T. C.; Liu, Y.; Riikilä, T.; Zwinger, T.; Timonen, J.; Moore, J.

    2014-12-01

    The algoritm of a first principles calving-simulation computer-code is outlined and demonstrated. The code is particle-based and uses Newtonian dynamics to simulate ice-fracture, motion and calving. The code can simulate real-size glacier but is only able to simualte individual calving events within a few tens of minutes in duration. The code couples to the Elmer/Ice ice flow-simulation code: Elmer is employed to produce various glacier geomteries, which are then tested for stability using the particle code. In this way it is possible to pin-point the location of calving fronts. The particle simulation code and field observations are engaged to investigate the criticality of calving glaciers. The calving mass and inter-event waiting times both have power-law distributions with the same critical exponents as found for Abelian sand-pile models. This indicate that calving glaciers share characteristics with Self-Organized Critical systems (SOC). This would explain why many glacier found in nature may become unstable as a result of even minor changes in their environment. An SOC calving glacier at the critical point will display so large fluctuations in calving rate that it will render the concept 'average calving rate' more or less useless. I.e. 'average calving rate' will depend on measurement time and always have fluctuaions in the range of 100% more or less independent of the averaging time.

  5. Gypsum under pressure: A first-principles study

    NASA Astrophysics Data System (ADS)

    Giacomazzi, Luigi; Scandolo, Sandro

    2010-02-01

    We investigate by means of first-principles methods the structural response of gypsum (CaSO4ṡ2H2O) to pressures within and above the stability range of gypsum-I (P≤4GPa) . Structural and vibrational properties calculated for gypsum-I are in excellent agreement with experimental data. Compression within gypsum-I takes place predominantly through a reduction in the volume of the CaO8 polyhedra and through a distortion of the hydrogen bonds. The distance between CaSO4 layers becomes increasingly incompressible, indicating a mechanical limit to the packing of water molecules between the layers. We find that a structure with collapsed interlayer distances becomes more stable than gypsum-I above about 5 GPa. The collapse is concomitant with a rearrangement of the hydrogen-bond network of the water molecules. Comparison of the vibrational spectra calculated for this structure with experimental data taken above 5 GPa supports the validity of our model for the high-pressure phase of gypsum.

  6. Designing substrates for silicene and germanene: First-principles calculations

    NASA Astrophysics Data System (ADS)

    Chen, M. X.; Zhong, Z.; Weinert, M.

    2016-08-01

    We propose a guideline for exploring substrates that stabilize the monolayer honeycomb structure of silicene and germanene while simultaneously preserving the Dirac states: in addition to having a strong binding energy to the monolayer, a suitable substrate should be a large-gap semiconductor with a proper work function such that the Dirac point lies in the gap and far from the substrate states when their bands align. We illustrate our idea by performing first-principles calculations for silicene and germanene on the Al-terminated (0001) surface of Al2O3 . The overlaid monolayers on Al-terminated Al2O3 (0001) retain the main structural profile of the low-buckled honeycomb structure via a binding energy comparable to the one between silicene and Ag(111). An unfolded band structure derived from the k -projection method reveals that a gapped Dirac cone is formed at the K point due to the structural distortion and the interaction with the substrate. The gaps of 0.4 and 0.3 eV, respectively, for the supported silicene and germanene suggest that they may have potential applications in nanoelectronics.

  7. Predicted boron-carbide compounds: A first-principles study

    SciTech Connect

    Wang, De Yu; Yan, Qian; Wang, Bing; Wang, Yuan Xu Yang, Jueming; Yang, Gui

    2014-06-14

    By using developed particle swarm optimization algorithm on crystal structural prediction, we have explored the possible crystal structures of B-C system. Their structures, stability, elastic properties, electronic structure, and chemical bonding have been investigated by first-principles calculations with density functional theory. The results show that all the predicted structures are mechanically and dynamically stable. An analysis of calculated enthalpy with pressure indicates that increasing of boron content will increase the stability of boron carbides under low pressure. Moreover, the boron carbides with rich carbon content become more stable under high pressure. The negative formation energy of predicted B{sub 5}C indicates its high stability. The density of states of B{sub 5}C show that it is p-type semiconducting. The calculated theoretical Vickers hardnesses of B-C exceed 40 GPa except B{sub 4}C, BC, and BC{sub 4}, indicating they are potential superhard materials. An analysis of Debye temperature and electronic localization function provides further understanding chemical and physical properties of boron carbide.

  8. Elastic, electronic and thermal properties of YSZ from first principles

    NASA Astrophysics Data System (ADS)

    Jin, Lei; Yu, Qinghe; Rauf, Abdul; Zhou, Chungen

    2012-01-01

    First principles calculations were performed to investigate the elastic, electronic and thermal properties of 14% cubic yttria-stabilized zirconia (YSZ) using the pseudo potential plane-wave method within the gradient generalized approximation (GGA) for the exchange and correlation potential. Computed lattice constant parameters are in good agreement with the available experimental results. The three independent elastic constants were computed by means of the stress-strain method, indicating that 14% cubic YSZ is a mechanically stable structure. From the knowledge of the elastic constants, a set of related properties, namely bulk, shear modulus, Young's modulus, sound velocity, Debye temperature, thermal capacity and minimum thermal conductivity are numerically estimated in the frame work of the Voigt-Reuss-Hill approximation for YSZ polycrystalline. The calculated bulk modulus, shear modulus, Young's modulus, sound velocity, Debye temperature, thermal capacity and minimum thermal conductivity are in reasonable agreement with the available experimental and theory data. Density of states, charge density and Mulliken population analysis show that the 14% cubic YSZ is covalent and possess ionic character.

  9. First-principles simulations at constant electric polarization

    NASA Astrophysics Data System (ADS)

    Dieguez, Oswaldo; Vanderbilt, David

    2005-03-01

    We develop a formalism to perform first-principles calculations for insulators at fixed electric polarization. As shown by Sai, Rabe, and Vanderbilt (SRV),ootnotetextN. Sai, K.M. Rabe, and D. Vanderbilt, Phys. Rev. B 66, 104108 (2002). such an approach allows one to map out the energy landscape as a function of polarization, providing a powerful tool for the theoretical investigation of polar materials. While the SRV method is only approximate because the effect of electric field is described using low-order Taylor expansions, our method is exact because we use the finite-fields approach of Souza, 'Iñiguez, and Vanderbilt.ootnotetextI. Souza, J. 'Iñiguez, and D. Vanderbilt, Phys. Rev. Lett. 89, 117602 (2002). We apply our method both to systems where the ionic contribution to the polarization dominates, and to systems where this is not the case. We show that the SRV method gives rather accurate results in the former case as expected, while the present exact method provides substantial improvements in the latter case.

  10. First principle active neutron coincidence counting measurements of uranium oxide

    NASA Astrophysics Data System (ADS)

    Goddard, Braden; Charlton, William; Peerani, Paolo

    2014-03-01

    Uranium is present in most nuclear fuel cycle facilities ranging from uranium mines, enrichment plants, fuel fabrication facilities, nuclear reactors, and reprocessing plants. The isotopic, chemical, and geometric composition of uranium can vary significantly between these facilities, depending on the application and type of facility. Examples of this variation are: enrichments varying from depleted (~0.2 wt% 235U) to high enriched (>20 wt% 235U); compositions consisting of U3O8, UO2, UF6, metallic, and ceramic forms; geometries ranging from plates, cans, and rods; and masses which can range from a 500 kg fuel assembly down to a few grams fuel pellet. Since 235U is a fissile material, it is routinely safeguarded in these facilities. Current techniques for quantifying the 235U mass in a sample include neutron coincidence counting. One of the main disadvantages of this technique is that it requires a known standard of representative geometry and composition for calibration, which opens up a pathway for potential erroneous declarations by the State and reduces the effectiveness of safeguards. In order to address this weakness, the authors have developed a neutron coincidence counting technique which uses the first principle point-model developed by Boehnel instead of the "known standard" method. This technique was primarily tested through simulations of 1000 g U3O8 samples using the Monte Carlo N-Particle eXtended (MCNPX) code. The results of these simulations showed good agreement between the simulated and exact 235U sample masses.

  11. Graphene mechanics: I. Efficient first principles based Morse potential.

    PubMed

    Costescu, Bogdan I; Baldus, Ilona B; Gräter, Frauke

    2014-06-28

    We present a computationally efficient pairwise potential for use in molecular dynamics simulations of large graphene or carbon nanotube systems, in particular, for those under mechanical deformation, and also for mixed systems including biomolecules. Based on the Morse potential, it is only slightly more complex and computationally expensive than a harmonic bond potential, allowing such large or mixed simulations to reach experimentally relevant time scales. By fitting to data obtained from quantum mechanics (QM) calculations to represent bond breaking in graphene patches, we obtain a dissociation energy of 805 kJ mol(-1) which reflects the steepness of the QM potential up to the inflection point. A distinctive feature of our potential is its truncation at the inflection point, allowing a realistic treatment of ruptured C-C bonds without relying on a bond order model. The results obtained from equilibrium MD simulations using our potential compare favorably with results obtained from experiments and from similar simulations with more complex and computationally expensive potentials.

  12. Defects in gallium nitride nanowires: First principles calculations

    NASA Astrophysics Data System (ADS)

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

    2010-08-01

    Atomic configurations and formation energies of native defects in an unsaturated GaN nanowire grown along the [001] direction and with (100) lateral facets are studied using large-scale ab initio calculation. Cation and anion vacancies, antisites, and interstitials in the neutral charge state are all considered. The configurations of these defects in the core region and outermost surface region of the nanowire are different. The atomic configurations of the defects in the core region are same as those in the bulk GaN, and the formation energy is large. The defects at the surface show different atomic configurations with low formation energy. Starting from a Ga vacancy at the edge of the side plane of the nanowire, a N-N split interstitial is formed after relaxation. As a N site is replaced by a Ga atom in the suboutermost layer, the Ga atom will be expelled out of the outermost layers and leaves a vacancy at the original N site. The Ga interstitial at the outmost surface will diffuse out by interstitialcy mechanism. For all the tested cases N-N split interstitials are easily formed with low formation energy in the nanowires, indicating N2 molecular will appear in the GaN nanowire, which agrees well with experimental findings.

  13. A Fortran program for calculating electron or hole mobility in disordered semiconductors from first-principles

    NASA Astrophysics Data System (ADS)

    Li, Zi; Zhang, Xu; Lu, Gang

    2011-12-01

    A Fortran program is developed to calculate charge carrier (electron or hole) mobility in disordered semiconductors from first-principles. The method is based on non-adiabatic ab initio molecular dynamics and static master equation, treating dynamic and static disorder on the same footing. We have applied the method to calculate the hole mobility in disordered poly(3-hexylthiophene) conjugated polymers as a function of temperature and electric field and obtained excellent agreements with experimental results. The program could be used to explore structure-mobility relation in disordered semiconducting polymers/organic semiconductors and aid rational design of these materials. Program summaryProgram title: FPMu Catalogue identifier: AEJV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 788 580 No. of bytes in distributed program, including test data, etc.: 8 433 024 Distribution format: tar.gz Programming language: Fortran 90 Computer: Any architecture with a Fortran 90 compiler Operating system: Linux, Windows RAM: Proportional to the system size, in our example, 1.2 GB Classification: 7.9 Nature of problem: Determine carrier mobility from first-principles in disordered semiconductors as a function of temperature, electric field and carrier concentration. Solution method: Iteratively solve master equation with carrier state energy and transition rates determined from first-principles. Restrictions: Mobility for disordered semiconductors where the carrier wave-functions are localized and the carrier transport is due to phonon-assisted hopping mechanism. Running time: Depending on the system size (about an hour for the example here).

  14. Exploiting periodic first-principles calculations in NMR spectroscopy of disordered solids.

    PubMed

    Ashbrook, Sharon E; Dawson, Daniel M

    2013-09-17

    Much of the information contained within solid-state nuclear magnetic resonance (NMR) spectra remains unexploited because of the challenges in obtaining high-resolution spectra and the difficulty in assigning those spectra. Recent advances that enable researchers to accurately and efficiently determine NMR parameters in periodic systems have revolutionized the application of density functional theory (DFT) calculations in solid-state NMR spectroscopy. These advances are particularly useful for experimentalists. The use of first-principles calculations aids in both the interpretation and assignment of the complex spectral line shapes observed for solids. Furthermore, calculations provide a method for evaluating potential structural models against experimental data for materials with poorly characterized structures. Determining the structure of well-ordered, periodic crystalline solids can be straightforward using methods that exploit Bragg diffraction. However, the deviations from periodicity, such as compositional, positional, or temporal disorder, often produce the physical properties (such as ferroelectricity or ionic conductivity) that may be of commercial interest. With its sensitivity to the atomic-scale environment, NMR provides a potentially useful tool for studying disordered materials, and the combination of experiment with first-principles calculations offers a particularly attractive approach. In this Account, we discuss some of the issues associated with the practical implementation of first-principles calculations of NMR parameters in solids. We then use two key examples to illustrate the structural insights that researchers can obtain when applying such calculations to disordered inorganic materials. First, we describe an investigation of cation disorder in Y2Ti(2-x)Sn(x)O7 pyrochlore ceramics using (89)Y and (119)Sn NMR. Researchers have proposed that these materials could serve as host phases for the encapsulation of lanthanide- and actinide

  15. Density and Compressibility of Liquid Water and Ice from First-Principles Simulations with Hybrid Functionals.

    PubMed

    Gaiduk, Alex P; Gygi, François; Galli, Giulia

    2015-08-01

    We determined the equilibrium density and compressibility of water and ice from first-principles molecular dynamics simulations using gradient-corrected (PBE) and hybrid (PBE0) functionals. Both functionals predicted the density of ice to be larger than that of water, by 15 (PBE) and 35% (PBE0). The PBE0 functional yielded a lower density of both ice and water with respect to PBE, leading to better agreement with experiment for ice but not for liquid water. Approximate inclusion of dispersion interactions on computed molecular-dynamics trajectories led to a substantial improvement of the PBE0 results for the density of liquid water, which, however, resulted to be slightly lower than that of ice.

  16. Performance of arsenene and antimonene double-gate MOSFETs from first principles

    NASA Astrophysics Data System (ADS)

    Pizzi, Giovanni; Gibertini, Marco; Dib, Elias; Marzari, Nicola; Iannaccone, Giuseppe; Fiori, Gianluca

    2016-08-01

    In the race towards high-performance ultra-scaled devices, two-dimensional materials offer an alternative paradigm thanks to their atomic thickness suppressing short-channel effects. It is thus urgent to study the most promising candidates in realistic configurations, and here we present detailed multiscale simulations of field-effect transistors based on arsenene and antimonene monolayers as channels. The accuracy of first-principles approaches in describing electronic properties is combined with the efficiency of tight-binding Hamiltonians based on maximally localized Wannier functions to compute the transport properties of the devices. These simulations provide for the first time estimates on the upper limits for the electron and hole mobilities in the Takagi's approximation, including spin-orbit and multi-valley effects, and demonstrate that ultra-scaled devices in the sub-10-nm scale show a performance that is compliant with industry requirements.

  17. Performance of arsenene and antimonene double-gate MOSFETs from first principles

    PubMed Central

    Pizzi, Giovanni; Gibertini, Marco; Dib, Elias; Marzari, Nicola; Iannaccone, Giuseppe; Fiori, Gianluca

    2016-01-01

    In the race towards high-performance ultra-scaled devices, two-dimensional materials offer an alternative paradigm thanks to their atomic thickness suppressing short-channel effects. It is thus urgent to study the most promising candidates in realistic configurations, and here we present detailed multiscale simulations of field-effect transistors based on arsenene and antimonene monolayers as channels. The accuracy of first-principles approaches in describing electronic properties is combined with the efficiency of tight-binding Hamiltonians based on maximally localized Wannier functions to compute the transport properties of the devices. These simulations provide for the first time estimates on the upper limits for the electron and hole mobilities in the Takagi's approximation, including spin–orbit and multi-valley effects, and demonstrate that ultra-scaled devices in the sub-10-nm scale show a performance that is compliant with industry requirements. PMID:27557562

  18. Performance of arsenene and antimonene double-gate MOSFETs from first principles.

    PubMed

    Pizzi, Giovanni; Gibertini, Marco; Dib, Elias; Marzari, Nicola; Iannaccone, Giuseppe; Fiori, Gianluca

    2016-01-01

    In the race towards high-performance ultra-scaled devices, two-dimensional materials offer an alternative paradigm thanks to their atomic thickness suppressing short-channel effects. It is thus urgent to study the most promising candidates in realistic configurations, and here we present detailed multiscale simulations of field-effect transistors based on arsenene and antimonene monolayers as channels. The accuracy of first-principles approaches in describing electronic properties is combined with the efficiency of tight-binding Hamiltonians based on maximally localized Wannier functions to compute the transport properties of the devices. These simulations provide for the first time estimates on the upper limits for the electron and hole mobilities in the Takagi's approximation, including spin-orbit and multi-valley effects, and demonstrate that ultra-scaled devices in the sub-10-nm scale show a performance that is compliant with industry requirements. PMID:27557562

  19. First-Principles Simulations for the Initial Stage of Graphene Growth Induced by Si Sublimation from Stepped SiC Surface

    NASA Astrophysics Data System (ADS)

    Ono, Youky; Yamasaki, Takahiro; Ohno, Takahisa

    2015-03-01

    An epitaxial graphene sheet can be obtained by heat sublimation of Si atoms from the stepped SiC surface. Although this method is expected as one of the most encouraging procedure to make clean sheets, its atomic scale growth mechanism is yet not understood in detail. In this study, the initial stage of the graphene growth processes on a stepped SiC(0001) surface are analyzed by first-principles molecular dynamics (FPMD) simulations. A first-principles calculation code ``PHASE'' which is appropriate for efficient large scale parallel calculations is used. Our FPMD simulations proceed as follows. Before the start, some of the Si atoms on the top layer are intentionally removed from the initial SiC substrate to emulate the Si heat sublimation. MD is executed for 1 psec. under the condition of high temperature and then relaxed. Next, additional Si atoms are removed from the 2nd top layer, and then the same MD is repeated again. We tracked the behaver of the redundant C atoms during the series of these procedures. Where, when and how do those C atoms start to re-create the new C-C networks will be discussed in detail by comparing the results from several different patterns of the SiC substrates. A portion of this research was supported by the grant from MEXT's project and carried out in partnership with the University of Tokyo.

  20. Risk reduction and the privatization option: First principles

    SciTech Connect

    Bjornstad, D.J.; Jones, D.W.; Russell, M.; Cummings, R.C.; Valdez, G.; Duemmer, C.L.

    1997-06-25

    The Department of Energy`s Office of Environmental Restoration and Waste Management (EM) faces a challenging mission. To increase efficiency, EM is undertaking a number of highly innovative initiatives--two of which are of particular importance to the present study. One is the 2006 Plan, a planning and budgeting process that seeks to convert the clean-up program from a temporally and fiscally open-ended endeavor to a strictly bounded one, with firm commitments over a decade-long horizon. The second is a major overhauling of the management and contracting practices that define the relationship between the Department and the private sector, aimed at cost reduction by increasing firms` responsibilities and profit opportunities and reducing DOE`s direct participation in management practices and decisions. The goal of this paper is to provide an independent perspective on how EM should create new management practices to deal with private sector partners that are motivated by financial incentives. It seeks to ground this perspective in real world concerns--the background of the clean-up effort, the very difficult technical challenges it faces, the very real threats to environment, health and safety that have now been juxtaposed with financial drivers, and the constraints imposed by government`s unique business practices and public responsibilities. The approach is to raise issues through application of first principles. The paper is targeted at the EM policy officer who must implement the joint visions of the 2006 plan and privatization within the context of the tradeoff between terminal risk reduction and interim risk management.

  1. First-principles study of codoping in lanthanum bromide

    NASA Astrophysics Data System (ADS)

    Erhart, Paul; Sadigh, Babak; Schleife, André; Åberg, Daniel

    2015-04-01

    Codoping of Ce-doped LaBr3 with Ba, Ca, or Sr improves the energy resolution that can be achieved by radiation detectors based on these materials. Here, we present a mechanism that rationalizes this enhancement on the basis of first-principles electronic structure calculations and point defect thermodynamics. It is shown that incorporation of Sr creates neutral VBr-SrLa complexes that can temporarily trap electrons. As a result, Auger quenching of free carriers is reduced, allowing for a more linear, albeit slower, scintillation light yield response. Experimental Stokes shifts can be related to different CeLa-SrLa-VBr triple complex configurations. Codoping with other alkaline as well as alkaline-earth metals is considered as well. Alkaline elements are found to have extremely small solubilities on the order of 0.1 ppm and below at 1000 K. Among the alkaline-earth metals the lighter dopant atoms prefer interstitial-like positions and create strong scattering centers, which has a detrimental impact on carrier mobilities. Only the heavier alkaline-earth elements (Ca, Sr, Ba) combine matching ionic radii with sufficiently high solubilities. This provides a rationale for the experimental finding that improved scintillator performance is exclusively achieved using Sr, Ca, or Ba. The present mechanism demonstrates that codoping of wide-gap materials can provide an efficient means for managing charge carrier populations under out-of-equilibrium conditions. In the present case dopants are introduced that manipulate not only the concentrations but also the electronic properties of intrinsic defects without introducing additional gap levels. This leads to the availability of shallow electron traps that can temporarily localize charge carriers, effectively deactivating carrier-carrier recombination channels. The principles of this mechanism are therefore not specific to the material considered here but can be adapted for controlling charge carrier populations and

  2. A digitally reconstructed radiograph algorithm calculated from first principles

    SciTech Connect

    Staub, David; Murphy, Martin J.

    2013-01-15

    Purpose: To develop an algorithm for computing realistic digitally reconstructed radiographs (DRRs) that match real cone-beam CT (CBCT) projections with no artificial adjustments. Methods: The authors used measured attenuation data from cone-beam CT projection radiographs of different materials to obtain a function to convert CT number to linear attenuation coefficient (LAC). The effects of scatter, beam hardening, and veiling glare were first removed from the attenuation data. Using this conversion function the authors calculated the line integral of LAC through a CT along rays connecting the radiation source and detector pixels with a ray-tracing algorithm, producing raw DRRs. The effects of scatter, beam hardening, and veiling glare were then included in the DRRs through postprocessing. Results: The authors compared actual CBCT projections to DRRs produced with all corrections (scatter, beam hardening, and veiling glare) and to uncorrected DRRs. Algorithm accuracy was assessed through visual comparison of projections and DRRs, pixel intensity comparisons, intensity histogram comparisons, and correlation plots of DRR-to-projection pixel intensities. In general, the fully corrected algorithm provided a small but nontrivial improvement in accuracy over the uncorrected algorithm. The authors also investigated both measurement- and computation-based methods for determining the beam hardening correction, and found the computation-based method to be superior, as it accounted for nonuniform bowtie filter thickness. The authors benchmarked the algorithm for speed and found that it produced DRRs in about 0.35 s for full detector and CT resolution at a ray step-size of 0.5 mm. Conclusions: The authors have demonstrated a DRR algorithm calculated from first principles that accounts for scatter, beam hardening, and veiling glare in order to produce accurate DRRs. The algorithm is computationally efficient, making it a good candidate for iterative CT reconstruction techniques

  3. First principles modeling of nonlinear incidence rates in seasonal epidemics.

    PubMed

    Ponciano, José M; Capistrán, Marcos A

    2011-02-01

    In this paper we used a general stochastic processes framework to derive from first principles the incidence rate function that characterizes epidemic models. We investigate a particular case, the Liu-Hethcote-van den Driessche's (LHD) incidence rate function, which results from modeling the number of successful transmission encounters as a pure birth process. This derivation also takes into account heterogeneity in the population with regard to the per individual transmission probability. We adjusted a deterministic SIRS model with both the classical and the LHD incidence rate functions to time series of the number of children infected with syncytial respiratory virus in Banjul, Gambia and Turku, Finland. We also adjusted a deterministic SEIR model with both incidence rate functions to the famous measles data sets from the UK cities of London and Birmingham. Two lines of evidence supported our conclusion that the model with the LHD incidence rate may very well be a better description of the seasonal epidemic processes studied here. First, our model was repeatedly selected as best according to two different information criteria and two different likelihood formulations. The second line of evidence is qualitative in nature: contrary to what the SIRS model with classical incidence rate predicts, the solution of the deterministic SIRS model with LHD incidence rate will reach either the disease free equilibrium or the endemic equilibrium depending on the initial conditions. These findings along with computer intensive simulations of the models' Poincaré map with environmental stochasticity contributed to attain a clear separation of the roles of the environmental forcing and the mechanics of the disease transmission in shaping seasonal epidemics dynamics.

  4. First Principles Design of Non-Centrosymmetric Metal Oxides

    NASA Astrophysics Data System (ADS)

    Young, Joshua Aaron

    The lack of an inversion center in a material's crystal structure can result in many useful material properties, such as ferroelectricity, piezoelectricity and non-linear optical behavior. Recently, the desire for low power, high efficiency electronic devices has spurred increased interest in these phenomena, especially ferroelectricity, as well as their coupling to other material properties. By studying and understanding the fundamental structure-property relationships present in non-centrosymmetric materials, it is possible to purposefully engineer new compounds with the desired "acentric" qualities through crystal engineering. The families of ABO3 perovskite and ABO2.5 perovskite-derived brownmillerite oxides are ideal for such studies due to their wide range of possible chemistries, as well as ground states that are highly tunable owing to strong electron-lattice coupling. Furthermore, control over the B-O-B bond angles through epitaxial strain or chemical substitution allows for the rapid development of new emergent properties. In this dissertation, I formulate the crystal-chemistry criteria necessary to design functional non-centrosymmetric oxides using first-principles density functional theory calculations. Recently, chemically ordered (AA')B2O 6 oxides have been shown to display a new form of rotation-induced ferroelectric polarizations. I now extend this property-design methodology to alternative compositions and crystal classes and show it is possible to induce a host of new phenomena. This dissertation will address: 1) the formulation of predictive models allowing for a priori design of polar oxides, 2) the optimization of properties exhibited by these materials through chemical substitution and cation ordering, and 3) the use of strain to control the stability of new phases. Completion of this work has led to a deeper understanding of how atomic structural features determine the physical properties of oxides, as well as the successful elucidation of

  5. First principle kinetic studies of zeolite-catalyzed methylation reactions.

    PubMed

    Van Speybroeck, Veronique; Van der Mynsbrugge, Jeroen; Vandichel, Matthias; Hemelsoet, Karen; Lesthaeghe, David; Ghysels, An; Marin, Guy B; Waroquier, Michel

    2011-02-01

    Methylations of ethene, propene, and butene by methanol over the acidic microporous H-ZSM-5 catalyst are studied by means of state of the art computational techniques, to derive Arrhenius plots and rate constants from first principles that can directly be compared with the experimental data. For these key elementary reactions in the methanol to hydrocarbons (MTH) process, direct kinetic data became available only recently [J. Catal.2005, 224, 115-123; J. Catal.2005, 234, 385-400]. At 350 °C, apparent activation energies of 103, 69, and 45 kJ/mol and rate constants of 2.6 × 10(-4), 4.5 × 10(-3), and 1.3 × 10(-2) mol/(g h mbar) for ethene, propene, and butene were derived, giving following relative ratios for methylation k(ethene)/k(propene)/k(butene) = 1:17:50. In this work, rate constants including pre-exponential factors are calculated which give very good agreement with the experimental data: apparent activation energies of 94, 62, and 37 kJ/mol for ethene, propene, and butene are found, and relative ratios of methylation k(ethene)/k(propene)/k(butene) = 1:23:763. The entropies of gas phase alkenes are underestimated in the harmonic oscillator approximation due to the occurrence of internal rotations. These low vibrational modes were substituted by manually constructed partition functions. Overall, the absolute reaction rates can be calculated with near chemical accuracy, and qualitative trends are very well reproduced. In addition, the proposed scheme is computationally very efficient and constitutes significant progress in kinetic modeling of reactions in heterogeneous catalysis.

  6. First-principles studies of Ni-Ta intermetallic compounds

    SciTech Connect

    Zhou Yi; Wen Bin; Ma Yunqing; Melnik, Roderick; Liu Xingjun

    2012-03-15

    The structural properties, heats of formation, elastic properties, and electronic structures of Ni-Ta intermetallic compounds are investigated in detail based on density functional theory. Our results indicate that all Ni-Ta intermetallic compounds calculated here are mechanically stable except for P21/m-Ni{sub 3}Ta and hc-NiTa{sub 2}. Furthermore, we found that Pmmn-Ni{sub 3}Ta is the ground state stable phase of Ni{sub 3}Ta polymorphs. The polycrystalline elastic modulus has been deduced by using the Voigt-Reuss-Hill approximation. All Ni-Ta intermetallic compounds in our study, except for NiTa, are ductile materials by corresponding G/K values and poisson's ratio. The calculated heats of formation demonstrated that Ni{sub 2}Ta are thermodynamically unstable. Our results also indicated that all Ni-Ta intermetallic compounds analyzed here are conductors. The density of state demonstrated the structure stability increases with the Ta concentration. - Graphical abstract: Mechanical properties and formation heats of Ni-Ta intermetallic compounds are discussed in detail in this paper. Highlights: Black-Right-Pointing-Pointer Ni-Ta intermetallic compounds are investigated by first principle calculations. Black-Right-Pointing-Pointer P21/m-Ni{sub 3}Ta and hc-NiTa{sub 2} are mechanically unstable phases. Black-Right-Pointing-Pointer Pmmn-Ni{sub 3}Ta is ground stable phase of Ni{sub 3}Ta polymorphs. Black-Right-Pointing-Pointer All Ni-Ta intermetallic compounds are conducting materials.

