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
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.
Stable and Efficient Linear Scaling First-Principles Molecular Dynamics for 10000+ Atoms.
Arita, Michiaki; Bowler, David R; Miyazaki, Tsuyoshi
2014-12-01
The recent progress of linear-scaling or O(N) methods in density functional theory (DFT) is remarkable. Given this, we might expect that first-principles molecular dynamics (FPMD) simulations based on DFT could treat more realistic and complex systems using the O(N) technique. However, very few examples of O(N) FPMD simulations exist to date, and information on the accuracy and reliability of the simulations is very limited. In this paper, we show that efficient and robust O(N) FPMD simulations are now possible by the combination of the extended Lagrangian Born-Oppenheimer molecular dynamics method, which was recently proposed by Niklasson ( Phys. Rev. Lett. 2008 , 100 , 123004 ), and the density matrix method as an O(N) technique. Using our linear-scaling DFT code Conquest, we investigate the reliable calculation conditions for accurate O(N) FPMD and demonstrate that we are now able to do practical, reliable self-consistent FPMD simulations of a very large system containing 32768 atoms. PMID:26583225
Gygi, F; Draeger, E W; de Supinski, B R; Yates, R K; Franchetti, F; Kral, S; Lorenz, J; Ueberhuber, C; Gunnels, J A; Sexton, J C
2005-04-25
We demonstrate that the Qbox code supports unprecedented large-scale First-Principles Molecular Dynamics (FPMD) applications on the BlueGene/L supercomputer. Qbox is an FPMD implementation specifically designed for large-scale parallel platforms such as BlueGene/L. Strong scaling tests for a Materials Science application show an 86% scaling efficiency between 1024 and 32,768 CPUs. Measurements of performance by means of hardware counters show that 37% of the peak FPU performance can be attained.
Gygi, F; Draeger, E; de Supinski, B; Yates, R K; Franchetti, F; Kral, S; Lorenz, J; Ueberhueber, C; Gunnels, J A; Sexton, J
2006-01-04
First-Principles Molecular Dynamics (FPMD) is an accurate, atomistic simulation approach that is routinely applied to a variety of areas including solid-state physics, chemistry, biochemistry and nanotechnology. FPMD enables one to perform predictive materials simulations, as no empirical or adjustable parameters are used to describe a given system. Instead, a quantum mechanical description of electrons is obtained by solving the Kohn-Sham equations within a pseudopotential plane-wave formalism. This rigorous first-principles treatment of electronic structure is computationally expensive and limits the size of tractable systems to a few hundred atoms on most currently available parallel computers. Developed specifically for large parallel systems at LLNL's Center for Applied Scientific Computing, the Qbox implementation of the FPMD method shows unprecedented performance and scaling on BlueGene/L.
A Scalable O(N) Algorithm for Large-Scale Parallel First-Principles Molecular Dynamics Simulations
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(N^{3}) 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.
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
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.
First principles molecular dynamics of molten NaCl
NASA Astrophysics Data System (ADS)
Galamba, N.; Costa Cabral, B. J.
2007-03-01
First principles Hellmann-Feynman molecular dynamics (HFMD) results for molten NaCl at a single state point are reported. The effect of induction forces on the structure and dynamics of the system is studied by comparison of the partial radial distribution functions and the velocity and force autocorrelation functions with those calculated from classical MD based on rigid-ion and shell-model potentials. The first principles results reproduce the main structural features of the molten salt observed experimentally, whereas they are incorrectly described by both rigid-ion and shell-model potentials. Moreover, HFMD Green-Kubo self-diffusion coefficients are in closer agreement with experimental data than those predicted by classical MD. A comprehensive discussion of MD results for molten NaCl based on different ab initio parametrized polarizable interionic potentials is also given.
First-principles semiclassical initial value representation molecular dynamics.
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
First principles molecular dynamics without self-consistent field optimization
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.
First principles molecular dynamics study of filled ice hydrogen hydrate.
Zhang, Jingyun; Kuo, Jer-Lai; Iitaka, Toshiaki
2012-08-28
We investigated structural changes, phase diagram, and vibrational properties of hydrogen hydrate in filled-ice phase C(2) by using first principles molecular dynamics simulation. It was found that the experimentally reported "cubic" structure is unstable at low temperature and/or high pressure: The "cubic" structure reflects the symmetry at high (room) temperature where the hydrogen bond network is disordered and the hydrogen molecules are orientationally disordered due to thermal rotation. In this sense, the "cubic" symmetry would definitely be lowered at low temperature where the hydrogen bond network and the hydrogen molecules are expected to be ordered. At room temperature and below 30 GPa, it is the thermal effects that play an essential role in stabilizing the structure in "cubic" symmetry. Above 60 GPa, the hydrogen bonds in the framework would be symmetrized and the hydrogen bond order-disorder transition would disappear. These results also suggest the phase behavior of other filled-ice hydrates. In the case of rare gas hydrate, there would be no guest molecules' rotation-nonrotation transition since the guest molecules keep their spherical symmetry at any temperature. On the contrary methane hydrate MH-III would show complex transitions due to the lower symmetry of the guest molecule. These results would encourage further experimental studies, especially nuclear magnetic resonance spectroscopy and neutron scattering, on the phases of filled-ice hydrates at high pressures and/or low temperatures. PMID:22938248
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.
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.
Excited-State Properties of Molecular Solids from First Principles.
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
Extreme Scale Computing for First-Principles Plasma Physics Research
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.
Dithiocarbamate anchoring in molecular wire junctions: a first principles study.
Li, Zhenyu; Kosov, Daniel S
2006-05-25
Recent experimental realization [J. Am. Chem. Soc., 127 (2005) 7328] of various dithiocarbamate self-assembly on gold surface opens the possibility for use of dithiocarbamate linkers to anchor molecular wires to gold electrodes. In this paper, we explore this hypothesis computationally. We computed the electron transport properties of 4,4'-bipyridine (BP), 4,4'-bipyridinium-1,1'-bis(carbodithioate) (BPBC), 4-(4'-pyridyl)-peridium-1-carbodithioate (BPC) molecule junctions based on the density functional theory and nonequilibrium Green's functions. We demonstrated that the stronger molecule-electrode coupling associated with the conjugated dithiocarbamate linker broadens transmission resonances near the Fermi energy. The broadening effect along with the extension of the pi conjugation from the molecule to the gold electrodes lead to enhanced electrical conductance for BPBC molecule. The conductance enhancement factor is as large as 25 at applied voltage bias 1.0 V. Rectification behavior is predicted for BPC molecular wire junction, which has the asymmetric anchoring groups. PMID:16706444
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).
Scaling First Principles Materials Science Codes to Thousands of Processors
NASA Astrophysics Data System (ADS)
Canning, Andrew; Raczkowski, David
2004-03-01
Modern supercomputers have been rapidly increasing in power in large part by using more processors rather than more powerful processors. The most powerful computer in the world at present as listed by www.top500.org is the Earth simulator in Japan (NEC SX6) which has 5120 vector processors and all the top 18 machines on the list have more than 1000 processors. In this talk I will present some novel computational algorithms for scaling up plane-wave based materials science codes to run on these large machines avoiding communication bottlenecks typical of these types of codes. I will present some performance results for some physical systems such as CdSe quantum dots on the IBM SP, Cray X1 and NEC SX6. (This work was supported by the Director, Office of Advanced Scientific Computing Research, Division of Mathematical, Information and Computational Sciences of the U.S. Department of Energy and the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory under contract number DE-AC03-76SF00098)
First Principle Molecular Dynamics Study of Melting in Silicon and Germanium
NASA Astrophysics Data System (ADS)
Wang, Xiaofei; Scandolo, Sandro; Car, Roberto
2003-03-01
We present a scheme to compute the phase diagrams of materials with Density Functional Theory (DFT). Our approach is based on first principle molecular dynamics simulations combined with the scaling algorithm proposed by M. Koning, A. Antonelli and S. Yip. (Phys. Rev. Lett. 83, 3973 (1999)) to improve the efficiency of thermodynamic integration techniques. This approach allows us to compute the free energy of a given material phase over a finite temperature range using a single simulation run. We have applied this scheme to study the melting transition in Silicon and Germanium, using both LDA and GGA approximations of density functional theory. Both approximations give qualitatively similar results. In the Silicon case, the calculated melting temperature is in better agreement with experiment when the GGA approximation is used.
Protein-Protein Interactions from Linear-Scaling First Principles Quantum Mechanical Calculations
NASA Astrophysics Data System (ADS)
Cole, Daniel; Skylaris, Chris-Kriton; Rajendra, Eeson; Venkitaraman, Ashok; Payne, Mike
2010-03-01
A modification of the MM-PBSA technique for calculating binding affinities of biomolecular complexes is presented. Classical molecular dynamics is used to explore the motion of the extended interface between two peptides derived from the BRC4 repeat of BRCA2 and the eukaryotic recombinase RAD51. The resulting trajectory is sampled using the linear-scaling density functional theory code, onetep, to determine from first principles, and with high computational efficiency, the relative free energies of binding of the ˜2800 atom receptor-ligand complexes. This new method provides the basis for computational interrogation of protein-protein and protein-ligand interactions, within fields ranging from chemical biological studies to small molecule binding behaviour, with both unprecedented chemical accuracy and affordable computational expense.
Protein-protein interactions from linear-scaling first-principles quantum-mechanical calculations
NASA Astrophysics Data System (ADS)
Cole, D. J.; Skylaris, C.-K.; Rajendra, E.; Venkitaraman, A. R.; Payne, M. C.
2010-08-01
A modification of the MM-PBSA technique for calculating binding affinities of biomolecular complexes is presented. Classical molecular dynamics is used to explore the motion of the extended interface between two peptides derived from the BRC4 repeat of BRCA2 and the eukaryotic recombinase RAD51. The resulting trajectory is sampled using the linear-scaling density functional theory code, onetep, to determine from first principles, and with high computational efficiency, the relative free energies of binding of the ~2800 atom receptor-ligand complexes. This new method provides the basis for computational interrogation of protein-protein and protein-ligand interactions within fields ranging from chemical biological studies to small-molecule binding behaviour, with both unprecedented chemical accuracy and affordable computational expense.
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.
A method of orbital analysis for large-scale first-principles simulations
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})
Determination of structure and properties of molecular crystals from first principles.
Szalewicz, Krzysztof
2014-11-18
CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be
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.
Redox condition in molten salts and solute behavior: A first-principles molecular dynamics study
NASA Astrophysics Data System (ADS)
Nam, Hyo On; Morgan, Dane
2015-10-01
Molten salts technology is of significant interest for nuclear, solar, and other energy systems. In this work, first-principles molecular dynamics (FPMD) was used to model the solute behavior in eutectic LiCl-KCl and FLiBe (Li2BeF4) melts at 773 K and 973 K, respectively. The thermo-kinetic properties for solute systems such as the redox potential, solute diffusion coefficients and structural information surrounding the solute were predicted from FPMD modeling and the calculated properties are generally in agreement with the experiments. In particular, we formulate an approach to model redox energetics vs. chlorine (or fluorine) potential from first-principles approaches. This study develops approaches for, and demonstrates the capabilities of, FPMD to model solute properties in molten salts.
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
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.
First-Principles Molecular Dynamics Calculations of the Equation of State for Tantalum
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
First-principles study of the electronic and molecular structure of protein nanotubes
NASA Astrophysics Data System (ADS)
Okamoto, Hajime; Takeda, Kyozaburo; Shiraishi, Kenji
2001-09-01
The electronic and molecular structures of protein nanotubes (PNT's) have been investigated theoretically by first-principles electronic structure calculations. The results have been discussed in comparison to those of the polypeptide open chains (POC's) and polypeptide closed rings (PCR's) in order to give a systematic understanding. Focusing on the intra-ring and inter-ring hydrogen bonds (HB's), we also investigate the PCR stacking mechanism. The present calculation reveals that PNT's are semiconductors and that an extra proton in the tube interior has the potential to be an electron acceptor.
Spin Crossover in Ferropericlase From First-Principles Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Holmstrom, E.; Stixrude, L. P.
2013-12-01
Ferropericlase is believed to be the second-most abundant mineral of the lower mantle of the Earth. It is experimentally known that with increasing pressure, the iron ions in the mineral begin to collapse from a high-spin to low-spin state. This spin crossover looks certain to have geophysical effects, and hence a good theoretical understanding of the phenomenon is necessary. Using first-principles molecular dynamics simulations in conjunction with thermodynamic integration, we construct a phase diagram of the spin crossover as a function of pressure and temperature. In addition, we predict that the mineral loses its electrically insulating character within the lower mantle.
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
Crystalline and liquid Si3 N4 characterization by first-principles molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Mauri, Aurelio; Celino, Massimo; Castellani, Niccoló; Erbetta, Davide
2011-05-01
Silicon nitride (Si3 N4) has a wide range of engineering applications where its mechanical and electronic properties can be effectively exploited. In particular, in the microelectronics field, the amorphous silicon nitride films are widely used as charge storage layer in metal-alumina-nitrideoxide nonvolatile memory devices. Atomic structure of amorphous silicon nitride is characterized by an high concentration of traps that control the electric behavior of the final device by the trappingde-trapping mechanism of the electrical charge occurring in its traps. In order to have a deep understanding of the material properties and, in particular, the nature of the electrical active traps a detailed numerical characterization of the crystalline and liquid phases is mandatory. For these reasons first-principles molecular dynamics simulations are extensively employed to simulate the crystalline Si3 N4 in its crystalline and liquid phases. Good agreement with experimental results is obtained in terms of density and formation entalpy. Detailed characterization of c-Si3 N4 electronic properties is performed in terms of band structure and band gap. Then constant temperature and constant volume first-principles molecular dynamics is used to disorder a stoichiometric sample of Si3 N4 . Extensive molecular dynamics simulations are performed to obtain a reliable liquid sample whose atomic structure does not depend on the starting atomic configuration. Detailed characterization of the atomic structure is achieved in terms of radial distribution functions and total structure factor.
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
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
NASA Astrophysics Data System (ADS)
Righi, Maria Clelia; Zilibotti, Giovanna; Corni, Stefano; Ferrario, Mauro; Bertoni, Carlo Maria
2016-05-01
Ab initio molecular dynamics offers an unexpected tool to understand many aspects of complex and macroscopic phenomena, like friction, lubrication, and surface passivation through chemical reactions induced by load and confinement, as found in recent works (Zilibotti et al., in Phys. Rev. Lett. 111:146101, 2013; De Barros Bouchet et al., J Phys Chem C 116:6966, 2012). Here we review the results of first-principle molecular dynamics simulations of diamond interfaces interacting with water molecules, at different concentrations. We found that the molecular confinement induced by the applied load promotes water dissociation. The consequent surface passivation prevents the formation of carbon bonds across the interface, reducing adhesion and friction. The possibility to extend the use of an atomistic approach to understand the kinetics of tribochemical reactions and their effects on friction will also be discussed.
Mechanisms of molecular doping of graphene: A first-principles study
NASA Astrophysics Data System (ADS)
Saha, Srijan Kumar; Chandrakanth, Reddy Ch.; Krishnamurthy, H. R.; Waghmare, U. V.
2009-10-01
Doping graphene with electron donating or accepting molecules is an interesting approach to introduce carriers into it, analogous to electrochemical doping accomplished in graphene when used in a field-effect transistor. Here, we use first-principles density-functional theory to determine changes in the electronic-structure and vibrational properties of graphene that arise from the adsorption of aromatic molecules such as aniline and nitrobenzene. Identifying the roles of various mechanisms of chemical interaction between graphene and a molecule, we bring out the contrast between electrochemical and molecular doping of graphene. Our estimates of various contributions to shifts in the Raman-active modes of graphene with molecular doping are fundamental to the possible use of Raman spectroscopy in (a) characterization of the nature and concentration of carriers in graphene with molecular doping, and (b) graphene-based chemical sensors.
Terahertz spectra of biotin based on first principle, molecular mechanical, and hybrid simulations.
Bykhovski, Alexei; Woolard, Dwight
2013-07-01
Terahertz (THz) absorption of biotin was simulated using the first principle and the density functional theory (DFT) both in the harmonic approximation and with corrections for the anharmonicity. Anharmonicity corrections were calculated using two different approaches. First, the perturbation theory-based first principle calculations were performed to include third- and fourth-order anharmonicity corrections in atomic displacements to harmonic vibrational states. Second, the atom-centered density matrix propagation molecular dynamics model that provides a good energy conservation was used to calculate the atomic trajectories, velocities, and a dipole moment time history of biotin at low and room temperatures. Predicted low-THz lines agree well with the experimental spectra. The influence of the polyethylene (PE) matrix embedment on the THz spectra of biotin at the nanoscale was studied using the developed hybrid DFT/molecular mechanical approach. While PE is almost transparent at THz frequencies, additional low-THz lines are predicted in the biotin/PE system, which reflects a dynamic interaction between biotin and a surrounding PE cavity. PMID:25055303
Three-dimensional diffusion of molecular hydrogen in graphdiyne: a first-principles study
NASA Astrophysics Data System (ADS)
Zhang, Hongyu; Zhao, Xiaoyang; Zhang, Meng; Luo, Youhua; Li, Guihua; Zhao, Mingwen
2013-12-01
First-principles calculations with van der Waals correction included are carried out to investigate the intercalation and diffusion of molecular hydrogen in single-layer and bulk graphdiyne, which is crucial for understanding and improving the hydrogen storage capacity of graphdiyne. Different intercalation sites and hydrogen molecular orientations have been considered and compared. It is found that configurations with the axis of the hydrogen molecule parallel to graphdiyne layers are favoured. In contrast to graphite where hydrogen diffusion is restricted within the interlayer space, the unique porous structure of graphdiyne enables three-dimensional diffusion of hydrogen (in-plane diffusion and out-plane diffusion) with moderate energy barriers, thus ensuring easy hydrogen loading and unloading. The in-plane diffusion barriers largely depend on the interlayer distance, whereas the interlayer spacing has little effect on the out-plane diffusion barriers. This experimentally available novel carbon allotrope is expected to find applications in hydrogen storage.
NASA Astrophysics Data System (ADS)
Tsukamoto, Shigeru; Caciuc, Vasile; Atodiresei, Nicolae; Blügel, Stefan
2012-06-01
In this first-principles study, we present density-functional calculations of the electronic structures and electron transport properties of organic molecular junctions with several anchoring groups containing atoms with different electronegativities, i.e., benzenediboronate (BDB), benzenedicarboxylate (BDC), and dinitrobenzene (DNB) molecular junctions sandwiched between two Cu(110) electrodes. The electronic-structure calculations exhibit a significant difference in the density of states not only at the anchoring groups but also at the aromatic rings of the molecular junctions, suggesting that the electron transport is specific for each system. Our transport calculations show that the BDB and DNB molecular junctions have finite electron transmissions at the zero-bias limit while the BDC molecular junction has a negligible electron transmission. Moreover, for the BDB and DNB systems, the electron transmission channels around the Fermi energy reveal fingerprint features, which provide specific functionalities for the molecular junctions. Therefore, our theoretical results demonstrate the possibility to precisely tune the electron transport properties of molecular junctions by engineering the anchoring groups at the single-atom level.
First Principles Molecular Modeling of Sensing Material Selection for Hybrid Biomimetic Nanosensors
NASA Astrophysics Data System (ADS)
Blanco, Mario; McAlpine, Michael C.; Heath, James R.
Hybrid biomimetic nanosensors use selective polymeric and biological materials that integrate flexible recognition moieties with nanometer size transducers. These sensors have the potential to offer the building blocks for a universal sensing platform. Their vast range of chemistries and high conformational flexibility present both a problem and an opportunity. Nonetheless, it has been shown that oligopeptide aptamers from sequenced genes can be robust substrates for the selective recognition of specific chemical species. Here we present first principles molecular modeling approaches tailored to peptide sequences suitable for the selective discrimination of small molecules on nanowire arrays. The modeling strategy is fully atomistic. The excellent performance of these sensors, their potential biocompatibility combined with advanced mechanistic modeling studies, could potentially lead to applications such as: unobtrusive implantable medical sensors for disease diagnostics, light weight multi-purpose sensing devices for aerospace applications, ubiquitous environmental monitoring devices in urban and rural areas, and inexpensive smart packaging materials for active in-situ food safety labeling.
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.
First principles molecular dynamics study of nitrogen vacancy complexes in boronitrene.
Ukpong, A M; Chetty, N
2012-07-01
We present the results of first principles molecular dynamics simulations of nitrogen vacancy complexes in monolayer hexagonal boron nitride. The threshold for local structure reconstruction is found to be sensitive to the presence of a substitutional carbon impurity. We show that activated nitrogen dynamics triggers the annihilation of defects in the layer through formation of Stone-Wales-type structures. The lowest energy state of nitrogen vacancy complexes is negatively charged and spin polarized. Using the divacancy complex, we show that their formation induces spontaneous magnetic moments, which is tunable by electron or hole injection. The Fermi level s-resonant defect state is identified as a unique signature of the ground state of the divacancy complex. Due to their ability to enhance structural cohesion, only the divacancy and the nitrogen vacancy carbon-antisite complexes are able to suppress the Fermi level resonant defect state to open a gap between the conduction and valence bands. PMID:22677800
Spin crossover in ferropericlase from first-principles molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Holmstrom, Eero; Stixrude, Lars
2014-05-01
Ferropericlase is the second-most abundant mineral of the lower mantle of the Earth. It is experimentally known that with increasing pressure, the iron ions in the mineral begin to collapse from a high-spin to low-spin state. This spin crossover alters various properties of the material, and hence a good theoretical understanding of the phenomenon is necessary. Using first-principles molecular dynamics simulations in conjunction with thermodynamic integration, we construct a phase diagram of the spin crossover as a function of pressure and temperature. In addition, we present the thermal equation of state of the mineral up to 140 GPa and 4000 K, and predict that the electrical conductivity of ferropericlase reaches semi-metallic values within the lower mantle.
A First Principles Molecular Dynamics Study Of Calcium Ion In Water
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
NASA Astrophysics Data System (ADS)
Osei-Kuffuor, Daniel; Fattebert, Jean-Luc
2014-01-01
We present the first truly scalable first-principles molecular dynamics algorithm with O(N) complexity and controllable accuracy, capable of simulating systems with finite band gaps of sizes that were previously impossible with this degree of accuracy. By avoiding global communications, we provide a practical computational scheme capable of extreme scalability. Accuracy is controlled by the mesh spacing of the finite difference discretization, the size of the localization regions in which the electronic wave functions are confined, and a cutoff beyond which the components of the overlap matrix can be omitted when computing selected elements of its inverse. We demonstrate the algorithm's excellent parallel scaling for up to 101 952 atoms on 23 328 processors, with a wall-clock time of the order of 1 min per molecular dynamics time step and numerical error on the forces of less than 7×10-4 Ha/Bohr.
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.
NASA Astrophysics Data System (ADS)
Reeves, Kyle; Yao, Yi; Kanai, Yosuke
Electronic stopping describes the transfer of energy from a highly-energetic charged particle to electrons in a material. This process induces massive electronic excitations via interaction between the material and the highly localized electric field from the charged particle. Understanding this phenomenon in condensed matter systems under proton irradiation has implications in various modern technologies. First-principles simulations, based on our recently-developed large-scale real-time time-dependent density functional theory approach, provide a detailed description of how electrons are excited via a non-equilibrium energy transfer from protons on the attosecond time scale. We apply this computational approach to the important case of liquid water under proton irradiation. Our work reveals several key features of the excitation dynamics at the mesoscopic and molecular levels which support a clearer understanding of the water radiolysis mechanism under proton irradiation. Importantly, we will demonstrate a first-principles determination of the energy transfer rate, (i.e. electronic stopping power) in liquid water, and a comparison to existing empirical models will be presented. We will conclude by discussing how the exchange-correlation approximation influences the calculation of the electronic stopping power.
Savage, C. M.; Schwenn, P. E.; Kheruntsyan, K. V.
2006-09-15
We investigate the quantum many-body dynamics of dissociation of a Bose-Einstein condensate of molecular dimers into pairs of constituent bosonic atoms and analyze the resulting atom-atom correlations. The quantum fields of both the molecules and atoms are simulated from first principles in three dimensions using the positive-P representation method. This allows us to provide an exact treatment of the molecular field depletion and s-wave scattering interactions between the particles, as well as to extend the analysis to nonuniform systems. In the simplest uniform case, we find that the major source of atom-atom decorrelation is atom-atom recombination which produces molecules outside the initially occupied condensate mode. The unwanted molecules are formed from dissociated atom pairs with nonopposite momenta. The net effect of this process--which becomes increasingly significant for dissociation durations corresponding to more than about 40% conversion--is to reduce the atom-atom correlations. In addition, for nonuniform systems we find that mode mixing due to inhomogeneity can result in further degradation of the correlation signal. We characterize the correlation strength via the degree of squeezing of particle number-difference fluctuations in a certain momentum-space volume and show that the correlation strength can be increased if the signals are binned into larger counting volumes.
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.
NASA Astrophysics Data System (ADS)
Zapol, Peter; Karpeyev, Dmitry; Maheshwari, Ketan; Zhong, Xiaoliang; Narayanan, Badri; Sankaranarayanan, Subramanian; Wilde, Michael; Heinonen, Olle; Rungger, Ivan
2015-03-01
The electronic conduction in Hf-oxide heterostructures for use in, e.g., resistive switching devices, depends sensitively on local oxygen stoichiometry and interactions at interfaces with metal electrodes. In order to model the electronic structure of different disordered configurations near interfaces, we have combined molecular dynamics (MD) simulations with first-principle based non-equilibrium Green's functions (NEGF) methods, including self-interaction corrections. We have developed an approach to generating automated workflows that combine MD and NEGF computations over many parameter values using the Swift parallel scripting language. A sequence of software tools transforms the result of one calculation into the input of the next allowing for a high-throughput concurrent parameter sweep. MD simulations generate systems with quenched disorder, which are then directly fed to NEGF and on to postprocessing. Different computations can be run on different computer platforms matching the computational load to the hardware resources. We will demonstrate results for metal-HfO2-metal heterostructures obtained using this workflow. Argonne National Laboratory's work was supported under U.S. Department of Energy Contract DE-AC02-06CH11357.
NASA Astrophysics Data System (ADS)
Kambayashi, Shaw; Chihara, Junzo
1996-06-01
A first-principles molecular dynamics (MD) scheme is presented on the basis of the density-functional (DF) theory with use of the the quantal hypernetted chain (QHNC) approximation. The DF theory brings about exact expressions for the ion-electron and ion-ion radial distribution functions (RDF) of an electron-ion mixture as a model of a simple liquid metal. These exact expressions prove that an ion-electron mixture can be treated as a one-component liquid interacting only via a pairwise interaction in the evaluation of the ion-ion RDF, and provide a set of integral equations: one is an exact integral equation for the ion-ion RDF and another for an effective ion-ion interaction, which depends on the ion configuration specified by the ion-ion RDF. Hence, after some approximations are introduced, the MD simulation can be performed to get the ion-ion RDF using the ion-ion interaction determined so as to be consistent to the ion-ion RDF: the MD simulation and the procedure to determine the effective interaction from the QHNC equation are performed iteratively. This MD simulation coupled with the QHNC equation (QHNC-MD method) for the effective interaction provides a first-principles calculation of structures of simple liquid metal: the ion-ion and electron-ion RDF's, the charge distributions of an ion and a pseudoatom, the effective ion-ion interaction and the ion-ion bridge function are evaluated in a self-consistent manner from the atomic number as the only input. We have applied this QHNC-MD method to Li, Na, K, Rb, and Cs near the melting temperature using up to 16 000 particles for the MD simulation. It is found that the convergence of the effective ion-ion interaction is fast enough for practical application to alkali metals; two MD runs are enough for convergence within accuracy of 3 to 4 digits, if the initial effective potential is properly set up. The structure factors, thus obtained, show excellent agreement with the experimental data observed by x-ray and
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).
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
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.
First Principles Study of Double Photoionization of H2 UsingExterior Complex Scaling
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.
Stiffness of Diphenylalanine-Based Molecular Solids from First Principles Calculations
NASA Astrophysics Data System (ADS)
Azuri, Ido; Hod, Oded; Gazit, Ehud; Kronik, Leeor
2013-03-01
Diphenylalanine-based peptide nanotubes were found to be unexpectedly stiff, with a Young modulus of 19 GPa. Here, we calculate the Young modulus from first principles, using density functional theory with dispersive corrections. This allows us to show that at least half of the stiffness of the material comes from dispersive interactions and to identify the nature of the interactions that contribute most to the stiffness. This presents a general strategy for the analysis of bioinspired functional materials.
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.
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
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
A unified electrostatic and cavitation model for first-principles molecular dynamics in solution
NASA Astrophysics Data System (ADS)
Scherlis, Damián A.; Fattebert, Jean-Luc; Gygi, François; Cococcioni, Matteo; Marzari, Nicola
2006-02-01
The electrostatic continuum solvent model developed by [Fattebert and Gygi J. Comput. Chem. 23, 662 (2002); Int. J. Quantum Chem. 93, 139 (2003)] is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. Our model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. We apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon.
A unified electrostatic and cavitation model for first-principles molecular dynamics in solution
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.
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.
A first principle particle mesh method for solution SAXS of large bio-molecular systems.
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
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.
NASA Astrophysics Data System (ADS)
Kara, Abdelkader; Matos, Jeronimo; Yildirim, Handan
2015-03-01
C6 coefficients are used to investigate the strength of the long-range interactions for weakly interacting dimers as a function of separation distance. These coefficients are useful both as a measure for the accuracy of the various van der Waals (vdW) inclusive methods as well as reference for use in large-scale molecular dynamics simulations. In the case of molecule-surface interaction, the C3 coefficient is the counterpart to the C6 coefficient that is used for testing the interaction of dimers. We will present the results of the vdW inclusive density functional theory (DFT) calculations evaluating the C3 coefficients for the adsorption of M/X(110) and X(111), with X: Ag, Au, Cu, Pt, Pd, Ni, Rh and M: Benzene, Thiophene, Sexithiophene, Pentacene and Olympicene, as described by the PBE exchange-correlation functional and the self-consistent vdW-DF, optimized vdW-DFs and vdW-DF2 functionals. Work supported by the U.S. Department of Energy Basic Energy Science under Contract No. DE-FG02-11ER16243.
NASA Astrophysics Data System (ADS)
Golovanov, Viacheslav; Golovanova, Viktoria; Rantala, Tapio T.
2016-02-01
First-principles density functional theory calculations in the generalized gradient approximation, with plane wave basis set and pseudopotentials, have been used to investigate the desorption pathways of molecular oxygen species adsorbed on the SnO2 (110) surface. Energetics of the thermodynamically favored precursors is studied in dependence on the surface charge provided either by surface defects or by donor type impurities from the near-surface region. The resonant desorption modes of O2 molecules are examined in the framework of ab initio atomic thermodynamics and relationship of these results to experimental observations is discussed.
Wang, Zhiguo; Gao, Fei; Li , Jingbo; Zu, Xiaotao T.; Weber, William J.
2009-02-18
Using first principles molecular dynamics simulations, the displacement threshold energy and defect configurations are determined in SiC nanotubes. The simulation results reveal that a rich variety of defect structures (vacancies, Stone-Wales defects, and antisite defects) are formed with threshold energies of from 11 to 64 eV. The threshold energy shows an anisotropic behavior and exhibits a dramatic decrease with decreasing tube diameter. The electronic structure can be altered by the defects formed by irradiation, which suggests that the electron irradiation may be a way to use defect engineering to tailor electronic properties of SiC nanotubes.
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.
NASA Astrophysics Data System (ADS)
Wright, Louise B.; Walsh, Tiffany R.
2012-12-01
The ability to exert molecular-level control at the aqueous interface between biomolecules and inorganic substrates is pivotal to advancing applications ranging from sustainable manufacturing to targeted therapeutics. Progress is hindered by a lack of structural information of these interfaces with atomic resolution. Molecular simulation is one approach to obtain such data, but can be limited by the reliability of the force-field used. First-principles simulations, in principle, can provide insights into such aqueous interfaces, but are resource-intensive, limiting previous first-principles studies to approximate the environment of liquid water. Here, we use Car-Parrinello simulations to investigate adsorption of two charged adsorbates that are functional groups common to all amino-acids—ethanoate and ammonium—at the interface between hydroxylated quartz and liquid water, directly incorporating full solvation effects at the interface. Our findings reveal the stable character of carboxylate-quartz binding, as well as the surprisingly indifferent nature of ammonium-quartz interactions, in liquid water.
Scaling laws for ignition at the National Ignition Facility from first principles.
Cheng, Baolian; Kwan, Thomas J T; Wang, Yi-Ming; Batha, Steven H
2013-10-01
We have developed an analytical physics model from fundamental physics principles and used the reduced one-dimensional model to derive a thermonuclear ignition criterion and implosion energy scaling laws applicable to inertial confinement fusion capsules. The scaling laws relate the fuel pressure and the minimum implosion energy required for ignition to the peak implosion velocity and the equation of state of the pusher and the hot fuel. When a specific low-entropy adiabat path is used for the cold fuel, our scaling laws recover the ignition threshold factor dependence on the implosion velocity, but when a high-entropy adiabat path is chosen, the model agrees with recent measurements. PMID:24229109
First-Principles Mobility Calculations and Atomic-Scale Interface Roughness in Nanoscale Structures
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.
First-principles molecular dynamics simulations at solid-liquid interfaces with a continuum solvent.
Sánchez, Verónica M; Sued, Mariela; Scherlis, Damián A
2009-11-01
Continuum solvent models have become a standard technique in the context of electronic structure calculations, yet no implementations have been reported capable to perform molecular dynamics at solid-liquid interfaces. We propose here such a continuum approach in a density functional theory framework using plane-wave basis sets and periodic boundary conditions. Our work stems from a recent model designed for Car-Parrinello simulations of quantum solutes in a dielectric medium [D. A. Scherlis et al., J. Chem. Phys. 124, 074103 (2006)], for which the permittivity of the solvent is defined as a function of the electronic density of the solute. This strategy turns out to be inadequate for systems extended in two dimensions: the dependence of the dielectric function on the electronic density introduces a new term in the Kohn-Sham potential, which becomes unphysically large at the interfacial region, seriously affecting the convergence of the self-consistent calculations. If the dielectric medium is properly redefined as a function of the atomic coordinates, a good convergence is obtained and the constant of motion is conserved during the molecular dynamics simulations. The Poisson problem is solved using a multigrid method, and in this way Car-Parrinello molecular dynamics simulations of solid-liquid interfaces can be performed at a very moderate computational cost. This scheme is employed to investigate the acid-base equilibrium at the TiO(2)-water interface. The aqueous behavior of titania surfaces has stimulated a large amount of experimental research, but many open questions remain concerning the molecular mechanisms determining the chemistry of the interface. Here we make an attempt to answer some of them, putting to the test our continuum model. PMID:19894999
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.
Mohamad, Mazmira; Ahmed, Rashid; Shaari, Amirudin; Goumri-Said, Souraya
2015-02-01
Escalating demand for sustainable energy resources, because of the rapid exhaustion of conventional energy resources as well as to maintain the environmental level of carbon dioxide (CO2) to avoid its adverse effect on the climate, has led to the exploitation of photovoltaic technology manifold more than ever. In this regard organic materials have attracted great attention on account of demonstrating their potential to harvest solar energy at an affordable rate for photovoltaic technology. 2-vinyl-4,5-dicyanoimidazole (vinazene) is considered as a suitable material over the fullerenes for photovoltaic applications because of its particular chemical and physical nature. In the present study, DFT approaches are employed to provide an exposition of optoelectronic properties of vinazene molecule and molecular crystal. To gain insight into its properties, different forms of exchange correlation energy functional/potential such as LDA, GGA, BLYP, and BL3YP are used. Calculated electronic structure of vinazene molecule has been displayed via HOMO-LUMO isosurfaces, whereas electronic structure of the vinazene molecular crystal, via electronic band structure, is presented. The calculated electronic and optical properties were analyzed and compared as well. Our results endorse vinazene as a suitable material for organic photovoltaic applications. PMID:25631921
NASA Astrophysics Data System (ADS)
Wang, Xiaoli; Hou, Dong; Zheng, Xiao; Yan, YiJing
2016-01-01
The magnetic anisotropy and Kondo phenomena in a mechanically stretched magnetic molecular junction are investigated by combining the density functional theory (DFT) and hierarchical equations of motion (HEOM) approach. The system is comprised of a magnetic complex Co(tpy-SH)2 sandwiched between adjacent gold electrodes, which is mechanically stretched in experiments done by Parks et al. [Science 328, 1370 (2010)]. The electronic structure and mechanical property of the stretched system are investigated via the DFT calculations. The HEOM approach is then employed to characterize the Kondo resonance features, based on the Anderson impurity model parameterized from the DFT results. It is confirmed that the ground state prefers the S = 1 local spin state. The structural properties, the magnetic anisotropy, and corresponding Kondo peak splitting in the axial stretching process are systematically evaluated. The results reveal that the strong electron correlations and the local magnetic properties of the molecule magnet are very sensitive to structural distortion. This work demonstrates that the combined DFT+HEOM approach could be useful in understanding and designing mechanically controlled molecular junctions.
Semiclassical Monte Carlo: A first principles approach to non-adiabatic molecular dynamics
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.
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.
NASA Astrophysics Data System (ADS)
Fu, Tao; Peng, Xianghe; Zhao, Yinbo; Feng, Chao; Tang, Shan; Hu, Ning; Wang, Zhongchang
2015-05-01
We develop the second nearest-neighbor modified embedded atom method (2NN MEAM) potential for vanadium nitride (VN) in terms of the individual vanadium and nitrogen. The potential parameters are determined by fitting the cohesive energy, lattice parameter, and elastic constants of the VN with the NaCl-type structure, which are obtained by first-principles calculations. We find that the developed potentials can be used to describe the fundamental physical properties of the V-N system with other lattice structures. The calculated tensile stress-strain curves of the VN layers by first principles agree with those obtained by molecular dynamic simulations, validating the use of the developed potential. The bond breaking and its growth and coalescence are found to play an important role in the formation of fracture. We also find that temperature influences markedly the breaking of bonds, which can be attributed to the deviation of atoms from their equilibrium positions due to the thermal activated vibration, or to the superposition of the thermal energy to the deformation energy. Moreover, no dislocations and slips are found throughout the deformation process.
First-principles molecular dynamics simulation of the Ca2UO2(CO3)3 complex in water.
Priest, Chad; Tian, Ziqi; Jiang, De-En
2016-06-14
Recent experiments have shown that the neutral Ca2UO2(CO3)3 complex is the dominant species of uranium in many uranyl-containing streams. However, the structure and solvation of such a species in water has not been investigated from first principles. Herein we present a first principles molecular dynamics perspective of the Ca2UO2(CO3)3 complex in water based on density functional theory and Born-Oppenheimer approximation. We find that the Ca2UO2(CO3)3 complex is very stable in our simulation timeframe for three different concentrations considered and that the key distances from our simulation are in good agreement with the experimental data from extended X-ray absorption fine structure (EXAFS) spectroscopy. More important, we find that the two Ca ions bind differently in the complex, as a result of the hydrogen-bonding network around the whole complex. This finding invites confirmation from time-resolved EXAFS and has implications in understanding the dissociative equilibrium of the Ca2UO2(CO3)3 complex in water. PMID:26901265
NASA Astrophysics Data System (ADS)
Shimojo, Fuyuki; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya
2008-06-01
Rapid reaction of a molten metal with an oxide is the key to understanding recently discovered fast reactions in nanothermite composites. We have investigated the thermite reaction of Fe2O3 with aluminum by molecular dynamics simulations with interatomic forces calculated quantum mechanically in the framework of the density functional theory. A redox reaction to form iron metal and Al2O3 initiates with the rapid formation of Al-O bonds at the interface within 1 ps, followed by the propagation of the combustion front with a velocity of 70 m/s for at least 5 ps at 2000 K. The reaction time for an oxygen atom to change character from Fe2O3 type to Al2O3 type at the interface is estimated to be 1.7±0.9ps , and bond-overlap population analysis has been used to calculate reaction rates.
Shimojo, Fuyuki; Nakano, Aiichiro; Kalia, Rajiv K; Vashishta, Priya
2008-06-01
Rapid reaction of a molten metal with an oxide is the key to understanding recently discovered fast reactions in nanothermite composites. We have investigated the thermite reaction of Fe2O3 with aluminum by molecular dynamics simulations with interatomic forces calculated quantum mechanically in the framework of the density functional theory. A redox reaction to form iron metal and Al2O3 initiates with the rapid formation of Al-O bonds at the interface within 1 ps, followed by the propagation of the combustion front with a velocity of 70 m/s for at least 5 ps at 2000 K. The reaction time for an oxygen atom to change character from Fe2O3 type to Al2O3 type at the interface is estimated to be 1.7+/-0.9 ps , and bond-overlap population analysis has been used to calculate reaction rates. PMID:18643332
Large-Scale Computations Leading to a First-Principles Approach to Nuclear Structure
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.
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.
Adeagbo, Waheed A; Doltsinis, Nikos L; Klevakina, Ksenia; Renner, Jörg
2008-05-16
Car-Parrinello molecular dynamics (CP-MD) simulations are performed at high temperature and pressure to investigate chemical interactions and transport processes at the alpha-quartz-water interface. The model system initially consists of a periodically repeated quartz slab with O-terminated and Si-terminated (1000) surfaces sandwiching a film of liquid water. At a temperature of 1000 K and a pressure of 0.3 GPa, dissociation of H(2)O molecules into H(+) and OH(-) is observed at the Si-terminated surface. The OH(-) fragments immediately bind chemically to the Si-terminated surface while Grotthus-type proton diffusion through the water film leads to protonation of the O-terminated surface. Eventually, both surfaces are fully hydroxylated and no further chemical reactions are observed. Due to the confinement between the two hydroxylated quartz surfaces, water diffusion is reduced by about one third in comparison to bulk water. Diffusion properties of dissolved SiO(2) present as Si(OH)(4) in the water film are also studied. We do not observe strong interactions between the hydroxylated quartz surfaces and the Si(OH)(4) molecule as would have been indicated by a substantial lowering of the Si(OH)(4) diffusion coefficient along the surface. No spontaneous dissolution of quartz is observed. To study the mechanism of dissolution, constrained CP-MD simulations are done. The associated free energy profile is calculated by thermodynamic integration along the reaction coordinate. Dissolution is a stepwise process in which two Si--O bonds are successively broken. Each bond breaking between a silicon atom at the surface and an oxygen atom belonging to the quartz lattice is accompanied by the formation of a new Si--O bond between the silicon atom and a water molecule. The latter loses a proton in the process which eventually leads to protonation of the oxygen atom in the cleaved quartz Si--O bond. The final solute species is Si(OH)(4). PMID:18404743
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).
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
Ikeshoji, Tamio; Ando, Yasunobu; Otani, Minoru; Tsuchida, Eiji; Takagi, Shigeyuki; Matsuo, Motoaki; Orimo, Shin-ichi
2013-09-23
We use first-principles molecular dynamics to study the electrochemical solid-solid interface between lithium metal and lithium electrolyte LiBH{sub 4}. An external bias is applied by using an effective screening medium. We observe large polarization in the LiBH{sub 4}, because the lithium cations in LiBH{sub 4} are shifted more on one side of the double-well potential of Li{sup +}. This results in a large potential drop in the interface region and a large double-layer capacity corresponding to ca. 70 μF/cm{sup 2}. H-coordination to the Li atoms plays an important role in the charge-transfer reaction and ion transfer.
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
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.
First-principles molecular dynamics study of water dissociation on the γ-U(1 0 0) surface.
Yang, Yu; Zhang, Ping
2015-05-01
Based on first-principles molecular dynamics simulations at finite temperatures, we systematically study the adsorption and dissociation of water molecules on the γ-U(1 0 0) surface. We predict that water molecules spontaneously dissociate upon approaching the native γ-U(1 0 0) surface. The dissociation results from electronic interactions between surface uranium 6d states and 1b2, 3a1, and 1b1 molecular orbitals of water. With segregated Nb atoms existing on the surface, adsorbing water molecules also dissociate spontaneously because Nb 3d electronic states can also interact with the molecular orbitals similarly. After dissociation, the isolated hydrogen atoms are found to diffuse fast on both the γ-U surface and that with a surface substitutional Nb atom, which is very similar to the 'Hot-Atom' dissociation of oxygen molecules on the Al(1 1 1) surface. From a series of consecutive molecular dynamics simulations, we further reveal that on both the γ-U surface and that with a surface substitutional Nb atom, one surface U atom will be pulled out to form the U-O-U structure after dissociative adsorption of 0.44 ML water molecules. This result indicates that oxide nucleus can form at low coverage of water adsorption on the two surfaces. PMID:25835568
First-principles molecular dynamics study of water dissociation on the γ-U(1 0 0) surface
NASA Astrophysics Data System (ADS)
Yang, Yu; Zhang, Ping
2015-05-01
Based on first-principles molecular dynamics simulations at finite temperatures, we systematically study the adsorption and dissociation of water molecules on the γ-U(1 0 0) surface. We predict that water molecules spontaneously dissociate upon approaching the native γ-U(1 0 0) surface. The dissociation results from electronic interactions between surface uranium 6d states and 1b2, 3a1, and 1b1 molecular orbitals of water. With segregated Nb atoms existing on the surface, adsorbing water molecules also dissociate spontaneously because Nb 3d electronic states can also interact with the molecular orbitals similarly. After dissociation, the isolated hydrogen atoms are found to diffuse fast on both the γ-U surface and that with a surface substitutional Nb atom, which is very similar to the ‘Hot-Atom’ dissociation of oxygen molecules on the Al(1 1 1) surface. From a series of consecutive molecular dynamics simulations, we further reveal that on both the γ-U surface and that with a surface substitutional Nb atom, one surface U atom will be pulled out to form the U-O-U structure after dissociative adsorption of 0.44 ML water molecules. This result indicates that oxide nucleus can form at low coverage of water adsorption on the two surfaces.
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
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.
NASA Astrophysics Data System (ADS)
Shimojo, Fuyuki; Nakano, Aiichiro; Kalia, Rajiv K.; Vashishta, Priya
2009-07-01
Integration of nanowires and nanoparticles of energetic materials into semiconducting structures is giving birth to "nanoenergetics-on-a-chip" technology. Understanding and controlling the reactions of nanoenergetic materials pose a theoretical challenge for combining quantum-mechanical accuracy with large scales to capture nanostructural effects. Recent developments in linear-scaling density functional theory have set a stage for first-principles molecular dynamics simulation of thermite reaction at an Al /Fe2O3 interface. Here, we report the finding of a concerted metal-oxygen flip mechanism that enhances mass diffusion and reaction rate at the interface. This mechanism leads to two-stage reactions, which may explain recent experimental observation in thermite nanowire arrays.
First-principles study of hydrogen-bonded molecular conductor κ -H3(Cat-EDT-TTF/ST)2
NASA Astrophysics Data System (ADS)
Tsumuraya, Takao; Seo, Hitoshi; Kato, Reizo; Miyazaki, Tsuyoshi
2015-07-01
We theoretically study hydrogen-bonded molecular conductors synthesized recently, κ -H3(Cat-EDT-TTF) 2 and its diselena analog, κ -H3(Cat-EDT-ST) 2, by first-principles density functional theory calculations. In these crystals, two H(Cat-EDT-TTF/ST) units share a hydrogen atom with a short O-H-O hydrogen bond. The calculated band structure near the Fermi level shows a quasi-two-dimensional character with a rather large interlayer dispersion due to the absence of insulating layers, in contrast with conventional molecular conductors. We discuss effective low-energy models based on H(Cat-EDT-TTF/ST) units and its dimers, respectively, where the microscopic character of the orbitals composing them are analyzed. Furthermore, we find a stable structure which is different from the experimentally determined structure, where the shared hydrogen atom becomes localized to one of the oxygen atoms, in which charge disproportionation between the two types of H(Cat-EDT-TTF) units is associated. The calculated potential energy surface for the H atom is very shallow near the minimum points; therefore the probability of the H atom can be delocalized between the two O atoms.
NASA Astrophysics Data System (ADS)
Banerjee, Paramita; Chandrakumar, K. R. S.; Das, G. P.
2016-05-01
To surmount the limitations of bulk MgH2 for the purpose of hydrogen storage, we report here, a detailed first principles density functional theory (DFT) based study on the structure and stability of neutral (Mgm) and positively charged (Mgm+) Mg nanoclusters of different sizes (m = 2, 4, 8 and 12) and their interaction with molecular hydrogen (H2). Our results demonstrate that H2 is weakly bound to the Mg nanoclusters through van der Waals interactions. Incorporation of Grimme's dispersion correction (D3) in the DFT based exchange-correlation functionals leads to improved accuracy of H2 interaction energy (IE) values that fall within an energy window (between physisorption and chemisorption) desirable for hydrogen storage. Energy decomposition analysis reveals the significance of polarization energy for these Mg-H2 binding. Ab-initio molecular dynamics simulation shows that complete dehydrogenation from these Mg nanoclusters occur at ∼100 °C which is a significant improvement over bulk MgH2 (∼300 °C).
First-principles molecular dynamics study of glassy GeS2: Atomic structure and bonding properties
NASA Astrophysics Data System (ADS)
Celino, M.; Le Roux, S.; Ori, G.; Coasne, B.; Bouzid, A.; Boero, M.; Massobrio, C.
2013-11-01
The structure of glassy GeS2 is studied in the framework of density functional theory, by using a fully self-consistent first-principles molecular dynamics (FPMD) scheme. A comparative analysis is performed with previous molecular dynamics data obtained within the Harris functional (HFMD) total energy approach. The calculated total neutron structure factor exhibits an unprecedented agreement with the experimental counterpart. In particular, the height of the first sharp diffraction peak (FSDP) improves considerably upon the HFMD results. Both the Ge and the S subnetworks are affected by a consistent number of miscoordinations, coexisting with the main tetrahedral structural motif. Glassy GeS2 features a short-range order quite similar to the one found in glassy GeSe2, a notable exception being the larger number of edge-sharing connections. An electronic structure localization analysis, based on the Wannier functions formalism, provides evidence of a more enhanced ionic character in glassy GeS2 when compared to glassy GeSe2.
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
NASA Astrophysics Data System (ADS)
Bauchy, M.; Kachmar, A.; Micoulaut, M.
2014-11-01
The structural, vibrational, electronic, and dynamic properties of amorphous and liquid AsxSe1-x (0.10
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}.
Ong, Mitchell T; Verners, Osvalds; Draeger, Erik W; van Duin, Adri C T; Lordi, Vincenzo; Pask, John E
2015-01-29
Lithium-ion battery performance is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact both the solvation and diffusivity of Li ions. In this work, we used first-principles molecular dynamics to examine the solvation and diffusion of Li ions in the bulk organic solvents ethylene carbonate (EC), ethyl methyl carbonate (EMC), and a mixture of EC and EMC. We found that Li ions are solvated by either carbonyl or ether oxygen atoms of the solvents and sometimes by the PF6(-) anion. Li(+) prefers a tetrahedrally coordinated first solvation shell regardless of which species are involved, with the specific preferred solvation structure dependent on the organic solvent. In addition, we calculated Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in the linear carbonate EMC compared to the cyclic carbonate EC. The magnitude of the diffusion coefficient correlates with the strength of Li(+) solvation. Corresponding analysis for the PF6(-) anion shows greater diffusivity associated with a weakly bound, poorly defined first solvation shell. These results can be used to aid in the design of new electrolytes to improve Li-ion battery performance. PMID:25523643
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.
Gee, Richard H; Kuo, I-Feng W; Chinn, Sarah C; Raber, Ellen
2012-03-14
Computational studies of condensed-phase chemical reactions are challenging in part because of complexities in understanding the effects of the solvent environment on the reacting chemical species. Such studies are further complicated due to the demanding computational resources required to implement high-level ab initio quantum chemical methods when considering the solvent explicitly. Here, we use first-principles molecular dynamics simulations to examine condensed-phase decontamination reactions of V-type nerve agents in an explicit aqueous solvent. Our results include a detailed study of hydrolysis, base-hydrolysis, and nucleophilic oxidation of both VX and R-VX, as well as their protonated counterparts (i.e., VXH(+) and R-VXH(+)). The decontamination mechanisms and chemical reaction energy barriers, as determined from our simulations, are found to be in good agreement with experiment. The results demonstrate the applicability of using such simulations to assist in understanding new decontamination technologies or other applications that require computational screening of condensed-phase chemical reaction mechanisms. PMID:22298156
NASA Astrophysics Data System (ADS)
Pratihar, Subha; Chandra, Amalendu
2011-01-01
The preferential solvation of solutes in mixed solvent systems is an interesting phenomenon that plays important roles in solubility and kinetics. In the present study, solvation of a lithium atom in aqueous ammonia solution has been investigated from first principles molecular dynamics simulations. Solvation of alkali metal atoms, like lithium, in aqueous and ammonia media is particularly interesting because the alkali metal atoms release their valence electrons in these media so as to produce solvated electrons and metal counterions. In the present work, first principles simulations are performed employing the Car-Parrinello molecular dynamics method. Spontaneous ionization of the Li atom is found to occur in the mixed solvent system. From the radial distribution functions, it is found that the Li ^+ ion is preferentially solvated by water and the coordination number is mostly four in its first solvation shell and exchange of water molecules between the first and second solvation shells is essentially negligible in the time scale of our simulations. The Li ^+ ion and the unbound electron are well separated and screened by the polar solvent molecules. Also the unbound electron is primarily captured by the hydrogens of water molecules. The diffusion rates of Li ^+ ion and water molecules in its first solvation shell are found to be rather slow. In the bulk phase, the diffusion of water is found to be slower than that of ammonia molecules because of strong ammonia-water hydrogen bonds that participate in solvating ammonia molecules in the mixture. The ratio of first and second rank orientational correlation functions deviate from 3, which suggests a deviation from the ideal Debye-type orientational diffusion. It is found that the hydrogen bond lifetimes of ammonia-ammonia pairs is very short. However, ammonia-water H-bonds are found to be quite strong when ammonia acts as an acceptor and these hydrogen bonds are found to live longer than even water-water hydrogen
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
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).
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)
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
Zhang, Yigang; Yin, Qing-Zhu
2012-11-27
Carbon (C) is one of the candidate light elements proposed to account for the density deficit of the Earth's core. In addition, C significantly affects siderophile and chalcophile element partitioning between metal and silicate and thus the distribution of these elements in the Earth's core and mantle. Derivation of the accretion and core-mantle segregation history of the Earth requires, therefore, an accurate knowledge of the C abundance in the Earth's core. Previous estimates of the C content of the core differ by a factor of ∼20 due to differences in assumptions and methods, and because the metal-silicate partition coefficient of C was previously unknown. Here we use two-phase first-principles molecular dynamics to derive this partition coefficient of C between liquid iron and silicate melt. We calculate a value of 9 ± 3 at 3,200 K and 40 GPa. Using this partition coefficient and the most recent estimates of bulk Earth or mantle C contents, we infer that the Earth's core contains 0.1-0.7 wt% of C. Carbon thus plays a moderate role in the density deficit of the core and in the distribution of siderophile and chalcophile elements during core-mantle segregation processes. The partition coefficients of nitrogen (N), hydrogen, helium, phosphorus, magnesium, oxygen, and silicon are also inferred and found to be in close agreement with experiments and other geochemical constraints. Contents of these elements in the core derived from applying these partition coefficients match those derived by using the cosmochemical volatility curve and geochemical mass balance arguments. N is an exception, indicating its retention in a mantle phase instead of in the core. PMID:23150591
NASA Astrophysics Data System (ADS)
Galamba, N.; Costa Cabral, B. J.
2007-09-01
The structure and self-diffusion of NaI and NaCl at temperatures close to their melting points are studied by first principles Hellmann-Feynman molecular dynamics (HFMD). The results are compared with classical MD using rigid-ion (RI) and shell-model (ShM) interionic potentials. HFMD for NaCl was reported before at a higher temperature [N. Galamba and B. J. Costa Cabral, J. Chem. Phys. 126, 124502 (2007)]. The main differences between the structures predicted by HFMD and RI MD for NaI concern the cation-cation and the anion-cation pair correlation functions. A ShM which allows only for the polarization of I- reproduces the main features of the HFMD structure of NaI. The inclusion of polarization effects for both ionic species leads to a more structured ionic liquid, although a good agreement with HFMD is also observed. HFMD Green-Kubo self-diffusion coefficients are larger than those obtained from RI and ShM simulations. A qualitative study of charge transfer in molten NaI and NaCl was also carried out with the Hirshfeld charge partitioning method. Charge transfer in molten NaI is comparable to that in NaCl, and results for NaCl at two temperatures support the view that the magnitude of charge transfer is weakly state dependent for ionic systems. Finally, Hirshfeld charge distributions indicate that differences between RI and HFMD results are mainly related to polarization effects, while the influence of charge transfer fluctuations is minimal for these systems.
NASA Astrophysics Data System (ADS)
Suzuki, Ai; Selvam, Parasuraman; Kusagaya, Tomonori; Takami, Seiichi; Kubo, Momoji; Imamura, Akira; Miyamoto, Akira
The decomposition reaction dynamics of 2,3,4,4',5-penta-chlorinated biphenyl (2,3,4,4',5-PeCB), 3,3',4,4',5-penta-chlorinated biphenyl (3,3',4,4',5-PeCB), and 2,3,7,8-tetra-chlorinated dibenzo-p-dioxin (2,3,7,8-TCDD) was clarified for the first time at atomic and electronic levels, using our novel tight-binding quantum chemical molecular dynamics method with first-principles parameterization. The calculation speed of our new method is over 5000 times faster than that of the conventional first-principles molecular dynamics method. We confirmed that the structure, energy, and electronic states of the above molecules calculated by our new method are quantitatively consistent with those by first-principles calculations. After the confirmation of our methodology, we investigated the decomposition reaction dynamics of the above molecules and the calculated dynamic behaviors indicate that the oxidation of the 2,3,4,4',5-PeCB, 3,3',4,4',5-PeCB, and 2,3,7,8-TCDD proceeds through an epoxide intermediate, which is in good agreement with the previous experimental reports and consistent with our static density functional theory calculations. These results proved that our new tight-binding quantum chemical molecular dynamics method with first-principles parameterization is an effective tool to clarify the chemical reaction dynamics at reaction temperatures.
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
NASA Astrophysics Data System (ADS)
Yin, Q.; Zhang, Y.
2012-12-01
The degree of chemical equilibration (hereafter as Ke), defined as the cumulative mass fraction of the metalic core in equilibrium with the silicate mantle during the Earth accretion processes, greatly influences determination of the timing of the Earth core formation [1]. If Ke is larger than ~0.4, Hf-W chronology implies a fast accretion in less than 30 Myr for the Earth. Otherwise, Hf-W data can only be used to constrain the Ke instead of timing [1]. Here we use the two-phase first-principles molecular dynamics (FPMD) [2] to constrain the solubility of light elements in liquid iron in equilibration with silicate melt at temperatures from 2500 to 4200 K, pressures from 20 to 120 GPa, and two compositions simplified from the "O-bearing" and "Si-bearing" bulk Earth model compositions of McDonough [3]. The solubility data are then used in the simulations of the many possible accretion scenarios of the Earth as outlined in [4], considering magma ocean depth, homogeneous vs heterogeneous accretion etc. For each accretion route, we calculate the effective core-mantle equilibration degree (Ke), where Kei and Wi are the core-mantle equilibration degree and the accreted mass fraction of the ith step, respectively. The successful Ke are selected based on the criterion that the resulting Earth's core must meet the required density deficit [5]. The Ke in those successful simulations are all found to be larger than 0.57, implying that the core-mantle differentiation has to occur early [1], within 30 millions years from the beginning of the solar system as originally stated [6]. Additional simulations (all at 3200 K and 40 GPa) are also made to calculate the partition coefficients of several other light elements. Combined with the bulk Earth compositions of these elements [3], it is found Si, O, and S are the major light elements in the core while C, P, Mg, H, N, and He are the minor elements in the core. We show [7] that FPMD calculations lend strong support to the classical
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
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
Fang, H. Z.; Shang, S. L.; Wang, Y.; Liu, Z. K.; Alfonso, D.; Alman, D. E.; Shin, Y. K.; Zou, C. Y.; Duin, A. C. T. van; Lei, Y. K.; Wang, G. F.