  7. Properties of ferroelectric ultrathin films from first principles

    NASA Astrophysics Data System (ADS)

    Bin-Omran, Saad

    First-principles-based methods are used to determine the response of polarization to epitaxial strain in films made of BaTiO3 (BT) and Pb(Zr0.5Ti0.5)O3 (PZT). Unlike in BT films, the strength of this response as well as its sign dramatically depend on the film's thickness and electrical boundary conditions in PZT films. A phenomenological model provides a rationale for these findings. Moreover, we reveal the effect of the depolarizing field on the paraelectric-to-ferroelectric phase transition in BaTiO3 and PZT ultrathin films. We found that with decreasing the beta screening parameter (i.e., when increasing the depolarizing field) (i) the Curie temperature, Tc, linearly decreases; (ii) the dielectric maximum epsilonmax increases; (iii) the phase transition becomes less diffuse. Furthermore, we investigate the effect of mechanical boundary conditions on the paraelectric-to-ferroelectric phase transition in BaTiO3 and PZT ultrathin films. It is predicted that (i) the phase transition temperature (Tc) increases due to the applied compressive strain; (ii) the epitaxial strain decreases the dielectric maximum epsilon max at any given value of the screening parameter beta; (iii) the diffusive character of the transition is larger in compressive films than in freestanding systems at a fixed beta. Also, we reveal that the nature of all paraelectric-to-ferroelectric phase transitions in the BaTiO3 and PZT ultrathin films (that are under different electric and mechanical boundary conditions) is of second-order.

  8. Impact of first-principles properties of deuterium–tritium on inertial confinement fusion target designs

    SciTech Connect

    Hu, S. X. Goncharov, V. N.; Boehly, T. R.; McCrory, R. L.; Skupsky, S.; Collins, L. A.; Kress, J. D.; Militzer, B.

    2015-05-15

    A comprehensive knowledge of the properties of high-energy-density plasmas is crucial to understanding and designing low-adiabat, inertial confinement fusion (ICF) implosions through hydrodynamic simulations. Warm-dense-matter (WDM) conditions are routinely accessed by low-adiabat ICF implosions, in which strong coupling and electron degeneracy often play an important role in determining the properties of warm dense plasmas. The WDM properties of deuterium–tritium (DT) mixtures and ablator materials, such as the equation of state, thermal conductivity, opacity, and stopping power, were usually estimated by models in hydro-codes used for ICF simulations. In these models, many-body and quantum effects were only approximately taken into account in the WMD regime. Moreover, the self-consistency among these models was often missing. To examine the accuracy of these models, we have systematically calculated the static, transport, and optical properties of warm dense DT plasmas, using first-principles (FP) methods over a wide range of densities and temperatures that cover the ICF “path” to ignition. These FP methods include the path-integral Monte Carlo (PIMC) and quantum-molecular dynamics (QMD) simulations, which treat electrons with many-body quantum theory. The first-principles equation-of-state table, thermal conductivities (κ{sub QMD}), and first principles opacity table of DT have been self-consistently derived from the combined PIMC and QMD calculations. They have been compared with the typical models, and their effects to ICF simulations have been separately examined in previous publications. In this paper, we focus on their combined effects to ICF implosions through hydro-simulations using these FP-based properties of DT in comparison with the usual model simulations. We found that the predictions of ICF neutron yield could change by up to a factor of ∼2.5; the lower the adiabat of DT capsules, the more variations in hydro-simulations. The FP

  9. Impact of first-principles properties of deuterium–tritium on inertial confinement fusion target designs

    DOE PAGES

    Hu, S. X.; Goncharov, V. N.; Boehly, T. R.; McCrory, R. L.; Skupsky, S.; Collins, L. A.; Kress, J. D.; Militizer, B.

    2015-04-20

    In this study, a comprehensive knowledge of the properties of high-energy-density plasmas is crucial to understanding and designing low-adiabat, inertial confinement fusion (ICF) implosions through hydrodynamic simulations. Warm-dense-matter (WDM) conditions are routinely accessed by low-adiabat ICF implosions, in which strong coupling and electron degeneracy often play an important role in determining the properties of warm dense plasmas. The WDM properties of deuterium–tritium (DT) mixtures and ablator materials, such as the equation of state, thermal conductivity, opacity, and stopping power, were usually estimated by models in hydro-codes used for ICF simulations. In these models, many-body and quantum effects were only approximatelymore » taken into account in the WMD regime. Moreover, the self-consistency among these models was often missing. To examine the accuracy of these models, we have systematically calculated the static, transport, and optical properties of warm dense DT plasmas, using first-principles (FP) methods over a wide range of densities and temperatures that cover the ICF “path” to ignition. These FP methods include the path-integral Monte Carlo (PIMC) and quantum-molecular dynamics (QMD) simulations, which treat electrons with many-body quantum theory. The first-principles equation-of-state table, thermal conductivities (KQMD), and first principles opacity table of DT have been self-consistently derived from the combined PIMC and QMD calculations. They have been compared with the typical models, and their effects to ICF simulations have been separately examined in previous publications. In this paper, we focus on their combined effects to ICF implosions through hydro-simulations using these FP-based properties of DT in comparison with the usual model simulations. We found that the predictions of ICF neutron yield could change by up to a factor of –2.5; the lower the adiabat of DT capsules, the more variations in hydro

  10. Impact of first-principles properties of deuterium–tritium on inertial confinement fusion target designs

    SciTech Connect

    Hu, S. X.; Goncharov, V. N.; Boehly, T. R.; McCrory, R. L.; Skupsky, S.; Collins, L. A.; Kress, J. D.; Militizer, B.

    2015-04-20

    In this study, a comprehensive knowledge of the properties of high-energy-density plasmas is crucial to understanding and designing low-adiabat, inertial confinement fusion (ICF) implosions through hydrodynamic simulations. Warm-dense-matter (WDM) conditions are routinely accessed by low-adiabat ICF implosions, in which strong coupling and electron degeneracy often play an important role in determining the properties of warm dense plasmas. The WDM properties of deuterium–tritium (DT) mixtures and ablator materials, such as the equation of state, thermal conductivity, opacity, and stopping power, were usually estimated by models in hydro-codes used for ICF simulations. In these models, many-body and quantum effects were only approximately taken into account in the WMD regime. Moreover, the self-consistency among these models was often missing. To examine the accuracy of these models, we have systematically calculated the static, transport, and optical properties of warm dense DT plasmas, using first-principles (FP) methods over a wide range of densities and temperatures that cover the ICF “path” to ignition. These FP methods include the path-integral Monte Carlo (PIMC) and quantum-molecular dynamics (QMD) simulations, which treat electrons with many-body quantum theory. The first-principles equation-of-state table, thermal conductivities (KQMD), and first principles opacity table of DT have been self-consistently derived from the combined PIMC and QMD calculations. They have been compared with the typical models, and their effects to ICF simulations have been separately examined in previous publications. In this paper, we focus on their combined effects to ICF implosions through hydro-simulations using these FP-based properties of DT in comparison with the usual model simulations. We found that the predictions of ICF neutron yield could change by up to a factor of –2.5; the lower the adiabat of DT capsules, the more variations in hydro

  11. Impact of first-principles properties of deuterium-tritium on inertial confinement fusion target designsa)

    NASA Astrophysics Data System (ADS)

    Hu, S. X.; Goncharov, V. N.; Boehly, T. R.; McCrory, R. L.; Skupsky, S.; Collins, L. A.; Kress, J. D.; Militzer, B.

    2015-05-01

    A comprehensive knowledge of the properties of high-energy-density plasmas is crucial to understanding and designing low-adiabat, inertial confinement fusion (ICF) implosions through hydrodynamic simulations. Warm-dense-matter (WDM) conditions are routinely accessed by low-adiabat ICF implosions, in which strong coupling and electron degeneracy often play an important role in determining the properties of warm dense plasmas. The WDM properties of deuterium-tritium (DT) mixtures and ablator materials, such as the equation of state, thermal conductivity, opacity, and stopping power, were usually estimated by models in hydro-codes used for ICF simulations. In these models, many-body and quantum effects were only approximately taken into account in the WMD regime. Moreover, the self-consistency among these models was often missing. To examine the accuracy of these models, we have systematically calculated the static, transport, and optical properties of warm dense DT plasmas, using first-principles (FP) methods over a wide range of densities and temperatures that cover the ICF "path" to ignition. These FP methods include the path-integral Monte Carlo (PIMC) and quantum-molecular dynamics (QMD) simulations, which treat electrons with many-body quantum theory. The first-principles equation-of-state table, thermal conductivities (κQMD), and first principles opacity table of DT have been self-consistently derived from the combined PIMC and QMD calculations. They have been compared with the typical models, and their effects to ICF simulations have been separately examined in previous publications. In this paper, we focus on their combined effects to ICF implosions through hydro-simulations using these FP-based properties of DT in comparison with the usual model simulations. We found that the predictions of ICF neutron yield could change by up to a factor of ˜2.5; the lower the adiabat of DT capsules, the more variations in hydro-simulations. The FP-based properties of DT

  12. Unified understanding of superconductivity and Mott transition in alkali-doped fullerides from first principles.

    PubMed

    Nomura, Yusuke; Sakai, Shiro; Capone, Massimo; Arita, Ryotaro

    2015-08-01

    Alkali-doped fullerides A 3C60 (A = K, Rb, Cs) are surprising materials where conventional phonon-mediated superconductivity and unconventional Mott physics meet, leading to a remarkable phase diagram as a function of volume per C60 molecule. We address these materials with a state-of-the-art calculation, where we construct a realistic low-energy model from first principles without using a priori information other than the crystal structure and solve it with an accurate many-body theory. Remarkably, our scheme comprehensively reproduces the experimental phase diagram including the low-spin Mott-insulating phase next to the superconducting phase. More remarkably, the critical temperatures T c's calculated from first principles quantitatively reproduce the experimental values. The driving force behind the surprising phase diagram of A 3C60 is a subtle competition between Hund's coupling and Jahn-Teller phonons, which leads to an effectively inverted Hund's coupling. Our results establish that the fullerides are the first members of a novel class of molecular superconductors in which the multiorbital electronic correlations and phonons cooperate to reach high T c s-wave superconductivity.

  13. First-principles study on dielectric function of isolated and bundled carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Yang, J. Y.; Liu, L. H.; Tan, J. Y.

    2015-06-01

    The dielectric function fundamentally determines the thermal radiative properties of nanomaterials. In this work, the first-principles method is applied to investigate the finite temperature dielectric function of isolated and bundled single-walled carbon nanotubes in the visible-ultraviolet spectral range without empirical models. The effects of diameter, intertube interactions and temperature on dielectric functions are discussed. The calculated extraordinary dielectric functions of four isolated (5,5), (6,6), (7,7) and (8,8) armchair nanotubes with different diameters are compared to study the diameter effect. It shows that the locations of absorption peaks of dielectric functions consistently shift to lower energy with increasing diameter. To analyze the influence of non-local intertube interactions, the dielectric functions of bundled (6,6) armchair nanotubes with varying intertube distance are calculated within the van der Waals theory. As nanotubes bundle together, the intertube interactions become strong and the absorption peaks enhance. The temperature effect is included into computing dielectric function of isolated (5,0) zigzag nanotubes via first-principles molecular dynamics method. It observes that the dominant absorption peak shifts to lower energy as temperature increases from 0 to 600 K. To interpret the temperature influence, the temperature perturbed density of states is presented.

  14. First-Principles Equation of State Calculations of First- and Second-Row Plasmas

    NASA Astrophysics Data System (ADS)

    Driver, K. P.; Soubiran, F.; Zhang, S.; Militzer, B.

    2015-12-01

    Theoretical studies of high energy density matter are a key component to improving our knowledge related to interiors of giant planets and stars, astrophysical processes, and new plasma energy technologies, such as inertial confined fusion. Path integral Monte Carlo (PIMC) and density functional theory molecular dynamics (DFT-MD) are simulation methods that provide consistent, first-principles descriptions of warm, dense matter and plasmas over a wide range of density and temperature conditions. Here, we report simulation results using these two methods for a number of first- and second-row elements. DFT-MD algorithms are well-suited for low temperatures, while PIMC has been restricted to relatively high temperatures due to the free-particle approximation of the nodal surface. For first-row elements, we find that the free-particle approximation is sufficient as long as the temperature is high enough to sufficiently ionize the second electronic shell of the atoms. For heavier, second-row elements, we have developed a new, localized nodal surface, which allows us to treat bound states within the PIMC formalism. By combining PIMC and DFT-MD pressures and internal energies, we produce a coherent, first-principles equation of state, bridging the entire warm dense matter regime. Pair-correlation functions and the density of electronic states reveal an evolving plasma structure. The degree of ionization is affected by both temperature and density. Finally, shock Hugoniot curves show an increase in compression as the first and second shells are ionized.

  15. Unified understanding of superconductivity and Mott transition in alkali-doped fullerides from first principles

    PubMed Central

    Nomura, Yusuke; Sakai, Shiro; Capone, Massimo; Arita, Ryotaro

    2015-01-01

    Alkali-doped fullerides A3C60 (A = K, Rb, Cs) are surprising materials where conventional phonon-mediated superconductivity and unconventional Mott physics meet, leading to a remarkable phase diagram as a function of volume per C60 molecule. We address these materials with a state-of-the-art calculation, where we construct a realistic low-energy model from first principles without using a priori information other than the crystal structure and solve it with an accurate many-body theory. Remarkably, our scheme comprehensively reproduces the experimental phase diagram including the low-spin Mott-insulating phase next to the superconducting phase. More remarkably, the critical temperatures Tc’s calculated from first principles quantitatively reproduce the experimental values. The driving force behind the surprising phase diagram of A3C60 is a subtle competition between Hund’s coupling and Jahn-Teller phonons, which leads to an effectively inverted Hund’s coupling. Our results establish that the fullerides are the first members of a novel class of molecular superconductors in which the multiorbital electronic correlations and phonons cooperate to reach high Tc s-wave superconductivity. PMID:26601242

  16. First-principles equation of state and electronic properties of warm dense oxygen

    SciTech Connect

    Driver, K. P. Soubiran, F.; Zhang, Shuai; Militzer, B.

    2015-10-28

    We perform all-electron path integral Monte Carlo (PIMC) and density functional theory molecular dynamics (DFT-MD) calculations to explore warm dense matter states of oxygen. Our simulations cover a wide density-temperature range of 1–100 g cm{sup −3} and 10{sup 4}–10{sup 9} K. By combining results from PIMC and DFT-MD, we are able to compute pressures and internal energies from first-principles at all temperatures and provide a coherent equation of state. We compare our first-principles calculations with analytic equations of state, which tend to agree for temperatures above 8 × 10{sup 6} K. Pair-correlation functions and the electronic density of states reveal an evolving plasma structure and ionization process that is driven by temperature and density. As we increase the density at constant temperature, we find that the ionization fraction of the 1s state decreases while the other electronic states move towards the continuum. Finally, the computed shock Hugoniot curves show an increase in compression as the first and second shells are ionized.

  17. Waltzing of a helium pair in tungsten: Migration barrier and trajectory revealed from first-principles

    SciTech Connect

    Niu, J. G.; Zhan, Q.; Geng, W. T.

    2014-06-15

    Despite well documented first-principles theoretical determination of the low migration energy (0.06 eV) of a single He in tungsten, fully quantum mechanical calculations on the migration of a He pair still present a challenge due to the complexity of its trajectory. By identifying the six most stable configurations of the He pair in W and decomposing its motion into rotational, translational, and rotational-translational routines, we are able to determine its migration barrier and trajectory. Our density functional theory calculations demonstrate a He pair has three modes of motion: a close or open circular two-dimensional motion in (100) plane with an energy barrier of 0.30 eV, a snaking motion along [001] direction with a barrier of 0.30 eV, and a twisted-ladder motion along [010] direction with the two He swinging in the plane (100) and a barrier of 0.31 eV. The graceful associative movements of a He pair are related to the chemical-bonding-like He-He interaction being much stronger than its migration barrier in W. The excellent agreement with available experimental measurements (0.24–0.32 eV) on He migration makes our first-principles result a solid input to obtain accurate He-W interatomic potentials in molecular dynamics simulations.

  18. First-principles prediction of the softening of the silicon shock Hugoniot curve

    DOE PAGES

    Hu, S. X.; Militzer, B.; Collins, L. A.; Driver, K. P.; Kress, J. D.

    2016-09-15

    Here, whock compression of silicon (Si) under extremely high pressures (>100 Mbar) was investigated by using two first-principles methods of orbital-free molecular dynamics (OFMD) and path integral Monte Carlo (PIMC). While pressures from the two methods agree very well, PIMC predicts a second compression maximum because of 1s electron ionization that is absent in OFMD calculations since Thomas–Fermi-based theories lack inner shell structure. The Kohn–Sham density functional theory is used to calculate the equation of state (EOS) of warm dense silicon for low-pressure loadings (P < 100 Mbar). Combining these first-principles EOS results, the principal Hugoniot curve of silicon formore » pressures varying from 0.80 Mbar to above ~10 Gbar was derived. We find that silicon is ~20% or more softer than what was predicted by EOS models based on the chemical picture of matter. Existing experimental data (P ≈ 1–2 Mbar) seem to indicate this softening behavior of Si, which calls for future strong-shock experiments (P > 10 Mbar) to benchmark our results.« less

  19. Strong n-type molecule as low bias negative differential resistance device predicted by first-principles study

    NASA Astrophysics Data System (ADS)

    Min, Y.; Zhong, C. G.; Dong, Z. C.; Zhao, Z. Y.; Zhou, P. X.; Yao, K. L.

    2016-10-01

    A first-principles study of the transport properties of two thiolated pentacenes sandwiching ethyl is performed. The thiolated pentacene molecule shows strong n-type characteristics when contact Ag lead because of low work function about metal Ag. A strong negative differential resistance (NDR) effect with large peak-to-valley ratio of 758% is present under low bias. Our investigations indicate that strong n- or p-type molecules can be used as low bias molecular NDR devices and that the molecular NDR effect based on molecular-level leaving not on molecular-level crossing has no hysteresis.

  20. First-principles opacity table of warm dense deuterium for inertial-confinement-fusion applications.

    PubMed

    Hu, S X; Collins, L A; Goncharov, V N; Boehly, T R; Epstein, R; McCrory, R L; Skupsky, S

    2014-09-01

    Accurate knowledge of the optical properties of a warm dense deuterium-tritium (DT) mixture is important for reliable design of inertial confinement fusion (ICF) implosions using radiation-hydrodynamics simulations. The opacity of a warm dense DT shell essentially determines how much radiation from hot coronal plasmas can be deposited in the DT fuel of an imploding capsule. Even for the simplest species of hydrogen, the accurate calculation of their opacities remains a challenge in the warm-dense matter regime because strong-coupling and quantum effects play an important role in such plasmas. With quantum-molecular-dynamics (QMD) simulations, we have derived a first-principles opacity table (FPOT) of deuterium (and the DT mixture by mass scaling) for a wide range of densities from ρ(D)=0.5 to 673.518g/cm(3) and temperatures from T=5000K up to the Fermi temperature T(F) for each density. Compared with results from the astrophysics opacity table (AOT) currently used in our hydrocodes, the FPOT of deuterium from our QMD calculations has shown a significant increase in opacity for strongly coupled and degenerate plasma conditions by a factor of 3-100 in the ICF-relevant photon-energy range. As conditions approach those of classical plasma, the opacity from the FPOT converges to the corresponding values of the AOT. By implementing the FPOT of deuterium and the DT mixture into our hydrocodes, we have performed radiation-hydrodynamics simulations for low-adiabat cryogenic DT implosions on the OMEGA laser and for direct-drive-ignition designs for the National Ignition Facility. The simulation results using the FPOT show that the target performance (in terms of neutron yield and energy gain) could vary from ∼10% up to a factor of ∼2 depending on the adiabat of the imploding DT capsule; the lower the adiabat, the more variation is seen in the prediction of target performance when compared to the AOT modeling. PMID:25314551

  1. First-principles modeling of titanate/ruthenate superlattices

    NASA Astrophysics Data System (ADS)

    Junquera, Javier

    2013-03-01

    The possibility to create highly confined two-dimensional electron gases (2DEG) at oxide interfaces has generated much excitement during the last few years. The most widely studied system is the 2DEG formed at the LaO/TiO2 polar interface between LaAlO3 and SrTiO3, where the polar catastrophe at the interface has been invoked as the driving force. More recently, partial or complete delta doping of the Sr or Ti cations at a single layer of a SrTiO3 matrix has also been used to generate 2DEG. Following this recipe, we report first principles characterization of the structural and electronic properties of (SrTiO3)5/(SrRuO3)1 superlattices, where all the Ti of a given layer have been replaced by Ru. We show that the system exhibits a spin-polarized two-dimensional electron gas extremely confined to the 4 d orbitals of Ru in the SrRuO3 layer, a fact that is independent of the level of correlation included in the simulations. For hybrid functionals or LDA+U, every interface in the superlattice behaves as minority-spin half-metal ferromagnet, with a magnetic moment of μ = 2.0 μB/SrRuO3 unit. The shape of the electronic density of states, half metallicity and magnetism are explained in terms of a simplified tight-binding model, considering only the t2 g orbitals plus (i) the bi-dimensionality of the system, and (ii) strong electron correlations. Possible applications are discussed, from their eventual role in thermoelectric applications to the possible tuning of ferromagnetic properties of the 2DEG with the polarization of the dielectric. Work done in collaboration with P. García, M. Verissimo-Alves, D. I. Bilc, and Ph. Ghosez. Financial support provided by MICINN Grant FIS2009-12721-C04-02, and by the European Union Grant No. CP-FP 228989-2 ``OxIDes.'' The authors thankfully acknowledge the computer resources, technical expertise and assistance provided by the BSC/RES.

  2. First principles evaluation of the photocatalytic properties of cuprous oxide

    NASA Astrophysics Data System (ADS)

    Bendavid, Leah Isseroff

    Cuprous oxide (Cu2O) is a semiconductor attractive for use as a photocatalyst in renewable fuel production, but has thus far exhibited low efficiencies in solar energy technologies. A thorough understanding of its photocatalytically relevant properties is needed to develop improved cuprous oxide-based photocatalysts. This dissertation uses first principles calculations founded in quantum mechanics to study the physical, optical, electronic, and chemical properties of cuprous oxide and to optimize its performance in solar energy applications. The key properties that affect efficiency include electronic excitations, the band gap, band edge positions, charge transport, defect trap states, catalyst stability, and surface chemistry. The band gap of Cu 2O, which defines the efficiency of solar energy absorption, is first calculated with hybrid density functional theory (DFT) followed by a single GW perturbation. We also design methods to calculate optical excitations using embedded correlated wavefunction theory. The low-index surfaces are characterized using DFT+U, where we identify the (111) surface as the most stable. This surface is employed in the derivation of the band edges of Cu2O, which demonstrate that Cu2O can provide the thermodynamic overpotential needed to drive water splitting and the reduction of CO2 to methanol. We also identify the adsorption mechanisms of weakly physisorbed CO2 and the more strongly adsorbed H2O on the Cu2O(111) surface. Effective charge transport is needed so that photoexcited carriers can reach the surface active sites prior to recombination. We study electron and hole transport in Cu2O using the small polaron model, and show that its localized description is inappropriate for carrier transport, which is better modeled using band theory. We then use an approach founded in band theory to analyze the cause of intrinsic trap states, which promote carrier recombination. We conclude that doping with Li can prevent trap state formation and

  3. ABINIT: First-principles approach to material and nanosystem properties

    NASA Astrophysics Data System (ADS)

    Gonze, X.; Amadon, B.; Anglade, P.-M.; Beuken, J.-M.; Bottin, F.; Boulanger, P.; Bruneval, F.; Caliste, D.; Caracas, R.; Côté, M.; Deutsch, T.; Genovese, L.; Ghosez, Ph.; Giantomassi, M.; Goedecker, S.; Hamann, D. R.; Hermet, P.; Jollet, F.; Jomard, G.; Leroux, S.; Mancini, M.; Mazevet, S.; Oliveira, M. J. T.; Onida, G.; Pouillon, Y.; Rangel, T.; Rignanese, G.-M.; Sangalli, D.; Shaltaf, R.; Torrent, M.; Verstraete, M. J.; Zerah, G.; Zwanziger, J. W.

    2009-12-01

    ABINIT [ http://www.abinit.org] allows one to study, from first-principles, systems made of electrons and nuclei (e.g. periodic solids, molecules, nanostructures, etc.), on the basis of Density-Functional Theory (DFT) and Many-Body Perturbation Theory. Beyond the computation of the total energy, charge density and electronic structure of such systems, ABINIT also implements many dynamical, dielectric, thermodynamical, mechanical, or electronic properties, at different levels of approximation. The present paper provides an exhaustive account of the capabilities of ABINIT. It should be helpful to scientists that are not familiarized with ABINIT, as well as to already regular users. First, we give a broad overview of ABINIT, including the list of the capabilities and how to access them. Then, we present in more details the recent, advanced, developments of ABINIT, with adequate references to the underlying theory, as well as the relevant input variables, tests and, if available, ABINIT tutorials. Program summaryProgram title: ABINIT Catalogue identifier: AEEU_v1_0 Distribution format: tar.gz Journal reference: Comput. Phys. Comm. Programming language: Fortran95, PERL scripts, Python scripts Computer: All systems with a Fortran95 compiler Operating system: All systems with a Fortran95 compiler Has the code been vectorized or parallelized?: Sequential, or parallel with proven speed-up up to one thousand processors. RAM: Ranges from a few Mbytes to several hundred Gbytes, depending on the input file. Classification: 7.3, 7.8 External routines: (all optional) BigDFT [1], ETSF IO [2], libxc [3], NetCDF [4], MPI [5], Wannier90 [6] Nature of problem: This package has the purpose of computing accurately material and nanostructure properties: electronic structure, bond lengths, bond angles, primitive cell size, cohesive energy, dielectric properties, vibrational properties, elastic properties, optical properties, magnetic properties, non-linear couplings, electronic and

  4. First-principles modelling of materials: From polythiophene to phosphorene

    NASA Astrophysics Data System (ADS)

    Ziletti, Angelo

    As a result of the computing power provided by the current technology, computational methods now play an important role in modeling and designing materials at the nanoscale. The focus of this dissertation is two-fold: first, new computational methods to model nanoscale transport are introduced, then state-of-the-art tools based on density functional theory are employed to explore the properties of phosphorene, a novel low dimensional material with great potential for applications in nanotechnology. A Wannier function description of the electron density is combined with a generalized Slater-Koster interpolation technique, enabling the introduction of a new computational method for constructing first-principles model Hamiltonians for electron and hole transport that maintain the density functional theory accuracy at a fraction of the computational cost. As a proof of concept, this new approach is applied to model polythiophene, a polymer ubiquitous in organic photovoltaic devices. A new low dimensional material, phosphorene - a single layer of black phosphorous - the phosphorous analogue of graphene was first isolated in early 2014 and has attracted considerable attention. It is a semiconductor with a sizable band gap, which makes it a perfect candidate for ultrathin transistors. Multi-layer phosphorene transistors have already achieved the highest hole mobility of any two-dimensional material apart from graphene. Phosphorene is prone to oxidation, which can lead to degradation of electrical properties, and eventually structural breakdown. The calculations reported here are some of the first to explore this oxidation and reveal that different types of oxygen defects are readily introduced in the phosphorene lattice, creating electron traps in some situations. These traps are responsible for the non-ambipolar behavior observed by experimental collaborators in air-exposed few-layer black phosphorus devices. Calculation results predict that air exposure of phosphorene

  5. First principles investigation of Fe and Al bearing phase H

    NASA Astrophysics Data System (ADS)

    Tsuchiya, J.; Tsuchiya, T.

    2015-12-01

    exploration of these hydrous phases, such as the spin transition of Fe in phase H and the possibility of further phase transition of this new hydrous mineral using first principles calculation techniques and discuss the possible effects of this hydrous phase at the bottom of lower mantle.

  6. A genetic algorithm for first principles global structure optimization of supported nano structures

    SciTech Connect

    Vilhelmsen, Lasse B.; Hammer, Bjørk

    2014-07-28

    We present a newly developed publicly available genetic algorithm (GA) for global structure optimisation within atomic scale modeling. The GA is focused on optimizations using first principles calculations, but it works equally well with empirical potentials. The implementation is described and benchmarked through a detailed statistical analysis employing averages across many independent runs of the GA. This analysis focuses on the practical use of GA’s with a description of optimal parameters to use. New results for the adsorption of M{sub 8} clusters (M = Ru, Rh, Pd, Ag, Pt, Au) on the stoichiometric rutile TiO{sub 2}(110) surface are presented showing the power of automated structure prediction and highlighting the diversity of metal cluster geometries at the atomic scale.

  7. Cold Baryogenesis from first principles in the two-Higgs doublet model with fermions

    NASA Astrophysics Data System (ADS)

    Mou, Zong-Gang; Saffin, Paul M.; Tranberg, Anders

    2015-06-01

    We present a first-principles numerical computation of the baryon asymmetry in electroweak-scale baryogenesis. For the scenario of Cold Baryogenesis, we consider a one fermion-family reduced CP-violating two Higgs-doublet model, including a classical SU(2)-gauge/two-Higgs sector coupled to one quantum left-handed fermion doublet and two right-handed singlets. Separately, the C(CP) breaking of the two-Higgs potential and the C and P breaking of the gauge-fermion interactions do not provide a baryon asymmetry. Only when combined does baryogenesis occur. Through large-scale computer simulations, we compute the asymmetry for one particularly favourable scalar potential. The numerical signal is at the boundary of what is numerically discernible with the available computer resources, but we tentatively find an asymmetry of | η| ≤ 3.5 × 10-7.