2014-01-28
This paper is concerned with the prediction of oxygen diffusivities in fcc nickel from first-principles calculations and large-scale atomic simulations. Considering only the interstitial octahedral to tetrahedral to octahedral minimum energy pathway for oxygen diffusion in fcc lattice, greatly underestimates the migration barrier and overestimates the diffusivities by several orders of magnitude. The results indicate that vacancies in the Ni-lattice significantly impact the migration barrier of oxygen in nickel. Incorporation of the effect of vacancies results in predicted diffusivities consistent with available experimental data. First-principles calculations show that at high temperatures the vacancy concentration is comparable to the oxygen solubility, and there is a strong binding energy and a redistribution of charge density between the oxygen atom and vacancy. Consequently, there is a strong attraction between the oxygen and vacancy in the Ni lattice, which impacts diffusion.
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.
NASA Astrophysics Data System (ADS)
Migaou, Amani; Sarpi, Brice; Guiltat, Mathilde; Payen, Kevin; Daineche, Rachid; Landa, Georges; Vizzini, Sébastien; Hémeryck, Anne
2016-05-01
First principles calculations, scanning tunneling microscopy, and Auger spectroscopy experiments of the adsorption of Mg on Ag(111) substrate are conducted. This detailed study reveals that an atomic scale controlled deposition of a metallic Mg monolayer perfectly wets the silver substrate without any alloy formation at the interface at room temperature. A liquid-like behavior of the Mg species on the Ag substrate is highlighted as no dot formation is observed when coverage increases. Finally a layer-by-layer growth mode of Mg on Ag(111) can be predicted, thanks to density functional theory calculations as observed experimentally.
Migaou, Amani; Sarpi, Brice; Guiltat, Mathilde; Payen, Kevin; Daineche, Rachid; Landa, Georges; Vizzini, Sébastien; Hémeryck, Anne
2016-05-21
First principles calculations, scanning tunneling microscopy, and Auger spectroscopy experiments of the adsorption of Mg on Ag(111) substrate are conducted. This detailed study reveals that an atomic scale controlled deposition of a metallic Mg monolayer perfectly wets the silver substrate without any alloy formation at the interface at room temperature. A liquid-like behavior of the Mg species on the Ag substrate is highlighted as no dot formation is observed when coverage increases. Finally a layer-by-layer growth mode of Mg on Ag(111) can be predicted, thanks to density functional theory calculations as observed experimentally. PMID:27208966
Homocoordination preference in NaCs and LiNa liquid alloys by first principles molecular dynamics
NASA Astrophysics Data System (ADS)
Costa Cabral, B. J.; Martins, J. L.
1999-09-01
We present structural and dynamics results based on Hellman-Feynman molecular dynamics for the liquid phase of the NaCs alloy at two Na concentrations (cNa=0.6 and 0.8) and for the Li0.61Na0.39 zero alloy at two temperatures (T=590 K and 690 K). For NaCs the calculated structure factor S(k) is in very good agreement with data from neutron scattering experiments and the partial structure factors are compared to semiexperimental, theoretical and classical molecular dynamics predictions. We predict similar values for the self-diffusion coefficients of Na and Cs atoms in the Na0.6Cs0.4 alloy. For LiNa the concentration-concentration structure factor is in good agreement with experimental data and our results for the dynamics are compared with data from classical molecular dynamics simulations.
Dissociative versus molecular adsorption of phenol on Si(100)2×1 : A first-principles calculation
NASA Astrophysics Data System (ADS)
Carbone, Marilena; Meloni, Simone; Caminiti, Ruggero
2007-08-01
We investigated the competitive adsorption of a bifunctional molecule, phenol, on Si(100)2×1 by ab initio calculations. We performed geometry optimizations of phenol adsorbed either molecularly or dissociatively, on five possible sites (top, bridge, valley bridge, cave, and pedestal), in the low coverage regime. We found that the dissociative adsorption of phenol on top of a silicon dimer is the most favorable adsorption configuration. In the group of dissociative adsorption the phenol initially placed on the bridge or the valley-bridge sites ends up as a toplike local minima. The pedestal and cave sites remain as low-adsorption energy “open” sites. In the group of molecular adsorption, a higher adsorption energy is associated to the adsorption through an addition reaction and loss of the aromatic character (bridge, valley-bridge, and pedestal sites). Standard butterfly or diagonal butterfly are the corresponding optimized geometries. Retention of aromatic character and lower adsorption energy are associated to the adsorption on the top and cave sites. The ordering of adsorption sites according to the adsorption energy shows a mixture of the dissociative and the molecular sites. In the case of adsorption on the top site, the adsorption energies after a rotation of the phenoxy fragment along the bonding axis and hydrogen migration on the surface are very similar. The bend of the phenoxy fragment on the surface, instead, is not favored (the adsorption energy is 1.004eV lower compared to the vertical position). Different electron density maps were calculated for different adsorption sites and modes. Finally, we investigated the possibility that molecularly adsorbed phenol behaves as a precursor for the dissociative one by nudged elastic band calculations. We found a barrier of the same order of magnitude of the thermodynamic energy at room temperature for the conversion of the valley-bridge molecular into the top dissociative site.
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.
Multi-scale First-Principles Modeling of Three-Phase System of Polymer Electrolyte Membrane Fuel Cel
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.
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.
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
NASA Astrophysics Data System (ADS)
Kimizuka, Hajime; Ogata, Shigenobu
We investigated the H diffusivity in face-centered cubic Pd and Al by performing path-integral molecular dynamics (PIMD) modeling in the framework of density functional theory (DFT); in our calculations, we took nuclear quantum effects into consideration. The DFT results showed that the H-migration barriers (Em) in Pd and Al exhibited similar values (approximately 0.16 eV), while the H atoms were stable at octahedral (O) sites for Pd and at tetrahedral (T) sites for Al. The PIMD-based free-energy profiles for H migration between the O-site and T-site were evaluated using the thermodynamic integration of the centroid forces at 150-600 K. We confirmed that the quantum effects significantly affected the Em and the difference between the energies of the H atom at the O-site and the T-site (EO - T); The Em and EO - T values in Pd at 300 K increased by 32% and 98%, respectively, relative to the classical limit. On the other hand, the Em and ET - O (i.e., -EO - T) values in Al at 300 K decreased by 3% and 41%, respectively. This suggested that the quantum nature of H nuclei was essential for understanding the H-diffusion kinetics in these metals even above ambient temperature.
Trinh, Thuat T; Rozanska, Xavier; Delbecq, Françoise; Tuel, Alain; Sautet, Philippe
2016-06-01
The condensation reactions between Ge(OH)4 and Si(OH)4 units in solution are studied to understand the mechanism and stable species during the initial steps of the formation process of Ge containing zeolites under basic conditions. The free energy of formation of (OH)3Ge-O-Ge-(OH)2O(-), (OH)3Si-O-Si-(OH)2O(-), (OH)3Ge-O-Si-(OH)2O(-) and (OH)3Si-O-Ge-(OH)2O(-) dimers is calculated with ab initio molecular dynamics and thermodynamic integration, including an explicit description of the water solvent molecules. Calculations show that the attack of the conjugated base (Ge(OH)3O(-) and Si(OH)3O(-)) proceeds with a smaller barrier at the Ge center. In addition, the formation of the pure germanate dimer is more favorable than that of the germano-silicate structure. These results explain the experimental observation of Ge-Ge and Si-Ge dimer species in solutions, with a few Si-Si ones. PMID:27172391
First-principles molecular dynamics study of the structure and dynamic behavior of liquid Li4BN3H10
NASA Astrophysics Data System (ADS)
Farrell, David E.; Shin, Dongwon; Wolverton, C.
2009-12-01
We have applied density-functional theory based ab initio molecular dynamics to examine Li4BN3H10 at temperatures both above and below the experimental melting point. We examine the structure of the liquid, diffusivity, vibrational spectra and compare to both experimental data and analogous properties from solid-state calculations. We find the following: (1) the liquid state, like the solid state, is primarily a mixture of Li+ , BH4- , and NH2- with ionic interactions between the BH4- and NH2- anions and the Li+ cations. (2) We observe the reaction of two amide anions exchanging hydrogen to form ammonia and an imide anion: 2NH2-→NH3+NH2- . (3) The liquid demonstrates wide bond-angle distributions in the BH4- and NH2- units and thus these anionic units are not simply rigid complexes. (4) The Li+ sublattice disorders before the anionic sublattices and the liquid exhibits very fast Li+ diffusion. We calculate the activation energy and pre-exponential factor for Li+ diffusivity in the liquid to be ˜20kJ/mol and 15×10-4cm2/s , respectively. (5) Finally, we find that the liquid contains the same generic types of vibrational modes as the solid, however the lower-frequency anionic vibration and rotation modes become more prominent with increasing temperature.
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
First-principles studies on molecular beam epitaxy growth of GaAs1-xBix
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
NASA Astrophysics Data System (ADS)
Liu, Zhe
The thermodynamic properties of two nano-scale precipitate-strengthened alloys, Fe-Cu and Al-TM(=Ti, Zr and Hf) systems, are investigated within framework of first-principles thermodynamics methods. In particular, thermodynamic properties of the metastable precipitate phases are calculated, where direct experimental measurements are not available. Atomic volumes, magnetic moments, mixing energies and elastic properties of bcc Fe1-xCux solid solutions are studied by first-principles calculations based on the cluster expansion (CE) framework. We introduce a generalization of the CE technique for the calculation of concentration-dependent elastic moduli in disordered phase. Calculated mixing energies, atomic volumes and magnetic moments agree well with measurements for metastable alloys prepared through non-equilibrium processing techniques. The variations of the bulk modulus B, shear moduli C44 and C', with respect to copper concentration are calculated for the disordered bcc phase. While the B and C44 are positive for all concentrations, C' is positive only for Cu concentrations less than 50 atomic%. The implications of present results are discussed in relation to the observed metastability of bcc Fe-Cu alloys, and the strengthening mechanism of nanoscale bcc precipitates in an alpha-Fe matrix. Vibrational entropy, which is often omitted in first-principles phase-diagram calculations, has been shown to be an essential contribution in the phase stability of many Al-based alloys. In this work, we study the effect of lattice vibrations on the solubility limit for Al-TM(=Ti, Zr and Hf) systems. We propose a transferable force constant approach (TFC), in which the relations between bond force constants, bond length and TM composition are assumed to be transferable among different structures, to substantially reduce the heavy computational expense associated with first-principles lattice dynamics calculations. Our results demonstrate that the TFC can predict the
NASA Astrophysics Data System (ADS)
Zonias, Nicholas; Lagoudakis, Pavlos; Skylaris, Chris-Kriton
2010-01-01
We present a computational study by density functional theory (DFT) of entire silicon nanorods with up to 1648 atoms without any periodicity or symmetry imposed. The nanorods have been selected to have varying aspect ratios and levels of surface passivation with hydrogen. The structures of the nanorods have been optimized using a density functional tight-binding approach, while energies and electronic properties have been computed using linear-scaling DFT with plane-wave accuracy with the ONETEP (Skylaris et al 2005 J. Chem. Phys. 122 084119) program. The aspect ratio and surface passivation (1 × 1 and 2 × 1 reconstructions) along with the size of the nanorods which leads to quantum confinement along all three dimensions, significantly affect their electronic properties. The structures of the nanorods also show interesting behaviour as, depending on their characteristics, they can in certain areas retain the structure of bulk silicon while in other parts significantly deviate from it.
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.
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.
Lee, Eunseok; Persson, Kristin A
2013-10-25
Nano-scaling of electrode materials is often used in battery applications to enhance performance, particularly relating to rate capability. However, for the high-voltage spinel LiNi0.5Mn1.5O4 conflicting results have been reported on the benefits of nano-scaling. In this study, we present first-principles calculations to investigate the effect of nano-scaling on LiNi0.5Mn1.5O4, specifically focusing on the roles and coupling between surface stability, cation ordering and phase behavior. We calculate and compare the surface energy for the low index facets (100), (110), and (111), and find that the most stable facet is dependent on the cation ordering at the surface layer. In this context, we predict a spontaneous surface reconstruction in the cation-ordered structure which leads to a deviation from the perfect surface cation ordering and results in an enhanced accessibility to solid solution behavior as a function of Li content. Our results imply that nano-scaling will be more beneficial for the cation-ordered structure, as compared to the disordered structure where the solid solution region is already intrinsically accessible for a broad range of Li concentrations. PMID:24067535
First-principles study of the nano-scaling effect on the electrochemical behavior in LiNi0.5Mn1.5O4
NASA Astrophysics Data System (ADS)
Lee, Eunseok; Persson, Kristin A.
2013-10-01
Nano-scaling of electrode materials is often used in battery applications to enhance performance, particularly relating to rate capability. However, for the high-voltage spinel LiNi0.5Mn1.5O4 conflicting results have been reported on the benefits of nano-scaling. In this study, we present first-principles calculations to investigate the effect of nano-scaling on LiNi0.5Mn1.5O4, specifically focusing on the roles and coupling between surface stability, cation ordering and phase behavior. We calculate and compare the surface energy for the low index facets (100), (110), and (111), and find that the most stable facet is dependent on the cation ordering at the surface layer. In this context, we predict a spontaneous surface reconstruction in the cation-ordered structure which leads to a deviation from the perfect surface cation ordering and results in an enhanced accessibility to solid solution behavior as a function of Li content. Our results imply that nano-scaling will be more beneficial for the cation-ordered structure, as compared to the disordered structure where the solid solution region is already intrinsically accessible for a broad range of Li concentrations.
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
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.
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
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.
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.
Wei, Donghui; Fang, Lei; Tang, Mingsheng; Zhan, Chang-Guo
2013-01-01
Proteasome is the major component of the crucial nonlysosomal protein degradation pathway in the cells, but the detailed reaction pathway is unclear. In this study, first-principles quantum mechanical/molecular mechanical free energy calculations have been performed to explore, for the first time, possible reaction pathways for proteasomal proteolysis/hydrolysis of a representative peptide, succinyl-leucyl-leucyl-valyl-tyrosyl-7-amino-4-methylcoumarin (Suc-LLVY-AMC). The computational results reveal that the most favorable reaction pathway consists of six steps. The first is a water-assisted proton transfer within proteasome, activating Thr1-Oγ. The second is a nucleophilic attack on the carbonyl carbon of a Tyr residue of substrate by the negatively charged Thr1-Oγ, followed by the dissociation of the amine AMC (third step). The fourth step is a nucleophilic attack on the carbonyl carbon of the Tyr residue of substrate by a water molecule, accompanied by a proton transfer from the water molecule to Thr1-Nz. Then, Suc-LLVY is dissociated (fifth step), and Thr1 is regenerated via a direct proton transfer from Thr1-Nz to Thr1-Oγ. According to the calculated energetic results, the overall reaction energy barrier of the proteasomal hydrolysis is associated with the transition state (TS3b) for the third step involving a water-assisted proton transfer. The determined most favorable reaction pathway and the rate-determining step have provided a reasonable interpretation of the reported experimental observations concerning the substituent and isotopic effects on the kinetics. The calculated overall free energy barrier of 18.2 kcal/mol is close to the experimentally-derived activation free energy of ~18.3–19.4 kcal/mol, suggesting that the computational results are reasonable. PMID:24111489
Wan, Liwen F; Prendergast, David
2014-10-15
The knowledge of Mg solvation structure in the electrolyte is requisite to understand the transport behavior of Mg ions and their dissolution/deposition mechanism at electrolyte/electrode interfaces. In the first established rechargeable Mg-ion battery system [D. Aurbach et al. Nature 2000, 407, 724], the electrolyte is of the dichloro complex (DCC) solution family, Mg(AlCl2BuEt)2/THF, resulting from the reaction of Bu2Mg and EtAlCl2 with a molar ratio of 1:2. There is disagreement in the literature regarding the exact solvation structure of Mg ions in such solutions, i.e., whether Mg(2+) is tetra- or hexacoordinated by a combination of Cl(-) and THF. In this work, theoretical insight into the solvation complexes present is provided based on first-principles molecular dynamics simulations (FPMD). Both Mg monomer and dimer structures are considered in both neutral and positively charged states. We found that, at room temperature, the Mg(2+) ion tends to be tetracoordinated in the THF solution phase instead of hexacoordinated, which is the predominant solid-phase coordination. Simulating the X-ray absorption spectra (XAS) at the Mg K-edge by sampling our FPMD trajectories, our predicted solvation structure can be readily compared with experimental measurements. It is found that when changing from tetra- to hexacoordination, the onset of X-ray absorption should exhibit at least a 1 eV blue shift. We propose that this energy shift can be used to monitor changes in the Mg solvation sphere as it migrates through the electrolyte to electrolyte/electrode interfaces and to elucidate the mechanism of Mg dissolution/deposition. PMID:25243732
First principle thousand atom quantum dot calculations
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.
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
Katcho, N. A.; Lomba, E.; Urones-Garrote, E.; Otero-Diaz, L. C.; Landa-Canovas, A. R.
2006-06-01
In this work we present an investigation on the composition dependence of the local structure in Se{sub x}Te{sub 1-x} crystalline alloys analyzing their experimental energy-loss spectra with the aid of a real-space multiple-scattering modeling approach and first-principles molecular dynamics. The concourse of this latter technique is essential for a proper modeling of the alloy spectra. From our results, it can be inferred that Se{sub x}Te{sub 1-x} alloys exhibit a high degree of substitutional disorder ruling out the existence of fully ordered alternating copolymer chains of Se and Te atoms.
NASA Astrophysics Data System (ADS)
Katcho, N. A.; Lomba, E.; Urones-Garrote, E.; Landa-Cánovas, A. R.; Otero-Díaz, L. C.
2006-06-01
In this work we present an investigation on the composition dependence of the local structure in SexTe1-x crystalline alloys analyzing their experimental energy-loss spectra with the aid of a real-space multiple-scattering modeling approach and first-principles molecular dynamics. The concourse of this latter technique is essential for a proper modeling of the alloy spectra. From our results, it can be inferred that SexTe1-x alloys exhibit a high degree of substitutional disorder ruling out the existence of fully ordered alternating copolymer chains of Se and Te atoms.
Culturing conceptions: From first principles
NASA Astrophysics Data System (ADS)
Roth, Wolff-Michael; Lee, Yew Jin; Hwang, Sungwon
2008-07-01
Over the past three decades, science educators have accumulated a vast amount of information on conceptions--variously defined as beliefs, ontologies, cognitive structures, mental models, or frameworks--that generally (at least initially) have been derived from interviews about certain topics. During the same time period, cultural studies has emerged as a field in which everyday social practices are interrogated with the objective to understand culture in all its complexity. Science educators have however yet to ask themselves what it would mean to consider the possession of conceptions as well as conceptual change from the perspective of cultural studies. The purpose of this article is thus to articulate in and through the analysis of an interview about natural phenomenon the first principles of such a cultural approach to scientific conceptions. Our bottom-up approach in fact leads us to develop the kind of analyses and theories that have become widespread in cultural studies. This promises to generate less presupposing and more parsimonious explanations of this core issue within science education than if conceptions are supposed to be structures inhabiting the human mind.
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.
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.
NASA Astrophysics Data System (ADS)
Haruyama, Jun; Hu, Chunping; Watanabe, Kazuyuki
2012-06-01
The femtosecond laser reaction dynamics of the 3,5-difluoro-3',5'-dibromo-biphenyl (DFDBrBPh) molecule is investigated using time-dependent density-functional theory combined with molecular-dynamics (TDDFT-MD) simulation. This work is based on a recent experiment that monitored torsional motion of the DFDBrBPh molecule by femtosecond time-resolved Coulomb explosion imaging [Madsen , Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.102.073007 102, 073007 (2009)]. The results confirm that the probe pulse triggers a Coulomb explosion and the kick pulse induces the torsional motion of two phenyl rings, using the experimental settings of the lasers. The Coulomb explosion dynamics simulation verifies that the F and Br atoms dissociate to the ion detector while maintaining their initial alignment with respect to the phenyl rings, which is the fundamental basis of Coulomb explosion imaging of molecular torsion. Furthermore, the period and amplitude of the torsional motion obtained by the simulation are consistent with the experimental values. This validates the ability of the TDDFT-MD method to reveal the underlying mechanism of experimentally observed molecular torsional dynamics.
NASA Astrophysics Data System (ADS)
Sebbari, K.; Domain, C.; Roques, J.; Perron, H.; Simoni, E.; Catalette, H.
2011-07-01
Density Functional Theory (DFT), based on both static and Born-Oppenheimer Molecular Dynamics approaches, has been used to investigate the effect of hydrogen bonds and temperature on the water monolayer adsorption on the rutile TiO2 (110) face. It was demonstrated that the difference between some previous theoretical results and experimental data is due to too slim slab thickness model and/or too small surface area. According to the present static calculations, water monolayer adsorbs molecularly on the five-fold titanium atoms of an optimised five-layer slab thickness, due to the stabilising lateral hydrogen bonds between molecules. From the molecular dynamics simulations, two adsorption mechanisms were described as a function of temperature. Finally, it was pointed out that the dynamics of water adsorption is strongly influenced by the structural model used. When temperature increases, the monolayer dissociates gradually. However, because of the periodic boundary conditions, the 1 × 1 surface unit needs to be extended to at least 2 × 5 to get an accurate representation of the monolayer dissociation ratio. In these conditions, this ratio is around 20%, 25% and 33% at 270, 350 and 425 K, respectively.
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.
Time-dependent first-principles approaches to PV materials
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.
NASA Astrophysics Data System (ADS)
Kim, Yong-Hyun; Zhang, S. B.
2006-03-01
Despite being one of the most important macroscopic measures and a long history even before the quantum mechanics, the concept of pH has rarely been mentioned in microscopic theories, nor being incorporated computationally into first-principles theory of aqueous solutions. Here, we formulate a theory for the pH dependence of solution formation energy by introducing the proton chemical potential as the microscopic counterpart of pH in atomistic solution models. Within the theory, the general acid-base chemistry can be cast in a simple pictorial representation. We adopt density-functional molecular dynamics to demonstrate the usefulness of the method by studying a number of solution systems including water, small solute molecules such as NH3 and HCOOH, and more complex amino acids with several functional groups. For pure water, we calculated the auto- ionization constant to be 13.2 with a 95 % accuracy. For other solutes, the calculated dissociation constants, i.e., the so- called pKa, are also in reasonable agreement with experiments. Our first-principles pH theory can be readily applied to broad solution chemistry problems such as redox reactions.
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.
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.
Lin, Bin; Dong, Huilong; Du, Chunmiao; Hou, Tingjun; Lin, Haiping; Li, Youyong
2016-02-19
The adsorption of small molecules (NH3, N2, H2 and CH4) on all-boron fullerene B40 is investigated by density functional theory (DFT) and the non-equilibrium Green's function (NEGF) for its potential application in the field of single-molecular gas sensors. The high adsorption energies (-1.09 to -0.75 eV) of NH3 on different adsorption sites of the B40 surface indicate that NH3 strongly chemisorbs to B40. The charge transfer induced by the NH3 adsorption results in a modification of the density of states (DOS) of B40 near the Fermi level, and therefore changes its electronic transport properties. For all possible adsorption sites, the adsorption of NH3 exclusively leads to a decrease of the conductance of B40. Taking into consideration that the non-polar gas molecules (e.g. N2, H2 and CH4) are only physisorbed and show negligible effect on the conductance properties of B40, we would expect that B40 can be used as a single-molecular gas sensor to distinguish NH3 from non-polar gas molecules at low bias. PMID:26775574
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.
NASA Astrophysics Data System (ADS)
Sebbari, K.; Roques, J.; Simoni, E.; Domain, C.; Perron, H.; Catalette, H.
2012-08-01
The effects of temperature and solvation on uranyl ion adsorption at the water/rutile TiO2(110) interface are investigated by Density Functional Theory (DFT) in both static and Born-Oppenheimer molecular dynamics approaches. According to experimental observations, uranyl ion can form two surface complexes in a pH range from 1.5 to 4.5. Based on these observations, the structures of the complexes at 293 K are first calculated in agreement with vacuum static calculations. Then, an increase in temperature (293 to 425 K) induces the reinforcement of uranyl ion adsorption due to the release of water molecules from the solvation shell of uranyl ion. Finally, temperature can modify the nature of the surface species.
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
NASA Astrophysics Data System (ADS)
Malysheva, L.; Onipko, A.; Valiokas, R.; Liedberg, B.
2005-09-01
We report orientation angles for the alkyl chain, amide group, and oligo(ethylene glycol) (OEG) portion within self-assembled monolayers (SAMs) of OEG-terminated and amide containing alkanethiolates which, depending on the OEG length and substrate temperature, display unique conformations — all-trans or helical. Optimized geometries of the molecular constituents, characteristic vibration frequencies and transition dipole moments are obtained by using DFT methods with gradient corrections. These ab initio data are subsequently used to simulate infrared reflection-absorption (RA) spectra associated with different conformations and orientations. The obtained results have generated a deeper knowledge of the internal SAM structure, which is crucial for understanding phase and folding characteristics, interaction with water and ultimately the protein repellent properties of OEG-containing SAMs.
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.
Chamber Clearing First Principles Modeling
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
NASA Astrophysics Data System (ADS)
Bankura, Arindam; Chandra, Amalendu
2012-03-01
We have investigated the solvation structure and migration kinetics of an excess proton and a hydroxide ion in water-ammonia mixed liquids of varying composition by means of ab initio molecular dynamics simulations. The excess proton is always found to be attached to an ammonia molecule to form the ammonium ion. Migration of the excess proton is found to occur very occasionally from one ammonia to the other but no proton transfer to a water molecule is observed during the entire simulations. Also, when the ammonium ion is solvated in water only, its hydrogen bond dynamics and rotation are found to occur at a faster rate than those in water-ammonia mixtures. For water-ammonia mixtures containing a proton less, the defect is found to stay like the hydroxide ion. For these systems, occasional proton transfer is found to occur only through the hydrogen bonded chains of water molecules in these water-ammonia mixtures. No proton transfer is found to take place from an ammonia molecule. The presence of ammonia molecules makes the realization of proper presolvated state of the hydroxide ion to accept a proton a more difficult process and, as a result, the rate of proton transfer and migration kinetics of the hydroxide ion in water-ammonia mixtures are found to be slower than that in liquid water and these rates are found to slow down further with increase of ammonia concentration.
First-principles studies on molecular beam epitaxy growth of GaAs_{1-x}Bi_{x}
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 GaAs_{1-x}Bi_{x} 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)-Ga_{sub}||Bi surface and a proposed q(1 x 1)-Ga_{sub}||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)-Ga_{sub}||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.
Woidy, Patrick; Bühl, Michael; Kraus, Florian
2015-04-28
Pentaammine dioxido uranium(VI) dibromide ammonia (1/1), [UO2(NH3)5]Br2·NH3, was synthesized in the form of yellow crystals by the reaction of uranyl bromide, UO2Br2, with dry liquid ammonia. The compound crystallizes orthorhombic in space group Cmcm and is isotypic to [UO2(NH3)5]Cl2·NH3 with a = 13.2499(2), b = 10.5536(1), c = 8.9126(1) Å, V = 1246.29(3) Å(3) and Z = 4 at 123 K. The UO2(2+) cation is coordinated by five ammine ligands and the coordination polyhedron can be best described as pentagonal bipyramid. Car-Parrinello molecular dynamics simulations are reported for [UO2(NH3)5](2+) in the gas phase and in liquid NH3 solution (using the BLYP density functional). According to free-energy simulations, solvation by ammonia has only a small effect on the uranyl-NH3 bond strength. PMID:25797497
Phonon-phonon interactions: First principles theory
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.
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
First principles nonequilibrium plasma mixing
NASA Astrophysics Data System (ADS)
Ticknor, C.; Herring, S. D.; Lambert, F.; Collins, L. A.; Kress, J. D.
2014-01-01
We have performed nonequilibrium classical and quantum-mechanical molecular dynamics simulations that follow the interpenetration of deuterium-tritium (DT) and carbon (C) components through an interface initially in hydrostatic and thermal equilibrium. We concentrate on the warm, dense matter regime with initial densities of 2.5-5.5 g/cm3 and temperatures from 10 to 100 eV. The classical treatment employs a Yukawa pair-potential with the parameters adjusted to the plasma conditions, and the quantum treatment rests on an orbital-free density functional theory at the Thomas-Fermi-Dirac level. For times greater than about a picosecond, the component concentrations evolve in accordance with Fick's law for a classically diffusing fluid with the motion, though, described by the mutual diffusion coefficient of the mixed system rather than the self-diffusion of the individual components. For shorter times, microscopic processes control the clearly non-Fickian dynamics and require a detailed representation of the electron probability density in space and time.
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
Intrinsic ferroelectric switching from first principles.
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
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.
Materials Databases Infrastructure Constructed by First Principles Calculations: A Review
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.
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.
NASA Astrophysics Data System (ADS)
Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi
2015-07-01
In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl- + CH3Cl → ClCH3 + Cl-) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.
Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi
2015-07-01
In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl(-) + CH3Cl → ClCH3 + Cl(-)) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF. PMID:26156461
Description of charge conjugation from first principles
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.
First-principles calculation of dielectric response in molecule-based materials.
Heitzer, Henry M; Marks, Tobin J; Ratner, Mark A
2013-07-01
The dielectric properties of materials are of fundamental significance to many chemical processes and the functioning of numerous solid-state device technologies. While experimental methods for measuring bulk dielectric constants are well-established, far less is known, either experimentally or theoretically, about the origin of dielectric response at the molecular/multimolecular scale. In this contribution we report the implementation of an accurate first-principles approach to calculating the dielectric response of molecular systems. We assess the accuracy of the method by reproducing the experimental dielectric constants of several bulk π-electron materials and demonstrating the ability of the method to capture dielectric properties as a function of frequency and molecular orientation in representative arrays of substituted aromatic derivatives. The role of molecular alignment and packing density on dielectric response is also examined, showing that the local dielectric behavior of molecular assemblies can diverge significantly from that of the bulk material. PMID:23734640
Interface Structure Prediction from First-Principles
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.
First-principles transversal DNA conductance deconstructed
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.
First principles determination of dislocation properties.
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.
First principles calculations for lithiated manganese oxides.
Prasad, R.
1998-12-23
First principles calculations within the local-spin-density-functional theory (LSDFF) framework are presented of densities of electronic states for MnO, LiMnO{sub 2} in the monoclinic and orthorhombic structures, cubic LiMn{sub 2}O{sub 4} spinel and {lambda}-MnO{sub 2} (delithiated spinel), all in antiferromagnetic spin configurations. The changes in energy spectra as the Mn oxidation state varies between 2+ and 4+ are illustrated. Preliminary calculations for Co-doped LiMnO{sub 2} are presented, and the destabilization of a monoclinic relative to a rhombohedral structure is discussed.
First principles semiclassical calculations of vibrational eigenfunctions.
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
Atomistic models of hydrogenated amorphous silicon nitride from first principles
NASA Astrophysics Data System (ADS)
Jarolimek, K.; de Groot, R. A.; de Wijs, G. A.; Zeman, M.
2010-11-01
We present a theoretical study of hydrogenated amorphous silicon nitride (a-SiNx:H) , with equal concentrations of Si and N atoms (x=1) , for two considerably different densities (2.0 and 3.0g/cm3 ). Densities and hydrogen concentration were chosen according to experimental data. Using first-principles molecular-dynamics within density-functional theory the models were generated by cooling from the liquid. Where both models have a short-range order resembling that of crystalline Si3N4 because of their different densities and hydrogen concentrations they show marked differences at longer length scales. The low-density nitride forms a percolating network of voids with the internal surfaces passivated by hydrogen. Although some voids are still present for the high-density nitride, this material has a much denser and uniform space filling. The structure factors reveal some tendency for the nonstoichiometric high-density nitride to phase separate into nitrogen rich and poor areas. For our slowest cooling rate (0.023 K/fs) we obtain models with a modest number of defect states, where the low (high) density nitride favors undercoordinated (overcoordinated) defects. Analysis of the structural defects and electronic density of states shows that there is no direct one-to-one correspondence between the structural defects and states in the gap. There are several structural defects that do not contribute to in-gap states and there are in-gap states that do only have little to no contributions from (atoms in) structural defects. Finally an estimation of the size and cooling rate effects on the amorphous network is reported.
Materials Databases Infrastructure Constructed by First Principles Calculations: A Review
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
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.
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
Numerical inductance calculations based on first principles.
Shatz, Lisa F; Christensen, Craig W
2014-01-01
A method of calculating inductances based on first principles is presented, which has the advantage over the more popular simulators in that fundamental formulas are explicitly used so that a deeper understanding of the inductance calculation is obtained with no need for explicit discretization of the inductor. It also has the advantage over the traditional method of formulas or table lookups in that it can be used for a wider range of configurations. It relies on the use of fast computers with a sophisticated mathematical computing language such as Mathematica to perform the required integration numerically so that the researcher can focus on the physics of the inductance calculation and not on the numerical integration. PMID:25402467
Transition Metal Nitrides: A First Principles Study
NASA Astrophysics Data System (ADS)
Pathak, Ashish; Singh, A. K.
2016-04-01
The present work describes the structural stability and electronic and mechanical properties of transition metal nitrides (TmNs: B1 cubic structure (cF8, Fm ‾ overline 3 m)) using first principles density functional theory (DFT) within generalized gradient approximation (GGA). The lattice constant of TmNs increases with increasing the atomic radii of the transition metals. Stability of the TmNs decreases from IVB to VIB groups due to increase in formation energy/atom. The bonding characteristics of these nitrides have been explained based on electronic density of states and charge density. All the TmNs satisfy Born stability criteria in terms of elastic constants except CrN and MoN that do not exist in equilibrium binary phase diagrams. The groups IVB and V-VIB nitrides are associated with brittle and ductile behaviour based on G/B ratios, respectively. The estimated melting temperatures of these nitrides exhibit reasonably good agreement with calculated with B than those of the C11 for all nitrides.
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.
Safeguards First Principle Initiative (SFPI) Cost Model
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.
First principle study of sodium decorated graphyne
NASA Astrophysics Data System (ADS)
Sarkar, Utpal; Bhattacharya, Barnali; Seriani, Nicola
2015-11-01
We present first-principles calculations of the electronic properties of Na-decorated graphyne. This structure of the graphyne family is a direct band gap semiconductor with a band gap of 0.44 eV in absence of sodium, but Na-decorated graphyne compounds are metallic, and can then be employed as carbon-based conductors. Metallization is due to charge donation from sodium to carbon. Pristine graphyne is more stable than Na-decorated graphyne, therefore is seems probable that, if this material should be employed as electrode in Na-ion batteries, it would lead to the formation of metallic sodium rather than well dispersed sodium ions. On the other side, this property might be useful if graphyne is employed in water desalination. Finally, the abrupt change from a semiconducting to a metallic state in presence of a small amount of sodium might be exploited in electronics, e.g. for the production of smooth metal-semiconductor interfaces through spatially selective deposition of sodium.
THERMODYNAMIC MODELING AND FIRST-PRINCIPLES CALCULATIONS
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.
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
Ziegler Natta heterogeneous catalysis by first principles computer experiments
NASA Astrophysics Data System (ADS)
Boero, M.; Parrinello, M.; Terakura, K.
1999-09-01
In this work we present a first attempt to study the polymerization process of ethylene in a realistic Ziegler-Natta heterogeneous system by means of first principles molecular dynamics. In particular, we simulate, in a very unbiased way, both the deposition of the catalyst TiCl 4 on the (110) active surface of a solid MgCl 2 support and the polymer chain formation. By using a constrained molecular dynamics approach, we work out the energetics and the reaction pathway of the polymerization process as it occurs in a laboratory or an industrial plant. The good agreement of the results of our simulations with the available experimental data indicates that these kinds of simulations can be used as a skilful approach to study the details of the reaction mechanism which are not accessible to experimental probes. This offers a tool to improve the production and/or to design reactants and products for practical use.
Transversity from First Principles in QCD
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.
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
First Principles Dynamics of Photoexcited DNA and RNA Bases
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.
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.
First principles electron transport simulations in the Kondo regime
NASA Astrophysics Data System (ADS)
Rungger, Ivan; Radonjic, Milos; Appelt, Wilhelm; Chioncel, Liviu; Droghetti, Andrea
When magnetic atoms, molecules or thin films are brought into contact with metals the electron-electron interaction leads to the appearance of the correlated Kondo state at low temperatures. In this talk we will present results for the electronic structure and conductance in the Kondo regime of recent STM and break junction experiments for stable radical molecules, which correspond to spin half molecular magnets. We will outline the methodological approach to evaluate the conductance of such systems from first principles, as implemented in the Smeagol electron transport code. The method combines the density functional theory (DFT) with Anderson impurity solvers within the continuum time quantum Monte Carlo (CTQMC) and numerical renormalization group (NRG) approaches.
First-principles theory, coarse-grained models, and simulations of ferroelectrics.
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
Vibrational and Thermophysical Properties of PETN from First Principles
NASA Astrophysics Data System (ADS)
Gonzalez, Joseph; Landerville, Aaron; Oleynik, Ivan
2015-06-01
Thermophysical properties are urgently sought as input for meso- and continuum-scale modeling of energetic materials (EMs). However, empirical data in this regard are often limited to specific pressures and temperatures. Such modeling of EMs can be greatly improved by inclusion of thermophysical properties over a wide range of pressures and temperatures, provided such data could be reliably obtained from theory. We demonstrate such a capability by calculating the equation of state, heat capacities, coefficients of thermal expansion, and Gruneissen parameters for pentaerythritol tetranitrate (PETN) using first-principles density functional theory, which includes proper description of van der Waals interactions and zero-point and thermal free energy contributions to pressure, the latter being calculated using the quasi-harmonic approximation. Further, we investigate the evolution of the vibration spectrum of PETN as a function of pressure.
Auger recombination in sodium-iodide scintillators from first principles
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.
Optimized Materials From First Principles Simulations: Are We There Yet?
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.
First principles modeling of grain boundaries in CdTe
NASA Astrophysics Data System (ADS)
Chan, Maria K. Y.; Sen, Fatih; Buurma, Christopher; Paulauskas, Tadas; Sun, Ce; Kim, Moon; Klie, Robert
The role of extended defects is of significant interest for semiconductors, especially photovoltaics since energy conversion efficiencies are often affected by such defects. In particular, grain boundaries in CdTe photovoltaics are enigmatic since the achievable efficiencies of CdTe photovoltaics are higher in polycrystalline devices as compared to single crystalline devices. Yet, despite recent advances, the efficiency of poly-CdTe devices are still substantially below the theoretical maximum. We carry out an atomistic-level study using Scanning Transmission Electron Microscopy (STEM), together with first principles density functional theory (DFT) modeling, in order to understand the properties of specific bicrystals, i.e. artificial grain boundaries, constructed using wafer bonding. We discuss examples of bicrystals, including some involving large scale DFT calculations, and trends in defect and electronic properties. This work was funded by DOE SunShot BRIDGE program.
Thermodynamics of Magnetic Systems from First Principles: WL-LSMS
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.
NASA Astrophysics Data System (ADS)
Kohno, Yuji; Mori, Kazuki; Hiyoshi, Reiko I.; Takahashi, Osamu; Ueda, Kazuyoshi
2016-06-01
Classical molecular dynamics (MD) calculations were performed to reveal the effect of high pressure on the crystal structure of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), an insensitive energetic material. The primary simulation cell consisted of 54 molecules in a triclinic cell, corresponding to 27 unit cells obtained by replicating the experimentally determined unit cell. Inter- and intra-molecular hydrogen bonds were maintained in the range of 1.0 atm to 20.0 GPa as pressure was incremented by 0.5 GPa. The pressure dependence of the interlayer distances (h1) and farthest intermolecular distance (d1) between nitro groups in the TATB crystal's unit cell was investigated in the same range. h1 decreased monotonously from 3.50 to 2.90 Å as pressure increased to 20.0 GPa. However, d1 increased considerably with pressure up to 4.0 GPa, most remarkably between 2.0 and 4.0 GPa. Thus, a unique structural change occurred in TATB crystal in this range. On the other hand, 1,3-diamino-2,4,6-trinitrobenzene (DATB) crystal showed a unique structural change between 7.0 and 8.0 GPa. These discrepancies are attributed to the different network systems of hydrogen bonding of these two molecules. To validate the MD calculation results, we conducted first-principles calculations. MD and first-principles calculations showed good agreement with previous experimental results.
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.
Transport Properties of Nanoscale Materials by First-principles Calculations
NASA Astrophysics Data System (ADS)
Mizuseki, Hiroshi; Belosludov, Rodion V.; Lee, S.-U.; Kawazoe, Yoshiyuki
2009-03-01
Molecular devices are potential candidates for the next step towards nanoelectronic technology. Our group has covered a wide range of nanoscale wires, which have potential application in molecular electronics using first-principles calculations and nonequilibrium Green's function formalism [1]. Our target materials are supramolecular enamel wires (covered wires) [2], connection between organic molecules and metal electrodes, self-assembled nanowires on silicon surface [3], porphyrin [4], phthalocyanine, metallocene [5], fused-ring thiophene molecules, length dependence of conductance in alkanedithiols and so on. Namely, we have investigated a relationship of the energy levels of delocalized frontier orbitals (HOMO and LUMO) and Fermi level of metal electrodes and estimate the electronic transport properties through atomic and molecular wires using Green's function approach. References [1] http://www-lab.imr.edu/˜mizuseki/nanowire.html [2] R. V. Belosludov, A. A. Farajian, H. Baba, H. Mizuseki, and Y. Kawazoe, Jpn. J. Appl. Phys., 44, 2823 (2005). [3] R. V. Belosludov, A. A. Farajian, H. Mizuseki, K. Miki, and Y. Kawazoe, Phys. Rev. B, 75, 113411 (2007). [4] S.-U. Lee, R. V. Belosludov, H. Mizuseki, and Y. Kawazoe, Small 4 (2008) 962. [5] S.-U Lee, R. V. Belosludov, H. Mizuseki, and Y. Kawazoe, J. Phys. Chem. C. 111 (2007) 15397.
First-principles design of nanomachines.
Banavar, Jayanth R; Cieplak, Marek; Hoang, Trinh Xuan; Maritan, Amos
2009-04-28
Learning from nature's amazing molecular machines, globular proteins, we present a framework for the predictive design of nanomachines. We show that the crucial ingredients for a chain molecule to behave as a machine are its inherent anisotropy and the coupling between the local Frenet coordinate reference frames of nearby monomers. We demonstrate that, even in the absence of heterogeneity, protein-like behavior is obtained for a simple chain molecule made up of just 30 hard spheres. This chain spontaneously switches between 2 distinct geometries, a single helix and a dual helix, merely because of thermal fluctuations. PMID:19359489
First-principles design of nanomachines
Banavar, Jayanth R.; Cieplak, Marek; Hoang, Trinh Xuan; Maritan, Amos
2009-01-01
Learning from nature's amazing molecular machines, globular proteins, we present a framework for the predictive design of nanomachines. We show that the crucial ingredients for a chain molecule to behave as a machine are its inherent anisotropy and the coupling between the local Frenet coordinate reference frames of nearby monomers. We demonstrate that, even in the absence of heterogeneity, protein-like behavior is obtained for a simple chain molecule made up of just 30 hard spheres. This chain spontaneously switches between 2 distinct geometries, a single helix and a dual helix, merely because of thermal fluctuations. PMID:19359489
First Principles Simulations of Nanoparticle Solids
NASA Astrophysics Data System (ADS)
Greenwood, Arin; Vörös, Márton; Galli, Giulia
Nanoparticle solids are gaining popularity as materials for optoelectronic devices such as solar cells. However, there is still much debate regarding the transport regime governing the charge carriers. To date, no comprehensive description of transport mechanisms in nanoparticle solids has been established, and there is a lack of computational studies predicting electron mobilities and transport rates at the ab initio level. In order to understand electron transport properties, it is an essential prerequisite to build realistic structural models of nanoparticle solids to use for prediction of electronic structure and eventually transport properties. Here we present Ab Initio Molecular Dynamics simulations of lead chalcogenide nanoparticles and surrounding ligands to extract relevant electronic structure properties for charge transport calculations. We tested the validity of recently observed ''band-like'' transport by assessing the formation of bands and their dependence on nanoparticle surface structure and ligands. Work supported by DOE-BES under DE-FG02-06ER46262.
Ions in solutions: Determining their polarizabilities from first-principles
NASA Astrophysics Data System (ADS)
Molina, John J.; Lectez, Sébastien; Tazi, Sami; Salanne, Mathieu; Dufrêche, Jean-François; Roques, Jérôme; Simoni, Eric; Madden, Paul A.; Turq, Pierre
2011-01-01
Dipole polarizabilities of a series of ions in aqueous solutions are computed from first-principles. The procedure is based on the study of the linear response of the maximally localized Wannier functions to an applied external field, within density functional theory. For most monoatomic cations (Li ^+, Na ^+, K ^+, Rb ^+, Mg ^{2+}, Ca ^{2+} and Sr ^{2+}) the computed polarizabilities are the same as in the gas phase. For Cs ^+ and a series of anions (F ^-, Cl ^-, Br ^- and I ^-), environmental effects are observed, which reduce the polarizabilities in aqueous solutions with respect to their gas phase values. The polarizabilities of H ^+_(aq), OH ^-_(aq) have also been determined along an ab initio molecular dynamics simulation. We observe that the polarizability of a molecule instantaneously switches upon proton transfer events. Finally, we also computed the polarizability tensor in the case of a strongly anisotropic molecular ion, UO _2^{2+}. The results of these calculations will be useful in building interaction potentials that include polarization effects.
First-principles stability study of clathrate hydrates under pressure
NASA Astrophysics Data System (ADS)
Thonhauser, Timo; Li, Qi; Kolb, Brian
2010-03-01
We present a first-principles DFT study of the structural stability of clathrate hydrates under pressure. These materials form under high pressure and low temperature and consist of polyhedral water cages that form an ice-like framework of hydrogen bonds. Clathrate hydrates can be filled with guest molecules such as methane or molecular hydrogen, in which case these materials and their stability are of interest for energy-storage solutions. Since the interactions between the water molecules themselves---but also between the water molecules and the guest molecules---is at least partly determined by van der Waals forces, we utilize the recently developed self-consistent van der Waals density functional vdW-DF (T. Thonhauser, V.R. Cooper, S. Li, A. Puzder, P. Hyldgaard, and D.C. Langreth, Phys. Rev. B 76, 125112 (2007)). For our simulations we consider the empty host lattice, as well as the host lattice filled with methane and molecular hydrogen, for pressures up to 1 GPa. Our results show that the system undergoes phase transitions from structure I to structure II and finally to structure H, in good agreement with experiment.
Stavrou, Elissaios; Riad Manaa, M; Zaug, Joseph M; Kuo, I-Feng W; Pagoria, Philip F; Kalkan, Bora; Crowhurst, Jonathan C; Armstrong, Michael R
2015-10-14
Recent theoretical studies of 2,6-diamino-3,5-dinitropyrazine-1-oxide (C4H4N6O5 Lawrence Livermore Molecule No. 105, LLM-105) report unreacted high pressure equations of state that include several structural phase transitions, between 8 and 50 GPa, while one published experimental study reports equation of state (EOS) data up to a pressure of 6 GPa with no observed transition. Here we report the results of a synchrotron-based X-ray diffraction study and also ambient temperature isobaric-isothermal atomistic molecular dynamics simulations of LLM-105 up to 20 GPa. We find that the ambient pressure phase remains stable up to 20 GPa; there is no indication of a pressure induced phase transition. We do find a prominent decrease in b-axis compressibility starting at approximately 13 GPa and attribute the stiffening to a critical length where inter-sheet distance becomes similar to the intermolecular distance within individual sheets. The ambient temperature isothermal equation of state was determined through refinements of measured X-ray diffraction patterns. The pressure-volume data were fit using various EOS models to yield bulk moduli with corresponding pressure derivatives. We find very good agreement between the experimental and theoretically derived EOS. PMID:26472388
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.
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 (C_{4}H_{4}N_{6}O_{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. As a result, we find very good agreement between the experimental and theoretically derived EOS.
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
NASA Astrophysics Data System (ADS)
Stavrou, Elissaios; Riad Manaa, M.; Zaug, Joseph M.; Kuo, I.-Feng W.; Pagoria, Philip F.; Kalkan, Bora; Crowhurst, Jonathan C.; Armstrong, Michael R.
2015-10-01
Recent theoretical studies of 2,6-diamino-3,5-dinitropyrazine-1-oxide (C4H4N6O5 Lawrence Livermore Molecule No. 105, LLM-105) report unreacted high pressure equations of state that include several structural phase transitions, between 8 and 50 GPa, while one published experimental study reports equation of state (EOS) data up to a pressure of 6 GPa with no observed transition. Here we report the results of a synchrotron-based X-ray diffraction study and also ambient temperature isobaric-isothermal atomistic molecular dynamics simulations of LLM-105 up to 20 GPa. We find that the ambient pressure phase remains stable up to 20 GPa; there is no indication of a pressure induced phase transition. We do find a prominent decrease in b-axis compressibility starting at approximately 13 GPa and attribute the stiffening to a critical length where inter-sheet distance becomes similar to the intermolecular distance within individual sheets. The ambient temperature isothermal equation of state was determined through refinements of measured X-ray diffraction patterns. The pressure-volume data were fit using various EOS models to yield bulk moduli with corresponding pressure derivatives. We find very good agreement between the experimental and theoretically derived EOS.
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).
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.
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
First principles simulations of fluid water: The radial distribution functions
NASA Astrophysics Data System (ADS)
Ortega, José; Lewis, James P.; Sankey, Otto F.
1997-03-01
We apply a recently developed first principles but simplified molecular dynamics method to the simulation of water at different conditions. The computational simplicity of this method allows its application to systems containing a significant number of molecules, yet still taking explicitly into account the quantum electronic structure of the system. In the present work we simulate a system of 216 H2O molecules with periodic boundary conditions at two different densities (ρ=1.0 g/cm3 and ρ=0.72 g/cm3 and temperatures ranging from ˜300 K to ˜580 K. The effect of density and temperature on the structure of water is analyzed by means of the partial radial distribution functions gOO, gOH and gHH . We find an important reduction of the hydrogen-bond peak for water at the supercritical conditions ρ= 0.72 g/cm3, T=580 K, in good agreement with recent experimental results.
First-principles pressure-temperature phase diagrams in metals
Moriarty, J.A.
1993-07-01
Using interatomic potentials derived from first-principles generalized pseudopotential theory, finite-temperature phase transitions in both simple and transition metals can be studied through a combination of analytic statistical methods and molecular-dynamics simulation. In the prototype simple metal-Mg, where volume and pair forces adequately describe the energetics, a complete and accurate phase diagram has thereby been obtained to 60 GPa. A rapidly temperature-dependent hcp-bcc phase line is predicted which ends in a triple point on the melting curve near 4 GPa. In central transition metals such as Mo or Fe, on the other hand, the energetics are complicated by d-state interactions which give rise to both many-body angular forces and enhanced electron-thermal contributions. We have made a detailed study of these phenomena and their impact on melting in the prototype case of Mo and a full melting curve to 2 Mbar has been obtained. In the case of Fe, we are examining the high-pressure phase diagram and the question of whether or not there exists a high-pressure, high-temperature solid bcc phase, as has been speculated. To date, we have shown that the bcc structure is both thermodynamically and mechanically unstable at high pressure and zero temperature, with a large and increasing bcc-hcp energy difference under compression.
First-Principles and Semi-Empirical Studies of Microclusters.
NASA Astrophysics Data System (ADS)
Chang, Audrey Young-Zee
The structural, electronic and magnetic properties of clusters have been a subject of intense investigation in recent years, due to many advancements in theoretical and experimental techniques. Since the bonding of atoms in clusters is often different from in bulk, clusters may assume different shapes and structures as the size varies. They therefore provide a model for understanding the transition and structural formation of bulk materials. In this dissertation, two different approaches for pursuing cluster study are carried out: one is based on a realistic but semi-empirical method, the other is more of a first-principles type of calculation. In the first part, the implementation and application of a dynamics simulated annealing scheme, introduced by Car and Parrinello, to a semi-empirical tight-binding model for studying the silicon clusters is presented. In searching for the ground state structures, Langevin molecular dynamics is employed to allow relaxation of the nuclei. For small silicon clusters, Si_{n} (n <= 10), a preference of close-packed structure with binding energies depending on the size are found. Relatively stable structures are observed for clusters of size 4, 6 and 7 which are in accordance with the experimentally found "magic number". In the second part, the study of transition-metal chromium clusters via a first-principles, all-electron, linear combination of Gaussian orbitals method is presented. Transition -metal elements are characterized by having contracted valence d-orbitals containing up to ten electrons, which make them a highly correlated system. The many-electron effects attributed to interactions among these electrons are manifested rather dramatically through the observed magnetic ordering. In this study, the magnetic and structural properties of chromium clusters, (Cr_{n} n <= 9), are investigated based on density functional theory. In bulk, the bcc chromium crystal has a weak antiferromagnetic coupling due to Fermi surfaces
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.
First-principles investigation of graphene-metal interfaces
NASA Astrophysics Data System (ADS)
Ross, Andrew; Adamska, Lyudmyla; Lin, You; Oleynik, Ivan
2011-03-01
Epitaxial growth of graphene on Ni(111) substrates is one promising method of large-scale, high-quality graphene wafer production, due to the small lattice mismatch between these two materials. We present results of first-principles density functional theory (DFT) investigation of thestructural, electronic, and magnetic properties of graphene/Ni(111) interfaces relevant to experimental studies of graphene growth on nickel substrates. DFT calculations were performed to identify the favored interface geometries and binding sites for different interface configurations. Additional adlayers of Ni and Cu were either adsorbed on top of the graphene/metal interface, or placed between the graphene and substrate to model processes of metal intercalation. It was also found that the interaction between graphene/Ni(111) and the top Cu adlayer is much weaker compared to that for Ni adlayer. The atomic, electronic, and magnetic properties of these interfaces, including induced magnetic moments in graphene/Ni(111) and Cu,Ni/graphene/Ni(111) systems are also discussed. This work was supported by NSF REU supplement to the award CCF-0726842.
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.
A First-Principle Kinetic Theory of Meteor Plasma Formation
NASA Astrophysics Data System (ADS)
Dimant, Yakov; Oppenheim, Meers
2015-11-01
Every second millions of tiny meteoroids hit the Earth from space, vast majority too small to observe visually. However, radars detect the plasma they generate and use the collected data to characterize the incoming meteoroids and the atmosphere in which they disintegrate. This diagnostics requires a detailed quantitative understanding of formation of the meteor plasma. Fast-descending meteoroids become detectable to radars after they heat due to collisions with atmospheric molecules sufficiently and start ablating. The ablated material then collides into atmospheric molecules and forms plasma around the meteoroid. Reflection of radar pulses from this plasma produces a localized signal called a head echo. Using first principles, we have developed a consistent collisional kinetic theory of the near-meteoroid plasma. This theory shows that the meteoroid plasma develops over a length-scale close to the ion mean free path with a non-Maxwellian velocity distribution. The spatial distribution of the plasma density shows significant deviations from a Gaussian law usually employed in head-echo modeling. This analytical model will serve as a basis for more accurate quantitative interpretation of the head echo radar measurements. Work supported by NSF Grant 1244842.
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.
NASA Astrophysics Data System (ADS)
Correa, Alfredo; Schleife, Andre; Kanai, Yosuke
2014-03-01
In order to understand the interaction of projectile atoms with targets under particle radiation in materials, e.g. in space applications or nuclear reactors, it is critical to investigate electronic and ionic contributions to stopping power. The goal of such efforts is detailed understanding of radiation damages as well as fundamental effects such as ion-electron interaction. While ionic stopping has been successfully modeled by molecular dynamics in the past, only recently a computational framework came within reach that is capable of accurately describing electronic stopping from first principles. Using our large-scale implementation of real-time time-dependent density functional theory in non-adiabatic Ehrenfest molecular dynamics, we are able to gain deep insight into electronic stopping for systems with hundreds of atoms and thousands of electrons, taking into account their quantum-mechanical electron-electron interaction. We discuss distinct contributions of valence and core electrons of aluminum target atoms to electronic stopping, and we study their importance for different projectile (hydrogen and helium atoms) velocities. There is striking influence of the stopping geometry especially for fast projectiles, and we find excellent agreement with experiment. Prepared by LLNL under Contract DE-AC52-07NA27344.
First-Principles Monte Carlo Simulations of Reaction Equilibria in Compressed Vapors.
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
First-Principles Monte Carlo Simulations of Reaction Equilibria in Compressed Vapors
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
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.
Magnetic Properties of Ni(2+)(aq) from First Principles.
Mareš, Jiří; Liimatainen, Helmi; Pennanen, Teemu O; Vaara, Juha
2011-10-11
The aqueous solution of the Ni(2+) ion was investigated using a first principles molecular dynamics (FPMD) simulation based on periodic density-functional theory (DFT) calculations. Statistical averages of the magnetic properties corresponding to the triplet spin state of the ion, the hyperfine coupling, g and zero-field splitting tensors, as well as the resulting paramagnetic nuclear magnetic resonance (pNMR) shielding terms were calculated using DFT from instantaneous simulation snapshots extracted from the FPMD trajectory. We report comprehensive tests of the reliability of systematically selected DFT functionals for the properties. The isotropic nuclear shielding of the (17)O nuclei can be obtained with good predictive power. The accuracy of the calculated (1)H shieldings is limited by the fact that the spin-density on the proton sites is not reproduced reliably with the tested functionals, rendering the dominant Fermi contact isotropic shielding term less well-defined. On the other hand, the dominant spin-dipole term of the shielding anisotropy, which gives a practically vanishing isotropic contribution, can be obtained with good reliability for both the (1)H and (17)O nuclei. The anisotropic shielding tensor can be thus utilized reliably in the calculation of Curie-type paramagnetic relaxation. We discuss the evolution of the pNMR properties through the first and second solvation shells of the ion, toward the bulk solvent. The magnetic properties of the dominant, six-coordinated solution are compared to those of the metastable, 5-fold coordinated intermediate occurring in the dissociative exchange process. PMID:26598159
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.
Electron Exchange and Conduction in Nontronite from First-Principles
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
Force field development from first principles for materials design
NASA Astrophysics Data System (ADS)
Chan, Maria; Kinaci, Alper; Narayanan, Badri; Sen, Fatih; Gray, Stephen; Davis, Michael; Sankaranaryanan, Subramanian
2015-03-01
The ability to perform accurate calculations efficiently is crucial for computational materials design. In this talk, we will discuss a stream-lined approach to force field development using first principles density functional theory training data and machine learning algorithms. We will also discuss the validation of this approach on precious metal nanoparticles.
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
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
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.
Hybrid first-principles/neural networks model for column flotation
Gupta, S.; Liu, P.H.; Svoronos, S.A.; Sharma, R.; Abdel-Khalek, N.A.; Cheng, Y.; El-Shall, H.
1999-03-01
A new model for phosphate column flotation is presented which for the first time relates the effects of operating variables such as frother concentration on column performance. This is a hybrid model that combines a first-principles model with artificial neural networks. The first-principles model is obtained from material balances on both phosphate particles and gangue (undesired material containing mostly silica). First-order rates of net attachment are assumed for both. Artificial neural networks relate the attachment rate constants to the operating variables. Experiments were conducted in a 6-in.-dia. (152-mm-dia.) laboratory column to provide data for neural network training and model validation. The model successfully predicts the effects of frother concentration, particle size, air flow rate and bubble diameter on grade and recovery.
Understanding and Predicting Thiolated Gold Nanoclusters from First Principles
Jiang, Deen
2010-01-01
This is an exciting time for studying thiolated gold nanoclusters. Single crystal structures of Au{sub 102}(SR){sub 44} and Au{sub 25}(SR){sub 18}{sup -} (-SR being an organothiolate group) bring both surprises and excitement in this field. First principles density functional theory (DFT) simulations turn out to be an important tool to understand and predict thiolated gold nanoclusters. In this review, I summarize the progresses made by us and others in applying first principles DFT to thiolated gold nanoclusters, as inspired by the recent experiments. First, I will give some experimental background on synthesis of thiolated gold nanoclusters, followed by a description of the recent experimental breakthroughs. Then I will introduce the superatom complex concept as a way to understand the electronic structure of thiolated gold nanoclusters or smaller nanoparticles. Next, I will describe in detail how first principles DFT is used to understand the Au-thiolate interface, predict structures for Au{sub 38}(SR){sub 24}, screen good dopants for the Au{sub 25}(SR){sub 18}{sup -} cluster, design the smallest magic thiolated gold cluster, and demonstrate the need for the trimer protecting motif. I will conclude with a grand challenge: the real time monitoring of nucleation of thiolated gold nanoclusters.