  8. First-Principles Investigation of Electronic Excitation Dynamics in Water under Proton Irradiation

    NASA Astrophysics Data System (ADS)

    Reeves, Kyle; Kanai, Yosuke

    2015-03-01

    A predictive and quantitative understanding of electronic excitation dynamics in water under proton irradiation is of great importance in many technological areas ranging from utilizing proton beam therapy to preventing nuclear reactor damages. Despite its importance, an atomistic description of the excitation mechanism has yet to be fully understood. Identifying how a high-energy proton dissipates its kinetic energy into the electronic excitation is crucial for predicting atomistic damages, later resulting in the formation of different chemical species. In this work, we use our new, large-scale first-principles Ehrenfest dynamics method based on real-time time-dependent density functional theory to simulate the electronic response of bulk water to a fast-moving proton. In particular, we will discuss the topological nature of the electronic excitation as a function of the proton velocity. We will employ maximally-localized functions to bridge our quantitative findings from first-principles simulations to a conceptual understanding in the field of water radiolysis.

  9. Electron field emission in nanostructures: A first-principles study

    NASA Astrophysics Data System (ADS)

    Driscoll, Joseph Andrew

    The objective of this work was to study electron field emission from several nanostructures using a first-principles framework. The systems studied were carbon nanowires, graphene nanoribbons, and nanotubes of varying composition. These particular structures were chosen because they have recently been identified as showing novel physical phenomena, as well as having tremendous industrial applications. We examined the field emission under a variety of conditions, including laser illumination and the presence of adsorbates. The goal was to explore how these conditions affect the field emission performance. In addition to the calculations, this dissertation has presented computational developments by the author that allowed these demanding calculations to be performed. There are many possible choices for basis when performing an electronic structure calculation. Examples are plane waves, atomic orbitals, and real-space grids. The best choice of basis depends on the structure of the system being analyzed and the physical processes involved (e.g., laser illumination). For this reason, it was important to conduct rigorous tests of basis set performance, in terms of accuracy and computational efficiency. There are no existing benchmark calculations for field emission, but transport calculations for nanostructures are similar, and so provide a useful reference for evaluating the performance of various basis sets. Based on the results, for the purposes of studying a non-periodic nanostructure under field emission conditions, we decided to use a real-space grid basis which incorporates the Lagrange function approach. Once a basis was chosen, in this case a real-space grid, the issue of boundary conditions arose. The problem is that with a non-periodic system, field emitted electron density can experience non-physical reflections from the boundaries of the calculation volume, leading to inaccuracies. To prevent this issue, we used complex absorbing potentials (CAPs) to absorb

  10. The Harvard Clean Energy Project: High-throughput screening of organic photovoltaic materials using first-principles electronic structure theory

    NASA Astrophysics Data System (ADS)

    Hachmann, Johannes; Olivares-Amaya, Roberto; Atahan-Evrenk, Sule; Amador-Bedolla, Carlos; Aspuru-Guzik, Alan

    2012-02-01

    We present the Harvard Clean Energy Project (CEP) which is concerned with the computational screening and design of new organic photovoltaic materials. CEP has established an automated, high-throughput, in silico framework to study millions of potential candidate structures. This presentation discusses the CEP branch which employs first-principles computational quantum chemistry for the characterization of molecular motifs and the assessment of their quality with respect to applications as electronic materials. In addition to finding specific structures with certain properties, it is the goal of CEP to illuminate and understand the structure-property relations in the domain of organic electronics. Such insights can open the door to a rational, systematic, and accelerated development of future high-performance materials. CEP is a large-scale investigation which utilizes the massive computational resource of IBM's World Community Grid. In this context, it is deployed as a screensaver application harvesting idle computing time on donor machines. This cyberinfrastructure paradigm has already allowed us to characterize 3.5 million molecules of interest in about 50 million DFT calculations.

  11. First-principles study on phase transition and ferroelectricity in lithium niobate and tantalate

    SciTech Connect

    Toyoura, Kazuaki Ohta, Masataka; Nakamura, Atsutomo; Matsunaga, Katsuyuki

    2015-08-14

    The phase transitions and ferroelectricity of LiNbO{sub 3} and LiTaO{sub 3} have been investigated theoretically from first principles. The phonon analyses and the molecular dynamics simulations revealed that the ferroelectric phase transition is not conventional displacive type but order-disorder type with strong correlation between cation displacements. According to the evaluated potential energy surfaces around the paraelectric structures, the large difference in ferroelectricity between the two oxides results from the little difference in short-range interionic interaction between Nb-O and Ta-O. As the results of the crystal orbital overlap population analyses, the different short-range interaction originates from the difference in covalency between Nb4d-O2p and Ta5d-O2p orbitals, particularly d{sub xz}-p{sub x}/d{sub yz}-p{sub y} orbitals (π orbitals), from the electronic point of view.

  12. First-principles approach to calculating energy level alignment at aqueous semiconductor interfaces

    DOE PAGES

    Kharche, Neerav; Muckerman, James T.; Hybertsen, Mark S.

    2014-10-21

    A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1b₁ energy level in water. The application to the specific cases of nonpolar (101¯0 ) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation and themore » dynamical fluctuations in the interface Zn-O and O-H bond orientations. As a result, these effects contribute up to 0.5 eV.« less

  13. First-principles approach to calculating energy level alignment at aqueous semiconductor interfaces

    SciTech Connect

    Kharche, Neerav; Muckerman, James T.; Hybertsen, Mark S.

    2014-10-21

    A first-principles approach is demonstrated for calculating the relationship between an aqueous semiconductor interface structure and energy level alignment. The physical interface structure is sampled using density functional theory based molecular dynamics, yielding the interface electrostatic dipole. The GW approach from many-body perturbation theory is used to place the electronic band edge energies of the semiconductor relative to the occupied 1b₁ energy level in water. The application to the specific cases of nonpolar (101¯0 ) facets of GaN and ZnO reveals a significant role for the structural motifs at the interface, including the degree of interface water dissociation and the dynamical fluctuations in the interface Zn-O and O-H bond orientations. As a result, these effects contribute up to 0.5 eV.

  14. First-principles quantum-mechanical investigations of biomass conversion at the liquid-solid interfaces

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

    We report first-principles density-functional calculations and ab initio molecular dynamics (MD) simulations for the reactions involving furfural, which is an important intermediate in biomass conversion, at the catalytic liquid-solid interfaces. The different dynamic processes of furfural at the water-Cu(111) and water-Pd(111) interfaces suggest different catalytic reaction mechanisms for the conversion of furfural. Simulations for the dynamic processes with and without hydrogen demonstrate the importance of the liquid-solid interface as well as the presence of hydrogen in possible catalytic reactions including hydrogenation and decarbonylation of furfural. Supported by DOE (DE-SC0004600). This research used the supercomputer resources of the XSEDE, the NERSC Center, and the Tandy Supercomputing Center.

  15. First principles study of the optical contrast in phase change materials.

    PubMed

    Caravati, S; Bernasconi, M; Parrinello, M

    2010-08-11

    We study from first principles the optical properties of the phase change materials Ge(2)Sb(2)Te(5) (GST), GeTe and Sb(2)Te(3) in the crystalline phase and in realistic models of the amorphous phase generated by quenching from the melt in ab initio molecular dynamics simulations. The calculations reproduce the strong optical contrast between the crystalline and amorphous phases measured experimentally and exploited in optical data storage. It is demonstrated that the optical contrast is due to a change in the optical matrix elements across the phase change in all the compounds. It is concluded that the reduction of the optical matrix elements in the amorphous phases is due to angular disorder in p-bonding which dominates the amorphous network in agreement with previous proposals (Huang and Robertson 2010 Phys. Rev. B 81 081204) based on calculations on crystalline models.

  16. Order-disorder phase boundary in ice VII-VIII investigated by first principles

    NASA Astrophysics Data System (ADS)

    Wentzcovitch, R. M.; Umemoto, K.; Baroni, S.; de Gironcoli, S.

    2009-12-01

    Phase boundaries among the various forms of ice are difficult to determine experimentally because of large hysteresis involved, especially at the lowest temperatures. Theoretically, there are also great challenges, including the order-disorder (OD) phenomenon. The ice VII-VIII boundary, a typical OD boundary, has been reasonably well constrained experimentally and is an ideal study case. We present a first principles quasiharmonic study consisting in the complete statistical sampling of molecular orientations within a 16 molecules supercell. This supercell size accounts well for several aspects of this transition, including the Clapeyron slope and the isotopic effect. Research supported by NSF grants ATM 0428774 (VLab) and EAR 0757903. Computations were performed at the Minnesota Supercomputing Institute.

  17. Towards a mulitphase equation of state of Carbon from first principles

    NASA Astrophysics Data System (ADS)

    Correa, Alfredo; Benedict, Lorin; Schwegler, Eric

    2007-03-01

    Ab initio molecular dynamics and electronic structure calculation had become one of the most useful tools to investigate properties of materials. Unfortunately these atomistic detailed results are rarely reused in calculations at a higher level of description, such as fluid dynamics and finite elements calculations. In this talk we present a concrete example showing the way that first principles results can be expressed in a way that is useful for hydrodynamics calculations, in particular we show how to build a analytic equation of state for Carbon that involves solid (diamond and BC8) and liquid phases. Applications of this newly obtained equation of state will be presented. This work was performed under the auspices of the U.S. Dept. of Energy at the University of California/Lawrence Livermore National Laboratory under contract no. W-7405-Eng-48.

  18. First principles calculation of electron ionization mass spectra for selected organic drug molecules.

    PubMed

    Bauer, Christoph Alexander; Grimme, Stefan

    2014-11-21

    This study presents a showcase for the novel Quantum Chemistry Electron Ionization Mass Spectrometry (QCEIMS) method on five FDA-approved drugs. The method allows a first-principles electronic structure-based prediction of EI mass spectra in principle for any molecule. The systems in this case study are organic substances of nominal masses between 404 and 853 atomic mass units and cover a wide range of functional groups and organic molecular structure motifs. The results demonstrate the widespread applicability of the QCEIMS method for the unbiased computation of EI mass spectra even for larger molecules. Its strengths compared to standard (static) or database driven approaches in such cases are highlighted. Weak points regarding the required computation times or the approximate character of the employed QC methods are also discussed. We propose QCEIMS as a viable and robust way of predicting EI mass spectra for sizeable organic molecules relevant to medicinal and pharmaceutical chemistry.

  19. First-Principles Investigations of Defects in Minerals

    NASA Astrophysics Data System (ADS)

    Verma, Ashok K.

    2011-07-01

    The ideal crystal has an infinite 3-dimensional repetition of identical units which may be atoms or molecules. But real crystals are limited in size and they have disorder in stacking which as called defects. Basically three types of defects exist in solids: 1) point defects, 2) line defects, and 3) surface defects. Common point defects are vacant lattice sites, interstitial atoms and impurities and these are known to influence strongly many solid-state transport properties such as diffusion, electrical conduction, creep, etc. In thermal equilibrium point defects concentrations are determined by their formation enthalpies and their movement by their migration barriers. Line and surface defects are though absent from the ideal crystal in thermal equilibrium due to higher energy costs but they are invariably present in all real crystals. Line defects include edge-, screw- and mixed-dislocations and their presence is essential in explaining the mechanical strength and deformation of real crystals. Surface defects may arise at the boundary between two grains, or small crystals, within a larger crystal. A wide variety of grain boundaries can form in a polycrystal depending on factors such growth conditions and thermal treatment. In this talk we will present our first-principles density functional theory based defect studies of SiO2 polymorphs (stishovite, CaCl2-, α-PbO2-, and pyrite-type), Mg2SiO4 polymorphs (forsterite, wadsleyite and ringwoodite) and MgO [1-3]. Briefly, several native point defects including vacancies, interstitials, and their complexes were studied in silica polymorphs upto 200 GPa. Their values increase by a factor of 2 over the entire pressure range studied with large differences in some cases between different phases. The Schottky defects are energetically most favorable at zero pressure whereas O-Frenkel pairs become systematically more favorable at pressures higher than 20 GPa. The geometric and electronic structures of defects and migrating

  20. Modeling of compositionally graded barium strontium titanate from first principles

    NASA Astrophysics Data System (ADS)

    Walizer, Laura Elizabeth

    Barium Strontium Titanate (BaxSr1-xTiO 3 or BST) is a Perovskite alloy of interest for both technological and intellectual reasons. Its ferroelectric and piezoelectric properties make it useful in a variety of electric components such as transducers and actuators, and BST in particular is a material of interest for the development of a ferroelectric RAM for computers.(1) The inclusion of SrTiO3, an incipient ferroelectric, and the fact that the properties of a BST system depend strongly on its relative composition of BaTiO3 (BT) and SrTiO3 (ST), make also this a material of high interest. (2) Compositionally graded systems are of further interest (see e.g., Refs. (3), (4), (5) and references therein), partly because their compositional grading leads to a built-in polarization gradient. Due to this, these systems could act as transcapacitors, devices which act as charge amplifiers in much the same way that transistors act as current amplifiers.(3), (4) Here, compositionally graded BST systems were modeled using a first-principles derived effective Hamiltonian method within Monte-Carlo simulation. (6) The graded systems under consideration had an average Ba composition of 70%. These systems were modeled under stress-free conditions, as well as, under epitaxial strain due to a SrTiO3 substrate. Both the degree of grading and the thickness of the layers were varied. The investigation revealed that graded BST systems behaved differently from bulk BST systems in several ways. First, some graded BST systems possessed both monodomain states qualitatively similar to those found in bulk systems (except that the polarization exhibited a "wave" behavior inside the graded systems), and also states with domain striping. Where this occurred, the monodomain state was lower in energy, and was therefore the ground-state, but the striped domain state was found to be metastable, representing a local energy minimum. Analyzing unstrained compositionally graded systems layer by layer

  1. First-principles scheme for spectral adjustment in nanoscale transport

    NASA Astrophysics Data System (ADS)

    García-Suárez, Víctor M.; Lambert, Colin J.

    2011-05-01

    We implement a general method for correcting the low-bias transport properties of nanoscale systems within an ab initio methodology based on linear combinations of atomic orbitals. This method consists of adjusting the molecular spectrum, i.e. shifting the position of the occupied and unoccupied molecular orbitals to match the experimental highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO (HL)) gap. Thus we show how the typical problem of an underestimated HL gap can be corrected, leading to quantitative and qualitative agreement with experiments. We show that an alternative method based on calculating the position of the relevant transport resonances and fitting them to Lorentzians can significantly underestimate the conductance and does not accurately reproduce the electron transmission coefficient between resonances. We compare this simple method in an ideal system of a benzene molecule coupled to featureless leads to more sophisticated approaches, such as GW, and find rather good agreement between both. We also present the results of a benzenedithiolate molecule between gold leads, where we study different coupling configurations for straight and tilted molecules, and show that this method yields the observed evolution of two-dimensional conductance histograms. We also explain the presence of low-conductance zones in such histograms by taking into account different coupling configurations.

  2. First-principles study of transition-metal nitrides as diffusion barriers against Al

    NASA Astrophysics Data System (ADS)

    Mei, Zhi-Gang; Yacout, Abdellatif M.; Kim, Yeon Soo; Hofman, Gerard; Stan, Marius

    2016-04-01

    Using density-functional theory based first-principles calculations we provided a comparative study of the diffusion barrier properties of TiN, ZrN, and HfN against Al for U-Mo dispersion fuel applications. We firstly examined the thermodynamic stability of these transition-metal nitrides with Al. The calculated heats of reaction show that both TiN and ZrN are thermodynamically unstable diffusion barrier materials, which might be decomposed by Al at relatively high temperatures. As a comparison, HfN is a stable diffusion barrier material for Al. To evaluate the kinetic stability of these nitride systems against Al diffusion, we investigated the diffusion mechanisms of Al in TiN, ZrN and HfN using atomic scale simulations. The effect of non-stoichiometry on the defect formation and Al migration was systematically studied.

  3. FInal Report: First Principles Modeling of Mechanisms Underlying Scintillator Non-Proportionality

    SciTech Connect

    Aberg, Daniel; Sadigh, Babak; Zhou, Fei

    2015-01-01

    This final report presents work carried out on the project “First Principles Modeling of Mechanisms Underlying Scintillator Non-Proportionality” at Lawrence Livermore National Laboratory during 2013-2015. The scope of the work was to further the physical understanding of the microscopic mechanisms behind scintillator nonproportionality that effectively limits the achievable detector resolution. Thereby, crucial quantitative data for these processes as input to large-scale simulation codes has been provided. In particular, this project was divided into three tasks: (i) Quantum mechanical rates of non-radiative quenching, (ii) The thermodynamics of point defects and dopants, and (iii) Formation and migration of self-trapped polarons. The progress and results of each of these subtasks are detailed.

  4. Thermoelectric properties of binary LnN (Ln=La and Lu): First principles study

    NASA Astrophysics Data System (ADS)

    Sreeparvathy P., C.; Gudelli, Vijay Kumar; Kanchana, V.; Vaitheeswaran, G.; Svane, A.; Christensen, N. E.

    2015-06-01

    First principles density functional calculations were carried out to study the electronic structure and thermoelectric properties of LnN (Ln = La and Lu) using the full potential linearized augmented plane wave (FP-LAPW) method. The thermoelectric properties were calculated by solving the Boltzmann transport equation within the constant relaxation time approximation. The obtained lattice parameters are in good agreement with the available experimental and other theoretical results. The calculated band gaps using the Tran-Blaha modified Becke-Johnson potential (TB-mBJ), of both compounds are in good agreement with the available experimental values. Thermoelectric properties like thermopower (S), electrical conductivity scaled by relaxation time (σ/τ) and power-factor (S2σ/τ) are calculated as functions of the carrier concentration and temperature for both compounds. The calculated thermoelectric properties are compared with the available experimental results of the similar material ScN.

  5. Thermoelectric properties of binary LnN (Ln=La and Lu): First principles study

    SciTech Connect

    Sreeparvathy, P. C.; Gudelli, Vijay Kumar; Kanchana, V.; Vaitheeswaran, G.; Svane, A.; Christensen, N. E.

    2015-06-24

    First principles density functional calculations were carried out to study the electronic structure and thermoelectric properties of LnN (Ln = La and Lu) using the full potential linearized augmented plane wave (FP-LAPW) method. The thermoelectric properties were calculated by solving the Boltzmann transport equation within the constant relaxation time approximation. The obtained lattice parameters are in good agreement with the available experimental and other theoretical results. The calculated band gaps using the Tran-Blaha modified Becke-Johnson potential (TB-mBJ), of both compounds are in good agreement with the available experimental values. Thermoelectric properties like thermopower (S), electrical conductivity scaled by relaxation time (σ/τ) and power-factor (S{sup 2}σ/τ) are calculated as functions of the carrier concentration and temperature for both compounds. The calculated thermoelectric properties are compared with the available experimental results of the similar material ScN.

  6. First principles investigation of the structure of a bacteriochlorophyll crystal

    SciTech Connect

    Marchi, M. |; Hutter, J.; Parrinello, M.

    1996-08-21

    In this communication we present an ab initio study of the crystal of methyl bacteriophorbide (MeBPheo) a, a bacteriochlorophyll derivative, and high-precision structure of which is available. Our main purpose has been to investigate the viability of the technique toward complex molecular systems relevant to biologically important phenomena, in this particular case photosynthesis. Here we present the following results: First, we show that DFT is capable of calculating nuclear positions in excellent agreement with the experimental X-ray structure. Second, the calculated electronic density of the HOMO orbital reveals a {pi} type bond between rings I and III, consistent with the one-dimensional chain structure of the MeBPheo a molecules in the crystal. Finally, after performing the optimization of the molecular geometry with one electron in the LUMO state, we find localized bond length changes near the ring II of the MeBPheo a. 19 refs., 3 figs.

  7. First principles-based multiscale modeling of ferroelectric polymers

    SciTech Connect

    Strachan, A. H.; Su, Haibin; Goddard, W. A. , III

    2004-01-01

    We use Density Functional Theory [within the generalized gradient approximation (DFT-GGA)] and molecular dynamics (MD) to characterize electromechanical properties of PVDF and its random copolymer with TrFE. Our simulations predict that large electrostrictive strains ({approx}5%) at extremely high frequencies (up to 10{sup 9} Hz) can be obtained in a poly(vinylidene fluoride) (PVDF) nano-actuator if the inter-chain packing density is appropriately chosen. We control the packing density by assembling the polymer chains on a Si <111> surface with 1/2 coverage. Under these conditions the equilibrium conformation of the polymer contains a combination of Gauche and Trans bonds which can be easily transformed to an all-Trans conformation by applying an electric field. Such molecular transformation is accompanied by a large deformation along the polymer chain direction.

  8. First principles study on the electronic structures and stability of Cr 7C 3 type multi-component carbides

    NASA Astrophysics Data System (ADS)

    Xiao, B.; Feng, J.; Zhou, C. T.; Xing, J. D.; Xie, X. J.; Chen, Y. H.

    2008-06-01

    First principles calculations were conducted to investigate the stabilities of six multi-component carbides of Cr 7C 3 by calculating the cohesive energy and formation enthalpy of them. The theoretical predictions were compared with the experimental results and they were in agreement with each other. The electronic structures of the six carbides were also calculated in order to provide more information about the relationship between the stability and crystal compositions at atomic scale.

  9. Ferroelectric Surface Chemistry: FIrst-principle study of NOx Decomposition

    NASA Astrophysics Data System (ADS)

    Kakekhani, Arvin; Ismail-Beigi, Sohrab

    2012-02-01

    NOx molecules are critical and regulated air pollutants produced during automotive combustion. As part of a long-term effort to design viable catalysts for NOx decomposition that operate at higher temperatures and thus would allow for greater fuel efficiency, we are studying NOx chemistry on ferroelectric perovskite surfaces. Changing the direction of the ferroelectric polarization can modify surface properties and thus can lead to switchable surface chemistry. We will discuss our results for NO and NO2 on the polar (001) surfaces of PbTiO3 as function of ferroelectric polarization, surface stoichiometry, and various molecular or dissociated binding modes.

  10. First-principles investigations on ionization and thermal conductivity of polystyrene for inertial confinement fusion applications

    DOE PAGES

    Hu, S. X.; Collins, L. A.; Goncharov, V. N.; Kress, J. D.; McCrory, R. L.; Skupsky, S.

    2016-04-14

    Using quantum molecular-dynamics (QMD) methods based on the density functional theory, we have performed first-principles investigations on the ionization and thermal conductivity of polystyrene (CH) over a wide range of plasma conditions (ρ = 0.5 to 100 g/cm3 and T = 15,625 to 500,000 K). The ionization data from orbital-free molecular-dynamics calculations have been fitted with a “Saha-type” model as a function of the CH plasma density and temperature, which exhibits the correct behaviors of continuum lowering and pressure ionization. The thermal conductivities (κQMD) of CH, derived directly from the Kohn–Sham molecular-dynamics calculations, are then analytically fitted with a generalizedmore » Coulomb logarithm [(lnΛ)QMD] over a wide range of plasma conditions. When compared with the traditional ionization and thermal conductivity models used in radiation–hydrodynamics codes for inertial confinement fusion simulations, the QMD results show a large difference in the low-temperature regime in which strong coupling and electron degeneracy play an essential role in determining plasma properties. Furthermore, hydrodynamic simulations of cryogenic deuterium–tritium targets with CH ablators on OMEGA and the National Ignition Facility using the QMD-derived ionization and thermal conductivity of CH have predicted –20% variation in target performance in terms of hot-spot pressure and neutron yield (gain) with respect to traditional model simulations.« less

  11. First-principles entropy calculations for liquid metals and warm dense matter

    NASA Astrophysics Data System (ADS)

    Desjarlais, Michael

    2013-06-01

    The total entropy is not an explicit or easily accessible quantity in first-principles molecular dynamics simulations. It is, however, an extremely important quantity for the calculation of total free energies and derived properties such as equilibrium phase boundaries. In shock experiments the entropy of the shock state determines the release isentrope. Recent advances in the calculation of the entropy for liquid metals and warm dense matter directly from the velocity history in quantum molecular dynamics simulations are presented. The method, a generalization of the 2PT method for classical molecular dynamics, significantly increases the accuracy of the method for systems with electronic entropy, spin degrees of freedom, and the softer interactions characteristic of liquid metals and warm dense matter. The results are compared to data and the results of indirect methods, such as coexistence simulations to determine phase boundaries. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  12. First-principles calculation of principal Hugoniot and K-shell X-ray absorption spectra for warm dense KCl

    SciTech Connect

    Zhao, Shijun; Zhang, Shen; Kang, Wei; Li, Zi; Zhang, Ping; He, Xian-Tu

    2015-06-15

    Principal Hugoniot and K-shell X-ray absorption spectra of warm dense KCl are calculated using the first-principles molecular dynamics (FPMD) method. Evolution of electronic structures as well as the influence of the approximate description of ionization on pressure (caused by the underestimation of the energy gap between conduction bands and valence bands) in the first-principles method are illustrated by the calculation. It is shown that approximate description of ionization in FPMD has small influence on Hugoniot pressure due to mutual compensation of electronic kinetic pressure and virial pressure. The calculation of X-ray absorption spectra shows that the band gap of KCl persists after the pressure ionization of the 3p electrons of Cl and K taking place at lower energy, which provides a detailed understanding to the evolution of electronic structures of warm dense matter.

  13. Development of a "First Principles" Water Potential with Flexible Monomers: Dimer Potential Energy Surface, VRT Spectrum, and Second Virial Coefficient.

    PubMed

    Babin, Volodymyr; Leforestier, Claude; Paesani, Francesco

    2013-12-10

    The development of a "first principles" water potential with flexible monomers (MB-pol) for molecular simulations of water systems from gas to condensed phases is described. MB-pol is built upon the many-body expansion of the intermolecular interactions, and the specific focus of this study is on the two-body term (V2B) representing the full-dimensional intermolecular part of the water dimer potential energy surface. V2B is constructed by fitting 40,000 dimer energies calculated at the CCSD(T)/CBS level of theory and imposing the correct asymptotic behavior at long-range as predicted from "first principles". The comparison of the calculated vibration-rotation tunneling (VRT) spectrum and second virial coefficient with the corresponding experimental results demonstrates the accuracy of the MB-pol dimer potential energy surface.

  14. First-principles calculation of ground and excited-state absorption spectra of ruby and alexandrite considering lattice relaxation

    NASA Astrophysics Data System (ADS)

    Watanabe, Shinta; Sasaki, Tomomi; Taniguchi, Rie; Ishii, Takugo; Ogasawara, Kazuyoshi

    2009-02-01

    We performed first-principles calculations of multiplet structures and the corresponding ground-state absorption and excited-state absorption spectra for ruby (Cr3+:α-Al2O3) and alexandrite (Cr3+:BeAl2O4) which included lattice relaxation. The lattice relaxation was estimated using the first-principles total energy and molecular-dynamics method of the CASTEP code. The multiplet structure and absorption spectra were calculated using the configuration-interaction method based on density-functional calculations. For both ruby and alexandrite, the theoretical absorption spectra, which were already in reasonable agreement with experimental spectra, were further improved by consideration of lattice relaxation. In the case of ruby, the peak positions and peak intensities were improved through the use of models with relaxations of 11 or more atoms. For alexandrite, the polarization dependence of the U band was significantly improved, even by a model with a relaxation of only seven atoms.

  15. First-principles Calculations of Nuclear Magnetic Resonance Chemical Shielding Tensors in Complex Ferroelectric Perovskites

    NASA Astrophysics Data System (ADS)

    Pechkis, Daniel Lawrence

    Nuclear magnetic resonance (NMR) spectroscopy is one of the most important experimental probes of local atomistic structure, chemical ordering, and dynamics. Recently, NMR has increasingly been used to study complex ferroelectric perovskite alloys, where spectra can be difficult to interpret. First-principles calculations of NMR spectra can greatly assist in this task. In this work, oxygen, titanium, and niobium NMR chemical shielding tensors, ŝ , were calculated with first-principles methods for ferroelectric transition metal prototypical ABO3 perovskites [SrTiO3, BaTiO 3, PbTiO3 and PbZrO3] and A(B,B')O3 perovskite alloys Pb(Zr1/2Ti1/2)O3 (PZT) and Pb(Mg1/3Nb2/3)O3 (PMN). The principal findings are 1) a large anisotropy between deshielded sigma xx(O) ≃ sigmayy(O) and shielded sigma zz(O) components; 2) a nearly linear dependence on nearest-distance transition-metal/oxygen bond length, rs, was found for both isotropic deltaiso(O) and axial deltaax(O) chemical shifts ( d̂=ŝ reference- ŝ ), across all the systems studied, with deltaiso(O) varying by ≃ 400 ppm; 3) the demonstration that the anisotropy and linear variation arise from large paramagnetic contributions to sigmaxx(O) and sigmayy(O), due to virtual transitions between O(2p) and unoccupied B(nd) states. Using these results, an argument against Ti clustering in PZT, as conjectured from recent 17O NMR magic-angle-spinning measurements, is made. The linear dependence of the chemical shifts on rs provides a scale for determining transition-metal/oxygen bond lengths from experimental 17O NMR spectra. As such, it can be used to assess the degree of local tetragonality in perovskite solid solutions for piezoelectric applications. Results for transition metal atoms show less structural sensitivity, compared to 17O NMR, in homovalent B-site materials, but could be more useful in heterovalent B-site perovskite alloys. This work shows that both 17O and B-site NMR spectroscopy, coupled with first principles

  16. First principles prediction of amorphous phases using evolutionary algorithms

    NASA Astrophysics Data System (ADS)

    Nahas, Suhas; Gaur, Anshu; Bhowmick, Somnath

    2016-07-01

    We discuss the efficacy of evolutionary method for the purpose of structural analysis of amorphous solids. At present, ab initio molecular dynamics (MD) based melt-quench technique is used and this deterministic approach has proven to be successful to study amorphous materials. We show that a stochastic approach motivated by Darwinian evolution can also be used to simulate amorphous structures. Applying this method, in conjunction with density functional theory based electronic, ionic and cell relaxation, we re-investigate two well known amorphous semiconductors, namely silicon and indium gallium zinc oxide. We find that characteristic structural parameters like average bond length and bond angle are within ˜2% of those reported by ab initio MD calculations and experimental studies.