Evolutionary approach for determining first-principles hamiltonians
NASA Astrophysics Data System (ADS)
Hart, Gus L. W.; Blum, Volker; Walorski, Michael J.; Zunger, Alex
2005-05-01
Modern condensed-matter theory from first principles is highly successful when applied to materials of given structure-type or restricted unit-cell size. But this approach is limited where large cells or searches over millions of structure types become necessary. To treat these with first-principles accuracy, one 'coarse-grains' the many-particle Schrödinger equation into 'model hamiltonians' whose variables are configurational order parameters (atomic positions, spin and so on), connected by a few 'interaction parameters' obtained from a microscopic theory. But to construct a truly quantitative model hamiltonian, one must know just which types of interaction parameters to use, from possibly 106-108 alternative selections. Here we show how genetic algorithms, mimicking biological evolution ('survival of the fittest'), can be used to distil reliable model hamiltonian parameters from a database of first-principles calculations. We demonstrate this for a classic dilemma in solid-state physics, structural inorganic chemistry and metallurgy: how to predict the stable crystal structure of a compound given only its composition. The selection of leading parameters based on a genetic algorithm is general and easily applied to construct any other type of complex model hamiltonian from direct quantum-mechanical results.
Evolutionary approach for determining first-principles hamiltonians.
Hart, Gus L W; Blum, Volker; Walorski, Michael J; Zunger, Alex
2005-05-01
Modern condensed-matter theory from first principles is highly successful when applied to materials of given structure-type or restricted unit-cell size. But this approach is limited where large cells or searches over millions of structure types become necessary. To treat these with first-principles accuracy, one 'coarse-grains' the many-particle Schrodinger equation into 'model hamiltonians' whose variables are configurational order parameters (atomic positions, spin and so on), connected by a few 'interaction parameters' obtained from a microscopic theory. But to construct a truly quantitative model hamiltonian, one must know just which types of interaction parameters to use, from possibly 10(6)-10(8) alternative selections. Here we show how genetic algorithms, mimicking biological evolution ('survival of the fittest'), can be used to distil reliable model hamiltonian parameters from a database of first-principles calculations. We demonstrate this for a classic dilemma in solid-state physics, structural inorganic chemistry and metallurgy: how to predict the stable crystal structure of a compound given only its composition. The selection of leading parameters based on a genetic algorithm is general and easily applied to construct any other type of complex model hamiltonian from direct quantum-mechanical results. PMID:15834412
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.
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. PMID:25721337
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.
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.
First principles study of the Young's modulus of Si <001> nanowires
Lee, B; Rudd, R E
2006-07-03
We report the results of first-principles calculations of the Young's modulus and other mechanical properties of hydrogen-passivated Si <001> nanowires. The nanowires are taken to have predominantly {l_brace}100{r_brace} surfaces, with small {l_brace}110{r_brace} facets according to the Wulff shape. The Young's modulus, the equilibrium length and the constrained residual stress of a series of prismatic beams of differing sizes is found to have a size dependence that scales like the surface area to volume ratio for all but the smallest beam. The results are compared with two different models (and the results of classical atomistic calculations based on an empirical potential). We discuss the physics of the hydrogen interactions on the surface and the charge density variations within the beam that may account for the discrepancies of the models and the first principles results.
First-principle optimal local pseudopotentials construction via optimized effective potential method
NASA Astrophysics Data System (ADS)
Mi, Wenhui; Zhang, Shoutao; Wang, Yanchao; Ma, Yanming; Miao, Maosheng
2016-04-01
The local pseudopotential (LPP) is an important component of orbital-free density functional theory, a promising large-scale simulation method that can maintain information on a material's electron state. The LPP is usually extracted from solid-state density functional theory calculations, thereby it is difficult to assess its transferability to cases involving very different chemical environments. Here, we reveal a fundamental relation between the first-principles norm-conserving pseudopotential (NCPP) and the LPP. On the basis of this relationship, we demonstrate that the LPP can be constructed optimally from the NCPP for a large number of elements using the optimized effective potential method. Specially, our method provides a unified scheme for constructing and assessing the LPP within the framework of first-principles pseudopotentials. Our practice reveals that the existence of a valid LPP with high transferability may strongly depend on the element.
NASA Astrophysics Data System (ADS)
Pratihar, Subha; Chandra, Amalendu
2011-01-01
First principles molecular dynamics simulations are carried out to investigate the solvation of an excess electron and a lithium atom in mixed water-ammonia cluster (H _2O) _5NH _3 at a finite temperature of 150 K. Both [(H _2O) _5NH _3] ^- and Li(H _2O) _5NH _3 clusters are seen to display substantial hydrogen bond dynamics due to thermal motion leading to many different isomeric structures. Also, the structures of these two clusters are found to be very different from each other and also very different from the corresponding neutral cluster without any excess electron or the metal atom. Spontaneous ionization of Li atom occurs in the case of Li(H _2O) _5NH _3. The spatial distribution of the singly occupied molecular orbital shows where and how the excess (or free) electron is primarily localized in these clusters. The populations of single acceptor (A), double acceptor (AA), and free (NIL) type water and ammonia molecules are found to be significantly high. The dangling hydrogens of these type of water or ammonia molecules are found to primarily capture the free electron. It is also found that the free electron binding motifs evolve with time due to thermal fluctuations and the vertical detachment energy of [(H _2O) _5NH _3] ^- and vertical ionization energy of Li(H _2O) _5NH _3 also change with time along the simulation trajectories. Assignments of the observed peaks in the vibrational power spectra are done and we found a one to one correlation between the time-averaged populations of water and ammonia molecules at different H-bonding sites with the various peaks of power spectra. The frequency-time correlation functions of OH stretch vibrational frequencies of these clusters are also calculated and their decay profiles are analyzed in terms of the dynamics of hydrogen bonded and dangling OH modes. It is found that the hydrogen bond lifetimes in these clusters are almost five to six times longer than that of pure liquid water at room temperature.
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.
Computation of Mössbauer isomer shifts from first principles
NASA Astrophysics Data System (ADS)
Zwanziger, J. W.
2009-05-01
Computation of the observables of a Mössbauer spectrum, primarily the isomer shift, from a first-principles approach is described. The framework used is density functional theory using the projector augmented wave formalism (DFT PAW), which enables efficient computation even of many-electron solids such as SnCl2. The proper PAW version of the isomer shift is derived and shown to be correct through comparison of computed shifts and experiment in a variety of compounds based on tin, germanium and zinc. The effects of pressure are considered as well as motional effects including the Lamb-Mössbauer factor and the second-order Doppler shift.
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.
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.
Superconductivity of compressed solid argon from first principles
NASA Astrophysics Data System (ADS)
Ishikawa, Takahiro; Asano, Masamichi; Suzuki, Naoshi; Shimizu, Katsuya
2015-02-01
We present first-principles calculations on the superconductivity of solid argon under high pressure. Solid argon is found to take the double hexagonal close-packed structure in pressure range from 420 to 690 GPa, where an insulator-to-metal transition occurs at around 590 GPa. The crystal structure transforms into the hexagonal close-packed structure at 690 GPa and into the face-centered cubic structure at 2300 GPa. The superconducting critical temperature is gradually increased with the successive phase transitions and reaches the maximum value of 12 K at 2600 GPa due to the enhancement of the Fermi surface nesting.
First-Principles Study of Impurities in TlBr
Du, Mao-Hua
2012-01-01
TlBr is a promising semiconductor material for room-temperature radiation detection. Material purification has been the driver for the recent improvement in the TlBr detector performance, mainly reflected by the significant increase in the carrier mobility-lifetime product. This suggests that impurities have significant impact on the carrier transport in TlBr. In this paper, first-principles calculations are used to study the properties of a number of commonly observed impurities in TlBr. The impurity-induced gap states are presented and their effects on the carrier trapping are discussed.
First-Principles Studies of Li Nucleation on Graphene.
Liu, Mingjie; Kutana, Alex; Liu, Yuanyue; Yakobson, Boris I
2014-04-01
We study the Li clustering process on graphene and obtain the geometry, nucleation barrier, and electronic structure of the clusters using first-principles calculations. We estimate the concentration-dependent nucleation barrier for Li on graphene. While the nucleation occurs more readily with increasing Li concentration, possibly leading to the dendrite formation and failure of the Li-ion battery, the existence of the barrier delays nucleation and may allow Li storage on graphene. Our electronic structure and charge transfer analyses reveal how the fully ionized Li adatoms transform to metallic Li during the cluster growth on graphene. PMID:26274475
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.
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.
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.
Large impurity effects in rubrene crystals: First-principles calculations
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.
Rare-earth pnictides and chalcogenides from first-principles.
Petit, L; Szotek, Z; Lüders, M; Svane, A
2016-06-01
This review tries to establish what is the current understanding of the rare-earth monopnictides and monochalcogenides from first principles. The rock salt structure is assumed for all the compounds in the calculations and wherever possible the electronic structure/properties of these compounds, as obtained from different ab initio methods, are compared and their relation to the experimental evidence is discussed. The established findings are summarised in a set of conclusions and provide outlook for future study and possible design of new materials. PMID:27165563
Rare-earth pnictides and chalcogenides from first-principles
NASA Astrophysics Data System (ADS)
Petit, L.; Szotek, Z.; Lüders, M.; Svane, A.
2016-06-01
This review tries to establish what is the current understanding of the rare-earth monopnictides and monochalcogenides from first principles. The rock salt structure is assumed for all the compounds in the calculations and wherever possible the electronic structure/properties of these compounds, as obtained from different ab initio methods, are compared and their relation to the experimental evidence is discussed. The established findings are summarised in a set of conclusions and provide outlook for future study and possible design of new materials.
Collective modes in light nuclei from first principles.
Dytrych, T; Launey, K D; Draayer, J P; Maris, P; Vary, J P; Saule, E; Catalyurek, U; Sosonkina, M; Langr, D; Caprio, M A
2013-12-20
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 6Li, 8Be, and 6He 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. PMID:24483740
First-Principles Study of LiPON Solid Electrolyte
NASA Astrophysics Data System (ADS)
Santosh, K. C.; Xiong, Ka; Cho, Kyeongjae
2011-03-01
There has been much interest in the thin-film solid electrolyte for solid state battery and ionics applications. LiPON is a representative material developed by Oak Ridge National Laboratory. In this work, we use first principles calculations based on the density functional theory to investigate the Li- ion migration mechanisms of LiPON family materials. We investigate atomic structures, electronic structures and defect formation energies of these materials. To determine the migration path of Li diffusion, the activation energies are calculated. This study helps us to understand fundamental mechanisms of Li-ion migration and to improve Li ion conductivity in the solid electrolytes.
First principles pseudopotential calculations on aluminum and aluminum alloys
Davenport, J.W.; Chetty, N.; Marr, R.B.; Narasimhan, S.; Pasciak, J.E.; Peierls, R.F.; Weinert, M.
1993-12-31
Recent advances in computational techniques have led to the possibility of performing first principles calculations of the energetics of alloy formation on systems involving several hundred atoms. This includes impurity concentrations in the 1% range as well as realistic models of disordered materials (including liquids), vacancies, and grain boundaries. The new techniques involve the use of soft, fully nonlocal pseudopotentials, iterative diagonalization, and parallel computing algorithms. This approach has been pioneered by Car and Parrinello. Here the authors give a review of recent results using parallel and serial algorithms on metallic systems including liquid aluminum and liquid sodium, and also new results on vacancies in aluminum and on aluminum-magnesium alloys.
Electromagnetic Response of ^{12}C: A First-Principles Calculation.
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
First Principles Phase Diagram Calculaions with the Maps Package
NASA Astrophysics Data System (ADS)
Burton, B. P.
2003-12-01
The MAPS, MIT ab initio software package (http://cms.northwestern.edu/Group.html) was used to perform first principles phase diagram calculations (FPPD) for the mineral systems: CaCO3}-MgCO{3; CdCO3}-MgCO{3; CaCO3}-MgCO{3; and NaCl-KCl. General characteristics of FPPD calculations will be reviewed and details of specific calculations will be discussed. Particular attention will be given to: the prediction of new stable ordered phases; metastable ordered phases; and the role of vibrational entropy in phase stability.
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.
First-principles studies of low tolerance factor perovskites
NASA Astrophysics Data System (ADS)
Kang, Sung Gu; Fennie, Craig J.
2014-03-01
Most perovskites form in the non-polar Pnma structure, however, materials found in the polar subgroup of this structure, e.g., space group Pna21, are rare. Here we study from first principles the structural and vibrational properties of twelve materials that span a wide range of tolerance factors (MgSnO3, ZnSnO3, MgTiO3, ZnTiO3, MgGeO3, ZnGeO3, CdSnO3, CaSnO3, CdTiO3, CaTiO3, CdGeO3, and CaGeO3) . We illustrate how low tolerance factor materials that have been artificially constrained to the Pnma structure do in fact display ferroelectric instabilities. Insight is gained by further studying the energetics for each material in the ilmenite, lithium niobate, and perovskite structures over a wide pressure range. Our first-principles results are shown to correlate with physical descriptors, such as tolerance factor, ionic radii, and electronegativity. The rationalized rules from our data analysis will guide to design the new ferroelectric/functional materials.
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.
First-Principles Studies of Conformation and Solution Effects on DNA Transport
NASA Astrophysics Data System (ADS)
Tan, Bikan
DNA charge transport (CT) has attracted considerable attention by the scientific community over the past 20 years. This interest reflects the potential of DNA CT to provide a sensitive route for signaling, whether in the construction of a nano-scale biosensor or as an enzymatic tool to detect damage in the genome. Research in DNA CT began as a quest to determine whether the DNA double helix with pi-stacked base pairs might share the conductive characteristics of pi-stacked solids. Physicists carried out sophisticated experiments to measure the conductivity of DNA. But the means to connect DNA to the electrodes, as well as the conditions under which the conductivity was measured are different among many experiments, as the results of the current measurements. DNA CT was seen to depend upon the connection between electrodes and DNA, and coupling between the DNA base pair stacks. Importantly, for those studies that utilized well-characterized connections to the DNA and preserved the duplex native conformation in buffered solution, significant electron conductivities were achieved. Certainly, the debate among researches has shifted from "Is DNA CT possible?" to "How does it work?". To investigate the remarkable characteristics of the double-helix molecule, we use a first-principle technique combined with molecular dynamics simulations to calculate the transport properties of B-DNA sandwiched between carbon nanotubes via alkane linkers. The quantum results using the NEGF method are calculated from snapshots recorded in MD trajectories. In chapter 1, we will go through the basic quantum and classic theories on which our calculations are based. The subject of DNA structure, electronic properties and its potential application in many fields will be introduced in chapter 2. In chapter 3, we discuss our results towards the understanding of the mechanism of DNA charge transport.
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.
NASA Astrophysics Data System (ADS)
van der Ven, Anton
2004-03-01
Many multiscale solid state phenomena involve the transport of chemical species over large distances. This is true of crack growth in corrosive environments as well as diffusional phase transformations. Often these phenomena occur over time scales that are too long for a direct atomistic simulation. Instead continuum methods that draw on phenomenological kinetic parameters such as diffusion coefficients or thermodynamic response functions such as informed cohesive zone models are necessary. A link between first principles atomistic methods and macroscopic kinetic parameters or response functions can be made with statistical mechanical coarse-graining techniques. For multicomponent crystalline solids, this involves integrating out fast degrees of freedom to generate a coarse-grained first-principles lattice model Hamiltonian that is suited for calculating both thermodynamic and kinetic properties, the latter with the help of Green-Kubo methods. We illustrate this approach by describing (i) a first principles calculation of diffusion coefficients in non-dilute alloys, essential input for continuum simulations of diffusional phase transformations and (ii) a first principles derivation of a cohesive zone model in the presence of highly mobile impurities. Cohesive zone models are used to describe the response of a solid ahead of the crack tip in continuum simulations of crack growth. We will show that for some systems, stress induced phase transformations can occur along the cohesive zone above a critical impurity chemical potential. The stress-induced transformation is accompanied by a saturation of the cohesive zone region with impurities and leads to a dramatic reduction of critical stress for decohesion.
First principles calculation of the effect of Coulomb collisions in partially ionized gases
Donkó, Z.
2014-04-15
Coulomb collisions, at appreciable ratios (η) of the electron to the neutral particle density, influence significantly the electron kinetics in particle swarms and in plasmas of gas discharges. This paper introduces a combination of Molecular Dynamics and Monte Carlo simulation techniques, to provide a novel, approximation-free, first principles calculation method for the velocity distribution function of electrons, and related swarm characteristics, at arbitrary η. Simulation results are presented for electrons in argon gas, for density ratios between zero and 10{sup −1}, representing the limits of a negligible electron density and an almost complete Maxwellization of the velocity distribution function, respectively.
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
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
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
Thermoelastic properties of α -iron from first-principles
NASA Astrophysics Data System (ADS)
Dragoni, Daniele; Ceresoli, Davide; Marzari, Nicola
2015-03-01
We calculate the thermomechanical properties of α -iron, and in particular its isothermal and adiabatic elastic constants, using first-principles total-energy and lattice-dynamics calculations, minimizing the quasiharmonic vibrational free energy under finite strain deformations. Particular care is made in the fitting procedure for the static and temperature-dependent contributions to the free energy, in discussing error propagation for the two contributions separately, and in the verification and validation of pseudopotential and all-electron calculations. We find that the zero-temperature mechanical properties are sensitive to the details of the calculation strategy employed, and common semilocal exchange-correlation functionals provide only fair to good agreement with experimental elastic constants, while their temperature dependence is in excellent agreement with experiments in a wide range of temperature almost up to the Curie transition.
First-principles prediction of disordering tendencies in pyrochlore oxides
NASA Astrophysics Data System (ADS)
Jiang, Chao; Stanek, C. R.; Sickafus, K. E.; Uberuaga, B. P.
2009-03-01
Using first-principles calculations, we systematically predict the order-disorder energetics of series of zirconate (A2Zr2O7) , hafnate (A2Hf2O7) , titanate (A2Ti2O7) , and stannate (A2Sn2O7) pyrochlores. The disordered defect-fluorite structure is modeled using an 88-atom two-sublattice special quasirandom structure (SQS) that closely reproduces the most relevant near-neighbor intrasublattice and intersublattice pair-correlation functions of the random mixture. The order-disorder transition temperatures of these pyrochlores estimated from our SQS calculations show overall good agreement with existing experiments. We confirm previous studies suggesting that the bonding in pyrochlores is not purely ionic and thus electronic effects also play a role in determining their disordering tendencies. Our results have important consequences for numerous applications, including nuclear waste forms and fast ion conductors.
First-principles study of interface doping in ferroelectric junctions
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
Helium diffusion in olivine based on first principles calculations
NASA Astrophysics Data System (ADS)
Wang, Kai; Brodholt, John; Lu, Xiancai
2015-05-01
As a key trace element involved in mantle evolution, the transport properties of helium in the mantle are important for understanding the thermal and chemical evolution of the Earth. However, the mobility of helium in the mantle is still unclear due to the scarcity of measured diffusion data from minerals under mantle conditions. In this study, we used first principles calculations based on density functional theory to calculate the absolute diffusion coefficients of the helium in olivine. Using the climbing images nudged elastic band method, we defined the diffusion pathways, the activation energies (Ea), and the prefactors. Our results demonstrate that the diffusion of helium has moderate anisotropy. The directionally dependent diffusion of helium in olivine can be written in Arrhenius form as follows.
Electromagnetic response of C12 : A first-principles calculation
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
First-principles study of hydrogen in perfect tungsten crystal
NASA Astrophysics Data System (ADS)
Xu, Jingcheng; Zhao, Jijun
2009-09-01
Tungsten-based materials are used as the first wall materials in ITER. Hydrogen impurities were introduced via bombarding with the reaction plasma, which are important for the behavior and stability of the tungsten wall. Using the first-principles density functional theory and planewave pseudopotential technique, we have simulated the behaviors of hydrogen atoms inside the perfect tungsten bcc lattice. The binding energies for different interstitial sites were compared to determine the optimal trapping site for the hydrogen atom inside the tungsten lattice. The diffusion barriers for hydrogen atom between nearby trapping sites and the interaction between two interstitial hydrogen atoms were also calculated. The implication of our theoretical results on the hydrogen diffusion and accumulation behavior was discussed.
First-principles modeling hydrogenation of bilayered boron nitride
NASA Astrophysics Data System (ADS)
Jing, Wang; Peng, Zhang; Xiang-Mei, Duan
2016-05-01
We have investigated the structural and electronic characteristics of hydrogenated boron-nitride bilayer (H–BNBN–H) using first-principles calculations. The results show that hydrogenation can significantly reduce the energy gap of the BN–BN into the visible-light region. Interestingly, the electric field induced by the interface dipoles helps to promote the formation of well-separated electron–hole pairs, as demonstrated by the charge distribution of the VBM and CBM. Moreover, the applied bias voltage on the vertical direction of the bilayer could modulate the band gap, resulting in transition from semiconductor to metal. We conclude that H–BNBN–H could improve the solar energy conversion efficiency, which may provide a new way for tuning the electronic devices to meet different environments and demands. Project supported by the National Natural Science Foundation of China (Grant No. 11574167).
High pressure polyhydrides of molybdenum: A first-principles study
NASA Astrophysics Data System (ADS)
Feng, Xiaolei; Zhang, Jurong; Liu, Hanyu; Iitaka, Toshiaki; Yin, Ketao; Wang, Hui
2016-07-01
We present results from first-principles calculations on molybdenum polyhydrides under pressure. In addition to the experimental ε-phase of MoH, we find several novel structures of MoH2 and MoH3 at pressures below 100 GPa. A hexagonal structure of MoH2 becomes stable with respect to decomposition into MoH and H2 above 9 GPa, and transforms into an orthorhombic structure at 24 GPa, which remains stable up to 100 GPa. MoH3 is unstable relative to decomposition into MoH and H2 over the whole pressure range studied. Electronic structure calculations reveal that molybdenum polyhydrides are metallic under pressure.
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.
Defects in AIN/GaN Superlattice: First Principle Calculations.
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
Hydrogen storage in LiH: A first principle study
NASA Astrophysics Data System (ADS)
Banger, Suman; Nayak, Vikas; Verma, U. P.
2014-04-01
First principles calculations have been performed on the Lithium hydride (LiH) using the full potential linearized augmented plane wave (FP-LAPW) method within the framework of density functional theory. We have extended our calculations for LiH+2H and LiH+6H in NaCl structure. The structural stability of three compounds have been studied. It is found that LiH with 6 added Hydrogen atoms is most stable. The obtained results for LiH are in good agreement with reported experimental data. Electronic structures of three compounds are also studied. Out of three the energy band gap in LiH is ˜3.0 eV and LiH+2H and LiH+6H are metallic.
Two Dimensional Ice from First Principles: Structures and Phase Transitions.
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
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.
Electronic Stopping Power in LiF from First Principles
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.
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.
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.
First-principles simulations of electrostatic interactions between dust grains
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.
First principles modeling of panchromatic dyes for solar cells applications.
NASA Astrophysics Data System (ADS)
di Felice, Rosa; Calzolari, Arrigo; Dong, Rui; Buongiorno Nardelli, Marco
2013-03-01
The state-of-the-art dye in Grätzel solar cells, N719, exhibits a total solar-to-electric conversion efficiency of 11.2%. However, it severely lacks absorption in the red and the near infrared regions of the electromagnetic spectrum, which represent more than 70% of the solar radiation spectrum. Using calculations from first principles in the time-dependent domain, we have studied the electronic and optical response of a novel class of panchromatic sensitizers that can harvest solar energy efficiently across the visible and near infrared regions, which have been recently synthesized [A. El-Shafei, M. Hussain, A. Atiq, A. Islam, and L. Han, J. Mater. Chem. 22, 24048 (2012)]. Our calculations show that, by tuning the properties of antenna groups, one can achieve a substantial improvement of the optical properties.
First-Principles Dielectric Spectra of Silicon: THz through UV
NASA Astrophysics Data System (ADS)
Lawler, H. M.; Dalosto, S.; Levine, Z. H.; Shirley, E. L.; Rehr, J. J.
2007-03-01
We present an implementation of the GW-Bethe-Salpeter-equation approach to first-principles calculations of dielectric response based in part on input from the plane-wave, pseudopotential code ABINIT. This work, together with lattice dynamical calculations, aims to develop versatile codes capable of calculating dielectric spectra in insulators for the full spectral range from THz to the UV. Below the bandgap, lattice vibrations absorb light in the THz range. These spectra are generally composed of sharp infrared-active features (absent by symmetry in silicon); weak, temperature dependent continuum effects from IR-active-multiphonon state hybridization; and contributions to the macroscopic polarization directly from multiphonon states. Above the bandgap, density-functional band structures are taken as a starting point for the inclusion of many-body interactions within the GW-BSE approximation. Emphasis will be on treating the excitionic effects and non-zero-momentum application of the modern theory of polarization with ABINIT.
NMR shifts for polycyclic aromatic hydrocarbons from first-principles
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.
First principle study of manganese doped cadmium sulphide sheet
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.
First principles pseudopotential calculations on aluminum and aluminum alloys
Davenport, J.W.; Chetty, N.; Marr, R.B.; Narasimhan, S.; Pasciak, J.E.; Peierls, R.F.; Weinert, M.; Rahman, T.S.
1994-12-31
Recent advances in computational techniques have led to the possibility of performing first principles calculations of the energetics of alloy formation on systems involving several hundred atoms. This includes impurity concentrations in the 1% range as well as realistic models of disordered materials (including liquids), vacancies, and grain boundaries. The new techniques involve the use of soft, fully nonlocal pseudopotentials, iterative diagonalization, and parallel computing algorithms. This approach has been pioneered by Car and Parrinello. Here the authors give a review of recent results using parallel and serial algorithms by their group on metallic systems including liquid aluminum and liquid sodium, and also new results on vacancies in aluminum and on aluminum-magnesium alloys.
First-principles study of silicon nitride nanotubes
NASA Astrophysics Data System (ADS)
Gao, Guohua; Kang, Hong Seok
2008-10-01
We have made a first-principles calculation of the topological, geometric, and electronic structures of nitrogen-doped armchair and zigzag silicon carbide nanotubes, where we have assumed that all carbon atoms have been substituted by nitrogen atoms. The doping was found to be substantially easier than for analogous carbon nanotubes. In addition, the doping process is cooperative, leading us to theoretically predict the stable existence of silicon nitride nanotubes (SiNNTs). For (n,n) SiNNTs, all kinds of chiral indices n are possible. These armchair tubes are semiconductors with much smaller band gaps than those of corresponding silicon carbide nanotubes, and the gap decreases with the tube diameter. For (n,0) chirality, only even-numbered chiral indices (n=2l) are possible. These nanotubes are also semiconductors with band gaps larger than those of armchair SiNNTs of similar diameters.
Carbon-rich icosahedral boron carbide designed from first principles
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.
First-principles study of thermal properties of borophene.
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
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.
Hadron Phenomenology from First-Principle QCD Studies
NASA Astrophysics Data System (ADS)
Papavassiliou, Joannis
2016-03-01
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.
Free-Carrier Absorption in Silicon from First Principles
NASA Astrophysics Data System (ADS)
Shi, Guangsha; Kioupakis, Emmanouil
The absorption of light by free carriers in semiconductors such as silicon results in intraband electron or hole excitations, and competes with optical transitions across the band gap. Free-carrier absorption therefore reduces the efficiency of optoelectronic devices such as solar cells because it competes with the generation of electron-hole pairs. In this work, we use first-principles calculations based on density functional theory to investigate direct and phonon-assisted free-carrier absorption in silicon. We determine the free-carrier absorption coefficient as a function of carrier concentration and temperature and compare to experiment. We also identify the dominant phonon modes that contributing to phonon-assisted free-carrier absorption processes, and analyze the results to evaluate the impact of this loss mechanism on the efficiency of silicon solar cells. This research was supported by the National Science Foundation CAREER award through Grant No. DMR-1254314. Computational resources were provided by the DOE NERSC facility.
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.
Structural instabilities in strontium titanate from first-principles calculations
NASA Astrophysics Data System (ADS)
Lasota, Christopher Andrew
For some time now, first-principles calculation methods have proven to be an effective tool for investigating the physics of condensed matter systems. The additional use of density functional theory (DFT) and the local density approximation (LDA) has permitted even complex materials to be studied on desktop workstations with remarkable success. The incorporation of linear response theory into these methods has extended their power, allowing investigation of important dynamical properties. Contained within the following pages are the results of a first-principles study of SrTiO3. This transition metal oxide is often grouped with ferroelectric materials, due to its similar composition and perovskite structure. Although it behaves as if it were to become ferroelectric, it fails to do so, even at the lowest temperatures. Using the LAPW method for bulk materials, the ground-state equilibrium properties for the cubic phase were found. Additional linear response calculations produced the phonon frequencies throughout the Brillouin zone. Imaginary values for these frequencies revealed two distinct regions of reciprocal space corresponding to structural instabilities of the ferroelectric (FE) and antiferrodistortive (AFD) types. A cell-doubling AFD transition to tetragonal structure is observed experimentally, so subsequent calculations were continued in this phase. Total energy calculations were performed for both FE and AFD distortions in this new phase, and it was found that the AFD instability is enhanced with decreasing lattice parameter, while the FE instability is diminished. Furthermore, these calculations suggest that this material is marginally stable against FE distortions, even at the 105 K volume.
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.
First principles theory for surface plasmon generation and decay to hot carriers
NASA Astrophysics Data System (ADS)
Sundararaman, Ravishankar; Narang, Prineha; Jermyn, Adam; Atwater, Harry A.; Goddard, William A., III
2014-03-01
Plasmonic resonances provide a promising pathway for efficiently capturing infrared photons from solar radiation and boosting photo-catalytic activity via local temperature enhancements and hot carrier generation. Previous calculations of plasmon decay to excited carriers employing a fully quantized model Hamiltonian [2] indicate strong plasmon polarization dependence and momentum anisotropy of the generated carriers, in contrast with classical theories. An accurate first principles calculation for this process must account for microscopic details at the atomic scale for the electronic states as well as the effect of the 10-100 nm length scale particle and antennae geometries on the plasmon resonances. Here, we present a first-principles multi-scale model of plasmonics combining electronic density-functional theory with electromagnetic models on longer length-scales, and investigate the role of electronic structure and geometry on plasmonic light absorption, decay and hot carrier generation. This material is based upon work performed by the Joint Center for Artificial Photosynthesis, a DOE Energy Innovation Hub, supported through the Office of Science of the U.S. Department of Energy under Award Number DE-SC0004993.
Truncated spherical-wave basis set for first-principles pseudopotential calculations
NASA Astrophysics Data System (ADS)
Monserrat, B.; Haynes, P. D.
2010-11-01
Analytic results for two- and three-centre integrals are derived for the truncated spherical-wave basis set designed for first-principles pseudopotential calculations within density-functional theory. These allow the overlap, kinetic energy and non-local pseudopotential matrix elements to be calculated efficiently and accurately. In particular, the scaling of the computational effort with maximum angular momentum component is dramatically improved and the projection method takes full account of the discontinuities in the basis functions arising from their localization within spherical regions.
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.
First Principles Modeling of Phonon Heat Conduction in Nanoscale Crystalline Structures
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
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.
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.
The Effects of Relativity on First-Principles Calculations
NASA Astrophysics Data System (ADS)
Semi, T.; Mattsson, A. E.; Wills, J. M.
2011-06-01
The construction of the equation of state for a given material is of central importance to its characterization. Hugoniots can be calculated using Density Functional Theory (DFT), and DFT points compared to available experimental results. By evaluating the accuracy in a relevant phase space, confidence is gained in the DFT method. This bolsters the dependability of DFT data in phase spaces in which experiment may be difficult or impossible to perform, and verifies its usefulness. The equation of state is comprised of the cold curve and thermal electronic and ionic terms. We discuss differences in the cold curve of Ce produced by first principles calculations using the Scalar Dirac equation with variational spin-orbit coupling treatment and that generated by the full relativistic formulation, both with the same DFT functionals. The relativistic effects of f-electrons in systems like Ce are expected to be of a magnitude substantial enough to be consequential to the description of these structures. ``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.''
Electronic structure and ionicity of actinide oxides from first principles
NASA Astrophysics Data System (ADS)
Petit, L.; Svane, A.; Szotek, Z.; Temmerman, W. M.; Stocks, G. M.
2010-01-01
The ground-state electronic structures of the actinide oxides AO , A2O3 , and AO2 ( A=U , Np, Pu, Am, Cm, Bk, and Cf) are determined from first-principles calculations, using the self-interaction corrected local spin-density approximation. Emphasis is put on the degree of f -electron localization, which for AO2 and A2O3 is found to follow the stoichiometry, namely, corresponding to A4+ ions in the dioxide and A3+ ions in the sesquioxides. In contrast, the A2+ ionic configuration is not favorable in the monoxides, which therefore become metallic. The energetics of the oxidation and reduction in the actinide dioxides is discussed, and it is found that the dioxide is the most stable oxide for the actinides from Np onward. Our study reveals a strong link between preferred oxidation number and degree of localization which is confirmed by comparing to the ground-state configurations of the corresponding lanthanide oxides. The ionic nature of the actinide oxides emerges from the fact that only those compounds will form where the calculated ground-state valency agrees with the nominal valency expected from a simple charge counting.
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).
First-principles design of organo-Sn polymeric dielectrics
NASA Astrophysics Data System (ADS)
Tran, Huan; Kumar, Arun; Wang, Chenchen; Baldwin, Aaron; Ma, Rui; Sotzing, Gregory; Ramprasad, Rampi
2014-03-01
Following on from recent computation-based suggestions that Sn-containing polymers may be promising dielectrics, one of them, poly (dimethyltin glutarate) (pDMTG), has been synthesized. The measured dielectric constant of pDMTG is ɛ ~= 7 . 4 , significantly higher than the current standard material used for high-energy-density applications, namely, polypropylene (ɛ ~= 2 . 2). By performing first-principles calculations at the level of density functional theory and using the minima-hopping method to predict the stable structures (given that just the composition is provided), we propose four structural models of pDMTG. Based on these models, various physical properties of pDMTG, e.g., dielectric constant, infrared spectra and refractive index, are determined to closely agree with experimental data. The calculated band gap of pDMTG is high (Eg ~= 6 . 1 eV), implying that pDMTG is a promising candidate for high-energy-density materials. The strategy that has lead to the synthesis and understanding of pDMTG shows that density functional theory is a powerful method to study and design new materials. Our work is supported by the Office of Naval Research through the Multidisciplinary University Research Initiative (MURI).
First-principles study of liquid and amorphous metals
NASA Astrophysics Data System (ADS)
Ganesh, Panchapakesan
Computer simulations using state of the art First-Principles ab-initio methods enable us to probe the structural features of novel materials like liquid metals and metallic glass forming alloys, both in their supercooled liquid state as well as in their quenched amorphous forms where available. The ab-initio nature of the calculations enable us to capture the chemical identity realistically at the atomistic level without any free parameters. The results show that even though elemental liquid metals like face-centered cubic (FCC) Cu and body-centered cubic (BCC) Fe (and W) have similar atomic structure at high temperature, which is also similar to jammed packing of hard-spheres, they differ quite appreciably even with slight supercooling. This difference enables us to further supercool Fe and W to a much greater degree than Cu. The origin of this difference between elemental metals with different crystalline ground states can be understood based on concepts of geometric frustration. Further, the role played by atoms of different sizes in controlling the geometric frustration in glass forming alloys has been investigated. Studies of Silicon in its supercooled regime have been made to investigate the existence of a possible structural transition. Attempts to clarify if the structural transition could be a thermodynamic phase transition have been made and changes in electronic properties accompanying this structural change have been studied.
First-Principle Characterization for Singlet Fission Couplings.
Yang, Chou-Hsun; Hsu, Chao-Ping
2015-05-21
The electronic coupling for singlet fission, an important parameter for determining the rate, has been found to be too small unless charge-transfer (CT) components were introduced in the diabatic states, mostly through perturbation or a model Hamiltonian. In the present work, the fragment spin difference (FSD) scheme was generalized to calculate the singlet fission coupling. The largest coupling strength obtained was 14.8 meV for two pentacenes in a crystal structure, or 33.7 meV for a transition-state structure, which yielded a singlet fission lifetime of 239 or 37 fs, generally consistent with experimental results (80 fs). Test results with other polyacene molecules are similar. We found that the charge on one fragment in the S1 diabatic state correlates well with FSD coupling, indicating the importance of the CT component. The FSD approach is a useful first-principle method for singlet fission coupling, without the need to include the CT component explicitly. PMID:26263271
First principles Tafel kinetics of methanol oxidation on Pt(111)
NASA Astrophysics Data System (ADS)
Fang, Ya-Hui; Liu, Zhi-Pan
2015-01-01
Electrocatalytic methanol oxidation is of fundamental importance in electrochemistry and also a key reaction in direct methanol fuel cell. To resolve the kinetics at the atomic level, this work investigates the potential-dependent reaction kinetics of methanol oxidation on Pt(111) using the first principles periodic continuum solvation model based on modified-Poisson-Boltzmann equation (CM-MPB), focusing on the initial dehydrogenation elementary steps. A theoretical model to predict Tafel kinetics (current vs potential) is established by considering that the rate-determining step of methanol oxidation (to CO) is the first Csbnd H bond breaking (CH3OH(aq) → CH2OH* + H*) according to the computed free energy profile. The first Csbnd H bond breaking reaction needs to overcome a large entropy loss during methanol approaching to the surface and replacing the adsorbed water molecules. While no apparent charge transfer is involved in this elementary step, the charge transfer coefficient of the reaction is calculated to be 0.36, an unconventional value for charge transfer reactions, and the Tafel slope is deduced to be 166 mV. The results show that the metal/adsorbate interaction and the solvation environment play important roles on influencing the Tafel kinetics. The knowledge learned from the potential-dependent kinetics of methanol oxidation can be applied in general for understanding the electrocatalytic reactions of organic molecules at the solid-liquid interface.
First-principles study of hydrogen storage materials
NASA Astrophysics Data System (ADS)
Ma, Zhu
2008-10-01
In this thesis, we use first-principles calculations to study the structural, electronic, and thermal properties of several complex hydrides. We investigate structural and electronic properties of Na-Li alanates. Although Na alanate can reversibly store H with Ti catalyst, its weight capacity needs to be improved. This can be accomplished by partial replacement of Na with lighter elements. We explore the structures of possible Na-Li alloy alanates, and study their phase stability. We also study the structural and thermal properties of Li/Mg/Li-Mg Amides/Imides. Current experimental results give a disordered model about the structure of Li-Mg Imide, in which the positions of Li and Mg are not specified. In addition the model gives a controversial composition stoichiometry. We try to resolve this controversy by searching for low-energy ordered phases. In the last part, we study the structural, energetic, and electronic properties of the La-Mg-Pd-H system. This quaternary system is another example of hydrogenation-induced metal-nonmetal transition without major reconstruction of metal host structure, and it is also with partial reversible H capacity. Experiment gives partially disordered H occupancy on two Wyckoff positions. Our calculation explains the structural and bonding characteristics observed in experiment.
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.
First-principles prediction of disordering tendencies in complex oxides
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.
First principles based mean field model for oxygen reduction reaction.
Jinnouchi, Ryosuke; Kodama, Kensaku; Hatanaka, Tatsuya; Morimoto, Yu
2011-12-21
A first principles-based mean field model was developed for the oxygen reduction reaction (ORR) taking account of the coverage- and material-dependent reversible potentials of the elementary steps. This model was applied to the simulation of single crystal surfaces of Pt, Pt alloy and Pt core-shell catalysts under Ar and O(2) atmospheres. The results are consistent with those shown by past experimental and theoretical studies on surface coverages under Ar atmosphere, the shape of the current-voltage curve for the ORR on Pt(111) and the material-dependence of the ORR activity. This model suggests that the oxygen associative pathway including HO(2)(ads) formation is the main pathway on Pt(111), and that the rate determining step (RDS) is the removal step of O(ads) on Pt(111). This RDS is accelerated on several highly active Pt alloys and core-shell surfaces, and this acceleration decreases the reaction intermediate O(ads). The increase in the partial pressure of O(2)(g) increases the surface coverage with O(ads) and OH(ads), and this coverage increase reduces the apparent reaction order with respect to the partial pressure to less than unity. This model shows details on how the reaction pathway, RDS, surface coverages, Tafel slope, reaction order and material-dependent activity are interrelated. PMID:22064886
Electrostatic engineering of strained ferroelectric perovskites from first principles
NASA Astrophysics Data System (ADS)
Cazorla, Claudio; Stengel, Massimiliano
2015-12-01
Design of novel artificial materials based on ferroelectric perovskites relies on the basic principles of electrostatic coupling and in-plane lattice matching. These rules state that the out-of-plane component of the electric displacement field and the in-plane components of the strain are preserved across a layered superlattice, provided that certain growth conditions are respected. Intense research is currently directed at optimizing materials functionalities based on these guidelines, often with remarkable success. Such principles, however, are of limited practical use unless one disposes of reliable data on how a given material behaves under arbitrary electrical and mechanical boundary conditions. Here we demonstrate, by focusing on the prototypical ferroelectrics PbTiO3 and BiFeO3 as test cases, how such information can be calculated from first principles in a systematic and efficient way. In particular, we construct a series of two-dimensional maps that describe the behavior of either compound (e.g., concerning the ferroelectric polarization and antiferrodistortive instabilities) at any conceivable choice of the in-plane lattice parameter, a , and out-of-plane electric displacement, D . In addition to being of immediate practical applicability to superlattice design, our results bring new insight into the complex interplay of competing degrees of freedom in perovskite materials and reveal some notable instances where the behavior of these materials depart from what naively is expected.
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).
First principles calculations for modern ceramic science and engineering
NASA Astrophysics Data System (ADS)
Tanaka, Isao; Oba, Fumiyasu
2008-02-01
The free energy of compounds can be theoretically obtained as a function of temperature, pressure and chemical potentials by a combination of a first principles method including phonon calculations and statistical approaches using cluster expansion and Monte Carlo simulations. The information is quite useful in ceramic science and engineering since experimental data are not abundantly available. As an example of phonon calculations, results for graphite in comparison to diamond are presented. The free energy difference among polymorphs of Ga2O3 is shown as a function of temperature as well. Theoretical calculations of x-ray absorption near edge structures (XANES) and electron energy loss near edge structures (ELNES) are also demonstrated. Proper inclusion of the core-hole effect is mandatory in the calculation. For 3d transition element L2,3 XANES/ELNES, a configuration interaction approach to take account of the correlation among the core-hole and the excited electron satisfactorily reproduces experimental spectra. As an example, results for Mn-doped ZnO are shown.
First-principles prediction of a native ferroelectric metal
NASA Astrophysics Data System (ADS)
Iniguez, Jorge; Filippetti, Alessio; Fiorentini, Vincenzo; Ricci, Francesco; Delugas, Pietro
The possibility that metals may support ferroelectricity is an intriguing open issue. Over the years, various compounds have been referred to as ferroelectric metals, including non-centrosymmetric metals as well as ferroelectrics whose polar distortion survives moderate metallicity induced by doping or proximity. Yet, we think none of these systems embodies a truly ferroelectric metal with native switchable polarization and native metallicity coexisting in a single phase. Here we report a first-principles prediction of such a material. We show that the layered perovskite Bi5Ti5O17 has a non-zero density of states at the Fermi level and metal-like conductivity, as well as a spontaneous polarization in zero field. Further, we predict that the polarization of Bi5Ti5O17 is switchable both in principle (the material complies with the sufficient symmetry requirements) and in practice (in spite of being a metal, Bi5Ti5O17 can sustain a sizable potential drop along the polar direction, as needed to revert its polarization by application of an electric bias). Our results also reveal striking behaviors - such as the self screening mechanism at work in thin Bi5Ti5O17 layers - emerging from the intimate interplay between polar distortions and free carriers in such an exotic material. Supported by MIUR-PRIN, Fondazione Banco di Sardegna, FNR Luxembourg, MINECO-Spain, CINECA-ISCRA and CESGA.
Safeguards First Principles Initiative at the Nevada Test Site
Geneva Johnson
2007-07-08
The Material Control and Accountability (MC&A) program at the Nevada Test Site (NTS) was selected as a test bed for the Safeguards First Principles Initiative (SFPI). The implementation of the SFPI is evaluated using the system effectiveness model and the program is managed under an approved MC&A Plan. The effectiveness model consists of an evaluation of the critical elements necessary to detect, deter, and/or prevent the theft or diversion of Special Nuclear Material (SNM). The modeled results indicate that the MC&A program established under this variance is still effective, without creating unacceptable risk. Extensive performance testing is conducted through the duration of the pilot to ensure the protection system is effective and no material is at an unacceptable risk. The pilot was conducted from January 1, 2007, through May 30, 2007. This paper will discuss the following activities in association with SFPI: 1. Development of Timeline 2. Crosswalk of DOE Order and SFPI 3. Peer Review 4. Deviation 5. MC&A Plan and Procedure changes 6. Changes implemented at NTS 7. Training 8. Performance Test
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.
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.
Realtime capable first principle based modelling of tokamak turbulent transport
NASA Astrophysics Data System (ADS)
Citrin, Jonathan; Breton, Sarah; Felici, Federico; Imbeaux, Frederic; Redondo, Juan; Aniel, Thierry; Artaud, Jean-Francois; Baiocchi, Benedetta; Bourdelle, Clarisse; Camenen, Yann; Garcia, Jeronimo
2015-11-01
Transport in the tokamak core is dominated by turbulence driven by plasma microinstabilities. When calculating turbulent fluxes, maintaining both a first-principle-based model and computational tractability is a strong constraint. We present a pathway to circumvent this constraint by emulating quasilinear gyrokinetic transport code output through a nonlinear regression using multilayer perceptron neural networks. This recovers the original code output, while accelerating the computing time by five orders of magnitude, allowing realtime applications. A proof-of-principle is presented based on the QuaLiKiz quasilinear transport model, using a training set of five input dimensions, relevant for ITG turbulence. The model is implemented in the RAPTOR real-time capable tokamak simulator, and simulates a 300s ITER discharge in 10s. Progress in generalizing the emulation to include 12 input dimensions is presented. This opens up new possibilities for interpretation of present-day experiments, scenario preparation and open-loop optimization, realtime controller design, realtime discharge supervision, and closed-loop trajectory optimization.
Predicted boron-carbide compounds: a first-principles study.
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. PMID:24929411
Predicted boron-carbide compounds: A first-principles study
NASA Astrophysics Data System (ADS)
Wang, De Yu; Yan, Qian; Wang, Bing; Wang, Yuan Xu; Yang, Jueming; Yang, Gui
2014-06-01
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.
Predicted boron-carbide compounds: A first-principles study
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.
First Principles Modelling of Oxygen Impurities in UN Nuclear Fuels
Kotomin, Eugene Alexej; Mastrikov, Yuri A.
2008-07-15
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.
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.
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.
Semiconducting Graphene on Silicon from First-Principles Calculations.
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. PMID:26213346
First-Principles Investigation of the Electronic Properties of Interfaces
NASA Astrophysics Data System (ADS)
Lucking, Michael C.
Modern technology depends on the interfaces between materials. Nanomaterials and 2D systems are also promising for future energy and electronics applications. The much larger surface to volume ration of these systems compared to their bulk counterparts makes the interface properties even more important. Understanding the properties of interfaces is vital for technological advancement. First-principles calculations utilizing Density Functional Theory (DFT) can be applied to interfaces and nanostructures to improve the understanding of these systems. I have used these methods to investigate several systems with energy and electronics applications. Several aspects of solar water splitting have been examined, leading to a method of calculating redox levels as well as alignments for amorphous materials. A derailed understanding of the hole transfer reaction on surfaces has also been developed, as well as an understanding of band edge engineering in the promising photocatalyst CoO. In the field if electronics, edge engineering possibilities have been discovered in MoS2, also leading to a general electron counting method that is widely applicable. The nature of the insulating state as well as a model for the transition to the superconducting state has been proposed in (Li,Fe)OHFeSe. The interface between STO and FeSe has also been investigated and the issues are discussed.
Auger recombination in InN from first principles
NASA Astrophysics Data System (ADS)
McAllister, Andrew; Kioupakis, Emmanouil
Group-III Nitride materials are used in numerous electronic and optoelectronic devices including solid-state lighting, energy conversion, sensor technologies, and high-power electronics. Indium nitride in particular is interesting for fast electronics and optoelectronics in the infrared. Auger recombination is a non-radiative carrier recombination process that would limit the efficiency of these devices. The small band gap (0.7 eV) and the high intrinsic free-electron concentrations in InN possibly make Auger recombination particularly important in this material. We used first-principles computational methods to determine the Auger recombination rates in InN. Our results suggest that direct Auger recombination is dominant in this material and that phonon-assisted Auger processes are not as important as in wider-gap nitrides such as GaN. This research was supported by the National Science Foundation CAREER award through Grant No. DMR-1254314. Computational resources were provided by the DOE NERSC facility.
Thermal conductivity of silicene from first-principles
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.
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.
First principle calculations of hexyl thiolate monolayer on Au(1 1 1)
NASA Astrophysics Data System (ADS)
Wu, Taiquan; Cao, Dan; Wang, Xinyan; Jiao, Zhiwei; Chen, Miaogen; Luo, Honglei; Zhu, Ping
2015-03-01
The first-principle technique has been employed to determine the structure of hexyl thiolate molecular chains, monolayers and the adsorption system. CASTEP calculation shows that hexyl thiolate monolayer is a self-assembly system. And the molecular orientation of the hexyl thiolate on the surface is not symmetrical, they have the simplex structure. The electron density confirms the result. Hexyl thiolate monolayer is adsorbed on the Au(1 1 1)-(√3 × √3)R30° surface in the bridge site with the angle between the Ssbnd C6 bond and the surface is 65°. The structural parameters in the adsorption system are the same to those in the monolayer.
Performance of arsenene and antimonene double-gate MOSFETs from first principles
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
Performance of arsenene and antimonene double-gate MOSFETs from first principles.
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
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
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
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
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 (K_{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
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
First-principles studies of Ni-Ta intermetallic compounds
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.
A digitally reconstructed radiograph algorithm calculated from first principles
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
Risk reduction and the privatization option: First principles
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.
A first-principles theoretical approach to heterogeneous nanocatalysis.
Negreiros, Fabio R; Aprà, Edoardo; Barcaro, Giovanni; Sementa, Luca; Vajda, Stefan; Fortunelli, Alessandro
2012-02-21
A theoretical approach to heterogeneous catalysis by sub-nanometre supported metal clusters and alloys is presented and discussed. Its goal is to perform a computational sampling of the reaction paths in nanocatalysis via a global search in the phase space of structures and stoichiometry combined with filtering which takes into account the given experimental conditions (catalytically relevant temperature and reactant pressure), and corresponds to an incremental exploration of the disconnectivity diagram of the system. The approach is implemented and applied to the study of propylene partial oxidation by Ag(3) supported on MgO(100). First-principles density-functional theory calculations coupled with a Reactive Global Optimization algorithm are performed, finding that: (1) the presence of an oxide support drastically changes the potential energy landscape of the system with respect to the gas phase, favoring configurations which interact positively with the electrostatic field generated by the surface; (2) the reaction energy barriers for the various mechanisms are crucial in the competition between thermodynamically and kinetically favored reaction products; (3) a topological database of structures and saddle points is produced which has general validity and can serve for future studies or for deriving general trends; (4) the MgO(100) surface captures some major features of the effect of an oxide support and appears to be a good model of a simple oxide substrate; (5) strong cooperative effects are found in the co-adsorption of O(2) and other ligands on small metal clusters. The proposed approach appears as a viable route to advance the role of predictive computational science in the field of heterogeneous nanocatalysis. PMID:22057595
First principles characterization of silicate sites in clay surfaces.
Alvim, Raphael S; Miranda, Caetano R
2015-02-21
Aluminosilicate clays like Montmorillonite (MMT) and Muscovite Mica (MT) have siloxane cavities on the basal plane. The hydroxyl groups localized in these cavities and van der Waals (vdW) forces contribute significantly to adsorption processes. However, the basal sites are found to be difficult to characterize experimentally. Here, (001) surfaces of MMT and MT clays were investigated using first-principles calculations to understand how these silicate surface sites are influenced by hydroxyl groups and the effective role of inner layer vdW interactions. Based on density-functional theory (DFT) within the generalized gradient approximation (GGA), different types of exchange-correlation functionals were tested to check the effect of vdW dispersion correction. Noncontact atomic force microscopy (nc-AFM), X-ray absorption spectroscopy (XAS) in the near-edge region and solid-state nuclear magnetic resonance (SS-NMR) spectroscopy were simulated. In both clays, the oxygen surface sites are directly affected by the intralayer interaction through hydroxyl groups. Our results indicated that the chemical environment of the hydroxyl groups is distinct in the MMT and MT structures. The vdW correction was essential for a better description of the surface oxygen sites and correctly describes the similarity between both clays. Particularly, the bulk apical oxygen sites in the MT structure are less influenced by vdW interaction. Compared to MMT, the silicon surface sites of MT are more sensitive to the intralayer changes in Si-Oapical-Al and with less effect of the hydroxyl groups. These results provide a clear understanding of influence of the siloxane cavity on the oxygen and silicon surface sites in aluminosilicates. PMID:25592132
First principles modeling of nonlinear incidence rates in seasonal epidemics.
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. PMID:21379320
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.
First-principles investigation of hydrous post-perovskite
NASA Astrophysics Data System (ADS)
Townsend, Joshua P.; Tsuchiya, Jun; Bina, Craig R.; Jacobsen, Steven D.
2015-07-01
A stable, hydrogen-defect structure of post-perovskite (hy-ppv, Mg1-xSiH2xO3) has been determined by first-principles calculations of the vibrational and elastic properties up to 150 GPa. Among three potential hy-ppv structures analyzed, one was found to be stable at pressures relevant to the lower-mantle D″ region. Hydrogen has a pronounced effect on the elastic properties of post-perovskite due to magnesium defects associated with hydration, including a reduction of the zero-pressure bulk (K0) and shear (G0) moduli by 5% and 8%, respectively, for a structure containing ∼1 wt.% H2O. However, with increasing pressure the moduli of hy-ppv increase significantly relative to ppv, resulting in a structure that is only 1% slower in bulk compressional velocity and 2.5% slower in shear-wave velocity than ppv at 120 GPa. In contrast, the reduction of certain anisotropic elastic constants (Cij) in hy-ppv increases with pressure (notably, C55, C66, and C23), indicating that hydration generally increases elastic anisotropy in hy-ppv at D″ pressures. Calculated infrared absorption spectra show two O-H stretching bands at ∼3500 cm-1 that shift with pressure to lower wavenumber by about 2 cm-1/GPa. At 120 GPa the hydrogen bonds in hy-ppv are still asymmetric. The stability of a hy-ppv structure containing 1-2 wt.% H2O at D″ pressures implies that post-perovskite may be a host for recycled or primordial hydrogen near the Earth's core-mantle boundary.
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. PMID:26601242
First-principles study of hypothetical boron crystals: Bn(n = 13, 14, 15)
NASA Astrophysics Data System (ADS)
Aydın, Sezgin; Şimşek, Mehmet
2012-11-01
First-principles simulations within density functional theory are performed to investigate structural, electronic and mechanical properties of hypothetical boron crystals Bn(n = 13, 14, 15). These hypothetical crystals are generated by inserting boron atom(s) to the space in three-dimensional network of α-boron (α-B12). The effects of inserted atom(s) and their site(s) on the lattice parameters, mechanical and electronic properties are discussed. Cohesive energies and formation enthalpies are calculated to discuss energetic stability of purposed compounds, and also the elastic constants are determined to study mechanical stability and mechanical properties such as bulk, shear and Young moduli. To check the phase stability, molecular dynamics simulations and transition state search calculations are performed and to emphasize distinction of the phases energy-volume curves for all phases are presented. From calculated density of states and Mulliken atomic charges/bond overlap populations, it is observed that the charge transfers exist between inserted boron atom(s) located at different sites and icosahedral boron atoms. By mean of the optimized ground state geometry and other first-principles results, the micro-hardnesses of each boron phases are calculated.
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.
Guan, Zhaoyong; Si, Chen; Hu, Shuanglin; Duan, Wenhui
2016-04-28
Based on first-principles calculations, we present the electronic and magnetic properties of a class of line defect-embedded zigzag graphene nanoribbons, with one edge saturated by two hydrogen atoms per carbon atom and the other edge terminated by only one hydrogen atom. Such edge-modified nanoribbons without line defects are found to be typical bipolar magnetic semiconductors (BMS). In contrast, when the line defect is introduced into the ribbons, the ground state is ferromagnetic, and the resulting nanoribbons can be tuned to spin-polarized metal, metal with Dirac point, or half-metal by varying the position of the line defect, owing to the defect-induced self-doping of the BMS. Specifically, when the line defect is far away from the edges of the ribbon, the system shows half-metallicity. We further confirm the structural and magnetic stability at room temperature by first-principles molecular dynamics simulations. Our findings reveal the possibility of building metal-free electronic/spintronic devices with magnetic/half-metallic graphene nanoribbons. PMID:27087060
First-principles equation of state and electronic properties of warm dense oxygen
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.
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.
Atta-Fynn, Raymond; Biswas, Parthapratim
2009-07-01
Localized basis ab initio molecular dynamics simulation within the density functional framework has been used to generate realistic configurations of amorphous silicon carbide (a-SiC). Our approach consists of constructing a set of smart initial configurations that conform to essential geometrical and structural aspects of the materials obtained from experimental data, which is subsequently driven via a first-principles force field to obtain the best solution in a reduced solution space. A combination of a priori information (primarily structural and topological) along with the ab initio optimization of the total energy makes it possible to model a large system size (1000 atoms) without compromising the quantum mechanical accuracy of the force field to describe the complex bonding chemistry of Si and C. The structural, electronic and vibrational properties of the models have been studied and compared to existing theoretical models and available data from experiments. We demonstrate that the approach is capable of producing large, realistic configurations of a-SiC from first-principles simulation that display its excellent structural and electronic properties. Our study reveals the presence of predominant short range order in the material originating from heteronuclear Si-C bonds with a coordination defect concentration as small as 5% and a chemical disorder parameter of about 8%. PMID:21828477
First-principles opacity table of warm dense deuterium for inertial-confinement-fusion applications.
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
A genetic algorithm for first principles global structure optimization of supported nano structures
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.
Doping of rhenium disulfide monolayers: a systematic first principles study.
Çakır, Deniz; Sahin, Hasan; Peeters, François M
2014-08-21
The absence of a direct-to-indirect band gap transition in ReS2 when going from the monolayer to bulk makes it special among the other semiconducting transition metal dichalcogenides. The functionalization of this promising layered material emerges as a necessity for the next generation technological applications. Here, the structural, electronic, and magnetic properties of substitutionally doped ReS2 monolayers at either the S or Re site were systematically studied by using first principles density functional calculations. We found that substitutional doping of ReS2 depends sensitively on the growth conditions of ReS2. Among the large number of non-metallic atoms, namely H, B, C, Se, Te, F, Br, Cl, As, P, and N, we identified the most promising candidates for n-type and p-type doping of ReS2. While Cl is an ideal candidate for n-type doping, P appears to be the most promising candidate for p-type doping of the ReS2 monolayer. We also investigated the doping of ReS2 with metal atoms, namely Mo, W, Ti, V, Cr, Co, Fe, Mn, Ni, Cu, Nb, Zn, Ru, Os and Pt. Mo, Nb, Ti, and V atoms are found to be easily incorporated in a single layer of ReS2 as substitutional impurities at the Re site for all growth conditions considered in this work. Tuning chemical potentials of dopant atoms energetically makes it possible to dope ReS2 with Fe, Co, Cr, Mn, W, Ru, and Os at the Re site. We observe a robust trend for the magnetic moments when substituting a Re atom with metal atoms such that depending on the electronic configuration of dopant atoms, the net magnetic moment of the doped ReS2 becomes either 0 or 1 μB. Among the metallic dopants, Mo is the best candidate for p-type doping of ReS2 owing to its favorable energetics and promising electronic properties. PMID:25001566
First Principles Modeling of Bimolecular Reactions with Diffusion
NASA Astrophysics Data System (ADS)
Hansen, S. K.; Scher, H.; Berkowitz, B.