  17. First principles prediction of amorphous phases using evolutionary algorithms.

    PubMed

    Nahas, Suhas; Gaur, Anshu; Bhowmick, Somnath

    2016-07-01

    We discuss the efficacy of evolutionary method for the purpose of structural analysis of amorphous solids. At present, ab initio molecular dynamics (MD) based melt-quench technique is used and this deterministic approach has proven to be successful to study amorphous materials. We show that a stochastic approach motivated by Darwinian evolution can also be used to simulate amorphous structures. Applying this method, in conjunction with density functional theory based electronic, ionic and cell relaxation, we re-investigate two well known amorphous semiconductors, namely silicon and indium gallium zinc oxide. We find that characteristic structural parameters like average bond length and bond angle are within ∼2% of those reported by ab initio MD calculations and experimental studies. PMID:27394098

  18. First Principles Charge Transfer Excitations in Curved Aromatic Materials

    NASA Astrophysics Data System (ADS)

    Zoppi, Laura; Martin Samos, Layla; Baldridge, Kim K.

    Understanding excitation properties and charge transport phenomena of curved π-conjugated materials is critical for a rational utilization of buckybowls as electrically active materials in solid-state devices. In this respect, the class of materials based on the smallest bowl-shaped fullerene fragment, corannulene, C20H10, offers a unique possibility for building up scaffolds with a tunable spectrum of structural and electronic properties. Here, GW-BSE based approaches are applied to investigation and prediction of charge transfer excitations of C20H10 materials systems at functional interfaces, with a special emphasis on design aspects of materials relevant in the experimental domain. Theoretical predictions together with experimental findings illustrate the possibility of integrating corannulene electronic functions in molecular devices

  19. First Principle Predictions of Isotopic Shifts in H2O

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Kwak, Dochan (Technical Monitor)

    2002-01-01

    We compute isotope independent first and second order corrections to the Born-Oppenheimer approximation for water and use them to predict isotopic shifts. For the diagonal correction, we use icMRCI wavefunctions and derivatives with respect to mass dependent, internal coordinates to generate the mass independent correction functions. For the non-adiabatic correction, we use scaled SCF/CIS wave functions and a generalization of the Handy method to obtain mass independent correction functions. We find that including the non-adiabatic correction gives significantly improved results compared to just including the diagonal correction when the Born-Oppenheimer potential energy surface is optimized for H2O-16. The agreement with experimental results for deuterium and tritium containing isotopes is nearly as good as our best empirical correction, however, the present correction is expected to be more reliable for higher, uncharacterized levels.

  20. Approaching actinide(+III) hydration from first principles.

    PubMed

    Wiebke, J; Moritz, A; Cao, X; Dolg, M

    2007-01-28

    A systematic computational approach to An(III) hydration on a density-functional level of theory, using quasi-relativistic 5f-in-core pseudopotentials and valence-only basis sets for the An(III) subsystems, is presented. Molecular structures, binding energies, hydration energies, and Gibbs free energies of hydration have been calculated for [An(III)(OH(2))(h)](3+) (h = 7, 8, 9) and [An(III)(OH(2))(h-1) * OH(2)](3+) (h = 8, 9), using large (7s6p5d2f1g)/[6s5p4d2f1g] An(III) and cc-pVQZ O and H basis sets within the COSMO implicit solvation model. An(III) preferred primary hydration numbers are found to be 8 for all An(III) at the gradient-corrected density-functional level of theory. Second-order Møller-Plesset perturbation theory predicts preferred primary hydration numbers of 9 and 8 for Ac(III)-Md(III) and No(III)-Lr(III), respectively.

  1. A generalized Poisson solver for first-principles device simulations

    NASA Astrophysics Data System (ADS)

    Bani-Hashemian, Mohammad Hossein; Brück, Sascha; Luisier, Mathieu; VandeVondele, Joost

    2016-01-01

    Electronic structure calculations of atomistic systems based on density functional theory involve solving the Poisson equation. In this paper, we present a plane-wave based algorithm for solving the generalized Poisson equation subject to periodic or homogeneous Neumann conditions on the boundaries of the simulation cell and Dirichlet type conditions imposed at arbitrary subdomains. In this way, source, drain, and gate voltages can be imposed across atomistic models of electronic devices. Dirichlet conditions are enforced as constraints in a variational framework giving rise to a saddle point problem. The resulting system of equations is then solved using a stationary iterative method in which the generalized Poisson operator is preconditioned with the standard Laplace operator. The solver can make use of any sufficiently smooth function modelling the dielectric constant, including density dependent dielectric continuum models. For all the boundary conditions, consistent derivatives are available and molecular dynamics simulations can be performed. The convergence behaviour of the scheme is investigated and its capabilities are demonstrated.

  2. A generalized Poisson solver for first-principles device simulations.

    PubMed

    Bani-Hashemian, Mohammad Hossein; Brück, Sascha; Luisier, Mathieu; VandeVondele, Joost

    2016-01-28

    Electronic structure calculations of atomistic systems based on density functional theory involve solving the Poisson equation. In this paper, we present a plane-wave based algorithm for solving the generalized Poisson equation subject to periodic or homogeneous Neumann conditions on the boundaries of the simulation cell and Dirichlet type conditions imposed at arbitrary subdomains. In this way, source, drain, and gate voltages can be imposed across atomistic models of electronic devices. Dirichlet conditions are enforced as constraints in a variational framework giving rise to a saddle point problem. The resulting system of equations is then solved using a stationary iterative method in which the generalized Poisson operator is preconditioned with the standard Laplace operator. The solver can make use of any sufficiently smooth function modelling the dielectric constant, including density dependent dielectric continuum models. For all the boundary conditions, consistent derivatives are available and molecular dynamics simulations can be performed. The convergence behaviour of the scheme is investigated and its capabilities are demonstrated. PMID:26827208

  3. First-Principles Computation of Graphene's Phonon Anharmonicity

    NASA Astrophysics Data System (ADS)

    Kornbluth, Mordechai; Marianetti, Chris A.

    Here we use density-functional theory to compute an interatomic potential for graphene, including anharmonicities up to at least fourth order. We generate all group-theoretically allowed terms within a hexagon via the recently-developed slave mode expansion. This expands the potential in terms of the normal modes of overlapping hexagons, while obeying the space group symmetry and homogeneity of free space. We further introduce the notion of cooperative modes, which combine strain and q = 0 phonons to yield the same pure mode amplitude on each hexagon. Within the cooperative subspace, cooperative modes allow for arbitrarily-precise meshing to directly compute energies, or calculation of the anharmonic coefficients via finite-difference. We demonstrate the power of our approach in the context of strained graphene, which is known to have a novel strain-driven soft mode at the K-point. We identify the dominant anharmonic terms which drive the soft K mode, and study the role of finite temperatures using molecular dynamics and Monte-Carlo simulations.

  4. Large scale molecular simulations of nanotoxicity.

    PubMed

    Jimenez-Cruz, Camilo A; Kang, Seung-gu; Zhou, Ruhong

    2014-01-01

    The widespread use of nanomaterials in biomedical applications has been accompanied by an increasing interest in understanding their interactions with tissues, cells, and biomolecules, and in particular, on how they might affect the integrity of cell membranes and proteins. In this mini-review, we present a summary of some of the recent studies on this important subject, especially from the point of view of large scale molecular simulations. The carbon-based nanomaterials and noble metal nanoparticles are the main focus, with additional discussions on quantum dots and other nanoparticles as well. The driving forces for adsorption of fullerenes, carbon nanotubes, and graphene nanosheets onto proteins or cell membranes are found to be mainly hydrophobic interactions and the so-called π-π stacking (between aromatic rings), while for the noble metal nanoparticles the long-range electrostatic interactions play a bigger role. More interestingly, there are also growing evidences showing that nanotoxicity can have implications in de novo design of nanomedicine. For example, the endohedral metallofullerenol Gd@C₈₂(OH)₂₂ is shown to inhibit tumor growth and metastasis by inhibiting enzyme MMP-9, and graphene is illustrated to disrupt bacteria cell membranes by insertion/cutting as well as destructive extraction of lipid molecules. These recent findings have provided a better understanding of nanotoxicity at the molecular level and also suggested therapeutic potential by using the cytotoxicity of nanoparticles against cancer or bacteria cells.

  5. Magnetoresistance in multilayer fullerene spin valves: A first-principles study

    NASA Astrophysics Data System (ADS)

    ćakır, Deniz; Otálvaro, Diana M.; Brocks, Geert

    2014-12-01

    Carbon-based molecular semiconductors are explored for application in spintronics because their small spin-orbit coupling promises long spin lifetimes. We calculate the electronic transport from first principles through spin valves comprising bi- and tri-layers of the fullerene molecules C60 and C70, sandwiched between two Fe electrodes. The spin polarization of the current, and the magnetoresistance depend sensitively on the interactions at the interfaces between the molecules and the metal surfaces. They are much less affected by the thickness of the molecular layers. A high current polarization (CP >90 %) and magnetoresistance (MR >100 %) at small bias can be attained using C70 layers. In contrast, the current polarization and the magnetoresistance at small bias are vanishingly small for C60 layers. Exploiting a generalized Jullière model we can trace the differences in spin-dependent transport between C60 and C70 layers to differences between the molecule-metal interface states. These states also allow one to interpret the current polarization and the magnetoresistance as a function of the applied bias voltage.

  6. Probing adhesion forces at the molecular scale

    SciTech Connect

    Thomas, R.C.; Houston, J.E.; Michalske, T.A.

    1996-12-31

    Measurements of adhesion forces at the molecular scale, such as those discussed here, are necessary to understand macroscopic boundary-layer behavior such as adhesion, friction, wear, lubrication, and many other important phenomena. The authors` recent interfacial force microscopy (IFM) studies have provided detailed information about the mechanical response of both self-assembled monolayer (SAM) films and the underlying substrates. In addition, they recently demonstrated that the IFM is useful for studying the chemical nature of such films. In this talk, the authors discuss a new method for studying surface interactions and chemical reactions using the IFM. To quantitatively measure the work of adhesion and bond energies between two organic thin films, they modify both a Au substrate and a Au probe with self-assembling organomercaptan molecules having either the same or different end groups (-CH{sub 3}, -NH{sub 2}, and -COOH), and then analyze the force-versus-displacement curves (force profiles) that result from the approach to contact of the two surfaces. Their results show that the magnitude of the adhesive forces measured between methyl-methyl interactions are in excellent agreement with van der Waals calculations using Lifshitz theory and previous experimentally determined values. Moreover, the measured peak adhesive forces scale as expected for van der Waals, hydrogen-bonding, and acid-base interactions.

  7. Plane Wave First-principles Materials Science Codes on Multicore Supercomputer Architectures

    NASA Astrophysics Data System (ADS)

    Canning, Andrew; Deslippe, Jack; Louie, Steven. G.; Scidac Team

    2014-03-01

    Plane wave first-principles codes based on 3D FFTs are one of the largest users of supercomputer cycles in the world. Modern supercomputer architectures are constructed from chips having many CPU cores with nodes containing multiple chips. Designs for future supercomputers are projected to have even more cores per chip. I will present new developments for hybrid MPI/OpenMP PW codes focusing on a specialized 3D FFTs that gives greatly improved scaling over a pure MPI version on multicore machines. Scaling results will be presented for the full electronic structure codes PARATEC and BerkeleyGW. using the new hybrid 3D FFTs, threaded libraries and OpenMP to gain greatly improved scaling to very large core count on Cray and IBM machines. Support for this work was provided through the Scientific Discovery through Advanced Computing (SciDAC) program funded by U.S. Department of Energy, Office of Science, Advanced Scientific Computing Research (and Basic Energy Sciences).

  8. First principles based multiparadigm modeling of electronic structures and dynamics

    NASA Astrophysics Data System (ADS)

    Xiao, Hai

    enabling the tunability of CBO. We predict that Na further improves the CBO through electrostatically elevating the valence levels to decrease the CBO, explaining the observed essential role of Na for high performance. Moreover we find that K leads to a dramatic decrease in the CBO to 0.05 eV, much better than Na. We suggest that the efficiency of CIGS devices might be improved substantially by tuning the ratio of Na to K, with the improved phase stability of Na balancing phase instability from K. All these defects reduce interfacial stability slightly, but not significantly. A number of exotic structures have been formed through high pressure chemistry, but applications have been hindered by difficulties in recovering the high pressure phase to ambient conditions (i.e., one atmosphere and room temperature). Here we use dispersion-corrected DFT (PBE-ulg flavor) to predict that above 60 GPa the most stable form of N2O (the laughing gas in its molecular form) is a 1D polymer with an all-nitrogen backbone analogous to cis-polyacetylene in which alternate N are bonded (ionic covalent) to O. The analogous trans-polymer is only 0.03-0.10 eV/molecular unit less stable. Upon relaxation to ambient conditions both polymers relax below 14 GPa to the same stable non-planar trans-polymer, accompanied by possible electronic structure transitions. The predicted phonon spectrum and dissociation kinetics validate the stability of this trans-poly-NNO at ambient conditions, which has potential applications as a new type of conducting polymer with all-nitrogen chains and as a high-energy oxidizer for rocket propulsion. This work illustrates in silico materials discovery particularly in the realm of extreme conditions. Modeling non-adiabatic electron dynamics has been a long-standing challenge for computational chemistry and materials science, and the eFF method presents a cost-efficient alternative. However, due to the deficiency of FSG representation, eFF is limited to low-Z elements with

  9. First principles Candu fuel model and validation experimentation

    SciTech Connect

    Corcoran, E.C.; Kaye, M.H.; Lewis, B.J.; Thompson, W.T.; Akbari, F.; Higgs, J.D.; Verrall, R.A.; He, Z.; Mouris, J.F.

    2007-07-01

    Many modeling projects on nuclear fuel rest on a quantitative understanding of the co-existing phases at various stages of burnup. Since the various fission products have considerably different abilities to chemically associate with oxygen, and the O/M ratio is slowly changing as well, the chemical potential (generally expressed as an equivalent oxygen partial pressure) is a function of burnup. Concurrently, well-recognized small fractions of new phases such as inert gas, noble metals, zirconates, etc. also develop. To further complicate matters, the dominant UO{sub 2} fuel phase may be non-stoichiometric and most of minor phases have a variable composition dependent on temperature and possible contact with the coolant in the event of a sheathing defect. A Thermodynamic Fuel Model to predict the phases in partially burned Candu nuclear fuel containing many major fission products has been under development. This model is capable of handling non-stoichiometry in the UO{sub 2} fluorite phase, dilute solution behaviour of significant solute oxides, noble metal inclusions, a second metal solid solution U(Pd-Rh-Ru)3, zirconate and uranate solutions as well as other minor solid phases, and volatile gaseous species. The treatment is a melding of several thermodynamic modeling projects dealing with isolated aspects of this important multi-component system. To simplify the computations, the number of elements has been limited to twenty major representative fission products known to appear in spent fuel. The proportion of elements must first be generated using SCALES-5. Oxygen is inferred from the concentration of the other elements. Provision to study the disposition of very minor fission products is included within the general treatment but these are introduced only on an as needed basis for a particular purpose. The building blocks of the model are the standard Gibbs energies of formation of the many possible compounds expressed as a function of temperature. To these data

  10. First-principles investigations on ionization and thermal conductivity of polystyrene for inertial confinement fusion applications

    NASA Astrophysics Data System (ADS)

    Hu, S. X.; Collins, L. A.; Goncharov, V. N.; Kress, J. D.; McCrory, R. L.; Skupsky, S.

    2016-04-01

    Using quantum molecular-dynamics (QMD) methods based on the density functional theory, we have performed first-principles investigations of the ionization and thermal conductivity of polystyrene (CH) over a wide range of plasma conditions (ρ = 0.5 to 100 g/cm3 and T = 15 625 to 500 000 K). The ionization data from orbital-free molecular-dynamics calculations have been fitted with a "Saha-type" model as a function of the CH plasma density and temperature, which gives an increasing ionization as the CH density increases even at low temperatures (T < 50 eV). The orbital-free molecular dynamics method is only used to gauge the average ionization behavior of CH under the average-atom model in conjunction with the pressure-matching mixing rule. The thermal conductivities (κQMD) of CH, derived directly from the Kohn-Sham molecular-dynamics calculations, are then analytically fitted with a generalized Coulomb logarithm [(lnΛ)QMD] over a wide range of plasma conditions. When compared with the traditional ionization and thermal conductivity models used in radiation-hydrodynamics codes for inertial confinement fusion simulations, the QMD results show a large difference in the low-temperature regime in which strong coupling and electron degeneracy play an essential role in determining plasma properties. Hydrodynamic simulations of cryogenic deuterium-tritium targets with CH ablators on OMEGA and the National Ignition Facility using the QMD-derived ionization and thermal conductivity of CH have predicted ˜20% variation in target performance in terms of hot-spot pressure and neutron yield (gain) with respect to traditional model simulations.

  11. First-principles calculation of thermodynamic stability of acids and bases under pH environment: A microscopic pH theory

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

    Despite being one of the most important thermodynamic variables, pH has yet to be incorporated into first-principles thermodynamics to calculate stability of acidic and basic solutes in aqueous solutions. By treating the solutes as defects in homogeneous liquids, we formulate a first-principles approach to calculate their formation energies under proton chemical potential, or pH, based on explicit molecular dynamics. The method draws analogy to first-principle calculations of defect formation energies under electron chemical potential, or Fermi energy, in semiconductors. From this, we propose a simple pictorial representation of the general theory of acid-base chemistry. By performing first-principles molecular dynamics of liquid water models with solutes, we apply the formulation to calculate formation energies of various neutral and charged solutes such as H+, OH-, NH3, NH4+, HCOOH, and HCOO- in water. The deduced auto-dissociation constant of water and the difference in the pKa values of NH3 and HCOOH show good agreement with known experimental values. Our first-principles approach can be further extended and applied to other bio- and electro-chemical molecules such as amino acids and redox reaction couples that could exist in aqueous environments to understand their thermodynamic stability.

  12. First-Principles Calculation of Thermodynamic Stability of Acids and Bases under pH Environment: A Microscopic pH Theory

    SciTech Connect

    Kim, Y. H.; Kim, K.; Zhang, S. B.

    2012-04-07

    Despite being one of the most important thermodynamic variables, pH has yet to be incorporated into first-principles thermodynamics to calculate stability of acidic and basic solutes in aqueous solutions. By treating the solutes as defects in homogeneous liquids, we formulate a first-principles approach to calculate their formation energies under proton chemical potential, or pH, based on explicit molecular dynamics. The method draws analogy to first-principle calculations of defect formation energies under electron chemical potential, or Fermi energy, in semiconductors. From this, we propose a simple pictorial representation of the general theory of acid-base chemistry. By performing first-principles molecular dynamics of liquid water models with solutes, we apply the formulation to calculate formation energies of various neutral and charged solutes such as H{sup +}, OH{sup -}, NH{sub 3}, NH{sub 4}{sup +}, HCOOH, and HCOO{sup -} in water. The deduced auto-dissociation constant of water and the difference in the pKa values of NH{sub 3} and HCOOH show good agreement with known experimental values. Our first-principles approach can be further extended and applied to other bio- and electro-chemical molecules such as amino acids and redox reaction couples that could exist in aqueous environments to understand their thermodynamic stability.

  13. First-principles calculation of thermodynamic stability of acids and bases under pH environment: a microscopic pH theory.

    PubMed

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

    2012-04-01

    Despite being one of the most important thermodynamic variables, pH has yet to be incorporated into first-principles thermodynamics to calculate stability of acidic and basic solutes in aqueous solutions. By treating the solutes as defects in homogeneous liquids, we formulate a first-principles approach to calculate their formation energies under proton chemical potential, or pH, based on explicit molecular dynamics. The method draws analogy to first-principle calculations of defect formation energies under electron chemical potential, or Fermi energy, in semiconductors. From this, we propose a simple pictorial representation of the general theory of acid-base chemistry. By performing first-principles molecular dynamics of liquid water models with solutes, we apply the formulation to calculate formation energies of various neutral and charged solutes such as H(+), OH(-), NH(3), NH(4)(+), HCOOH, and HCOO(-) in water. The deduced auto-dissociation constant of water and the difference in the pKa values of NH(3) and HCOOH show good agreement with known experimental values. Our first-principles approach can be further extended and applied to other bio- and electro-chemical molecules such as amino acids and redox reaction couples that could exist in aqueous environments to understand their thermodynamic stability. PMID:22482545

  14. High P-T experiments and first principles calculations of the diffusion of Si, O, Cr in liquid iron

    NASA Astrophysics Data System (ADS)

    Posner, Esther; Rubie, David C.; Frost, Daniel J.; Vlček, Vojtěch; Steinle-Neumann, Gerd

    2016-04-01

    Diffusion transport properties of molten iron and iron alloys at high pressures and temperatures are important for understanding large-scale geodynamic processes and thermochemical evolution of planetary interiors, such as the time and length scales of metal-silicate equilibration during core formation and chemical exchange across core-mantle boundaries during cooling. The density of the Earth's outer core is ˜10% too low to be composed of pure Fe-Ni and is assumed to contain significant concentrations of light elements, such as Si, S, O, and/or C, in addition to siderophile transition metals (V, Cr, Mn, W) which are depleted in the Earth's mantle relative to chondrites. The chemical diffusivity of light and siderophile elements in liquid iron under P -T conditions of the Earth's core and its formation are therefore required to constrain the composition and potential chemical stratification of planetary cores, in addition to the kinetics of chemical buoyancy from inner core crystallization that partially drives the geodynamo. In order to better understand the effects of pressure and temperature on Si, O, and Cr diffusion in liquid iron, we have conducted (1) chemical diffusion-couple experiments combined with numerical modeling of diffusion profiles to account for non-isothermal annealing, and (2) first principles molecular dynamic (FP-MD) calculations from ambient pressure to 135 GPa and 2200-5500 K. Experimental diffusion couples comprised of highly polished cylindrical disks of 99.97% Fe and metallic Fe alloy were contained within an MgO capsule and annealed within the P -T range 1873-2653 K and 1-18 GPa using a multi-anvil apparatus. A series of experiments are conducted at each pressure using variable heating rates, final quench temperatures (Tf), and time duration at Tf. Recovered capsules were cut and polished parallel to the axis of the cylindrical sample and measured using EMPA 10 μm-step line scans. To extend our dataset to P -T conditions of the Earth

  15. High P-T experiments and first principles calculations of the diffusion of Si, O, Cr in liquid iron

    NASA Astrophysics Data System (ADS)

    Posner, Esther; Rubie, David C.; Frost, Daniel J.; Vlček, Vojtěch; Steinle-Neumann, Gerd

    2016-04-01

    Diffusion transport properties of molten iron and iron alloys at high pressures and temperatures are important for understanding large-scale geodynamic processes and thermochemical evolution of planetary interiors, such as the time and length scales of metal-silicate equilibration during core formation and chemical exchange across core-mantle boundaries during cooling. The density of the Earth's outer core is ˜10% too low to be composed of pure Fe-Ni and is assumed to contain significant concentrations of light elements, such as Si, S, O, and/or C, in addition to siderophile transition metals (V, Cr, Mn, W) which are depleted in the Earth's mantle relative to chondrites. The chemical diffusivity of light and siderophile elements in liquid iron under P -T conditions of the Earth's core and its formation are therefore required to constrain the composition and potential chemical stratification of planetary cores, in addition to the kinetics of chemical buoyancy from inner core crystallization that partially drives the geodynamo. In order to better understand the effects of pressure and temperature on Si, O, and Cr diffusion in liquid iron, we have conducted (1) chemical diffusion-couple experiments combined with numerical modeling of diffusion profiles to account for non-isothermal annealing, and (2) first principles molecular dynamic (FP-MD) calculations from ambient pressure to 135 GPa and 2200-5500 K. Experimental diffusion couples comprised of highly polished cylindrical disks of 99.97% Fe and metallic Fe alloy were contained within an MgO capsule and annealed within the P -T range 1873-2653 K and 1-18 GPa using a multi-anvil apparatus. A series of experiments are conducted at each pressure using variable heating rates, final quench temperatures (Tf), and time duration at Tf. Recovered capsules were cut and polished parallel to the axis of the cylindrical sample and measured using EMPA 10 μm-step line scans. To extend our dataset to P -T conditions of the Earth

  16. First-principles investigation of cubic BaRuO3: A Hund's metal

    NASA Astrophysics Data System (ADS)

    Dasari, Nagamalleswararao; Yamijala, S. R. K. C. Sharma; Jain, Manish; Dasgupta, T. Saha; Moreno, Juana; Jarrell, Mark; Vidhyadhiraja, N. S.

    2016-08-01

    A first-principles investigation of cubic BaRuO3, by combining density functional theory with dynamical mean-field theory and a hybridization expansion continuous time quantum Monte Carlo solver, has been carried out. Nonmagnetic calculations with appropriately chosen on-site Coulomb repulsion U and Hund's exchange J for single-particle dynamics and static susceptibility show that cubic BaRuO3 is in a spin-frozen state at temperatures above the ferromagnetic transition point. A strong redshift with increasing J of the peak in the real frequency dynamical susceptibility indicates a dramatic suppression of the Fermi liquid coherence scale as compared to the bare parameters in cubic BaRuO3. The self-energy also shows clear deviation from Fermi liquid behavior that manifests in the single-particle spectrum. Such a clean separation of energy scales in this system provides scope for an incoherent spin-frozen (SF) phase that extends over a wide temperature range, to manifest in non-Fermi liquid behavior and to be the precursor for the magnetically ordered ground state.

  17. How to generate a significant effective temperature for cold dark matter, from first principles

    NASA Astrophysics Data System (ADS)

    McDonald, Patrick

    2011-04-01

    I show how to reintroduce velocity dispersion into perturbation theory (PT) calculations of structure in the Universe, i.e., how to go beyond the pressureless fluid approximation, starting from first principles. This addresses a possible deficiency in uses of PT to compute clustering on the weakly non-linear scales that will be critical for probing dark energy. Specifically, I show how to derive a non-negligible value for the (initially tiny) velocity dispersion of dark matter particles, langleδν2rangle , where δν is the deviation of particle velocities from the local bulk flow. The calculation is essentially a renormalization of the homogeneous (zero order) dispersion by fluctuations 1st order in the initial power spectrum. For power law power spectra with n > -3, the small-scale fluctuations diverge and significant dispersion can be generated from an arbitrarily small starting value — the dispersion level is set by an equilibrium between fluctuations generating more dispersion and dispersion suppressing fluctuations. For an n = -1.4 power law normalized to match the present non-linear scale, the dispersion would be ~ 100kms-1. This n corresponds roughly to the slope on the non-linear scale in the real ΛCDM Universe, but ΛCDM contains much less initial small-scale power — not enough to bootstrap the small starting dispersion up to a significant value within linear theory (viewed very broadly, structure formation has actually taken place rather suddenly and recently, in spite of the usual ``hierarchical'' description). The next order PT calculation drives the ΛCDM dispersion up into balance with growing structure, and should eventually account for dispersion effects seen recently in simulations (I have not yet carried out that calculation).

  18. A first principles study on the CVD graphene growth on copper surfaces: A carbon atom incorporation to graphene edges

    NASA Astrophysics Data System (ADS)

    Tajima, Nobuo; Kaneko, Tomoaki; Nara, Jun; Ohno, Takahisa

    2016-11-01

    Carbon atom reactions in the chemical vapor deposition (CVD) processes for graphene production on copper surfaces have been studied by first principles molecular dynamics (MD) simulations at a typical CVD growth temperature. This study focuses on the processes of a carbon atom incorporation to graphene edges. The energy barriers of these carbon atom incorporation reactions have been calculated as ~ 1 eV, which are comparable or slightly larger than the barriers of carbon atom dimerization. We have also found that the surface copper atoms form step like structures to terminate the carbon dangling bonds at graphene edges, which are markedly different from the graphene-copper interactions observed in static calculations.

  19. Structure of hydrophobic hydration of benzene and hexafluorobenzene from first principles

    SciTech Connect

    Allesch, M; Schwegler, E; Galli, G

    2006-10-23

    We report on the aqueous hydration of benzene and hexafluorobenzene, as obtained by carrying out extensive (>100 ps) first principles molecular dynamics simulations. Our results show that benzene and hexafluorobenzene do not behave as ordinary hydrophobic solutes, but rather present two distinct regions, one equatorial and the other axial, that exhibit different solvation properties. While in both cases the equatorial regions behave as typical hydrophobic solutes, the solvation properties of the axial regions depend strongly on the nature of the {pi}-water interaction. In particular, {pi}-hydrogen and {pi}-lone pair interactions are found to dominate in benzene and hexafluorobenzene, respectively, which leads to substantially different orientations of water near the two solutes. We present atomic and electronic structure results (in terms of Maximally Localized Wannier Functions) providing a microscopic description of benzene- and hexafluorobenzene-water interfaces, as well as a comparative study of the two solutes. Our results point at the importance of an accurate description of interfacial water in order to characterize hydration properties of apolar molecules, as these are strongly influenced by subtle charge rearrangements and dipole moment redistributions in interfacial regions.

  20. First-Principles Investigations on Thermal Conductivity and Average Ionization of CH Ablators Under Extreme Conditions

    NASA Astrophysics Data System (ADS)

    Hu, S. X.; Goncharov, V. N.; McCrory, R. L.; Skupsky, S.; Collins, L. A.; Kress, J. D.

    2015-11-01

    A plastic CH ablator (polystyrene) is often used for inertial confinement fusion (ICF) target designs. Upon intense laser or x-ray ablations, a CH ablator can be shocked to warm-dense-matter (WDM) conditions. Many-body coupling and quantum electron degeneracy are expected to play an essential role in determining the properties of such warm dense plasmas. Using ab initio methods of quantum molecular dynamics (QMD), we have performed investigations on the principal Hugoniot of a CH ablator, the first-principles equation-of-state table of CH, and its effect on ICF simulations. In this presentation, we focus on the thermal conductivity and average ionization of CH-ablators under a wide range of plasma temperatures and densities. The resulting thermal conductivity (κ) and average ionization () show large differences from the usual model predictions in the WDM regime. These results, being fitted with analytical functions of plasma density and temperature, have been incorporated into radiation -hydrodynamics codes. Their effects on the ICF implosion simulations will be presented. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944 and the Scientific Campaign 10 at LANL under Contract No. DE-AC52-06NA25396.

  1. Electronic and magnetic properties of nonmetal atoms doped blue phosphorene: First-principles study

    NASA Astrophysics Data System (ADS)

    Zheng, Huiling; Yang, Hui; Wang, Hongxia; Du, Xiaobo; Yan, Yu

    2016-06-01

    Using first-principles calculations, we study the geometrical structure, electronic structure and magnetic properties of substitutionally doped blue phosphorene with a series of nonmetallic atoms, including F, Cl, B, N, C, Si and O. The calculated formation energies and molecular dynamics simulations indicate that F, Cl, B, N, C, Si and O doped blue phosphorene are stable. Moreover, the substitutional doping of F, Cl, B and N cannot induce the magnetism in blue phosphorene due to the saturation or pairing of the valence electron of dopant and its neighboring P atoms. In contrast, ground states of C, Si and O doped blue phosphorene are spin-polarized and the magnetic moments induced by a doping atom are all 1.0 μB, which is attributed to the appearance of an unpaired valence electron of C and Si and the formation of a nonbonding 3p electron of a neighboring P atom around O. Furthermore, the magnetic coupling between the moments induced by two C, Si and O are found to be long-range anti-ferromagnetic and the origin of the coupling can be attributed to the p-p hybridization interaction involving polarized electrons.

  2. First-principles based atomistic modeling of phase stability in PMN-xPT.

    PubMed

    Sepliarsky, M; Cohen, R E

    2011-11-01

    We have performed molecular dynamics simulations using a shell model potential developed by fitting first-principles results to describe the behavior of the relaxor-ferroelectric (1 - x)PbMg(1/3)Nb(2/3)O(3)-xPbTiO(3) (PMN-xPT) as a function of concentration and temperature, using site occupancies within the random site model. In our simulations, PMN is cubic at all temperatures and behaves as a polar glass. As a small amount of Ti is added, a weak polar state develops, but structural disorder dominates, and the symmetry is rhombohedral. As more Ti is added the ground state is clearly polar and the system is ferroelectric, but with easy rotation of the polarization direction. In the high Ti content region, the solid solution adopts ferroelectric behavior similar to PT, with tetragonal symmetry. The ground state sequence with increasing Ti content is R-M(B)-O-M(C)-T. The high-temperature phase is cubic at all compositions. Our simulations give the slopes of the morphotropic phase boundaries, crucial for high-temperature applications. We find that the phase diagram of PMN-xPT can be understood within the random site model. PMID:21997277

  3. Assembling a bi-coordinated Cr complex for ferromagnetic nanorings: insight from first-principles calculations.

    PubMed

    Zhu, Guizhi; Liu, Junyi; Sun, Qiang; Jena, Puru

    2016-07-21

    Motivated by the recent synthesis of bi-coordinated transition metal-organic complexes [Samuel, et al., Chem. Sci., 2015, 6, 3148], we have studied the structure and magnetic properties of a series of bi-coordinated transition metal based nanorings by folding quasi-1D chains. Among the cyclic alkyl(amino)carbine (CAAC) based quasi-1D chains (TM-CAAC, TM = Cr, Mn, Fe, Co, Ni), only Cr-CAAC is found to be ferromagnetic. First-principles calculations combined with Heisenberg-Dirac-van Vleck models were performed to understand the onset of robust ferromagnetism in Cr-based systems. With increasing size, the infrared intensity increases and the exchange energy oscillates. In particular, when the number, n, of TM-CAAC units is even and larger than 3, the magnetic coupling in nanorings is stronger than that in quasi-1D chains. The band gap changes very slowly with size. More importantly, compared with the highly coordinated Cr single molecular magnets, the low coordination of Cr ions enhances magnetic moment and stabilizes ferromagnetic coupling. PMID:27315141

  4. First-principles study of the stability of calcium-decorated carbon nanostructures

    NASA Astrophysics Data System (ADS)

    Cazorla, C.; Shevlin, S. A.; Guo, Z. X.

    2010-10-01

    In view of the interest in calcium-decorated carbon nanostructures motivated by potential biotechnological and nanotechnological applications, we have carried out a systematic and thorough first-principles computational study of the energetic and structural properties of these systems. We use density-functional theory (DFT) and ab initio molecular dynamic simulations to determine minimum energy configurations, binding energy profiles and the thermodynamic stability of Ca-decorated graphene and carbon nanotubes (CNT) as function of doping concentration. In graphene, we predict the existence of an equilibrium (3×3)R30° commensurate CaC6 monolayer that remains stable without clustering at low and room temperatures. For carbon nanotubes, we demonstrate that uniformly Ca-decorated zigzag (n≤10,0) CNT become stable against clustering at moderately large doping concentrations while Ca-coated armchair (n,n) CNT exhibit a clear thermodynamic tendency for Ca aggregation. In both Ca-doped graphene and CNT systems, we estimate large energy barriers (˜1eV) for atomic aggregation processes, which indicates that Ca clustering in carbon nanosurfaces may be kinematically hindered. Finally, we demonstrate via comparison of DFT and Møller-Plesset second-order perturbation calculations that DFT underestimates significantly the weak interaction between a Ca dopant and a coronene molecule, and also that the Ca-coronene system is not physically comparable to Ca-doped graphene due to lack of electronic π-d orbitals hybridization near the Fermi energy level.

  5. Infrared radiative properties of alumina up to the melting point: A first-principles study

    NASA Astrophysics Data System (ADS)

    Yang, J. Y.; Xu, M.; Liu, L. H.

    2016-11-01

    The high thermal emission of alumina dominates the radiative heat transfer of rocket exhaust plume. Yet numerous experimental measurements on radiative properties of alumina at high temperatures vary considerably from each other and cannot provide physical insight into the underlying mechanism. In this work, the ab initio molecular dynamics (AIMD) method and ab initio parameterized Drude model are combined to predict the radiative properties of alumina for temperatures up to 2327 K (the melting point) in the spectral range 1-12 μm. Contributed by different microscopic processes, the optical absorption of alumina in the spectral range 1-4 and 4-12 μm is described by two distinct methods. In the spectral range 4-12 μm, the multi-phonon process mainly contributes to optical absorption and can be simulated by the AIMD method based on the linear response theory. While in the spectral range 1-4 μm, the optical absorption is mainly caused by intrinsic carriers and can be effectively described by the ab initio parameterized Drude model. The first-principles calculations can successfully predict the infrared radiative properties of alumina at high temperatures and well reproduce the literature experiments. Moreover, the theoretical simulations verify that alumina can retain its semiconducting character even in the liquid phase and there emerges sharp increase in the near-infrared optical absorption of alumina upon melting.

  6. 2-Chlorophenol adsorption on Cu(1 0 0): First-principles density functional study

    NASA Astrophysics Data System (ADS)

    Altarawneh, Mohammednoor; Radny, Marian W.; Smith, Phillip V.; Mackie, John C.; Kennedy, Eric M.; Dlugogorski, Bogdan Z.

    2008-04-01

    Interactions between a 2-chlorophenol molecule and the Cu(1 0 0) surface have been analyzed using a first-principles density functional theory (DFT) plane-wave method as the first step in gaining a detailed understanding at the molecular level of the copper catalyzed formation of PCDD/F's (dioxin compounds). While the 2-chlorophenol molecule is found to be only very weakly bound to the Cu(1 0 0) surface in a number of vertical and flat-lying configurations, its dissociation into either 2-hydroxyl-phenyl (C 6H 4OH) or benzyne (C 6H 4) results in chemisorption on the surface. The dissociative reaction (2-chlorophenol + Cu surface → 2-chlorophenoxy + H-Cu surface), which is an initial and key step in the catalytic process, is also found to be exothermic on two considered sites. The 2-chlorophenoxy radical on the Cu(1 0 0) surface transforms into a mono chloro-phenolate and is more stable than the gas-phase species by about 1.74 eV. The most stable configurations occur when the benzyne moiety, hydroxyl group and chlorine atom are all separately chemisorbed on the surface with an overall stability of 0.97 eV.

  7. Isolation of pristine MXene from Nb₄AlC₃ MAX phase: a first-principles study.

    PubMed

    Mishra, Avanish; Srivastava, Pooja; Mizuseki, Hiroshi; Lee, Kwang-Ryeol; Singh, Abhishek K

    2016-04-28

    Synthesis of pristine MXene sheets from MAX phase is one of the foremost challenges in getting a complete understanding of the properties of this new technologically important 2D-material. Efforts to exfoliate Nb4AlC3 MAX phase always lead to Nb4C3 MXene sheets, which are functionalized and have several Al atoms attached. Using the first-principles calculations, we perform an intensive study on the chemical transformation of MAX phase into MXene sheets by inserting HF, alkali atoms and LiF in Nb4AlC3 MAX phase. Calculated bond-dissociation energy (BDE) shows that the presence of HF in MAX phase always results in functionalized MXene, as the binding of H with MXene is quite strong while that with F is weak. Insertion of alkali atoms does not facilitate pristine MXene isolation due to the presence of chemical bonds of almost equal strength. In contrast, weak Li-MXene and strong Li-F bonding in Nb4AlC3 with LiF ensured strong anisotropy in BDE, which will result in the dissociation of the Li-MXene bond. Ab initio molecular dynamics calculations capture these features and show that at 500-650 K, the Li-MXene bond indeed breaks leaving a pristine MXene sheet behind. The approach and insights developed here for chemical exfoliation of layered materials bonded by chemical bonds instead of van der Waals can promote their experimental realization. PMID:27045339

  8. First-principles study of amorphous Ga4Sb6Te3 phase-change alloys

    NASA Astrophysics Data System (ADS)

    Bouzid, Assil; Gabardi, Silvia; Massobrio, Carlo; Boero, Mauro; Bernasconi, Marco

    2015-05-01

    First-principles molecular dynamics simulations within the density functional theory framework were performed to generate amorphous models of the Ga4Sb6Te3 phase change alloy by quenching from the melt. We find that Ga-Sb and Ga-Te are the most abundant bonds with only a minor amount of Sb-Te bonds participating to the alloy network. Ga and four-coordinated Sb atoms present a tetrahedral-like geometry, whereas three-coordinated Sb atoms are in a pyramidal configuration. The tetrahedral-like geometries are similar to those of the crystalline phase of the two binary compounds GaTe and GaSb. A sizable fraction of Sb-Sb bonds is also present, indicating a partial nanoscale segregation of Sb. Despite the fact that the composition Ga4Sb6Te3 lies on the pseudobinary Ga Sb -Sb2Te3 tie line, the amorphous network can be seen as a mixture of the two binary compounds GaTe and GaSb with intertwined elemental Sb.

  9. Water confined in nanotubes and between graphene sheets: A first principle study

    SciTech Connect

    Cicero, G; Grossman, J C; Schwegler, E; Gygi, F; Galli, G

    2008-10-17

    Water confined at the nanoscale has been the focus of numerous experimental and theoretical investigations in recent years, y yet there is no consensus on such basic properties et as diffusion and the nature of hydrogen bonding (HB) under confinement. Unraveling these properties is important to understand fluid flow and transport at the nanoscale, and to shed light on the solvation of biomolecules. Here we report on a first principle, computational study focusing on water confined between prototypical non polar substrate, i.e. , single wall carbon nanotubes and graphene sheets, 1 to 2.5 nm apart. The results of our molecular dynamics simulations show the presence of a thin, interfacial liquid layer ({approx} 5 Angstroms) whose microscopic structure and thickness are independent of the distance between confining layers. The prop properties of the hydrogen bonded network are very similar to those of the bulk outside the interfacial region, even in the case of strong confinement , confinement. Our findings indicate that the perturbation induced by the presence of confining media is extremely local in liquid water, and we propose that many of the effects attributed to novel phases under confinement are determined by subtle electronic structure rearrangements occurring at the interface with the confining medium.

  10. Temperature effects in first-principles solid state calculations of the chemical shielding tensor made simple

    SciTech Connect

    Monserrat, Bartomeu Needs, Richard J.; Pickard, Chris J.

    2014-10-07

    We study the effects of atomic vibrations on the solid-state chemical shielding tensor using first principles density functional theory calculations. At the harmonic level, we use a Monte Carlo method and a perturbative expansion. The Monte Carlo method is accurate but computationally expensive, while the perturbative method is computationally more efficient, but approximate. We find excellent agreement between the two methods for both the isotropic shift and the shielding anisotropy. The effects of zero-point quantum mechanical nuclear motion are important up to relatively high temperatures: at 500 K they still represent about half of the overall vibrational contribution. We also investigate the effects of anharmonic vibrations, finding that their contribution to the zero-point correction to the chemical shielding tensor is small. We exemplify these ideas using magnesium oxide and the molecular crystals L-alanine and β-aspartyl-L-alanine. We therefore propose as the method of choice to incorporate the effects of temperature in solid state chemical shielding tensor calculations using the perturbative expansion within the harmonic approximation. This approach is accurate and requires a computational effort that is about an order of magnitude smaller than that of dynamical or Monte Carlo approaches, so these effects might be routinely accounted for.

  11. Transition metal decorated graphene-like zinc oxide monolayer: A first-principles investigation

    SciTech Connect

    Lei, Jie; Xu, Ming-Chun; Hu, Shu-Jun

    2015-09-14

    Transition metal (TM) atoms have been extensively employed to decorate the two-dimensional materials, endowing them with promising physical properties. Here, we have studied the adsorption of TM atoms (V, Cr, Mn, Fe, and Co) on graphene-like zinc oxide monolayer (g-ZnO) and the substitution of Zn by TM using first-principles calculations to search for the most likely configurations when TM atoms are deposited on g-ZnO. We found that when a V atom is initially placed on the top of Zn atom, V will squeeze out Zn from the two-dimensional plane then substitute it, which is a no barrier substitution process. For heavier elements (Cr to Co), although the substitution configurations are more stable than the adsorption ones, there is an energy barrier for the adsorption-substitution transition with the height of tens to hundreds meV. Therefore, Cr to Co prefers to be adsorbed on the hollow site or the top of oxygen, which is further verified by the molecular dynamics simulations. The decoration of TM is revealed to be a promising approach in terms of tuning the work function of g-ZnO in a large energy range.

  12. Temperature effects in first-principles solid state calculations of the chemical shielding tensor made simple

    NASA Astrophysics Data System (ADS)

    Monserrat, Bartomeu; Needs, Richard J.; Pickard, Chris J.

    2014-10-01

    We study the effects of atomic vibrations on the solid-state chemical shielding tensor using first principles density functional theory calculations. At the harmonic level, we use a Monte Carlo method and a perturbative expansion. The Monte Carlo method is accurate but computationally expensive, while the perturbative method is computationally more efficient, but approximate. We find excellent agreement between the two methods for both the isotropic shift and the shielding anisotropy. The effects of zero-point quantum mechanical nuclear motion are important up to relatively high temperatures: at 500 K they still represent about half of the overall vibrational contribution. We also investigate the effects of anharmonic vibrations, finding that their contribution to the zero-point correction to the chemical shielding tensor is small. We exemplify these ideas using magnesium oxide and the molecular crystals L-alanine and β-aspartyl-L-alanine. We therefore propose as the method of choice to incorporate the effects of temperature in solid state chemical shielding tensor calculations using the perturbative expansion within the harmonic approximation. This approach is accurate and requires a computational effort that is about an order of magnitude smaller than that of dynamical or Monte Carlo approaches, so these effects might be routinely accounted for.

  13. Band offsets at the crystalline / hydrogenated amorphous silicon interface from first-principles

    NASA Astrophysics Data System (ADS)

    Hazrati, Ebrahim; Jarolimek, Karol; de Wijs, Gilles A.; InstituteMolecules; Materials Team

    2015-03-01

    The heterojunction formed between crystalline silicon (c-Si) and hydrogenated amorphous silicon (a-Si:H) is a key component of a new type of high-efficiency silicon solar cell. Since a-Si:H has a larger band gap than c-Si, band offsets are formed at the interface. A band offset at the minority carrier band will mitigate recombination and lead to an increased efficiency. Experimental values of band offsets scatter in a broad range. However, a recent meta-analysis of the results (W. van Sark et al.pp. 405, Springer 2012) gives a larger valence offset (0.40 eV) than the conduction offset (0.15 eV). In light of the conflicting reports our goal is to calculate the band offsets at the c-Si/a-Si:H interface from first-principles. We have prepared several atomistic models of the interface. The crystalline part is terminated with (111) surfaces on both sides. The amorphous structure is generated by simulating an annealing process at 1100 K, with DFT molecular dynamics. Once the atomistic is ready it can be used to calculate the electronic structure of the interface. Our preliminary results show that the valence offset is larger than the conduction band offset.

  14. Composition-Dependent Phase Concentrations from First Principles: Simulating Combinatorial Libraries of Transition Metal Oxides

    NASA Astrophysics Data System (ADS)

    Li, Guo; Yan, Qimin; Zhou, Lan; Newhouse, Paul; Gregoire, John; Neaton, Jeffrey

    To identify material phases in experimental combinatorial libraries, we develop a theoretical model as a complementary approach to accelerate phase identification. In this approach, samples in a combinatorial library are simulated as mixtures in chemical equilibria. Each of these mixtures contains all the solid-state phases, which can possibly exist in the library. Using the total energies of these phases obtained in first-principle calculations, we calculate the Gibbs free energy changes in the corresponding chemical reactions, and subsequently evaluate the equilibrium concentrations of the phases in every sample according to the law of mass action. Furthermore, to test this approach, we simulate pseudobinary libraries MnxV1-xOy and CuxV1-xOy. Interestingly, we find that the composition-dependent phase concentrations calculated within our approach agree well with the experimental results measured with XRD spectroscopy. This work supported by DOE (the JCAP under Award Number DE-SC0004993 and the Molecular Foundry of LBNL), and computational resources provided by NERSC.

  15. First-principles Equations of State and Shock Hugoniots of First- and Second-Row Plasmas

    NASA Astrophysics Data System (ADS)

    Driver, Kevin; Soubiran, Francois; Zhang, Shuai; Militzer, Burkhard

    A first-principles methodology for studying high energy density physics and warm dense matter is important for the stewardship of plasma science and guiding inertial confinement fusion experiments. In order to address this challenge, we have been developing the capability of path integral Monte Carlo (PIMC) for studying dense plasmas comprised of increasingly heavy elements, including nitrogen, oxygen, and neon. In recent work, we have extended PIMC methodology beyond the free-particle node approximation by implementing localized nodal surfaces capable of describing bound plasma states in second-row elements, such as silicon. We combine results from PIMC with results from density functional theory molecular dynamics (DFT-MD) calculations to produce a coherent equation of state that bridges the entire WDM regime. Analysis of pair-correlation functions and the electronic density of states reveals an evolving plasma structure and ionization process that is driven by temperature and pressure. We also compute shock Hugoniot curves for a wide range of initial densities, which generally reveal an increase in compression as the second and first shells are ionized. This work is funded by the NSF/DOE Partnership in Basic Plasma Science and Engineering (DE-SC0010517).

  16. First principles kinetic Monte Carlo study on the growth patterns of WSe2 monolayer

    NASA Astrophysics Data System (ADS)

    Nie, Yifan; Liang, Chaoping; Zhang, Kehao; Zhao, Rui; Eichfeld, Sarah M.; Cha, Pil-Ryung; Colombo, Luigi; Robinson, Joshua A.; Wallace, Robert M.; Cho, Kyeongjae

    2016-06-01

    The control of domain morphology and defect level of synthesized transition metal dichalcogenides (TMDs) is of crucial importance for their device applications. However, current TMDs synthesis by chemical vapor deposition and molecular beam epitaxy is in an early stage of development, where much of the understanding of the process-property relationships is highly empirical. In this work, we use a kinetic Monte Carlo coupled with first principles calculations to study one specific case of the deposition of monolayer WSe2 on graphene, which can be expanded to the entire TMD family. Monolayer WSe2 domains are investigated as a function of incident flux, temperature and precursor ratio. The quality of the grown WSe2 domains is analyzed by the stoichiometry and defect density. A phase diagram of domain morphology is developed in the space of flux and the precursor stoichiometry, in which the triangular compact, fractal and dendritic domains are identified. The phase diagram has inspired a new synthesis strategy for large TMD domains with improved quality.

  17. First Principles Calculation of Intial Oxidation Processes of Si(001) Surface

    NASA Astrophysics Data System (ADS)

    Tsuyoshi, Uda; Koichi, Kato; Kiyoyuki, Terakura

    1997-08-01

    Oxidation of the Si(001) surface, one of the most important processes in the modern Si technology, was studied using the first-principles calculation technique with spin-polarized gradient approximation. The spontaneous dissociative chemisorption occurs only in the exceptional case, where incident O2 molecule attacks the center between the two surface dimers with its molecular axis parallel to a dimer row. In other cases, rather large activation energy is needed for dissociative chemisorption of an O2 molecule. It increases as the chemisorption site becomes deeper from the surface. This is in accordance qualitatively with the recent finding by scanning reflection electron microscopy (SREM) that the oxidation occurs in a layer-by-layer reaction mode. The calculated activation energies, however, are considerably larger than the observed ones. In particular, the calculated barrier energy for backbond oxidation is more than 0.8 eV, while the first sub-surface, including backbonds, is observed to be oxidized with almost no activation energy. We have found that the barrierless backbond oxidation can be realized along a reaction path via the spontaneously chemisorbed meta-stable states on the Si top-layer mentioned earlier. Since this channel is very narrow, our model also explains why the initial sticking coefficient of O2 molecule is small despite of the fact that the barrierless oxidation takes place along this path. This work was partly supported by the New Energy and Industrial Technology Development Organization (NEDO).

  18. Water solubility in calcium aluminosilicate glasses investigated by first principles techniques

    SciTech Connect

    Bouyer, Frederic; Geneste, Gregory; Ispas, Simona; Kob, Walter; Ganster, Patrick

    2010-12-15

    First-principles techniques have been employed to study the reactivity of water into a calcium aluminosilicate glass. In addition to the well known hydrolysis reactions Si-O-Si+H{sub 2}O{yields}Si-OH+Si-OH and Si-O-Al+H{sub 2}O{yields}Si-OH+Al-OH, a peculiar mechanism is found, leading to the formation of an AlO{sub 3}-H{sub 2}O entity and the breaking of Al-O-Si bond. In the glass bulk, most of the hydrolysis reactions are endothermic. Only a few regular sites are found reactive (i.e. in association with an exothermic reaction), and in that case, the hydrolysis reaction leads to a decrease of the local disorder in the amorphous vitreous network. Afterwards, we suggest that ionic charge compensators transform into network modifiers when hydrolysis occurs, according to a global process firstly suggested by Burnham in 1975. Our theoretical computations provide a more general model of the first hydrolysis steps that could help to understand experimental data and water speciation in glasses. -- Graphical Abstract: Reactivity within glass bulk: structures obtained after hydrolyses reactions (endothermic and exothermic processes) and mechanisms involving Si-OH, Al-OH, Si-OH-Al groups within aluminosilicates glasses (through ab initio molecular dynamics): formation of the Si-OH-Al entity coupled with an H exchange-Frederic Bouyer and Gregory Geneste. Display Omitted

  19. Solvated ions as defects in liquid water: A first-principles perspective

    NASA Astrophysics Data System (ADS)

    Schwegler, Eric; Pham, Tuan Anh; Govoni, Marco; Galli, Giulia

    Understanding the electronic properties of solvated ions is crucial in order to control and engineer aqueous electrolytes for a wide variety of emerging energy and environmental technologies, including photocatalytic water splitting. In this talk, we present a strategy to evaluate electronic energy levels of simple solvated ions in aqueous solutions, using a combination of first-principles molecular dynamics simulations and many-body perturbation theory within the GW approximation. We considered CO32- , HCO3-,NO3-,NO2-ions and we show that by analogy to defects in semiconductors, these solvated ions may be classified as deep or shallow defects in liquid water. In particular CO32- and NO2-ions behave as shallow defects, while HCO3-and NO3-as deep ones. We also show that the inclusion of many-body corrections constitutes significant improvement over conventional density functional theory calculations, yielding satisfactory agreement with photoemission experiments. Part of this work was supported by the U.S. Department of Energy at the LLNL under Contract DE-AC52-07NA27344. T.A.P acknowledge the support from the Lawrence Fellowship. Part of this work was supported by LDRD at ANL.

  20. Liquid iron-hydrogen alloys at outer core conditions by first-principles calculations

    NASA Astrophysics Data System (ADS)

    Umemoto, Koichiro; Hirose, Kei

    2015-09-01

    We examined the density, bulk sound (compressional) velocity, and Grüneisen parameter of liquid pure Fe, Fe100H28 (0.50 wt % H), Fe88H40 (0.81 wt % H), and Fe76H52 (1.22 wt % H) at Earth's outer core pressure and temperature (P-T) conditions (~100 to 350 GPa, 4000 to 7000 K) based on first-principles molecular dynamics calculations. The results demonstrate that the thermodynamic Grüneisen parameter of liquid iron alloy decreases with increasing pressure, temperature, and hydrogen concentration, indicating a relatively small temperature gradient in the outer core when hydrogen is present. Along such temperature profile, both the density and compressional velocity of liquid iron containing ~1 wt % hydrogen match seismological observations. It suggests that hydrogen could be a primary light element in the core, although the shear velocity of the inner core is not reconciled with solid Fe-H alloy and thus requires another impurity element.

  1. Thermoelectric transport properties of warm dense molybdenum from first-principles simulations

    NASA Astrophysics Data System (ADS)

    French, Martin; Haill, Thomas; Desjarlais, Michael; Mattsson, Thomas

    2013-10-01

    Molybdenum, with its high melting point, significant electrical conductivity, and high material strength, is a technologically important material in general and has in particular recently been proposed as a driver material in high-pressure strength experiments on Sandia's Z-machine. To simulate and understand the processes in these experiments with magneto-hydrodynamic simulations, accurate models for the electrical and thermal conductivity are needed for a wide range of thermodynamic parameters. Here, we present novel results for the electrical and thermal conductivity of molybdenum in various states ranging from the solid to the dense plasma phase. The results were obtained with first-principles simulation techniques that combine density functional theory with molecular dynamics and linear response theory. We find good agreement between our theoretical results and available experimental data. Sandia National Laboratories is a multiprogram laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the US Department of Energy's National Nuclear Security Administration under Contract No. DE-AC04-94AL85000.