2013-12-01
We consider three approaches to modeling A + B → C irreversible reactions in natural media: 1) a discretized diffusion-reaction equation (DRE), 2) a particle tracking (PT) scheme in which reaction occurs if and only if an A and B particle pair are within a fixed distance, r (the "reaction radius"), and 3) a PT scheme using an alternative to the fixed reaction radius: a collocation probability distribution derived directly from first principles. Each approach has advantages. In some cases a discretized DRE may be the most computationally efficient method. For PT simulations, robust codes exist based on use of a fixed reaction radius. And finally, collocation probabilities may be derived directly from the Fick's Law constant, D, which is a well-established property for most species. In each approach, a single parameter governs the 'promiscuity' of the reaction (i.e. the thermodynamic favorability of reaction, predicated on the particles being locally well mixed). For the DRE, fixed-reaction-radius PT, and collocation-based PT, these parameters are, respectively: a second-order decay rate, r, and D. We established a number of new results enhancing these approaches and relating them to each other (and to nature). In particular, a thought experiment concerning a simple system in which the predictions of each approach can be computed analytically was used to derive formulas establishing a universal one-to-one correspondence among each of the governing parameters. We thus showed the conditions for equivalence of the three approaches, and grounded both the DRE approach and the fixed-radius PT approach in the Fick's Law D. We further showed that the existing collocation-based PT theory is based on a probability distribution that is only correct for infinitesimally small times, but which can be modified to be accurate for larger times by means of continuous time random walk analysis and first-passage probability distributions. Finally, we employed a novel mathematical
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
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.
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
Lee, B; Rudd, R E
2006-10-19
We report the results of first-principles density functional theory calculations of the Young's modulus and other mechanical properties of hydrogen-passivated Si {l_angle}001{r_angle} nanowires. The nanowires are taken to have predominantly {l_brace}100{r_brace}surfaces, with small {l_brace}110{r_brace} facets according to the Wulff shape. The Young's modulus, the equilibrium length and the constrained residual stress of a series of prismatic beams of differing sizes are found to have size dependences that scale like the surface area to volume ratio for all but the smallest beam. The results are compared with a continuum model and the results of classical atomistic calculations based on an empirical potential. We attribute the size dependence to specific physical structures and interactions. In particular, the hydrogen interactions on the surface and the charge density variations within the beam are quantified and used both to parameterize the continuum model and to account for the discrepancies between the two models and the first-principles results.
Chevreau, Hubert; Duyker, Samuel G; Peterson, Vanessa K
2015-12-01
Metal-organic frameworks (MOFs) are promising solid sorbents, showing gas selectivity and uptake capacities relevant to many important applications, notably in the energy sector. To improve and tailor the sorption properties of these materials for such applications, it is necessary to gain an understanding of their working mechanisms at the atomic and molecular scale. Specifically, it is important to understand how features such as framework porosity, topology, chemical functionality and flexibility underpin sorbent behaviour and performance. Such information is obtained through interrogation of structure-function relationships, with neutron powder diffraction (NPD) being a particularly powerful characterization tool. The combination of NPD with first-principles density functional theory (DFT) calculations enables a deep understanding of the sorption mechanisms, and the resulting insights can direct the future development of MOF sorbents. In this paper, experimental approaches and investigations of two example MOFs are summarized, which demonstrate the type of information and the understanding into their functional mechanisms that can be gained. Such information is critical to the strategic design of new materials with targeted gas-sorption properties. PMID:26634721
Phonon thermal transport in Bi2Te3 from first principles
NASA Astrophysics Data System (ADS)
Hellman, Olle; Broido, David A.
2014-10-01
We present first-principles calculations of the thermal and thermal transport properties of Bi2Te3 that combine an ab initio molecular dynamics (AIMD) approach to calculate interatomic force constants (IFCs) along with a full iterative solution of the Peierls-Boltzmann transport equation for phonons. The newly developed AIMD approach allows determination of harmonic and anharmonic interatomic forces at each temperature, which is particularly appropriate for highly anharmonic materials such as Bi2Te3. The calculated phonon dispersions, heat capacity, and thermal expansion coefficient are found to be in good agreement with measured data. The lattice thermal conductivity, κl, calculated using the AIMD approach nicely matches measured values, showing better agreement than the κl obtained using temperature-independent IFCs. A significant contribution to κl from optic phonon modes is found. Already at room temperature, the phonon line shapes show a notable broadening and onset of satellite peaks reflecting the underlying strong anharmonicity.
First principle investigation of iron pentacarbonyl energetic solid at high pressure
NASA Astrophysics Data System (ADS)
Nguyen Cong, Kien; Steele, Brad; Landerville, Aaron; Oleynik, Ivan
2015-06-01
Polymeric phase of carbon mono-oxide (p-CO), an extended non-molecular solid, is extremely energetic, and therefore represents a new class of low-Z energetic materials. Recently, iron penta-carbonyl Fe(CO)5 has been experimentally investigated as a p-CO precursor: the presence of transition metal ions is believed to stabilize p-CO at ambient conditions. Since p-CO forms at high pressures, it becomes important to investigate the high-pressure behavior of Fe(CO)5 as well. In this work, first-principles evolutionary structure search method is used to predict the crystal phases of Fe(CO)5 at high pressure. Known experimental structure of phase I is confirmed. Moreover, previously unknown structure of phase II is predicted. The Raman spectra, calculated as a function of pressure, were used to demonstrate that the phase III, predicted by a recent experiment, is identical to phase II.
First-principles study on phase transition and ferroelectricity in lithium niobate and tantalate
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.
Improved calculation of Si sputter yield via first principles derived interatomic potential
NASA Astrophysics Data System (ADS)
Hossain, M. Z.; Freund, J. B.; Johnson, H. T.
2009-04-01
Silicon sputter yield under medium energy Ar+ ion bombardment is calculated via molecular dynamics, using a highly accurate interatomic potential for Ar-Si interactions derived from first-principles calculations. Unlike the widely used universal repulsive potentials such as the Moliere or ZBL parameterizations, this new potential, referred to as DFT-ArSi, is developed via localized basis density functional theory. Sputter yields for Si obtained with the DFT-ArSi potential at 500 eV and 1 keV incident energies are found to be within 6% and 2% of experimental results, respectively, while errors using existing potentials are typically on the order of 11%. The DFT-ArSi potential differs from existing empirical potentials in the ˜1 Å interatomic separation range which is shown to be the most important range for modeling low-to-medium energy ion bombardment.
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.
First-principles study of the amorphization of stishovite by isotropic volume expansion
NASA Astrophysics Data System (ADS)
Misawa, Masaaki; Shimojo, Fuyuki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya
Simple synthesis of ceramics with high hardness and high toughness from Earth-abundant materials is one of the most important issues in materials science. Nishiyama et al. synthesized nano-crystalline stishovite with extremely high toughness and high hardness via compression and decompression of silica, and proposed fracture-induced amorphization mechanisms for the toughning. Furthermore, it was shown that the toughening mechanisms are effective even in nanoscale order. Our first-principles molecular dynamics simulations have shown rapid amorphization of stishovite within picoseconds under increasing volume, thus substantiating the proposed amorphization mechanisms. Furthermore, we have calculated the critical stress, energy difference, and energy barrier for the crystalline-to-amorphous structural transition.
First-principles approach to calculating energy level alignment at aqueous semiconductor interfaces
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
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.
First-principles approach to calculating energy level alignment at aqueous semiconductor interfaces
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.
Solvation Structure and Dynamics of Ni(2+)(aq) from First Principles.
Mareš, Jiří; Liimatainen, Helmi; Laasonen, Kari; Vaara, Juha
2011-09-13
The aqueous solution of Ni(2+) was investigated using first principles molecular dynamics (FPMD) simulation based on periodic density-functional theory (DFT) calculations. The experimental structural parameters of the Ni(aq) complex are reproduced well by the simulation. An exchange event of the water molecule in the first solvation shell is observed, supporting the proposed dissociative mechanism of exchange. The calculated dynamic characteristics of the surrounding water molecules indicate too slow translational diffusion in comparison to experimental results, in agreement with other FPMD studies employing a similar level of theory. We also find that the reorientational dynamics of water are an order of magnitude slower as compared to experimental data. On the other hand, the angular momentum dynamics are in better agreement with the experimental data than the previously reported results from MD simulations employing empirical force fields. The obtained MD trajectory can supply accurate structures for the calculation of magnetic properties. PMID:26605483
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
Thermoelectric properties of binary LnN (Ln=La and Lu): First principles study
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.
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.
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.
Continuous wavelet transform analysis of one-dimensional quantum bound states from first principles
Handy, C.R.; Murenzi, R.
1996-11-01
Over the last decade, Handy and Bessis have developed a moment-problem-based, multiscale quantization theory, the eigenvalue moment method (EMM), which has proven effective in solving singular, strongly coupled, multidimensional Schr{umlt o}dinger Hamiltonians. We extend the scope of EMM by demonstrating its essential role in the generation of wavelet transforms for one-dimensional quantum systems. Combining this with the function-wavelet reconstruction formulas currently available, we are able to recover the wave function systematically, from first principles, through a multiscale process proceeding from large spatial scales to smaller ones. This accomplishment also addresses another outstanding problem, that of reconstructing a function from its moments. For the class of problems considered, the combined EMM-wavelet analysis yields a definitive solution. {copyright} {ital 1996 The American Physical Society.}
First Principles based thermo-kinetic modeling of electrocatalytic processes at fuel cell cathodes
NASA Astrophysics Data System (ADS)
Gadre, Milind Jayram
Fuel Cells are promising alternative-energy technologies for the future. The design of efficient, cost-effective materials to catalyze the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) is a major hurdle facing the large-scale commercialization of these technologies. Perovskites of transition metal oxides and related hetero-structures are promising, cheap materials for oxygen electro-catalysis. Understanding the detailed nature of OER and ORR catalytic activity of various surfaces of perovskite oxides can help design highly active perovskite cathodes. My research work involves first principles based thermo-kinetic modeling of various oxygen electro-catalytic processes on the surfaces of transition metal perovskites, to develop detailed mechanistic understanding of oxygen reduction/evolution reactions, and to suggest ways to engineer better cathode materials.
FInal Report: First Principles Modeling of Mechanisms Underlying Scintillator Non-Proportionality
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.
First principles-based multiscale modeling of ferroelectric polymers
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.
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.
Molecular Scale Simulation of Homopolymer Wall Slip
NASA Astrophysics Data System (ADS)
Dorgan, John R.; Rorrer, Nicholas A.
2013-04-01
The first molecular scale simulation of highly entangled polydisperse homopolymers that is capable of capturing all three regions—no slip, weak slip, and strong slip—of the hydrodynamic boundary condition is presented. An on-lattice dynamic Monte Carlo technique capable of correctly capturing both unentangled and entangled polymer dynamics is used to study the molecular details of wall slip phenomena for homopolymers and energetically neutral walls. For unentangled chains (those exhibiting Rouse dynamics) weak slip is not present but evidence of strong slip is manifest at very high shear rates. For entangled chains (of sufficient length to exhibit reptation dynamics), both weak and strong slip are observed. Consistent with numerous experimental studies, disentanglement and cohesive failure occur at high shear rates. Disentanglement is clearly evidenced in a nonlinear velocity profile that exhibits shear banding, in an excess of chain ends at the slip plane, and perhaps most importantly in a nonmonotonic stress versus shear rate response. The chain end density exhibits a pretransitional periodicity prior to disentanglement. Unentangled Rouse chains do not show this pretransitional response or a bifurcation in their stress versus shear rate response. Finally, it is shown that when polydispersity is introduced, slip phenomena are severely reduced and the inherent constitutive bifurcation is limited to a small region. Predictions are in post facto agreement with many experiments, are distinct from existing results obtained using molecular dynamics simulation techniques, and shed light on fundamental mechanisms of polymer wall slip.
Molecular scale simulation of homopolymer wall slip.
Dorgan, John R; Rorrer, Nicholas A
2013-04-26
The first molecular scale simulation of highly entangled polydisperse homopolymers that is capable of capturing all three regions--no slip, weak slip, and strong slip--of the hydrodynamic boundary condition is presented. An on-lattice dynamic Monte Carlo technique capable of correctly capturing both unentangled and entangled polymer dynamics is used to study the molecular details of wall slip phenomena for homopolymers and energetically neutral walls. For unentangled chains (those exhibiting Rouse dynamics) weak slip is not present but evidence of strong slip is manifest at very high shear rates. For entangled chains (of sufficient length to exhibit reptation dynamics), both weak and strong slip are observed. Consistent with numerous experimental studies, disentanglement and cohesive failure occur at high shear rates. Disentanglement is clearly evidenced in a nonlinear velocity profile that exhibits shear banding, in an excess of chain ends at the slip plane, and perhaps most importantly in a nonmonotonic stress versus shear rate response. The chain end density exhibits a pretransitional periodicity prior to disentanglement. Unentangled Rouse chains do not show this pretransitional response or a bifurcation in their stress versus shear rate response. Finally, it is shown that when polydispersity is introduced, slip phenomena are severely reduced and the inherent constitutive bifurcation is limited to a small region. Predictions are in post facto agreement with many experiments, are distinct from existing results obtained using molecular dynamics simulation techniques, and shed light on fundamental mechanisms of polymer wall slip. PMID:23679746
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.
NASA Astrophysics Data System (ADS)
Zhao, Shijun; Zhang, Shen; Kang, Wei; Li, Zi; Zhang, Ping; He, Xian-Tu
2015-06-01
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.
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.
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
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.
Vibrational spectrum and electron-phonon coupling of doped solid picene from first principles
NASA Astrophysics Data System (ADS)
Boeri, Lilia; Subedi, Alaska
2012-02-01
The search for new intercalated hydrocarbon superconductors was initiated by the report of a superconducting critical temperature (Tc) of 18 K in K- and Rb- doped picene (C22H14), followed by phenanthrene, coronene and di-benz-picene (27 K). These compounds, formed by justappoxed benzene rings, bear a strong resemblance both to fullerenes and intercalated graphites. Using first-principles linear response calculations have performed calculations of the phonon spectrum and electron-phonon (ep) interaction, we have shown that the coupling of the high-energy C bond-stretching phonons to the π molecular orbitals for a doping of 3 electrons per picene molecule is sufficiently strong to reproduce the experimental Tc of 18 K within Migdal-Eliashberg theory. For hole doping, we predicted a similar coupling leading to a maximum Tc of 6 K. However, we argue that, due to its molecular nature, picene may belong to the same class of strongly correlated ep superconductors as fullerides [1]. Our results are in agreement with estimates based on molecular orbital models;we also discuss possible reasons and implications of the discrepancy with linear response calculations that include explicitely the dopant.
NMR chemical shifts in periodic systems from first principles
NASA Astrophysics Data System (ADS)
Sebastiani, Daniel; Goward, Gillian; Schnell, Ingo; Parrinello, Michele
2002-08-01
A recently developed ab-initio method for the calculation of NMR chemical shifts and magnetic susceptibilities in systems under periodic boundary conditions is presented and applied to a hydrogen-bonded molecular crystal. The calculations can unambiguously assign the chemical shifts to individual atoms in experimental spectra, and can further serve for the validation of simulated atomic trajectories and geometries. Apart from the example presented, the method can be applied to crystalline and amorphous insulators, as well as to isolated molecules using a supercell technique. The results are in good agreement with experiment.
NASA Astrophysics Data System (ADS)
Yadav, Vivek Kumar; Chandra, Amalendu
2013-06-01
A first principles study of the dynamics of supercritical methanol is carried out by means of ab initio molecular dynamics simulations. In particular, the fluctuation dynamics of hydroxyl stretch frequencies, hydrogen bonds, dangling hydroxyl groups, and orientation of methanol molecules are investigated for three different densities at 523 K. Apart from the dynamical properties, various equilibrium properties of supercritical methanol such as the local density distributions and structural correlations, hydrogen bonding aspects, frequency-structure correlations, and dipole distributions of methanol molecules are also investigated. In addition to the density dependence of various equilibrium and dynamical properties, their dependencies on dispersion interactions are also studied by carrying out additional simulations using a dispersion corrected density functional for all the systems. It is found that the hydrogen bonding between methanol molecules decreases significantly as we move to the supercritical state from the ambient one. The inclusion of dispersion interactions is found to increase the number of hydrogen bonds to some extent. Calculations of the frequency-structure correlation coefficient reveal that a statistical correlation between the hydroxyl stretch frequency and the nearest hydrogen-oxygen distance continues to exist even at supercritical states of methanol, although it is weakened with increase of temperature and decrease of density. In the supercritical state, the frequency time correlation function is found to decay with two time scales: One around or less than 100 fs and the other in the region of 250-700 fs. It is found that, for supercritical methanol, the times scales of vibrational spectral diffusion are determined by an interplay between the dynamics of hydrogen bonds, dangling OD groups, and inertial rotation of methanol molecules and the roles of these various components are found to vary with density of the supercritical solvent. Effects
First-Principles Investigation of Li Intercalation Kinetics in Phospho-Olivines
NASA Astrophysics Data System (ADS)
Malik, Rahul
This thesis focuses broadly on characterizing and understanding the Li intercalation mechanism in phospho-olivines, namely LiFePO 4 and Li(Fe,Mn)PO4, using first-principles calculations. Currently Li-ion battery technology is critically relied upon for the operation of electrified vehicles, but further improvements mainly in cathode performance are required to ensure widespread adoption, which in itself requires learning from existing commercial cathode chemistries. LiFePO4 is presently used in commercial Li-ion batteries, known for its rapid charge and discharge capability but with underwhelming energy density. This motivates the three central research efforts presented herein. First, we investigate the modified phase diagram and electrochemical properties of mixed olivines, such as Li(Fe,Mn)PO4, which offer improved theoretical energy density over LiFePO4 (due to the higher redox voltage associated with Mn2+/Mn3+). The Lix(Fe1-yMny)PO4 phase diagram is constructed by Monte Carlo simulation on a cluster expansion Hamiltonian parametrized by first-principles determined energies. Deviations from the equilibrium phase behavior and voltages of pure LiFePO4 and LiMnPO 4 are analyzed and discussed to good agreement with experimental observations. Second, we address why LiFePO4 exhibits superior rate performance strictly when the active particle size is brought down to the nano-scale. By considering the presence of immobile point defects residing in the 1D Li diffusion path, specifically by calculating from first principles both defect formation energies and Li migration barriers in the vicinity of likely defects, the Li diffusivity is recalculated and is found to strongly vary with particle size. At small particle sizes, the contribution from defects is small, and fast 1D Li diffusion is accessible. However, at larger particle sizes (microm scale and above) the contribution from defects is much larger. Not only is Li transport impeded, but it is also less anisotropic in
Böttcher, D; Ernst, A; Henk, J
2011-07-27
The magnetization dynamics of Co nanoislands on Cu(111) is studied on the atomic scale by means of the stochastic Landau-Lifshitz-Gilbert equation. The exchange and anisotropy constants of the spin Hamiltonian are computed from first principles. We focus on hysteresis loops and magnetic switching in dependence on temperature, island size, and strength of an external magnetic field. The magnetic switching of nanoislands whose magnetization is reversed on the sub-nanosecond time scale is found consistent with the Stoner-Wohlfarth theory. We separate the superparamagnetic from the ferromagnetic regime and provide evidence that nanodomains can exist at least on a sub-picosecond time scale. PMID:21715954
First principles prediction of amorphous phases using evolutionary algorithms.
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
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.
First-principles simulations of liquid ZnTe
NASA Astrophysics Data System (ADS)
Jain, Manish; Godlevsky, Vitaliy V.; Derby, Jeffrey J.; Chelikowsky, James R.
2002-01-01
We report the results of ab initio molecular-dynamic simulations of liquid ZnTe near the melting point temperature. In agreement with experiment, we find that l-ZnTe retains its open tetrahedral environment upon melting with a coordination near four. In addition, we find atoms of Te in l-ZnTe often form transitory chains just as in l-CdTe. We compare our calculated structure factor to experiment and also determine the conductivity of the melt. l-ZnTe has a semiconductorlike conductivity similar to CdTe. We also calculate the dynamic properties of the liquid and predict self-diffusion constants of DZn=1.0×10-4 cm2/s and DTe=3.2×10-5 cm2/s.
Vibrational transition moments of CH4 from first principles
NASA Astrophysics Data System (ADS)
Yurchenko, Sergei N.; Tennyson, Jonathan; Barber, Robert J.; Thiel, Walter
2013-09-01
New nine-dimensional (9D), ab initio electric dipole moment surfaces (DMSs) of methane in its ground electronic state are presented. The DMSs are computed using an explicitly correlated coupled cluster CCSD(T)-F12 method in conjunction with an F12-optimized correlation consistent basis set of the TZ-family. A symmetrized molecular bond representation is used to parameterise these 9D DMSs in terms of sixth-order polynomials. Vibrational transition moments as well as band intensities for a large number of IR-active vibrational bands of 12CH4 are computed by vibrationally averaging the ab initio dipole moment components. The vibrational wavefunctions required for these averages are computed variationally using the program TROVE and a new ‘spectroscopic’ 12CH4 potential energy surface. The new DMSs will be used to produce a hot line list for 12CH4.
First principles prediction of an insensitive high energy density material.
Hirshberg, Barak; Denekamp, Chagit
2013-10-28
A new high performance yet insensitive explosive is proposed, based on an extensive computational study of tris(tetrazolyl)amine in the solid state and in the gas phase. The calculations for the solid state employ the PBE density functional with empirical dispersion correction while the gas phase calculations use the higher level of B3LYP and MP2. Two stable crystalline structures of tris(tertrazolyl)amine were located belonging to P1 and P21 space groups. The crystal structures obtained reveal that solid tris(tertrazolyl)amine is organized in layers with a very small interlayer spacing, due to π stacking, as well as significant inter and intra-molecular hydrogen bonding. Application of these results to the calculation of the detonation velocity and pressure indicate high performance for both phases, especially the P21 phase. At the same time the small value found for the interlayer spacing and the significant hydrogen bonding suggest relatively high stability. These results point to a promising new explosive material with a balance between high performance and insensitivity. PMID:24042364
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.
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.
A generalized Poisson solver for first-principles device simulations.
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
First-principles study of Casimir repulsion in metamaterials.
Yannopapas, Vassilios; Vitanov, Nikolay V
2009-09-18
We examine theoretically the Casimir effect between a metallic plate and several types of magnetic metamaterials in pursuit of Casimir repulsion, by employing a rigorous multiple-scattering theory for the Casimir effect. We first examine metamaterials in the form of two-dimensional lattices of inherently nonmagnetic spheres such as spheres made from materials possessing phonon-polariton and exciton-polariton resonances. Although such systems are magnetically active in infrared and optical regimes, the force between finite slabs of these materials and metallic slabs is plainly attractive since the effective electric permittivity is larger than the magnetic permeability for the studied spectrum. When lattices of magnetic spheres made from superparamagnetic composites are employed, we achieve not only Casimir repulsion but almost total suppression of the Casimir effect itself in the micrometer scale. PMID:19792414
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.
Probing adhesion forces at the molecular scale
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.
First-principles insights into interaction of CO, NO, and HCN with Ag{sub 8}
Torbatian, Zahra; Hashemifar, S. Javad Akbarzadeh, Hadi
2014-02-28
We use static as well as time-dependent first-principles computations to study interaction of the CO, NO, and HCN molecules with the Ag{sub 8} nanocluster. The many-body based GW correction is applied for accurate description of the highest occupied (HOMO) and the lowest unoccupied (LUMO) molecular orbital levels. It is argued that the adsorption of these molecules changes the stable structure of Ag{sub 8} from Td to the more chemically active D{sub 2d} symmetry. We discuss that the CO, NO, and HCN molecules prefer to adsorb on the atom of the cluster with significant contribution to both HOMO and LUMO, for the accomplishment of the required charge transfers in the systems. The charge back donation is found to leave an excess energy of about 110 meV on the NO molecular bond, evidencing potential application of silver clusters for NO reduction. It is argued that CO and specially NO exhibit strong physical interaction with the silver cluster and hence significantly modify the electronic and optical properties of the system, while HCN makes very week physical bonds with the cluster. The optical absorption spectra of the Ag{sub 8} cluster before and after molecule adsorption are computed and a nontrivial red shift is observed in the NO and HCN adsorbed clusters.
First principles effective electronic couplings for hole transfer in natural and size-expanded DNA
Migliore, Agostino; Corni, Stefano; Varsano, Daniele; Klein, Michael L.; Di Felice, Rosa
2009-01-01
Hole transfer processes between base pairs in natural DNA and size-expanded DNA (xDNA) are studied and compared, by means of an accurate first principles evaluation of the effective electronic couplings (also known as transfer integrals), in order to assess the effect of the base augmentation on the efficiency of charge transport through double-stranded DNA. According to our results, the size expansion increases the average electronic coupling, and thus the CT rate, with potential implications in molecular biology and in the implementation of molecular nanoelectronics. Our analysis shows that the effect of the nucleobase expansion on the charge-transfer (CT) rate is sensitive to the sequence of base pairs. Furthermore, we find that conformational variability is an important factor for the modulation of the CT rate. From a theoretical point of view, this work offers a contribution to the CT chemistry in π-stacked arrays. Indeed, we compare our methodology against other standard computational frameworks that have been adopted to tackle the problem of CT in DNA, and unravel basic principles that should be accounted for in selecting an appropriate theoretical level. PMID:19537767
von Lilienfeld-Toal, Otto Anatole
2010-11-01
The design of new materials with specific physical, chemical, or biological properties is a central goal of much research in materials and medicinal sciences. Except for the simplest and most restricted cases brute-force computational screening of all possible compounds for interesting properties is beyond any current capacity due to the combinatorial nature of chemical compound space (set of stoichiometries and configurations). Consequently, when it comes to computationally optimizing more complex systems, reliable optimization algorithms must not only trade-off sufficient accuracy and computational speed of the models involved, they must also aim for rapid convergence in terms of number of compounds 'visited'. I will give an overview on recent progress on alchemical first principles paths and gradients in compound space that appear to be promising ingredients for more efficient property optimizations. Specifically, based on molecular grand canonical density functional theory an approach will be presented for the construction of high-dimensional yet analytical property gradients in chemical compound space. Thereafter, applications to molecular HOMO eigenvalues, catalyst design, and other problems and systems shall be discussed.
First principle computation of biomolecule-ligand interaction
NASA Astrophysics Data System (ADS)
Chachiyo, Teepanis
We have determined the calibration constants for the SDFT prediction of 57Fe Mossbauer parameters. The calibration constants are basis set and exchange-correlation functional specific. The basis set is 6-311G* whereas the exchange-correlation functional are UB3LYP, UBLYP, UBPW91, and UMPW1PW91. This method is used to predict the binding conformation of a dioxygen molecule to the P intermediate of methane monooxygenase whose experimental binding structure is presently unknown. When O2 binds to the diiron cluster in a mu-1,2-peroxo fashion, the associated theoretical Mossbauer parameters are in good agreement with the experimental values. An efficient method for locating minimum energy crossing points is introduced and tested on the phenyl cation. An agreement of the present method and previous works is satisfactory. The convergence rate obeys a logarithmic law and is verified on the phenyl cation. Due to its rapid convergence rate, the method is suitable for a large molecular system. As an application of the new methodology, the crossing points of the cation of [Fe(ptz)6](BF4) 2 were studied in order to identify the geometrical parameters of the spin crossing points between S=0 ↔ S=1, and S=1 ↔ S=2. The calculation shows that the transition from a singlet ground state to the triplet intermediate state is accompanied by almost 0.3A bond length elongation of the axial ligands. We have implemented an approximation scheme that allows one to study protein system such as a ligand-protein binding conformation and a protein active site geometry optimization. The scheme, named E-MFCC, is a significant improvement over the previous MFCC approximation originally put forth by Zhang et al. The geometry optimization of some small test systems utilizing the E-MFCC scheme introduces an error on the order of 10-2A as compared to the all-atom calculation.
Experimental and first-principles characterization of functionalized magnetic nanoparticles.
Antipas, Georgios S E; Statharas, Eleftherios; Tserotas, Philippos; Papadopoulos, Nikolaos; Hristoforou, E
2013-06-24
Magnetic iron oxide nanoparticles synthesized by coprecipitation and thermal decomposition yield largely monodisperse size distributions. The diameters of the coprecipitated particles measured by X-ray diffraction and transmission electron microscopy are between approximately 9 and 15 nm, whereas the diameters of thermally decomposed particles are in the range of 8 to 10 nm. Coprecipitated particles are indexed as magnetite-rich and thermally decomposed particles as maghemite-rich; however, both methods produce a mixture of magnetite and maghemite. Fourier transform IR spectra reveal that the nanoparticles are coated with at least two layers of oleic acid (OA) surfactant. The inner layer is postulated to be chemically adsorbed on the nanoparticle surface whereas the rest of the OA is physically adsorbed, as indicated by carboxyl O-H stretching modes above 3400 cm(-1). Differential thermal analysis (DTA) results indicate a double-stepped weight loss process, the lower-temperature step of which is assigned to condensation due to physically adsorbed or low-energy bonded OA moieties. Density functional calculations of Fe-O clusters, the inverse spinel cell, and isolated OA, as well as OA in bidentate linkage with ferrous and ferric atoms, suggest that the higher-temperature DTA stage could be further broken down into two regions: one in which condensation is due ferrous/ferrous- and/or ferrous/ferric-OA and the other due to condensation from ferrous/ferric- and ferric/ferric-OA complexes. The latter appear to form bonds with the OA carbonyl group of energy up to fivefold that of the bond formed by the ferrous/ferrous pairs. Molecular orbital populations indicate that such increased stability of the ferric/ferric pair is due to the contribution of the low-lying Fe(3+) t(2g) states into four bonding orbitals between -0.623 and -0.410 a.u. PMID:23649714
Hydrolysis of cisplatin--a first-principles metadynamics study.
Lau, Justin Kai-Chi; Ensing, Bernd
2010-09-21
Cisplatin, or cis-[Pt(NH(3))(2)Cl(2)], was the first member of a new revolutionary class of anticancer drugs that is still used today for the treatment of a wide variety of cancers. The mode of action of cisplatin starts inside the cell with the hydrolysis of Pt-Cl bonds to form a Pt-aqua complex. The solvent environment plays an essential role in many biochemical processes in general, and is expected to have a particular strong effect on the activation (hydrolysis) of cisplatin and cisplatin derivatives. To investigate these solvent effects, we have studied the explicit solvent structures during cisplatin hydrolysis by means of Car-Parrinello molecular dynamics simulations. Since hydrolysis is an activated process, and thus a rare event on the simulation timescale, we have applied the metadynamics sampling technique to map out the free energy landscape from which the reaction mechanism and activation free energy are obtained. Our simulations show that hydrogen bonding between solvent water molecules and metal complexes in the hydrolyzed product systems is stronger than that in the reactant cisplatin system. In addition, the free energy profiles from our metadynamics simulations for the cisplatin hydrolysis shows that the second hydrolysis of cisplatin is thermodynamically favourable, which is in good agreement with experimental results and previous static density functional theory calculations. The reactant channels for both hydrolysis steps are rather wide and flat, indicative of a continuous spectrum of allowed mechanisms with no strong preference for either concerted dissociative or concerted associative pathways. Three or five coordinated metastable intermediates do not exist in aqueous solution. PMID:20582358
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).