  2. First Principles.

    ERIC Educational Resources Information Center

    Cappelletti, John

    1989-01-01

    Details the following thoughts on directing for the theater: select the play, read the play, read the play again, ask questions, discover the spine, form a concept, cast the play, listen to the actors, make it move, make it spontaneous, make it real, look for obstacles, make it relevant, and make it important. (PRA)

  3. First-principles modeling of catalysts: novel algorithms and reaction mechanisms

    NASA Astrophysics Data System (ADS)

    Richard, Bryan Goldsmith

    A molecular level understanding of a reaction mechanism and the computation of rates requires knowledge of the stable structures and the corresponding transition states that connect them. Temperature, pressure, and environment effects must be included to bridge the 'materials gap' so one can reasonably compare ab initio (first-principles, i.e., having no empirical parameters) predictions with experimental measurements. In this thesis, a few critical problems pertaining to ab initio modeling of catalytic systems are addressed; namely, 1) the issue of building representative models of isolated metal atoms grafted on amorphous supports, 2) modeling inorganic catalytic reactions in non-ideal solutions where the solvent participates in the reaction mechanism, and 3) bridging the materials gap using ab initio thermodynamics to predict the stability of supported nanoparticles under experimental reaction conditions. In Chapter I, a background on first-principles modeling of heterogeneous and homogenous catalysts is provided. Subsequently, to address the problem of modeling catalysis by isolated metal atoms on amorphous supports, we present in Chapter II a sequential-quadratic programming algorithm that systematically predicts the structure and reactivity of isolated active sites on insulating amorphous supports. Modeling solution phase reactions is also a considerable challenge for first-principles modeling, yet when done correctly it can yield critical kinetic and mechanistic insight that can guide experimental investigations. In Chapter III, we examine the formation of peroxorhenium complexes by activation of H2O2, which is key in selective oxidation reactions catalyzed by CH3ReO3 (methyltrioxorhenium, MTO). New experiments and density functional theory (DFT) calculations were conducted to better understand the activation of H2O2 by MTO and to provide a strong experimental foundation for benchmarking computational studies involving MTO and its derivatives. It was found

  4. Radiation effects from first principles : the role of excitons in electronic-excited processes.

    SciTech Connect

    Wong, Bryan Matthew

    2009-09-01

    Electron-hole pairs, or excitons, are created within materials upon optical excitation or irradiation with X-rays/charged particles. The ability to control and predict the role of excitons in these energetically-induced processes would have a tremendous impact on understanding the effects of radiation on materials. In this report, the excitonic effects in large cycloparaphenylene carbon structures are investigated using various first-principles methods. These structures are particularly interesting since they allow a study of size-scaling properties of excitons in a prototypical semi-conducting material. In order to understand these properties, electron-hole transition density matrices and exciton binding energies were analyzed as a function of size. The transition density matrices allow a global view of electronic coherence during an electronic excitation, and the exciton binding energies give a quantitative measure of electron-hole interaction energies in these structures. Based on overall trends in exciton binding energies and their spatial delocalization, we find that excitonic effects play a vital role in understanding the unique photoinduced dynamics in these systems.

  5. Rare-earth vs. heavy metal pigments and their colors from first principles.

    PubMed

    Tomczak, Jan M; Pourovskii, Leonid V; Vaugier, Loig; Georges, Antoine; Biermann, Silke

    2013-01-15

    Many inorganic pigments contain heavy metals hazardous to health and environment. Much attention has been devoted to the quest for nontoxic alternatives based on rare-earth elements. However, the computation of colors from first principles is a challenge to electronic structure methods, especially for materials with localized f-orbitals. Here, starting from atomic positions only, we compute the colors of the red pigment cerium fluorosulfide as well as mercury sulfide (classic vermilion). Our methodology uses many-body theories to compute the optical absorption combined with an intermediate length-scale modelization to assess how coloration depends on film thickness, pigment concentration, and granularity. We introduce a quantitative criterion for the performance of a pigment. While for mercury sulfide, this criterion is satisfied because of large transition matrix elements between wide bands, cerium fluorosulfide presents an alternative paradigm: the bright red color is shown to stem from the combined effect of the quasi-2D and the localized nature of states. Our work shows the power of modern computational methods, with implications for the theoretical design of materials with specific optical properties.

  6. Active Pharmaceutical Ingredients: Prediction of Physical-Chemical Properties from First Principles

    NASA Astrophysics Data System (ADS)

    Valenzano, Loredana

    2013-03-01

    Polymorphism in active pharmaceutical ingredients (APIs) plays a crucial role both for medical and intellectual property concerns but despite ongoing efforts, experimental and computational investigations of the existence and the physical-chemical properties of the same compound in different forms is still an open question.While comparison between computed and experimental values for properties derived from differences between states is often promising (such as bulk modulus), results are disappointing for absolute values (such as density). Quantum mechanical computational methods describe the systems at 0K, experimentally properties are often evaluated at room temperature. Therefore it is not surprising that results determined from first principles dramatically differ from those obtained experimentally. By applying a quantum mechanical periodic approach that takes into account long range London dispersion forces fitted for solid materials, and by imposing different cell volumes corresponding to different thermodynamic conditions, we show how results from calculations at 0K (structures, vibrational spectra, elastic constants) may be compared to experimental values at higher temperatures, helping to foster a stronger linkage between computational and experimental work on systems such as APIs. Where experimental results are not available, our work represents an innovative approach in addressing the properties of APIs. Our results can also serve as foundation for the developing of new force fields to be adopted within a multi-scale computational approach.

  7. Adhesion of the iron-chromium oxide interface from first-principles theory.

    PubMed

    Punkkinen, M P J; Kokko, K; Levämäki, H; Ropo, M; Lu, S; Delczeg, L; Zhang, H L; Delczeg-Czirjak, E K; Johansson, B; Vitos, L

    2013-12-11

    We determine the interface energy and the work of separation of the Fe/Cr2O3 interface using first-principles density functional theory. Starting from different structures, we put forward a realistic interface model that is suitable to study the complex metal-oxide interaction. This model has the lowest formation energy and corresponds to an interface between Fe and oxygen terminated Cr2O3. The work of separation is calculated to be smaller than the intrinsic adhesion energy of pure Fe or Cr2O3, suggesting that stainless steel surfaces should preferentially break along the metal-oxide interface. The relative stabilities and magnetic interactions of the different interfaces are discussed. Next we introduce Cr atoms into the Fe matrix at different positions relative to the interface. We find that metallic Cr segregates very strongly to the (FeCr)/Cr2O3 interface, and increases the separation energy of the interface, making the adhesion of the oxide scale mechanically more stable. The Cr segregation is explained by the enthalpy of formation.

  8. First-principles modeling of biological systems and structure-based drug-design.

    PubMed

    Sgrignani, Jacopo; Magistrato, Alessandra

    2013-03-01

    Molecular modeling techniques play a relevant role in drug design providing detailed information at atomistic level on the structural, dynamical, mechanistic and electronic properties of biological systems involved in diseases' onset, integrating and supporting commonly used experimental approaches. These information are often not accessible to the experimental techniques taken singularly, but are of crucial importance for drug design. Due to the enormous increase of the computer power in the last decades, quantum mechanical (QM) or first-principles-based methods have become often used to address biological issues of pharmaceutical relevance, providing relevant information for drug design. Due to their complexity and their size, biological systems are often investigated by means of a mixed quantum-classical (QM/MM) approach, which treats at an accurate QM level a limited chemically relevant portion of the system and at the molecular mechanics (MM) level the remaining of the biomolecule and its environment. This method provides a good compromise between computational cost and accuracy, allowing to characterize the properties of the biological system and the (free) energy landscape of the process in study with the accuracy of a QM description. In this review, after a brief introduction of QM and QM/MM methods, we will discuss few representative examples, taken from our work, of the application of these methods in the study of metallo-enzymes of pharmaceutical interest, of metal-containing anticancer drugs targeting the DNA as well as of neurodegenerative diseases. The information obtained from these studies may provide the basis for a rationale structure-based drug design of new and more efficient inhibitors or drugs.

  9. Phase diagrams for clathrate hydrates of methane, ethane, and propane from first-principles thermodynamics.

    PubMed

    Cao, Xiaoxiao; Huang, Yingying; Li, Wenbo; Zheng, Zhaoyang; Jiang, Xue; Su, Yan; Zhao, Jijun; Liu, Changling

    2016-01-28

    Natural gas hydrates are inclusion compounds composed of major light hydrocarbon gaseous molecules (CH4, C2H6, and C3H8) and a water clathrate framework. Understanding the phase stability and formation conditions of natural gas hydrates is crucial for their future exploitation and applications and requires an accurate description of intermolecular interactions. Previous ab initio calculations on gas hydrates were mainly limited by the cluster models, whereas the phase diagram and equilibrium conditions of hydrate formation were usually investigated using the thermodynamic models or empirical molecular simulations. For the first time, we construct the chemical potential phase diagrams of type II clathrate hydrates encapsulated with methane/ethane/propane guest molecules using first-principles thermodynamics. We find that the partially occupied structures (136H2O·1CH4, 136H2O·16CH4, 136H2O·20CH4, 136H2O·1C2H6, and 136H2O·1C3H8) and fully occupied structures (136H2O·24CH4, 136H2O·8C2H6, and 136H2O·8C3H8) are thermodynamically favorable under given pressure-temperature (p-T) conditions. The theoretically predicted equilibrium pressures for pure CH4, C2H6 and C3H8 hydrates at the phase transition point are consistent with the experimental data. These results provide valuable guidance for establishing the relationship between the accurate description of intermolecular noncovalent interactions and the p-T equilibrium conditions of clathrate hydrates and other molecular crystals.

  10. Phase diagrams for clathrate hydrates of methane, ethane, and propane from first-principles thermodynamics.

    PubMed

    Cao, Xiaoxiao; Huang, Yingying; Li, Wenbo; Zheng, Zhaoyang; Jiang, Xue; Su, Yan; Zhao, Jijun; Liu, Changling

    2016-01-28

    Natural gas hydrates are inclusion compounds composed of major light hydrocarbon gaseous molecules (CH4, C2H6, and C3H8) and a water clathrate framework. Understanding the phase stability and formation conditions of natural gas hydrates is crucial for their future exploitation and applications and requires an accurate description of intermolecular interactions. Previous ab initio calculations on gas hydrates were mainly limited by the cluster models, whereas the phase diagram and equilibrium conditions of hydrate formation were usually investigated using the thermodynamic models or empirical molecular simulations. For the first time, we construct the chemical potential phase diagrams of type II clathrate hydrates encapsulated with methane/ethane/propane guest molecules using first-principles thermodynamics. We find that the partially occupied structures (136H2O·1CH4, 136H2O·16CH4, 136H2O·20CH4, 136H2O·1C2H6, and 136H2O·1C3H8) and fully occupied structures (136H2O·24CH4, 136H2O·8C2H6, and 136H2O·8C3H8) are thermodynamically favorable under given pressure-temperature (p-T) conditions. The theoretically predicted equilibrium pressures for pure CH4, C2H6 and C3H8 hydrates at the phase transition point are consistent with the experimental data. These results provide valuable guidance for establishing the relationship between the accurate description of intermolecular noncovalent interactions and the p-T equilibrium conditions of clathrate hydrates and other molecular crystals. PMID:26745181

  11. Global smoothing and continuation for large-scale molecular optimization

    SciTech Connect

    More, J.J.; Wu, Zhijun

    1995-10-01

    We discuss the formulation of optimization problems that arise in the study of distance geometry, ionic systems, and molecular clusters. We show that continuation techniques based on global smoothing are applicable to these molecular optimization problems, and we outline the issues that must be resolved in the solution of large-scale molecular optimization problems.

  12. First Principles Simulations fo the Supercritical Behavior of Ore Forming Fluids

    SciTech Connect

    Weare, John H

    2013-04-19

    Abstract of Selected Research Progress: I. First-principles simulation of solvation structure and deprotonation reactions of ore forming metal ions in very nonideal solutions: Advances in algorithms and computational performance achieved in this grant period have allowed the atomic level dynamical simulation of complex nanoscale materials using interparticle forces calculated directly from an accurate density functional solution to the electronic Schr dinger equation (ab-initio molecular dynamics, AIMD). Focus of this program was on the prediction and analysis of the properties of environmentally important ions in aqueous solutions. AIMD methods have provided chemical interpretations of these very complex systems with an unprecedented level of accuracy and detail. The structure of the solvation region neighboring a highly charged metal ion (e.g., 3+) in an aqueous solution is very different from that of bulk water. The many-body behaviors (polarization, charge transfer, etc.) of the ion-water and water-water interactions in this region are difficult to capture with conventional empirical potentials. However, a large numbers of waters (up to 128 waters) are required to fully describe chemical events in the extended hydrations shells and long simulation times are needed to reliably sample the system. Taken together this makes simulation at the 1st principles level a very large computational problem. Our AIMD simulation results using these methods agree with the measured octahedral structure of the 1st solvation shell of Al3+ at the 1st shell boundary and a calculated radius of 1.937 (exp. 1.9). Our calculated average 2nd shell radius agrees remarkably well with the measured radius, 4.093 calculated vs. the measured value of 4.0-4.15 . Less can be experimentally determined about the structure of the 2nd shell. Our simulations show that this shell contains roughly 12 water molecules, which are trigonally coordinated to the 1st shell waters. This structure cannot be

  13. A first principles atmospheric propagation & characterization tool: the laser environmental effects definition and reference (LEEDR)

    NASA Astrophysics Data System (ADS)

    Fiorino, Steven T.; Bartell, Richard J.; Krizo, Matthew J.; Caylor, Gregory L.; Moore, Kenneth P.; Harris, Thomas R.; Cusumano, Salvatore J.

    2008-02-01

    The Air Force Institute of Technology Center for Directed Energy (AFIT/CDE) has developed a first principles atmospheric propagation and characterization model called the Laser Environmental Effects Definition and Reference or LEEDR. This package enables the creation of profiles of temperature, pressure, water vapor content, optical turbulence, and atmospheric particulates and hydrometeors as they relate to line-by-line layer extinction coefficient magnitude at wavelengths from the UV to the RF. Worldwide seasonal, diurnal, and geographical variability in these parameters is accessed from probability density function (PDF) databases using a variety of recently available resources to include the Extreme and Percentile Environmental Reference Tables (ExPERT), the Master Database for Optical Turbulence Research in Support of the Airborne Laser, and the Global Aerosol Data Set (GADS). GADS provides aerosol constituent number densities on a 5° x 5° grid worldwide. ExPERT mapping software allows the LEEDR operator to choose from specific site or regional upper air data to characterize correlated molecular absorption, aerosol absorption and scattering by percentile. The integration of the Surface Marine Gridded Climatology database, the Advanced Navy Aerosol Model (ANAM), and the Navy Surface Layer Optical Turbulence (NSLOT) model provides worldwide coverage over all ocean regions on a 1° x 1° grid. Molecular scattering is computed based on Rayleigh theory. Molecular absorption effects are computed for the top 13 absorbing species using line strength information from the HITRAN 2004 database in conjunction with a community standard molecular absorption continuum code. Aerosol scattering and absorption are computed with the Wiscombe Mie model. Each atmospheric particulate/hydrometeor is evaluated based on its wavelength-dependent forward and off-axis scattering characteristics and absorption effects on laser energy delivered at any wavelength from 0.355 μm to 8.6 m

  14. Communication: Towards first principles theory of relaxation in supercooled liquids formulated in terms of cooperative motion

    NASA Astrophysics Data System (ADS)

    Freed, Karl F.

    2014-10-01

    A general theory of the long time, low temperature dynamics of glass-forming fluids remains elusive despite the almost 20 years since the famous pronouncement by the Nobel Laureate P. W. Anderson, "The deepest and most interesting unsolved problem in solid state theory is probably the theory of the nature of glass and the glass transition" [Science 267, 1615 (1995)]. While recent work indicates that Adam-Gibbs theory (AGT) provides a framework for computing the structural relaxation time of supercooled fluids and for analyzing the properties of the cooperatively rearranging dynamical strings observed in low temperature molecular dynamics simulations, the heuristic nature of AGT has impeded general acceptance due to the lack of a first principles derivation [G. Adam and J. H. Gibbs, J. Chem. Phys. 43, 139 (1965)]. This deficiency is rectified here by a statistical mechanical derivation of AGT that uses transition state theory and the assumption that the transition state is composed of elementary excitations of a string-like form. The strings are assumed to form in equilibrium with the mobile particles in the fluid. Hence, transition state theory requires the strings to be in mutual equilibrium and thus to have the size distribution of a self-assembling system, in accord with the simulations and analyses of Douglas and co-workers. The average relaxation rate is computed as a grand canonical ensemble average over all string sizes, and use of the previously determined relation between configurational entropy and the average cluster size in several model equilibrium self-associating systems produces the AGT expression in a manner enabling further extensions and more fundamental tests of the assumptions.

  15. Electrical conductivity in oxygen-deficient phases of tantalum pentoxide from first-principles calculations

    SciTech Connect

    Bondi, Robert J. Desjarlais, Michael P.; Thompson, Aidan P.; Brennecka, Geoff L.; Marinella, Matthew J.

    2013-11-28

    We apply first-principles density-functional theory (DFT) calculations, ab-initio molecular dynamics, and the Kubo-Greenwood formula to predict electrical conductivity in Ta{sub 2}O{sub x} (0 ≤ x ≤ 5) as a function of composition, phase, and temperature, where additional focus is given to various oxidation states of the O monovacancy (V{sub O}{sup n}; n = 0,1+,2+). In the crystalline phase, our DFT calculations suggest that V{sub O}{sup 0} prefers equatorial O sites, while V{sub O}{sup 1+} and V{sub O}{sup 2+} are energetically preferred in the O cap sites of TaO{sub 7} polyhedra. Our calculations of DC conductivity at 300 K agree well with experimental measurements taken on Ta{sub 2}O{sub x} thin films (0.18 ≤ x ≤ 4.72) and bulk Ta{sub 2}O{sub 5} powder-sintered pellets, although simulation accuracy can be improved for the most insulating, stoichiometric compositions. Our conductivity calculations and further interrogation of the O-deficient Ta{sub 2}O{sub 5} electronic structure provide further theoretical basis to substantiate V{sub O}{sup 0} as a donor dopant in Ta{sub 2}O{sub 5}. Furthermore, this dopant-like behavior is specific to the neutral case and not observed in either the 1+ or 2+ oxidation states, which suggests that reduction and oxidation reactions may effectively act as donor activation and deactivation mechanisms, respectively, for V{sub O}{sup n} in Ta{sub 2}O{sub 5}.

  16. Communication: Towards first principles theory of relaxation in supercooled liquids formulated in terms of cooperative motion.

    PubMed

    Freed, Karl F

    2014-10-14

    A general theory of the long time, low temperature dynamics of glass-forming fluids remains elusive despite the almost 20 years since the famous pronouncement by the Nobel Laureate P. W. Anderson, "The deepest and most interesting unsolved problem in solid state theory is probably the theory of the nature of glass and the glass transition" [Science 267, 1615 (1995)]. While recent work indicates that Adam-Gibbs theory (AGT) provides a framework for computing the structural relaxation time of supercooled fluids and for analyzing the properties of the cooperatively rearranging dynamical strings observed in low temperature molecular dynamics simulations, the heuristic nature of AGT has impeded general acceptance due to the lack of a first principles derivation [G. Adam and J. H. Gibbs, J. Chem. Phys. 43, 139 (1965)]. This deficiency is rectified here by a statistical mechanical derivation of AGT that uses transition state theory and the assumption that the transition state is composed of elementary excitations of a string-like form. The strings are assumed to form in equilibrium with the mobile particles in the fluid. Hence, transition state theory requires the strings to be in mutual equilibrium and thus to have the size distribution of a self-assembling system, in accord with the simulations and analyses of Douglas and co-workers. The average relaxation rate is computed as a grand canonical ensemble average over all string sizes, and use of the previously determined relation between configurational entropy and the average cluster size in several model equilibrium self-associating systems produces the AGT expression in a manner enabling further extensions and more fundamental tests of the assumptions. PMID:25318708

  17. Communication: Towards first principles theory of relaxation in supercooled liquids formulated in terms of cooperative motion.

    PubMed

    Freed, Karl F

    2014-10-14

    A general theory of the long time, low temperature dynamics of glass-forming fluids remains elusive despite the almost 20 years since the famous pronouncement by the Nobel Laureate P. W. Anderson, "The deepest and most interesting unsolved problem in solid state theory is probably the theory of the nature of glass and the glass transition" [Science 267, 1615 (1995)]. While recent work indicates that Adam-Gibbs theory (AGT) provides a framework for computing the structural relaxation time of supercooled fluids and for analyzing the properties of the cooperatively rearranging dynamical strings observed in low temperature molecular dynamics simulations, the heuristic nature of AGT has impeded general acceptance due to the lack of a first principles derivation [G. Adam and J. H. Gibbs, J. Chem. Phys. 43, 139 (1965)]. This deficiency is rectified here by a statistical mechanical derivation of AGT that uses transition state theory and the assumption that the transition state is composed of elementary excitations of a string-like form. The strings are assumed to form in equilibrium with the mobile particles in the fluid. Hence, transition state theory requires the strings to be in mutual equilibrium and thus to have the size distribution of a self-assembling system, in accord with the simulations and analyses of Douglas and co-workers. The average relaxation rate is computed as a grand canonical ensemble average over all string sizes, and use of the previously determined relation between configurational entropy and the average cluster size in several model equilibrium self-associating systems produces the AGT expression in a manner enabling further extensions and more fundamental tests of the assumptions.

  18. Formaldehyde adsorption and decomposition on rutile (110): A first-principles study

    NASA Astrophysics Data System (ADS)

    Liu, Liming; Zhao, Jin

    2016-10-01

    We investigated the adsorption and decomposition of formaldehyde (HCHO) molecule on stoichiometric rutile TiO2(110) surface using first principles-calculations. By comparing the adsorption energy of one bidentate and two monodentate configurations, we found the bidentate configuration is the most stable one because of an additional C-O bond formation. The monodentate configuration can change into the bidentate configuration by overcoming a small barrier less than 0.1 eV. Then, we investigated the decomposition of HCHO which involves two deprotonation processes starting from different adsorption structures. The energy barrier of the first deprotonation is 1.3 eV and 1.1 eV for bidentate and monodentate configurations. After the first deprotonation, an adsorbed formate HCOO specie is formed. The second deprotonation needs 1.74 eV and 1.64 eV for bidentate and monodentate configurations, respectively. After that, an adsorbed CO2 is formed. It can desorb from the surface after overcoming a small barrier of 0.12 eV. In principle, it is also possible to obtain a CO molecule from the surface. Yet a large energy barrier higher than 1.74 eV needs to be overcome. By analyzing the energy level alignment of molecular orbitals with TiO2 energy band edges, we discussed the photocatalytic activity of the reactants and intermediates during the decomposition process. Our results give a clear description of the adsorption structure and thermal decomposition process of HCHO on rutile TiO2(110) surface. The discussion of photocatalytic reactivity based on energy level alignment provides valuable insights to understand the combined photocatalytic and thermally catalytic reactions.

  19. First-Principles Approach to Energy Level Alignment at Aqueous Semiconductor Interfaces

    NASA Astrophysics Data System (ADS)

    Hybertsen, Mark

    2015-03-01

    We have developed a first principles method to calculate the energy level alignment between semiconductor band edges and reference energy levels at aqueous interfaces. This alignment is fundamental to understand the electrochemical characteristics of any semiconductor electrode in general and the potential for photocatalytic activity in particular. For example, in the search for new photo-catalytic materials, viable candidates must demonstrate both efficient absorption of the solar spectrum and an appropriate alignment of the band edge levels in the semiconductor to the redox levels for the target reactions. In our approach, the interface-specific contribution to the electrostatic step across the interface is evaluated using density functional theory (DFT) based molecular dynamics to sample the physical interface structure and the corresponding change in the electrostatic potential at the interface. The reference electronic levels in the semiconductor and in the water are calculated using the GW approach, which naturally corrects for errors inherent in the use of Kohn-Sham energy eigenvalues to approximate the electronic excitation energies in each material. Taken together, our calculations provide the alignment of the semiconductor valence band edge to the centroid of the highest occupied 1b1 level in water. The known relationship of the 1b1 level to the normal hydrogen electrode completes the connection to electrochemical levels. We discuss specific results for GaN, ZnO, and TiO2. The effect of interface structural motifs, such as different degrees of water dissociation, and of dynamical characteristics, will be presented together with available experimental data. Work supported by the US Department of Energy, Office of Basic Energy Sciences under Contract No. DE-AC02-98CH10886.

  20. Liquid Iron Alloys with Hydrogen at Outer Core Conditions by First Principles

    NASA Astrophysics Data System (ADS)

    Umemoto, K.; Hirose, K.

    2015-12-01

    Since the density of the outer core deduced from seismic data is about 10% lower than that of pure iron at core pressures and temperatures (P-T), it is widely believed that the outer core includes one or more light elements. Although intensive experimental and theoretical studies have been performed so far, the light element in the core has not yet been identified. Comparison of the density and sound velocity of liquid iron alloys with observations, such as the PREM, is a promising way to determine the species and quantity of light alloying component(s) in the outer core. Here we report the results of a first-principles molecular dynamics study on liquid iron alloyed with hydrogen, one of candidates of the light elements. Hydrogen had been much less studied than other candidates. However, hydrogen has been known to reduce the melting temperature of Fe-H solid [1]. Furthermore, very recently, Nomura et al. argued that the outer core may include 24 at.% H in order to be molten under relatively low temperature (< 3600 K) [2]. Since then hydrogen has attracted strong interests. We clarify the effects of hydrogen on density and sound velocity of liquid iron alloys under outer core P-T conditions. It is shown that ~1 wt% hydrogen can reproduce PREM density and sound velocity simultaneously very well. In addition, we show the presence of hydrogen rather reduces Gruneisen parameters. It indicates that, if hydrogen exists in the outer core, temperature profile of the outer core could be changed considerably from one estimated so far. [1] Sakamaki, K., E. Takahashi, Y. Nakajima, Y. Nishihara, K. Funakoshi, T. Suzuki, and Y. Fukai, Phys. Earth Planet. Inter., 174, 192-201 (2009). [2] Nomura, R., K. Hirose, K. Uesugi, Y. Ohishi, A. Tsuchiyama, A. Miyake, and Y. Ueno, Science 31, 522-525 (2014).

  1. Two-dimensional near-ultraviolet spectroscopy of aromatic residues in amyloid fibrils: a first principles study.

    PubMed

    Jiang, Jun; Mukamel, Shaul

    2011-02-14

    We report a first principles study of two dimensional electronic spectroscopy of aromatic side chain transitions in the 32-residue β-amyloid (Aβ(9-40)) fibrils in the near ultraviolet (250-300 nm). An efficient exciton Hamiltonian with electrostatic fluctuations (EHEF) algorithm is used to compute the electronic excitations in the presence of environmental fluctuations. The through-space inter- and intra-molecular interactions are calculated with high level quantum mechanics (QM) approaches, and interfaced with molecular mechanics (MM) simulations. Distinct two dimensional near ultraviolet (2DNUV) spectroscopic signatures are identified for different aromatic transitions, and the couplings between them. 2DNUV signals associated with the transition couplings are shown to be very sensitive to the change of residue-residue interactions induced by residue mutations. Our simulations suggest that 2DNUV spectra could provide a useful local probe for the structure and kinetics of fibrils.

  2. First-principles thermoelasticity of transition metals at high pressure: Tantalum prototype in the quasiharmonic limit

    NASA Astrophysics Data System (ADS)

    Orlikowski, Daniel; Söderlind, Per; Moriarty, John A.

    2006-08-01

    The thermoelastic properties of tantalum have been investigated over its theoretical high-pressure bcc solid phase (up to 26000K at 10Mbar ) using an advanced first-principles approach that accurately accounts for cold, electron-thermal, and ion-thermal contributions in materials where anharmonic effects are small. Specifically, we have combined ab initio full-potential linear-muffin-tin-orbital electronic-structure calculations for the cold and electron-thermal contributions to the elastic moduli with phonon contributions for the ion-thermal part calculated using model generalized pseudopotential theory. For the latter, a summation of terms over the Brillouin zone is performed within the quasiharmonic approximation, where each term is composed of a strain derivative of the phonon frequency at a particular k point. At ambient pressure, the resulting temperature dependence of the Ta elastic moduli is in excellent agreement with ultrasonic measurements. The experimentally observed anomalous behavior of C44 at low temperatures is shown to originate from the electron-thermal contribution. At higher temperatures, the main contribution to the temperature dependence of the elastic moduli comes from thermal expansion, but inclusion of the electron- and ion-thermal contributions is essential to obtain quantitative agreement with experiment. In addition, the pressure dependence of the moduli at ambient temperature compares well with recent diamond-anvil-cell measurements to 1.05Mbar . Moreover, the calculated longitudinal and bulk sound velocities in polycrystalline Ta at higher pressure and temperature in the vicinity of shock melting (˜3Mbar) agree well with data obtained from shock experiments. However, at high temperatures along the melt curve above 1Mbar , the B' shear modulus becomes negative, indicating the onset of unexpectedly strong anharmonic effects. Finally, the assumed temperature dependence of the Steinberg-Guinan strength model obtained from scaling with the

  3. First Principles Calculations for X-ray Resonant Spectra and Elastic Properties

    SciTech Connect

    Lee, Yongbin

    2004-01-01

    In this thesis, we discuss applications of first principles methods to x-ray resonant spectra and elastic properties calculation. We start with brief reviews about theoretical background of first principles methods, such as density functional theory, local density approximation (LDA), LDA+U, and the linear augmented plane wave (LAPW) method to solve Kohn-Sham equations. After that we discuss x-ray resonant scattering (XRMS), x-ray magnetic circular dichroism (XMCD) and the branching problem in the heavy rare earths Ledges. In the last chapter we discuss the elastic properties of the second hardest material AlMgB14.

  4. First-principles Theory of the Momentum-dependent Local Ansatz for Correlated Electron System

    NASA Astrophysics Data System (ADS)

    Chandra, Sumal; Kakehashi, Yoshiro

    The momentum-dependent local-ansatz (MLA) wavefunction describes well correlated electrons in solids in both the weak and strong interaction regimes. In order to apply the theory to the realistic system, we have extended the MLA to the first-principles version using the tight-binding LDA+U Hamiltonian. We demonstrate for the paramagnetic Fe that the first-principles MLA can describe a reasonable correlation energy gain and suppression of charge fluctuations due to electron correlations. Furthermore, we show that the MLA yields a distinct momentum dependence of the momentum distribution, and thus improves the Gutzwiller wavefunction.

  5. Research on regularized mean-variance portfolio selection strategy with modified Roy safety-first principle.

    PubMed

    Atta Mills, Ebenezer Fiifi Emire; Yan, Dawen; Yu, Bo; Wei, Xinyuan

    2016-01-01

    We propose a consolidated risk measure based on variance and the safety-first principle in a mean-risk portfolio optimization framework. The safety-first principle to financial portfolio selection strategy is modified and improved. Our proposed models are subjected to norm regularization to seek near-optimal stable and sparse portfolios. We compare the cumulative wealth of our preferred proposed model to a benchmark, S&P 500 index for the same period. Our proposed portfolio strategies have better out-of-sample performance than the selected alternative portfolio rules in literature and control the downside risk of the portfolio returns. PMID:27386363

  6. First principles calculation of thermal expansion coefficients of pure and Cr doped α-alumina crystals

    NASA Astrophysics Data System (ADS)

    Tohei, Tetsuya; Watanabe, Yuito; Lee, Hak-Sung; Ikuhara, Yuichi

    2016-10-01

    We have performed theoretical analysis of thermal expansion behavior of alumina crystals under finite temperature based on first principles phonon state calculations. Liner thermal expansion coefficients of a pure α-alumina crystal have been evaluated based on quasi-harmonic approximation including crystalline anisotropy. The Cr doping effect on the alumina crystal has also been examined and found that the doping can cause a noticeable change on the thermal expansion coefficient. The present results demonstrate that the first principles theoretical approach can be helpful for reproducing or predicting thermal expansion behaviors including dopant effects, which may pave a way for possible control of thermal expansion of materials by doping or alloying.

  7. Temporal scaling of molecular evolution in primates and other mammals.

    PubMed

    Gingerich, P D

    1986-05-01

    Molecular clocks are routinely tested for linearity using a relative rate test and routinely calibrated against the geological time scale using a single or average paleontologically determined time of divergence between living taxa. The relative rate test is a test of parallel rate equality, not a test of rate constancy. Temporal scaling provides a test of rates, where scaling coefficients of 1.0 (isochrony) represent stochastic rate constancy. The fossil record of primates and other mammals is now known in sufficient detail to provide several independent divergence times for major taxonomic groups. Molecular difference should scale negatively or isochronically (scaling coefficients less than 1.0) with divergence time: where two or more divergence times are available, molecular difference appears to scale positively (scaling coefficient greater than 1.0). A minimum of four divergence times are required for adequate statistical power in testing the linear model: scaling is significantly nonlinear and positive in six of 11 published investigations meeting this criterion. All groups studied show some slowdown in rates of molecular change over Cenozoic time. The break from constant or increasing rates during the Mesozoic to decreasing rates during the Cenozoic appears to coincide with extraordinary diversification of placental mammals at the beginning of this era. High rates of selectively neutral molecular change may be concentrated in such discrete events of evolutionary diversification.

  8. Thermal conductivity and dielectric functions of alkali chloride XCl (X = Li, Na, K and Rb): a first-principles study

    NASA Astrophysics Data System (ADS)

    Xu, M.; Yang, J. Y.; Liu, L. H.

    2016-07-01

    The macroscopic physical properties of solids are fundamentally determined by the interactions among microscopic electrons, phonons and photons. In this work, the thermal conductivity and infrared–visible–ultraviolet dielectric functions of alkali chlorides and their temperature dependence are fully investigated at the atomic level, seeking to unveil the microscopic quantum interactions beneath the macroscopic properties. The microscopic phonon–phonon interaction dominates the thermal conductivity which can be investigated by the anharmonic lattice dynamics in combination with Peierls–Boltzmann transport equation. The photon–phonon and electron–photon interaction intrinsically induce the infrared and visible–ultraviolet dielectric functions, respectively, and such microscopic processes can be simulated by first-principles molecular dynamics without empirical parameters. The temperature influence on dielectric functions can be effectively included by choosing the thermally equilibrated configurations as the basic input to calculate the total dipole moment and electronic band structure. The overall agreement between first-principles simulations and literature experiments enables us to interpret the macroscopic thermal conductivity and dielectric functions of solids in a comprehensive way.

  9. Thermal conductivity and dielectric functions of alkali chloride XCl (X = Li, Na, K and Rb): a first-principles study

    NASA Astrophysics Data System (ADS)

    Xu, M.; Yang, J. Y.; Liu, L. H.

    2016-07-01

    The macroscopic physical properties of solids are fundamentally determined by the interactions among microscopic electrons, phonons and photons. In this work, the thermal conductivity and infrared-visible-ultraviolet dielectric functions of alkali chlorides and their temperature dependence are fully investigated at the atomic level, seeking to unveil the microscopic quantum interactions beneath the macroscopic properties. The microscopic phonon-phonon interaction dominates the thermal conductivity which can be investigated by the anharmonic lattice dynamics in combination with Peierls-Boltzmann transport equation. The photon-phonon and electron-photon interaction intrinsically induce the infrared and visible-ultraviolet dielectric functions, respectively, and such microscopic processes can be simulated by first-principles molecular dynamics without empirical parameters. The temperature influence on dielectric functions can be effectively included by choosing the thermally equilibrated configurations as the basic input to calculate the total dipole moment and electronic band structure. The overall agreement between first-principles simulations and literature experiments enables us to interpret the macroscopic thermal conductivity and dielectric functions of solids in a comprehensive way.

  10. Scale bridging in molecular simulation. Recurrent problems and current options

    NASA Astrophysics Data System (ADS)

    Hartmann, Carsten; Delle Site, Luigi

    2015-09-01

    Multiscale and multiphysics approaches have become an integral part of the molecular modeling and simulation toolbox and are used to attack various real-world problems that would be out of reach without these techniques. This special topics issue is devoted to a critical appraisal of some of the most popular scale bridging techniques for molecular simulation. It features regular articles and a "Discussion and Debate" section, in which experts in the field discuss specific articles and general aspects of scale bridging techniques.

  11. Molecular scale dynamics of large ring polymers.

    PubMed

    Gooßen, S; Brás, A R; Krutyeva, M; Sharp, M; Falus, P; Feoktystov, A; Gasser, U; Pyckhout-Hintzen, W; Wischnewski, A; Richter, D

    2014-10-17

    We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture. PMID:25361284

  12. Molecular scale dynamics of large ring polymers.

    PubMed

    Gooßen, S; Brás, A R; Krutyeva, M; Sharp, M; Falus, P; Feoktystov, A; Gasser, U; Pyckhout-Hintzen, W; Wischnewski, A; Richter, D

    2014-10-17

    We present neutron scattering data on the structure and dynamics of melts from polyethylene oxide rings with molecular weights up to ten times the entanglement mass of the linear counterpart. The data reveal a very compact conformation displaying a structure approaching a mass fractal, as hypothesized by recent simulation work. The dynamics is characterized by a fast Rouse relaxation of subunits (loops) and a slower dynamics displaying a lattice animal-like loop displacement. The loop size is an intrinsic property of the ring architecture and is independent of molecular weight. This is the first experimental observation of the space-time evolution of segmental motion in ring polymers illustrating the dynamic consequences of their topology that is unique among all polymeric systems of any other known architecture.

  13. Expanding the scale of molecular biophysics

    NASA Astrophysics Data System (ADS)

    Levine, Herbert

    2016-10-01

    Here, I argue that some of the secrets of complex biological function rely on assemblies of many heterogeneous proteins that together enable sophisticated sensing and actuating processes. Evolution seems to delight in making these structures and in continually elaborating upon their capabilities. Developing tools that can go beyond the few protein limit, both on the experimental frontier and from a theoretical, conceptual framework, should be an extremely high priority for the next generation of molecular biophysicists.

  14. A concurrent multiscale micromorphic molecular dynamics

    SciTech Connect

    Li, Shaofan Tong, Qi

    2015-04-21

    In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation.

  15. First-principles calculations of shear moduli for Monte Carlo-simulated Coulomb solids

    NASA Technical Reports Server (NTRS)

    Ogata, Shuji; Ichimaru, Setsuo

    1990-01-01

    The paper presents a first-principles study of the shear modulus tensor for perfect and imperfect Coulomb solids. Allowance is made for the effects of thermal fluctuations for temperatures up to the melting conditions. The present theory treats the cases of the long-range Coulomb interaction, where volume fluctuations should be avoided in the Ewald sums.

  16. Integration of first-principles methods and crystallographic database searches for new ferroelectrics: Strategies and explorations

    SciTech Connect

    Bennett, Joseph W.; Rabe, Karin M.

    2012-11-15

    In this concept paper, the development of strategies for the integration of first-principles methods with crystallographic database mining for the discovery and design of novel ferroelectric materials is discussed, drawing on the results and experience derived from exploratory investigations on three different systems: (1) the double perovskite Sr(Sb{sub 1/2}Mn{sub 1/2})O{sub 3} as a candidate semiconducting ferroelectric; (2) polar derivatives of schafarzikite MSb{sub 2}O{sub 4}; and (3) ferroelectric semiconductors with formula M{sub 2}P{sub 2}(S,Se){sub 6}. A variety of avenues for further research and investigation are suggested, including automated structure type classification, low-symmetry improper ferroelectrics, and high-throughput first-principles searches for additional representatives of structural families with desirable functional properties. - Graphical abstract: Integration of first-principles methods with crystallographic database mining, for the discovery and design of novel ferroelectric materials, could potentially lead to new classes of multifunctional materials. Highlights: Black-Right-Pointing-Pointer Integration of first-principles methods and database mining. Black-Right-Pointing-Pointer Minor structural families with desirable functional properties. Black-Right-Pointing-Pointer Survey of polar entries in the Inorganic Crystal Structural Database.

  17. Course-Level Implementation of First Principles, Goal Orientations, and Cognitive Engagement: A Multilevel Mediation Model

    ERIC Educational Resources Information Center

    Lee, Sunghye; Koszalka, Tiffany A.

    2016-01-01

    The First Principles of Instruction (FPI) represent ideologies found in most instructional design theories and models. Few attempts, however, have been made to empirically test the relationship of these FPI to instructional outcomes. This study addresses whether the degree to which FPI are implemented in courses makes a difference to student…

  18. Real-space method for first-principles electron transport calculations: Self-energy terms of electrodes for large systems

    NASA Astrophysics Data System (ADS)

    Ono, Tomoya; Tsukamoto, Shigeru

    2016-01-01

    We present a fast and stable numerical technique to obtain the self-energy terms of electrodes for first-principles electron transport calculations. Although first-principles calculations based on the real-space finite-difference method are advantageous for execution on massively parallel computers, large-scale transport calculations are hampered by the computational cost and numerical instability of the computation of the self-energy terms. Using the orthogonal complement vectors of the space spanned by the generalized Bloch waves that actually contribute to transport phenomena, the computational accuracy of transport properties is significantly improved with a moderate computational cost. To demonstrate the efficiency of the present technique, the electron transport properties of a Stone-Wales (SW) defect in graphene and silicene are examined. The resonance scattering of the SW defect is observed in the conductance spectrum of silicene since the σ* state of silicene lies near the Fermi energy. In addition, we found that one conduction channel is sensitive to a defect near the Fermi energy, while the other channel is hardly affected. This characteristic behavior of the conduction channels is interpreted in terms of the bonding network between the bilattices of the honeycomb structure in the formation of the SW defect. The present technique enables us to distinguish the different behaviors of the two conduction channels in graphene and silicene owing to its excellent accuracy.

  19. First principles study of atomic-scale nanowires and dynamical transverse spin susceptibility

    NASA Astrophysics Data System (ADS)

    Ke, Liqin

    This dissertation includes two independent theoretical studies: (a) structure and electron transport in Au and Co nanowires by using the local-density approximation (LDA), and (b) studies of the dynamical transverse spin susceptibility in Fe, Ni, Co and FeSe. Ballistic conductance calculations of infinite zigzag chains of Co and Au, and multi-atom Au nanowires, were calculated within the Landauer-Buttiker formalism. The Co chain was spin polarized, and the majority spin channel exhibits quantized conductance. But because of the close spacing of Co d levels, the minority channel does not. In contrast, Au is not spin polarized, and shows well-behaved quantization. The deformation of an atomic Au wire placed between Au electrodes was investigated theoretically. It was found that the lowest phonon eigenstates are associated with lateral motion of atoms in the middle of the chain. Large displacements which resulted in wire breakage were studied, and the energy barrier associated with this process has been calculated. At certain stages of the wire breaking process, atomic fluctuations become very large, which results in an intrinsic conductance fluctuation, even at arbitrarily low temperature. The theoretical background and calculational formalism of the dynamical transverse spin susceptibility is presented in two approximations, the Rigid Spin Approximation (RSA) and the time-dependent LDA. The latter was implemented with a recently developed full product basis (FPB) method. In the RSA case, the exchange-correlation kernel is determined indirectly from a sum rule. The theory was applied to bcc-Fe, fcc-Ni, hcp-Co, and to FeSe in the Neel magnetic structure. In the FeSe case, intra-pocket and inter-pocket mechanisms were found to govern the low energy bare susceptibility. The enhanced susceptibility was found to consist of some admixture of Stoner excitations and spin wave parts.

  20. Free energies and mechanisms of water exchange around Uranyl from first principles molecular dynamics

    SciTech Connect

    Atta-Fynn, Raymond; Bylaska, Eric J.; De Jong, Wibe A.

    2012-02-01

    From density functional theory (DFT) based ab initio (Car-Parrinello) metadynamics, we compute the activation energies and mechanisms of water exchange between the first and second hydration shells of aqueous Uranyl (UO{sub 2}{sup 2+}) using the primary hydration number of U as the reaction coordinate. The free energy and activation barrier of the water dissociation reaction [UO{sub 2}(OH{sub 2}){sub 5}]{sup 2+}(aq) {yields} [UO{sub 2}(OH{sub 2})4]{sup 2+}(aq) + H{sub 2}O are 0.7 kcal and 4.7 kcal/mol respectively. The free energy is in good agreement with previous theoretical (-2.7 to +1.2 kcal/mol) and experimental (0.5 to 2.2 kcal/mol) data. The associative reaction [UO{sub 2}(OH{sub 2}){sub 5}]{sup 2+}(aq) + H{sub 2}O {yields} [UO{sub 2}(OH{sub 2})6]{sup 2+}(aq) is short-lived with a free energy and activation barrier of +7.9 kcal/mol and +8.9 kca/mol respectively; it is therefore classified as associative-interchange. On the basis of the free energy differences and activation barriers, we predict that the dominant exchange mechanism between [UO{sub 2}(OH{sub 2}){sub 5}]{sup 2+}(aq) and bulk water is dissociative.

  1. First-Principles Molecular Dynamics of Melts in the MgO-SiO2 System

    NASA Astrophysics Data System (ADS)

    Karki, Bijaya; de Koker, Nico; Bhattarai, D.; Stixrude, Lars

    2008-03-01

    We have recently completed simulations of five melt compositions in the MgO-SiO2 system within density functional theory. These results allow us to investigate the structural and thermodynamical, transport properties of melts along the MgO-SiO2 join as a function of pressure. In particular, we have found that the mixing in MgO-SiO2 system is significantly non-ideal at low pressures with negative excess volume and enthalpy of mixing. With increasing pressure, the volume of mixing decreases rapidly to a value close to zero at pressures above 50 GPa whereas the enthalpy of mixing remains negative. The radial distribution functions and coordination environments are found to show interesting changes with varying composition. Also, the effects of composition on diffusivity are shown to be substantial at low pressures whereas the effects are increasingly suppressed with increasing pressure.

  2. First-principles study of molecular NO dissociation on Ir(100) surface

    NASA Astrophysics Data System (ADS)

    Erikat, I. A.; Hamad, B. A.; Khalifeh, J. M.

    2014-02-01

    The dissociation of NO on Ir(100) surface is investigated using density functional theory (DFT). The pathway and transition state (TS) of the dissociation of NO molecule are determined using climbing image nudge elastic band (CI-NEB). The prerequisite state of NO dissociation is determining the most stable sites of the reactant and products. We found that the most energetically stable sites are the hollow for N atom and the bridge for NO molecule as well as O atom. We found that the bending of NO is the first step of the dissociation reaction due to the increase of the back-donation from the d-band of Ir to 2 π ∗ orbital of NO, which causes the weakening of NO bond. The dissociation energy barrier of NO molecule on Ir(100) surface is 0.49 eV.

  3. Fullerene and nanotube growth: new insights using first principles and molecular dynamics.

    PubMed

    Cruz-Silva, Rodolfo; Araki, Takumi; Hayashi, Takuya; Terrones, Humberto; Terrones, Mauricio; Endo, Morinobu

    2016-09-13

    Shortly after the discovery of fullerenes, many researchers pointed out that carbon nanotubes could be considered as elongated fullerenes. However, the detailed formation mechanism for both structures has been a topic of debate for several years, and consequently it has been difficult to draw a clear connection between the two systems. While the synthesis conditions appear to be different for both fullerenes and nanotubes, here, we demonstrate that it is highly likely that, at an initial growth stage, single-walled carbon nanotubes begin to grow from a hemisphere-like fullerene cap. More importantly, by analysing the minimum-energy path, it is shown that the insertion of C2 fragments drives the transformation of this fullerene cap into an elongated structure that leads to the formation of very short carbon nanotubes.This article is part of the themed issue 'Fullerenes: past, present and future, celebrating the 30th anniversary of Buckminster Fullerene'.

  4. Fullerene and nanotube growth: new insights using first principles and molecular dynamics.

    PubMed

    Cruz-Silva, Rodolfo; Araki, Takumi; Hayashi, Takuya; Terrones, Humberto; Terrones, Mauricio; Endo, Morinobu

    2016-09-13

    Shortly after the discovery of fullerenes, many researchers pointed out that carbon nanotubes could be considered as elongated fullerenes. However, the detailed formation mechanism for both structures has been a topic of debate for several years, and consequently it has been difficult to draw a clear connection between the two systems. While the synthesis conditions appear to be different for both fullerenes and nanotubes, here, we demonstrate that it is highly likely that, at an initial growth stage, single-walled carbon nanotubes begin to grow from a hemisphere-like fullerene cap. More importantly, by analysing the minimum-energy path, it is shown that the insertion of C2 fragments drives the transformation of this fullerene cap into an elongated structure that leads to the formation of very short carbon nanotubes.This article is part of the themed issue 'Fullerenes: past, present and future, celebrating the 30th anniversary of Buckminster Fullerene'. PMID:27501974

  5. A simplified implementation of van der Waals density functionals for first-principles molecular dynamics applications

    NASA Astrophysics Data System (ADS)

    Wu, Jun; Gygi, François

    2012-06-01

    We present a simplified implementation of the non-local van der Waals correlation functional introduced by Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)] and reformulated by Román-Pérez et al. [Phys. Rev. Lett. 103, 096102 (2009)]. The proposed numerical approach removes the logarithmic singularity of the kernel function. Complete expressions of the self-consistent correlation potential and of the stress tensor are given. Combined with various choices of exchange functionals, five versions of van der Waals density functionals are implemented. Applications to the computation of the interaction energy of the benzene-water complex and to the computation of the equilibrium cell parameters of the benzene crystal are presented. As an example of crystal structure calculation involving a mixture of hydrogen bonding and dispersion interactions, we compute the equilibrium structure of two polymorphs of aspirin (2-acetoxybenzoic acid, C9H8O4) in the P21/c monoclinic structure.

  6. The future of nanofabrication and molecular scale devices in nanomedicine.

    PubMed

    Freitas, R A

    2002-01-01

    Nanotechnology is engineering and manufacturing at the molecular scale, and the application of nanotechnology to medicine is called nanomedicine. Nanomedicine subsumes three mutually overlapping and progressively more powerful molecular technologies. First, nanoscale-structured materials and devices that can be fabricated today hold great promise for advanced diagnostics and biosensors, targeted drug delivery and smart drugs, and immunoisolation therapies. Second, biotechnology offers the benefits of molecular medicine via genomics, proteomics, and artificial engineered microbes. Third, in the longer term, molecular machine systems and medical nanorobots will allow instant pathogen diagnosis and extermination, chromosome replacement and individual cell surgery in vivo, and the efficient augmentation and improvement of natural physiological function. Current research is exploring the fabrication of designed nanostructures, nanoactuators and nanomotors, microscopic energy sources, and nanocomputers at the molecular scale, along with the means to assemble them into larger systems, economically and in great numbers.

  7. Design of Ni-base superalloys and MCrAlY coatings from first-principles and computational thermodynamics

    NASA Astrophysics Data System (ADS)

    Liu, Xuan

    This thesis explores the thermodynamics of Ni-base superalloys and metallic coatings used in the protection of these alloys. First, a thermodynamic description of the Nb-Re binary system is developed by means of the CALculation of PHAse Diagrams (CALPHAD) method supplemented by first-principles calculations based on density functional theory (DFT) and experimental data in the literature. In addition to terminal solution phases in the Nb-Re system, there are two intermetallic phases, sigma (sigma) and chi (chi), all modeled with sublattice models. Special quasi-random structures (SQS) are employed to mimic the random mixing of the bcc, hcp, and fcc solid solution phases from first-principles. Finite temperature thermodynamic properties of end-members and dilute mixing in each sublattice of the complex sigma and chi phases are predicted from first-principles calculations and the Debye-Gruneisen model. The utility of the Debye-Gruneisen model is then investigated with respect to its fitting parameter known as the scaling factor, and it is found that the prediction of finite-temperature properties can be improved by modification of this factor. This scaling factor is studied using bcc, fcc, hcp systems and the Mg-Zn binary system due to the abundance of thermodynamic data. Predicted Debye temperatures (thetaD), using a calculated scaling factor, show good agreement with experiments and improvements over the scaling factor derived by Moruzzi et al. Finite-temperature thermodynamic properties of intermetallics are investigated to show the efficiency and improved accuracy of the calculated scaling factor. However, for the intermetallic Mg2Zn11, the Debye-Gruneisen model cannot account for anomalous lattice dynamics at low temperatures. The calculated scaling factor is then used throughout the present work for finite-temperature predictions. Another missing piece of the literature includes the thermodynamics of Al-Co-Cr-Ni bond coat system used in the protection of

  8. Unified first principles description from warm dense matter to ideal ionized gas plasma: electron-ion collisions induced friction.

    PubMed

    Dai, Jiayu; Hou, Yong; Yuan, Jianmin

    2010-06-18

    Electron-ion interactions are central to numerous phenomena in the warm dense matter (WDM) regime and at higher temperature. The electron-ion collisions induced friction at high temperature is introduced in the procedure of ab initio molecular dynamics using the Langevin equation based on density functional theory. In this framework, as a test for Fe and H up to 1000 eV, the equation of state and the transition of electronic structures of the materials with very wide density and temperature can be described, which covers a full range of WDM up to high energy density physics. A unified first principles description from condensed matter to ideal ionized gas plasma is constructed.

  9. A Cu-amyloid β complex activating Fenton chemistry in Alzheimer's disease: Learning with multiple first-principles simulations

    NASA Astrophysics Data System (ADS)

    La Penna, Giovanni; Hureau, Christelle; Faller, Peter

    2014-10-01

    Amyloid β peptides form complexes with copper, both in vitro and in vivo, relatively soluble in water as oligomers and active as catalysts for oxidation of organic substrates by hydrogen peroxide, a species always present in cells and in their aerobic environment. All these species are present in the synapse, thus making a connection between the amyloid cascade hypothesis and the oxidative damages by reactive oxygen species in neurons, when pathological dishomeostasis of amyloid peptides and metal ions occur. In order to understand the structural features of these toxic complexes, we built several models of Cu-Aβ peptides in monomeric and dimeric forms and we found, performing multiple first-principles molecular dynamics simulations, that Cu-induced dimers are more active than monomers in converting hydrogen peroxide into aggressive hydroxyl radicals.

  10. Probing the intrinsic failure mechanism of fluorinated amorphous carbon film based on the first-principles calculations

    NASA Astrophysics Data System (ADS)

    Zhang, Ren-Hui; Wang, Li-Ping; Lu, Zhi-Bin

    2015-03-01

    Fluorinated amorphous carbon films exhibit superlow friction under vacuum, but are prone to catastrophic failure. Thus far, the intrinsic failure mechanism remains unclear. A prevailing view is that the failure of amorphous carbon film results from the plastic deformation of substrates or strong adhesion between two contacted surfaces. In this paper, using first-principles and molecular dynamics methodology, combining with compressive stress-strain relation, we firstly demonstrate that the plastic deformation induces graphitization resulting in strong adhesion between two contacted surfaces under vacuum, which directly corresponds to the cause of the failure of the films. In addition, sliding contact experiments are conducted to study tribological properties of iron and fluorinated amorphous carbon surfaces under vacuum. The results show that the failure of the film is directly attributed to strong adhesion resulting from high degree of graphitization of the film, which are consistent with the calculated results.

  11. All-electron first-principles GW+Bethe-Salpeter calculation for optical absorption spectra of sodium clusters

    SciTech Connect

    Noguchi, Yoshifumi; Ohno, Kaoru

    2010-04-15

    The optical absorption spectra of sodium clusters (Na{sub 2n}, n{<=} 4) are calculated by using an all-electron first-principles GW+Bethe-Salpeter method with the mixed-basis approach within the Tamm-Dancoff approximation. In these small systems, the excitonic effect strongly affects the optical properties due to the confinement of exciton in the small system size. The present state-of-the-art method treats the electron-hole two-particle Green's function by incorporating the ladder diagrams up to the infinite order and therefore takes into account the excitonic effect in a good approximation. We check the accuracy of the present method by comparing the resulting spectra with experiments. In addition, the effect of delocalization in particular in the lowest unoccupied molecular orbital in the GW quasiparticle wave function is also discussed by rediagonalizing the Dyson equation.

  12. [First-principles study of vibrational Raman spectra of amorphous carbon].