First principles predictions of van der Waals bonded inorganic crystal structures: Test case, HgCl2
Cooper, Valentino R; Donald, Kelling J
2015-01-01
We study the crystals structure and stability of four possible polymorphs of HgCl2 using first principles density functional theory. Mercury (II) halides are a unique class of materials which, depending on the halide species, form in a wide range of crystal structures, ranging from densely packed solids to layered materials and molecular solids. Predicting the groundstate structure of any member of this group from first principles, therefore, requires a general purpose functional that treats van der Waals bonding and covalent/ionic bonding adequately. Here, we demonstrate that the non-local van der Waals density functional paired with the C09 exchange functional meets this bar for HgCl2. In particular, this functional is able to predict the correct groundstate among the structures tested as well as having extremely good agreement with the experimentally known crystal structure. These results highlight the maturity of this functional and open the door to using this method for truly first principles crystal structure predictions.
Defects in gallium nitride nanowires: first principles calculations
Wang, Zhiguo; Li, Jingbo; Gao, Fei; Weber, William J.
2010-08-15
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 nitrogen related defects are more stable than the gallium related defects under nitrogen-rich conditions. The configurations of these defects in the core region of the nanowire are same as those in the bulk GaN. The relaxation of vacancies is generally small, but the relaxation around antisite defects is large. The nitrogen interstitial relaxes into a split interstitial configuration. The configurations of the defects in the outermost free surface region are different than those in the core. A Ga atom on the outmost surface is replaced by a Ga interstital, and is ejected on to the surface to become an adsorbed atom. A gallium atom at the outermost surface can also be ejected out to become an adsorbed atom. Nitrogen interstitials form a split-interstitial configuration with one of the nearest-neighbor nitrogens. For a Ga vacancy at the edge of the side plane of the nanowire, nitrogen atom at a gallium site and nitrogen interstitial often induced the formation of N2 molecules with low formation energy, which agrees well with experiment findings [Nano Letters 9, 1844 (2009)].
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.
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.
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
NASA Astrophysics Data System (ADS)
Sun, Huayang; Kang, Dongdong; Dai, Jiayu; Ma, Wen; Zhou, Liangyuan; Zeng, Jiaolong
2016-03-01
The equation of states (EOS) and electronic structures of argon with temperatures from 0.02 eV to 3 eV and densities from 0.5 g/cm3 to 5.5 g/cm3 are calculated using the pair potential and many-body potential molecular dynamics and the density functional theory (DFT) molecular dynamics with van der Waals (vdW) corrections. First-principles molecular dynamics is implemented above 2.0 g/cm3. For the cases of low densities below 3 g/cm3, we performed pair potential molecular dynamics in order to obtain the ionic configurations, which are used in density functional theory to calculate the EOS and electronic structures. We checked the validity of different methods at different densities and temperatures, showing their behaviors by comparing EOS. DFT without vdW correction works well above 1 eV and 3.5 g/cm3. Below 1 eV and 2.0 g/cm3, it overestimates the pressure apparently and results in incorrect behaviors of the internal energy. With vdW corrections, the semi-empirical force-field correction (DFT-D2) method gives consistent results in the whole density and temperature region, and the vdW density functional (vdW-DF2) method gives good results below 2.5 g/cm3, but it overestimates the pressure at higher densities. The interactions among the atoms are overestimated by the pair potential above 1 eV, and a temperature dependent scaled pair potential can be used to correct the ionic configurations of the pair potential up to 3 eV. The comparisons between our calculations and the experimental multi-shock compression results show that the Hugoniot line of DFT-D2 and DFT tends to give larger pressure than the results of the self-consistent fluid variational theory, and the difference increases with the density. The electronic energy gap exists for all our cases up to 5.5 g/cm3 and 1 eV. The effect of vdW interactions on the electronic structures are also discussed.
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.
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
First principles Candu fuel model and validation experimentation
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
NASA Astrophysics Data System (ADS)
Niklasson, Anders; Cawkwell, Marc
2012-02-01
Born-Oppenheimer molecular dynamics (BOMD) based on density functional theory offers a very accurate quantum mechanical approach to atomistic simulations that is more reliable and general compared to classical MD. Unfortunately, BOMD simulations are often limited by a high computational cost or by problems such as unbalanced phase space trajectories, numerical instabilities and a systematic long-term energy drift. These problems become particularly severe in combination with reduced complexity or linear scaling algorithms that are necessary for the study of large systems. We have recently taken some steps toward a new generation of first principles MD, which combines some of the best features of regular BOMD and Car-Parrinello MD, while avoiding their most serious shortcomings. The new dynamics is given in terms of an extended Lagrangian (XL), where auxiliary extended electronic degrees of freedom are added to the nuclear part. Our framework enables accurate geometric integration of both the nuclear and electronic degrees of freedom that provide a time-reversible and energy conserving dynamics on the ground state BO potential energy surface that is stable also under approximate SCF convergence. XL-BOMD provides a surprisingly simple and general framework for atomistic simulations
First principles studies of interface dielectric properties of polymer/metal-oxide nanocomposites
NASA Astrophysics Data System (ADS)
Yu, Liping
This thesis is devoted to studying interface dielectric properties of polymer nanocomposites from first principles. We aim to understand at atomic scale the role of interface effects and the dielectric finite size effects of nanoparticles in determining the effective dielectric properties of polymer nanocomposites. To study surface effects from first principles, we first investigate the two common methods, namely dipole correction and Coulomb cutoff, used to eliminate the artificial effects introduced by using the supercell approximation. We implement Coulomb cutoff technique in a plane-wave-based density functional theory code and compare it with dipole correction for the same system under the same conditions. By comparison, both methods are shown to be equivalent and able to remove the artificial effects of periodic images very accurately. We also find that a combination of these two methods offers an easy way to distinguish the localized bound states of interest from highly delocalized unoccupied states while using a relatively small supercell, and to ascertain the convergence of the results with respect to supercell size. To understand the dielectric properties at the atomic scale, we develop a new nanoscale averaging model to connect the macroscopic quantities to the corresponding microscopic ones. This model allows us to compute the spatially resolved local dielectric permittivity, including the critically important ionic contributions, for interfaces and other complex structures. In this model, a simple way of evaluating real-space decay length of the nonlocal dielectric functions is also proposed. By using the dipole correction and our averaging model in supercells, we calculate the optical and static local dielectric permittivity profiles for polymer (polypropylene)/metal-oxide (PbTiO3 and alumina) nanocomposites. Our ab-initio results show that metal-oxide/polymer interface effects are very localized and are mostly confined to the metal-oxide surface side
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 (
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
First-principles studies of conformation and solution effects on DNA transport
NASA Astrophysics Data System (ADS)
Tan, Bikan; Hodak, Miroslav; Lu, Wenchang; Bernholc, Jerry
2014-03-01
The electrical conductivity of DNA molecules is of fundamental interest in the life sciences. We use first-principles techniques combined with molecular dynamical (MD) simulations to calculate transport properties of B-DNA connected to carbon nanotubes via alkane linkers. The quantum transport properties are calculated for over a hundred of snapshots recorded in MD trajectories. We discover that the DNA conformation and especially the overlaps between sequential guanine bases play a critical role in electron transport. DNA charge transport is indeed governed by charge delocalization with wavefunctions extent controlled by geometrical overlaps. Solvent atoms also affect the conductivity, with counterions decreasing the conductance by a factor of 2-3. In addition, we find that water molecules around the double helix screen the negatively-charged phosphate groups suppressing the conductance of DNA. Comparing transport properties of 4-base-pair (BP) with 10-BP DNA, we find weak distance dependence of the conductivity. Finally, we discuss the effect of sequence on DNA conductivity.
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.
Water confined in nanotubes and between graphene sheets: A first principle study
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.
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.
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.
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).
Two-dimensional arsenic monolayer sheet predicted from first-principles
NASA Astrophysics Data System (ADS)
Pu, Chun-Ying; Ye, Xiao-Tao; Jiang, Hua-Long; Zhang, Fei-Wu; Lu, Zhi-Wen; He, Jun-Bao; Zhou, Da-Wei
2015-03-01
Using first-principles calculations, we investigate the two-dimensional arsenic nanosheet isolated from bulk gray arsenic. Its dynamical stability is confirmed by phonon calculations and molecular dynamics analyzing. The arsenic sheet is an indirect band gap semiconductor with a band gap of 2.21 eV in the hybrid HSE06 functional calculations. The valence band maximum (VBM) and the conduction band minimum (CBM) are mainly occupied by the 4p orbitals of arsenic atoms, which is consistent with the partial charge densities of VBM and CBM. The charge density of the VBM G point has the character of a π bond, which originates from p orbitals. Furthermore, tensile and compressive strains are applied in the armchair and zigzag directions, related to the tensile deformations of zigzag and armchair nanotubes, respectively. We find that the ultimate strain in zigzag deformation is 0.13, smaller than 0.18 of armchair deformation. The limit compressive stresses of single-layer arsenic along armchair and zigzag directions are -4.83 GPa and -4.76 GPa with corresponding strains of -0.15 and -0.14, respectively. Projected supported by the Henan Joint Funds of the National Natural Science Foundation of China (Grant Nos. U1304612 and U1404608), the National Natural Science Foundation of China (Grant Nos. 51374132 and 11404175), the Special Fund for Theoretical Physics of China (Grant No. 11247222), and Nanyang Normal University Science Foundation, China (Grant Nos. ZX2012018 and ZX2013019).
First-principles calculations for the tunnel ionization rate of atoms and molecules
Otobe, T.; Yabana, K.; Iwata, J.-I.
2004-05-01
We present first-principles calculations for the tunnel ionization rate of some atoms and molecules in a static intense electric field. The Gamow state is calculated to describe the ionization process in the Kohn-Sham formalism with the self-interaction correction. The tunnel ionization rate is obtained from the imaginary part of the Gamow state eigenvalue. The ionization rates of rare-gas atoms Ar and Xe and diatomic molecules N{sub 2}, O{sub 2}, and F{sub 2} are investigated. The calculations describe well the observed behavior of the tunnel ionization. The results also show good correspondence with the Ammosov-Delone-Krainov model for rare-gas atoms. We find that the properties of the highest occupied orbital have significant effects on the ionization rate. In particular, our calculation reproduces the suppression of the ionization rate of O{sub 2} molecule in comparison with that of Xe atom. We also find that the ionization rates of O{sub 2} and F{sub 2} molecules are very sensitive to the relative angle between the electric field and the molecular axis, reflecting properties of the highest occupied orbital.
Controlled catalytic properties of iron nanoparticles on doped graphene: A first-principles study
NASA Astrophysics Data System (ADS)
Kim, Sol; Jhi, Seung-Hoon
2014-03-01
Iron is an important catalyst in Fischer-Tropsch synthesis (FTS). Recently carbon-material- supported iron nanoparticles were reported as a good catalyst better than bulk iron surface. Here we employed B- and N-doped graphene as supporting materials for iron nanoparticles and studied the change in d-band center of iron nanoparticles which is a key factor in gas adsorption. We then investigated the molecular adsorption of H2 and CO on the nanoparticles using first-principle calculations. It was found that B doping enhances the binding energy of the Fe13 on the graphene, which lowers the d-band center of Fe13, but N doping reduces it. Difference in the work-function and subsequently in the charge transfer causes such behavior in the binding energies. We showed that the adsorption of H2 and CO on the Fe-graphene substrate is strongly correlated with the d-band center modulated by the doping concentration. We also found that the stability of Fe nanoparticle was enhanced by graphene doping.
First principles study of Al/SrTiO3 interface formation
NASA Astrophysics Data System (ADS)
Hamze, Ali; Posadas, Agham; Kormondy, Kristy; Demkov, Alexander
Two-dimensional electron gasses (2DEGs) at the interfaces of oxides have been the subject of much interest in recent years due to their relatively high carrier mobilities and potential for use in all-oxide devices. In particular, the γ-Al2O3 (γ-alumina)-SrTiO3 (STO) system has been the focus of much research. It exhibits a 2DEG at the interface with a carrier mobility ranging from 103-105 cm2V-1 s-1, depending on the thickness of the STO and how the γ-alumina film was grown. It is believed that Al atoms steal oxygen from the STO substrate at growth temperature and thus create a conductive channel in STO near the interface. We investigate the initial studies of the interface formation using density functional theory. The results of first principles calculations are compared with those of x-ray photoemission spectroscopy (XPS) performed in situ on thin Al films deposited on STO by molecular beam epitaxy. Analysis of the Al 2p XPS spectrum shows one layer of aluminum is fully oxidized during growth at 40°C and 4 layers of aluminum are fully oxidized during growth at 600°C. Furthermore, the Ti 2p XPS spectrum shows the titanium atoms are reduced, which is consistent with the presence of oxygen vacancies in STO.
Toward a Monte Carlo program for simulating vapor-liquid phase equilibria from first principles
McGrath, M; Siepmann, J I; Kuo, I W; Mundy, C J; Vandevondele, J; Sprik, M; Hutter, J; Mohamed, F; Krack, M; Parrinello, M
2004-10-20
Efficient Monte Carlo algorithms are combined with the Quickstep energy routines of CP2K to develop a program that allows for Monte Carlo simulations in the canonical, isobaric-isothermal, and Gibbs ensembles using a first principles description of the physical system. Configurational-bias Monte Carlo techniques and pre-biasing using an inexpensive approximate potential are employed to increase the sampling efficiency and to reduce the frequency of expensive ab initio energy evaluations. The new Monte Carlo program has been validated through extensive comparison with molecular dynamics simulations using the programs CPMD and CP2K. Preliminary results for the vapor-liquid coexistence properties (T = 473 K) of water using the Becke-Lee-Yang-Parr exchange and correlation energy functionals, a triple-zeta valence basis set augmented with two sets of d-type or p-type polarization functions, and Goedecker-Teter-Hutter pseudopotentials are presented. The preliminary results indicate that this description of water leads to an underestimation of the saturated liquid density and heat of vaporization and, correspondingly, an overestimation of the saturated vapor pressure.
Transition metal decorated graphene-like zinc oxide monolayer: A first-principles investigation
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.
Transition metal decorated graphene-like zinc oxide monolayer: A first-principles investigation
NASA Astrophysics Data System (ADS)
Lei, Jie; Xu, Ming-Chun; Hu, Shu-Jun
2015-09-01
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.
Structure of hydrophobic hydration of benzene and hexafluorobenzene from first principles
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.
Water solubility in calcium aluminosilicate glasses investigated by first principles techniques
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
NASA Astrophysics Data System (ADS)
Nguyen, Ngoc Linh; Borghi, Giovanni; Ferretti, Andrea; Marzari, Nicola
The determination of spectral properties of the DNA and RNA nucleobases from first principles can provide theoretical interpretation for experimental data, but requires complex electronic-structure formulations that fall outside the domain of applicability of common approaches such as density-functional theory. In this work, we show that Koopmans-compliant functionals, constructed to enforce piecewise linearity in energy functionals with respect to fractional occupation-i.e., with respect to charged excitations-can predict not only frontier ionization potentials and electron affinities of the nucleobases with accuracy comparable or superior with that of many-body perturbation theory and high-accuracy quantum chemistry methods, but also the molecular photoemission spectra are shown to be in excellent agreement with experimental ultraviolet photoemsision spectroscopy data. The results highlight the role of Koopmans-compliant functionals as accurate and inexpensive quasiparticle approximations to the spectral potential, which transform DFT into a novel dynamical formalism where electronic properties, and not only total energies, can be correctly accounted for.
NASA Astrophysics Data System (ADS)
Kim, Sejoong; Marzari, Nicola
2013-06-01
We present a first-principles approach for inelastic quantum transport calculations based on maximally localized Wannier functions. Electronic-structure properties are obtained from density-functional theory in a plane-wave basis, and electron-vibration coupling strengths and vibrational properties are determined with density-functional perturbation theory. Vibration-induced inelastic transport properties are calculated with nonequilibrium Green's function techniques; since these are based on a localized orbital representation we use maximally localized Wannier functions. Our formalism is applied first to investigate inelastic transport in a benzene molecular junction connected to monoatomic carbon chains. In this benchmark system the electron-vibration self-energy is calculated either in the self-consistent Born approximation or by lowest-order perturbation theory. It is observed that upward and downward conductance steps occur, which can be understood using multieigenchannel scattering theory and symmetry conditions. In a second example, where the monoatomic carbon chain electrode is replaced with a (3,3) carbon nanotube, we focus on the nonequilibrium vibration populations driven by the conducting electrons using a semiclassical rate equation and highlight and discuss in detail the appearance of vibrational cooling as a function of bias and the importance of matching the vibrational density of states of the conductor and the leads to minimize joule heating and breakdown.
First-principle study on the surface atomic relaxation properties of sphalerite
NASA Astrophysics Data System (ADS)
Liu, Jian; Wen, Shu-ming; Xian, Yong-jun; Bai, Shao-jun; Chen, Xiu-min
2012-09-01
The surface properties of sphalerite (ZnS) were theoretically investigated using first principle calculations based on the density functional theory (DFT). DFT results indicate that both the (110) and the (220) surfaces of sphalerite undergo surface atom relaxation after geometry optimization, which results in a considerable distortion of the surface region. In the normal direction, i.e., perpendicular to the surface, S atoms in the first surface layer move outward from the bulk ( d 1), whereas Zn atoms move toward the bulk ( d 2), forming an S-enriched surface. The values of these displacements are 0.003 nm for d 1 and 0.021 nm for d 2 on the (110) surface, and 0.002 nm for d 1 and 0.011 nm for d 2 on the (220) surface. Such a relaxation process is visually interpreted through the qualitative analysis of molecular mechanics. X-ray photoelectron spectroscopic (XPS) analysis provides the evidence for the S-enriched surface. A polysulphide (S{/n 2-}) surface layer with a binding energy of 163.21 eV is formed on the surface of sphalerite after its grinding under ambient atmosphere. This S-enriched surface and the S{/n 2-} surface layer have important influence on the flotation properties of sphalerite.
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.
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.
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.
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.
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
First-Principles calculation of surface stress evolution of Ge quantum dots
NASA Astrophysics Data System (ADS)
Lu, Guang-Hong; Cuma, Martin; Liu, Feng
2004-03-01
Ge quantum dots (huts) form on Si(001) surface after growth of a wetting layer of 3-4 monolayers, having a highly ordered structure bounded by (105) facets. Surface stress/strain plays an important role in their stabilization. Recent experiments [1,2] of Ge growth on Si(105) surface have suggested a continuous evolution toward compression with increasing Ge coverage to stabilize Ge/Si(105) facets. However, quantitative information of surface stress of Ge/Si(105) facet, and hence the surface stress on Ge dots is still lacking, which causes a big gap in our understanding. Therefore, we have performed large-scale first-principles calculations to evaluate evolution of surface energy and surface stress in the Ge-covered Si (105) surface, as a function of Ge coverage. We show a very large tensile surface stress present in clean Si(105) surface induced by surface reconstruction, which continuously evolve toward compression with increasing Ge coverage, confirming the qualitative suggestion by experiments. Quantitatively, only moderate reduction of tensile surface stress occurs for the first two layers of Ge deposition, and the surface stress actually remains to be tensile until 5-layer of Ge coverage. This work is supported by DOE. [1] Y. Fujikawa, K. Akiyama, T. Nagao, T. Sakurai, M.G. Lagally, T. Hashimoto, Y. Morikawa, and K. Terakura, Phys. Rev. Lett. 88, 176101 (2002) [2] P. Raiteri,D.B. Migas, L. Miglio, A. Rastelli, and H. von Kanel, Phys. Rev. Lett. 88, 256103 (2002)
NASA Astrophysics Data System (ADS)
Wang, Yanli; Ding, Yi
2015-06-01
Arsenene and antimonene, i.e. two-dimensional (2D) As and Sb monolayers, are the recently proposed cousins of phosphorene (Angew. Chem. Int. Ed., 54, 3112 (2015)). Through first-principle calculations, we systematically investigate electronic and transport properties of the corresponding As and Sb nanoribbons, which are cut from the arsenene and antimonene nanosheets. We find that different from the 2D systems, band features of As and Sb nanoribbons are dependent on edge shapes. All armchair As/Sb nanoribbons keep the indirect band gap feature, while the zigzag ones transfer to direct semiconductors. Quantum confinement in nanoribbons enhances the gap sizes, for which both the armchair and zigzag ones have a gap scaling rule inversely proportional to the ribbon width. Comparing to phosphorene, the large deformation potential constants in the As and Sb nanoribbons cause small carrier mobilities in the orders of magnitude of 101-102 cm2/Vs. Our study demonstrates that the nanostructures of group-Vb elements would possess different electronic properties for the P, As, and Sb ones, which have diverse potential applications for nanoelectronics and nanodevices.
Rare-earth vs. heavy metal pigments and their colors from first principles
Tomczak, Jan M.; Pourovskii, Leonid V.; Vaugier, Loig; Georges, Antoine; Biermann, Silke
2013-01-01
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. PMID:23302689
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.
First-principles investigation of the structural changes in Li-rich cathode composites
NASA Astrophysics Data System (ADS)
Dixit, Hemant; Zhou, Wu; Nanda, Jagjit; Idrobo, Juan-Carlos; Cooper, Valentino; Materials Science and Technology Division Collaboration
2014-03-01
Lithium ion batteries have high energy densities and are widely used in consumer electronics. However, it is essential to improve their power rate and cycle life for long-term usage. Cathode materials containing Li-excess layered oxide compounds, xLi2MnO3(1- x)LiMO2, (where M=Mn, Co, Ni and x= 0.2-0.7) have two times higher capacities than the conventional cathode material but during cycling a decrease in energy density and a concomitant development of a low voltage plateau are often observed. Furthermore, recent experimental studies have observed the formation and clustering of the anti-site defects near the surface. Thus a detailed understanding of the structural changes at the atomic scale of these Li-rich composites is essential to establish the correlation between the structural and electrochemical property. We present first-principles density functional theory study of the structural and electronic properties in Li-rich cathode composites. These cathode composites are modelled as solid solutions of the LiMnO2 (R 3 m) and Li2MnO3 (C2m) phases. We discuss the stability of the proposed model, the diffusion energy barriers of Li+ ions calculated using nudged-elastic band method and the formation energies of the antisite defects.
Analytical study of Yang-Mills theory in the infrared from first principles
NASA Astrophysics Data System (ADS)
Siringo, Fabio
2016-06-01
Pure Yang-Mills SU(N) theory is studied in the Landau gauge and four dimensional space. While leaving the original Lagrangian unmodified, a double perturbative expansion is devised, based on a massive free-particle propagator. In dimensional regularization, all diverging mass terms cancel exactly in the double expansion, without the need to include mass counterterms that would spoil the symmetry of the Lagrangian. No free parameters are included that were not in the original theory, yielding a fully analytical approach from first principles. The expansion is safe in the infrared and is equivalent to the standard perturbation theory in the UV. At one-loop, explicit analytical expressions are given for the propagators and the running coupling and are found in excellent agreement with the data of lattice simulations. A universal scaling property is predicted for the inverse propagators and shown to be satisfied by the lattice data. Higher loops are found to be negligible in the infrared below 300 MeV where the coupling becomes small and the one-loop approximation is under full control.
Global smoothing and continuation for large-scale molecular optimization
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.
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
First-principles study of high-conductance DNA sequencing with carbon nanotube electrodes
NASA Astrophysics Data System (ADS)
Chen, X.; Rungger, I.; Pemmaraju, C. D.; Schwingenschlögl, U.; Sanvito, S.
2012-03-01
Rapid and cost-effective DNA sequencing at the single nucleotide level might be achieved by measuring a transverse electronic current as single-stranded DNA is pulled through a nanometer-sized pore. In order to enhance the electronic coupling between the nucleotides and the electrodes and hence the current signals, we employ a pair of single-walled close-ended (6,6) carbon nanotubes (CNTs) as electrodes. We then investigate the electron transport properties of nucleotides sandwiched between such electrodes by using first-principles quantum transport theory. In particular, we consider the extreme case where the separation between the electrodes is the smallest possible that still allows the DNA translocation. The benzene-like ring at the end cap of the CNT can strongly couple with the nucleobases and therefore it can both reduce conformational fluctuations and significantly improve the conductance. As such, when the electrodes are closely spaced, the nucleobases can pass through only with their base plane parallel to the plane of CNT end caps. The optimal molecular configurations, at which the nucleotides strongly couple to the CNTs, and which yield the largest transmission, are first identified. These correspond approximately to the lowest energy configurations. Then the electronic structures and the electron transport of these optimal configurations are analyzed. The typical tunneling currents are of the order of 50 nA for voltages up to 1 V. At higher bias, where resonant transport through the molecular states is possible, the current is of the order of several μA. Below 1 V, the currents associated to the different nucleotides are consistently distinguishable, with adenine having the largest current, guanine the second largest, cytosine the third and, finally, thymine the smallest. We further calculate the transmission coefficient profiles as the nucleotides are dragged along the DNA translocation path and investigate the effects of configurational variations
First Principles Simulations fo the Supercritical Behavior of Ore Forming Fluids
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
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
McDaniel, Jesse G; Choi, Eunsong; Son, Chang-Yun; Schmidt, J R; Yethiraj, Arun
2016-01-14
The conformational properties of polymers in ionic liquids are of fundamental interest but not well understood. Atomistic and coarse-grained molecular models predict qualitatively different results for the scaling of chain size with molecular weight, and experiments on dilute solutions are not available. In this work, we develop a first-principles force field for poly(ethylene oxide) (PEO) in the ionic liquid 1-butyl 3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) using symmetry adapted perturbation theory (SAPT). At temperatures above 400 K, simulations employing both the SAPT and OPLS-AA force fields predict that PEO displays ideal chain behavior, in contrast to previous simulations at lower temperature. We therefore argue that the system shows a transition from extended to more compact configurations as the temperature is increased from room temperature to the experimental lower critical solution temperature. Although polarization is shown to be important, its implicit inclusion in the OPLS-AA force is sufficient to describe the structure and energetics of the mixture. The simulations emphasize the difference between ionic liquids from typical solvents for polymers. PMID:26690901
Application of First Principles Ni-Cd and Ni-H2 Battery Models to Spacecraft Operations
NASA Technical Reports Server (NTRS)
Timmerman, Paul; Bugga, Ratnakumar; DiStefano, Salvador
1997-01-01
The conclusions of the application of first principles model to spacecraft operations are: the first principles of Bi-phasic electrode presented model provides an explanation for many behaviors on voltage fading on LEO cycling.
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
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.
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.
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.
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).
Temporal scaling of molecular evolution in primates and other mammals.
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. PMID:3444400
Data set for diffusion coefficients of alloying elements in dilute Mg alloys from first-principles
Zhou, Bi-Cheng; Shang, Shun-Li; Wang, Yi; Liu, Zi-Kui
2015-01-01
Diffusion coefficients of alloying elements in Mg are critical for the development of new Mg alloys for lightweight applications. Here we present the data set of the temperature-dependent dilute tracer diffusion coefficients for 47 substitutional alloying elements in hexagonal closed packed (hcp) Mg calculated from first-principles calculations based on density functional theory (DFT) by combining transition state theory and an 8-frequency model. Benchmark for the DFT calculations and systematic comparison with experimental diffusion data are also presented. The data set refers to “Diffusion coefficients of alloying elements in dilute Mg alloys: A comprehensive first-principles study” by Zhou et al. [1]. PMID:26702419
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
First Principles Calculations for X-ray Resonant Spectra and Elastic Properties
Yongbin Lee
2006-05-01
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 AlMgB{sub 14}.
A concurrent multiscale micromorphic molecular dynamics
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.
NASA Astrophysics Data System (ADS)
Hu, S. X.
2014-10-01
Accurate knowledge of the properties of warm dense deuterium/tritium (DT) is essential to reliably design inertial confinement fusion (ICF) implosions. In the warm-dense-matter regime, routinely accessed by low-adiabat ICF implosions, strong-coupling and degeneracy effects play an important role in determining plasma properties. Using first-principles methods of both path-integral Monte Carlo and quantum molecular-dynamics (QMD), we have performed systematic investigation of the equation of state, thermal conductivity, and opacity for DT over a wide range of densities and temperatures. These first-principles properties have been incorporated into our hydrocodes. When compared to hydro simulations using standard plasma models, significant differences in 1-D target performance have been identified for simulations of DT implosions. For low-adiabat (α <= 2) DT plasma conditions, the QMD-predicted opacities are 10 to 100 × higher than predicted by the cold-opacity-patched astrophysical opacity table. The thermal conductivity could be 3 to 10 × larger than the Lee-More model prediction. These enhancements can modify the shell adiabat and shock dynamics in lower- α ICF implosions, which could lead to ~ 40 variations in peak density and neutron yield. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.
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.
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.
Molecular Scale Dynamics of Large Ring Polymers
NASA Astrophysics Data System (ADS)
Gooßen, S.; Brás, A. R.; Krutyeva, M.; Sharp, M.; Falus, P.; Feoktystov, A.; Gasser, U.; Pyckhout-Hintzen, W.; Wischnewski, A.; Richter, D.
2014-10-01
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.
Molecular scale dynamics of large ring polymers.
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
Wetting and spreading at the molecular scale
NASA Technical Reports Server (NTRS)
Koplik, Joel; Banavar, Jayanth R.
1994-01-01
We have studied the microscopic aspects of the spreading of liquid drops on a solid surface by molecular dynamics simulations of coexisting three-phase Lennard-Jones systems of liquid, vapor and solid. We consider both spherically symmetric atoms and chain-like molecules, and a range of interaction strengths. As the attraction between liquid and solid increases we observed a smooth transition in spreading regimes, from partial to complete to terraced wetting. In the terraced case, where distinct monomolecular layers spread with different velocities, the layers are ordered but not solid, with qualitative behavior resembling recent experimental findings, but with interesting differences in the spreading rate.
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.
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.
First principles study of structural, electronic and magnetic properties of magnesium
NASA Astrophysics Data System (ADS)
Abdel Rahim, G. P.; Rodríguez M, J. A.; Moreno-Armenta, M. G.
2016-02-01
We investigated the structural, electronic, and magnetic properties of Mg, in the CS (simple cubic), NiAs (Nickel arsenide), FCC (rock-salt), R (Rhombohedral), Diamond and WZ (wurtzite) phases. Calculations were performed using the first-principles pseudo-potential method within the framework of spin-density functional theory (DFT).
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.