    PubMed

    Niu, Li; Zhu, Jia-qi; Gao, Wei; Du, Shan-yi

    2009-09-01

    The vibrational density of states and nonresonant reduced Raman spectra of amorphous carbon at densities of 2.6, 2.9 and 3.2 g x cm(-3) were calculated by the use of a first-principles plane-wave pesudopotential method. Three structural models were generated by liquid-quench method using Car-Parinello molecular dynamics, their vibrational frequencies and eigenmodes were determined using the linear response approach, and Raman coupling tensors were calculated using the finite electric field method. The calculated results show that the sp3 fraction increases from 50% to 84.4%, the sp2 configuration changes from mainly rings to short chains, the position of the G peak moves to higher frequencies, the intensity ratio of D and G peaks decreases, the position of the T peak moves to lower frequencies and the intensity ratio of T and G peaks increases as density increases from 2.6 to 3.2 g x cm(-3). The authors' calculated Raman spectra show an overall good agreement with experimental spectra. The analysis in terms of atomic vibrations confirms that the G and D peaks both come from sp2 C contribution, G peak is due to the stretching vibration of any pair of sp2 atoms and the T peak is due to the C-C sp3 vibration. The authors' analysis also confirms that the dispersion of G and T peaks is due to bond-length changes. The bond length of chains (olefins) is shorter than that of rings, so their vibrational frequency is higher and the G-peak position moves to higher frequencies with increasing the sp3 fraction. The number of sp3-sp2 type bonds decreases as the sp3 fraction increases. These bonds are shorter than pure sp3-sp3 bonds, hence the T-peak position moves to lower frequencies. The research results provide a theoretic basis for analyzing experimental Raman spectra of amorphous carbon. PMID:19950647

  13. First-principles thermal conductivity of warm-dense deuterium plasmas for inertial confinement fusion applications.

    PubMed

    Hu, S X; Collins, L A; Boehly, T R; Kress, J D; Goncharov, V N; Skupsky, S

    2014-04-01

    Thermal conductivity (κ) of both the ablator materials and deuterium-tritium (DT) fuel plays an important role in understanding and designing inertial confinement fusion (ICF) implosions. The extensively used Spitzer model for thermal conduction in ideal plasmas breaks down for high-density, low-temperature shells that are compressed by shocks and spherical convergence in imploding targets. A variety of thermal-conductivity models have been proposed for ICF hydrodynamic simulations of such coupled and degenerate plasmas. The accuracy of these κ models for DT plasmas has recently been tested against first-principles calculations using the quantum molecular-dynamics (QMD) method; although mainly for high densities (ρ > 100 g/cm3), large discrepancies in κ have been identified for the peak-compression conditions in ICF. To cover the wide range of density-temperature conditions undergone by ICF imploding fuel shells, we have performed QMD calculations of κ for a variety of deuterium densities of ρ = 1.0 to 673.518 g/cm3, at temperatures varying from T = 5 × 103 K to T = 8 × 106 K. The resulting κQMD of deuterium is fitted with a polynomial function of the coupling and degeneracy parameters Γ and θ, which can then be used in hydrodynamic simulation codes. Compared with the "hybrid" Spitzer-Lee-More model currently adopted in our hydrocode lilac, the hydrosimulations using the fitted κQMD have shown up to ∼20% variations in predicting target performance for different ICF implosions on OMEGA and direct-drive-ignition designs for the National Ignition Facility (NIF). The lower the adiabat of an imploding shell, the more variations in predicting target performance using κQMD. Moreover, the use of κQMD also modifies the shock conditions and the density-temperature profiles of the imploding shell at early implosion stage, which predominantly affects the final target performance. This is in contrast to the previous speculation that κQMD changes mainly the

  14. Nuclear Quantum Effects in Ice Phases and Water from First Principles Calculations

    NASA Astrophysics Data System (ADS)

    Pamuk, Betul

    Despite the simplicity of the molecule, condensed phases of water show many physical anomalies, some of which are still unexplained to date. This thesis focuses on one striking anomaly that has been largely neglected and never explained. When hydrogen (1H) is replaced by deuterium (2 D), zero point fluctuations of the heavy isotope causes ice to expand, whereas in normal isotope effect, heavy isotope causes volume contraction. Furthermore, in a normal isotope effect, the shift in volume should decrease with increasing temperature, while, in ice, the volume shift increases with increasing temperature and persists up to the melting temperature and also exists in liquid water. In this dissertation, nuclear quantum effects on structural and cohesive properties of different ice polymorphs are investigated. We show that the anomalous isotope effect is well described by first principles density functional theory with van der Waals (vdW-DF) functionals within the quasi-harmonic approximation. Our theoretical modeling explains how the competition between the intra- and inter-molecular bonding of ice leads to an anomalous isotope effect in the volume and bulk modulus of ice. In addition, we predict a normal isotope effect when 16O is replaced by 18O, which is experimentally confirmed. Furthermore, the transition from proton disordered hexagonal phase, ice Ih to proton ordered hexagonal phase, ice XI occurs with a temperature difference between 1H and 2D of 6K, in good agreement with experimental value of 4K. We explain, for first time for that this temperature difference is entirely due to the zero point energy. In the second half of this thesis, we expand our study to the other ice phases: ice Ic, ice IX, ice II, ice VIII, clathrate hydrates, and low and high density amorphous ices. We employ the methodology that we have developed to investigate the isotope effect in structures with different configurations. We show that there is a transition from anomalous isotope effect

  15. First-Principles Computer Simulations of Dense Plasmas and Application to the Interiors of Giant Planets

    NASA Astrophysics Data System (ADS)

    Militzer, Burkhard

    2013-06-01

    This presentation will review three recent applications of first-principles computer simulation techniques to study matter at extreme temperature-pressure conditions that are of relevance to astrophysics. First we report a recent methodological advance in all-electron path integral Monte Carlo (PIMC) that allowed us to extend this method beyond hydrogen and helium to elements with core electrons [1]. We combine results from PIMC and with density functional molecular dynamics (DFT-MD) simulations and derive a coherent equation of state (EOS) for water and carbon plasmas in the regime from 1-50 Mbar and 104-109 K that can be compared to laboratory shock wave experiments. Second we apply DFT-MD simulations to characterize superionic water in the interiors of Uranus and Neptune. By adopting a thermodynamic integration technique, we derive the Gibbs free energy in order to demonstrate the existence of a phase transformation from body-centered cubic to face-centered cubic superionic water [2]. Finally we again use DFT-MD to study the interiors of gas giant planets. We determine the EOS for hydrogen-helium mixtures spanning density-temperature conditions in the deep interiors of giant planets, 0.2-9.0 g/cc and 1000-80000 K [3]. We compare the simulation results with the semi-analytical EOS model by Saumon and Chabrier. We present a revision to the mass-radius relationship which makes the hottest exoplanets increase in radius by ~0.2 Jupiter radii at fixed entropy and for masses greater than 0.5 Jupiter masses. This change is large enough to have possible implications for some discrepant inflated giant exoplanets. We conclude by demonstrating that all materials in the cores of giant planets, ices, MgO, SiO2, and iron, will all dissolve into metallic hydrogen. This implies the cores of Jupiter and Saturn have been at least partially eroded. [1] K. P. Driver, B. Militzer, Phys. Rev. Lett. 108 (2012) 115502. [2] H. F. Wilson, M. L. Wong, B. Militzer, http://arxiv.org/abs/1211

  16. First-principles thermal conductivity of warm-dense deuterium plasmas for inertial confinement fusion applications

    NASA Astrophysics Data System (ADS)

    Hu, S. X.; Collins, L. A.; Boehly, T. R.; Kress, J. D.; Goncharov, V. N.; Skupsky, S.

    2014-04-01

    Thermal conductivity (κ) of both the ablator materials and deuterium-tritium (DT) fuel plays an important role in understanding and designing inertial confinement fusion (ICF) implosions. The extensively used Spitzer model for thermal conduction in ideal plasmas breaks down for high-density, low-temperature shells that are compressed by shocks and spherical convergence in imploding targets. A variety of thermal-conductivity models have been proposed for ICF hydrodynamic simulations of such coupled and degenerate plasmas. The accuracy of these κ models for DT plasmas has recently been tested against first-principles calculations using the quantum molecular-dynamics (QMD) method; although mainly for high densities (ρ > 100 g/cm3), large discrepancies in κ have been identified for the peak-compression conditions in ICF. To cover the wide range of density-temperature conditions undergone by ICF imploding fuel shells, we have performed QMD calculations of κ for a variety of deuterium densities of ρ = 1.0 to 673.518 g/cm3, at temperatures varying from T = 5 × 103 K to T = 8 × 106 K. The resulting κQMD of deuterium is fitted with a polynomial function of the coupling and degeneracy parameters Γ and θ, which can then be used in hydrodynamic simulation codes. Compared with the "hybrid" Spitzer-Lee-More model currently adopted in our hydrocode lilac, the hydrosimulations using the fitted κQMD have shown up to ˜20% variations in predicting target performance for different ICF implosions on OMEGA and direct-drive-ignition designs for the National Ignition Facility (NIF). The lower the adiabat of an imploding shell, the more variations in predicting target performance using κQMD. Moreover, the use of κQMD also modifies the shock conditions and the density-temperature profiles of the imploding shell at early implosion stage, which predominantly affects the final target performance. This is in contrast to the previous speculation that κQMD changes mainly the

  17. [First-principles study of vibrational Raman spectra of amorphous carbon].

    PubMed

    Niu, Li; Zhu, Jia-qi; Gao, Wei; Du, Shan-yi

    2009-09-01

    The vibrational density of states and nonresonant reduced Raman spectra of amorphous carbon at densities of 2.6, 2.9 and 3.2 g x cm(-3) were calculated by the use of a first-principles plane-wave pesudopotential method. Three structural models were generated by liquid-quench method using Car-Parinello molecular dynamics, their vibrational frequencies and eigenmodes were determined using the linear response approach, and Raman coupling tensors were calculated using the finite electric field method. The calculated results show that the sp3 fraction increases from 50% to 84.4%, the sp2 configuration changes from mainly rings to short chains, the position of the G peak moves to higher frequencies, the intensity ratio of D and G peaks decreases, the position of the T peak moves to lower frequencies and the intensity ratio of T and G peaks increases as density increases from 2.6 to 3.2 g x cm(-3). The authors' calculated Raman spectra show an overall good agreement with experimental spectra. The analysis in terms of atomic vibrations confirms that the G and D peaks both come from sp2 C contribution, G peak is due to the stretching vibration of any pair of sp2 atoms and the T peak is due to the C-C sp3 vibration. The authors' analysis also confirms that the dispersion of G and T peaks is due to bond-length changes. The bond length of chains (olefins) is shorter than that of rings, so their vibrational frequency is higher and the G-peak position moves to higher frequencies with increasing the sp3 fraction. The number of sp3-sp2 type bonds decreases as the sp3 fraction increases. These bonds are shorter than pure sp3-sp3 bonds, hence the T-peak position moves to lower frequencies. The research results provide a theoretic basis for analyzing experimental Raman spectra of amorphous carbon.

  18. First-principles quantum mechanical investigations: Catalytic reactions of furfural on Pd(111) and at the water/Pd(111) interface

    NASA Astrophysics Data System (ADS)

    Xue, Wenhua

    Bio-oils have drawn more and more attention from scientists as a promising new clean, cheap energy source. One of the most interesting relevant issues is the effect of catalysts on the catalytic reactions that are used for producing bio-oils. Furfural, as a very important intermediate during these reactions, has attracted significant studies. However, the effect of catalysts, including particularly the liquid/solid interface formed by a metal catalyst and liquid water, in the catalytic reactions involving furfural still remains elusive. In this research, we performed ab initio molecular dynamics simulations and first-principles density-functional theory calculations to investigate the atomic-scale mechanisms of catalytic hydrogenation of furfural on the palladium surface and at the liquid/state interface formed by the palladium surface and liquid water. We studied all the possible mechanisms that lead to formation of furfuryl alcohol (FOL), formation of tetrahydrofurfural (THFAL), and formation of tetrahydrofurfurfuryl alcohol (THFOL). We found that liquid water plays a significant role in the hydrogenation reactions. During the reaction in the presence of water and the palladium catalyst, in particular, water directly participates in the hydrogenation of the aldehyde group of furfural and facilitates the formation of FOL by reducing the activation energy. Our calculations show that water provides hydrogen for the hydrogenation of the aldehyde group, and at the same time, a pre-existing hydrogen atom, which is resulted from dissociation of molecular hydrogen (experimentally, molecular hydrogen is always supplied for hydrogenation) on the palladium surface, is bonded to water, making the water molecule intact in structure. In the absence of water, on the other hand, formation of FOL and THFAL on the palladium surface involves almost the same energy barriers, suggesting a comparable selectivity. Overall, as water reduces the activation energy for the formation of FOL

  19. Molecular-Scale Electronics: From Concept to Function.

    PubMed

    Xiang, Dong; Wang, Xiaolong; Jia, Chuancheng; Lee, Takhee; Guo, Xuefeng

    2016-04-13

    Creating functional electrical circuits using individual or ensemble molecules, often termed as "molecular-scale electronics", not only meets the increasing technical demands of the miniaturization of traditional Si-based electronic devices, but also provides an ideal window of exploring the intrinsic properties of materials at the molecular level. This Review covers the major advances with the most general applicability and emphasizes new insights into the development of efficient platform methodologies for building reliable molecular electronic devices with desired functionalities through the combination of programmed bottom-up self-assembly and sophisticated top-down device fabrication. First, we summarize a number of different approaches of forming molecular-scale junctions and discuss various experimental techniques for examining these nanoscale circuits in details. We then give a full introduction of characterization techniques and theoretical simulations for molecular electronics. Third, we highlight the major contributions and new concepts of integrating molecular functionalities into electrical circuits. Finally, we provide a critical discussion of limitations and main challenges that still exist for the development of molecular electronics. These analyses should be valuable for deeply understanding charge transport through molecular junctions, the device fabrication process, and the roadmap for future practical molecular electronics.

  20. Interplay of oxygen octahedral rotations and electronic instabilities in strontium ruthenate Ruddlesden-Poppers from first principles

    NASA Astrophysics Data System (ADS)

    Voss, Johannes; Fennie, Craig J.

    2011-03-01

    The Ruddlesden-Popper ruthenates Sr n+1 Ru n O3 n + 1 display a broad range of electronic phases including p -wave superconductivity, electronic nematicity, and ferromagnetism. Elucidating the role of the number of perovskite blocks, n , in the realization of these differently ordered electronic states remains a challenge. Additionally dramatic experimental advances now enable the atomic scale growth of these complex oxide thin films on a variety of substrates coherently, allowing for the application of tunable epitaxial strain and subsequently the ability to control structural distortions such as oxygen octahedral rotations. Here we investigate from first principles the effect of oxygen octahedral rotations on the electronic structure of Sr 2 Ru O4 and Sr 3 Ru 2 O7 . We discuss possible implications for the physics of the bulk systems and point towards new effects in thin films.

  1. First-principles quantum-mechanical investigations: The role of water in catalytic conversion of furfural on Pd(111)

    NASA Astrophysics Data System (ADS)

    Xue, Wenhua; Borja, Miguel Gonzalez; Resasco, Daniel E.; Wang, Sanwu

    2015-03-01

    In the study of catalytic reactions of biomass, furfural conversion over metal catalysts with the presence of water has attracted wide attention. Recent experiments showed that the proportion of alcohol product from catalytic reactions of furfural conversion with palladium in the presence of water is significantly increased, when compared with other solvent including dioxane, decalin, and ethanol. We investigated the microscopic mechanism of the reactions based on first-principles quantum-mechanical calculations. We particularly identified the important role of water and the liquid/solid interface in furfural conversion. Our results provide atomic-scale details for the catalytic reactions. Supported by DOE (DE-SC0004600). This research used the supercomputer resources at NERSC, of XSEDE, at TACC, and at the Tandy Supercomputing Center.

  2. First-principles study on stability of transition metal solutes in aluminum by analyzing the underlying forces

    SciTech Connect

    Liu, Wei; Xu, Yichun; Li, Xiangyan; Wu, Xuebang Liu, C. S.; Liang, Yunfeng; Wang, Zhiguang

    2015-05-07

    Although there have been some investigations on behaviors of solutes in metals under strain, the underlying mechanism of how strain changes the stability of a solute is still unknown. To gain such knowledge, first-principles calculations are performed on substitution energy of transition metal solutes in fcc Al host under rhombohedral strain (RS). Our results show that under RS, substitution energy decreases linearly with the increase of outermost d radius r{sub d} of the solute due to Pauli repulsion. The screened Coulomb interaction increases or decreases the substitution energy of a solute on condition that its Pauling electronegativity scale ϕ{sub P} is less or greater than that of Al under RS. This paper verifies a linear relation of substitution energy change versus r{sub d} and ϕ{sub P} under RS, which might be instructive for composition design of long life alloys serving in high stress condition.

  3. Local fields in conductor surface electromigration: A first-principles study in the low-bias ballistic limit

    SciTech Connect

    Bevan, Kirk H; Zhu, Wenguang; Stocks, George Malcolm; Guo, Hong; Zhang, Zhenyu

    2012-01-01

    Utilizing first-principles quantum transport calculations, we investigate the role of local fields in conductor surface electromigration. A nanometer-thick Ag(100) thin film is adopted as our prototypical conductor, where we demonstrate the existence of intense local electric fields at atomic surface defects under an external bias. It is shown that such local fields can play an important role in driving surface electromigration and electrical breakdown. The intense fields originate from the relatively short (atomic-scale) screening lengths common to most elemental metals. This general short-range screening trend is established self-consistently within an intuitive picture of linear response electrostatics. The findings shed new light on the underlying physical origins of surface electromigration and point to the possibility of harnessing local fields to engineer electromigration at the nanoscale.

  4. Lack of support for adaptive superstructure NiPt7 : Experiment and first-principles calculations

    NASA Astrophysics Data System (ADS)

    Schönfeld, B.; Engelke, M.; Ruban, A. V.

    2009-02-01

    Order and effective interaction parameters on the Pt-rich side of solid Ni-Pt alloys have been investigated by experimental and first-principles theoretical techniques. Diffuse x-ray scattering was taken from single-crystalline Ni-87.8at.%Pt aged at 603 K to set up a state of thermal equilibrium. From the separated short-range order scattering, effective pair interaction parameters were determined. These experimentally deduced values do not produce the suggested NiPt7 superstructure at lower temperatures. Instead of that, phase separation into NiPt3 regions with L12 structure and a Pt-rich matrix is observed in Monte Carlo simulations and supported by x-ray scattering of Ni-75.2at.%Pt . First-principles calculations at 0 K also show that the suggested NiPt7 phase is unstable against decomposition into NiPt3 and Pt.

  5. "Watching" Polaron Pair Formation from First-Principles Electron-Nuclear Dynamics.

    PubMed

    Donati, Greta; Lingerfelt, David B; Petrone, Alessio; Rega, Nadia; Li, Xiaosong

    2016-09-22

    The formation of polaron pairs is one of the important photophysical processes that take place after the excitation in semiconducting organic polymers. First-principles Ehrenfest excited-state dynamics is a unique tool to investigate ultrafast photoinduced charge carrier dynamics and related nonequilibrium processes involving correlated electron-nuclear dynamics. In this work the formation of polaron pairs and their dynamical evolution in an oligomer of seven thiophene units is investigated with a combined approach of first-principles exciton-nuclear dynamics and wavelet analysis. The real-time formation of a polaron pair can be observed in the dipole evolution during the excited-state dynamics. The possible driving force of the polaron pair formation is investigated through qualitative correlation between the structural dynamics and the dipole evolution. The time-dependent characteristics and spectroscopic consequences of the polaron pair formation are probed using the wavelet analysis. PMID:27571540

  6. Dispersion correction derived from first principles for density functional theory and Hartree-Fock theory.

    PubMed

    Guidez, Emilie B; Gordon, Mark S

    2015-03-12

    The modeling of dispersion interactions in density functional theory (DFT) is commonly performed using an energy correction that involves empirically fitted parameters for all atom pairs of the system investigated. In this study, the first-principles-derived dispersion energy from the effective fragment potential (EFP) method is implemented for the density functional theory (DFT-D(EFP)) and Hartree-Fock (HF-D(EFP)) energies. Overall, DFT-D(EFP) performs similarly to the semiempirical DFT-D corrections for the test cases investigated in this work. HF-D(EFP) tends to underestimate binding energies and overestimate intermolecular equilibrium distances, relative to coupled cluster theory, most likely due to incomplete accounting for electron correlation. Overall, this first-principles dispersion correction yields results that are in good agreement with coupled-cluster calculations at a low computational cost.

  7. Magnetically induced phonon splitting in A Cr2O4 spinels from first principles

    NASA Astrophysics Data System (ADS)

    Wysocki, Aleksander L.; Birol, Turan

    2016-04-01

    We study the magnetically-induced phonon splitting in cubic A Cr2O4 (A =Mg , Zn, Cd) spinels from first principles and demonstrate that the sign of the splitting, which is experimentally observed to be opposite in CdCr2O4 compared to ZnCr2O4 and MgCr2O4 , is determined solely by the particular magnetic ordering pattern observed in these compounds. We further show that this interaction between magnetism and phonon frequencies can be fully described by the previously proposed spin-phonon coupling model [C. J. Fennie and K. M. Rabe, Phys. Rev. Lett. 96, 205505 (2006)], 10.1103/PhysRevLett.96.205505 that includes only the nearest neighbor exchange. Using this model with materials specific parameters calculated from first principles, we provide additional insights into the physics of spin-phonon coupling in this intriguing family of compounds.

  8. Spin-state transition induced half metallicity in a cobaltate from first principles

    NASA Astrophysics Data System (ADS)

    Ou, Xuedong; Fan, Fengren; Li, Zhengwei; Wang, Hongbo; Wu, Hua

    2016-02-01

    Half metal is a promising spintronic material. Here, we explore, using first principles calculations, a spin-state transition induced half metallicity in a layered cobaltate via a physical or chemical pressure. Our exemplary first principles study shows that the layered cobaltate Sr2CoO3F would undergo a transition, under a pressure of 5.4 GPa, from a high-spin antiferromagnetic insulator to an intermediate-spin ferromagnetic half-metal. The former phase is associated with a superexchange in a Mott insulator, and the latter one is due to a broad band formation and a kinetic energy gain of the partially occupied eg orbital. Note that the above transition could also be induced by a chemical pressure via doping in (Sr1-xCax)2CoO3F (x > 0.3). This work suggests that a cobaltate would be of a particular interest if stabilized into an intermediate-spin state.

  9. First-Principles Studies of the Excited States of Chromophore Monomers and Dimers

    NASA Astrophysics Data System (ADS)

    Hamed, Samia; Sharifzadeh, Sahar; Neaton, Jeffrey

    2015-03-01

    Elucidation of the energy transfer mechanism in natural photosynthetic systems remains an exciting challenge. Through the careful analysis of excited states on individual chromophores and dimers - and the predictive first-principles methods used to compute them - we are building towards an understanding of the nature of excitation transfer among arrays of chromophores embedded in protein environments. Excitation energies, transition dipoles, and natural transition orbitals for the important low-lying singlet and triplet states of experimentally-relevant chromophores are obtained from first-principles time-dependent density functional theory (TDDFT) and many body perturbation theory. The effect of the Tamm-Dancoff approximation and the performance of several exchange-correlation functionals, including an optimally-tuned range-separated hybrid, are evaluated with TDDFT, and compared to MBPT calculations and experiments. This work has been supported by the DOE; computational resources have been provided by NERSC.

  10. Exchange and spin-orbit induced phenomena in diluted (Ga,Mn)As from first principles

    NASA Astrophysics Data System (ADS)

    Kudrnovský, J.; Drchal, V.; Turek, I.

    2016-08-01

    Physical properties induced by exchange interactions (Curie temperature and spin stiffness) and spin-orbit coupling (anomalous Hall effect, anisotropic magnetoresistance, and Gilbert damping) in the diluted (Ga,Mn)As ferromagnetic semiconductor are studied from first principles. Recently developed Kubo-Bastin transport theory and nonlocal torque operator formulation of the Gilbert damping as formulated in the tight-binding linear muffin-tin orbital method are used. The first-principles Liechtenstein mapping is employed to construct an effective Heisenberg Hamiltonian and to estimate Curie temperature and spin stiffness in the real-space random-phase approximation. Good agreement of calculated physical quantities with experiments on well-annealed samples containing only a small amount of compensating defects is obtained.

  11. Magnetically induced phonon splitting in ACr2O4 spinels from first principles

    DOE PAGES

    Wysocki, Aleksander L.; Birol, Turan

    2016-04-22

    We study the magnetically-induced phonon splitting in cubic ACr2O4 (A=Mg, Zn, Cd) spinels from first principles and demonstrate that the sign of the splitting, which is experimentally observed to be opposite in CdCr2O4 compared to ZnCr2O4 and MgCr2O4, is determined solely by the particular magnetic ordering pattern observed in these compounds. We further show that this interaction between magnetism and phonon frequencies can be fully described by the previously proposed spin-phonon coupling model [C. J. Fennie and K. M. Rabe, Phys. Rev. Lett. 96, 205505 (2006)] that includes only the nearest neighbor exchange. In conclusion, using this model with materialsmore » specific parameters calculated from first principles, we provide additional insights into the physics of spin-phonon coupling in this intriguing family of compounds.« less

  12. First-Principles Momentum-Dependent Local Ansatz Wavefunction and Momentum Distribution Function Bands of Iron

    NASA Astrophysics Data System (ADS)

    Kakehashi, Yoshiro; Chandra, Sumal

    2016-04-01

    We have developed a first-principles local ansatz wavefunction approach with momentum-dependent variational parameters on the basis of the tight-binding LDA+U Hamiltonian. The theory goes beyond the first-principles Gutzwiller approach and quantitatively describes correlated electron systems. Using the theory, we find that the momentum distribution function (MDF) bands of paramagnetic bcc Fe along high-symmetry lines show a large deviation from the Fermi-Dirac function for the d electrons with eg symmetry and yield the momentum-dependent mass enhancement factors. The calculated average mass enhancement m*/m = 1.65 is consistent with low-temperature specific heat data as well as recent angle-resolved photoemission spectroscopy (ARPES) data.

  13. Lattice Anharmonicity and Thermal Conductivity from Compressive Sensing of First-Principles Calculations

    DOE PAGES

    Zhou, Fei; Nielson, Weston; Xia, Yi; Ozolins, Vidvuds

    2014-10-27

    First-principles prediction of lattice thermal conductivity KL of strongly anharmonic crystals is a long-standing challenge in solid state physics. Using recent advances in information science, we propose a systematic and rigorous approach to this problem, compressive sensing lattice dynamics (CSLD). Compressive sensing is used to select the physically important terms in the lattice dynamics model and determine their values in one shot. Non-intuitively, high accuracy is achieved when the model is trained on first-principles forces in quasi-random atomic configurations. The method is demonstrated for Si, NaCl, and Cu12Sb4S13, an earth-abundant thermoelectric with strong phononphonon interactions that limit the room-temperature KLmore » to values near the amorphous limit.« less

  14. Lattice Anharmonicity and Thermal Conductivity from Compressive Sensing of First-Principles Calculations

    SciTech Connect

    Zhou, Fei; Nielson, Weston; Xia, Yi; Ozolins, Vidvuds

    2014-10-27

    First-principles prediction of lattice thermal conductivity KL of strongly anharmonic crystals is a long-standing challenge in solid state physics. Using recent advances in information science, we propose a systematic and rigorous approach to this problem, compressive sensing lattice dynamics (CSLD). Compressive sensing is used to select the physically important terms in the lattice dynamics model and determine their values in one shot. Non-intuitively, high accuracy is achieved when the model is trained on first-principles forces in quasi-random atomic configurations. The method is demonstrated for Si, NaCl, and Cu12Sb4S13, an earth-abundant thermoelectric with strong phononphonon interactions that limit the room-temperature KL to values near the amorphous limit.

  15. Lattice Anharmonicity and Thermal Conductivity from Compressive Sensing of First-Principles Calculations

    SciTech Connect

    Zhou, Fei; Nielson, Weston; Xia, Yi; Ozoliņš, Vidvuds

    2014-10-01

    First-principles prediction of lattice thermal conductivity κL of strongly anharmonic crystals is a long-standing challenge in solid-state physics. Making use of recent advances in information science, we propose a systematic and rigorous approach to this problem, compressive sensing lattice dynamics. Compressive sensing is used to select the physically important terms in the lattice dynamics model and determine their values in one shot. Nonintuitively, high accuracy is achieved when the model is trained on first-principles forces in quasirandom atomic configurations. The method is demonstrated for Si, NaCl, and Cu12Sb4S13, an earth-abundant thermoelectric with strong phonon-phonon interactions that limit the room-temperature κL to values near the amorphous limit.

  16. Methane Oxidation over PdO(101) Revealed by First-Principles Kinetic Modeling.

    PubMed

    Van den Bossche, Maxime; Grönbeck, Henrik

    2015-09-23

    The catalytic oxidation of methane to carbon dioxide and water over PdO(101) is investigated with first-principles based microkinetic modeling. Extensive exploration of the reaction landscape allows for determination of preferred pathways at different reaction conditions. The predicted kinetic behavior is in good agreement with a range of experimental findings including reaction orders in methane, water, and oxygen as well as apparent activation energies. The results consolidate the role of the PdO(101) surface in the activity of PdO catalysts and offer starting points for computational design of materials with improved catalytic activity. Moreover, the study demonstrates the predictive power of first-principles based kinetic modeling for oxide surfaces when hybrid functionals are applied in conjugation with kinetic models that go beyond the mean-field approximation. PMID:26333148

  17. First-principles analysis of anharmonic nuclear motion and thermal transport in thermoelectric materials

    SciTech Connect

    Tadano, Terumasa; Tsuneyuki, Shinji

    2015-12-31

    We show a first-principles approach for analyzing anharmonic properties of lattice vibrations in solids. We firstly extract harmonic and anharmonic force constants from accurate first-principles calculations based on the density functional theory. Using the many-body perturbation theory of phonons, we then estimate the phonon scattering probability due to anharmonic phonon-phonon interactions. We show the validity of the approach by computing the lattice thermal conductivity of Si, a typical covalent semiconductor, and selected thermoelectric materials PbTe and Bi{sub 2}Te{sub 3} based on the Boltzmann transport equation. We also show that the phonon lifetime and the lattice thermal conductivity of the high-temperature phase of SrTiO{sub 3} can be estimated by employing the perturbation theory on top of the solution of the self-consistent phonon equation.

  18. Structure of the (111) surface of bismuth: LEED analysis and first-principles calculations

    SciTech Connect

    Moenig, H.; Wells, J.; Hofmann, Ph.; Sun, J.; Pohl, K.; Koroteev, Yu.M.; Bihlmayer, G.; Chulkov, E.V.

    2005-08-15

    The surface structure of Bi(111) was investigated by low-energy electron diffraction (LEED) intensity analysis for temperatures between 140 and 313 K and by first-principles calculations. The diffraction pattern reveals a (1x1) surface structure and LEED intensity versus energy simulations confirm that the crystal is terminated with a Bi bilayer. Excellent agreement is obtained between the calculated and measured diffraction intensities in the whole temperature range. The first interlayer spacing shows no significant relaxation at any temperature while the second interlayer spacing expands slightly. The Debye temperatures deduced from the optimized atomic vibrational amplitudes for the two topmost layers are found to be significantly lower than in the bulk. The experimental results for the relaxations agree well with those of our first-principles calculation.

  19. First-principles insights into f magnetism: A case study on some magnetic pyrochlores

    NASA Astrophysics Data System (ADS)

    Deilynazar, Najmeh; Khorasani, Elham; Alaei, Mojtaba; Javad Hashemifar, S.

    2015-11-01

    First-principles calculations are performed to investigate f magnetism in A2Ti2O7 (A=Eu, Gd, Tb, Dy, Ho, Er, Yb) magnetic pyrochlore oxides. The Hubbard U parameter and the relativistic spin orbit correction are applied for a more accurate description of the electronic structure of the systems. It is argued that the main obstacle for the first-principles study of these systems is the multi-minima solutions of their electronic configuration. Among the studied pyrochlores, Gd2Ti2O7 shows the least multi-minima problem. The crystal electric field theory is applied for phenomenological comparison of the calculated spin and orbital moments with the experimental data.

  20. Integration of first-principles methods and crystallographic database searches for new ferroelectrics: Strategies and explorations

    NASA Astrophysics Data System (ADS)

    Bennett, Joseph W.; Rabe, Karin M.

    2012-11-01

    In this concept paper, the development of strategies for the integration of first-principles methods with crystallographic database mining for the discovery and design of novel ferroelectric materials is discussed, drawing on the results and experience derived from exploratory investigations on three different systems: (1) the double perovskite Sr(Sb1/2Mn1/2)O3 as a candidate semiconducting ferroelectric; (2) polar derivatives of schafarzikite MSb2O4; and (3) ferroelectric semiconductors with formula M2P2(S,Se)6. A variety of avenues for further research and investigation are suggested, including automated structure type classification, low-symmetry improper ferroelectrics, and high-throughput first-principles searches for additional representatives of structural families with desirable functional properties.